UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-Q

(Mark One)


☒			QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended ~~June 30, 2019~~March 31, 2020


☐			TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from ________ to ________

Commission file number: ~~001-34962~~001-34962

ZOGENIX, INC.

(Exact Name of Registrant as Specified in its Charter)

____________________________________________


Delaware	20-5300780
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification No.)

5959 Horton Street, Suite 500 Emeryville, California 94608		~~94608~~
(Address of Principal Executive ~~Offices)~~		(Offices and Zip Code)

510-550-8300

(Registrant’s Telephone Number, Including Area Code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class

Trading Symbol

Name of each exchange on which registered

Common Stock, par value $0.001 per share

ZGNX

The Nasdaq Global Market

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. x☒ Yes ☐ No

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes x☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer

x☒

Accelerated filer

Non-accelerated filer

Smaller reporting company

Emerging growth company

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). ☐ Yes x☒ No

The number of outstanding shares of the registrant’s common stock, par value $0.001 per share, as of ~~July 31, 2019~~April 30, 2020 was ~~42,541,503.~~55,340,691.

ZOGENIX, INC.

~~FORM~~Form 10-Q

For the Quarterly Period Ended ~~June 30, 2019~~March 31, 2020

~~Table of Contents~~TABLE OF CONTENTS


			Page
PART I. FINANCIAL INFORMATION

Item 1.	Financial Statements	3

	Condensed Consolidated Balance Sheets as of ~~June~~ 30 ~~, 2019~~March 31, 2020 and December 31, ~~2018~~2019	31

	Condensed Consolidated Statements of Operations for the Three ~~and Six~~ Months Ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	42

	Condensed Consolidated Statements of Comprehensive Loss for the Three ~~and Six~~ Months Ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	53

	Condensed Consolidated Statements of ~~Stockholders'~~Stockholders’ Equity for the ~~Six~~ Three Months Ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	74

	Condensed Consolidated Statements of Cash Flows for the ~~Six~~Three Months Ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	65

	Notes to the Condensed Consolidated Financial Statements	86

Item 2.	~~Management's~~Management ’s Discussion and Analysis of Financial Condition and Results of Operations	2118

Item 3.	Quantitative and Qualitative Disclosures about Market Risk	3126

Item 4.	Controls and Procedures	3126

PART II. OTHER INFORMATION

Item 1.	Legal Proceedings	3227

Item 1A.	Risk Factors	3227

Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	3429

Item 3.	Defaults Upon Senior Securities	3529

Item 4.	Mine Safety Disclosures	3529

Item 5.	Other Information	3529

Item 6.	Exhibits	3630

	Signatures	3731

PART I – FINANCIAL INFORMATION

Item 1. Financial Statements

Zogenix, Inc.

Condensed Consolidated Balance Sheets (Unaudited)

(in thousands, except par value)


		June 30, 2019		December 31, 2018			March 31, 2020		December 31, 2019
Assets:	Assets:					Assets:
Current assets:	Current assets:					Current assets:
Cash and cash equivalents	Cash and cash equivalents	$	50,788	$	68,454	Cash and cash equivalents	$	269,975	$	62,070

Marketable securities	Marketable securities	412,180		445,733		Marketable securities	150,218		189,085

Prepaid expenses		7,701		6,718
Other current assets		5,113		11,825
Other receivable						Other receivable	19,741		—
Prepaid expenses and other current assets						Prepaid expenses and other current assets	13,647		11,084
Acquisition holdback placed in escrow						Acquisition holdback placed in escrow	25,000		25,000

Total current assets	Total current assets	475,782		532,730		Total current assets	478,581		287,239
Property and equipment, net	Property and equipment, net	10,141		2,870		Property and equipment, net	9,560		9,424
Operating lease right-of-use assets	Operating lease right-of-use assets	8,110		—		Operating lease right-of-use assets	8,546		7,774
Intangible assets		102,500		102,500
Indefinite-lived intangible assets						Indefinite-lived intangible assets	102,500		102,500
Goodwill	Goodwill	6,234		6,234		Goodwill	6,234		6,234
Other noncurrent assets	Other noncurrent assets	1,850		3,997		Other noncurrent assets	1,485		1,079

Total assets	Total assets	$	604,617	$	648,331	Total assets	$	606,906	$	414,250
Liabilities and stockholders’ equity:	Liabilities and stockholders’ equity:					Liabilities and stockholders’ equity:
Current liabilities:	Current liabilities:					Current liabilities:
Accounts payable	Accounts payable	$	3,012	$	7,989	Accounts payable	$	7,887	$	7,979
Accrued and other current liabilities	Accrued and other current liabilities	20,946		18,086		Accrued and other current liabilities	25,803		30,117
Acquisition holdback liability						Acquisition holdback liability	24,444		24,444
Deferred revenue, current	Deferred revenue, current	6,027		—		Deferred revenue, current	5,696		5,927
Current portion of operating lease liabilities	Current portion of operating lease liabilities	1,402		—		Current portion of operating lease liabilities	1,383		1,322
Current portion of contingent consideration	Current portion of contingent consideration	34,800		32,300		Current portion of contingent consideration	23,600		25,600

Total current liabilities	Total current liabilities	66,187		58,375		Total current liabilities	88,813		95,389

Deferred revenue, noncurrent	Deferred revenue, noncurrent	8,404		—		Deferred revenue, noncurrent	6,407		7,425
Operating lease liabilities, net of current portion	Operating lease liabilities, net of current portion	11,186		—		Operating lease liabilities, net of current portion	11,454		10,752
Contingent consideration, net of current portion	Contingent consideration, net of current portion	35,700		45,900		Contingent consideration, net of current portion	32,300		38,200
Deferred income taxes	Deferred income taxes	17,425		17,425		Deferred income taxes	17,425		17,425
Other long-term liabilities		—		3,830

Total liabilities	Total liabilities	138,902		125,530		Total liabilities	156,399		169,191
Commitments and contingencies	Commitments and contingencies					Commitments and contingencies
Stockholders’ equity:	Stockholders’ equity:					Stockholders’ equity:
Preferred stock, $0.001 par value; 10,000 shares authorized; none issued and outstanding		—		—
Common stock, $0.001 par value; 100,000 and 50,000 shares authorized and 42,498 and 42,078 shares issued and outstanding at June 30, 2019 and December 31, 2018, respectively		42		42
Preferred stock, $0.001 par value; 10,000 shares authorized; NaN issued and outstanding						Preferred stock, $0.001 par value; 10,000 shares authorized; NaN issued and outstanding	—		—
Common stock, $0.001 par value; 100,000 shares authorized; and 55,341 and 45,272 shares issued and outstanding at March 31, 2020 and December 31, 2019, respectively						Common stock, $0.001 par value; 100,000 shares authorized; and 55,341 and 45,272 shares issued and outstanding at March 31, 2020 and December 31, 2019, respectively	55		45
Additional paid-in capital	Additional paid-in capital	1,233,866		1,218,710		Additional paid-in capital	1,591,497		1,360,092
Accumulated deficit	Accumulated deficit	(768,919)		(695,954)		Accumulated deficit	(1,141,257)		(1,115,457)
Accumulated other comprehensive income	Accumulated other comprehensive income	726		3		Accumulated other comprehensive income	212		379
Total stockholders’ equity	Total stockholders’ equity	465,715		522,801		Total stockholders’ equity	450,507		245,059
Total liabilities and stockholders’ equity	Total liabilities and stockholders’ equity	$	604,617	$	648,331	Total liabilities and stockholders’ equity	$	606,906	$	414,250

See accompanying notes to the unaudited condensed consolidated financial statements.

Zogenix, Inc. | Q1 2020 Form 10-Q | 1

Zogenix, Inc.

Condensed Consolidated Statements of Operations (Unaudited)

(in thousands, except per share amounts)


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018		2019		2018			2020		2019
Collaboration revenue	Collaboration revenue	$	1,069	$	—	$	1,069	$	—	Collaboration revenue	$	1,249	$	—
Operating expenses:	Operating expenses:									Operating expenses:
Research and development	Research and development	27,096		26,741		51,448		49,721		Research and development	33,240		24,352
Selling, general and administrative	Selling, general and administrative	15,459		8,577		26,377		16,647		Selling, general and administrative	21,318		10,918
Acquired in-process research and development expense										Acquired in-process research and development expense	1,500		—
Change in fair value of contingent consideration	Change in fair value of contingent consideration	(700)		(2,500)		2,300		(2,500)		Change in fair value of contingent consideration	(7,900)		3,000
Total operating expenses	Total operating expenses	41,855		32,818		80,125		63,868		Total operating expenses	48,158		38,270
Loss from operations	Loss from operations	(40,786)		(32,818)		(79,056)		(63,868)		Loss from operations	(46,909)		(38,270)
Other income (expense):	Other income (expense):									Other income (expense):
Interest income	Interest income	2,983		1,029		6,139		1,862		Interest income	1,088		3,156

Other income (expense)		40		2,950		(48)		2,987
Other income (expense), net										Other income (expense), net	20,021		(88)
Total other income	Total other income	3,023		3,979		6,091		4,849		Total other income	21,109		3,068
Net loss										Net loss	$	(25,800)	$	(35,202)

Net loss per share, basic and diluted										Net loss per share, basic and diluted	$	(0.54)	$	(0.83)

Net loss from continuing operations		(37,763)		(28,839)		(72,965)		(59,019)
Loss from discontinued operations, net of tax		—		(198)		—		(198)
Net loss		$	(37,763)	$	(29,037)	$	(72,965)	$	(59,217)
Net loss per share, basic and diluted:
Continuing operations		$	(0.89)	$	(0.82)	$	(1.72)	$	(1.68)
Discontinued operations		—		(0.01)		—		(0.01)
Total		$	(0.89)	$	(0.83)	$	(1.72)	$	(1.69)

Weighted average common shares used in the calculation of basic and diluted net loss per common share		42,458		35,355		42,348		35,099
Weighted average number of shares used in the calculation of basic and diluted net loss per common share										Weighted average number of shares used in the calculation of basic and diluted net loss per common share	48,185		42,236

See accompanying notes to the unaudited condensed consolidated financial statements.

Zogenix, Inc. | Q1 2020 Form 10-Q | 2

Zogenix, Inc.

Condensed Consolidated Statements of Comprehensive Loss (Unaudited)

(in thousands)


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018		2019		2018			2020		2019
Net loss	Net loss	$	(37,763)	$	(29,037)	$	(72,965)	$	(59,217)	Net loss	$	(25,800)	$	(35,202)
Other comprehensive income (loss):
Change in unrealized gains on marketable securities		353		—		723		—
Other comprehensive (loss) income, net of tax:										Other comprehensive (loss) income, net of tax:

Change in unrealized (losses) gains related to marketable securities										Change in unrealized (losses) gains related to marketable securities	(172)		370
Foreign currency translation adjustments										Foreign currency translation adjustments	5		—
Total other comprehensive (loss) income										Total other comprehensive (loss) income	(167)		370
Comprehensive loss	Comprehensive loss	$	(37,410)	$	(29,037)	$	(72,242)	$	(59,217)	Comprehensive loss	$	(25,967)	$	(34,832)

See accompanying notes to the unaudited condensed consolidated financial statements.

Zogenix, Inc. | Q1 2020 Form 10-Q | 3

Zogenix, Inc.

Condensed Consolidated Statements of Stockholders' Equity (Unaudited)

(in thousands)


		Six Months Ended June 30, 2019																															Three Months Ended March 31, 2020
		Common Stock					Additional Paid-in Capital		Accumulated Other Comprehensive Income		Accumulated Deficit					Total Stockholders’ Equity			Common Stock											Additional Paid-in Capital			Accumulated Other Comprehensive Income			Accumulated Deficit	Total Stockholders’ Equity
		Shares	Amount																Shares		Accumulated Other Comprehensive Income				Accumulated Deficit				Total Stockholders’ Equity
Balance at December 31, 2018		42,078	$	42	$	1,218,710							$	3			$	(695,954)												$	522,801
Balance at December 31, 2019													Balance at December 31, 2019		45,272				$	45			$	1,360,092			$	379			$	(1,115,457)		$	245,059
Net loss	Net loss	—	—		—		—		(35,202)		(35,202)		Net loss		—				—			—				—				(25,800)			(25,800)
Other comprehensive income		—	—		—		370		—		370
Other comprehensive loss													Other comprehensive loss		—				—			—				(167)				—			(167)
Issuance of common stock, net of offering costs													Issuance of common stock, net of offering costs		9,798				10			221,698				—				—			221,708
Issuance of common stock under employee equity plans	Issuance of common stock under employee equity plans	380	—		5,293		—		—		5,293		Issuance of common stock under employee equity plans		297				—			3,882				—				—			3,882
Shares repurchased for tax withholdings related to net share settlement of employee equity awards	Shares repurchased for tax withholdings related to net share settlement of employee equity awards	(12)	—		(606)		—		—		(606)		Shares repurchased for tax withholdings related to net share settlement of employee equity awards		(26)				—			(569)				—				—			(569)
Stock-based compensation	Stock-based compensation	—	—		4,223		—		—		4,223		Stock-based compensation		—				—			6,394				—				—			6,394
Balance at March 31, 2019		42,446	$	42	$	1,227,620	$	373	$	(731,156)	$	496,879
Net loss		—	—		—		—		(37,763)		(37,763)
Other comprehensive income		—	—		—		353		—		353
Issuance of common stock under employee equity plans		52	—		888		—		—		888
Stock-based compensation		—	—		5,358		—		—		5,358
Balance at June 30, 2019		42,498	$	42	$	1,233,866	$	726	$	(768,919)	$	465,715
Balance at March 31, 2020													Balance at March 31, 2020		55,341				$	55		$	1,591,497			$	212			$	(1,141,257)		$	450,507


		Six Months Ended June 30, 2018																															Three Months Ended March 31, 2019
		Common Stock					Additional Paid-in Capital		Accumulated Other Comprehensive Income		Accumulated Deficit					Total Stockholders’ Equity			Common Stock											Additional Paid-in Capital			Accumulated Other Comprehensive Income			Accumulated Deficit	Total Stockholders’ Equity
		Shares	Amount																Shares		Accumulated Other Comprehensive Income				Accumulated Deficit				Total Stockholders’ Equity
Balance at December 31, 2017		34,808	$	35	$	873,526							$	—			$	(572,040)												$	301,521
Balance at December 31, 2018													Balance at December 31, 2018		42,078				$	42			$	1,218,710			$	3			$	(695,954)		$	522,801
Net loss	Net loss	—	—		—		—		(30,180)		(30,180)		Net loss		—				—			—				—				(35,202)			(35,202)
Other comprehensive income													Other comprehensive income		—				—			—				370				—			370

Issuance of common stock under employee equity plans	Issuance of common stock under employee equity plans	198	—		1,930		—		—		1,930		Issuance of common stock under employee equity plans		380				—			5,293				—				—			5,293
Shares repurchased for tax withholdings related to net share settlement of employee equity awards	Shares repurchased for tax withholdings related to net share settlement of employee equity awards	(33)	—		(1,411)		—		—		(1,411)		Shares repurchased for tax withholdings related to net share settlement of employee equity awards		(12)				—			(606)				—				—			(606)
Stock-based compensation	Stock-based compensation	—	—		1,912		—		—		1,912		Stock-based compensation		—				—			4,223				—				—			4,223
Balance at March 31, 2018		34,973	$	35	$	875,957	$	—	$	(602,220)	$	273,772
Net loss									(29,037)		(29,037)
Issuance of common stock, net of offering costs		740	1		30,251		—		—		30,252
Issuance of common stock under employee equity plans		114	—		1,838		—		—		1,838
Shares repurchased for tax withholdings related to net share settlement of employee equity awards		—	—		(18)		—		—		(18)
Stock-based compensation		—	—		3,059		—		—		3,059
Balance at June 30, 2018		35,827	$	36	$	911,087	$	—	$	(631,257)	$	279,866
Balance at March 31, 2019													Balance at March 31, 2019		42,446				$	42		$	1,227,620			$	373			$	(731,156)		$	496,879

See accompanying notes to the unaudited condensed consolidated financial statements.

Zogenix, Inc. | Q1 2020 Form 10-Q | 4

Zogenix, Inc.

Condensed Consolidated Statements of Cash Flows (Unaudited)

(in thousands)


		Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018			2020		2019
Cash flow from operating activities:	Cash flow from operating activities:					Cash flow from operating activities:
Net loss	Net loss	$	(72,965)	$	(59,217)	Net loss	$	(25,800)	$	(35,202)
Adjustments to reconcile net loss from continuing operations to net cash used in operating activities:
Adjustments to reconcile net loss to net cash used in operating activities:						Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	Stock-based compensation	9,581		4,971		Stock-based compensation	6,394		4,223
Depreciation and amortization	Depreciation and amortization	552		50		Depreciation and amortization	357		191
Noncash lease expense						Noncash lease expense	339		—
Net accretion and amortization of investments in marketable securities						Net accretion and amortization of investments in marketable securities	(215)		(1,703)

Net accretion and amortization of investments in marketable securities		(3,299)		—
Change in fair value of warrant liabilities	Change in fair value of warrant liabilities	158		31		Change in fair value of warrant liabilities	(162)		303
Change in fair value of contingent purchase consideration		2,300		(2,500)
Acquired in-process research and development expense						Acquired in-process research and development expense	1,500		—
Change in fair value of contingent consideration						Change in fair value of contingent consideration	(7,900)		3,000
Changes in operating assets and liabilities:	Changes in operating assets and liabilities:					Changes in operating assets and liabilities:
Accounts receivable						Accounts receivable	—		(15,500)

Prepaid expenses and other current assets		6,071		(3,482)
Other receivable						Other receivable	(19,741)		—
Prepaid expenses, escrow holdback and other current assets						Prepaid expenses, escrow holdback and other current assets	(722)		5,270
Other assets	Other assets	(5,963)		2,891		Other assets	(405)		(6,580)
Accounts payable, accrued and other liabilities	Accounts payable, accrued and other liabilities	(5,193)		1,689		Accounts payable, accrued and other liabilities	(4,435)		(7,096)
Operating lease liability	Operating lease liability	12,588		—		Operating lease liability	(452)		12,767
Deferred revenue	Deferred revenue	14,431		—		Deferred revenue	(1,249)		15,500
Net cash used in operating activities	Net cash used in operating activities	(41,739)		(55,567)		Net cash used in operating activities	(52,491)		(24,827)
Cash flows from investing activities:	Cash flows from investing activities:					Cash flows from investing activities:
Cash paid for in-process research and development asset						Cash paid for in-process research and development asset	(1,500)		—
Purchases of marketable securities	Purchases of marketable securities	(251,782)		—		Purchases of marketable securities	(15,695)		(145,826)
Proceeds from maturities of marketable securities	Proceeds from maturities of marketable securities	289,357		—		Proceeds from maturities of marketable securities	54,605		171,225

Purchases of property and equipment	Purchases of property and equipment	(8,922)		(84)		Purchases of property and equipment	(193)		(4,535)
Net cash provided by (used in) investing activities		28,653		(84)
Net cash provided by investing activities						Net cash provided by investing activities	37,217		20,864
Cash flows from financing activities:	Cash flows from financing activities:					Cash flows from financing activities:
Payment of contingent consideration	Payment of contingent consideration	(10,000)		—		Payment of contingent consideration	—		(10,000)
Proceeds from issuance of common stock under equity incentive plans	Proceeds from issuance of common stock under equity incentive plans	6,026		5,427		Proceeds from issuance of common stock under equity incentive plans	2,040		4,379
Taxes paid related to net share settlement of equity awards	Taxes paid related to net share settlement of equity awards	(606)		(1,426)		Taxes paid related to net share settlement of equity awards	(569)		(582)
Proceeds from issuance of common stock, net of issuance costs	Proceeds from issuance of common stock, net of issuance costs	—		30,250		Proceeds from issuance of common stock, net of issuance costs	221,708		—
Net cash (used in) provided by financing activities		(4,580)		34,251
Net cash provided by (used in) financing activities						Net cash provided by (used in) financing activities	223,179		(6,203)
Net decrease in cash and cash equivalents	Net decrease in cash and cash equivalents	(17,666)		(21,400)		Net decrease in cash and cash equivalents	207,905		(10,166)
Cash and cash equivalents, beginning of the period	Cash and cash equivalents, beginning of the period	68,454		293,503		Cash and cash equivalents, beginning of the period	62,070		68,454
Cash and cash equivalents, end of the period	Cash and cash equivalents, end of the period	$	50,788	$	272,103	Cash and cash equivalents, end of the period	$	269,975	$	58,288

Noncash financing activities:
Purchases of property and equipment in accounts payable and accrued liabilities		$	662	$	—

See accompanying notes to the unaudited condensed consolidated financial statements.

