Human Immunodeficiency Virus Protease Ligand Specificity Conferred by Residues Outside of the Active Site Cavity<sup>,</sup>

Hoog, Susan S.; Towler, Eric M.; Zhao, Baoguang; Doyle, Michael L.; Debouck, Christine; Abdel-Meguid, Sherin S.

doi:10.1021/bi960179j

Cited by 40 publications

(50 citation statements)

References 21 publications

(38 reference statements)

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“…Earlier studies showed that PR 1 bearing the substitutions, V32I, I47V, and V82I, altered the inhibition but not the binding mode of a tripeptide inhibitor. 16,17 These residues are the sites of drug resistance mutations V32I, I47V, and various substitutions of Val82 in HIV-1 (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Tie¹,

Wang²,

Boross³

et al. 2012

Protein Science

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Clinical inhibitor amprenavir (APV) is less effective on HIV-2 protease (PR 2 ) than on HIV-1 protease (PR 1 ). We solved the crystal structure of PR 2 with APV at 1.5 Å resolution to identify structural changes associated with the lowered inhibition. Furthermore, we analyzed the PR 1 mutant (PR 1M ) with substitutions V32I, I47V, and V82I that mimic the inhibitor binding site of PR 2 . PR 1M more closely resembled PR 2 than PR 1 in catalytic efficiency on four substrate peptides and inhibition by APV, whereas few differences were seen for two other substrates and inhibition by saquinavir (SQV) and darunavir (DRV). High resolution crystal structures of PR 1M with APV, DRV, and SQV were compared with available PR 1 and PR 2 complexes. Val/Ile32 and Ile/Val47 showed compensating interactions with SQV in PR 1M and PR 1 , however, Ile82 interacted with a second SQV bound in an extension of the active site cavity of PR 1M . Residues 32 and 82 maintained similar interactions with DRV and APV in all the enzymes, whereas Val47 and Ile47 had opposing effects in the two subunits. Significantly diminished interactions were seen for the aniline of APV bound in PR 1M and PR 2 relative to the strong hydrogen bonds observed in PR 1 , consistent with 15-and 19-fold weaker inhibition, respectively. Overall, PR 1M partially replicates the specificity of PR 2 and gives insight into drug resistant mutations at residues 32, 47, and 82. Moreover, this analysis provides a structural explanation for the weaker antiviral effects of APV on HIV-2.

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Section: Introductionmentioning

confidence: 99%

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Tie¹,

Wang²,

Boross³

et al. 2012

Protein Science

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“…In addition, the HIV-1 mutant protease containing all four changes was only slightly resistant to the inhibitors, leading to the conclusion that the four active-site residues would be insufficient to explain the differences in inhibitor sensitivity between HIV-1 and HIV-2 proteases. This observation was further explored by Hoog et al, who solved the structure of an HIV-1 protease containing V32I, I47V, and V82I, complexed with the tripeptide analogue inhibitor SB203386 and compared it to previously solved structures of WT HIV-1 and simian immunodeficiency virus (SIV) complexed with the same inhibitor (28). They concluded that ligand specificity was imparted not only by the three active-site residues tested but also by changes outside the active center.…”

Section: Discussionmentioning

confidence: 99%

“…In HIV-1, a substitution at any one of these residues confers multi-PI resistance (26), and common drug resistance mutations at positions 32, 47, and 82 encode the corresponding wild-type (WT) amino acids from HIV-2. Early structural and biochemical studies showed that these residues contribute to substrate selectivity (27,28), as well as inhibitor sensitivity (29), although most of these observations were made using investigational PI which were never licensed. More recently, crystallographic studies have linked three of the four residues (32, 47, and 82) to differential amprenavir (APV) and DRV sensitivities (30)(31)(32)(33).…”

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confidence: 99%

Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors

Raugi

Smith

Gottlieb

2016

J Virol

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Protease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2 ROD9 molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PR⌬4) and compared the phenotypic sensitivities (50% effective concentration [EC 50 ]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PR⌬4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PR⌬4 enzyme. These models suggest that the amprenavir sensitivity of PR⌬4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2= pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2. IMPORTANCEProteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine FDA-approved HIV-1 protease inhibitors (PI) are active against HIV-2. The underlying reasons for intrinsic PI resistance in HIV-2 are not known. We examined the contributions of four amino acids in the ligand-binding pocket of the enzyme that differ between HIV-1 and HIV-2 by constructing HIV-2 clones encoding the corresponding HIV-1 amino acids and testing the PI susceptibilities of the resulting viruses. We found that the HIV-2 clone containing all four changes (PR⌬4) was as susceptible as HIV-1 to all nine PI. We also modeled the PR⌬4 enzyme structure and compared it to existing crystallographic structures of HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir. Our findings demonstrate that four positions in the ligand-binding cleft of protease are the primary cause of HIV-2 PI resistance.

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“…One group of residues is located in the interconnecting loop composed of residues 80 through 84. This region has been proposed as one of the important determinants in substrate selection [39,40]. Proteases are partioned in subsites based on information about the substrate structures they process.…”

Section: Residues In the Best Internally Predictive And Best Externalmentioning

confidence: 99%

Inhibition and substrate recognition – a computational approach applied to HIV protease

Vinkers

Jonge

Daeyaert

et al. 2003

J Comput Aided Mol Des

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SummaryWe have developed a computational approach in which an inhibitor's strength is determined from its interaction energy with a limited set of amino acid residues of the inhibited protein. We applied this method to HIV protease. The method uses a consensus structure built from X-ray crystallographic data. All inhibitors are docked into the consensus structure. Given that not every ligand-protein interaction causes inhibition, we implemented a genetic algorithm to determine the relevant set of residues. The algorithm optimizes the q 2 between the sum of interaction energies and the observed inhibition constants. The best possible predictive model resulting has a q 2 of 0.63. External validation by examining the predictivity for compounds not used in derivation of the model leads to a prediction accuracy between 0.9 and 1.5 log 10 unit. Out of 198 residues in the whole protein, the best internally predictive model defines a subset of 20 residues and the best externally predictive model one of 9 residues. These residues are distributed over the subsites of the enzyme. This approach provides insight in which interactions are important for inhibiting HIV protease and it allows for quantitative prediction of inhibitor strength.

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Human Immunodeficiency Virus Protease Ligand Specificity Conferred by Residues Outside of the Active Site Cavity^,

Cited by 40 publications

References 21 publications

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors

Inhibition and substrate recognition – a computational approach applied to HIV protease

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Human Immunodeficiency Virus Protease Ligand Specificity Conferred by Residues Outside of the Active Site Cavity,

Cited by 40 publications

References 21 publications

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors

Inhibition and substrate recognition – a computational approach applied to HIV protease

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Product

Resources

About

Human Immunodeficiency Virus Protease Ligand Specificity Conferred by Residues Outside of the Active Site Cavity^,