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 .
Priority
This application was filed on and is a U.S. national Stage application under 35 U.S.C. 371 of International Patent Application No. PCT/EP2021/076448 filed 09/27/2021, which claims the benefit of the priority of European Patent Application No. EP20198728.6 filed 09/28/2020.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements submitted on 03/24/2023 has been considered by the examiner.
Claim Status
Claims 1-18 are being examined on the merits in this office action.
Drawings
The drawings are objected to because Figs. 1-2, 5-6, 9, and 15-16 are not legible. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 112
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 1, 6-11, 13, 15-18 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 1, 6, 11 and 18, claim 1 contains a parenthesis in line 3. It is unclear whether the limitations in the parenthesis are a required part of the claimed invention. Further, claim 6 contains parenthesis on line 4-5; claim 11 contains parenthesis in line 2; and claim 18 contains parenthesis on line 3.
Regarding claim 9, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). claim 10, 13, 15 and 17 have a similar issue.
Claims 7-8 depend on claim 1 and recites the limitation "…for purifying a target molecule…" in line 2. There is insufficient antecedent basis for this limitation in the claim because independent claim 1 does not recite purifying a target protein.
Claim 16 depends on claim 1 and recites the limitation “…wherein the increase in contact time…”. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 102
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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-6, and 18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. (US20150353597A1– hereinafter “Chen”).
Chen teaches a method comprising: contacting a first fusion protein comprising the protein of interest (POI) fused to the C-terminus of an intein C-fragment with a second fusion protein comprising an intein N-fragment and a purification tag to form a complex between the first fusion protein and the second fusion protein; cleaving the POI from the intein C-fragment, wherein the protein is released from the complex and isolating the POI [0008-0009]. Chen teaches that the method further comprises washing the complex with buffer before the cleavage, wherein the method comprise contacting the complex with one or more cleavage inhibitors (claim 65). Chen teaches contacting the complex buffers comprising imidazole [0104], which is an example of a heteroaromatic compound.
Regarding claim 2, Chen teaches that the intein complex is formed during a protein purification process (claim 35).
Regarding claim 3, Chen teaches wherein the first step is performed at a pH of 8.0 and later washing in buffer at a pH of 6.0 [0095].
Regarding claim 4, Chen teaches in other embodiments where both steps are performed at pH of 8.0 [0104].
Regarding claim 5-6, Chen teaches contacting the complex buffers comprising imidazole [0104], which is an example of a heteroaromatic compound. Examiner further notes that imidazole compound of Chen is not substituted thus reads on unsubstituted imidazole.
Regarding claim 18, Chen teaches a method comprising: contacting a first fusion protein comprising the protein of interest (POI) fused to the C-terminus of an intein C-fragment with a second fusion protein comprising an intein N-fragment and a purification tag to form a complex between the first fusion protein and the second fusion protein; cleaving the POI from the intein C-fragment, wherein the protein is released from the complex and isolating the POI [0008-0009]. Chen teaches that the method further comprises washing the complex with buffer before the cleavage, wherein the method comprise contacting the complex with one or more cleavage inhibitors (claim 65). Chen teaches contacting the complex buffers comprising imidazole [0104], which is an example of a heteroaromatic compound. Chen teaches that the N- and C-exteins are joined via a peptide bond [0059, 0068].
Claim Rejections - 35 USC § 103
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.
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.
Claims 7-17 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US20150353597A1– hereinafter “Chen”) as applied to claim 1 above, and further in view of Han et al. (Biochem. and Biophy. Res. Comm. 482 (2017) 120-125).
The teachings of Chen are disclosed above and incorporated herein by reference.
Chen does not teach a first flow rate as recited in claim 7.
Han teaches an intein fusion protein and methods of purifying (Abstract). Han teaches that the first separation step was performed on a Chelating Sepharose Fast Flow column (1.0 × 6.5 cm), and that the activation of protein splicing was performed by flushing the column via the cleavage buffer (0.05 M PBS) at different pH levels (5.0, 5.5, 6.0, 6.5, 7.0) to optimize the conditions of intein splicing. Han teaches that the resin was incubated in the cleavage buffer for 24 h at 25 °C temperature. After splicing at the optimal conditions, elution was performed at a flow rate of 2.0 mL/min with four steps using the following buffers: buffer C, buffer D, 0.5 M imidazole and 0.05 M EDTA. The 0.5 M imidazole eluent was adjusted to pH 3.6 with 0.05 M phosphoric acid (Page 121, section 2.4). Han teaches that the protein was still bound to the resin and was finally eluted with 0.5 M imidazole (Fig. 2B, elution fraction C peak; Page 123, section 3.3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method taught by Chen and incorporate the method steps of Han for improved solubility (Abstract). One of ordinary skill in the art would be motivated and would have had a reasonable expectation of success in modifying Chen with the teachings of Han of purifying the fusion protein since Han teaches that the protein had improved solubility with a purity of over 95% (Abstract).
