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Saeed S, Shahzadi I, Zahoor AF, Al-Mutairi AA, Kamal S, Faisal S, Irfan A, Al-Hussain SA, Muhammed MT, Zaki MEA. Exploring theophylline-1,2,4-triazole tethered N-phenylacetamide derivatives as antimicrobial agents: unraveling mechanisms via structure-activity relationship, in vitro validation, and in silico insights. Front Chem 2024; 12:1372378. [PMID: 38645776 PMCID: PMC11026557 DOI: 10.3389/fchem.2024.1372378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Theophylline, a nitrogen-containing heterocycle, serves as a promising focal point for medicinal researchers aiming to create derivatives with diverse pharmacological applications. In this work, we present an improved synthetic method for a range of theophylline-1,2,4-triazole-S-linked N-phenyl acetamides (4a‒g) utilizing ultrasound-assisted synthetic approach. The objective was to assess the effectiveness of synthesized theophylline-1,2,4-triazoles (4a‒g) as inhibitors of HCV serine protease and as antibacterial agents against B. subtilis QB-928 and E. coli AB-274. Theophylline-1,2,4-triazoles were obtained in good to excellent yields (69%-95%) in a shorter time than conventional approach. 4-Chlorophenyl moiety containing theophylline-1,2,4-triazole 4c displayed significantly higher inhibitory activity against HCV serine protease enzyme (IC50 = 0.015 ± 0.25 mg) in comparison to ribavirin (IC50 = 0.165 ± 0.053 mg), but showed excellent binding affinity (-7.55 kcal/mol) with the active site of serine protease, better than compound 4c (-6.90 kcal/mol) as well as indole-based control compound 5 (-7.42 kcal/mol). In terms of percentage inhibition of serine protease, 2-chlorophenyl compound 4b showed the maximum percentage inhibition (86%), more than that of the 3,4-dichlorophenyl compound 4c (76%) and ribavirin (81%). 3,4-Dimethylphenyl-based theophylline-1,2,4-triazole 4g showed the lowest minimum inhibitory concentration (MIC = 0.28 ± 0.50 μg/mL) against the B. subtilis bacterial strain as compared to the standard drug penicillin (MIC = 1 ± 1.50 μg/mL). The other 4-methylphenyl theophylline-1,2,4-triazole 4e (MIC = 0.20 ± 0.08 μg/mL) displayed the most potent antibacterial potential against E. coli in comparison to the standard drug penicillin (MIC = 2.4 ± 1.00 μg/mL). Molecular docking studies further helped in an extensive understanding of all of the interactions between compounds and the enzyme active site, and DFT studies were also employed to gain insights into the molecular structure of the synthesized compounds. The results indicated that theophylline-linked triazole derivatives 4b and 4c showed promise as leading contenders in the fight against the HCV virus. Moreover, compounds 4e and 4g demonstrated potential as effective chemotherapeutic agents against E. coli and B. subtilis, respectively. To substantiate these findings, additional in vivo studies and clinical trials are imperative, laying the groundwork for their integration into future drug design and development.
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Affiliation(s)
- Sadaf Saeed
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Irum Shahzadi
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Aamal A. Al-Mutairi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Shagufta Kamal
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sami A. Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Türkiye
| | - Magdi E. A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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2
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Noh SS, Shin HJ. Role of Virus-Induced EGFR Trafficking in Proviral Functions. Biomolecules 2023; 13:1766. [PMID: 38136637 PMCID: PMC10741569 DOI: 10.3390/biom13121766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Since its discovery in the early 1980s, the epidermal growth factor receptor (EGFR) has emerged as a pivotal and multifaceted player in elucidating the intricate mechanisms underlying various human diseases and their associations with cell survival, proliferation, and cellular homeostasis. Recent advancements in research have underscored the profound and multifaceted role of EGFR in viral infections, highlighting its involvement in viral entry, replication, and the subversion of host immune responses. In this regard, the importance of EGFR trafficking has also been highlighted in recent studies. The dynamic relocation of EGFR to diverse intracellular organelles, including endosomes, lysosomes, mitochondria, and even the nucleus, is a central feature of its functionality in diverse contexts. This dynamic intracellular trafficking is not merely a passive process but an orchestrated symphony, facilitating EGFR involvement in various cellular pathways and interactions with viral components. Furthermore, EGFR, which is initially anchored on the plasma membrane, serves as a linchpin orchestrating viral entry processes, a crucial early step in the viral life cycle. The role of EGFR in this context is highly context-dependent and varies among viruses. Here, we present a comprehensive summary of the current state of knowledge regarding the intricate interactions between EGFR and viruses. These interactions are fundamental for successful propagation of a wide array of viral species and affect viral pathogenesis and host responses. Understanding EGFR significance in both normal cellular processes and viral infections may not only help develop innovative antiviral therapies but also provide a deeper understanding of the intricate roles of EGFR signaling in infectious diseases.
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Affiliation(s)
- Se Sil Noh
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hye Jin Shin
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
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Alamri MA, Mirza MU, Adeel MM, Ashfaq UA, Tahir ul Qamar M, Shahid F, Ahmad S, Alatawi EA, Albalawi GM, Allemailem KS, Almatroudi A. Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15060659. [PMID: 35745579 PMCID: PMC9228520 DOI: 10.3390/ph15060659] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/17/2022] Open
Abstract
Rift valley fever virus (RVFV) is the causative agent of a viral zoonosis that causes a significant clinical burden in domestic and wild ruminants. Major outbreaks of the virus occur in livestock, and contaminated animal products or arthropod vectors can transmit the virus to humans. The viral RNA-dependent RNA polymerase (RdRp; L protein) of the RVFV is responsible for viral replication and is thus an appealing drug target because no effective and specific vaccine against this virus is available. The current study reported the structural elucidation of the RVFV-L protein by in-depth homology modeling since no crystal structure is available yet. The inhibitory binding modes of known potent L protein inhibitors were analyzed. Based on the results, further molecular docking-based virtual screening of Selleckchem Nucleoside Analogue Library (156 compounds) was performed to find potential new inhibitors against the RVFV L protein. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity analysis of these compounds was also performed. Besides, the binding mechanism and stability of identified compounds were confirmed by a 50 ns molecular dynamic (MD) simulation followed by MM/PBSA binding free energy calculations. Homology modeling determined a stable multi-domain structure of L protein. An analysis of known L protein inhibitors, including Monensin, Mycophenolic acid, and Ribavirin, provide insights into the binding mechanism and reveals key residues of the L protein binding pocket. The screening results revealed that the top three compounds, A-317491, Khasianine, and VER155008, exhibited a high affinity at the L protein binding pocket. ADME analysis revealed good pharmacodynamics and pharmacokinetic profiles of these compounds. Furthermore, MD simulation and binding free energy analysis endorsed the binding stability of potential compounds with L protein. In a nutshell, the present study determined potential compounds that may aid in the rational design of novel inhibitors of the RVFV L protein as anti-RVFV drugs.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 16273, Saudi Arabia;
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada;
| | - Muhammad Muzammal Adeel
- 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
- Correspondence: (M.T.u.Q.); (K.S.A.)
