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`UNITED STATES PATENT AND TRADEMARK OFFICE
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`UNITED STATES DEPARTMENT OF COMMERCE
`United States Patent and Trademark Office
`Address: COMMISSIONER FOR PATENTS
`P.O. Box 1450
`Alexandria1 Virginia 22313- 1450
`wwwusptogov
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`APPLICATION NO.
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` F ING DATE
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`FIRST NAMED INVENTOR
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`ATTORNEY DOCKET NO.
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`CONF {MATION NO.
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`11/739,180
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`04/24/2007
`
`Thomas Kelleher
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`C062—02/03 US
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`8837
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`Intellectual Property Department
`Cubist Pharmaceuticals, Inc.
`65 Hayden Avenue
`Lexington, MA 02421
`
`KAM, CHIH MIN
`PAPER NUMBER
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`ART UNIT
`1656
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`MAIL DATE
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`11/30/2010
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`DELIVERY MODE
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`PAPER
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`Please find below and/or attached an Office communication concerning this application or proceeding.
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`The time period for reply, if any, is set in the attached communication.
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`PTOL—90A (Rev. 04/07)
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`Page 1
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`CUBIST 2104
`AGILA v. CUBIST
`IPR2015-00142
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`Page 1
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`CUBIST 2104
`AGILA v. CUBIST
`IPR2015-00142
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`Office Action Summary
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`Application No.
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`Applicant(s)
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`11/739,180
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`Examiner
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`CHIH-MIN KAM
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`KELLEHER ET AL.
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`Art Unit
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`1656 -
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`-- The MAILING DA TE of this communication appears on the cover sheet with the correspondence address --
`Period for Reply
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`A SHORTENED STATUTORY PERIOD FOR REPLY IS SET TO EXPIRE 3 MONTH(S) OR THIRTY (30) DAYS,
`WHICHEVER IS LONGER, FROM THE MAILING DATE OF THIS COMMUNICATION.
`Extensions of time may be available under the provisions of 37 CFR 1.136(a).
`In no event however may a reply be timely filed
`after SIX (6) MONTHS from the mailing date of this communication.
`If NO period for reply is specified above, the maximum statutory period will apply and will expire SIX (6) MONTHS from the mailing date of this communication.
`-
`- Failure to reply within the set or extended period for reply will, by statute, cause the application to become ABANDONED (35 U.S.C. § 133).
`Any reply received by the Office later than three months after the mailing date of this communication, even if timely filed, may reduce any
`earned patent term adjustment. See 37 CFR 1.704(b).
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`Status
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`1)IXI Responsive to communication(s) filed on 22 September 2010.
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`2a)I:I This action is FINAL.
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`2b)IZI This action is non-final.
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`3)I:I Since this application is in condition for allowance except for formal matters, prosecution as to the merits is
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`closed in accordance with the practice under EX parte Quayle, 1935 CD. 11, 453 O.G. 213.
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`Disposition of Claims
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`4)IXI Claim(s) 1-29 31-36 38-44 47-52 54-56 and 58-160 is/are pending in the application.
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`4a) Of the above Claim(s)
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`is/are withdrawn from consideration.
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`5)IZI Claim(s) 2-7 and 115 is/are allowed.
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`6)IXI Claim(s) 1 8-29 31-36 38-44 47-52 54-56 58-114 and 116-160 is/are rejected.
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`7)I:I Claim(s) _ is/are objected to.
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`8)I:I Claim(s) _ are subject to restriction and/or election requirement.
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`Application Papers
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`9)I:I The specification is objected to by the Examiner.
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`10)IZ The drawing(s) filed on 24 April 2007 is/are: a)IZI accepted or b)I:I objected to by the Examiner.
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`Applicant may not request that any objection to the drawing(s) be held in abeyance. See 37 CFR 1.85(a).
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`Replacement drawing sheet(s) including the correction is required if the drawing(s) is objected to. See 37 CFR 1.121(d).
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`11)I:I The oath or declaration is objected to by the Examiner. Note the attached Office Action or form PTO-152.
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`Priority under 35 U.S.C. § 119
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`12)I:I Acknowledgment is made of a claim for foreign priority under 35 U.S.C. § 119(a)—(d) or (f).
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`a)I:I All
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`b)I:I Some * c)I:I None of:
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`1.I:I Certified copies of the priority documents have been received.
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`2.I:I Certified copies of the priority documents have been received in Application No.
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`
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`3.I:I Copies of the certified copies of the priority documents have been received in this National Stage
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`application from the International Bureau (PCT Rule 17.2(a)).
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`* See the attached detailed Office action for a list of the certified copies not received.
