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
Applicant’s election of Group (I) with the addition of Compound 955
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as the elected compound species in the reply filed on 07/20/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 5-8, 11-12, 16, 18-19, and 28-29 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention and species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 07/20/2026.
Priority
The present application claims priority to U.S. Provisional Patent Application No.
63/291319, filed December 17, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 01/14/2025 and 07/20/2026 has been considered by the examiner.
Status of claims
Claims 1-11, 13-19, and 28-29 are pending. Claims 12, 20-27, and 30-50 are canceled. Claims 5-8, 11-12, 16, 18-19, and 28-29 are withdrawn. Claims 1-4, 9-10, 13-15 and 17 are examined in accordance to the elected species.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-4, 9-10, 13, and 17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 is directed to a compound of Formula (I), or a pharmaceutically acceptable salt thereof, wherein A is a kinase inhibitor and L1 is selected from an exceptionally broad collection of substituted C1-C20 alkylene, optionally substituted C1-C20 heteroalkylene, optionally substituted C1-C20 alkenylene, optionally substituted C1-C20 heteroalkenylene, optionally substituted C1-C20 alkynylene, optionally substituted C1-C20 heteroalkynylene, optionally substituted C3-C14 carbocyclylene, or optionally substituted 3- to 14-membered heterocyclylene groups.
Thus, claim 1 does not merely encompass the particular kinase-biding moiety and linker of elected compound 955. Rather, the claim encompasses a combinatorial genus in which both the kinase-biding component A and the intervening L1 may vary extensively.
The specification provides generic statements corresponding to these alternatives and states, inter alia, that L1 may comprise the various alkylene, heteroalkylene, unsaturated, carbocyclic and heterocyclic genera recited in the claim. The specification further defines “optionally substituted” broadly, contemplating substitution at one or more substitutable positions with permissible substituents and stating that the invention is not limited to the exemplary substituents. The disclosure of the presently provided examples, however, is concentrated in substantially narrower structural regions. For example, the specification specifically depicts linker species containing particular amide/PEG, alkyl/amide, ester/ether, and piperazine-containing architecture and provides specific compounds constructed therefrom. The experimental Scheme 1 likewise prepares a defined series of compounds by varying a relatively limited collection of linker precursors.
The disclosure has not been shown to provide representative species reflecting the substantial structural diversity encompassed by, for example, optionally substituted C1-C20 alkenylene, heteroalkynylene, alkynylene. Heteroalkylnylene, C3-C14 carbocyclylene and 3-to-14-membered heterocyclylene linkers, across the additionally variable genus wherein A may be a kinase inhibitor. Nor does the specification identify a common structural characteristic, beyond membership within Formula (I) and the desired functional designation of A as a kinase inhibitor, from which one of ordinary skill would recognize possession of the full scope of A x L1 genus.
Mere disclosure of a broad list of possible substituents or components does not, without more, establish possession of every combination obtainable by selecting members from those lists. See MPEP §2163.02; Fujikawa v. Wattanasin, 93 F.3d 1559, 1571 (Fed. Cir. 1996). Current PTO guidance likewise explains that here substantial variation exists within a genus, the adequately disclosed species must reflect that variation, or the disclosure must establish the necessary common attributes of structure-function-correlation.
The limitations of dependent claims 2-4, 9-10, 13 respectively narrow A and L1 but do not cure the deficiency with respect to the full claimed genus.
Accordingly, the specification does not reasonably coney possession of the full genus encompassed by claim 1.
Claims 1-4, 9-10, 13, and 17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the exemplified compounds, including the specifically disclosed compounds encompassed by claims 14 and 15, does not reasonably provide enablement for the full scope of the genus of compounds of Formula (I). The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
The Wands factors identified in re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988), include the breadth of the claims, the nature of the invention, the state of the prior art, level of ordinary skill, predictability of the art, amount of direction supplied, existence of working examples, and quantity of working examples, and quantity of experimentation required. MEPE §2164.01(A) and 2164.08.
The factors are considered together below.
Breadth of the claims
The breadth of the claims is substantial. A is functionally defined as a kinase inhibitor,
without restriction to a particular structural scaffold or kinase class. At the same time L1 encompasses numerous independently broad structural genera extending to 20 carbon atoms and including saturated, unsaturated, heteroatoms-containing, carbocyclic, and heterocyclic structures, each additionally subject to optional substitution. The claims therefore encompass a very large combinatorial space in which substantial structural variation is permitted simultaneously in the kinase-binding moiety and the linker.
