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 .
Applicant’s amendments and arguments, filed 7/20/2026, have been entered and carefully considered, but are not completely persuasive.
Claims 1-20, 24-25, 27, 29, 33, 35, 39-42 are pending in this application. Claims 2-6, 8-9, 11, 17-20, 24-25, 27, 29, 33, 35, 39-40 stand withdrawn from consideration as being drawn to inventions or species non-elected without traverse, 1/20/2026.
Newly submitted claims 41-42 are directed to a species that is independent or distinct from the species originally claimed for the following reasons: Claims 41-42 define differing methods, utilizing differing subsets of atomic coordinates. The elected species was Species e) “A method of identifying a compound that modulates Rel hydrolase/synthetase using a 3D structure represented by the full coordinates of Table 3 (p248, Rel-ppGpp-complex, closed form)”, and the Rel protein comprises both activities.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claims 41-42 have withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Claims 1, 7, 10, 12-16 are under examination.
The substitute specification filed 7/20/2026 has been entered and the objection to the specification is withdrawn.
The objection to claim 7 is withdrawn.
The rejection of the claims under 35 USC 112b, for reciting an improper Markush grouping, is withdrawn.
The rejections under 35 USC 103 have been withdrawn.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
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, 7, 10, 12-16 are 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.
The metes and bounds of claim 1 remain unclear, with respect to the steps required to identify a ligand that modulates one of two activities of the Rel protein. Claim 1 now recites “generating a three-dimensional structure represented by a set of atomic coordinates… through a three-dimensional protein structure rendering software program, and assessing a degree of fit….” however, the term “generating” does not set forth how the coordinates are to be used in any particular process, to identify any ligand or compound. The phrase encompasses any possible way to “generate” a representation of a set of coordinates, without direction or specificity. While breadth is not the same as indefiniteness, one of skill would not be apprised as to how Applicant intends the particular elected coordinate set is to be utilized to achieve the desired goal: the 3D representation, and the candidate ligand fitting. Claims 1, 7, 10 and 12 are not limited to computer-implemented methods, nor do they provide any potential sets of candidate compounds/ ligands which could possibly be “fitted” to the three-dimensional structures in a computer-implemented docking process. The portion or structural region of the protein represented by the structural coordinates to which the ligand is to be fitted is not specified beyond the crystal structure recited in elected Table 3. Within the unspecified docking process, it is unclear at what point a “degree of fit” achieves the goal of identifying a compound that modulates the enzymatic activity, as no thresholds, reference data or ground truth information are provided for any type of comparison, nor is the fitted ligand tested in silico, in vitro or in vivo for any modulating ability. It is unclear if any degree of fit (0% to 100%) to any part of the recited structure results in the identification of a modulator of the enzymatic activities. The plain meaning of the term “modulates” encompasses any change, such as blocking, amplifying or reducing a given activity. The claim fails to provide any steps to determine what modulation is made by the structural docking/fitting as claimed. The term “assessing a degree of fit” does not set forth how the fit is assessed “through a docking score by a docking modeling algorithm”, or how the degree of fit is linked to any modulation of either recited activity. The claim fails to particularly point out and distinctly claim the necessary and sufficient steps and data required to carry out the desired process “identifying compounds that modulate Rel hydrolase and/or Rel synthetase”. Claim 1 does not clearly end with the identification of a modulator of either activity, as a measurement of 0% degree of fit for a candidate ligand would indicate no binding and no modulation.
The metes and bounds of claim 12 are unclear with respect to how the candidate is to be tested for the given activity. The candidate compound is not clearly physically provided or synthesized such that it could be tested in claim 1 or claim 12. While breadth of the claim is not equal to indefiniteness, one of skill would not be apprised as to the particular steps Applicant intended to be carried out to identify the modulation of the synthetase or hydrolase activity.
The metes and bounds of claim 13 are unclear with respect to the computer-implementation of the method of claim 1. Step a) of claim 1 is directed to “generating a three-dimensional structure by reading of said atomic coordinates on using 3D rendering software…” The 3D rendering software is not clearly the same software recited in claim 1 (“through a three-dimensional protein structure rendering software program”). The metes and bounds of “reading of said… coordinates on using 3D rendering software” are unclear, with respect to how “reading” the coordinates results in the generation of a complex 3D protein/ enzyme structure.
