Cubist Pharmaceuticals (CBST) 8-K Cubist Increases Revenue 30% to $231 Million In the Second Quarter

Exhibit 99.1

FOR IMMEDIATE RELEASE

CUBIST INCREASES REVENUE 30% TO $231 MILLION IN THE SECOND QUARTER

·CUBICIN Net Revenues of $212 Million, Up 20% Over Q2 2011

·Q2 2012 Non-GAAP Diluted EPS Increased 28% Over Q2 2011 to $0.68; Q2 GAAP Diluted EPS was $0.58

·Non-GAAP Adjusted Operating Income for Q2 2012 Increased 23% Over Q2 2011 to $71 Million; Q2 GAAP Operating Income was $62 Million

Lexington, Mass., July 19, 2012 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) today announced results for the second quarter ended June 30, 2012.  The Company will host a conference call and webcast today at 5:00 p.m. ET (details below).

Financial Highlights for the Second Quarter of 2012 (unaudited)

·For the second consecutive quarter, total net revenues grew 30% over the same period in 2011. Q2 2012 total net revenues were $230.6 million, compared to $176.8 million in Q2 2011.

·U.S. CUBICIN® (daptomycin for injection) net product revenues increased 19% to $200.2 million from $168.6 million in Q2 2011; CUBICIN international revenues increased 47% to $11.4 million, compared to $7.7 million in Q2 2011.

·Non-GAAP diluted earnings per share (EPS) increased 28% to $0.68, compared to $0.53 in Q2 2011; GAAP diluted EPS was $0.58, compared to a loss of $0.34 per share in Q2 2011.

·Non-GAAP adjusted operating income increased 23% to $71.1 million, compared to $57.7 million in Q2 2011; GAAP operating income was $61.5 million, compared to an operating loss of $24.2 million in Q2 2011.

Michael Bonney, CEO of Cubist, said, “With another strong quarter, driven by revenue growth of 30% and a marked increase in bottom line growth, we are very pleased with the first half of 2012. We’re off to a strong start as we drive towards our Building Blocks of Growth five-year goals, and we look forward to a promising second half of 2012 as we continue to focus on creating long-term shareholder value.”

Cubist recorded a $5 million bonus from Optimer Pharmaceuticals, Inc. in the second quarter of 2012, for achieving the first year revenue target, bringing DIFICID® (fidaxomicin) service revenues for the quarter to $8.7 million. ENTEREG® (alvimopan), acquired through our acquisition of Adolor Corporation in December 2011, net product revenues were $9.7 million in Q2 2012.

As of June 30, 2012, Cubist had $854 million in cash, cash equivalents and investments. The total number of Cubist’s common shares outstanding as of June 30, 2012 was 63,751,433.

Recent Company Highlights

·On July 12, 2012, Cubist announced the initiation of its pivotal Phase 3 studies evaluating the efficacy and safety of CB-315 in patients with Clostridium difficile-associated diarrhea, or CDAD, with enrollment of a patient in the first of two planned identical global trials.

65 Hayden Avenue, Lexington, MA 02421  P 781.860.8660  F 781.861.0566  www.cubist.com

·On July 2, 2012, Cubist announced the promotion of Robert J. Perez, former Executive Vice President and Chief Operating Officer (COO), to President and COO; the promotion of Michael Tomsicek, former Vice President of Corporate Finance, to Senior Vice President and Deputy Chief Financial Officer; and the appointment of Thomas Rollins, former Senior Vice President of Program Management and R&D Planning at Sunovian Pharmaceutical Inc., to Senior Vice President of Program and Portfolio Management.

·On June 11, 2012, Cubist announced a five-year strategic roadmap, Building Blocks of Growth, which focuses on driving top- and bottom-line growth, future pipeline developments, and cultural enhancements that will position Cubist to deliver long-term, sustainable growth.

