DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Upon further consideration the restriction dated 8/22/2025 is withdrawn. Pursuant to the procedures set forth in MPEP § 821.04(B), claims 1-14 and 20, previously withdrawn from consideration (in Applicant’s response received 10/29/2025) as a result of a restriction requirement, are hereby rejoined and fully examined for patentability under 37 CFR 1.104, as presented in the claims dated 3/10/2022.
Because all claims previously withdrawn from consideration under 37 CFR 1.142 have been rejoined, the restriction requirement as set forth in the Office action mailed on 8/22/2025 is hereby withdrawn. In view of the withdrawal of the restriction requirement as to the rejoined inventions, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Status of Claims
Claims 1-14 and 20 are pending and examined on the merits.
Priority
The instant application filed on 3/10/2022 claims the benefit of priority to U.S. Provisional Patent Application No. 63/159,888 filed on 3/11/2021. Thus, the effective filing date of the claims is 3/11/2021.
The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The Third-Party Submission Under 37 CFR 1.290 filed on 5/2/2023 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-5, 7, and 20 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1 and 20 recite "a minimal synthon cap" (claim 1) and "a synthon cap" (claim 20), which is not a term of art and it is unclear what the term encompasses. Looking to the instant specification, a minimal synthon cap is only referred to as a methyl or phenyl group, and in the context of being needed to "cap" or terminate reactive groups of the scaffold that are often highly polar or charged and may distort docking results (para.0036). To further prosecution, "a minimap synthon cap" is interpreted as being a methyl or phenyl group.
Claim 3 recites "the first R position is only R1 or only R2 for two-component compounds". It is not clear what the limitation is meant to achieve, as the terms "R1" or "R2" are understood to be generic placeholders in chemistry/organic chemistry, and could take on the "value" of many different chemical or functional groups or side chains. In any case, the claim seems to be trying to limit the combination of groups, however, a "first R position" can only take on a single type of group at one time, rendering this interpretation moot. The specification nor the drawings illuminate the meaning of this limitation, therefore, to further prosecution, the claim is interpreted as not further limiting claim 1.
Claim 4 recites "the large libraries of compounds include Enamine REadily AvailabLe for synthesis (REAL) compound libraries, REAL Space compound libraries, or any other libraries that can be defined as a limited set of Markush scaffolds with two or more R-groups (synthons)". Claims must be complete in themselves and cannot rely on external documents to define their boundaries, therefore the metes and bounds of the claim are not clear because they at least partially rely on named databases or libraries. Additionally, the claim is indefinite because named databases or libraries such as those listed have no requirement to remain static, and therefore their contents have the potential to change over time. To further prosecution, the limitation is interpreted as "the large libraries of compounds include any libraries that can be defined as a limited set of Markush scaffolds with two or more R-groups (synthons)".
Claim 5 recites "the second R position is capped with a minimal synthon cap because the reaction scaffolds are often highly polar or charged", which contains a statement of purpose. Statements of intended use or purpose do not limit a claim, and do not define structure or steps. To further prosecution, the claim is interpreted as simply "the second R position is capped with a minimal synthon cap".
Claim 7 recites "the filtering or screening includes" in line 1 of the claim. There is insufficient antecedent basis for “the filtering or screening”. To further prosecution, the limitation is interpreted as depending from claim 6 where "filtering or screening" are first introduced.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-14 and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1 and 20: “docking the proxy compounds to the target receptor structure by docking of a flexible ligand to predict binding scores and ligand-receptor interaction information and to select a first set of best-scoring proxy compounds” (claim 1) and “docking the proxy compounds to at least one of a cannabinoid CB1 receptor and a cannabinoid CB2 receptor by docking of a flexible ligand to select a first set of best-scoring proxy compounds” (claim 20); and “performing docking for the fully enumerated compounds in at least two R positions to select a first set of best docking compounds” (claim 1) and “performing docking of the fully enumerated compounds in at least two R positions to select compounds that dock to at least one of a cannabinoid CB1 receptor and a cannabinoid CB2 receptor” (claim 20) provides an evaluation and organizing information (predicting binding scores, organizing interaction information, and selecting best-scoring compounds) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 6: “filtering or screening the first best set of proxy compounds for diversity” provides an evaluation (filtering requires an evaluation or comparison) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 8: “selecting of compounds with higher chances for successful enumeration, as defined by distances to specific atoms of a pocket” provides an evaluation (selecting requires an evaluation or comparison [of distances in this case]) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 12: “filtering for physical-chemical properties, drug-likeness, novelty, and chemical diversity to select a final set of best docking compounds” provides an evaluation (filtering and selecting requires an evaluation or comparison) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas.
