DETAILED ACTION
Status of Application
Claims 1-12 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 of claims 3-7, 9-10, and 12 as submitted in a communication filed on 07/19/2024 is acknowledged.
Applicant’s election with traverse of Group I, claims 1-4, drawn to a mutant α-L-fucosidase as submitted in communication filed on 07/13/2026 is acknowledged.
Applicant’s traverse is on the grounds that it would not pose an undue burden on the Examiner to examine all the claims together. Applicant’s arguments have been fully considered but not deemed persuasive to withdraw the restriction requirement. It is noted that It would be erroneous to assume that a reference that teaches a polypeptide would necessarily teach a method of using a polypeptide. Therefore, contrary to Applicant’s assertions, a comprehensive search of all the claims would require class/subclass searches which are not necessarily co-extensive as well as different keyword searches in the patent/non-patent literature. Thus, an examination of all the claimed inventions would impose an undue burden on the Office. The requirement is deemed proper and therefore is made FINAL.
Claims 5-12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 07/19/2024.
Claims 1-4 are at issue and will be examined to the extent they encompass the elected invention.
Priority
Acknowledgment is made of applicant' s claim for domestic priority under 35
U.S.C. 119 (e) to provisional Application No. 63/529439 filed on 07/28/2023.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 07/19/2024 and 02/11/2025 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Rejections - 35 USC § 103 (AIA )
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.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over Klontz et al. (Nature Communications 11.1 (2020): 6204; hereby “Klontz”)(Cited in IDS).
In regards to Clams 1-3, Klontz teaches the structure and dynamics of an α-fucosidase, called AlfC (abstract). Klontz teaches the crystal structures of AlfC, combined with mutational and kinetic analyses (abstract). It was noted that the crystal structure of the α-L-fucosidase of Klontz (Uniprot ID: A0A422MHI3_LACPA) has 100% sequence identity to the α-L-fucosidase of SEQ ID NO:1 (See alignment below). Klontz teaches an approach, wherein point mutations were performed on the disordered region of AlfC near the active site, which is between amino acid residues 247-266 (Fig. 2g and pages 6 [1]-[2]). Klontz teaches that a mutation at position 274 to alanine can convert AlfC from a hydrolase into an efficient transfucosidase (Page 2 [2]). Klontz teaches that position 274 is an acid/base candidate (Fig. 2f and pages 6 [1]-[2]). Klontz discloses that mutating the acid/base results in a large (~104-fold) decrease in kcat and a decrease in KM (higher affinity) (pages 6 [1]). Klontz discloses that some mutants have a 2-fold increase in enzymatic activity compared to wildtype α-L-fucosidase (pages 6 [1]-[2]). In regards to claim 4, Klontz teaches the defucosylation of IgG, wherein antibodies are treated with an endoglycosidase and α-fucosidase (Fig 1). Klontz does not expressly teach the substitution of lysine at position 247.
RESULT 1
A0A422MHI3_LACPA
ID A0A422MHI3_LACPA Unreviewed; 344 AA.
AC A0A422MHI3; K0NB39;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 10-JUN-2026, entry version 36.
DE RecName: Full=alpha-L-fucosidase {ECO:0000256|ARBA:ARBA00012662};
DE EC=3.2.1.51 {ECO:0000256|ARBA:ARBA00012662};
GN ORFNames=BN194_28780 {ECO:0000313|EMBL:CCK23825.1}, C0Q90_12685
GN {ECO:0000313|EMBL:PLC45420.1};
OS Lacticaseibacillus paracasei (Lactobacillus paracasei).
OC Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
OC Lacticaseibacillus.
