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
Application Status
**The Non-Final Office action mailed on 10/07/2025 is hereby vacated and a new Non-Final Office action is hereby presented in this Office action.
This application is a 371 of PCT/US2020/054859, filed on 04/07/2022.
Claims 1-53, 54-56, 60-62, 63-67, and 68-72 are currently pending in the instant application.
The preliminary amendment filed on 07/01/2025, amending claims 29-30, and 32-33, canceling claims 57-59, and adding new claims 68-72 is acknowledged.
Election/Restriction
Applicant's election of Claims 54-56, 68-69, and 70-72, drawn to a protein expressed in a mammalian cell comprising a first unnatural amino acid (UAA) that is a tryptophan analog and a second UAA that is a leucine analog, in the response filed on 07/01/2025 is acknowledged.
Since, Applicants did not elect any Groups of the restriction requirement, which is required as per Restriction requirement, the Examiner is hereby considers election as without traverse, and applicants are reminded to acknowledge of the election clearly in the next response, but mentioned to examine claims 54-56, 68-69, and 70-72, which are corresponds to Group VI.
Accordingly, Claims 1-49, 50-53, and 60-67 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Applicants request for rejoinder is noted. However, current claims of elected Group VI are not allowable at this time. When Group VI would be allowable, rejoinder request would be evaluated at that time.
The requirement is still deemed proper and is therefore made FINAL.
Claims 54-56, 68-69, and 70-72 are present for examination.
The groupings of the restricted groups are shown below again for the clarification.
Group, I claim(s) 1-49, drawn to a method of producing a protein comprising a first unnatural amino acid (UAA) and a second different UAA, the method comprising culturing a mammalian cell with: (i) a nucleic acid comprising a nucleotide sequence encoding a first tRNA including SEQ ID Nos: 49-54, and 108-113, comprising an anticodon that hybridizes to a first codon selected from UAG, UGA, and UAA, and is capable of being charged with the first UAA; (ii) a nucleic acid comprising a nucleotide sequence encoding a first aminoacyl- tRNA synthetase including SEQ ID Nos: 44-48, capable of charging the first tRNA with the first UAA: (iii) a nucleic acid comprising a nucleotide sequence encoding a second tRNA comprising an anticodon that hybridizes to a second codon selected from UAG, UGA, and UAA, and is capable of being charged with the second UAA, wherein the first and second tRNA do not contain the same anticodon; (iv) a nucleic acid comprising a nucleotide sequence encoding a second aminoacyl-tRNA synthetase capable of charging the second tRNA with the second UAA; and (v) a nucleic acid comprising a nucleotide sequence encoding the protein comprising the first codon and the second codon; under conditions that permit the first tRNA, when expressed in the cell and charged with the first UAA, to hybridize to the first codon and direct the incorporation of the first UAA into the protein, and the second tRNA, when expressed in the cell and charged with the second UAA, to hybridize to the second codon and direct the incorporation of the second UAA into the protein; wherein the amount of the protein comprising the first and second UAA expressed by the cell is at least 10% of the amount of a reference protein expressed by the same cell or a similar cell, wherein the reference protein is an otherwise identical protein that does not comprise the first and second UAA.
Group, II claim(s) 50, drawn to a method of producing a protein comprising a tryptophan analog and a leucine analog, the method comprising culturing a mammalian cell with: (i) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E. coli tryptophanyl-tRNA comprising an anticodon that hybridizes to a UGA codon, and is capable of being charged with the tryptophan analog; (ii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E. coli tryptophanyl-tRNA synthetase capable of charging the derivative of the .coli tryptophanyl-tRNA with the tryptophan analog; (iii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E.coli tyrosyl-tRNA comprising an anticodon that hybridizes to UAG codon, and is capable of being charged with the tyrosine analog; (iv) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E. coli tyrosyl-tRNA synthetase capable of charging the derivative of the E. coli tyrosyl- tRNA with the tyrosine analog; and (v) a nucleic acid comprising a nucleotide sequence encoding the protein comprising the UGA codon and the UAG codon; under conditions that permit the derivative of the E. coli tryptophanyl-tRNA, when expressed in the cell and charged with the tryptophan analog, to hybridize to the UGA codon and direct the incorporation of the tryptophan into the protein, and the derivative of the E. coli tyrosyl-tRNA, when expressed in the cell and charged with the tyrosine analog, to hybridize to the UAG codon and direct the incorporation of the tyrosine analog into the protein.
