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 Claims
Claims 1-5, 7-11, 13, 14, 16, 18-21 and 23-25 are pending.
Claims 3-5, 7, 10, 11, 13, 16, 18, 21 and 23-25 are amended.
Claims 1-5, 7-11, 13, 14, 16, 18-21 and 23-25 are currently under examination on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. The U.S. effective filing date of all claims under examination is set at 03/15/2021 based on the provisional application 63/161,312 (filed 03/15/2021).
Information Disclosure Statement
The information disclosure statements (IDS) submitted are being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiencies –
The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Amino acid sequences appearing in the drawings of FIGs. 5 and 8-11 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Amino acid sequence of 5xGS appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, inserting the required sequence identifiers into the Brief Description of the Drawings and inserting the required sequence identifiers into the specification, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities:
The specification on Pg 5 line 11 discloses "The circuits shown in Figure 3" which appears to be a typographical error because Figure 3 does not show circuits but shows a bar graph.
Appropriate correction is required.
The use of the term nanobody, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 112(b)
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 2, 4, 16 and 18-20 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.
Claims 2 and 4 contains the trademark/trade name “nanobody”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe an extracellular binding domain which comprises a single-domain antibody and, accordingly, the identification/description is indefinite.
Claim 16 recites the phrase “The cell of claim 8 any of claims 8, 14 and 15,”. It is unclear which claim(s) claim 16 is dependent upon. In addition, claim 15 is a cancelled claim and it is, therefore, unclear what is meant by claim 15.
Claims 18-20 recite “the first binding moiety”. There is insufficient antecedent basis for “the first binding moiety” in the claims because claim 1 does not recite “a first binding moiety”.
Claim Rejections - 35 USC § 103 (first)
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.
Claims 1-4, 7, 8, 14, 16, 18, 20, 21 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Choe et al. (WO2019099689A1 Date Published 2019-05-23) in view of Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916) and Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144).
Choe et al. teaches chimeric polypeptides that can modulate cellular processes following cleavage of a force sensor cleavage domain that is induced upon binding of a specific binding member of the chimeric polypeptide with its binding partner and methods of using force sensor cleavage domain-containing chimeric polypeptides to modulate cellular functions (Abstract). They teach that the chimeric polypeptides can include fusion proteins with a heterologous amino acid sequence that are expressed in mammalian cells engineered to include a nucleic acid that encodes the chimeric polypeptide (paragraphs [0032], [00272] and [00273]). They also teach that the chimeric polypeptides include: an extracellular domain comprising a first member of a binding pair; a force sensor cleavage domain comprising a proteolytic cleavage site; a transmembrane domain; and an intracellular domain (paragraph [0052]).
Choe et al. teaches that binding of a first member of the binding pair of the chimeric polypeptide to a second member of the binding pair can induce cleavage of the force sensor cleavage domain at the proteolytic cleavage site, thereby releasing the intracellular domain (paragraph [0052]). They teach that the second member of the binding pair can be a cell surface protein molecule (paragraphs [00182], [00183] and [00186]). They also teach that intracellular domains can include Notch intracellular domains, non-Notch intracellular domains, an enzyme or a portion thereof, or an enzyme domain (paragraphs [0052] and [00211]). Further, they teach that the released intracellular domain of Notch can bind to target proteins including the CSL (CBFl/Su(Fl)/Lag-l) transcription factor complex, IKKa and LEF1 (paragraph [0054]), which are non-antibody binding domains. As confirmed by the teachings of Yuan et al., CSL is a transcription factor of Notch signaling that is primarily localized to the nucleus of cells (Abstract, Figure 2 and Pg. 34904 column right second paragraph lines 5-7), i.e. CSL is a target protein that is not localized at the plasma membrane.
Choe et al. teaches that the first member of the specific binding pair of the chimeric polypeptide can be a single chain Fv (scFv), a sdAb VH (single domain antibody variable domains), a cell-surface receptor, or a ligand for a cell-surface receptor (paragraphs [00138] and [00184] to [00186]). They teach that the force sensor cleavage domain of the chimeric polypeptide can include Delta cleavage domains derived from a Delta protein or homolog thereof that comprise at least one proteolytic cleavage site of the Delta protein (paragraphs [0051], [0082] and [0083]). They also teach circuits that comprises the chimeric protein as described above (paragraphs [00334] and [0035]). They further teach in Aspects 65, 66 and 67, a method of modulating an activity of a cell that expresses a chimeric polypeptide, the method comprising: contacting the cell with a second member of the specific binding pair, wherein binding of the first member of the specific binding pair to the second member of the specific binding pair induces cleavage of the chimeric polypeptide at the proteolytic cleavage site, thereby releasing the intracellular domain, wherein release of the intracellular domain modulates the activity of the cell, wherein said contacting is carried out in vivo, ex vivo, or in vitro, and wherein the second member of the specific binding pair is on the surface of a second cell (paragraph [00341]).
Choe et al. does not specifically teach a cleavable fusion protein comprising: (a) an extracellular binding domain comprising a first protein binding domain, wherein the first protein binding domain specifically binds to a cell surface protein; (b) a force sensing region; (c) a transmembrane domain; (d) one or more force-dependent cleavage sites that are cleaved when the force sensing region is activated; and (e) an intracellular domain comprising: an intracellular domain comprising: i. a second protein binding domain, wherein the second protein binding domain specifically binds to a target protein; and ii. a degradation domain, wherein the degradation domain is a E3 ligase-recruiting domain.