·In May 2012, at two scientific meetings, Cubist presented the results from Phase 2 studies of CB-5945 in patients with chronic non-cancer pain and opioid-induced constipation (OIC). The studies each met the primary endpoint of change from baseline in the number of spontaneous bowel movements (SBMs). Phase 3 studies are planned to begin by the end of 2012.

·On April 17, 2012, Cubist announced that its Phase 4 study of ENTEREG in patients undergoing radical cystectomy met its primary endpoint of time to achieve recovery of both upper and lower GI function. Additionally, all secondary endpoints, including length of hospital stay, achieved statistical significance. Cubist expects to submit a supplemental New Drug Application (sNDA) with the U.S. Food and Drug Administration (FDA) by the end of 2012.

“As we look to build on our tremendous momentum as a growing leader in the acute care/hospital environment, our Building Blocks of Growth will help us to sharpen our focus and measure our future success,” said Michael Bonney.  “The next five years present many exciting opportunities for Cubist, and we have already taken important steps to capture them, including making key senior executive promotions and new hires that enhance our existing team.  Together, we look forward to delivering important new medicines for patients and driving long-term value for our customers and shareholders.”

Use of Non-GAAP Financial Measures

Non-GAAP net income, non-GAAP EPS and non-GAAP adjusted operating income exclude non-operational activities.  As a result, Cubist uses these measures to assess and analyze its operational results and trends and to make financial and operational decisions.  Cubist also believes these non-GAAP financial measures are useful to investors because they provide greater transparency regarding Cubist’s operating performance.  These non-GAAP financial measures should not be considered an alternative to measurements required by GAAP, such as operating income, net income and EPS, and should not be considered measures of Cubist’s liquidity.  In addition, these non-GAAP financial measures are unlikely to be comparable with non-GAAP information provided by other companies.  Reconciliations between non-GAAP financial measures and GAAP financial measures are included in the tables accompanying this press release after the unaudited condensed consolidated financial statements.

***********************CONFERENCE CALL & WEBCAST INFORMATION***********************

CUBIST 2Q 2012 FINANCIAL RESULTS

Thursday, July 19, 2012 at 5:00 p.m. ET

U.S./Canada Attendee Dial-in: (855) 319-7654

International Attendee Dial-in: (484) 756-4327

Attendee Passcode: 13972921

24-HOUR REPLAY U.S./CANADA: (855) 859-2056

24-HOUR REPLAY INTERNATIONAL: (404) 537-3406

CALL WILL ALSO BE BROADCAST LIVE, LISTEN ONLY, VIA THE WEB AT:

www.tinyurl.com/cubist2Q12

Attendee Password: 071912

Replay will be available for 90 days via the Internet at www.cubist.com

*********************************************************************************

About Cubist

Cubist Pharmaceuticals, Inc. is a biopharmaceutical company focused on the research, development, and commercialization of pharmaceutical products that address significant unmet medical needs in the acute care environment. Cubist is headquartered in Lexington, Mass. Additional information can be found at Cubist’s web site at www.cubist.com.

Cubist Safe Harbor Statement

This press release includes forward-looking statements, including, without limitation, statements regarding:  (i) the favorable results of our Phase 2 clinical studies of CB-5945 and our expectations on the anticipated timing of our Phase 3 clinical studies for CB-5945; and (ii) our expectations regarding the submission of an sNDA for the use of ENTEREG by the end of 2012.Each forward-looking statement is subject to risks and uncertainties that could cause actual results to differ materially from those expressed or implied by such statement.Applicable risks and uncertainties include, among others: (i) our ability to successfully develop CB-5945 on the timelines that we expect; (ii) the timing and outcome of discussions with regulatory agencies, including the FDA, regarding ENTEREG, the timing of our submission of an sNDA, if any, and the actual safety and efficacy of ENTEREG for the indications in which it is being studied; and (iii) those additional factors discussed under the caption “Risk Factors” in our recent periodic filings with the Securities and Exchange Commission. We caution investors not to place considerable reliance on the forward-looking statements contained in this press release.These forward-looking statements speak only as of the date of this document, and we undertake no obligation to update or revise any of these statements.

