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Ren J, Vaid TM, Lee H, Ojeda I, Johnson ME. Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations. J Comput Aided Mol Des 2023; 37:53-65. [PMID: 36427108 PMCID: PMC9839505 DOI: 10.1007/s10822-022-00490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present an investigation of HCV NS3/4A inhibitors based on a sulfonamidobenzamide scaffold. Inhibitor interactions with HCV NS3/4A were explored by molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. All of the inhibitors adopt similar molecular docking poses in the catalytic site of the protease that are stabilized by hydrogen bond interactions with G137 and the catalytic S139, which are known to be important for potency and binding stability. The quantitative assessments of binding free energies from MM/PBSA correlate well with the experimental results, with a high coefficient of determination, R2 of 0.92. Binding free energy decomposition analyses elucidate the different contributions of Q41, F43, H57, R109, K136, G137, S138, S139, A156, M485, and Q526 in binding different inhibitors. The importance of these sidechain contributions was further confirmed by computational alanine scanning mutagenesis. In addition, the sidechains of K136 and S139 show crucial but distinct contributions to inhibitor binding with HCV NS3/4A. The structural basis of the potency has been elucidated, demonstrating the importance of the R155 sidechain conformation. This extensive exploration of binding energies and interactions between these compounds and HCV NS3/4A at the atomic level should benefit future antiviral drug design.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- BeiGene (Beijing) Co., Ltd, No. 30 Science Park Road, Zhong-Guan-Cun Life Sciences Park, Changping District, Beijing, 102206, People's Republic of China
| | - Tasneem M Vaid
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Isabel Ojeda
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
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Hazra M, Dubey RC. Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV. J Biomol Struct Dyn 2022:1-20. [PMID: 35993498 DOI: 10.1080/07391102.2022.2113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.
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Affiliation(s)
- Mousumi Hazra
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
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Abstract
Pestiviruses like bovine viral diarrhoea virus (BVDV) and classical swine fever virus (CSFV) belong to the family Flaviviridae. A special feature of the Flaviviridae is the importance of nonstructural (NS) proteins for both genome replication and virion morphogenesis. The NS2-3-4A region and its regulated processing by the NS2 autoprotease and the NS3/4A protease plays a central role in the pestiviral life cycle. We report the identification and characterization of a novel internal cleavage in BVDV NS2, which is mediated by the NS3/4A protease. Further mapping using the NS2 of BVDV-1 strain NCP7 showed that cleavage occurs between L188 and G189. This cleavage site represents a novel sequence motif recognized by the NS3/4A protease and is conserved between the pestivirus species A, B and D. Inhibition of this internal NS2 cleavage by mutating the cleavage site did not cause obvious effects on RNA replication or virion morphogenesis in cultured cell lines. Accordingly, this novel internal NS2 cleavage adds an additional layer to the already complex polyprotein processing of Pestiviruses and might further extend the repertoires of the multifunctional NS2. However, unravelling of the functional relevance of this novel processing event in NS2, therefore, awaits future in vivo studies.
