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 .
DETAILED ACTION
This application is a US national phase of PCT/EP2020/062645, filed May 7,
2020, with foreign application EP19173389.8, filed May 8, 2019. Applicant’s amendment filed April 28, 2025 is acknowledged. Claims 10 and 12-21 are canceled, and claims 7, 24, and 33 are amended. Currently claims 1-9, 11, and 22-38 are pending and under examination.
The previous objections, 112(b) rejection, and 101 rejection in the Final office action mailed February 28, 2025 are withdrawn due to Applicant’s amendment to the claims and remarks filed April 28, 2025.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on April 28, 2025 has been entered.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-4, 7-9, 22-23, 26-27, 34, 35, 37, 38 are rejected under 35 U.S.C. 103 as being obvious over Thomas-White et al. (NCBI Accession # PKY96525.1, Direct Submission, Submitted 17-DEC-2017, Biology, Loyola University Chicago, 1032 W Sheridan Rd., Biology Department, LSB 317B, Chicago, IL 60660, USA, previously cited in PTO-892 mailed 8/30/2024, hereinafter “Thomas”) in view of Bumgarner et al. (NCBI Accession # PNP86798.1, Direct Submission, Submitted (29-MAR-2017) Microbiology, University of Washington, Box 358070, 1410 NE Campus Parkway, Seattle, WA 98195, USA, previously cited in PTO-892 mailed 8/30/2024, hereinafter “Bumgarner”), as evidenced by Donovan et al. (APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 2006, p. 2988–2996, previously cited in PTO-892 mailed 8/30/2024, hereinafter “Donovan”) and Schmelcher et al. (Future Microbiol. 2012 October ; 7(10): 1147–1171, previously cited in PTO-892 mailed 8/30/2024, hereinafter “Schmelcher”).
Regarding claims 1, 3-4, 7, 22-23, 34, 35, 37, 38, Thomas teaches a 1,4-beta-N-acetylmuramidase [Gardnerella vaginalis] (Accession # PKY96525.1) with 100% sequence identity to SEQ ID NO: 2, 93% sequence identity to SEQ ID NO: 28, and 95% sequence identity to SEQ ID NO: 31 (See sequence comparison below). The 1,4-beta-N-acetylmuramidase also consists of a linker region between the catalytic domain (SEQ ID NO:2) and cell-wall binding domain (SEQ ID NO: 28) that is the amino acid sequence according to SEQ ID NO: 46 recited in claim 7 (See annotation of sequence below). The GenPept information sheet for PKY96525.1 teaches that the enzyme is a GH25_LytC-like enzyme, and the LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains, and indicates it has cell-wall binding domains (CBD) (pg. 2, “Region”).
Sequence comparison of PYK96525.1 and SEQ ID NO: 2
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771
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Sequence comparison of PYK96525.1 and SEQ ID NO: 28
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545
805
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Sequence comparison of PYK96525.1 and SEQ ID NO: 31
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485
807
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Annotated PYK96525.1: Red: SEQ ID NO:2; Yellow: L10 linker region SEQ ID NO: 46; Blue: SEQ ID NO: 31; Green: SEQ ID NO: 28
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580
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Thomas does not teach the polypeptide comprises a sequence of at least 96% identity to SEQ ID NO: 31.
However, Bumgarner teaches a 1,4-beta-N-acetylmuramidase [Gardnerella vaginalis] (Accession # PNP86798.1) with 100% sequence identity to SEQ ID NO: 31 (See sequence comparison below). As evidenced by Donovan, fusion proteins of peptidoglycan hydrolase (i.e., endolysins) maintain their parental specificities according to each domain (title, pg. 2989, col. 2, para 1). Donovan further evidences that it is not uncommon for peptidoglycan hydrolases to possess multiple hydrolytic domains or for these domains to act independently of each other and even maintain their enzymatic activities in the presence of a nonfunctional second domain (pg. 2989, col. 1, para 4). It is further noted that domains from different genomes of different prophages in a recombinant endolysin is a well-understood evolutionary phenomenon. As evidenced by Schmelcher, natural chimeras exist, such as the Listeria phage endolysin PlyPSA, which has a cell-wall binding domain highly similar to other Listeria phage lysins, and an enzymatic domain related to amidase domains from Bacillus and Clostridium phages (pg. 11, para 1).
