`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`UNITED STATES DEPARTMENT OF COMMERCE
`United States Patent and Trademark Office
`Address: COMMISSIONER FOR PATENTS
`P.O. Box 1450
`Alexandria1 Virginia 22313- 1450
`wwwusptogov
`
`APPLICATION NO.
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`
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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
`
`C062—02/03 US
`
`8837
`
`Intellectual Property Department
`Cubist Pharmaceuticals, Inc.
`65 Hayden Avenue
`Lexington, MA 02421
`
`KAM, CHIH MIN
`PAPER NUMBER
`
`ART UNIT
`1656
`
`MAIL DATE
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`08/1 1/2009
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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 2211
`AGILA V. CUBIST
`IPR2015-00143
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`CUBIST 2211
`AGILA v. CUBIST
`IPR2015-00143
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`

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`
`
`Application No.
`
`Applicant(s)
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`11/739,18O
`
`KELLEHER ET AL.
`
`Office Action Summary
`
`Examiner
`
`CHIH-MIN KAM
`
`Art Unit
`
`1656 -
`
`-- The MAILING DA TE of this communication appears on the cover sheet with the correspondence address --
`Period for Reply
`
`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).
`
`Status
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`1)IXI Responsive to communication(s) filed on 15 May 2009.
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`2a)IZI This action is FINAL.
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`2b)I:I 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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`
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`Disposition of Claims
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`4)IZI Claim(s) 1-29 31-36 38-44 46-52 and 54-57 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)I:I Claim(s) _ is/are allowed.
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`6)IXI Claim(s) 1-5 8-29 31 -34 38-42 46-50 and 54-57 is/are rejected.
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`7)IZI Claim(s) 6 7 35 36 43 44 51 and 52 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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`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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`Attach ment(s)
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`1) D Notice of References Cited (PTO-892)
`2) D Notice of Draftsperson‘s Patent Drawing Review (PTO-948)
`3) |:| Information Disclosure Statement(s) (PTO/SB/08)
`Paper No(s)/Mai| Date
`.
`U.S. Patent and Trademark Office
`
`4) E Interview Summary (PTO-413)
`Paper N0(S)/IVI3II Date.w -
`5) I:I Notice of Informal Patent Application
`6) D Other:
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`PTOL-326 (Rev. 08-06)
`
`Office Action Summary
`
`Part of Paper No./Mai| Date 20090808
`
`Page 2
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`Page 2
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`

`

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`
`
`
`CHlH-MIN KAM
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`1656
`
`
`
`
`
`
`
`
`Application No.
`Applicant(s)
`
`_
`Interwew Summary
`
`11/739,180
`KELLEH ER ET AL.
`
`Examiner
`Art Unit
`
`
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`All participants (applicant, applicant’s representative, PTO personnel):
`
`(1 ) CHlH-MlN KAM.
`
`(2) Jill Mandelblatt.
`
`Date of Interview: 14 Max 2009.
`
`(3)William De Vaul.
`
`(4)
`
`.
`
`Type:
`
`b)I:I Video Conference
`a)IX] Telephonic
`c)l:I Personal [copy given to: 1)I:I applicant
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`2)[:I applicant's representative]
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`Exhibit shown or demonstration conducted:
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`If Yes, brief description:
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`d)l:| Yes
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`e)I:I No.
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`Claim(s) discussed: pending claims.
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`Identification of prior art discussed: Baker et al. (US RE39,071E1.
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`Agreement with respect to the claims f)I:I was reached.
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`g)IZ] was not reached. h)I:I NlA.
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`Substance of Interview including description of the general nature of what was agreed to if an agreement was
`reached, or any other comments: Discussing the Baker reference regarding the purity of daptomycin {LY 146032),
`applicants would present the arguments and evidence indicating the purity of LY146032 in Baker'sreference is best
`93% in the coming amendment.
`.
`
`(A fuller description, if necessary, and a copy of the amendments which the examiner agreed would render the claims
`allowable, if available, must be attached. Also, where no copy of the amendments that would render the claims
`allowable is available, a summary thereof must be attached.)