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Affiliation(s)
- Thomas Walther
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany.,Present address: EUROIMMUN AG, Luebeck, Germany
| | - Barbara Bruhn
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
| | - Olaf Isken
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
| | - Norbert Tautz
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
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Boonma T, Nutho B, Darai N, Rungrotmongkol T, Nunthaboot N. Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study. J Biomol Struct Dyn 2021; 40:5283-5294. [PMID: 33430709 DOI: 10.1080/07391102.2020.1869587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Hepatitis C virus (HCV) NS3/4A serine protease is a promising drug target for the discovery of anti-HCV drugs. However, its amino acid mutations, particularly A156T, commonly lead to rapid emergence of drug resistance. Paritaprevir and glecaprevir, the newly FDA-approved HCV drugs, exhibit distinct resistance profiles against the A156T mutation of HCV NS3/4A serine protease. To illustrate their different molecular resistance mechanisms, molecular dynamics simulations and binding free energy calculations were carried out on the two compounds complexed with both wild-type (WT) and A156T variants of HCV NS3/4A protease. QM/MM-GBSA-based binding free energy calculations revealed that the binding affinities of paritaprevir and glecaprevir towards A156T NS3/4A were significantly reduced by ∼4 kcal/mol with respect to their WT complexes, which were in line with the experimental resistance folds. Moreover, the relatively weak intermolecular interactions with amino acids such as H57, R155, and T156 of NS3 protein, the steric effect and the destabilized protein binding surface, which is caused by the loss of salt bridge between R123 and D168, are the main contributions for the higher fold-loss in potency of glecaprevir due to A156T mutation. An insight into the difference of molecular mechanism of drug resistance against the A156T substitution among the two classes of serine protease inhibitors could be useful for further optimization of new generation HCV NS3/4A inhibitors with enhanced inhibitory potency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thitiya Boonma
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nitchakan Darai
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand.,Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
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Lim SK, Othman R, Yusof R, Heh CH. Rational drug discovery: Ellagic acid as a potent dual-target inhibitor against hepatitis C virus genotype 3 (HCV G3) NS3 enzymes. Chem Biol Drug Des 2020; 97:28-40. [PMID: 32657543 DOI: 10.1111/cbdd.13756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/15/2020] [Accepted: 06/28/2020] [Indexed: 12/19/2022]
Abstract
Structure-based virtual screening (SBVS) has served as a popular strategy for rational drug discovery. In this study, we aimed to discover novel benzopyran-based inhibitors that targeted the NS3 enzymes (NS3/4A protease and NS3 helicase) of HCV G3 using a combination of in silico and in vitro approaches. With the aid of SBVS, six novel compounds were discovered to inhibit HCV G3 NS3/4A protease and two phytochemicals (ellagic acid and myricetin) were identified as dual-target inhibitors that inhibited both NS3/4A protease and NS3 helicase in vitro (IC50 = 40.37 ± 5.47 nm and 6.58 ± 0.99 µm, respectively). Inhibitory activities against the replication of HCV G3 replicons were further assessed in a cell-based system with four compounds showed dose-dependent inhibition. Compound P8 was determined to be the most potent compound from the cell-based assay with an EC50 of 19.05 µm. The dual-target inhibitor, ellagic acid, was determined as the second most potent (EC50 = 32.37 µm) and the most selective in its inhibitory activity against the replication of HCV replicons, without severely affecting the viability of the host cells (selectivity index > 6.18).
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Affiliation(s)
- See Khai Lim
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia.,Center for Natural Products Research and Drug Discovery (CENAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
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Ren J, Ojeda I, Patel M, Johnson ME, Lee H. Exploring small molecules with pan-genotypic inhibitory activities against hepatitis C virus NS3/4A serine protease. Bioorg Med Chem Lett 2019; 29:2349-2353. [PMID: 31201062 DOI: 10.1016/j.bmcl.2019.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023]
Abstract
Among the many Hepatitis C virus (HCV) genotypes and subtypes, genotypes 1b and 3a are most prevalent in United States and Asia, respectively. A total of 132 commercially available analogs of a previous lead compound were initially investigated against wild-type HCV genotype 1b NS3/4A protease. Ten compounds showed inhibitory activities (IC50 values) below 10 µM with comparable direct binding affinities (KD values) determined by surface plasmon resonance (SPR). To identify pan-genotypic inhibitors, these ten selected compounds were tested against four additional genotypes (1a, 2a, 3a, and 4) and three drug-resistant mutants (A156S, R155K, and V36M). Four new analogs have been identified with better activities against all five tested genotypes than the prior lead compound. Further, the original lead compound did not show activity against genotype 3a NS3/4A, whereas four newly identified compounds exhibited IC50 values below 33 µM against genotype 3a NS3/4A. Encouragingly, the best new compound F1813-0710 possessed promising activity toward genotype 3a, which is a huge improvement over the previous lead compound that had no effect on genotype 3a. This intriguing observation was further analyzed by molecular docking and molecular dynamics (MD) simulations to understand their different binding interactions, which should benefit future pan-genotypic inhibitor design and drug discovery.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Isabel Ojeda
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Maulik Patel
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA.
| | - Hyun Lee
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Biophysics Core at Research Resource Center, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA.
