1
|
Wypych RM, LaPlante SR, White PW, Martin SF. Structure-thermodynamics-relationships of hepatitis C viral NS3 protease inhibitors. Eur J Med Chem 2020; 192:112195. [PMID: 32151833 DOI: 10.1016/j.ejmech.2020.112195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
Thermodynamic parameters were determined for structurally-related inhibitors of HCV NS3 protease to assess how binding entropies and enthalpies vary with incremental changes at the P2 and P3 inhibitor subsites. Changing the heterocyclic substituent at P2 from a pyridyl to a 7-methoxy-2-phenyl-4-quinolyl group leads to a 710-fold increase in affinity. Annelating a benzene ring onto a pyridine ring leads to quinoline-derived inhibitors having higher affinities, but the individual enthalpy and entropy contributions are markedly different for each ligand pair. Introducing a phenyl group at C2 of the heterocyclic ring at P2 uniformly leads to higher affinity analogs with more favorable binding entropies, while adding a methoxy group at C7 of the quinoline ring at P2 provides derivatives with more favorable binding enthalpies. Significant enthalpy/entropy compensation is observed for structural changes made to inhibitors lacking a 2-phenyl substituent, whereas favorable changes in both binding enthalpies and entropies accompany structural modifications when a 2-phenyl group is present. Overall, binding energetics of inhibitors having a 2-phenyl-4-quinolyl group at P2 are dominated by entropic effects, whereas binding of the corresponding norphenyl analogs are primarily enthalpy driven. Notably, the reversal from an entropy driven association to an enthalpy driven one for this set of inhibitors also correlates with alternate binding modes. When the steric bulk of the side chain at P3 is increased from a hydrogen atom to a tert-butyl group, there is a 770-fold improvement in affinity. The 30-fold increase resulting from the first methyl group is solely the consequence of a more favorable change in entropy, whereas subsequent additions of methyl groups leads to modest increases in affinity that arise primarily from incremental improvements in binding enthalpies accompanied with smaller favorable entropic contributions.
Collapse
Affiliation(s)
- Rachel M Wypych
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA
| | - Steven R LaPlante
- Université du Québec, INRS-Centre Armand Frappier Santé et Biotechnologie, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
| | - Peter W White
- Boehringer Ingelheim (Canada) Limited, Research and Development, 2100 rue Cunard, Laval, Quebec, H7S 2G5, Canada
| | - Stephen F Martin
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA.
| |
Collapse
|
2
|
Rosenquist Å, Samuelsson B, Johansson PO, Cummings MD, Lenz O, Raboisson P, Simmen K, Vendeville S, de Kock H, Nilsson M, Horvath A, Kalmeijer R, de la Rosa G, Beumont-Mauviel M. Discovery and Development of Simeprevir (TMC435), a HCV NS3/4A Protease Inhibitor. J Med Chem 2014; 57:1673-93. [DOI: 10.1021/jm401507s] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Maxwell D. Cummings
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19002, United States
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Kenny Simmen
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Herman de Kock
- Galapagos NV Generaal De Wittelaan, L11A3-2800, Mechelen, Belgium
| | | | | | | | - Guy de la Rosa
- Janssen Global Services, LLC, Titusville, New Jersey 08560, United States
| | | |
Collapse
|
3
|
LaPlante SR, Padyana AK, Abeywardane A, Bonneau P, Cartier M, Coulombe R, Jakalian A, Wildeson-Jones J, Li X, Liang S, McKercher G, White P, Zhang Q, Taylor SJ. Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus. J Med Chem 2014; 57:2074-90. [DOI: 10.1021/jm401432c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Steven R. LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | - Pierre Bonneau
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Mireille Cartier
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - René Coulombe
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Araz Jakalian
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | | | - Ginette McKercher
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Peter White
