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Wong-Sam A, Wang YF, Kneller DW, Kovalevsky AY, Ghosh AK, Harrison RW, Weber IT. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. J Mol Graph Model 2022; 117:108315. [PMID: 36108568 PMCID: PMC10091457 DOI: 10.1016/j.jmgm.2022.108315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/14/2023]
Abstract
Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical isolate including 10 mutations associated with resistance to lopinavir and darunavir. Compared to the wild-type protease, PR10x exhibits ∼3-fold decrease in catalytic efficiency and Ki values of 2-3 orders of magnitude worse for darunavir, lopinavir, and potent investigational inhibitor GRL-519. Crystal structures of the mutant were solved in a ligand-free form and in complex with GRL-519. The structures show altered interactions in the active site, flap-core interface, hydrophobic core, hinge region, and 80s loop compared to the corresponding wild-type protease structures. The ligand-free crystal structure exhibits a highly curled flap conformation which may amplify drug resistance. Molecular dynamics simulations performed for 1 μs on ligand-free dimers showed extremely large fluctuations in the flaps for PR10x compared to equivalent simulations on PR with a single L76V mutation or wild-type protease. This analysis offers insight about the synergistic effects of mutations in highly resistant variants.
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Affiliation(s)
- Andres Wong-Sam
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Y Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert W Harrison
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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