DETAILED ACTION
Applicant's response, filed 17 February 2026, has been fully considered. The following rejections
and/or objections are either reiterated or newly applied. They constitute the complete set presently
being applied to the instant application.
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 .
Priority
The instant application claims benefit of priority to U.S. Application No. 17/866,281 filed on 5/4/2020. The claim to the benefit of priority is acknowledged. As such, the effective filing date of claims 16-22, 26, and 30-31 is 5/4/2020.
Election/Restriction
REQUIREMENT FOR UNITY OF INVENTION
As provided in 37 CFR 1.475(a), a national stage application shall relate to one invention only or to a group of inventions so linked as to form a single general inventive concept (“requirement of unity of invention”). Where a group of inventions is claimed in a national stage application, the requirement of unity of invention shall be fulfilled only when there is a technical relationship among those inventions involving one or more of the same or corresponding special technical features. The expression “special technical features” shall mean those technical features that define a contribution which each of the claimed inventions, considered as a whole, makes over the prior art.
The determination whether a group of inventions is so linked as to form a single general inventive concept shall be made without regard to whether the inventions are claimed in separate claims or as alternatives within a single claim. See 37 CFR 1.475(e).
When Claims Are Directed to Multiple Categories of Inventions:
As provided in 37 CFR 1.475 (b), a national stage application containing claims to different categories of invention will be considered to have unity of invention if the claims are drawn only to one of the following combinations of categories:
(1) A product and a process specially adapted for the manufacture of said product; or
(2) A product and a process of use of said product; or
(3) A product, a process specially adapted for the manufacture of the said product, and a use of the said product; or
(4) A process and an apparatus or means specifically designed for carrying out the said process; or
(5) A product, a process specially adapted for the manufacture of the said product, and an apparatus or means specifically designed for carrying out the said process.
Otherwise, unity of invention might not be present. See 37 CFR 1.475 (c).
Restriction is required under 35 U.S.C. 121 and 372.
This application contains the following inventions or groups of inventions which are not so linked as to form a single general inventive concept under PCT Rule 13.1.
In accordance with 37 CFR 1.499, applicant is required, in reply to this action, to elect a single invention to which the claims must be restricted.
Group 1, claims 16-22, 26, and 30-31, drawn to a method of designing a therapeutic scaffold.
Group 2, claims 32, 36, and 42, drawn to a method of treating cancer.
The groups of inventions listed above do not relate to a single general inventive concept under PCT Rule 13.1 because, under PCT Rule 13.2, they lack the same or corresponding special technical features for the following reasons:
Groups 1 and 2 lack unity of invention because the groups do not share the same or corresponding technical feature.
During a telephone conversation with Celin Conde on 3/13/2026 a provisional election was made without traverse to prosecute the invention of Group 1, claims 16-22, 26, and 30-31. Affirmation of this election must be made by applicant in replying to this Office action. Claims 32, 36, and 42 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
The examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
Claim Status
Claims 16-22, 26, and 30-31 are pending.
Claims 1-15, 23-25, 27-29, and 32-47 are withdrawn.
Claims 16-22, 26, and 30-31 are rejected.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 10/26/2022, 10/30/2023, and 2/17/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: Figure 1A-Items 2 and 3. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The use of the term Taxotere, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 26 is objected to because of the following informalities: there is a duplicate word in line 2 - “constituents”. Appropriate correction is required.
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.
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 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.
Claims 16-17, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Bergmann et al. (Journal of Chemical Information and Modeling (2009) 658-669) and Heikamp et al. (Chemical Biology & Drug Design (2017) 655-667).
Claim 16 is directed to a method of designing a scaffold by creating a 3D distance net, screening small fragments and deconstructing the structure.
Bergmann et al. teaches in the abstract “A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex”, on page 658, column 2, paragraph 1 “The complex is described by geometrical descriptors of the scaffold binding site as well as a 3D interaction energy map of the binding site computed by GRID using five different chemical probes. The scaffolds in the database to be searched are described geometrically as well as by atom-pair descriptions of atom types to be fitted onto the GRID computed map. This allows for a ranking of scaffolds in a database according to how well they fit into the scaffold binding site”, on page 659, column 2, paragraph 2 “Three types of descriptors are used to describe the receptor: (a) the distance between anchor points of the query scaffold, (b) the dihedral angle between the anchor points and their connecting points on the query scaffold, and, finally, (c) a GRID derived molecular interaction profile of the receptor related to the GRIND descriptors”, on page 659, column 1, paragraph 2 “The binding site definition starts by selecting a fragment from a protein-bound ligand to be replaced with a fragment from a selected database. The selected fragment, in the following termed the query scaffold, is removed from the binding site. The query scaffold is used to indicate the geometry of the attachment points of the scaffold to the remaining parts of the ligand as well as to define the binding pocket for the receptor interaction profile computation”, reading on a method of designing a scaffold of a therapeutic agent directed against a drug-resistant target comprising: a) creating a three-dimensional fishing net of the distances in the DFG phosphate conformation (3D surface net) of the drug resistant target using an algorithmic phosphate detector; b) screening a library of small fragment to capture small fragment that specifically binds to the 3D surface net of the target, thereby identifying a scaffold structure of the therapeutic agent.
