Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking

Abstract

Modeling studies were performed on HCV NS5B Polymerase in an effort to design new inhibitors. The binding models of five different scaffold inhibitors were investigated and compared by using molecular dynamics simulations, free energy calculation and decomposition. Our results show Tyr448 plays the most critical role in the binding of most inhibitors. In addition, favorable contributions of residues Pro197, Arg200, Cys366, Met414 and Tyr448 in a deep hydrophobic pocket prove to be important for the selectivity of inhibitors. Furthermore, an optimized docking protocol was presented based on cross-docking the five inhibitors in the palm binding site of this enzyme using the Autodock program. This protocol was used later to virtually screen NCI and Maybridge diversity set libraries. The binding site was profiled via the statistics and analysis of the hydrogen bond networks formed between the receptor and the top-ranked diversity set compounds. Based on our detailed binding site analysis two useful rules were proposed to guide the selection of promising hits.Response to Reviewers: Question1: It is a pity that nothing in detail is discussed about found structures resulting from the virtual screening. Did the authors find new promising ligands with high (higher than the template ligands?) affinity and are they structurally diverse or similar to the used ones?Answer: We have found some promising compounds after the virtual screening. They are structurally diverse. Most of them form hydrogen bonds with the critical residues such as Tyr448 and have strong hydrophobic interaction with the residues in the deep hydrophobic pocket mentioned in our article. These compounds are under biological test.Question2: Additionally to figure 5 at least one figure should be added, showing the amino acid residues of the active site with the discussed most important interactions with one (the best?) ligand. This would considerably help to understand the discussion without looking in the original pdb-files. AbstractModeling studies were performed on HCV NS5B Polymerase in an effort to design new inhibitors. The binding models of five different scaffold inhibitors were investigated and compared by using molecular dynamics simulations, free energy calculation and decomposition. Our results show Tyr448 plays the most critical role in the binding of most inhibitors. In addition, favorable contributions of residues Pro197, Arg200, Cys366, Met414 and Tyr448 in a deep hydrophobic pocket prove to be important for the selectivity of inhibitors.Furthermore, an optimized docking protocol was presented based on cross-docking the five inhibitors in the palm binding site of this enzyme using the Autodock program. This protocol was used later to virtually screen NCI and Maybridge diversity set libraries. The binding site was profiled via the statistics and analysis of the hydrogen bond networks formed between the receptor and the top-ranked diversity set compounds. Based on our detailed binding site analysis two useful rules were proposed to ...

Computational study enlightens the structural role of the alcohol acyltransferase DFGWG motif

“…No dramatic differences were observed among the systems and the final ranking of affinities of complexes regarding the contribution of solvation (ΔG solpol +ΔG sol-npol ); on the contrary, the differences in ΔG bind values of the different complexes depend mainly on van der Waals contributions (Table 3). It has been claimed that the MM-GBSA method systematically gives unrealistically low values for the absolute value of ΔG bind , overestimating the stability of the complexes in relation to the uncomplexed form [30,32]. Therefore, the absolute ΔG bind values shown here are probably unrealistically low; however, the affinities of VpAAT1 and the different VpAAT1-mutants for the ligands are likely to be uniformly weaker, despite this underestimation.…”

“…Additionally, the MM-GBSA method is attractive because it allows the decomposition of the electrostatic solvation free energy into atomic contributions in a straightforward manner and results can be obtained much faster than other approaches such as free energy perturbation methods or the MM-PBSA model [33,34]. On the other hand, the effect of point substitutions on protein structure has been used previously with many positive results [32][33][34], the per-atom contributions can be added over atom groups such as residues, backbones and side-chains, to obtain their contributions to the total binding free energy. Thus, the effect of Y52A, D381A and 381E mutations was calculated at the atomic level using the MM-GBSA method.…”

“…Free energy of binding calculations using MM-GBSA methods are based on MDS of the given protein-ligand complexes in explicit solvents [31,32]. These methods have been used widely to predict binding affinities of biomolecular complexes.…”

Structure-based virtual screening, synthesis and SAR of novel inhibitors of hepatitis C virus NS5B polymerase

“…In contrast, compound 3 , bearing the rhodanine scaffold proved to be a suitable “hit” for development of more potent novel analogs, through SAR optimization and chemical synthesis (Table 2). Previous studies have reported the IC 50 values for lead molecules identified through virtual screening, ranging from 20 μM for the 3D Pharmo DB TM set51 to 1 μM for compounds originating from the French National Library/Prestwick commercial library and the NCI library put together 50. Our “hit” compound 3 , though it exhibited a higher IC 50 value of 55 μM, a systematic SAR exploration and one step synthetic derivatization around a selected parent heterocyclic core of compound 7 , ultimately yielded compound 28 (IC 50 = 7.7 μM), the most potent NS5B inhibitor of this series.…”

Ligand and Structure Based Virtual Screening Strategies for Hit-Finding and Optimization of Hepatitis C Virus (HCV) Inhibitors

“…The compounds active in the RC assay were also evaluated in the HCV replicon assay. As suggested, lower than expected EC 50 values are partly derived from the cellular toxicity An interesting work was recently presented by Li et al [47] Molecular dynamics simulations, free energy decomposition and docking were used in an effort to investigate and compare five different molecular scaffolds of HCV NS5B inhibitors. As many Xray structures of HCV NS5B polymerase complexed with NNIs are publicly available, the authors selected five of them (1YVF, 2GC8, 2GIQ, 2JC0, 2QE5) based on the following criteria: the protein is HCV NS5B polymerase genotype 1b, the NNIs all bind to the same palm binding site and these five NNIs represent different scaffolds.…”