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`Attachment(s)
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`4) D Interview Summary (PTO-413)
`1) D Notice of References Cited (PTO-892)
`Paper No(s)/Mai| Date. _
`2) D Notice of Draftsperson‘s Patent Drawing Review (PTO-948)
`3) IZI Information Disclosure Statement(s) (PTO/SB/08)
`5) I:I Notice of Informal Patent Application
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`Paper No(s)/Mai| Date 9/22/10.
`6) D Other:
`U.S. Patent and Trademark Office
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`PTOL-326 (Rev. 08-06)
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`Office Action Summary
`Page 2
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`Part of Paper No./Mai| Date 20101127
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`

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`Application/Control Number: 11/739,180
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`Page 2
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`Art Unit: 1656
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`DETAILED ACTION
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`Status of the Claims
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`1.
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`Claims 1-29, 31-36, 38-44, 47-52, 54-56 and 58-160 are pending.
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`Applicants’ amendment filed September 22, 2010 is acknowledged. Claims 2, 3, 6, 8, 9,
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`11, 38, 47-52, 58, 59 and 61 have been amended, claims 46 and 57 have been cancelled, and new
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`claims 64-160 have been added. Therefore, claims 1-29, 31-36, 38-44, 47-52, 54-56 and 58-160
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`are examined.
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`Withdrawn Claim Obiections
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`2.
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`The previous objection to claims 2-7, 31-36, 39-44, 47-52, 59 and 61-63 is withdrawn in
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`View of applicants’ amendment to the claims in the amendment filed September 22, 2010.
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`Withdrawn Claim Re 'ections - 35 USC I 02
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`3.
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`The previous rejection of claims 8-29, 38, 46, 55-56, 58 and 60 under 35 USC. 102(e) as
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`being as anticipated by Baker et al. (US RE39,071 E) is withdrawn in View of applicants’
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`amendment to the claims, applicants’ cancellation of the claims, and applicants’ response at
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`pages 23-24 in the amendment filed September 22, 2010.
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`Withdrawn Claim Reiections - Obviousness Twe Double Patenting
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`4.
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`The preVious rejection of claims 8-9, 46, 55, 57, 58 and 60 under the judicially created
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`doctrine of obViousness-type double patenting as being unpatentable over claims 18-20, 26, 28
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`and 29 of US. Patent RE39,071 E is withdrawn in View of applicants’ amendment to the claims,
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`and applicants’ cancellation of the claims in the amendment filed September 22, 2010.
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`New Claim Rejections - 35 USC § 112
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`The following is a quotation of the second paragraph of 35 USC. 112:
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`Page 3
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`Application/Control Number: 11/739,180
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`Page 3
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`Art Unit: 1656
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`The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the
`subject matter which the applicant regards as his invention.
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`5.
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`Claims 8-29, 31-36, 38-44, 47-52, 55-56, 58-114 and 116-160 are rejected under 35
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`USC. 112, second paragraph, as being indefinite for failing to particularly pointing out and
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`distinctly claiming the subject matter which the applicant regards as his invention.
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`6.
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`Claims 8-29, 31-36, 38-44, 47-52, 55-56, 58-114 and 116-160 are indefinite because of
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`the use of the term “impurities 1-14”. The term cited renders the claim indefinite, it is not clear
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`what these impurities are, and how they are defined. Claims 8-29, 31-36, 38-44, 47-52, 55-56,
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`59-61, 63-114 and 116-160 are included in this rejection for being dependent on a rejected claim
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`and not correcting the deficiency of the claims from which they depend.
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`7.
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`Claims 8-29, 31-36, 38-44, 47-52, 55-56, 95-113 and 116-160 are indefinite because of
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`the use of the term “The composition” or “the composition”, while the independent claim (i.e.,
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`claim 62) recites the term “Daptomycin”, not “A composition”.
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`Claim Rejections - 35 USC § 1 02
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`The following is a quotation of the appropriate paragraphs of 35 USC. 102 that form the
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`basis for the rejections under this section made in this Office action:
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`A person shall be entitled to a patent unless ,
`(e) the invention was described in a patent granted on an application for patent by another filed in the United
`States before the invention thereof by the applicant for patent, or on an international application by another who
`has fulfilled the requirements of paragraphs (1), (2), and (4) of section 371(c) of this title before the invention
`thereof by the applicant for patent.
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`The changes made to 35 USC. 102(e) by the American Inventors Protection Act of 1999
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`(AIPA) and the Intellectual Property and High Technology Technical Amendments Act of 2002
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`do not apply when the reference is a US. patent resulting directly or indirectly from an
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`international application filed before November 29, 2000. Therefore, the prior art date of the
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`Application/Control Number: 11/739,180
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`reference is determined under 35 U.S.C. 102(e) prior to the amendment by the AIPA (pre-AIPA
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`35 U.S.C. 102(e)).
