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 .
Claim Status
Claims 1, 7 were amended.
Claims 1, 3, 7, 9, 11, 19, 27-29, 31-32, 43-44, 46, 54, 57-59 are examined on the merits.
Priority
The application a 371 of PCT/US20/65024, that claims the benefit of U.S. Provisional Application No. 62/949,023, filed on December 17, 2019 is acknowledged.
Reopening of Prosecution
This Office Action is in response to Applicant’s response filed March 6, 2026. The finality of the Office Action mailed January 8, 2026 has been reconsidered and is withdrawn.
Withdrawn Rejections
The rejection of claims 1, 3, 7, 9, 11, 19, 27-29, 31-32, 43-44, 46, 54 and 57-59, under 35 U.S 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of Applicant’s amendment of the claims in the reply filed 03/06/2026.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 3, 7, 27-29, 31-32, 58 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Eyckerman et al. (“Eyckerman”, STKE, 2002, cited as reference 7 on IDS filed 09/07/2022).
Regarding claims 1, 3, 7, Eyckerman teaches a novel mammalian two-hybrid system that is based on insights in type I cytokine receptor signal transduction. Cytokine receptor clustering following ligand binding triggers the cross-activation of associated Janus kinase (JAK) (e.g. paragraph 3rd, page 2). Eyckerman teaches that the cells are transfected with the bait plasmid, the prey plasmid, and a STAT-dependent reporter gene (pXP2d2-rPAP1-luci). The stimulation of the reporter gene is used as a measure of the interaction between the bait and prey proteins. The cells are also transfected with a constitutively expressed reporter gene (pUT651 encoding β-galactosidase) to normalize transfection variations (e.g., paragraph 5th, page 9) (It reads on plurality of the cells expressing a ligand depend chimeric receptor). Eyckerman teaches that a heterologous bait polypeptide is fused to a receptor variant lacking functional STAT3 recruitment sites. In the configuration shown, a receptor chimera consisting of the extracellular domain of the homodimeric EpoR fused to the transmembrane and cytosolic domains of the LR-F3 is used. Tyrosine to phenylalanine mutations eliminate the functional STAT3 recruitment site at position 1138 and also other recruitment sites at positions 985 and 1077 linking to the Ras pathway and to JAK-STAT signaling inhibitors. A heterologous prey polypeptide is fused to a receptor fragment of gp130 containing four functional STAT3 recruitment sites. If bait and prey interact, the recruited receptor fragment is phosphorylated upon ligand-induced receptor activation, and a STAT3-dependent signal is obtained. This process can be monitored using a STAT3 responsive reporter gene (e.g. paragraph 3rd, page 2; Fig. 1B [see below]). Eyckerman teaches that in analytical experiments, the reporter gene signal can be low. In some cases, swapping of bait and prey proteins may lead to higher reporter induction in analytical MAPPIT experiments (It reads on fusing the prey protein to the first receptor and the bait fused to gp130 containing functional STAT recruitment sites). This difference may be explained by a sterical configuration leading to better activation of the JAK-STAT pathway (e.g., paragraph 3rd, page 17 [troubleshooting]) (It reads on avoiding the bait protein being trapped within the cell organelle and avoiding the bait protein to interact with transmembrane domains of the second receptor of the chimeric receptor).
Both the instant claims and Eyckerman describe a two-hybrid split system where one target protein is fused to the mutated receptor and the other to the is fused to the mobile STAT recruiting fragment, this swapping of the generic names “bait” and “pray” does not stablish a patentable distinction.
Regarding the limitation in claim 7 wherein the bait protein does not substantially interact with the non-prey portion of the chimeric receptor”, this limitation does not require a specific technical feature which is not specified by the instant claim 1.
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Regarding claims 27-28, Eyckerman teaches a novel mammalian two-hybrid system that is based on insights in type I cytokine receptor signal transduction. Cytokine receptor clustering following ligand binding triggers the cross-activation of associated Janus kinase (JAK) (e.g., paragraph 3rd, page 2).
Regarding claim 29, Eyckerman teaches a receptor chimera consisting of the extracellular domain of the homodimeric EpoR fused to the transmembrane and cytosolic domains of the LR-F3 is used (e.g., Fig. 1B) (It reads on ligand-binding domain from EpoR).
