DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant's election without traverse of invention Group I, claims 1-22 without traverse, and of the amylase variant species of claim 21, and of the feature species N at position 40, R at position 91, F at position 100, S at position 281, N at position 172, R at position 116, and pairwise deletions at positions 181 and 182, and SEQ ID NO: 1 as the SEQ ID NO species, without traverse, in the reply filed on 5/28/2025, is acknowledged. Claims 23-28, are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Claims 1-20 and 22 are withdrawn as they do not read on the elected species.
Status of the Claims
The amendment of 5/28/2025 has been entered. Claims 1-28 are pending (claim set as filed on 02/21/2023). Claims 1-20, and 22-28 are withdrawn as discussed above under Election/Restrictions.
Claim 21 is currently under examination and was examined on its merits.
Priority
This application filed on 04/21/2022 claims priority to PCT application no. PCT/US2020/056428, filed on 10/20/2020, and claims priority to provisional application no. PRO 62/925,273, filed on 10/24/2019.
Information Disclosure Statement
No Information Disclosure Statement (IDS) has been filed in this application. Applicant is reminded that each individual associated with the filing and prosecution of a patent application has a duty of candor and good faith in dealing with the U.S. Patent and Trademark Office, which includes a duty to disclose to the Office all information known to that individual to be material to patentability (see 37 C.F.R. 1.56).
Claim Objections
Claim 21 is objected to because of the following informalities:
In claim 21, line 6, “postion” should read “position”.
Claim Rejections - 35 USC § 112 (b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
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.
Claim 21 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 21 recites ‘[a] recombinant, variant, non-naturally-occurring a-amylase
comprising three or more of the following features: (a) D or N at position 40 and/or R at position 91 and (b) Fat position 100, Y at position 263, D at position 288, M, N or R at position 324 and/or L at position 364, optionally in combination with (c) H at position 169, M at position 183M, N or S at position 281, N or R at position 172, P at position 190, E, Q or R at position 244, R at position 474, R at pos[i]tion 116, optionally
in combination with pairwise deletions at positions 181 and 182 or 183 and 184’, which renders the claim indefinite since it is unclear if the phrase ‘three or more features’ relates to the recited (a), (b), and (c), to subsets of individual modifications (for example, F at position 100, Y at position 263, D at position 288, M, N or R at position 324), or to individual amino acid positions of modifications (for example, ‘F at position 100’).
The phrase ‘and/or’ recited in line 2 of claim 21 renders the claim indefinite since it is unclear if ‘and/or’ recited in line 2 relates to ‘R at position 91’, or to ‘R at position 91’ and further limitations following ‘R at position 91’. If further limitations are included, it is unclear which of the listed following limitations after ‘R at positions 91’ are encompassed.
The phrase ‘and/or’ recited in line 4 of claim 21 renders the claim indefinite since it is unclear if ‘and/or’ recited in line 4 relates to ‘L at position 364’, or to ‘L at position 364’ and further limitations following ‘L at position 364’. If further limitations are included, it is unclear which of the listed following limitations after ‘L at position 364’ are encompassed. The phrase ‘and/or’ recited in line 4 further renders the claim indefinite since it is unclear if ‘and/or’ in line 4 refers back to ‘R at position 324’, or to ‘F at position 100, Y at position 263, D at position 288, M, N or R at position 324’.
The phrase ‘optionally in combination with’ recited in line 4 of claim 21 renders the claim indefinite since it is unclear if ‘optionally in combination with’ relates to ‘(c) H at position 169, M at position 183M, N or S at position 281, N or R at position 172, P at position 190, E, Q or R at position 244, R at position 474, R at pos[i]tion 116’, or to ‘(c) H at position 169, M at position 183M, N or S at position 281, N or R at position 172, P at position 190, E, Q or R at position 244, R at position 474, R at pos[i]tion 116, optionally in combination with pairwise deletions at positions 181 and 182 or 183 and 184’. It is further unclear if ‘optionally in combination with’ recited in line 4 refers back to ‘L at position 364’, or to ‘L at position 364’ and further limitations recited before ‘L at position 364’. If further limitations before ‘L at position 364’ are included, it is unclear which of the further limitations before ‘L at position 364’ are encompassed.
The phrase ‘optionally in combination with’ recited in line 6 of claim 21 renders the claim indefinite since it is unclear if ‘optionally in combination with’ refers back to (c), or to (a), (b), and (c).
