Combining 3-D Quantitative Structure−Activity Relationship with Ligand Based and Structure Based Alignment Procedures for in Silico Screening of New Hepatitis C Virus NS5B Polymerase Inhibitors

Abstract

The viral NS5B RNA-dependent RNA-polymerase (RdRp) is one of the best-studied and promising targets for the development of novel therapeutics against hepatitis C virus (HCV). Allosteric inhibition of this enzyme has emerged as a viable strategy toward blocking replication of viral RNA in cell based systems. Herein, we describe how the combination of a complete computational procedure together with biological studies led to the identification of novel molecular scaffolds, hitherto untested toward NS5B polymerase. Structure based 3-D quantitative structure-activity relationship (QSAR) models were generated employing NS5B non-nucleoside inhibitors (NNIs), whose bound conformations were readily available from the protein database (PDB). These were grouped into two training sets of structurally diverse NS5B NNIs, based on their binding to the enzyme thumb (15 NNIs) or palm (10 NNIs) domains. Ligand based (LB) and structure based (SB) alignments were rigorously investigated to assess the reliability on the correct molecular alignment for unknown binding mode modeled compounds. Both Surflex and Autodock programs were able to reproduce with minimal errors the experimental binding conformations of 24 experimental NS5B allosteric inhibitors. Eighty-one (thumb) and 223 (palm) modeled compounds taken from literature were LB and SB aligned and used as external validation sets for the development of 3-D QSAR models. Low error of prediction proved the 3-D QSARs to be useful scoring functions for the in silico screening procedure. Finally, the virtual screening of the NCI Diversity Set led to the selection for enzymatic assays of 20 top-scoring molecules for each final model. Among the 40 selected molecules, preliminary data yielded four derivatives exhibiting IC(50) values ranging between 45 and 75 microM. Binding mode analysis of hit compounds within the NS5B polymerase thumb domain showed that one of them, NSC 123526, exhibited a docked conformation which was in good agreement with the thumb training set most active compound (6).

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches

“…A total of 262 published compounds with known activities and unknown binding modes [15][16][17][18][19][45][46][47][48] (Supplementary Material Table SM-1) were collected. As an extension of previously reported applications [39,42,[45][46][47], in order to evaluate the 3-D QSAR model predictive abilities, either ligand-based (LB) or SB molecular alignments were ruled out by means of the programs Surflex-Sim [48], Omega/Rocs [49][50][51][52] and Balloon/ShaEP [53][54][55] for the LB and AutoDock4 [56], AutoDock Vina (herein just Vina), DOCK, Plants, ParaDocks and Surflex-Dock for the SB. Only the LB and SB best performing programs were then used to align the external test set compounds (see Test Set Selection section) and assess the 3-D QSAR models by means of pIC 50 predicted values (Fig.…”

“…The 27 VEGFR-2/inhibitors complexes (Table 2) were submitted to a previously reported [45] molecular modeling protocol as follows: (1) using the UCSF Chimera [57] MatchMaker the complexes were SB superimposed using 2OH4 as template, the one having the best number of residues-resolution combination (510 residues, 2.05 Å ); (2) all crystal water molecules were removed, and hydrogen atoms were added using the leap module of AMBER suite;…”

Synthesis, biological evaluation and docking analysis of a new series of methylsulfonyl and sulfamoyl acetamides and ethyl acetates as potent COX-2 inhibitors

“…Before performing any docking study, the most suitable docking program within a series of 8 program/scoring combinations function was assessed by a previously described cross-docking protocol 17,18 applied on the available experimental co-crystallized complexes for either COX-1 (18 complexes, Table 3) or COX-2 (14 complexes, Table 4). Briefly, each energy minimized COX complex was divided into ligand and protein (see Section 4).…”

“…In particular, all the compounds found active against either COX-1 or COX-2 enzymes (Tables 1 and 5) were modeled and cross-docked into all the available COX-1/COX-2 experimental structures following the same protocol as in the docking assessment. The lowest energy poses were selected 17 as the likely binding modes for the newly synthesized compounds. Compound 4 was the only one found with an appreciable inhibitory activity against COX-1 (36% at 10 lM) and its lowest energy bound pose was found in the proteins 2OYU ( Fig.…”

Novel Cinnamyl Hydroxyamides and 2‐Aminoanilides as Histone Deacetylase Inhibitors: Apoptotic Induction and Cytodifferentiation Activity

“…In all cases the lowest energy docked conformation belonged to the most populated cluster. In the case of HDAC4 100 runs for each structure were generated (cross-Docking [62] ) and the results of either set of dockings were clustered using the AutoDock internal clustering algorithm.…”