1
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Martino SD, Petri GL, De Rosa M. Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn? J Med Chem 2024; 67:885-921. [PMID: 38179950 DOI: 10.1021/acs.jmedchem.3c01971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.
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Affiliation(s)
- Simona Di Martino
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Giovanna Li Petri
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Maria De Rosa
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
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2
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Del Rosario García-Lozano M, Dragoni F, Gallego P, Mazzotta S, López-Gómez A, Boccuto A, Martínez-Cortés C, Rodríguez-Martínez A, Pérez-Sánchez H, Manuel Vega-Pérez J, Antonio Del Campo J, Vicenti I, Vega-Holm M, Iglesias-Guerra F. Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses. Bioorg Chem 2023; 133:106408. [PMID: 36801791 DOI: 10.1016/j.bioorg.2023.106408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC50) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC50 6.6 µM and 1.9 µM respectively) and DENV (IC50 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.
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Affiliation(s)
- María Del Rosario García-Lozano
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; SeLiver Group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital CSIC University of Seville, Seville, Spain
| | - Filippo Dragoni
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy
| | - Paloma Gallego
- Unit for Clinical Management of Digestive Diseases and CIBERehd, Valme University Hospital, 41014 Seville, Spain
| | - Sarah Mazzotta
- Department of Chemistry, University of Milan, 20133 Milan, Italy
| | - Alejandro López-Gómez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | - Adele Boccuto
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy; VisMederi Research srl, Siena, Italy
| | - Carlos Martínez-Cortés
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - Alejandro Rodríguez-Martínez
- Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva sn, 18071 Granada, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy.
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
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3
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Lin HY, Chang SY, Teng HH, Wu HJ, Li HY, Cheng CC, Chuang CK, Lin HY, Lin SP, Cheng WC. Discovery of small-molecule protein stabilizers toward exogenous alpha-l-iduronidase to reduce the accumulated heparan sulfate in mucopolysaccharidosis type I cells. Eur J Med Chem 2023; 247:115005. [PMID: 36563498 DOI: 10.1016/j.ejmech.2022.115005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/16/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
Synthesis of a series of l-iduronic acid (IdoA)- and imino-IdoA-typed C-glycosides for modulating α-l-iduronidase (IDUA) activity is described. In an enzyme inhibition study, IdoA-typed C-glycosides were more potent than imino-IdoA analogs, with the most potent IdoA-typed C-glycoside 27c showing an IC50 value of 1 μM. On the other hand, co-treatment of 12 with rh-α-IDUA in mucopolysaccharidosis type I (MPS I) fibroblasts exhibited a nearly 3-fold increase of the IDUA activity, resulting in a clear reduction of the accumulated heparan sulfate (HS) compared to the exogenous enzyme treatment alone. This is the first report of small molecules facilitating IDUA stabilization, enhancing enzyme activity, and reducing accumulated HS in MPS I cell-based assays, which reveals that small molecules as rh-α-IDUA stabilizers to improve enzyme replacement therapy (ERT) efficacy toward MPS I is feasible and promising.
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Affiliation(s)
- Hung-Yi Lin
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Shih-Ying Chang
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Hsuan-Hsuan Teng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Hsi-Ju Wu
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Huang-Yi Li
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Chia-Chun Cheng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Chih-Kuang Chuang
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan
| | - Hsiang-Yu Lin
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan; Department of Pediatrics and Rare Disease Center, MacKay Memorial Hospital, Taipei, 10449, Taiwan
| | - Shuan-Pei Lin
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan; Department of Pediatrics and Rare Disease Center, MacKay Memorial Hospital, Taipei, 10449, Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan; Department of Chemistry, National Cheng Kung University, Tainan City, 701, Taiwan.
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4
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Wan H, Aravamuthan V, Pearlstein RA. Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory. ACS Pharmacol Transl Sci 2020; 3:1111-1143. [PMID: 33330838 PMCID: PMC7671103 DOI: 10.1021/acsptsci.0c00089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/01/2023]
Abstract
![]()
The
SARS-CoV-2 main protease (Mpro) is of major interest
as an antiviral drug target. Structure-based virtual screening efforts,
fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2
Mpro crystal structures, are underway in many laboratories.
However, little is known about the dynamic enzyme mechanism, which
is needed to inform both assay development and structure-based inhibitor
design. Here, we apply biodynamics theory to characterize the structural
dynamics of substrate-induced Mpro activation under nonequilibrium conditions. The catalytic cycle
is governed by concerted dynamic structural
rearrangements of domain 3 and the m-shaped loop (residues 132–147)
on which Cys145 (comprising the thiolate nucleophile and half of the
oxyanion hole) and Gly143 (comprising the second half of the oxyanion
hole) reside. In particular, we observed the following: (1) Domain
3 undergoes dynamic rigid-body rotation about the domain 2–3
linker, alternately visiting two primary conformational states (denoted
as M1pro ↔
M2pro); (2)
The Gly143-containing crest of the m-shaped loop undergoes up and
down translations caused by conformational changes within the rising
stem of the loop (Lys137–Asn142) in response to domain 3 rotation
and dimerization (denoted as M1/downpro ↔ 2·M2/uppro) (noting that the Cys145-containing
crest is fixed in the up position). We propose that substrates associate
to the M1/downpro state, which promotes the M2/downpro state, dimerization (denoted as 2·M2/uppro–substrate),
and catalysis. Here, we explore the state transitions of Mpro under nonequilibrium conditions, the mechanisms by which they are
powered, and the implications thereof for efficacious inhibition under in vivo conditions.
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Affiliation(s)
- Hongbin Wan
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vibhas Aravamuthan
- Vibhas Aravamuthan - NIBR Informatics, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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5
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Agback P, Woestenenk E, Agback T. Probing contacts of inhibitor locked in transition states in the catalytic triad of DENV2 type serine protease and its mutants by 1H, 19F and 15 N NMR spectroscopy. BMC Mol Cell Biol 2020; 21:38. [PMID: 32450796 PMCID: PMC7249419 DOI: 10.1186/s12860-020-00283-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/11/2020] [Indexed: 11/25/2022] Open
Abstract
Background Detailed structural knowledge of enzyme-inhibitor complexes trapped in intermediate state is the key for a fundamental understanding of reaction mechanisms taking place in enzymes and is indispensable as a structure-guided drug design tool. Solution state NMR uniquely allows the study of active sites of enzymes in equilibrium between different tautomeric forms. In this study 1H, 19F and 15 N NMR spectroscopy has been used to probe the interaction contacts of inhibitors locked in transition states of the catalytic triad of a serine protease. It was demonstrated on the serotype II Dengue virus NS2B:NS3pro serine protease and its mutants, H51N and S135A, in complex with high-affinity ligands containing trifluoromethyl ketone (tfk) and boronic groups in the C-terminal of tetra-peptides. Results Monitoring 19F resonances, shows that only one of the two isomers of the tfk tetra-peptide binds with NS2B:NS3pro and that access to the bulk of the active site is limited. Moreover, there were no bound water found in proximity of the active site for any of the ligands manifesting in a favorable condition for formation of low barrier hydrogen bonds (LBHB) in the catalytic triad. Based on this data we were able to identify a locked conformation of the protein active site. The data also indicates that the different parts of the binding site most likely act independently of each other. Conclusions Our reported findings increases the knowledge of the detailed function of the catalytic triad in serine proteases and could facilitate the development of rational structure based inhibitors that can selectively target the NS3 protease of Dengue type II (DENV2) virus. In addition the results shows the usefulness of probing active sites using 19F NMR spectroscopy.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
| | - Esmeralda Woestenenk
- Protein Expression and Characterization Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
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6
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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.
