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 .
Priority
The instant application, filed 02/23/2023 is a Continuation of 16766083 , filed 05/21/2020, now abandoned.
16766083 is a National Stage entry of PCT/US2018/065784 , International Filing Date: 12/14/2018
PCT/US2018/065784 Claims Priority from Provisional Application 62599608 , filed 12/15/2017.
Benefit of priority is to December 15, 2017.
Information Disclosure Statement
The Examiner has considered the reference(s) provided in the 7/10/23, 4/4/24, 1/10/25, 8/26/25 and 9/19/25 Information Disclosure Statements, except as noted therein, and provides a signed and dated copy of each herewith.
Claim Status
Claims 1, 6, 7, 12-16, 20, 21, 45, 63, 64, 77, 91, 108, 115-121 are currently pending and under examination.
Claims 1, 6, 7, 12-16, 20, 21, 45, 63, 64, 77, 91, 108, 115-121 are rejected.
Claim Interpretation
The term “stapled protein/peptide” is discussed at pages 20+. The examination will be guided by the definition and example at page 20-21:
…. Accordingly, the stapled (cross-linked) polypeptides described herein have improved biological activity relative to a corresponding non-stapled (un-cross-linked) polypeptide.
"Peptide stapling" is a term coined from a synthetic methodology wherein two olefin- containing side-chains (e.g., cross-linkable side chains) present in a polypeptide chain are covalently joined (e.g., "stapled together") using a ring-closing metathesis (RCM) reaction to form a cross-linked ring ….
The term “protein degrader” is not limited to a protein that degrades or destroys a protein for degradation, but includes a protein that binds to/recruits the actually protein degrader to the vicinity of the protein for degradation. At page 11, a protein degrader is:
….the second protein is a degrader protein, such as, e.g., an E3 ubiquitin ligase or a substrate adaptor for an E3 ubiquitin ligase. …
The term “peptide degron” is defined at page 35:
This disclosure features peptide degrons that bind a protein that is the substrate adaptor for an ubiquitin E3 ligase. In some instances, the degrons bind a WD-40 protein that is the substrate adaptor for an ubiquitin E3 ligase. The degron binds to the substrate recognition domain of the Ubiquitin E3 ligase in a shallow groove and is tolerant of elaboration (i.e., conjugation of a stapled peptide sequence) at either the N- or C-terminus. Exemplary substrate adaptors for an ubiquitin E3 ligase include MDM2, …
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code.
See the ‘http/’ at page 11, 12, 27, 49, 53, and 57.
Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
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.
Claims 45, 116, 119 are 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 45 is drawn to a modified first protein, yet there is no other second protein mentioned within the claim. Also, it is not clear what is intended by a structurally disordered region. Claims 116 and 119 depending from claim 45 also are rejected under this section.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 21, 45, 63, 91, 108, 115, 116, 118, 119, 120, 121, and separately claims 64 and 77 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Each of claims 21, 45 and 91 encompass large to huge genera of species that possess a respectively claimed property
For claim 21 that the peptide binds a WD40-repeat protein that is a substrate adapter for an E3 ubiquitin ligase, and can have at least one of any of amino acid deletions, substitutions, and insertions,
Also for claim 45 that the peptide of the modified protein binds a WD40-repeat protein that is a substrate adapter for an E3 ubiquitin ligase, and can have at least one of any of amino acid deletions, substitutions, and insertions, and
For claim 91 that the peptide that binds COP1 protein comprises a modified version of the amino acid sequence DQIVPEY (SEQ ID NO:25) and can have at least one of any of amino acid deletions, substitutions, and insertions (thus allowing deviating completely from DQIVPEY so long as any de minimis binding to COP1 protein exists).
Although applicant has listed known sequences, such as natural degrons, see for example pages 37-40, there is a paucity of meaningful teachings, examples, disclosures regarding linkers relevant to the genus, and structure/function associations to achieve possession of the respective large genera of claims 21, 45 and 91. The limited modified species that are presented are far from representative of these claimed genera, and there are no relevant and substantial teachings as to how to obtain species commensurate with a respective claimed genus rather than a species that does not fall within the respective claim metes and bounds, which may be an unexpected, undesired product as well as resulting in an unfavorable outcome if administered in accordance with any of the claimed methods.
