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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 11/14/2025 has been entered.
Application Status
This action is written in response to applicant’s correspondence received on 11/14/2025. Claims 1-16 are pending. Claims 1 and 11 have been amended. Claims 3-9 and 15-16 have been withdrawn from consideration. Claims 1-2 and 10-14 are currently under examination.
Claim Rejections - 35 USC § 112 – Updated in Response to Amendment
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 1-2 and 10-13 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.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Regents of the University of California v. Eli Lilly & Co, 119 F.3d at 1568, 43 USPQ2d at 1406.
Regarding claim 1, claim 1 is directed to a recombinant microorganism for producing a nicotinamide derivative, where the microorganism is transformed to express a NAMPT which is composed of an amino acid sequence with 90% homology to SEQ ID NOs 3 or 6, where the NAMPT converts nicotinamide and phosphoribosyl pyrophosphate into nicotinamide mononucleotide. Claim 1 further limits the genus of microorganism to “bacterium,” (bacteria). Thus, Claim 1 encompasses the entirety of the genus “bacteria,” where the genus bacteria is further recited with functional limitations such as the capacity to be genetically manipulated (transformed) to express a functional NAMPT. This claim language is problematic because it is known in the art that not all bacteria can be transformed or genetically modified to act as recombinant microorganisms, as presently recited. Claim 1 further recites a genus of NAMPT enzymes, namely, enzymes which are 90% identical to SEQ ID NOs 3 or 6. The genus of enzymes that are 90% identical to SEQ ID NOs 3 or 6 has not been demonstrated in the specification by representative species in a degree sufficient to show possession of this genus because, as discussed further below, it is known in the art that minor changes and point mutations can dramatically affect NAMPT enzymes causing unpredictability.
With regards to the specification, the Applicant appears to have cloned various NAMPT enzymes into vectors and tested their efficiency with regards to generating NMN (examples on pages 37-58). For instance, the Applicant has tested various NAMPT enzymes from a number of species to determine their efficiency of converting nicotinamide to NMN (paragraph 177). The Applicants tested various vectors comprising different NAMPT enzymes which were expressed in E. coli for their ability to convert nicotinamide into NMN by measuring NMN levels after culturing (see Examples 1-11 on pages 51-54). However, all of the tests appear to have been performed in E. coli cells, specifically the BL21 strain. Each of the NAMPT were codon-optimized for E. coli cells. No testing was performed in other bacteria (e.g., gram-positive bacteria, obligate intracellular pathogens, etc.). Thus, the Applicant has tested a limited number of NAMPTs in a given condition for their ability to convert nicotinamide to NMN in one bacteria type (E. coli, specifically the BL21 strain). This is problematic because the art teaches that unpredictability concerning the ability to genetically manipulate different species of bacteria.
Regarding the state of the art, it is known that NAMPT functionality is relatively uncharacterized in other bacteria. For instance, Houry (Houry D et al. Struct Biol. 2023 Sep;215(3):108004, of record) is a research article that focuses on structural determinants of NAMPT activity as it relates to substrate specificity (Title, Abstract, and throughout). Houry teaches that recent studies indicate that NAMPT rarely occurs in prokaryotes, which would include bacteria (page 2, left column, second paragraph); as such, there exists unpredictability concerning the introduction of a foreign NAMPT into a bacteria which normally does not encode such an enzyme. Furthermore, Houry teaches that structural mechanisms involving only recently characterized posttranslational modifications affect the functionality of NAMPT, where such enhancements of NAMPT activity are unknown/uncharacterized in the genus of bacteria NAMPTs (Abstract). Thus, mechanistic underpinnings of NAMPT activity differ between individual species of bacteria as presently recited. For instance, Houry teaches that posttranslational modifications play a key role in NAMPT functionality (Abstract). It is reasonable to infer that different bacterial cells with varying capacities for posttranslational modifications would function differently, as taught by Macek (Macek B et al. Nat Rev Microbiol. 2019 Nov;17(11):651-664, see Abstract). Given that it is known that posttranslational modifications (PTMs) affect the functionality of NAMPT enzymes and that PTMs are rare and highly unpredictable in bacteria (Macek, Abstract), the Applicant has not demonstrated possession of the genus bacteria with respect to claim 1 which requires functional language (i.e., a functional NAMPT enzyme capable of carrying out enzymatic conversions). Furthermore, the teaching that NAMPTs are rare in prokaryotes, per Houry, casts further doubts on the functionality of the recited SEQ ID NOs in other bacteria (e.g., P. aeuroginosa or C. burnetti). The Applicant has not sufficiently characterized the genus of bacteria commensurate in scope with the recited claims and specification.