Sequence comparison of PNP86798.1 and SEQ ID NO: 31
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Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to synthesize a polypeptide with naturally occurring domains from the Gardnerella vaginalis endolysin polypeptide PYK96525.1 comprising a N-terminal domain having 100% sequence identity to instant SEQ ID NO: 2, a C-terminal domain comprising a 1,4-beta-N-acetylmuramidase, and a linker comprising NVGLNGCKNGGS as taught by Thomas, and substitute the C-terminal domain with a different naturally occurring Gardnerella vaginalis endolysin 1,4-beta-N-acetylmuramidase domain PNP86798.1 that has 100% sequence identity to SEQ ID NO: 31 as taught by Bumgarner. One of ordinary skill in the art would have substituted known C-terminal domains of 1,4-beta-N-acetylmuramidase that are specific for Gardnerella vaginalis, as substituting different domains are known to maintain their parental specificities according to each domain as evidenced by Donovan. Further, it would have been prima facie obvious to construct a polypeptide comprising 1, 2, or 3 C-terminal domains as taught by Thomas.
Regarding claims 2, 8, 9, 26, 27, Thomas and Bumgarner do not teach the specific activities recited in claims 2, 8, 9, 26, and 27. However, the activity claimed are inherent to the known proteins, and as evidenced by Donovan, fusion proteins of peptidoglycan hydrolase (i.e., endolysins) maintain their parental specificities according to each domain (title, pg. 2989, col. 2, para 1). Donovan further discloses that it is not uncommon for peptidoglycan hydrolases to possess multiple hydrolytic domains or for these domains to act independently of each other and even maintain their enzymatic activities in the presence of a nonfunctional second domain (pg. 2989, col. 1, para 4). It is further noted that domains from different genomes of different prophages in a recombinant endolysin is a well-understood evolutionary phenomenon. As evidenced by Schmelcher, natural chimeras exist, such as the Listeria phage endolysin PlyPSA, which has a cell-wall binding domain highly similar to other Listeria phage lysins, and an enzymatic domain related to amidase domains from Bacillus and Clostridium phages (pg. 11, para 1). "Products of identical chemical composition cannot have mutually exclusive properties." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). Thus, if the prior art teaches the identical chemical structure, the properties applicant discloses and/or claims are necessarily present.
Claims 5-6, 24-25, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Thomas in view of Bumgarner as evidenced by Donovan and Schmelcher as applied to claims 1-4, 7-9, 22-23, 26-27, 34, 35, 37, 38 above, and further in view of Thomas-White et al. (NCBI Accession # PKZ59243, Direct Submission, Submitted (17-DEC-2017) Biology, Loyola University Chicago, 1032 W Sheridan Rd., Biology Department, LSB 317B, Chicago, IL 60660, USA, previously cited in PTO-892 mailed 8/30/2024, hereinafter “Thomas2”) and Schmelcher.
Thomas teaches PYK96525.1 that comprises a N-terminal domain that has 100% sequence identity to SEQ ID NO: 2, and 2 CBDs with a first domain comprising 93% sequence identity to SEQ ID NO: 28 located N-terminally to a second domain comprising 95% sequence identity to SEQ ID NO: 31, and a linker region. Bumgarner teaches PNP86798.1 that comprises a domain that has 100% sequence identity to SEQ ID NO: 31. Neither Thomas or Bumgarner teach a polypeptide that comprises a sequence that has at least 96% or 100% identity to SEQ ID NO: 28.
However, Thomas2 teaches a 1,4-beta-N-acetylmuramidase [Gardnerella vaginalis] (Accession # PKZ59243) with 100% sequence identity to SEQ ID NO: 28 (See sequence comparison below).
None of the prior art teach the specific combination of these two C-terminal domains taught by Bumgarner and Thomas2.
However, Schmelcher teaches evaluation of the effects of combining multiple CBDs on the binding properties (pg. 11, para 2). Schmelcher teaches their laboratory was able to demonstrate that combining the CBD of Listeria phage endolysin Ply500 (CBD500), which is specific for serovar 4, 5, and 6 strains, with that of PlyP35, which recognizes the majority of serovar 1, 2, and 3 strains, resulted in heterologous GFP fusion constructs that are able to recognize and brightly decorate a broad spectrum of Listeria cells from all species and serovars (pg. 11, para 2). Further, Schmelcher discloses new results from the laboratory with staphylococcal lysins suggest that binding affinity can be further potentiated with increasing copies of the same CBD in one fusion construct (pg. 11, para 2).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to synthesize a Gardnerella vaginalis endolysin polypeptide PYK96525.1 containing 2 CBDs as taught by Thomas, and substitute the CBDs with PKZ59243 taught by Thomas2 and PNP86798.1 taught by Bumgarner. One of ordinary skill in the art would have been motivated to substitute strain specific CBDs to create a highly effective endolysin that would increase cell-wall binding and exhibit enhanced lytic activities as taught by Schmelcher (pg. 12, para 1).