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | |
Collapse
|
4
|
Aydin C, Mukherjee S, Hanson AM, Frick DN, Schiffer CA. The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities. Protein Sci 2013; 22:1786-98. [PMID: 24123290 DOI: 10.1002/pro.2378] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 12/15/2022]
Abstract
Hepatitis C (HCV) protein 3/4A (NS3/4A) is a bifunctional enzyme comprising two separate domains with protease and helicase activities, which are essential for viral propagation. Both domains are stable and have enzymatic activity separately, and the relevance and implications of having protease and helicase together as a single protein remains to be explored. Altered in vitro activities of isolated domains compared with the full-length NS3/4A protein suggest the existence of interdomain communication. The molecular mechanism and extent of this communication was investigated by probing the domain-domain interface observed in HCV NS3/4A crystal structures. We found in molecular dynamics simulations that the two domains of NS3/4A are dynamically coupled through the interface. Interestingly, mutations designed to disrupt this interface did not hinder the catalytic activities of either domain. In contrast, substrate cleavage and DNA unwinding by these mutants were mostly enhanced compared with the wild-type protein. Disrupting the interface did not significantly alter RNA unwinding activity; however, the full-length protein was more efficient in RNA unwinding than the isolated protease domain, suggesting a more direct role in RNA processing independent of the interface. Our findings suggest that HCV NS3/4A adopts an "extended" catalytically active conformation, and interface formation acts as a switch to regulate activity. We propose a unifying model connecting HCV NS3/4A conformational states and protease and helicase function, where interface formation and the dynamic interplay between the two enzymatic domains of HCV NS3/4A potentially modulate the protease and helicase activities in vivo.
Collapse
Affiliation(s)
- Cihan Aydin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | | | | | | | | |
Collapse
|
5
|
Abian O, Vega S, Sancho J, Velazquez-Campoy A. Allosteric inhibitors of the NS3 protease from the hepatitis C virus. PLoS One 2013; 8:e69773. [PMID: 23936097 PMCID: PMC3728351 DOI: 10.1371/journal.pone.0069773] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/15/2013] [Indexed: 12/14/2022] Open
Abstract
The nonstructural protein 3 (NS3) from the hepatitis C virus processes the non-structural region of the viral precursor polyprotein in infected hepatic cells. The NS3 protease activity has been considered a target for drug development since its identification two decades ago. Although specific inhibitors have been approved for clinical therapy very recently, resistance-associated mutations have already been reported for those drugs, compromising their long-term efficacy. Therefore, there is an urgent need for new anti-HCV agents with low susceptibility to resistance-associated mutations. Regarding NS3 protease, two strategies have been followed: competitive inhibitors blocking the active site and allosteric inhibitors blocking the binding of the accessory viral protein NS4A. In this work we exploit the intrinsic Zn+2-regulated plasticity of the protease to identify a new type of allosteric inhibitors. In the absence of Zn+2, the NS3 protease adopts a partially-folded inactive conformation. We found ligands binding to the Zn+2-free NS3 protease, trap the inactive protein, and block the viral life cycle. The efficacy of these compounds has been confirmed in replicon cell assays. Importantly, direct calorimetric assays reveal a low impact of known resistance-associated mutations, and enzymatic assays provide a direct evidence of their inhibitory activity. They constitute new low molecular-weight scaffolds for further optimization and provide several advantages: 1) new inhibition mechanism simultaneously blocking substrate and cofactor interactions in a non-competitive fashion, appropriate for combination therapy; 2) low impact of known resistance-associated mutations; 3) inhibition of NS4A binding, thus blocking its several effects on NS3 protease.
