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
Claims 1-3, 5-10, 13-15, 17 and 22 are pending. Claim 22 is withdrawn.
Claims 1-3, 5-10, 13-15 and 17 are under examination herein.
Priority
This application is a 371 of PCT/EP2021/054510 filed 2/24/2021, which claims benefit of SWITZERLAND 00215/20 filed on 2/24/2020.
The effective filing date of the current application is February 24, 2020.
Claim Objections
Claim 1 is objected to because of the following informalities: b) subitems “i.” and “ii.” which include a period. It is suggested that the identifier be amended to use a parenthesis as in “i)” and “ii)”. See MPEP 608.01(m), first paragraph.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Maintained rejection: Claims 1-3, 5-10, 13-15 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Samain (WO 2007/101862 A1, published on September 13, 2007; previously cited) in view of Shoda et al. (“A facile enzymatic synthesis of cellooligosaccharide derivatives using β-lactosyl fluoride”, Carbohydrate Research, 1993, Vol. 249, Issue 1, pp.127-137; previously cited) and Yokoyama (“Methods of synthesis of glycosyl fluorides”, Carbohydrate Research, 2000, Vol. 327, Issues 1-2, pp.5-14; previously cited).
Regarding claim 1, Samain teaches a method of producing oligosaccharides comprising the step of consisting of culturing a microorganism in a culture medium, optionally comprising an exogenous precursor, wherein said microorganism comprises heterologous genes encoding a CMP-Neu5Ac synthetase, a sialic acid synthase, a GlcNAc-6-phosphate 2 epimerase and a sialyltransferase (description p.47, claim 1). Samain teaches using metabolically engineered Escherichia coli strains overexpressing Neisseria meningitidis genes for α-2,3-Sialyltransferase and for CMP-Neu5Ac synthase to eventually produce sialyllactose (description p.2 lines 4-14).
Samain does not teach wherein the exogenous precursor is a compound of General Formula I.
However, Shoda teaches a convenient method for the preparation of cellooligosaccharide derivatives using β-lactosyl fluoride as the glycosyl donor (abstract). Shoda teaches that the reaction gave rise to a β-cellotrioside derivative (abstract). Shoda further teaches that a cellotetraoside derivative has been successfully prepared and using the resulting β-cellotrioside as the starting material (abstract).
Yokoyama teaches that glycosyl fluorides are versatile sugar donors in the synthesis of natural products and carbohydrates (p.5, 1st column). Yokoyama teaches that glycosyl fluorides have been utilized for effective glycosylation reactions because of their enhanced stability, ease of handling and higher stereoselectivity compared with other glycosyl halides (p.5 2nd column last paragraph to p.6, 1st sentence).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Samain to replace the lactose precursor taught by Samain with lactosyl fluoride taught by Shoda to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to do so because Yokoyama teaches that glycosyl fluorides have enhanced stability, ease of handling and higher stereoselectivity compared with other glycosyl halides. One of ordinary skill would have found it beneficial to select lactosyl fluoride because Yokohama teaches that glycosyl fluorides are versatile sugar donors in the synthesis of natural products and carbohydrates.
Regarding claim 2, Samain teaches the microorganism is an E. coli strain which is LacY+, LacZ- and optionally MelA- (description p.48, claim 7).
Regarding claim 3, Samain teaches wherein the heterologous sialyltransferase gene is a bifunctional α-2,3 and α-2,8 sialyltransferase (description p.48, claim 12).
Regarding claim 5, Samain teaches the exogenous precursor is selected from lactose, galactose, β-galactoside and α-galactoside (description p.48, claim 8).
Regarding claims 6-7 and 10, Samain teaches the exogenous precursor is selected from lactose (description p.48, claim 8), whose structure contains an OH group in the R1 and R2 positions as required by instant General Formula Ia (relevant to claims 6 and 7). Samain teaches the exogenous precursor can be lactose, which corresponds to a structure where R5 and R7 are OH, and R12, R13, R14, R15 and R16 are each independently hydrogen (description p.48, claim 8), as required by instant General Formula IIb (relevant to claim 10).
Samain does not teach wherein glycosidic bond
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is a glycosidic bond.
