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 .
DETAILED ACTION
Claim Status
Claims 37 and 43-51 are pending. Claims 37 and 43-51 are under examination. Claims 37 and 43-51 are rejected.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 08/06/2025 has been entered. No request for suspension of action was filed.
Filing Receipt
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Note: A new filing receipt is needed to reflect the power of attorney filed 11/15/2024. The acceptance of the Power of attorney was mailed 11/22/2024.
Election/Restrictions
Applicant elected without traverse Group VI claims 37 and 43-51 in a response filed 03/11/2024.
Applicant elected the immediately below specie.
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The specie is found to be free of the prior art. The search of the specie was expanded to include the species in the below 102 and 103 rejections.
The search of the elected specie did result in art. Sharma et al. (Design and synthesis of molecular probes for the determination of the target of the anthelmintic drug praziquantel, Bioorganic & Medicinal Chemistry Letters, 24(11), 2469-2472, Published 2014) and Sharma et al. SI (Supplemental Information, pages 1-23, Published 2014). See page 6 of Sharma et al. SI as seen below. The elected specie is within compound 4 of Scheme S1 disclosed by Sharma et al. SI. However, Compound 4 of Sharma et al. SI does not anticipate nor render the elected specie obvious.
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Response to Amendments/Arguments
Applicant's amendments and arguments filed 08/06/2025 are acknowledged and
have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below in original or modified form is herein withdrawn.
112(a) and 112(b) rejections of claims 37 and 43-51 in the final mailed 02/06/2025 are withdrawn. The claim amendments have overcome the rejections.
The 102 rejection of claims 37, 43-50 as anticipated by Kambe et al (Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells, JACS, 136, 10777-10782, Published 07-2014) with Supp. Information pages 1-67, Published 07-2014) in the final mailed 02/06/2025 are withdrawn. The claim amendments have overcome the rejections.
The 102 rejection of claims 37, 43-47 and 50 as anticipated by MacKinnon et al.
(Target Identification by Diazirine Photo-Cross-Linking and Click Chemistry, Curr Protoc Chem Biol, 1, 55-73, Published 12-2008) in the final mailed 02/06/2025 are withdrawn. The claim amendments have overcome the rejections.
The 103(a) rejection of claims 37, 43-51 over Kambe et al (Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells, JACS, 136, 10777-10782, Published 07-2014) and Statsyuk et al. (USPGPub 2018/0170878, Published 06-2018) in the final mailed 02/06/2025 are withdrawn. The claim amendments have overcome the rejections.
The 103(a) rejection of claims 37, 43-51 over MacKinnon et al. (Target Identification by Diazirine Photo-Cross-Linking and Click Chemistry, Curr Protoc Chem Biol, 1, 55-73, Published 12-2008) and Statsyuk et al. (USPGPub 2018/0170878, Published 06-2018) in the final mailed 02/06/2025 has been modified. The modifications were necessitated by amendment.
The following 112(a), 112(b), 102, and 103 rejections constitute the complete set of rejections and/or objections presently being applied to the instant application. The rejections were necessitated by amendment.
Response to Arguments
Applicant's arguments filed 08/06/2025 have been fully considered but they are not persuasive.
Applicant argues
The prior art MacKinnon et al. does not give a hint of a pair of disproportionation being detected. In fact, a protein does not contain two conjugated double bonds in its primary structure.
Examiner’s response
The pair of disproportionation products are produced by a carbene reaction with the claimed compound A as claimed. Thus any prior art that reacts the claimed carbene with the claimed compound A will result in the pair of disproportionation products. Detection of the products is not a claim limitation.
Proteins have aromatic residues phenylalanine, tyrosine and tryptophan as evidence by Lanzarotti et al. (Aromatic-Aromatic Interactions in Proteins: beyond the Dimer, J. Chemical Information and Modeling, 51, pp. 1623-1633, Published 2011). The current specification allows for two conjugated double bonds to be in ring systems (p. 23). Benzene has at least two conjugated double bonds.
