7LMX | pdb_00007lmx

A HIGHLY SPECIFIC INHIBITOR OF INTEGRIN ALPHA-V BETA-6 WITH A DISULFIDE

PDB DOI: https://doi.org/10.2210/pdb7LMX/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-06 Released: 2022-08-10
Deposition Author(s): Dong, X., Bera, A.K., Roy, A., Shi, L., Springer, T.A., Baker, D.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.262 (Depositor), 0.267 (DCC)
R-Value Work:
0.228 (Depositor), 0.233 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8.

Roy, A., Shi, L., Chang, A., Dong, X., Fernandez, A., Kraft, J.C., Li, J., Le, V.Q., Winegar, R.V., Cherf, G.M., Slocum, D., Poulson, P.D., Casper, G.E., Vallecillo-Zuniga, M.L., Valdoz, J.C., Miranda, M.C., Bai, H., Kipnis, Y., Olshefsky, A., Priya, T., Carter, L., Ravichandran, R., Chow, C.M., Johnson, M.R., Cheng, S., Smith, M., Overed-Sayer, C., Finch, D.K., Lowe, D., Bera, A.K., Matute-Bello, G., Birkland, T.P., DiMaio, F., Raghu, G., Cochran, J.R., Stewart, L.J., Campbell, M.G., Van Ry, P.M., Springer, T., Baker, D.

(2023) Nat Commun 14: 5660-5660

PubMed: 37704610 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-41272-z
Primary Citation Related Structures:
7LMV, 7LMX, 8TCF, 8TCG

PubMed 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.

Organizational Affiliation

Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.

Encodia Inc, 5785 Oberlin Drive, San Diego, CA, 92121, USA.

Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.

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.

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.

Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China.

Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.

Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.

Denali Therapeutics, South San Francisco, CA, USA.

Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.

Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.

Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.

Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA.

Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.

Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.

Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.

Alchemab Therapeutics Ltd, Cambridge, UK.

Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG, England.

Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA.

Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.

Dept of Medicine, University of Washington, Seattle, WA, USA.

Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA. melody@fredhutch.org.

Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA. pvanry@byu.edu.

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. springer@crystal.harvard.edu.

Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. dabaker@uw.edu.

Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA. dabaker@uw.edu.