However, Shoda teaches β-lactosyl fluoride (Gal-Glc-F, 1) is smoothly hydrolyzed to lactose, with a regio- and stereo-selective β-(1,4)-glycosidic bond formation between the lactose unit of 1 and the D-glucose unit of the acceptor (p.128, 1st paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have replaced the lactose taught by Samain with the β-lactosyl fluoride containing a glycosidic bond taught by Shoda, because Shoda teaches that β-lactosyl fluoride (Gal-Glc-F, 1) is smoothly hydrolyzed to lactose, with a regio- and stereo-selective β-(1,4)-glycosidic bond formation between the lactose unit of 1 and the D-glucose unit of the acceptor. One of ordinary skill in the art would have found it beneficial to replace lactose with β-lactosyl fluoride because of its enhanced stability, ease of handling and higher stereoselectivity as taught by Yokoyama.
Regarding claim 8, Samain teaches the strain is devoid of β-galactosidase activity (description p.22, lines 9-10). Samain teaches the microorganism is LacZ – (β galactosidase) (description p.48, claim 7).
Regarding claim 9, Samain teaches the exogenous precursor is lactose (description p.48, claim 8), which is a disaccharide moiety.
Regarding claim 13, Samain teaches that the heterologous sialyltransferase gene may be selected from an α-2,3 sialyltransferase (description p.10, lines 13-15). Samain teaches a Neu5Acα-3Galβ-4Glc (GM3) molecule produced from Galβ-4Glc using α-2,3 sialyltransferase (Figure 2).
Regarding claim 14, Samain teaches that the heterologous sialyltransferase gene may be selected from an α-2,3 sialyltransferase (description p.10, lines 13-15). Samain also teaches wherein the heterologous sialyltransferase gene is a bifunctional α-2,3 and α-2,8 sialyltransferase (description p.10, lines 13-15; p.48, claim 12). Samain teaches an oligosaccharide moiety for the ganglioside GD3 that is Neu5Acα-8Neu5Acα-3Galβ-4Glc (description p.3, line 24). Samain teaches that GD3 can be formed by transferring a sialyl moiety from an activated sialic acid molecule produced internally to the Neu5Acα-3Galβ-4Glc (GM3) to form Neu5Acα-8Neu5Acα-3Galβ-4Glc which is GD3 (description p.23, lines 1-4; Figure 5; Figure 6). Samain further teaches the production of GD3, wherein the heterologous sialyltransferase gene is a bifunctional α-2,3 and α-2,8 sialyltransferase, such as the cstII gene from Campylobacter jejuni deposited under ATCC Accession No. 43438, which catalyzes the transfer of a sialyl moiety from an activated sialic acid molecule produced internally to the Neu5Acα-3Galβ-4Glc (GM3) to form Neu5Acα-8Neu5Acα-3Galβ-4Glc (GD3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method taught by Samain to combine the α-2,3 sialyltransferase with a bifunctional α-2,3 and α-2,8 sialyltransferase to produce the ganglioside GD3, because Samain teaches that GD3 is formed by adding a sialyl moiety to GM3 to obtain a GD3.
Regarding claim 15, Samain teaches the microorganism further comprises heterologous sequences encoding β-1,4GalNActransfersase and β-1,3-Galactosyltransferase, which β-1,4GalNActransfersase transfers a UDP-GalNac residue to sialyllactose (GM3) to form GalNAcβ-4(Neu5Acα-3)Galβ-4Glc (GM2) and the β-1,3-Galactosyltransferase transfers a Galactosyl residue to GM2 to form GM1 (description p.49, claim 14).
Regarding claim 17, Samain teaches the process of the invention is based on the active uptake of an exogenous precursor (description p.4, lines 21-22). Samain teaches that the expression “exogenous precursor” is intended to denote a compound involved in the biosynthetic pathway of the oligosaccharide according to the invention that is internalized by the cells (description p.4, lines 25-27). Samain teaches the metabolically engineered pathway for the production of several sugars such as GM3, GD3 and GT3 in Figure 5. Samain further teaches oligosaccharide moieties of the gangliosides selected from:
GM3 (3'sialyllactose, Neu5Acα-3Galβ-4Glc) and oligosaccharides comprising the GM3 motif;
GD3 Neu5Acα-8Neu5Acα-3Galβ-4Glc;
GT3 (Neu5Acα-8Neu5Acα-8Neu5Acα-3Galβ-4Glc);
GM2 GalNAcβ-4(Neu5Acα-3)Galβ-4Glc;
GMl Galβ-3GalNAcβ-4(Neu5Acα-3 )Galβ-4Glc;
GDla Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-3)Galβ-4Glc;
GTla Neu5Acα-8Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-3)Galβ-4Glc;
GD2 GalNAcβ-4(Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GT2 GalNAcβ-4(Neu5Acaα8Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GDlb Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GTlb Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GQlb Neu5Acα-8Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GTlc Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GQlc, Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GPlc Neu5Acα-8Neu5Acα-3Galβ-3GalNAcβ-4(Neu5Acα-8Neu5Acα-8Neu5Acα3)Galβ-4Glc;
GDla Neu5Acα-3Galβ-3(Neu5Acα-6)GalNAcβ-4Galβ-4Glc; and
Fucosyl-GMl Fucα-2Galβ-3GalNAcβ-4(Neu5Acα-3)Galβ-4Glc (description p.3 line 21-p.4 line 9). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Samain to replace the exogenous precursor of lactose with one of the oligosaccharide moieties taught by Samain to arrive at the claimed invention. Samain teaches that various oligosaccharide glycosyl moieties are formed and can be sialyated to produce other glycoside moieties which are recognized as being part of particular gangliosides such as GM3. One of ordinary skill in the art would reasonably expect that replacing one exogenous precursor saccharide with another would predictably result in the production of the desired glycosyl moiety because Samain teaches the pathways of various sugar productions and relevant oligosaccharide intermediates, and it was known in the art at the time of invention that exogenous precursors comprising glycosyl moieties with fluorides could be converted by glycosyltransferases to glycosyl fluorides of interest as discussed above in the rejection of claim 1.