Zogenix, Inc. | Q1 2020 Form 10-Q | 5

Zogenix, Inc.

Notes to Condensed Consolidated Financial Statements (Unaudited)

Note 1 – Organization, ~~and~~ Basis of Presentation and Liquidity

Zogenix, Inc. and subsidiaries (the Company, we, us or our) is a global pharmaceutical company committed to developing and commercializing transformative therapies to improve the lives of patients and their families living with rare diseases. We are ~~currently~~primarily focused on developing and commercializing ~~central nervous system (CNS) therapies to address rare or orphan childhood-onset~~two therapeutic product candidates: Fintepla, a low-dose fenfluramine investigational therapy for two pediatric epilepsy ~~disorders. Our lead product candidate, Fintepla (ZX008, fenfluramine) is currently being developed~~disorders, Dravet syndrome and Lennox-Gastaut Syndrome (LGS); and MT1621, an investigational deoxynucleoside substrate enhancement therapy for the treatment of ~~seizures associated with Dravet syndrome~~thymidine kinase 2 deficiency (TK2d), an inherited mitochondrial DNA depletion disorder that predominantly affects children and ~~Lennox-Gastaut syndrome (LGS).~~ is often fatal.

We operate in ~~one~~1 business segment—the research, development and commercialization of pharmaceutical products and our headquarters are located in Emeryville, California.

Basis of Presentation

The accompanying condensed consolidated financial statements include the accounts of Zogenix, Inc. and its wholly-owned subsidiaries. Intercompany accounts and transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared pursuant to the rules and regulations of the Securities and Exchange Commission (SEC) for interim financial reporting. In the opinion of management, the condensed consolidated financial statements reflect all adjustments, which are normal and recurring in nature, necessary for fair financial statement presentation. The results of operations for any interim period are not necessarily indicative of results of operations for any future period. Certain information and footnote disclosures normally included in annual consolidated financial statements prepared in accordance with generally accepted accounting principles in the United States (GAAP) have been condensed or omitted. Accordingly, these unaudited interim condensed consolidated financial statements and accompanying notes should be read in conjunction with the consolidated financial statements and related notes included in our ~~2018~~2019 Annual Report on Form 10-K (2019 Form 10-K), which was filed with the SEC on ~~February 28, 2019.~~March 2, 2020.

Certain prior period amounts within the accompanying unaudited condensed consolidated financial statements have been reclassified to conform to current period presentation. These reclassifications did not affect our financial position, net loss, comprehensive loss, or cash flows as of and for the periods presented.

Future Funding Requirements

As of March 31, 2020, our cash, cash equivalents and marketable securities totaled $420.2 million. Excluding gains from two discrete business divestitures, we have incurred significant net losses and negative cash flows from operating activities since inception resulting in an accumulated deficit of ~~$768.9 million~~$1.1 billion as of ~~June 30, 2019.~~March 31, 2020. We expect to continue to incur significant operating losses and negative cash flows from operations as we continue to advance our product candidates through development and commercialization. Additionally, ~~pursuant to our acquisition of Brabant Pharma Limited (Brabant) in 2014 to obtain worldwide development and commercialization rights to Fintepla,~~ we are ~~required~~obligated to make ~~additional~~future milestone payments tothat are contingent upon the ~~former owners~~successful achievement of ~~Brabant in the event we achieve~~ certain regulatory and ~~sales milestones with~~sales-based milestone events related to Fintepla ~~(See Note 5).~~and certain regulatory milestone events related to MT1621. Historically, we have relied primarily on the proceeds from equity offerings to finance our operations. Until such time, if ever, we can generate a sufficient amount of revenue to finance our cash requirements, we may need to continue to rely on additional financing to achieve our business objectives. However, if such financing is not available at adequate levels when needed, we may be required to significantly delay, scale back or discontinue one or more of our product development programs or commercialization efforts or other aspects of our business plans, and our operating results and financial condition would be adversely affected.

Zogenix, Inc. | Q1 2020 Form 10-Q | 6

Note 2 – Summary of Significant Accounting Policies

Use of Estimates

The preparation of our condensed consolidated financial statements ~~in conformity with GAAP~~ requires ~~management~~us to make estimates, judgments and assumptions that may affect the reported amounts ~~reported in~~of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the ~~condensed consolidated financial statements~~results of which form the basis for making judgments about the carrying values of assets, liabilities and ~~accompanying notes.~~equity and the amount of revenues and expenses. Actual results may differ from those estimates.

~~Revenue Recognition~~

We analyze our collaboration arrangements to assess whether such arrangements, or transactions between arrangement participants, involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities or are more akin to a vendor-customer relationship. In making this evaluation, we consider whether the activities of the collaboration are considered to be distinct and deemed to be within the scope of the collaborative arrangement guidance and those that are more reflective of a vendor-

customer relationship and, therefore, within the scope of the revenue with contracts with customers guidance. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement.

For elements of collaboration arrangements that are not accounted for pursuant to the revenue from contracts with customers guidance, an appropriate recognition method is determined and applied consistently, generally by analogy to the revenue from contracts with customers guidance. Amounts related to transactions with a counterparty in a collaborative arrangement that is not a customer are presented as collaboration revenue and on a separate line item from revenue recognized from contracts with customers, if any, in our condensed consolidated statements of operations.

Amounts received prior to satisfying the revenue recognition criteria are recorded as deferred revenue in the condensed consolidated balance sheets. If the related efforts underlying the deferred revenue is expected to be satisfied within the next twelve months this will be classified in current liabilities. Unconditional rights to receive consideration in advance of performance are recorded as receivables and deferred revenue in the condensed consolidated balance sheets when we have a contractual right to bill and receive the payment, performance is expected to commence shortly and there is less than a year between billing and performance. Amounts recognized for satisfied performance obligations prior to the right to payment becoming unconditional are recorded as contract assets in the condensed consolidated balance sheets. If we expect to have an unconditional right to receive consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer.

For arrangements or transactions between arrangement participants determined to be within the scope of the contracts with customers guidance, we perform the following steps to determine the appropriate amount of revenue to be recognized as we fulfill our obligations: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) we satisfy each performance obligation.

At contract inception, we assess the goods or services promised in a contract with a customer and identify those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the performance obligation does not provide the customer with a material right.

We consider the terms of the contract and our customary business practices to determine the transaction price. The transaction price is the amount of consideration to which we expect to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur.

If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative stand-alone selling prices unless the transaction price is variable and meets the criteria to be allocated entirely to one or more, but not all, performance obligations in the contract. The relative selling price for each performance obligation is based on observable prices if it is available. If observable prices are not available, we estimate stand-alone selling price for the performance obligation utilizing the estimated cost of the performance obligation with an estimated assumed margin. Once the transaction price has been allocated to a performance obligation using the applicable methodology, it is not subject to reassessment for subsequent changes in stand-alone selling prices.

Revenue is recognized when, or as, we satisfy a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset. For performance obligations that are satisfied over time, we recognize revenue using an input or output measure of progress that best depicts our satisfaction of the relevant performance obligation. Revenues from performance obligations associated with a purchase order of Fintepla will be recognized when the customer obtains control of our product, which will occur at a point in time which may be upon shipment or delivery to the customer.

After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the overall transaction price is allocated to the performance obligations on the same methodology as at contract inception.

identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations.

Significant Accounting Policies

~~Our other~~The significant accounting policies and estimates used in the preparation of the accompanying condensed consolidated financial statements are described in Note 2, Summary of ~~Notes~~Significant Accounting Policies of notes to ~~Consolidated Financial Statements included~~the consolidated financial statements in our ~~2018 Annual Report on~~2019 Form 10-K. ~~As a result of entering into a collaborative arrangement~~There have been no material changes in ~~March 2019 and the adoption of the new lease accounting standard, we have updated our revenue recognition and lease accounting policies as detailed below. There were no other changes to~~ our significant accounting policies during the three months ended March 31, 2020 other than the recently adopted accounting pronouncements set forth below.

Impact of COVID-19 Pandemic

In March 2020, the World Health Organization declared the global novel coronavirus disease (COVID-19) outbreak a pandemic. To date, our operations have not been significantly impacted by the COVID-19 outbreak. However, we cannot predict the specific extent, duration, or full impact that the COVID-19 outbreak will have on our financial condition and operations, including ongoing and planned clinical trials, the timelines for receiving feedback or approvals from ~~those disclosed~~regulatory authorities, and a potential product launch in the midst of a pandemic.

Management is monitoring the potential impact of the COVID-19 pandemic, if any, on the carrying value of our ~~2018 Annual Report~~indefinite-lived in-process research and development (IPR&D) intangible asset, goodwill, long-lived assets and right-of-use assets. The full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations and financial condition, will depend on ~~Form 10-K. See Notes 3~~future developments that are highly uncertain, including as a result of new information that may emerge concerning COVID-19 and 7the actions taken to contain it or treat COVID-19, as well as the economic impact on local, regional, national and international markets. If the financial markets and/or the overall economy are impacted for ~~additional details related~~an extended period, our business, results of operations and financial condition may be adversely affected.

Income Taxes

On March 27, 2020, The Coronavirus Aid, Relief and Economic Security Act (CARES Act) was signed into law which lifts certain limitations originally imposed by the Tax Cuts and Jobs Act of 2017 (Tax Act). The CARES Act, among other provisions, retroactively and temporarily (for taxable years beginning before January 1, 2021) suspends application of the 80%-of-income limitation on the use of net operating losses, which was enacted as part of the Tax Act. It also provides that net operating losses arising in any taxable year beginning after December 31, 2017, and before January 1, 2021 are generally eligible to be carried back up to five years. The enactment of the CARES Act did not result in any material adjustments to our ~~collaborative arrangement and~~income tax provision for the ~~adoption~~three months ended March 31, 2020 or to our net deferred tax assets as of March 31, 2020. Given our history of losses, we do not expect the provisions of the ~~new lease accounting standard, respectively.~~CARES Act to have a material impact on our annual effective tax rate or condensed consolidated financial statements in 2020; however, we will continue to evaluate the impact of tax legislation and will update our disclosures as additional information and interpretive guidance becomes available.

Recently Adopted Accounting Pronouncements

Accounting Standards Update (ASU) ~~2018-18,~~ ~~Collaborative Arrangements: Clarifying the Interaction between Topic 808 and Topic 606~~ (ASU 2018-18) makes targeted improvements for collaborative arrangements by (1) clarifying that certain transactions between collaborative arrangement participants should be accounted for as revenue under the contract with customer guidance (Topic 606) when the collaborative arrangement participant is a customer, (2) adding unit of account guidance to assess whether the collaborative arrangement, or a part of the arrangement, is with a customer and (3) precluding a company from presenting transactions with collaborative arrangement participants that are not directly related to sales to third parties together with revenue from contracts with customers. Entities must apply the guidance retrospectively as of the date of their initial application of Topic 606 and should recognize the cumulative effect of initially applying the amendments as an adjustment to opening retained earnings as of the later of (1) the earliest annual period presented and (2) the annual period that includes the date of the entity’s initial application of Topic 606. ASU 2018-18 is effective for fiscal years beginning after December 15, 2019, including interim periods therein. Early adoption is permitted. We elected to early adopt this standard effective January 1, 2019 and have applied its guidance to our arrangement entered into in March 2019 with Nippon Shinyaku Co., Ltd. (See Note 3). No retrospective adjustment to our condensed consolidated financial statements was required as a result of our application of these amendments.

In August 2018, the SEC adopted the final rule under SEC Release No. 33-10532, Disclosure Update and Simplification, amending certain disclosure requirements that were redundant, duplicative, overlapping, outdated or superseded. Additionally, the amendments expanded the disclosure requirements on the analysis of stockholders’ equity for interim financial statements. Under the amendments, a summary of changes in each caption of stockholders’ equity presented in the consolidated balance sheets must be provided in a note or separate statement, and we have provided this disclosure beginning with the first quarter of 2019.

~~Leases~~

~~In February 2016, the FASB issued ASU No. 2016-02,~~ ~~Leases~~ ~~(Topic 842)~~. Topic 842 establishes a right-of-use asset model that requires all lessees to recognize ROU assets and liabilities for leases with a duration greater than one year on the balance sheet as well as provide disclosures with respect to certain qualitative and quantitative information regarding the amount, timing and uncertainty of cash flows arising from leases.

We adopted Topic 842 effective January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance. Consequently, prior period financial information and related disclosures have not been adjusted and will continue to be presented in accordance with the previous lease standard. In addition, we elected the package of transition provisions available for existing contracts, which allowed us to carryforward our historical assessments of (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct lease costs for existing leases. We did not elect the practical expedient allowing the use-of-hindsight which would require us to reassess the lease term of our leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the current contract portfolio.

The adoption of Topic 842 did not have a material impact on our condensed consolidated statements of operations and cash flows. The impact on the accompanying condensed consolidated balance sheet as of January 1, 2019 was as follows (in thousands):

December 31, 2018 Adjustments Due to the
Adoption of Topic 842 January 1, 2019
Assets
Operating lease right-of-use assets $ — $ 8,641 $ 8,641
Liabilities
Other accrued liabilities $ 1,845 $ (363) $ 1,482
Current portion of operating lease liabilities — 1,058 1,058
Operating lease liabilities, net of current portion — 11,776 11,776
Other long-term liabilities 3,830 (3,830) —
Total $ 5,675 $ 8,641 $ 14,316

Upon adoption on January 1, 2019, we recorded operating lease ROU assets and lease liabilities of $8.6 million and $12.8 million, respectively, with the difference between ROU assets and lease liabilities attributed to the reclassifications of deferred rent and lease incentive obligations, a cease-use liability and initial direct leasing costs as a component of ROU assets.

Prior to January 1, 2019, we recognized related rent expense on a straight-line basis over the term of the lease. Incentives granted under our operating lease, including allowances for leasehold improvements and rent holidays, were recognized as reductions to rent expense on a straight-line basis over the term of the lease. Deferred rent consisted of the difference between rent expense recognized on a straight-line basis and cash rent payments. Subsequent to the adoption of Accounting Standards Update (ASU) 2016-02 and related amendments (collectively, Topic 842) on January 1, 2019, we determine whether the arrangement is or contains a lease at the inception of the arrangement and if such a lease is classified as a financing lease or operating lease at lease commencement. All of our leases are classified as operating leases. Leases with a term greater than one year are included in operating lease right-of-use assets (ROU asset), current portion of lease liabilities, and lease liabilities, net of current portion in our condensed consolidated balance sheet at June 30, 2019. If a lease contains an option to renew, the renewal option is included in the calculation of lease liabilities if we are reasonably certain at lease commencement the renewal option will be exercised. Lease liabilities and their corresponding ROU assets are measured at the present value of the remaining lease payments, discounted at an appropriate incremental borrowing rate at lease commencement, or as of January 1, 2019, for our existing leases. Management uses judgment to estimate the appropriate incremental borrowing rate, which is the rate incurred to borrow on a collateralized basis over a similar term an amount equal to the lease payments in a similar economic environment. Certain adjustments to the ROU asset may be required for items such as initial direct lease costs, lease incentives, scheduled rent escalations and impairment charges if we determine the ROU asset is impaired. Operating lease expense is recognized on a straight-line basis over the lease term.

We elected the post-transition practical expedient to not separate lease components from non-lease components for all existing lease classes. We also elected a policy of not recording leases on our condensed balance sheets when a lease has a term of one year or less.

~~Recent Accounting Pronouncements Not Yet Effective~~

~~ASU~~ 2016-13, Financial Instruments—Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments~~requires that certain~~ revises the measurement of credit losses for most financial ~~assets be~~instruments measured at amortized cost, ~~net~~including trade receivables, from an incurred loss methodology to an expected loss methodology which results in earlier recognition of ~~an allowance for estimated~~ credit ~~losses such~~losses. Under the incurred loss model, a loss is not recognized until it is probable that the ~~net receivable represents~~loss-causing event has already occurred. The standard introduces a forward-looking expected credit loss model that requires an estimate of the ~~present value of~~ expected ~~cash collection. In addition, this standard update requires that certain financial assets be measured at amortized cost reflecting an allowance for estimated~~ credit losses ~~expected to occur~~ over the life of the ~~assets. The estimate of credit losses must be based on~~instrument by considering all relevant information including historical ~~information,~~experience, current conditions, and reasonable and supportable forecasts that affect collectability. In addition, the ~~collectability~~standard also modifies the impairment model for available-for-sale debt securities, which are measured at fair value, by eliminating the consideration for the length of ~~the amounts. This~~time fair value has been less than amortized cost when assessing credit loss for a debt security and provides for reversals of credit losses through income upon credit improvement. The standard ~~update is~~became effective for us onbeginning January 1, 2020. Based on the composition of our investment portfolio, which reflects our primary investment objective of capital

Zogenix, Inc. | Q1 2020 ~~with early~~Form 10-Q | 7

preservation, the adoption ~~permitted. We expect to adopt~~of this ~~ASU on January 1, 2020 and are currently evaluating the effect that the updated~~ standard ~~will~~did not have a material impact on our condensed consolidated financial statements ~~and~~or related disclosures.