OX NCBI_TaxID=1597 {ECO:0000313|EMBL:CCK23825.1};
RN [1] {ECO:0000313|EMBL:CCK23825.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=W56 {ECO:0000313|EMBL:CCK23825.1};
RX PubMed=23144392; DOI=10.1128/JB.01386-12;
RA Hochwind K., Weinmaier T., Schmid M., van Hemert S., Hartmann A.,
RA Rattei T., Rothballer M.;
RT "Draft Genome Sequence of Lactobacillus casei W56.";
RL J. Bacteriol. 194:6638-6638(2012).
RN [2] {ECO:0000313|EMBL:PLC45420.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DUP 13076 {ECO:0000313|EMBL:PLC45420.1};
RX PubMed=29449394;
RA Muyyarikkandy M.S., Alqahtani F.H., Mandoiu I., Amalaradjou M.A.;
RT "Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits
RT Potent Antipathogenic Effects against Salmonella enterica Serovars
RT Enteritidis, Typhimurium, and Heidelberg.";
RL Genome Announc. 6:e00065-e00018(2018).
RN [3] {ECO:0007829|PDB:6O18, ECO:0007829|PDB:6O1A}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).
RX PubMed=33277506; DOI=10.1038/s41467-020-20044-z;
RA Klontz E.H., Li C., Kihn K., Fields J.K., Beckett D., Snyder G.A.,
RA Wintrode P.L., Deredge D., Wang L.X., Sundberg E.J.;
RT "Structure and dynamics of an alpha-fucosidase reveal a mechanism for
RT highly efficient IgG transfucosylation.";
RL Nat. Commun. 11:6204-6204(2020).
CC -!- FUNCTION: Alpha-L-fucosidase is responsible for hydrolyzing the alpha-
CC 1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the
CC carbohydrate moieties of glycoproteins.
CC {ECO:0000256|ARBA:ARBA00004071}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 29 family.
CC {ECO:0000256|ARBA:ARBA00007951}.
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DR EMBL; HE970764; CCK23825.1; -; Genomic_DNA.
DR EMBL; PKQJ01000018; PLC45420.1; -; Genomic_DNA.
DR RefSeq; WP_012492118.1; NC_010999.1.
DR PDB; 6O18; X-ray; 2.55 A; A/B/C/D=1-344.
DR PDB; 6O1A; X-ray; 2.60 A; A/B/C/D=1-344.
DR PDB; 6O1C; X-ray; 2.60 A; A/B/C/D/E/F/G/H=1-344.
DR PDB; 6O1I; X-ray; 3.55 A; A/B/C/D=1-344.
DR PDB; 6O1J; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-344.
DR PDB; 6OHE; X-ray; 3.14 A; A/B/C/D=1-344.
DR CAZy; GH29; Glycoside Hydrolase Family 29.
DR KEGG; lce:LC2W_2937; -.
DR KEGG; lcw:BN194_28780; -.
DR PATRIC; fig|1215914.3.peg.3019; -.
DR BRENDA; 3.2.1.127; 2884.
DR BRENDA; 3.2.1.51; 2884.
DR GO; GO:0005764; C:lysosome; IEA:TreeGrafter.
DR GO; GO:0004560; F:alpha-L-fucosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0006004; P:fucose metabolic process; IEA:InterPro.
DR GO; GO:0016139; P:glycoside catabolic process; IEA:TreeGrafter.
DR Gene3D; 3.20.20.80; Glycosidases; 1.
DR InterPro; IPR016286; FUC_metazoa-typ.
DR InterPro; IPR017853; GH.
DR InterPro; IPR000933; Glyco_hydro_29.
DR InterPro; IPR057739; Glyco_hydro_29_N.
DR PANTHER; PTHR10030; ALPHA-L-FUCOSIDASE; 1.
DR PANTHER; PTHR10030:SF37; ALPHA-L-FUCOSIDASE-RELATED; 1.
DR Pfam; PF01120; Alpha_L_fucos; 1.
DR PIRSF; PIRSF001092; Alpha-L-fucosidase; 1.
DR SMART; SM00812; Alpha_L_fucos; 1.