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7
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Naguib MM, Mohamed MR, M Ali MA, Karim AM. Development of an efficient in vivo cell-based assay system for monitoring hepatitis C virus genotype 4a NS3/4A protease activity. INDIAN J PATHOL MICR 2019; 62:391-398. [PMID: 31361226 DOI: 10.4103/ijpm.ijpm_774_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Hepatitis C virus (HCV) represents a serious worldwide healthcare problem. No protective vaccines against HCV have been developed yet due to the fact that HCV is rapidly mutable, allowing the virus to escape from the neutralizing antibodies. Understanding of HCV was initially hampered by the inability to achieve viral replication in cell culture. Given its essential roles in viral polyprotein processing and immune evasion, HCV NS3/4A protease is a prime target for antiviral chemotherapy. We aimed to establish in vivo cell-based assay system for monitoring the activity of NS3/4A protease from HCV genotype 4a, the predominant genotype in Egypt, and the Middle East. Furthermore, the developed system was used to evaluate the inhibitory potency of a series of computer-designed chemically-synthesized compounds against NS3/4A protease from HCV genotype 4a. Materials and Methods Native as well as mutant cleavage sites to NS3/4A protease were cloned in frame into β-galactosidase gene of TA cloning vector. The target specificity of HCV NS3/4A was evaluated by coexpression of β-galactosidase containing the protease cleavage site with NS3/4A protease construct in bacterial cells. The activity of β-galactosidase was colorimetrically estimated in the cell lysate using orthonitro phenyl β-D-galactopyanoside (ONPG) as a substrate. Results and Conclusions We successfully developed an efficient cell-based system based on the blue/white selection of bacterial cells that are able to express functional/nonfunctional β-galactosidase enzyme.
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Affiliation(s)
- Mohamed M Naguib
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed R Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed A M Ali
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Amr M Karim
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
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Ezat AA, Elshemey WM. A comparative study of the efficiency of HCV NS3/4A protease drugs against different HCV genotypes using in silico approaches. Life Sci 2018; 217:176-184. [PMID: 30528183 DOI: 10.1016/j.lfs.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/21/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
AIMS To investigate the efficacy of Direct Acting Antivirals (DAAs) in the treatment of different Hepatitis C Virus (HCV) genotypes. MAIN METHODS Homology modeling is used to predict the 3D structures of different genotypes while molecular docking is employed to predict genotype - drug interactions (Binding Mode) and binding free energy (Docking Score). KEY FINDINGS Simeprevir (TMC435) and to a lesser degree MK6325 are the best drugs among the studied drugs. The predicted affinity of drugs against genotype 1a is always better than other genotypes. P2-P4 macrocyclic drugs show better performance against genotypes 2, 3 and 5. Macrocyclic drugs are better than linear drugs. SIGNIFICANCE HCV is one of the major health problems worldwide. Until the discovery of DAAs, HCV treatment faced many failures. DAAs target key functional machines of the virus life cycle and shut it down. NS3/4A protease is an important target and several drugs have been designed to inhibit its functions. There are several NS3/4A protease drugs approved by Food and Drug Administration (FDA). Unfortunately, the virus exhibits resistance against these drugs. This study is significant in elucidating that no one drug is able to treat different genotypes with the same efficiency. Therefore, treatment should be prescribed based on the HCV genotype.
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Affiliation(s)
- Ahmed A Ezat
- Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt.
