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Farouk F, Ibrahim IM, Sherif S, Abdelhamed HG, Sharaky M, Al-Karmalawy AA. Investigating the effect of polymerase inhibitors on cellular proliferation: Computational studies, cytotoxicity, CDK1 inhibitory potential, and LC-MS/MS cancer cell entrapment assays. Chem Biol Drug Des 2024; 103:e14500. [PMID: 38467555 DOI: 10.1111/cbdd.14500] [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: 10/07/2023] [Revised: 02/04/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Directly acting antivirals (DAAs) are a breakthrough in the treatment of HCV. There are controversial reports on their tendency to induce hepatocellular carcinoma (HCC) in HCV patients. Numerous reports have concluded that the HCC is attributed to patient-related factors while others are inclined to attribute this as a DAA side-effect. This study aims to investigate the effect of polymerase inhibitor DAAs, especially daclatasivir (DLT) on cellular proliferation as compared to ribavirin (RBV). The interaction of DAAs with variable cell-cycle proteins was studied in silico. The binding affinities to multiple cellular targets were investigated and the molecular dynamics were assessed. The in vitro effect of the selected candidate DLT on cancer cell proliferation was determined and the CDK1 inhibitory potential in was evaluated. Finally, the cellular entrapment of the selected candidates was assessed by an in-house developed and validated LC-MS/MS method. The results indicated that polymerase inhibitor antiviral agents, especially DLT, may exert an anti-proliferative potential against variable cancer cell lines. The results showed that the effect may be achieved via potential interaction with the multiple cellular targets, including the CDK1, resulting in halting of the cellular proliferation. DLT exhibited a remarkable cell permeability in the liver cancer cell line which permits adequate interaction with the cellular targets. In conclusion, the results reveal that the polymerase inhibitor (DLT) may have an anti-proliferative potential against liver cancer cells. These results may pose DLT as a therapeutic choice for patients suffering from HCV and are liable to HCC development.
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Affiliation(s)
- Faten Farouk
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Salma Sherif
- Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | | | - Marwa Sharaky
- Pharmacology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Biochemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
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2
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Sun JG, Nie P, Herdewijn P, Li XJ. Exploring the synthetic approaches and clinical prowess of established macrocyclic pharmaceuticals. Eur J Med Chem 2024; 264:116051. [PMID: 38104377 DOI: 10.1016/j.ejmech.2023.116051] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Macrocyclic compounds, characterized by cyclic structures, often originate from either modified forms of unicyclic canonical molecules or natural products. Within the field of medicinal chemistry, there has been a growing fascination with drug-like macrocycles in recent years, primarily due to compelling evidence indicating that macrocyclization can significantly influence both the biological and physiochemical properties, as well as the selectivity, when compared to their acyclic counterparts. The approval of contemporary pharmaceutical agents like Lorlatinib underscore the notable clinical relevance of drug-like macrocycles. Nonetheless, the synthesis of these drug-like macrocycles poses substantial challenges, primarily stemming from the complexity of ring-closing reactions, which are inherently dependent on the size and geometry of the bridging linker, impacting overall yields. Nevertheless, macrocycles offer a promising avenue for expanding the synthetic toolkit in medicinal chemistry, enabling the creation of bioactive compounds. To shed light on the subject, we delve into the clinical prowess of established macrocyclic drugs, spanning various therapeutic areas, including oncology, and infectious diseases. Case studies of clinically approved macrocyclic agents illustrate their profound impact on patient care and disease management. As we embark on this journey through the world of macrocyclic pharmaceuticals, we aim to provide a comprehensive overview of their synthesis and clinical applications, shedding light on the pivotal role they play in modern medicine.
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Affiliation(s)
- Jian-Gang Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Peng Nie
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Xiao-Jing Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
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3
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Bafna K, Cioffi CL, Krug RM, Montelione GT. Structural similarities between SARS-CoV2 3CL pro and other viral proteases suggest potential lead molecules for developing broad spectrum antivirals. Front Chem 2022; 10:948553. [PMID: 36353143 PMCID: PMC9638714 DOI: 10.3389/fchem.2022.948553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/08/2022] [Indexed: 09/01/2023] Open
Abstract
Considering the significant impact of the recent COVID-19 outbreak, development of broad-spectrum antivirals is a high priority goal to prevent future global pandemics. Antiviral development processes generally emphasize targeting a specific protein from a particular virus. However, some antiviral agents developed for specific viral protein targets may exhibit broad spectrum antiviral activity, or at least provide useful lead molecules for broad spectrum drug development. There is significant potential for repurposing a wide range of existing viral protease inhibitors to inhibit the SARS-CoV2 3C-like protease (3CLpro). If effective even as relatively weak inhibitors of 3CLpro, these molecules can provide a diverse and novel set of scaffolds for new drug discovery campaigns. In this study, we compared the sequence- and structure-based similarity of SARS-CoV2 3CLpro with proteases from other viruses, and identified 22 proteases with similar active-site structures. This structural similarity, characterized by secondary-structure topology diagrams, is evolutionarily divergent within taxonomically related viruses, but appears to result from evolutionary convergence of protease enzymes between virus families. Inhibitors of these proteases that are structurally similar to the SARS-CoV2 3CLpro protease were identified and assessed as potential inhibitors of SARS-CoV2 3CLpro protease by virtual docking. Several of these molecules have docking scores that are significantly better than known SARS-CoV2 3CLpro inhibitors, suggesting that these molecules are also potential inhibitors of the SARS-CoV2 3CLpro protease. Some have been previously reported to inhibit SARS-CoV2 3CLpro. The results also suggest that established inhibitors of SARS-CoV2 3CLpro may be considered as potential inhibitors of other viral 3C-like proteases.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Christopher L. Cioffi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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4
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Shiner B, Huybrechts K, Gui J, Rozema L, Forehand J, Watts BV, Jiang T, Hoyt JE, Esteves J, Schnurr PP, Ray K, Gradus JL. Comparative Effectiveness of Direct-Acting Antivirals for Posttraumatic Stress Disorder in Veterans Affairs Patients With Hepatitis C Virus Infection. Am J Epidemiol 2022; 191:1614-1625. [PMID: 35689641 PMCID: PMC9989349 DOI: 10.1093/aje/kwac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 01/29/2023] Open
Abstract
We recently conducted an exploratory study that indicated that several direct-acting antivirals (DAAs), highly effective medications for hepatitis C virus (HCV) infection, were also associated with improvement in posttraumatic stress disorder (PTSD) among a national cohort of US Department of Veterans Affairs (VA) patients treated between October 1, 1999, and September 30, 2019. Limiting the same cohort to patients with PTSD and HCV, we compared the associations of individual DAAs with PTSD symptom improvement using propensity score weighting. After identifying patients who had available baseline and endpoint PTSD symptom data as measured with the PTSD Checklist (PCL), we compared changes over the 8-12 weeks of DAA treatment. The DAAs most prescribed in conjunction with PCL measurement were glecaprevir/pibrentasvir (GLE/PIB; n = 54), sofosbuvir/velpatasvir (SOF/VEL; n = 54), and ledipasvir/sofosbuvir (LDV/SOF; n = 145). GLE/PIB was superior to LDV/SOF, with a mean difference in improvement of 7.3 points on the PCL (95% confidence interval (CI): 1.1, 13.6). The mean differences in improvement on the PCL were smaller between GLE/PIB and SOF/VEL (3.0, 95% CI: -6.3, 12.2) and between SOF/VEL and LDV/SOF (4.4, 95% CI: -2.4, 11.2). While almost all patients were cured of HCV (92.5%) regardless of the agent received, PTSD outcomes were superior for those receiving GLE/PIB compared with those receiving LDV/SOF, indicating that GLE/PIB may merit further investigation as a potential PTSD treatment.
