DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
2. Claims 11-15 and 29-44 are presently pending. Applicant’s election of Group II (claims 1-15) and species: SEQ ID NO: 26 in the reply filed on March 5, 2026 is acknowledged. Claims 1-10 and 16-28 are canceled; claims 11 and 14 are presently amended; claims 29-44 are new. Election was made without traverse in the reply filed on May 15, 2026. Accordingly, claims 11-15 and 29-44 are presently subject to examination. In addition, SEQ IDs NOs: 2, 7, 13 (contained within SEQ ID NO: 26) and 34, (the nucleic acid encoding SEQ ID NO: 26) are presently subject to examination since they are encompassed by the elected species: the fusion protein of SEQ ID NO: 26.
Information Disclosure Statement
3. 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.
Specification Objections
4. The instant specification is objected to for the following reasons:
a. There are trademarks in this application that do not meet the requirements.
The use of the term (e.g., “eBiosciences” at page 25, line 2), 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. Applicant should review the specification for other trademarks and make corrections as required.
Claim Rejections - 35 USC § 112
5. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description
6. Claims 11-15 and 29-44 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter later claimed. The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, disclosure of drawings, or by disclosure of relevant identifying characteristics, for example, structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the Applicants were in possession of the claimed genus.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that:
"applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
The claims are directed to polynucleotide comprising a nucleotide sequence encoding a fusion protein of comprising: (a) a first polypeptide comprising Interleukin-2 (IL-2) or a functional variant or fragment thereof; and (b) a second polypeptide comprising an extracellular domain of lnterleukin-2 Receptor alpha (IL-2Rα) or a functional variant or fragment thereof, wherein said fusion protein has IL-2 activity, wherein the first polypeptide and the second polypeptide are linked via a linker. The claims include % variants of SEQ ID NOs: 2 (the IL-2), 7 (the IL-2Rα ECD), 13 (the (GGGS)3 linker), 26 (the fusion protein), and 34 (the nucleotide sequence of the fusion protein); and a variant comprising at least one mutation in the ECD of IL-2Rα (claim 40, for example); wherein the fusion protein "has IL-2 activity" (from claim 11). However, while the specification teaches the IL-2 of SEQ ID NO: 2, linker of SEQ ID NO: 13, and the IL-2Rα of SEQ ID NO:7, and one variant of the hIL-2Rα of SEQ ID NO: 7 with 2 amino acid substitutions, no % variant thereof meeting the limitations of the claims was ever identified or particularly described.
The claimed immunomodulatory molecules must possess specific functions, such as "has IL-2 activity," but there is only one structure presented that correlates with this function. The specification only sets forth the construct of SEQ ID NO: 26 specifically as potentially having the required functions, but this species is not sufficiently representative of such a broad genus of fusion proteins having IL-2 activity as instantly claimed.
A. No Written Description for Variants or Portions of the Claim-Recited Features
The claimed invention recites variants and portions of the claim-recited fusion protein and its components because the claims recite: “at least 90% sequence identity” (claim 30), “at least 85% sequence identity” (claims 38-39, 44), unspecified mutations (which includes insertions and deletions (claim 40)), or no structure at all (i.e., claim 11); and the broadest reasonable interpretation for this recitation is: the claim language reads on fusion proteins comprising fragments of the features. However, the specification only demonstrates fusion proteins of SEQ ID NO: 26, which comprises SEQ ID NOs: 2, 7, and 13; and additional fusion proteins having alternative linkers, none of which is a fragment of the (GGGS)3 linker (SEQ ID NO: 13) comprised in SEQ ID NO: 26 (see, e.g., FIG. 4).
The specification therefore only demonstrates constructs having a single IL-2 sequence (SEQ ID NO: 2), a single IL-2Rα ECD sequence (SEQ ID NO: 7), and a single (GGGS)3 sequence (SEQ ID NO: 13). No specific fragments of these features are demonstrated in the specification. The specification provides no identification of any particular portions of the polypeptides of SEQ ID NO: 2, 7 and 13 that must be conserved, and there is no teaching in the specification regarding which 10-15% of the sequence structures can be varied while retaining the desired functional property. Further, there is no correlation between any structure and "IL-2 activity" of the polypeptides disclosed, based on which those of ordinary skill in the art could predict which amino acids can vary from SEQ ID NO: 2, 7, 13, 26, or encoded by the nucleotide SEQ ID NO: 34 without losing the activity. For example, FIG. 4A of the shows there was a significant difference in activity of the fusion protein when (GGGGS)4 linker was used as compared to the instantly claimed (GGGS)3 linker of SEQ ID NO: 13.
The claims recite functional language of the fusion protein, such as “functional fragment” of the IL-2 and IL-2Rα ECD, and that the fusion protein has “IL-2 activity,” however a definition by function does not suffice to define the genus because it is only an indication of what the fusion protein does, rather than what it is; therefore, it is only a definition of a useful result rather than a definition of what achieves that result. In addition, because the genus of fusion proteins is highly variable (i.e., each molecule comprising a fragment of a feature would necessarily have a unique structure; see MPEP 2434), the generic description of the substance is insufficient to describe the genus. Thus, the encompassed fusion proteins having fragments of the claim-recited features have no correlation between their structure and function.
To address this issue, a brief assessment of the state of the art regarding fragments of amino acid sequence is made herein, showing that it is unpredictable how a fragment of a short amino acid sequence will function, let alone fragments of longer amino sequences comprising domains of fusion proteins:
Souza‐Silva et al. ("Peptide fragments of bradykinin show unexpected biological activity not mediated by B1 or B2 receptors." British Journal of Pharmacology 179.12 (2022): 3061-3077) teaches regarding fragments of the 9 amino acid Bradykinin sequence: “BK-(1–7) and BK-(1–5) are produced in vivo from BK-(1–9). Both peptides induced NO production in all cell types tested. However, unlike BK-(1–9), NO production elicited by BK-(1–7) or BK-(1–5) was not inhibited by B1 or B2 receptor antagonists.” Souza‐Silva et al. at abstract. Therefore, it was unpredictable that fragments of this 9 amino acid sequence had substantially different biological activity compared to the full-length amino acid sequence.
In contrast, Zablocki et al. ("Potent in vitro and in vivo inhibitors of platelet aggregation based upon the Arg-Gly-Asp-Phe sequence of fibrinogen. A proposal on the nature of the binding interaction between the Arg-guanidine of RGDX mimetics and the platelet GP IIb-IIIa receptor." Journal of medicinal chemistry 36.13 (1993): 1811-1819) teaches regarding a fragment of the 4 amino acid RGDF sequence that surprisingly: “[p]reviously, we had shown that the inherent inhibitory potency of Arg-Gly-Asp-Phe [RGDF] for disrupting the fibrinogen-GP Ilb-IIIa interaction can be enhanced 15-fold by removing the Arg-NH2 and the Arg-Gly amide bond to obtain 8-guanidinooctanoyl-Asp-Phe[GOA-Asp Phe]” Zablocki et al. at introduction. In other words, the fragment of the 4 amino acid sequence showed a large increase in inhibitory activity compared to the full-length tetrapeptide.