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claims 1 and 20: “generating a list of proxy compounds comprising reaction scaffolds” provides insignificant extra-solution activities (generating a list is a pre-solution activity involving data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
“iteratively enumerating the first set of best-scoring proxy compounds so that at least one capped R position is replaced with a full range of corresponding synthons to produce fully enumerated compounds” provides insignificant extra-solution activities (iterative enumeration is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 12: “synthesis and testing that is a subset of the first set of best docking compounds” provides insignificant extra-solution activities (synthesis and testing of a subset of compounds is a post-solution activity involving sample manipulation and data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
The steps for generating lists, iterative enumeration, and synthesis and testing of compounds are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre- and post-solution activities involving data gathering, and data and sample manipulation steps (see MPEP 2106.04(d)(2)).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The limitations for generating lists, iterative enumeration, and synthesis and testing of compounds are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-14 and 20 are not patent eligible.
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.
Claims 1-3, 5-12, and 14 rejected under 35 U.S.C. 103 as being unpatentable over Lobanov et al. (US-7416524) in view of Zhou et al. (Zhou et al. "Pharmacophore-based 3D-QSAR modeling, virtual screening and molecular docking analysis for the detection of MERTK inhibitors with novel scaffold." Combinatorial chemistry & high throughput screening 19.1 (2016): 73-96).
Regarding claims 1 and 3, Lobanov teaches a method for efficiently screening of large libraries of compounds to identify the best compounds that dock to receptor (Abstract "A system, method, and computer program product for fast and efficient searching of large virtual combinatorial libraries based on a fitness function").
Lobanov also teaches generating a list of proxy compounds comprising reaction scaffolds and enumerated with corresponding synthons only in a first R position while a second R position is capped with a minimal synthon cap to become a capped R position (Page 33 col 1 line 49 "Generally, a universally applicable program has been developed for generating virtual libraries. As input, this program takes lists of reagents supplied in Structure-Data File (SDF) format, [], or Simplified Molecular Input Line Entry Specification (SMILES) format").
Lobanov also teaches docking the proxy compounds to the target receptor structure by docking of a flexible ligand to predict binding scores and ligand-receptor interaction information and to select a first set of best-scoring proxy compounds (Page 33 col 2 line 46 "Besides similarity and diversity (i.e., dissimilarity), other selection criteria can also be employed. Examples include selecting compounds having desired properties or property distributions as determined by a property prediction algorithm or a quantitative structure-activity model, or exhibiting an optimal fit to a biological receptor as determined by a biomolecular docking algorithm. Compound can also be selected based on 2D and 3D QSAR predictions, and receptor complementarity", and page 36 col 2 line 48 "the desired number (e.g., K) of the highest-ranking (most similar) compounds are selected from the enumerated "focused" library (i.e., second set of enumerated compounds) based on their similarity scores or dissimilarity scores. Alternatively, the highest-ranking K compounds can be selected without prior sorting. For example, any compound having a dissimilarity value lower than a threshold value can be selected").
Lobanov also teaches iteratively enumerating the first set of best-scoring proxy compounds so that at least one capped R position is replaced with a full range of corresponding synthons to produce fully enumerated compounds (Page 41 col 1 line 1 "The list of "preferred" reagents was then used to produce the "focused" library (Step 112) and all reagent combinations associated with that "focused" library were enumerated").
Lobanov does not explicitly teach performing docking for the fully enumerated compounds in at least two R positions to select a first set of best docking compounds.