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Affiliation(s)
- Brian Shiner
- Correspondence to Dr. Brian Shiner, VA Medical Center, 215 N. Main Street, White River Junction, VT 05009 (e-mail: )
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5
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Lafridi H, Almalki FA, Ben Hadda T, Berredjem M, Kawsar SMA, Alqahtani AM, Esharkawy ER, Lakhrissi B, Zgou H. In silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site. J Biomol Struct Dyn 2022; 41:2260-2273. [PMID: 35075979 DOI: 10.1080/07391102.2022.2029571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An array of computational approaches DFT/QSAR/POM methods has been used for a better understanding of drug properties regarding 13 inhibitor derivatives containing either P2 cyclopentane P1 carboxylic acid moiety (1-9) or a P1 cyclopropyl acyl sulfonamide (10-13). To further recognize binding interactions and their activity trends, molecular docking studies were carried out with the use of HCV, which can be used to accurately predict the interactions of ligands with the receptor. The QSAR models are developed through the use of Multiple Linear Regression (MLR) together with Principal Component Analysis (PCA) methods. The statistical results indicate the multiple correlation coefficient R2 = 0.840, which shows favorable estimation stability, as well as showing a significant correlation between the HCV NS3 protease of the studied compounds and their electron-accepting ability. The POM analysis of the Physico-chemical properties of compounds 1-13, shows that they are bearing (O1, O2) and/or (O1, O2, O3) antiviral pockets, whereby all oxygen atoms are Osp2 and bearing negative charges. Similar to the reference ligand (F9K), the most active compound 10 was bound deeply into the binding cavity of NS3 protease making interactions with the residues Gly137, His57, Ala157, and His528. The anti-hepatitis pharmacophore site is similar to the anti-HIV pharmacophore site.
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Affiliation(s)
- Hind Lafridi
- Material Sciences, Processes, Environment and Modeling, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco.,Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia.,Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Eman R Esharkawy
- Department of Plant Ecology and Range Management, Ecology and Dry Lands Agriculture Division, Desert Research Center, Mathef El-Mataria, Egypt.,Department of Chemistry, Science Faculty for Girls, Northern Border University ARAR, North Region, Saudi Arabia
| | - Brahim Lakhrissi
- Laboratory of Organic Chemistry, Catalysis, and Environment, Department of Chemistry, Faculty of Sciences, Ibn Tofaïl University, Kenitra, Morocco
| | - Hsaine Zgou
- Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
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6
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Dultz G, Srikakulam SK, Konetschnik M, Shimakami T, Doncheva NT, Dietz J, Sarrazin C, Biondi RM, Zeuzem S, Tampé R, Kalinina OV, Welsch C. Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability. J Biol Chem 2021; 297:101031. [PMID: 34339738 PMCID: PMC8405986 DOI: 10.1016/j.jbc.2021.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022] Open
Abstract
The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.
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Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany; Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken, Germany
| | - Michael Konetschnik
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julia Dietz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ricardo M Biondi
- Molecular Targeting, Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Medical Faculty, Saarland University, Homburg, Germany; Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany.
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7
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Havranek B, Islam SM. An in silico approach for identification of novel inhibitors as potential therapeutics targeting COVID-19 main protease. J Biomol Struct Dyn 2021; 39:4304-4315. [PMID: 32544024 PMCID: PMC7309303 DOI: 10.1080/07391102.2020.1776158] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023]
Abstract
Respiratory disease caused by a novel coronavirus, COVID-19, has been labeled a pandemic by the World Health Organization. Very little is known about the infection mechanism for this virus. More importantly, there are no drugs or vaccines that can cure or prevent a person from getting COVID-19. In this study, the binding affinity of 2692 protease inhibitor compounds that are known in the protein data bank, are calculated against the main protease of the novel coronavirus with docking and molecular dynamics (MD). Both the docking and MD methods predict the macrocyclic tissue factor-factor VIIa (PubChem ID: 118098670) inhibitor to bind strongly with the main protease with a binding affinity of -10.6 and -10.0 kcal/mol, respectively. The TF-FVIIa inhibitors are known to prevent the coagulation of blood and have antiviral activity as shown in the case of SARS coronavirus. Two more inhibitors, phenyltriazolinones (PubChem ID: 104161460) and allosteric HCV NS5B polymerase thumb pocket 2 (PubChem ID: 163632044) have shown antiviral activity and also have high affinity towards the main protease of COVID-19. Furthermore, these inhibitors interact with the catalytic dyad in the active site of the COVID-19 main protease that is especially important in viral replication. The calculated theoretical dissociation constants of the proposed COVID-19 inhibitors are found to be very similar to the experimental dissociation constant values of similar protease-inhibitor systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Shahidul M. Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
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8
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Zhang H, Zheng X, Li J, Liu Q, Huang XX, Ding H, Suzuki R, Muramatsu M, Song SJ. Flavonoid-triazolyl hybrids as potential anti-hepatitis C virus agents: Synthesis and biological evaluation. Eur J Med Chem 2021; 218:113395. [PMID: 33838584 DOI: 10.1016/j.ejmech.2021.113395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/06/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022]
Abstract
A series of flavonoid-triazolyl hybrids were synthesized and evaluated as novel inhibitors of hepatitis C virus (HCV). The results of anti-HCV activity assays showed that most of the synthesized derivatives at a concentration of 100 μg/mL inhibited the generation of progeny virus. Among these derivatives, 10m and 10r exhibited the most potent anti-HCV activity and inhibited the production of HCV in a dose-dependent manner. Interestingly, 10m and 10r had no significant inhibitory effect on viral translation or replication. Additional action mechanism studies revealed that the most potent compounds, 10m and 10r, significantly inhibited viral entry to 34.0% and 52.0%, respectively, at 10 μM. These results suggest further effective application of 10m and 10r as potential HCV preventive agents.
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Affiliation(s)
- Han Zhang
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xin Zheng
- Department of Cardiology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan
| | - Jichong Li
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingbo Liu
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Huaiwei Ding
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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9
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Perelson AS, Ke R. Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics. Clin Pharmacol Ther 2021; 109:829-840. [PMID: 33410134 DOI: 10.1002/cpt.2160] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Modern viral kinetic modeling and its application to therapeutics is a field that attracted the attention of the medical, pharmaceutical, and modeling communities during the early days of the AIDS epidemic. Its successes led to applications of modeling methods not only to HIV but a plethora of other viruses, such as hepatitis C virus (HCV), hepatitis B virus and cytomegalovirus, which along with HIV cause chronic diseases, and viruses such as influenza, respiratory syncytial virus, West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which generally cause acute infections. Here we first review the historical development of mathematical models to understand HIV and HCV infections and the effects of treatment by fitting the models to clinical data. We then focus on recent efforts and contributions of applying these models towards understanding SARS-CoV-2 infection and highlight outstanding questions where modeling can provide crucial insights and help to optimize nonpharmaceutical and pharmaceutical interventions of the coronavirus disease 2019 (COVID-19) pandemic. The review is written from our personal perspective emphasizing the power of simple target cell limited models that provided important insights and then their evolution into more complex models that captured more of the virology and immunology. To quote Albert Einstein, "Everything should be made as simple as possible, but not simpler," and this idea underlies the modeling we describe below.
