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
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 5/6/26 has been entered.
2. Applicants’ response filed 5/6/26 to Final Office Action mailed 11/6/25 is acknowledged.
3. Applicant’s prior election of Group I to host cell [claims 94, 96-108, 111, 114 & 115-117 (new)] in the reply filed on 3/12/25 is acknowledged. Species election of Insect demethylase protein/DNA of SEQ ID Nos. 152/151 is also acknowledged.
4. Claims withdrawn:
Claims 109-110 & 112-113 & 118-120 and all non-elected sequences are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
5. Applicant's amendment and arguments filed 5/6/26 have been fully considered but they are not deemed to be persuasive. The reasons are discussed following the rejection(s).
6. Any objection or rejection of record which is not expressly repeated in this Office Action has been overcome by Applicant’s response and withdrawn
7. 35 U.S.C. § 112, first paragraph (Written Description)
Claims 94, 96-108, 111, 114 & 115-117 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Instant claims 94, 96-108, 111, 114 & 115-117 are directed to the following genus claims.
94. A genetically modified host cell comprising a pathway having enhanced production of one or more benzylisoquinoline alkaloids wherein the host cell expresses of one or more heterologous insect genes encoding one or more insect demethylases capable of converting thebaine into northebaine, thebaine into oripavine, thebaine into nororipavine and/or oripavine into nororipavine; wherein the host cell is a fungal cell, wherein the one or more insect demethylases comprises a polypeptide which is at least 80% identical to the insect demethylase comprised in SEQ ID NO: 152
96. The cell of claims 94, wherein the one or more insect demethylases comprises a polypeptide encoded by a polynucleotide which is 70% identical to the comprising SEQ ID NO: 251, or genomic DNA thereof.
Dependent claims 97-108, 111, 114 & 115-117 add further limitations but does not address the written description requirement.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, 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 that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that a representative number of species means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The instant specification, however, only provides description of: A genetically modified host cell comprising a pathway having enhanced production of one or more benzylisoquinoline alkaloids wherein the cell expresses a heterologous insect gene of SEQ ID NO: 153 encoding an Heliothis virescens P450 protein mutant (I256V) demethylase of SEQ ID NO: 152 capable of converting thebaine into northebaine, thebaine into oripavine, thebaine into nororipavine and/or oripavine into nororipavine; wherein the host cell is a eukaryote selected from the group consisting of a mammalian, an insect, a plant, or a fungal cell, wherein the one or more insect demethylases comprises a polypeptide which is at least 95% identical to the one or more insect demethylases comprised in SEQ ID NO: 152 and comprises one or more conserved amino acids substitutions at positions G103, H111, K167, E198, R219, L223, I256, A259, L273, V284, I309, L314, 0517, L160, N216, R443 corresponding to SEQ ID NO: 152.
While other insect species, for example demethylases from Helicoverpa armigera of SEQ ID NO: 140, 142, 144, etc. are disclosed, the specification does not contain any disclosure or description of the structure and function of all amino acid/DNA sequences that are at least 80%/70% identical to SEQ ID NO: 152/151, or a derivative derived from such a sequence by insertion, deletion or substitution, and encoding a protein of SEQ ID NO: 152 which has the enzymatic activity of a demethylase. The species disclosed from Heliothis virescens is not representative of the genus claimed.
This is further supported by the following sequence comparison of Applicants’ SEQ ID NO: 152 and AC A0A2A4JAK3 a 90.4% query match but an entirely different protein viz., Helicoverpa armigera GIP protein sequence.
ID A0A2A4JAK3_HELVI 523 AA.
AC A0A2A4JAK3;
DT 20-DEC-2017, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2017, sequence version 1.
DT 05-FEB-2025, entry version 22.
DE RecName: Full=unspecific monooxygenase {ECO:0000256|ARBA:ARBA00012109};
DE EC=1.14.14.1 {ECO:0000256|ARBA:ARBA00012109};
GN ORFNames=B5V51_5222 {ECO:0000313|EMBL:PCG68452.1};
OS Heliothis virescens (Tobacco budworm moth).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea;
OC Noctuidae; Heliothinae; Heliothis.
OX NCBI_TaxID=7102 {ECO:0000313|EMBL:PCG68452.1};
RN [1] {ECO:0000313|EMBL:PCG68452.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HvINT- {ECO:0000313|EMBL:PCG68452.1};
RC TISSUE=Whole body {ECO:0000313|EMBL:PCG68452.1};
RA Fritz M.L., Deyonke A.M., Papanicolaou A., Micinski S., Westbrook J.,
RA Gould F.;
RT "Contemporary evolution of a Lepidopteran species, Heliothis virescens, in
RT response to modern agricultural practices.";
RL Submitted (SEP-2017) to the EMBL/GenBank/DDBJ databases.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0016705; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; IEA:InterPro.