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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.
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7
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In Silico Screening for Potent Anti-HCV Compounds with Inhibitory Activities Toward the NS3/4A Protease. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9750-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Li HY, Lee JD, Chen CW, Sun YC, Cheng WC. Synthesis of (3S,4S,5S)-trihydroxylpiperidine derivatives as enzyme stabilizers to improve therapeutic enzyme activity in Fabry patient cell lines. Eur J Med Chem 2018; 144:626-634. [PMID: 29289886 DOI: 10.1016/j.ejmech.2017.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
A series of 3S,4S,5S-trihydroxylated piperidines bearing structural diversity at C-2 or C-6 positions has been synthesized and tested to determine their ability to stabilize the activity of recombinant human α-Galactosidase A (rh-α-Gal A). Hit molecules were identified by rapid inhibitory activity screening, and then further investigated for their ability to protect this enzyme from thermo-induced denaturation and enhance its activity in Fabry patient cell lines. Our study resulted in the identification of a new class of small molecules as enzyme stabilizers for the potential treatment of Fabry disease. Of these, stabilizer 21 was the most effective, showing a 12-fold increase in rh-α-Gal A activity in Fabry disease cell lines.
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Affiliation(s)
- Huang-Yi Li
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 115, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, 155, Linong Street, Section 2, Taipei 112, Taiwan
| | - Jay-Der Lee
- Department of Chemistry, National Taiwan Normal University, 162, Section 1, Heping East Road, Taipei 106, Taiwan
| | - Chiao-Wen Chen
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Ying-Chieh Sun
- Department of Chemistry, National Taiwan Normal University, 162, Section 1, Heping East Road, Taipei 106, Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, National Cheng-Kung University, 1, University Road, Tainan 701, Taiwan.
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9
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Cheng WC, Lin CK, Li HY, Chang YC, Lu SJ, Chen YS, Chang SY. A combinatorial approach towards the synthesis of non-hydrolysable triazole–iduronic acid hybrid inhibitors of human α-l-iduronidase: discovery of enzyme stabilizers for the potential treatment of MPSI. Chem Commun (Camb) 2018; 54:2647-2650. [DOI: 10.1039/c7cc09642a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis and bioevaluation of substituent-diverse triazole–iduronic acid hybrid molecules are highlighted.
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Affiliation(s)
- Wei-Chieh Cheng
- Genomics Research Center
- Academia Sinica
- Taipei
- Taiwan
- Department of Chemistry
| | | | - Huang-Yi Li
- Department of Life Sciences and Institute of Genome Sciences
- National Yang-Ming University
- Taipei
- Taiwan
| | - Yu-Chien Chang
- Department of Chemistry
- National Cheng Kung University
- Tainan City
- Taiwan
| | | | - Yu-Shin Chen
- Genomics Research Center
- Academia Sinica
- Taipei
- Taiwan
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10
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Hamad HA, Thurston J, Teague T, Ackad E, Yousef MS. The NS4A Cofactor Dependent Enhancement of HCV NS3 Protease Activity Correlates with a 4D Geometrical Measure of the Catalytic Triad Region. PLoS One 2016; 11:e0168002. [PMID: 27936126 PMCID: PMC5148068 DOI: 10.1371/journal.pone.0168002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022] Open
Abstract
We are developing a 4D computational methodology, based on 3D structure modeling and molecular dynamics simulation, to analyze the active site of HCV NS3 proteases, in relation to their catalytic activity. In our previous work, the 4D analyses of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) yielded divergent, gradual and genotype-dependent, 4D conformational instability measures, which strongly correlate with the known disparate catalytic activities among genotypes. Here, the correlation of our 4D geometrical measure is extended to intra-genotypic alterations in NS3 protease activity, due to sequence variations in the NS4A activating cofactor. The correlation between the 4D measure and the enzymatic activity is qualitatively evident, which further validates our methodology, leading to the development of an accurate quantitative metric to predict protease activity in silico. The results suggest plausible “communication” pathways for conformational propagation from the activation subunit (the NS4A cofactor binding site) to the catalytic subunit (the catalytic triad). The results also strongly suggest that the well-sampled (via convergence quantification) structural dynamics are more connected to the divergent catalytic activity observed in HCV NS3 proteases than to rigid structures. The method could also be applicable to predict patients’ responses to interferon therapy and better understand the innate interferon activation pathway.
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Affiliation(s)
- Hamzah A. Hamad
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Jeremy Thurston
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Thomas Teague
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Edward Ackad
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Mohammad S. Yousef
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- * E-mail:
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11
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Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
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12
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Parsy C, Alexandre FR, Brandt G, Caillet C, Cappelle S, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos L, Leroy F, Liuzzi M, Loi AG, Moulat L, Musiu C, Rahali H, Roques V, Seifer M, Standring D, Surleraux D. Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease. Bioorg Med Chem Lett 2014; 24:4444-4449. [DOI: 10.1016/j.bmcl.2014.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 10/24/2022]
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13
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Hotiana HA, Haider MK. Structural modeling of HCV NS3/4A serine protease drug-resistance mutations using end-point continuum solvation and side-chain flexibility calculations. J Chem Inf Model 2013; 53:435-51. [PMID: 23305404 DOI: 10.1021/ci3004754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational methods of modeling protein-ligand interactions have gained widespread application in modern drug discovery. In continuum solvation-based methods of binding affinity estimation, limited description of solvent environment and protein flexibility is traded for a time scale that fits medicinal chemistry test cycles. The results of this speed-accuracy trade-off have been promising in terms of modeling structure-activity relationships of ligand series against protein targets. The potential of these approaches in recapitulating structural and energetic effects of resistance mutations, which involve large changes in binding affinity, remains relatively unexplored. We used continuum solvation binding affinity predictions and graph theory-based flexibility calculations to model thirteen drug resistance mutations in HCV NS3/4A serine protease, against three small-molecule inhibitors, with a 2-fold objective: quantitative assessment of binding energy predictions against experimental data and elucidation of structural/energetic determinants of resistance. The results show statistically significant correlation between predicted and experimental binding affinities, with R(2) and predictive index of up to 0.83 and 0.91, respectively. The level of accuracy was consistent with what has been reported for the inverse problem of binding affinity estimation of congeneric ligands against the same target. The quality of predictions was poor for mutations involving induced-fit effects, primarily, because of the lack of entropy terms. Flexibility analysis explained this discrepancy by indicating characteristic changes in side-chain mobility of a key binding site residue. The combined results from two approaches provide novel insights regarding the molecular mechanism of resistance. NS3/4A inhibitors, with large P2 substituents, derive high affinity with optimal van der Waals interactions in the S2 subsite, in order to overcome unfavorable desolvation and entropic cost of induced-fit effects. High-level resistance mutations tend to increase the desolvation and/or entropic barrier to ligand binding. The lead optimization strategies should, therefore, address the balance of these opposing energetic contributions in both the wild-type and mutant target.
