Characterizing the structural variability of HIV-2 protease upon the binding of diverse ligands using a structural alphabet approach

Abstract

The HIV-2 protease (PR2) is an important target for designing new drugs against the HIV-2 infection. In this study, we explored the structural backbone variability of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. 77% of PR2 positions are structurally variable, meaning they exhibit different local conformations in PR2 structures. This variability was observed all along the structure, particularly in the elbow and flap regions. A part of these backbone changes observed between the 18 PR2 is induced by intrinsic flexibility, and ligand binding putatively induces others occurring in the binding pocket. These latter changes could be important for PR2 adaptation to diverse ligands and are accompanied by changes outside the binding pocket. In addition, the study of the link between structural variability of the pocket and PR2–ligand interactions allowed us to localize pocket regions important for ligand binding and catalytic function, regions important for ligand recognition that adjust their backbone in response to ligand binding and regions important for the pocket opening and closing that have large intrinsic flexibility. Finally, we suggested that differences in ligand effectiveness for PR2 could be partially explained by different backbone deformations induced by these ligands. To conclude, this study is the first characterization of the PR2 structural variability considering ligand diversity. It provides information about the recognition of PR2 to various ligands and its mechanisms to adapt its local conformation to bound ligands that could help understand the resistance of PR2 to its inhibitors, a major antiretroviral class.

Communicated by Ramaswamy H. Sarma

Keywords:

• HIV-2 protease
• structural variability
• structural deformation upon ligand binding
• structural alphabet
• ligand specificity

Acknowledgements

We thank Yasaman Karami and Natacha Cerisier for proofreading this manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by an ANRS Grant to B.V., D.D., A.C.C. and L.R. D.T. was supported by an ANRS fellowship.