ASU 2017-04, ~~Intangibles-Goodwill~~Intangibles—Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairmentsimplifies how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. Step 2 measures a goodwill impairment loss by comparing the implied fair value of a reporting unit’s goodwill with the carrying amount of that goodwill. The implied fair value for a reporting unit is determined in the same manner as the amount of goodwill recognized in a business acquisition of the reporting unit. Under the ~~amendments in ASU 2017-04,~~standard, an entity ~~should~~shall recognize an impairment charge for the amount by which the carrying amount of a reporting unit exceeds its fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. The ~~updated guidance requires a prospective adoption. ASU 2017-04 is~~standard became effective for ~~fiscal years~~us beginning ~~after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted~~

~~for goodwill impairment tests performed on testing dates after~~ January 1, ~~2017. We are currently evaluating the timing and effect that the updated~~2020. The adoption of this standard ~~will~~did not have a material impact on our condensed consolidated financial statements ~~and~~or related ~~disclosures.~~disclosures; however, any prospective goodwill impairment losses recognized will be measured in accordance with the updated guidance.

ASU 2018-13,Fair Value Measurement (Topic 820): Disclosure ~~Framework—~~Framework—Changes to the Disclosure Requirements for Fair Value Measurementmodifies the disclosure requirements in Topic 820 ~~Fair Value Measurement,~~ by removing certain disclosure requirements related to the fair value hierarchy, modifying existing disclosure requirements related to measurement uncertainty and adding new disclosure requirements, such as disclosing the ~~changes in unrealized gains and losses for the period included in other comprehensive income for recurring Level 3 fair value measurements held at the end of the reporting period and disclosing the~~ range and weighted average of significant unobservable inputs used to develop Level 3 fair value measurements. This standard became effective for us beginning January 1, 2020 and the adoption of this standard did not have a material impact on our condensed consolidated financial statements. For the new disclosures regarding our Level 3 fair value measurements, see Note 5, Fair Value Measurements to these condensed consolidated financial statements.

ASU 2019-12, Simplifying the Accounting for Income Taxes (Topic 740) removes certain exceptions to the general principles in Topic 740 related to the approach for intraperiod tax allocation, the methodology for calculating income taxes in an interim period and the recognition of deferred tax liabilities for outside basis differences. The new guidance also simplifies aspects of the accounting for franchise taxes and enacted changes in tax laws or rates and clarifies the accounting for transactions that result in a step-up in the tax basis of goodwill. This ASU is effective for ~~public companies~~us for ~~fiscal years~~all interim and annual periods beginning ~~after December 15, 2019, including interim periods within that fiscal year. Early~~January 1, 2021, with early adoption ~~is permitted for any removed or modified disclosures.~~permitted. We ~~are currently evaluating the timing and effect that the updated~~early adopted ASU 2019-12 beginning January 1, 2020 on a prospective basis. The adoption of this standard ~~will~~did not have a material impact on our condensed consolidated financial statements and related disclosures.

The only aspect of ASU 2019-12 that is currently applicable to us is the removal of the exception related to intraperiod tax allocation. Beginning in 2020, we will apply the general methodology regarding the intraperiod allocation of tax expense. After the adoption of ASU 2019-12, in periods where we have a loss from continuing operations, we will determine the amount of taxes attributable to continuing operations without regard to the tax effect of other items, including changes in unrealized gains related to marketable securities.

Recent Accounting Pronouncements

We have reviewed recently issued accounting pronouncements and concluded they are either not applicable to our business or no material effect is expected on our condensed consolidated financial statements as a result of future adoption.

Note 3 – Collaborative Arrangement

In March 2019, we entered into an agreement (Shinyaku Agreement) with Nippon Shinyaku Co., Ltd. (Shinyaku) for the exclusive distribution of Fintepla in Japan for the treatment of Dravet syndrome and LGS. As part of the Shinyaku Agreement, we are responsible for completing the global clinical development and all regulatory approval activities for Fintepla to support the submission of new drug applications in Japan for Dravet syndrome and LGS. Upon regulatory approval of Fintepla in Japan, Shinyaku will act as our exclusive distributor for Fintepla and will be responsible for the commercialization activities including the promotion, marketing, sale and distribution of Fintepla in Japan. Upon regulatory approval of Fintepla in Japan, Shinyaku will also act as our exclusive distributor for commercial shipment and distribution of Fintepla in Japan. If we pursue global development of Fintepla for indications other than Dravet syndrome or LGS, Shinyaku has the option to participate in the development for such indications in Japan, subject to cost sharing requirements pursuant to the agreement. Activities under the Shinyaku Agreement will be governed by a joint steering committee (JSC) consisting of three representatives from each party to the agreement. All decisions of the JSC are to be made by a unanimous vote with tie-breaking rights provided to each party for certain matters related to development, regulatory approval and ~~commercialization.~~commercializationselect distribution activities of Fintepla in that territory.

Zogenix, Inc. | Q1 2020 Form 10-Q | 8

Shinyaku has agreed to support development and regulatory approval of Fintepla in Japan by actively participating in the design of non-clinical, clinical and manufacturing requirements needed for regulatory submission, actively planning and participating in product labeling decisions and discussions with the Japanese Ministry of Health, Labor and Welfare (MHLW) and obtained distribution exclusivity through the payment of ~~$20.0 million, of which $15.5 million was received shortly after~~an initial fixed consideration. Pursuant to the ~~execution~~terms of the agreement, Shinyaku agreed to make aggregate fixed payments of $20.0 million to us in scheduled installments. As of March 31, 2020, we have received $17.0 million with the ~~remainder payable over~~remaining balance due within the next ~~two years.~~ year. We will be actively running the clinical trials, performing manufacturing validation activities, preparing regulatory filings and holding discussions with MHLW, and negotiating pricing. We and Shinyaku have agreed to proportionally share the Japan specific development costs that may arise outside of the initial development plan and any post-approval clinical study costs in Japan. In addition, we can earn up to $66.0 million from Shinyaku for the achievement of certain regulatory milestones ~~related to~~for the treatment of Dravet syndrome and ~~the treatment of~~ LGS.

~~After~~ If regulatory approval of Fintepla is received in Japan, ~~has been obtained,~~ we have agreed to supply Shinyaku with Fintepla upon receipt of purchase orders at our actual manufacturing cost plus a fixed transfer price mark-up, a fixed percentage of Shinyaku's net sales of Fintepla in Japan for such fiscal year, and a net price mark-up based on a percent of the applicable aggregate sales of Fintepla by Shinyaku for such fiscal year. The net price mark-up percentage increases with Shinyaku’s sales of Fintepla annual net sales in Japan and ranges between mid-twenties and is capped at a low thirties of the aggregate annual net sales for an applicable fiscal year.

In addition, we can earn up to an additional $42.5 million tied to the achievement of certain net sales milestones by Shinyaku through the term of the ~~agreement.~~

~~The Shinyaku Agreement~~agreement, which generally expires in September of 2045, unless earlier terminated by either party for a change in control, a material breach, bankruptcy, dissolution, or winding up of such other party. The Shinyaku Agreement may be also terminated by either party: (1) with one year prior written notice to the other party on or after the date of the first commercial sale of a competing generic version of the Fintepla in Japan, (2) if, prior to the launch of the Fintepla in Japan, a party has a good faith concern, based on credible evidence, that such launch is not likely to be possible with commercially reasonable efforts, or (3) if a party believes Fintepla poses a substantial safety concern. We may also terminate the agreement following the second anniversary of the first commercial sale of the Fintepla in Japan if Shinyaku has failed to achieve or maintain certain diligence obligations under the Shinyaku Agreement. Shinyaku may also terminate the agreement if, prior to the launch of the Fintepla in Japan, Shinyaku has a good faith concern that Fintepla will not be commercially viable in Japan.2045.

~~We concluded that~~The collaborative activities under the Shinyaku Agreement prior to regulatory approval are within the scope of the accounting guidance related to collaborative arrangements ~~guidance~~ as both parties are active participants and are exposed to significant risks and rewards dependent on the success of commercializing Fintepla in Japan. Since Shinyaku is not a customer as it does not obtain an output of our development and regulatory approval activities for Fintepla as they were not provided a license to ~~its~~our intellectual property or the ability to manufacture the product, and we do not consider performing development and regulatory approval services to be a part of our ongoing activities. Shinyaku will only become a customer and subject to revenue from contracts from customers accounting guidance after regulatory approval of Fintepla in Japan occurs and Shinyaku places purchase orders with us.To date, Shinyaku has not provided us with any purchase orders and thus no revenue has been recognized for the supply of Fintepla.

We considered the revenue from contracts with customers guidance by analogy in determining the unit of account, and the recognition and measurement of such unit of account for collaborative activities under the Shinyaku Agreement and concluded that there are two development programs akin to performance obligations related to collaborative activities for development and regulatory approval efforts for Dravet and LGS. ~~Participation on the JSC was concluded to be both quantitatively and qualitatively immaterial in the context of the Shinyaku Agreement.~~We are the principal as it relates to the collaborative development and regulatory approval activities primarily because we are responsible for the acceptability of the results of the work of the third-party vendors that are used to assist us in performing such activities. Therefore, such collaboration revenue ~~has been~~is presented on a gross basis in our condensed consolidated statements of operations apart from research and development expenses ~~incurred.~~incurred.

Since Shinyaku was not provided a license to our intellectual property or the ability to manufacture Fintepla, Shinyaku will only become a customer, and payments made under the Shinyaku Agreement will only be subject to the accounting guidance related to revenue from contracts from customers, after regulatory approval of Fintepla in Japan occurs and Shinyaku places purchase orders with us.

The initial collaboration consideration consisted solely of the fixed consideration payments of $20.0 million and was allocated on a relative standalone selling price basis to ~~each associated~~the two identified development ~~program was determined using the most likely method~~programs akin to ~~consist solely of the fixed consideration payments of $20.0 million.~~performance obligations related to collaborative activities for development and regulatory approval efforts for Dravet syndrome and LGS. Analogizing to the revenue from contracts with customers variable consideration guidance, all potential regulatory milestone payment consideration will be included in the collaboration consideration if and when it is probable that a significant reversal in the amount of cumulative collaboration consideration recognized will not occur when the uncertainty associated with the variable collaboration consideration is subsequently resolved. At contract inception and through ~~June 30, 2019,~~March 31, 2020, this consideration was fully constrained as the achievement of the events tied to these regulatory milestone payments was highly dependent on factors outside our control.

Collaboration revenue is being recognized over time as the collaborative activities related to each development program are rendered. We determined an input method is a reasonable representative depiction of the performance of the collaborative activities under the Shinyaku Agreement. The method of measuring progress towards completion incorporates actual internal and external costs incurred, relative to total internal and external costs expected to be incurred over an estimated period to satisfy the collaborative activities. The period over which total costs are estimated reflects our estimate of the period over which it will perform the collaborative activities for each development program. ~~We expect to recognize collaboration revenue for each development program over periods ranging from~~ ~~three~~ ~~to four years.~~ Changes in estimates of total internal and external costs expected to be incurred are recognized in the period of change as a cumulative catch-up adjustment to collaboration revenue.

Zogenix, Inc. | Q1 2020 Form 10-Q | 9

As of June 30, 2019, we had received $15.5 million out of the $20.0 million in fixed consideration. The remaining $4.5 million will be billed in accordance with the terms of the agreement and will be recorded when there is an unconditional right to receive this payment. For the three ~~and six~~ months ended ~~June 30, 2019,~~March 31, 2020, we recognized collaboration revenue of ~~$1.1~~$1.2 million. As of ~~June 30, 2019, we~~March 31, 2020, $12.1 million related to this agreement was recorded ~~$14.4 million in~~as deferred revenue, which is classified as either current or net of current portion in the accompanying condensed consolidated balance sheets based on the period over which the collaboration revenue is expected to be recognized. We expect to recognize collaboration revenue related to these collaborative activities through the end of 2023.

We concluded that the supply of Fintepla to Shinyaku will be within the scope of the revenue from contracts with customers guidance if regulatory approval in Japan occurs and when a purchase order is received from Shinyaku. Such activity is considered to be a vendor customer relationship as Shinyaku will be a party that has contracted with an us to obtain goods or services that are an output of our ordinary activities in exchange for consideration and selling approved commercial product to a customer is expected to be part of our ongoing activities. Each purchase order for a shipment of Fintepla will be identified as a separate performance obligation as we did not grant Shinyaku intellectual property rights. The agreed upon price for the supply of Fintepla (cost plus a fixed transfer price mark-up, fixed percentage of aggregate sales of Fintepla by Shinyaku per year, the net price mark-up and sales milestones) to Shinyaku does not represent a material right, and therefore is not a performance obligation, and such pricing on an aggregate basis represents the standalone selling price a distributor would typically pay for such a product in that region or market. There are also no minimum purchase commitments. The transaction price to be allocated to the performance obligation will include the fixed consideration associated with the cost-plus price of Fintepla and variable consideration associated with a fixed percentage of aggregate sales of Fintepla by Shinyaku per year, the net price mark-up and sales milestones subject to the constraint. As of June 30, 2019, Shinyaku has not provided us with any purchase orders and thus no revenue has been recognized for the supply of Fintepla.

Note 4 – Cash, Cash Equivalents and Marketable Securities

The following tables summarize the amortized cost and the estimated fair value of our cash, cash equivalents and marketable securities as of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018~~2019 (in thousands):

June 30, 2019
Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value
Current assets:
Cash $ 18,157 $ — $ — $ 18,157
Cash equivalents:
Commercial paper 17,443 — — 17,443
Money market funds 15,188 — — 15,188
Total cash equivalents 32,631 — — 32,631
Total cash and cash equivalents 50,788 — — 50,788
Marketable securities:
Commercial paper 153,691 — — 153,691
Corporate debt securities 83,108 431 (5) 83,534
Certificate of deposits 70,175 — — 70,175
U.S. Treasuries 104,480 300 — 104,780
Total marketable securities 411,454 731 (5) 412,180
Total cash, cash equivalents and marketable securities $ 462,242 $ 731 $ (5) $ 462,968


		December 31, 2018															March 31, 2020
		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value			Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Current assets:	Current assets:									Current assets:
Cash	Cash	$	5,222	$	—	$	—	$	5,222	Cash	$	11,271	$	—	$	—	$	11,271
Cash equivalents:										Cash equivalents:

Cash equivalents:
Money market funds	Money market funds	63,232		—		—		63,232		Money market funds	224,070		—		—		224,070

Commercial paper										Commercial paper	34,634		—		—		34,634
Total cash and cash equivalents	Total cash and cash equivalents	68,454		—		—		68,454		Total cash and cash equivalents	269,975		—		—		269,975
Marketable securities:	Marketable securities:									Marketable securities:
Commercial paper	Commercial paper	152,940		—		—		152,940		Commercial paper	39,528		—		—		39,528
Corporate debt securities	Corporate debt securities	60,622		58		(75)		60,605		Corporate debt securities	70,543		273		(66)		70,750
Certificate of deposits	Certificate of deposits	128,647		—		—		128,647		Certificate of deposits	39,940		—		—		39,940
U.S. Treasury securities		103,521		31		(11)		103,541

Total marketable securities	Total marketable securities	445,730		89		(86)		445,733		Total marketable securities	150,011		273		(66)		150,218
Total cash, cash equivalents and marketable securities	Total cash, cash equivalents and marketable securities	$	514,184	$	89	$	(86)	$	514,187	Total cash, cash equivalents and marketable securities	$	419,986	$	273	$	(66)	$	420,193



	December 31, 2019
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Current assets:
Cash	$	43,058	$	—	$	—	$	43,058


Cash equivalents:
Money market funds	11,527		—		—		11,527
Commercial paper	7,485		—		—		7,485
Total cash and cash equivalents	62,070		—		—		62,070
Marketable securities:
Commercial paper	73,366		—		—		73,366
Corporate debt securities	74,038		381		(2)		74,417
Certificate of deposits	41,302		—		—		41,302

Total marketable securities	188,706		381		(2)		189,085
Total cash, cash equivalents and marketable securities	$	250,776	$	381	$	(2)	$	251,155

Zogenix, Inc. | Q1 2020 Form 10-Q | 10

The following table summarizes the cost and fair value of marketable securities based on stated effective maturities as of ~~June 30, 2019~~March 31, 2020 (in thousands):


		Amortized Cost		Fair Value			Amortized Cost		Fair Value
Due within one year	Due within one year	$	361,446	$	361,814	Due within one year	$	127,968	$	128,147
Due between one and two years	Due between one and two years	50,008		50,366		Due between one and two years	22,043		22,071
Total	Total	$	411,454	$	412,180	Total	$	150,011	$	150,218

~~There~~We regularly review our available-for-sale marketable securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, market data, issuer-specific factors, and current economic conditions. For all marketable securities that have been ~~no significant realized gains or losses on available-for-sale securities for the periods presented. As of June 30, 2019, available-for-sale debt securities that were~~ in a continuous loss position ~~but~~as of March 31, 2020, we have the ability and intent to hold until maturity or recovery. We determined the gross unrealized losses were ~~not~~caused by market fluctuations. There have been no specific facts or circumstances that have arisen to indicate that there has been any significant deterioration in the creditworthiness of the issuers of these securities. As such, we determined no allowance for credit losses was deemed ~~to be~~necessary.

Accrued interest receivable is recorded in “Prepaid expenses and other ~~than temporarily impaired were not material.~~current assets” on our condensed consolidated balance sheets and was $0.7 million and $0.6 million as of March 31, 2020 and December 31, 2019, respectively.

See Note 5 for further information regarding the fair value of our financial instruments.

Zogenix, Inc. | Q1 2020 Form 10-Q | 11

Note 5 – Fair Value Measurements

Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. A three-level valuation hierarchy has been established under GAAP for disclosure of fair value measurements. The valuation hierarchy is based on the transparency of inputs to the valuation of an asset or liability as of the measurement date. The three levels are defined as follows:


Level 1:			Observable inputs such as quoted prices in active markets;
Level 2:			Inputs, other than the quoted prices in active markets, that are observable either directly or indirectly; and
Level 3:			Unobservable inputs in which there is little or no market data, which require the reporting entity to develop its own assumptions.

Our financial instruments consist primarily of cash and cash equivalents, marketable securities, ~~accounts receivable,~~ other current assets, accounts payable and accrued liabilities, contingent consideration liabilities and our outstanding common stock warrant liabilities. Certain cash equivalents, marketable securities, contingent consideration liabilities and common stock warrant liabilities are reported at their respective fair values on our condensed consolidated balance sheets. The remaining financial instruments are carried at cost which approximates their respective fair values because of the short-term nature of these financial instruments. See Note 4 for further information regarding the amortized cost of our financial assets.