Sequence comparison of PKZ59243.1 and SEQ ID NO: 28
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Claims 11, 28-31, and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Thomas and Bumgarner as evidenced by Donovan and Schmelcher as applied to claims 1-4, 7-9, 22-23, 26-27, 34, 35, 37, 38 above, and further in view of Briers et al. (WO2012085259A2, cited in PTO-892 mailed 2/28/2025, hereinafter “Briers”).
Thomas and Bumgarner teach the polypeptide of claims 28-31 and 33 as discussed above, but do not teach a pharmaceutical composition comprising said polypeptide.
However, Briers teaches a fusion protein composed of an enzyme having the activity of degrading the cell wall of Gram-negative bacteria and/or Gram-positive bacteria and at least two peptide stretches fused to the enzyme at the N- or C-terminus (abstract). Briers teaches the fusion protein comprises a first amino acid sequence e.g. an endolysin, with a second and a third amino acid sequence, wherein the second and third amino acid sequences are preferably peptide stretches, in particular selected from the group consisting of cationic, polycationic, hydrophobic, amphipathic, sushi and antimicrobial peptides, preferably, said second and third amino acid sequence is foreign to and not substantially homologous with any domain of the first amino acid sequence (pg. 5, para 3). Briers teaches endolysins comprise at least one "enzymatically active domain" (EAD) having at least one of the following activities: N-acetyl-muramidase, inter alia, which is the same type of catalytic domain of the claimed invention (pg. 7, para 2). Briers teaches in addition, the endolysins may also contain regions which are enzymatically inactive and bind to the cell wall of the host bacteria, wherein said regions are CBDs (cell wall binding domains) (pg. 7, para 2). Briers teaches the composition is a pharmaceutical composition, said process comprising admixing one or more fusion protein and/or one or more hosts transformed with a nucleic acid comprising a nucleotide sequence encoding a fusion protein with a pharmaceutically acceptable diluent, excipient or carrier (pg. 41, para 1).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to synthesize A Gardnerella vaginalis endolysin polypeptide PYK96525.1 comprising a N-terminal domain having 100% sequence identity to instant SEQ ID NO: 2, a C-terminal domain comprising a 1,4-beta-N-acetylmuramidase, and a linker as taught by Thomas, and substitute the C-terminal domain with a different Gardnerella vaginalis endolysin 1,4-beta-N-acetylmuramidase domain PNP86798.1 that has 100% sequence identity to SEQ ID NO: 31 as taught by Bumgarner, and make a pharmaceutical composition comprising the polypeptide as taught by Briers. One of ordinary skill in the art would have been motivated to make a pharmaceutical composition comprising the endolysin with a pharmaceutically acceptable diluent, as this is a well-understood, routine, and conventional laboratory practice as taught by Briers.
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over Thomas, Bumgarner, and Briers as evidenced by Donovan and Schmelcher as applied to claims 11, 28-31, and 33 above, and further in view of Thomas2 and Schmelcher.
Thomas teaches PYK96525.1 that comprises a N-terminal domain that has 100% sequence identity to SEQ ID NO: 2, and 2 CBD’s with a first domain comprising 93% sequence identity to SEQ ID NO: 28 located N-terminally to a second domain comprising 95% sequence identity to SEQ ID NO: 31, and a linker region. Bumgarner teaches PNP86798.1 that comprises a domain that has 100% sequence identity to SEQ ID NO: 31. Briers teaches a pharmaceutical compositions comprising a structurally similar endolysin polypeptide comprising enzymatic domains and CBDs as the claimed polypeptide. None of Thomas, Bumgarner, and Briers teach a polypeptide that comprises a sequence that has at least 95% identity to SEQ ID NO: 28.
However, Thomas2 teaches a 1,4-beta-N-acetylmuramidase [Gardnerella vaginalis] (Accession # PKZ59243) with 100% sequence identity to SEQ ID NO: 28 (See sequence comparison above).