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Ghadah M. Albalawi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
- Department of Laboratory and Blood Bank, King Fahd Specialist Hospital, Tabuk 47717, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
- Correspondence: (M.T.u.Q.); (K.S.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
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Wu S, Yuan H, Fan H, Xu Y, Liu Z, Wu X, Wu M, Zhang X, Shi T, Zhang T. Evolutionary characteristics and immune mutation of hepatitis C virus genotype 1b among intravenous drug users in mainland, China. J Viral Hepat 2022; 29:209-217. [PMID: 35075775 DOI: 10.1111/jvh.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/08/2022] [Indexed: 12/09/2022]
Abstract
China is one of the countries with the heaviest burden of hepatitis C virus (HCV) worldwide, especially subtype 1b. To better control hepatitis C, insights into the characteristics of dynamic spread and genomic mutations are urgently needed. We retrieved sequences of HCV-1b NS5B among intravenous drug users (IDUs) and general people (Non-IDUs) in China from 2000 to 2011 in NCBI. Bayesian phylogenetic and phylogeographic analyses were used to evaluate the transmission dynamics of HCV-1b. Non-synonymous substitutions were detected to illustrate immune adaptation. Evolutionary history demonstrated that HCV-1b effective population size experienced a sharp increase in 1990. HCV-1b sequences among IDUs had a higher estimated evolutionary rate (5.7185 × 10-3 substitutions/site/year) than overall (7.7332 × 10-4 ). 105/136 (77.2%) of HCV-1b sequences clustered into 38 networks. The average non-synonymous HCV-1b immune epitopes among IDUs were 0.211, higher than non-IDUs, especially in the HLA-A*02 molecular recognition region. All of these posed significant challenges for the prevention and treatment of HCV. Heterogeneity and genetic linkages of HCV-1b suggest that evolutionary surveillance of HCV in cities in east-central China and among IDUs could not be neglected.
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Affiliation(s)
- Sheng Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, China.,School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Fan
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Yiyun Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Zhenqiu Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, China.,School of Life Sciences, Fudan University, Shanghai, China
| | - Xuefu Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Mingshan Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Xin Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Tingting Shi
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Shanghai Institute of Infectious Diseases and Biosafety, Shanghai, China.,Yiwu Research Institute, Fudan University, Yiwu, China
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Elgoud Said AA, Afifi AH, Ali TFS, Samy MN, Abdelmohsen UR, Fouad MA, Attia EZ. NS3/4A helicase inhibitory alkaloids from Aptenia cordifolia as HCV target. RSC Adv 2021; 11:32740-32749. [PMID: 35493564 PMCID: PMC9042107 DOI: 10.1039/d1ra06139a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/29/2021] [Indexed: 01/16/2023] Open
Abstract
Chemical investigation of Aptenia cordifolia roots extract, using chromatographic and spectroscopic techniques, resulted in isolation and identification of eight known compounds. The basic ethyl acetate fraction (alkaloidal fraction) afforded O-methylsceletenone, epinine, 4-methoxy phenethylamine, and N-methyl tyramine while, the acidic ethyl acetate fraction (non-alkaloidal fraction) afforded only cis-N-coumaroyl tyramine. Moreover, the petroleum ether fraction afforded capric acid, tricosanol, and a mixture of β-sitosterol & stigma sterol. Upon screening of anti HCV activity of these three fractions, only the basic ethyl acetate fraction had high activity against HCV with an IC50 value equal to 2.4 μg mL-1 which provoked us to carry out structure based in silico virtual screening on the drug targets of HCV of isolated alkaloidal compounds as well as the previously dereplicated alkaloids through metabolomics from the antiviral active fraction. The tortuosamine compound exhibited the strongest binding to the active site of NS3/4A helicase with a binding affinity (-7.1 kcal mol-1) which is very close to the native ligand (-7.7 kcal mol-1).
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Affiliation(s)
- Asmaa Abo Elgoud Said
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University 61519 Minia Egypt +20-86-2369075 +20-86-2347759
| | - Ahmed H Afifi
- Department of Pharmacognosy, Division of Pharmaceutical Industries, National Research Center Dokki 12622 Giza Egypt
| | - Taha F S Ali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University 61519 Minia Egypt
| | - Mamdouh Nabil Samy
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University 61519 Minia Egypt +20-86-2369075 +20-86-2347759
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University 61519 Minia Egypt +20-86-2369075 +20-86-2347759
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone 61111 New Minia City Egypt
| | - Mostafa A Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University 61519 Minia Egypt +20-86-2369075 +20-86-2347759
| | - Eman Zekry Attia
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University 61519 Minia Egypt +20-86-2369075 +20-86-2347759
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Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
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Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
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Robello M, Barresi E, Baglini E, Salerno S, Taliani S, Settimo FD. The Alpha Keto Amide Moiety as a Privileged Motif in Medicinal Chemistry: Current Insights and Emerging Opportunities. J Med Chem 2021; 64:3508-3545. [PMID: 33764065 PMCID: PMC8154582 DOI: 10.1021/acs.jmedchem.0c01808] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the years, researchers in drug discovery have taken advantage of the use of privileged structures to design innovative hit/lead molecules. The α-ketoamide motif is found in many natural products, and it has been widely exploited by medicinal chemists to develop compounds tailored to a vast range of biological targets, thus presenting clinical potential for a plethora of pathological conditions. The purpose of this perspective is to provide insights into the versatility of this chemical moiety as a privileged structure in drug discovery. After a brief analysis of its physical-chemical features and synthetic procedures to obtain it, α-ketoamide-based classes of compounds are reported according to the application of this motif as either a nonreactive or reactive moiety. The goal is to highlight those aspects that may be useful to understanding the perspectives of employing the α-ketoamide moiety in the rational design of compounds able to interact with a specific target.
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Affiliation(s)
- Marco Robello
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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El-Garawani I, Hassab El-Nabi S, Gadallah M, Abdelsameea E. Association between IFN-λ 3 Gene Polymorphisms and Outcome of Treatment with Direct Acting Antivirals in Chronic HCV-Infected Egyptian Patients. Immunol Invest 2021; 50:12-22. [PMID: 32024403 DOI: 10.1080/08820139.2020.1722158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background: Single nucleotide polymorphisms (SNPs) of the interferon lambda 3 (IFN-λ 3) gene are associated with viral clearance and treatment response in chronic hepatitis C virus (HCV) infection. Aim: to assess whether specific IFN-λ 3 gene SNP, known as rs12979860 (C > T), could predict the outcome of treatment with direct acting antivirals (DAAs) among Egyptian patients with chronic HCV genotype 4 infection. Methods: Tetra-primer (ARMS-PCR) and PCR-RFLP methods were used for SNP genotyping in 100 chronic HCV-infected patients and 50 healthy subjects as control group. Results: The CC (wild type) genotype of rs12979860 was identified in 20 patients, 50% of them achieved sustained virological response (SVR). SNP genotype TT was found in 17 patients and only 2 of them (11.76%) were responders. The frequency of CT genotypes was significantly higher in responders than in non-responders (p= .021). In contrast, the frequency of TT genotypes was significantly higher in non-responders (42.85%, p< .001). On univariate and multivariate logistic regression analyses of the significant predictors of SVR, there were six predictive factors (Age, diabetes mellitus, AST, albumin, type of therapy and IFN-λ 3 genotype). Conclusion: The TT genotype and T allele were significantly associated with failure to achieve SVR. However, CT genotype of IFN-λ 3 (rs12979860) may be considered as a predictor for SVR in patients who received DAAs.
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Affiliation(s)
- Islam El-Garawani
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Sobhy Hassab El-Nabi
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Marwa Gadallah
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Eman Abdelsameea
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University , Shibin Al Kawm, Egypt
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9
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Tunghirun C, Narkthong V, Chaicumpa W, Chimnaronk S. Interference of dengue replication by blocking the access of 3' SL RNA to the viral RNA-dependent RNA polymerase. Antiviral Res 2020; 182:104921. [PMID: 32835694 DOI: 10.1016/j.antiviral.2020.104921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/25/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023]
Abstract
The four circulating serotypes of dengue virus (DENV) occasionally cause potentially fetal symptoms of severe dengue, which there is currently no specific treatment available. Extensive efforts have been made to inhibit viral replication processes by impeding the activity of an exclusive RNA-dependent RNA polymerase (RdRp) in the viral non-structural protein 5 (NS5). In our earlier work, we identified the characteristic, specific interaction between the C-terminal thumb subdomain of RdRp and an apical loop in the 3' stem-loop (SL) element in the DENV RNA genome, which is fundamental for viral replication. Here, we demonstrated a new approach for interfering viral replication via blocking of 3' SL RNA binding to RdRp by the single-chain variable fragments (scFvs). We isolated and cloned 3 different human scFvs that bound to RdRp from DENV serotype 2 and interfered with 3' SL-binding, utilizing a combination of phage-display panning and Alpha methods. When tagged with a cell penetrating peptide, a selected scFv clone, 2E3, entered cells and partially colocalized with NS5 in the cytoplasm of infected HuH-7 cells. 2E3 significantly inhibited DENV RNA replication with sub-nanomolar EC50 values and significantly reduced the production of infectious particles. The molecular docking models suggested that 2E3 recognized both palm and thumb subdomains of RdRp, and interacted with Lys841, a key residue involved in RNA binding. Our results provide a new potential therapeutic molecule specific for flaviviral infection.