The dependent claims narrow the kinase target but continue to encompass structurally diverse kinase inhibitors and the full L1 genus. Claim 17 incorporated claim1’s compound genus.
This factor weighs substantially toward undue experimenting.
Nature of the invention
The claimed compounds are bifunctional molecules whose biological properties depend
merely upon the ability to synthesize covalently connected components but upon interaction among the component ligands, linker target protein, and cellular environment.
Gao et al. (ACS Med. Chem. Lett. 2020, 11, 237−240) describes the conventional PROTAC architecture as comprising a target protein, an E3 ligase ligand, and a linker. See page 237.
The nature of the invention therefore involves more than routine formation of a covalent bond between independently known fragments where biological behavior would necessarily follow from the identities of the fragments.
State of the prior art and (D) predictability
The prior art demonstrates both that skilled artisans were capable of constructing
individual bifunctional degraders and that biological performance across structural space were not governed by a generally predictive design rule.
Gao expressly identifies as unresolved challenges, how to understand PROTAC degradation activity, selectivity, and off-target effect across different targets, cell lines and animal models, as well as know to rationally design PROTACs. Gao also identified efficient selection of suitable target protein ligands as a continuing challenge. See page 238.
Troup et al. (Explor Target Antitumor Ther. 2020; 1:273-312) explains that linker length and composition play critical role in PROTAC physiological properties and bioactivity and identifies limitations of the traditional trial-and-error approach to linker selection. See page 279. More significantly, Troup reports that empirical optimization commonly involved libraries of different linker compositions, lengths and connecting groups. One cited program synthesized more than 50 PROTACs, while another synthesized more than 40, and Troup explains that an optimal linker for one warhead/anchor combination generally does not translate across different E3-ligase anchors. See page 290. Troup further observes that cellular activity of a PROTAC is difficult to predict because linker changes can materially affect permeability, metabolic stability, solubility, and related properties. See page 301.
The evidence therefore does not establish that individual bifunctional compounds could not be rationally designed or synthesized. It established instead that successful results obtained for particular ligand/linker combinations could not simply be extrapolated throughout the structurally diverse universe encompassed by claim 1.
Level of ordinary skill
The level of ordinary skill in this field is high. The skilled artisan would possess substantial knowledge of medical chemistry, organic synthesis, kinase pharmacology and bifunctional degrader design.
This factor weighs against undue experimentation to the extent ordinary synthetic transformations and routine assays are involved. However, a high level of skill does not supply the missing predictive relationship across the full claimed structural genus. The issue is therefore not whether the skilled artisan could synthesize and test candidate compounds, but the amount and nature of experimentation required to identify operative compounds throughout the claimed scope.
Amount of direction or guidance supplied
The specification further states that compound may be made or modified using
methods known in organic synthesis and that reaction schemes, optimization, scale-up and protocols may be determined by the skilled artisan. Such guidance supports enablement of the disclosed and closely related species. However, the disclosure does not provide a predictive rule identifying which combinations throughout the broad kinase inhibitor A x L1 genus will retain the required kinase-inhibitory character and otherwise exhibit the biological properties underlying the disclosed bifunctional constructs. Nor does it provide sufficient guidance for selecting among the extensive structural alternatives without substantial empirical investigation.
This factor therefore weighs toward undue experimentation for the full genu even though it weighs against such a conclusion for individual disclosed species.
Applicant provides actual compounds, including the elected compound 955, and
provide biological testing for multiple linker-containing species.
This factor weighs against undue experimentation for those compounds and sufficiently close structurally related analogs. However, it does not establish enablement throughout the vastly broader genus where A and L1 can vary simultaneously across structurally diverse classes.
Current PTO guidance recognizes that representative examples may enable a genus where the skilled artisan would reasonably expect the genus to behave similarly, but additional evidence is appropriate where adequate reasons sh0ow that the genus as a whole cannot be practiced without undue experimentation. MEPE §2164.01(a).
Quantity of experimentation
The evidence indicates that the required experimentation would not merely consist of
routine confirmation of a predictable result.
Troup reports programs requiring synthesis and evaluation of more than 40 or 50 candidate degraders even where substantial portions of the molecules were already fixed, and expressly states that optimal linker solutions do not necessarily translate between ligand/anchor combinations.