Regarding claim 7, Chen teaches a method of purifying a protein of interest (POI) comprising providing a first fusion protein comprising the POI and an intein C-fragment, wherein the POI is fused to the C-terminus of the intein C-fragment, providing a second fusion protein comprising an intein N-fragment and a purification tag, contacting the first fusion protein with the second fusion protein in binding buffer, wherein the second fusion protein is attached to a resin that binds to the purification tag, wherein the purification tag is capable of specifically binding a purification resin, wherein a complex between the first fusion protein and the second fusion protein is formed; wherein the binding buffer inhibits a C-terminal protein cleavage of the first fusion protein between the POI and the intein C-fragment; inducing the C-terminal protein cleavage of the first fusion protein between the POI and the intein C-fragment whereby the POI is released; and separating the POI from the first fusion protein and the C-terminus of the intein C-fragment [0008]. Chen teaches that the purification method is a chitin mediated chromatography method [0033, 0084, 0092]. Han teaches that the first separation step was performed on a Chelating Sepharose Fast Flow column (1.0 × 6.5 cm), and that the activation of protein splicing was performed by flushing the column via the cleavage buffer (0.05 M PBS) at different pH levels (5.0, 5.5, 6.0, 6.5, 7.0) to optimize the conditions of intein splicing. Han teaches that the resin was incubated in the cleavage buffer for 24 h at 25 °C temperature. After splicing at the optimal conditions, elution was performed at a flow rate of 2.0 mL/min with four steps using the following buffers: buffer C, buffer D, 0.5 M imidazole and 0.05 M EDTA (Page 121, section 2.4). Further, Han teaches a first separation step followed another step of elution with 0.5 M imidazole (Fig. 2B, elution fraction C peak; Page 123, section 3.3).
Regarding claim 8, Chen teaches a method of purifying a protein of interest (POI) comprising providing a first fusion protein comprising the POI and an intein C-fragment, wherein the POI is fused to the C-terminus of the intein C-fragment, providing a second fusion protein comprising an intein N-fragment and a purification tag, contacting the first fusion protein with the second fusion protein in binding buffer, wherein the second fusion protein is attached to a resin that binds to the purification tag, wherein the purification tag is capable of specifically binding a purification resin, wherein a complex between the first fusion protein and the second fusion protein is formed; wherein the binding buffer inhibits a C-terminal protein cleavage of the first fusion protein between the POI and the intein C-fragment; inducing the C-terminal protein cleavage of the first fusion protein between the POI and the intein C-fragment whereby the POI is released; and separating the POI from the first fusion protein and the C-terminus of the intein C-fragment [0008]. Chen teaches that the purification method is a chitin mediated chromatography method [0033, 0084, 0092]. Chen teaches binding the complex to an affinity resin before inducing the C-terminal protein cleavage; and regenerating the affinity resin by dissociating the intein C-fragment from the second fusion protein (claim 73). Further, Han teaches that the first separation step was performed on a Chelating Sepharose Fast Flow column (1.0 × 6.5 cm), and that the activation of protein splicing was performed by flushing the column via the cleavage buffer (0.05 M PBS) at different pH levels (5.0, 5.5, 6.0, 6.5, 7.0) to optimize the conditions of intein splicing. Han teaches that the resin was incubated in the cleavage buffer for 24 h at 25 °C temperature. After splicing at the optimal conditions, elution was performed at a flow rate of 2.0 mL/min with four steps using the following buffers: buffer C, buffer D, 0.5 M imidazole and 0.05 M EDTA. The 0.5 M imidazole eluent was adjusted to pH 3.6 with 0.05 M phosphoric acid (Page 121, section 2.4). It would have been obvious to combine the teachings of Chen and Han for enhanced purification of the protein.