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Affiliation(s)
- Alan S Perelson
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ruian Ke
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
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10
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Dinesh DC, Tamilarasan S, Rajaram K, Bouřa E. Antiviral Drug Targets of Single-Stranded RNA Viruses Causing Chronic Human Diseases. Curr Drug Targets 2021; 21:105-124. [PMID: 31538891 DOI: 10.2174/1389450119666190920153247] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid (RNA) viruses associated with chronic diseases in humans are major threats to public health causing high mortality globally. The high mutation rate of RNA viruses helps them to escape the immune response and also is responsible for the development of drug resistance. Chronic infections caused by human immunodeficiency virus (HIV) and hepatitis viruses (HBV and HCV) lead to acquired immunodeficiency syndrome (AIDS) and hepatocellular carcinoma respectively, which are one of the major causes of human deaths. Effective preventative measures to limit chronic and re-emerging viral infections are absolutely necessary. Each class of antiviral agents targets a specific stage in the viral life cycle and inhibits them from its development and proliferation. Most often, antiviral drugs target a specific viral protein, therefore only a few broad-spectrum drugs are available. This review will be focused on the selected viral target proteins of pathogenic viruses containing single-stranded (ss) RNA genome that causes chronic infections in humans (e.g. HIV, HCV, Flaviviruses). In the recent past, an exponential increase in the number of available three-dimensional protein structures (>150000 in Protein Data Bank), allowed us to better understand the molecular mechanism of action of protein targets and antivirals. Advancements in the in silico approaches paved the way to design and develop several novels, highly specific small-molecule inhibitors targeting the viral proteins.
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Affiliation(s)
| | - Selvaraj Tamilarasan
- Section of Microbial Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kaushik Rajaram
- Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, India
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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11
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Abstract
Over the past 60 years, more than 100 antiviral drugs or their combinations have been approved for clinical use. Antiviral drugs can be classified according to their chemical nature (e.g., small-molecules, peptides, biologics) or mechanisms of drug actions against specific viral proteins (e.g., polymerase inhibitors, protease inhibitors, glycoprotein inhibitors). This article provides an overview of antiviral classifications in 10 important human viruses: hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), human cytomegalovirus (HCMV), herpes simplex virus (HSV), variola virus (human smallpox), varicella zoster virus (VZV), influenza virus, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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12
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Lim YS, Mai HN, Nguyen LP, Kang SM, Tark D, Hwang SB. Adenosylhomocysteinase like 1 interacts with nonstructural 5A and regulates hepatitis C virus propagation. J Microbiol 2020; 59:101-109. [PMID: 33355889 DOI: 10.1007/s12275-021-0470-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022]
Abstract
Hepatitis C virus (HCV) life cycle is highly dependent on cellular proteins for viral propagation. In order to identify the cellular factors involved in HCV propagation, we previously performed a protein microarray assay using the HCV nonstructural 5A (NS5A) protein as a probe. Of ∼9,000 human cellular proteins immobilized in a microarray, adenosylhomocysteinase like 1 (AHCYL1) was among 90 proteins identified as NS5A interactors. Of these candidates, AHCYL1 was selected for further study. In the present study, we verified the physical interaction between NS5A and AHCYL1 by both in vitro pulldown and coimmunoprecipitation assays. Furthermore, HCV NS5A interacted with endogenous AHCYL1 in Jc1-infected cells. Both NS5A and AHCYL1 were colocalized in the cytoplasmic region in HCV-replicating cells. siRNAmediated knockdown of AHCYL1 abrogated HCV propagation. Exogenous expression of the siRNA-resistant AHCYL1 mutant, but not of the wild-type AHCYL1, restored HCV protein expression levels, indicating that AHCYL1 was required specifically for HCV propagation. Importantly, AHCYL1 was involved in the HCV internal ribosome entry site-mediated translation step of the HCV life cycle. Finally, we demonstrated that the proteasomal degradation pathway of AHCYL1 was modulated by persistent HCV infection. Collectively, these data suggest that HCV may modulate the AHCYL1 protein to promote viral propagation.
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Affiliation(s)
- Yun-Sook Lim
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Han N Mai
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.,Ilsong Institute of Life Science, Hallym University, Anyang, 14066, Republic of Korea
| | - Lap P Nguyen
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Sang Min Kang
- Laboratory for Infectious Disease Prevention, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Dongseob Tark
- Laboratory for Infectious Disease Prevention, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Soon B Hwang
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea. .,Ilsong Institute of Life Science, Hallym University, Anyang, 14066, Republic of Korea.
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13
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Dultz G, Shimakami T, Schneider M, Murai K, Yamane D, Marion A, Zeitler TM, Stross C, Grimm C, Richter RM, Bäumer K, Yi M, Biondi RM, Zeuzem S, Tampé R, Antes I, Lange CM, Welsch C. Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors. J Biol Chem 2020; 295:13862-13874. [PMID: 32747444 PMCID: PMC7535904 DOI: 10.1074/jbc.ra120.013898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/26/2020] [Indexed: 12/20/2022] Open
Abstract
Inhibitors against the NS3-4A protease of hepatitis C virus (HCV) have proven to be useful drugs in the treatment of HCV infection. Although variants have been identified with mutations that confer resistance to these inhibitors, the mutations do not restore replicative fitness and no secondary mutations that rescue fitness have been found. To gain insight into the molecular mechanisms underlying the lack of fitness compensation, we screened known resistance mutations in infectious HCV cell culture with different genomic backgrounds. We observed that the Q41R mutation of NS3-4A efficiently rescues the replicative fitness in cell culture for virus variants containing mutations at NS3-Asp168 To understand how the Q41R mutation rescues activity, we performed protease activity assays complemented by molecular dynamics simulations, which showed that protease-peptide interactions far outside the targeted peptide cleavage sites mediate substrate recognition by NS3-4A and support protease cleavage kinetics. These interactions shed new light on the mechanisms by which NS3-4A cleaves its substrates, viral polyproteins and a prime cellular antiviral adaptor protein, the mitochondrial antiviral signaling protein MAVS. Peptide binding is mediated by an extended hydrogen-bond network in NS3-4A that was effectively optimized for protease-MAVS binding in Asp168 variants with rescued replicative fitness from NS3-Q41R. In the protease harboring NS3-Q41R, the N-terminal cleavage products of MAVS retained high affinity to the active site, rendering the protease susceptible for potential product inhibition. Our findings reveal delicately balanced protease-peptide interactions in viral replication and immune escape that likely restrict the protease adaptive capability and narrow the virus evolutionary space.
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Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Markus Schneider
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Kazuhisa Murai
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Daisuke Yamane
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Antoine Marion
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Tobias M Zeitler
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Claudia Stross
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christian Grimm
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Rebecca M Richter
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Katrin Bäumer
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Ricardo M Biondi
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter and Cluster of Excellence-Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Christian M Lange
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany.
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14
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B UR, Tandon H, Pradhan MK, Adhikesavan H, Srinivasan N, Das S, Jayaraman N. Potent HCV NS3 Protease Inhibition by a Water-Soluble Phyllanthin Congener. ACS OMEGA 2020; 5:11553-11562. [PMID: 32478245 PMCID: PMC7254805 DOI: 10.1021/acsomega.0c00786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/30/2020] [Indexed: 05/04/2023]
Abstract
NS3/4A protease of hepatitis C virus (HCV) plays an important role in viral RNA replication. A 1,4-diphenylbutanedicarboxylic acid derivative, namely, phyllanthin, extracted from the leaf of a herbal plant, Phyllanthus amarus, inhibits HCV NS3/4A protease and replication activities. However, the reduced aqueous solubility, high toxicity, and poor oral bioavailability are major impediments with phyllanthin. We herein present a design approach to generate phyllanthin congeners in order to potentiate inhibition activity against protease. The phyllanthin congeners were synthesized by chemical methods and subjected to systematic biological studies. One of the congeners, annotated as D8, is identified as a novel and potent inhibitor of the HCV-NS3/4Aprotease activity in vitro and the viral RNA replication in cell culture. Structural analysis using the computational-based docking approach demonstrated important noncovalent interactions between D8 and the catalytic residues of the viral protease. Furthermore, D8 was found to be significantly nontoxic in cell culture. More importantly, oral administration of D8 in BALB/c mice proved its better tolerability and bioavailability, as compared to native phyllanthin. Taken together, this study reveals a promising candidate for developing anti-HCV therapeutics to control HCV-induced liver diseases.
