De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8 PMID: 37704610

ADC Targets in Oncology

2026-04-10

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

Nat Commun. 2023 Sep 13;14(1):5660. doi: 10.1038/s41467-023-41272-z.

Anindya Roy ^# ¹ , Lei Shi ^# ¹ ² , Ashley Chang ^# ³ , Xianchi Dong ⁴ ⁵ ⁶ , Andres Fernandez ⁷ , John C Kraft ¹ , Jing Li ⁴ , Viet Q Le ⁴ , Rebecca Viazzo Winegar ³ , Gerald Maxwell Cherf ⁸ ⁹ , Dean Slocum ⁴ , P Daniel Poulson ³ , Garrett E Casper ³ , Mary L Vallecillo-Zúniga ³ , Jonard Corpuz Valdoz ³ , Marcos C Miranda ¹ ¹⁰ , Hua Bai ¹ , Yakov Kipnis ¹ ¹¹ , Audrey Olshefsky ¹ ¹² , Tanu Priya ¹³ ¹⁴ , Lauren Carter ¹ , Rashmi Ravichandran ¹ , Cameron M Chow ¹ , Max R Johnson ¹ , Suna Cheng ¹ , McKaela Smith ¹ , Catherine Overed-Sayer ¹⁵ ¹⁶ , Donna K Finch ¹⁵ ¹⁷ , David Lowe ¹⁵ ¹⁸ , Asim K Bera ¹ , Gustavo Matute-Bello ¹⁹ , Timothy P Birkland ²⁰ , Frank DiMaio ¹ , Ganesh Raghu ²⁰ ²¹ , Jennifer R Cochran ⁸ , Lance J Stewart ¹ , Melody G Campbell ²² , Pam M Van Ry ²³ , Timothy Springer ²⁴ , David Baker ²⁵ ²⁶

Affiliations

1. Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
2. Encodia Inc, 5785 Oberlin Drive, San Diego, CA, 92121, USA.
3. Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
4. Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA.
5. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
6. Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China.
7. Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
8. Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
9. Denali Therapeutics, South San Francisco, CA, USA.
10. Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
11. Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
12. Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
13. Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
14. Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
15. Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
16. Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
17. Alchemab Therapeutics Ltd, Cambridge, UK.
18. Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG, England.
19. Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA.
20. Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.
21. Dept of Medicine, University of Washington, Seattle, WA, USA.
22. Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA. [email protected].
23. Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA. [email protected].
24. Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA. [email protected].
25. Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. [email protected].
26. Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA. [email protected].
# Contributed equally.

Abstract

The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated Cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and Other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD Integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 Inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed Integrin binding proteins with high selectivity.