However, Zhou teaches performing a docking procedure for high-throughput virtual screening using at least two key elements contributing to ligand activity (Page 1 Abstract "For the pharmacophore model, two hydrogen bond donors (D), one hydrogen bond receptor (A), and two hydrophobic groups (H) were considered as the key elements contributing to ligand activity. [] Subsequently, docking procedure was applied on these hits, and 840 compounds were obtained through high-throughput virtual screening (HTVS)").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Lobanov as taught by Zhou in order to efficiently and effectively search large virtual combinatorial libraries (page 1 col 2 last paragraph "To screen from the drug-like database and discover MERTK inhibitors with new scaffold, the pharmacophore model was used in searching hits matched with all the pharmacophoric features"). One skilled in the art would have a reasonable expectation of success because both approaches are concerned with virtually screening compounds utilizing 3D QSAR modeling.
Regarding claims 2 and 5, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Lobanov also teaches the minimal synthon cap is methyl or phenyl (Figure 3 shows a portion of a large virtual combination library that includes compounds containing methyl and/or phenyl groups, which could be a first or second R position).
Regarding claim 6, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Lobanov also teaches filtering or screening the first best set of proxy compounds for diversity (Page 30 col 2 line 59 "Examples of fitness functions that can be used with the present invention include, but are not limited to, similarity to one or more query structures, diversity, and presence of desired properties").
Regarding claim 7, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. While the referenced prior art does not explicitly state a 20% threshold for reaction diversity specifically, the claimed feature is simply the result of optimizing a known parameter (diversity), which is routinely cited by Lobanov as a specific desired result-effective variable of the screening process. Therefore, it would have been obvious to optimize the percent of selected resulting compounds to achieve the desired performance.
Regarding claim 8, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Zhou also teaches docking the compounds to the target receptor structure further includes selecting of compounds with higher chances for successful enumeration, as defined by distances to specific atoms of a pocket (Page 2 col 1 first paragraph "The scaling of van der waals radii and other parameters was set as default values", page 2 col 2 paragraph 2 "The prepared ligands were then subjected to generating conformer in the Macromodel module of Schrödinger using a Macromodel torsion angle search approach. OPLS_2005 was employed as force field for minimization of returned conformers with solvent using None, “Electrostatic Treatment” using Distance-dependent", and page 21 col 1 paragraph 1 " The returned hits were required to satisfy all the five pharmacophore features within the intersite distance matching tolerance").
Regarding claims 9-11, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Lobanov also teaches: the iteratively enumerating comprises a single iteration for two-component reactions with only two R groups (claim 9); the iteratively enumerating comprises a plurality of iterations for three-component reactions with three R groups (claim 10); and the iteratively enumerating comprises repeatedly enumerating a plurality of iterations when the compounds are 4- and 5- component compounds until the compounds are fully enumerated with library synthons (claim 11) (The section titled "Virtual Combinatorial Libraries" on page 32 col 1 line 61 outlines the distinction between enumerated and non-enumerated virtual combinatorial libraries, the former of which they give an example out to a three-dimensional combinatorial matrix of reagents which could easily be expanded to any number of reagent dimensions desired).
Regarding claim 12, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Lobanov also teaches the performing the docking for the fully enumerated compounds further includes filtering for physical-chemical properties, drug-likeness, novelty, and chemical diversity to select a final set of best docking compounds for synthesis and testing that is a subset of the first set of best docking compounds (Page 30 col 2 line 59 "Examples of fitness functions that can be used with the present invention include, but are not limited to, similarity to one or more query structures, diversity, and presence of desired properties" and page 33 col 2 line 4 "The role of virtual combinatorial libraries in drug discovery is to provide computational access to compounds that can be readily synthesized and tested for biological activity. The role of the computational tools is to identify which compounds from the library need to be tested to achieve the desired objective").
Regarding claim 14, Lobanov in view of Zhou teach the methods of Claims 1 on which this claim depends/these claims depend, respectively. Zhou also teaches the receptors have receptor structures represented by 3D coordinates of the receptor atoms (The software used here, Schrödinger, represents molecular structures using 3D coordinates).
Claim 4 rejected under 35 U.S.C. 103 as being unpatentable over Lobanov et al. (US-7416524) in view of Zhou et al. (Zhou et al. "Pharmacophore-based 3D-QSAR modeling, virtual screening and molecular docking analysis for the detection of MERTK inhibitors with novel scaffold." Combinatorial chemistry & high throughput screening 19.1 (2016): 73-96) as applied to claims 1-3, 5-12, and 14 above, and further in view of Barnard et al. (Barnard et al. "Use of Markush structure analysis techniques for descriptor generation and clustering of large combinatorial libraries." Journal of Molecular Graphics and Modelling 18.4-5 (2000): 452-463).
