DETAILED ACTION
Status of the Application
Claims 1, 2, 5, 6, 9-13, 15, 16, 19, 22, 23, 24-26, and 28-30 are pending.
Claims 1, 2, 5, 6, 9-13, 15, 16, 19, 22, 23, 24-26, and 28-30 are under examination.
The following Office Action is in response to Applicant's communication dated 12/20/2023.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1, 2, 5, 6, 9-12, 15, 16, 19, 22, and 23 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Chee et al. (U.S. PGPub 2021/0302431 A1).
Regarding claim 1, Chee discloses a method of identifying a target protein, the method comprising:
(i) contacting a sample comprising the target protein with a chemical probe that comprises a functional unit that specifically interacts with the target protein; (e.g. contacting the macromolecule with a binding agent [paragraph 0015]
(ii) loading the sample on a chip comprising a plurality of sample wells; (e.g. loading sample containing macromolecules associated with recording tags joined to a solid support [paragraph 0014], wherein “solid support” can be any support surface including chips, wells disc, etc.[paragraph 0332])
(iii) detecting the sample on the chip, wherein at least a subset of the plurality of sample wells comprises the target protein bound to the chemical probe; (e.g. transferring the information from binding agent to recording tags upon binding events [paragraph 0016])
(iv) sequencing the contents of at least the subset of the plurality of sample wells comprising the target protein bound to the chemical probe, thereby identifying the target protein. (e.g. sequencing the recoding tag [paragraph 0019]. Peptide sequencing also disclosed in Fig 15 with description on paragraph 0272)
Regarding claim 2, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses the sample is a biological sample or a whole proteome [paragraph 0408].
Regarding claim 5, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses
step (i) further comprises immobilizing the target protein at a base of each of the wells of the subset of the plurality of sample wells; and step (e.g. macromolecules associated with recording tags joined to a solid support [paragraph 0014], wherein “solid support” can be any support surface including chips, wells disc, etc.[paragraph 0332])
step (iii) further comprises detecting the target protein. (e.g. transferring the information from binding agent to recording tags upon binding events [paragraph 0016])
Regarding claim 6, Chee discloses a method of identifying a target protein of claim 5 as discussed fully above and incorporated here. Chee further discloses the target protein is immobilized to the base of the well via a secondary complex. [Fig. 2C]
Regarding claim 9, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses the chemical probe is a small molecule (e.g. binding agents may include a peptide, a polypeptide, a protein, carbohydrate, or a small molecule [paragraph 0314]), wherein the small molecule is a drug (e.g. affinity ligand [0420]), a synthetic analogue of alkyl-CoA, a nucleoside triphosphate (NTP) [paragraph 0472], a nucleoside diphosphate (NDP), a nucleoside monophosphate (NMP) [paragraph 0474], a nucleotide, a small molecule that binds covalently to the target protein, or a small molecule that binds non-covalently to the target protein (e.g. binding agent may form a covalent association or non-covalent association with the macromolecule[paragraph 0314]).
Regarding claim 10, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses the functional unit comprises a chemical warhead, optionally wherein the chemical warhead is an electrophilic warhead, a photocaged radical warhead, or nucleophilic warhead. (e.g. The Staudinger ligation, a bio-orthogonal reaction where a phosphine nucleophilically attacks the azide. The intermediate aza-ylide then undergoes intramolecular nucleophilic attack on an electrophilic center [paragraph 0422]).
Regarding claim 11, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses the chemical probe further comprises an orthogonal reactive group, optionally wherein the orthogonal reactive group is a CLICK handle, an alkyne, a cyclopropene, a tetrazine, a cyclopropene partnered with a dioxolane-fused transcyclooctene (TCO), or a tetrazine partnered with a dioxolane-fused transcyclooctene (TCO). [paragraph 0422].
Regarding claim 12, Chee discloses a method of identifying a target protein of claim 1 as discussed fully above and incorporated here. Chee further discloses the method is automated or manual. (The analysis workflow is performed through various instrumentations and manual laboratory procedures [paragraph 0419, 0493, 0597, and 0606 etc.]