Group, III claim(s) 51, drawn to a method of producing a protein comprising a tryptophan analog and a tyrosine analog, the method comprising culturing a mammalian cell with: (i) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E.coli tryptophanyl-tRNA comprising an anticodon that hybridizes to a TGA codon, and is capable of being charged with the tryptophan analog; (ii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E.coli tryptophanyl-tRNA synthetase capable of charging the derivative of the .co/i tryptophanyl-tRNA with the tryptophan analog; (iii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an M. barkeri pyrrolysyl-tRNA comprising an anticodon that hybridizes to UAG codon, and is capable of being charged with the pyrrolysine analog; (iv) a nucleic acid comprising a nucleotide sequence encoding a derivative of an M. barkeri pyrrolysyl-tRNA synthetase capable of charging the derivative of the M. barkeri pyrrolysyl-tRNA with the pyrrolysine analog; and (v) a nucleic acid comprising a nucleotide sequence encoding the protein comprising the UGA codon and the UAG codon; under conditions that permit the derivative of the E.coli tryptophanyl-tRNA, when expressed in the cell and charged with the tryptophan analog, to hybridize to the UGA codon and direct the incorporation of the tryptophan into the protein, and the derivative of the E. cob pyrrolysyl-tRNA, when expressed in the cell and charged with the pyrrolysine analog, to hybridize to the UAG codon and direct the incorporation of the pyrrolysine analog into the protein.
Group, IV claim(s) 52, drawn to a method of producing a protein comprising a tryptophan analog and a pyrrolysine analog, the method comprising culturing a mammalian cell with: (i) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E.coli tryptophanyl-tRNA comprising an anticodon that hybridizes to a TGA codon, and is capable of being charged with the tryptophan analog; (ii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an E.co/i tryptophanyl-tRNA synthetase capable of charging the derivative of the .co/i tryptophanyl-tRNA with the tryptophan analog;(iii) a nucleic acid comprising a nucleotide sequence encoding a derivative of an M. barkeri pyrrolysyl-tRNA comprising an anticodon that hybridizes to UAG codon, and is capable of being charged with the pyrrolysine analog; (iv) a nucleic acid comprising a nucleotide sequence encoding a derivative of an M. barkeri pyrrolysyl-tRNA synthetase capable of charging the derivative of the A.I barkeri pyrrolysyl-tRNA with the pyrrolysine analog; and (v) a nucleic acid comprising a nucleotide sequence encoding the protein comprising the UGA codon and the UAG codon; under conditions that permit the derivative of the E.coli tryptophanyl-tRNA, when expressed in the cell and charged with the tryptophan analog, to hybridize to the UGA codon and direct the incorporation of the tryptophan into the protein, and the derivative of the E. cob pyrrolysyl-tRNA, when expressed in the cell and charged with the pyrrolysine analog, to hybridize to the UAG codon and direct the incorporation of the pyrrolysine analog into the protein.
Group, V claim(s) 53, 63-66, and 67, drawn to a protein comprising a first unnatural amino acid (UAA) and a second UAA produced by the method of claim 1 (elected group).
Group, VI claim(s) 54-56, 68-69 and 70-72, drawn to a protein expressed in a mammalian cell comprising a first unnatural amino acid (UAA) that is a tryptophan analog and a second UAA that is a leucine analog.
Group, VII claim(s) 60-62, drawn to a protein expressed in a mammalian cell comprising a first unnatural amino acid (UAA) that is a tryptophan analog and a second UAA that is a pyrrolysine analog.