However, these deficiencies are made up in the teachings of Neklesa et al.
Neklesa et al. teaches a method for targeted protein degradation using the PROTAC technology wherein PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase complex, thus causing ubiquitination and degradation of the target protein by the proteasome (Abstract). They teach that due to their catalytic nature and the pre-requisite ubiquitination step, exquisitely potent molecules with a high degree of degradation selectivity can be designed into PROTAC molecules (Abstract). They also teach in Fig. 1 a schematic of the PROTAC technology which shows the PROTAC comprising a first part that is a ligand for target protein binding and a second part that is a ligand for recruiting E3 ligase. Fig. 1 of Neklesa et al. further teaches that the recruitment of E3 ligase to a target protein produces a trimeric complex formation that leads to the transfer of ubiquitins to the target protein. Upon dissociation of the complex, the polyubiquitinated target protein is recognized by the proteasome and degraded, while the PROTAC molecule can be recycled for subsequent rounds of degradation (Fig. 1).
One of ordinary skill in the art would have been motivated, with a reasonable expectation of success, to perform a combined method of generating a cleavable fusion protein that comprises: (a) an extracellular binding domain comprising a first protein binding domain, wherein the first protein binding domain specifically binds to a cell surface protein; (b) a force sensing region; (c) a transmembrane domain; (d) a force-dependent cleavage site that is cleaved when the force sensing region is activated; and (e) an intracellular domain comprising: a second protein binding domain, wherein the second protein binding domain specifically binds to a target protein and when the fusion protein is expressed in a mammalian cell, binding of the first binding domain to the cell surface protein induces proteolytic cleavage of the force-dependent cleavage site to release the intracellular domain as taught by Choe et al. and modify the intracellular domain that specifically binds a target protein as taught by Choe et al. to include the E3 ligase-recruiting ligand or domain as taught by Neklesa et al. such that the intracellular domain comprises both a domain that specifically binds to target protein and an E3 ligase-recruiting domain that is a degradation domain, because Choe et al. teaches that such a chimeric fusion protein has the property of undergoing force-dependent proteolytic cleavage to release an intracellular domain upon binding of the extracellular first binding domain to the cell surface protein and because Neklesa et al. teaches that a bifunctional PROTAC molecule that comprises a first ligand for target protein binding and a second ligand for recruiting E3 ligase is capable of performing targeted protein ubiquitination and degradation by proteasomes in a catalytic, selective, potent and recyclable manner with superior outcomes when compared to other modalities (Abstract, Fig. 1 and Section 2). In addition, Choe et al. teaches that binding triggered and/or force-dependent modulation of cellular activities that is afforded by the said cleavable chimeric fusion protein provides the ability to program cells to detect signals from their neighboring cells, and autonomously transduce such signaling inputs into desired activity outputs without needing to employ commonly used inducible cell systems (e.g., chemically inducible, optically inducible, etc.) that require a user-provided input to control the change in activity of a population of cells (paragraphs [0004] and [0005]). Further, by including a PROTAC molecule as part of the intracellular domain of a fusion protein expressed in a cell, it provides the advantage of overcoming bioavailability of a PROTAC molecule as was described by Neklesa et al. as a hurdle to the use of PROTACs (Pg. 143 column right first full paragraph lines 15-17). The motivation to generate and use a cleavable fusion protein that comprises an extracellular domain and a releasable intracellular molecule that can target ubiquitination/degradation of the targeted proteins would be to enable precise, localized, and on-demand destruction of specifically targeted intracellular proteins upon encountering a distinct external stimulus which corresponds to protein binding on the extracellular cell surface. This is an example of (A) Combining prior art elements according to known methods to yield predictable results; and (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. See MPEP 2143. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art, absent unexpected results.
With regards to instant claim 18, a protein circuit comprising:
i. a fusion protein generated by performing the combined method of Choe et al. and Neklesa et al.; and ii. the target protein as taught by Choe et al. and Neklesa et al.; would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter the degradation of the target protein upon binding of the first binding moiety of the fusion protein to the cell surface protein on another cell.
With regards to instant claim 20, the protein circuit as taught by Choe et al. and Neklesa et al., wherein the target protein is not localized to the plasma membrane for the CSL transcription factor as taught by Choe et al. and Yuan et al., would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to increase the degradation of the targeted CSL transcription factor upon binding of the first binding moiety of the fusion protein to the cell surface protein on another cell.
With regards to instant claim 21, a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell as taught by Choe et al., wherein: (a) the first cell comprises: i. the fusion protein generated by performing the combined method of Choe et al. and Neklesa et al.; and ii. the target protein as taught by Choe et al. and Neklesa et al.; and (b) the second cell comprises the cell surface protein on its surface as taught by Choe et al.; would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter degradation of the target protein upon binding of the first cell to the second cell via the fusion protein generated by the combined method.
With regards to instant claim 25, the method for modulating degradation of a target protein as taught by Choe et al. and Neklesa et al., wherein the target protein is not localized to the plasma membrane for the CSL transcription factor as taught by Choe et al. and Yuan et al., would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to increase the degradation of the targeted CSL transcription factor upon the step of introducing the first cell to the second cell.
