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 .
Status of the Application
Claim(s) 1-20 are pending and under examination
The following Office Action is in response to Applicant's communication dated 04/13/2024.
Drawings
The drawings are objected to because:
Specific deficiency - Sequences appearing in the drawings for Figs. 2A, 3A, 3C are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
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(s) 5 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 5 recites “irregular secondary structure”, which is unclear because the claim does not provide an objective standard by which one of ordinary skill in the art can determine whether a secondary structure is “irregular”. Although the specification states “ The loop regions typically have irregular secondary structures.”[¶0016], the specification does not define the term or provide any structural criteria (e.g. dihedral angle, hydrogen bonding pattern, structural assignments, or other measurable parameters) for distinguishing a regular secondary structure from an irregular secondary structure. Since one of ordinary skill in the art cannot determine with reasonable certainty the scope of protection, the metes and bounds of the claim are unascertainable.
For purposes of examination only, and to facilitate a complete analysis of the claim, the Examiner interprets “irregular secondary structures” as encompassing an unstructured or disordered loop region lacking common secondary structures, such as beta strand or alpha helix. This is consistent with the specification, which distinguishes the regions having secondary structures, such as alpha helices and beta strands, from the connecting loop regions that are being described as having irregular secondary structures [¶0016]. This interpretation is adopted solely for examination and does not resolve the lack of clarity in the claim language.
Claim Rejections - 35 USC § 103
Koepnick et al., Rossmann et al., and Sahtoe et al.
Claim(s) is/are rejected under 35 U.S.C. 103 as being unpatentable over Koepnick et al. (Nature. 2019;570(7761):390-394) in view of Rossmann et al.(Protein Eng Des Sel. 2017;30(6):419-430, disclosed in IDS) and Sahtoe et al.(bioRxiv 2023.01.13.523785).
Regarding claims 1 and 5-8, Koepnick discloses the de novo protein Peak6 (PDB 6MRS), having the amino acid sequence as shown in figure below.
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Koepnick’s Peak6 corresponds to the recited sequence of claim 1 with regards to alpha1, alpha2, beta1, beta2, beta3, and beta4 sequences. In addition, Peak6 loop1-5/X1-5 regions contain 7, 5, 5, 4, 4 amino acids respectively. Hence, Koepnick teaches the claimed sequence and X1-X5 lengths.
Koepnick does not teach to replace the loop regions that results X1 to be other than RKMGVTM, X2 to be other than RSGNE, X3 to be other than IKGLH, X4 to be other than GVET, or X5 to be other than HGDT.
Rossmann teaches peptide display system (RAD display), which screening peptide sequences are presented within a loop region of a stable protein scaffold. [Abstract and Fig. 1]. Rossmann teaches that peptide display commonly employ a small, highly soluble and thermostable protein core capable of tolerating insertions into loop sequences and successfully shown RadA scaffold tolerates sequence diversity within its L2 loop [Introduction]. Rossman also teaches peptide display of different lengths and compositions, producing libraries of variants by varying residues at selected positions [Fig. 1].
One of ordinary skill in the art would have recognized from Rossmann that modification of a solvent accessible loop of a folded stable protein scaffold is a known technique to generate protein displaying different peptide sequences. Additionally, Sahtoe discloses that such protein engineering techniques is applicable to Koepnick’s foldit scaffold 2003333_0006 (i.e. Peak6) and modify the same scaffold to function as a peptide binder, which include introducing chain break in the connecting loop between beta strands 3 and 4, corresponding to the X5 region in current claim [Abstract, Materials and methods, and Fig S1].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to apply Rossmann’s known loop sequence diversification technique to at least one of Koepnick’s X1-X5 loop regions in Peak6 scaffold to provide Peak6 scaffold displaying different peptide sequences, with a reasonable expectation of success since Rossmann shows that sequence diverse peptide loops can be accommodated by a stable folded protein scaffold. Sahtoe specifically confirmed that Koepnick’s Peak6 itself, including the beta3-4 connection region, is amendable to protein engineering. Modification of even one amino acid within any of X1-X5 would cause loop to differ from its native Peak6 sequence while remaining within the claimed 2-10 amino acid range and retain more than 80% sequence identity. A skilled artisan would have been motivated to use Peak6 as a scaffold to design binders by modifying loop region because the display system can serve as a flexible and robust platform for the selection or characterization of peptides in a variety of applications ranging from basic research tool to drug discovery [Rossmann discussion], or serve as binders to amyloid forming segments of these proteins could have utility both as diagnostics and therapeutics [Sahtoe Introduction].
Regarding claim 4, Koepnick discloses X1, X2, X3, X4 and X5 comprise different amino acid sequences. (e.g. the native Peak 6 protein already provide the concept that five different loops contain five different sequences [see picture above]).
Regarding claim 10 and 11, Rossmann teaches displayed protein may comprises a cysteine and His6 tag at N-terminal (e.g. expression of all constructs in bacteria is regulated by the T7lac promoter and designed to facilitate flexibility in purification and biophysical applications by including options for addition of an N-terminal His6-tag and a unique cysteine that allows for site-specific labeling and directional immobilization through the very N-terminus of the display protein. Plasmids were constructed to express His6-Cys-tagged [“RAD scaffold design” section]).