As but one example of the latter, Ackloo et al., J. Med. Chem. 2025, 68, 1092−1112, teaches that the WD40 repeat family is one of the largest protein families, so determining specificity for the desired modified peptides with appropriate and not inappropriate affinity and binding represents challenges that are neither addressed nor resolved in the application as filed.
For these reasons claims 21, 45 and 91 are rejected under this section; applicant was not in possession of what is claimed therein at the time of filing.
The other claims listed above, depending from one of claims 21, 45, and 91, also are rejected based on the respective rejection of one of claims 21, 45 and 91, and further as indicated immediately below.
As to each of claims 63, 115 and 116, there is insufficient support and examples for the range of possible diseases and disorders that are encompassed by the claim, including a lack of actual examples demonstrating the desired treating effect that is commensurate with the breadth and diversity of the species of diseases, disorders and chimeric polypeptides.
Claim 64 is more limiting than the above independent claims, however also suffers from a lack of sufficient support – such as from examples, structure/function associations, and how to determine locations for stapling for making constructs that span across the range of viral, bacterial and animal proteins that are targeted by the ‘protein-targeting stapled peptide’. As such there is a lack of support (possession) commensurate for what is claimed. This also applies to method claim 77 which administers the peptide small molecule fusion of claim 64, this method claim additionally lacking sufficient support (possession) for the range of possible diseases and disorders that are encompassed by the claim, including a lack of actual examples demonstrating the desired treating effect that is commensurate with the breadth and diversity of the species of diseases, disorders and peptide small molecule fusion molecules, the latter including disclosure as to how to determine placement of the stapling.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 12, 13, 15, 16, 117 is/are rejected under 35 U.S.C. 102a1as being anticipated by Cromm et al. (PCT-237; September 21, 2017; Targeted protein degradation: from chemical biology to drug discovery. Cell Chem Biol. 24(9): 1181-1190), cited in the 7/10/23 IDS so not provided herewith.
Cromm et al. teach Proteolysis Targeting Chimeras (PROTACs) at page 1182-1187. PROTACs comprise an first moiety that binds to a protein of interest (POI), which is the Protein for Degradation (PD) set forth in the instant claims, and a second moiety that binds to endogenous E3 ligase. The E3 ligase binds to ubiquitin which degrades the POI.
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Therefore, Cromm et al. teach a chimera comprising a first moiety that binds to a first protein for degradation and a second protein that binds to a protein degrader (Claim 1, 16).
At page 1184, last paragraph, Cromm et al. teach small molecule PROTACs using the nutlin3a replacing the peptide E3 ligands, wherein the nutlin3a binds to bind a protein that is the substrate adaptor for an ubiquitin E3 ligase that is MDM2.
At page 1185, para. 1, Cromm et al. teach the VHL ligand binding moiety, and at para. 2 the thalidomide binding moiety attached to cereblon CRBN. See Figure 4.
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Therefore, Cromm et al. teach a chimera comprising a first moiety that binds to a first protein for degradation and a second moiety that is a small molecule that binds to a protein degrader that is the substrate adaptor for a ubiquitin E3 ligase that is MDM2 (Claim 15).
Therefore, Cromm et al. teach a chimera comprising a first moiety that is a small molecule (Claim 12), and a second moiety that is a peptide degron (Claim 13).
At page 1184, right col., para. 1, Cromm et al. teach that PROTACs comprising a VHL binding domain have been used in live animals (Claim 117).
Claim(s) 1, 6, 7, 16, 20 and 117 is/are rejected under 35 U.S.C. 102a1as being anticipated by Richardson et al. (2017; Towards the development of a peptide-PROTAC conjugate targeting a viral protein: Rational design and optimization of a stapled alpha-helical peptide that binds HPV16 E2 protein. Abstracts of Papers American Chemical Society 254: 96, cited in 7/10/23 IDS so not provided).
Richardson et al. teach a PROTAC comprising an alpha-helical modified stapled peptide moiety based on the C-terminus of BRD4, which binds HPV16 E2 protein. The entire construct is described as a heterobivalent ligand composed of a small molecule PROTAC conjugated to a peptide with affinity for HPV16 protein. A library-developed identified stapled peptide has low micromolar affinity for HPV16 E2.