DR CDD; cd11056; CYP6-like; 1.
PNG
media_image1.png
867
757
media_image1.png
Greyscale
According to MPEP 2163, to satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v.Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed.Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116.
The scope of each genus includes many members of demethylase enzymes with widely differing structural, chemical, and physical characteristics. Furthermore, each genus is highly variable because a significant number of structural differences between genus members exit. The specification does not describe and define any structural features and amino acid sequences commonly possessed by each genus. There is no art-recognized correlation between any structure of a demethylase and sequences having varying sequence homology, i.e., 80% or 70% of SEQ ID NO: 152/151 (protein/DNA). Those of ordinary skill in the art would not be able to identify without further testing what specific DNA sequences would encode a protein having demethylase activity and be effective in catalyzing a product/byproduct, wherein when the product is northebaine then the by-product is thebaine N-oxide and/or northebaine oxaziridine and when the product is nororipavine then the by-product is oripavine N-oxide and/or nororipavine oxaziridine.
Alternatively, the genus of polynucleotides (at least 70% of SEQ ID NO: 151) that comprise these DNA molecules and encoding many different proteins may be obtained with the aid of a computer by a skilled artisan. However, there is no teaching regarding which 30% of the sequence that can be varied and still result in a DNA encoding a protein having demethylase activity. An important consideration is that structure is not necessarily a reliable indicator of function. The instant specification provides no disclosure relating similarity or identity of structure to conservation of function. General knowledge in the art provides guidance to modification of some amino acids that are tolerated without losing a protein’s tertiary structure.
The claim includes a genus that can be analyzed at several levels sequentially for the purpose of focusing the issue. First, the disclosure of SEQ ID NO: 152/151 combined with pre-existing knowledge in the art regarding the genetic code and its redundancies would have put one in possession of the genus of nucleic acids that encode SEQ ID NO: 152 (the encoding protein). With the aid of a computer, one of skill in the art could identify all of the nucleic acid sequences with at least 70% sequence identity with SEQ ID NO: 152/151. However, there is no teaching regarding which 20% of the amino acids can vary from SEQ ID NO: 152 and still result in a protein that retains demethylase activity. Further, there is no disclosed or art-recognized correlation between any structure other than SEQ ID NO: 152 and demethylase activity. An important consideration is that structure is not necessarily a reliable indicator of function. In this example, there is no disclosure relating similarity of structure to conservation of function. General knowledge in the art included the knowledge that some amino acid variations are tolerated without losing a protein’s tertiary structure. The results of amino acid substitutions have been studied so extensively that amino acids are grouped in so-called “exchange groups” of similar properties because substituting within the exchange group is expected to conserve the overall structure. For example, the expectation from replacing leucine with isoleucine would be that the protein would likely retain its tertiary structure. On the other hand, when non-exchange group members are substituted, e.g., proline for tryptophan, the expectation would be that the substitution would not likely conserve the protein’s tertiary structure. Given what is known in the art about the likely outcome of substitutions on structure, those in the art would have likely expected the applicant to have been in possession of a genus of proteins having a tertiary structure similar to SEQ ID NO: 152 from Heliothis virescens P450 protein mutant (I256V) although the claim is not so limited. However, conservation of structure is not necessarily a surrogate for conservation of function. In this case, there is no disclosed correlation between structure and function. There is no disclosure of the active site amino acid residues responsible for the catalytic activity. While general knowledge in the art may have allowed one of skill in the art to identify other proteins expected to have the same or similar tertiary structure, in this case there is no general knowledge in the art about similar proteins to SEQ ID NO: 152 to suggest that general similarity of structure confers the activity. Accordingly, one of skill in the art would not accept the disclosure of SEQ ID NO: 152 (or the encoding DNA of SEQ ID NO: 151) as representative of other proteins having demethylase activity. The specification, taken with the pre-existing knowledge in the art of amino acid substitution and the genetic code, fails to satisfy the written description requirement of 35 U.S.C. 112, first paragraph.
8. Applicants’ arguments (previous): Applicants argue that “The software output uses one dot or two dots in the output to indicate the degree of conservation. Examples of tolerated conservative substitutions are those corresponding to I256V, L160M, N216S, R443K of SEQ ID NO: 152. In a particular embodiment the demethylase comprises comprise one or more conserved amino acids corresponding to amino acids selected from positions G103, Hll, K167, E198, R219, L223, I256, A259, L273, V284, I309, L314, Q517, L160, N216 and/or R443 of SEQ ID NO: 152 (Hv CYP AOA2A4JAM9) or any conservative substitutions thereof and comprises a polypeptide which is at least 60% identical to the
insect demethylase comprised in SEQ ID NO: 152.”
Present Application [0207] (emphasis added).
