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WO-2026096827-A2 - ENGINEERED THERAPEUTIC PROTEIMER COMPOSITIONS AND RELATED METHODS

WO2026096827A2WO 2026096827 A2WO2026096827 A2WO 2026096827A2WO-2026096827-A2

Abstract

The present invention pertains to the field of protein engineering, molecular imaging, molecular diagnostics, and biopharmaceutics. Provided herein are six unique Proteimer protein scaffolds (TEX-S2/S3, TEX-S4, YTHDF3, PUM, DARPin, and Aca2) that demonstrate specificity and affinity comparable to antibodies across a broad range of therapeutic targets. Methods and protocols are provided for generating non-native protein aptamers, Proteimers, which are capable of binding to a diverse set of targets, including RNA, DNA, proteins, post-translational modifications, peptides, small molecules, and prosthetic groups. This platform supports the creation of biotherapeutic aptamers from Proteimer scaffolds for the treatment of various diseases.

Inventors

  • CHO, HYUNDAE
  • CHO, Hannah K.

Assignees

  • CROSSLIFE TECHNOLOGIES INC.

Dates

Publication Date
20260507
Application Date
20251030
Priority Date
20241030

Claims (20)

  1. 1 . A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 8 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 18, 19, 25, 26, 29, 102, 105 and 106 of TEX-S2 (SEQ ID NO:2).
  2. 2. The non-native variant proteimer of claim 1 , wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, and 8.
  3. 3. A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 12 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 18, 19, 22, 25, 26, 29, 40, 46, 102, 105, 106, and 136 of TEX-S3 (SEQ ID NO:4).
  4. 4. The non-native variant proteimer of claim 3, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12.
  5. 5 The variant proteimer of claims 3-4, wherein the proteimer is selected from the group consisting of SEQ ID NOs: 16 (SNCA-B), 17 (SNCA-C), 21 (APPS3- 5), 22 (APPS3-11 ), 24 (TEX-T1 ), 25 (TEX-T2), 27 (TEX-CD19-6), 28 (TEX CD19-8), and 30-110.
  6. 6. The variant proteimer of claims 3-5, wherein the proteimer is selected from the group consisting of SEQ ID NOs: 16 (SNCA-B), 17 (SNCA-C), 21 (APPS3- 5), 22 (APPS3-11 ), 24 (TEX-T1 ), 25 (TEX-T2), 27 (TEX-CD19-6), 28 (TEX CD19-8).
  7. 7. A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 12 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 31 , 32, 35, 38, 39, 42, 53, 59, 115, 118, 119, and 149 of TEX-S4 (SEQ ID NO:6).
  8. 8. The non-native variant proteimer of claim 7, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12. - 55 - 128617-0002W001/10028904 9 Docket No: 128617-0002WQ01
  9. 9. A non-native variant proteimer, relative to wild-type YTHDF3, comprising any combination of one up to all 11 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 40, 54, 55, 57, 84, 108, 113, 129, 147, 149, and 150 of YTHDF3 (SEQ ID NO:8).
  10. 10. The non-native variant proteimer of claim 9, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11.
  11. 11 . The variant proteimer of claims 9-10, wherein the proteimer is selected from the group consisting of SED ID NOs: 124-138.
  12. 12. A non-native variant proteimer, relative to wild-type PUM, comprising any combination of one up to all 24 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 37, 38, 41 , 73, 74, 77, 109, 110, 113, 145, 146, 149, 181 , 182, 185, 217, 218, 221 , 253, 254, 257, 296, 297, and 300 of PUM (SEQ ID NQ:10).
  13. 13. The non-native variant proteimer of claim 12, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, and 24.
  14. 14. A non-native variant proteimer, relative to wild-type DARPin, comprising any combination of one up to all 21 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 32, 34, 35, 37, 45, 46, 58, 65, 67, 68, 70, 78, 79, 91 , 98, 100, 101 , 103, 111 , 112, and 124 of DARPin (SEQ ID NO:12).
  15. 15. The non-native variant proteimer of claim 14, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, and 21.
  16. 16. A non-native variant proteimer, relative to wild-type Aca2, comprising any combintion of one up to all 14 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 28, 30, 31 , 33, 34, 39, 45, 149, 151 , 152, 154, 155, 160, and 166 of Aca2 (SEQ ID NO: 14). - 56 - 128617-0002W001/10028904 9 Docket No: 128617-0002W001
  17. 17. The non-native variant proteimer of claim 16, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, and 14.
  18. 18. The variant proteimer of claims 16-17, wherein the proteimer is selected from the group consisting of SED ID NOs:141-148.
  19. 19. A non-native variant proteimer, relative to a wild-type nanobody, comprising any combination of one up to all 22 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 28, 29, 30, 31 , 32, 34, 35, 37, 56, 57, 58, 61 , 103, 104, 105, 106, 107, 108, 109, 110, 111 , and 112 of the nanobody (SEQ ID NO: 18).
  20. 20. The non-native variant proteimer of claim 19, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , and 22.