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Affiliation(s)
- Chairat Tunghirun
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Veerakorn Narkthong
- Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sarin Chimnaronk
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand; Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Elfiky AA, Ismail A. Molecular dynamics and docking reveal the potency of novel GTP derivatives against RNA dependent RNA polymerase of genotype 4a HCV. Life Sci 2019; 238:116958. [PMID: 31628915 DOI: 10.1016/j.lfs.2019.116958] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 01/17/2023]
Abstract
AIM To work on Hepatitis C Virus (HCV), one of the major causes of liver cirrhosis and hepatocellular carcinoma, polymerase of genotype 4a that have no solved structures deposited in the protein data bank (PDB) yet. Understanding the dynamics and testing some novel inhibitors are also covered. MATERIALS AND METHODS Molecular Dynamics Simulation (MDS) is performed for a period of 1 μs on comparatively modeled then validated NS5b of subtype 4a. Following MDS analysis, molecular docking is performed to test the inhibitory performance of eight novels suggested guanosine derivatives using 181 different conformations of the protein model gathered during the MDS run after the equilibration period. KEY FINDINGS The results yield that the eight modified, at position 2', GTP derivatives (fluorine, Hydroxyl, and sulphonyl oxydanyl) have binding energies comparable to the parent molecule, GTP. Besides, the eight suggested compounds have lower binding energies (and hence better in binding) compared to sofosbuvir (a drug approved by FDA in 2013 against HCV) and ribavirin (a wide range acting antiviral drug used before against HCV). SIGNIFICANCE Combined molecular dynamics and molecular docking are able to test the hypothesis of HCV polymerase dynamics doesn't affect the nucleotides (or nucleotide inhibitors) binding to its active site. Despite the reported highly dynamic subtype 4a of HCV; all the nucleotide inhibitors under the study are able to, tightly, bind to NS5b of genotype 4a. This behavior is reported before for the Zika virus polymerase, as well.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Alaa Ismail
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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Stereoselective synthesis and biological evaluation as inhibitors of hepatitis C virus RNA polymerase of GSK3082 analogues with structural diversity at the 5-position. Eur J Med Chem 2019; 171:401-419. [DOI: 10.1016/j.ejmech.2019.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 01/27/2023]
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12
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In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors. Sci Rep 2019; 9:6809. [PMID: 31048746 PMCID: PMC6497722 DOI: 10.1038/s41598-019-43129-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 04/17/2019] [Indexed: 01/05/2023] Open
Abstract
The Crimean-Congo Hemorrhagic Fever virus (CCHFV) is a segmented negative single-stranded RNA virus (-ssRNA) which causes severe hemorrhagic fever in humans with a mortality rate of ~50%. To date, no vaccine has been approved. Treatment is limited to supportive care with few investigational drugs in practice. Previous studies have identified viral RNA dependent RNA Polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Since no crystal structure is available yet, we report the structural elucidation of CCHFV-RdRp by in-depth homology modeling. Even with low sequence identity, the generated model suggests a similar overall structure as previously reported RdRps. More specifically, the model suggests the presence of structural/functional conserved RdRp motifs for polymerase function, the configuration of uniform spatial arrangement of core RdRp sub-domains, and predicted positively charged entry/exit tunnels, as seen in sNSV polymerases. Extensive pharmacophore modeling based on per-residue energy contribution with investigational drugs allowed the concise mapping of pharmacophoric features and identified potential hits. The combination of pharmacophoric features with interaction energy analysis revealed functionally important residues in the conserved motifs together with in silico predicted common inhibitory binding modes with highly potent reference compounds.
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13
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Wang Z, Chen Z, Li J, Huang J, Zheng C, Liu JP. Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase. J Biomol Struct Dyn 2019; 38:1071-1082. [PMID: 30915896 DOI: 10.1080/07391102.2019.1593244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q2 of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q2 of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhenming Chen
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jing Huang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Chenni Zheng
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Immunology, Central Eastern Clinical School, Monash University, Melbourne, Vitoria, Australia.,Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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14
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Elfiky AA. Novel Guanosine Derivatives as Anti-HCV NS5b Polymerase: A QSAR and Molecular Docking Study. Med Chem 2019; 15:130-137. [PMID: 30324891 DOI: 10.2174/1573406414666181015152511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 06/01/2018] [Accepted: 09/30/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND IDX-184 is a guanosine derivative having a potent inhibitory performance against HCV NS5b polymerase. OBJECTIVE To test three different groups of 2'C - modified analogues of guanosine nucleotide against HCV polymerase. METHOD Using combined Quantitative Structure-Activity Relationships (QSAR) and molecular docking, the suggested compounds are studied. RESULTS Examining the docked structures of the compounds with experimentally solved NS5b structure (PDB ID: 2XI3) revealed that most of the compounds have the same mode of interaction as that of guanosine nucleotide and hence, NS5b inhibition is possible. CONCLUSION It is revealed that sixteen modifications have a better binding affinity to NS5b compared to guanosine. In addition, seven more compounds are better in NS5b binding compared to the approved drug, sofosbuvir, and the compound under clinical trials, IDX-184. Hence, these compounds could be potent HCV NS5b inhibitors. Summary Points: Novel guanosine modifications were introduced in silico and optimized using QM. QSAR and docking calculations are performed to test the binding affinity of the compounds to HCV NS5b active site. Comparison between the binding affinities and the mode of interactions of the compounds and both GTP and IDX-184 is performed. Structural mining to quantify the mode of binding of the compounds to NS5b active site pocket.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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15
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Abstract
Coronaviruses (CoVs) are a major group of viruses known to be responsible for wide spectrum of diseases in multiple species. The CoVs affecting human population are referred to as human coronaviruses (HCoVs). They lead to multiple respiratory diseases, such as common cold, pneumonia, bronchitis, severe acute respiratory syndrome, and Middle East respiratory syndrome. CoVs are RNA viruses that require RNA-dependent RNA polymerases (RdRPs) for various steps in their life cycle. Action of RdRP is needed in several steps in the life cycle of CoVs and thus RdRPs constitute potential targets for drugs and other therapeutic interventions for the treatment of diseases caused by CoVs. The chapter therefore presents a detailed discussion on the structure and functions of CoV polymerases and the development of their potential inhibitors.
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16
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Ganta NM, Gedda G, Rathnakar B, Satyanarayana M, Yamajala B, Ahsan MJ, Jadav SS, Balaraju T. A review on HCV inhibitors: Significance of non-structural polyproteins. Eur J Med Chem 2018; 164:576-601. [PMID: 30639895 PMCID: PMC7185800 DOI: 10.1016/j.ejmech.2018.12.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) mortality and morbidity is a world health misery with an approximate 130–150 million chronically HCV tainted and suffering individuals and it initiate critical liver malfunction like cirrhosis, hepatocellular carcinoma or liver HCV cancer. HCV NS5B protein one of the best studied therapeutic target for the identification of new drug candidates to be added to the combination or multiple combination medication recently approved. During the past few years, NS5B has thus been an important object of attractive medicinal chemistry endeavors, which induced to the surfacing of betrothal preclinical drug molecules. In this scenario, the current review set limit to discuss research published on NS5B and few other therapeutic functional inhibitors concentrating on hit investigation, hit to lead optimization, ADME parameters evaluation, and the SAR data which was out for each compound type and similarity taken into consideration. The discussion outlined in this specific review will surly helpful and vital tool for those medicinal chemists investigators working with HCV research programs mainly pointing on NS5B and set broad spectrum identification of creative anti HCV compounds. This mini review also tells each and every individual compound ability related how much they are active against NS5B and few other targets. Hepatitis C infection causes severe liver cirrhosis and carcinoma. The new acute HCV infections are raising every year and mortality rate become serious concern. The plausible list of anti-HCV drugs and clinical agents were listed in this review. The divergent medicinal scaffolds as anti-HCV agents were presented as per their targets.
