9XMM

Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide

Summary for 9XMM

• Entry DOI: 10.2210/pdb9xmm/pdb
• EMDB information: 67027
• Descriptor: Integrin alpha-V heavy chain, Integrin beta-6, ALA-TRP-ARG-GLY-ASP-CHG-CYS-ASN-PRO, ... (9 entities in total)
• Functional Keywords: integrin, complex, bicyclic peptide, cell adhesion
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 120349.18

Authors

Wang, J.C.,An, Y.N. (deposition date: 2025-11-11, release date: 2026-04-15, Last modification date: 2026-05-27)

Primary citation

Yang, H.,Dong, W.,An, Y.,He, Z.,Pan, H.,Pan, W.,Tan, J.,Sun, J.,Shen, C.,Su, W.,Wang, J.,Sussmuth, R.D.,Yao, G.
Ansamer-Controlled Bicyclic Peptides as Integrin alpha v beta 6 Targeting Agents.
Angew.Chem.Int.Ed.Engl., 65:-, 2026

PubMed Abstract: Bicyclic peptides are promising candidates for peptide-drug conjugates due to their structural rigidity and high target specificity. Recently, it became more apparent that some peptides form nonclassical conformational isomers, termed ansamers. These conformational isomers designated as P and M are non-interconvertible and separable, thus broaden the chemical space of the peptide template. In this study, we incorporated the RGD motif into a bicyclic peptide and systematically assessed the inhibitory activities of the P and M isomers against various integrins. The molecule 10-M exhibited high selectivity and potent inhibitory activity against the αvβ6 integrin, whereas 10-P, its conformational counterpart, lacked such activity. The cryo-EM structure of αvβ6 bound to 10-M shows, that it adopts a conformation with the cyclohexane sidechain of the amino acid Chg engaging in hydrophobic interactions with Ile183 and the disulfide bond within the β6 SDL2 loop. Compared to the linear peptide A20FMDV, a broadly applied αvβ6 inhibitor, 10-M displays faster cellular internalization and also sustains prolonged enrichment within tumor tissues. Moreover, employing 10-M a designed toxin-drug conjugate exhibits remarkable tumor-suppressing effects in vivo. These findings reveal how conformational isomers of ansamers affect biological activity-and highlight their potential for the identification of new bioactive molecules.

PubMed: 41937119
DOI: 10.1002/anie.1254428

Experimental method

ELECTRON MICROSCOPY (2.88 Å)