title: Effect of D168V mutation in NS3/4A HCV protease on susceptibilities of faldaprevir and danoprevir.
abstract: Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency. The D168V mutation was shown to interrupt the hydrogen bonding network of Q80R155D168R123 embedded in the extended S2 and partial S4 subsites of the NS3 protein and as a result the R123 side chain was displaced and moved out from the binding pocket. By means of MM/PBSA and MM/GBSA binding free energy calculations, the FDV and DNV binding affinities were shown to be significantly reduced by ∼10-15 kcal mol-1and ∼4-9 kcal mol-1relative to the wild-type complexes, respectively, which somewhat agrees with the experimental resistance folds.
authors.affiliation: Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
authors.forename: Arthitaya
authors.initials: A
authors.lastname: Meeprasert
authors.affiliation: Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
authors.forename: Supot
authors.initials: S
authors.lastname: Hannongbua
authors.affiliation: Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
authors.forename: Nawee
authors.initials: N
authors.lastname: Kungwan
authors.affiliation: Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand and PhD Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. t.rungrotmongkol@gmail.com thanyada.r@chula.ac.th.
authors.forename: Thanyada
authors.initials: T
authors.lastname: Rungrotmongkol
mesh_terms: D019943:Amino Acid Substitution; D000621:Aminoisobutyric Acids; D001665:Binding Sites; D020134:Catalytic Domain; D003062:Codon; D003521:Cyclopropanes; D024882:Drug Resistance, Viral; D016174:Hepacivirus / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D006860:Hydrogen Bonding; D054833:Isoindoles; D007769:Lactams / Q000737:chemistry / Q000494:pharmacology*; D047029:Lactams, Macrocyclic; D007930:Leucine / Q000031:analogs & derivatives; D008958:Models, Molecular; D008968:Molecular Conformation; D009154:Mutation; D009842:Oligopeptides / Q000737:chemistry / Q000494:pharmacology*; D011392:Proline / Q000031:analogs & derivatives; D011485:Protein Binding; D011804:Quinolines; D013449:Sulfonamides / Q000737:chemistry / Q000494:pharmacology*; D013844:Thiazoles / Q000737:chemistry / Q000494:pharmacology*; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000621:Aminoisobutyric Acids; D003062:Codon; D003521:Cyclopropanes; D054833:Isoindoles; D007769:Lactams; D047029:Lactams, Macrocyclic; D007930:Leucine; D009842:Oligopeptides; D011392:Proline; D011804:Quinolines; D013449:Sulfonamides; D013844:Thiazoles; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C093542:NS4 protein, hepatitis C virus; C553752:danoprevir; C552340:faldaprevir