DETAILED ACTION
Status of the Application
Claims 1-7 and 10-19 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A preliminary amendment filed on 10/15/2024, amending claims 1, 3, 4, 6, 7 and 10-16, cancelling claims 8-9, adding claims 18-19 and amending the specification to include a cross-reference to related applications and a reference to sequence listing submitted electronically paragraph is acknowledged.
Priority
This application is a 371 of PCT/JP2022/047741 filed on 12/23/2022 and claims
foreign priority under 35 U.S. C. 119(a)-(d) to JP2022-079708 filed on 05/13/2022, JP2022-079712 filed on 05/13/2022, JP2022-079711 filed on 05/13/2022 and JP2021-215094 filed on 12/28/2021.
Specification
The disclosure is objected to because of the following informalities: Under name in Table 4 on page 126, "Enzyme" is misspelled "Enzymme" .
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a) Written Description
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 1-7 and 10-19 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 in part to a polypeptide comprising a sequence having 90% or higher sequence identity to an amino acid sequence represented by SEQ ID NO: 1 with one amino acid residue thereof engineered, and having higher catalytic activity than a polypeptide consisting of the amino acid sequence represented by SEQ ID NO: 1 for a reductive amination reaction between at least one compound A represented by the following formula (1) or a salt thereof and at least one compound B represented by the following formula (2) or a salt thereof or an intramolecular reductive amination reaction of at least one compound B represented by the formula (2) or a salt thereof under at least one reaction condition:
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128
220
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wherein in the formula (1),
R¹ and R² each independently represent a hydrogen atom, an alkyl group, an alkenyl group,
an alkynyl group, a cycloalkyl group, an aryl group, a heterocyclyl group, or a heteroaryl
group, these groups are optionally substituted, and at least one of R¹ and R² is a hydrogen
atom,
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125
324
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87
333
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171
317
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wherein in the formula (2),
X represents a carbon atom, Y represents a hydrogen atom, a group represented by the formula (1’) or a group represented by formula (3), n represents an integer of between 0 and 2, and R6 represents a hydrogen atom, an optionally substituted aliphatic hydrocarbon group having between 1 and 6 carbon atoms, an optionally substituted aryl group having between 5 and 12 carbon atoms, an optionally substituted heteroaryl group having 5 and 12 ring-constituting atoms, a group containing a nitrogen atom, or a group containing an oxygen atom; in the formula (1’),
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72
57
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Represents a binding point to X, and R1a is a group by removing a hydrogen atom from the group represented by R1 in the formula (1), and is not a hydrogen atom;
In the formula (3),
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72
57
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Represents a binding point to X, m represents an integer of between 0 and 6, p is 0 or 1, q is 0 or 1, r is 0 or 1, Z1 represents an optionally substituted alkylene group, or an ether bond-containing group having between 1 and 6 carbon atoms, and when m is 2 or larger, a plurality of Z1 are the same of different, Z2 represents a carbon atom, R³, R⁴ and R⁵ each independently represent a hydrogen atom, an optionally substituted aliphatic hydrocarbon group having between 1 and 6 carbon atoms, an optionally substituted aryl group having between 5 and 12 carbon atoms, an optionally substituted heteroaryl group having between 5 and 12 ring-constituting atoms, a group containing a nitrogen atom, or a group containing an oxygen atom, any two or more of R³, R⁴, and R⁵ are optionally bonded to each other to form a ring structure together with Z², the ring structure is optionally a cycloalkyl group, an aryl group, a heterocyclyl group, or a heteroaryl group, and these groups are optionally substituted, R³, R⁴, and R⁵ each optionally form a double bond or a triple bond with Z², and when any one of R³, R⁴, and R⁵ is bonded to Z² through a double bond or a triple bond, at least one of p, q and r is 0; and when one of R¹ and R² in the formula (1) is a methyl group and the other moiety is a hydrogen atom, in the formula (2), Y is a group represented by the formula (3), m is 0, and two or more of R³ to R⁵ are not a hydrogen atom, and wherein the polypeptide comprises a sequence having the engineering of an amino acid residue positioned at a site corresponding to at least one amino acid residue selected from the group consisting of: a histidine residue at position 44, a threonine residue at position 156, a histidine residue at position 182, a glutamine residue at position 186, a tryptophan residue at position 253, and a lysine residue at position 260 in the amino acid sequence represented by SEQ ID NO: 1. Claims 2-3, 7, and 10-19 depend directly or indirectly therefrom claim 1.
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, precise definition, such as by structure, formula, [or] chemical ‘requires a 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.
Claim 1 recites a polypeptide that comprises a sequence having 90% or higher sequence identity to an amino acid sequence represented by SEQ ID NO: 1 with one amino acid residue thereof engineered, but the specification does not reasonably convey possession of the full breadth of variants encompassed by the claim. The disclosure appears to support, at most sequences that have three amino acids engineered which is around 99% sequence identity to SEQ ID NO: 1. The claim encompasses a large genus of proteins that can have up to 33 amino acid modifications within SEQ ID NO:1
(
0.1
×
332
=
33.2
)
; SEQ ID NO: 1 has 332 amino acids. The specification provides no clue as to whether all of the possible modifications encompassed by the % sequence identity recited would result in a variant of the polypeptide of SEQ ID NO: 1 able to have increased catalytic activity or even able to catalyze the recited reactions. The claims encompass a large genus of proteins sharing a limited number of structural features. A sufficient written description of a genus of polypeptides may be achieved by a recitation of a representative number of polypeptides defined by their amino acid sequence or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, the recited structural feature, i.e., “90% or higher sequence identity to SEQ ID NO: 1, is not representative of all the members of the genus of proteins recited since there is no information as to which are the structural elements within the polypeptide of SEQ ID NO: 1 that are essential for the desired activity. Claims 2-3, 7, and 10-19 all require the polypeptide of claim 1.