Cubist, CUBICIN and ENTEREG are registered trademarks of Cubist Pharmaceuticals, Inc.

DIFICID is a registered trademark of Optimer Pharmaceuticals, Inc.

Contacts:
INVESTORS:	MEDIA:
Cubist Pharmaceuticals, Inc.	Cubist Pharmaceuticals, Inc.
Eileen C. McIntyre	Julie DiCarlo
Senior Director, Investor Relations	Senior Director, Corporate Communications
(781) 860-8533	(781) 860-8063
eileen.mcintyre@cubist.com	julie.dicarlo@cubist.com
Tables Follow

CUBIST PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

UNAUDITED

(in thousands)

	June 30,		December 31,
	2012		2011
ASSETS
Cash, cash equivalents and investments	$	854,418	$	867,695
Accounts receivable, net	90,126		87,800
Inventory	72,422		70,000
Property and equipment, net	168,763		168,425
Deferred tax assets, net	14,384		16,189
In-process research and development	311,400		311,400
Other assets	349,145		365,946
Total assets	$	1,860,658	$	1,887,455
LIABILITIES AND STOCKHOLDERS’ EQUITY
Accounts payable and accrued expenses	$	156,621	$	177,378
Deferred tax liabilities, net	132,226		143,177
Deferred revenue	37,242		31,524
Contingent consideration	223,757		248,234
Debt and other liabilities, net	424,564		487,285
Total liabilities	974,410		1,087,598
Total stockholders’ equity	886,248		799,857
Total liabilities and stockholders’ equity	$	1,860,658	$	1,887,455

CUBIST PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF INCOME

UNAUDITED

(in thousands, except share and per share data)

	Three months ended						Six months ended
	June 30,						June 30,
	2012			2011			2012			2011
Revenues:
U.S. CUBICIN product revenues, net	$	200,180		$	168,575		$	384,887		$	322,291
U.S. ENTEREG product revenues, net	9,706			—			19,148			—
Total U.S. product revenues, net	209,886			168,575			404,035			322,291
International product revenues	11,363			7,747			24,017			16,047
Service revenues	8,665			—			12,329			—
Other revenues	653			516			1,878			1,031
Total revenues, net	230,567			176,838			442,259			339,369
Costs and expenses:
Cost of product revenues	58,891			38,976			112,843			75,553
Research and development	67,206			41,871			118,378			82,287
Contingent consideration	2,694			81,816			5,523			82,914
Selling, general and administrative	40,255			38,341			84,035			78,505
Total costs and expenses	169,046			201,004			320,779			319,259
Operating income (loss)	61,521			(24,166		)	121,480			20,110
Other income (expense), net	(11,273		)	(6,961		)	(19,786		)	(13,768		)
Income (loss) before income taxes	50,248			(31,127		)	101,694			6,342
Provision (benefit) for income taxes	7,125			(10,512		)	25,777			4,372
Net income (loss)	$	43,123		$	(20,615	)	$	75,917		$	1,970
Basic earnings (loss) per share	0.68			(0.34		)	1.20			0.03
Diluted earnings (loss) per share	0.58		(1)	(0.34		)	1.04		(1)	0.03
Shares used in calculating:
Basic earnings (loss) per share	63,498,953			60,517,553			63,250,165			59,991,068
Diluted earnings (loss) per share	81,166,329			60,517,553			81,001,476			61,828,807

(1) Includes add back of interest expense, debt issuance costs and debt discount amortization on 2.50% notes to income, net of tax effect

CUBIST PHARMACEUTICALS, INC.

