Design of nevirapine derivatives insensitive to the K103N and Y181C HIV-1 reverse transcriptase mutants

Relative assessment of different statistical instruments and measures for the prediction of promising outcomes using docking, virtual screening and ADMET analysis against HIV-RT

Reverse transcriptase is the most therapeutic target for the discovery of novel, potent, and non-toxic new anti-retroviral drugs. In the present work, various docking software such as Sybyl Surflex-Dock, OpenEye FRED, and Hermes GOLD were evaluated for their efficiency to reproduce known cognate inhibitors' conformations. Three metrics were used and compared to assess the performance of the applied scoring functions, i.e. enrichment factor, receiver operating characteristic (ROC) curves, and Bedroc analysis. Twelve different scoring functions of three softwares were used to assess their ability to rank the cognate ligand within the active site of its proteins. The extensive virtual screening task was performed on eight crystal structures, and the performance of docking and scoring was assessed by their ability to efficiently detect known active compounds enriched in the top-ranked of the list among a randomly selected dataset of the ten thousand compounds of the NCI database. The effectiveness of post-docking relaxation in Surflex was also evaluated. The top 20, 50, and 100 compounds were selected based on consensus scoring functions from all 48 proteins with different ligand complexes. Further, the shortlisted leads were subjected to ADMET via using Discovery Studio. The results further implicate the importance of various statistical tools that should be followed before large-scale virtual screening for the drug discovery process. In silico results demonstrating the experiment was successful. The study of the research covers the combinatorial in silico techniques such as benchmarking of the softwares and scoring functions, statistical tools applied for screening and different conformations of HIV-RT crystal structures for virtual screening with rigid and flexible molecular docking and molecular dynamics simulation approach. This study reveals a clear roadmap to identify novel scaffolds against HIV-RT for antiretroviral therapy, thus providing the remedial solutions of HIV related infections and other diseases caused by malfunctioning of the target protein.Communicated by Ramaswamy H. Sarma.

Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection

The HIV replication cycle offers multiple targets for chemotherapeutic intervention, including the viral exterior envelope glycoprotein, gp120; viral co-receptors CXCR4 and CCR5; transmembrane glycoprotein, gp41; integrase; reverse transcriptase; protease and so on. Most currently used anti-HIV drugs are reverse transcriptase inhibitors or protease inhibitors. The expanding application of simulation to drug design combined with experimental techniques have developed a large amount of novel inhibitors that interact specifically with targets besides transcriptase and protease. This review presents details of the anti-HIV inhibitors discovered with computer-aided approaches and provides an overview of the recent five-year achievements in the treatment of HIV infection and the application of computational methods to current drug design.

Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase--evidence from molecular dynamics simulations and MM-PBSA calculations

The important role of the bridge water molecule in the binding of HIV-1 reverse transcriptase (RT) inhibitor complex was elucidated by molecular dynamics (MD) simulations using an MM-PBSA approach. Binding free energies and thermodynamic property differences for nevirapine bound to wild type and Y181C HIV-1 reverse transcriptase were investigated, and the results were compared with available experimental data. MD simulations over 3 ns revealed that the bridge water formed three characteristic hydrogen bonds to nevirapine and two residues, His235 and Leu234, in the binding pocket. The energetic derived model, which was determined from the consecutive addition of a water molecule, confirmed that only the contribution from the bridge water was essential in the binding configuration. Including this bridge water in the MM-PBSA calculations reoriented the binding energies from -32.20 to -37.65 kcal/mol and -28.07 to -29.82 kcal/mol in the wild type and Y181C HIV-1 RT, respectively. From the attractive interactions via the bridge water, His235 and Leu234 became major contributions. We found that the bridge water is the key in stabilizing the bound complex; however, in the Y181C RT complex this bridge water showed weaker hydrogen bond formation, lack of attractive force to nevirapine and lack of binding efficiency, leading to the failure of nevirapine against the Y181C HIV-1 RT. Moreover, the dynamics of Val179, Tyr181Cys, Gly190 and Leu234 in the binding pocket showed additional attractive energetic contributions in helping nevirapine binding. These findings that the presence of a water molecule in the hydrophobic binding site plays an important role are a step towards a quantitative understanding of the character of bridge water in enzyme-inhibitor binding. This can be helpful in developing designs for novel non-nucleoside HIV-1 RT inhibitors active against the mutant enzyme.