Koepnick et al., Rossmann et al., Sahtoe et al., and Prior et al.
Claim(s) 2 and 3 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koepnick et al. (Nature. 2019;570(7761):390-394) in view of Rossmann et al.(Protein Eng Des Sel. 2017;30(6):419-430, disclosed in IDS), Sahtoe et al.(bioRxiv 2023.01.13.523785), and Prior et al. (US20070050855A1, EFD: August 30th 2002).
Regarding claims 2 and 3, Koepnick, Rossmann, and Sahtoe do not disclose that the five loop regions each comprises an identical sequence of three to six amino acids.
Prior discloses modification of a protein scaffold at multiple solvent exposed loop regions and expressly teaches the same therapeutic peptide may be inserted into all five loops of scaffold to create a pentavalent molecule with increased avidity for the antigen, receptor, or targeting molecule, which the therapeutic protein binds. [abstract and ¶0093].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to modify Peak6 scaffold by placing the same display peptide in all five loop regions to increase increased avidity toward binding partner, per Prior explicit teaching.
Koepnick et al., Rossmann et al., Sahtoe et al., and Zhang et al.
Claim(s) 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koepnick et al. (Nature. 2019;570(7761):390-394) in view of Rossmann et al.(Protein Eng Des Sel. 2017;30(6):419-430, disclosed in IDS), Sahtoe et al.(bioRxiv 2023.01.13.523785), and Zhang et al. (Nucleic Acids Res. 2005;33(7):2302-2309).
Regarding claim 9, Rossmann teaches modification of a surface exposed scaffold loop need not disrupt the underling protein fold, specifically discloses the removal of RadA loop does not affect protein stability and peptide insertion at loop region position away from the scaffold core is unlikely to interfere with folding and stability [“RAD scaffold design” section]. Sahtoe further teaches that beta3-beta4 loop of Koepnick’s Peak6 itself can be engineered. Zhang teaches that a TM-score greater than 0.5 is indicative of proteins having the same overall fold [“How many folds are there in the PDB?“ section].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art modifying an X-loop of Peak6 according to Rossmann and Sahtoe would have reasonably expected the result protein to retain overall Peak6 fold and exhibit a TM-score of at least 0.5 relative to the native Peak6.
Koepnick et al., Rossmann et al., Sahtoe et al., and Mallick et al.
Claim(s) 12, 13, 19, and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koepnick et al. (Nature. 2019;570(7761):390-394) in view of Rossmann et al.(Protein Eng Des Sel. 2017;30(6):419-430, disclosed in IDS), Sahtoe et al.(bioRxiv 2023.01.13.523785), and Mallick et al. (WO2019036055A2, Published: Febuary 18th 2019).
Regarding claims 12 and 13, Koepnick, Rossmann, and Sahtoe do not disclose an affinity reagent (e.g. antibody or nucleic acid aptamer) is non-covalently bound to X1, X2, X3, X4 or X5.
Mallick discloses selecting affinity reagent with desired affinity and specificity and toward targeted peptide epitopes [abstract], wherein affinity reagent can be antibody or aptamer [¶0005].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to use antibody or nucleic acid aptamer as binding reagent for epitope displayed within X1, X2, X3, X4 or X5 because method enable selection and characterization of affinity reagents that bind to multiple epitopes instead of just a single one. This technique allows the use of a single reagent for wider screening tasks rather than needing a unique reagent for every single target as conventional method [¶0002-0003].
Regarding claims 19 and 20, Koepnick, Rossmann, and Sahtoe do not disclose an array of different proteins, including protein of claim 1, is attached to the solid support.
Mallick discloses selecting affinity reagent with desired affinity and specificity and toward targeted peptide epitopes [abstract], wherein the target proteins immobilized on a solid support [Fig. 1, Fig. 3B, and ¶, ].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to immobilize Koepnick’s Peak6 on a solid support, as taught by Mallick, to efficiently characterize binding affinities of affinity reagents across a number of unknown proteins [¶0061], enable high throughput screening.
Koepnick et al., Rossmann et al., Sahtoe et al., and Ma et al.
Claim(s) 14-18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koepnick et al. (Nature. 2019;570(7761):390-394) in view of Rossmann et al.(Protein Eng Des Sel. 2017;30(6):419-430, disclosed in IDS), Sahtoe et al.(bioRxiv 2023.01.13.523785), and Ma et al.(Mol Cell Proteomics. 2012;11(8):501-511).
Regarding claims 14-18, Koepnick, Rossmann, and Sahtoe do not disclose that X1, X2, X3, X4, or X5 comprises an amino acid sequence selected from the group consisting of HHH, HRH, YFR, WNK, FRRF, RFRF, WFR, LEEL, YWL, HFR, FST, DPY, FWR, DTR, DTV, RWWR, RDE, HSP, DPY, DTR, SLF, and DDY.
Ma teaches insertion of His8 tag (8 consecutive histidine residues) into exposed surface loop of a folded protein [Abstract and method section].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to insert a His8 tag to one of the X1-X5 loop regions of Peak6 to enable efficient affinity purification for proteins of interest [page 501].
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KHAI QUYNH TIEN PHAM/ Examiner, Art Unit 1684
/JEREMY C FLINDERS/ Primary Examiner, Art Unit 1684
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