The claim is substantially broader still because it permits simultaneous variation of both A and L1.
Accordingly, practicing the full scope would require selecting structurally diverse kinase inhibitors, selecting and constructing numerous linker architectures, preparing the resulting compounds, and empirically determining which combinations retain the requisite kinase-inhibitor characteristic and operative biological properties.
The experimentation is therefore not merely large in number, it is iterative and screening-oriented in the absence of a disclosed general predictive relationship.
Conclusion
On balance, although the level of skill is high, known synthetic methods are available, and Applicant provides working examples, those considerations are outweighed for the full scope of Claims 1-4, 9-10, 13, and 17 by the extraordinary breadth of the claimed structural space, limited guidance for traversing that space, the state of predictability, and the quantity of empirical experimentation required.
Accordingly, the specification does not teach the skilled artisan how to make and use the full scope of claims 1-4, 9-10, 13, and 17 without undue experimentation.
Clarification of the prior art rejection below:
The foregoing conclusion should not be understood as a finding that a skilled artisan could not synthesize an individual compound such as elected compound 955, or that every modification of a known bifunctional compound would lack a reasonable expectation of success. Rather, the enablement deficiency concerns extrapolation across the full A x L1 genus.
As explained below, the prior art provides specific teachings directed toward the particular structural components and attachment positions of 955. A specific prior-art pathway rendering one species obvious does not supply Applicant with enablement of the substantial larger genus encompassed by claims 1-4, 9-10, 13, and 17.
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 1-4, 9-10, and 13-15 are rejected under 35 U.S.C. 103 as being unpatentable over Olsen et al. (Nature Chemical Biology, Vol 14, February 2018, pages 163-170) in view of Zhang et al. (Aging Cell. 2018;17: e12780, pages 1-14) and Foley et al. (US2011/0053938 A1), Wang et al. (CN110845445A), and Troupe et al. (Explor Target Antitumor Ther. 2020; 1:273-312).
Olsen teaches the design and preparation of THAL-SNS-032
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, a bifunctional compound comprising the multi-targeted cyclin-dependent kinase inhibitor SNS-0.32 conjugated through a 3-polyethylene (PEG) linker to a second protein-binding moiety, thalidomide. Olsen teaches that SNS-0.32 is a potent inhibitor of cyclin-dependent kinases, including CDK9, and explains that thalidomide conjugation was employed as a strategy for targeted protein degradation. See Results, page 164; and Discussion Section.) Olsen specifically teaches that THAL-SNS-032 is formed by conjugating SNS-032 to thalidomide and induces potent and selective degradation of CDK9 in a CRBN-dependent manner.
Particularly relevant to the presently claimed compounds, Olsen teaches that, based upon structural information obtained from the SNS-032/CDK2 co-crystal structure (PDP 5D1J), the solvent-exposed piperidine nitrogen of SNS-032 was selected as the site for derivatization and was connected through a three-polyethylene-glycol linker to thalidomide. See Results Section. Olsen therefore expressly identifies the same piperidine nitrogen present in the A moiety of the presently elected species as an accessible and suitable attachment point for construction of a bifunctional conjugate.
Olsen further demonstrates that derivatization at this position does not abolish the kinase-inhibitor activity of the SNS-032 moiety. Specifically, THAL-SNS-032 retained nanomolar biochemical inhibition of CDK/CycB (171 nM), CDK2/CycA (62 nM), CHD1/CyH/MNAT1 (398 nM), and CDK9/CycT1 (4nM). Chemical-proteomic analysis further showed similar kinase-binding profiles for SNS-032 and THAL-SNS-032 in cell lysates, indicating that the linker/imide modification did not interfere materially with kinase binding. See Results.
Thus, Olsen teaches the A portion of the presently elected compound, including its CDK/CKD9-inhibitor property, and expressly teaches derivatization through the same solvent-exposed piperidine nitrogen employed as the attachment site in elected compound 955.
Olsen does not, however, teach selected compound 955 because Olsen employs a PEG-containing linker terminating in thalidomide rather than presently claimed piperazine-containing linker terminating in a piperlongumine-derived moiety.