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Affiliation(s)
- Hajira Ahmed Hotiana
- Undergraduate Program in Science, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
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14
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Alaee M, Rajabi P, Sharifi Z, Farajollahi MM. Immunoreactivity assessment of hepatitis C virus NS3 protease and NS5A proteins expressed in TOPO cloning system. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2012; 47:282-91. [PMID: 23040046 DOI: 10.1016/j.jmii.2012.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/30/2012] [Accepted: 08/09/2012] [Indexed: 01/29/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is a major cause of acute and chronic liver disease. Numerous screening assays based on the detection of immunoresponses to HCV structural and nonstructural proteins have been designed. Various studies have demonstrated genotype-specific differences in anti-HCV antibody responses to different HCV proteins. METHODS Full-length NS3 protease and N-terminally truncated NS5A were expressed using pET TOPO 102/D system. Antigenicity of the purified recombinant proteins was assessed by immunoblotting and indirect enzyme-linked immunosorbent assay (ELISA). Furthermore, anti-HCV antibody responses to the recombinant proteins were evaluated in three prevalent genotypes in Iran. RESULTS We were able to express and purify NS5A and NS3 protease using TOPO cloning system. The HCV NS3 protease and NS5A produced in BL21 Star (DE3) was immunoreactive. Our results demonstrate that NS3 protease and NS5A have good immunoreactivity, but they are not sufficient for detecting all HCV-positive sera. No significant genotype-specific differences were detected in immunoresponses to the recombinant proteins. CONCLUSION In conclusion, we successfully isolated, expressed, and purified substantial amount of HCV NS3 protease and N-terminally truncated NS5A, and used them as capturing antigens in a screening ELISA assay with high sensitivity, reproducibility, and specificity. Accordingly, it is well confirmed that TOPO cloning system can be used as a dynamic system in order to express higher amount of immunoreactive viral proteins.
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Affiliation(s)
- Mahsa Alaee
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Peyman Rajabi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Zohreh Sharifi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mohammad Morad Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
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15
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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.
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Affiliation(s)
- Daisuke Takaya
- RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan
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16
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Zhu H, Briggs JM. Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease. Proteins 2011; 79:2428-43. [DOI: 10.1002/prot.23064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 04/01/2011] [Accepted: 04/19/2011] [Indexed: 11/11/2022]
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17
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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.
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Affiliation(s)
- Christopher T Lemke
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada.
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18
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Gallo M, Bottomley MJ, Pennestri M, Eliseo T, Paci M, Koch U, Bazzo R, Summa V, Carfì A, Cicero DO. Structural characterization of the Hepatitis C Virus NS3 protease from genotype 3a: The basis of the genotype 1b vs. 3a inhibitor potency shift. Virology 2010; 405:424-38. [DOI: 10.1016/j.virol.2010.05.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 04/30/2010] [Accepted: 05/26/2010] [Indexed: 11/25/2022]
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19
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Rodríguez A, Oliva C, González M. A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B. Phys Chem Chem Phys 2010; 12:8001-15. [PMID: 20520921 DOI: 10.1039/c002116d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The reaction mechanism of the NS3/NS4A protease with the NS4B/5A and NS4A/4B natural substrates has been investigated using the QM/MM (quantum mechanics/molecular mechanics) approach, and some calculations have been performed on the reaction with the NS5A/5B natural substrate. This study widely extends a previous contribution of our group on the reaction mechanism with the NS5A/5B substrate, the main goal here being to understand the differences found between the reaction mechanism of each natural substrate and the role played by the enzymatic residues in the catalytic cycle. This knowledge will ultimately help in developing new NS3/NS4A protease inhibitors. The two first steps of the mechanism have been considered: Acylation and breaking of the peptide bond, with emphasis on the former one (rate limiting process). Energy and free energy profiles for both steps have been calculated at the AM1/MM level and corrected by means of MP2 ab initio calculations, being evident the importance of correlation energy. Acylation is the rate limiting step in all cases and occurs through a tetracoordinated intermediate, as previously suggested for other serine proteases. Specificities in the NS4B/5A mechanism can be attributed to the presence of a Proline residue in the substrate P2 position. The analysis of structures and energies confirm the importance of the oxyanion hole in the electrostatic stabilization of the tetracoordinated intermediate. Finally, the role of other residues, e.g., Arg-155 and Asp-79, has been explained, and the viability of Arg-155 mutants and its resistance to some protease inhibitors has been understood thanks to virtual mutation studies.
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Affiliation(s)
- Alejandro Rodríguez
- Departament de Química Física i IQTC, Universitat de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain
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20
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Geitmann M, Dahl G, Danielson UH. Mechanistic and kinetic characterization of hepatitis C virus NS3 protein interactions with NS4A and protease inhibitors. J Mol Recognit 2010; 24:60-70. [DOI: 10.1002/jmr.1023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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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
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22
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Gallo M, Pennestri M, Bottomley MJ, Barbato G, Eliseo T, Paci M, Narjes F, De Francesco R, Summa V, Koch U, Bazzo R, Cicero DO. Binding of a Noncovalent Inhibitor Exploiting the S′ region Stabilizes the Hepatitis C virus NS3 Protease Conformation in the Absence of Cofactor. J Mol Biol 2009; 385:1142-55. [DOI: 10.1016/j.jmb.2008.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/17/2008] [Accepted: 11/12/2008] [Indexed: 12/09/2022]
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23
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Bandyopadhyay D, Mehler EL. Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment. Proteins 2008; 72:646-59. [PMID: 18247345 DOI: 10.1002/prot.21958] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A general method has been developed to characterize the hydrophobicity or hydrophilicity of the microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating a quantitative property descriptor (QPD) based on the relative (to water) hydrophobicity of the MENV. Values of the QPD were calculated for a test set of 733 proteins to analyze the modulating effects on amino acid residue properties by the MENV in which they are imbedded. The QPD values and solvent accessibility were used to derive a partitioning of residues based on the MENV hydrophobicities. From this partitioning, a new hydrophobicity scale was developed, entirely in the context of protein structure, where amino acid residues are immersed in one or more "MENVpockets." Thus, the partitioning is based on the residues "sampling" a large number of "solvents" (MENVs) that represent a very large range of hydrophobicity values. It was found that the hydrophobicity of around 80% of amino acid side chains and their MENV are complementary to each other, but for about 20%, the MENV and their imbedded residue can be considered as mismatched. Many of these mismatches could be rationalized in terms of the structural stability of the protein and/or the involvement of the imbedded residue in function. The analysis also indicated a remarkable conservation of local environments around highly conserved active site residues that have similar functions across protein families, but where members have relatively low sequence homology. Thus, quantitative evaluation of this QPD is suggested, here, as a tool for structure-function prediction, analysis, and parameter development for the calculation of properties in proteins.
