Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
DETAILED ACTION
Application Status
This application is a CON of US patent application 16/008,924, filed on 07/15/2022.
Claims 45-59, and 63-64 are currently pending in this patent application.
In response to a previous Office action, a Final Rejection Office action (mailed on 08/04/2025), Applicants filed a response and a claims amendment, amending claims 45, 48-59, and 64, and canceling claim 62 on 02/04/2026 is acknowledged.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 02/04/2026 has been entered.
Claims 45-59 and 63-64 are present for examination.
Applicants' arguments filed on 02/04/2026, have been fully considered and are deemed persuasive to overcome some of the rejections previously applied. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Priority
Acknowledgement is made of applicants claim for priority of US patent applications 16/008,924, filed on 06/14/2018, now US patent 11393556, and 14/776,532, filed on 09/14/2014, now US patent 10025900, and US Provisional application 61/793,598, filed on 03/15/2013.
New-Claim Rejections – pre-AIA 35 U.S.C. § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived 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 under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
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 45-59 and 62-64 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Mayo et al. (Method for the generation of proteins with new enzymatic function, US PGPUB 2002/018393A1, publication 12/05/2002, see IDS) in view of Zanghellini et al (New algorithms and an in silico bench mark for computational enzyme design. Protein Science (2006), 15: 2785-2794, see IDS), and Schramm et al. (Transition state variation in enzymatic reaction. ( Current opinion in Chemical Biology (2001), 5: 556-563, see, PTO892).
The Broadest Reasonable Interpretation (BRI) of claim 45, which is drawn to a method for selecting and making a full-length protein having glycosidase (synonym- hydrolase) activity, the method comprising: (a) obtaining a template structure of a wild-type template protein, wherein the template protein is a glycosidase; (b) preparing a functional site description of the template protein based on the template structure, wherein the functional site description comprises (i) amino acid identities for each functional site amino acid residue, (ii) rotameric states for each functional residue, (iii) rotameric states for a ligand, and (iv) geometric placement of the functional residues with respect to the ligand; (c) computationally selecting, from a database of candidate proteins, one or more candidate proteins having structural homology to the template structure of the template protein and/or sequence homology to an amino acid sequence of the template protein; (d) providing a structural model for each of the one or more candidate proteins amino acid sequences; (e) evaluating each structural model relative to the functional site description of the template protein by computationally docking ligand(s), reaction substrate(s), transition state(s), or reaction product(s) relating to the glycosidase activity to each structural model, (f) selecting, based on the evaluation, at least one candidate protein that satisfies the functional site description of the template protein; and_(g) recombinantly expressing and confirming the selected at least one candidate protein has the glycosidase activity, thereby making the full-length protein having the enzymatic glycosidase activity.
Regarding claims 45-59 and 62-64, Mayo et al. teach a method of generating (making) a protein having enzyme-like activity (title, abstract, Para. [0023]), the method comprising: (a) preparing a functional site description based on at least one template protein structure having the enzymatic activity, or having structural or sequence homology to a protein with the desired enzymatic function, or design of proteins with novel functions (Para. 23) including the function or activity of “glycosidase or hydrolase” (see, para 82-83) as well as hydrolase and the desired protein (enzyme) and could be named as “glycosylhydrolase or glycosidase”; and the scaffold protein can be computationally modeled to incorporate a novel catalytic enzymatic activity or function or property, (Para. 41); active site domains that mimic naturally occurring chemical reactions, modeled on known enzymatic principles, can be designed and inserted into a protein scaffold to generate a protein with enzymes-like activity, (Para. 48); de novo active site domains may be designed and inserted into a protein scaffold to generate proteins with novel enzyme-like activities, (Para. 49); template protein backbone structure of the variant protein substantially corresponds to the template protein backbone structure of a human target protein, (Para. 131); (b) computationally selecting one or more of amino acid sequences having structural homology and/or sequence homology to the template protein structure, providing a structural model for each said amino acid sequence, and candidate variant proteins can be generated in variety of computational ways, using a variety of protein design cycles, including structure-based methods or sequence-based methods, or combinations thereof, (Para. 109); variant candidate proteins of the invention have an amino acid sequence that differs from the scaffold protein, (Para. 113); overall homology of the protein sequence to the target sequence is 75% to 99% homology to the template protein (para 118); computational methods can be used to insert the active site domain and change the identity of the surrounding amino acids to other amino acids to optimize the catalytic reaction (Para. 57); and it is possible only to model a portion of a protein, for example a domain of a larger protein, (Para. 91); using an ORBIT computational program, each position in the protein structure of thioredoxin protein was modeled, (Para. 211); a combinatorial complexity (para 70-73) of approximately 1026 amino acid sequence that corresponded to 10101 rotamer sequences were scanned in approximately two days on 14195 MHz R10000 processors running in parallel, (Para. 212); (c) selecting the amino acid sequences satisfying the functional site description and computational