Bergmann et al. does not teach the use of a fragmentation algorithm and deconstructing the structure.
Heikamp et al. teaches in the abstract “The first step in hit optimization is the identification of the pharmacophore, which is normally achieved by deconstruction of the hit molecule to generate “deletion analogues.” In silico fragmentation approaches often focus on the generation of small fragments that do not describe properly the fragment space associated to the deletion analogues. We present significant modifications to the molecular fragmentation programme molBLOCKS, which allows the exhaustive sampling of the fragment space associated with a molecule to generate all possible molecular fragments. This generates larger fragments, by combining the smallest fragments. Additionally, it has been modified to deal with the problem of changing pharmacophoric properties through fragmentation, by highlighting bond cuts”, reading on using a fragmentation algorithm to deconstruct the resistant drug structure and construct the scaffold of a therapeutic agent from the surface net structure and the captured small fragment, thereby designing the scaffold of the therapeutic agent.
It would have been obvious at the time of first filing to have modified the teachings of Bergmann et al. for a 3D method of representing distances in scaffold conformation and screening small fragments, with the teachings of Heikamp et al. for the use of a fragmentation algorithm for the deconstruction of drug structure to construct a scaffold, as the latter teaches in the abstract “This fragment set was found to be more diverse than those generated by standard fragmentation programmes and was relevant to drug discovery as it contains the key fragments representing the pharmacophoric elements associated with ligand recognition. The use of dummy atoms to highlight bond cuts further increases the information content of fragments by visualizing their previous bonding pattern”. One would have had a reasonable expectation of success given that the former screens the scaffolds against a small fragment database, and the latter merely suggests a new method of deconstructing small fragments for that same screening. Therefore, it would have been obvious at the time of first filing to have modified the teachings of each and to be successful.
Claim 17 is directed to the method of claim 16 but further specifies the target as a kinase and the therapeutic as a kinase inhibitor.
Bergmann et al. teaches in the abstract “SHOP was used for suggesting new inhibitors of p38 MAP kinase”, reading on wherein the target is a kinase, and the therapeutic agent is a kinase inhibitor.
Claim 20 is directed to the method of claim 16 but further specifies that the target be an intermediate conformation and the 3D net is an intermediate.
Heikamp et al. teaches on page 657, column 1, paragraph 3 “in some cases, it might be useful to create not just the smallest possible fragments but some intermediate fragments as well”, reading on wherein the drug-resistant target is in a DFG INTERMEDIATE conformation, and wherein the 3D surface net is a 3D INTERMEDIATE surface net (3D INTER net).
Claims 18-19, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Bergmann et al. (Journal of Chemical Information and Modeling (2009) 658-669) and Heikamp et al. (Chemical Biology & Drug Design (2017) 655-667) as applied to claims 16-17, and 20 above, and further in view of Gani et al. (Chemical Biology & Drug Design (2013) 506-519).
Claim 18 is directed to the method of claim 16 but further specifies a mutation in a target causing a conformation change.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach a mutation in a target causing a conformation change.
Gani et al. teaches in the abstract “we have taken a retrospective approach to evaluate virtual screening methods for the leukemia target kinase ABL1 and its drug-resistant mutant ABL1-T315L”, and on page 507, column 2, paragraph 4 “Five crystal structures of T315I mutants of ABL1 kinase domain in complex with inhibitors were taken for analysis, along with structures for four of these inhibitors that have been co-crystallized also with the ABL1-wt kinase domain. These structures, summarized in Table 2, were used forVS of dual active inhibitors and of inactive ligands. Because four pairs of structures, each with one inhibitor binding both the wt and T315I forms, are included, the test set includes a range of inhibitor-associated flexibilities, DFG conformational states, and allows direct comparisons of the effects of gatekeeper mutations”, reading on wherein a mutation in a gene encoding the target results in a change in the conformation of the phosphate on the target.