Description

Docket No: 128617-0002W001 Engineered Therapeutic Proteimer Compositions and Related Methods FIELD OF INVENTION [0001] The present invention is related to the field of protein engineering, molecular imaging, molecular diagnostics, and biopharmaceutics. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING [0002] The contents of the electronic sequence listing (Sequence_Listing-128617- 0002W001 .xml; Size: 188,831 bytes; and Date of Creation: October 30, 2025) is herein incorporated by reference in its entirety. BACKGROUND [0003] Biotherapeutics is a growing field that has revolutionized modem medicine. The growth has been stimulated by antibody technologies that can target a wide range of conditions such as autoimmune/autoinflammatory diseases and cancer. [0004] Engineered protein scaffolds that bind with high specificity to target molecules are growing tools that have provided a powerful platform for creating novel biopharmaceutical technologies that can work similarly to monoclonal antibodies. Such technologies provide cost-effective and modular approaches to create aptamers that bind to biomarkers or therapeutic targets with high affinity. To date, several scaffolds have been engineered to create drug products for a wide range of diseases, many of which have entered late-stage clinical trials. The growth of these promising technologies has inspired the field of aptamer biopharmaceutical technologies. These aptamers are beneficial because of their high stability which allows for advance engineering that cannot be conducted on antibodies. [0005] The screening and design of proteins have emerged as key avenues in therapeutic discovery, leveraging the vast diversity of natural protein structures, functions, and interactions. Although life-changing, antibody therapeutics remain costly to manufacture and the process of drug discovery is laborious. Therefore, improved methods for generating novel biotherapeutics are in high demand. SUMMARY [0006] Provided herein are invention Proteimers (Protein-Based Aptamers) that capitalize on the diversity of natural protein, facilitating the high-throughput - 1 - 128617-0002W001/10028904 9 Docket No: 128617-0002WQ01 development of high-affinity binders targeting small molecules, proteins, and nucleic acids. [0007] Accordingly, provided herein are the following items: 1 . A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 8 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 18, 19, 25, 26, 29, 102, 105 and 106 of TEX-S2 (SEQ ID NO:2). 2. The non-native variant proteimer of item 1 , wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, and 8. 3. A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 12 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 18, 19, 22, 25, 26, 29, 40, 46, 102, 105, 106, and 136 of TEX-S3 (SEQ ID NO:4). 4. The non-native variant proteimer of item 3, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12. 5 The variant proteimer of items 3-4, wherein the proteimer is selected from the group consisting of SEQ ID NOs: 16 (SNCA-B), 17 (SNCA-C), 21 (APPS3-5), 22 (APPS3-11 ), 24 (TEX-T1 ), 25 (TEX-T2), 27 (TEX-CD19-6), 28 (TEX CD19-8), and 30-110. 6. The variant proteimer of items 3-5, wherein the proteimer is selected from the group consisting of SEQ ID NOs: 16 (SNCA-B), 17 (SNCA-C), 21 (APPS3-5), 22 (APPS3-11 ), 24 (TEX-T1 ), 25 (TEX-T2), 27 (TEX-CD19-6), 28 (TEX CD19-8). 7. A non-native variant proteimer, relative to wild-type TEX264, comprising any combination of one up to all 12 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 31 , 32, 35, 38, 39, 42, 53, 59, 115, 118, 119, and 149 of TEX-S4 (SEQ ID NO:6). - 2 - 128617-0002W001/10028904 9 Docket No: 128617-0002WQ01 8. The non-native variant proteimer of item 7, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12. 9. A non-native variant proteimer, relative to wild-type YTHDF3, comprising any combination of one up to all 11 of variant amino acid residues, wherein the variant amino acid residues correspond to residues 40, 54, 55, 57, 84, 108, 113, 129, 147, 149, and 150 of YTHDF3 (SEQ ID NO:8). 10. The non-native variant proteimer of item 9, wherein the number of variant amino acid residues is selected from the group consisting of: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10. and 11. 11 . The variant proteimer of items 9-10, wherein the proteimer is selected from the group consisting of SED ID NOs: 124-138. 12. A non-native variant proteimer, relative to wild-type PUM, comprising any combination of one up to all 24 of variant amino acid residues, wherein the variant