The above juxtaposition of a fragmenting a short amino acid sequence resulting in substantially different biological activity as illustrated by Souza‐Silva et al. compared to fragmenting a different short amino acid sequence resulting in a large increase in (inhibitory) activity illustrated by Zablocki et al. shows it is very unpredictable what effects will be obtained with all the possible fusion proteins comprising fragments of features as instantly claimed. Therefore, neither the art nor the specification provides a sufficient representative number of fusion proteins comprising fragments of IL-2, IL-2Rα, and linker to meet the written description requirement for instant claims encompassing fusion proteins having fragments of these features.
It is therefore unknown how the genus of fusion proteins comprising fragments of IL-2, IL-2Rα, and (GGGS)3 linker would recognize target molecules and regulate immune response. Applicant has not shown possession of a representative number of species that have the claimed function(s). The specification therefore provides insufficient written description to support the genus of fusion proteins comprising fragments of IL-2, IL-2Rα, and (GGGS)3 linker encompassed by the claims. Given all of the above, Applicant does not have written description for “variants” or “portions” of the IL-2, IL-2Rα, and (GGGS)3 linker.
B. No Written Description for the Breath of the Claims
Claims 11-15, 29-38, and 40-43 are very broad because the claims either do not recite SEQ ID NOs at all (e.g., claim 11), or only recite SEQ ID NOs for one of the three required domains of the fusion protein (IL-2, IL-2Rα ECD, or (GGGS)3 linker). These claims therefore fail to recite necessary features of the fusion protein, such as the specific IL-2, IL-2Rα ECD, or (GGGS)3 linker demonstrated in the specification.
As shown above, the specification only provides one example a fusion protein that reads on elected species: SEQ ID NO: 26. Therefore, the breadth of the claims encompasses a broad genus of fusion proteins with unknown functionality. To address this issue, a brief assessment of the state of the art regarding unpredictability in fusion protein design is made herein.
Silacci et al. ("Linker length matters, fynomer-Fc fusion with an optimized linker displaying picomolar IL-17A inhibition potency." Journal of Biological Chemistry 289.20 (2014): 14392-14398) is directed to Fynomer-Fc fusion proteins for inhibiting IL-17A. Silacci et al. at title. In this instance, the linker design and length “influenced significantly the potency of [the] Fc fusion proteins.” Silacci et al. at conclusion.
Chen et al. ("Fusion protein linkers: property, design and functionality." Advanced drug delivery reviews 65.10 (2013): 1357-1369) is a review of linkers in fusion protein design. Chen et al. teaches that “successful construction of a recombinant fusion protein requires two indispensable elements: the component proteins and the linkers. The choice of the component proteins is based on the desired functions of the fusion protein product and, in most cases, is relatively straightforward. On the other hand, the selection of a suitable linker to join the protein domains together can be complicated and is often neglected in the design of fusion proteins. Direct fusion of functional domains without a linker may lead to many undesirable outcomes, including misfolding of the fusion proteins, low yield in protein production, or impaired bioactivity. Therefore, the selection or rational design of a linker to join fusion protein do mains is an important, yet underexplored, area in recombinant fusion protein technology.” Chen et al. at introduction.
Challener ("Fusion proteins pose manufacturability challenges." BioPharm International 30.5 (2017): 30-31) is directed to challenges in fusion protein manufacturing. Challener at title. Challener teaches that “Achieving and maintaining proper folding for each of the components in fusion proteins is a major challenge in the molecular design of these products. Issues can arise when domains are taken out of their natural context, or a domain is combined with a second domain with which it does not fold well. As a result, combining the different components of the fusion protein that do not naturally occur together can lead to instability with the composite molecule, creating manufacturing challenges such as aggregation[.]” Challener at the need for stabilization. Therefore, “[a] key aspect of improving the manufacturability of fusion proteins lies with their design, which should be focused on minimizing the subsequent residual liabilities that remain for process development.” Challener at new design strategies.
Therefore, careful design of a fusion protein’s configuration—including the linkers used to fuse the various domains of the fusion protein—is critical to the functionality of the fusion protein, and also requires validation / experimentation to solve the well-known challenges associated with this technology. Accordingly, without actually performing the required experiments, it is unpredictable what species of the instantly claimed genus of immunomodulatory molecules are functional and have “IL-2 activity.”
Given all of the above, Applicant does not have written description for the genus of fusion proteins instantly claimed—Applicant instead has possession of: a fusion protein specifically comprising each of of SEQ ID NO: 2, 7, and 13 (i.e., SEQ ID NO: 26), and no fragments thereof.
MPEP § 2163.02 states, “[a]n objective standard for determining compliance with the written description requirement is, 'does the description clearly allow person of ordinary skill in the art to recognize that he or she invented what is claimed’”. The courts have decided: the purpose of the "written description" requirement is broader than to merely explain how to "make and use"; the Applicant must convey with reasonable clarity to those skilled in the art, that as of the filing date sought, he or she was in possession of the invention. The invention is for purposes of the “written description” inquiry, whatever is now claimed. See Vas-Cath, Inc v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991).
Furthermore, the written description provision of 35 USC §112 is severable from its enablement provision; and adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993). And Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. Moreover, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was “ready for patenting” by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has the Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed.
Therefore, for all these reasons the specification lacks adequate written description, and one of skill in the art cannot reasonably conclude that Applicant had possession of the claimed invention at the time the instant application was filed.
7. 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 34 and 36-37 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.
The claims recite polynucleotides comprising or consisting of SEQ ID NOs rather than polynucleotides comprising or consisting of amino acids set forth in the SEQ ID NOs. Polynucleotides comprise or consist of nucleic acids that encode amino acids; it is therefore unclear how a polynucleotide can comprise or consist of a “SEQ ID NO,” which is neither a nucleic or amino acid. Appropriate clarification and/or correction is requested.
Claim Rejections - 35 USC § 102
8. 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
9. Note: Applicant has elected species: SEQ ID NO: 26, a IL-2 / IL-2Rα fusion protein; SEQ ID NOs: 2, 7, 13, and 34 read on the elected species and are also subject to examination.
Claims 11-12, 14-15, 29, 34-35, and 37-44 are rejected under 35 U.S.C 102 (a)(2) as anticipated by Frelinger et al. (US20130089516A1, published April 11, 2013).
Claim 11 is directed to polynucleotide comprising a nucleotide sequence encoding a fusion protein of comprising: (a) a first polypeptide comprising Interleukin-2 (IL-2) or a functional variant or fragment thereof; and (b) a second polypeptide comprising an extracellular domain of lnterleukin-2 Receptor alpha (IL-2Rα) or a functional variant or fragment thereof, wherein said fusion protein has IL-2 activity, wherein the first polypeptide and the second polypeptide are linked via a linker.
Claim 12 is directed to a host cell comprising the polynucleotide of claim 11.
Claim 14 is directed to a method for making a fusion protein, the method comprising introducing into a host cell the polynucleotide of claim 11 and expressing the fusion protein in the host cell.
Claim 15 is drawn to the method of claim 14, wherein the polynucleotide encoding the fusion protein is operably linked to a promoter active in the host cell.
Claim 29 is drawn to the polynucleotide of claim 11, wherein the linker comprises a glycine/serine linker.
Claim 34 is drawn to the polynucleotide of claim 11, wherein the first polypeptide has at least 85% sequence identity to SEQ ID NO: 2.
Claim 35 is drawn to the polynucleotide of claim 11, wherein the first polypeptide comprises the amino acid sequence as set forth in SEQ ID NO: 2.