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Affiliation(s)
- Uma Reddy B
- Microbiology and
Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Manoj K. Pradhan
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560 012, India
| | | | | | - Saumitra Das
- Microbiology and
Cell Biology, Indian Institute of Science, Bangalore 560 012, India
- National Institute
of Biomedical Genomics, Kalyani 741 251, India
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15
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Bafna K, Krug RM, Montelione GT. Structural Similarity of SARS-CoV2 M pro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.12153615.v1. [PMID: 32511291 PMCID: PMC7263768 DOI: 10.26434/chemrxiv.12153615] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
During the current COVID-19 pandemic more than 160,000 people have died worldwide as of mid-April 2020, and the global economy has been crippled. Effective control of the SARS-CoV2 virus that causes the COVID-19 pandemic requires both vaccines and antivirals. Antivirals are particularly crucial to treat infected people during the period of time that an effective vaccine is being developed and deployed. Because the development of specific antiviral drugs can take a considerable length of time, an important approach is to identify existing drugs already approved for use in humans which could be repurposed as COVID-19 therapeutics. Here we focus on antivirals directed against the SARS-CoV2 Mpro protease, which is required for virus replication. A structural similarity search showed that the Hepatitis C virus (HCV) NS3/4A protease has a striking three-dimensional structural similarity to the SARS-CoV2 Mpro protease, particularly in the arrangement of key active site residues. We used virtual docking predictions to assess the hypothesis that existing drugs already approved for human use or clinical testing that are directed at the HCV NS3/4A protease might fit well into the active-site cleft of the SARS-CoV2 protease (Mpro). AutoDock docking scores for 12 HCV protease inhibitors and 9 HIV-1 protease inhibitors were determined and compared to the docking scores for an α-ketoamide inhibitor of Mpro, which has recently been shown to inhibit SARS-CoV2 virus replication in cell culture. We identified eight HCV protease inhibitors that bound to the Mpro active site with higher docking scores than the α-ketoamide inhibitor, suggesting that these protease inhibitors may effectively bind to the Mpro active site. These results provide the rationale for us to test the identified HCV protease inhibitors as inhibitors of the SARS-CoV2 protease, and as inhibitors of SARS-CoV2 virus replication. Subsequently these repurposed drugs could be evaluated as COVID-19 therapeutics.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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16
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Bafna K, Krug RM, Montelione GT. Structural Similarity of SARS-CoV2 M pro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.12153615.v1. [PMID: 32511291 PMCID: PMC7263768 DOI: 10.26434/chemrxiv.12153615.v1+10.26434/chemrxiv.12153615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/20/2024]
Abstract
During the current COVID-19 pandemic more than 160,000 people have died worldwide as of mid-April 2020, and the global economy has been crippled. Effective control of the SARS-CoV2 virus that causes the COVID-19 pandemic requires both vaccines and antivirals. Antivirals are particularly crucial to treat infected people during the period of time that an effective vaccine is being developed and deployed. Because the development of specific antiviral drugs can take a considerable length of time, an important approach is to identify existing drugs already approved for use in humans which could be repurposed as COVID-19 therapeutics. Here we focus on antivirals directed against the SARS-CoV2 Mpro protease, which is required for virus replication. A structural similarity search showed that the Hepatitis C virus (HCV) NS3/4A protease has a striking three-dimensional structural similarity to the SARS-CoV2 Mpro protease, particularly in the arrangement of key active site residues. We used virtual docking predictions to assess the hypothesis that existing drugs already approved for human use or clinical testing that are directed at the HCV NS3/4A protease might fit well into the active-site cleft of the SARS-CoV2 protease (Mpro). AutoDock docking scores for 12 HCV protease inhibitors and 9 HIV-1 protease inhibitors were determined and compared to the docking scores for an α-ketoamide inhibitor of Mpro, which has recently been shown to inhibit SARS-CoV2 virus replication in cell culture. We identified eight HCV protease inhibitors that bound to the Mpro active site with higher docking scores than the α-ketoamide inhibitor, suggesting that these protease inhibitors may effectively bind to the Mpro active site. These results provide the rationale for us to test the identified HCV protease inhibitors as inhibitors of the SARS-CoV2 protease, and as inhibitors of SARS-CoV2 virus replication. Subsequently these repurposed drugs could be evaluated as COVID-19 therapeutics.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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17
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Bafna K, Krug RM, Montelione GT. Structural Similarity of SARS-CoV2 M pro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.12153615.v1. [PMID: 32511291 PMCID: PMC7263768 DOI: 10.26434/chemrxiv.12153615.v1 10.26434/chemrxiv.12153615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
During the current COVID-19 pandemic more than 160,000 people have died worldwide as of mid-April 2020, and the global economy has been crippled. Effective control of the SARS-CoV2 virus that causes the COVID-19 pandemic requires both vaccines and antivirals. Antivirals are particularly crucial to treat infected people during the period of time that an effective vaccine is being developed and deployed. Because the development of specific antiviral drugs can take a considerable length of time, an important approach is to identify existing drugs already approved for use in humans which could be repurposed as COVID-19 therapeutics. Here we focus on antivirals directed against the SARS-CoV2 Mpro protease, which is required for virus replication. A structural similarity search showed that the Hepatitis C virus (HCV) NS3/4A protease has a striking three-dimensional structural similarity to the SARS-CoV2 Mpro protease, particularly in the arrangement of key active site residues. We used virtual docking predictions to assess the hypothesis that existing drugs already approved for human use or clinical testing that are directed at the HCV NS3/4A protease might fit well into the active-site cleft of the SARS-CoV2 protease (Mpro). AutoDock docking scores for 12 HCV protease inhibitors and 9 HIV-1 protease inhibitors were determined and compared to the docking scores for an α-ketoamide inhibitor of Mpro, which has recently been shown to inhibit SARS-CoV2 virus replication in cell culture. We identified eight HCV protease inhibitors that bound to the Mpro active site with higher docking scores than the α-ketoamide inhibitor, suggesting that these protease inhibitors may effectively bind to the Mpro active site. These results provide the rationale for us to test the identified HCV protease inhibitors as inhibitors of the SARS-CoV2 protease, and as inhibitors of SARS-CoV2 virus replication. Subsequently these repurposed drugs could be evaluated as COVID-19 therapeutics.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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18
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Bafna K, Krug RM, Montelione GT. Structural Similarity of SARS-CoV2 M pro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020. [PMID: 32511291 DOI: 10.26434/chemrxiv.12153615.v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
During the current COVID-19 pandemic more than 160,000 people have died worldwide as of mid-April 2020, and the global economy has been crippled. Effective control of the SARS-CoV2 virus that causes the COVID-19 pandemic requires both vaccines and antivirals. Antivirals are particularly crucial to treat infected people during the period of time that an effective vaccine is being developed and deployed. Because the development of specific antiviral drugs can take a considerable length of time, an important approach is to identify existing drugs already approved for use in humans which could be repurposed as COVID-19 therapeutics. Here we focus on antivirals directed against the SARS-CoV2 Mpro protease, which is required for virus replication. A structural similarity search showed that the Hepatitis C virus (HCV) NS3/4A protease has a striking three-dimensional structural similarity to the SARS-CoV2 Mpro protease, particularly in the arrangement of key active site residues. We used virtual docking predictions to assess the hypothesis that existing drugs already approved for human use or clinical testing that are directed at the HCV NS3/4A protease might fit well into the active-site cleft of the SARS-CoV2 protease (Mpro). AutoDock docking scores for 12 HCV protease inhibitors and 9 HIV-1 protease inhibitors were determined and compared to the docking scores for an α-ketoamide inhibitor of Mpro, which has recently been shown to inhibit SARS-CoV2 virus replication in cell culture. We identified eight HCV protease inhibitors that bound to the Mpro active site with higher docking scores than the α-ketoamide inhibitor, suggesting that these protease inhibitors may effectively bind to the Mpro active site. These results provide the rationale for us to test the identified HCV protease inhibitors as inhibitors of the SARS-CoV2 protease, and as inhibitors of SARS-CoV2 virus replication. Subsequently these repurposed drugs could be evaluated as COVID-19 therapeutics.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
