Prosecution Insights
Last updated: October 23, 2026
Application No. 18/321,684

ACTIVITY-BASED PROBE COMPOUNDS, COMPOSITIONS, AND METHODS OF USE

Non-Final OA §112§DP
Filed
May 22, 2023
Priority
Mar 15, 2013 — provisional 61/794,296 +4 more
Examiner
PERREIRA, MELISSA JEAN
Art Unit
1618
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
The Board of Trustees of the Leland Stanford Junior University
OA Round
1 (Non-Final)
52%
Grant Probability
Moderate
1-2
OA Rounds
4m
Est. Remaining
78%
With Interview

Examiner Intelligence

Grants 52% of resolved cases
52%
Career Allowance Rate
436 granted / 837 resolved
-7.9% vs TC avg
Strong +26% interview lift
Without
With
+25.7%
Interview Lift
resolved cases with interview
Typical timeline
3y 9m
Avg Prosecution
38 currently pending
Career history
881
Total Applications
across all art units

Statute-Specific Performance

§101
2.1%
-37.9% vs TC avg
§103
56.1%
+16.1% vs TC avg
§102
12.7%
-27.3% vs TC avg
§112
16.6%
-23.4% vs TC avg
Black line = Tech Center average estimate • Based on career data from 837 resolved cases