`
`THE FORMAL WRITTEN REPLY TO THE LAST OFFICE ACTION MUST INCLUDE THE SUBSTANCE OF THE
`
`If a reply to the last Office action has already been filed, APPLICANT IS
`INTERVIEW. (See MPEP Section 713.04).
`GIVEN A NON-EXTENDABLE PERIOD OF THE LONGER OF ONE MONTH OR THIRTY DAYS FROM THIS
`
`INTERVIEW DATE, OR THE MAILING DATE OF THIS INTERVIEW SUMMARY FORM, WHICHEVER IS LATER, TO
`FILE A STATEMENT OF THE SUBSTANCE OF THE INTERVIEW. See Summary of Record of Interview
`requirements on reverse side or on attached sheet.
`
`
`
`
`
` U.S. Patentand Trademark Office
`PTOL-413 (Rev. 04-03)
`Interview Summary
`Paper No. 20090808
`
`Page 3
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`Page 3
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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, 46-52 and 54-57 are pending.
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`Applicants’ amendment filed May 15, 2009 is acknowledged. Claim 1 has been
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`amended, and new claims 54-57 have been cancelled. Therefore, claims 1-29, 31-36, 38-44, 46-
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`52 and 54-57 are examined.
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`Claim Rejections - 35 USC § 1 02/1 03
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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(0) of this title before the invention
`thereof by the applicant for patent.
`
`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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`reference is determined under 35 USC. 102(e) prior to the amendment by the AIPA (pre-AIPA
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`35 USC. 102(e)).
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`The following is a quotation of 35 USC. 103(a) which forms the basis for all
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`obviousness rejections set forth in this Office action:
`
`(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in
`section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are
`such that the subject matter as a whole would have been obvious at the time the invention was made to a person
`having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the
`manner in which the invention was made.
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`Page 4
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`Page 4
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`

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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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`2.
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`Claims 1-5, 8-29, 31-34, 38-42, 46-50 and 54-57 are rejected under 35 U.S.C. 102(e) as
`
`anticipated by or, in the alternative, under 35 U.S.C. 103(a) as unpatentable over Baker et al. (US
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`RE39,071 E, reissue ofU.S. Patent 5,912,226, filed December 16, 1991).
`
`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, claim
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`8). Baker et al. also teach the preparation of a pharmaceutical formulation comprising the
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`purified daptomycin (LY146032) with pharmaceutical carriers or excipients (column 9, lines 47-
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`59; claims 9, 38, 46 and 55-57). Although Baker et al. do not specifically disclose the
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`daptomycin (LY146032) that is essentially pure (i.e., at least 98% of a sample being daptomycin
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`as defined at page 11, lines 23-26 of the instant specification); that is substantially free of
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`anhydro-daptomycin (no more than 1%; page 11, lines 27-29) and substantially free of [3-isomer
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`of daptomycin (no more than 1%); that is essentially free of anhydro-daptomycin (no more than
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`0.5%; page 12, lines 1-3) and substantially free of [3-isomer of daptomycin (no more than 1%);
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`that is free of anhydro-daptomycin (no more than 0.1%; page 12, lines 4-6) and substantially free
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`of [3-isomer of daptomycin (no more than 1%), the reference does indicate the daptomycin
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`(LY146032) is in substantially pure form and contains less than 2.5% of a combined total of
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`anhydro-daptomycin and beta-isomer of daptomycin. Furthermore, Baker et al. discloses a
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`composition or pharmaceutical composition comprising substantially pure daptomycin, which
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`meets the criteria of claim 1(a)-1(d) and 1(g), and its dependent claims because the term
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`Page 5
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`Page 5
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`Application/Control Number: 11/739,180
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`Page 4
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`Art Unit: 1656
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`“comprising” indicates the composition can contain something else besides substantially or
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`essentially pure daptomycin. Since claim 1(a)-1(d) and 1(g) merely recites substantially or
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`essentially pure daptomycin that may contain slight amount of anhydro-daptomycin and beta-
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`isomer of daptomycin, it is obVious that a composition comprising LY146032 that is
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`substantially pure taught by Baker et al., which encompass the embodiments of essentially pure