Response to Arguments
Applicant argues that the glycosylation reaction is performed on the exogenous precursor to form the glycosyl fluoride of interest, thus both the exogenous precursor and the product of the glycosylation reaction are fluorides (See Remarks dated 1/9/26, p.13, 1st paragraph). Applicant argues that the office action acknowledges Samain does not use an exogenous precursor of General Formula I, and states that Shoda teaches a method using β-lactosyl fluoride as a glycosyl donor, however Shoda does not disclose or suggest that β-lactosyl fluoride is used to produce a glycosyl fluoride nor that a glycosylation reaction can or should be performed on β-lactosyl fluoride (See Remarks dated 1/9/2026, p.13 last paragraph).
Applicant further argues that in the method described by Shoda, a mixed solvent system of acetonitrile and acetate buffer is used to favor condensation over hydrolysis of the substrate to lactose, which would be incompatible with the method described by Samain, since it is well known in the art that microorganisms such as E. coli barely tolerate solvents with LogP values lower than 3.4-3.8, and refers to applicant-supplied reference Zhang et al (See Remarks dated 1/9/2026, p.14 1st paragraph).
Applicant argues that Shoda would lead a skilled person away form using a microbial fermentation for the production of an oligosaccharide fluoride, because according to Shoda, the exogenous fluoride and the oligosaccharide fluoride would be prone to hydrolysis of the C-F bond in absence of an organic solvent in the medium; and further a skilled person would find it surprising that hydrolyses of the exogenous precursor of General Formula I is not observed during the microbial fermentation and that the glycosyl fluoride of interest can be isolated from the medium (See Remarks dated 1/9/2026, p.14 last paragraph).
Applicant argues that Yokoyama does not remedy the fact that Shoda only teaches the use of β-lactosyl fluoride as a glycosyl donor, and Yokoyama teaches that glycosyl fluorides are versatile sugar donors in the synthesis of natural products (See Remarks dated 1/9/2026, p.14 last 2 lines to p.15. top 3 lines).
Applicant's arguments filed January 9, 2026 have been fully considered but they are not persuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). One of ordinary skill would have been motivated to modify the method of Samain, i.e. to replace the lactose precursor taught by Samain with β-lactosyl fluoride taught by Shoda, because Yokoyama teaches that glycosyl fluorides have enhanced stability, ease of handling and higher steroselectivity.
One of ordinary skill would understand that Shoda’s experimental solvent conditions of acetonitrile and acetate buffer would not be applicable in the biological system of Samain, because Samain teaches a method of culturing a microorganism in a culture medium to produce oligosaccharides, and as demonstrated by applicant-supplied reference by Zhang et al., it is well-known in the art that microorganisms are not typically cultured in acetonitrile and/or acetate buffer. The modification is to replace lactose taught by Samain with β-lactosyl fluoride taught by Shoda in the method of Samain.
While Applicant argues that one of ordinary skill would find it surprising to isolate the glycosyl fluoride from the culture medium, it is noted that this is an optional step recited in claim 1 step c. Regarding Applicant’s argument directed to hydrolysis of the C-F bond in the absence of an organic solvent in the medium, the argument is directed to a claim limitation not required by the claimed invention.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/DEEPA MISHRA/Examiner, Art Unit 1657
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