See the current specification page 35, Table 2. Wherein the compound 2,4-Dihydroxyacetophenone has a benzene ring which results in a pair of isomers. The benzene ring has three conjugated double bonds which comprises two conjugated double bonds. Therefore, benzene has the claimed two conjugated double bonds.
For the reasons stated above the below rejections are maintained as set forth below.
Claim Interpretation
The claimed identification is met when the remaining limitations of claim 37 are met.
The disproportionation products comprising F and F’ are interpreted to be produced when compound A having two conjugated double bonds undergoes a carbene reaction (elected specie) with a first functional group of a linker precursor molecule C. The linker precursor molecule C comprises the first functional group, a linker moiety and a second functional group, wherein the second functional group of the linker precursor molecule C remains unreacted.
Due to disproportionation resulting from a carbene reaction of the organic compound A, any reaction of the claimed carbene with the claimed compound A would result in the claimed pair of disproportionation reaction products.
Concerning the limitation of “two conjugated bonds”, this is being interpreted as “at least two conjugated bonds. See the current specification page 35, Table 2. Wherein the compound 2,4-Dihydroxyacetophenone has a benzene ring which results in a pair of isomers. The benzene ring has three conjugated double bonds which comprises two conjugated double bonds. Therefore, benzene has the claimed two conjugated double bonds. Note: the specification allows for the two conjugated bonds to be in ring structures (p. 23). “In some embodiments, at least one of the two conjugated double bonds is in a ring system, such as a cycloalkyl ring”.
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 37 and 43-51 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. This is a new matter rejection.
The phrase “molecular weight of two hydrogen atoms” in claim 37 does not find support in the original disclosure and is therefore new matter. The specification contemplates the “molecular weight…. plus 2,”. See the current specification page 21.
However, the molecular weight of 2 hydrogen atoms is not contemplated by the specification. The number 2, as utilized in the original disclosure may or may not be two hydrogen atoms. The molecular weight of 2 does not implicitly imply the molecular weight of two hydrogen atoms. To specify two hydrogen atoms, 2.016 g/mol would necessarily have to be recited or a showing of the loss or addition of two hydrogen (Example 14 does not depict the loss or addition of two hydrogen). Additionally, Plus or minus 2 g/mol may be two hydrogen atoms or may imply plus or minus some other entity not recited.
Applicant cites Example 14 within the original disclosure to suggest support for
the “molecular weight of 2 hydrogen atoms”. See immediately below, taken from
remarks filed 11/15/2025 page 1.
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The structure of abietic acid has 8 hydrogen in the two fused rings having
Unsaturation (purportedly the two conjugated double bonds). Compound (A) has 7 hydrogen. Compound (B) has 11 hydrogen. See above. The molecular weight of plus or minus two hydrogen atoms is not present.
The published version of the original specification was reviewed to ensure
references to “paragraphs 2-4 on page 12, paragraphs 3-5 on page 23” existed. They
do not.
Applicant has not pointed out where the amended claim is supported, nor does there appear to be a written description of the claim limitation. See MPEP 2163.04; see also Hyatt v. Dudes, 492 F.3d 1365, 1370, 83 USPQ2d 1373, 1376 (Fed. Cir. 2007) (holding that “[MPEP] § 2163.04 [subsection] (I)(B) as written is a lawful formulation of the prima facie standard for a lack of written description rejection.”).
The newly added limitation of identifying an organic compound A from a mixture does not have antecedent basis in the original disclosure. Nowhere in the original disclosure is the compound A found in a mixture and is identified from the mixture.
The limitation “disproportionation reaction products produced by carbene or nitrene or free-radical reaction of the organic compound A” does not have support in the original disclosure.
Disproportionation is separate from the reaction of compound A with the carbene or nitrene or free-radical reaction (site non-selective reactions).