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`daptomycin at least 98% pure (claims 1(a), 2, 31, 39, 47), the embodiments of substantially free
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`of anhydro-daptomycin (no more than 1%) and substantially free of [3-isomer of daptomycin (no
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`more than 1%; claims 1(b), 3, 32, 40, 48), the embodiments of essentially free of anhydro-
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`daptomycin (no more than 0.5%) and substantially free of [3-isomer of daptomycin (no more than
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`1%; claims 1(c), 4, 33, 41, 49), and the embodiments of free of anhydro-daptomycin (no more
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`than 0.1%) and substantially free of [3-isomer of daptomycin (no more than 1%; claims 1(d), 5,
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`34, 42, 50). It is also obvious that claims 11-29 are not patentable because the product by
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`process claims are limited by and defined by the process, determination of patentability is based
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`on the product itself, and the patentability of a product does not depend on its method of
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`production (see MPEP 2113). In the instant case, the composition comprising daptomycin that is
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`substantially free of anhydro-daptomycin and beta-isomer of daptomycin (less than 2.5%
`
`impurity) as indicated in the patent is not different from the claimed composition comprising
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`essentially or substantially pure daptomycin (>98% daptomycin), even though the daptomycin of
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`reference is purified by a different process. Baker et al. also disclose an antibiotic composition
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`comprised of a combination of a compound of formula 1 (i.e., anhydro-A21978C; column 1,
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`lines 14-21), a compound of formula 2 (isomer of A21978C) and a compound of formula 3 (the
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`Page 6
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`Application/Control Number: 11/739,180
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`Page 5
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`Art Unit: 1656
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`parent cyclic peptide of A21978C; LY146032) or pharmaceutically acceptable salts (Reissue:
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`claim 18; claim 10 of instant application).
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`Resgonse t0 Arguments
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`Applicants indicate that Baker did not provide LY146032 that is at least 97.5% pure
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`because (A) other impurities are implied in Baker, (B) a dozen other impurities later discovered
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`by Applicants were unappreciated in Baker and were at least 7% in Baker's later work, and (C)
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`Baker's later work teaches at best 93% purity. Regarding item A, applicants argue that Baker did
`
`not discuss overall purity of daptomycin in the composition, and Baker does not disclose the
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`purity level of daptomycin in the sample but discloses the level of anhydro-daptomycin and beta-
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`isomer of daptomycin in relation to daptomycin. Baker implies that other degradants are present,
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`but are not predominant in the pH range that optimizes the transpeptidation reactions. Regarding
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`item B, applicants argue that Baker likely had less than 93% LY146032 because it did not
`
`recognize existence of other impurities and Baker's later work (US. Patent 4,874,843) shows
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`undetermined impurities at least as great as 7%. Regarding item C, applicants argue that Baker's
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`later work (US. Patent 4,874,843) describes at best 93% purity. Furthermore, the Applicants
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`described the use of the purification method from the '843 patent in Example 2 of the present
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`application (See page 52, lines 1-5), and the purity level of the composition was 91%. Moreover,
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`Applicants' use of the HPLC method described in the present invention revealed that the
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`daptomycin purified by the '843 patent's method in Example 2 of the present application
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`contained fourteen impurities (anhydro daptomyein, beta-isomer of daptomycin and 12
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`additional impurities; see Example 10, page 57, line 10- page 60, line 8), It was Applicants'
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`present discovery of the impurities and the resulting method to produce more pure forms of
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`Page 7
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`Page 7
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`

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`Application/Control Number: 11/739,180
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`Page 6
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`Art Unit: 1656
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`daptomyein that are non-obvious over Baker. In view of the foregoing, the rejection should be
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`withdrawn (pages 8-12 of the response).