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Affiliation(s)
- Debashree Bandyopadhyay
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA
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24
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Morillas M, Eberl H, Allain FT, Glockshuber R, Kuennemann E. Novel Enzymatic Activity Derived from the Semliki Forest Virus Capsid Protein. J Mol Biol 2008; 376:721-35. [DOI: 10.1016/j.jmb.2007.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 11/13/2007] [Accepted: 11/16/2007] [Indexed: 10/22/2022]
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25
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Bäck M, Johansson PO, Wångsell F, Thorstensson F, Kvarnström I, Ayesa S, Wähling H, Pelcman M, Jansson K, Lindström S, Wallberg H, Classon B, Rydergård C, Vrang L, Hamelink E, Hallberg A, Rosenquist S, Samuelsson B. Novel potent macrocyclic inhibitors of the hepatitis C virus NS3 protease: Use of cyclopentane and cyclopentene P2-motifs. Bioorg Med Chem 2007; 15:7184-202. [PMID: 17845856 DOI: 10.1016/j.bmc.2007.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 07/02/2007] [Accepted: 07/06/2007] [Indexed: 01/23/2023]
Abstract
Several highly potent novel HCV NS3 protease inhibitors have been developed from two inhibitor series containing either a P2 trisubstituted macrocyclic cyclopentane- or a P2 cyclopentene dicarboxylic acid moiety as surrogates for the widely used N-acyl-(4R)-hydroxyproline in the P2 position. These inhibitors were optimized for anti HCV activities through examination of different ring sizes in the macrocyclic systems and further by exploring the effect of P4 substituent removal on potency. The target molecules were synthesized from readily available starting materials, furnishing the inhibitor compounds in good overall yields. It was found that the 14-membered ring system was the most potent in these two series and that the corresponding 13-, 15-, and 16-membered macrocyclic rings delivered less potent inhibitors. Moreover, the corresponding P1 acylsulfonamides had superior potencies over the corresponding P1 carboxylic acids. It is noteworthy that it has been possible to develop highly potent HCV protease inhibitors that altogether lack the P4 substituent. Thus the most potent inhibitor described in this work, inhibitor 20, displays a K(i) value of 0.41 nM and an EC(50) value of 9 nM in the subgenomic HCV replicon cell model on genotype 1b. To the best of our knowledge this is the first example described in the literature of a HCV protease inhibitor displaying high potency in the replicon assay and lacking the P4 substituent, a finding which should facilitate the development of orally active small molecule inhibitors against the HCV protease.
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Affiliation(s)
- Marcus Bäck
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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26
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Oliva C, Rodríguez A, González M, Yang W. A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate. Proteins 2007; 66:444-55. [PMID: 17094110 DOI: 10.1002/prot.21190] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics and molecular mechanics (QM/MM) calculations were carried out to characterize the reaction mechanism of the NS3 protease with its preferred substrate (NS5A/5B). The main purpose of this study was to locate the barrier states and intermediates along the distinguished coordinate path (DCP) involved in this process. These structures, and in particular the one corresponding to the first barrier state and intermediate (B1 and I1), could be a starting point for the synthesis of inhibitors of this protease, which could be used to treat hepatitis C. The two first steps of the reaction mechanism were studied, i.e., the acylation step and the breaking of the peptide bond. The first step takes place through a tetracoordinated intermediate, as suggested from previous works on other Serine proteases. The importance of the different amino acid residues was also considered (perturbation study where the MM charges of each residue were set to zero independently). The residues of the oxyanion hole were confirmed as the most important for the electrostatic stabilization of the tetracoordinate intermediate. Moreover, the role of other residues, e.g., Arg-155 and Asp-79, was also explained.
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Affiliation(s)
- Carolina Oliva
- Departament de Química Física i Centre de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/ Martí i Franquès 1, 08028 Barcelona, Spain.
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27
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Thorstensson F, Wångsell F, Kvarnström I, Vrang L, Hamelink E, Jansson K, Hallberg A, Rosenquist S, Samuelsson B. Synthesis of novel potent hepatitis C virus NS3 protease inhibitors: Discovery of 4-hydroxy-cyclopent-2-ene-1,2-dicarboxylic acid as a N-acyl-l-hydroxyproline bioisostere. Bioorg Med Chem 2007; 15:827-38. [PMID: 17107807 DOI: 10.1016/j.bmc.2006.10.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 10/17/2006] [Accepted: 10/23/2006] [Indexed: 11/22/2022]
Abstract
Potent tetrapeptidic inhibitors of the HCV NS3 protease have been developed incorporating 4-hydroxy-cyclopent-2-ene-1,2-dicarboxylic acid as a new N-acyl-l-hydroxyproline mimic. The hydroxycyclopentene template was synthesized in eight steps from commercially available (syn)-tetrahydrophthalic anhydride. Three different amino acids were explored in the P1-position and in the P2-position the hydroxyl group of the cyclopentene template was substituted with 7-methoxy-2-phenyl-quinolin-4-ol. The P3/P4-positions were then optimized from a set of six amino acid derivatives. All inhibitors were evaluated in an in vitro assay using the full-length NS3 protease. Several potent inhibitors were identified, the most promising exhibiting a K(i) value of 1.1nM.
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28
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Zhou H, Singh NJ, Kim KS. Homology modeling and molecular dynamics study of West Nile virus NS3 protease: A molecular basis for the catalytic activity increased by the NS2B cofactor. Proteins 2006; 65:692-701. [PMID: 16972281 DOI: 10.1002/prot.21129] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The West Nile virus (WNV) NS3 serine protease, which plays an important role in assembly of infective virion, is an attractive target for anti-WNV drug development. Cofactors NS2B and NS4A increase the catalytic activity of NS3 in dengue virus and Hepatitis C virus, respectively. Recent studies on the WNV-NS3 characterize the catalytically active form of NS3 by tethering the 40-residue cofactor NS2B. It is suggested that NS2B is essential for the NS3 activity in WNV, while there is no information of the WNV-NS3-related crystal structure. To understand the role of NS2B/substrate in the NS3 catalytic activity, we built a series of models: WNV-NS3 and WNV-NS3-NS2B and WNV-NS3-NS2B-substrate using homology modeling and molecular modeling techniques. Molecular dynamics (MD) simulations were performed for 2.75 ns on each model, to investigate the structural stabilization and catalytic triad motion of the WNV NS3 protease with and without NS2B/substrate. The simulations show that the NS3 rearrangement occurs upon the NS2B binding, resulting in the stable D75-OD1...H51-NH hydrogen bonding. After the substrate binds to the NS3-NS2B active site, the NS3 protease becomes more stable, and the catalytic triad is formed. These results provide a structural basis for the activation and stabilization of the enzyme by its cofactor and substrate.
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Affiliation(s)
- Hong Zhou
- Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Hyojadong, Namgu, Pohang 790-784, Korea
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29
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Exploiting Ligand and Receptor Adaptability in Rational Drug Design Using Dynamics and Structure-Based Strategies. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_2006_087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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30
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Johansson PO, Bäck M, Kvarnström I, Jansson K, Vrang L, Hamelink E, Hallberg A, Rosenquist A, Samuelsson B. Potent inhibitors of the hepatitis C virus NS3 protease: Use of a novel P2 cyclopentane-derived template. Bioorg Med Chem 2006; 14:5136-51. [PMID: 16675222 DOI: 10.1016/j.bmc.2006.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/30/2006] [Accepted: 04/04/2006] [Indexed: 11/18/2022]
Abstract
The HCV NS3 protease is essential for replication of the hepatitis C virus (HCV) and therefore constitutes a promising new drug target for anti-HCV therapy. Several potent and promising HCV NS3 protease inhibitors, some of which display low nanomolar activities, were identified from a series of novel inhibitors incorporating a trisubstituted cyclopentane dicarboxylic acid moiety as a surrogate for the widely used N-acyl-(4R)-hydroxyproline in the P2 position.