DR SUPFAM; SSF51445; (Trans)glycosidases; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:6O18, ECO:0007829|PDB:6O1A};
KW Glycosidase {ECO:0000256|ARBA:ARBA00023295};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Signal {ECO:0000256|ARBA:ARBA00022729}.
FT DOMAIN 6..333
FT /note="Glycoside hydrolase family 29 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF01120"
SQ SEQUENCE 344 AA; 39219 MW; DE27CE0DADC8E6C4 CRC64;
Query Match 100.0%; Score 1879; Length 344;
Best Local Similarity 100.0%;
Matches 344; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MNDNVAWFKQAKYGMMIHWGLYSLLAGEYRGESSSAYAEWIQSKFQIPNAEYGNLATAFN 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MNDNVAWFKQAKYGMMIHWGLYSLLAGEYRGESSSAYAEWIQSKFQIPNAEYGNLATAFN 60
Qy 61 PLYFDAKKIVALAKQCGMQYLVVTTKHHDGFAMYHSKVDAYNVYDATPFHRDIIGELAEA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PLYFDAKKIVALAKQCGMQYLVVTTKHHDGFAMYHSKVDAYNVYDATPFHRDIIGELAEA 120
Qy 121 CQKAGLKFGLYYSQDLDWHDPNGGGYKSNDVETAGTTWDNSWDFPDEDQKNFDLCFDNKI 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 CQKAGLKFGLYYSQDLDWHDPNGGGYKSNDVETAGTTWDNSWDFPDEDQKNFDLCFDNKI 180
Qy 181 LPQIKEIMSNYGDIATAWFDVPMTLSEAQSQTIYDTVRELQPNCLINSRLGNGKYDFVSL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LPQIKEIMSNYGDIATAWFDVPMTLSEAQSQTIYDTVRELQPNCLINSRLGNGKYDFVSL 240
Qy 241 GDNEIPKNKEDMNKTDVDYNEITGFKPSPLGLYETAGTINDSWGFSYHDQNWKTPRTLYR 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GDNEIPKNKEDMNKTDVDYNEITGFKPSPLGLYETAGTINDSWGFSYHDQNWKTPRTLYR 300
Qy 301 YKQHLNDFGINYLLNVGLDPLGRVPMMAEENLLAAKALEDEANR 344
||||||||||||||||||||||||||||||||||||||||||||
Db 301 YKQHLNDFGINYLLNVGLDPLGRVPMMAEENLLAAKALEDEANR 344
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to mutate residues in the disordered region near the active site, such as residue 247, to determine the roles of the amino acids in the disordered region or field for other mutations that have increased substrate affinity and/or enzymatic activity. A person of ordinary skill in the art is motivated to modify the amino acid residue at position 247 of an α-L-fucosidase having at least 95% sequence identity to SEQ ID NO: 1, including substituting a lysine at position 247 with alanine (equivalent to SEQ ID NO:5) because Klontz specifically investigates an alanine substitution at position 247 and teaches that mutations within the disorder region near the active site can affect enzyme function. Accordingly, one of ordinary skill is motivated to investigate residue substitutions within this region by point mutagenesis to determine the contribution of such residues to enzyme function and to identify mutants having altered or desirable enzymatic properties, including substrate affinity. One of ordinary skill in the art has a reasonable expectation of success at producing the claimed mutants because Klontz demonstrates that residues associated with that disorder region are amendable to substitution mutations that can result in improved enzymatic properties. Furthermore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have the mutant α-L-fucosidase discussed above in a composition comprising at least one glycosidase. A person of ordinary skill in the art is motivated to have said composition because the use of α-L-fucosidase with an endoglycosidase for defucosylation of IgG is taught by Klontz. One of ordinary skill in the art has a reasonable expectation of success because Klontz teaches the use of of α-L-fucosidase with a endoglycosidase for carrying out glycan-processing reactions. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claim is in condition for allowance.
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/S.L.S./Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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