Claim Rejections - 35 USC § 103 (second)
Claims 1-5, 7, 8, 14, 16, 18, 20, 21 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Choe et al. (WO2019099689A1 Date Published 2019-05-23), Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916) and Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144), as applied to claims 1-4, 7, 8, 14, 16, 18, 20, 21 and 25, and further in view of Kanemaki (Eur J Physiol 465, 419–425; 2013).
The combined teachings of Choe et al., Yuan et al. and Neklesa et al. render obvious instant claims 1-4, 7, 8, 14, 16, 18, 20, 21 and 25 as discussed above in the first 103 which is incorporated here in its entirety.
Choe et al., Yuan et al. and Neklesa et al. do not specifically teach the cleavable fusion protein of instant claim 1, wherein the degradation domain is a degron.
However, these deficiencies are made up in the teachings of Kanemaki.
Kanemaki teaches a protein domain called “degron” is capable of inducing rapid proteolysis by the proteasome is well suited to be used for the conditional depletion of a protein of interest (Abstract). They teach that degron fusion proteins have been developed by exploiting various pathways that lead to proteasomal degradation (Abstract). They also teach that degrons can be conditionally induced to further fine tune their degradation activities (Table 1A).
One of ordinary skill in the art would have been motivated, with a reasonable expectation of success, to perform the combined method of generating a cleavable fusion protein as taught by Choe et al. and Neklesa et al. and by substituting the E3-ligase binding ligand as taught by Neklesa with the degron protein domain as taught by Kanemaki because Kanemaki teaches that degron fusion proteins can be used for the conditional proteasomal degradation of a protein of interest which are advantageous in terms of specificity, reversibility, and the time required for depletion of said proteins (Abstract and Table 1A). This is an example of (B) Simple substitution of one known element for another to obtain predictable results. See MPEP 2143. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art, absent unexpected results.
Claim Rejections - 35 USC § 103 (third)
Claims 1-4, 7-11, 13, 14, 16, 18-21 and 23-25 are rejected under 35 U.S.C. 103 as being unpatentable over Choe et al. (WO2019099689A1 Date Published 2019-05-23), Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916) and Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144), as applied to claims 1-4, 7, 8, 14, 16, 18, 20, 21 and 25, and further in view of Wu et al. (Science 350, aab4077; 2015).
The combined teachings of Choe et al., Yuan et al. and Neklesa et al. render obvious instant claims 1-4, 7, 8, 14, 16, 18, 20, 21 and 25 as discussed above in the first 103 which is incorporated here in its entirety.
Choe et al., Yuan et al. and Neklesa et al. do not specifically teach a cell comprising the fusion protein of instant claim 1, wherein the cell further comprises the target protein that is localized to the plasma membrane; or wherein the target protein is a transmembrane protein; or wherein the target protein is associated with a transmembrane protein; or wherein the target protein is an immune receptor.
They also do not specifically teach the method of modulating degradation of a target protein according to instant claim 21, wherein the target protein is a chimeric antigen receptor.
However, these deficiencies are made up in the teachings of Wu et al.
Wu et al. teaches a chimeric antigen receptor (CAR) that can be switched on or off for titratable and reversible control over CAR T cell activity to address concerns about the potential for severe toxicity of cellular therapeutics that primarily stem from a lack of precise control over the activity of the therapeutic cells once they are infused into patients (Structured Abstract: Results and Rationale). They teach in Fig. 1C a conventional CAR design. They also teach in the figure on Pg. 293 and in Fig. 2A and 2B the schematic representation of an ON-switch CAR that is split into two parts wherein Part I of the receptor features an extracellular antigen-binding scFv domain, a CD8α hinge and transmembrane domain, in addition to a FKBP domain for heterodimerization and Part II comprises a CD8α transmembrane domain for membrane anchoring and a FRB* domain for heterodimerization, where localization of both receptor parts are at the plasma membrane.
One of ordinary skill in the art would have been motivated, with a reasonable expectation of success, to perform the combined method of generating the cleavable fusion protein as taught by Choe et al. and Neklesa et al. and by substituting the intracellular domain that is the Notch intracellular domain as taught by Choe et al. with the FRB* heterodimerization domain as taught by Wu et al., and further including a CAR at the plasma membrane of the cell as taught by Wu et al. wherein the CAR is a transmembrane protein as well as an immune receptor that is modified to comprise the FKBP heterodimerization domain as taught by Wu et al. and which is the target binding protein of FRB* on the cleavable fusion protein, and wherein the target protein is associated with the CD8α transmembrane domain of the CAR as taught by Wu et al. such that the claimed cleavable fusion protein, expressed alongside CARs on T cells, can function by interacting and binding tumor antigens on tumor cells which in turn causes cleavage/release of the degradation domains when bound, thus allowing persistent expression of the CAR to effect tumor cell killing; alternatively the CAR is degraded when tumor antigen is no longer present due to lack of release of the degradation domain of the cleavable fusion protein which enables heterodimerization of the FRB* on the cleavable fusion protein with the FKBP domain on the CAR and which result in subsequent degradation of the CAR since the T cell is no longer needed to interact with the tumor cell to effect killing of said tumor cell. The motivation to express such a claimed cleavable fusion protein in T cells that also express CARs is to include an additional control mechanism that would allow for the engineered CAR T cell to be switched “on” or “off” to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity as taught by Wu et al. (Abstract). This is an example of (B) Simple substitution of one known element for another to obtain predictable results; (A) Combining prior art elements according to known methods to yield predictable results; and (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. See MPEP 2143. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art, absent unexpected results.