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`8.
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`Claims 1 and 54 are rejected under 35 U.S.C. 102(e) as anticipated by Baker et al. (US
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`RE39,071 E, reissue ofU.S. Patent 5,912,226, filed December 16, 1991).
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`Baker et al. teach an antibacterial composition comprising daptomycin (LY146032)
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`obtained in substantially pure form, which refers to daptomycin that contains less than 2.5% of a
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`combined total of anhydro-daptomycin and beta-isomer of daptomycin (column 8, lines 50-60;
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`Examples 4 and 5; claim 1(g), 54), where daptomycin is purified by a procedure using Diaion
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`HP-20 resin column, followed by HPLC and another HP-20 resin column (Examples 1-5). Baker
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`et al. also teach the preparation of a pharmaceutical formulation comprising the purified
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`daptomycin (LY146032) with pharmaceutical carriers or excipients (column 9, lines 47-59), and
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`an antibiotic composition comprised of a combination of a compound of formula 1 (i.e.,
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`anhydro-A21978C; column 1, lines 14-21), a compound of formula 2 (isomer of A21978C) and a
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`compound of formula 3 (the parent cyclic peptide of A21978C; LY146032) or pharmaceutically
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`acceptable salts (Reissue: claim 18).
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`Resgonse t0 Arguments
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`Applicants indicate that the purity of daptomycin in Baker can only be interpreted as
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`defined by Baker, thus Baker can be interpreted to read that there is 97.5% of daptomycin over a
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`daptomycin plus anhydro-daptomycin (“A”) plus beta isomer daptomycin (“B”) composition.
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`The present application describes daptomycin purity relative to daptomycin plus anhydro-
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`daptomycin (impurity No. 13) plus beta isomer daptomycin (impurity No. 8) plus 12 other
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`impurities (impurities 1-7, 9-12 and 14) as described in Table 3 of the specification. Thus, Baker
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`uses a different purity and does not teach purity over the 14 daptomycin impurities. Applicants
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`also indicate that Baker methods yield at best about 93% pure daptomycin measured under the
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`current application while it yields 97.5% purity under its own teachings. Applicants further
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`assert that eVidence of inherency and/or notice of facts to support the inherency of the present
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`claims have not been provided. Regarding product-by process claims, claims 11-29 have been
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`amended to depend on claim 62 or claim 115, thus the basis for rejection is overcome. Therefore,
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`Baker does not anticipate claims 1 and 54, the rejection under 35 U.S.C. 102 (e) should be
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`withdrawn (pages 21-24 of the response).
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`Applicants’ response has been fully considered. Regarding claim 1(g) and claim 54, the
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`arguments are not found persuasive because of the following reasons. Baker et al. teach an
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`antibacterial composition comprising daptomycin (LY146032) obtained in substantially pure
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`form, which refers to daptomycin that contains less than 2.5% of a combined total of anhydro-
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`daptomycin and beta-isomer of daptomycin (column 8, lines 50-60; Examples 4 and 5). Since
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`Baker et al. do not indicate other impurities besides anhydro-daptomycin and beta-isomer of
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`daptomycin are contained in the daptomycin (LY146032) in substantially pure form, it reads that
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`the daptomycin has more than 97.5% purity. While Baker implies that other degradants are
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`present, but are not predominant in the pH range that optimizes the transpeptidation reactions,
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`the reference does not indicate other degradants are present m the purification procedure
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`(column 8, lines 45-49). While Baker's later work (US. Patent 4,874,843) shows undetermined
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`impurities at least as great as 7%, and daptomycin has at best 93% purity, the ‘843 patent only
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`use a single HP-20 resin column to purify daptomycin with a yield of 50-60% (Example 1-2),
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`which is different from the purification procedure (i.e., Diaion HP-20 resin column, followed by
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`Application/Control Number: 11/739,180
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`HPLC and another HP-20 resin column) used by Baker et al. in the US RE39,071 E (e.g., with a
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`very low yield in Example 3). Thus, even Baker (US. Patent 4,874,843) shows undetermined
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`impurities at least as great as 7%, and daptomycin has at best 93% purity, it does not mean that
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`the daptomycin purified by Baker et a]. in the US RE39,071 E has at best 93% purity since the
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`purification procedures used by two patents are different. As shown in Example 2 of the present
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`application, the purity level of the daptomycin was 91% using the purification method from the
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`'843 patent, and the daptomycin sample was filrther confirmed to contain fourteen impurities
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`(Example 10), which does not mean the daptomycin purified by Baker et al. in the US RE39,071
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`E would have at best 93% purity when a different purification procedure is used. The
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`daptomycin purified by Baker et al. in the US RE39,071 E is obtained in substantially pure form
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`that contains less than 2.5% of a combined total of anhydro-daptomycin and beta-isomer of
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`daptomycin as taught by Baker et al. is not different from the claimed composition as indicated
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`in claims 1(g) and 54 because the claimed substantially pure daptomycin has also >97% purity
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`without indicating the existence of other 14 impuritites. Therefore, the rejection of claim 1(g)
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`and claim 54 are maintained.