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Affiliation(s)
- Per-Ola Johansson
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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31
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Cuerrier D, Moldoveanu T, Inoue J, Davies PL, Campbell RL. Calpain Inhibition by α-Ketoamide and Cyclic Hemiacetal Inhibitors Revealed by X-ray Crystallography,. Biochemistry 2006; 45:7446-52. [PMID: 16768440 DOI: 10.1021/bi060425j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calpains are intracellular calcium-activated cysteine proteases whose unregulated proteolysis following the loss of calcium homeostasis can lead to acute degeneration during ischemic episodes and trauma, as well as Alzheimer's disease and cataract formation. The determination of the crystal structure of the proteolytic core of mu-calpain (muI-II) in a calcium-bound active conformation has made structure-guided design of active site inhibitors feasible. We present here high-resolution crystal structures of rat muI-II complexed with two reversible calpain-specific inhibitors employing cyclic hemiacetal (SNJ-1715) and alpha-ketoamide (SNJ-1945) chemistries that reveal new details about the interactions of inhibitors with this enzyme. The SNJ-1715 complex confirms that the free aldehyde is the reactive species of the cornea-permeable cyclic hemiacetal. The alpha-ketoamide warhead of SNJ-1945 binds with the hydroxyl group of the tetrahedral adduct pointing toward the catalytic histidine rather than the oxyanion hole. The muI-II-SNJ-1945 complex shows residue Glu261 displaced from the S1' site by the inhibitor, resulting in an extended "open" conformation of the domain II gating loop and an unobstructed S1' site. This conformation offers an additional template for structure-based drug design extending to the primed subsites. An important role for the highly conserved Glu261 is proposed.
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Affiliation(s)
- D Cuerrier
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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32
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Baxter NJ, Roetzer A, Liebig HD, Sedelnikova SE, Hounslow AM, Skern T, Waltho JP. Structure and dynamics of coxsackievirus B4 2A proteinase, an enyzme involved in the etiology of heart disease. J Virol 2006; 80:1451-62. [PMID: 16415022 PMCID: PMC1346940 DOI: 10.1128/jvi.80.3.1451-1462.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 2A proteinases (2A(pro)) from the picornavirus family are multifunctional cysteine proteinases that perform essential roles during viral replication, involving viral polyprotein self-processing and shutting down host cell protein synthesis through cleavage of the eukaryotic initiation factor 4G (eIF4G) proteins. Coxsackievirus B4 (CVB4) 2A(pro) also cleaves heart muscle dystrophin, leading to cytoskeletal dysfunction and the symptoms of human acquired dilated cardiomyopathy. We have determined the solution structure of CVB4 2A(pro) (extending in an N-terminal direction to include the C-terminal eight residues of CVB4 VP1, which completes the VP1-2A(pro) substrate region). In terms of overall fold, it is similar to the crystal structure of the mature human rhinovirus serotype 2 (HRV2) 2A(pro), but the relatively low level (40%) of sequence identity leads to a substantially different surface. We show that differences in the cI-to-eI2 loop between HRV2 and CVB4 2A(pro) translate to differences in the mechanism of eIF4GI recognition. Additionally, the nuclear magnetic resonance relaxation properties of CVB4 2A(pro), particularly of residues G1 to S7, F64 to S67, and P107 to G111, reveal that the substrate region is exchanging in and out of a conformation in which it occupies the active site with association and dissociation rates in the range of 100 to 1,000 s(-1). This exchange influences the conformation of the active site and points to a mechanism for how self-processing can occur efficiently while product inhibition is avoided.
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Affiliation(s)
- Nicola J Baxter
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
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33
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Niyomrattanakit P, Winoyanuwattikun P, Chanprapaph S, Angsuthanasombat C, Panyim S, Katzenmeier G. Identification of residues in the dengue virus type 2 NS2B cofactor that are critical for NS3 protease activation. J Virol 2004; 78:13708-16. [PMID: 15564480 PMCID: PMC533897 DOI: 10.1128/jvi.78.24.13708-13716.2004] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteolytic processing of the dengue virus polyprotein is mediated by host cell proteases and the virus-encoded NS2B-NS3 two-component protease. The NS3 protease represents an attractive target for the development of antiviral inhibitors. The three-dimensional structure of the NS3 protease domain has been determined, but the structural determinants necessary for activation of the enzyme by the NS2B cofactor have been characterized only to a limited extent. To test a possible functional role of the recently proposed Phix(3)Phi motif in NS3 protease activation, we targeted six residues within the NS2B cofactor by site-specific mutagenesis. Residues Trp62, Ser71, Leu75, Ile77, Thr78, and Ile79 in NS2B were replaced with alanine, and in addition, an L75A/I79A double mutant was generated. The effects of these mutations on the activity of the NS2B(H)-NS3pro protease were analyzed in vitro by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of autoproteolytic cleavage at the NS2B/NS3 site and by assay of the enzyme with the fluorogenic peptide substrate GRR-AMC. Compared to the wild type, the L75A, I77A, and I79A mutants demonstrated inefficient autoproteolysis, whereas in the W62A and the L75A/I79A mutants self-cleavage appeared to be almost completely abolished. With exception of the S71A mutant, which had a k(cat)/K(m) value for the GRR-AMC peptide similar to that of the wild type, all other mutants exhibited drastically reduced k(cat) values. These results indicate a pivotal function of conserved residues Trp62, Leu75, and Ile79 in the NS2B cofactor in the structural activation of the dengue virus NS3 serine protease.
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Affiliation(s)
- Pornwaratt Niyomrattanakit
- Laboratory of Molecular Virology, Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Phutthamonthon 4 Rd., Nakornpathom 73170, Thailand
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Goudreau N, Brochu C, Cameron DR, Duceppe JS, Faucher AM, Ferland JM, Grand-Maître C, Poirier M, Simoneau B, Tsantrizos YS. Potent Inhibitors of the Hepatitis C Virus NS3 Protease: Design and Synthesis of Macrocyclic Substrate-Based β-Strand Mimics. J Org Chem 2004; 69:6185-201. [PMID: 15357576 DOI: 10.1021/jo049288r] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring beta-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.