With regards to instant claim 19, one of ordinary skill in the art would have been motivated, with a reasonable expectation of success, to perform a combined method of generating the protein circuit comprising a fusion protein as taught by Choe et al., Neklesa et al. and Wu et al., and a target protein wherein the target protein is fused to a CAR that is localized to the plasma membrane as taught by Wu et al., and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell decreases degradation of the target protein because when the first binding moiety of the fusion protein is not bound to the cell surface protein on another cell, the fusion protein stays intact allowing the intracellular domain that comprises the E3 ligase-recruiting domain and the FRB*domain to bind and form a heterodimer with the FKBP domain of the CAR in the presence of rapamycin. This dimerization would in turn allow the E3 ligase-recruiting domain of the intracellular domain to ubiquitinylate the modified CAR, resulting in proteasomal degradation.
With regards to instant claims 21 and 23, a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell as taught by Choe et al., wherein: (a) the first cell comprises: i. the fusion protein generated by performing the combined method of Choe et al., Neklesa et al. and Wu et al.; and ii. the target protein is a FKBP domain located on the C terminus of a CAR that is localized to the plasma membrane as taught by Wu et al.; and (b) the second cell comprises the cell surface protein on its surface as taught by Choe et al.; the step of introducing the first cell to the second cell would result in the release of the intracellular domain thereby removing the intracellular domain comprising the E3-ligase recruiting domain away from the CAR at the plasma membrane, which would in turn result in a decrease in the degradation of the CAR that is fused to the target protein.
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.
First NSDP: U.S. Patent No. 12065479
Claims 1-5, 7-11, 13, 14, 16, 18-21 and 23-25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 and 13 of U.S. Patent No. 12065479 (Date Published 2024-08-20) in view of Choe et al. (WO2019099689A1 Date Published 2019-05-23), Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916), Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144), Kanemaki (Eur J Physiol 465, 419–425; 2013) and Wu et al. (Science 350, aab4077; 2015).
Patented claim 1 is drawn in part to a chimeric polypeptide comprising, from N terminus to C terminus:
a) an extracellular domain comprising a first member of a binding pair;
b) a non-Notch force sensor cleavage domain comprising a proteolytic cleavage site;
c) a cleavable transmembrane domain; and
d) an intracellular domain that is not a Notch intracellular signaling domain and does not induce expression of Notch target genes,
wherein binding of the first member of the specific binding pair to the second member of the specific binding pair, present on a cell, induces cleavage at the proteolytic cleavage site thereby releasing the intracellular domain.
Patented claim 2 recites to the chimeric polypeptide according to claim 1, wherein the first member of the binding pair comprises at least a portion of a receptor that binds a ligand and the second member of the binding pair comprises at least a portion of the ligand.
Patented claim 3 recites the chimeric polypeptide according to claim 1, wherein the first member of the binding pair comprises at least a portion of a ligand that binds a receptor and the second member of the binding pair comprises at least a portion of the receptor.
Patented claim 4 recites the chimeric polypeptide according to claim 1, wherein the first member of the binding pair comprises an antibody.
Patented claim 5 is drawn in part to the chimeric polypeptide according to claim 4, wherein the antibody is a nanobody, a single chain variable fragment (scFv) or a single domain antibody (sdAb).
Patented claim 6 recites the chimeric polypeptide according to claim 1, wherein the intracellular domain comprises a transcriptional activator or repressor.
Patented claim 7 recites a nucleic acid encoding the chimeric polypeptide according to claim 1.
Patented claim 13 is drawn in part to a method of modulating an activity of a cell that expresses a chimeric polypeptide, the method comprising:
contacting the cell with a second member of the specific binding pair, wherein binding of the first member of the specific binding pair to the second member of the specific binding pair induces cleavage of the chimeric polypeptide at the proteolytic cleavage site, thereby releasing the intracellular domain, wherein release of the intracellular domain modulates the activity of the cell, wherein the chimeric polypeptide comprises, from N terminus to C terminus:
a) an extracellular domain comprising a first member of a binding pair;
b) a non-Notch force sensor cleavage domain comprising a proteolytic cleavage site;
c) a cleavable transmembrane domain; and
d) an intracellular domain that is not a Notch intracellular signaling domain and does not induce expression of Notch target genes,
wherein binding of the first member of the specific binding pair to the second member of the specific binding pair, present on a cell, induces cleavage at the proteolytic cleavage site thereby releasing the intracellular domain,
Patent claims do not specifically teach the chimeric protein wherein the first member of the binding pair specifically binds to a cell surface protein; or one or more force-dependent cleavage sites that are cleaved when the force sensing domain is activated; or an intracellular domain comprising: i. a second protein binding domain, wherein the second protein binding domain specifically binds to a target protein; and ii. a degradation domain, wherein the degradation domain is a degron or E3 ligase- recruiting domain, and when the fusion protein is expressed in a mammalian cell.