Regarding claim 9, Han teaches that the first separation step was performed on a Chelating Sepharose Fast Flow column (1.0 × 6.5 cm), and that the activation of protein splicing was performed by flushing the column via the cleavage buffer (0.05 M PBS) at different pH levels (5.0, 5.5, 6.0, 6.5, 7.0) to optimize the conditions of intein splicing. Han teaches that the resin was incubated in the cleavage buffer for 24 h at 25 °C temperature. After splicing at the optimal conditions, elution was performed at a flow rate of 2.0 mL/min with four steps using the following buffers: bufferC, bufferD, 0.5 M imidazole and 0.05 M EDTA. The 0.5 M imidazole eluent was adjusted to pH 3.6 with 0.05 M phosphoric acid (Page 121, section 2.4). it would have been obvious to combine the teachings of Chen and Han for enhanced purification of the protein. Examiner notes that the first step is at a pH of 8.0, and the second step is at a pH of 3.6 which is lower. It would have been obvious to combine the teachings of Chen and Han for enhanced purification of the protein (Abstract).
Regarding claim 10, Han teaches that the method steps were conducted at the same pH of 8.0, and that the buffer is phosphate-buffered saline (Page 121, whole section 2.3).
Regarding claim 11, Chen teaches loading the protein in a resin column and washed 4 times with 10 column volumes and incubated in the buffer A [0095]. Further, Han teaches that the resin was incubated in the cleavage buffer for 24 h at 25 °C temperature and after splicing at the optimal conditions, elution was performed at a flow rate of 2.0 mL/min (Page 122, left col., line 1-9).
Regarding claim 12, Chen teaches that the purification method is a chitin mediated chromatography method [0033, 0084, 0092]. Chen teaches binding the complex to an affinity resin before inducing the C-terminal protein cleavage; and regenerating the affinity resin by dissociating the intein C-fragment from the second fusion protein (claim 73). Chen teaches addition of E.coli cells [0103].
Regarding claim 13, Chen teaches that the chitin resin was thoroughly washed with pH 11.4 buffer to remove cleaved C* from NC1A-CBD on the column [0085, 0095] and that the buffer contained zinc chloride [0095] which is a salt.
Regarding claim 14, Chen teaches that the second fusion protein is attached to a resin that binds to the purification tag or affinity tag, wherein the purification tag is capable of specifically binding a purification resin, wherein a complex between the first fusion protein and the second fusion protein is formed [0008] and that the affinity tag includes 6x histidine [0007], which reads on amino functional group.
Regarding claim 15, Han teaches Fast Flow column equilibrated with 0.05 M PBS (pH 8.0) at a flow rate of 1.0 mL/min and then elution was performed at a flow rate of 2.0 mL/min with four steps using the following buffers: buffer C, buffer D, 0.5 M imidazole and 0.05 M EDTA (Page 121, right col. Section 2.4). It would have been obvious to combine the teachings of Chen and Han for enhanced purification of the protein (Abstract).
Regarding claim 16, Chen teaches that the method led to high purity yields of up to 84 mg per liter [0071-0072, 0088]. With regards to the percent yield recited, MPEP 2111.04 states: claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure. In the instant case, the limitation expresses the intended result of the method step of claim 1 and is given little patentable weight.
Regarding claim 17, Chen renders obvious the method of claim 1. Chen further teaches that the protein of interest is selected from a bioactive peptide, an enzyme, an enzyme inhibitor, an enzymatic catalytic site, a DNA-binding protein, an isolated protein domain, a ligand for receptors, a receptor, a growth factor, a cytokine, a structural protein, an antibody, an antibody fragment, an epitope, an epitope-binding region, an antigen, an allergen (claim 72).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-2, 7-8, 12-14, and 17 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 9-12, 14-15, and 18 of copending Application No. 17/796,720. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the copending application recite a method for purifying a target molecule in a sample, the method comprising the steps of (a) providing a sample containing a fusion protein comprising an intein-C polypeptide joined to a target molecule by a peptide bond (intein-C tagged target molecule);(b) contacting the sample with a chromatography resin comprising a covalently- linked N-terminal intein polypeptide, under conditions in which the intein-C polypeptide in the fusion protein binds to the intein-N polypeptide in the resin to form an intein complex;(c) optionally washing the resin containing the intein complex to remove unbound contaminants;(d) exposing the intein complex to conditions sufficient to release the target molecule from the intein-C polypeptide;(e) regenerating the chromatographic resin by contacting the resin with a composition having a pH in aqueous solution of about 1 to about 4; so as to disrupt the intein-N intein-C complex and release the intein-C polypeptide from the chromatography resin; and (f) optionally, performing at least one additional purification cycles by repeating steps (a) to (e) at least once, wherein the regenerated chromatography resin obtained from step (e) or optional step (f) retains at least about 60%, preferably at least about 70% and more preferably at least about 80% of its C-terminal intein binding capacity after each purification cycle (claim 1).