RECONCILIATION OF GAAP TO NON-GAAP FINANCIAL INFORMATION

UNAUDITED

(in thousands, except share and per share data)

	Three months ended						Six months ended
	June 30,						June 30,
	2012			2011			2012			2011
Reconciliation of GAAP net income (loss) to non-GAAP proforma net income
GAAP net income (loss)	$	43,123		$	(20,615	)	$	75,917		$	1,970
Non-cash debt discount amortization	4,654			4,569			9,481			9,054
Loss on partial extinguishment of 2.25% Notes	3,728			—			3,728			—
ENTEREG intangible asset amortization	4,589			—			9,177			—
ENTEREG inventory step-up	834			—			1,369			—
Expenses related to the acquisition of Adolor	1,448			—			5,037			—
Contingent consideration	2,694			81,816			5,523			82,914
Reversal of reserve for uncertain tax positions	(10,961		)	—			(10,961		)	—
Non-cash tax adjustment	4,825			(24,228		)	21,974			(11,189		)
Non-GAAP proforma net income	$	54,934		$	41,542		$	121,245		$	82,749
Non-GAAP basic earnings per share	$	0.87		$	0.69		$	1.92		$	1.38
Non-GAAP diluted earnings per share	$	0.68	(1)	$	0.53	(1)	$	1.50	(1)	$	1.08	(1)
Shares used in calculating:
Non-GAAP basic earnings per share	63,498,953			60,517,553			63,250,165			59,991,068
Non-GAAP diluted earnings per share	84,076,269			81,961,313			84,231,134			80,802,339

(1) Includes add back of interest expense and debt issuance costs on 2.25% notes and 2.50% notes to income, net of tax effect

	Three months ended					Six months ended
	June 30,					June 30,
	2012		2011			2012		2011
Reconciliation of GAAP operating income (loss) to non-GAAP adjusted operating income
Operating income (loss)	$	61,521	$	(24,166	)	$	121,480	$	20,110
ENTEREG intangible asset amortization	4,589		—			9,177		—
ENTEREG inventory step-up	834		—			1,369		—
Expenses related to the acquisition of Adolor	1,448		—			5,037		—
Contingent consideration	2,694		81,816			5,523		82,914
Non-GAAP adjusted operating income	$	71,086	$	57,650		$	142,586	$	103,024

CUBIST PHARMACEUTICALS, INC.

RECONCILIATION OF GAAP TO NON-GAAP FINANCIAL INFORMATION

UNAUDITED

(in thousands, except share and per share data)

	Three months ended						Six months ended
	June 30,						June 30,
	2012			2011			2012			2011
Reconciliation of GAAP basic earnings per share to non-GAAP basic earnings per share
Non-GAAP basic net income - from table above	$	54,934		$	41,542		$	121,245		$	82,749
GAAP and Non-GAAP basic shares	63,498,953			60,517,553			63,250,165			59,991,068
GAAP basic earnings (loss) per share	$	0.68		$	(0.34	)	$	1.20		$	0.03
Non-GAAP adjustments - from table above	0.19			1.03			0.72			1.35
Non-GAAP basic earnings per share	$	0.87		$	0.69		$	1.92		$	1.38
Reconciliation of GAAP diluted earnings per share to non-GAAP diluted earnings per share
Non-GAAP basic net income - from table above	$	54,934		$	41,542		$	121,245		$	82,749
Non-GAAP dilutive adjustments	2,417		(1)	1,969		(1)	4,906		(1)	4,119		(1)
Non-GAAP diluted net income	$	57,351		$	43,511		$	126,151		$	86,868
GAAP diluted shares	81,166,329			60,517,553			81,001,476			61,828,807
Non-GAAP dilutive adjustments	2,909,940		(2)	21,443,760		(2)	3,229,658		(2)	18,973,532		(2)
Non-GAAP diluted shares	84,076,269			81,961,313			84,231,134			80,802,339
GAAP diluted earnings (loss) per share	$	0.58		$	(0.34	)	$	1.04		$	0.03
Non-GAAP dilutive adjustments	0.10			0.87			0.46			1.05
Non-GAAP diluted earnings per share	$	0.68		$	0.53		$	1.50		$	1.08

(1) Includes add back of interest expense and debt issuance costs on 2.25% notes and 2.50% notes to income, net of tax effect

(2) Weighted average shares issued on full conversion