Collapse
Affiliation(s)
- Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- IIS Aragón, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- * E-mail: (OA); (AVC)
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Javier Sancho
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragon, Zaragoza, Spain
- * E-mail: (OA); (AVC)
| |
Collapse
|
6
|
Bilodeau F, Bailey MD, Bhardwaj PK, Bordeleau J, Forgione P, Garneau M, Ghiro E, Gorys V, Halmos T, Jolicoeur ES, Leblanc M, Lemke CT, Naud J, O’Meara J, White PW, Llinàs-Brunet M. Synthesis and optimization of a novel series of HCV NS3 protease inhibitors: 4-Arylproline analogs. Bioorg Med Chem Lett 2013; 23:4267-71. [DOI: 10.1016/j.bmcl.2013.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
|
7
|
Vega S, Neira JL, Marcuello C, Lostao A, Abian O, Velazquez-Campoy A. NS3 protease from hepatitis C virus: biophysical studies on an intrinsically disordered protein domain. Int J Mol Sci 2013; 14:13282-306. [PMID: 23803659 PMCID: PMC3742187 DOI: 10.3390/ijms140713282] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/04/2013] [Accepted: 06/13/2013] [Indexed: 12/14/2022] Open
Abstract
The nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors), suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially) disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data.
Collapse
Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
| | - Jose L. Neira
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- Institute of Molecular and Cell Biology, Miguel Hernandez University, Elche (Alicante) 03202, Spain
| | - Carlos Marcuello
- Advanced Microscopy Laboratory (LMA), Institute of Nanoscience of Aragon (INA), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (C.M.); (A.L.)
| | - Anabel Lostao
- Advanced Microscopy Laboratory (LMA), Institute of Nanoscience of Aragon (INA), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (C.M.); (A.L.)
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- IIS Aragon–Aragon Health Science Institute (I+CS), Zaragoza 50009, Spain
- Network Biomedical Research Center on Hepatic and Digestive Diseases (CIBERehd), Barcelona 08036, Spain
- Authors to whom correspondence should be addressed; E-Mails: (O.A.); (A.V.-C.); Tel.: +34-976-761-000 (ext. 5417) (O.A.); +34-976-762-996 (A.V.-C.); Fax: +34-976-762-990 (O.A. & A.V.-C.)
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
- Department of Biochemistry and Cellular and Molecular Biology, Faculty of Sciences, University of Zaragoza, Zaragoza 50009, Spain
- Authors to whom correspondence should be addressed; E-Mails: (O.A.); (A.V.-C.); Tel.: +34-976-761-000 (ext. 5417) (O.A.); +34-976-762-996 (A.V.-C.); Fax: +34-976-762-990 (O.A. & A.V.-C.)
| |
Collapse
|
8
|
Verga-Gérard A, Porcherot M, Meyniel-Schicklin L, André P, Lotteau V, Perrin-Cocon L. Hepatitis C virus/human interactome identifies SMURF2 and the viral protease as critical elements for the control of TGF-β signaling. FASEB J 2013; 27:4027-40. [PMID: 23781096 DOI: 10.1096/fj.13-229187] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
TGF-β signaling induces epithelial to mesenchymal transition (EMT) and plays an important role in hepatocellular carcinoma (HCC) development. Clinical observations indicate that hepatitis C virus (HCV) chronic infection, which is a major cause of HCC, induces TGF-β signaling perturbations. Here, we investigate the mechanisms by which HCV nonstructural proteins interfere with TGF-β signaling, in human hepatoma cell lines expressing HCV subgenomic replicon. A transcriptomic study showed that TGF-β stimulation of these cells resulted in a protumoral gene expression profile and in up-regulation of EMT-related genes compared to control interferon-treated cells not expressing HCV proteins. We found that the viral protease NS3-4A interacted with SMURF2, a negative regulator of TGF-β signaling. In cells expressing HCV subgenomic replicon or NS3-4A, TGF-β stimulation induced an increased expression of SMAD-dependent genes compared to control cells. This enhanced signaling was suppressed by SMURF2 overexpression and mimicked by SMURF2 silencing. In addition, NS3-4A expression resulted in an increased and prolonged TGF-β-induced phosphorylation of SMAD2/3 that was abrogated by SMURF2 overexpression. Neither NS3-4A protease activity nor SMURF2 ubiquitin-ligase activity was required to affect TGF-β signaling. Therefore, by targeting SMURF2, NS3-4A appears to block the negative regulation of TGF-β signaling, increasing the responsiveness of cells to TGF-β.
