Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1<i>H</i>-Benzylindole Derivatives through Fluorine Substitutions

Ferro, Stefania; Luca, Laura De; Barreca, Maria Letizia; Iraci, Nunzio; Grazia, Sara De; Christ, Frauke; Witvrouw, Myriam; Debyser, Zeger; Chimirri, Alba

doi:10.1021/jm8009266

Cited by 38 publications

(32 citation statements)

References 34 publications

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“…Thus, this predicted binding mode allows raltegravir to both (1) interact strongly with the two Mg’s and to also (2) impede the chemistry that the side-chain of His67 likely performs during the catalytic cycle of integrase 34. This binding mode involves interactions with T66, N155, and K159, which are all known to be important for the function of HIV integrase 1,7,10,35…”

Section: Resultsmentioning

confidence: 99%

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

Perryman

Forli

Morris

et al. 2010

Journal of Molecular Biology

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Human immunodeficiency virus type 1 (HIV-1) integrase is one of three virally encoded enzymes essential for replication and, therefore, a rational choice as a drug target for the treatment of HIV-1 infected individuals. In 2007 raltegravir became the first integrase inhibitor approved for use in the treatment of HIV infected patients, more than a decade since the approval of the first protease inhibitor (saquinavir, Hoffman La-Roche, 1995) and two decades since the approval of the first reverse transcriptase inhibitor (retrovir, Glaxo Smithkline, 1987). The slow progress towards a clinically effective HIV-1 integrase inhibitor can at least in part be attributed to a poor structural understanding of this key viral protein. Here we describe the development of a restrained molecular dynamics protocol that produces a more accurate model of the active site of this drug target. This model provides an advance on previously described models as it ensures that the catalytic DDE motif makes correct, monodentate, interactions with the two active site magnesium ions. Dynamic restraints applied to this coordination state create models with the correct solvation sphere for the metal ion complex and highlight the coordination sites available for metal binding ligands. Applying appropriate dynamic flexibility to the core domain allowed the inclusion of multiple conformational states in subsequent docking studies. These models have allowed us to (1) explore the effects of key drug resistance mutations on the dynamic flexibility and conformational preferences of HIV integrase and to (2) study raltegravir binding in the context of these dynamic models of both wild type and the G140S/Q148H drug resistant enzyme.

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Section: Resultsmentioning

confidence: 99%

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

Perryman

Forli

Morris

et al. 2010

Journal of Molecular Biology

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“…Shown in Fig. 1, XZ89 and CHI-1043 are structurally distinct from any of the four compounds used to verify the MD approach (21,56). INSTI 1 is similar to RAL (16).…”

Section: Verificationmentioning

confidence: 94%

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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“…Recently, a HIV-1 IN-Mg 2+ -DNA model that mimics the product of 3' processing has been reported [27,68]. This complex has now been used as template to build the analogous SIVmac251 two metal-IN-DNA complex, starting from the available coordinates of the CCD in the RCSB Protein Data Bank.…”

Section: Methodsmentioning

confidence: 99%

Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy

et al. 2010

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BackgroundIn this study we successfully created a new approach to ART in SIVmac251 infected nonhuman primates. This drug regimen is entirely based on drugs affecting the pre-integration stages of replication and consists of only two nucleotidic/nucleosidic reverse transcriptase inhibitors (Nt/NRTIs) and raltegravir, a promising new drug belonging to the integrase strand transfer inhibitor (INSTI) class.ResultsIn acutely infected human lymphoid CD4+ T-cell lines MT-4 and CEMx174, SIVmac251 replication was efficiently inhibited by raltegravir, which showed an EC90 in the low nanomolar range. This result was confirmed in primary macaque PBMCs and enriched CD4+ T cell fractions. In vivo monotherapy with raltegravir for only ten days resulted in reproducible decreases in viral load in two different groups of animals. When emtricitabine (FTC) and tenofovir (PMPA) were added to treatment, undetectable viral load was reached in two weeks, and a parallel increase in CD4 counts was observed. In contrast, the levels of proviral DNA did not change significantly during the treatment period, thus showing persistence of this lentiviral reservoir during therapy.ConclusionsIn line with the high conservation of the three main amino acids Y143, Q148 and N155 (responsible for raltegravir binding) and molecular docking simulations showing similar binding modes of raltegravir at the SIVmac251 and HIV-1 IN active sites, raltegravir is capable of inhibiting SIVmac251 replication both in tissue culture and in vivo. This finding may help to develop effective ART regimens for the simian AIDS model entirely based on drugs adopted for treatment in humans. This ART-treated AIDS nonhuman primate model could be employed to find possible strategies for virus eradication from the body.

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Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions

Cited by 38 publications

References 34 publications

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

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

Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy

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