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Affiliation(s)
- Narayana Murthy Ganta
- Department of Pharmaceutical Chemistry, Vishnu Institute of Pharmaceutical Education and Research, Narsapur, Medak, Telangana, 502313, India
| | - Gangaraju Gedda
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Bethi Rathnakar
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Mavurapu Satyanarayana
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Bhaskar Yamajala
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Surender Singh Jadav
- CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India.
| | - Tuniki Balaraju
- Deapartment of Chemistry, Material Science Centre, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, WB, 741 246, India.
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17
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Liang HP, Hak H, Ji JM. A study on the relationship between HCV NS3 and endogenous IRF-3. EUR J INFLAMM 2018. [DOI: 10.1177/2058739218784453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This study aims to investigate the relationship between hepatitis C virus (HCV) NS3/4A and endogenous interferon regulatory factor-3 (IRF-3). The localization of endogenous IRF-3 protein before and after virus infection was analyzed by immunofluorescence assay (IFA). IFA results revealed that the synergistic action of transfection and HCV virus infection could more effectively reduce the nuclear translocation of endogenous IRF-3 in HeLa cells, compared to the activation of Sendai virus infection alone. The highest nuclear translocation of endogenous IRF-3 in transfected HeLa cells occurred at 24 h after Sendai virus infection. Our study was consistent with a published paper, which revealed that HCV NS3/4A protease could suppress the activation of IRF-3 and was indispensable in the transcription of interferon (IFN)-α/β.
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Affiliation(s)
- Hong-Ping Liang
- Department of Clinical Laboratory, Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Hotta Hak
- Department of Microbiology and Genomics, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Jian-Min Ji
- Department of Clinical Laboratory, Shanxi Provincial People’s Hospital, Taiyuan, China
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18
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Elfiky AA. Zika virus: novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase. Future Virol 2017. [DOI: 10.2217/fvl-2017-0081] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Aim: During the last 2 years, the zika virus (ZIKV) outbreak has rapidly spread worldwide to more than 80 countries. In the last decade, nucleotide inhibitors (NIs) have been widely studied against different viruses such as HCV and human coronaviruses. Materials & methods: In this study, four novel guanosine derivatives were tested in silico against ZIKV polymerase. Discussion: The modified guanosines at position 2′ in the ribose ring gave comparable binding energies to that of GTP; hence, it could compete with GTP for the ZIKV polymerase active site and halt viral replication. Conclusion: The suggested guanosine derivatives had a higher affinity than ribavirin (wide range antiviral drug) in binding to ZIKV polymerase.
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Affiliation(s)
- Abdo A Elfiky
- Lecturer at Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
- Junior Associate at Quantitative Life Science Department, The Abdus Salam International Center for Theoretical Physics, Trieste, Italy
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19
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Moriishi K. The potential of signal peptide peptidase as a therapeutic target for hepatitis C. Expert Opin Ther Targets 2017; 21:827-836. [DOI: 10.1080/14728222.2017.1369959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kohji Moriishi
- Department of Microbiology, Graduate School of Medical Science, University of Yamanashi, Yamanashi, Japan
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20
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Elfiky AA, Ismail AM. Molecular modeling and docking revealed superiority of IDX-184 as HCV polymerase inhibitor. Future Virol 2017. [DOI: 10.2217/fvl-2017-0027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: IDX-184 is a nonstructural 5b nucleoside inhibitor (NI) that was under clinical trials against HCV. This work adopts a molecular modeling approach in order to study the interaction between IDX-184 and HCV polymerase from four different genotypes. Methods: Comparisons to the native nucleotide (Guanosine triphosphate) and other NIs were performed using interaction descriptors, calculated using semiempirical quantum mechanics and molecular docking. Results: IDX-184 shows potent binding to the active site of the polymerases. In addition, IDX-184 was better than Sofosbuvir and Ribavirin when docked into polymerase active site (even with experimentally solved structure). Conclusion: Analysis of the interaction descriptors and docking complexes suggests IDX-184 as a superior NI against the studied HCV subtypes.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, PO Box 12613, Giza, Egypt
- Quantitative Life Science Department, The Abdus Salam International Center for Theoretical Physics, Strada Costiera, 11 I34151, Trieste, Italy
| | - Alaa M Ismail
- Biophysics Department, Faculty of Sciences, Cairo University, PO Box 12613, Giza, Egypt
- Biochemistry Department, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2R3, AB, Canada
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21
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Ganta KK, Mandal A, Debnath S, Hazra B, Chaubey B. Anti-HCV Activity from Semi-purified Methanolic Root Extracts of Valeriana wallichii. Phytother Res 2017; 31:433-440. [PMID: 28078810 DOI: 10.1002/ptr.5765] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 01/10/2023]
Abstract
Hepatitis C virus (HCV) is a serious global health problem affecting approximately 130-150 million individuals. Presently available direct-acting anti-HCV drugs have higher barriers to resistance and also improved success rate; however, cost concerns limit their utilization, especially in developing countries like India. Therefore, development of additional agents to combat HCV infection is needed. In the present study, we have evaluated anti-HCV potential of water, chloroform, and methanol extracts from roots of Valeriana wallichii, a traditional Indian medicinal plant. Huh-7.5 cells infected with J6/JFH chimeric HCV strain were treated with water, chloroform, and methanol extracts at different concentrations. Semi-quantitative reverse transcription polymerase chain reaction result demonstrated that methanolic extract showed reduction in HCV replication. The methanolic extract was fractionated by thin layer chromatography, and the purified fractions (F1, F2, F3, and F4) were checked for anti-HCV activity. Significant viral inhibition was noted only in F4 fraction. Further, intrinsic fluorescence assay of purified HCV RNA-dependent RNA polymerase NS5B in the presence of F4 resulted in sharp quenching of intrinsic fluorescence with increasing amount of plant extract. Our results indicated that methanolic extract of V. wallichii and its fraction (F4) inhibited HCV by binding with HCV NS5B protein. The findings would be further investigated to identify the active principle/lead molecule towards development of complementary and alternative therapeutics against HCV. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Krishna Kumar Ganta
- Functional Genomics Lab, Centre for Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Anirban Mandal
- Functional Genomics Lab, Centre for Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukalyani Debnath
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Banasri Hazra
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Binay Chaubey
- Functional Genomics Lab, Centre for Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
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22
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Tomei L, Altamura S, Paonessa G, De Francesco R, Migliaccio G. Review HCV Antiviral Resistance: The Impact of in vitro Studies on the Development of Antiviral Agents Targeting the Viral NS5B Polymerase. ACTA ACUST UNITED AC 2016; 16:225-45. [PMID: 16130521 DOI: 10.1177/095632020501600403] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The high prevalence of the disease caused by hepatitis C virus (HCV) and the limited efficacy of interferon-based therapies have stimulated the search for safer and more effective drugs. The development of inhibitors of the HCV NS5B RNA polymerase represents a promising strategy for identifying novel anti-HCV therapeutics. However, the high genetic diversity, mutation rate and turnover of HCV are expected to favour the emergence of drug resistance, limiting the clinical usefulness of polymerase inhibitors. Thus, the characterization of the drug-resistance profile of these antiviral agents is considered crucial for identifying the inhibitors with a higher probability of clinical success. In the absence of an efficient in vitro infection system, HCV sub-genomic replicons have been used to study viral resistance to both nucleoside and non-nucleoside NS5B inhibitors. While these studies suggest that drug-resistant viruses are likely to evolve in vivo, they provide a wealth of information that should help in the identification of inhibitors with improved and distinct resistance profiles that might be used for combination therapy.
