Binding of a noncovalent inhibitor exploiting the S' region stabilizes the hepatitis C virus NS3 protease conformation in the absence of cofactor.
We present the first structure of a noncovalent inhibitor bound to the protease domain of hepatitis C virus NS3 protein (NS3p), solved by NMR. The inhibitor exploits interactions with the S' region of NS3p to form a long-lived complex, although the absence of negative charges strongly reduces the association rate. The inhibitor stabilizes the N-terminal domain of NS3p and the substrate-binding site, and correctly aligns catalytic His-Asp residues. These actions were previously attributed exclusively to the cofactor NS4A, which interacts with the N-terminal domain of the NS3p and functions as an activator in vivo. The structure of the inhibitor/NS3p complex is very similar to that of the NS3p-NS4A complex, showing that binding of the NS4A cofactor is not the only event leading to a stable active-site conformation.
Gallo
Mariana
M
Department of Chemical Science and Technology, Università di Roma Tor Vergata Via della Ricerca Scientifica 1, 00133 Rome, Italy.
Pennestri
Matteo
M
Bottomley
Matthew James
MJ
Barbato
Gaetano
G
Eliseo
Tommaso
T
Paci
Maurizio
M
Narjes
Frank
F
De Francesco
Raffaele
R
Summa
Vincenzo
V
Koch
Uwe
U
Bazzo
Renzo
R
Cicero
Daniel O
DO
D000577:Amides / Q000494:pharmacology; D001224:Aspartic Acid / Q000378:metabolism; D002352:Carrier Proteins / Q000378:metabolism*; D002384:Catalysis / Q000187:drug effects; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004795:Enzyme Stability / Q000187:drug effects; D006639:Histidine / Q000378:metabolism; D006860:Hydrogen Bonding / Q000187:drug effects; D047908:Intracellular Signaling Peptides and Proteins; D007700:Kinetics; D008958:Models, Molecular; D011480:Protease Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017186:Titrimetry; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D014764:Viral Proteins / Q000378:metabolism*; D014867:Water; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
D000577:Amides; D001224:Aspartic Acid; D002352:Carrier Proteins; D006639:Histidine; D047908:Intracellular Signaling Peptides and Proteins; D011480:Protease Inhibitors; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; D014867:Water; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C455041:NS4A cofactor peptide, Hepatitis C virus