Pages 11 through 12 differentiate the site non-selective reactions from the disproportionation. The site non-selective reactions involve the carbene, nitrene or free-radical chemistry. Whereas the disproportionation does not involve the site non-selective reactions on page 12 of the specification.
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 37 and 43-51 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.
Claim 37 is indefinite due to two conflicting chemistries. A carbene reaction does not necessarily result in a disproportionation. For example, the elected specie, a diazirine results in a carbene. See immediately below showing carbene formation.
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The resulting carbene reacts with Compound A and not necessarily on the two conjugated double bonds. Without explanation a disproportionation is also occurring with the carbene per claim 37.
Below is a depiction of the disproportionation of abietic acid (Compound A in Example 14). A carbene is not necessary.
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Claim 37 is also indefinite because the claim does not specify as to where the carbene or nitrene or free radical originate from. For example, the carbene or nitrene or free radical may originate from the first functional group or from the organic compound A.
Moving on, the newly added limitation of identifying an organic compound A from a mixture is indefinite due to two conflicting interpretations. Either the organic compound A having two conjugated double bonds resides in a mixture or a pair of disproportionation reaction products constitutes the mixture.
Claim 37 is also indefinite for the use of the unidentified isomer compound E.
Compound E may just be compound F and F’ with varying amounts of hydrogen atoms. However, clarification is needed.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 37, 43-46 and 48-49 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lawrence et al. (3-Aryl-3-(trifluoromethyl)diazirines as Versatile Photoactivated “Linker” Molecules for the Improved Covalent Modification of Graphitic and Carbon Nanotube Surfaces, Chem. Mater., 23, pp. 3740-3751, Published 2011).
Lawrence et al. disclose the below reaction of compound A and linker precursor molecule C (p. 3743, left column, sec. 2.3.).
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Compound A being the multiwalled carbon nanotube and the linker precursor molecule C being 3-[3-(trifluoromethyl)diazirin-3-yl]phenyl ferrocene monocarboxylate. The carbon nanotube has at least two conjugated double bonds. The current specification allows for two conjugated double bonds to be in ring systems (p. 23).
The substituted alkylene with an aryl is the linker (an arylene claim 48). The carboxylate being the second functional group (claim 46). The initial oxygen in the O-C(O)- group being the oxygen in claim 49.
Per the claim interpretation, the disproportionation products comprising F and F’ are produced in the above reaction, due to compound A having two conjugated double bonds which undergoes a carbene reaction with the claimed linker precursor molecule C. The limitations of the 2 hydrogen and the molecular weight of isomer E are also met.
Substantially identical methods yield substantially identical products. See MPEP 2112.01 I. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Both the prior art and the claimed invention have a carbene reaction with compound A having two conjugated double bonds with a first functional group of the linker precursor molecule C. Due to the methods of the prior art and those of the invention being substantially identical, the products would have been substantially identical.
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.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 37, 43-51 is/are rejected under 35 U.S.C. 103 as being unpatentable over MacKinnon et al. (Target Identification by Diazirine Photo-Cross-Linking and Click Chemistry, Curr Protoc Chem Biol, 1, 55-73, Published 12-2008) and Statsyuk et al. (USPGPub 2018/0170878, Published 06-2018) and as evidence by Lanzarotti et al. (Aromatic-Aromatic Interactions in Proteins: beyond the Dimer, J. Chemical Information and Modeling, 51, pp. 1623-1633, Published 2011). The modifications to this reaction were necessitated by amendment.
Scope of the Prior Art
MacKinnon et al. teach the formation of the carbene and an individual diazirine
with alkyne handle compound covalently bond to a protein target, and detection by
conjugation (p. 17). The protein target is the claimed organic compound A. Concerning the two conjugated double bonds, aromatic residues are widespread in proteins as evidence by Lanzarotti et al. (Abstract). The aromatic residues are phenylalanine, tyrosine and tryptophan (Bridging pages 1623-1624). These amino acids have a benzene ring and therefore have the two double conjugated bonds required to be present in compound A. The current specification allows for two conjugated double bonds to be in ring systems (p. 23).