Claim 37 is drawn to the polynucleotide of claim 11, wherein the second polypeptide comprises at least 85% sequence identity to SEQ ID NO: 7.
Claim 38 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises the amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 43, 44, 45, 46, 54, 55, 56, 57, 58, 59, 60, or 61.
Claim 39 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises the amino acid sequence having at least 85% sequence identity to SEQ ID NO: 26.
Claim 40 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises at least one mutation in the extracellular domain of IL-2Rα.
Claim 41 is drawn to the polynucleotide of claim 11, wherein the fusion protein has an increased IL-2 potency when compared to native or recombinant IL-2.
Claim 42 is drawn to the polynucleotide of claim 11, wherein the fusion protein has an increased persistent IL-2 stimulation of TL-2R bearing lymphocytes in vivo when compared to native or recombinant IL-2.
Claim 43 is drawn to the polynucleotide of claim 11, wherein the fusion protein further comprises a leader peptide.
Claim 44 is drawn to the polynucleotide of claim 11, wherein the polynucleotide comprises a nucleic acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 29-34.
Frelinger et al. is directed to chimeric nucleic acid sequences encoding chimeric polypeptides (see the abstract). Frelinger et al. discloses an IL-2 / IL-2Rα fusion protein, wherein the IL-2 / IL-2Rα are linked by a linker. See, e.g., Frelinger et al. at FIG. 2A, reproduced below for Applicant’s convenience:
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Felinger et al. also discloses nucleic acid sequences encoding the amino acid sequence. An alignment of Frelinger et al.’s SEQ ID NO: 29 to instant SEQ ID NO: 34 is provided at the end of this section for Applicant’s convenience. (Claim 11; and Claim 44 since the sequence identity is >85%)
Frelinger et al. further discloses non-viral methods for delivering an expression vector comprising a nucleic acid encoding the polypeptide to host cells; that the vector may have promoters operably linked, e.g., CMV promoter, SV40 promoter, β-actin promoter, for controlling transcription from the vectors in mammalian host cells. Frelinger et al. at para. [0051]-[0054]. Felinger et al. therefore discloses a method comprising introducing into a host cell a polynucleotide and expressing the IL-2 / IL-2Rα fusion protein in the host cell. (Claims 12 and 14-15)
Frelinger et al. further discloses that the linker may be glycine/serine linker at para. [0025]. (Claim 29)
Frelinger et al. further discloses the nucleic acid sequence encodes a peptide comprising the amino acid sequence of instant SEQ ID NO: 2. An alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 26 is provided at the end of this section for Applicant’s convenience (note: instant SEQ ID NO: 2 consists of the first 133 amino acids below (see instant Table 1), which are and are 100% identical between the aligned sequences). (Claims 34-35; and Claims 38-39 since the since the sequence identity of the entire fusion protein shown above is >85%)
Frelinger et al. further discloses the IL-Rα of the fusion protein at least 85% sequence identity to SEQ ID NO: 7. An alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 7 is provided at the end of this section for Applicant’s convenience. (Claim 37)
Frelinger et al. further discloses the fusion protein may comprise at least one mutation anywhere, including the extracellular domain of IL-2Rα at para. [0027, 0029, 0032] (e.g., “As with all peptides, polypeptides, and proteins, including fragments thereof, it is understood that additional modifications in the amino acid sequence of the chimeric polypeptides can occur that do not alter the nature or function of the peptides, polypeptides, or proteins. Such modifications include conservative amino acid substitutions and are discussed in greater detail below”; “provided are polypeptides or nucleic acids that have at least, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 percent identity to one of SEQ ID NOs:1-50)”; “Protein modifications include amino acid sequence modifications. Modifications in amino acid sequence may arise naturally as allelic variations (e.g., due to genetic polymorphism), may arise due to environmental influence (e.g, by exposure to ultraviolet light), or may be produced by human intervention (e.g., by mutagenesis of cloned DNA sequences), such as induced point, deletion, insertion and substitution mutants. These modifications can result in changes in the amino acid sequence, provide silent mutations, modify a restriction site, or provide other specific mutations.” (Claim 40)
Frelinger et al. does not explicitly disclose wherein the fusion protein has an increased IL-2 potency when compared to native or recombinant IL-2 (i.e., claim 41); or wherein the fusion protein has an increased persistent IL-2 stimulation of TL-2R bearing lymphocytes in vivo when compared to native or recombinant IL-2 (i.e., claim 42). However, as discussed above Frelinger et al. discloses the structure of the IL-2 / IL-2Rα fusion protein instantly claimed—to the extent these properties are associated with the structure recited in instant claim 11, the properties are also inherently disclosed by Frelinger et al. (Claims 41-42)
Last, Frelinger et al. also discloses wherein the fusion protein further comprises a leader peptide, i.e. the secretory peptide of the unprocessed form of the fusion protein, e.g., the first 20 amino acids of instant SEQ ID NO: 27 (see instant Table 1). Frelinger et al. discloses this feature by its SEQ ID NO: 45 as well; an alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 27 is provided at the end of this section for Applicant’s convenience, demonstrating a 20 amino acid leader sequence omitted from the above alignments with Frelinger et al.’s SEQ ID NO: 45. (Claim 43)
Accordingly, Frelinger et al. anticipates claims 11-12, 14-15, 29, 34-35, and 37-44.
