A synergy of activity, stability, and inhibitor‐interaction of HIV ‐1 protease mutants evolved under drug‐pressure

ABSTRACT Pradimicin A (PRM-A), an antifungal nonpeptidic benzonaphtacenequinone antibiotic, is a low-molecular-weight (molecular weight, 838) carbohydrate binding agent (CBA) endowed with a selective inhibitory activity against human immunodeficiency virus (HIV). It invariably inhibits representative virus strains of a variety of HIV-1 clades with X4 and R5 tropisms at nontoxic concentrations. Time-of-addition studies revealed that PRM-A acts as a true virus entry inhibitor. PRM-A specifically interacts with HIV-1 gp120 and efficiently prevents virus transmission in cocultures of HUT-78/HIV-1 and Sup T1 cells. Upon prolonged exposure of HIV-1-infected CEM cell cultures, PRM-A drug pressure selects for mutant HIV-1 strains containing N-glycosylation site deletions in gp120 but not gp41. A relatively long exposure time to PRM-A is required before drug-resistant virus strains emerge. PRM-A has a high genetic barrier, since more than five N-glycosylation site deletions in gp120 are required to afford moderate drug resistance. Such mutated virus strains keep full sensitivity to the other known clinically used anti-HIV drugs. PRM-A represents the first prototype compound of a nonpeptidic CBA lead and, together with peptide-based lectins, belongs to a conceptually novel type of potential therapeutics for which drug pressure results in the selection of glycan deletions in the HIV gp120 envelope.

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SJP-L-5 inhibits HIV-1 polypurine tract primed plus-strand DNA elongation, indicating viral DNA synthesis initiation at multiple sites under drug pressure

Scientific Reports ◽

10.1038/s41598-018-20954-5 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 1

Author(s):

Xing-Jie Zhang ◽

Rui-Rui Wang ◽

Huan Chen ◽

Rong-Hua Luo ◽

Liu-Meng Yang ◽

...

Keyword(s):

Dna Synthesis ◽

Drug Pressure ◽

Viral Dna ◽

Polypurine Tract ◽

Hiv 1

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Kinetic Characterization and Cross-Resistance Patterns Of HIV-1 Protease Mutants Selected under Drug Pressure

Biochemistry ◽

10.1021/bi00029a002 ◽

1995 ◽

Vol 34 (29) ◽

pp. 9282-9287 ◽

Cited By ~ 179

Author(s):

Sergei V. Gulnik ◽

Leonid I. Suvorov ◽

Beishan Liu ◽

Betty Yu ◽

Barry Anderson ◽

...

Keyword(s):

Cross Resistance ◽

Kinetic Characterization ◽

Drug Pressure ◽

Resistance Patterns ◽

Hiv 1

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Mutations Proximal to Sites of Autoproteolysis and the α-Helix That Co-evolve under Drug Pressure Modulate the Autoprocessing and Vitality of HIV-1 Protease

Biochemistry ◽

10.1021/acs.biochem.5b00759 ◽

2015 ◽

Vol 54 (35) ◽

pp. 5414-5424 ◽

Cited By ~ 8

Author(s):

John M. Louis ◽

Lalit Deshmukh ◽

Jane M. Sayer ◽

Annie Aniana ◽

G. Marius Clore

Keyword(s):

Drug Pressure ◽

Α Helix ◽

Hiv 1

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An inhibitor-interaction intermediate of HIV-1 protease, revealed by Isothermal Titration Calorimetry and NMR spectroscopy

10.1101/404996 ◽

2018 ◽

Author(s):

Shahid N Khan ◽

John D Persons ◽

Michel Guerrero ◽

Tatiana V. Ilina ◽

Masayuki Oda ◽

...

Keyword(s):

Heat Flow ◽

Isothermal Titration Calorimetry ◽

Titration Calorimetry ◽

Drug Resistant ◽

Wild Type ◽

Binding Experiment ◽

Direct Experiment ◽

Resistant Mutants ◽

Inhibitor Interaction ◽

Hiv 1

AbstractSome of drug-resistant mutants of HIV-1 protease (PR), such as a clinically-relevant drug- resistant PR mutant (Flap+(I54V)) containing L10I, G48V, I54V and V82A mutations, produce significant changes in the balance between entropy and enthalpy of the drug-PR interactions, compared to the wild-type (WT) PR. Here, to gain a comprehensive understanding of the entropy-enthalpy compensation effects, we compared nuclear magnetic resonance (NMR), fluorescence spectroscopy and isothermal titration calorimetry (ITC) data of a WT PR with Flap+(I54V)and related mutants: (1) Flap+(I54V); (2) Flap+(I54A)which evolves from Flap+(I54V)in the continued presence of inhibitor yet does not exhibit entropy-enthalpy compensation; and (3) Flap+(I54), a control mutant that contains only L10I, G48V and V82A mutations. Our data indicate that WT and Flap+(I54A)show enthalpy-driven inhibitor-interaction, while Flap+(I54)and Flap+(I54V)exhibit entropy-driven inhibitor interaction. Interestingly, Flap+(I54A)exhibited significantly slower heat flow in the competitive ITC experiment with a strong binder, darunavir, and a weak binder, acetyl-pepstatin, but did not exhibit such slow heat flow in the direct inhibitor-titration experiments. NMR confirmed replacement of the weak binder by the strong binder in a competitive manner. This difference in the heat flow of the competitive binding experiment compared to the direct experiment can only be explained by assuming an inhibitor-bound intermediate pathway. A similar, but attenuated, tendency for slow heat flow was also detected in the competitive experiment with WT. Overall, our data suggests that an inhibitor-bound intermediate affects the entropy-enthalpy compensation of inhibitor-PR interaction.