Zhang teaches that piperlongumine (PL) is a biologically active intracellular protein-binding compound associated with ubiquitin-proteasome-dependent protein degradation. Zhang employed a PL-derived chemical probe to identify PL-binding proteins in cells and identified hundreds of such proteins, ultimately identifying 172 potential senolytic PL targets. Gene-oncology analysis showed that PL-binding targets were associated with, inter alia, protein transport and localization, autophagy, TOR signaling, protein phosphorylation, and ubiquitination. See §2.2, “Identification and validation of OXR1 as a target of PL.”
Zhang further teaches that PL directly binds oxidation resistance 1 (OXR1) and induces degradation of OXR1 though the ubiquitin-proteasome system in senescent cells. Zhang additionally reports that PL-induced reduction of OXR1 protein occurs post-transcriptionally and is associated with proteasomal degradation and demonstrates accumulation of polyubiquitinated proteins following PL treatment. §2.3 and Fig. 2.
Accordingly, Zhang would have provided one of ordinary skill in the art with reason to investigate PL as a biologically active protein-binding/degradation-associated moiety for incorporation into a bifunctional molecule of the type taught by Olsen.
The Examiner does not rely upon Zhang as teaching that PL is itself an E3 ligase ligand or that PL recruits a particular E3 ligase. Rather, Zhang is relied upon for its express teaching that PL binds intracellular proteins and is capable of producing ubiquitin-proteasome-associated degradation of a directly bound intracellular protein.
Foley teaches that PL is amenable to structural derivatization at the aromatic oxygen corresponding to the attachment position employed in the presently elected species. Specifically, Foley expressly teaches its compounds may be produced using piperlongumine as a starting material. See ¶ [0011]. Foley further teaches that PL derivatives may readily be prepared synthetically and identifies known literature concerning synthesis and derivatization of piperlongumine. See ¶[0055] Moreover specifically, Foley’s scheme I and Example 1 teach treating piperlongumine with AlCl3 to selectively remove an aromatic methyl group and thereby prepare the corresponding phenolic intermediate BPS-02083-01. Foley reports preparation of this intermediate from piperlongumine in 66% yield. See ¶[0084].
Foley then teaches reacting that phenolic PL intermediate with 2-morpholinoethanol in the presence of triphenylphosphine and DEAD to form an ether-linked PL derivative bearing an alkyl chain terminating in a nitrogen-containing heterocycle. See ¶[0085] and Scheme I. Foley therefore demonstrates experimentally that the PL aromatic methoxy position corresponding to the oxygen attachment region employed in compound 955 can be converted into a phenolic exit vector and subsequently functionalized with an O-linked side chain containing a nitrogen heterocycle. This teaching provides both a known site and known chemistry for incorporating PL into a larger conjugated molecule.
Wang teaches linker technology for preparing bifunctional small-molecule PROTAC compounds, including piperazine-containing linker structures. Wang specifically teaches Boc-protected amino-piperazine-1-alkyl ketone and azido-piperazine-1-alkyl ketone linker compounds and teaches use of these compounds to prepare intermediates for thalidomide-based functional small-molecule PROTACs. See claim 1 and ¶ 7. Wang therefore establishes that carbonyl-containing piperazine linkers were known as synthetically useful linker architectures for connecting the constituent ligand portions of bifunctional degradation molecules.
Troup in this section concerning PROTAC linker design, teach that PROTACs comprise two ligand components joined through a linker and that linker length and composition critically affect physiochemical properties and biological activity. Troup further teaches that the field had progressed from simple alkyl and polyethylene-glycol linkers toward more sophisticated functional linker structures. See Abstract and “Linker design strategies Section.” Troup further explains that modification of linker composition, including introduction of more polar and rigidifying structural features, such as piperazine was a recognized approach for optimizing properties including permeability, metabolic stability, and solubility. See pages 283 and 301.
Accordingly, Troup supplies an express reason why one of ordinary skill, beginning with Olsen’s PEG-linked bifunctional SNS-032 construct, would consider alternative linker architectures such as piperazine-containing linker structure expressly taught by Wang.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to modify the bifunctional SNS-032 construct of Olsen by employing a piperazine-containing linker of the type taught by Wang and by connecting the distal end of such linker to a PL aromatic-oxygen attachment site taught by Foley. Olsen expressly identifies the solvent exposed piperidine nitrogen of SNS-032 as an appropriate exit vector for attachment to a linker and demonstrates experimentally that derivatization at that position preserves potent CDK kinase inhibition. See Results. Thus, one of ordinary skill would have understood that this nitrogen provides a suitable point at which alternative bifunctional linker architecture could be installed without destroying the kinase-binding activity function of the SNS-032-derived moiety.