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Affiliation(s)
- Nathalie Goudreau
- Department of Chemistry, Boehringer Ingelheim Ltd., Research and Development, 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5
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35
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Frecer V, Kabelác M, De Nardi P, Pricl S, Miertus S. Structure-based design of inhibitors of NS3 serine protease of hepatitis C virus. J Mol Graph Model 2004; 22:209-20. [PMID: 14629979 DOI: 10.1016/s1093-3263(03)00161-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have designed small focused combinatorial library of hexapeptide inhibitors of NS3 serine protease of the hepatitis C virus (HCV) by structure-based molecular design complemented by combinatorial optimisation of the individual residues. Rational residue substitutions were guided by the structure and properties of the binding pockets of the enzyme's active site. The inhibitors were derived from peptides known to inhibit the NS3 serine protease by using unusual amino acids and alpha-ketocysteine or difluoroaminobutyric acid, which are known to bind to the S1 pocket of the catalytic site. Inhibition constants (Ki) of the designed library of inhibitors were predicted from a QSAR model that correlated experimental Ki of known peptidic inhibitors of NS3 with the enthalpies of enzyme-inhibitor interaction computed via molecular mechanics and the solvent effect contribution to the binding affinity derived from the continuum model of solvation. The library of the optimised inhibitors contains promising drug candidates-water-soluble anionic hexapeptides with predicted Ki* in the picomolar range.
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Affiliation(s)
- Vladimír Frecer
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, I-34012, Trieste, Italy
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36
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Shokhen M, Albeck A. Identification of protons position in acid-base enzyme catalyzed reactions: The hepatitis C viral NS3 protease. Proteins 2004; 55:245-50. [PMID: 15048818 DOI: 10.1002/prot.20058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
General acid-base catalysis is a key element of the catalytic activity of most enzymes. Therefore, any explicit molecular modeling of enzyme-catalyzed chemical reactions requires correct identification of protons location on the catalytic groups. In this work, we apply our quantum mechanical/self-consistent reaction field in virtual solvent [QM/SCRF(VS)] method for identification of the position of protons shared by the enzyme catalytic groups and the polar groups of the inhibitor in a covalent tetrahedral complex (TC) of the hepatitis C virus NS3 protease with a peptidyl alpha-ketoacid inhibitor. To identify the relevant protonation states, we have analyzed relative stabilities of R and S configurations of the TC that depend on the specific proton distribution over the polar groups and correlated it with experimental NMR and X-ray crystallography data, both at low and neutral pH ranges. The tentative assignment of the single resonance in the (13)C NMR spectrum of the hemiketal carbon at physiological pH to the S configuration of TC is confirmed. Both R and S configurations are equally stable at acidic pH in our modeling, in good agreement with the (13)C NMR observation.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel.
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37
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Guo Z, Durkin J, Fischmann T, Ingram R, Prongay A, Zhang R, Madison V. Application of the lambda-dynamics method to evaluate the relative binding free energies of inhibitors to HCV protease. J Med Chem 2004; 46:5360-4. [PMID: 14640544 DOI: 10.1021/jm030040o] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The lambda-dynamics method was used to calculate the relative binding free energies of inhibitors to the hepatitis C virus (HCV) protease. A total of seven HCV protease p-side product inhibitors were used in this study. The inhibitors are 6-mer peptides spanning P6-P1 (Ac-Asp-d-Glu-Leu-Ile-Cha-P1-CO(2)H). For this protein, S1 is a major hydrophobic pocket for binding. Binding of various residues to this pocket was investigated through free energy simulations and experimental inhibition constants. Several 300 ps lambda-dynamics simulations in explicit solvent were performed. The relative binding free energy was estimated from these simulations. From a single simulation, the inhibitors can be correctly classified into highly potent and weakly potent groups. The multiple simulations give an accurate rank ordering of inhibitor potency; computed and experimental binding free energies agree with 0.6 kcal/mol for five of the seven inhibitors. In addition, free energy perturbation (FEP) calculations were carried out to validate the results from lambda-dynamics. A total of 6 ligand pairs were compared. For each pair, 5-11 windows were used to map one ligand to the other. The cumulative simulation time was over 2 ns for each ligand pair. For four of the six ligand pairs, the lambda-dynamics free energy difference fits better than the FEP difference to the experimental value. The fact that the lambda-dynamics method achieved similar results in only a fraction of the total simulation time for FEP further demonstrates the robustness of the lambda-dynamics method.
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Affiliation(s)
- Zhuyan Guo
- Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
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38
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Tsantrizos YS. The design of a potent inhibitor of the hepatitis C virus NS3 protease:BILN 2061?From the NMR tube to the clinic. Biopolymers 2004; 76:309-23. [PMID: 15386268 DOI: 10.1002/bip.20127] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The virally encoded serine protease NS3/NS4A is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. Until very recently, the design of inhibitors for the HCV NS3 protease was limited to large peptidomimetic compounds with poor pharmacokinetic properties, making drug discovery an extremely challenging endeavor. In our quest for the discovery of a small-molecule lead that could block replication of the hepatitis C virus by binding to the HCV NS3 protease, the critical protein-polypeptide interactions between the virally encoded NS3 serine protease and its polyprotein substrate were investigated. Lead optimization of a substrate-based hexapeptide, guided by structural data, led to the understanding of the molecular dynamics and electronic effects that modulate the affinity of peptidomimetic ligands for the active site of this enzyme. Macrocyclic beta-strand scaffolds were designed that allowed the discovery of potent, highly selective, and orally bioavailable compounds. These molecules were the first HCV NS3 protease inhibitors reported that inhibit replication of HCV subgenomic RNA in a cell-based replicon assay at low nanomolar concentrations. Optimization of their biopharmaceutical properties led to the discovery of the clinical candidate BILN 2061. Oral administration of BILN 2061 to patients infected with the hepatitis C genotype 1 virus resulted in an impressive reduction of viral RNA levels, establishing proof-of-concept for HCV NS3 protease inhibitors as therapeutic agents in humans.
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Affiliation(s)
- Youla S Tsantrizos
- Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval (Québec) H7S 2G5, Canada.
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39
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Richer MJ, Juliano L, Hashimoto C, Jean F. Serpin mechanism of hepatitis C virus nonstructural 3 (NS3) protease inhibition: induced fit as a mechanism for narrow specificity. J Biol Chem 2003; 279:10222-7. [PMID: 14701815 DOI: 10.1074/jbc.m313852200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hepatitis C virus (HCV) nonstructural 3 (NS3) serine protease disrupts important cellular antiviral signaling pathways and plays a pivotal role in the proteolytic maturation of the HCV polyprotein precursor. This recent discovery has fostered the search for NS3 protease inhibitors. However, the enzyme's unusual induced fit behavior and peculiar molecular architecture have imposed considerable obstacles to the development of small molecule inhibitors. In this article, we demonstrate that such unique induced fit behavior and the chymotrypsin-like catalytic domain can provide the structural plasticity necessary to generate protein-based inhibitors of the NS3 protease. We took advantage of the macromolecular scaffold of a Drosophila serpin, SP6, which intrinsically supports chymotrypsin-like enzyme inhibition, to design a novel class of potent and selective inhibitors. We show that altering the SP6 reactive site loop (RSL) resulted in the development of the first effective (K(i) of 34 nm) and selective serpin, SP6(EVC/S), directed at the NS3 protease. SP6(EVC/S) operates as a suicide substrate inhibitor, and its partitioning between the complex-forming and proteolytic pathways for the NS3 protease is HCV NS4A cofactor-dependent and -specific. Once bound to the protease active site, SP6(EVC/S) partitions with equal probability to undergo proteolysis by NS3 at the C-terminal site of the engineered RSL, (P(6))Glu-Ile-(P(4))Val-Met-Thr-(P(1))Cys- downward arrow -(P(1)')Ser, or to form a covalent acyl-enzyme complex characteristic of cognate protease-serpin pairs. Our results also reveal a novel cofactor-induced serpin mechanism of enzyme inhibition that could be explored for developing effective and selective inhibitors of other important induced fit viral proteases of the Flaviviridae family such as the West Nile virus NS3 endoprotease.
