HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

Andres Wong-Sam; Yuan Fang Wang; Daniel W. Kneller; Andrey Y. Kovalevsky; Arun K. Ghosh; Robert W. Harrison; Irene T. Weber

doi:10.1016/j.jmgm.2022.108315

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

Andres Wong-Sam, Yuan Fang Wang, Daniel W. Kneller, Andrey Y. Kovalevsky, Arun K. Ghosh, Robert W. Harrison, Irene T. Weber

Single Crystal Diffraction

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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 K_i 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.

Original language	English
Article number	108315
Journal	Journal of Molecular Graphics and Modelling
Volume	117
DOIs	https://doi.org/10.1016/j.jmgm.2022.108315
State	Published - Dec 2022

Funding

This work was supported by the National Institute of Health (grant numbers AI150461 ITW and RWH, AI150466 AKG ); an NIH diversity supplement (AW-S); and a fellowship from the Molecular Basis of Disease Program of Georgia State University (AW-S). We are grateful to Dr. Johnson Agniswamy for valuable discussions. Clinical inhibitors were obtained from the AIDS Reagent Program, Division of AIDS, NIAID, NIH. We thank the SER-CAT staff at the Advanced Photon Source, Argonne National Laboratory , for assistance during X-ray data collection. Supporting institutions may be found at http://www.ser-cat.org/members.html . Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38. This work was supported by the National Institute of Health (grant numbers AI150461 ITW and RWH, AI150466 AKG); an NIH diversity supplement (AW-S); and a fellowship from the Molecular Basis of Disease Program of Georgia State University (AW-S).We are grateful to Dr. Johnson Agniswamy for valuable discussions. Clinical inhibitors were obtained from the AIDS Reagent Program, Division of AIDS, NIAID, NIH. We thank the SER-CAT staff at the Advanced Photon Source, Argonne National Laboratory, for assistance during X-ray data collection. Supporting institutions may be found at http://www.ser-cat.org/members.html. Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38.

Funders	Funder number
National Institutes of Health	AI150461
U.S. Department of Energy
National Institute of Allergy and Infectious Diseases	R37AI150466
Office of Science
Basic Energy Sciences	W-31-109-Eng-38
Argonne National Laboratory
Georgia State University

Keywords

Darunavir
Drug resistance
GRL-519
HIV Protease
HIV/AIDS
Lopinavir
Molecular dynamics
X-ray crystallography

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.jmgm.2022.108315

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title = "HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics",

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.",

keywords = "Darunavir, Drug resistance, GRL-519, HIV Protease, HIV/AIDS, Lopinavir, Molecular dynamics, X-ray crystallography",

author = "Andres Wong-Sam and Wang, {Yuan Fang} and Kneller, {Daniel W.} and Kovalevsky, {Andrey Y.} and Ghosh, {Arun K.} and Harrison, {Robert W.} and Weber, {Irene T.}",

note = "Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",

year = "2022",

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doi = "10.1016/j.jmgm.2022.108315",

language = "English",

volume = "117",

journal = "Journal of Molecular Graphics and Modelling",

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T1 - HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

AU - Wong-Sam, Andres

AU - Wang, Yuan Fang

AU - Kneller, Daniel W.

AU - Kovalevsky, Andrey Y.

AU - Ghosh, Arun K.

AU - Harrison, Robert W.

AU - Weber, Irene T.

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

KW - Darunavir

KW - Drug resistance

KW - GRL-519

KW - HIV Protease

KW - HIV/AIDS

KW - Lopinavir

KW - Molecular dynamics

KW - X-ray crystallography

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SN - 1093-3263

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JO - Journal of Molecular Graphics and Modelling

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ER -

HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics

Abstract

Funding

Keywords

UN SDGs

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