Abstract
The RNA-dependent RNA polymerase NS5B is a key enzyme of the replication of hepatitis C virus (HCV) and a major therapeutic target. Applying a novel continuous assay with highly purified protein and a fluorescent RNA-template we provide for the first time a comprehensive mechanistic description of the enzymatic reaction. Using fluorescence spectroscopy, the kinetics of NS5B was confirmed to consist of two half-reactions, namely substrate binding and turnover. Determining the binding constants of the substrates and the rate constants of individual reaction steps, NS5B was shown to bind the template single-stranded RNA with high affinity (nanomolar range) and in a stepwise process that reflects the substrate positioning. As demonstrated by CD, NTP(s) binding caused a tertiary structural change of the enzyme into an active conformation. The second half-reaction was dissected into a sequential polymerization and a subsequent, rate-limiting product release reaction. Taking advantage of these tools, we analyzed the mechanism of action of the NS5B inhibitor HCV-796, which was shown to interfere with the formation of double-stranded RNA by blocking the second half-reaction.
Publication types
-
Research Support, N.I.H., Extramural
-
Research Support, Non-U.S. Gov't
MeSH terms
-
Benzofurans / chemistry*
-
Benzofurans / pharmacology
-
Enzyme Inhibitors / chemistry*
-
Enzyme Inhibitors / pharmacology
-
Hepacivirus / enzymology*
-
Hepacivirus / genetics
-
Protein Structure, Tertiary
-
RNA, Double-Stranded / chemistry*
-
RNA, Double-Stranded / genetics
-
RNA, Double-Stranded / metabolism
-
RNA, Viral / biosynthesis
-
RNA, Viral / chemistry*
-
RNA, Viral / genetics
-
RNA-Dependent RNA Polymerase / antagonists & inhibitors*
-
RNA-Dependent RNA Polymerase / chemistry*
-
RNA-Dependent RNA Polymerase / genetics
-
RNA-Dependent RNA Polymerase / metabolism
-
Recombinant Proteins / antagonists & inhibitors
-
Recombinant Proteins / chemistry
-
Recombinant Proteins / genetics
-
Recombinant Proteins / metabolism
-
Sulfonamides / chemistry*
-
Sulfonamides / pharmacology
-
Viral Nonstructural Proteins / antagonists & inhibitors*
-
Viral Nonstructural Proteins / chemistry*
-
Viral Nonstructural Proteins / genetics
-
Viral Nonstructural Proteins / metabolism
-
Virus Replication / drug effects
-
Virus Replication / physiology
Substances
-
Benzofurans
-
Enzyme Inhibitors
-
HCV 796
-
RNA, Double-Stranded
-
RNA, Viral
-
Recombinant Proteins
-
Sulfonamides
-
Viral Nonstructural Proteins
-
NS-5 protein, hepatitis C virus
-
RNA-Dependent RNA Polymerase