Priority
Acknowledgement is made of applicants claim for priority of US Provisional application62/912,171, filed on 10/08/2019.
Drawing Objections
Drawings submitted on 04/07/2022 are not accepted by the Examiner because the drawings are not clearly legible. Appropriate correction is required
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.
Claims 54-56, 68, are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 54 is indefinite in the recitation “analog’, in the context of amino acids tryptophan and leucine, which is confusing as to the scope of the amino acids tryptophan and leucine. It is not clear whether this phrase includes structural analog having functional activity as tryptophan and leucine or not. Clarification is required.
Claims 71, and 72 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claims 71 and 72 are indefinite in the recitation “fragment thereof’, in the context of antibody, which are confusing as to the scope of antibody of interest. It is not clear whether this phrase includes structural fragments of antibody of interest having functional activity or not. Clarification is required.
Claims 71, and 72 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 71 is indefinite in the recitation “any other polypeptide or protein’, in the context of antibody, which are confusing as to the scope of antibody of interest. The specification does not define anything about “other polypeptide or protein”, which is unknown rendering the metes and bounds of the term unclear, confusing and indefinite. Clarification is required.
Claim 72 is rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
Claim 72 recites the phrase “e.g.,” renders the claim(s) indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim Rejections - 35 U.S.C. § 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
According to MPEP 2143:
“Exemplary rationales that may support a conclusion of obviousness include:
(A) Combining prior art elements according to known methods to yield
predictable results;
(B) Simple substitution of one known element for another to obtain predictable
results;
(C) Use of known technique to improve similar devices (methods, or products)
in the same way;
(D) Applying a known technique to a known device (method, or product) ready
for improvement to yield predictable results;
(E) “ Obvious to try ” – choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success;
(F) Known work in one field of endeavor may prompt variations of it for use in
either the same field or a different one based on design incentives or other market
forces if the variations are predictable to one of ordinary skill in the art;
(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art
reference teachings to arrive at the claimed invention.
Note that the list of rationales provided is not intended to be an all-inclusive list. Other rationales to support a conclusion of obviousness may be relied upon by Office personnel.”
Claims 54-56, 68-71, and 72 are rejected under 35 U.S.C. 103 as being unpatentable over Chatterjee et al. (Universal platform for genetic code expression. US 2017/0349891 A1, publication 12/07/2017, claim priority of 62/345,308, filed on 06/03/2016, see IDS) in view of Zheng et al. (Expanding the Scope of Single- and Double-Noncanonical Amino Acid Mutagenesis in Mammalian Cells Using Orthogonal Poly-specific Leucyl-tRNA Synthetases. Biochemistry 2018, 57, 441-441, Epub ).
Claim 54 is interpreted under BRI as any protein expressed in a mammalian cell comprising a first unnatural amino acid (UAA) that is a tryptophan analog and a second UAA that is a leucine analog.