The following tables summarize assets and liabilities recognized or disclosed at fair value on a recurring basis as of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018~~2019 (in thousands):


		June 30, 2019															March 31, 2020
		Level 1		Level 2		Level 3		Total			Level 1		Level 2		Level 3		Total
Assets:	Assets:									Assets:
Cash equivalents:	Cash equivalents:									Cash equivalents:
Commercial paper	Commercial paper	$	—	$	17,443	$	—	$	17,443	Commercial paper	$	—	$	34,634	$	—	$	34,634
Money market funds	Money market funds	15,188		—		—		15,188		Money market funds	224,070				—		224,070

Marketable securities:	Marketable securities:									Marketable securities:
Commercial paper	Commercial paper	—		153,691		—		153,691		Commercial paper	—		39,528		—		39,528
Corporate debt securities	Corporate debt securities	—		83,534		—		83,534		Corporate debt securities	—		70,750		—		70,750
Certificate of deposits	Certificate of deposits	—		70,175		—		70,175		Certificate of deposits	—		39,940		—		39,940
U.S. Treasury securities		—		104,780		—		104,780

Total assets⁽¹⁾	Total assets⁽¹⁾	$	15,188	$	429,623	$	—	$	444,811	Total assets (1)	$	224,070	$	184,852	$	—	$	408,922
Liabilities:	Liabilities:									Liabilities:
Common stock warrant liabilities⁽²⁾	Common stock warrant liabilities⁽²⁾	$	—	$	—	$	501	$	501	Common stock warrant liabilities⁽²⁾	$	—	$	—	$	36	$	36
Contingent consideration liabilities⁽³⁾	Contingent consideration liabilities⁽³⁾	—		—		70,500		70,500		Contingent consideration liabilities⁽³⁾	—		—		55,900		55,900
Total liabilities	Total liabilities	$	—	$	—	$	71,001	$	71,001	Total liabilities	$	—	$	—	$	55,936	$	55,936


		December 31, 2018															December 31, 2019
		Level 1		Level 2		Level 3		Total			Level 1		Level 2		Level 3		Total
Assets:	Assets:									Assets:
Cash equivalents:	Cash equivalents:									Cash equivalents:
Money market funds	Money market funds	$	63,232	$	—	$	—	$	63,232	Money market funds	$	11,527	$	—	$	—	$	11,527
Commercial paper										Commercial paper	—		7,485		—		$	7,485
Marketable securities:	Marketable securities:									Marketable securities:
Commercial paper	Commercial paper	—		152,940		—		152,940		Commercial paper	—		73,366		—		73,366
Corporate debt securities	Corporate debt securities	—		60,605		—		60,605		Corporate debt securities	—		74,417		—		74,417
Certificate of deposits	Certificate of deposits	—		128,647		—		128,647		Certificate of deposits	—		41,302		—		41,302
U.S. Treasury securities		—		103,541		—		103,541

Total assets⁽¹⁾	Total assets⁽¹⁾	$	63,232	$	445,733	$	—	$	508,965	Total assets (1)	$	11,527	$	196,570	$	—	$	208,097
Liabilities:	Liabilities:									Liabilities:
Common stock warrant liabilities⁽²⁾		$	—	$	—	$	343	$	343
Contingent consideration liabilities⁽³⁾		—		—		78,200		78,200
Common stock warrant liabilities										Common stock warrant liabilities	$	—	$	—	$	198	$	198
Contingent consideration liabilities										Contingent consideration liabilities	—		—		63,800		63,800
Total liabilities	Total liabilities	$	—	$	—	$	78,543	$	78,543	Total liabilities	$	—	$	—	$	63,998	$	63,998

(1)

~~(1)~~ Fair value is determined by taking into consideration valuations obtained from third-party pricing services. The third-party pricing services utilize industry standard valuation models, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. These inputs include reported trades of and broker/dealer quotes on the same or similar securities; issuer credit spreads; benchmark securities; and other observable inputs.

~~(2) Represents~~Contingent Consideration Liability

Pursuant to the ~~fair value of common stock warrants outstanding that may require cash settlement under certain circumstances. We estimated the fair value~~terms of the ~~warrant liabilities using~~Brabant purchase agreement in 2014 in which we acquired worldwide development and commercialization rights to Fintepla, we are obligated to make future milestone payments that are contingent upon the ~~Black-Scholes valuation model. As~~successful achievement of ~~June 30, 2019~~certain regulatory and ~~December 31, 2018, common stock warrant liabilities relate~~sales-based milestone events related to ~~warrants issued in July 2011 in connection with a debt financing arrangement.~~Fintepla. The ~~warrants entitle the holder to purchase up to 28,125 shares~~potential amount of ~~our common stock at an exercise price of $72.00 per share and expires in July 2021.~~

~~(3) In connection with a prior acquisition in 2014,~~future payments that we may be required to ~~pay future contingent consideration upon the achievement of specified development, regulatory approval or sales-based milestone events. We estimated the fair value~~make is between 0, if none of the ~~contingent consideration liabilities on the acquisition date using~~remaining milestones are achieved, to a ~~probability-weighted income approach, which reflects the probability and timing~~maximum of future payments. This fair value measurement is based on significant Level 3 inputs such as the anticipated timelines and probability of achieving development, regulatory approval or sales-based milestone events and projected revenues. $75.0 million.

The resulting probability-weighted cash flows are discounted at risk-adjusted interest rates. Subsequent to the acquisition date, at each reporting period prior to settlement, we revalue these liabilities by performingfollowing table provides a review of the assumptions listed above and record increases or decreases in the fair value of these contingent consideration liabilities. In the absence of any significant changes in key assumptions, the quarterly determination of fair values of these contingent consideration liabilities would primarily reflect the passage of time and risk-adjusted interest rates. Significant judgment is used in determining Level 3 inputs and fair value measurements as of the acquisition date and for each subsequent reporting period. Updates to assumptions could have a significant impact on our results of operations in any given period and actual results may differ from estimates. For example, significant increases in the probability of achieving a milestone or projected revenues would result in a significantly higher fair value measurement while significant decreases in the estimated probability of achieving a milestone or projected revenues would result in a significantly lower fair value measurement. Significant increases in the discount rate or in the anticipated timelines would result in a significantly lower fair value measurement while significant decreases in the discount rate or anticipated timelines would result in a significantly higher fair value measurement. The acquisition provides for aggregate contingent consideration of up to $95.0 million, of which $10.0 million was paid in March 2019. As of June 30, 2019, the estimated fair valuereconciliation of our contingent consideration liabilities was $70.5 million, of which $34.8 million has been classified as current liabilities. The classification was based upon our reasonable expectation as to the timing of settlement of certain specified milestones.

~~The following tables provide a reconciliation of liabilities~~liability measured at fair value on a recurring basis using significant unobservable inputs (Level 3) for the three ~~and six~~ months ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~ (in thousands):

~~Contingent Consideration Liabilities~~

Three Months Ended June 30, Six Months Ended June 30,
2019 2018 2019 2018
Balance at beginning of period $ 71,200 $ 76,900 $ 78,200 $ 76,900
Change in fair value (700) (2,500) 2,300 (2,500)
Settlements — — (10,000) —
Balance at end of period $ 70,500 $ 74,400 $ 70,500 $ 74,400

~~Common Stock Warrant Liabilities~~


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018		2019		2018			2020		2019
Balance at beginning of period	Balance at beginning of period	$	646	$	495	$	343	$	512	Balance at beginning of period	$	63,800	$	78,200
Change in fair value	Change in fair value	(145)		48		158		31		Change in fair value	(7,900)		3,000
Settlements										Settlements	—		(10,000)
Balance at end of period	Balance at end of period	$	501	$	543	$	501	$	543	Balance at end of period	$	55,900	$	71,200

The ~~changes~~decrease in fair value of our contingent consideration for the ~~liabilities shown~~three months ended March 31, 2020 was primarily due to changes to our probability-weighted estimates for achieving regulatory/commercial milestones and the use of a higher discount rate to reflect an increase in ~~the tables above are recorded through change~~credit-adjusted interest rates. The increase in fair value of our contingent consideration for the three months ended March 31, 2019 was primarily due to the inclusion of sales in Japan in our forecast associated with the execution of the Shinyaku Agreement, which accelerated the estimated timing of when certain sales milestones will be reached, and a market driven decrease in the discount rate.

The following table summarizes the significant unobservable inputs used in the fair value measurement of our contingent consideration liabilities ~~within operating expense and~~as of March 31, 2020.


Fair Value as of March 31, 2020 (in thousands)	Valuation Technique	Unobservable Input	Range	Weighted Average (1)
$55,900	Discounted cash flow	Discount rate	6.5% — 14.8%	9.8%
			Probability of payment	0% — 85.1%	85.1%
			Projected year of payment	2020 — 2030	2022

(1)Unobservable inputs were weighted by the ~~change in~~relative fair value of ~~common stock warrant liabilities within other income (expense) in~~ the ~~condensed consolidated statements~~contingent consideration liability. For projected year of ~~operations.~~payment, the amount represents the median of the inputs and is not a weighted average.

~~There were no transfers between levels during~~The weighted average discount rate was calculated based on the ~~periods presented. See Note 4 for further information regarding the amortized cost~~relative fair value of our ~~financial instruments.~~contingent consideration obligations. Significant increases or decreases in projected revenues, probabilities of payment, discount rates or the time until payment is made would have resulted in a significantly lower or higher fair value measurement as of March 31, 2020.

Note 6 – Accrued and Other Current Liabilities

The following table provides details of accrued and other current liabilities (in thousands):


		June 30, 2019		December 31, 2018			March 31, 2020		December 31, 2019
Accrued clinical trial expenses	Accrued clinical trial expenses	$	11,627	$	10,621	Accrued clinical trial expenses	$	14,215	$	18,666
Accrued compensation	Accrued compensation	4,328		5,277		Accrued compensation	4,930		7,179
Other accrued liabilities	Other accrued liabilities	4,490		1,845		Other accrued liabilities	6,622		4,074
Common stock warrant liabilities	Common stock warrant liabilities	501		343		Common stock warrant liabilities	36		198
Total accrued and other current liabilities	Total accrued and other current liabilities	$	20,946	$	18,086	Total accrued and other current liabilities	$	25,803	$	30,117

Note 7 – Leases

We have ~~two noncancellable~~ operating leases consisting of ~~administrative and research and development~~ office space for our Emeryville, California headquarters and for our various subsidiaries. In March 2020, our operating lease for our former headquarters in San Diego, California ~~that expire~~and the co-terminus sublease arrangement with our sublessee expired in ~~May 2027 and March~~accordance with the terms of the leases. In February 2020, ~~respectively. Our Emeryville~~we entered into a lease ~~includes~~for office space in Maidenhead, United Kingdom, for a ~~renewal option~~five-year term with aggregate lease payments of approximately $1.5 million. Operating lease assets represent our right to use an underlying asset for ~~an additional five years, which was not included in our determination~~the lease term. Operating lease liabilities represent the present value of lease payments over the lease term, under the legacy lease standard as renewal was not reasonably assured at the inception of the lease. As a result, the renewal option to extend the lease was not included in determining our ROU assets and lease liabilities. Our former headquarters has been subleased todiscounted using an ~~unrelated third party for the remainder~~estimate of our original lease term. As of June 30, 2019, we do not have any material finance leases or service contracts with lease arrangements. Our lease agreements do not contain any material residual value guarantees or material restrictive covenants.secured incremental borrowing rate.

The components of lease costs, which were included in our condensed consolidated statements of operations, were as follows (in thousands):


	Three Months Ended March 31,
	2020		2019
Lease costs
Operating lease cost	$	567	$	499
Short-term lease cost (1)	157		328
Sublease income	(115)		(145)
Total	$	609	$	682

(1)

Three Months Ended
June 30, 2019 Six Months Ended
June 30, 2019
Lease costs
Operating lease cost $ 496 $ 995
Short-term lease cost⁽¹⁾
220 548
Sublease income (145) (290)
Total $ 571 $ 1,253

⁽¹⁾Short-term lease cost included $0.2 million related to a short-term lease that expired in March 2019.

Cash paid for amounts included in the measurement of lease liabilities for the ~~six~~three months ended ~~June 30,~~March 31, 2020 and 2019 was $0.6 million and ~~was~~$0.3 million, respectively. The amounts were included in net cash used in operating activities in our condensed consolidated statements of cash flows. Right-of-use assets obtained in exchange for new operating lease liabilities were $1.2 million for the three months ended March 31, 2020.

Zogenix, Inc. | Q1 2020 Form 10-Q | 14

Maturities of operating lease liabilities as of ~~June 30, 2019~~March 31, 2020 and ~~lease commitments under noncancellable operating leases as of~~ December 31, ~~2018~~2019 were as follows (in thousands):


		June 30, 2019		December 31, 2018			March 31, 2020		December 31, 2019
2019 (remaining 6 months and 12 months, respectively)		$	1,164	$	1,777
2020		1,788		1,788
2020 (remaining 9 months and 12 months, respectively)						2020 (remaining 9 months and 12 months, respectively)	$	1,533	$	1,986
2021	2021	1,839		1,839		2021	2,292		1,957
2022	2022	1,894		1,894		2022	2,230		1,894
2023	2023	1,951		1,951		2023	2,287		1,951
2024						2024	2,300		2,010
Thereafter	Thereafter	7,111		7,296		Thereafter	5,103		5,101
Total lease payments	Total lease payments	15,747		$	16,545	Total lease payments	15,745		14,899
Less imputed interest	Less imputed interest	(3,159)				Less imputed interest	(2,908)		(2,825)
Total operating lease liabilities	Total operating lease liabilities	$	12,588			Total operating lease liabilities	$	12,837	$	12,074


	~~June 30, 2019~~
~~Current portion of operating lease liabilities~~	$	~~1,402~~
~~Operating lease liabilities, net of current portion~~	~~11,186~~
~~Total lease liabilities~~	$	~~12,588~~


	March 31, 2020		December 31, 2019
Current portion of operating lease liabilities	$	1,383	$	1,322
Operating lease liabilities, net of current portion	11,454		10,752
Total lease liabilities	$	12,837	$	12,074

As of ~~June 30, 2019,~~March 31, 2020, the weighted average remaining lease term was ~~7.5~~6.8 years and the weighted average discount rate, weighted based on the remaining balance of lease payments, was ~~6.0%~~6.2%.

Note 8 – ~~Common Stock~~Stockholders’ Equity and Stock-Based Compensation

~~Increase in Authorized Shares~~Sale of Common Stock

In ~~May 2019, our stockholders approved and~~March 2020, we ~~filed~~completed an ~~amendment to our Fifth Amended and Restated Certificate~~underwritten public offering of ~~Incorporation, as amended, to increase the total number of authorized~~9,798,000 shares of our common stock at an offering price of $23.50 per share, including 1,278,000 shares sold pursuant to the underwriters’ full exercise of their option to purchase additional shares. Net proceeds realized from ~~50,000,000~~the offering amounted to ~~100,000,000.~~approximately $221.7 million, after deducting commissions and other offering expenses.

Equity Incentive Plans

We have issued stock-based awards from various equity incentive and stock purchase plans, as more fully described in Note 12, Stock-Based Compensation to the consolidated financial statements ~~and related notes included~~ in our ~~2018 Annual Report on~~2019 Form 10-K.

At December 31, 2018, 1,550,351 shares were available for grant under our 2010 Equity Incentive Award Plan (2010 Plan). Pursuant to its evergreen provision, the number of shares reserved for issuance under the 2010 Plan automatically increases on January 1 of each year, commencing on January 1, 2013, and on each January 1 through and including January 1, 2020, in an amount equal to 4% of the total number of shares of common stock outstanding on December 31 of the preceding year, or a lesser number of shares as determined by our board of directors. On January 1, 2019, the increase in shares reserved for issuance pursuant to the evergreen provision was limited to 589,619 shares as the 2010 Plan’s maximum 7,500,000 shares reserved for issuance was reached.

In May 2019, our stockholders approved the amendment and restatement of our 2010 Plan (2010 Restated Plan), which provided an increase in the number of shares of common stock reserved for issuance pursuant to awards granted under our 2010

Plan from 7,500,000 to 11,500,000 and an extension of the term of the 2010 Plan through March 2029. In addition, the 2010 Restated Plan eliminated the evergreen provision that provided for an annual increase in the number of shares available for issuance under the 2010 Plan on January 1 of each year discussed above. Following its approval, all future issuance of equity awards will be granted under the 2010 Restated Plan (other than the shares available for purchase under our 2010 Employee Stock Purchase Plan). As of June 30, 2019, 5,226,029 shares were available for future issuance under the 2010 Restated Plan.

Stock Options

The following is a summary of stock option activity for the ~~six~~three months ended ~~June 30, 2019~~March 31, 2020 (in thousands, except per share data):


		Shares	Weighted- Average Exercise Price per Share			Shares	Weighted- Average Exercise Price per Share
Outstanding at December 31, 2018		3,744	$	20.69
Outstanding at December 31, 2019					Outstanding at December 31, 2019	4,253	$	29.59
Granted	Granted	924	50.28		Granted	841	30.11
Exercised	Exercised	(386)	14.83		Exercised	(230)	16.87
Canceled	Canceled	(46)	34.57		Canceled	(65)	37.07
Outstanding at June 30, 2019		4,236	$	27.53
Outstanding at March 31, 2020					Outstanding at March 31, 2020	4,799	$	30.19

Restricted Stock Units

The following is a summary of restricted stock unit activity for the ~~six~~three months ended ~~June 30, 2019~~March 31, 2020 (in thousands, except per share data):

Shares Weighted- Average Fair Value per Share at Grant Date
Outstanding at December 31, 2018 289 $ 25.56
Granted 169 52.56
Vested (31) 42.65
Canceled (16) 26.15
Outstanding at June 30, 2019 411 $ 35.33

Zogenix, Inc. | Q1 2020 Form 10-Q | 15


	Shares	Weighted- Average Fair Value per Share at Grant Date
Outstanding at December 31, 2019	439	$	36.97
Granted	216	27.36
Vested	(66)	48.41
Canceled	(8)	37.56
Outstanding at March 31, 2020	581	$	32.11

Stock-Based Compensation Expense Allocation

The following table summarizes the components of total stock-based compensation expense included in the condensed consolidated statements of operations (in thousands):


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018		2019		2018			2020		2019
Research and development	Research and development	$	2,074	$	1,062	$	3,509	$	1,743	Research and development	$	2,729	$	1,435
Selling, general and administrative	Selling, general and administrative	3,284		1,997		6,072		3,228		Selling, general and administrative	3,665		2,788

Total	Total	$	5,358	$	3,059	$	9,581	$	4,971	Total	$	6,394	$	4,223

Note 9 – Net Loss Per Share

Basic net loss ~~from continuing operations~~ per share is calculated by dividing net loss ~~from continuing operations~~ by the weighted average number of shares outstanding for the period. Diluted net loss ~~from continuing operations~~ per share is calculated by dividing net loss ~~from continuing operations~~ by the weighted average number of shares of common stock and potential dilutive common stock equivalents outstanding during the period if the effect is dilutive. ~~The Company’s~~Our potentially dilutive shares of common stock include outstanding stock options, restricted stock units and warrants to purchase common stock.