Patent claims also do not specifically teach the chimeric protein wherein the force sensing region and/or the one or more force-dependent cleavage sites are from a Delta/Serrate/Lag2 (DSL) superfamily protein; or wherein the second protein binding domain is a scFv, a nanobody, or a non-antibody binding domain; or wherein the degradation domain is a degron; or a cell comprising the chimeric protein, wherein the cell further comprises the target protein; or wherein the target protein is localized to the plasma membrane; or wherein the target protein is a transmembrane protein; or wherein the target protein is associated with a transmembrane protein; or wherein the target protein is an immune receptor; or wherein the target protein is not localized to the plasma membrane.
Patent claims further do not specifically teach a protein circuit comprising i. a chimeric protein; and ii. the target protein; wherein binding of the first binding moiety of the chimeric protein to the cell surface protein on another cell releases the intracellular domain and alters degradation of the target protein; or wherein the target protein is localized to the plasma membrane and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell decreases degradation of the target protein; or wherein the target protein is not localized to the plasma membrane and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell increases degradation of the target protein.
Patent claims also further do not specifically teach a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell, wherein: (a) the first cell comprises: i. the chimeric protein; and ii. the target protein; and (b) the second cell comprises the cell surface protein on its surface, wherein binding of the first cell to the second cell via the fusion protein releases the intracellular domain, thereby altering degradation of the target protein; or wherein the target protein is localized to the plasma membrane and the introducing step results in a decrease in degradation of the target protein; or wherein the target protein is a chimeric antigen receptor; or wherein the target protein is not localized to the plasma membrane and the introducing step results in an increase in degradation of the target protein.
However, these deficiencies are made up in the teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al.
The teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al. have been described in the 103 rejections above.
It would be obvious to generate a cleavable fusion protein by modifying the chimeric protein as recited by the Patent to include the intracellular domain that comprises a target-protein-binding domain as taught by Choe et al. attached to the E3-ligase recruiting domain as taught by Neklesa et al. to arrive at an intracellular domain that comprises both a domain that specifically binds to the target protein of the CSL complex (that is not localized to the plasma membrane as taught by Yuan et al.) and an E3 ligase-recruiting domain that is a degradation domain, because Choe et al. teaches that said chimeric fusion protein has the property of undergoing force-dependent proteolytic cleavage to release an intracellular domain upon binding of the extracellular first binding domain to the cell surface protein and because Neklesa et al. teaches that a bifunctional molecule that comprises a first ligand for target protein binding and a second ligand for recruiting E3 ligase is capable of performing targeted protein ubiquitination and degradation by proteasomes in a catalytic, selective, potent and recyclable manner with superior outcomes when compared to other modalities. The motivation to generate and use a cleavable fusion protein that comprises the extracellular domain of the Patent and the introduced releasable intracellular target-binding and degradation domains of Choe et al. and Neklesa et al. respectively that can target ubiquitination/degradation of the targeted proteins would be to enable precise, localized, and on-demand destruction of specifically targeted intracellular proteins upon encountering a distinct external stimulus that corresponds to protein binding on the extracellular cell surface.
In addition, it would be obvious to generate a cleavable fusion protein by performing modification of the Patented chimeric protein to include domains as taught by Choe et al. and Neklesa et al. above, and further substituting the E3-ligase recruiting domain taught by Neklesa et al. for the degron domain as taught by Kanemaki because Kanemaki teaches that degron fusion proteins can be used for the conditional proteasomal degradation of a protein of interest which are advantageous in terms of specificity, reversibility, and the time required for depletion of said proteins.
Further, it would be obvious to generate a cleavable fusion protein by performing modification of the Patented chimeric protein to include domains as taught by Choe et al. and Neklesa et al. above, and further substituting the intracellular domain that is the Notch intracellular domain as taught by Choe et al. with the FRB* heterodimerization domain as taught by Wu et al., and even further including a CAR at the plasma membrane of the cell as taught by Wu et al. wherein the CAR is a transmembrane protein as well as an immune receptor that is modified to comprise the FKBP heterodimerization domain which is the target protein or binding partner of FRB* on the fusion protein, and wherein the target protein is associated with the CD8α transmembrane domain of the CAR as taught by Wu et al. such that the generated cleavable fusion protein, expressed alongside CARs on T cells, can function by interacting and binding tumor antigens on tumor cells which in turn causes cleavage/release of the degradation domains when bound, thus allowing persistent expression of the CAR to effect tumor cell killing; alternatively the CAR is degraded when tumor antigen is no longer present due to lack of release of the degradation domain of the cleavable fusion protein which enables heterodimerization of the FRB* on the cleavable fusion protein with the FKBP domain on the CAR and which result in subsequent degradation of the CAR since the T cell is no longer needed to interact with the tumor cell to effect killing of said tumor cell. The motivation to express such a claimed cleavable fusion protein in T cells that also express CARs is to include an additional control mechanism that would allow for the engineered CAR T cell to be switched “on” or “off” to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity as taught by Wu et al. (Abstract).
Moreover, it would be obvious to generate a protein circuit by performing the combined method of the Patented chimeric protein, Chou et al. and Neklesa et al. as described above and including a target protein as taught by Choe et al. and Neklesa et al. because the generated protein circuit would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter the degradation of the target protein upon binding of the first binding moiety of the fusion protein to the cell surface protein on another cell.
