HIV-1 IN Inhibitors: 2010 Update and Perspectives

Marchand, Christophe; Maddali, Kasthuraiah; Métifiot, Mathieu; Pommier, ﻿Yves

doi:10.2174/156802609789630910

Cited by 81 publications

(88 citation statements)

References 146 publications

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“…Clinically relevant IN inhibitors show selectivity for the ST reaction and only weakly inhibit 3= processing (45). These compounds are referred to as IN strand transfer inhibitors (INSTIs).…”

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Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate with In Vitro Activity

Johnson

Métifiot

Pommier

et al. 2012

Antimicrob Agents Chemother

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The design of novel integrase (IN) inhibitors has been aided by recent crystal structures revealing the binding mode of these compounds with a full-length prototype foamy virus (PFV) IN and synthetic viral DNA ends. Earlier docking studies relied on incomplete structures and did not include the contribution of the viral DNA to inhibitor binding. Using the structure of PFV IN as the starting point, we generated a model of the corresponding HIV-1 complex and developed a molecular dynamics (MD)-based approach that correlates with the in vitro activities of novel compounds. Four well-characterized compounds (raltegravir, elvitegravir, MK-0536, and dolutegravir) were used as a training set, and the data for their in vitro activity against the Y143R, N155H, and G140S/Q148H mutants were used in addition to the wild-type (WT) IN data. Three additional compounds were docked into the IN-DNA complex model and subjected to MD simulations. All three gave interaction potentials within 1 standard deviation of values estimated from the training set, and the most active compound was identified. Additional MD analysis of the raltegravir-and dolutegravir-bound complexes gave internal and interaction energy values that closely match the experimental binding energy of a compound related to raltegravir that has similar activity. These approaches can be used to gain a deeper understanding of the interactions of the inhibitors with the HIV-1 intasome and to identify promising scaffolds for novel integrase inhibitors, in particular, compounds that retain activity against a range of drug-resistant mutants, making it possible to streamline synthesis and testing. . This leaves a conserved CA sequence with a free hydroxyl on each of the 3= ends of the viral DNA and a 2-nucleotide overhang on each of the 5= ends. In the second reaction, IN uses the newly created 3= hydroxyl to attack the phosphodiester backbone of the host genome (strand transfer [ST]). Depending on the retrovirus, the two viral ends are inserted 4 to 6 bases apart, creating a small duplication in the target DNA flanking the provirus (5 nucleotides in the case of HIV-1 and 4 for prototype foamy virus [PFV]) (50). Cellular enzymes repair the gaps, leaving the double-stranded proviral DNA stably integrated into the genome of the infected cell.Integrases consist of three functionally distinct domains that have been characterized by biochemical and mutational analyses. The N-terminal domain (NTD; residues 1 to 50) contains a zincbinding HHCC motif and contributes to multimer formation (7,8). The C-terminal domain (CTD; identified as residues 212 to 288 in deletion studies) nonspecifically binds DNA (18,20,34,42). The catalytic core domain (CCD; residues 50 to 212) contains the catalytic triad DD35E motif that is well conserved among the retroviral integrase superfamily (7,11,19,32). This active site coordinates two metal ions and binds one viral DNA end. Although IN complexes exist in solution in different multimeric states, recent crystallographic data confirmed that the functi...

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confidence: 99%

Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate with In Vitro Activity

Johnson

Métifiot

Pommier

et al. 2012

Antimicrob Agents Chemother

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“…The U.S. Food and Drug Administration (FDA) approval of raltegravir (3) for experienced patients, and more recently for naive patients, has significantly impacted AIDS therapy (10). However, clinical resistance to RAL emerges due to mutations in IN (13,17). Biochemical characterization of recombinant mutant IN enzymes demonstrated that RAL resistance involves one of three main mutations: Y143R, G140S-Q148H, and N155H (14,16,18).…”

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MK-0536 Inhibits HIV-1 Integrases Resistant to Raltegravir

Métifiot

Johnson

Smith

et al. 2011

Antimicrob Agents Chemother

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“…It has been reported that halogen substitution on the aryl group showed significant potency and selectivity against IN and viral replication in cell culture 13 . Several IN inhibitors containing different halogen substitution on the aryl group had been tested in the clinic, including MK-2048, GS-9137 and MK-0518 ( Figure 1) 14,15 . Especially MK-0518, also known as raltegravir, was the first IN inhibitor drug approved by the United States Food and Drug Administration (US FDA).…”

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confidence: 99%