title: Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis.
abstract: Hepatitis C virus (HCV) bifunctional NS3/4A is an attractive anti-HCV drug target, as both the protease and helicase functions are required for viral infection and replication. Although the first generation of NS3/4A protease inhibitors (PIs) has focused almost exclusively on the interaction with the protease domain alone, recent studies have shown that PIs also inhibit the full-length NS3/4A protein. However, the detailed molecular mechanism of the interaction between protease inhibitors, as well as the peptide substance with the full-length NS3/4A protein, remains poorly understood. Herein, starting from the recently determined crystal structure of an inhibitor (inhibitor ) bound to the full-length NS3/4A protein, the structures of the full-length NS3/4A complexed with inhibitor ITMN-191 (by InterMune/Roche; Phase II) and substrate 4B5A (the viral cleavage product peptide) were built. Then, residue interaction network (RIN) analysis, molecular dynamics (MD) simulation, binding free energy calculation, decomposition of free energies on per-residue and dynamic substrate recognition pattern analysis were employed to uncover the structural and energetic basis of inhibitor and substrate binding mode in the binding cleft located at the interface of the protease and helicase domains of the full-length NS3/4A. The results from our study reveal that both the protease and helicase residues of the NS3/4A participate in the interactions with the inhibitor , ITMN-191 and 4B5A. Additional analysis of the NS3/4A substrate and inhibitor envelopes reveals the areas where the consensus inhibitor volume extended beyond the substrate envelope. These areas correspond to drug resistance mutations including Arg155, Ala156 and Asp168 at the protease active site as well as the two conserved helicase residues Gln526 and His528 that strongly interact with the inhibitors. Thus, the findings of this study will be very useful for understanding the interaction mechanism between the inhibitor (substrate) and NS3/4A and also for the rational design and development of new potent molecules targeting the full-length NS3/4A.
authors: State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China.
authors: Weiwei
authors: W
authors: Xue
authors: Meixia
authors: M
authors: Wang
authors: Xiaojie
authors: X
authors: Jin
authors: Huanxiang
authors: H
authors: Liu
authors: Xiaojun
authors: X
authors: Yao
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D000998:Antiviral Agents / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003521:Cyclopropanes; D024882:Drug Resistance, Viral / Q000235:genetics; D016174:Hepacivirus / Q000737:chemistry / Q000201:enzymology; D054833:Isoindoles; D007700:Kinetics; D007769:Lactams / Q000737:chemistry*; D047029:Lactams, Macrocyclic; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011392:Proline / Q000031:analogs & derivatives; D011480:Protease Inhibitors / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D020365:RNA Helicases / Q000737:chemistry*; D013449:Sulfonamides / Q000737:chemistry*; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000596:Amino Acids; D000998:Antiviral Agents; D003521:Cyclopropanes; D054833:Isoindoles; D007769:Lactams; D047029:Lactams, Macrocyclic; D011392:Proline; D011480:Protease Inhibitors; D020365:RNA Helicases; D013449:Sulfonamides; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C553752:danoprevir