Office Action

§112 §DP
DETAILED ACTION Notice of Pre-AIA or AIA Status The present application is being examined under the pre-AIA first to invent provisions. Claims Status Claims 38-55 are pending in the application. 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 49 and 54 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 instant claims 49 and 54 recite D-T wherein D-T is PNG media_image1.png 106 180 media_image1.png Greyscale and therefore comprises two different D moieties which is confusing and unclear. Claim 38 is 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 instant claim is confusing and unclear as the compounds of formula (I) comprise a structure containing so many possible variations including the combination of undefined and infinite targeting elements, quenchers and fluorescent labels. The L3 alkyl linker that may be optionally replaced with a heteroatom has an undefined length and may or may not be present. Therefore, the compounds may have different sizes, reactivities and functions. The compounds of the instant claims comprise numerous different structures so that the scope of the claims cannot be determined. While breadth alone is not indefinite, the instant claims have an almost unlimited number of possible combinations of chemical moieties that it is not possible to determine the metes and bounds of the claims. The dependent claims fall therewith. Claim 38 is rejected on the judicially-created basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature. A Markush claim contains an “improper Markush grouping” if: (1) the species of the Markush group do not share a single structural similarity,” or (2) the species do not share a common use. Members of a Markush group share a "single structural similarity” when they belong to the same recognized physical or chemical class or to the same recognized physical or chemical class or to the same art-recognized class. Members of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent (see Federal Register, Vol. 76, No. 27, Wednesday, February 9, 2011, p. 7166, left and middle columns, bridging paragraph). The claims are directed to the compounds of formula (I) comprising a Markush structure containing so many possible variations, such as the combination of undefined and infinite targeting elements, quenchers and fluorescent label. The L3 alkyl linker that may be optionally replaced with a heteroatom has an undefined length and may or may not be present. Therefore, the compounds may have different sizes, reactivities and functions. The compounds of the instant claims comprise numerous different structures so that the scope of the claim cannot be determined, instant claims have an almost unlimited number of possible combinations of chemical moieties and there is nothing of record to show a common chemical core that is specifically tied to a function in the almost unlimited breadth of the claimed compounds. Applicant attention is directed to the third paragraph of MPEP 803.02 which discloses: “Since the decisions in In re Weber, 580 F.2d 455, 198 USPQ 328 (CCPA 1978) and In re Haas, 580 F.2d 461, 198 USPQ 334 (CCPA 1978), it is improper for the Office to refuse to examine that which Applicants regard as their invention, unless the subject matter in a claim lacks unity of invention. In re Harnisch, 631 F.2d 716, 206 USPQ 300 (CCPA 1980); and Ex parte Hozumi, 3 USPQ2d 1059 (Bd. Pat. App. & Int. 1984). Broadly, unity of invention exists where compounds included within a Markush group (1) share a common utility, and (2) share a substantial structural feature essential to that utility.” In the instant case, if it is asserted that the claims share a common utility, it is noted the only shared structure is the substituted phenoxy moiety that does not allow the genus to have an art recognized classification. Hence, the Markush grouping is improper. In response to this rejection, Applicant should either amend the claim(s) to recite only individual species or grouping of species that share a substantial structural feature as well as a common use that flows from the substantial structural feature, or present a sufficient showing that the species recited in the alternative of the claims(s) in fact share a substantial structural feature as well as a common use that flows from the substantial structural feature. This is a rejection on the merits and may be appealed to the Board of Patent Appeals and Interferences in accordance with 35 U.S.C. §134 and 37 CFR 41.31(a)(1) (emphasis provided). The dependent claims fall therewith. 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. Claims 38-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 11,655,236B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. 11,655,236B2 comprise PNG media_image2.png 58 78 media_image2.png Greyscale wherein D-T is PNG media_image3.png 82 148 media_image3.png Greyscale , D is a fluorescent cyanine label; L1 is an optional linker; AA1 is an amino acid side chain; U is O; L is PNG media_image4.png 92 164 media_image4.png Greyscale and R is QC-1 quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising AA1 is an amino acid side chain; D is a fluorescent label; U is O, L1 is a linker; L3 is a linker and Q is a quencher, such as QC-1. The compounds of the instant claims and U.S. Patent No. 11,655,236B2 are used in the method of imagine cells having cysteine protease activity and the method of labeling a cysteine cathepsin protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of U.S. Patent No. 11,655,236B2 and of the instant claims have an analogous structure and are used in analogous methods for imaging cysteine protease via fluorescence. Claims 38-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of U.S. Patent No. 10,829,477B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. 10,829,477B2 comprise PNG media_image2.png 58 78 media_image2.png Greyscale wherein D-T is PNG media_image3.png 82 148 media_image3.png Greyscale , D is a fluorescent label; L1 is a linker; AA1 is an amino acid side chain; U is O,N or S; L is PNG media_image4.png 92 164 media_image4.png Greyscale and R is QSY or QC-1 quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising AA1 is an amino acid side chain; D is a fluorescent label; L1 is a linker; L3 is a linker and Q is a quencher, such as QSY or QC-1. The compounds of the instant claims and U.S. Patent No. 10,829,477B2 are used in the method of imagine cells having cysteine protease activity and the method of labeling a protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of U.S. Patent No. 10,829,477B2 and of the instant claims have an analogous structure and are used in analogous methods for imaging protease via fluorescence. Claims 38-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-22 of U.S. Patent No. 10,100,037B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. 10,100,037B2 comprise formula (II) PNG media_image6.png 112 258 media_image6.png Greyscale wherein L1 is a linker; L3 is a linker; D is a fluorescent label; AA1 is an amino acid side chain; U is O,N or S; Q is QSY quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising L1 is a linker; L3 is a linker; D is a fluorescent label; AA1 is an amino acid side chain; D is a fluorescent label; and Q is a quencher, such as QSY. The compounds of the instant claims and U.S. Patent No. 10,100,037B2 are used in the method of imagine cells having cysteine protease activity and the method of labeling a protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of U.S. Patent No. 10,100,037B2 and of the instant claims have an analogous structure and are used in analogous methods for imaging a protease via fluorescence. Claims 38-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 10,869,936B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. 10,869,936B2 comprise formula (II) PNG media_image6.png 112 258 media_image6.png Greyscale wherein L1 is a linker; L3 is a linker; D is a benzoindole dye; AA1 is an amino acid side chain; U is O,NH or S; Q is QSY or QC-1 quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising L1 is a linker; L3 is a linker; D is Cy5; AA1 is an amino acid side chain; D is a cyanine dye; and Q is a quencher, such as QSY or QC-1. The compounds of the instant claims and U.S. Patent No. 10,869,936B2 are used in the method of imagine cells having cysteine protease activity and the method of labeling a protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of U.S. Patent No. 10,869,936B2 and of the instant claims have an analogous structure and are used in analogous methods for imaging a protease via fluorescence. Claims 38-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,059,482B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. 12,059,482B2 comprise formula (II) PNG media_image6.png 112 258 media_image6.png Greyscale wherein L1 is a linker; L3 is a linker; D is a benzoindole dye; AA1 is an amino acid side chain; U is O,NH or S; Q is QSY or QC-1 quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising L1 is a linker; L3 is a linker; D is Cy5; AA1 is an amino acid side chain; D is a cyanine dye; and Q is a quencher, such as QSY or QC-1. The compounds of the instant claims and U.S. Patent No. 12,059,482B2 are used in the method of imagine cells having cysteine protease activity and the method of labeling a protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of U.S. Patent No. 12,059,482B2 and of the instant claims have an analogous structure and are used in analogous methods for imaging a protease via fluorescence. Claims 38-55 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 18/748,881 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the compounds of U.S. Patent No. copending Application No. 18/748,881 comprise formula (II) PNG media_image7.png 120 326 media_image7.png Greyscale wherein L1 is a linker; L3 is a linker; D is a benzoindole dye substituted with a sulfonate or a carbonate; AA1 is an amino acid side chain; U is O,NH or S; Q is QSY or QC-1 quencher that encompasses the compounds of the instant claims, such as formula (II) PNG media_image5.png 126 316 media_image5.png Greyscale comprising L1 is a linker; L3 is a linker; D is Cy5; AA1 is an amino acid side chain; D is a cyanine dye; and Q is a quencher, such as QSY or QC-1. The compounds of the instant claims and copending Application No. 18/748,881 are used in the method of imagine cells having cysteine protease activity and the method of labeling a cathepsin cysteine protease/the method of visualizing a tumor in an animal to measure a detectable signal, such as fluorescence, respectively. Therefore, the compounds of copending Application No. 18/748,881 and of the instant claims have an analogous structure and are used in analogous methods for imaging a protease via fluorescence. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Conclusion No claims are allowed at this time. Any inquiry concerning this communication or earlier communications from the examiner should be directed to MELISSA JEAN PERREIRA whose telephone number is (571)272-1354. The examiner can normally be reached M9-3, T9-3, W9-3, Th9-2, F9-2. 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, Michael Hartley can be reached at 571-272-0616. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /MELISSA J PERREIRA/Examiner, Art Unit 1618
Read full office action

Prosecution Timeline

May 22, 2023
Application Filed
Sep 29, 2026
Non-Final Rejection mailed — §112, §DP (current)

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Study what changed to get past this examiner. Based on 5 most recent grants.

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Prosecution Projections

1-2
Expected OA Rounds
52%
Grant Probability
78%
With Interview (+25.7%)
3y 9m (~4m remaining)
Median Time to Grant
Low
PTA Risk
Based on 837 resolved cases by this examiner. Grant probability derived from career allowance rate.

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