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Affiliation(s)
- Martin J Richer
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, Canada
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40
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Abstract
The limitations of current treatment for chronic hepatitis C virus (HCV) infection have prompted the development of novel therapeutic strategies targeting events specific to viral replication. Over the past decade, advances in the study of HCV molecular biology have led to the identification of cis-acting RNA sequences and viral enzymatic activities which present attractive targets for inhibition. High-resolution, three-dimensional structures of the HCV serine protease, helicase and RNA-dependent RNA polymerase have been determined through X-ray crystallographic studies. More recently, solution structures of these proteins and the HCV internal ribosome entry site have been evaluated by nuclear magnetic resonance spectroscopy and electron microscopy. Mutational analysis and structural characterization of these macromolecules in complex with bound substrates, cofactors and inhibitors has further defined the various electrochemical interactions which mediate protein-protein, protein-RNA and other intermolecular contacts. This review will discuss the available structural data with respect to the rational design of HCV enzyme inhibitors and the development of antisense-based therapeutic strategies, such as RNA interference.
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Affiliation(s)
- R M Smith
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT 06030-1845, USA
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41
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Gregorio GV, Choudhuri K, Ma Y, Pensati P, Iorio R, Grant P, Garson J, Bogdanos DP, Vegnente A, Mieli-Vergani G, Vergani D. Mimicry between the hepatitis C virus polyprotein and antigenic targets of nuclear and smooth muscle antibodies in chronic hepatitis C virus infection. Clin Exp Immunol 2003; 133:404-13. [PMID: 12930368 PMCID: PMC1808793 DOI: 10.1046/j.1365-2249.2003.02229.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autoantibodies to smooth muscle (SMA) and nuclear components (ANA) arise in the natural course of chronic infection with hepatitis C virus. In view of the growing evidence for 'molecular mimicry' as a mechanism of autoimmunity we investigated whether cross-reactive immune reactions between host smooth muscle/nuclear components and HCV antigens may contribute to the formation of SMA and ANA in chronic HCV infection. Computer-assisted protein database search methods were used to identify three smooth muscle (smoothelin698-717, myosin1035-1054, vimentin69-88) and three nuclear (matrin722-741, histone H2A11-30, replication protein A133-152) host antigens with the highest local sequence similarity to the HCV polyprotein and 20-mer peptides corresponding to these regions were constructed. Sera from 51 children with chronic HCV infection [median age: 8 (2-16); 27 boys], 26 SMA positive and five ANA positive, were tested for reactivity to the synthesized HCV peptides and their human homologues by enzyme linked immunosorbent assay (ELISA). Sera from patients with HBV infection and chronic liver disease of different aetiologies were used as controls. 'Double reactivity' to HCV peptides and smooth muscle/nuclear homologues was associated strongly with HCV infection (P < 0.001 for both). Humoral cross-reactivity was established as the basis for double recognition by competition ELISA. Double-reactivity to smooth muscle and HCV peptide antigens correlated with SMA positivity by indirect immunofluouresence (P = 0.05). Of 15 patients double-reactive to myosin1035-1054 and its HCV homologue, 13 recognized whole myosin by immunoblot. These results suggest that ANA and SMA in chronic HCV infection may arise, at least in part, as a consequence of cross-reactive immune responses to HCV and host smooth muscle/nuclear antigens.
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Affiliation(s)
- G V Gregorio
- Institute of Liver Studies and Department of Child Health, King's College Hospital, GKT Medical School, London, UK
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42
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Orvieto F, Koch U, Matassa VG, Muraglia E. Novel, potent phenethylamide inhibitors of the hepatitis C virus (HCV) NS3 protease: probing the role of P2 aryloxyprolines with hybrid structures. Bioorg Med Chem Lett 2003; 13:2745-8. [PMID: 12873506 DOI: 10.1016/s0960-894x(03)00536-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthesis of hybrid HCV NS3 protease/NS4A inhibitors having the 4,4-difluoroaminobutyric acid (difluoroAbu) phenethylamides as P1-P1' and quinolyloxyprolines as P2 fragments led to 7 (IC(50) 54 nM). Molecular modelling suggests that this potent tripeptide inhibitor utilizes interactions in the S1', S1, S2, S3 and S4 sites of the protease.
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Affiliation(s)
- Federica Orvieto
- Medicinal Chemistry Department, IRBM-MRL Rome, V Pontina Km 30,600, 00040 Pomezia, Rome, Italy
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Affiliation(s)
- Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
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44
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Abstract
Inhibitor design against viral targets must take into account the peculiar characteristics of viral biology-in particular, the plasticity of their replicative machinery. This includes maturational cleavage of the polyprotein, which is mediated by virally encoded proteases. Designing against a movable target is particularly challenging, but at the same time it offers new opportunities. Here we describe our experience with the NS3/4A (NS: nonstructural) serine protease of human hepatitis C virus (HCV). By extensive use of combinatorial peptide libraries, various inhibitor types were generated, including product inhibitors, serine traps, P-P' inhibitors, and prime side inhibitors. The latter represent a first case for a serine protease. A key finding, derived from structural studies utilizing these inhibitors, was that NS3 is an induced-fit protease, requiring both the NS4A cofactor protein and the substrate to fully activate its catalytic machinery. In the absence of cofactor and/or substrate, NS3 exists in solution as a large conformational ensemble, which can be matched by a correspondingly large set of peptide inhibitors, each one stabilizing a given conformer. In the perspective of inhibiting viral proteases in general, we suggest that combinatorial ligand ensembles may be a powerful tool, to contrast the adaptive potential of the viral quasispecies.
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Affiliation(s)
- Elisabetta Bianchi
- Biopolymers Laboratory, Department of Molecular & Cell Biology, IRBM P. Angeletti, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy
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45
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Casbarra A, Piaz FD, Ingallinella P, Orrù S, Pucci P, Pessi A, Bianchi E. The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure. Protein Sci 2002; 11:2102-12. [PMID: 12192066 PMCID: PMC2373603 DOI: 10.1110/ps.0206602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We recently reported a new class of inhibitors of the chymotrypsin-like serine protease NS3 of the hepatitis C virus. These inhibitors exploit the binding potential of the S' site of the protease, which is not generally used by the natural substrates. The effect of prime-site occupancy was analyzed by circular dichroism spectroscopy and limited proteolysis-mass spectrometry. Generally, nonprime inhibitors cause a structural change in NS3. Binding in the S' site produces additional conformational changes with different binding modes, even in the case of the NS3/4A cofactor complex. Notably, inhibitor binding either in the S or S' site also has profound effects on the stabilization of the protease. In addition, the stabilization propagates to regions not in direct contact with the inhibitor. In particular, the N-terminal region, which according to structural studies is endowed with low structural stability and is not stabilized by nonprime inhibitors, was now fully protected from proteolytic degradation. From the perspective of drug design, P-P' inhibitors take advantage of binding pockets, which are not exploited by the natural HCV substrates; hence, they are an entry point for a novel class of NS3/4A inhibitors. Here we show that binding of each inhibitor is associated with a specific structural rearrangement. The development of a range of inhibitors belonging to different classes and an understanding of their interactions with the protease are required to address the issue of the most likely outcome of viral protease inhibitor therapy, that is, viral resistance.