Claim 4 is directed in part to a polypeptide comprising a sequence having 90% or higher sequence identity to an amino acid sequence represented by SEQ ID NO: 1 with one amino acid residue thereof engineered, and having higher catalytic activity than a polypeptide consisting of the amino acid sequence represented by SEQ ID NO: 17 for a reductive amination reaction between an alkylamine or a salt thereof and at least one compound represented by the following formula (2') or a salt thereof under at least one reaction condition:
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172
303
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wherein Y' represents a C₃ to C₈ cycloalkyl group or a C₆ to C₉ aralkyl group, and the aralkyl group is optionally substituted by a C₁ to C₃ alkyl group or a halogen atom. Claims 5-6 depend directly therefrom claim 4.
Claim 4 recites a polypeptide that comprises a sequence having 90% or higher sequence identity to an amino acid sequence represented by SEQ ID NO: 1 with one amino acid residue thereof engineered and having higher catalytic activity than a polypeptide consisting of the amino acid sequence represented by SEQ ID NO:17, but the specification does not reasonably convey possession of the full breadth of variants encompassed by the claim. The disclosure appears to support, at most sequences that have three amino acids engineered which is around 99% sequence identity to SEQ ID NO: 1. The claim encompasses a large genus of proteins that can have up to 33 amino acid modifications within SEQ ID NO:1
(
0.1
×
332
=
33.2
)
; SEQ ID NO: 1 has 332 amino acids. Claims 5-6 require the polypeptide of claim 4.
Due to the fact that the specification only discloses a few species of the genus, and the lack of description of any additional species by any relevant, identifying characteristics or properties, one of skill in the art would not recognize from the disclosure that Applicant was in possession of the claimed invention.
Claims 1-7 and 10-19 are rejected under 35 U.S.C.112, first paragraph, because the specification, while being enabling for the polypeptide of SEQ ID NO: 1 and mutants having up to 3 mutations that have higher catalytic activity, does not reasonably provide enablement for all variants of the polypeptide of SEQ ID NO: 1 having 90% or higher sequence identity to the polypeptide of SEQ ID NO: 1. 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.
Factors to be considered in determining whether undue experimentation is
required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed.
Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breath of the claims. The factors which have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breath of the claims. Claims 1-7 and 10-19 encompass variants of the polypeptide of SEQ ID NO: 1 having higher catalytic activity and 90% or higher sequence identity to the polypeptide of SEQ ID NO:1. The enablement provided is not commensurate in scope with the claim due to extremely large number of proteins encompassed by the claims for which a significant portion of their structure is unknown. In the instant case, the specification enables the polypeptide of SEQ ID NO:1 and mutants with 1 to 3 amino acid substitutions that have higher catalytic activity.
The amount of direction or guidance presented and the existence of working examples. The specification discloses a limited number of variants of the polypeptide of SEQ ID NO: 1 having higher catalytic activity as working examples, while also providing examples of mutants that do not have increased activity. However, the specification is silent with regard to the structural elements required in any polypeptide having the recited structural characteristics such that the polypeptide would use the specific substrates of claims 1, 4, 13, 14 and 15. No correlation between structure and the ability to use the specific substrates recited in the claims has been presented or is known in the art. While the claimed variants can have up to 33 modifications within SEQ ID NO: 1 (90% sequence identity), there is no information or guidance as to which 33 amino acids residues in the polypeptide of SEQ ID NO: 1 can be modified and which ones are to be conserved to create a variant displaying higher catalytic activity compared to SEQ ID NO: 1.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. While methods of generating or isolating variants of a polypeptide were known in the art at the time of the invention, it was not routine in the art to screen by a trial-and-error process for all variants of the polypeptide of SEQ ID NO: 1 having 90% or higher sequence identity to the polypeptide of SEQ ID NO: 1 and determine which ones have the ability to catalyze the recited reactions. In the absence of (a) a rational and predictable scheme for modifying any residue in the polypeptide of SEQ ID NO: 1 such that the resulting variant would have higher catalytic activity, and/or (ii) a correlation between structure and activity, one of skill in the art would have to test an essentially infinite number of proteins to determine which ones can utilize the recited reactants and catalyze the recited reactions.
Therefore, taking into consideration the extremely broad scope of the claim, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of
the claims.
Closest Prior Art
The prior are does teach mutations (F117L, M141V or M141L) to the gene DpkA, which is SEQ ID NO: 1, that increase the catalytic activity, see Table 2, pg. 6 of Mindt et al. (Frontiers in Bioengineering and Biotechnology, published 09/26/2019) and Kerbs et al. (Microorganisms, published 04/13/2021) which introduced an amino acid exchange in the enzyme’s substrate binding pocket (F117L) to produce sarcosine and N-ethyl-glycine (see 3.2., pg. 7). However, the art does not teach any of the amino acid substitutions at the positions taught in claim 1, a histidine residue at position 44, a threonine residue at position 156, a histidine residue at position 182, a glutamine residue at position 186, a tryptophan residue at position 253, and a lysine residue at position 260 in the amino acid sequence represented by SEQ ID NO: 1. Based on the crystal structure of DpkA (PDB ID: 1WTJ, Goto et al. (Journal of Biological Chemistry, published 12/09/2005), the mutations in claim 1 are not just limited to the substrate binding pocket which makes the amino acid substitutions none obvious and would require more than routine experimentation to discover an increase in catalytic activity, which has been shown in the instant application to vary not only with the mutation but also the substrate.
Conclusion
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DALTON KIEFER, PhD whose telephone number is (571)272-1235. The examiner can normally be reached M-F 7:30-5 EST.
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/DALTON EDWARD KIEFER/Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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