title: Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335.
abstract: Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.
authors.affiliation: Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada. christopher.lemke@boehringer-ingelheim.com
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Lemke
authors.forename: Nathalie
authors.initials: N
authors.lastname: Goudreau
authors.forename: Songping
authors.initials: S
authors.lastname: Zhao
authors.forename: Oliver
authors.initials: O
authors.lastname: Hucke
authors.forename: Diane
authors.initials: D
authors.lastname: Thibeault
authors.forename: Montse
authors.initials: M
authors.lastname: Llinàs-Brunet
authors.forename: Peter W
authors.initials: PW
authors.lastname: White
mesh_terms: D000621:Aminoisobutyric Acids; D002352:Carrier Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D020134:Catalytic Domain; D017321:Clinical Trials, Phase I as Topic; D018360:Crystallography, X-Ray; D016174:Hepacivirus / Q000201:enzymology*; D006526:Hepatitis C / Q000188:drug therapy / Q000201:enzymology; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D007930:Leucine / Q000031:analogs & derivatives; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry* / Q000627:therapeutic use; D011392:Proline / Q000031:analogs & derivatives; D011480:Protease Inhibitors / Q000737:chemistry* / Q000627:therapeutic use; D011485:Protein Binding; D011804:Quinolines; D013844:Thiazoles / Q000737:chemistry* / Q000627:therapeutic use; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000621:Aminoisobutyric Acids; D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; D007930:Leucine; D009842:Oligopeptides; D011392:Proline; D011480:Protease Inhibitors; D011804:Quinolines; 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; C455041:NS4A cofactor peptide, Hepatitis C virus; C552340:faldaprevir