Regarding claim 31, Eyckerman teaches the bait protein is fused to a mutant receptor chimera that still allows JAK activation, but from which STAT target sites have been eliminated (e.g., paragraph 3rd, page 2). Eyckerman teaches that a heterologous bait polypeptide is fused to a receptor variant lacking functional STAT3 recruitment sites. In the configuration shown, a receptor chimera consisting of the extracellular domain of the homodimeric EpoR fused to the transmembrane and cytosolic domains of the LR-F3 is used (e.g., Fig. 1B).
Regarding claim 32, Eyckerman teaches a heterologous prey polypeptide is fused to a receptor fragment of gp130 containing four functional STAT3 recruitment sites (e.g., Fig. 1B).
Regarding claim 58, Eyckerman teaches system allows stable expression of complex prey cDNA libraries cloned in ecotropic retroviral
vectors and prevents health hazards associated with the use of amphotropic vectors. (e.g., paragraph 1st, page 11).
Claims 1, 3, 7, 27-29, 32 and 59 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Braun et al. (“Braun”, Nat. Methods. 2009).
Regarding claims 1, 3, 7, Braun teaches MAPPIT: A bait-protein is fused to a hybrid erythropoietin-leptin receptor and the prey is fused to gp130 (e.g., paragraph 4th, page 3; Fig. 1) (It reads on ligand-dependent chimeric receptor proteins). Braun teaches that for the MAPPIT experiments, HEK-293T cells were transfected in 96-well plates. Twenty-four hours after transfection cells were stimulated with ligand (Epo) or left untreated for an additional 24 hours, followed by measurement of luciferase activity in triplicate. All interactions were tested in two configurations (e.g., paragraph 4th, page 8; Supplementary Fig. 5) (It reads on plurality of the cells expressing ligand depend chimeric receptor). Braun teaches MAPPIT: a bait-protein is fused to a hybrid erythropoietin-leptin receptor and the prey is fused to gp130. Upon stimulation with erythropoietin JAK2 molecules trans-phosphorylate each other and if bait and prey interact the activated JAKs will phosphorylate gp130, which in turn recruits and subsequently activates STAT3, which then activates transcription of a reporter (e.g., Fig. 2b). Braun teaches that all interactions were tested in two configurations (swapping bait and prey) (e.g., paragraph 1st, page 9; Supplementary Fig. 5a [see below]) (swapping bait and prey: It reads on fusing the prey protein to the first receptor and the bait fused to gp130 containing functional STAT recruitment sites). Braun teaches that if there is (2) wrong cellular localization: remove targeting sequences, use a subdomain or swap bait and prey. (3) Toxicity of bait or prey: use a mutated protein or subdomain.
(4) Steric hindrance: swap bait and prey, use subdomains or fuse prey N-terminally (e.g., paragraph 11th, page 30, Supplementary Protocol 2, troubleshooting) (By swapping bait and prey: It reads on avoiding the bait protein being trapped within the cell organelle and avoiding the bait protein to interact with transmembrane domains of the second receptor of the chimeric receptor).
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Regarding claims 27-29, Braun teaches Braun teaches MAPPIT: a bait-protein is fused to a hybrid erythropoietin-leptin receptor (e.g., Fig. 2b).
Regarding claim 32, Braun teaches prey is fused to gp130 (e.g., Fig. 2b).
Regarding claim 59, Braun teaches (4) Steric hindrance: swap bait and prey, use subdomains or fuse prey N-terminally (e.g., paragraph 11th, page 30, Supplementary Protocol 2, troubleshooting).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 9, 11, 19 and 54 are rejected under 35 U.S.C. 103 as being unpatentable over Eyckerman et al. (“Eyckerman”, STKE, 2002, cited as reference 7 on IDS filed 09/07/2022) as applied to claim 1, 3, 7, 27-29, 31-32, 58 above, and further in view of Eyckerman et al. (“021”, US 2003/0100021 A1, cited as reference 1 on IDS filed 09/07/2022).
The teachings of Eyckerman are described above and applied as before.