It would have been obvious at the time of first filing to have modified the teachings of Bergmann et al. and Heikamp et al. for the method of claim 16, with the teachings of Gani et al. for the screening of ABL1 and its drug resistant mutant as the latter teaches in the abstract “the addition of target structural information via docking improves enrichment, and explicit consideration of multiple target conformations (i.e. types I and II) achieves best enrichment of active versus inactive ligands, even without assuming knowledge of the binding mode. We believe that this study can be extended to other therapeutically important kinases in prospective virtual screening studies”. One would have had a reasonable expectation of success given that the former are designing scaffolds for drug design and the latter is merely specifying a particular subset of drugs and targets for drug design. Therefore, it would have been obvious at the time of first filing to have modified the teachings of each and to be successful.
Claim 19 is directed to the method of claim 18 and thus claim 16, but further specifies the mutation induces a phosphate into a DFG intermediate conformation.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach that the mutation induces a phosphate into a DFG intermediate conformation.
Gani et al. teaches in the abstract “we have taken a retrospective approach to evaluate virtual screening methods for the leukemia target kinase ABL1 and its drug-resistant mutant ABL1-T315L”, and on page 507, column 2, paragraph 4 “Five crystal structures of T315I mutants of ABL1 kinase domain in complex with inhibitors were taken for analysis, along with structures for four of these inhibitors that have been co-crystallized also with the ABL1-wt kinase domain. These structures, summarized in Table 2, were used forVS of dual active inhibitors and of inactive ligands. Because four pairs of structures, each with one inhibitor binding both the wt and T315I forms, are included, the test set includes a range of inhibitor-associated flexibilities, DFG conformational states, and allows direct comparisons of the effects of gatekeeper mutations”, reading on wherein the mutation induces a phosphate to be in a DFG INTERMEDIATE conformation.
Claim 30 is directed to the method of claim 16 but further specifies the kinase as ABL1 mutant T315I.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach that the kinase is ABL1 mutant T315I.
Gani et al. teaches in the abstract “we have taken a retrospective approach to evaluate virtual screening methods for the leukemia target kinase ABL1 and its drug-resistant mutant ABL1-T315L”, and on page 507, column 2, paragraph 4 “Five crystal structures of T315I mutants of ABL1 kinase domain in complex with inhibitors were taken for analysis, along with structures for four of these inhibitors that have been co-crystallized also with the ABL1-wt kinase domain. These structures, summarized in Table 2, were used forVS of dual active inhibitors and of inactive ligands. Because four pairs of structures, each with one inhibitor binding both the wt and T315I forms, are included, the test set includes a range of inhibitor-associated flexibilities, DFG conformational states, and allows direct comparisons of the effects of gatekeeper mutations”, reading on wherein the target is kinase ABL1 mutant T315I.
Claims 20-21, 26, and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Bergmann et al. (Journal of Chemical Information and Modeling (2009) 658-669) and Heikamp et al. (Chemical Biology & Drug Design (2017) 655-667) as applied to claims 16-17, and 20 above, and further in view of Richters et al. (Journal of Medicinal Chemistry (2013) 5757-5772).
Claim 20 is directed to the method of claim 17 and thus claim 16, but further specifies the exclusion of regions of high frequency of drug-resistant mutation.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach the exclusion of regions of high frequency of drug-resistant mutation.
Richters et al. teaches on page 5758, column 1, paragraph 2 “One of the most prominent and striking mutations is the replacement of the gatekeeper residue, a position that is known to control access to the ATP-binding site affecting inhibitor selectivity, with a bulkier and often more lipophilic residue, as is the case for T670I of the KIT oncogenic drug-resistant variant in GIST. The primary gain of function mutation V559D in the juxtamembrane region of KIT leads to constitutive activation, while the secondary mutation T670I at the gatekeeper position is accompanied by insensitivity toward imatinib as a first line therapy.20,21 Similarly the oncogenic fusion protein Bcr-Abl in CML results in stabilization of the active kinase conformation leading to a constitutively active protein. Additionally, the amino acid exchange of threonine for isoleucine at the gatekeeper position 315 (T315I) causes a steric repulsion that prohibits inhibitors from binding within the active site and causes resistance to imatinib.22 Moreover, this substitution at position 315 represents the only variant out of more than 50 drug-resistant mutations occurring in the catalytic domain of Bcr-Abl that is presently unfeasible to address in cancer therapy with small molecule inhibitors23 with one exception: the type II inhibitor ponatinib (Figure 1a) recently received accelerated approval by the FDA while still running in phase III clinical trials, but treatment potentially produces severe side effects such as hepatotoxicity and arterial thrombosis.24,25 Therefore, current efforts in kinase research focus on overcoming these mutant variants by developing allosteric inhibitors that exclusively bind outside the ATP binding site and lock the kinase in its inactive form”, reading on wherein creating the three-dimensional fishing net comprises excluding regions of high frequency of drug resistance mutation of the kinase.