Collapse
Affiliation(s)
- Amandine Verga-Gérard
- 1Centre International de Recherche en Infectiologie, INSERM U1111, 21 av. Tony Garnier, F-69007 Lyon, France.
| | | | | | | | | | | |
Collapse
|
9
|
McCauley JA, Rudd MT, Liverton NJ. HCV NS3/4a Protease Inhibitors: Simeprevir (TMC‐435350), Vaniprevir (MK‐7009) and MK‐5172. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hepatitis C virus (HCV) infection continues to represent a major health issue, with estimates of 130–170 million people infected worldwide. Recent developments in the HCV NS3/4a protease inhibitor area have significantly improved treatment options for patients. However, a more dramatic paradigm shift in the treatment of HCV infection appears all but certain in coming years, with a move to all oral combination therapy with direct‐acting antivirals (DAAs). HCV protease inhibitors have the potential to play a significant role in these DAA combination therapies. This chapter discusses in detail the design and discovery of three HCV NS3/4a protease inhibitors in clinical development: simeprevir (TMC‐435350), vaniprevir (MK‐7009) and MK‐5172.
Collapse
Affiliation(s)
- John A. McCauley
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
| | - Michael T. Rudd
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
| | - Nigel J. Liverton
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
| |
Collapse
|
10
|
O'Meara JA, Lemke CT, Godbout C, Kukolj G, Lagacé L, Moreau B, Thibeault D, White PW, Llinàs-Brunet M. Molecular mechanism by which a potent hepatitis C virus NS3-NS4A protease inhibitor overcomes emergence of resistance. J Biol Chem 2012; 288:5673-81. [PMID: 23271737 DOI: 10.1074/jbc.m112.439455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although optimizing the resistance profile of an inhibitor can be challenging, it is potentially important for improving the long term effectiveness of antiviral therapy. This work describes our rational approach toward the identification of a macrocyclic acylsulfonamide that is a potent inhibitor of the NS3-NS4A proteases of all hepatitis C virus genotypes and of a panel of genotype 1-resistant variants. The enhanced potency of this compound versus variants D168V and R155K facilitated x-ray determination of the inhibitor-variant complexes. In turn, these structural studies revealed a complex molecular basis of resistance and rationalized how such compounds are able to circumvent these mechanisms.
Collapse
Affiliation(s)
- Jeff A O'Meara
- Boehringer Ingelheim (Canada) Limited, Research and Development, Laval, Quebec H7S 2G5, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Saalau-Bethell SM, Woodhead AJ, Chessari G, Carr MG, Coyle J, Graham B, Hiscock SD, Murray CW, Pathuri P, Rich SJ, Richardson CJ, Williams PA, Jhoti H. Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function. Nat Chem Biol 2012; 8:920-5. [PMID: 23023261 PMCID: PMC3480716 DOI: 10.1038/nchembio.1081] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/23/2012] [Indexed: 01/23/2023]
Abstract
Here we report a highly conserved new binding site located at the interface between the protease and helicase domains of the hepatitis C virus (HCV) NS3 protein. Using a chemical lead, identified by fragment screening and structure-guided design, we demonstrate that this site has a regulatory function on the protease activity via an allosteric mechanism. We propose that compounds binding at this allosteric site inhibit the function of the NS3 protein by stabilizing an inactive conformation and thus represent a new class of direct-acting antiviral agents.