ALIGNMENT INSTANT SEQ ID NO 34 TO FRELINGER ET AL. SEQ ID NO: 29
US-13-639-006-29
Sequence 29, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 29
LENGTH: 1233
TYPE: DNA
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 92.3%; Score 1091.4; Length 1233;
Best Local Similarity 94.7%;
Matches 1156; Conservative 0; Mismatches 26; Indels 39; Gaps 1;
Qy 1 ATGGACAGGATGCAACTCCTGTCTTGCATTGCACTAAGTCTTGCACTTGTCACAAACAGT 60
||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 7 ATGTACAGGATGCAACTCCTGTCTTGCATTGCACTAAGTCTTGCACTTGTCACAAACAGT 66
Qy 61 GCACCTACTTCAAGTTCTACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGAT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 67 GCACCTACTTCAAGTTCTACAAAGAAAACACAGCTACAACTGGAGCATTTACTTCTGGAT 126
Qy 121 TTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 127 TTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTC 186
Qy 181 ACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACATCTTCAGTGTCTAGAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 187 ACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACATCTTCAGTGTCTAGAA 246
Qy 241 GAAGAACTCAAACCTCTGGAGGAAGTGCTAAATTTAGCTCAAAGCAAAAACTTTCACTTA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 247 GAAGAACTCAAACCTCTGGAGGAAGTGCTAAATTTAGCTCAAAGCAAAAACTTTCACTTA 306
Qy 301 AGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 307 AGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAA 366
Qy 361 ACAACATTCATGTGTGAATATGCTGATGAGACAGCAACCATTGTAGAATTTCTGAACAGA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 367 ACAACATTCATGTGTGAATATGCTGATGAGACAGCAACCATTGTAGAATTTCTGAACAGA 426
Qy 421 TGGATTACCTTTTGTCAAAGCATCATCTCAACACTGA----------------------- 457
|||||||||||||||||||||||||||||||||||||
Db 427 TGGATTACCTTTTGTCAAAGCATCATCTCAACACTGACTCACAGCAGCAAGCTGCAGGAA 486
Qy 458 ----------------CTGGTGGAGGTTCTGGTGGAGGTTCAGGTGGAGGTTCGGAGCTC 501
||||||| ||| ||| || || ||| | ||||||
Db 487 TTCGGTGGCGGTGGCTCTGGTGGCGGTGGCTCTGGTGGCGGTGGCTCTGGTACCGAGCTC 546
Qy 502 TGTGACGATGACCCGCCAGAGATCCCACACGCCACATTCAAAGCCATGGCCTACAAGGAA 561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 547 TGTGACGATGACCCGCCAGAGATCCCACACGCCACATTCAAAGCCATGGCCTACAAGGAA 606
Qy 562 GGAACCATGTTGAACTGTGAATGCAAGAGAGGTTTCCGCAGAATAAAAAGCGGGTCACTC 621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 607 GGAACCATGTTGAACTGTGAATGCAAGAGAGGTTTCCGCAGAATAAAAAGCGGGTCACTC 666
Qy 622 TATATGCTCTGTACAGGAAACTCTAGCCACTCGTCCTGGGACAACCAATGTCAATGCACA 681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 667 TATATGCTCTGTACAGGAAACTCTAGCCACTCGTCCTGGGACAACCAATGTCAATGCACA 726
Qy 682 AGCTCTGCCACTCGGAACACAACGAAACAAGTGACACCTCAACCTGAAGAACAGAAAGAA 741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 727 AGCTCTGCCACTCGGAACACAACGAAACAAGTGACACCTCAACCTGAAGAACAGAAAGAA 786
Qy 742 AGGAAAACCACAGAAATGCAAAGTCCAATGCAGCCAGTGGACCAAGCGAGCCTTCCAGGT 801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 787 AGGAAAACCACAGAAATGCAAAGTCCAATGCAGCCAGTGGACCAAGCGAGCCTTCCAGGT 846
Qy 802 CACTGCAGGGAACCTCCACCATGGGAAAATGAAGCCACAGAGAGAATTTATCATTTCGTG 861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 847 CACTGCAGGGAACCTCCACCATGGGAAAATGAAGCCACAGAGAGAATTTATCATTTCGTG 906
Qy 862 GTGGGGCAGATGGTTTATTATCAGTGCGTCCAGGGATACAGGGCTCTACACAGAGGTCCT 921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 907 GTGGGGCAGATGGTTTATTATCAGTGCGTCCAGGGATACAGGGCTCTACACAGAGGTCCT 966
Qy 922 GCTGAGAGCGTCTGCAAAATGACCCACGGGAAGACAAGGTGGACCCAGCCCCAGCTCATA 981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 967 GCTGAGAGCGTCTGCAAAATGACCCACGGGAAGACAAGGTGGACCCAGCCCCAGCTCATA 1026
Qy 982 TGCACAGGTGAAATGGAGACCAGTCAGTTTCCAGGTGAAGAGAAGCCTCAGGCAAGCCCC 1041
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1027 TGCACAGGTGAAATGGAGACCAGTCAGTTTCCAGGTGAAGAGAAGCCTCAGGCAAGCCCC 1086
Qy 1042 GAAGGCCGTCCTGAGAGTGAGACTTCCTGCCTCGTCACAACAACAGATTTTCAAATACAG 1101
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1087 GAAGGCCGTCCTGAGAGTGAGACTTCCTGCCTCGTCACAACAACAGATTTTCAAATACAG 1146
Qy 1102 ACAGAAATGGCTGCAACCATGGAGACGTCCATATTTACAACAGAGTACCAGGGTGGACAT 1161
|||||||||||||||||||||||||||||||||||||||||||||||||||| | |||
Db 1147 ACAGAAATGGCTGCAACCATGGAGACGTCCATATTTACAACAGAGTACCAGGTAGCACAC 1206
Qy 1162 CACCATCACCATCACTAATAA 1182
||||| ||||| ||||||| |
Db 1207 CACCACCACCACCACTAATGA 1227
ALIGNMENT INSTANT SEQ ID NO 26 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 98.1%; Score 1912; Length 392;
Best Local Similarity 96.5%;
Matches 359; Conservative 1; Mismatches 4; Indels 8; Gaps 1;
Qy 1 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 80
Qy 61 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 81 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 140
Qy 121 WITFCQSIISTLT--------GGGSGGGSGGGSELCDDDPPEIPHATFKAMAYKEGTMLN 172
||||||||||||| ||| || | |:|||||||||||||||||||||||||||
Db 141 WITFCQSIISTLTHSSKLQEFGGGGSGGGGSGTELCDDDPPEIPHATFKAMAYKEGTMLN 200
Qy 173 CECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRNTTKQVTPQPEEQKERKTTE 232
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 201 CECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRNTTKQVTPQPEEQKERKTTE 260
Qy 233 MQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVC 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 261 MQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVC 320
Qy 293 KMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCLVTTTDFQIQTEMAA 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 321 KMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCLVTTTDFQIQTEMAA 380
Qy 353 TMETSIFTTEYQ 364
||||||||||||
Db 381 TMETSIFTTEYQ 392
ALIGNMENT INSTANT SEQ ID NO 7 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 100.0%; Score 1203; Length 392;
Best Local Similarity 100.0%;
Matches 219; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQ 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 174 ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQ 233
Qy 61 CTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYH 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 234 CTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYH 293
Qy 121 FVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 294 FVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQA 353
Qy 181 SPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 219
|||||||||||||||||||||||||||||||||||||||
Db 354 SPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 392
ALIGNMENT INSTANT SEQ ID NO 27 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
APPLICANT: University of Rochester
TITLE OF INVENTION: Protease Activated Cytokines
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 97.7%; Score 1997; Length 392;
Best Local Similarity 96.4%;
Matches 378; Conservative 1; Mismatches 5; Indels 8; Gaps 1;
Qy 1 MDRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRML 60
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRML 60
Qy 61 TFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSE 120
Qy 121 TTFMCEYADETATIVEFLNRWITFCQSIISTLT--------GGGSGGGSGGGSELCDDDP 172
||||||||||||||||||||||||||||||||| ||| || | |:|||||||
Db 121 TTFMCEYADETATIVEFLNRWITFCQSIISTLTHSSKLQEFGGGGSGGGGSGTELCDDDP 180
Qy 173 PEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATR 232
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATR 240
Qy 233 NTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMV 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 NTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMV 300
Qy 293 YYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPE 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 YYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPE 360
Qy 353 SETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 384
||||||||||||||||||||||||||||||||
Db 361 SETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 392
Claim Rejections - 35 USC § 103
10. 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.
11. Note: Applicant has elected species: SEQ ID NO: 26, a IL-2 / IL-2Rα fusion protein; SEQ ID NOs: 2, 7, 13, and 34 read on the elected species and are also subject to examination.
Claims 11-15, 29, 34-35, and 37-44 are rejected under 35 U.S.C. 103 as being unpatentable over Frelinger et al. (US20130089516A1, published April 11, 2013) in view of Taniguchi et al. ("Structure and expression of a cloned cDNA for human interleukin-2." Nature 302.5906 (1983): 305-310).
Claim 11 is directed to polynucleotide comprising a nucleotide sequence encoding a fusion protein of comprising: (a) a first polypeptide comprising Interleukin-2 (IL-2) or a functional variant or fragment thereof; and (b) a second polypeptide comprising an extracellular domain of lnterleukin-2 Receptor alpha (IL-2Rα) or a functional variant or fragment thereof, wherein said fusion protein has IL-2 activity, wherein the first polypeptide and the second polypeptide are linked via a linker.