Further in claim 13, it is unclear what structures were intended by Applicant to be used to carry out the subsequent steps of “fitting” and “selecting.” The metes and bounds of step b) are unclear with respect to how Applicant intended the fitting to be carried out in a computer modeling process. Neither claim 13 nor claim 1 actually provide any candidate compound of any particular structure which is to be fitted to the elected form of the Rel protein. It is unclear whether a representation of the candidate compound is obtained and fitted in silico to the structure generated in step a) in a conventional docking process, or some other process. It is not the direction of a particular modeling or docking process carried out on a particular 3D structure, with and without a 3D representation of a candidate compound, followed by energetic modeling. Further, it is unclear whether the newly amended step b) is intended to replace the step b) of claim 1, or whether it further comprises pose modeling. Claim 1 step b) is directed to “conformation” modeling of the Rel protein interaction with the candidate, while step b) is now directed to “pose modeling of said candidate compound on said Rel structure.” It is unclear what the difference in scope is between each step b).
The metes and bounds of claim 14 are unclear with respect to how the superimposition between the 3D structure representing the elected Rel protein form, and the candidate compound are to be carried out. No structure of a candidate compound is clearly provided by claims 1, or 13. This claim is written using results-based language but fails to particularly set forth how the result is to be obtained. The recitation of superimposition doesn’t specify how it is to be carried out in a way that satisfies all the requirements of claims 13 and 1, including assessing the degree of fit.
The metes and bounds of claim 15 are unclear with respect to how, in particular, the “docking modeling” is to be carried out in the method of claim 13. No structure of a candidate compound is clearly provided by claims 1, or 13. This claim is written using results-based language but fails to particularly set forth how the result is to be obtained. The recitation of superimposition doesn’t specify how it is to be carried out in a way that satisfies all the requirements of claims 13 and 1, including assessing the degree of fit.
The metes and bounds of claim 16 are unclear with respect to how the “binding” of any structural representation of a candidate compound to an amino acid residue of the structural representation of the elected Rel protein is identified. This claim is written using results-based language but fails to particularly set forth how the result is to be obtained. Claim 13 does not identify any particular binding between the representation of the candidate and a specific amino acid of the representation of elected Rel protein. Claim 13 does not clearly determine “pose geometry” as now recited in claim 16. The claim does not clearly set forth how “pose geometry” allows for the identification of binding to at least one amino acid without steric interference.
While claims are read in light of the specification, limitations from the specification cannot be read into the claims. MPEP 2111, 2173.02. See also In re Prater, Superguide Corp. v DirecTV Enterprises, Inc.
Applicant’s arguments:
Applicant’s arguments have been carefully considered but are not completely persuasive, as indefiniteness remains or was introduced by amendment.
MPEP 2173: “The essential inquiry pertaining to this requirement is whether the claims set out and circumscribe a particular subject matter with a reasonable degree of clarity and particularity. "As the statutory language of ‘particular[ity]' and 'distinct[ness]' indicates, claims are required to be cast in clear—as opposed to ambiguous, vague, indefinite—terms. It is the claims that notify the public of what is within the protections of the patent, and what is not." Packard, 751 F.3d at 1313, 110 USPQ2d at 1788.”
Conclusion
No claim is allowed.
With respect to rejoinder of other species of the method of claim 1, MPEP 821.04 notes: “In order to be eligible for rejoinder, a claim to a nonelected invention must depend from or otherwise require all the limitations of an allowable claim. A withdrawn claim that does not require all the limitations of an allowable claim will not be rejoined… 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.”
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY K ZEMAN whose telephone number is 5712720723. The examiner can normally be reached on 8am-2pm M-F. Email may be sent to mary.zeman@uspto.gov if the appropriate permissions have been filed.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry Riggs can be reached on 571 270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY K ZEMAN/ Primary Examiner, Art Unit 1686