A reconciliation of the numerators and denominators used in computing net loss ~~from continuing operations~~ per share is as follows (in thousands, except per share amounts):


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018		2019		2018			2020		2019
Numerator:	Numerator:									Numerator:
Net loss from continuing operations		$	(37,763)	$	(28,839)	$	(72,965)	$	(59,019)
Net loss										Net loss	$	(25,800)	$	(35,202)

Denominator:	Denominator:									Denominator:
Shares used in per share calculation	Shares used in per share calculation	42,458		35,355		42,348		35,099		Shares used in per share calculation	48,185		42,236

Net loss from continuing operations per share, basic and diluted		$	(0.89)	$	(0.82)	$	(1.72)	$	(1.68)
Net loss per share, basic and diluted										Net loss per share, basic and diluted	$	(0.54)	$	(0.83)

The following table presents the potential shares of common stock outstanding that were excluded from the ~~computation~~calculation of diluted net loss ~~from continuing operations~~ per share for the periods presented because including them would have been anti-dilutive (in thousands):


		Three Months Ended June 30,			Six Months Ended June 30,				Three Months Ended March 31,
		2019	2018	2019	2018		2020	2019
Shares subject to outstanding common stock options		4,227	3,816	3,973	3,648
Shares subject to outstanding stock options						Shares subject to outstanding stock options	4,450	3,716
Shares subject to outstanding restricted stock units	Shares subject to outstanding restricted stock units	415	292	355	279	Shares subject to outstanding restricted stock units	485	295
Shares subject to outstanding warrants to purchase common stock	Shares subject to outstanding warrants to purchase common stock	28	38	28	38	Shares subject to outstanding warrants to purchase common stock	28	28
Total	Total	4,670	4,146	4,356	3,965	Total	4,963	4,039

Zogenix, Inc. | Q1 2020 Form 10-Q | 16

Note 10 – United Kingdom (U.K.) Research and Development ~~Incentives~~(R&D) Tax Relief Scheme

We ~~carry out~~conduct extensive research and development activities that benefit from ~~the~~ U.K.’s small and medium-sized ~~enterprise (SME) research and development~~enterprises (SMEs) R&D tax ~~credit regime, whereby we may either~~relief scheme. Under this tax relief scheme, a SME has an option to receive an enhanced U.K. tax deduction on ~~our~~its eligible ~~research and development~~R&D activities or, when an SME entity is in a net operating loss position, can elect to surrender net operating losses that arise from its eligible ~~research and development~~R&D activities in exchange for a cash payment from the U.K. tax authorities. ~~These refundable cash credits, which~~As the tax incentives may be received without regard to an entity’s actual tax liability, they are not subject to accounting for income ~~taxes and have been~~taxes. Amounts recognized by us for cash payment claims under the SME R&D tax relief scheme are recorded as a component of other ~~income.~~

~~In December 2018, we filed~~income after an election for tax relief has been made by submitting a claim for a discrete tax year and collectability is deemed probable and reasonably assured.

As of December 31, 2019, we submitted claims as an SME for a ~~$7.1~~total amount of $19.7 million, ~~refundable~~consisting of tax credit cash ~~credit~~rebates of $9.9 million and $9.8 million for our ~~2016~~2017 and 2018 tax ~~year, which~~years, respectively. In April 2020, we received correspondence from the U.K. tax authorities informing us the claim has been approved. As a result, the amount of the claim was ~~received in February 2019. We~~ recorded ~~this amount~~as other receivable on the condensed consolidated balance sheet at March 31, 2020 and recognized as a component of other income on the condensed consolidated statement of operations for the ~~year-ended December~~three months ended March 31, ~~2018. As of the date hereof,~~2020. For our 2019 tax year, we have not ~~filed claims~~yet decided whether to seek tax relief by surrendering some of our losses for ~~any refundable~~a tax credit cash ~~credit for~~rebate claim or electing to receive enhanced U.K. tax deductions on our ~~2017 or 2018~~eligible research and development activities. Under the U.K’s tax ~~years, nor have we recorded any balances related to claims for these years or for~~legislation, there is a two-year window after the ~~2019~~end of a tax year ~~as collectability is deemed not probable or reasonably assured.~~

to seek relief under this tax relief scheme.

20Zogenix, Inc. | Q1 2020 Form 10-Q | 17

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.

Forward-Looking Statements

This Quarterly Report on Form 10-Q contains forward-looking statements that involve substantial risks and uncertainties. These forward-looking statements include, but are not limited to, statements about:

•the ~~timing of the resubmission of the NDA for Fintepla~~

•~~the~~ progress and timing of clinical trials of our ~~lead~~ product ~~candidate Fintepla;~~candidates Fintepla and MT1621;

•the safety and efficacy of our product candidates;

•the impact of COVID-19 pandemic;

•the timing of submissions to, and decisions made by the U.S. Food and Drug Administration (FDA) and other regulatory agencies, including foreign regulatory agencies, with regards to the demonstration of the safety and efficacy of our product candidates and adequacy of the manufacturing processes related to our product candidates to the satisfaction of the FDA and such other regulatory agencies;

•our ability to obtain, maintain and successfully enforce adequate patent and other intellectual property or regulatory exclusivity protection of our product candidates and the ability to operate our business without infringing the intellectual property rights of others;

•the goals of our development activities and estimates of the potential markets for our product candidates, and our ability to compete within those markets;

•our ability to obtain and maintain adequate levels of coverage and reimbursement from third-party payors for any of our product candidates that may be approved for sale, the extent of such coverage and reimbursement and the willingness of third-party payors to pay for our products versus less expensive therapies;

•the impact of healthcare reform laws; and

•projected cash needs and our expected future revenues, operations and expenditures.

The forward-looking statements are contained principally in the sections entitled “Risk Factors” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations.” In some cases, you can identify forward-looking statements by the following words: “may,” “will,” “could,” “would,” “should,” “expect,” “intend,” “plan,” “anticipate,” “believe,” “estimate,” “predict,” “project,” “potential,” “continue,” “ongoing” or the negative of these terms or other comparable terminology, although not all forward-looking statements contain these words. These statements relate to future events or our future financial performance or condition and involve known and unknown risks, uncertainties and other factors that could cause our actual results, levels of activity, performance or achievement to differ materially from those expressed or implied by these forward-looking statements. We discuss many of these risks, uncertainties and other factors in this Quarterly Report on Form 10-Q in greater detail under the heading “Item 1A – Risk Factors.”

Given these risks, uncertainties and other factors, we urge you not to place undue reliance on these forward-looking statements, which speak only as of the date of this report. You should read this Quarterly Report on Form 10-Q completely and with the understanding that our actual future results may be materially different from what we expect. For all forward-looking statements, we claim the protection of the safe harbor for forward-looking statements contained in the Private Securities Litigation Reform Act of 1995. We undertake no obligation to revise or update publicly any forward-looking statements, whether as a result of new information, future events or otherwise, unless required by law.

Fintepla^® and Zogenix™ are our trademarks. All other trademarks, trade names and service marks appearing in this Quarterly Report on Form 10-Q are the property of their respective owners. Use or display by us of other parties’ trademarks, trade dress or products is not intended to and does not imply a relationship with, or endorsements or sponsorship of, us by the trademark or trade dress owner.

Unless the context requires otherwise, references in this Quarterly Report on Form 10-Q to “Zogenix,” “we,” “us” and “our” refer to Zogenix, Inc., a Delaware corporation, and its consolidated subsidiaries.

The condensed consolidated financial statements and this Management’s Discussion and Analysis of Financial Condition and Results of Operations should be read in conjunction with the consolidated financial statements and notes thereto for the year ended December 31, ~~2018~~2019 and the related Management’s Discussion and Analysis of Financial Condition and Results of Operations, both of which are contained in our ~~2018~~2019 Annual Report on Form ~~10-K.~~

10-K, which was filed with the SEC on March 2, 2020 (2019 Form 10-K).

21Zogenix, Inc. | Q1 2020 Form 10-Q | 18

Overview

We are a global pharmaceutical company committed to developing and commercializing transformative therapies to improve the lives of patients and their families living with rare diseases. We are ~~currently~~primarily focused on developing and commercializing ~~central nervous system (CNS) therapies to address rare or orphan childhood-onset~~two therapeutic product candidates: Fintepla, a low-dose fenfluramine investigational therapy for two pediatric epilepsy ~~disorders.~~disorders, Dravet syndrome and Lennox-Gastaut syndrome (LGS); and MT1621, an investigational deoxynucleoside substrate enhancement therapy for the treatment of thymidine kinase 2 deficiency (TK2d), an inherited mitochondrial DNA depletion disorder.

Fintepla for Patients with Rare Epilepsy Disorders

We own and control worldwide development and commercialization rights to Fintepla, our lead product candidate,~~, other than in Japan where~~ for which we have submitted a new drug application (NDA) to the United States Food and Drug Administration (FDA) and a Marketing Authorization Application (MAA) to the European Medicines Agency (EMA) seeking approval to market and sell the product for the treatment of seizures associated with Dravet syndrome, a rare and devastating pediatric epilepsy disorder. In March 2019, we entered into an exclusive distribution agreement with Nippon Shinyaku Co., Ltd. ~~(Shinyaku).~~ ~~Fintepla is low-dose fenfluramine under development for~~to support the ~~treatment~~sales and distribution of ~~seizures associated with two rare and catastrophic forms of childhood-onset epilepsy: Dravet syndrome and Lennox-Gastaut syndrome (LGS).~~the product in Japan, if approved.

~~Key Development Programs~~

~~Fintepla for Patients with~~ Dravet Syndrome

Dravet syndrome is a rare form of pediatric-onset epilepsy with life threatening consequences for patients and for which current treatment options are very limited. Fintepla has received orphan drug designation inIn February 2019, following the United States and the European Union (EU) for the treatment of Dravet syndrome. In addition, Fintepla for the treatment of Dravet syndrome received Fast Track designation from the U.S. Food and Drug Administration (FDA) in January 2016. In September 2016, we initiated Part 1completion of Study 1 and Study 1504, ~~a two-part, double blind, randomized,~~our two ~~arm~~global pivotal Phase 3 clinical ~~trial~~trials of Fintepla, in Dravet syndrome patients who are taking stiripentol with valproate and/or clobazam as part of their baseline standard care. Part 1 investigated the pharmacokinetic profile and safety of Fintepla when co-administered with the stiripentol regimen (stiripentol with valproate and/or clobazam). Based on the results of the pharmacokinetic and safety portion of the trial, in February 2017 we initiated the safety and efficacy portion of Study 1504 utilizing a dose of Fintepla 0.5mg/kg/day (20mg/day maximum). Study 1504, a two-arm study, compared Fintepla versus placebo across the titration and 12-week maintenance periods at multiple sites located the Netherlands, United States, Canada, Germany, the United Kingdom and Spain. In January 2018, we announced patient enrollment was complete at 87 patients, with 43 patients randomized into the Fintepla-arm and 44 patients randomized to the placebo arm.

In July 2018, we reported positive top-line results from Cohort 2 of Study 1504. The study results, which are consistent with those reported in Study 1, successfully met the primary objective of demonstrating that Fintepla, at a dose of 0.5 mg/kg/day, when co-administered with stiripentol regimen (stiripentol with valproate and/or clobazam), was superior to placebo as adjunctive therapy in the treatment of Dravet syndrome in children and young adults based on change in the frequency of convulsive seizures between the 6-week baseline observation period and the 15-week treatment period (p<0.001). In the trial, Fintepla at a dose of 0.5 mg/kg/day also demonstrated statistically significant improvements versus placebo in all key secondary measures, the proportion of patients with clinically meaningful reductions in seizure frequency (50% or greater) and longest seizure-free interval. Fintepla was generally well-tolerated in this study, with the adverse events consistent with those observed in Study 1 and the known safety profile of fenfluramine without any signs or symptoms of valvular heart disease (valvulopathy) or pulmonary hypertension.

Upon completion of our Fintepla Phase 3 trials, eligible patients were permitted to enroll in an ongoing open-label extension (OLE) trial to study the long-term safety and effectiveness of Fintepla (Study 1503). In December 2018, we presented interim data from Study 1503 regarding the effectiveness and overall safety of Fintepla observed in the study, including the long-term cardiovascular assessments and findings at the 72nd Annual Meeting of the American Epilepsy Society. A total of 232 patients from Study 1503 were included in the interim analysis of the OLE trial. As of March 13, 2018, the interim cutoff date, the median duration of treatment with Fintepla was 256 days and the range was 58-634 days (equivalent to 161 patient-years of exposure to Fintepla). In this interim analysis population of 232 patients, a total of 22 (9.5%) patients had discontinued treatment for the following reasons: lack of efficacy (16), subject withdrawal (2), adverse event (1), Sudden Unexpected Death in Epilepsy (SUDEP) (1), physician decision (1), and withdrawal by caregiver (1). Approximately 90% of patients remained in the study at the time of the interim analysis. The median percent reduction in monthly convulsive seizure frequency over the entire OLE treatment period was 66.8% (compared with baseline frequency established in the core Phase 3 studies). Over the same period, 64.4% of children and young adults showed a >50% reduction in convulsive seizure frequency and 41.2% showed a >75% reduction.

The occurrence of adverse events was consistent with the Phase 3 placebo-controlled studies. The most common adverse events occurring in more than 10% of children and young adults were pyrexia (22%), nasopharyngitis (20%), decreased appetite (16%), influenza (12%), diarrhea (11%), and upper respiratory tract infection (10%). A total of 13.4% of children lost >7% body weight at some point during the trial; in 42% of those children weight loss abated during the period covered by the interim analysis. Over the course of the OLE treatment period included in the interim analysis, one patient died from SUDEP that was deemed unrelated to Fintepla. A total of 703 color doppler echocardiograms were performed to assess cardiovascular

health at baseline, week 4 or 6, and then every 3 months during the OLE trial. No patient developed valvular heart disease (valvulopathy) or pulmonary arterial hypertension at any time after daily treatment with Fintepla.

~~In February 2019,~~ we completed our rolling submission of ~~a New Drug Application (NDA)~~an NDA with the FDA and submitted a ~~Marketing Authorization Application (MAA)~~MAA to the ~~European Medicines Agency (EMA)~~EMA for Fintepla for the treatment of seizures associated with Dravet syndrome. ~~The~~In March 2019, the EMA ~~has~~ accepted the MAA and initiated its ~~review.~~

review and we currently anticipate a decision on the MAA in the fourth quarter of 2020. In April 2019, we received a Refusal to File (RTF) letter from the FDA regarding our NDA for Fintepla for the treatment of seizures associated with Dravet syndrome. ~~Upon its preliminary review, the FDA determined that the NDA submitted in February~~In September 2019, was not sufficiently complete to permit a substantive review. In the RTF letter, the FDA cited two reasons for the RTF decision: first, certain non-clinical studies were not submitted to allow assessment of the chronic administration of fenfluramine; and, second, the application contained an incorrect version of a clinical dataset, which prevented the completion of the review process that is necessary to support the filing of the NDA.

~~We held~~following a Type A meeting with the FDA in May 2019 to review the ~~two~~ issues identified in the RTF ~~letter. Based on~~letter, we resubmitted the ~~final meeting minutes received,~~NDA and in November 2019, the FDA ~~has agreed with our plan to resubmit~~accepted the NDA for filing. The FDA granted priority review for the NDA for Fintepla, ~~without~~which established a target action date of six months from the ~~inclusion~~date of ~~the new chronic toxicity studies requested in the RTF letter. With regards to the second issue, we conducted and discussed~~receipt, with an assigned Prescription Drug User Fee Act, (PDUFA) date of March 25, 2020. As part of their review, the FDA ~~a root cause analysis identifying the issue with the incorrect clinical dataset submitted~~requested additional information from us including, but not limited to, additional data to conduct additional efficacy analyses from our two pivotal studies in ~~the original NDA, and~~Dravet syndrome. On February 27, 2020, we announced that the FDA ~~has requested that we include certain findings from our analysis in~~extended the ~~resubmitted~~PDUFA target action date to June 25, 2020, which provides the FDA additional time to review the NDA. ~~We intend to resubmit the NDA for Fintepla in the third quarter of 2019.~~

Lennox-Gastaut Syndrome

Fintepla ~~for Patients with LGS~~

~~LGS~~ is another rare, refractory, debilitating pediatric-onset epilepsy with life threatening consequences for patients and for which current treatment options are limited and suboptimal. Beginning in first quarter of 2016, we funded an open-label, dose-finding, investigator-initiated study of the effectiveness and tolerability of Fintepla as an adjunctive therapy in patients with LGS. In December 2016, we presented initial data from an interim analysis of the first 13 patients to have completed at least 12 weeks of this Phase 2 clinical trial at the 70th Annual Meeting of the AES. In this interim analysis, Fintepla was observed to provide clinically meaningful improvement in major motor seizure frequency in patients with severe refractory LGS, with 7 out of 13 patients (54%) achieving at least a 50% reduction in the number of major motor seizures, at doses below the 0.8 mg/kg/day maximum allowed dose. In addition, Fintepla was generally well tolerated without any observed signs or symptoms of valvulopathy or pulmonary hypertension. We believe these data indicate that Fintepla has the potential to be a safe and effective adjunctive treatment of major motor seizures for patients with LGS. Based on the strength of the LGS data generated, in the first quarter of 2017, we submitted an Investigational New Drug Application (IND) to the FDA to initiate a Phase 3 program of Fintepla in LGS. Our IND for Fintepla as a potential treatment for LGS became effective in April 2017. In the first half of 2017, Fintepla received orphan drug designationalso under late-stage development for the treatment of seizures associated with LGS, ~~from the FDA in the United States~~another rare and ~~the EMA in the EU.~~

~~Study 1601~~

devastating form of childhood-onset epilepsy. In November 2017, we announced the initiation of Study 1601, our double-blind, placebo-controlled, multicenter global Phase 3 clinical trial of Fintepla as an adjunctive treatment for seizures in patients with ~~LGS (Study 1601).~~LGS. In February 2020, we announced positive top-line results from Study 1601, ~~is planned for up to 85 sites in North America, Europe, Asia-Pacific, South America, South Africa and Australia and is divided in two parts. Part 1 is~~which met its primary objective of demonstrating that Fintepla at a ~~double-blind, placebo-controlled investigation to assess the safety, tolerability and efficacy~~dose of ~~Fintepla when added to a patient’s current anti-epileptic therapy. The trial will include two dose levels of Fintepla (0.2~~0.7 mg/kg/day ~~and 0.8 mg/kg/day, up~~was superior to ~~a maximum daily dose~~placebo in reducing the frequency of 30 mg), as well as placebo. After establishing baseline seizure frequency for 4 weeks, randomized patients will be titrated to their dose over a 2-week titration period, followed by a 12-week fixed dose maintenance period. The primary endpoint ofdrop seizures, based on the ~~clinical trial is~~ change ~~in the number of seizures that result in drops~~ between baseline and the ~~combined~~ titration and maintenance ~~periods at the 0.8~~treatment period (p=0.0012). The same dose of Fintepla (0.7 mg/kg/~~day dose compared to placebo. The~~day) also demonstrated improvements versus placebo in key secondary ~~endpoints include change~~efficacy measures, including a significant reduction in the ~~number~~proportion of patients with a clinically meaningful reduction (≥50%) in drop seizure frequency (p=0.0150). A decrease in the frequency of drop seizures between baseline and the ~~combined titration~~treatment period was observed for a lower dose of Fintepla (0.2 mg/kg/day) compared to placebo, but this change did not reach statistical significance (p=0.0915). In Study 1601, Fintepla was generally well-tolerated, with the adverse events consistent with those observed in our two prior Phase 3 studies in Dravet syndrome. The most common adverse events (≥10%) in the Fintepla-treated groups were decreased appetite, somnolence, fatigue, vomiting, diarrhea, seizure and ~~maintenance periods at~~pyrexia. The incidence of serious treatment emergent adverse events was 11.5% (n=10) in the 0.7 mg/kg/day group, 4.5% (n=4) in the 0.2 mg/kg/day ~~dose,~~group, and 4.6% (n=4) in the ~~proportion~~placebo group. Patients who completed the double-blind phase of ~~patients achieving a 50% reduction in drop seizures. Part 2 of the clinical trial will be~~Study 1601 and were eligible could enter a 12-month ~~OLE~~open label extension study to evaluate the long-term safety, tolerability and effectiveness of Fintepla. ~~In July 2019, we completed enrollment for Study 1601~~We are now focused on finalizing the studies and data required to support a supplemental NDA (sNDA) and intend to meet with ~~a total of 263 randomized patients, with approximately 87 subjects per treatment arm. We expect top-line data from this study will be available~~the FDA in the ~~first quarter~~second half of ~~2020.~~2020 to discuss an sNDA planned submission.