processing results in a set of optimized variant candidate sequences with putative enzyme-like activity, (Para. 111); (d) recombinantly expressing and confirming said desired function, for at least one amino acid sequence, thereby making the protein having the desired function; (candidate proteins are recombinant, (Para. 137); protein may be made using recombinant techniques, through the expression of a recombinant nucleic acid, (Para. 139); (e) producing the protein having the desired function in a host cell or in vitro translation system (recombinant nucleic acid is made and reintroduced into a host cell, (Para. 138); numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells (Para. 175). Mayo et al. further teaches that the desired function is binding to one or more ligands (active site domains that mimic naturally occurring chemical reactions can be designed and inserted into a protein scaffold, (Para. 48); active site domains may be designed and inserted into a protein scaffold to generate ligand binding proteins, (Para. 50)). Mayo et al. also teach the ligand, which is a small molecule, a hormone, a protein or peptide including glycosidase or glycosylhydrolase enzyme (see, para 82-83) as well as dehydrogenase enzyme; (Para. 51, 52, 197), wherein the desired function is an enzymatic activity, and where the desired functionality includes substrate specificity (once made, the candidate proteins are tested for enzymatic activities or attributes such as substrate specificity, (Para. 206); double reciprocal analysis of an enzyme like protein PZD2 catalyzed PNPA hydrolysis in the presence and absence of inhibitor shows the hallmark features of competitive inhibition implying that PNPG is able to bind in the active site and block PNPA binding, (Para. 229, Fig. 9). Mayo et al. further teaches the amino acid sequences are selected that have amino acid identit (ies) and corresponding to three-dimensional structure that satisfy the functional site description, i.e., computational methods can be used to insert the active site domain and change the identity of the surrounding amino acids to other amino acids to optimize the catalytic reaction (Para. 57); structural alignment of structurally related proteins can be identified to generate sequence alignments (Para. 60); rotamer/template energies are calculated for the interaction of every possible rotamer at every variable residue position with the backbone, using some or all of the scoring functions, (Para. 93); then, rotamer/rotamer interaction energy of each possible rotamer is compared with every possible rotamer at all other variable residue positions, (Para. 94); as will be appreciated by those in the art, once an optimized sequence or set of sequences is generated, a variety of sequence space sampling methods can be done (Para. 101); a set of rotamers representing some high energy state of the substrate is generated, that can include the transition state of a targeted chemical reaction, (Para. 66); and D26I protein was predicted by ORBIT program in an independent calculation and results in increased thermodynamic stability similar to the previously reported D26A protein, (Para. 219), wherein amino acid sequences that satisfy the functional site description are selected by binding (contemplating docking) a ligand(s), substrate(s), or transition state(s) relating to the desired function (active site domains may be designed and inserted into a protein scaffold to generate ligand binding proteins, (Para. 47-50); basic principles of enzymatic catalysis including proximity and orientation of substrate molecules, transition state stabilization, acid-base catalysis, and covalent catalysis may be used as guidelines for building an active site domain (Para 26), wherein the functional site description comprises amino acid identities for each functional site amino acid residue (computational methods can be used to insert the active site domain and change the identity of the surrounding amino acids to other amino acids to optimize the catalytic reaction, (Para. 57); computational processing results in a set of optimized variant candidate sequences with putative enzyme-like activity, (Para. 111), rotameric states for each functional residue (as will be appreciated by those in the art, once an optimized sequence or set of sequences is generated, a variety of sequence space sampling methods can be done, (Para. 101); a set of rotamers representing some high energy state of the substrate is generated, structural alignment of structurally related proteins can be done to generate sequence alignments, (Para. 60), wherein the functional site description comprises one or more of: a structural model of one or more of reaction substrate(s), transition state(s), and reaction product(s) (basic principles of enzymatic catalysis including proximity and orientation of substrate molecules, transition state stabilization, acid-base catalysis, and covalent catalysis may be used as guidelines for building an active site domain, (Para. 26); amino acid identities for each functional site amino acid residue, (computational methods may be applied to optimize the amino acids in the surrounding area, to accommodate substrate binding and catalysis (Para. 25); rotameric states for each functional residue, rotameric states for each substrate, rotameric states for each transition state, rotameric states for each reaction product (rotamer/template energies are calculated for the interaction of every possible rotamer at every variable residue position with the backbone, using some or all of the scoring functions, (Para. 93); then, rotamer/rotamer interaction energy of each possible rotamer is compared with every possible rotamer at all other variable residue positions, (Para. 94); as will be appreciated by those in the art, once an optimized sequence or set of sequences is generated, a variety of sequence space sampling methods can be done, (Para. 101); a set of rotamers representing some high energy state of the substrate is generated, that can include the transition state of a targeted chemical reaction (Para 66); the term "high energy state" is meant to include high energy states of the substrate on some reaction pathway, high energy states of the substrate/protein complex on some reaction pathway, transition states