| | - Wael M Elshemey
- Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
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Choi Y, Yoon S, Matsumoto K, Ohta Y, Lee S, Yu KS, Jang IJ. Pharmacokinetic characteristics of telaprevir in healthy Korean male subjects and comparisons with Japanese. Drug Des Devel Ther 2018; 12:1045-1051. [PMID: 29750017 PMCID: PMC5933357 DOI: 10.2147/dddt.s148117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Introduction Telaprevir, a reversible selective inhibitor of viral protease and a potential blocker of viral replication, is indicated for the treatment of hepatitis C virus genotype 1 infection. In this study, the pharmacokinetic profile, safety, and tolerability of telaprevir and the effect of food on telaprevir exposure were evaluated in healthy Korean subjects, and compared with data from a previous study in Japanese male subjects. Methods The single ascending dose study was conducted in 3 dose-based groups (500, 750, and 1,250 mg, six subjects each) in a fasted state. In the multiple dose study, eight subjects in the fed state received 750 mg of telaprevir once on Day 1 and every 8 hours from Day 2 until the morning of Day 6. Serial blood samples for pharmacokinetic analysis were collected for up to 24 hours in the single ascending dose study and for 6 days in the multiple dose study. Individual pharmacokinetic parameters were calculated using a non-compartmental analysis method. Safety and tolerability profiles were evaluated throughout the study. Results Following multiple administrations of telaprevir, maximum plasma concentrations (Cmax), area under the concentration–time curve (AUC0–8), and Ctrough (concentration at 8 h after drug administration) increased by ~2.41-fold. Compared to fasted state values, mean Cmax and AUC0–24 increased by 4.92- and 4.81-fold, respectively, after food intake. The Cmax and AUCinf of Korean subjects were 26%–34% higher than those of Japanese subjects; however, these differences were not clinically significant. All observed adverse events were mild and there was no discontinuation due to AEs. Conclusion In conclusion, the telaprevir’s pharmacokinetic characteristics were similar in Korean and Japanese subjects. Telaprevir was well tolerated in a single dose of up to 1,250 mg and in multiple doses of 750 mg.
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Affiliation(s)
- Yewon Choi
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Republic of Korea
| | - Seonghae Yoon
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Republic of Korea
| | - Kyoko Matsumoto
- Ikuyaku Integrated Value Development Division, Mitsubishi Tanabe Pharma Corporation, Osaka, Japan
| | - Yoshiyasu Ohta
- Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Tokyo, Japan
| | - SeungHwan Lee
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Republic of Korea
| | - Kyung-Sang Yu
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Republic of Korea
| | - In-Jin Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Republic of Korea
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Abstract
Over the last 2 decades, covalent inhibitors have gained much popularity and is living up to its reputation as a powerful tool in drug discovery. Covalent inhibitors possess many significant advantages including increased biochemical efficiency, prolonged duration and the ability to target shallow, solvent exposed substrate-binding domains. However, rapidly mounting concerns over the potential toxicity, highly reactive nature and general lack of selectivity have negatively impacted covalent inhibitor development. Recently, a great deal of emphasis by the pharmaceutical industry has been placed toward the development of novel approaches to alleviate the major challenges experienced through covalent inhibition. This has unexpectedly led to the emergence of "selective" covalent inhibitors. The purpose of this review is not only to provide an overview from literature but to introduce a technical guidance as to how to initiate a systematic "road map" for the design of selective covalent inhibitors which we believe may assist in the design and development of optimized potential selective covalent HCV NS3/4A viral protease inhibitors.
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Affiliation(s)
- Letitia Shunmugam
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Pritika Ramharack
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa. .,College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU, Tallahassee, FL, 32307, USA.
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11
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Kataoka H, Ohe T, Takahashi K, Nakamura S, Mashino T. Novel fullerene derivatives as dual inhibitors of Hepatitis C virus NS5B polymerase and NS3/4A protease. Bioorg Med Chem Lett 2016; 26:4565-4567. [PMID: 27597249 DOI: 10.1016/j.bmcl.2016.08.086] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 11/26/2022]
Abstract
We evaluated the Hepatitis C virus (HCV) NS5B polymerase and HCV NS3/4A protease inhibition activities of a new set of proline-type fullerene derivatives. All of the compounds had the potential to inhibit both the enzymes, indicating that the fullerene derivatives may be dual inhibitors against NS5B and NS3/4A and could be novel lead compounds for the treatment of HCV infections.
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Affiliation(s)
- Hiroki Kataoka
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, Japan
| | - Tomoyuki Ohe
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, Japan.
| | - Kyoko Takahashi
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, Japan
| | - Shigeo Nakamura
- Department of Chemistry, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, Japan
| | - Tadahiko Mashino
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, Japan.