~~Collaborative Arrangement with Nippon Shinyaku~~Other Potential Indications

In ~~March 2019, we entered into an agreement (Shinyaku Agreement) with Nippon Shinyaku Co., Ltd. (Shinyaku) for the exclusive distribution of Fintepla in Japan for the treatment of~~addition to Dravet syndrome and ~~LGS. As part of the Shinyaku Agreement,~~LGS, we are ~~responsible~~evaluating Fintepla in other rare epileptic syndromes and diseases, including an ongoing investigator-initiated study being conducted in Sunflower Syndrome. Sunflower Syndrome is a rare, drug-resistant epileptic disorder with photo-induced seizures characterized by episodes of hand-waving while looking towards bright light, as well as absence and generalized tonic-clonic seizures.

The investigator-initiated open-label, Phase 2 study evaluated the efficacy and tolerability of Fintepla as an adjunctive antiepileptic treatment for ~~completing the global clinical development and all regulatory approval activities for Fintepla~~patients with Sunflower Syndrome. On April 22, 2020, we held a conference call with investors to ~~support the submission of new drug applications in Japan for Dravet syndrome and LGS. Shinyaku will be responsible for the~~

23Zogenix, Inc. | Q1 2020 Form 10-Q | 19

~~commercialization activities~~discuss investigator-reported interim data of this study. Following a four-week baseline period, during which patients observed a baseline median convulsive seizure frequency (MCSF) of 121 seizures per day (range 11-240), patients received 0.2 mg/kg/day Fintepla which was added to their current treatment regimen, and were dose titrated over a two month period to determine maximum tolerability (maximum dose of 26 mg/day), with an overall treatment period of three months (2 month titration period, one month full dose). Of the ten patients enrolled in the trial, nine patients completed the trial. Following treatment with Fintepla, MCSF was reduced by 84% compared to the pre-treatment baseline (p < 0.001). Fintepla was generally well-tolerated and the most common adverse events were minor loss of appetite and fatigue (n=2).

MT1621 for Patients with TK2 Deficiency

In September 2019, we acquired all the outstanding equity interests of Modis Therapeutics, Inc. (Modis), a privately-held biopharmaceutical company based in Oakland, California. Modis holds an exclusive worldwide license from Columbia University in New York City to certain intellectual property rights owned or controlled by Columbia University to develop and commercialize MT1621. MT1621 is an investigational deoxynucleoside-combination substrate enhancement therapy in development for the treatment of TK2d, a rare, debilitating, and often fatal genetic mitochondrial DNA depletion disorder that primarily affects infants and children and for which there are currently no approved therapies. Modis previously completed the RETRO study, a potentially pivotal Phase 2 global retrospective study of MT1621 in 38 pediatric and adult patients with TK2d (median age of disease onset, 2.5 years) treated at eight clinical sites in the United States, Spain and Israel. Subjects received MT1621 for a median of 71 weeks (range 92 days – 7 years). In October 2019, we announced positive top-line results from the RETRO study in which 94.7% of treated patients had either improved (68%) or stabilized (26%) overall responses in major functional domains. A survival analysis using a time-dependent Cox regression model showed that the difference in probability of survival between treated patients and untreated natural history control patients was statistically significant (p<0.0006). Among clinical responders, a subset demonstrated profound responses, in some cases reacquiring previously lost motor milestones such as ambulation, respiratory function and feeding. Safety data from RETRO indicated that MT1621 was generally well-tolerated. Most reported adverse events were considered not related to study drug (199 of 292), with mild or moderate diarrhea being the most common treatment-related adverse event (AE), occurring in 63% of patients. Serious AEs (SAEs) were reported in 14 subjects (37%). The majority of SAEs were deemed related to TK2d; two patients experienced three adverse events related to study drug alone (kidney stone, kidney stone removal, diarrhea). Two adult-onset patients stopped treatment due to asymptomatic increases in aminotransferase liver enzymes (no increase in bilirubin levels), which resolved upon discontinuation of treatment. In April 2020, we held an End of Phase 2 meeting with the FDA and are scheduled to meet with the FDA in June 2020 to receive feedback with respect to chemistry, manufacturing, and controls (CMC). In addition, we plan to seek feedback from regulatory authorities in Europe during the third quarter of 2020 to determine the path forward to a potential submission of an MAA.

Business Update Regarding COVID-19

The current COVID-19 worldwide pandemic has presented substantial public health and economic challenges and is affecting our employees, patients and their families and caregivers, communities and business operations, as well as the U.S. and global economies and financial markets. International and U.S. governmental authorities in impacted regions are taking actions in an effort to slow the spread of COVID-19, including issuing varying forms of “stay-at-home” orders, and restricting business functions outside of one’s home. In response, we have implemented a work from home policy for all employees across all facilities, following the ~~promotion, marketing, sale~~guidelines or directives issued by federal, state and ~~distribution~~local government agencies in the U.S. as well as the U.K. government. To date, we have been able to continue to supply Fintepla and MT1621 to our patients currently enrolled in our clinical trials and do not currently anticipate any interruptions in supply. While we are currently continuing the clinical trials we have underway in sites across the globe, we expect that COVID-19 precautions may directly or indirectly impact the timeline for some of ~~Fintepla in Japan. Upon regulatory approval~~our clinical trials. For example, due to the challenges of ~~Fintepla in Japan, Shinyaku will also act as~~enrolling new patients posed by the COVID-19 pandemic, we have paused the initiation of our ~~exclusive distributor for commercial shipment and distribution~~exploratory Phase 2 study (the “basket study”), which is a study designed to understand the characteristics of ~~Fintepla in Japan. If we pursue global development of Fintepla for indications~~rare epilepsy disorders other than Dravet syndrome orand LGS ~~Shinyaku has the option to participate~~in separate cohorts and evaluate whether Fintepla is safe and effective versus placebo in these patient populations. Any delays in the development for such indications in Japan, subject to cost sharing requirements pursuant to the agreement. Activities under the Shinyaku Agreement will be governed by a joint steering committee (JSC) consistingcompletion of three representatives from each party to the agreement. All decisions of the JSC are to be made by a unanimous vote with tie-breaking rights provided to each party for certain matters related to development, regulatory approval and commercialization.

Shinyaku has agreed to support development and regulatory approval of Fintepla in Japan by actively participating in the design of non-clinical, clinical and manufacturing requirements needed for regulatory submission, actively planning and participating in product labeling decisions and discussions with the Japanese Ministry of Health, Labor and Welfare (MHLW) and obtained distribution exclusivity through the payment of $20.0 million, of which $15.5 million was received shortly after the execution of the agreement with the remainder payable over the next two years. We will be actively running theour clinical trials ~~performing manufacturing validation activities, preparing regulatory filings~~ and ~~holding discussions with MHLW,~~any disruption in our supply chain could have a material adverse effect on our business, results of operations and ~~negotiating pricing. We~~financial condition. The full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations and ~~Shinyaku have agreed to proportionally share the Japan specific development costs~~financial condition, will depend on future developments that are highly uncertain, including as a result of new information that may arise outside of the initial development plan and any post-approval clinical study costs in Japan. In addition, we can earn up to $66.0 million from Shinyaku for the achievement of certain regulatory milestones related to the treatment of Dravet syndromeemerge concerning COVID-19 and the ~~treatment of LGS.~~

~~After regulatory approval of Fintepla in Japan has been obtained, we have agreed~~actions taken to supply Shinyaku with Fintepla upon receipt of purchase orders at our actual manufacturing cost plus a fixed transfer price mark-up, a fixed percentage of Shinyaku's net sales of Fintepla in Japan for such fiscal year,contain it or treat COVID-19, as well as the economic impact on local, regional, national and a net price mark-up based on a percent of the applicable aggregate sales of Fintepla by Shinyaku for such fiscal year. The net price mark-up percentage increases with Shinyaku’s sales of Fintepla annual net sales in Japan and ranges between mid-twenties and is capped at a low thirties of the aggregate annual net sales for an applicable fiscal year.

~~In addition, we can earn up to an additional $42.5 million tied to the achievement of certain net sales milestones by Shinyaku through the term of the agreement.~~

The Shinyaku Agreement expires in September of 2045, unless earlier terminated by either party for a change in control, a material breach, bankruptcy, dissolution, or winding up of such other party. The Shinyaku Agreement may be also terminated by either party: (1) with one year prior written notice to the other party on or after the date of the first commercial sale of a competing generic version of the Fintepla in Japan, (2) if, prior to the launch of the Fintepla in Japan, a party has a good faith concern, based on credible evidence, that such launch is not likely to be possible with commercially reasonable efforts, or (3) if a party believes Fintepla poses a substantial safety concern. We may also terminate the agreement following the second anniversary of the first commercial sale of the Fintepla in Japan if Shinyaku has failed to achieve or maintain certain diligence obligations under the Shinyaku Agreement. Shinyaku may also terminate the agreement if, prior to the launch of the Fintepla in Japan, Shinyaku has a good faith concern that Fintepla will not be commercially viable in Japan.international markets.

Critical Accounting Policies and Estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our condensed consolidated financial statements, which have been prepared in conformity with GAAP. The preparation of these consolidated

Zogenix, Inc. | Q1 2020 Form 10-Q | 20

financial statements requires us to make estimates and assumptions that affect the reported amounts of assets, liabilities, expenses and related disclosures. We evaluate our estimates and assumptions on an ongoing basis. Our estimates are based on historical experience and various other assumptions that we believe to be reasonable under the circumstances. Actual results could differ from those estimates.

We consider an accounting estimate to be critical if: (1) the accounting estimate requires us to make assumptions about matters that were highly uncertain at the time the accounting estimate was made, and (2) changes in the estimate that are reasonably likely to occur from period to period, or use of different estimates that we reasonably could have used in the current period, would have a material impact on our financial condition or results of operations. Our critical accounting policies and estimates are described in the Management’s Discussion and Analysis of Financial Condition and Results of Operations section of our ~~2018 Annual Report on~~2019 Form 10-K. As a result of entering into the Shinyaku Agreement in March 2019 and the adoption of the new lease accounting standard, we have updated our revenue recognition and lease accounting policies as detailed below. There were no ~~other significant~~material changes to our critical accounting policies during the ~~six~~three months ended ~~June 30, 2019,~~March 31, 2020, as compared to the critical accounting policies and estimates disclosed in our ~~2018 Annual Report on~~2019 Form 10-K.

~~Revenue Recognition~~

Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the stand-alone selling prices of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations.

~~Leases~~

Recent Accounting Pronouncements

For information with respect to recent accounting pronouncements that are of significance or potential significance to us, see Note 2, ~~“Summary~~Summary of Significant Accounting ~~Policies” in~~Policies, to the ~~notes to~~ condensed consolidated financial statements in Part I, Item 1 of this Quarterly Report on Form 10-Q.

Results of Operations

Comparison of Three ~~and Six~~ Months Ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~

Collaboration Revenue


		Three Months Ended June 30,										Six Months Ended June 30,									Three Months Ended March 31,
(in thousands)	(in thousands)	2019		2018		Change		2019		2018		Change		(in thousands)	2020		2019		Change
Collaboration revenue	Collaboration revenue	$	1,069	$	—	$	1,069	$	1,069	$	—	$	1,069	Collaboration revenue	$	1,249	$	—	$	1,249

We currently do not have an approved product for sale. Collaboration revenue increased from prior periods as a result of our Shinyaku Agreement entered into in March 2019 and related performance of such collaboration activities under the agreement. We may also be entitled to receive additional milestone payments pursuant to the Shinyaku Agreement upon the occurrence of specific events. ~~Due to~~As the recognition of this collaboration revenue is based on costs incurred to date relative to total estimated costs at completion when measuring progress and the uncertainty of when the events underlying various milestones are resolved, we expect our collaboration revenue will fluctuate from period to period.

Research and Development Expenses


		Three Months Ended June 30,										Six Months Ended June 30,									Three Months Ended March 31,
(in thousands)	(in thousands)	2019		2018		Change		2019		2018		Change		(in thousands)	2020		2019		Change
Research and development	Research and development	$	27,096	$	26,741	$	355	$	51,448	$	49,721	$	1,727	Research and development	$	33,240	$	24,352	$	8,888

Research and development expenses consist of expenses incurred in developing, testing and seeking marketing approval of our product candidates, including: payments made to third-party clinical research organizations (CROs) and investigational sites, which conduct our clinical trials on our behalf, and consultants; expenses associated with regulatory submissions, pre-clinical development and clinical trials; payments to third-party manufacturers, which produce our active pharmaceutical ingredient and finished product; pre-launch inventory, personnel related expenses, such as salaries, benefits, travel and other related expenses, including stock-based compensation; and facility, maintenance, depreciation and other related expenses.

~~We utilize contract manufacturing organizations,~~For each of our research and development programs, we incur both external and internal costs. External costs include clinical and non-clinical activities performed by CROs, ~~contract laboratories and independent contractors to produce~~lab services, purchases of product candidate ~~material~~materials and manufacturing development costs. We track external research and development expenses for ~~the conduct~~each of our ~~pre-clinical studies and clinical trials.~~key development programs. We ~~track third-party~~have not tracked internal costs by program. We recognize the expenses associated with the services provided by CROs based on estimated progress toward completion at the end of each reporting period. We coordinate clinical trials through a number of contracted investigational sites and recognize the associated expense based on a ~~number of factors, including actual~~program-by-program basis because our research and ~~estimated subject enrollment~~development employees and ~~visits, direct pass-through costs and other clinical site fees.~~ infrastructure resources are utilized across our product candidate development programs.

Zogenix, Inc. | Q1 2020 Form 10-Q | 21

The table below sets forth ~~information regarding~~components of our research and development expenses for the periods presented.


	Three Months Ended March 31,
(in thousands)	2020		2019		Change
Fintepla for Dravet syndrome	$	7,311	$	9,620	$	(2,309)
Fintepla for LGS	7,943		6,003		1,940
MT1621	1,652		—		1,652
Other (1)	797		466		331
Total external costs	17,703		16,089		1,614
Internal costs	15,537		8,263		7,274
Total	$	33,240	$	24,352	$	8,888

————————————

(1)Other external costs ~~for our major development~~include early-phase exploratory research programs.

Three Months Ended June 30, Six Months Ended June 30,
(in thousands) 2019 2018 Change 2019 2018 Change
Fintepla for Dravet syndrome $ 11,047 $ 15,239 $ (4,192) $ 20,666 $ 29,102 $ (8,436)
Fintepla for LGS 6,668 4,176 2,492 12,671 6,881 5,790
Other(1) 9,381 7,326 2,055 18,111 13,738 4,373
Total $ 27,096 $ 26,741 $ 355 $ 51,448 $ 49,721 $ 1,727

(1) Other research and development expenses include employee and infrastructure resources that are not tracked on a program-by-program basis, as well as pre-clinical development costs incurred for other product candidates.

In October 2014, we acquired worldwide development and commercialization rights to Fintepla through an acquisition of a business ~~acquisition~~ and have since incurred significant expenditures related to conducting clinical trials of Fintepla. Research and development expenses related to Fintepla for Dravet syndrome decreased by ~~$4.2 million and $8.4~~$2.3 million for the three ~~and six~~ months ended ~~June 30, 2019, respectively,~~March 31, 2020 compared to the same ~~periods~~period in ~~2018~~2019 primarily due to wind-down of clinical activities related to our Phase 3 trials Study 1501 and Study 1504. Research and development spend related to Fintepla for LGS increased by ~~$2.5 million and $5.8~~$1.9 million in the same year-over-year ~~periods, respectively,~~period reflecting the progression and expansion of our clinical trial activities within Study ~~1601,~~1601. External costs increased by $1.7 million due to our spend on the MT1621 development program, which ~~was initiated~~we acquired through our acquisition of Modis in ~~November 2017. Other~~September 2019. Internal costs for research and development ~~expenses~~activities increased by ~~$2.1 million and $4.4~~$7.3 million for the three ~~and six~~ months ended ~~June 30, 2019, respectively,~~March 31, 2020 compared to the same ~~periods~~period in ~~2018. The increase was~~2019 primarily ~~attributable~~driven by additions to ~~personnel-related costs from~~ headcount, ~~additions.~~including, in part, former Modis employees who continued their employment with us.

Selling, General and Administrative Expenses


		Three Months Ended June 30,										Six Months Ended June 30,									Three Months Ended March 31,
(in thousands)	(in thousands)	2019		2018		Change		2019		2018		Change		(in thousands)	2020		2019		Change
Selling	Selling	$	7,517	$	2,266	$	5,251	$	11,432	$	4,711	$	6,721	Selling	$	10,352	$	3,915	$	6,437
General and administrative	General and administrative	7,942		6,311		1,631		14,945		11,936		3,009		General and administrative	10,966		7,003		3,963
Total selling, general and administrative	Total selling, general and administrative	$	15,459	$	8,577	$	6,882	$	26,377	$	16,647	$	9,730	Total selling, general and administrative	$	21,318	$	10,918	$	10,400

Selling expense consists primarily of salaries and benefits of sales and marketing ~~management~~personnel and market research expenses for product candidates that are in development. General and administrative expenses consist primarily of salaries and related costs for personnel in executive, finance, accounting, business development and internal support functions. In addition, general and administrative expenses include professional fees for legal, consulting and accounting services.

Selling expense increased by ~~$5.3 million and $6.7~~$6.4 million for the three ~~and six~~ months ended ~~June 30, 2019. respectively,~~March 31, 2020 compared to the same ~~periods~~period in ~~2018~~2019 and was primarily attributable to increased personnel-related costs as a result of headcount additions ~~as well as increased marketing programs and projects~~ in preparation for the potential approval and commercialization of Fintepla for Dravet syndrome.

General and administrative expense increased by ~~$1.6 million and $3.0~~$4.0 million for the three ~~and six~~ months ended ~~June 30, 2019, respectively,~~March 31, 2020 compared to the same period in ~~2018~~2019 and was primarily attributable to increased personnel-related costs, including stock-based compensation and professional services.

Acquired In-Process Research and Development Expense

Acquired in-process research and development (IPR&D) expense consists of a transaction accounted for as an IPR&D asset acquisition. For the three months ended March 31, 2020, we incurred $1.5 million in aggregate monthly option maintenance fees for the right to license an IPR&D asset.