The instant claims recite a method for releasing a target molecule from an intein complex comprising (i) a fusion protein comprising an intein-C polypeptide joined to the target molecule by a peptide bond (intein-C tagged target molecule); and (ii) an intein-N polypeptide, the method comprising the steps of: (a) contacting the intein-C tagged target molecule with the intein-N polypeptide, for a first time period sufficient to form the intein complex; and (b) releasing the target molecule from the intein complex by: (i) contacting the intein complex with a medium effective to remove the target molecule, for a second time period which is longer than the first time period; and/or (ii) contacting the intein complex with a heteroaromatic compound comprising at least one ring nitrogen atom (claim 1), that the method comprises purifying a target molecule, the method comprising the step of (a) contacting the intein-C tagged target molecule with the intein-N polypeptide on a chromatography resin at a first flow rate so as to form the intein complex; and (b) releasing the target molecule from the intein complex (claim 7).
The claims of the copending application anticipate the instant claims
Regarding claim 2, the claims of copending application recite that the method is for purifying a target molecule (claim 1).
Regarding claims 7-8, the claims of the copending application recite a method for purifying a target molecule in a sample, the method comprising the steps of (a) providing a sample containing a fusion protein comprising an intein-C polypeptide joined to a target molecule by a peptide bond (intein-C tagged target molecule);(b) contacting the sample with a chromatography resin comprising a covalently- linked N-terminal intein polypeptide, under conditions in which the intein-C polypeptide in the fusion protein binds to the intein-N polypeptide in the resin to form an intein complex;(c) optionally washing the resin containing the intein complex to remove unbound contaminants;(d) exposing the intein complex to conditions sufficient to release the target molecule from the intein-C polypeptide;(e) regenerating the chromatographic resin by contacting the resin with a composition having a pH in aqueous solution of about 1 to about 4; so as to disrupt the intein-N intein-C complex and release the intein-C polypeptide from the chromatography resin; and (f) optionally, performing at least one additional purification cycles by repeating steps (a) to (e) at least once, wherein the regenerated chromatography resin obtained from step (e) or optional step (f) retains at least about 60%, preferably at least about 70% and more preferably at least about 80% of its C-terminal intein binding capacity after each purification cycle (claim 1), that step further comprises regenerating the chromatographic resin by contacting the resin with at least one detergent (claim 3), further comprising the step of performing at least one purification cycle wherein the resin is contacted with a basic composition having a pH in aqueous solution of about 9 or higher (claim 6), wherein the intein-C tagged target molecule is prepared by attaching an intein-C polypeptide to a target molecule to obtain a fusion protein, and expressing the fusion protein in an expression system (claim 9), further comprising the step of isolating the target molecule obtained from step (d) (claim 15).
Regarding claim 12, the claims of the copending application recite wherein step (b) comprises contacting the chromatography resin with a cell culture supernatant comprising the intein-C tagged target molecule (claim 10).
Regarding claim 13, the claims of the copending application recite wherein step (c) is performed, and comprises washing the chromatography resin with a washing buffer prior to releasing the target molecule from the intein-C polypeptide (claim 11-12, 14).
Regarding claim 14, the claims of the copending application recite wherein the intein-N polypeptide is attached to the chromatography resin through a functional group selected from the group consisting of hydroxyl, thiol, epoxide, amino, carbonyl epoxide and carboxylic acid (claim 19).
Regarding claim 17, the claims of the copending application recite wherein the target molecule is a protein (claim 18).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Mercy H. Sabila whose telephone number is (571)272-2562. The examiner can normally be reached Monday - Friday 5:00 am - 3:00 pm.
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/MERCY H SABILA/Examiner, Art Unit 1654