Claim 12 is directed to a host cell comprising the polynucleotide of claim 11.
Claim 13 is directed to the host cell of claim 12, wherein the host cell comprises a CHO cell or a COS cell.
Claim 14 is directed to a method for making a fusion protein, the method comprising introducing into a host cell the polynucleotide of claim 11 and expressing the fusion protein in the host cell.
Claim 15 is drawn to the method of claim 14, wherein the polynucleotide encoding the fusion protein is operably linked to a promoter active in the host cell.
Claim 29 is drawn to the polynucleotide of claim 11, wherein the linker comprises a glycine/serine linker.
Claim 34 is drawn to the polynucleotide of claim 11, wherein the first polypeptide has at least 85% sequence identity to SEQ ID NO: 2.
Claim 35 is drawn to the polynucleotide of claim 11, wherein the first polypeptide comprises the amino acid sequence as set forth in SEQ ID NO: 2.
Claim 37 is drawn to the polynucleotide of claim 11, wherein the second polypeptide comprises at least 85% sequence identity to SEQ ID NO: 7.
Claim 38 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises the amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 43, 44, 45, 46, 54, 55, 56, 57, 58, 59, 60, or 61.
Claim 39 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises the amino acid sequence having at least 85% sequence identity to SEQ ID NO: 26.
Claim 40 is drawn to the polynucleotide of claim 11, wherein the fusion protein comprises at least one mutation in the extracellular domain of IL-2Rα.
Claim 41 is drawn to the polynucleotide of claim 11, wherein the fusion protein has an increased IL-2 potency when compared to native or recombinant IL-2.
Claim 42 is drawn to the polynucleotide of claim 11, wherein the fusion protein has an increased persistent IL-2 stimulation of TL-2R bearing lymphocytes in vivo when compared to native or recombinant IL-2.
Claim 43 is drawn to the polynucleotide of claim 11, wherein the fusion protein further comprises a leader peptide.
Claim 44 is drawn to the polynucleotide of claim 11, wherein the polynucleotide comprises a nucleic acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 29-34.
Frelinger et al. is directed to chimeric nucleic acid sequences encoding chimeric polypeptides (see the abstract). Frelinger et al. teaches an IL-2 / IL-2Rα fusion protein, wherein the IL-2 / IL-2Rα are linked by a linker. See, e.g., Frelinger et al. at FIG. 2A, reproduced below for Applicant’s convenience:
PNG
media_image1.png
268
580
media_image1.png
Greyscale
Felinger et al. also teaches nucleic acid sequences encoding the amino acid sequence. An alignment of Frelinger et al.’s SEQ ID NO: 29 to instant SEQ ID NO: 34 is provided at the end of this section for Applicant’s convenience. Frelinger et al. further teaches non-viral methods for delivering an expression vector comprising a nucleic acid encoding the polypeptide to host cells; that the vector may have promoters operably linked, e.g., CMV promoter, SV40 promoter, β-actin promoter, for controlling transcription from the vectors in mammalian host cells. Frelinger et al. at para. [0051]-[0054]. Felinger et al. therefore teaches a method comprising introducing into a host cell a polynucleotide and expressing the IL-2 / IL-2Rα fusion protein in the host cell. Frelinger et al. further teaches that the linker may be glycine/serine linker at para. [0025]. Frelinger et al. further teaches the nucleic acid sequence encodes a peptide comprising the amino acid sequence of instant SEQ ID NO: 2. An alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 26 is provided at the end of this section for Applicant’s convenience (note: instant SEQ ID NO: 2 consists of the first 133 amino acids below (see instant Table 1), which are and are 100% identical between the aligned sequences). Frelinger et al. further teaches the IL-Rα of the fusion protein at least 85% sequence identity to SEQ ID NO: 7. An alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 7 is provided at the end of this section for Applicant’s convenience. Frelinger et al. further teaches the fusion protein may comprise at least one mutation anywhere, including the extracellular domain of IL-2Rα at para. [0027, 0029, 0032] (e.g., “As with all peptides, polypeptides, and proteins, including fragments thereof, it is understood that additional modifications in the amino acid sequence of the chimeric polypeptides can occur that do not alter the nature or function of the peptides, polypeptides, or proteins. Such modifications include conservative amino acid substitutions and are discussed in greater detail below”; “provided are polypeptides or nucleic acids that have at least, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 percent identity to one of SEQ ID NOs:1-50)”; “Protein modifications include amino acid sequence modifications. Modifications in amino acid sequence may arise naturally as allelic variations (e.g., due to genetic polymorphism), may arise due to environmental influence (e.g, by exposure to ultraviolet light), or may be produced by human intervention (e.g., by mutagenesis of cloned DNA sequences), such as induced point, deletion, insertion and substitution mutants. These modifications can result in changes in the amino acid sequence, provide silent mutations, modify a restriction site, or provide other specific mutations.” Frelinger et al. does not explicitly disclose wherein the fusion protein has an increased IL-2 potency when compared to native or recombinant IL-2 (i.e., claim 41); or wherein the fusion protein has an increased persistent IL-2 stimulation of TL-2R bearing lymphocytes in vivo when compared to native or recombinant IL-2 (i.e., claim 42). However, as discussed above Frelinger et al. discloses the structure of the IL-2 / IL-2Rα fusion protein instantly claimed—to the extent these properties are associated with the structure recited in instant claim 11, the properties are also necessarily present in Frelinger et al. Frelinger et al. also teaches wherein the fusion protein further comprises a leader peptide, i.e. the secretory peptide of the unprocessed form of the fusion protein, e.g., the first 20 amino acids of instant SEQ ID NO: 27 (see instant Table 1). Frelinger et al. discloses this feature by its SEQ ID NO: 45 as well; an alignment of Frelinger et al.’s SEQ ID NO: 45 to instant SEQ ID NO: 27 is provided at the end of this section for Applicant’s convenience, demonstrating a 20 amino acid leader sequence omitted from the above alignments with Frelinger et al.’s SEQ ID NO: 45. (Claims 11-12, 14-15, 29, 34-35, and 37-44)
Frelinger et al. teaches the importance of solubility of the IL-2Rα receptor to the fusion protein at e.g., para. [0074] and [0094]. Frelinger et al. teaches at para. [0025] regarding linkers: “The linker sequence serves to provide flexibility between the first and third polypeptides, such that the third polypeptide is capable of inhibiting the activity of the first polypeptide. The linker sequence can be located between the first and second polypeptide or the second and third polypeptide. Optionally, the chimeric polypeptide comprises at least one linker sequence, two or more linker sequences, or four linker sequences. The at least one linker sequence, two or more linker sequences, or four linker sequences can be the same or different linker sequences. Optionally, the linker sequence comprises GGGGS (SEQ ID NO:6), GSGSGS (SEQ ID NO:7), or G(SGGG)2SGGT (SEQ ID NO:8). The chimeric polypeptide can further comprise an amino acid sequence comprising a histidine tag.” Frelinger et al. therefore explicitly teaches GGGS linkers that can be combined with the same or different linkers, and a GSGGGSGGGSGGT linker, but does explicitly teach the instantly claimed GGGSGGGSGGGS linker of SEQ ID NO: 13. Frelinger et al. at e.g., para. [0055] teaches that tag sequences can be included on the fusion protein, e.g. histidine tag, to facilitate purification of the fusion protein. Frelinger et al. at FIG. 2A shows a 6x histidine tag attached to the C-terminus of the fusion protein. Frelinger et al. at para. [0055] also teaches the tag may instead be located at the N-terminus. As discussed above, Frelinger et al. also discloses a sequence comprising instant SEQ ID NO:2 and a 20 amino acid N-terminus leader / signaling peptide.