Regarding claim 15, Chee discloses a chip comprising a plurality of wells and a target protein bound to a chemical probe immobilized to a base of at least a subset of the plurality of wells (e.g. macromolecules associated with recording tags joined to a solid support [paragraph 0014], wherein “solid support” can be any support surface including chips, wells disc, etc.[paragraph 0332]), optionally wherein the chemical probe comprises a functional unit that specifically interacts with the target protein [paragraphs 0422, 0459, and 0460].
Regarding claim 16, Chee discloses a chip of claim 15 as discussed fully above and incorporated here. Chee further discloses the plurality of wells comprises at least 96 wells (e.g. 1.6 million 75-picoliter wells [paragraph 0419]).
Regarding claim 19, Chee discloses a chip of claim 15 as discussed fully above and incorporated here. Chee further discloses the chemical probe is a small molecule (e.g. binding agents may include a peptide, a polypeptide, a protein, carbohydrate, or a small molecule [paragraph 0314]), wherein the small molecule is a drug (e.g. affinity ligand [0420]), a synthetic analogue of alkyl-CoA, a nucleoside triphosphate (NTP) [paragraph 0472], a nucleoside diphosphate (NDP), a nucleoside monophosphate (NMP) [paragraph 0474], a nucleotide, a small molecule that binds covalently to the target protein, or a small molecule that binds non-covalently to the target protein (e.g. binding agent may form a covalent association or non-covalent association with the macromolecule[paragraph 0314]).
Regarding claim 22, Chee discloses a chip of claim 15 as discussed fully above and incorporated here. Chee further discloses the functional unit comprises a chemical warhead, optionally wherein the chemical warhead is an electrophilic warhead, a photocaged radical warhead, or nucleophilic warhead. (e.g. The Staudinger ligation, a bio-orthogonal reaction where a phosphine nucleophilically attacks the azide. The intermediate aza-ylide then undergoes intramolecular nucleophilic attack on an electrophilic center [paragraph 0422]).
Regarding claim 23, Chee discloses a chip of claim 15 as discussed fully above and incorporated here. Chee further discloses the chemical probe further comprises an orthogonal reactive group, optionally wherein the orthogonal reactive group is a CLICK handle, an alkyne, a cyclopropene, a tetrazine, a cyclopropene partnered with a dioxolane-fused transcyclooctene (TCO), or a tetrazine partnered with a dioxolane-fused transcyclooctene (TCO). [paragraph 0422].
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.
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.
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.
Claim(s) 13, 24-26, and 28-30 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chee et al. (U.S. PGPub 2021/0302431 A1).
Regarding claim 13, Chee discloses a method of identifying a target protein of claim 12 as discussed fully above and incorporated here. Chee further discloses using NGS platforms (e.g. Illumina 454, and SOLiD) employing flow cells and automated sequencing reactions performed within sequencing instruments [paragraph 0419]. Since neither claim 13 or applicant’s specification define any particular architectures for the “single instrument” limitation, Chee’s disclosure reasonably encompasses the limitation disclosed in claim 13. According, it would have been obvious to one of ordinary skill in the art to perform the automated method within single instrument in order to streamline automated analysis and reduce sample handling.
Regarding claim 24, Chee discloses a method of identifying two or more protein homologues, the method comprising:
(i) contacting a sample comprising the two or more protein homologues with a chemical probe that comprises a functional unit that binds to a shared feature of the two or more protein homologues; (e.g. binding agents engineered to bind specific peptide features and scaffolds capable of recognizing amino acid residues [paragraph 0314]).