Furthermore, it would be obvious to generate a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell as recited by the Patent method, wherein: (a) the first cell comprises: i. the fusion protein generated by performing the combined method of the Patent, Choe et al. and Neklesa et al.; and ii. the target protein as taught by Choe et al. and Neklesa et al.; and (b) the second cell comprises the cell surface protein on its surface as taught by Choe et al. and as recited by the Patent, because the generated method would result in the release of the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter degradation of the target protein upon binding of the first cell to the second cell via the fusion protein generated by the combined method.
Second NSDP: Copending Appln 18/020611
Claims 1-5, 7-11, 13, 14, 16, 18-21 and 23-25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 13-19, 21-24 and 29 of copending Application No. 18/020611 in view of Choe et al. (WO2019099689A1 Date Published 2019-05-23), Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916), Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144), Kanemaki (Eur J Physiol 465, 419–425; 2013) and Wu et al. (Science 350, aab4077; 2015).
Although the copending claims and instant claims are not identical, they are both drawn to a cell comprising a fusion protein comprising: a transmembrane domain; a target-binding domain that specifically binds to a target protein; and a degradation domain, wherein the degradation domain is a degron or E3 ligase-recruiting domain, wherein the fusion protein is expressed in a mammalian cell; wherein the target-binding domain is a scFv or nanobody; wherein the target-binding domain is a non-antibody target-binding domain; wherein the target is a CAR (copending claims 1, 2, 4, 6, 13, 14 and 24).
Copending claim 15 is drawn to a cell comprising the fusion protein of copending claim 1, wherein the target-binding domain is a synthetic leucine zipper.
Copending claim 19 is drawn to a cell of copending claim 1, wherein the target protein is exogenous to the cell and comprises a synthetic leucine zipper and binding between the fusion protein and the target protein is via leucine zippers.
Copending claims do not specifically teach a cleavable fusion protein comprising:(a) an extracellular binding domain comprising a first protein binding domain, wherein the first protein binding domain specifically binds to a cell surface protein; a force sensing region; one or more force-dependent cleavage sites that are cleaved when the force sensing region is activated; and an intracellular domain comprising: a second protein binding domain, wherein the second protein binding domain specifically binds to a target protein; and a degradation domain, wherein the degradation domain is a degron or E3 ligase- recruiting domain, and when the fusion protein is expressed in a mammalian cell, binding of the first binding domain to the cell surface protein induces proteolytic cleavage of the one or more force-dependent cleavage site to release the intracellular domain; or wherein the extracellular binding domain comprises a scFv, a nanobody, a cell-surface receptor or a ligand for a cell-surface receptor; or wherein the force sensing region and/or the one or more force-dependent cleavage sites are from a Delta/Serrate/Lag2 (DSL) superfamily protein.
Copending claims also do not specifically teach a cell comprising the fusion protein wherein the cell further comprises the target protein and wherein the target protein is localized to the plasma membrane; or wherein the target protein is a transmembrane protein; or wherein the target protein is associated with a transmembrane protein; or wherein the target protein is an immune receptor; or wherein the target protein is not localized to the plasma membrane.
Copending claims further do not specifically teach a protein circuit comprising i. a fusion protein; and ii. the target protein; wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell releases the intracellular domain and alters degradation of the target protein; or wherein the target protein is localized to the plasma membrane and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell decreases degradation of the target protein; or wherein the target protein is not localized to the plasma membrane and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell increases degradation of the target protein.
Copending claims also further do not specifically teach a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell, wherein: (a) the first cell comprises: i. the fusion protein; and ii. the target protein; and (b) the second cell comprises the cell surface protein on its surface, wherein binding of the first cell to the second cell via the fusion protein releases the intracellular domain, thereby altering degradation of the target protein; or wherein the target protein is localized to the plasma membrane and the introducing step results in a decrease in degradation of the target protein; or wherein the target protein is not localized to the plasma membrane and the introducing step results in an increase in degradation of the target protein.
However, these deficiencies are made up in the teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al.
The teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al. have been described in the 103 rejections above.
It would be obvious to generate a cleavable fusion protein by substituting the transmembrane domain and intracellular domain of the chimeric protein as taught by Choe et al. with the fusion protein that comprises a transmembrane protein, a target-binding domain and a degradation domain as recited by the copending claims because Choe et al. teaches that chimeric fusion proteins that comprise an extracellular first member binding pair, a force sensor cleavage domain comprising a proteolytic cleavage site; a transmembrane domain; and an intracellular domain, upon binding of the first binding member to the second member binding pair on the cell surface of a second cell, cleavage of the force sensor cleavage domain at the proteolytic cleavage site is induced, thereby releasing the intracellular domain that comprises the target-binding domain and E3-ligase recruiting domain or degron to effect degradation of target protein because Neklesa et al. teaches that a bifunctional molecule that comprises a first ligand for target protein binding and a second ligand for recruiting E3 ligase is capable of performing targeted protein ubiquitination and degradation by proteasomes in a catalytic, selective, potent and recyclable manner with superior outcomes when compared to other modalities. The motivation to generate and use a cleavable fusion protein that comprises an extracellular binding domain and a releasable intracellular molecule that can target ubiquitination/degradation of the targeted proteins would be to enable precise, localized, and on-demand destruction of specifically targeted intracellular proteins upon encountering a distinct external stimulus which corresponds to protein binding on the extracellular cell surface.