Eyckerman does not teach a bait protein associated with a scaffold as it is required by instant claim 9. Eyckerman does not teach small molecules which binds to the pray or bait protein, as required by instant claims 11, 19. Eyckerman does not teach F506 as a bait protein, as required by claim 54. However, this is cured by “021”.
“021 teaches a method to detect compound-compound binding using a recombinant receptor and/or a prey polypeptide is disclosed, a eukaryotic cell carrying a recombinant receptor of the present invention is transformed or transfected with a vector library encoding prey polypeptides (e.g., paragraph 0031). “021” teaches the pMET7-flag-gp130 vector, (indicating that the “pray protein is fused to FLAG tag) (e.g., paragraph 0145), Flag tag can be interpreted as a “scaffold” since there is no definition of “scaffold” in the specifications. “021” teaches recombinant receptor may bind a small molecule. Alternatively, the prey polypeptide of the present invention may also bind to the small molecule, such that bait and prey are linked together by the small molecule. The small molecule may be present in the host cell as a compound produced by the cell or as a compound taken up by the cell from the medium (e.g., paragraph 0034). “021” teaches use of MAPPIT to screen compound-compound interactions comprising non-polypeptide compounds (e.g., paragraph 00273). Eyckerman teaches an experiment which is performed with Fujisporin, whereby FK506 is chemically linked to cyclosporin A. Alternatively, bivalent compounds are obtained by fusing FK506 to tetracycline or to a steroid ligand; such hybrid compounds have the capacity to interact with the protein partners FKBP12 and cyclophilin (or tetracycline/steroid receptors) (e.g., paragraph 0274; Example 9).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to combine the teachings of Eyckerman -a protocol to evaluate protein-protein interaction using a chimeric receptor, comprising an extracellular ligand-bonding domain like EpoR fused to a cytoplasmic domain of a second receptor and bait fused to gp130 containing STAT3 recruitment sites or swapping the bait with the prey, with the teachings of “021” the prey polypeptide may also bind to the small molecule, such that bait and prey are linked together by the small molecule, such as FK506. A skill artisan would have had a reasonable expectation of success because both Eyckerman and “021” teach the same recombinant receptor comprising an extracellular ligand-binding domain that comprises a heterologous bait polypeptide, then it would have been obvious to use this system to evaluate protein-protein interactions mediated by small molecules.
One of ordinary skill in the art before the effective filing date of the invention would have been motivated to develop a method in order to identify small molecules that target protein-protein interactions using a chimeric receptor that includes a prey polypeptide that binds to the bait polypeptide upon interaction with the small molecule.
Claims 43-44 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Eyckerman et al. (“Eyckerman”, STKE, 2002) and Eyckerman et al. (“021”, US 2003/0100021 A1, cited as reference 1 on IDS filed 09/07/2022) as applied to claim 1, 3, 7, 9, 11, 19, 27-29, 31-32, 54, 58 and 59 above, and further in view of Wells et al. (“Wells”, WO 2013/112625 A1, published August 2013).
Eyckerman and “021” do not teach the E3 ligase substrate binding unit, as required by instant claim 43. Eyckerman does not teach the bait is contacted with the prey before interaction with the prey protein, as required by claim 44. Eyckerman and “021” do not teach the compound is selected from thalidomide, lenalidomide, pomalidomide, CC-220, CC-122, CC-885, or a derivative or analog thereof, as required by claim 46. However, this is cured by Wells.