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12
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Jittavisutthikul S, Seesuay W, Thanongsaksrikul J, Thueng-in K, Srimanote P, Werner RG, Chaicumpa W. Human Transbodies to HCV NS3/4A Protease Inhibit Viral Replication and Restore Host Innate Immunity. Front Immunol 2016; 7:318. [PMID: 27617013 PMCID: PMC4999588 DOI: 10.3389/fimmu.2016.00318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
A safe and effective direct acting anti-hepatitis C virus (HCV) agent is still needed. In this study, human single chain variable fragments of antibody (scFvs) that bound to HCV NS3/4A protein were produced by phage display technology. The engineered scFvs were linked to nonaarginines (R9) for making them cell penetrable. HCV-RNA-transfected Huh7 cells treated with the transbodies produced from four different transformed E. coli clones had reduced HCV-RNA inside the cells and in the cell spent media, as well as fewer HCV foci in the cell monolayer compared to the transfected cells in culture medium alone. The transbodies-treated transfected cells also had up-expression of the genes coding for the host innate immune response, including TRIF, TRAF3, IRF3, IL-28B, and IFN-β. Computerized homology modeling and intermolecular docking predicted that the effective transbodies interacted with several critical residues of the NS3/4A protease, including those that form catalytic triads, oxyanion loop, and S1 and S6 pockets, as well as a zinc-binding site. Although insight into molecular mechanisms of the transbodies need further laboratory investigation, it can be deduced from the current data that the transbodies blocked the HCV NS3/4A protease activities, leading to the HCV replication inhibition and restoration of the virally suppressed host innate immunity. The engineered antibodies should be tested further for treatment of HCV infection either alone, in combination with current therapeutics, or in a mixture with their cognates specific to other HCV proteins.
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Affiliation(s)
- Surasak Jittavisutthikul
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
| | - Watee Seesuay
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
| | - Jeeraphong Thanongsaksrikul
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Pathum-thani, Thailand
| | - Kanyarat Thueng-in
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
- School of Pathology, Institute of Medicine, Suranaree University of Technology, Nakhon Ratchasima Province, Thailand
| | - Potjanee Srimanote
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Pathum-thani, Thailand
| | - Rolf G. Werner
- Industrial Technology, Faculty of Science, University of Tuebingen, Tuebingen, Germany
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Pathum-thani, Thailand
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13
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Palanisamy N, Lennerstrand J. Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach. Interdiscip Sci 2016; 10:143-156. [PMID: 27311576 DOI: 10.1007/s12539-016-0177-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 05/17/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023]
Abstract
The hepatitis C virus (HCV), of the family flaviviridae, is one of the major causes of chronic liver diseases. Until the year 2012, HCV infections were treated using PEG-interferon and ribavirin combinations, which have a low cure rate and severe side effects. Currently, many direct-acting antivirals (DAAs) are available, e.g. protease inhibitors, NS5A and polymerase inhibitors. These drugs have proven to be efficient in interferon-free treatment combinations and capable of enhancing the cure rate to above 90 %. Unlike PEG-interferon and ribavirin combinations, DAAs select for resistance in HCV. The R155K mutation in the HCV was found to resist all the currently available protease inhibitors. Here, we studied biophysical parameters like pocket (cavity) geometries and stabilizing residues of HCV 1a NS3/4A protease in wild type and mutants. We also studied HCV 1a NS3/4A protease's catalytic residues: their accessibility, energy, flexibility and binding to Phase II oral protease inhibitor vedroprevir (GS-9451), and compared these parameters between wild type and mutant(s). All these studies were performed using various bioinformatics tools (e.g. Swiss-PdbViewer and Schrödinger's Maestro) and web servers (e.g. DoGSiteScorer, SRide, ASA-View, WHAT IF, elNémo, CABS-flex, PatchDock and PLIP). From our study, we found that introduction of R155K, A156T or D168A mutation to wild-type NS3/4A protease increases the pocket's volume, surface (in the R155K mutant, surface decreases), lipo surface and depth and decreases the number of stabilizing residues. Additionally, differences in catalytic residues' solvent accessibility, energy, root-mean-square deviation (RMSD) and flexibility between wild type and mutants might explain changes in the protease activity and the resistance to protease inhibitors.
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Affiliation(s)
- Navaneethan Palanisamy
- Synthetic Biology Group, Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 267 (BioQuant), 69120, Heidelberg, Germany.
- The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany.