One of ordinary skill in the art would not be able to determine the metes and bounds of the claim 21, and thus could not clearly determine how to avoid infringement of the claim.
In the interest of compact prosecution, the Examiner is interpreting claim 21 to the broadest embodiment claimed.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Lassila et al. (WO 2018/184004 A1, published on 10/04/2018), hereinafter ‘Lassila’, in view of Cascao-Pereira et al. (US 2014/0287477 A1, published on 09/25/2014), hereinafter ‘Cascao-Pereira’, and Betts et al. (“Amino acid properties and consequences of substitutions”, published in Feb 2003, Bioinformatics for Geneticists, pages 289-316), hereinafter ‘Betts’.
Lassila’s general disclosure relates to “compositions and methods relating to variant alpha-amylases” (see entire document, including abstract).
Regarding claim 21, pertaining to the recombinant, variant, non-naturally-occurring α-amylase of claim 1, Lassila teaches a recombinant, variant, non-naturally-occurring α-amylase (“a recombinant variant of a parent a-amylase is provided”, “Disclosed are compositions and methods relating to variant α-amylases containing a plurality of combinable mutations”, “The combinatorial variants are based on an α-amylase from a Bacillus sp., herein, referred to as "BspAmy24”. The amino acid sequence of the mature form of the BspAmy24 α-amylase polypeptide is shown below as SEQ ID NO: 1"; paragraphs [002], [007], [0071]). The Examiner notes that the instant specification discloses that the sequences of instant SEQ ID NO: 1 and Lassila’s SEQ ID NO:1 are identical (“The variants are most closely related to an a-amylase from a Bacillus sp., herein, referred to as AA2560, and previously identified as BspAmy24 (SEQ ID NO: 1) in WO 2018/184004.”; see instant specification, paragraph [0061]).
Additionally, Lassila teaches “variant α-amylase enzymes that include combinations of mutations that improve their performance in industrial applications” (paragraph [0071]), and that “[t]he variant a-amylases are useful, for example, for starch liquefaction and saccharification, cleaning starchy stains, textile desizing, baking, and brewing“ (paragraph [002]). Lassila further discloses wherein “not all mutations produce the same effect in different molecules and not all mutations can be combined” (paragraph [006]), and that “[t]he need exists for robust engineered a-amylases molecules.” (paragraph [006]).
Lassila does not teach wherein the recombinant, variant non-naturally-occurring α-amylase comprises the three features N at position 40, R at position 91, and F at position 100, using SEQ ID NO: 1 for numbering.
Cascao-Pereira’s general disclosure relates to compositions and methods relating to variant maltohexaose-forming alpha-amylases (see entire document including abstract).
Regarding claim 21, pertaining to the variant α-amylase, Cascao-Pereira teaches a variant α-amylase (“a variant α-amylase polypeptide derived from a parental α-amylase polypeptide is provided comprising at least one combinable mutation at a productive amino acid position”, paragraph [0007], see claim 1).
Pertaining to individual amino acid positions 40, 91, and 100, wherein SEQ ID NO:1 is used for numbering, Cascao-Pereira teaches wherein “the parent enzyme is Amy707 α-amylase derived from Bacillus sp. 707 (#707) having the amino acid sequence of SEQ ID NO: 3” (see paragraph [0246]), and wherein “α-amylase variants that include combinable mutations were identified by making a site evaluation library (SEL) based on Amy707 (SEQ ID NO: 3)” (see paragraph [0248]). The Examiner notes that the positions 40, 91, and 100 of Amy707 correspond to the positions 40, 91, and 100 of instant SEQ ID NO: 1 (please see the sequence alignment of instant SEQ ID NO: 1 and Cascao-Pereira’s SEQ ID NO: 3 attached to this Office action).
Pertaining to individual amino acid positions 40, 91, and 100, Cascao-Pereira teaches a suitability score of individual amino acids in specific positions in Bacillus sp. α-amylase SEQ ID NO: 3, wherein a suitability score indicates mutations that are more suitable for combinatorial variants (“"suitability score" refers to the ability of one or more combinable mutations to be used to make combinatorial variants, based on the performance criteria for combinability […] in which each of the mutations fall. A higher suitability score indicates a mutation or mutations that are more suitable for use in making combinatorial variants.”, “The suitability scores of individual substitutions in Amy707 are shown in Table C. The position numbering is based on the amino acid sequence of the mature Amy707 polypeptide (SEQ ID NO: 3).”, “SEQ ID NO: 3 sets forth the amino acid sequence of the mature form of Bacillus sp. 707 α-amylase”; paragraphs [0088], [0198], [0253], [0551], see Table C).
