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
Claims 1-4,7-8,10-15,17,19-24 and 27 are pending.
During a preliminary amendment of this application, the applicant, on date 10/14/2025 elected Group III (claims 19, 21-23 ), drawn to a method of identifying a peptide that binds a target protein comprising 19. incubating in a reaction vessel: a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a (a) first split intein, and (iii) a target protein; a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, (b) and (iii) a second fragment of the transcription factor; wherein the first and second split inteins belong to the same intein; and an inducible promoter operably linked to at least one reporter gene, wherein the (c) transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor, and detecting transcription of the reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein. Applicant did not mention whether they elected with traverse or without traverse and also do not argue against elected ion restriction requirement, therefore examiner consider the election without traverse. Claims 1-4,7-8,10-15,17,20,24 and 27of election/restriction-office action of date 8/13/2025 is withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions.
The requirement is therefore made FINAL.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 5/22/2025 in compliance with the provisions of 37 CFR 1.97. Accordingly, the examiner has considered the IDS statements.
Claim Rejections, 35 U.S.C 112 (a) Paragraph
The following is a quotation of the first paragraph of 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 19, 21-23 are rejected under 35 U.S.C. 112(a), as containing 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(s), at the time the application was filed, had possession of the claimed invention.
It is noted that MPEP 2111.01 states that "[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow." method of identifying a peptide that binds a target protein comprising incubating in a reaction vessel: a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a (a) first split intein, and (iii) a target protein; a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, (b) and (iii) a second fragment of the transcription factor; wherein the first and second split inteins belong to the same intein; and an inducible promoter operably linked to at least one reporter gene, wherein the (c) transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor, and detecting transcription of the reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein “ can be use of any fusion protein comprising any peptide having any structure that bind any target protein having any structure. Therefore in light of the specification, claims are broadly interpreted to use any peptide that bind any target protein.
The Court of Appeals for the Federal Circuit has recently held that a "written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." University of California v. Eli Lilly and Co., 1997 U.S. App. LEXIS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993). To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these (paraphrased from Enzo Biochemical).University of Rochester v. G.D. Searle & Co. (69 USPQ2d 1886 (2004)) specifically points to the applicability of both Lilly and Enzo Biochemical to methods of using products, wherein said products lack adequate written description. While in University of Rochester v. G.D. Searle & Co. the methods were held to lack written description because not a single example of the product used in the claimed methods was described, the same analysis applies wherein the product, used in the claimed methods, must have adequate written description (see Enzo paraphrased above).
There is no structure-function correlation with a method of identifying a genus of genus of peptide having many structures that are able to bind any target protein having any structure and having any function. The specification discloses peptide having comprises a sequence selected from SEQ ID NOs: 6-25 able to bind target protein comprises a viral receptor binding domain (RBD) of the SARS-CoV-2 spike protein, wherein the RBD comprises SEQ ID NO: 71. Therefore one of skill in the art would not recognize from the disclosure that applicants were in possession of the claimed invention.
The genus of polypeptide that bind a genus of target protein having required in the claimed invention is an extremely large structurally and functionally variable genus. An argument can be made that the recited genus of is adequately described by the disclosure of the structure of peptide having comprises a sequence selected from SEQ ID NOs: 6-25 able to bind target protein comprises a viral receptor binding domain (RBD) of the SARS-CoV-2 spike protein, wherein the RBD comprises SEQ ID NO: 71. However, the art clearly teaches there is a practical limits to predict function of a polypeptide based structural homology:
A. Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that "Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, and page 105).
B. Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340,) also highlight the difficulties associated with "Prediction of protein function from protein sequence and structure": "To reason from sequence and structure to function is to step onto much shakier ground", closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein's role fundamentally (page 323, paragraph 1).
C. This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polypeptides do not necessarily share the same function and many functionally similar proteins will have little or no structural homology to disclosed proteins. For example, proteins having similar structure have different activities (structure does not always correlate to function); Witkowski et al., (Biochemistry 38:11643-11650, 1999) teaches that one conservative amino acid substitution transforms a beta -ketoacyl synthase into a malonyl decarboxylase and completely eliminates beta-ketoacyl synthase activity. The art also teaches that functionally similar molecules have different structures; Kisselev L., (Structure, 2002, Vol. 10: 8-9) teach that polypeptide release factors in prokaryotes and eukaryotes have same function but different structures.
As stated above, no information beyond the characterization of a few species; such as the structure of disclosure of the structure of peptide having comprises a sequence selected from SEQ ID NOs: 6-25 able to bind target protein comprises a viral receptor binding domain (RBD) of the SARS-CoV-2 spike protein, wherein the RBD comprises SEQ ID NO: 71 respectively has been provided by the applicants’, which would indicate that they had the possession of the claimed genus of polypeptides. The claimed genera of polypeptides and the encoding polynucleotides have widely variable structures and associated functions. As it is discussed above, a minor changes in structure may result in changes affecting function, since, the specification provided no additional information (species/variant/mutant) correlating structure with function, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Furthermore, "Possession may not be shown by merely describing how to obtain possession of members of the claimed ,genus or how to identify their common structural features" (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895). A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the .gene does (function), rather what it is (structure), see University of California v. Eli Lilly & Co., 43 USPQ2d 1938, thus above claims lack adequate written description.
Applicants' are referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Conclusion
Claims 19, 21-23 are rejected. No claim is allowed.
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examiner should be directed to Mohammad Meah whose telephone number is 571-272-
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/MOHAMMAD Y MEAH/Examiner, Art Unit 1652