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`Applicants’ response has been fully considered. However, the arguments are not found
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`persuasive because of the following reasons. Regarding item A, Baker et a]. 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-
`
`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
`
`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
`
`(column 8, lines 45-49). Regarding items B and C, while Baker's later work (US. Patent
`
`4,874,843) shows undetermined impurities at least as great as 7%, and daptomycin has at best
`
`93% purity, the ‘843 patent only use a single HP-20 resin column to purify daptomycin, which is
`
`different from the purification procedure (i.e., Diaion HP-20 resin column, followed by HPLC
`
`and another HP-20 resin column) used by Baker et al. in the US RE39,071 E. Thus, even Baker
`
`(US. Patent 4,874,843) shows undetermined impurities at least as great as 7%, and daptomycin
`
`has at best 93% purity, it does not mean that the daptomycin purified by Baker et al. in the US
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`RE39,071 E has at best 93% purity since the purification procedures used by two patents are
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`different. As shown in Example 2 of the present application, the purity level of the daptomycin
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`was 91% using the purification method from the '843 patent, and the daptomycin sample was
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`Page 8
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`Page 8
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`Application/Control Number: 11/739,180
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`Page 7
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`Art Unit: 1656
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`fiarther confirmed to contain fourteen impurities (Example 10), which does not mean the
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`daptomycin purified by Baker et al. in the US RE39,071 E would have at best 93% purity when a
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`different purification procedure is used. Even if the daptomycin purified by Baker et al. in the
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`US RE39,071 E does not have 97.5% purity, the composition comprising daptomycin
`
`(LY146032) obtained in substantially pure form that contains less than 2.5% of a combined total
`
`of anhydro-daptomycin and beta-isomer of daptomycin as taught by Baker et al. is not different
`
`from the claimed composition as indicated in claim 1(a)-1(d) and 1(g) because the term
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`“comprising” indicates the composition can contain something else besides substantially or
`
`essentially pure daptomycin in a composition comprising substantially or essentially pure
`
`daptomycin. Therefore, the rejection of claim 1(a)—1(d) and its dependent claims are maintained.
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`Claim Objections
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`3.
`
`Claims 6-7, 35-36, 43-44 and 51-52 are objected to because the claims are dependent
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`from a rejected claim, but would be allowable if rewritten in independent form including all of
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`the limitations of the base claim and any intervening claims.
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`Page 9
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`Page 9
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`

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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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`Conclusion
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`4.
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`Claims 1-5, 8-29, 31-34, 38-42, 46-50 and 54-57 are rejected; and claims 6-7, 35-36, 43-
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`44 and 51-52 are objected to.
`
`Applicant's amendment necessitated the new ground(s) of rejection presented in this
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`Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a).
`
`Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
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`A shortened statutory period for reply to this final action is set to expire THREE
`
`MONTHS from the mailing date of this action. In the event a first reply is filed within TWO
`
`MONTHS of the mailing date of this final action and the advisory action is not mailed until after
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`the end of the THREE-MONTH shortened statutory period, then the shortened statutory period
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`will expire on the date the advisory action is mailed, and any extension fee pursuant to 37
`
`CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event,
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`however, will the statutory period for reply expire later than SIX MONTHS from the date of this
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`final action.
`
`Any inquiry concerning this communication or earlier communications from the
`
`examiner should be directed to Chih-Min Kam whose telephone number is (571) 272-0948. The
`
`examiner can normally be reached on 8.00-4230, Mon-Fri.
`
`If attempts to reach the examiner by telephone are unsuccessful, the examiner’s
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`supervisor, Jon Weber can be reached at 571-272-0925. 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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`Page 10
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`Page 10
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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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`Information regarding the status of an application may be obtained from the Patent
`
`Application Information Retrieval (PAIR) system. Status information for published applications
`
`may be obtained from either Private PAIR or Public PAIR. Status information for unpublished
`
`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).
`
`/Chih-Min Kam/
`
`Primary Examiner, Art Unit 1656
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`CMK
`
`August 8, 2009
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`Page 11
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`Page 11
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