Regarding claims 54-56, 68-71, and 72, Chatterjee et al. also teach a composition comprising an E. coli tryptophanyl-tRNA synthetase (EcTrp-RS) wherein the EcTrp-RS aminoacylates an E. coli tryptophanyl tRNA (Ec-tRNATrp) with a tryptophan analog over the naturally-occurring tryptophan amino acid, wherein the analog is selected from the group consisting of: 5-hydroxytryptophan (5-HTP), 5-azidotryptophan, 5-propargyloxytryptophan, 5-aminotryptophan, 5-methoxytryptophan, 5-O-allyltryptophan, or 5-bromotryptophan, composition comprising an E. coli tryptophanyl-tRNA synthetase (EcTrp-RS) wherein the EcTrp-RS comprises the amino acid sequence of SEQ ID NO: 91, or a homologous bacteria-derived Trp-RS, and wherein the EcTrp-RS is mutated to replace the serine at position 8 with alanine; the valine at position 144 is replaced with either serine, glycine or alanine; and the valine at position 146 is replaced with either alanine, isoleucine or cysteine. Chatterjee et al. further teach a method of producing a protein in a cell with one, or more, tryptophan analogs to incorporate at specified positions in the protein, the method comprising, (a) culturing the cell in a culture medium under conditions suitable for growth, wherein the cell comprises a nucleic acid that encodes a protein with one, or more, amber (stop codons UAA, and UAG) or opal (UAG and UAA) selector codons, wherein the cell further comprises an Ec-tRNATrp that recognizes the selector codon(s), and wherein the cell further comprises an EcTrp-RS (aminoacyl tRNA synthetase) that aminoacylates the Ec-tRNATrP with a tryptophan analog; (b) contacting the cell culture medium with one, or more, tryptophan analogs under conditions suitable for incorporation of the one, or more, tryptophan analogs into the protein in response to the selector codon(s), thereby producing the protein with one, or more tryptophan analogs, wherein the EcTrp-RS comprises the amino acid sequence of SEQ ID NO: 91, or a homologous bacteria-derived Trp-RS, and wherein the EcTrp-RS is mutated to replace the serine at position 8 with alanine; the valine at position 144 is replaced with either serine, glycine or alanine; and the valine at position 146 is replaced with either alanine, isoleucine or cysteine, wherein the Ec-tRNATrp polynucleotide sequence comprises SEQ ID NO: 1 or SEQ ID NO: 3, or a homologous bacteria-derived tRNA comprising at least about 80% sequence identity with SEQ ID NO: 1 or 3, wherein the tRNA has an anti-codon loop comprising a sequence that specifically binds to a selector sequence of an mRNA selected from the group consisting of an amber codon (UAA or UGA) or an opal codon (UAG and UAA) selector codons, wherein the cell further comprises an Ec-tRNATrp that recognizes the selector c, wherein the tryptophan analog is selected from the group consisting of: 5-azidotryptophan, 5-propargyloxytryptophan, 5-aminotryptophan, 5-methoxytryptophan, 5-O-allyltryptophan, or 5-bromotryptophan, wherein the cell is an E. coli cell or a eukaryotic cell, wherein the cell further comprises a second tRNA/RS pair that is orthogonal to the cell, wherein the second pair does not cross-react with the EcTrp-RS/tRNA pair and that recognizes an amber (selector codon in the protein, wherein the protein produced contains one, or more tryptophan analogs and one, or more, distinct unnatural amino acid other than a tryptophan analog. Chatterjee et al. further teach methods for producing orthogonal aminoacyl synthetase-tRNA pairs for incorporating unnatural amino acids into specific sites in proteins produced in E. coli and mammalian cells, the method comprising a. functionally replacing an endogenous aminoacyl synthetase-tRNA pair in an E. coli host cell with a counter-part aminoacyl synthetase-tRNA pair orthogonal to E. coli and mammalian cells, resulting in an altered translational machinery (ATM) E. coli and liberating the endogenous E. coli aminoacyl synthetase-tRNA pair, wherein the liberated E. coli aminoacyl synthetase-tRNA pair is orthogonal to the ATM E. coli and mammalian cells; b. reintroducing the liberated E. coli aminoacyl synthetase-tRNA pair into the ATM E. coli cell as a nonsense suppressor under conditions suitable for genetically selecting and identifying a variant E. coli aminoacyl synthetase that preferentially aminoacylates a tRNA with an unnatural amino acid over a natural amino acid, thereby producing an orthogonal aminoacyl synthetase-tRNA pair for incorporating unnatural amino acids into specific sites in proteins including antibody, GFP, recombinant proteins or therapeutic proteins produced in E. coli and mammalian cells, wherein second tRNA/RS pair that is orthogonal to the cell, wherein the second pair recognizes an amber selector codon in the protein, but does not cross-react with the first RS/tRNA pair (e.g., EcTrp-RS/tRNAtrp), and Chatterjee et al. teach methods and compositions for selecting and identifying (contemplating detecting) orthogonal aminoacyl synthetase-tRNA pairs and their use to incorporate unnatural amino acids in a site-specific manner in proteins, and identifying (contemplating detecting), wherein the protein is a novel E . coli tryptophanyl synthetase-tRNA pair that functions as both an opal and amber suppressor and that incorporates tryptophan analogs 5-HTP into proteins (see, whole document in particular abstract, para 20, 32, 34, 35, 38, 40, 59, 66, 69, 72, 73, 74, Fig. 3B, 6, 9, 11, Table 1, and claims 1-31).