Wells teaches a catalytic tagging system to search for target substrates. Identification of substrates for specific baits is accomplished by utilizing an orthogonal system consisting of an E1 activating enzyme, an E2 ubiquitin-like conjugating enzyme, and baits that are fused to the E2 ubiquitin-like conjugating enzyme (e.g., abstract). Wells teaches that the bait comprises a peptide, a protein, a small molecule, a nucleic acid, or a carbohydrate; the bait is a modified version of an E3 ligase and wherein the E3 ligase lacks a RING domain; modified version of the E3 ligase comprises a substrate binding domain and wherein the modified version of the E3 ligase is capable of fusing to an E2 ubiquitin-like conjugating enzyme. The bait is a small molecule, the small molecule is selected from the group consisting of dasatinib, imatinib, nilotinib, thalidomide, lenalidomide, and pomalidomide. The substrate is specific for the bait (e.g., paragraph 0007; Fig below; Fig. 5).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to combine the teaching of Eyckerman and “021” a method to evaluate protein-protein and protein-small molecule interactions using a chimeric receptor, comprising an extracellular ligand-binding domain like EpoR fused to a cytoplasmic domain of a second receptor fused to a prey and a fragment gp130 containing STAT3 recruitment sites, with the teachings of Wells - identification of substrates for specific baits is accomplished by utilizing an orthogonal system consisting of an E1 activating enzyme, an E2 ubiquitin-like conjugating enzyme, and baits that are fused to the E2 ubiquitin-like conjugating enzyme the modified version of the E3 ligase is capable of fusing to an E2 ubiquitin-like conjugating enzyme as a bait capable of binding. A skill artisan would have had a reasonable expectation of success in substituting the bait chimeric protein of the chimeric extracellular ligand-domain system with the E3-ligase bait for identifying substrates of E3 ligase because 1) Eyckerman and “021” discloses a recombinant receptor comprising an extracellular ligand-binding domain that comprises a heterologous bait polypeptide, that can detect small molecule/protein interaction, II) Wells discloses a system of enzymes like E3 ligase as a bait that facilitates the identification substrates, then it would have been obvious to use this systems to identify substrates of E3 ligases.
One of ordinary skill in the art before the effective filing date of the invention would have been motivated to develop a method in order to screen and identify agents that target protein-protein interactions, such substrates of E3 ligases using a chimeric receptor. This approach can be applied to macro-molecular interactions, including protein-protein, protein-lipid, protein-nucleic acid and protein-small ligand interactions, which are critical for the majority of biological functions for almost every living system (Wells, et al.).
Claim 57 is rejected under 35 U.S.C. 103 as being unpatentable over Eyckerman et al. (“Eyckerman”, STKE, 2002) as applied to claim 1, 3, 7, 27-29, 31-32, 58 and 59 above, and further in view of Lievens et al. (“Lievens”, Cytokine & Growth Factor Reviews, 2011).
Eyckerman does not teach the method is a microarray based screening format, as required by claim 57. However, this is cured by Lievens.
Lievens teaches MAPPIT (mammalian protein–protein interaction trap) is a two-hybrid interaction mapping technique based on functional complementation of a type I cytokine receptor signaling pathway (e.g., abstract). Lievens teaches MAPPIT has been developed into a multifunctional technology suite with applications in basic and translational areas of biology. Recent interest has focused on extending the scale of MAPPIT assays, both towards protein network mapping, protein–protein interface modeling and PPI inhibitor screening. For example, in the case of the ArrayMAPPIT screening platform, the prey collection will be further increased following the growth pace of the hORFeome collection. To permit a further increase in throughput, robustness and cost-efficiency, the platform is being downscaled to the level of a cell microarray. This
downscaling will also facilitate the use of MAPPIT as a primary screening tool in large-scale interactomics projects (e.g., paragraph 2nd, page 328).
Based on these teachings, it would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to combine the teaching of Eyckerman a method to evaluate protein-protein interactions using a chimeric receptor, comprising an extracellular ligand-binding domain like EpoR fused to a cytoplasmic domain of a second receptor fused to a prey and a fragment gp130 containing STAT3 recruitment sites, with teachings of Lievens scale of MAPPIT assays, both towards protein network mapping, protein–protein interface modeling and PPI inhibitor screening, ArrayMAPPIT or cell microarray. A skill artisan would have had a reasonable expectation of success because both Eyckerman and Lievens teach the same two-hybrid interaction mapping technique based on functional complementation of a type I cytokine receptor signaling pathway, then it would have been obvious to use this system to scale up to use in number of application like interactomics, drug screening and compound target profiling.
One of ordinary skill in the art before the effective filing date of the invention would have been motivated to develop a method for scaling up MAPPIT assays for towards protein network mapping, protein–protein interface modeling and PPI inhibitor screening as a primary screening tool in large-scale interactomics projects .
Conclusion
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/JULIO WASHINGTON GOMEZ RODRIGUEZ/Examiner, Art Unit 1637
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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