Therefore, Richardson et al. teach a chimera comprising a first moiety that binds to a protein for degradation and a second moiety which binds to the protein degrader, this based on the construct being a PROTAC (Claims 1, 16), wherein the first moiety is a stapled protein (Claim 6, 7), and wherein the PROTAC is for the therapeutic use in preventing the progression and/or transmission of HPV (Claims 20, 117).
Claim(s) 91 and 45 is/are rejected under 35 U.S.C. 102a1 as being anticipated by Uljon et al. (2016; Structural basis for substrate selectivity of the E3 ligase COP1. Structure 24: 687-696), cited in 7/10/23 IDS so not provided.
Uljon et al. teach COP1 peptide substrates at Figure 5A, comprising:
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The Trib2 peptide comprises two amino acid substitutions of DQIVPEY, per Figure 5A has an IC50 of 2.4 uM binding affinity to COP1, and per Figure 5B competes nearly as effectively as the Trib1 peptide. Trib2 anticipates claim 91.
Because the Trib2 peptide also meets the binding limitation of claim 45, and considering that the instant specification at page 70 indicates that Tribble proteins have structurally disordered regions, so this limitation would be met by the Trib2 peptide that has mutations in the COP1 binding site.
Accordingly, claim 45 also is anticipated by Uljon.
Claim Rejections - 35 USC § 103
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 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.
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(s) 1, 14, 64 and 77 is/are rejected under 35 U.S.C. 103 as being unpatentable over Montrose and Krissansen, Biochemical and Biophysical Research Communications 453 (2014) 735–740 (“MK”) in view of Walensky and Bird, J. Med. Chem. 2014, 57, 6275−6288 (“WB”).
Claim 1 is set forth above, and claim 14 depends from claim 1 and requires that the second moiety of claim 1 comprises a stapled peptide that binds to the protein degrader.
Claim 64 is directed to a peptide small molecule fusion comprising: (a) a protein- targeting stapled peptide and a thalidomide degron moiety; or (b) a protein-targeting stapled peptide and a Von Hippel-Lindau (VHL) degron moiety.
MK teaches and evaluates PROTAC peptide constructs including a CPP portion, an oligomerization domain of X-protein, and an ODD domain, see Fig. 1 and associated text. The ODD domain is found in commonly employed degrons of PROTACs, and derives from the hypoxia inducible factor (HIF-1a), which is recognized by the von Hippel-Lindau (pVHL) E3 ligase. Thus, the construct of Fig. 1, part C, that terminates with the ODD comprises a VHL degron moiety.
However, this construct, although comprising the X-protein targeting peptide, this peptide, LCLRPVGAESRGRPVSGPFG (the oligomerization domain of X-protein) is not stapled.
The level of skill in the art is high.
WB teaches advantages of stapling peptides, which include conferring α-helical structure, protease resistance, cellular penetrance, and biological activity, Abstract.
Based on the teachings of WB, one of ordinary skill in the art would have been motivated to modify the LCLRPVGAESRGRPVSGPFG (the oligomerization domain of X-protein) of the above-noted PROTAC comprising the ODD in order to improve one or more of the properties taught by WB. There would have been a reasonable expectation of success given the teachings of WB and the length of the noted oligomerization domain, the latter providing multiple alternatives for achieving a suitable stapling to improve one or more properties.
Accordingly, claim 64 would have been obvious.
Because MK also teaches that the purpose of affecting the X-protein with one of its PROTACs is to antagonize and destroy the cancer-forming X-protein of the hepatitis B virus, Title, Abstract, claim 77 would have been obvious.
Additionally, the modified PROTAC that makes obvious claim 64 also makes obvious the more generic claim 1. Further, based on the teachings of advantages of stapled peptides by WB, one of ordinary skill in the art would have been motivated by the opportunity of further improvement in such construct, employing the teachings of WB, to also staple the ‘second moiety’ peptide of the modified PROTAC. There would have been a reasonable expectation of success given the teachings of WB and the general knowledge and skill in the art regarding structure and function required for suitable binding.
Accordingly, claim 14 would have been obvious.
Claim(s) 108, 115, 120 and 121, and also claims 21 and 118, is/are rejected under 35 U.S.C. 103 as being unpatentable over Montrose and Krissansen, Biochemical and Biophysical Research Communications 453 (2014) 735–740 (“MK”) in view of Uljon et al. (2016; Structural basis for substrate selectivity of the E3 ligase COP1. Structure 24: 687-696), and Walensky and Bird, J. Med. Chem. 2014, 57, 6275−6288 (“WB”).
