title: Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site.
abstract: The hepatitis C virus (HCV) polymerase is required for replication of the viral genome and is a key target for therapeutic intervention against HCV. We have determined the crystal structures of the HCV polymerase complexed with two indole-based allosteric inhibitors at 2.3- and 2.4-Angstroms resolution. The structures show that these inhibitors bind to a site on the surface of the thumb domain. A cyclohexyl and phenyl ring substituents, bridged by an indole moiety, fill two closely spaced pockets, whereas a carboxylate substituent forms a salt bridge with an exposed arginine side chain. Interestingly, in the apoenzyme, the inhibitor binding site is occupied by a small alpha-helix at the tip of the N-terminal loop that connects the fingers and thumb domains. Thus, these molecules inhibit the enzyme by preventing formation of intramolecular contacts between these two domains and consequently precluding their coordinated movements during RNA synthesis. Our structures identify a novel mechanism by which a new class of allosteric inhibitors inhibits the HCV polymerase and open the way to the development of novel antiviral agents against this clinically relevant human pathogen.
authors.affiliation: Istituto di Ricerche di Biologia Molecolare P. Angeletti, Pomezia (Rome), Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Di Marco
authors.forename: Cinzia
authors.initials: C
authors.lastname: Volpari
authors.forename: Licia
authors.initials: L
authors.lastname: Tomei
authors.forename: Sergio
authors.initials: S
authors.lastname: Altamura
authors.forename: Steven
authors.initials: S
authors.lastname: Harper
authors.forename: Frank
authors.initials: F
authors.lastname: Narjes
authors.forename: Uwe
authors.initials: U
authors.lastname: Koch
authors.forename: Michael
authors.initials: M
authors.lastname: Rowley
authors.forename: Raffaele
authors.initials: R
authors.lastname: De Francesco
authors.forename: Giovanni
authors.initials: G
authors.lastname: Migliaccio
authors.forename: Andrea
authors.initials: A
authors.lastname: Carfí
mesh_terms: D000495:Allosteric Site; D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000494:pharmacology; D001665:Binding Sites; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D000998:Antiviral Agents; D004791:Enzyme Inhibitors; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase