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 .
Status of the Application
Claims 1, 2, 11-26, and 28-29 are pending.
Claims 2, 11-12, 16-20, 22, 24-26 and 28-29 are amended.
Claims 3-10, and 27 are canceled.
Claims 1, 2, 11-26, and 28-29 have been examined on the merits.
Priority
This application, U.S. Application number 17/915500, is a national stage entry of International Application Number PCT/IL2021/050357, filed on 03/29/2021, which claims for domestic priority under 35 U.S.C. 119(e) to provisional applications No. 63/049685 filed on 07/09/2020 as well as for foreign priority under 35 U.S.C. 119(a)-(d) to foreign application No. IL273684 filed on 03/29/2020.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 11/09/2022, 01/17/2023, 12/13/2023, 12/21/2023, 04/09/2025, and 10/16/2025 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97., and have been considered by the examiner.
Drawings
The drawings submitted on 09/29/2022 have been reviewed and are accepted by the Examiner for examination purposes.
Claim Objections
Claim 17 is objected to due to the recitation of “the genetically modified human GCase comprises a thermal stability …”. Given the thermal stability is a property, not a component, of the claimed GCase, the recited phrase should be revised to “the genetically modified human GCase has a thermal stability …”. Appropriate correction is required.
Claim 19 is objected to because of the recitation of “of any one of claim 1”. The phrase should be corrected to “of claim 1”. Appropriate correction is required.
Claim 20 is objected to due to the recitation of “… polynucleotide comprising a nucleic acid sequence encoding … GCase”. Given it’s the nucleic acid, not the sequence, being a part of the polynucleotide for encoding the GCase, the recited phrase should be changed to “… polynucleotide comprising a nucleic acid encoding … GCase”. Appropriate correction is required.
Claim 21 is objected to due to the recitation of “any one of SEQ ID NO: 3, 5 … 23 or 26”. The recited limitation should be corrected to “any one of SEQ ID NOs: 3, 5 … 23 and 26” to be consistent with the standard language for a Markush group. In addition, the recited “the nucleic acid sequence” should be changed to “the nucleic acid having a sequence” for the reason indicated above in the objection to claim 20. Appropriate correction is required.
Claim 22 is objected to due to the recitation of “expression of said nucleic acid sequence”. The recited “said nucleic acid sequence” should be changed to “said nucleic acid” for the reason indicated above in the objection to claim 20. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b), or 112, Second Paragraph
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 11, 16-19, and 26 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 pre-AIA the applicant regards as the invention.
Claim 11 is indefinite due to the recitation of “amino acids at coordinates D127, F128 … W381, N396, wherein the coordinates … are not modified. It is noted that no connection word (e.g. “and” or “or”) is placed between the “W381” and “N396”. It is unclear whether the mutations recited in the base claim 1 are at coordinates with any one or a combination of these unmodified amino acids recited in the claim 11. For the purpose of examination, the recited phrase is interpreted as “the genetically modified human GCase further comprises unmodified amino acids at coordinates D127, F128 … W381, and N396 corresponding to SEQ ID NO: 2”, according to the disclosure of the specification.
Claim 16 is indefinite due to the recitation of “… GCase is capable of catalyzing hydrolysis of said GlcCer … kcat/Km (M-1min-1)”. A parenthetical phrase is akin to “for example”. Given multiple different units may be used for a ratio of kcat/Km, the recited parenthetical phrase renders the claim indefinite because it does not clearly indicate if the limitation in the parentheses is required or simply an example. For the purpose of examination, the recited phrase is interpreted as “… GCase is capable of catalyzing hydrolysis of said GlcCer at a level of kcat/Km of at least about 0.2 x 106 M-1min-1.
Claims 17-19 are indefinite due to the recitation of “under the same conditions”. The claim does not recite any comparison phrase. It is unclear which specific conditions can be considered as “the same conditions”.
The claim 18 is also indefinite due to the recitation of “… GCase comprises at least 2 times intracellular expression level in eukaryotic cells …”. There is not sufficient antecedence basis for the limitation of “at least 2 times intracellular expression level in eukaryotic cells”. The claim is directed to a genetically modified enzyme, not to an eukaryotic cell that expresses the genetically modified enzyme. Given the claim does not previously define any expression of enzyme in eukaryotic cells, it is unclear where the eukaryotic cells come from.
Claim 26 is indefinite due to the recitation of “a cell comprising same”. It is unclear whether the recited “same” refers to the isolated polynucleotide or to the GCase previously recited in the claim.
Claim Interpretation
Claims 1 and 2 recite the mutation limitations of “K224N/G”, “H145K/R”, “T334F/Y/K”, “N102D/E”, “L103N/E/R”, “I406T/A”, “L420M/I”, and/or “D104N/G”. The forward slash (/) in the limitations is interpreted as an alternative term "or" based on the disclosure of the specification. For example, the mutation “K224N/G” is interpreted as substituting K at the position of 224 with N or G.
Claim Rejections - 35 USC § 112(a) or 112, First Paragraph
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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, 11, 16-20, 22-26, and 28-29 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(s), at the time the application was filed, had possession of the claimed invention.
The claims are directed in part to: (a) a genetically modified human beta-glucocerebrosidase (GCase): (i) comprising an amino acid sequence at least 85 % identical to SEQ ID NO: 2, (ii) comprising mutations L34P, K224N/G, T369E and N370D at coordinates correspond to the SEQ ID NO: 2, and (iii) being capable of catalyzing hydrolysis of a glycolipid glucosylceramide (GlcCer); (b) an isolated polynucleotide comprising a nucleic acid encoding the GCase having at least 85 % identical to SEQ ID NO: 2; (c) a nucleic acid construct comprising the polynucleotide/nucleic acid encoding the GCase having at least 85 % identical to SEQ ID NO: 2; (d) an isolated cell comprising the polynucleotide/nucleic acid encoding the GCase having at least 85 % identical to SEQ ID NO: 2; (e) a pharmaceutical composition comprising as an active ingredient the GCase having at least 85 % identical to SEQ ID NO: 2; and (f) a method of treating a disease associated with GCase deficiency or a Gaucher disease in a subject, comprising administering to the subject a therapeutically effective amount of the GCase having at least 85 % identical to SEQ ID NO: 2, or the isolated polynucleotide or a cell comprising the polynucleotide encoding the GCase having at least 85 % identical to SEQ ID NO: 2. The dependent claims 16-18 further define that the GCase has catalytic activity at a kcat/Km level of at least 0.2 x 106 M-1min-1, has a higher thermal stability compared to a wild-type GCase, or is expressed in eukaryotic cells at a level two times higher than that of a wild type GCase.
It is noted that the amino acid sequence of SEQ ID NO:2 has a total of 497 amino acids; and the at least 85%identity to SEQ ID NO:2 would allow up to 75 amino acids in the sequence of SEQ ID NO:2 to be mutated by amino acids substitution, deletion, and/or insertion, for generating the claimed genetically modified GCase having at least 85% identity to SEQ ID NO:2. It is also noted that Claim 1 does not define specific positions where the mutations occurs, except for the 4 substitution mutations at positions 34, 224, 369, and 370; Claim 2 limits the GCase of claim 1 by further including as few as one additional substitution mutation; and Claim 11 limits the GCase of claim 1 by defining a total of 13 unmodified amino acids. As such, even combining all the 3 claims together and excluding these 18 positions defined by claims 1-2 and 11, the at least 85% identity to SEQ ID NO:2 still allows up to 70 amino acids to be mutated at any of the remaining 479 positions throughout the sequence of SEQ ID NO:2. Furthermore, the claims do not define any specific types of mutations in the remaining 479 positions of the GCase enzyme. As such, the GCase may have any types of mutations (substitution, deletion, and/or insertion of any amino acids) at any of 479 positions of the SEQ ID NO:2 sequence. As known to one of ordinary skill in the art, there are 20 different amino acids, which may be used to mutate amino acids at the 479 positions of the GCase enzyme. Accordingly, the GCase mutants that meet the claimed at least 85% identity to SEQ ID NO: 2 encompasses an extremely large number of different variants and mutants derived from the wild type polypeptide of SEQ ID NO: 2.
The specification of the instant application does not provide any information about the structural - functional relationship for the 497 amino acids in the GCase of SEQ ID NO: 2. Given the claims do not define specific structures at the remaining 479 amino acids of the GCase having at least 85 % identical to SEQ ID NO: 2, an extremely large numbers of polynucleotide comprising a nucleic acid encoding various different mutants having at least 85% identity to SEQ ID NO: 2 must be constructed, each of them must be cloned into an expression construct and into a host cell, and then further screened for identifying genetically modified GCase mutants that have the claimed characteristics including: being capable of catalyzing hydrolysis of GlcCer, having the catalytic activity at a kcat/Km level of at least 0.2 x 106 M-1min-1, having a higher thermal stability compared to a wild-type GCase, and being expressed in eukaryotic cells at a level two times higher than that of a wild type GCase. As such, an effective high-throughput process is necessary for mutating, cloning and expressing nucleic acids encoding various mutants having at least 85% identity to SEQ ID NO: 2, as well as further screening genetically modified GCase mutant for identifying those having the claimed characteristics, so as to apply them to patients in the method for treating a disease associated with GCase deficiency or specifically Gaucher disease. However, the working examples 1-10 in the specification only constructed and analyzed 10 GCase mutants (D2-D7 and D13-D16). There is no disclosure in the specification or the prior art regarding how to carrying out a high-throughput process for effectively mutagenizing, cloning, and expressing GCase mutants, as well as effectively screening them and determining which substitutions, deletions or insertions in the SEQ ID NO: 2, encompassed by the claimed scope, would result in GCase mutants having the claimed characteristics.
In order for the written description provision of 35 USC 112, first paragraph to be satisfied, Applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed. For example, MPEP 2163 states in part,
An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004) (The patent at issue claimed a method of selectively inhibiting PGHS-2 activity by administering a non-steroidal compound that selectively inhibits activity of the PGHS-2 gene product, however the patent did not disclose any compounds that can be used in the claimed methods. While there was a description of assays for screening compounds to identify those that inhibit the expression or activity of the PGHS-2 gene product, there was no disclosure of which peptides, polynucleotides, and small organic molecules selectively inhibit PGHS-2. The court held that “without such disclosure, the claimed methods cannot be said to have been described.”).
Without additional information, the skilled artisan cannot envision which substitutions, deletions or insertions of the polypeptide of SEQ ID NO: 2 would result in a genetically modified GCase encompassed by the claims, which is capable of catalyzing hydrolysis of GlcCer, having catalytic activity at a kcat/Km level of at least 0.2 x 106 M-1min-1 and a higher thermal stability compared to a wild-type GCase, and being expressed at a level higher than that of wild type GCase. Adequate written description requires more than a mere statement that it is part of the invention.
Therefore, the full breadth of “comprising an amnio acid sequence at least 85% identical to SEQ ID NO: 2” encompassed by the claims do not meet the written description provision of 35 USC 112, first paragraph.
Allowable Subject Matter
The subject matter of Claims 1, 2, 11-26, and 28-29 is not taught or suggested by the prior art for the reasons indicated below.
Okkels et al. (WO 01/49830 A2, 2001, cited in IDS) is the closest prior art to the subject matter of claims 1, 20, 22, 24-26, and 28. Okkels et al. teach that Gaucher disease is one of inherited lysosomal storage diseases and is caused by a deficiency in a lysosomal enzyme, i.e. acid β-glucosidase, also termed glucocerebrosidase, and human glucocerebrosidase consists of 497 amino acids (page 1/lines 14-19 and 21, page 2/lines 14-15 and 24-25, page 3/lines 3-4 and 12-13). Okkels et al. also teach improving in vivo bioactivity of lysosomal enzyme (e.g. glucocerebrosidase) through modifying the lysosomal enzyme/glucocerebrosidase, thereby providing an improved treatment of lysosomal storage diseases (e.g. Gaucher disease) (page 4/lines 20-23, Claim 19). Okkels et al. specifically teach: (i) a genetically modified glucocerebrosidase/polypeptide comprising one or more substitution mutations relative to the amino acid sequence of parent glucocerebrosidase/polypeptide (Claims 19-20); (ii) an isolated polynucleotide encoding the glucocerebrosidase (Claim 45); (iii) an expression vector (i.e. a nucleic acid construct) comprising the polynucleotide encoding the glucocerebrosidase (Claim 46); (iv) a host cell comprising the expression vector that expresses the glucocerebrosidase (Claim 47); and (v) a pharmaceutical composition comprising the glucocerebrosidase/polypeptide and a pharmaceutically acceptable carrier (Claim 56); and (vi) a method of treating Gaucher disease in a patient, comprising: administering an effective amount of glucocerebrosidase/polypeptide to the patient (Claim 60). Okkels et al. further teach the one or more substitution mutations in the genetically modified glucocerebrosidase/polypeptide are selected from a Markush group, in which K224N+Q226T and K224N+Q226S are listed among a list of different substitution mutations (see Claim 20/line 7) (Note: K224N reads on one of the 4 substitution mutations recited in the instant claim 1). Listed below is the amino acid sequence alignment between “Qy”, the sequence of SEQ ID NO: 2 recited in the instant claim 1, and “Db”, the sequence of a genetically modified glucocerebrosidase taught by Okkels et al. (AAU05675), which shows there are three amino acid mismatches (including K224N+Q226S) among the alignment of 497 amino acids. The locations of L34, K224, T369, and N370 recited in the instant claim 1 are highlighted,
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Furthermore, Okkels et al. teach that the genetically modified glucocerebrosidase comprises one or more amino acids substituted with an asparagine residue “N”, wherein the one or more amino acids are selected from a Markush group, in which L34 is listed among a list of different amino acids (Claim 21/line 5). Thus, the genetically modified glucocerebrosidase may further comprise a substitution mutation L34N. However, the mutation L34N is distinct from the L34P recited in the instant claim 1, thus not meeting the limitation in the claim 1.
Overall, the genetically modified glucocerebrosidase taught by Okkels et al. differs from the genetically modified glucocerebrosidase of the instant claim 1 in that the genetically modified glucocerebrosidase of Okkels et al. comprises only the mutation K224N, but not the mutations L34P, T369E, and N370D.
Grabowski et al. (Chapter 3: Cell Biology and Biochemistry of Acid β-Glucosidase: The Gaucher Disease Enzyme, pages 49-66, 2006, in Book-Gaucher disease) teach that Gaucher disease is caused by defective functions of acid β-glucosidase (i.e. glucocerebrosidase, GCase) (page 50/lines 1-5); and the N370S mutation in GCase enzyme is common in Gaucher disease patients and has been the target used for attempts to activate the enzyme (page 58, para 2). Grabowski et al. further teach when the N370D mutation created in the human GCase produces a catalytically active enzyme with an increased enzyme activity (page 60/last 4 lines). Thus, Given Grabowski et al. teach N370D mutation increases enzyme activity, it would have been obvious to one of ordinary skill in the art to further combine N370D with K224N of Okkels et al. to arrive at a genetically mortified GCase enzyme having N370D and K224N mutations. However, no teachings of Grabowski et al. indicate other two mutations i.e. L34P and T369E, recited in the instant claim 1 are beneficial to the activity or function of the GCase enzyme. Grabowski et al. do not teach using either L34 or T369 amino acid as targets of mutation for improving the enzyme activities, while Grabowski et al. teach several other amino acids in the GCase enzyme are critical for glucosylation and catalytic activities of the GCase, which include E235, E340, V394, I161, M123V, K198E, M416V, R463P, and Cys of 4, 16, 19, 26, 126, 248, and 342 (page 54/last para, page 60/lines 1-8, page 61/para 2/lines 5-7 and 9-11, Fig. 3.2). Thus, the claimed GCase enzyme of the claim 1 is not obvious over the combined teachings of Okkels et al. and Grabowski et al.