Pertaining to amino acid N in position 40, Cascao-Pereira teaches wherein amino acid N in position 40 has the highest suitability score, which is higher than wild-type amino acid T in position 40 in SEQ ID NO: 3 (see Table C on page 11 and SEQ ID NO: 3).
Pertaining to amino acid F in position 100, Cascao-Pereira teaches wherein amino acid F in position 100 has a higher suitability score than wild-type amino acid Y in position 100 in SEQ ID NO: 3 (see Table C on page 12 and SEQ ID NO: 3).
Pertaining to amino acid R in position 91, Cascao-Pereira et al. discloses wherein amino acid R in position 91 has the same suitability score as wild-type amino acid S in SEQ ID NO: 3 (see Table C on page 11; and SEQ ID NO: 3).
Additionally, Cascao-Pereira teaches wherein “[t]he variant α-amylases are useful, for example, for starch liquefaction and saccharification, cleaning starchy stains, textile desizing, baking, and brewing.” (paragraph [0002]).
Betts’ general disclosure relates to “the nature of mutations and the properties of amino acids in a variety of different protein contexts” (see entire document, including page 292, paragraph 2).
Pertaining to amino acid substitutions with phenylalanine, Betts teaches wherein tyrosine can be substituted with phenylalanine, since both amino acids are aromatic amino acids (“Tyrosine can be substituted by other aromatic amino acids. See Phenylalanine.”, “Phenylalanine can be substituted with other aromatic or hydrophobic amino acids. It particularly prefers to exchange with tyrosine”; page 301, paragraph 9; page 302, paragraph 5; see Fig. 14.3 on page 297).
Pertaining to the amino acid arginine, Betts teaches that “[a]rginines are also frequently involved in salt-bridges where they pair with a negatively charged aspartate or glutamate to create stabilizing hydrogen bonds that can be important for protein stability” (see page 304, paragraph 1).
While Lassila does not teach wherein a recombinant, variant, non-naturally-occuring α-amylase comprises the three features N at position 40, R at position 91, and F at position 100, using SEQ ID NO: 1 for numbering, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to have combined Lassila’s α-amylase variant based on BspAmy24 with Cascao-Pereira’s teachings on suitable amino acids in specific positions of an α-amylase variant and with Betts’ teachings on tyrosine amino acid substitution and on properties of arginine, to have created a recombinant, variant, non-naturally-occuring α-amylase comprising the three features N at position 40, R at position 91, and F at position 100, using SEQ ID NO: 1 for numbering. One would have been motivated to do so, in order to have created a superior α-amylase variant with enhanced stability and an improved ability for starch liquefaction and saccharification, cleaning starchy stains, textile desizing, baking, or brewing (see Lassila and Cascao-Pereira above). A skilled artisan would have reasonably expected success in combining Lassila’s teachings with Cascao-Pereira’s and Betts’ teachings, since Lasilla’s and Cascao-Pereira’s teachings are both directed to Bacillus derived alpha-amylase variants used for starch liquefaction and saccharification, cleaning starchy stains, textile desizing, baking, and brewing (see Lassila and Cascao-Pereira’s above), and since Lassila’s, Cascao-Pereira’s, and Betts’ teachings are all directed to amino acid mutations in proteins (see Lassila, Cascao-Pereira, and Betts above).
Double Patenting
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. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); 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); 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) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 21 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 17/066,764 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both claim sets provide for similar compositions comprising a variant α-amylase. ‘764 provides a variant α-amylase comprising amino acid substitutions, wherein the α-amylase variant comprises the amino acids N in position 40, R in position 91, and F in position 100, R at position 116, N at position 172, and S at position 281 (see (g), in line 17 of claim 1), and pairwise deletions at positions 181 and 182, using SEQ ID NO: 1 for numbering.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
Correspondence Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SANDRA ZINGARELLI whose telephone number is (703)756-1799. The examiner can normally be reached M-F 9-5.
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/SANDRA ZINGARELLI/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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