It would have been obvious at the time of first filing to have modified the teachings of Bergmann et al. and Heikamp et al. for the method of claim 16, with the teachings of Richters et al. for the exclusion of regions subject to drug resistance mutation as the latter teaches in the abstract “Using protein X-ray crystallography, we confirm the anticipated binding mode in cSrc, which proved to be essential for overcoming the respective resistances. More importantly, the novel compounds effectively inhibit clinically relevant gatekeeper mutants of KIT and Abl in biochemical and cellular studies”. One would have had a reasonable expectation of success given that Richters et al. is merely limiting the regions under investigation and not modifying the method itself, merely the data being used. Therefore, it would have been obvious at the time of first filing to have modified the teachings of each and to be successful.
Claim 21 is directed to the method of claim 20 and thus claim 16, but further specifies the exclusion of HVR regions 1-7.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach the exclusion of HVR regions 1-7.
Richters et al. teaches on page 5758, column 1, paragraph 2 “One of the most prominent and striking mutations is the replacement of the gatekeeper residue, a position that is known to control access to the ATP-binding site affecting inhibitor selectivity, with a bulkier and often more lipophilic residue, as is the case for T670I of the KIT oncogenic drug-resistant variant in GIST. The primary gain of function mutation V559D in the juxtamembrane region of KIT leads to constitutive activation, while the secondary mutation T670I at the gatekeeper position is accompanied by insensitivity toward imatinib as a first line therapy.20,21 Similarly the oncogenic fusion protein Bcr-Abl in CML results in stabilization of the active kinase conformation leading to a constitutively active protein. Additionally, the amino acid exchange of threonine for isoleucine at the gatekeeper position 315 (T315I) causes a steric repulsion that prohibits inhibitors from binding within the active site and causes resistance to imatinib.22 Moreover, this substitution at position 315 represents the only variant out of more than 50 drug-resistant mutations occurring in the catalytic domain of Bcr-Abl that is presently unfeasible to address in cancer therapy with small molecule inhibitors23 with one exception: the type II inhibitor ponatinib (Figure 1a) recently received accelerated approval by the FDA while still running in phase III clinical trials, but treatment potentially produces severe side effects such as hepatotoxicity and arterial thrombosis.24,25 Therefore, current efforts in kinase research focus on overcoming these mutant variants by developing allosteric inhibitors that exclusively bind outside the ATP binding site and lock the kinase in its inactive form”. However, Richters et al. does not explicitly teach the exclusion of the HVR regions, however, when designing a scaffold it would have been obvious to a person skilled in the art to exclude regions that are not conserved but are rather subject to extreme amounts of variation, as the binding of the molecule for inactivation is paramount to the drugs success, and variability would result in inconsistent binding, thereby reading on wherein regions of high frequency of drug resistance mutation of the kinase comprises HVR regions 1-7.
Claim 26 is directed to the method of claim 16 but further specifies that the therapeutic is defined by derivation constituents left open to generate a combinatorial array of analogs.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach the therapeutic agent being defined by two derivation constituents left open to generate a combinatorial array of analogs.
Richters et al. teaches in Figure 1(A) “General scaffold of a 1,4-fused type II hybrid inhibitor, 1, composed of type I and type III fragments, as well as hybrid compound 2, as an initial rationally designed molecule to target cSrc wild-type and T338M”, and in Table 1 “Overview of Rationally Designed Small Molecule Library Consisting of Variably Fused 1,4- and 1,3-Fused Hybrid Derivatives as Well as Fragments and Compounds with Replaced Pyrazolo Part”, reading on wherein the scaffold of the therapeutic agent is defined by two derivation constituents left open to generate a combinatorial array of analogs.
Claim 31 is directed to the method of claim 30 and thus claim 16, but further specifies the scaffold structure.
Bergmann et al. and Heikamp et al. teach the method of claim 16 as previously described.
Bergmann et al. and Heikamp et al. teach the scaffold structure.
Richters et al. teaches in Figure 1(A) “General scaffold of a 1,4-fused type II hybrid inhibitor, 1, composed of type I and type III fragments, as well as hybrid compound 2, as an initial rationally designed molecule to target cSrc wild-type and T338M”, reading on the scaffold structures provided.
Conclusion
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/K.N.A./Examiner, Art Unit 1687
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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