Claim 108 is directed to a chimeric fusion polypeptide comprising a protein-targeting stapled peptide and a peptide of claim 91.
MK teaches and evaluates PROTAC peptide constructs including a CPP portion, an oligomerization domain of X-protein, and an ODD domain, see Fig. 1 and associated text. The ODD domain is found in commonly employed degrons of PROTACs, and derives from the hypoxia inducible factor (HIF-1a), which is recognized by the von Hippel-Lindau (pVHL) E3 ligase. Thus, the construct of Fig. 1, part C, that terminates with the ODD comprises a VHL degron moiety.
MK does not teach a peptide that meets the requirements of claim 91, however Uljon does, and teaches that the Trib2 peptide comprises two amino acid substitutions of DQIVPEY, per Figure 5A has an IC50 of 2.4 uM binding affinity to COP1, and per Figure 5B competes nearly as effectively as the Trib1 peptide.
The level of skill in the art is high.
Given the affinity of Trib2 to COP1, one of ordinary skill in the art would have been motivated to substitute in the Trib2 peptide toward achieving improved binding and efficacy of such modified PROTAC of MH. This is simple substitution of a peptide having a similar role in the PROTAC, and there would have been a reasonable expectation of success in view of the known function(s) of the respective peptides.
Neither MH nor Uljon teach that any peptide is stapled.
Based on the teachings of WB, one of ordinary skill in the art would have been motivated to modify the LCLRPVGAESRGRPVSGPFG (the oligomerization domain of X-protein) of the above-noted PROTAC comprising the ODD in order to improve one or more of the properties taught by WB. There would have been a reasonable expectation of success given the teachings of WB and Uljon and the length of the Trib2 peptide, the latter providing multiple alternatives for achieving a suitable stapling to improve one or more properties.
Accordingly, the chimeric fusion polypeptide of claim 108 would have been obvious.
Because MK also teaches that the purpose of affecting the X-protein with one of its PROTACs is to antagonize and destroy the cancer-forming X-protein of the hepatitis B virus, Title, Abstract, claim 115 would have been obvious. Because administering the modified PROTAC would reasonably be expected by one of ordinary skill in the art to be in the form of a pharmaceutical composition that includes a pharmaceutically acceptable carrier and/or vehicle, claims 120 and 121 would have been obvious.
Additionally, because the Trib2 peptide comprises a sequence that is a variant of a natural binding sequence that binds to a WD40-repeat protein that is a substrate adaptor for an E3 ubiquitin ligase, this comprising at least one substitution thereof, the basis for rejection of the chimeric fusion polypeptide of claim 108 as applied to claim 21 renders claim 21 obvious, as does the basis for rejection of claim 121 as applied to claim 118 render obvious claim 118.
Claim(s) 119 and 120 is/are rejected under 35 U.S.C. 103 as being unpatentable over Uljon et al. (2016; Structural basis for substrate selectivity of the E3 ligase COP1. Structure 24: 687-696), as evidenced by Mohan “Buffers”, 32 pages, Calbiochem 2003 (“Mohan”).
Claim 45 from which claim 119 depends is rejected above.
The level of ordinary skill in the art is high.
A modified protein of Uljon, such as Trib2, which differs from so is modified from Trib1 as indicated in Fig. 5A of Uljon, prepared as an aqueous buffered solution, which as evidenced by Mohan is ordinary and customary for proteins preparations (peptides having shorter lengths but the same amphipathic character), renders obvious claims 119 and 120.
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.
Claims 1, 6, 7, 12-16, 20, 21, 45, 63, 64, 77, 91, 108, 115-121 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 3, 4, 22, 48, 51, 53 of copending Application No. 18030433 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference application claims begin with a similar very broad claim 1 and then are directed to or include species that anticipate instant claims 1, 6, 7, 12-16, 21, 45, 64, 91, 108 (for 64, 91 and 108 see reference application claim 22 and preceding noted claims), and 117-121, and method claims 20, 63, 77, 115, 116 (see reference application claims 51 and 53 and preceding noted claims).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
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/Joseph Fischer/
Examiner, Art Unit 1658
Prosecution Insights