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Affiliation(s)
- Licia Tomei
- Istituto di Ricerche di Biologia Molecolare P Angeletti, Pomezia-Roma, Italy
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23
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Galiano V, Garcia-Valtanen P, Micol V, Encinar JA. Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:3163-3181. [PMID: 27784988 PMCID: PMC5066851 DOI: 10.2147/dddt.s117369] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds) to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (ΔG <−10.5 kcal/mol) were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo.
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Affiliation(s)
- Vicente Galiano
- Physics and Computer Architecture Department, Miguel Hernández University (UMH), Elche, Spain
| | - Pablo Garcia-Valtanen
- Experimental Therapeutics Laboratory, Hanson and Sansom Institute for Health Research, School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia
| | - Vicente Micol
- Molecular and Cell Biology Institute, Miguel Hernández University (UMH), Elche, Spain; CIBER: CB12/03/30038, Physiopathology of the Obesity and Nutrition, CIBERobn, Instituto de Salud Carlos III, Palma de Mallorca, Spain
| | - José Antonio Encinar
- Molecular and Cell Biology Institute, Miguel Hernández University (UMH), Elche, Spain
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24
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Elfiky AA. Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials. J Med Virol 2016; 88:2044-2051. [PMID: 27604059 DOI: 10.1002/jmv.24678] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/19/2022]
Abstract
In the last few months, a new Zika virus (ZIKV) outbreak evolved in America. In accordance, World Health Organization (WHO) in February 2016 declared it as Public Health Emergency of International Concern (PHEIC). ZIKV infection was reported in more than 60 countries and the disease was spreading since 2007 but with little momentum. Many antiviral drugs are available in market or in laboratories under clinical trials, could affect ZIKV infection. In silico docking study were performed on the ZIKV polymerase to test some of Hepatitis C Virus (HCV) drugs (approved and in clinical trials). The results show potency of almost all of the studied compounds on ZIKV polymerase and hence inhibiting the propagation of the disease. In addition, the study suggested two nucleotide inhibitors (IDX-184 and MK0608) that may be tested as drugs against ZIKV infection. J. Med. Virol. 88:2044-2051, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Abdo A Elfiky
- Faculty of Science, Biophysics Department, Cairo University, Giza, Egypt. ,
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25
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Benzaria S, Bardiot D, Bouisset T, Counor C, Rabeson C, Pierra C, Storer R, Loi AG, Cadeddu A, Mura M, Musiu C, Liuzzi M, Loddo R, Bergelson S, Bichko V, Bridges E, Cretton-Scott E, Mao J, Sommadossi JP, Seifer M, Standring D, Tausek M, Gosselin G, La Colla P. 2′-C-Methyl Branched Pyrimidine Ribonucleoside Analogues: Potent Inhibitors of RNA Virus Replication. ACTA ACUST UNITED AC 2016; 18:225-42. [PMID: 17907380 DOI: 10.1177/095632020701800406] [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] [Indexed: 11/16/2022]
Abstract
RNA viruses are the agents of numerous widespread and often severe diseases. Their unique RNA-dependent RNA polymerase (RDRP) is essential for replication and, thus, constitutes a valid target for the development of selective chemotherapeutic agents. In this regard, we have investigated sugar-modified ribonucleoside analogues as potential inhibitors of the RDRP. Title compounds retain ‘natural’ pyrimidine bases, but possess a β-methyl substituent at the 2′-position of the D- or L-ribose moiety. Evaluation against a broad range of RNA viruses, either single-stranded positive (ssRNA), single-stranded negative (ssRNA−) or double-stranded (dsRNA), revealed potent activities for D-2′- C-methyl-cytidine and -uridine against ssRNA+, and dsRNA viruses. None of the L-enantiomers were active. Moreover, the 5′-triphosphates of the active D-enantiomers were found to inhibit the bovine virus diarrhoea virus polymerase. Thus, the 2′-methyl branching of natural pyrimidine ribonucleosides transforms physiological molecules into potent, broad-spectrum antiviral agents that merit further development.
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Affiliation(s)
- Samira Benzaria
- Laboratoire Coopératif Idenix-CNRS-Université Montpellier II, Montpellier, France
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26
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Elfiky AA, Elshemey WM. IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study. Med Chem Res 2016; 25:1005-1008. [PMID: 32214769 PMCID: PMC7080126 DOI: 10.1007/s00044-016-1533-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/10/2016] [Indexed: 01/21/2023]
Abstract
Abstract Quantitative structure-activity relationship (QSAR) parameters are good indicators for the reactivity of direct-acting antiviral drugs. Since molecular structure is related to molecular function, careful selection of molecular substitutions will result in more drugs that are potent. In this work, QSAR parameters are selected in order to compare the four drugs used as nucleotide inhibitors (NIs) for non-structural 5B (NS5B) RNA-dependent RNA polymerase (RdRp) of hepatitis C virus (HCV). These drugs are: ribavirin (widely used over the last 20 years), sofosbuvir (approved on December 2013 by FDA), and finally IDX-184 and R7128 (phase IIb of clinical trial drugs). The nucleotide analogues uracil (U), guanine (G), and cytosine (C) from which these drugs are fabricated are also compared to that group of drugs. QSAR parameters suggested that the drug IDX-184 is the best among all of the studied NIs. It also shows that NIs are always more reactive than their parent nucleotide. Graphical Abstract The active site environment of 12 amino acids coordinated with IDX-184 through two Mg2+. The interaction with HCV subtypes 1a, 2b, and 3b is better than 4a subtype.
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Affiliation(s)
- Abdo A Elfiky
- 1Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.,2Biochemistry and Structural Biology, Center of Molecular Protein Science CMPS, Lund University, Lund, Sweden
| | - Wael M Elshemey
- 1Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
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27
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Design, synthesis, structure information and biochemical activity of new floro substituted organotin(IV) carboxylates. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 154:99-107. [PMID: 26708070 DOI: 10.1016/j.jphotobiol.2015.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 10/11/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022]
Abstract
Four new triorganotin(IV) complexes with general formula R3SnL (R=C4H9, C6H5, and L=3-[(fluorophenylamido)]propenoic acid, 3-[(fluorophenylamido)]propanoic acid) were synthesized and characterized by elemental analyses, FT-IR, NMR ((1)H, (13)C and (119)Sn), mass spectrometry and single crystal X-ray structural analysis. The disappearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra of the compounds conform the formation of the compound and suggests that the complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date shows the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than 250. Crystallographic data for compound 2 showed that tin has distorted tetrahedral geometry with 433.42° angle around the central tin atom. The compounds (1-4) bind to DNA, resulting hypochromism shifts in UV-visible spectroscopy suggesting an intercalative mode of interactions. The compound-DNA interaction results (UV-visible and Viscometery) encourage using the compounds against HCV. The compounds (1-4) were screened for anti-HCV activity using Huh7.5 cell (human hepatoma cell) by the Gaussia Luciferase Assay and found to be biologically active. Based on Gaussia Luciferase Assay, compound 3 (Tributylstannic [3-(2-fluorophenylamido)propionate]) was taken for quantitative analysis by "QRT-PCR" using the serum of HCV patients and was found to have substantial anti-HCV activity. This work, demonstrated that compound 3 may be used as a potential anti-HCV agent in the future.