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Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history

PLoS Biology ◽

10.1371/journal.pbio.3001010 ◽

2020 ◽

Vol 18 (12) ◽

pp. e3001010

Author(s):

Eva Bons ◽

Christine Leemann ◽

Karin J. Metzner ◽

Roland R. Regoes

Keyword(s):

Evolutionary Dynamics ◽

Fitness Landscape ◽

Large Population ◽

Parallel Evolution ◽

Cell Types ◽

Drug Pressure ◽

Evolutionary Paths ◽

The Impact ◽

Hiv 1

An often-returning question for not only HIV-1, but also other organisms, is how predictable evolutionary paths are. The environment, mutational history, and random processes can all impact the exact evolutionary paths, but to which extent these factors contribute to the evolutionary dynamics of a particular system is an open question. Especially in a virus like HIV-1, with a large mutation rate and large population sizes, evolution is expected to be highly predictable if the impact of environment and history is low, and evolution is not neutral. We investigated the effect of environment and mutational history by analyzing sequences from a long-term evolution experiment, in which HIV-1 was passaged on 2 different cell types in 8 independent evolutionary lines and 8 derived lines, 4 of which involved a switch of the environment. The experiments lasted for 240–300 passages, corresponding to approximately 400–600 generations or almost 3 years. The sequences show signs of extensive parallel evolution—the majority of mutations that are shared between independent lines appear in both cell types, but we also find that both environment and mutational history significantly impact the evolutionary paths. We conclude that HIV-1 evolution is robust to small changes in the environment, similar to a transmission event in the absence of an immune response or drug pressure. We also find that the fitness landscape of HIV-1 is largely smooth, although we find some evidence for both positive and negative epistatic interactions between mutations.

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Anatomy and pathology of HIV-1 peptidase

Essays in Biochemistry ◽

10.1042/bse0380113 ◽

2002 ◽

Vol 38 ◽

pp. 113-127 ◽

Cited By ~ 2

Author(s):

Ben M Dunn

Keyword(s):

Feline Immunodeficiency Virus ◽

Drug Target ◽

Concerted Effort ◽

Drug Pressure ◽

The Past ◽

Immunodeficiency Virus ◽

Hiv Type 1 ◽

Hiv 1

The peptidase of the HIV type 1 (HIV PR) is required for the replication of and further infection by the virus. A concerted effort has taken place in the past 15 years to understand the properties of this enzyme, as it serves as an excellent drug target for control of the virus. Owing to drug pressure, many mutations arise during turnover of the virus and some of these lead to resistance to the effects of the inhibitors. Recent advances in the understanding of the changes these mutations cause to the enzyme and its interaction with substrates and inhibitors have been described. In addition, studies of closely related retroviral enzymes from simian immunodeficiency virus, feline immunodeficiency virus and HIV-2 have expanded the structure-function paradigm. The role of the flexibility of ligands and of the enzyme in active-site interactions is discussed.

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Natural polymorphisms in the protease gene modulate the replicative capacity of non-B HIV-1 variants in the absence of drug pressure

Journal of Clinical Virology ◽

10.1016/j.jcv.2006.05.001 ◽

2006 ◽

Vol 36 (4) ◽

pp. 264-271 ◽

Cited By ~ 41

Author(s):

Africa Holguín ◽

Carlos Suñe ◽

François Hamy ◽

Vincent Soriano ◽

Thomas Klimkait

Keyword(s):

Protease Gene ◽

Replicative Capacity ◽

Drug Pressure ◽

Hiv 1

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Mutations in HIV-1gagandpolCompensate for the Loss of Viral Fitness Caused by a Highly Mutated Protease

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00465-12 ◽

2012 ◽

Vol 56 (8) ◽

pp. 4320-4330 ◽

Cited By ~ 30

Author(s):

Milan Kožíšek ◽

Sandra Henke ◽

Klára Grantz Šašková ◽

Graeme Brendon Jacobs ◽

Anita Schuch ◽

...

Keyword(s):

Highly Active Antiretroviral Therapy ◽

Viral Fitness ◽

Drug Pressure ◽

Viral Loads ◽

Highly Active ◽

Subtype B ◽

Hiv 1

ABSTRACTDuring the last few decades, the treatment of HIV-infected patients by highly active antiretroviral therapy, including protease inhibitors (PIs), has become standard. Here, we present results of analysis of a patient-derived, multiresistant HIV-1 CRF02_AG recombinant strain with a highly mutated protease (PR) coding sequence, where up to 19 coding mutations have accumulated in the PR. The results of biochemical analysisin vitroshowed that the patient-derived PR is highly resistant to most of the currently used PIs and that it also exhibits very poor catalytic activity. Determination of the crystal structure revealed prominent changes in the flap elbow region and S1/S1′ active site subsites. While viral loads in the patient were found to be high, the insertion of the patient-derived PR into a HIV-1 subtype B backbone resulted in reduction of infectivity by 3 orders of magnitude. Fitness compensation was not achieved by elevated polymerase (Pol) expression, but the introduction of patient-derivedgagandpolsequences in a CRF02_AG backbone rescued viral infectivity to near wild-type (wt) levels. The mutations that accumulated in the vicinity of the processing sites spanning the p2/NC, NC/p1, and p6pol/PR proteins lead to much more efficient hydrolysis of corresponding peptides by patient-derived PR in comparison to the wt enzyme. This indicates a very efficient coevolution of enzyme and substrate maintaining high viral loadsin vivounder constant drug pressure.

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