Additionally, the Applicant is broadly claiming that the bacteria of claim 1 are recombinant microorganisms which express a non-native NAMPT via transformation of a vector. Such claim language reasonably implies that the bacteria are capable of being grown in a lab, genetically manipulated via transformation, and capable of expression of recombinant proteins. However, it is known in the art that not all bacteria have tools available for such genetic manipulation and transformation. For example, obligate intracellular pathogens such as Coxiella burnetti are known to be difficult to manipulate genetically, as discussed by Beare (Beare et al., “Coxiella burnetti: Recent Advances and New Perspectives in Research of the Q Fever Bacterium,” text book published by Springer, 2012, Chapter 13, pages 249-267, Abstract and Summary, final paragraph). Beare teaches that, in general, it is known that there are significant hurdles when performing genetic transformation with obligate intracellular pathogens (Abstract). Thus, there is unpredictability surrounding the broad genus of “bacteria” with regards to whether or not such bacteria are capable of being genetically manipulated as presently claimed.
The research article McClure (McClure EE et al. Nat Rev Microbiol. 2017 Sep;15(9):544-558) further corroborates the point that obligate intracellular pathogens are difficult to manipulate genetically by teaching that:
“the refinement of genetic manipulation methods for all obligate intracellular bacteria has proven exceedingly difficult,” (page 1, right column, second paragraph).
There is therefore unpredictability surrounding the presently recited genus of bacteria, where such bacteria are further required to be able to be transformed and express recombinant proteins, where furthermore the recombinant NAMPT proteins are recited with functional limitations to perform enzymatic functions requiring PTMs whose status across the genus bacteria are widely uncharacterized and unknown.
Additionally, regarding claim 1, claim 1 recites that the NAMPT is composed of a polypeptide with 90% sequence homology to SEQ ID NOs 3 or 6 and therefore recites variants of NAMPTs that can vary by as much as 10% in relation to SEQ ID NOs 3 and 6. The Applicant has not offered examples of mutagenic analysis of SEQ ID NOs 3 and 6, and was not in possession of the claimed genus of SEQ ID NO 3 and 6 variants, as mutation in NAMPTs confer unpredictable structural/functional effects as known in the art (see below)
The enzyme activity of NAMPT enzymes is known to be unpredictable in the art as taught by Rongzhao (US 2018/0162895 A1, provided in Applicant’s IDS filed 9/17/2021). For instance, Rongzhao teaches that minor variations in NAMPT amino acid sequences can have a significant effect on the enzymatic activity of a given NAMPT (e.g., Table 1). Table 1 of Rongzhao teaches that point mutations can affect the enzymatic activity of a NAMPT by anywhere from 1.2-6.9 times (Table 1). Thus, the broad genus of “NAMPT” composed of SEQ ID NOs 3 or 6 with up to 10% variation (over 40 mutations in either SEQ ID NOs 3 and 6) recited in the claims comprises unpredictable variations in enzyme activity, where minor changes can have large effects on the enzymatic activity of a given NAMPT.
Additionally, Audrito (Audrito V et al. Front Oncol. 2020 Mar 19;10:358, of record) teaches that catalytic activity of NAMPT changes with various point mutations, that such functional mutational studies must be characterized empirically, and that some point mutations significantly decrease or abolish NAMPT enzymatic activity (page 5, left column, first paragraph). Thus, Audrito teaches that the genus of the enzyme NAMPT is subject to unknown variations in enzymatic catalytic activity based on minor changes to the protein, some of which can significantly decrease catalytic activity (page 5, left column, first paragraph). The Applicant has not performed functional and/or structural mutational analysis on the recited SEQ ID NOs (3 and 6). Given the known unpredictability of NAMPT enzymes and their intolerance to minor mutational changes with respect to overall functionality, a greater burden exists on the Applicant to characterize the recited enzymes/SEQ ID NOs to show possession of the claimed subject matter.
Additionally, it is also known in the art that different NAMPT enzymes have inherently different enzymatic activities and NMN conversion efficiencies when transformed into a microorganism such as E. coli, as taught in Figure 2B of Marinescu (Marinescu GC et al. Sci Rep. 2018 Aug 16;8(1):12278, provided in Applicant’s IDS filed 9/17/2021). As seen in Figure 2B of Marinescu, the NAMPT gene from H. ducreyi appears to have significantly more conversion efficiency of NMN compared with that of both M. musculus and S. oneidensis (Figure 2B). Thus, NAMPT enzymes and their NMN conversion efficiency are inherently unpredictable and must be determined empirically as taught by Marinescu (Figure 2B). Enzymes in the genus NAMPT therefore clearly have different enzymatic activities and the Applicant has not disclosed common features which predict which NAMPTs of the recited genus, with up to 10% mutation, would function as presently recited (i.e., with the functional limitation recited of “NAMPT”).