Collapse
|
12
|
Schultz B, Yang H, Delaney WE. Biochemical evaluation of HCV NS3 protease inhibitors. ACTA ACUST UNITED AC 2012; Chapter 13:Unit13B.7. [PMID: 21898332 DOI: 10.1002/0471141755.ph13b07s54] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes assays for characterizing the potency and mechanism of action of NS3 protease inhibitors. Determination of IC(50) values is described using in vitro expressed and purified NS3 protease. This assay can also be used for the rapid exploration of structure-activity relationships. Another protocol describes using the full-length NS3/4A complexes expressed in HCV replicon cell lines for a rapid alternative method for assessing protease activity without requiring conventional protein expression and purification. A method is then provided for determination of inhibitor K(i), which more accurately assesses the potency of inhibitors compared to the IC(50) assay, particularly for potent inhibitors that reach the sensitivity limit for the basic IC(50) assay. The final protocol describes how to determine the reversibility of inhibitor binding to the enzyme, an important parameter that can affect the pharmacodynamic properties of a compound.
Collapse
|
13
|
A macrocyclic HCV NS3/4A protease inhibitor interacts with protease and helicase residues in the complex with its full-length target. Proc Natl Acad Sci U S A 2011; 108:21052-6. [PMID: 22160684 DOI: 10.1073/pnas.1110534108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV NS3 protein is essential for viral polyprotein processing and RNA replication and hence viral replication. It is composed of an N-terminal serine protease domain and a C-terminal helicase/NTPase domain. For full activity, the protease requires the NS4A protein as a cofactor. HCV NS3/4A protease is a prime target for developing direct-acting antiviral agents. First-generation NS3/4A protease inhibitors have recently been introduced into clinical practice, markedly changing HCV treatment options. To date, crystal structures of HCV NS3/4A protease inhibitors have only been reported in complex with the protease domain alone. Here, we present a unique structure of an inhibitor bound to the full-length, bifunctional protease-helicase NS3/4A and show that parts of the P4 capping and P2 moieties of the inhibitor interact with both protease and helicase residues. The structure sheds light on inhibitor binding to the more physiologically relevant form of the enzyme and supports exploring inhibitor-helicase interactions in the design of the next generation of HCV NS3/4A protease inhibitors. In addition, small angle X-ray scattering confirmed the observed protease-helicase domain assembly in solution.
Collapse
|
14
|
Takaya D, Yamashita A, Kamijo K, Gomi J, Ito M, Maekawa S, Enomoto N, Sakamoto N, Watanabe Y, Arai R, Umeyama H, Honma T, Matsumoto T, Yokoyama S. A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors. Bioorg Med Chem 2011; 19:6892-905. [PMID: 21992802 DOI: 10.1016/j.bmc.2011.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/12/2011] [Accepted: 09/12/2011] [Indexed: 01/09/2023]
Abstract
Hepatitis C virus (HCV) is an etiologic agent of chronic liver disease, and approximately 170 million people worldwide are infected with the virus. HCV NS3-4A serine protease is essential for the replication of this virus, and thus has been investigated as an attractive target for anti-HCV drugs. In this study, we developed our new induced-fit docking program (genius), and applied it to the discovery of a new class of NS3-4A protease inhibitors (IC(50)=1-10 μM including high selectivity index). The new inhibitors thus identified were modified, based on the docking models, and revealed preliminary structure-activity relationships. Moreover, the genius in silico screening performance was validated by using an enrichment factor. We believe our designed scaffold could contribute to the improvement of HCV chemotherapy.
Collapse
Affiliation(s)
- Daisuke Takaya
- RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Lemke CT, Goudreau N, Zhao S, Hucke O, Thibeault D, Llinàs-Brunet M, White PW. Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335. J Biol Chem 2011; 286:11434-43. [PMID: 21270126 PMCID: PMC3064199 DOI: 10.1074/jbc.m110.211417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/17/2011] [Indexed: 11/06/2022] Open
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.