The individual diazirine with alkyne handle compound is seen immediately below.
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The individual diazirine with alkyne handle compound reads on claim 37, 43-47 and 50 with the diazirine being the first functional group, the alkyne handle being the second functional group and in between the diazirine and alkyne handle being the linker. Concerning claim 43, the linker is an optionally substituted alkylene.
MacKinnon et al. teach photo-affinity labeling (PAL) represents a useful
biochemical strategy for target identification in complex protein mixtures (p. 1, immediately under the Keywords heading).
MacKinnon et al. goes on to teach alkyl diazirines hold unique advantages. The first being compact size (p. 2 top). MacKinnon et al. teach an alkyl diazirine with an alkyne handle (p. 2 bottom). MacKinnon et al. teach the benefits of an alkyne handle (p. 2 middle).
Ascertaining the Difference
MacKinnon et al. does not teach the last compound in claim 51 as seen
immediately below.
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Secondary Reference
Statsyuk teaches photocrosslinking reagents, crosslinkable proteins displaying such photocrosslinking reagents, crosslinked protein-protein complexes, and methods of use thereof ([0004]), which are used for mapping proteins with the reagents and analysis via techniques such as mass spectrometry ([0007]). Statsyuk is therefore analogous art because it is in the same field of endeavor as MacKinnon et al. Statsuyk also teaches the immediately displayed compound above (page 10, lower right
column).
Obviousness
It would have been prima facie obvious for an ordinary artisan before the effective filing date of the claimed invention to have tried the diazirine compound taught by Statsyuk in the photo-affinity labeling (PAL) taught by MacKinnon et al. to arrive at the current invention with a reasonable expectation of success. The ordinary artisan would have done so to identify targets in complex protein mixtures. The ordinary artisan would have tried the diazirine compound taught by Statsyuk because of its small size and the existence of diazirine and alkyne handle.
Per the claim interpretation, the disproportionation products comprising F and F’ are produced in the above reaction, due to compound A having two conjugated double bonds which undergoes a carbene reaction with the claimed linker precursor molecule C. The limitations of the 2 hydrogen and the molecular weight of isomer E are also met.
Substantially identical methods yield substantially identical products. See MPEP 2112.01 I. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Both the prior art and the claimed invention have a carbene reaction with compound A having two conjugated double bonds with a first functional group of the linker precursor molecule C. Due to the methods of the prior art and those of the invention being substantially identical, the products would have been substantially identical.
The limitations of the 2 hydrogen and the molecular weight of isomer E are also met.
Claim(s) 37, 43-49 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smith et al. (Photoaffinity labeling in target- and binding-site identification, Future Med Chem., ; 7(2): pp. 159–183, Published 2015).
Scope of the Prior Art
Smith et al. teach the immediately below photoaffinity probe diazirine-alkyne linkers (p. 30, Table 1).
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Additionally, the immediately below compound (p. 33, Table 1).
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Note: the above photoaffinity probes have optionally substituted arylene (43), alkynes,
C(O)-O- (46), and O’s (48, 49).
The alkyne group is the second functional group. The diazirine (N=N ring) generates the carbene. See page 26 of Smith et al.
Smith et al. teach the general design for photoaffinity probes wherein an alkyne
and azide functionality on the two halves allows a conjugation step through 1,3-cycloaddition step (p. 24, Figure 1).
Concerning compound A, Smith teach furospinosulin-1 (seen immediately below) (p. 9).
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The above heterocycle group has two conjugated double bonds.
Smith et al. goes on to teach the photoaffinity probes were synthesized using the photophore benzophenone to deconvolute the mechanism of action of the furospinosulin-1 (p. 9).
Smith et al. teach the diazirine is a photophore (p. 11, entry 13 of Table 1).