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, 751 85, Uppsala, Sweden.
| | - Johan Lennerstrand
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, 751 85, Uppsala, Sweden
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Ashfaq UA, Jalil A, Ul Qamar MT. Antiviral phytochemicals identification from Azadirachta indica leaves against HCV NS3 protease: an in silico approach. Nat Prod Res 2015; 30:1866-9. [PMID: 26274064 DOI: 10.1080/14786419.2015.1075527] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hepatitis C virus (HCV) is a major health problem across the world affecting the people of all age groups. It is the main cause of hepatitis and at chronic stage causes liver cirrhosis and hepatocellular carcinoma. Various therapeutics are made against HCV but still there is a need to find out potential therapeutics to combat the virus. The goal of this study is to identify the phytochemicals of Azadirachta indica leaves having antiviral activity against HCV NS3 protease through molecular docking and simulation approach. Results show that the compound 3-Deacetyl-3-cinnamoyl-azadirachtin possesses good binding properties with HCV NS3/4A protease. It can be concluded from this study that Deacetyl-3-cinnamoyl-azadirachtin may serve as a potential inhibitor against NS3/4A protease.
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Affiliation(s)
- Usman Ali Ashfaq
- a Department of Bioinformatics and Biotechnology , Government College University Faisalabad (GCUF) , Faisalabad , Pakistan
| | - Asma Jalil
- a Department of Bioinformatics and Biotechnology , Government College University Faisalabad (GCUF) , Faisalabad , Pakistan
| | - Muhammad Tahir Ul Qamar
- a Department of Bioinformatics and Biotechnology , Government College University Faisalabad (GCUF) , Faisalabad , Pakistan.,b Center of Agricultural Biochemistry and Biotechnology (CABB) , University of Agriculture (UAF) , Faisalabad , Pakistan
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15
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Sarrazin C, Lathouwers E, Peeters M, Daems B, Buelens A, Witek J, Wyckmans Y, Fevery B, Verbinnen T, Ghys A, Schlag M, Baldini A, De Meyer S, Lenz O. Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region. Antiviral Res 2015; 116:10-6. [PMID: 25614456 DOI: 10.1016/j.antiviral.2015.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/19/2014] [Accepted: 01/11/2015] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) NS3 polymorphism Q80K is mainly found in patients with HCV genotype (G) 1a, and has been associated with a reduced treatment response to simeprevir with pegylated interferon (P) and ribavirin (R). Prevalence of Q80K among G1 patients may vary geographically. Q80K prevalence in the North-American G1 population in a recent study was 34%. We conducted a post hoc meta-analysis of Q80K polymorphism prevalence among HCV G1-infected patients enrolled in simeprevir and telaprevir Phase II/III studies. Baseline HCV NS3/4A protease sequences were analysed by population sequencing to determine Q80K prevalence. Overall, of 3349 patients from 25 countries in the European region analysed, 35.8%, 63.8% and 0.3% of patients had G1a, G1b and other/unknown HCV G1 subtypes, respectively. Q80K was detected at baseline in 7.5% of HCV G1 patients overall. Examination by subtype showed that 19.8%, 0.5% and 18.2% of patients with G1a, G1b and other/unknown HCV G1 subtypes had the Q80K polymorphism, respectively. Among countries in the European region with sequencing data available for either ⩾20 patients with G1a and/or ⩾40 G1 patients overall, the Q80K prevalence in G1 ranged from 0% in Bulgaria to 18.2% in the UK. Q80K prevalence also varied within G1a across different countries. HCV subtype 1a was correctly determined in 99% of patients by the LiPA v2 assay. A low overall prevalence of Q80K was observed in HCV G1-infected patients in the European region, compared with North America. However, the prevalence varied by country, due to differing ratios of G1a/G1b and differing Q80K prevalence within the G1a populations.
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Affiliation(s)
- Christoph Sarrazin
- Johann Wolfgang Goethe University Hospital, Medical Department 1, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Erkki Lathouwers
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Monika Peeters
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bjorn Daems
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Annemie Buelens
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - James Witek
- Janssen Research & Development LLC, 1125 Trenton Harbourton Rd, Titusville, NJ 08560, United States.
| | - Yves Wyckmans
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bart Fevery
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Thierry Verbinnen
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Anne Ghys
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Michael Schlag
- Janssen-Cilag, Vorgartenstraße 206B, 1020 Vienna, Austria.
| | - Alessandra Baldini
- Janssen Cilag, 1 Rue Camille Desmoulins, 92130 Issy-les-Moulineaux, France.
| | - Sandra De Meyer
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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