The artisan would further have had reason to investigate alternative linker composition because Troup teaches that linker composition is an important design variable affecting the physiochemical and biological properties of bifunctional degraders and describes the development of linker structures beyond conventional PEG and alkyl chains. See Abstract and page 274. Wang provides the corresponding concrete structural teaching by disclosing piperazine-containing carbonyl linkers specifically intended for construction of bifunctional small-molecule PROTAC compounds.
One of ordinary skill would additionally have had reason to employ PL as the distal biological active protein-binding moiety because Zhang teaches that PL binds to intracellular protein and can induce ubiquitin-proteasome-dependent degradation of a directly bound protein OXR1. Finally, Foley removes uncertainty concerning whether PL could be chemically incorporated into such a conjugate at the attachment position appearing in the presently elected compound. Foley experimentally demonstrates selective demethylation of PL to expose the corresponding phenolic oxygen with an O-linked chain terminating in a nitrogen-containing heterocycle.
The combination therefore does not depend upon selecting arbitrary attachment sites on either terminal ligand. Rather, both relevant exit vectors were expressly known in the art. Olsen identifies the solvent-exposed piperidine nitrogen of SNS-032, while Foley identifies and experimentally functionalize the relevant Pl aromatic oxygen.
One of ordinary skill in the art would have had a reasonably expectation of successfully preparing the resulting conjugated compound and retaining the claimed kinase-inhibitory character of its SNS-032-derived A moiety based on the combined teaching of the references.
Thus, reasonably expectation relied upon by the Examiner concerns successful construction of the specifically suggest conjugate and retention of the kinase-binding/inhibitory property required of the SNS-032-derived A moiety.
The Examiner does not take the position that every modification of a PROTAC linker would predictably retain identical degradation potency, selectivity, pharmacokinetic, or other biological properties, not is such a showing necessary to establish the obviousness of the presently claimed compound structure. The claims presently rejection encompass the compound as a chemical composition and does not require any particular DC50, Dmax, degradation potency, or degree of CKD9 degradation. This distinction is also consistent with the state of the art discussed by Troup; empirical optimization may be required to identify optimal degradation properties, but such optimization does not negate the specific structural teachings and known synthetic exit vectors relied upon above.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Olsen et al. (Nature Chemical Biology, Vol 14, February 2018, pages 163-170) in view of Zhang et al. (Aging Cell. 2018;17: e12780, pages 1-14) and Foley et al. (US2011/0053938 A1), Wang et al. (CN110845445A), and Troupe et al. (Explor Target Antitumor Ther. 2020; 1:273-312) as applied to claims 1-4, 9-10, and 13-15.
The combination of Olsen, Zhang, Foley, Wang, and Troup renders the compound of claim 1 obvious for the reasons set forth above.
The combination of Olsen, Zhang, Foley, Wang, and Troup collectively does not teach a pharmaceutical composition comprising the compound of claims 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient as recited in claim 17. However, Foley teaches pharmaceutical compositions comprising its piperlongumine-derived compounds and conventional pharmaceutical acceptable formulation components.
Specifically, Foley teaches that the disclosed compounds may be formulated in solid dosage forms, including tablets, capsules, particles, powders, and sachets, and teaches preparation of such dosage forms by mixing the compound with appropriate formulation components, including conventional, diluents, excipients and carriers. See ¶¶[0064]-[0068].Moreover, Foley’s own claim 4 expressly claim “a pharmaceutical composition comprising one or more compounds of claim 1, or its pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier/excipient.
It would have been obvious to one of ordinary skill in the art at the time the invention was filed to formulate the compound resulting from the combination discussed above, including the elected compound 955, together with a pharmaceutically acceptable excipient as required by claim 17. One of ordinary skill would have been motivated to do so in order to provide the compound in a conventional pharmaceutical form suitable for administration, as expressly taught by foley. The skilled artisan would have had a reasonable expectation of success because Foley teaches that such compounds can be formulated using ordinary methods and expressly identifies conventional pharmaceutically acceptable formulation components suitable for that purpose.
Conclusion
Claims 1-4, 9-10, 13-15 and 17 are not allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEAN P CORNET whose telephone number is (571)270-7669. The examiner can normally be reached Monday-Thursday from 7.00am-5.30pm.
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/JEAN P CORNET/Primary Examiner, Art Unit 1628