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`Claim Rejections-Obviousness Type Double Patenting
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`The nonstatutory double patenting rejection is based on a judicially created doctrine
`grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or
`improper timewise extension of the "right to exclude" granted by a patent and to prevent possible
`harassment by multiple assignees. See In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed.
`Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686
`F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA
`1970);and, In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
`A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) may be used to
`overcome an actual or provisional rejection based on a nonstatutory double patenting ground
`provided the conflicting application or patent is shown to be commonly owned with this
`application. See 37 CFR 1.130(b).
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`Application/Control Number: 11/739,180
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`Effective January 1, 1994, a registered attorney or agent of record may sign a terminal
`disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37
`CFR 3.73(b).
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`9.
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`Claims 1 and 54 are rejected under the judicially created doctrine of obviousness-type
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`double patenting as being unpatentable over claims 18-20, 26 and 28 of US. Patent RE39,071 E.
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`Although the conflicting claims are not identical, they are not patentably distinct from each other
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`because claims 1 and 54 in the instant application disclose a composition comprising
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`substantially pure daptomycin (i.e., >97% purity daptomycin). This is obvious variation in view
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`of claims 18-20, 26 and 28 of the patent which disclose an antibiotic composition comprised of a
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`combination of a compound of formula 1 (i.e., anhydro-daptomycin), a compound of formula 2
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`(i.e., beta-isomer of daptomycin) and a compound of formula 3 (i.e., daptomycin, A21978C), or
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`pharmaceutically acceptable salts thereof, wherein the total amount of the compound of formula
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`1 and the compound of formula 2 or salts thereof, in the combination is less than 6 weight
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`percent; or a pharmaceutical formulation comprising a combination of a compound of formula 1
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`(i.e., anhydro-daptomycin), a compound of formula 2 (i.e., beta-isomer of daptomycin) and a
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`compound of formula 3 (i.e., daptomycin, A21978C), or pharmaceutically acceptable salts
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`thereof, wherein the total amount of the compound of formula 1 and the compound of formula 2
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`or salts thereof, in the combination is less than 6 weight percent. Both claims of instant
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`application and the patent are directed to a composition comprising substantially pure
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`daptomycin (i.e., >97% purity daptomycin); or a pharmaceutical composition comprising the
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`composition and a pharmaceutically acceptable carrier or excipient. Thus, claims 1 and 54 in
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`present application and claims 18-20, 26 and 28 of the patent are obvious variations of a
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`composition comprising substantially pure daptomycin (i.e., >97% purity daptomycin).
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`Application/Control Number: 11/739,180
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`Page 8
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`Art Unit: 1656
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`Resgonse t0 Arguments
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`Applicants indicate that they reserve their right to file a terminal disclaimer upon an
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`indication of allowance of these claims over Baker under 35 U.S.C. § 102(e) as requested above
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`or to cancel such claims in a further amendment (page 24 of the response).
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`Applicants’ response has been considered and the rejection is maintained.
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`Conclusion
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`10.
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`Claims 1, 8-29, 31-36, 38-44, 47-52, 54-56, 58-114 and 116-160 are rejected; and claims
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`2-7 and 115 are free of art.
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`Any inquiry concerning this communication or earlier communications from the
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`examiner should be directed to Chih-Min Kam whose telephone number is (571) 272-0948. The
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`examiner can normally be reached on 8.00-4230, Mon-Fri.
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`If attempts to reach the examiner by telephone are unsuccessful, the examiner’s
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`supervisor, Manjunath Rao can be reached at 571-272-0939. The fax phone number for the
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`organization where this application or proceeding is assigned is 571-273-8300.
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`Information regarding the status of an application may be obtained from the Patent
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`Application Information Retrieval (PAIR) system. Status information for published applications
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`may be obtained from either Private PAIR or Public PAIR. Status information for unpublished
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`applications is available through Private PAIR only. For more information about the PAIR
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`system, see http://pair-direct.uspto. gov. Should you have questions on access to the Private PAIR
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`system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free).
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`/Chih-Min Kam/
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`Primary Examiner, Art Unit 1656
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`Page 9
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`Application/Control Number: 11/739,180
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`Page 9
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`Art Unit: 1656
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`CMK
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`November 27, 2010
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`Page 10
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