| | - Robert M Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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19
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Plant-Derived Purification, Chemical Synthesis, and In Vitro/In Vivo Evaluation of a Resveratrol Dimer, Viniferin, as an HCV Replication Inhibitor. Viruses 2019; 11:v11100890. [PMID: 31547617 PMCID: PMC6832221 DOI: 10.3390/v11100890] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/03/2019] [Accepted: 09/20/2019] [Indexed: 02/08/2023] Open
Abstract
Oligostilbenoid compounds, a group of resveratrol multimers, display several anti-microbial activities through the neutralization of cytotoxic oxidants, and by inhibiting essential host and viral enzymes. In our previous study, we identified a series of oligostilbenoid compounds as potent hepatitis C virus (HCV) replication inhibitors. In particular, vitisin B, a resveratrol tetramer, exhibited the most dramatic anti-HCV activity (EC50 = 6 nM and CC50 > 10 μM) via the disruption of the viral helicase NS3 (IC50 = 3 nM). However, its further development as an HCV drug candidate was halted due to its intrinsic drawbacks, such as poor stability, low water solubility, and restricted in vivo absorption. In order to overcome these limitations, we focused on (+)-ε-viniferin, a resveratrol dimer, as an alternative. We prepared three different versions of (+)-ε-viniferin, including one which was extracted from the grapevine root (EVF) and two which were chemically synthesized with either penta-acetylation (SVF-5Ac) or no acetylation (SVF) using a newly established synthesis method. We confirmed their anti-HCV replication activities and minimal cytotoxicity by using genotype 1b and 2a HCV replicon cells. Their anti-HCV replication action also translated into a significant reduction of viral protein expression. Anti-HCV NS3 helicase activity by EVF was also verified in vitro. Finally, we demonstrated that SVF has improved pharmacokinetic properties over vitisin B. Overall, the favorable antiviral and pharmacokinetic properties of these three versions of viniferin warrant their further study as members of a promising new class of anti-HCV therapeutics.
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20
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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] [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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21
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Zhu XB, Zhuo LY, Yue M, Liu M, Zang F, Fan HZ, Wu JJ, Xia XS, Zhang AM, Yu RB, Huang P. Genetic variants in IFIH1 and DDX58 influence hepatitis C virus clearance in Chinese Han population. J Med Virol 2019; 91:1097-1103. [PMID: 30633820 DOI: 10.1002/jmv.25398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/26/2018] [Accepted: 01/05/2019] [Indexed: 12/17/2022]
Abstract
AIMS To investigate the association between two RIG-I-like receptor gene polymorphisms and hepatitis C virus (HCV) infection in Chinese Han population. METHODS The current study genotyped two selected SNPs (IFIH1 rs3747517 and DDX58 rs9695310) using TaqMan allelic discrimination assay to assess their association with the susceptibility and clinical outcome of HCV infection among 3065 participants (1545 non-HCV infection individuals, 568 spontaneous HCV clearance cases, and 952 persistent infection patients). RESULTS IFIH1 rs3747517 (dominant model: Adjusted odds ratio [OR] = 1.34, 95% confidence interval [CI] = 1.07-1.68; P = 0.009) and DDX58 rs9695310 (dominant model: Adjusted OR = 1.43, 95% CI = 1.15-1.78; P = 0.001) were associated with chronic hepatitis C (CHC). And the risk of CHC increased when people were carrying more unfavorable rs3747517-GA/AA and rs9695310-GC/CC genotypes from zero to two with the chronic rates of 56.72%, 59.38%, and 69.01%, respectively (Ptrend < 0.001). CONCLUSION Genetic variations at IFIH1 rs3747517 and DDX58 rs9695310 were independent predictors of chronic hepatitis C in Chinese Han population.
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Affiliation(s)
- Xiao-Bo Zhu
- Department of Pharmacy, The People's Hospital of Danyang, Danyang, China
| | - Ling-Yun Zhuo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mei Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao-Zhi Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jing-Jing Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xue-Shan Xia
- Department of Bioengineering, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Department of Bioengineering, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Rong-Bin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
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Doncheva NT, Domingues FS, McGivern DR, Shimakami T, Zeuzem S, Lengauer T, Lange CM, Albrecht M, Welsch C. Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants. J Mol Biol 2019; 431:2354-2368. [PMID: 31051172 DOI: 10.1016/j.jmb.2019.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 12/24/2022]
Abstract
A variety of amino acid substitutions in the NS3-4A protease of the hepatitis C virus lead to protease inhibitor (PI) resistance. Many of these significantly impair the replication fitness of the resistant variants in a genotype- and subtype-dependent manner, a critical factor in determining the probability with which resistant variants will persist. However, the underlying molecular mechanisms are unknown. Here, we present a novel residue-interaction network approach to determine how near-neighbor interactions of PI resistance mutations in NS3-4A can impact protease functional sites dependent on their genomic background. We constructed subtype-specific consensus residue networks for subtypes 1a and 1b from protease structure ensembles combined with biological properties of protein residues and evolutionary amino acid conservation. By applying local and global network topology analysis and visual exploration, we characterize PI resistance-associated sites and outline differences in near-neighbor interactions. We find local residue-interaction patterns and features at protease functional sites that are subtype specific. The noncovalent bonding patterns indicate higher fitness costs conferred by PI resistance mutations in a subtype 1b genomic background and explain the prevalence of Q80K and R155K in subtype 1a. Based on local residue interactions, we predict a subtype-specific role for the protease residue NS3-Q80 in molecular mechanisms related to the assembly of infectious virus particles that is supported by experimental data on the capacity of Q80K variants to replicate and produce infectious virus in subtype 1a and 1b cell culture.
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Affiliation(s)
- Nadezhda T Doncheva
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | | | - David R McGivern
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Christian M Lange
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany
| | - Mario Albrecht
- Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria
| | - Christoph Welsch
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany.
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Alazard-Dany N, Denolly S, Boson B, Cosset FL. Overview of HCV Life Cycle with a Special Focus on Current and Possible Future Antiviral Targets. Viruses 2019; 11:v11010030. [PMID: 30621318 PMCID: PMC6356578 DOI: 10.3390/v11010030] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C infection is the leading cause of liver diseases worldwide and a major health concern that affects an estimated 3% of the global population. Novel therapies available since 2014 and 2017 are very efficient and the WHO considers HCV eradication possible by the year 2030. These treatments are based on the so-called direct acting antivirals (DAAs) that have been developed through research efforts by academia and industry since the 1990s. After a brief overview of the HCV life cycle, we describe here the functions of the different targets of current DAAs, the mode of action of these DAAs and potential future inhibitors.