Collapse
Affiliation(s)
- Christopher T Lemke
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada.
| | | | | | | | | | | | | |
Collapse
|
16
|
Cummings MD, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist A, Samuelsson B, Raboisson P, Simmen K. Induced-fit binding of the macrocyclic noncovalent inhibitor TMC435 to its HCV NS3/NS4A protease target. Angew Chem Int Ed Engl 2010; 49:1652-5. [PMID: 20166108 DOI: 10.1002/anie.200906696] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
17
|
Cummings M, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist Å, Samuelsson B, Raboisson P, Simmen K. Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
18
|
Massariol MJ, Zhao S, Marquis M, Thibeault D, White PW. Protease and helicase activities of hepatitis C virus genotype 4, 5, and 6 NS3-NS4A proteins. Biochem Biophys Res Commun 2009; 391:692-7. [PMID: 19944069 DOI: 10.1016/j.bbrc.2009.11.122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 11/19/2009] [Indexed: 02/05/2023]
Abstract
The bifunctional NS3 protease-helicase of hepatitis C virus (HCV), together with its cofactor protein NS4A, is an important target for antiviral drugs which can cure HCV infections. HCV strains are divided into six major genotypes based on sequence diversity, and the great majority of reports on NS3 have focused exclusively on genotype 1 proteins. Here we report the cloning, expression, and preliminary characterization of NS3-NS4A gene products from HCV genotypes 4, 5, and 6. This work complements our earlier characterization of genotype 2 and 3 proteins [17]. We compare NS3-NS4A protease and helicase activities of genotypes 4a, 5a, and 6a to those of common reference strains Con1 (genotype 1b) and JFH1 (genotype 2a). The specific activities of the proteases of the newly isolated proteins were similar to those of the reference proteins. Furthermore, the reference inhibitor BILN 2061 had similar activity against all of the proteins except for that of JFH1, which had an apparent K(i) that was 11-fold higher relative to Con1. RNA and DNA unwinding activities were also similar for genotypes 1, 4, 5, and 6 proteins, but significantly higher for genotype 2 JFH1. With the availability of these proteins, inhibitors developed based on their activity against genotype 1 can be tested against all the other major genotypes, providing a path to improved treatment for all HCV patients.
Collapse
Affiliation(s)
- Marie-Josée Massariol
- Boehringer Ingelheim (Canada) Ltd, Department of Biological Sciences, 2100 Cunard St, Laval, QC, Canada
| | | | | | | | | |
Collapse
|
19
|
Dahl G, Arenas OG, Danielson UH. Hepatitis C Virus NS3 Protease Is Activated by Low Concentrations of Protease Inhibitors. Biochemistry 2009; 48:11592-602. [DOI: 10.1021/bi9016928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Göran Dahl
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
| | - Omar Gutiérrez Arenas
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
| | - U. Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
| |
Collapse
|
20
|
Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol 2009; 83:12895-906. [PMID: 19793813 DOI: 10.1128/jvi.00942-09] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The flavivirus genome comprises a single strand of positive-sense RNA, which is translated into a polyprotein and cleaved by a combination of viral and host proteases to yield functional proteins. One of these, nonstructural protein 3 (NS3), is an enzyme with both serine protease and NTPase/helicase activities. NS3 plays a central role in the flavivirus life cycle: the NS3 N-terminal serine protease together with its essential cofactor NS2B is involved in the processing of the polyprotein, whereas the NS3 C-terminal NTPase/helicase is responsible for ATP-dependent RNA strand separation during replication. An unresolved question remains regarding why NS3 appears to encode two apparently disconnected functionalities within one protein. Here we report the 2.75-A-resolution crystal structure of full-length Murray Valley encephalitis virus NS3 fused with the protease activation peptide of NS2B. The biochemical characterization of this construct suggests that the protease has little influence on the helicase activity and vice versa. This finding is in agreement with the structural data, revealing a single protein with two essentially segregated globular domains. Comparison of the structure with that of dengue virus type 4 NS2B-NS3 reveals a relative orientation of the two domains that is radically different between the two structures. Our analysis suggests that the relative domain-domain orientation in NS3 is highly variable and dictated by a flexible interdomain linker. The possible implications of this conformational flexibility for the function of NS3 are discussed.
Collapse
|