None of the prior art references teach the specific combination of these two C-terminal domains taught by Bumgarner and Thomas2. However, Schmelcher teaches evaluation of the effects of combining multiple CBDs on the binding properties (pg. 11, para 2). Schmelcher teaches their laboratory was able to demonstrate that combining the CBD of Listeria phage endolysin Ply500 (CBD500), which is specific for serovar 4, 5, and 6 strains, with that of PlyP35, which recognizes the majority of serovar 1, 2, and 3 strains, resulted in heterologous GFP fusion constructs that are able to recognize and brightly decorate a broad spectrum of Listeria cells from all species and serovars (pg. 11, para 2). Further, Schmelcher discloses new results from the laboratory with staphylococcal lysins suggest that binding affinity can be further potentiated with increasing copies of the same CBD in one fusion construct (pg. 11, para 2).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to make a pharmaceutical composition as taught by Briers comprising a Gardnerella vaginalis endolysin polypeptide PYK96525.1 containing 2 CBDs as taught by Thomas, and substitute the CBDs with PKZ59243 taught by Thomas2 and PNP86798.1 taught by Bumgarner. One of ordinary skill in the art would have been motivated to substitute strain specific CBDs to create a highly effective endolysin that would increase cell-wall binding and exhibit enhanced lytic activities as taught by Schmelcher (pg. 12, para 1).
Response to Arguments
Applicant’ s arguments, see pgs. 9-13, filed 4/28/2025, with respect to the U.S.C. 101 rejection have been fully considered and are persuasive. The 101 rejection of claims 1-9, 11, and 22-38 has been withdrawn.
Applicant's arguments filed April 28, 2025 have been fully considered but they are not persuasive.
Regarding Applicant’s arguments directed to the 103 rejections, Applicant argues the references do not provide enough motivation to combine to arrive at the claimed invention. Applicant argues the Examiner has merely demonstrated each of the claimed elements were independently known in the art, and has not provided evidence of a motivation to combine, specifically for selecting the specific sequences as opposed to the multitude of other Gardnerella phages, pointing to the NCBI database of 49.422 different endolysins. Applicant argues the skilled artisan with the cited prior art in-hand would have had no expectation that the claimed polypeptides would have been effective in killing Gardnerella, and would result in increased killing activity compared to naturally occurring endolysins.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). As discussed in the 103 rejection, the claimed sequences were known in the prior art, as well as the practice for combining CBD and catalytic domains from different phages targeting different strains and species to enhance endolysin activity, as evidenced by Schmelcher and Donovan. One of ordinary skill in the art would have been motivated to try recombining known domains for more effective killing of species the domains naturally target. The examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). Applicant's argument that the prior art does not explicitly teach recombinant Gardnerella phages is not a basis for the obviousness rejection, since the prior art teaches the routine practice of recombining phage domains for enhanced endolysin activities, which would motivate one of ordinary skill in the art to look for known domains in the art and construct the claimed polypeptides of the present invention, thus the 103 rejections are maintained.
Regarding Applicant’s arguments directed to unexpected results, Applicant argues any alleged prima facie case of obviousness would be overcome by the unexpectedly superior activity of the claimed recombinant proteins and points to the specification discloses that “[s]urprisingly and unexpectedly, the inventor discovered that several recombinant endolysins have a stronger activity than any natural endolysin (H1B1 to H12B12), especially when viewed across all 4 Gardnerella strains tested (see FIGS. 8A to 8D), particularly H2B10, H2B11, and H2B12 have activity ranks 1, 2, and 3, respectively, and each is more active than any natural endolysin (see Table 5C).” Applicant argues overall, the polypeptides comprising H2 (i.e., SEQ ID NO: 2) and B10 (i.e., SEQ ID NO: 28 or 29), B11 (i.e., SEQ ID NO: 30 or 31), B12 (i.e., SEQ ID NO: 32 or 33), or B3 (i.e., SEQ ID NO: 19 or 20) exhibited the highest killing activity against Gardnerella (e.g., Example 4; Tables 5A-5C and 7; and Figures 8A-8D). Applicant argues each of these claimed polypeptides exhibited greater killing activity than H2B2 (EL2), which is identical to the endolysin disclosed in Thomas. In other words, the claimed polypeptides unexpectedly demonstrated greater killing activity than the closest prior art identified by the Examiner.
In response, the Examiner recognizes Applicant has demonstrated enhanced killing activity toward Gardnerella using the recombinant endolysins H2B3, H2B10, H2B11, and H2B12 which all contain the linker SEQ ID NO’s 45-46. However there is no evidence that recombinant endolysins using any kind of linker, endolysins with less than 2 cell-wall binding domains, or more than 2 cell-wall binding domains, and endolysins with any kind of combinations between SEQ ID NO: 2 and SEQ ID NO’s: 19, 20, and 28-33 would exhibit this unexpected enhanced killing activity. For these endolysins encompassed by the broad wording of claim 1 and not solving the technical problem, there is no data showing that they have any unexpected or surprising activity over naturally occurring endolysins. Thus, the subject-matter of claim 1 is considered to be directed to an arbitrary selection of an endolysin which the skilled person would arrive to without any inventive skills.
Conclusion
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/JESSICA EDWARDS/
Examiner
Art Unit 1657
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636