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Affiliation(s)
- Nathalie Alazard-Dany
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Solène Denolly
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Bertrand Boson
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
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Unexpected Replication Boost by Simeprevir for Simeprevir-Resistant Variants in Genotype 1a Hepatitis C Virus. Antimicrob Agents Chemother 2018; 62:AAC.02601-17. [PMID: 29661883 DOI: 10.1128/aac.02601-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/10/2018] [Indexed: 12/15/2022] Open
Abstract
Simeprevir is a novel NS3/4A protease inhibitor (PI) of hepatitis C virus (HCV). The baseline polymorphism NS3-Q80K is frequently observed in genotype (GT) 1a HCV and often associated with treatment failure in simeprevir-containing regimens. We aimed to elucidate mechanisms of treatment failure due to NS3-Q80K. We included a Q80R mutation in our study and generated a series of Huh-7.5 cell lines, each of which harbored either wild-type GT 1a strain H77S.3 or the Q80K or Q80R variant. The cells were cultured with increasing concentrations of simeprevir, and NS3 domain sequences were determined. The mutations identified by sequence analyses were subsequently introduced into H77S.3. The sensitivity of each mutant to the NS3/4A PIs simeprevir, asunaprevir, grazoprevir, and paritaprevir was analyzed. We introduced the mutations into GT 1b strain N.2 and compared the sensitivity to simeprevir with that of GT 1a strain H77S.3. While simeprevir treatment selected mutations at residue D168, such as D168A/V in the wild-type virus, an additional mutation at residue R155, R155K, was selected in Q80K/R variants at simeprevir concentrations of <2.5 μM. Sensitivity analyses showed that simeprevir concentrations of <1 μM significantly boosted the replication of Q80K/R R155K variants. Interestingly, this boost was not observed with the other NS3/4A PIs or in Q80R R155Q/G/T/W variants or GT 1b isolates. The boosted replication of the Q80K+R155K variant by simeprevir could be related to treatment failure in simeprevir-containing antiviral treatments in GT 1a HCV-infected patients with the NS3-Q80K polymorphism. This result provides new insight into how resistance-associated variants can cause treatment failure.
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Cory TJ, Mu Y, Gong Y, Kodidela S, Kumar S. Sofosbuvir + velpatasvir + voxilaprevir for the treatment of hepatitis C infection. Expert Opin Pharmacother 2018; 19:749-757. [PMID: 29634360 DOI: 10.1080/14656566.2018.1459567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Hepatitis C is a disease with a significant global impact. Over the last several years, the treatment of the disease has been revolutionized. Therapy has transformed over the last several years with the approval of second generation direct acting antivirals, and currently utilized medications for the treatment of hepatitis C are significantly more efficacious with better safety profiles than previously approved treatments. Treatment for individuals who have failed therapy on direct acting antivirals has, until recently, been complex and difficult to treat, but the approval of sofosbuvir/velpatasvir/voxilaprevir represents a new therapeutic option for these individuals. Areas covered: Sofosbuvir/velpatasvir/voxilaprevir is a recently approved therapeutic combination for the treatment of hepatitis C. This article reviews the studies leading to the approval of the combination, and its efficacy and safety profile. Expert opinion: Sofosbuvir/velpatasvir/voxilaprevir fills one of the previously unfilled niches for the treatment of hepatitis C, that of the treatment of individuals who have failed therapy with resistant virus. With the filling of this niche, there appears to be a general slowing of the development of new therapeutics. Although understandable, in the long term, there are considerable risks associated with the decreased development of new drugs to treat hepatitis C.
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Affiliation(s)
- Theodore J Cory
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Ying Mu
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Yuqing Gong
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Sunitha Kodidela
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Santosh Kumar
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
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The discovery and optimization of naphthalene-linked P2-P4 Macrocycles as inhibitors of HCV NS3 protease. Bioorg Med Chem Lett 2018; 28:43-48. [DOI: 10.1016/j.bmcl.2017.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022]
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NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA. J Virol 2017; 92:JVI.01253-17. [PMID: 29070684 PMCID: PMC5730761 DOI: 10.1128/jvi.01253-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/10/2017] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C viruses (HCV) encode a helicase enzyme that is essential for viral replication and assembly (nonstructural protein 3 [NS3]). This helicase has become the focus of extensive basic research on the general helicase mechanism, and it is also of interest as a novel drug target. Despite the importance of this protein, mechanistic work on NS3 has been conducted almost exclusively on variants from HCV genotype 1. Our understanding of NS3 from the highly active HCV strains that are used to study HCV genetics and mechanism in cell culture (such as JFH-1) is lacking. We therefore set out to determine whether NS3 from the replicatively efficient genotype 2a strain JFH-1 displays novel functional or structural properties. Using biochemical assays for RNA binding and duplex unwinding, we show that JFH-1 NS3 binds RNA much more rapidly than the previously studied NS3 variants from genotype 1b. Unlike NS3 variants from other genotypes, JFH-1 NS3 binds RNA with high affinity in a functionally active form that is capable of immediately unwinding RNA duplexes without undergoing rate-limiting conformational changes that precede activation. Unlike other superfamily 2 (SF2) helicases, JFH-1 NS3 does not require long 3′ overhangs, and it unwinds duplexes that are flanked by only a few nucleotides, as in the folded HCV genome. To understand the physical basis for this, we solved the crystal structure of JFH-1 NS3, revealing a novel conformation that contains an open, positively charged RNA binding cleft that is primed for productive interaction with RNA targets, potentially explaining robust replication by HCV JFH-1. IMPORTANCE Genotypes of HCV are as divergent as different types of flavivirus, and yet mechanistic features of HCV variants are presumed to be held in common. One of the most well-studied components of the HCV replication complex is a helicase known as nonstructural protein 3 (NS3). We set out to determine whether this important mechanical component possesses biochemical and structural properties that differ between common strains such as those of genotype 1b and a strain of HCV that replicates with exceptional efficiency (JFH-1, classified as genotype 2a). Indeed, unlike the inefficient genotype 1b NS3, which has been well studied, JFH-1 NS3 is a superhelicase with strong RNA affinity and high unwinding efficiency on a broad range of targets. Crystallographic analysis reveals architectural features that promote enhanced biochemical activity of JFH-1 NS3. These findings show that even within a single family of viruses, drift in sequence can result in the acquisition of radically new functional properties that enhance viral fitness.
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Viral Oncology: Molecular Biology and Pathogenesis. J Clin Med 2017; 6:jcm6120111. [PMID: 29186062 PMCID: PMC5742800 DOI: 10.3390/jcm6120111] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/17/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023] Open
Abstract
Oncoviruses are implicated in approximately 12% of all human cancers. A large number of the world's population harbors at least one of these oncoviruses, but only a small proportion of these individuals go on to develop cancer. The interplay between host and viral factors is a complex process that works together to create a microenvironment conducive to oncogenesis. In this review, the molecular biology and oncogenic pathways of established human oncoviruses will be discussed. Currently, there are seven recognized human oncoviruses, which include Epstein-Barr Virus (EBV), Human Papillomavirus (HPV), Hepatitis B and C viruses (HBV and HCV), Human T-cell lymphotropic virus-1 (HTLV-1), Human Herpesvirus-8 (HHV-8), and Merkel Cell Polyomavirus (MCPyV). Available and emerging therapies for these oncoviruses will be mentioned.