of the substrate on some reaction pathway, transition states of the substrate/protein complex on some reaction pathway, (Para. 67); another variation is to bias the score for amino acids that occur in the sequence alignment, thereby increasing the likelihood that they are found during computational screening but still allowing consideration of other amino acids, (Para. 59); and the functional residues with respect to said reaction substrate(s) and/or transition state(s) (structural alignment of structurally related proteins can be done to generate sequence alignments, (Para. 60). Mayo et al. further teaches the functional site description is constructed using one or more of: molecular mechanics, x-ray crystallography (para 77) and molecular dynamics, transition state analog (para 23, 26) or a suitable combination thereof (generally, high thermodynamic stability suggests the protein can tolerate the destabilizing mutations that are required to build an active site, (Para. 42); it is desirable to have candidate variant proteins with similar enzyme-like activity that are more stable than the scaffold protein or the wild-type enzyme, (Para. 145). Mayo et al. also teaches use of structural homology alignment software FASTA, (Para [0119]), for domain database DALI (Para. 60), and for homology BLAST or PSI-BLAST (Para. 61, 121-124]) and for homology modeling using ROSETA program (Para. 61). Mayo et al. further teach structural homology models of the sequence homologs are X-ray structures, three-dimensional protein structure (Para. 39, 70, 80, 131-132]). Mayo et al. teach the amino acid sequences are scored by computationally docking the ligand(s), and optimizing the positioning of the amino acid side chain and main chain atoms by minimizing the energy of the ligand(s)-structure interaction, the protein structure energy and/or the internal energy of ligand(s) (basic principles of enzymatic catalysis including proximity and orientation of substrate molecules, transition state stabilization, acid-base catalysis, and covalent catalysis may be used as guidelines for building an active site domain, (Para. 26); generally, high thermodynamic stability suggests the protein can tolerate the destabilizing mutations that are required to build an active site (Para, 42); ligand binding proteins may be designed using computational methods, such that rotamers are used to build the active site domain ground state, or low energy state, rather than high energy state rotamers, (Para. 50); it is desirable to have candidate variant proteins with enzyme-like activity that are more stable than the scaffold protein or the wild-type enzyme, (Para, 145). Mayo et al. further teach the ligand(s) comprises one or two of the transition state(s) related to the desired function (for designs directed at generating enzyme-like proteins, a set of rotamers representing some high energy state of the substrate is generated, where the high energy state of the substrate may include the transition state of a targeted chemical reaction, or some intermediate state on the reaction pathway of a targeted chemical reaction (Para, 66); for designs directed at generating ligand binding proteins, a set of rotamers representing some low energy or ground state is generated (Para, 66); the term "high energy state" is meant to include high energy states of the substrate on some reaction pathway, high energy states of the substrate/protein complex on some reaction pathway, transition states of the substrate on some reaction pathway, transition states of the substrate/protein complex on some reaction pathway, intermediate states of the substrate on some reaction pathway, intermediate states of the substrate/protein complex on some reaction pathway, low energy states of the substrate, low energy states of the substrate/protein complex, ground states of the substrate, and ground states of the substrate/protein complex (Para, 67). Mayo et al. also teach the amino acid sequences are scored by computationally docking the ligand(s), reaction substrate(s), or transition state(s) (basic principles of enzymatic catalysis including proximity and orientation of substrate molecules, transition state stabilization, acid-base catalysis, and covalent catalysis may be used as guidelines for building an active site domain, (Para, 26); generally, high thermodynamic stability suggests the protein can tolerate the destabilizing mutations that are required to build an active site (Para, 42); ligand binding proteins may be designed using computational methods, such that rotamers are used to build the active site domain ground state, or low energy state, rather than high energy state rotamers (Para, 50); it is desirable to have candidate variant proteins with enzyme-like activity that are more stable than the scaffold protein or the wild-type enzyme, (Para, 145), and optimizing the positioning of the amino acid side chain and main chain atoms by minimizing the energy of the ligand(s), reaction substrate(s)/ transition state(s)-structure interaction, the protein structure energy and/or the internal energy of the ligand(s), substrate(s)/transition state(s)/product(s) (computational processing results in a set of optimized variant candidate sequences with putative enzyme-like activity (Para, 111); computational methods may be applied to optimize the amino acids in the surrounding area, to accommodate substrate binding and catalysis, (Para. 25); another variation is to bias the score for amino acids that occur in the sequence alignment, thereby increasing the likelihood that they are found during computational screening but still allowing consideration of other amino acids, (Para. 59). Mayo et al. further teaches that to have candidate variant proteins with enzyme-like activity that are more stable than the scaffold protein or the wild-type enzyme with higher sequence identity or homology and the variation between target sequence with template sequence 20% to 25%, and percent identities are 75% to 95% compared to the template protein having enzyme activity (Para. 118, 119, 123). Mayo et al. also teach protein having enzyme activity subject to directed evolution and mutagenesis techniques with repeating the same techniques to obtain a better mutant having improved enzymatic activity (Para. 26, 80, 141).
