UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE TO

TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1)

OF THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 2)

CUBIST PHARMACEUTICALS, INC.

(Name of Subject Company (Issuer))

CUBIST PHARMACEUTICALS, INC.

(Name of Filing Persons (Issuer))

2.50% Convertible Senior Notes due 2017

1.125% Convertible Senior Notes due 2018

1.875% Convertible Senior Notes due 2020

(Title of Class of Securities)

229678 AD9

229678 AF4

229678 AH0

(CUSIP Number of Class of Securities)

Sunil A. Patel

2000 Galloping Hill Road

K1-3045

Kenilworth, NJ 07033

(908) 740-4000

(Name, address and telephone number of person authorized to receive notices and communications on behalf of filing persons)

with copies to:

Andrew F. Fowler

David Schwartz

Hughes Hubbard & Reed LLP

One Battery Park Plaza

New York, NY 10004

Phone: (212) 837-6000

CALCULATION OF FILING FEE

Check the appropriate boxes to designate any transactions to which the statement relates:

Check the following box if the filing is a final amendment reporting the results of the tender offer:  x

INTRODUCTORY STATEMENT

This Amendment No. 2 amends and supplements the Tender Offer Statement on Schedule TO-I filed with the Securities and Exchange Commission (as amended and supplemented from time to time, the “Schedule TO”) by Cubist Pharmaceuticals, Inc. (the “Company”) with respect to the right of each holder (each, a “Holder”) of (i) the Company’s 2.50% Convertible Senior Notes due 2017 (the “2017 Convertible Notes”), (ii) the Company’s 1.125% Convertible Senior Notes due 2018 (the “2018 Convertible Notes”), and (iii) the Company’s 1.875% Convertible Senior Notes due 2020 (the “2020 Convertible Notes” and together with the 2017 Convertible Notes and 2018 Convertible Notes, the “Notes”), to require the Company to repurchase, at the Holder’s option, 100% of the principal amount of the Notes, plus accrued and unpaid interest thereon to, but excluding, February 23, 2015 (unless such Fundamental Change Repurchase Date falls after a Regular Record Date and on or prior to the corresponding Interest Payment date, in which case the Company shall pay the full amount of accrued and unpaid interest payable on such Interest Payment Date to the Holder of record at the close of business on such Regular Record Date), pursuant to the terms and conditions of the Fundamental Change Repurchase Right Notice, Notice of Right to Convert, Notice of Entry into Supplemental Indenture and Offer to Repurchase dated January 22, 2015 filed as Exhibit (a)(1) to the Schedule TO, as amended and supplemented by the Amendment and Supplement dated January 27, 2015 to Fundamental Change Repurchase Right Notice, Notice of Right to Convert, Notice of Entry into Supplemental Indenture and Offer to Repurchase dated January 22, 2015 filed as Exhibit (a)(1)(i) to the Schedule TO (as so amended and supplemented, the “ Notice”).

This Schedule TO was, and this Amendment is, intended to satisfy the disclosure requirements of Rule 13e-4(c)(2) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”).

Items 1 through 9, and Item 11.

Items 1 through 9 and Item 11 of the Schedule TO are hereby amended and supplemented by adding the following text thereto:

In accordance with the terms of the Notice, the Fundamental Change Repurchase Right expired at the end of the day, immediately after 11:59 p.m., Eastern time, on February 19, 2015 (the “Fundamental Change Expiration Time”), and was not extended. The Company has been advised by the Paying Agent, Conversion Agent and Information Agent that none of the Notes were validly surrendered for repurchase prior to the Fundamental Change Expiration Time. A copy of the press release announcing the final results of the tender offer is filed as Exhibit (a)(5)(i) and incorporated by reference herein.

Item 12. Exhibits.

Item 12 of the Schedule TO is hereby amended and supplemented to include the following exhibit:

SIGNATURE

After due inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: February 23, 2015

EXHIBIT INDEX

Exhibit (a)(5)(i)

Merck, on Behalf of Its Wholly Owned Subsidiary Cubist Pharmaceuticals, Announces Results of Tender Offer for Cubist’s 2.50% Convertible Senior Notes Due 2017, 1.125% Convertible Senior Notes Due 2018 and 1.875% Convertible Senior Notes Due 2020

KENILWORTH, N.J., Feb. 23, 2015 - Merck (NYSE: MRK), known as MSD outside the United States and Canada, on behalf of its wholly owned subsidiary Cubist Pharmaceuticals, Inc., today announced the results of its tender offer (the “Convertible Notes Tender Offer”) pursuant to which each holder of Cubist’s 2.50% Convertible Senior Notes due 2017 (the “2017 Convertible Notes”), 1.125% Convertible Senior Notes due 2018 (the “2018 Convertible Notes”) and 1.875% Convertible Senior Notes due 2020 (the “2020 Convertible Notes” and together with the 2017 Convertible Notes and 2018 Convertible Notes, the “Convertible Notes”) had the right (the “Fundamental Change Repurchase Right”), at such holder’s option, to require Cubist to repurchase for cash all of such holder’s Convertible Notes, or any portion of the principal amount thereof that is equal to $1,000 or an integral multiple of $1,000 principal amount. The Fundamental Change Repurchase Right expired at the end of the day, immediately after 11:59 p.m., Eastern time, on Feb. 19, 2015 (the “Fundamental Change Expiration Time”), and was not extended. Cubist has been advised by The Bank of New York Mellon Trust Company, N.A., the Paying Agent and Conversion Agent for the Convertible Notes Tender Offer, and Mackenzie Partners, the Information Agent for the Convertible Notes Tender Offer, that none of the Notes were validly surrendered for repurchase prior to the Fundamental Change Expiration Time.

About Merck

Today’s Merck is a global health care leader working to help the world be well. Merck is known as MSD outside the United States and Canada. Through our prescription medicines, vaccines, biologic therapies and animal health products, we work with customers and operate in more than 140 countries to deliver innovative health solutions. We also demonstrate our commitment to increasing access to health care through far-reaching policies, programs and partnerships. For more information, visit www.merck.com and connect with us on Twitter, Facebook and YouTube.

Merck Forward-Looking Statement

This news release includes “forward-looking statements” within the meaning of the safe harbor provisions of the U.S. Private Securities Litigation Reform Act of 1995. These statements are based upon the current beliefs and expectations of Merck’s management and are subject to significant risks and uncertainties. If underlying assumptions prove inaccurate or risks or uncertainties materialize, actual results may differ materially from those set forth in the forward-looking statements.

Risks and uncertainties include but are not limited to, general industry conditions and competition; general economic factors, including interest rate and currency exchange rate fluctuations; the impact of pharmaceutical industry regulation and health care legislation in the United States and internationally; global trends toward health care cost containment; technological advances, new products and patents attained by competitors; challenges inherent in new product development, including obtaining regulatory approval; Merck’s ability to accurately predict future market conditions; manufacturing difficulties or delays; financial instability of international economies and sovereign risk; dependence on the effectiveness of Merck patents and other protections for innovative products; and the exposure to litigation, including patent litigation, and/or regulatory actions.

Merck undertakes no obligation to publicly update any forward-looking statement, whether as a result of new information, future events or otherwise except as required by applicable law. Additional factors that could cause results to differ materially from those described in the forward-looking statements can be found in Merck’s 2013 Annual Report on Form 10-K and the company’s other filings with the Securities and Exchange Commission (SEC) available at the SEC’s Internet site (www.sec.gov).