Frelinger et al. does not explicitly disclose wherein the host cell comprising the construct comprises a CHO cell or a COS cell as required by instant claim 13.
Taniguchi et al. teaches using COS host cell for IL-2 constructs.
Taniguchi et al. is a report on the first cloning and sequence analysis of a cDNA coding for human IL-2 (see the abstract). Taniguchi et al. examined properties of the IL-2 secreted from IL-2 transfected COS cells. Taniguchi et al at pg. 307 “IL-2 activity from monkey cells.”
As will be touched on further below, Taniguchi et al. also teaches that the first 20 amino acids of IL-2 (absent from SEQ ID NO: 2) is the leader / signaling peptide of IL-2, which is cleaved by the cell during the secretion process. Taniguchi et al. at pg. 307, first full paragraph.
It was prima facie obvious at the time of the claimed invention to use COS cells of Taniguchi et al. to express the construct as taught by Frelinger et al because Taniguchi et al was to first to demonstrate that IL2 could be successfully expressed in COS cells. The person of ordinary skill in the art would be motivated to comprise an IL-2 construct in COS cells because there is a reasonable expectation of success that what originally worked in 1983 would still work today. As discussed above, Frelinger et al. also suggests comprising its IL-2 in mammalian cells, but does not provide specific examples; and it is also obvious to substitute one known element for another to obtain predictable results.
KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) discloses that “The simple substitution of one known, equivalent element for another is likely to be obvious when it does no more than yield predictable results”. The claim would have been obvious because the substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. In the instant case, Taniguchi et al. disclose that the instantly claimed COS cell (a mammalian cell) was known as suitable cell for comprising IL-2 constructs therein. Thus, the substitution of COS cells for the generic mammalian cells of Frelinger et al. would have yielded the predictable result that the instantly claimed IL-2 construct could also be comprised in COS cells. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Accordingly, Frelinger et al. in view of Taniguchi et al renders claims 11-15, 29, 34-35, and 37-44 obvious.
12. Claims 30-33 are rejected under 35 U.S.C. 103 as being unpatentable over Frelinger et al. in view of Taniguchi et al. as applied to claims 11-15, 29, 34-35, and 37-44 above, and further in view of Mal et al. ("Functional silencing of TATA-binding protein (TBP) by a covalent linkage of the N-terminal domain of TBP-associated factor 1." Journal of Biological Chemistry 282.30 (2007): 22228-22238).
Claim 30 is drawn to the polynucleotide of claim 11, wherein the linker comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 11, 12, 13, 14, 15, 40, 41, 50, 51, or 52.
Claim 31 is drawn to the polynucleotide of claim 11, wherein the linker comprises the amino acid sequence as set forth in any one of SEQ ID NOs: 11, 12, 13, 14, 15, 40, 41, 50, 51, or 52.
Claim 32 is drawn to the polynucleotide of claim 11, wherein the linker comprises the amino acid sequence as set forth in SEQ ID NO: 13.
Claim 33 is drawn to the polynucleotide of claim 11, wherein the linker consists of the amino acid sequence as set forth in SEQ ID NO: 13.
Frelinger et al. in view of Taniguchi et al. have been described above.
Frelinger et al. in view of Taniguchi et al. does not explicitly disclose wherein the linker comprises or consists of the amino acid sequence as set forth in SEQ ID NO: 13.
Mal et al. teaches a fusion protein having a linker consisting of instant SEQ ID NO: 13.
Mal et al. is directed to testing linkers that enable silencing of fusion proteins having TATA-binding protein attached by linkers to TAF molecules that bind and inhibit the TATA-binding protein (see the abstract). Mal et al. tested three (GGGS)x linkers and determined that (GGGS)3 linker (i.e., instant SEQ ID NO: 13) was the best of the three tested for suppressing TATA-binding protein activity and also markedly improved solubility of the fusion protein. Id.
It was prima facie obvious at the time of the claimed invention to use the (GGGS)3 linker of Mal et al. in the IL-2 / IL-2Rα fusion protein as taught by Frelinger et al because Mal et al. teaches the exact same linker for use in a fusion protein to improve the solubility of the fusion protein. A person of ordinary skill in the art would be motivated to try the linker because Frelinger et al. teaches similar linkers, and also that the linkers can be different than those explicitly provided for. Frelinger et al. also explicitly provides a GSGGGSGGGSGGT linker, which only differs from instantly claimed SEQ ID NO: 13 in that the first two amino acids (GS) must replace the last amino acid (T). As noted above, Frelinger et al. also teaches the importance of solubility of the fusion protein, and so a person of ordinary skill in the art would be motivated to look to similar linkers known in the art that improve solubility. Mal et al. provides the instantly claimed linker for this very purpose. Accordingly, it would have been obvious to use the instantly claimed linker in the IL-2 / IL-2Rα fusion protein of Frelinger et al. It is also obvious to substitute one known element for another to obtain predictable results.
KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) discloses that “The simple substitution of one known, equivalent element for another is likely to be obvious when it does no more than yield predictable results”. The claim would have been obvious because the substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. In the instant case, Mal et al. disclose that the instantly-claimed linker was known for use in fusion proteins and that it conferred superior solubility characteristics. Thus, the substitution of the linker of Mal et al. for the very similar linkers of Frelinger et al. would have yielded the predictable result of a soluble and functional fusion protein because both the fusion proteins of Mal et al. and Frelinger et al. operate by the same mechanism: inhibiting a first moiety (e.g., IL-2 or TATA-binding protein) with a second linker-attached moiety (e.g., IL-2Rα or TAF molecule). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Accordingly, claims 11-15, 29-35, and 37-44 are rendered obvious by Frelinger et al. in view of Taniguchi et al., and further in view of Mal et al.
13. Claim 36 is rejected under 35 U.S.C. 103 as being unpatentable over Frelinger et al., in view of Taniguchi et al. and Mal et al. as applied to claims 11-15, 29-35, and 37-44 above, and in light of Gillies (WO 2003048334 A2, published June 12, 2003). Note: as discussed above, Frelinger et al. teaches that tag sequences may be included on the N-terminus of the fusion protein (i.e., the IL-2 side) for purification purposes; and Taniguchi et al. teaches that the N-terminal 20 amino acids of IL-2 are cleaved during secretion (thereby rendering instant SEQ ID NO: 2, having the first 20 amino acids of unprocessed IL-2 omitted). If a tag was located at the N-terminus of these 20 amino acids, it too would be cleaved off the fusion protein and not be useful for purifying the secreted fusion protein because it would no longer be connected to the fusion protein.
Claim 36 is drawn to the polynucleotide of claim 11, wherein the first polypeptide (i.e., IL-2) consists of SEQ ID NO: 2.
Frelinger et al. in view of Taniguchi et al. and Mal et al. have been described above.
