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 .
In response to the restriction requirement, Applicant elected claims 2 and 4-6 for further examination. As a result, claims 3 and 7-12 are withdrawn from further prosecution.
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.
Claim 2 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are:
The claim recites the step of “calculating, using the computer system, a difference in binding free energy between the partitioned lead compound and each potential lead compound” without further defining what such difference in binding free energy is for or how such difference in binding free energy is used in predicting whether each potential lead compound will bind to the biomolecular target. The claim language is unclear on the connection between the step of calculating the difference in binding free energy and the step of predicting whether each potential lead compound will bind to the biomolecular target.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 2 and 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 and 6-8 of U.S. Patent No. 11,710,543.
Although the claims at issue are not identical, they are not patentably distinct from each other because the patented claims simply teach all claim limitations of the claim in the current application.
Regarding to claim 2: a method of screening potential lead compounds for suitability as a candidate for a pharmaceutical application, the method comprising the steps of:
inputting information about an initial lead compound into a computer system, the initial lead compound being known to bind to a biomolecular target involved in a metabolic or signaling pathway associated with a disease condition or pathology or to an infectivity or survival of a microbial pathogen (claim 1, lines 4-8);
providing a first database of known chemical reactions for access by the computer system (claim 1, lines 9-10);
providing a second database of known compound cores for access by the computer system (claim 1, lines 4-8);
partitioning, using the computer system, the initial lead compound into atoms defining a partitioned lead compound comprising a lead compound core and atoms defining a lead compound non-core, wherein the initial lead compound is partitioned using a computational retrosynthetic analysis of the initial lead compound based on information from the first database (claim 1, lines 10-15);
generating, using the computer system, a plurality of potential lead compounds each having a respective one of a plurality of alternative cores from the second database to replace the lead compound core in the initial lead compound (claim 1, lines 16-20);
calculating, using the computer system, a difference in binding free energy between the partitioned lead compound and each potential lead compound (claim 1, lines 21-23); and
predicting, using the computer system, whether each potential lead compound will bind to the biomolecular target; and reporting, by the computer system, a predicted active set of potential lead compounds based on the prediction (claim 1, lines 24-27).
Regarding to claim 4: wherein the difference in binding free energy is calculated using a free energy calculation technique (claim 6).
Regarding to claim 5: wherein the generation of at least one potential lead compound comprises creating an additional covalent bond or annihilating an existing covalent bond, or both creating an additional first covalent bond and annihilating an existing second covalent bond different from the first covalent bond (claim 7).
Regarding to claim 6: wherein the binding free energy difference calculation uses using a soft bond potential to calculate a bonded stretch interaction energy of existing covalent bonds for annihilation and additional covalent bonds for creation (claim 8).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 2 and 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tseng et al. (US 2013/0226549) in view of Shenkin et al. (US 2009/0287465).
Tseng et al. discloses a method of screening potential lead compounds for suitability as a candidate for a pharmaceutical application, the method comprising the steps of:
inputting information about an initial lead compound into a computer system (paragraph [0055]: docking a lead compound into a target molecule to obtain the information of the lead compound and its binding site);
providing a first database of known chemical reactions for access by the computer system (paragraph [0007]: The reaction database);
providing a second database of known compound fragments for access by the computer system (paragraph [0031]: Fragment database. Paragraph [0073]: The library of potential substitution fragments);
partitioning, using the computer system, the initial lead compound into fragments (paragraph [0056]: Decomposing the docked lead compound to form fragments), wherein the initial lead compound is partitioned using a computational retrosynthetic analysis of the initial lead compound based on information from the first database (paragraph [0007]: Retrosynthetic transformations automatically is generated from the reaction database);
generating, using the computer system, a plurality of potential lead compounds each having a respective one of a plurality of alternative fragments from the second database (paragraph [0048]: Potential compounds with various combinations of fragments are generated with stronger potency);
calculating, using the computer system, a difference in binding free energy between the partitioned lead compound and each potential lead compound; and predicting, using the computer system, whether each potential lead compound will bind to the biomolecular target; and reporting, by the computer system, a predicted active set of potential lead compounds based on the prediction (paragraph [0031]: The newly proposed compounds are ranked on the basis of a calculated binding fee energy).
Tseng et al. however is silent wherein the partitioning partitions the initial lead compound into atoms defining a partitioned lead compound comprising a lead compound core and atoms defining a lead compound non-core, wherein the plurality of alternative fragments from the second database is for replacing the lead compound core in the initial lead compound wherein the reference compound, and wherein the initial lead compound being known to bind to a biomolecular target involved in a metabolic or signaling pathway associated with a disease condition or pathology or to an infectivity or survival of a microbial pathogen.
Shenkin et al. discloses a method of deriving an optimized compound from a reference compound by replacing its core with a new core (Abstract), wherein the reference compound
being known to bind to a biomolecular target involved in a metabolic or signaling pathway associated with a disease condition or pathology or to an infectivity or survival of a microbial pathogen (paragraphs [0083]-[0084]: Reference compound and biological target) and being partitioned into atoms defining a partitioned lead compound comprising a lead compound core and atoms defining a lead compound non-core (paragraphs [0010], [0088], [0089]: The reference compound comprises its core and the side chains (non-core) defined as the peripheral molecular fragments).
Therefore, it would have been obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to modify Tseng’s method to partition the initial lead compound into a core and a non-core and replace its core with a new core in order to generate an optimized compound as taught by Shenkin et al. (Abstract).
CONTACT INFORMATION
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LAM S NGUYEN whose telephone number is (571)272-2151.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, DOUGLAS RODRIGUEZ, can be reached on 571-431-0716. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/LAM S NGUYEN/ Primary Examiner, Art Unit 2853