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Affiliation(s)
- Annarita Casbarra
- Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte Santangelo, Via Cinthia, 80126 Napoli, Italy
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46
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Tsumoto K, Misawa S, Ohba Y, Ueno T, Hayashi H, Kasai N, Watanabe H, Asano R, Kumagai I. Inhibition of hepatitis C virus NS3 protease by peptides derived from complementarity-determining regions (CDRs) of the monoclonal antibody 8D4: tolerance of a CDR peptide to conformational changes of a target. FEBS Lett 2002; 525:77-82. [PMID: 12163165 DOI: 10.1016/s0014-5793(02)03090-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have synthesized and characterized peptides derived from complementarity-determining regions (CDRs) of 8D4, a mouse monoclonal antibody against NS3 protease domain of hepatitis C virus. 8D4 inhibits enzymatic activity without its cofactor, NS4A peptide. One of the synthetic peptides derived from CDRs, CDR1 of the heavy-chain (CDR-H1) peptide strongly inhibited NS3 protease activity competitively in the absence of NS4A and non-competitively in the presence of NS4A. Moreover, cyclic CDR-H1 peptides bridged by disulfide inhibited NS3 protease more potently. The chain length of the CDR-H1 peptide is critical for strong inhibition, even when the peptide is circularized. This finding suggests the importance of peptide conformation. In contrast to a cognate antibody molecule, CDR-derived peptides may provide good ligands for target molecules by having a tolerance to conformational changes of the targets caused by cofactor binding or mutation.
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Affiliation(s)
- Kouhei Tsumoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 980-8579, Sendai, Japan.
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47
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Colarusso S, Gerlach B, Koch U, Muraglia E, Conte I, Stansfield I, Matassa VG, Narjes F. Evolution, synthesis and SAR of tripeptide alpha-ketoacid inhibitors of the hepatitis C virus NS3/NS4A serine protease. Bioorg Med Chem Lett 2002; 12:705-8. [PMID: 11844706 DOI: 10.1016/s0960-894x(01)00843-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
N-terminal truncation of the hexapeptide ketoacid 1 gave rise to potent tripeptide inhibitors of the hepatitis C virus NS3 protease/NS4A cofactor complex. Optimization of these tripeptides led to ketoacid 30 with an IC50 of 0.38 microM. The SAR of these tripeptides is discussed in the light of the recently published crystal structures of a ternary tripetide/NS3/NS4A complexes.
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Affiliation(s)
- Stefania Colarusso
- Department of Chemistry, IRBM, MRL Rome, Via Pontina Km 30.600, Pomezia, 00040, Rome, Italy
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Archer SJ, Camac DM, Wu ZJ, Farrow NA, Domaille PJ, Wasserman ZR, Bukhtiyarova M, Rizzo C, Jagannathan S, Mersinger LJ, Kettner CA. Hepatitis C virus NS3 protease requires its NS4A cofactor peptide for optimal binding of a boronic acid inhibitor as shown by NMR. CHEMISTRY & BIOLOGY 2002; 9:79-92. [PMID: 11841941 DOI: 10.1016/s1074-5521(01)00096-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
NMR spectroscopy was used to characterize the hepatitis C virus (HCV) NS3 protease in a complex with the 24 residue peptide cofactor from NS4A and a boronic acid inhibitor, Ac-Asp-Glu-Val-Val-Pro-boroAlg-OH. Secondary-structure information, NOE constraints between protease and cofactor, and hydrogen-deuterium exchange rates revealed that the cofactor was an integral strand in the N-terminal beta-sheet of the complex as observed in X-ray crystal structures. Based upon chemical-shift perturbations, inhibitor-protein NOEs, and the protonation state of the catalytic histidine, the boronic acid inhibitor was bound in the substrate binding site as a transition state mimic. In the absence of cofactor, the inhibitor had a lower affinity for the protease. Although the inhibitor binds in the same location, differences were observed at the catalytic site of the protease.
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Abstract
The Hepatitis C virus is a positive-stranded RNA virus which is the causal agent for a chronic liver infection afflicting more than 170,000,000 people world-wide. The HCV genome is approximately 9.6 kb in length and the proteome encoded is a polyprotein of a little more than 3000 amino acid residues. This polyprotein is processed by a combination of host and viral proteases into structural and non-structural proteins. The functions of most of these proteins have been established by analogy to other viruses and by sequence homology to known proteins, as well as subsequent biochemical analysis. Two of the non-structural proteins, NS4b and NS5a, are still of unknown function. The development of antivirals for this infectious agent has been hampered by the lack of robust and economical cell culture and animal infection systems. Recent progress in the molecular virology of HCV has come about due to the definition of molecular clones, which are infectious in the chimpanzee, the development of a subgenomic replicon system in Huh7 cells, and the description of a transgenic mouse model for HCV infection. Recent progress in the structural biology of the virus has led to the determination of high resolution three-dimensional structures of a number of the key virally encoded enzymes, including the NS3 protease, NS3 helicase, and NS5b RNA-dependent RNA polymerase. In some cases these structures have been determined in complex with substrates, co-factors (NS4a), and inhibitors. Finally, a variety of techniques have been used to define host factors, which may be required for HCV replication, although this work is just beginning.
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Affiliation(s)
- S Rosenberg
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
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50
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Lee YJ, Kang H, Rho SH, Eom SH, Park WJ. Assessment of substrate specificity of hepatitis G virus NS3 protease by a genetic method. Biochem Biophys Res Commun 2001; 286:171-5. [PMID: 11485324 DOI: 10.1006/bbrc.2001.5354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The RNA genome of hepatitis G virus (HGV) encodes a large polyprotein that is processed to mature proteins by viral-encoded proteases. The HGV NS3 protease is responsible for the cleavage of the HGV polyprotein at four different locations. No conserved sequence motif has been identified for the cleavage sites of the NS3 protease. To determine the substrate specificity of the NS3 protease, amino acid sequences cleaved by the NS3 protease were obtained from randomized sequence libraries by using a screening method referred to as GASP (Genetic Assay for Site-specific Proteolysis). Based on statistical analyses of the obtained cleavable sequences, a consensus substrate sequence was deduced: Gln-Glu-Thr-Leu-Val downward arrow Ser, with the scissile bond located between Val and Ser. The relevance of this peptide as a cleavable substrate was further supported by molecular modeling of the NS3 protease. Our result would provide an insight on the molecular activity of the NS3 protease and may be useful for the design of substrate-based inhibitors.
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Affiliation(s)
- Y J Lee
- Department of Life Science and National Research Laboratory of Proteolysis, Kwangju Institute of Science and Technology, 1 Oryong-dong, Puk-gu, Kwangju 500-712, Korea
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