Frelinger et al. in view of Taniguchi et al. and Mal et al. does not explicitly disclose wherein the first polypeptide of the fusion protein (i.e., IL-2) consists of SEQ ID NO: 2.
Gillies demonstrates that fusions to the N-terminus of IL-2 routinely remove the leader / signaling peptide thereby mooting the cleavage issue and rendering fusion proteins comprising a IL-2 sequence consisting of SEQ ID NO: 2.
Gillies is directed to IL-2 fusion proteins. Gillies produces at least 10 distinct N-terminal IL-2 fusion proteins (see Table 1). As shown in the alignment at the end of this rejection, Gillies et al. used instant SEQ ID NO: 2 to accomplish the N-terminal fusions.
It was therefore prima facie obvious at the time of the claimed invention to remove the IL-2 leader / signaling peptide from the fusion protein as taught by Frelinger et al. to arrive at instantly claimed fusion protein wherein the comprised IL-2 consists of instant SEQ ID NO: 2 because: Frelinger et al. teaches a purification tag may be placed at the N-terminus of the IL-2 of the fusion protein, and view of Taniguchi et al. / in light of Gillies et al., it was known that this requires removing the leader / signaling peptide. Removing the leader / signaling peptide results in the IL-2 of Frelinger et al. consisting of instant SEQ ID NO: 2. A person of ordinary skill in the art would have a reasonable expectation of success that using a sequence consisting of SEQ ID NO: 2 would work since this exact sequence was used in other IL-2 fusion protein contexts before the time of the claimed invention, as demonstrated by the above alignment to Gillies. It is also obvious to substitute one known element for another to obtain predictable results.
KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) discloses that “The simple substitution of one known, equivalent element for another is likely to be obvious when it does no more than yield predictable results”. The claim would have been obvious because the substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. In the instant case, Gillies disclose that the instantly claimed SEQ ID NO: 2, lacking leader /signaling peptide, was known. Thus, the substitution of instantly claimed SEQ ID NO: 2 for the unprocessed IL-2 sequence of Frelinger et al. would have yielded the predictable result of a functional IL-2 / IL-2Rα fusion protein, and additionally allow for inclusion of N-terminal purification tags as suggested by Frelinger et al. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Accordingly, claims 11-15 and 29-44 are rendered obvious by Frelinger et al. in view of Taniguchi et al., Mal et al., and in light of Gillies et al.
ALIGNMENT INSTANT SEQ ID NO 34 TO FRELINGER ET AL. SEQ ID NO: 29
US-13-639-006-29
Sequence 29, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 29
LENGTH: 1233
TYPE: DNA
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 92.3%; Score 1091.4; Length 1233;
Best Local Similarity 94.7%;
Matches 1156; Conservative 0; Mismatches 26; Indels 39; Gaps 1;
Qy 1 ATGGACAGGATGCAACTCCTGTCTTGCATTGCACTAAGTCTTGCACTTGTCACAAACAGT 60
||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 7 ATGTACAGGATGCAACTCCTGTCTTGCATTGCACTAAGTCTTGCACTTGTCACAAACAGT 66
Qy 61 GCACCTACTTCAAGTTCTACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGAT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 67 GCACCTACTTCAAGTTCTACAAAGAAAACACAGCTACAACTGGAGCATTTACTTCTGGAT 126
Qy 121 TTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 127 TTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTC 186
Qy 181 ACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACATCTTCAGTGTCTAGAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 187 ACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACATCTTCAGTGTCTAGAA 246
Qy 241 GAAGAACTCAAACCTCTGGAGGAAGTGCTAAATTTAGCTCAAAGCAAAAACTTTCACTTA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 247 GAAGAACTCAAACCTCTGGAGGAAGTGCTAAATTTAGCTCAAAGCAAAAACTTTCACTTA 306
Qy 301 AGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 307 AGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAA 366
Qy 361 ACAACATTCATGTGTGAATATGCTGATGAGACAGCAACCATTGTAGAATTTCTGAACAGA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 367 ACAACATTCATGTGTGAATATGCTGATGAGACAGCAACCATTGTAGAATTTCTGAACAGA 426
Qy 421 TGGATTACCTTTTGTCAAAGCATCATCTCAACACTGA----------------------- 457
|||||||||||||||||||||||||||||||||||||
Db 427 TGGATTACCTTTTGTCAAAGCATCATCTCAACACTGACTCACAGCAGCAAGCTGCAGGAA 486
Qy 458 ----------------CTGGTGGAGGTTCTGGTGGAGGTTCAGGTGGAGGTTCGGAGCTC 501
||||||| ||| ||| || || ||| | ||||||
Db 487 TTCGGTGGCGGTGGCTCTGGTGGCGGTGGCTCTGGTGGCGGTGGCTCTGGTACCGAGCTC 546
Qy 502 TGTGACGATGACCCGCCAGAGATCCCACACGCCACATTCAAAGCCATGGCCTACAAGGAA 561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 547 TGTGACGATGACCCGCCAGAGATCCCACACGCCACATTCAAAGCCATGGCCTACAAGGAA 606
Qy 562 GGAACCATGTTGAACTGTGAATGCAAGAGAGGTTTCCGCAGAATAAAAAGCGGGTCACTC 621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 607 GGAACCATGTTGAACTGTGAATGCAAGAGAGGTTTCCGCAGAATAAAAAGCGGGTCACTC 666
Qy 622 TATATGCTCTGTACAGGAAACTCTAGCCACTCGTCCTGGGACAACCAATGTCAATGCACA 681
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 667 TATATGCTCTGTACAGGAAACTCTAGCCACTCGTCCTGGGACAACCAATGTCAATGCACA 726
Qy 682 AGCTCTGCCACTCGGAACACAACGAAACAAGTGACACCTCAACCTGAAGAACAGAAAGAA 741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 727 AGCTCTGCCACTCGGAACACAACGAAACAAGTGACACCTCAACCTGAAGAACAGAAAGAA 786
Qy 742 AGGAAAACCACAGAAATGCAAAGTCCAATGCAGCCAGTGGACCAAGCGAGCCTTCCAGGT 801
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 787 AGGAAAACCACAGAAATGCAAAGTCCAATGCAGCCAGTGGACCAAGCGAGCCTTCCAGGT 846
Qy 802 CACTGCAGGGAACCTCCACCATGGGAAAATGAAGCCACAGAGAGAATTTATCATTTCGTG 861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 847 CACTGCAGGGAACCTCCACCATGGGAAAATGAAGCCACAGAGAGAATTTATCATTTCGTG 906
Qy 862 GTGGGGCAGATGGTTTATTATCAGTGCGTCCAGGGATACAGGGCTCTACACAGAGGTCCT 921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 907 GTGGGGCAGATGGTTTATTATCAGTGCGTCCAGGGATACAGGGCTCTACACAGAGGTCCT 966
Qy 922 GCTGAGAGCGTCTGCAAAATGACCCACGGGAAGACAAGGTGGACCCAGCCCCAGCTCATA 981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 967 GCTGAGAGCGTCTGCAAAATGACCCACGGGAAGACAAGGTGGACCCAGCCCCAGCTCATA 1026
Qy 982 TGCACAGGTGAAATGGAGACCAGTCAGTTTCCAGGTGAAGAGAAGCCTCAGGCAAGCCCC 1041
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1027 TGCACAGGTGAAATGGAGACCAGTCAGTTTCCAGGTGAAGAGAAGCCTCAGGCAAGCCCC 1086
Qy 1042 GAAGGCCGTCCTGAGAGTGAGACTTCCTGCCTCGTCACAACAACAGATTTTCAAATACAG 1101
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1087 GAAGGCCGTCCTGAGAGTGAGACTTCCTGCCTCGTCACAACAACAGATTTTCAAATACAG 1146
Qy 1102 ACAGAAATGGCTGCAACCATGGAGACGTCCATATTTACAACAGAGTACCAGGGTGGACAT 1161
|||||||||||||||||||||||||||||||||||||||||||||||||||| | |||
Db 1147 ACAGAAATGGCTGCAACCATGGAGACGTCCATATTTACAACAGAGTACCAGGTAGCACAC 1206