Mayo et al. do not teach geometric placement of functional residues of amino acids in a protein (for claim 45), and do not teach glycosidase (glucosyl-hydrolase) enzyme can be used as a protein template for designing new enzyme with desired functional activity (for claim 45, 54, 63 and 64).
However, Zanghellini et al. (inventor) teach a new algorithms and an in-silico benchmark for computational enzyme design, and further teach creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge, for computational protein design. Zanghellini et al. also teach two new algorithms for enzyme design that employ hashing techniques to allow searching through large numbers of protein scaffolds for optimal catalytic site placement., and an in silico benchmark, based on the recapitulation of the active sites of native enzymes, that allows rapid evaluation and testing of enzyme design methodologies, wherein benchmark test consists of designing sites for each of 10 different chemical reactions in backbone scaffolds derived from 10 enzymes catalyzing the reactions, the new methods succeed in identifying the native site in the native scaffold and ranking it within the top five designs for six of the 10 reactions, wherein the new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design. Zanghellini et al. further teach endoglucanase Cel5A, which is an EC class hydrolase having function of glycosidase, which can be used as a template protein (see, title, abstract, Table 1)
Alexandre Zanghellini et al. (inventor) do not explicitly teach using glycosidase enzyme as a template protein (for claim 45, 54, 63, and 64).
However, Schramm et al. teach transition state variation in enzymatic reactions, which is also associated with geometric variation of the transition state structures, and further teach that said transition state variation in enzyme catalysed reaction are found in glycosidase enzyme, where both retention and inversion occur with similar substrates depending on the geometric placement of carboxyl groups that are involved in transition state formation of an enzyme-substrate reactions, where glucosidases are a type of glycosidase, which are enzymes that break down complex carbohydrates into simpler sugars, i.e., glucosidases belong to the diverse class of glycosidase (glycoside hydrolase) enzyme, and thus, glycosidase enzyme of Schramm et al. is in fact glucosidase and meets the claim limitation of claim 63 (abstract, pg556, left Col para 2).
Therefore, It would have been obvious to one of ordinary skilled in the art in the same field at the time of the invention was made to combine the teachings of Mayo et al., Alexandre Zanghellini et al. and Schramm et al.to use geometric hashing of functional residues of amino acids in a protein in terms of conformational structure, activity and functional properties of a protein or enzyme, and endoglucanase Cel5A, which is an EC class hydrolase having function of glycosidase, which can be used as a template protein as taught by Alexandre Zanghellini et al., and transition state variation in enzyme catalysed reactions are found in the glycosidase enzyme as taught by Schramm et al., and modify Mayo et al. to de novo computational design of a protein and generating said designed protein having enzyme-like activity by mutating amino acid residues to arrive the claimed invention.
One of ordinary skilled in the art would have been motivated to predict and express an optimized conformation of a target protein with geometric placement of amino acids in said protein to achieve and compare protein structure conformation to a template protein having enzymatic activity, which is scientifically, commercially, financially beneficial, and has tremendous effect on Research and Development.
One of ordinary skilled in the art would have a reasonable expectation of success because Mayo et al. and Alexandre Zanghellini et al could successfully made or generate a protein having enzyme-like activity, by (a) preparing a functional site description based on at least one template protein structure having the enzymatic activity, or having structural or sequence homology to a protein with the desired enzymatic function (design of proteins with novel functions; scaffold protein can be computationally modeled to incorporate a novel catalytic activity or function or property, wherein the protein having enzyme activity is dehydrogenase having improved activity compared to control template protein. Thus, the above references render the claims prima facie obvious to one of ordinary skill in the art.
Conclusion
Status of the claims:
Claims 45-59 and 63-64 stand/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 from 9:00 AM - 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, PhD.
Primary Patent Examiner
Art Unit 1656 (Recombinant Enzymes and Protein Crystallography)
US Patent and Trademark Office (USPTO)
Ph. (571)-272-8137 and Fax (571)-273-8137
/IQBAL H CHOWDHURY/
Primary Examiner, Art Unit 1656