Chatterjee et al. do not teach producing modified protein containing unnatural amino acids Leucine analog such as LCA or Cys-N3 and using mammalian cells to express the modified protein (for claim 54).
However, Zheng et al. teach expanding the scope of single- and double-noncanonical (unnatural) amino acid mutagenesis in mammalian cell HEK293T(mammalian) cells, using orthogonal poly-specific Leucyl-tRNA synthetases, and further teach Engineered aminoacyl-tRNA synthetase/ tRNA pairs that enable site-specific incorporation of noncanonical amino acids (ncAAs) including C5-Az (synonym Cys-5-N3 as claimed) into proteins including EGFP-C5-Az, a fluorescence protein, in living cells, which have emerged as powerful tools in chemical biology. Zheng et al. also teach that the Escherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair, which is a promising candidate for ncAA mutagenesis in mammalian cells, and show that two highly polyspecific Ec-Leu-RS mutants can efficiently charge a large array of useful ncAAs into proteins expressed in mammalian cells, while discriminating against the 20 canonical amino acids, and combining with an opal-suppressing pyrrolysyl pair, these EcLeuRS variants further enabled site-specific incorporation of different combinations of two distinct ncAAs into proteins expressed in mammalian cells (see, title, abstract, pg442, left Col, para 1, pg443, left Col, para 1-2, Fig. 3, 4).
Therefore, it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention as a whole before the effective filing date of the invention was made by combining the teachings of Chatterjee et al., and Zheng et al. for producing modified EGFP or antibody protein containing unnatural amino acids tagged to 5-HTP or 4-fluophenylalanine (4-FPA), incorporating at least 30% to 40% or 60% of the protein by replacing phenylalanine with 5-HTP or FPA compared to non-modified protein in particular EGFP, or antibody as taught by Chatterjee et al. and Zheng et al. and producing modified protein containing unnatural amino acids using mammalian cells 293T to express the modified protein, and covalent bonding of UAAs to modified protein as taught by Chatterjee et al. and Zheng et al. and modify Chatterjee et al. for producing modified protein containing unnatural amino acids tagged to 5-HTP or 4-fluophenylalanine (4-FPA) or leucine analog Cys-5Az (leucine analog) incorporating into the protein by replacing phenylalanine and leucine with 5-HTP or FPA, and Cys-5-Az compared to non-modified protein in mammalian cells293T cells to arrive the claimed invention.
One of ordinary skilled in the art would have been motivated to make proteins or enzymes incorporated unnatural amino acids 5-HTP or 4-FPA and Cys-5-Az in order to produce modified protein having new properties including enhanced stability, enhanced activity, creating advanced therapeutics such as drug conjugates and enhanced biocatalysis, which is pharmaceutically, clinically and financially beneficial.
One of ordinary skilled in the art would have a reasonable expectation of success because Chatterjee et al. and Zheng et al. could successfully produce in an engineered E. coli cell or mammalian 293T cells in vivo or in vitro.
Thus, the above references render the claims prima facie obvious to one of ordinary skill in the art.
Conclusion
Status of the claims:
Claims 54-56, 68-71, and 72 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to IQBAL H CHOWDHURY whose telephone number is (571)272-8137. The examiner can normally be reached on M-F, at 9:00-5:00 PM.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath N. Rao, can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Iqbal H. Chowdhury, Primary Patent Examiner
Art Unit 1656 (Recombinant Enzymes and Protein Crystallography)
US Patent and Trademark Office
Ph. (571)-272-8137 and Fax (571)-273-8137
/IQBAL H CHOWDHURY/
Primary Examiner, Art Unit 1656