Qy 1162 CACCATCACCATCACTAATAA 1182
||||| ||||| ||||||| |
Db 1207 CACCACCACCACCACTAATGA 1227
ALIGNMENT INSTANT SEQ ID NO 26 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 98.1%; Score 1912; Length 392;
Best Local Similarity 96.5%;
Matches 359; Conservative 1; Mismatches 4; Indels 8; Gaps 1;
Qy 1 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 21 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 80
Qy 61 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 81 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 140
Qy 121 WITFCQSIISTLT--------GGGSGGGSGGGSELCDDDPPEIPHATFKAMAYKEGTMLN 172
||||||||||||| ||| || | |:|||||||||||||||||||||||||||
Db 141 WITFCQSIISTLTHSSKLQEFGGGGSGGGGSGTELCDDDPPEIPHATFKAMAYKEGTMLN 200
Qy 173 CECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRNTTKQVTPQPEEQKERKTTE 232
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 201 CECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRNTTKQVTPQPEEQKERKTTE 260
Qy 233 MQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVC 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 261 MQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVC 320
Qy 293 KMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCLVTTTDFQIQTEMAA 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 321 KMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCLVTTTDFQIQTEMAA 380
Qy 353 TMETSIFTTEYQ 364
||||||||||||
Db 381 TMETSIFTTEYQ 392
ALIGNMENT INSTANT SEQ ID NO 7 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 100.0%; Score 1203; Length 392;
Best Local Similarity 100.0%;
Matches 219; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQ 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 174 ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQ 233
Qy 61 CTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYH 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 234 CTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYH 293
Qy 121 FVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 294 FVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQA 353
Qy 181 SPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 219
|||||||||||||||||||||||||||||||||||||||
Db 354 SPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 392
ALIGNMENT INSTANT SEQ ID NO 27 TO FRELINGER ET AL. SEQ ID NO: 45
US-13-639-006-45
Sequence 45, US/13639006
Publication No. US20130089516A1
GENERAL INFORMATION
APPLICANT: University of Rochester
TITLE OF INVENTION: Protease Activated Cytokines
FILE REFERENCE: 10028-027WO1
CURRENT APPLICATION NUMBER: US/13/639,006
CURRENT FILING DATE: 2012-10-02
PRIOR APPLICATION NUMBER: US 61/320,360
PRIOR FILING DATE: 2010-04-02
NUMBER OF SEQ ID NOS: 68
SEQ ID NO 45
LENGTH: 392
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Synthetic Construct
Query Match 97.7%; Score 1997; Length 392;
Best Local Similarity 96.4%;
Matches 378; Conservative 1; Mismatches 5; Indels 8; Gaps 1;
Qy 1 MDRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRML 60
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRML 60
Qy 61 TFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSE 120
Qy 121 TTFMCEYADETATIVEFLNRWITFCQSIISTLT--------GGGSGGGSGGGSELCDDDP 172
||||||||||||||||||||||||||||||||| ||| || | |:|||||||
Db 121 TTFMCEYADETATIVEFLNRWITFCQSIISTLTHSSKLQEFGGGGSGGGGSGTELCDDDP 180
Qy 173 PEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATR 232
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATR 240
Qy 233 NTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMV 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 NTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMV 300
Qy 293 YYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPE 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 YYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPE 360
Qy 353 SETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 384
||||||||||||||||||||||||||||||||
Db 361 SETSCLVTTTDFQIQTEMAATMETSIFTTEYQ 392
Geneseq alignment of instant SEQ ID NO: 2
ID AAO30889 standard; protein; 133 AA.
XX
AC AAO30889;
XX
DT 15-JUN-2007 (revised)
DT 22-SEP-2003 (first entry)
XX
DE Human mature interleukin-2 (IL-2) protein.
XX
KW Cytokine; interleukin-2; IL-2; cancer; viral infection; immune disorder;
KW gene therapy; human; BOND_PC; interleukin 2;
KW interleukin 2 [Homo sapiens]; synthetic interleukin 2 (133 AA);
KW synthetic interleukin 2 (133 AA) [synthetic construct]; GO5134; GO19209;
KW GO30217; GO30307; GO5125; GO5576; GO5615; GO6916; GO6955; GO7155; GO7267;
KW GO8284; GO30101.
XX
OS Homo sapiens.
XX
CC PN WO2003048334-A2.
XX
CC PD 12-JUN-2003.
XX
CC PF 04-DEC-2002; 2002WO-US038780.
XX
PR 04-DEC-2001; 2001US-0337113P.
PR 12-APR-2002; 2002US-0371966P.
XX
CC PA (EMDL-) EMD LEXIGEN RES CENT CORP.
XX
CC PI Gillies SD;
XX
DR WPI; 2003-513757/48.
DR PC:NCBI; gi22219362.
DR PC:BIND; 341840, 341838, 341837.
XX
CC PT New fusion protein comprising a non-IL-2 moiety fused to a mutant IL-2
CC PT moiety, useful for preparing a composition for treating cancer, viral
CC PT infections or immune disorders.
XX
CC PS Disclosure; Page 48-49; 71pp; English.
XX
CC The invention relates to cytokine fusion proteins with increased
CC therapeutic index and methods for increasing the therapeutic index of
CC such fusion proteins. The fusion protein comprises a non-interleukin-2
CC (IL-2) moiety fused to a mutant IL-2 moiety. It is useful for preparing a
CC composition for treating cancer, viral infections or immune disorders.
CC The fusion protein is also used in gene therapy. The present sequence is
CC human mature IL-2 protein. This sequence is used to illustrate the method
CC of the invention
CC
CC Revised record issued on 15-JUN-2007 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 133 AA;
%
Result Query Filing
No. Score Match Length ID Date Dups Description
-------------------------------------------------------------------------------------------------------------
1 680 100.0 133 AAB01941 -- 970 Wild-type human interleukin-2 (hIL-2).
ALIGNMENT:
Query Match 100.0%; Score 680; Length 133;
Best Local Similarity 100.0%;
Matches 133; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLE 60
Qy 61 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 EELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNR 120
Qy 121 WITFCQSIISTLT 133
|||||||||||||
Db 121 WITFCQSIISTLT 133
Conclusion
14. No claim is allowed.
15. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRANDON R SCHWECHTER whose telephone number is (571)272-1270. The examiner can normally be reached M-Th 7-5 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Vanessa Ford can be reached at 20857. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BRANDON R SCHWECHTER/
Examiner, Art Unit 1674
/VANESSA L. FORD/ Supervisory Patent Examiner, Art Unit 1674
Prosecution Insights