Lobanov et al. in view of Zhou et al. are applied to claims 1-3, 5-12, and 14.
Regarding claim 4, Lobanov in view of Zhou teach the method of Claim 1 on which this claim depends/these claims depend.
Lobanov nor Zhou explicitly teach the large libraries of compounds include any libraries that can be defined as a limited set of Markush scaffolds with two or more R-groups.
However, Barnard teaches a combinatorial library encompassing Markush representations having a Markush core and may involve several disconnected segments linked in various ways by multiply connected R-groups (Page 3 col 1 paragraph 1 "Although combinatorial libraries may not add any fundamentally novel means of expression to the Markush structure types found in patents, Markush representations for libraries may introduce complexities not normally encountered in patents. This can apply particularly where the library involves diversity in the scaffold, such as can be obtained using multicomponent syntheses. In these cases, the Markush core may be quite small and may involve several disconnected segments linked in various ways by multiply connected R-groups (possibly directly connected to each other)").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Lobanov and Zhou as taught by Barnard in order to reduce storage size of the virtual combinatorial library by only storing reduced representations of desired compounds (Lobanov, page 30 col 1 line 51 "Additionally, the storage requirements for a fully enumerated virtual combinatorial library can be prohibitive. Since in these cases neither the generation nor the storage of fully enumerated libraries and their associated descriptors is feasible, there is a need for systems and methods that can identify the desired compounds without enumerating the entire library" and Barnard, page 1 Abstract "This article outlines a system in which a Markush structure representation is used for analysis of a combinatorial library, giving savings in terms of storage and processing requirements when compared with an enumerated library"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with reducing storage and processing requirements for analysis of enumerated libraries.
Claims 13 and 20 rejected under 35 U.S.C. 103 as being unpatentable over Lobanov et al. (US-7416524) in view of Zhou et al. (Zhou et al. "Pharmacophore-based 3D-QSAR modeling, virtual screening and molecular docking analysis for the detection of MERTK inhibitors with novel scaffold." Combinatorial chemistry & high throughput screening 19.1 (2016): 73-96) as applied to claims 1-3, 5-12, and 14 above, and further in view of Sapundzhi (Sapundzhi, "Scoring functions and modeling of structure-activity relationships for cannabinoid receptors." (2019): 139-145).
Lobanov et al. in view of Zhou et al. are applied to claims 1-3, 5-12, and 14.
Regarding claims 13 and 20, Lobanov in view of Zhou teach the method of Claim 1 on which claim 13 depends, and which claim 20 shares significant limitations.
Lobanov nor Zhou explicitly teach the receptors are a cannabinoid CB1 receptor and a cannabinoid CB2 receptor.
However, Sapundzhi teaches designing a ligand-receptor model for CB1 and CB2 receptors (Abstract "Computer-aided drug design could help much in the field of bioinformatics and biomedical engineering if there is a good model of CB1 and CB2 receptors and a suitable algorithm for the obtained ligand-receptor complex. The purpose of this article is to find the most appropriate scoring function and model for docking between cannabinoid ligands and cannabinoid receptors that correlate well with the data from biological activity of the compounds").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Lobanov and Zhou as taught by Sapundzhi in order to find the most appropriate scoring function and model for docking of ligands with specific receptors (Sapundzhi, page 1 abstract "The purpose of this article is to find the most appropriate scoring function and model for docking between cannabinoid ligands and cannabinoid receptors that correlate well with the data from biological activity of the compounds" and Lobanov, Page 33 col 2 line 46 "Besides similarity and diversity (i.e., dissimilarity), other selection criteria can also be employed. Examples include selecting compounds having desired properties or property distributions as determined by a property prediction algorithm or a quantitative structure-activity model, or exhibiting an optimal fit to a biological receptor as determined by a biomolecular docking algorithm"). One skilled in the art would have a reasonable expectation of success because both methods use a scoring function for docking between molecules and receptors.
Conclusion
No claims are allowed.
Inquiries
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/R.A.P./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686