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Venkatesan A, Rambabu M, Jayanthi S, Febin Prabhu Dass J. Pharmacophore feature prediction and molecular docking approach to identify novel anti-HCV protease inhibitors. J Cell Biochem 2017; 119:960-966. [PMID: 28691304 DOI: 10.1002/jcb.26262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 02/06/2023]
Abstract
Discovering a potential drug for HCV treatment is a challenging task in the field of drug research. This study initiates with computational screening and modeling of promising ligand molecules. The foremost modeling method involves the identification of novel compound and its molecular interaction based on pharmacophore features. A total of 197 HCV compounds for NS3/4A protein target were screened for our study. The pharmacophore models were generated using PHASE module implemented in Schrodinger suite. The pharmacophore features include one hydrogen bond acceptor, one hydrogen bond donor, and three hydrophobic sites. As a result, based on mentioned hypothesis the model ADHHH.159 corresponds to the CID 59533233. Furthermore, docking was performed using maestro for all the 197 compounds. Among these, the CID 59533313 and 59533233 possess the best binding energy of -11.75 and -10.40 kcal/mol, respectively. The interactions studies indicated that the CID complexed with the NS3/4A protein possess better binding affinity with the other compounds. Further the compounds were subjected to calculate the ADME properties. Therefore, it can be concluded that these two compounds could be a potential alternative drug for the development of HCV.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Majji Rambabu
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Sivaraman Jayanthi
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
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30
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Son K, Nguyen TTT, Choi JW, Pham LV, Luong TTD, Lim YS, Hwang SB. Rad51 Interacts with Non-structural 3 Protein of Hepatitis C Virus and Regulates Viral Production. Front Microbiol 2017; 8:1249. [PMID: 28729862 PMCID: PMC5498509 DOI: 10.3389/fmicb.2017.01249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is a leading cause of chronic liver disease affecting over 170 million people worldwide. Chronic infection with HCV progresses to liver fibrosis, cirrhosis, and hepatocellular carcinoma. HCV exploits host cellular factors for viral propagation. To investigate the cellular factors required for HCV propagation, we screened a siRNA library targeting human cell cycle genes using cell culture grown HCV-infected cells. In the present study, we selected and characterized a gene encoding Rad51. Rad51, a member of a conserved recombinase family, is an essential factor for homologous recombination and repair of double-strand DNA breaks. We demonstrated that siRNA-mediated knockdown of Rad51 significantly inhibited HCV propagation without affecting HCV RNA replication. Silencing of Rad51 impaired secretion of infectious HCV particles and thus intracellular viruses were accumulated. We showed that HCV NS3 specifically interacted with Rad51 and accumulated Rad51 in the cytosol. Furthermore, Rad51 was coprecipitated with NS3 and HCV RNA. By employing membrane flotation and protease protection assays, we also demonstrated that Rad51 was co-fractionated with HCV NS3 on the lipid raft. These data indicate that Rad51 may be a component of the HCV RNA replication complex. Collectively, these data suggest that HCV may exploit cellular Rad51 to promote viral propagation and thus Rad51 may be a potential therapeutic target for HCV.
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Affiliation(s)
- Kidong Son
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea.,Environmental Health Research Department, National Institute of Environmental ResearchIncheon, South Korea
| | - Tram T T Nguyen
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
| | - Jae-Woong Choi
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
| | - Long V Pham
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
| | - Trang T D Luong
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
| | - Yun-Sook Lim
- National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
| | - Soon B Hwang
- Department of Biomedical Gerontology, Graduate School of Hallym UniversityChuncheon, South Korea.,National Research Laboratory of Hepatitis C Virus and Ilsong Institute of Life Science, Hallym UniversityAnyang, South Korea
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Benzine T, Brandt R, Lovell WC, Yamane D, Neddermann P, De Francesco R, Lemon SM, Perelson AS, Ke R, McGivern DR. NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains. PLoS Pathog 2017; 13:e1006343. [PMID: 28594932 PMCID: PMC5464671 DOI: 10.1371/journal.ppat.1006343] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/10/2017] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) RNA is synthesized by the replicase complex (RC), a macromolecular assembly composed of viral non-structural proteins and cellular co-factors. Inhibitors of the HCV NS5A protein block formation of new RCs but do not affect RNA synthesis by pre-formed RCs. Without new RC formation, existing RCs turn over and are eventually lost from the cell. We aimed to use NS5A inhibitors to estimate the half-life of the functional RC of HCV. We compared different cell culture-infectious strains of HCV that may be grouped based on their sensitivity to lipid peroxidation: robustly replicating, lipid peroxidation resistant (LPOR) viruses (e.g. JFH-1 or H77D) and more slowly replicating, lipid peroxidation sensitive (LPOS) viruses (e.g. H77S.3 and N.2). In luciferase assays, LPOS HCV strains declined under NS5A inhibitor therapy with much slower kinetics compared to LPOR HCV strains. This difference in rate of decline was not observed for inhibitors of the NS5B RNA-dependent RNA polymerase suggesting that the difference was not simply a consequence of differences in RNA stability. In further analyses, we compared two isoclonal HCV variants: the LPOS H77S.3 and the LPOR H77D that differ only by 12 amino acids. Differences in rate of decline between H77S.3 and H77D following NS5A inhibitor addition were not due to amino acid sequences in NS5A but rather due to a combination of amino acid differences in the non-structural proteins that make up the HCV RC. Mathematical modeling of intracellular HCV RNA dynamics suggested that differences in RC stability (half-lives of 3.5 and 9.9 hours, for H77D and H77S.3, respectively) are responsible for the different kinetics of antiviral suppression between LPOS and LPOR viruses. In nascent RNA capture assays, the rate of RNA synthesis decline following NS5A inhibitor addition was significantly faster for H77D compared to H77S.3 indicating different half-lives of functional RCs. Inhibitors targeting the HCV NS5A protein are a key component of highly effective interferon-free combination therapies for chronic hepatitis C. Despite their high potency against HCV, the precise details of their mode of action are poorly understood. They are known to block assembly and release of virus particles from infected hepatocytes, resulting in a rapid drop in viral RNA in the blood. Additionally they block formation of intracellular membrane structures that are the site of viral RNA synthesis in infected hepatocytes. By preventing membrane remodeling, NS5A inhibitors effectively block formation of new RCs within the cell. Following addition of NS5A inhibitors to infected cell cultures, the kinetics of antiviral suppression were found to vary between different HCV strains, independent of specific differences in NS5A sequence. Using an integrated experimental and mathematical modeling approach, we provide evidence that the rate of decline of viral RNA abundance in infected cells treated with NS5A inhibitors is determined by the stability or half-life of the functional HCV RC.
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Affiliation(s)
- Tiffany Benzine
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan Brandt
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William C. Lovell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daisuke Yamane
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Petra Neddermann
- INGM -Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Raffaele De Francesco
- INGM -Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Stanley M. Lemon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David R. McGivern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle. Antimicrob Agents Chemother 2016; 60:3563-78. [PMID: 27021330 DOI: 10.1128/aac.02929-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/21/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) NS3 protease inhibitors (PIs) are important components of novel HCV therapy regimens. Studies of PI resistance initially focused on genotype 1. Therefore, knowledge about the determinants of PI resistance for the highly prevalent genotypes 2 to 6 remains limited. Using Huh7.5 cell culture-infectious HCV recombinants with genotype 1 to 6 NS3 protease, we identified protease positions 54, 155, and 156 as hot spots for the selection of resistance substitutions under treatment with the first licensed PIs, telaprevir and boceprevir. Treatment of a genotype 2 isolate with the newer PIs vaniprevir, faldaprevir, simeprevir, grazoprevir, paritaprevir, and deldeprevir identified positions 156 and 168 as hot spots for resistance; the Y56H substitution emerged for three newer PIs. Substitution selection also depended on the specific recombinant. The substitutions identified conferred cross-resistance to several PIs; however, most substitutions selected under telaprevir or boceprevir treatment conferred less resistance to certain newer PIs. In a single-cycle production assay, across genotypes, PI treatment primarily decreased viral replication, which was rescued by PI resistance substitutions. The substitutions identified resulted in differential effects on viral fitness, depending on the original recombinant and the substitution. Across genotypes, fitness impairment induced by resistance substitutions was due primarily to decreased replication. Most combinations of substitutions that were identified increased resistance or fitness. Combinations of resistance substitutions with fitness-compensating substitutions either rescued replication or compensated for decreased replication by increasing assembly. This comprehensive study provides insight into the selection patterns and effects of PI resistance substitutions for HCV genotypes 1 to 6 in the context of the infectious viral life cycle, which is of interest for clinical and virological HCV research.