Further, it would be obvious to generate a cleavable fusion protein by substituting the copending fusion protein into the chimeric protein as taught by Choe et al., and further including the synthetic leucine zipper as the target-binding domain, as well as including the target protein that comprises a synthetic leucine zipper such that the binding between the intracellular domain target-binding domain and the target protein is via leucine zippers, and even further including the target that is a CAR at the plasma membrane of the cell as recited by the copending claims, wherein the CAR is a transmembrane protein as well as an immune receptor that is modified to comprise the synthetic leucine zipper which is the target protein or binding partner of the other synthetic leucine zipper on the fusion protein, because the resulting generated cleavable fusion protein, expressed alongside CARs on T cells, can function by interacting and binding tumor antigens on tumor cells which in turn causes cleavage/release of the degradation domains when bound, thus allowing persistent expression of the CAR to effect tumor cell killing; alternatively the CAR is degraded when tumor antigen is no longer present due to lack of release of the degradation domain of the cleavable fusion protein which enables dimerization of the synthetic leucine zipper on the cleavable fusion protein with the synthetic leucine zipper on the CAR and which results in subsequent degradation of the CAR since the T cell is no longer needed to interact with the tumor cell to effect killing of said tumor cell. The motivation to express such a generated cleavable fusion protein in T cells that also express CARs is to include an additional control mechanism that would allow for the engineered CAR T cell to be switched “on” or “off” to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity as taught by Wu et al. (Abstract).
Moreover, it would be obvious to generate a protein circuit by performing the combined method of the copending claimed fusion protein and Chou et al. as described above and including a target protein as taught by Choe et al., or including a target protein that is a CAR as recited by the copending claims, because the generated protein circuit would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter the degradation of the target protein upon binding of the first binding moiety of the fusion protein to the cell surface protein on another cell.
Furthermore, it would be obvious to generate a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell as taught by Choe et al., wherein: (a) the first cell comprises: i. the fusion protein generated by performing the combined method of the copending claims and Choe et al.; and ii. the target protein as taught by Choe et al. or as recited by the copending claims; and (b) the second cell comprises the cell surface protein on its surface as taught by Choe et al., because the generated method would result in the release of the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter degradation of the target protein upon binding of the first cell to the second cell via the fusion protein generated by the combined method.
This is a provisional nonstatutory double patenting rejection.
Third NSDP: Copending Appln 18/278377
Claims 1-5, 7-11, 13, 14, 16, 18-21 and 23-25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of copending Application No. 18/278,377 in view of Choe et al. (WO2019099689A1 Date Published 2019-05-23), Yuan et al. (J Biol Chem. 2012 Oct 12;287(42):34904-34916), Neklesa et al. (Pharmacology & Therapeutics Volume 174, June 2017, Pages 138-144), Kanemaki (Eur J Physiol 465, 419–425; 2013) and Wu et al. (Science 350, aab4077; 2015).
Although the copending claims and instant claims are not identical, they are both drawn to a fusion protein comprising: (a) an extracellular domain comprising a first binding moiety that is capable of specifically binding to a first cell surface marker; (b) a transmembrane domain; and (c) an intracellular domain comprising: i. a first domain that specifically binds to a corresponding target domain in a target protein; and ii. a degradation domain, wherein the degradation domain is a degron or E3 ligase- recruiting domain; wherein the extracellular domain of the fusion protein comprises a scFv, a nanobody or a ligand for a cell-surface receptor (copending claim 1).
Copending claims 8 and 9 and instant claims are also both drawn to a cell comprising said fusion protein, or a nucleic acid containing the same; wherein the cell further comprises the target protein, wherein the target protein is localized at the plasma membrane and comprises a target dimerization domain to which the first dimerization domain of (c)(i) binds; wherein the target protein is a transmembrane protein; wherein the target protein is associated with a transmembrane protein; wherein the target protein is a chimeric antigen receptor.
Copending claim 19 and instant claims are further both drawn in part to a protein circuit comprising i. said fusion protein; and ii. a target protein, wherein binding of the first binding moiety of the fusion protein to cell surface markers alters degradation of the target protein.
Further, copending claim 21 and instant claims are drawn in part to a method for modulating degradation of a target protein, comprising introducing a first cell to a second cell, wherein:(a) the first cell comprises: i. said fusion protein; and ii. a target protein; and (b) the second cell comprises, on its surface, the first and second cell surface markers; thereby altering degradation of the target protein.
Copending claim 3 is drawn to a fusion protein of copending claim 1, wherein the first domain and the target domain are synthetic leucine zipper domains.
Copending claims do not specifically teach a cleavable fusion protein that further comprises: a force sensing region; one or more force-dependent cleavage sites that are cleaved when the force sensing region is activated; and when the fusion protein is expressed in a mammalian cell, binding of the first binding domain to the cell surface protein induces proteolytic cleavage of the one or more force-dependent cleavage site to release the intracellular domain; or wherein the force sensing region and/or the one or more force-dependent cleavage sites are from a Delta/Serrate/Lag2 (DSL) superfamily protein.