Smith et al. teach target deconvolution is an important part of drug discovery and development with screening to discover new bioactive molecules (p. 6).
Smith goes on to teach, “In general terms, target deconvolution can be split into two categories; affinity-based methods and expression cloning-based methods. A fundamental aspect, however, of all the technologies used for target identification is the affinity of the small molecule to its target protein. The strength of the association between a reversibly binding ligand and its target(s) determines whether the interaction will persist through experimental procedures for target detection and/or isolation. Photoaffinity probes can overcome this by permanently capturing targets with weak affinity through the formation of the covalent attachment”.
Ascertain the Differences
Smith et al. does not teach using the diazirine-alkyne linkers to deconvolute the mechanism of action of the furospinosulin-1
Obviousness
It would have been prima facie obvious for an ordinary artisan before the effective filing date of the claimed invention to have utilized the diazirine-alkyne linkers in place of the benzophenone linkers to deconvolute the mechanism of action of the furospinosulin-1 and arrive at the current invention. The ordinary artisan would have done so with a reasonable expectation of success because both the diazirine-alkyne and benzophenone linkers are photophores.
Due to the prior art teaching a reaction of a carbene with compound A having two conjugated double bonds, the ordinary artisan practicing the combined methods of Smith et al. as written above, would have practiced methods that were substantially identical to the instant methods.
Substantially identical methods yield substantially identical products. See MPEP 2112.01 I. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
The limitations of the 2 hydrogen and the molecular weight of isomer E are also met.
Claim(s) 50-51 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smith et al. (Photoaffinity labeling in target- and binding-site identification, Future Med Chem., ; 7(2): pp. 159–183, Published 2015) as applied to claims 37, 43-49 and in further view of Statsyuk et al. (USPGPub 2018/0170878, Published 06-2018).
Scope of the Prior Art
The combinational teachings of Smith et al. are written in the above 103 rejection and are incorporated by reference.
Additional teachings of Smith et al. include photoaffinity labeling (PAL) with proteins (p. 1). Smith et al. teach alkynes and azides both are successfully utilized in click chemistry (p. 3).
Ascertain the Differences
Smith et al. does not teach the immediately below photoaffinity probe.
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Secondary References
Statsyuk teaches photocrosslinking reagents, crosslinkable proteins displaying such photocrosslinking reagents, crosslinked protein-protein complexes, and methods of use thereof ([0004]), which are used for mapping proteins with the reagents and analysis via techniques such as mass spectrometry ([0007]). The teachings of Statsyuk are therefore, overlapping in nature to the teachings of Smith et al. with respect to photo linkers utilized with proteins. Statsyuk is analogous art to the invention because Statsuyk also teach the immediately below displayed compound (page 10, lower right
column).
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Obviousness
It would have been prima facie obvious for an ordinary artisan before the effective filing date of the claimed invention to have utilized the diazirine-azide linker taught by Statsuyk in place of the diazirine-alkyne linkers to deconvolute the mechanism of action of the furospinosulin-1 and arrive at the current invention. The ordinary artisan would have done so with a reasonable expectation of success because both the alkynes and azides are successfully utilized in click chemistry. The ordinary artisan would have looked to Statsuyk because both Smith et al. and Statsuyk teach photo induced linking with proteins.
Due to the prior art teaching a reaction of a carbene with compound A having two conjugated double bonds, the ordinary artisan practicing the combined methods of Smith et al. and Statsuyk as written above, would have been substantially identical to the instant methods.
Substantially identical methods yield substantially identical products. See MPEP 2112.01 I. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
The limitations of the 2 hydrogen and the molecular weight of isomer E are also met.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BLAINE G DOLETSKI whose telephone number is (571)272-2766. The examiner can normally be reached M-F 7-4 EST.
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/B.G.D/Examiner, Art Unit 1692 /Andrew D Kosar/Supervisory Patent Examiner, Art Unit 1625