(ii) loading the sample on a chip comprising a plurality of sample wells; (e.g. loading sample containing macromolecules associated with recording tags joined to a solid support [paragraph 0014], wherein “solid support” can be any support surface including chips, wells disc, etc.[paragraph 0332])
(iii) detecting the sample on the chip, wherein at least a subset of the plurality of samples wells comprises at least one of the two or more protein homologues; (e.g. transferring the information from binding agent to recording tags upon binding events [paragraph 0016])
(iv) sequencing the contents of at least the subset of the plurality of sample wells thereby identifying each protein of the plurality of target proteins. (e.g. sequencing the recoding tag [paragraph 0019]. Peptide sequencing also disclosed in Fig 15 with description on paragraph 0272)
The limitation reciting “two or more protein homologues” does not distinguish the claimed method over Chee. One of ordinary skill in the art would have understood that “protein homologues” refer to protein that share sequence similarity, structural and/or functional features such as conserved motifs, domains, or active sites. Chee discloses contacting proteins or peptides with engineered binding agents that selectively recognize peptide features or amino acid residues [paragraph 0314]. Such binding agents recognize structural or sequence features that are conserved across multiple proteins. Proteins sharing such conserved sequence or structural elements corresponds to homologous proteins under broadest reasonable interpretation. Accordingly, Chee teaches binding agents interact with multiple proteins that share the conserved feature, which corresponds to identifying two or more protein homologues in claim 24.
Regarding claim 25, Chee discloses a method of identifying two or more protein homologues of claim 24 as discussed fully above and incorporated here. Although Chee does not explicitly disclose binding agents contact with amino acid sequences that share at least 80%, 85%, 90%, or 95% sequence similarity, Chee discloses contacting proteins with binding agents that recognize specific peptide sequence and/or features and listed numerous scaffold binding agents capable of recognizing defined peptide motifs, including Affilin, , a T cell receptor, monobody, a single domain antibody, etc. [paragraph 0484]. Such binding agents are known in the art to bind specific peptide motifs or epitopes with high specificity. A person of ordinary skill in the art would understand that proteins or peptides that bind to the same probe need to share significant sequence similarity in the binding region. Hence, additional sequence similarity limitation of claim 25 is obvious in view of Chee.
Regarding claim 26, Chee discloses a method of identifying two or more protein homologues of claim 24 as discussed fully above and incorporated here. Chee further discloses the shared feature of the two or more protein homologues is a protein domain, active site, allosteric site, or post-translational modification [paragraph 0116].
Regarding claim 28, Chee discloses a method of identifying two or more protein homologues of claim 24 as discussed fully above and incorporated here. Chee further discloses the chemical probe is a small molecule (e.g. binding agents may include a peptide, a polypeptide, a protein, carbohydrate, or a small molecule [paragraph 0314]), wherein the small molecule is a drug (e.g. affinity ligand [0420]), a synthetic analogue of alkyl-CoA, a nucleoside triphosphate (NTP) [paragraph 0472], a nucleoside diphosphate (NDP), a nucleoside monophosphate (NMP) [paragraph 0474], a nucleotide, a small molecule that binds covalently to the target protein, or a small molecule that binds non-covalently to the target protein (e.g. binding agent may form a covalent association or non-covalent association with the macromolecule[paragraph 0314]).
Regarding claim 29, Chee discloses a method of identifying two or more protein homologues of claim 24 as discussed fully above and incorporated here. Chee further discloses the functional unit comprises a chemical warhead, optionally wherein the chemical warhead is an electrophilic warhead, a photocaged radical warhead, or nucleophilic warhead. (e.g. The Staudinger ligation, a bio-orthogonal reaction where a phosphine nucleophilically attacks the azide. The intermediate aza-ylide then undergoes intramolecular nucleophilic attack on an electrophilic center [paragraph 0469]).
Regarding claim 29, Chee discloses a method of identifying two or more protein homologues of claim 24 as discussed fully above and incorporated here. Chee further discloses the chemical probe further comprises an orthogonal reactive group, optionally wherein the orthogonal reactive group is a CLICK handle, an alkyne, a cyclopropene, a tetrazine, a cyclopropene partnered with a dioxolane-fused transcyclooctene (TCO), or a tetrazine partnered with a dioxolane-fused transcyclooctene (TCO). [paragraph 0422].
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