Copending claims also do not specifically teach a cell comprising the fusion protein wherein the cell further comprises the target protein and wherein the target protein is not localized to the plasma membrane.
Copending claims further do not specifically teach a protein circuit comprising i. the said fusion protein; and ii. the target protein; wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell releases the intracellular domain and alters degradation of the target protein; or wherein the target protein is not localized to the plasma membrane and wherein binding of the first binding moiety of the fusion protein to the cell surface protein on another cell increases degradation of the target protein.
Copending claims also further do not specifically teach a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell, wherein: (a) the first cell comprises: i. the said fusion protein; and ii. the target protein; and (b) the second cell comprises the cell surface protein on its surface, wherein binding of the first cell to the second cell via the fusion protein releases the intracellular domain, thereby altering degradation of the target protein; or wherein the target protein is localized to the plasma membrane and the introducing step results in a decrease in degradation of the target protein; or wherein the target protein is not localized to the plasma membrane and the introducing step results in an increase in degradation of the target protein.
However, these deficiencies are made up in the teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al.
The teachings of Choe et al., Yuan et al., Neklesa et al., Kanemaki and Wu et al. have been described in the 103 rejections above.
It would be obvious to generate a cleavable fusion protein by modifying the fusion protein as recited by the copending claims to include the force sensing region and the force-dependent cleavage sites that are cleaved when the force sensing region is activated as taught by Choe et al. because Choe et al. teaches that chimeric fusion proteins that comprise a first member binding pair, a force sensor cleavage domain comprising a proteolytic cleavage site; a transmembrane domain; and an intracellular domain, upon binding of the first binding member to the second member binding pair on the cell surface of a second cell, cleavage of the force sensor cleavage domain at the proteolytic cleavage site is induced, thereby releasing the intracellular domain that comprises the domain that specifically binds to a corresponding target domain in a target protein and E3-ligase recruiting domain or degron to effect degradation of target protein because Neklesa et al. teaches that a bifunctional molecule that comprises a first ligand for target protein binding and a second ligand for recruiting E3 ligase is capable of performing targeted protein ubiquitination and degradation by proteasomes in a catalytic, selective, potent and recyclable manner with superior outcomes when compared to other modalities. The motivation to generate and use a cleavable fusion protein that comprises an extracellular binding domain and a releasable intracellular molecule that can target ubiquitination/degradation of the targeted proteins would be to enable precise, localized, and on-demand destruction of specifically targeted intracellular proteins upon encountering a distinct external stimulus which corresponds to protein binding on the extracellular cell surface.
Further, it would be obvious to generate a cleavable fusion protein by including the force sensing region and the force-dependent cleavage sites as taught by Choe et al. into the recited copending fusion protein, and further including the synthetic leucine zipper as the target-binding domain, as well as including the target protein that comprises a synthetic leucine zipper such that the binding between the intracellular domain target-binding domain and the target protein is via leucine zippers, and even further including the target that is a CAR at the plasma membrane of the cell as recited by the copending claims, wherein the CAR is a transmembrane protein as well as an immune receptor that is modified to comprise the synthetic leucine zipper which is the target protein or binding partner of the other synthetic leucine zipper on the fusion protein, because the resulting generated cleavable fusion protein, expressed alongside CARs on T cells, can function by interacting and binding tumor antigens on tumor cells which in turn causes cleavage/release of the degradation domains when bound, thus allowing persistent expression of the CAR to effect tumor cell killing; alternatively the CAR is degraded when tumor antigen is no longer present due to lack of release of the degradation domain of the cleavable fusion protein which enables dimerization of the synthetic leucine zipper on the cleavable fusion protein with the synthetic leucine zipper on the CAR and which results in subsequent degradation of the CAR since the T cell is no longer needed to interact with the tumor cell to effect killing of said tumor cell. The motivation to express such a generated cleavable fusion protein in T cells that also express CARs is to include an additional control mechanism that would allow for the engineered CAR T cell to be switched “on” or “off” to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity as taught by Wu et al. (Abstract).
Moreover, it would be obvious to generate a protein circuit by performing the combined method of the copending claimed fusion protein and Chou et al. as described above and including a target protein as taught by Choe et al., or including a target protein that is a CAR as recited by the copending claims, because the generated protein circuit would have the property of releasing the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter the degradation of the target protein upon binding of the first binding moiety of the fusion protein to the cell surface protein on another cell.
Furthermore, it would be obvious to generate a method for modulating degradation of a target protein, comprising: introducing a first cell to a second cell as recited by the copending claims, wherein: (a) the first cell comprises: i. the fusion protein generated by performing the combined method of the copending claims and Choe et al.; and ii. the target protein as taught by Choe et al. or as recited by the copending claims; and (b) the second cell comprises the cell surface protein on its surface as taught by Choe et al. or as recited by the copending claims, because the generated method would result in the release of the intracellular domain that can bind to the target protein and simultaneously bind to E3-ligase to alter degradation of the target protein upon binding of the first cell to the second cell via the fusion protein generated by the combined method.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
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/YIE-CHIA LEE (TONYA)/Examiner, Art Unit 1642
/SEAN E AEDER/Primary Examiner, Art Unit 1642
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