Thus, the Applicant was not in possession of the genus of mutant NAMPTs with “90%” sequence identify to either SEQ ID NO 3 or 6, where such mutants retain their recited functionality (i.e, NAMPT enzymes) because such a genus would need to be determined experimentally/empirically.
Claims 2 and 10-13 depend from claim 1 and do resolve each of the 112(a) issues above.
For instance, claim 2 narrows the scope of the claims to recite that the NAMPT is composed of SEQ ID NOs 3 or 6. However, claim 2 depends from claim 1 and therefore broadly encompasses the unpredictable genus of “bacterium” recited in claim 1.
Furthermore, claim 11 further narrows claim 1 by reciting that the microorganism is E. coli. However, claim 11 still recites the unpredictable genus of NAMPTs with 90% sequence homology to SEQ ID NOs 3 and 6.
Response to Arguments and Amendments
The Applicant’s arguments and amendments submitted 11/14/2025 have been considered but are not persuasive to place the application in condition for allowance. The Applicant has amended independent claim 1 to recite “bacterium;” however, this genus was not shown to be in possession by the Applicant for the reasons discussed in the 112(a) rejection, above. Furthermore, the genus of NAMPT recited in claim 1 and dependent claims 10-13, where the NAMPT is 90% identical to SEQ ID NOs 3 or 6 was not shown to be possessed by the Applicant, as was originally argued in the Final rejection mailed 7/14/2025. Thus, the merits of the 112(a) rejection have not been addressed by amendment or argument.
Allowable Subject Matter
Claim 14 is allowable. Regarding claim 14, claim 14 recites a vector comprising a sequence which is 99% identical to SEQ ID NOs 2 or 5. SEQ ID NOs 2 and 5 encode codon-optimized versions of NAMPT enzymes from Sphingopyxis sp. C-I and C. pinensis, optimized to be expressed in E. coli, respectively. Both of the NAMPT protein sequences encoded by SEQ ID NOs 2 and 5 are known NAMPT sequences, as shown in NCBI WP 062182430 (NCBI BLAST search, accession number WP 062182430, published 3/28/2016) and NCBI WP 012788281 (NCBI BLAST search, accession number WP 012788281, published 5/17/2013) respectively. Thus, the sequences of these NAMPTs, as well as the fact that these sequences were functional NAMPTs was known in the art at the time of filing.
Furthermore, with regards to expressing foreign NAMPTs in E. coli cells, Sinclair (US 2016/0287621 A1, supplied in Applicant’s IDS filed 9/17/2021) teaches a recombinant microorganism for producing a nicotinamide derivative, where the microorganism has been engineered to express a NAMPT from a vector (Figures 2-3, paragraphs 161-164). Furthermore, Sinclair teaches that the cell type can be an E. coli cell (paragraph 113). Thus, it was known in the art that foreign NAMPTs could be expressed in E. coli cells, and furthermore, the NAMPTs encoded by SEQ ID NOs 2 and 5 were known NAMPTs at the time of filing.
However, there does not appear to be a teaching or suggestion in the art to specifically use the recited sequences as NAMPTs in E. coli. For instance, a practitioner would not be reasonably guided to using the recited NAMPTs, to engineer said sequences and optimize them in E. coli cells, as it was not apparent at the time of filing that NAMPTs from Sphingopyxis sp. C-I or C. pinensis would offer any specific advantage when used with the teachings of Sinclair. Thus, claim 14, which recites sequences of E. coli codon-optimized NAMPT proteins from Sphingopyxis sp. C-I (SEQ ID NO 2) and C. pinensis (SEQ ID NO 5) appears to be free of the art.
Furthermore, the Applicant has reduced to practice such vectors, used in E. coli cells, and demonstrated that such NAMPTs are effective for their intended use for the production of nicotinamide (see Example V-1 and V-2, pages 51-54). Thus, a practitioner is reasonably enabled to use the invention as presently recited, where said vector is optimized for E. coli cells.
Additionally, it appears that there is a degree of variability concerning the performance of different NAMPTs when cloned into E. coli. Thus, the findings can be viewed as being unpredictable (compare the variable NMN conversion efficiencies in paragraphs 257-260, NMN production in Examples 1-11, and uptake and excretion efficiencies).
Furthermore, claim 14 recites proteins which are heterologous to E. coli cells which have been codon-optimized for said E. coli cells. Thus, claim 14 is not drawn to a naturally occurring product of nature. Furthermore, ABSS sequence searches for SEQ ID NOs 2 and 5 were conducted, as well as BLAST searches (patent and nr/nt databases), and SEQ ID NOs 2 and 5 were found to be free of the art.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached at (571)-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636