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Nouroz F, Shaheen S, Mujtaba G, Noreen S. An overview on hepatitis C virus genotypes and its control. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2015. [DOI: 10.1016/j.ejmhg.2015.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms. Viruses 2015; 7:4438-60. [PMID: 26258787 PMCID: PMC4576190 DOI: 10.3390/v7082829] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/25/2022] Open
Abstract
RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication within the infected cells. RdRP function is critical not only for the virus life cycle but also for its adaptive potential. The combination of low fidelity of replication and the absence of proofreading and excision activities within the RdRPs result in high mutation frequencies that allow these viruses a rapid adaptation to changing environments. In this review, we summarize the current knowledge about structural and functional aspects on RdRP catalytic complexes, focused mainly in the Picornaviridae family. The structural data currently available from these viruses provided high-resolution snapshots for a range of conformational states associated to RNA template-primer binding, rNTP recognition, catalysis and chain translocation. As these enzymes are major targets for the development of antiviral compounds, such structural information is essential for the design of new therapies.
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Zhao C, Wang Y, Ma S. Recent advances on the synthesis of hepatitis C virus NS5B RNA-dependent RNA-polymerase inhibitors. Eur J Med Chem 2015; 102:188-214. [PMID: 26276434 DOI: 10.1016/j.ejmech.2015.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C is a viral liver infection considered as the major cause of cirrhosis and hepatocellular carcinoma (HCC). The HCV NS5B polymerase, an RNA-dependent RNA polymerase, is essential for HCV replication, which is able to catalyze the synthesis of positive (genomic) and negative (template) strand HCV RNA, but has no functional equivalent in mammalian cells. Therefore, the NS5B polymerase has emerged as an attractive target for the development of specifically targeted antiviral therapy for HCV (DAA, for direct-acting antivirals). Recently, a growing number of compounds have been reported as the NS5B polymerase inhibitors, some of which especially have been licensed in clinical trials. This review describes recent advances on the synthesis of the NS5B polymerase inhibitors, focusing on the merits and demerits of their synthetic methods. In particular, inspiration from the synthesis and the future direction of the NS5B polymerase inhibitors are highlighted.
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Affiliation(s)
- Can Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China.
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Wang H, Gao H, Duan S, Song X. Inhibition of microRNA-199a-5p reduces the replication of HCV via regulating the pro-survival pathway. Virus Res 2015; 208:7-12. [PMID: 26027911 DOI: 10.1016/j.virusres.2015.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that post-transcriptionally regulate the pathological processes of various liver diseases including hepatitis C virus (HCV) infection. In the present study, we demonstrated that HCV infection enhanced the expression of miR-199a-5p in HCV infected human hepatocytes and Huh7.5.1cells, as well as liver biopsy specimens. Inhibition of miR-199a-5p decreased HCV replication not only in terms of HCV RNA, but also the protein levels of NS3 and NS5A. Furthermore, we discovered that miR-199a-5p knockdown in Huh7.5.1 cells infected with genotype 2a (JFH1) or genotype 1b (SN1a) resulted in the remarkable inhibition of pro-survival pathways, as observed by the down-regulation of p-Akt, p-ERK and β-catenin protein levels. Moreover, pre-treatment with the pro-survival pathway specific activator prominently ablated the inhibition of HCV replication induced by miR-199a-5p knockdown. Collectively, our results highlight the up-regulation of miR-199a-5p expression with HCV infection and the promotion of HCV replication by miR-199a-5p. Moreover, miR-199a-5p may facilitate HCV replication by regulating pro-survival pathways through PI3K/Akt, Ras/ERK and Wnt/β-catenin. miR-199a-5p might be a potential drug target for developing a novel strategy to combat HCV infection.
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Affiliation(s)
- Hongwei Wang
- Department of Infection Diseases, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Haili Gao
- Department of Infection Diseases, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Shupeng Duan
- Department of Infection Diseases, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Xinwen Song
- Department of Infection Diseases, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China.
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Wang H, Geng L, Chen BZ, Ji M. Computational study on the molecular mechanisms of drug resistance of Narlaprevir due to V36M, R155K, V36M+R155K, T54A, and A156T mutations of HCV NS3/4A protease. Biochem Cell Biol 2014; 92:357-69. [DOI: 10.1139/bcb-2014-0039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Narlaprevir is a novel NS3/4A protease inhibitor of hepatitis C virus (HCV), and it has been tested in a phase II clinical trial recently. However, distinct drug-resistance of Narlaprevir has been discovered. In our study, the molecular mechanisms of drug-resistance of Narlaprevir due to the mutations V36M, R155K, V36M+R155K, T54A, and A156T of NS3/4A protease have been investigated by molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis. The predicted binding free energies of Narlaprevir towards the wild-type and five mutants show that the mutations V36M, R155K, and T54A lead to low-level drug resistance and the mutations V36M+R155K and A156T lead to high-level drug resistance, which is consistent with the experimental data. The analysis of the individual energy terms indicates that the van der Waals contribution is important for distinguishing the binding affinities of these six complexes. These findings again show that the combination of different molecular modeling techniques is an efficient way to interpret the molecular mechanism of drug-resistance. Our work mainly elaborates the molecular mechanism of drug-resistance of Narlaprevir and further provides valuable information for developing novel, safer, and more potent HCV antiviral drugs in the near future.
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Affiliation(s)
- Huiqun Wang
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Lingling Geng
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Bo-Zhen Chen
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Mingjuan Ji
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
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Pourbasheer E, Aalizadeh R, Shokouhi Tabar S, Ganjali MR, Norouzi P, Shadmanesh J. 2D and 3D Quantitative Structure–Activity Relationship Study of Hepatitis C Virus NS5B Polymerase Inhibitors by Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis Methods. J Chem Inf Model 2014; 54:2902-14. [DOI: 10.1021/ci500216c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Eslam Pourbasheer
- Department
of Chemistry, Payame Noor University (PNU), P. O. Box 19395-3697, Tehran, Iran
| | | | - Samira Shokouhi Tabar
- Department
of Chemistry, Payame Noor University (PNU), P. O. Box 19395-3697, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center
of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P.O. Box 143981-7435, Tehran, Iran
- Biosensor
Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences
Institute, Tehran University of Medical Sciences, P. O. Box,
14114-13137, Tehran, Iran
| | - Parviz Norouzi
- Center
of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P.O. Box 143981-7435, Tehran, Iran
- Biosensor
Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences
Institute, Tehran University of Medical Sciences, P. O. Box,
14114-13137, Tehran, Iran
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Shah FA, Fatima K, Sabir S, Ali S, Fischer A, Qadri MI. Design, synthesis, and Gaussia luciferase Assay of triorganotin(IV)-based HCV inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1242-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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Durantel D, Escuret V, Zoulim F. Current and emerging therapeutic approaches to hepatitis C infection. Expert Rev Anti Infect Ther 2014; 1:441-54. [PMID: 15482141 DOI: 10.1586/14787210.1.3.441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hepatitis C virus is a frequent disease infecting an estimated 3% of the worlds population. It represents a major health problem and must be combated by all means. The aim of this review is to discuss the current treatment methods, including interferon-alpha, either standard or pegylated, and ribavirin. Emerging treatments will also be discussed for this potentially curable disease.