Futerman et al. (WO 2004/091475, cited in IDS) teach a method of computationally generating, based on the 3-D structural information of glucocerebrosidase, a set of amino acid residues having amino acid sequence of coordinates essential for normal activity of glucocerebrosidase; and Futerman et al. provide a total of 6 different sets of amino acid residues at coordinates to be applied for constructing glucocerebrosidase mutants (abstract, Claims 9 and 16). However, none of these 6 sets of amino acid residues teaches or suggests a combination of the 4 amino acid residues (i.e. L34, K224, T369, and N370) for constructing the mutations at coordinates L34P, K224N/G, T369E, and N370D in the genetically modified glucocerebrosidase of the instant claim 1. Thus, further combining the teachings of Futerman et al. with those of Okkels et al. and Grabowski et al. would not render the claimed GCase enzyme of the claim 1 to be obvious.
Mason et al. (WO 2019/173756, 2019, cited in IDS) teach a method of treating patients having or at a risk of developing Parkinson’s disease by administering pluripotent cells expressing glucocerebrosidase (GBA) or its variants/mutants with at least 85% identity (abstract, page 1/lines 29-34, page 17/lines 7-11). Mason et al. teach the mutations V394L, D409H, L444P , N370S, and R496H in GBA of patients cause severe or mild pathogenic conditions (page 16/lines 37-41, page 24/lines 25-26). However, Mason et al. do not teach any specific mutations in the variants used for treating patients and they do not teach any of the mutations (i.e. L34P, K224N/G, T369E, or N370D) in the genetically modified glucocerebrosidase of the instant claim 1. Thus, further combining the teachings of Mason et al. with those of Okkels et al. and Grabowski et al. would not render the claimed GCase enzyme of the claim 1 to be obvious.
Kumar et al. (Metabolic Brain Disease, 2018, 33: 1835-1845, cited in IDS) identified the most common mutations in glucocerebrosidase which are known to cause Gaucher disease and represent a risk of developing Parkinson’s disease, including K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H; and they used computational analysis of these mutations to understand association between Parkinson’s and Gaucher diseases (abstract, page 1845/1st full para). However, Kumar et al. only studies the mutations that cause Gaucher disease. There are no teachings in Kumar et al. about genetically modifying glucocerebrosidase for improving its functions or activities; and there is no teaching about specific mutations (i.e. L34P, K224N/G, T369E, or N370D) in the genetically modified glucocerebrosidase of the instant claim 1. Thus, further combining the teachings of Kumar et al. with those of Okkels et al. and Grabowski et al. would not render the claimed GCase enzyme of the claim 1 to be obvious.
Therefore, the genetically modifying human glucocerebrosidase in claim 1, 2, 11-19 as well as a pharmaceutical composition comprising the glucocerebrosidase of the claim 1 as recited in claim 25 are unobvious over the art of record. Accordingly, the isolated polynucleotide encoding the glucocerebrosidase of the claim 1 as recited in claims 20-21, the nucleic acid construct as well as the isolated cell comprising the isolated polynucleotide of claim 20 as recited in claims 22-24, and the method of using the glucocerebrosidase of claim 1 for treating a subject as recited in claims 26 and 28-29 are also unobvious over the art of record. Therefore, The subject matter of the claims 1, 2, 11-26, and 28-29 is free of the art.
Claims 12-15 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claim is in condition for allowance.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Qing Xu, Ph.D., whose telephone number is (571) 272-3076. The examiner can normally be reached on Monday-Friday from 9:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath N. Rao, can be reached at (571) 272-0939. Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to the receptionist whose telephone number is (571) 272-1600.
/Qing Xu/
Patent Examiner
Art Unit 1656
/MANJUNATH N RAO/Supervisory Patent Examiner, Art Unit 1656