Prior to this amendment, claim 99 included similar limitations. Given such guidance, it is well within the understanding and skill of a person skilled in the art to produce demethylase variants within 60% SEQ ID of SEQ ID NO: 152, having preserved one or more of positions G103
PNG
media_image2.png
13
46
media_image2.png
Greyscale
K167, E198, R219, L223, I256, A259, L273, V284, I309, L314, Q517, L160, N216and/or R443. More specifically, a person skilled in the art would understand that the cited portions include demethylase variants within 60% SEQ ID of SEQ ID NO: 152.
Accordingly, Applicant respectfully disagrees with this characterization. Nevertheless, without acquiescing to the rejection, without waiver or disclaimer, and solely to expedite prosecution, claim 94 is amended to include the subject matter of claim 99 specifying the conserved region. Moreover, the optional feature of claim 94 is separated and reintroduce in new dependent claim 114.
Response: Applicants’ arguments are considered but not found to be persuasive because of the 30-40% modifications of SEQ ID Nos.152/151 that is sought in the host cell construction as well as the any conservative substitution claimed; and which is discussed above in the rejection under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph.
9. Applicants arguments (new):
The specification teaches that the cell of the invention "may be an eukaryote cell selected from the group consisting of mammalian, insect, plant, or fungal cells" and further specifies that "...the cell is a fungal cell selected from the phylas consisting of Ascomycota, Basidiomycota, Neocallimastigomycota, Glomeromycota, Blastocladiomycota, Chytridiomycota, Zygomycota, Oomycota and Microsporidia." See Specification as filed, [0303]. The working examples further demonstrate successful expression of insect demethylases, including SEQ ID NO: 152, in Saccharomyces cerevisiae yeast strains - a fungal cell - and their successful conversion of thebaine to northebaine and oripavine to nororipavine. See Specification at [0676]-[0685].
Further, the working examples demonstrate the superiority of a broad range of moth demethylases, including SEQ ID NO: 152 and its variants, across multiple experimental conditions. See Specification as filed, [0680]-[0689], Tables 5-1 through 5-8. Specifically, Example 5 demonstrates that expression of demethylase Hv_CYP_AOA2A4JAM9 (SEQ ID NO: 152) from Heliothis virescens in yeast exhibited an N-demethylation of thebaine to northebaine of approximately 44% and N-demethylation of oripavine to nororipavine of approximately 36%, without significant presence of oxaziridines or N-oxides - representing approximately 279% more conversion of oripavine to nororipavine compared to the best fungal demethylase. Id. Example 5 further shows the successful activity of a wide array of insect demethylases corresponding to SEQ ID NOs: 140, 142, 144, 146, 148, 152, 154, 156, 158, 162, 164, 166, 168,
170, 172, 174, 176, 178, 182, 184, 186, 188, 190, 192, 194, 196, 827, 829, 831, 833, 835, 837, 839, and 841, all of which exhibited demethylase activity in S. cerevisiae yeast host cells. See Specification as filed, [0152], Tables 5-1 through 5-8. The specification additionally describes and characterizes variants of SEQ ID NO: 152, including single mutants (e.g., Al10S, Al10N) and a triple mutant (Al10N+H242P+V224I), which retained and in certain instances improved demethylase activity. See Specification as filed, [0837]-[0838], Tables 41-5, 41-6. The triple mutant A110N+H242P+V224I, for example, demonstrated 8% more nororipavine production compared to the wild-type SEQ ID NO: 152. See Specification as filed, [0838]. These variants were further tested with transporters in Examples 45 and 46, confirming their functional activity in yeast across bioconversion of both thebaine and oripavine. See Specification as filed, [0865]- [0870], Tables 45-1, 46-1.
As such, the breadth of experimental data in the working examples provides a person of ordinary skill in the art with a sufficient basis to understand that the specification describes a representative number of species within the genus of polypeptides at least 80% identical to SEQ ID NO: 152 having the claimed demethylase activity. The specification further discloses analysis comparing the best-performing insect demethylases that identifies shared structural sequence features in the form of conserved amino acid positions. See Specification as filed, [0207]. This structural and functional characterization, combined with the narrowed claim scope, fully satisfies the written description requirement.
Accordingly, Applicant respectfully requests the withdrawal of the rejections of independent claim 94 and dependent claims therefrom under 35 U.S.C. § 112(a).
Response: Applicants’ arguments are considered but not found to be persuasive because what is argued is not reflected in the new claims. In fact the new claims are further non-descriptive in view of deletion of specific mutants from claim 94. The rejection is therefore maintained.
10. No claim is allowed.
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to TEKCHAND SAIDHA whose telephone number is (571)272-0940. The examiner can normally be reached on M-F 8.00-5.30. 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, Robert B Mondesi can be reached on 408 918 7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/TEKCHAND SAIDHA/
Primary Examiner, Art Unit 1652
Recombinant Enzymes, Hoteling
Telephone: (571) 272-0940
Fax: (571) 273-0940
Prosecution Insights