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Tributyltin(IV)[3-(3′,5′-dimethylphenylamido)propanoate] as a potent HCV inhibitor, its delivery study, controlled release and binding sites using CTAB as a standard cell membrane. Appl Organomet Chem 2013. [DOI: 10.1002/aoc.3079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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37
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Imran M, Manzoor S, Ashraf J, Khalid M, Tariq M, Khaliq HM, Azam S. Role of viral and host factors in interferon based therapy of hepatitis C virus infection. Virol J 2013; 10:299. [PMID: 24079723 PMCID: PMC3849893 DOI: 10.1186/1743-422x-10-299] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/24/2013] [Indexed: 02/07/2023] Open
Abstract
The current standard of care (SOC) for hepatitis C virus (HCV) infection is the combination of pegylated interferon (PEG-IFN), Ribavirin and protease inhibitor for HCV genotype 1. Nevertheless, this treatment is successful only in 70-80% of the patients. In addition, the treatment is not economical and is of immense physical burden for the subject. It has been established now, that virus-host interactions play a significant role in determining treatment outcomes. Therefore identifying biological markers that may predict the treatment response and hence treatment outcome would be useful. Both IFN and Ribavirin mainly act by modulating the immune system of the patient. Therefore, the treatment response is influenced by genetic variations of the human as well as the HCV genome. The goal of this review article is to summarize the impact of recent scientific advances in this area regarding the understanding of human and HCV genetic variations and their effect on treatment outcomes. Google scholar and PubMed have been used for literature research. Among the host factors, the most prominent associations are polymorphisms within the region of the interleukin 28B (IL28B) gene, but variations in other cytokine genes have also been linked with the treatment outcome. Among the viral factors, HCV genotypes are noteworthy. Moreover, for sustained virological responses (SVR), variations in core, p7, non-structural 2 (NS2), NS3 and NS5A genes are also important. However, all considered single nucleotide polymorphisms (SNPs) of IL28B and viral genotypes are the most important predictors for interferon based therapy of HCV infection.
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Affiliation(s)
- Muhammad Imran
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
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Kozlov MV, Kleymenova AA, Romanova LI, Konduktorov KA, Smirnova OA, Prasolov VS, Kochetkov SN. Benzohydroxamic acids as potent and selective anti-HCV agents. Bioorg Med Chem Lett 2013; 23:5936-40. [PMID: 24035094 DOI: 10.1016/j.bmcl.2013.08.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/14/2013] [Accepted: 08/18/2013] [Indexed: 01/30/2023]
Abstract
A diverse collection of 40 derivatives of benzohydroxamic acid (BHAs) of various structural groups were synthesized and tested against hepatitis C virus (HCV) in full-genome replicon assay. Some of these compounds demonstrated an exceptional activity, suppressing viral replication at sub-micromolar concentrations. The compounds were inactive against key viral enzymes NS3, and NS5B in vitro assays, suggesting host cell inhibition target(s). The testing results were consistent with metal coordination by the BHAs hydroxamic group in complex with a target(s). Remarkably, this class of compounds did not suppress poliomyelitis virus (PV) propagation in RD cells indicating a specific antiviral activity of BHAs against HCV.
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Affiliation(s)
- Maxim V Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia.
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Structural and antigenic definition of hepatitis C virus E2 glycoprotein epitopes targeted by monoclonal antibodies. Clin Dev Immunol 2013; 2013:450963. [PMID: 23935648 PMCID: PMC3722892 DOI: 10.1155/2013/450963] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/10/2013] [Indexed: 12/24/2022]
Abstract
Hepatitis C virus (HCV) is the major cause of chronic liver disease as well as the major indication for liver transplantation worldwide. Current standard of care is not completely effective, not administrable in grafted patients, and burdened by several side effects. This incomplete effectiveness is mainly due to the high propensity of the virus to continually mutate under the selective pressure exerted by the host immune response as well as currently administered antiviral drugs. The E2 envelope surface glycoprotein of HCV (HCV/E2) is the main target of the host humoral immune response and for this reason one of the major variable viral proteins. However, broadly cross-neutralizing monoclonal antibodies (mAbs) directed against HCV/E2 represent a promising tool for the study of virus-host interplay as well as for the development of effective prophylactic and therapeutic approaches. In the last few years many anti-HCV/E2 mAbs have been evaluated in preclinical and clinical trials as possible candidate antivirals, particularly for administration in pre- and post-transplant settings. In this review we summarize the antigenic and structural characteristics of HCV/E2 determined through the use of anti-HCV/E2 mAbs, which, given the absence of a crystal structure of this glycoprotein, represent currently the best tool available.
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40
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Elfiky AA, Elshemey WM, Gawad WA, Desoky OS. Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. Protein J 2013; 32:75-80. [PMID: 23322006 DOI: 10.1007/s10930-013-9462-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The current available treatment for hepatitis C virus (HCV)-the causative of liver cirrhosis and development of liver cancer-is a dual therapy using modified interferon and ribavirin. While this regimen increases the sustained viral response rate up to 40-80 % in different genotypes, unfortunately, it is poorly tolerated by patients. PSI-7977, a prodrug for PSI-7409, is a Non-Structural 5b (NS5b) polymerase nucleoside inhibitor that is currently in phase III clinical trials. The activated PSI-7977 is a direct acting antiviral (DAA) drug that acts on NS5b polymerase of HCV through a coordination bond with the two Mg(+2) present at the GDD active site motif. The present work utilizes a molecular modeling approach for studying the interaction between the activated PSI-7977 and the 12 amino acids constituting a 5 Å region surrounding the GDD active triad motif for HCV genotypes 1a, 2b, 3b and 4a. The analysis of the interaction parameters suggests that PSI-7977 is probably a better DAA drug for HCV genotypes 1a and 3b rather than genotypes 2b and 4a.
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Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
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Characterization of vaniprevir, a hepatitis C virus NS3/4A protease inhibitor, in patients with HCV genotype 1 infection: safety, antiviral activity, resistance, and pharmacokinetics. Antiviral Res 2013; 99:214-20. [PMID: 23747481 DOI: 10.1016/j.antiviral.2013.05.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 11/23/2022]
Abstract
Vaniprevir is a competitive inhibitor of the hepatitis C virus (HCV) NS3/4A protease that has potent anti-HCV activity in preclinical models. This placebo-controlled dose-ranging study assessed the safety, tolerability, and antiviral efficacy of vaniprevir monotherapy in patients with genotype 1 chronic HCV infection. Treatment-naive and treatment-experienced non-cirrhotic adult patients with baseline HCV RNA >10(6)IU/ml were randomized to receive placebo or vaniprevir at doses of 125 mg qd, 600 mg qd, 25mg bid, 75 mg bid, 250 mg bid, 500 mg bid, and 700 mg bid for 8 days. Forty patients (82.5% male, 75% genotype 1a) received at least one dose of placebo or vaniprevir. After 1 week of vaniprevir, the decrease in HCV RNA from baseline ranged from 1.8 to 4.6 log₁₀IU/ml across all treatment groups, and there was a greater than dose-proportional increase in vaniprevir exposure at doses above 75 mg bid. The most commonly reported drug-related adverse events (AEs) were diarrhea (n=5) and nausea (n=5). No pattern of laboratory or ECG abnormalities was observed, all AEs resolved during the study, and there were no discontinuations due to AEs. No serious AEs were reported. Resistance-associated amino acid variants were identified at positions R155 and D168 in patients infected with genotype 1a virus. Vaniprevir monotherapy demonstrated potent antiviral activity in patients with chronic genotype 1 HCV infection, and was generally well tolerated with no serious AEs or discontinuations due to AEs. Further development of vaniprevir, including studies in combination with other anti-HCV agents, is ongoing.
