In-Silico docking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate.

Andrea Savarino

doi:10.1186/1742-4690-4-21

Abstract

BackgroundHIV-1 integrase (IN) is an emerging drug target, as IN strand transfer inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials. One credible theory sees INSTIs as docking at the cellular (acceptor) DNA-binding site after IN forms a transitional complex with viral (donor) DNA. However, mapping of the DNA and INSTI binding sites within the IN catalytic core domain (CCD) has been uncertain.MethodsStructural superimpositions were conducted using the SWISS PDB and Cn3D free software. Docking simulations of INSTIs were run by a widely validated genetic algorithm (GOLD).ResultsStructural superimpositions suggested that a two-metal model for HIV-1 IN CCD in complex with small molecule, 1-(5-chloroindol-3-yl)-3-(tetrazoyl)-1,3-propandione-ene (5CITEP) could be used as a surrogate for an IN/viral DNA complex, because it allowed replication of contacts documented biochemically in viral DNA/IN complexes or displayed by a crystal structure of the IN-related enzyme Tn5 transposase in complex with transposable DNA. Docking simulations showed that the fitness of different compounds for the catalytic cavity of the IN/5CITEP complex significantly (P < 0.01) correlated with their 50% inhibitory concentrations (IC50s) in strand transfer assays in vitro. The amino acids involved in inhibitor binding matched those involved in drug resistance. Both metal binding and occupation of the putative viral DNA binding site by 5CITEP appeared to be important for optimal drug/ligand interactions. The docking site of INSTIs appeared to overlap with a putative acceptor DNA binding region adjacent to but distinct from the putative donor DNA binding site, and homologous to the nucleic acid binding site of RNAse H. Of note, some INSTIs such as 4,5-dihydroxypyrimidine carboxamides/N-Alkyl-5-hydroxypyrimidinone carboxamides, a highly promising drug class including raltegravir/MK-0518 (now in clinical trials), displayed interactions with IN reminiscent of those displayed by fungal molecules from Fusarium sp., shown in the 1990s to inhibit HIV-1 integration.ConclusionThe 3D model presented here supports the idea that INSTIs dock at the putative acceptor DNA-binding site in a IN/viral DNA complex. This mechanism of enzyme inhibition, likely to be exploited by some natural products, might disclose future strategies for inhibition of nucleic acid-manipulating enzymes.

Highlights

human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an emerging drug target, as IN strand transfer inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials
The lack of 5' cleavage before strand transfer is a major difference between HIV-1 IN and transposases such as Tn5, Tn7 and Tn10, which release a blunt-end transposable element from donor DNA [8,9]. 5' strand cleavage has been shown for Tn5 and Tn10 transposons to occur via a two-step process whereby the 3' OH generated from the initial strand cleavage attacks the 5' strand to form a hairpin, followed by cleavage of the hairpin by attack from an activated water molecule [8,9] (Fig. 1)
The Tn5 transposase/transposable DNA complex shows similarities with and differences from the HIV-1 IN/viral DNA interaction To map the donor DNA-binding site within the catalytic site of IN, previous work used the crystal structure of inhibitor 5CITEP in complex with HIV-1 IN catalytic core domain (CCD) described by Goldgur et al [22], or a structure of Tn5 transposase in complex with transposable DNA [19]

Summary

Introduction

HIV-1 integrase (IN) is an emerging drug target, as IN strand transfer inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials. Despite the decade-long studies in this field (reviewed in: [2]), several questions on the interactions of IN with its inhibitors have remained unanswered [1,2] These include: the docking site, possible interactions with metal ions and viral DNA, the amino acids involved in binding, the role of drug resistance mutations, and the conformations assumed by the inhibitors in complex with the enzyme. Elucidation of these issues is crucial, given the strict requirement of IN for insertion of proviral DNA into the cell genome, leading to retroviral latency and persistence during therapy [5]. The lack of 5' cleavage before strand transfer is a major difference between HIV-1 IN and transposases such as Tn5, Tn7 and Tn10, which release a blunt-end transposable element from donor DNA [8,9]. 5' strand cleavage has been shown for Tn5 and Tn10 transposons to occur via a two-step process whereby the 3' OH generated from the initial strand cleavage attacks the 5' strand to form a hairpin, followed by cleavage of the hairpin by attack from an activated water molecule [8,9] (Fig. 1)

Methods

Results

Conclusion