Zogenix, Inc. | Q1 2020 Form 10-Q | 22

Change in Fair Value of Contingent Consideration


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
(in thousands)	(in thousands)	2019		2018		2019		2018		(in thousands)	2020		2019
Change in fair value of contingent consideration	Change in fair value of contingent consideration	$	(700)	$	(2,500)	$	2,300	$	(2,500)	Change in fair value of contingent consideration	$	(7,900)	$	3,000

The contingent consideration liability relates to milestone payments under an existing agreement in connection with our prior acquisition of Fintepla. At each reporting period, the estimated fair value of the liability is determined by applying the income approach which utilizes variable inputs, such as the probability of success for achieving regulatory/commercial milestones, anticipated future cash flows, risk-free adjusted discount rates, and nonperformance risk. Any change in the fair value is recorded as contingent consideration (income) expense.

~~For the three months ended June 30, 2019, the estimated~~The decrease in fair value of our contingent consideration ~~liabilities decreased by $0.7 million as a result of having to resubmit our February 2019 NDA for Fintepla~~ for the ~~treatment of seizures associated with Dravet syndrome, which resulted in a slight adjustment~~three months ended March 31, 2020 was primarily due to changes to our ~~projected FDA approval timelines. For~~probability-weighted estimates for achieving regulatory/commercial milestones and the ~~six months ended June 30, 2019, the estimated~~use of a higher discount rate to reflect an increase in credit-adjusted interest rates. The increase in fair value of our contingent consideration ~~liabilities increased by $2.3 million~~for the three months ended March 31, 2019 was primarily due to the inclusion of sales in Japan in our forecast associated with the execution of the Shinyaku Agreement, which accelerated the estimated timing of when certain sales milestones will be reached, and a market driven decrease in the discount rate.

Other Income (Expense)


		Three Months Ended June 30,						Six Months Ended June 30,							Three Months Ended March 31,
(in thousands)	(in thousands)	2019		2018		2019		2018		(in thousands)	2020		2019
Other income (expense):	Other income (expense):									Other income (expense):
Interest income	Interest income	$	2,983	$	1,029	$	6,139	$	1,862	Interest income	$	1,088	$	3,156
Other income, net	Other income, net	40		2,950		(48)		2,987		Other income, net	20,021		(88)
Total other income	Total other income	$	3,023	$	3,979	$	6,091	$	4,849	Total other income	$	21,109	$	3,068

The ~~increase~~decrease in interest income for the three ~~and six~~ months ended ~~June 30, 2019~~March 31, 2020 compared to the same ~~periods~~period in ~~2018~~2019 was attributable to ~~interest earned from higher~~lower average cash and investment balances as we ~~invested~~funded our ~~proceeds from our 2018 capital raises~~acquisition of Modis in ~~marketable securities.~~September 2019 with cash on hand.

The ~~decrease~~increase in other income, net for the three ~~and six~~ months ended ~~June 30, 2019~~March 31, 2020 compared to the same ~~periods~~period in ~~2018~~2019 was primarily ~~attributable~~due to ~~$3.0~~$19.7 million of other income recognized infor a cash rebate claim submitted under the ~~prior year periods related to our~~ U.K.’s small and medium-sized enterprise and research and development tax ~~credit regime~~relief scheme for qualifying expenditures incurred in tax years 2017 and 2018. For our 2019 tax year, we have not yet decided whether to seek tax relief by surrendering some of our losses for a tax credit cash rebate claim or electing to receive enhanced U.K. tax deductions on our eligible research and development activities. Under the ~~2015~~U.K’s tax ~~year.~~legislation, there is a two-year window after the end of a tax year to seek relief under this tax relief scheme.

Liquidity and Capital Resources

Excluding gains from two discrete business divestitures, we have incurred significant net losses and negative cash flows from operating activities since inception. We had an accumulated deficit of ~~$768.9 million~~$1.1 billion at ~~June 30, 2019.~~March 31, 2020. We expect to continue to incur significant operating losses and negative cash flows from operations to advance our product candidates through development and commercialization. Additionally, ~~upon acceptance of our regulatory submission for Fintepla by the FDA and regulatory approval of Fintepla by the FDA or EMA, if at all,~~ we ~~will owe~~are obligated to make future milestone payments ~~under an existing agreement in connection with our prior acquisition~~that are contingent upon the successful achievement of ~~Fintepla.~~certain substantive development, regulatory and sales-based milestone events related to Fintepla and MT1621. As of ~~June 30, 2019,~~March 31, 2020, we derive collaboration revenue from our Shinyaku Agreement related to development and commercialization activities for Fintepla in Japan. We do not know when, or if, we will generate any revenue from product sales and do not expect to generate significant revenue from product sales unless and until we obtain regulatory approval of and commercialize ~~Fintepla.~~our product candidates. To date, we have relied primarily on the proceeds from equity offerings to finance our operations.

In March 2020, we completed an underwritten public offering of 9,798,000 shares of our common stock at an offering price of $23.50 per share, including 1,278,000 shares sold pursuant to the underwriters’ full exercise of their option to purchase additional shares. Net proceeds realized from the offering amounted to approximately $221.7 million, after deducting commissions and other offering expenses. As of ~~June 30, 2019,~~March 31, 2020, our cash, cash equivalents and marketable securities totaled ~~$463.0~~$420.2 million. We believe our existing capital resources are sufficient to meet our projected operating requirements for at least the next 12 months.

Zogenix, Inc. | Q1 2020 Form 10-Q | 23

Our principal uses of cash are research and development expenses, selling, general and administrative expenses and other working capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

•the rate of progress and cost of our clinical trials and other product development programs for Fintepla, MT1621 and our other product candidates and any other product candidates that we may develop, in-license or acquire;

•the timing of regulatory approval ~~for any~~ of our ~~other~~ product candidates and the commercial success of any approved products;

•the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights associated with Fintepla, MT1621 and any of our other product candidates;

•the timing and amounts of the milestone or other payments we must make related to Fintepla and MT1621;

•the costs of establishing or outsourcing sales, marketing and distribution capabilities, should we elect to do so;

•the costs, terms and timing of completion of outsourced commercial manufacturing supply arrangements for any product candidate; ~~and~~

•the effect of competing technological and market ~~developments.~~developments; and

•any delays and cost increases that result from the COVID-19 pandemic.

Until we can generate a sufficient amount of revenue to finance our cash requirements, if ever, we may need to continue to rely on additional financing to achieve our business objectives. However, we may not be able to secure such financing in a timely manner or on favorable terms, if at ~~all.~~all, and this risk could be exacerbated by the impact of COVID-19 on global economic conditions. If future funds are raised through issuance of equity or debt securities, these securities may have rights, preferences and privileges senior to those of our existing stockholders. If we raise additional funds through collaboration, licensing or other similar arrangements, it may be necessary to relinquish valuable rights to our potential products or proprietary technologies, or grant licenses on terms that are not favorable to us. Without additional funds at the time we need such funding, we may be forced to delay, scale back or eliminate some of our research and development activities, or other operations and potentially delay product development in an effort to provide sufficient funds to continue ~~its~~our operations. If any of these events occurs, our ability to achieve the development and commercialization goals could be adversely affected.

The following table presents selected information from our statements of cash flows (in thousands):


		Six Months Ended June 30,							Three Months Ended March 31,
		2019		2018			2020		2019
Cash and cash equivalents, beginning of the period	Cash and cash equivalents, beginning of the period	$	68,454	$	293,503	Cash and cash equivalents, beginning of the period	$	62,070	$	68,454
Net cash used in operating activities	Net cash used in operating activities	(41,739)		(55,567)		Net cash used in operating activities	(52,491)		(24,827)
Net cash provided by (used in) investing activities		28,653		(84)
Net cash (used in) provided by financing activities		(4,580)		34,251
Net cash provided by investing activities						Net cash provided by investing activities	37,217		20,864
Net cash provided by (used in) financing activities						Net cash provided by (used in) financing activities	223,179		(6,203)
Net decrease in cash and cash equivalents	Net decrease in cash and cash equivalents	(17,666)		(21,400)		Net decrease in cash and cash equivalents	207,905		(10,166)
Cash and cash equivalents, end of the period	Cash and cash equivalents, end of the period	$	50,788	$	272,103	Cash and cash equivalents, end of the period	$	269,975	$	58,288

Operating Activities

For the ~~six~~three months ended ~~June 30,~~March 31, 2020, net cash used in operating activities of $52.5 million was primarily attributable to research and development spend related to ongoing open-label clinical trials for Fintepla and manufacturing process development for Fintepla and MT1621, commercial preparedness and planning expenses including additions in headcount to build out our sales force of key account managers and general and administrative costs to support our business objectives.

For the three months ended March 31, 2019, net cash used in operating activities of ~~$41.7~~$24.8 million was primarily attributable to a net loss of ~~$73.0~~$35.2 million, plus the net effect of non-cash items of ~~$9.3~~$6.0 million, primarily from stock-based compensation, and a net cash inflow from changes in operating assets and liabilities of $21.9 million. Cash inflows from changes in operating assets and liabilities included the receipt of a $15.5 million upfront payment in connection with the Shinyaku Agreement entered into in March 2019. Changes in other operating assets and liabilities were primarily attributable to the timing of payments for prepaid and accrued clinical trial costs and accrued expenses in the normal course of business.

For the six months ended June 30, 2018, net cash used in operating activities of $55.6 million was primarily attributable to a net loss of $59.2 million, plus the net effect of non-cash items of $2.6 million, including stock-based compensation and changes in the estimated fair value of contingent consideration, and a net cash inflow from changes in operating assets and liabilities of ~~$1.1~~$4.4 million.

Zogenix, Inc. | Q1 2020 Form 10-Q | 24

Investing Activities

For the ~~six~~three months ended ~~June 30,~~March 31, 2020, net cash provided by investing activities of $37.2 million was attributable to the net purchase and maturities of our available-for-sale marketable securities of $38.9 million.

For the three months ended March 31, 2019, net cash provided by investing activities of ~~$28.7~~$20.9 million was attributable to ~~$289.4 million related to~~ maturities of marketable ~~securities,~~securities. These cash inflows were offset by ~~cash outflows of $251.8 million for~~ purchases of marketable securities and ~~$8.9 million in capital spend primarily related~~property and equipment, the majority of which was attributable to the build-out of our ~~new~~ headquarters, which we began to occupy in early March 2019.

~~For the six months ended June 30, 2018, net cash used in investing activities was attributable to purchases of property and equipment.~~

Financing Activities

For the ~~six~~three months ended ~~June 30,~~March 31, 2020, net cash provided by financing activities of $223.2 million primarily consisted of net proceeds realized from the issuance of 9,798,000 million shares of our common stock in a public offering and $1.5 million in net proceeds received from the issuance of common stock pursuant to our equity incentive plans.

For the three months ended March 31, 2019, net cash used in financing activities of ~~$4.6~~$6.2 million consisted of a $10.0 million payment of contingent consideration related to a prior acquisition and cash used to remit withholding taxes of $0.6 million related to the vesting of restricted stock units that were net share-settled by us to cover the required withholding tax. These cash outflows were offset by ~~$6.0~~$4.4 million of proceeds from common stock issuances pursuant to our equity incentive plans.

For the six months ended June 30, 2018, net cash provided by financing activities of $34.3 million consisted of net proceeds from sales of common stock of $30.3 million under an at-the-market offering and $5.4 million in proceeds received from the issuance of common stock under equity incentive plans. These cash inflows were offset by cash used to remit withholding taxes of $1.4 million related to the vesting of restricted stock units that were net share-settled by us to cover the required withholding tax.

Contractual Obligations

There were no material changes outside the ordinary course of our business during the ~~six~~three months ended ~~June 30, 2019~~March 31, 2020 to the information regarding our contractual obligations that was disclosed in Management’s Discussion and Analysis of Financial Condition and Results of Operations included in our ~~2018 Annual Report on~~2019 Form 10-K.

Off-Balance Sheet Arrangements

As of ~~June 30, 2019,~~March 31, 2020, we did not have any off-balance sheet arrangements, as defined in Item 303(a)(4)(ii) of Regulation S-K.

Zogenix, Inc. | Q1 2020 Form 10-Q | 25

Item 3. Quantitative and Qualitative Disclosures About Market Risk

For quantitative and qualitative disclosures about market risk, see Item 7A, ~~“Quantitative~~Quantitative and Qualitative Disclosures About Market ~~Risk”~~Risk, of our ~~2018 Annual Report on~~2019 Form 10-K. Our exposures to market risk have not changed materially since December 31, ~~2018.~~2019.

Item 4. Controls and Procedures

Conclusions Regarding the Effectiveness of Disclosure Controls and Procedures

We maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in our Exchange Act reports is recorded, processed, summarized and reported within the timelines specified in the Securities and Exchange Commission’s rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, management recognized that any controls and procedures, no matter how well designed and operated, can only provide reasonable assurance of achieving the desired control objectives, and in reaching a reasonable level of assurance, management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

As required by SEC Rule 13a-15(b), we carried out an evaluation, under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer, of the effectiveness of the design and operation of our disclosure controls and procedures as of the end of the period covered by this report. Based on the foregoing, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective as of ~~June 30, 2019~~March 31, 2020 at the reasonable assurance level.

Changes in Disclosure Controls and Procedures

There were no changes in our internal control over financial reporting during the three months ended ~~June 30, 2019~~March 31, 2020 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Zogenix, Inc. | Q1 2020 Form 10-Q | 26

PART II – OTHER INFORMATION

Item 1. Legal Proceedings

~~There have been no material updates to the legal proceedings as set forth in “Item 3. Legal Proceedings” in our 2018 Annual Report on Form 10-K other than as set forth below:~~

On April 12, 2019, a plaintiff stockholder filed a class action lawsuit against us and certain of our executive officers alleging violations of Sections 10(b) and 20(a) of the Securities Exchange Act in the United States District Court for the Northern District of California captioned Lake v. Zogenix, Case No. 3:19-cv-01975-RS. The plaintiff ~~seeks~~sought to represent a class of investors who purchased our stock between February 6, 2019 and April 8, 2019, and ~~alleges~~alleged that certain statements made during this period regarding the prospects for our ~~New Drug Application~~NDA for Fintepla were false or misleading. ~~The plaintiff seeks damages, interest, costs, attorneys’ fees, and other unspecified equitable relief. We~~On October 4, 2019, we filed a motion to dismiss the complaint in the action. On January 27, 2020, the court entered an order dismissing the complaint without prejudice. Rather than amend the complaint, the plaintiffs opted to voluntarily dismiss their claims. A final judgment in favor of Zogenix and our executive officers ~~believe~~was filed on February 13, 2020.

On January 17, 2020, a plaintiff stockholder filed a shareholder derivative lawsuit against our directors and officers alleging violations of Sections 10(b) and 20(a) of the ~~claims alleged~~Securities Exchange Act, breach of fiduciary duties, unjust enrichment, and waste of corporate assets, in the ~~complaint~~United States District Court for the Northern District of California captioned Lui v. Farr, Case No. 3:20-cv-00390. The plaintiff alleged that certain statements regarding the prospects for our NDA for Fintepla were false or misleading, and that we failed to maintain adequate internal controls in connection with its FDA submission process. Following dismissal of the Lake v. Zogenix securities class action, the plaintiff stockholder opted to voluntarily dismiss his suit. On April 2, 2020, the Court entered an order dismissing the action without prejudice pursuant to the parties’ stipulation.

We may become involved in various legal proceedings and claims that arise in the ordinary course of business. Such matters are ~~without merit~~subject to uncertainty and ~~intend to vigorously defend against them.~~there can be no assurance that such legal proceedings will not have a material adverse effect on our business, results of operations, financial position or cash flows.

Item 1A. Risk Factors

There have been no material changes in our risk factors from those disclosed in Part I, Item 1A of our ~~2018 Annual Report on~~2019 Form 10-K, other than as set forth below.

Our ~~success depends substantially on~~business is subject to risks arising from epidemic diseases, such as the recent COVID-19 pandemic.

The current COVID-19 worldwide pandemic has presented substantial public health and economic challenges and is affecting our ~~only product candidate~~employees, patients, communities and business operations, as well as the U.S. and global economy and financial markets. International and U.S. governmental authorities in ~~development, Fintepla. We cannot be certain that Fintepla~~impacted regions are taking actions in an effort to slow the spread of COVID-19, including issuing varying forms of “stay-at-home” orders, and restricting business functions outside of one’s home. In response, we have implemented a work from home policy for all employees across all facilities, following the guidelines or ~~our product candidates will receive regulatory approval or be successfully commercialized.~~

Wedirectives issued by federal, state and local government agencies in the U.S. as well as the U.K. government. To date, we have ~~only one product candidate in clinical development,~~been able to continue to supply Fintepla and MT1621 to our patients currently enrolled in our clinical trials and do not currently anticipate any interruptions in supply. In addition, while we are continuing the clinical trials we have underway in sites across the globe, we expect that COVID-19 precautions may directly or indirectly impact the timeline for some of our clinical trials. For example, due to the challenges of enrolling new patients posed by the COVID-19 pandemic, we have paused the initiation of our exploratory Phase 2 basket study, which is designed to understand the characteristics of rare epilepsy disorders other than Dravet syndrome and Lennox-Gastaut syndrome in separate cohorts and evaluate whether Fintepla is safe and effective versus placebo in these patient populations. As the COVID-19 pandemic continues to spread around the globe, we may experience disruptions that could severely impact our business, ~~depends substantially on its successful development~~clinical trials and ~~commercialization. We currently have no drug products approved for sale,~~manufacturing and ~~we may not be able to develop marketable drug products~~supply chains, including:

•interruption or delays in the ~~future. Fintepla and our product candidates will require additional clinical and pre-clinical development,~~operations of the FDA, EMA or other regulatory authorities, which may impact review and approval ~~in multiple jurisdictions, substantial investment, access to sufficient commercial manufacturing capacity~~timelines of our NDA and significant marketing efforts before we can generate any revenues from product sales. The research, testing, manufacturing, labeling, approval, sale, marketing, distribution and promotion of drug products are subject to extensive regulation by the FDA and other regulatory authorities in the United States and other countries, whose regulations differ from country to country.

We are not permitted to market our product candidates in the United States until we receive approval of a NDA from the FDA, or in any foreign countries until we receive the requisite approval from the regulatory authorities of such countries, and we may never receive such regulatory approvals. In February 2019, we completed our rolling submission of a NDA with the FDA and submitted a MAA ~~to the EMA~~ for Fintepla for the treatment of seizures associated with Dravet ~~syndrome. The EMA has accepted the MAA~~syndrome;

•further delays or difficulties in enrolling patients in our clinical trials;

•delays or difficulties in clinical site initiation, including difficulties in recruiting clinical site investigators and ~~initiated its review. However, on April 5, 2019, we received a RTF letter~~clinical site staff;

•diversion of healthcare resources away from the ~~FDA regarding~~conduct of clinical trials, including the diversion of hospitals serving as our ~~NDA for Fintepla for~~clinical trial sites and hospital staff supporting the ~~treatment~~conduct of seizures associated with Dravet syndrome. The RTF letter provided the FDA’s determination that the NDA, as submitted on February 5, 2019, was not sufficiently complete to permit a substantive review of the NDA. In the RTF letter, the FDA cited two reasons for the RTF decision: first, certain non-clinical studies were not submitted to allow assessment of the chronic administration of fenfluramine; and, second, the application contained an incorrect version of aour clinical dataset, which prevented the completion of the review process that is necessary to support the filing of the NDA. The FDA did not request or recommend in the RTF letter that we conduct any additional clinical efficacy or safety studies.