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Naderi M, Saeedi A, Moradi A, Kleshadi M, Zolfaghari MR, Gorji A, Ghaemi A. Interleukin-12 as a genetic adjuvant enhances hepatitis C virus NS3 DNA vaccine immunogenicity. Virol Sin 2013; 28:167-73. [PMID: 23709057 DOI: 10.1007/s12250-013-3291-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/28/2013] [Indexed: 01/27/2023] Open
Abstract
Hepatitis C virus (HCV) chronic infection is a worldwide health problem, and numerous efforts have been invested to develop novel vaccines. An efficient vaccine requires broad immune response induction against viral proteins. To achieve this goal, we constructed a DNA vaccine expressing nonstructural 3 (NS3) gene (pcDNA3.1-HCV-NS3) and assessed the immune response in C57BL/6 mice. In this study, the NS3 gene was amplified with a nested-reverse transcriptase-polymerase chain reaction (RT-PCR) method using sera of HCV-infected patients with genotype 1a. The resulting NS3 gene was subcloned into a pcDNA3.1 eukaryotic expression vector, and gene expression was detected by western blot. The resultant DNA vaccine was co-administered with interleukin-12 (IL-12) as an adjuvant to female C57BL/6 mice. After the final immunizations, lymphocyte proliferation, cytotoxicity, and cytokine levels were assessed to measure immune responses. Our data suggest that co-administration of HCV NS3 DNA vaccine with IL-12 induces production of significant levels of both IL-4 and interferon (IFN)-γ (p<0.05). Cytotoxicity and lymphocyte proliferation responses of vaccinated mice were significantly increased compared to control (p<0.05). Collectively, our results demonstrated that co-administration of HCV NS3 and IL-12 displayed strong immunogenicity in a murine model.
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Affiliation(s)
- Malihe Naderi
- Department of Microbiology, Qom branch, Islamic Azad University, Qom 37185-364, Iran
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Garriga D, Ferrer-Orta C, Querol-Audí J, Oliva B, Verdaguer N. Role of motif B loop in allosteric regulation of RNA-dependent RNA polymerization activity. J Mol Biol 2013; 425:2279-87. [PMID: 23542342 DOI: 10.1016/j.jmb.2013.03.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/15/2013] [Accepted: 03/21/2013] [Indexed: 01/22/2023]
Abstract
Increasing amounts of data show that conformational dynamics are essential for protein function. Unveiling the mechanisms by which this flexibility affects the activity of a given enzyme and how it is controlled by other effectors opens the door to the design of a new generation of highly specific drugs. Viral RNA-dependent RNA polymerases (RdRPs) are not an exception. These enzymes, essential for the multiplication of all RNA viruses, catalyze the formation of phosphodiester bonds between ribonucleotides in an RNA-template-dependent fashion. Inhibition of RdRP activity will prevent genome replication and virus multiplication. Thus, RdRPs, like the reverse transcriptase of retroviruses, are validated targets for the development of antiviral therapeutics. X-ray crystallography of RdRPs trapped in multiple steps throughout the catalytic process, together with NMR data and molecular dynamics simulations, have shown that all polymerase regions contributing to conserved motifs required for substrate binding, catalysis and product release are highly flexible and some of them are predicted to display correlated motions. All these dynamic elements can be modulated by external effectors, which appear as useful tools for the development of effective allosteric inhibitors that block or disturb the flexibility of these enzymes, ultimately impeding their function. Among all movements observed, motif B, and the B-loop at its N-terminus in particular, appears as a new potential druggable site.
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Affiliation(s)
- Damià Garriga
- Institut de Biología Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri i Reixac 10-12, 08028 Barcelona, Spain
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44
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Viral enzymes containing magnesium: Metal binding as a successful strategy in drug design. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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45
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Yanvarev DV, Korovina AN, Usanov NN, Kochetkov SN. Non-hydrolysable analogues of inorganic pyrophosphate as inhibitors of hepatitis C virus RNA-dependent RNA-polymerase. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s1068162012020124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Moriishi K, Matsuura Y. Exploitation of lipid components by viral and host proteins for hepatitis C virus infection. Front Microbiol 2012; 3:54. [PMID: 22347882 PMCID: PMC3278987 DOI: 10.3389/fmicb.2012.00054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/31/2012] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV), which is a major causative agent of blood-borne hepatitis, has chronically infected about 170 million individuals worldwide and leads to chronic infection, resulting in development of steatosis, cirrhosis, and eventually hepatocellular carcinoma. Hepatocellular carcinoma associated with HCV infection is not only caused by chronic inflammation, but also by the biological activity of HCV proteins. HCV core protein is known as a main component of the viral nucleocapsid. It cooperates with host factors and possesses biological activity causing lipid alteration, oxidative stress, and progression of cell growth, while other viral proteins also interact with host proteins including molecular chaperones, membrane-anchoring proteins, and enzymes associated with lipid metabolism to maintain the efficiency of viral replication and production. HCV core protein is localized on the surface of lipid droplets in infected cells. However, the role of lipid droplets in HCV infection has not yet been elucidated. Several groups recently reported that other viral proteins also support viral infection by regulation of lipid droplets and core localization in infected cells. Furthermore, lipid components are required for modification of host factors and the intracellular membrane to maintain or up-regulate viral replication. In this review, we summarize the current status of knowledge regarding the exploitation of lipid components by viral and host proteins in HCV infection.
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Affiliation(s)
- Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, University of Yamanashi Chuo-shi, Yamanashi, Japan
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Weiser BM, Tellinghuisen TL. Structural biology of the hepatitis C virus proteins. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e175-e226. [PMID: 24064309 DOI: 10.1016/j.ddtec.2011.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Roh C, Jo SK. (−)-Epigallocatechin gallate inhibits hepatitis C virus (HCV) viral protein NS5B. Talanta 2011; 85:2639-42. [DOI: 10.1016/j.talanta.2011.08.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 02/02/2023]
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Label free inhibitor screening of hepatitis C virus (HCV) NS5B viral protein using RNA oligonucleotide. SENSORS 2011; 11:6685-96. [PMID: 22163979 PMCID: PMC3231669 DOI: 10.3390/s110706685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/22/2011] [Accepted: 06/27/2011] [Indexed: 01/26/2023]
Abstract
Globally, over 170 million people (ca. 3% of the World's population) are infected with the hepatitis C virus (HCV), which can cause serious liver diseases such as chronic hepatitis, evolving into subsequent health problems. Driven by the need to detect the presence of HCV, as an essential factor in diagnostic medicine, the monitoring of viral protein has been of great interest in developing simple and reliable HCV detection methods. Despite considerable advances in viral protein detection as an HCV disease marker, the current enzyme linked immunosorbent assay (ELISA) based detection methods using antibody treatment have several drawbacks. To overcome this bottleneck, an RNA aptamer become to be emerged as an antibody substitute in the application of biosensor for detection of viral protein. In this study, we demonstrated a streptavidin-biotin conjugation method, namely, the RNA aptamer sensor system that can quantify viral protein with detection level of 700 pg mL(-1) using a biotinylated RNA oligonucleotide on an Octet optical biosensor. Also, we showed this method can be used to screen inhibitors of viral protein rapidly and simply on a biotinylated RNA oligonucleotide biosensor. Among the inhibitors screened, (-)-Epigallocatechin gallate showed high binding inhibition effect on HCV NS5B viral protein. The proposed method can be considered a real-time monitoring method for inhibitor screening of HCV viral protein and is expected to be applicable to other types of diseases.
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Ashfaq UA, Yousaf MZ, Aslam M, Ejaz R, Jahan S, Ullah O. siRNAs: potential therapeutic agents against hepatitis C virus. Virol J 2011; 8:276. [PMID: 21645341 PMCID: PMC3118364 DOI: 10.1186/1743-422x-8-276] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 06/06/2011] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus is a major cause of chronic liver diseases which can lead to permanent liver damage, hepatocellular carcinoma and death. The presently available treatment with interferon plus ribavirin, has limited benefits due to adverse side effects such as anemia, depression and "flu-like" symptoms. Needless to mention, the effectiveness of interferon therapy is predominantly, if not exclusively, limited to virus type 3a and 3b whereas in Europe and North America the majority of viral type is 1a and 2a. Due to the limited efficiency of current therapy, RNA interference (RNAi) a novel regulatory and powerful silencing approach for molecular therapeutics through a sequence-specific RNA degradation process represents an alternative option. Several reports have indicated the efficiency and specificity of synthetic and vector based siRNAs inhibiting HCV replication. In the present review, we focused that combination of siRNAs against virus and host genes will be a better option to treat HCV.
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Affiliation(s)
- Usman A Ashfaq
- Division of Molecular Medicine, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
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