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Lin B, He S, Yim HJ, Liang TJ, Hu Z. Evaluation of antiviral drug synergy in an infectious HCV system. Antivir Ther 2016; 21:595-603. [PMID: 27035622 DOI: 10.3851/imp3044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) have greatly improved the treatment of HCV infection. To improve response and prevent resistance, combination regimens have been the focus of clinical development. Regimens are often first assessed in vitro, with most combination studies to date using subgenomic replicon systems, which do not replicate the complete HCV life cycle and preclude study of entry and assembly inhibitors. Infectious full-length HCV systems have been developed and are being used to test drug efficacy. METHODS Using cell-based HCV Con1b replicon and an infectious full-length HCV (HCVcc-Luc) infection system, we systematically tested the synergy, additivity or antagonism of combinations of protease, NS5A and nucleotide NS5B inhibitor classes as well as the combination of these DAAs with host-targeting agent cyclosporin A or non-antibody entry inhibitor (S)-chlorcyclizine. Two computational software packages, MacSynergyII and CalcuSyn, were used for data analysis. RESULTS Combinations between different classes showed good consistency across the two viral assay systems and two software platforms. Combinations between NS5A and nucleotide NS5B inhibitors were synergistic, while combinations of protease inhibitors with the other two classes were additive to slightly antagonistic. As expected, combinations of antivirals of the same class were additive. Combination studies between these DAA classes and cyclosporin A or (S)-chlorcyclizine demonstrated additive to synergistic effects and highly synergistic effects, respectively. Combinations of these drugs did not show any added or unexpected cytotoxicity. CONCLUSIONS Our results show that in vitro combination studies of anti-HCV DAAs in the HCVcc system may provide useful guidance for drug combination designs in clinical studies. We also demonstrate that these DAAs in combination with host-targeting agents or entry inhibitors may improve HCV treatment response.
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Affiliation(s)
- Billy Lin
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shanshan He
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hyung Joon Yim
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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Natural HCV variants with increased replicative fitness due to NS3 helicase mutations in the C-terminal helix α18. Sci Rep 2016; 6:19526. [PMID: 26787124 PMCID: PMC4726148 DOI: 10.1038/srep19526] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/14/2015] [Indexed: 12/12/2022] Open
Abstract
High replicative fitness is a general determinant of a multidrug resistance phenotype and may explain lower sensitivity to direct-acting antiviral agents (DAAs) in some hepatitis C virus genotypes. Genetic diversity in the molecular target site of peptidomimetic NS3 protease inhibitors could impact variant replicative fitness and potentially add to virologic treatment failure. We selected NS3 helicase residues near the protease natural substrate in the NS3 domain interface and identified natural variants from a public database. Sequence diversity among different genotypes was identified and subsequently analyzed for potential effects of helicase variants on protein structure and function, and phenotypic effects on RNA replication and DAA resistance. We found increased replicative fitness in particular for amino acid substitutions at the NS3 helicase C-terminal helix α18. A network of strongly coupled residue pairs is identified. Helix α18 is part of this regulatory network and connects several NS3 functional elements involved in RNA replication. Among all genotypes we found distinct sequence diversity at helix α18 in particular for the most difficult-to-treat genotype 3. Our data suggest sequence diversity with implications for virus replicative fitness due to natural variants in helicase helix α18.
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Lee S, Yoon KD, Lee M, Cho Y, Choi G, Jang H, Kim B, Jung D, Oh J, Kim G, Oh J, Jeong Y, Kwon HJ, Bae SK, Min D, Windisch MP, Heo T, Lee C. Identification of a resveratrol tetramer as a potent inhibitor of hepatitis C virus helicase. Br J Pharmacol 2016; 173:191-211. [PMID: 26445091 PMCID: PMC4813382 DOI: 10.1111/bph.13358] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND PURPOSE Hepatitis C virus (HCV) infection is responsible for various chronic inflammatory liver diseases. Here, we have identified a naturally occurring compound with anti-HCV activity and have elucidated its mode of antiviral action. EXPERIMENTAL APPROACH Luciferase reporter and real-time RT-PCR assays were used to measure HCV replication. Western blot, fluorescence-labelled HCV replicons and infectious clones were employed to quantitate expression levels of viral proteins. Resistant HCV mutant mapping, in vitro NS3 protease, helicase, NS5B polymerase and drug affinity responsive target stability assays were also used to study the antiviral mechanism. KEY RESULTS A resveratrol tetramer, vitisin B from grapevine root extract showed high potency against HCV replication (EC50 = 6 nM) with relatively low cytotoxicity (EC50 >10 μM). Combined treatment of vitisin B with an NS5B polymerase inhibitor (sofosbuvir) exhibited a synergistic or at least additive antiviral activity. Analysis of a number of vitisin B-resistant HCV variants suggested an NS3 helicase as its potential target. We confirmed a direct binding between vitisin B and a purified NS3 helicase in vitro. Vitisin B was a potent inhibitor of a HCV NS3 helicase (IC50 = 3 nM). In vivo, Finally, we observed a preferred tissue distribution of vitisin B in the liver after i.p. injection in rats, at clinically attainable concentrations. Conclusion and Implications Vitisin B is one of the most potent HCV helicase inhibitors identified so far. Vitisin B is thus a prime candidate to be developed as the first HCV drug derived from natural products.
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Affiliation(s)
- Sungjin Lee
- College of PharmacyDongguk UniversityGoyangKorea
| | - Kee Dong Yoon
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Myungeun Lee
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Yoojin Cho
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Gahee Choi
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Hongje Jang
- Department of ChemistrySeoul National UniversitySeoulKorea
| | - BeomSeok Kim
- Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeoulKorea
| | - Da‐Hee Jung
- Department of Bio and Nano ChemistryKookmin UniversitySeoulKorea
| | - Jin‐Gyo Oh
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Geon‐Woo Kim
- Department of BiotechnologyYonsei UniversitySeoulKorea
| | - Jong‐Won Oh
- Department of BiotechnologyYonsei UniversitySeoulKorea
| | - Yong‐Joo Jeong
- Department of Bio and Nano ChemistryKookmin UniversitySeoulKorea
| | - Ho Jeong Kwon
- Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeoulKorea
| | - Soo Kyung Bae
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Dal‐Hee Min
- Department of ChemistrySeoul National UniversitySeoulKorea
| | - Marc P Windisch
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Tae‐Hwe Heo
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Choongho Lee
- College of PharmacyDongguk UniversityGoyangKorea
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Abstract
Mathematically modelling changes in HCV RNA levels measured in patients who receive antiviral therapy has yielded many insights into the pathogenesis and effects of treatment on the virus. By determining how rapidly HCV is cleared when viral replication is interrupted by a therapy, one can deduce how rapidly the virus is produced in patients before treatment. This knowledge, coupled with estimates of the HCV mutation rate, enables one to estimate the frequency with which drug resistant variants arise. Modelling HCV also permits the deduction of the effectiveness of an antiviral agent at blocking HCV replication from the magnitude of the initial viral decline. One can also estimate the lifespan of an HCV-infected cell from the slope of the subsequent viral decline and determine the duration of therapy needed to cure infection. The original understanding of HCV RNA decline under interferon-based therapies obtained by modelling needed to be revised in order to interpret the HCV RNA decline kinetics seen when using direct-acting antiviral agents (DAAs). There also exist unresolved issues involving understanding therapies with combinations of DAAs, such as the presence of detectable HCV RNA at the end of therapy in patients who nonetheless have a sustained virologic response.
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Affiliation(s)
- Alan S Perelson
- Theoretical Biology and Biophysics, MS-K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeremie Guedj
- INSERM, IAME, UMR 1137, 16 Rue Henri Huchard, F-75018 Paris, France
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