We held an Type A meeting with the FDA in May 2019 to review the two issues identified in the RTF letter. Based on the final meeting minutes received, the FDA has agreed with our plan to resubmit the NDA for Fintepla without the inclusion of the new chronic toxicity studies requested in the RTF letter. With regards to the second issue, we conducted and discussed with the FDA a root cause analysis identifying the issue with the incorrect clinical dataset submitted in the original NDA, and the FDA has requested that we include certain findings from our analysis in the resubmitted NDA. We intend to resubmit the NDA for Fintepla in the third quarter of 2019. trials;However, we cannot provide any assurance that we be able to adequately address the issues raised to FDA’s satisfaction or that the FDA will accept the resubmitted Fintepla NDA for filing, or that the FDA will ultimately approve our NDA following a substantive review. The FDA may determine later to require us to conduct additional non-clinical or clinical studies or may otherwise impose other requirements to be completed before or after approval of the NDA. In addition, the RTF letter could cause potential delays by the EMA on an approvability decision, or otherwise negatively affect such decision. Obtaining regulatory approval for a product candidate is a lengthy, expensive and uncertain process, and may not be successful. Any failure to obtain regulatory approval of Fintepla or our product candidates, or failure to obtain such approval for all of the indications and labeling claims we deem desirable, would limit our ability to generate future revenues, would potentially harm the development prospects of Fintepla and would have a material and adverse impact on our business.

32Zogenix, Inc. | Q1 2020 Form 10-Q | 27

~~Even if we successfully obtain regulatory approvals~~•interruption of key clinical trial activities, such as clinical trial site monitoring, due to ~~market~~limitations on travel imposed or recommended by federal or state governments, employers and others or interruption of clinical trial subject visits and study procedures, which may impact the integrity of subject data and clinical study endpoints;

•interruption of, or delays in receiving, supplies of our product candidates from our ~~revenues will~~contract manufacturing organizations due to staffing shortages, production slowdowns or stoppages and disruptions in delivery systems, including interruption of supply if Fintepla is approved for marketing;

•delays in clinical sites receiving the supplies and materials needed to conduct our clinical trials and interruption in global shipping that may affect the transport of clinical trial materials;

•limitations on employee resources that would otherwise be ~~dependent,~~focused on the conduct of our clinical trials, including because of sickness of employees or their families or the desire of employees to avoid contact with large groups of people;

•delays in receiving feedback or approvals from the FDA, EMA or other regulatory authorities with respect to future clinical trials or regulatory submissions, including for MT1621;

•changes in local regulations as part onof a response to COVID-19 which may require us to change the ways in which our clinical trials are conducted, which may result in unexpected costs, or to discontinue the clinical trials altogether;

•delays in necessary interactions with local regulators, ethics committees and other important agencies and contractors due to limitations in employee resources or forced furlough of government employees;

•refusal of the FDA or EMA to accept data from clinical trials in affected geographies; and

•difficulties launching or commercializing products, including due to reduced access to doctors as a result of social distancing protocols.

In addition, the spread of COVID-19 has had and may continue to severely impact the trading price of shares of our common stock and could further severely impact our ability to ~~commercialize~~raise additional capital on a timely basis or at all.

The COVID-19 pandemic continues to rapidly evolve. The extent to which the COVID-19 may impact our business, including our clinical trials, manufacturing and supply chains and financial condition will depend on future developments, which are highly uncertain and cannot be predicted with confidence, such ~~products as well~~ as the ~~size~~geographic spread of the ~~markets in~~disease, the ~~territories for which we gain regulatory approval. If~~duration of the ~~markets for our product candidates are not as significant as we estimate, our business~~pandemic, travel restrictions and ~~prospects will be harmed.~~

Any breakthrough therapy designation that we may receive from the FDA for our product candidates may not lead to a faster development or regulatory review or approval process, and it does not increase the likelihood that our product candidates will receive marketing approval.

~~In February 2018, the FDA granted breakthrough therapy designation for Fintepla~~social distancing in the United States ~~for the treatment of Dravet syndrome. The FDA has subsequently rescinded this breakthrough therapy designation because there are now two approved therapies for the disease~~ and ~~therefore, the administrative criteria for designation are no longer met. A breakthrough therapy is defined as a drug that is intended, alone~~other countries, business closures or in combination with one or more other drugs, to treat a serious or life-threatening disease or condition, and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over existing therapies on one or more clinically significant endpoints. For drugs that have been designated as breakthrough therapies, interaction and communication between the FDAbusiness disruptions and the ~~sponsor~~effectiveness of the trial can help to identify the most efficient path for clinical development while minimizing the number of patients placed in ineffective control regimens. Drugs designated as breakthrough therapies by the FDA are also eligible for accelerated approval. Designation as a breakthrough therapy is within the discretion of the FDA. Accordingly, even if we believe one of our product candidates meets the criteria for designation as a breakthrough therapy, the FDA may disagree and instead determine not to make such designation. We cannot be sure that any evaluation we may make of our product candidates as qualifying for breakthrough therapy designation will meet the FDA’s expectations. In any event, the receipt of a breakthrough therapy designation for a product candidate may not result in a faster development process, review or approval compared to drugs considered for approval under conventional FDA procedures and does not assure ultimate approval by the FDA. In addition, even if one or more of our product candidates qualify as breakthrough therapies, the FDA may later decide that such product candidates no longer meet the conditions for qualification such as the case with Finteplaactions taken in the United States ~~for~~and other countries to contain and treat the ~~treatment~~disease.

To the extent the COVID-19 pandemic adversely affects our business and financial results, it may also have the effect of ~~Dravet syndrome,~~heightening many of the other risks described in this section and in the “Risk Factors” section of our 2019 Form 10-K.

Disruptions at the FDA and other government agencies caused by funding shortages or ~~decide~~global health concerns could hinder their ability to hire, retain or deploy key leadership and other personnel, or otherwise prevent new or modified products from being developed, approved or commercialized in a timely manner or at all, which could negatively impact our business.

The ability of the FDA to review and approve new products can be affected by a variety of factors, including government budget and funding levels, statutory, regulatory, and policy changes, the FDA’s ability to hire and retain key personnel and accept the payment of user fees, and other events that may otherwise affect the FDA’s ability to perform routine functions. Average review times at the agency have fluctuated in recent years as a result. In addition, government funding of other government agencies that fund research and development activities is subject to the political process, which is inherently fluid and unpredictable. Disruptions at the FDA and other agencies may also slow the time ~~period~~necessary for ~~FDA review~~new drugs or ~~approval will not~~modifications to approved drugs to be ~~shortened. While we do not expect~~reviewed and/or approved by necessary government agencies, which would adversely affect our business. For example, over the ~~rescission of breakthrough therapy designation to limit~~last several years, including for 35 days beginning on December 22, 2018, the ~~potential for receiving priority review status for our planned resubmitted NDA for Fintepla,~~U.S. government has shut down several times and certain regulatory agencies, such as the FDA, have had to furlough critical FDA employees and stop critical activities.

Separately, in response to the COVID-19 pandemic, on March 10, 2020 the FDA announced its intention to postpone most foreign inspections of manufacturing facilities and products through April 2020, and subsequently, on March 18, 2020, the FDA announced its intention to temporarily postpone routine surveillance inspections of domestic manufacturing facilities. Regulatory authorities outside the United States may ~~not grant priority review status which would result~~adopt similar restrictions or other policy measures in response to the COVID-19 pandemic. If a ~~longer review period for~~prolonged government shutdown occurs, or if global health concerns continue to prevent the ~~NDA.~~

~~We are dependent on numerous third parties in our manufacturing supply chain, all of which are currently single source suppliers, for~~FDA or other regulatory authorities from conducting their regular inspections, reviews, or other regulatory activities, it could significantly impact the ~~clinical supply of Fintepla, and if we experience problems with any of these suppliers, the development of Fintepla could be delayed.~~

~~We outsource all manufacturing and packaging~~ability of the ~~clinical trial materials for Fintepla~~FDA or other regulatory authorities to ~~third parties. For example, in February 2019, we entered into~~timely review and process our regulatory

Zogenix, Inc. | Q1 2020 Form 10-Q | 28

submissions, including FDA’s ability to make a ~~master supply agreement with Aptuit (Oxford) Limited, an Evotec company (Aptuit), pursuant to~~decision by the June 25, 2020 PDUFA target action date, which Aptuit will be our commercial manufacturer and supplier of the fenfluramine active pharmaceutical ingredient (API). In addition, in July 2019 we entered into supply agreement with Penn Pharmaceutical Services Limited, trading as PCI Pharma Services (PCI Pharma), pursuant to which PCI Pharma will be our commercial manufacturer and supplier for Fintepla. Fintepla, if approved, would require to complete process validation under FDA regulations, for which there can be no assurance of success. We may never be able to establish additional sources of supply for Fintepla.

Suppliers, including Aptuit and PCI Pharma, are subject to regulatory requirements covering, among other things, testing, quality control and record keeping relating to our product candidate, and are subject to ongoing inspections by regulatory agencies. Failure by any of our suppliers to comply with applicable regulations may result in long delays and interruptions, and increase our costs, while we seek to secure another supplier who meets all regulatory requirements, including obtaining regulatory approval to utilize the new supplier. Accordingly, the loss of any of our current suppliers could have a material adverse effect on our ~~business, results of operations, financial condition and prospects.~~

~~Reliance on suppliers entails risks to which we would not be subject if we manufactured our product candidate ourselves, including:~~

•~~reliance on the third parties for regulatory compliance and quality assurance;~~

•the possible breach of the manufacturing agreements by the third parties because of factors beyond our control or the insolvency of any of these third parties or other financial difficulties, labor unrest, natural disasters or other factors adversely affecting their ability to conduct their business; and

•the possibility of termination or non-renewal of the agreements by the third parties, at a time that is costly or inconvenient for us, because of our breach of the manufacturing agreement or based on their own business priorities.business.

If our contract manufacturers or suppliers are unable to provide the quantities of our product candidate required for our clinical trials and, if approved, for commercial sale, on a timely basis and at commercially reasonable prices, and we are unable to find one or more replacement manufacturers or suppliers capable of production at a substantially equivalent cost, in substantially equivalent volumes and quality, and on a timely basis, we would likely be unable to meet demand for our products and would have to delay or terminate our pre-clinical or clinical trials, and we would lose potential revenue. It may also take a significant period of time to establish an alternative source of supply for our products, product candidates and components and to have any such new source approved by the FDA or any applicable foreign regulatory authorities. Furthermore, any of the above factors could cause the delay or suspension of initiation or completion of clinical trials, regulatory submissions or required approvals of our product candidates, cause us to incur higher costs and could prevent us from commercializing our product candidates successfully.

~~Our operating results may fluctuate significantly, which makes our future operating results difficult to predict.~~

Our quarterly and annual operating results may fluctuate significantly in the future, which makes it difficult for us to predict our future operating results. From time to time, in addition to the existing Shinyaku Agreement, we may enter into collaborative arrangements with other companies that include development funding and significant upfront and milestone payments and/or royalties, which may become an important source of our revenue. Accordingly, our revenue may depend on development funding and the achievement of development and clinical milestones under current and any potential future collaborative arrangements and sales of our products, if approved. Furthermore, revenues may consist of the recognition of deferred revenue from upfront, nonrefundable payments that we received from Shinyaku or payments we may receive under future collaboration agreements and the timing of recognizing deferred revenue is subject to significant management judgments, including estimating total costs at completion. These upfront and milestone payments may vary significantly from period to period and any such variance could cause a significant fluctuation in our operating results from one period to the next. As a result, any period-to-period comparisons of our operating results may not be meaningful. Accordingly, the results of any one period should not be relied upon as an indication of future performance.

The United Kingdom’s proposed withdrawal from the European Union may have a negative effect on global economic conditions, financial markets and our business, which could reduce the price of our common stock.

We are a company with worldwide operations, including significant business operations in Europe, and our wholly owned subsidiary Zogenix Europe Limited is incorporated under the laws of England and Wales. Following a national referendum in which a majority of voters in the United Kingdom elected to withdraw from the European Union, the government of the United Kingdom formally initiated the process for withdrawal in March 2017. The terms of any withdrawal are subject to a complex and ongoing negotiation between the United Kingdom and the European Union whose result and timing remain unclear and which has created significant political and economic uncertainty about the future trading relationship between the United Kingdom and the European Union in the event of a withdrawal, particularly in light of the possibility that an immediate, so-called “no deal” withdrawal could occur without a negotiated agreement.

These developments, or the perception that any of them could occur, have had and may continue to have a material adverse effect on global economic conditions and the stability of global financial markets, and could significantly reduce global market liquidity and restrict the ability of key market participants to operate in certain financial markets. Asset valuations, currency exchange rates and credit ratings have been and may continue to be subject to increased market volatility. Lack of clarity about future United Kingdom laws and regulations as the United Kingdom determines which European Union laws to replace or replicate in the event of a withdrawal, including financial laws and regulations, tax and free trade agreements, tax and customs laws, intellectual property rights, environmental, health and safety laws and regulations, immigration laws, employment laws and transport laws could increase costs, disrupt supply chains, depress economic activity and restrict our access to capital.

If the United Kingdom and the European Union are unable to negotiate acceptable withdrawal terms, barrier-free access between the United Kingdom and other European Union member states or among the European economic area overall could be diminished or eliminated. Any of these factors could have a material adverse effect on our business, financial condition and results of operations, affect our strategy in the European pharmaceutical market. and reduce the price of our common stock.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

Unregistered Sales of Equity Securities

None.

Use of Proceeds

Not applicable.

Item 3. Defaults Upon Senior Securities

None.

Item 4. Mine Safety Disclosures

Not applicable.

Item 5. Other Information

None.

Zogenix, Inc. | Q1 2020 Form 10-Q | 29

Item 6. Exhibits

EXHIBIT INDEX


Exhibit Number						Exhibit Description

3.1⁽¹⁾						Fifth Amended and Restated Certificate of Incorporation of the Registrant

3.2⁽⁴⁾⁽²⁾						Certificate of Amendment of Fifth Amended and Restated Certificate of Incorporation of the Registrant

3.3⁽⁵⁾⁽³⁾						Certificate of Amendment of Fifth Amended and Restated Certificate of Incorporation of the Registrant

3.4* 3.4⁽⁴⁾						Certificate of Amendment of Fifth Amended and Restated Certificate of Incorporation of the Registrant

3.5⁽¹⁾						Fifth Amended and Restated ~~Bylaws~~Certificate of Incorporation of the Registrant

4.1⁽²⁾⁽⁵⁾						Form of the Registrant’s Common Stock Certificate

~~4.5~~4.2⁽³⁾⁽⁶⁾						Warrant dated July 18, 2011 issued by the Registrant to Healthcare Royalty Partners (formerly Cowen Healthcare Royalty Partners II, L.P.)

~~10.1~~⁽⁶)†						~~Zogenix, Inc. 2010 Equity Incentive Award Plan~~

~~31.1~~31.1*						Certification of Chief Executive Officer pursuant to Section 302 of the Public Company Accounting Reform and Investor Protection Act of 2002 (18 U.S.C. §1350, as adopted)

~~31.2~~31.2*						Certification of Chief Financial Officer pursuant to Section 302 of the Public Company Accounting Reform and Investor Protection Act of 2002 (18 U.S.C. §1350, as adopted)

32.1**						Certification of Chief Executive Officer pursuant to Section 906 of the Public Company Accounting Reform and Investor Protection Act of 2002 (18 U.S.C. §1350, as adopted)

32.2**						Certification of Chief Financial Officer pursuant to Section 906 of the Public Company Accounting Reform and Investor Protection Act of 2002 (18 U.S.C. §1350, as adopted)

~~101.INS~~101*						Inline XBRL ~~Instance~~ Document -Set for the ~~instance document does not appear~~condensed consolidated financial statements and accompanying notes in ~~the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.~~Part I, Item 1, “Financial Statements” of this Quarterly Report on Form 10-Q.

~~101.SCH~~104*						Inline XBRL ~~Taxonomy Extension Schema Document.~~

~~101.CAL~~						for the cover page of this Quarterly Report on Form 10-Q, included in the Exhibit 101 Inline XBRL ~~Taxonomy Extension Calculation Linkbase Document.~~

~~101.DEF~~						~~Inline XBRL Taxonomy Extension Definition Linkbase Document.~~

~~101.LAB~~						~~Inline XBRL Taxonomy Extension Label Linkbase Document.~~

~~101.PRE~~						~~Inline XBRL Taxonomy Extension Presentation Linkbase Document.~~Document Set.

____________________

*Filed herewith.

(1)Incorporated by reference to Amendment No. 2 to the Registrant’s Registration Statement on Form S-1 filed on October 27, 2010.

(2)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on November 8, 2012.

(3)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on August 10, 2015.

(4)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on August 6, 2019.

(5)Incorporated by reference to Amendment No. 3 to the Registrant’s Registration Statement on Form S-1 filed on November 4, 2010.

~~(3)~~(6)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on August 12, 2011.

~~(4)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on November 8, 2012.~~

~~(5)Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q filed on August 10, 2015.~~

~~(6)Incorporated by reference to the Registrant's Current Report on Form 8-K filed on May 22, 2019.~~

†Indicates management contract or compensatory plan.

*Filed herewith.

**These certifications are being furnished solely to accompany this quarterly report pursuant to 18 U.S.C. Section 1350, and are not being filed for purposes of Section 18 of the Securities Exchange Act of 1934 and are not subject to the liability of that section. These certifications are not to be incorporated by reference into any filing of Zogenix, Inc., whether made before or after the date hereof, regardless of any general incorporation language in such ~~filing.~~filing herewith.

36Zogenix, Inc. | Q1 2020 Form 10-Q | 30

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.



			ZOGENIX, INC.

Date:	~~August 6, 2019~~May 5, 2020	By:	/s/ Stephen J. Farr
			President and Chief Executive Officer
			(Principal Executive Officer)

Date:	~~August 6, 2019~~May 5, 2020	By:	/s/ Michael P. Smith
			Executive Vice President, Chief Financial Officer ~~Treasurer~~ and ~~Secretary~~Treasurer
			(Principal Financial and Accounting Officer)


	December 31, 2018		Adjustments Due to the Adoption of Topic 842		January 1, 2019
Assets
Operating lease right-of-use assets	$	—	$	8,641	$	8,641

Liabilities
Other accrued liabilities	$	1,845	$	(363)	$	1,482
Current portion of operating lease liabilities	—		1,058		1,058
Operating lease liabilities, net of current portion	—		11,776		11,776
Other long-term liabilities	3,830		(3,830)		—
Total	$	5,675	$	8,641	$	14,316


	Three Months Ended June 30, 2019		Six Months Ended June 30, 2019
Lease costs
Operating lease cost	$	496	$	995
Short-term lease cost⁽¹⁾	220		548
Sublease income	(145)		(290)
Total	$	571	$	1,253