1
|
Chu H, Wang L, Wang J, Zhang Y, Jin N, Liu F, Li Y. Genomic profile of eGFP-tagged senecavirus A subjected to serial plaque-to-plaque transfers. Microb Pathog 2024; 191:106661. [PMID: 38657711 DOI: 10.1016/j.micpath.2024.106661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. This virus possesses a positive-sense, single-stranded RNA genome, approximately 7200 nt in length, composed of a single 5' untranslated region, encoding region and 3' untranslated region. In this study, a recombinant SVA tagged with enhanced green fluorescent protein (eGFP) sequence, rSVA-eGFP, was rescued from its cDNA clone using reverse genetics. The passage-5 (P5) rSVA-eGFP was totally subjected to 55 rounds of consecutive fluorescent plaque-to-fluorescent plaque (FP-FP) transfers, and one extra common passaging in vitro. The P61 viral stock was analyzed by next-generation sequencing. The result showed ten single-nucleotide mutations (SNMs) in the rSVA-eGFP genome, including nine transitions and only one transversion. The P61 progeny still showed a complete eGFP sequence, indicating no occurrence of copy-choice recombination within the eGFP region during serial FP-FP transfers. In other words, this progeny was genetically deficient in the recombination of eGFP sequence (RES), namely, an RES-deficient strain. Out of ten SNMs, three were missense mutations, leading to single-amino acid mutations (SAAMs): F15V in L protein, A74T in VP2, and E53R in 3D protein. The E53R was predicted to be spatially adjacent to the RNA channel of 3D protein, perhaps involved in the emergence of RES-deficient strain. In conclusion, this study uncovered a global landscape of rSVA-eGFP genome after serial FP-FP transfers, and moreover shed light on a putative SAAM possibly related to the RES-deficient mechanism.
Collapse
Affiliation(s)
- Huanhuan Chu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ningyi Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Yan Li
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China.
| |
Collapse
|
2
|
Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
| |
Collapse
|
3
|
Kyaw T, Drummond G, Bobik A, Peter K. Myocarditis: causes, mechanisms, and evolving therapies. Expert Opin Ther Targets 2023; 27:225-238. [PMID: 36946552 DOI: 10.1080/14728222.2023.2193330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Myocarditis is a severe lymphocyte-mediated inflammatory disorder of the heart, mostly caused by viruses and immune checkpoint inhibitors (ICIs). Recently, myocarditis as a rare adverse event of mRNA vaccines for SARS-CoV-2 has caused global attention. The clinical consequences of myocarditis can be very severe, but specific treatment options are lacking or not yet clinically proven. AREAS COVERED This paper offers a brief overview of the biology of viruses that frequently cause myocarditis, focusing on mechanisms important for viral entry and replication following host infection. Current and new potential therapeutic targets/strategies especially for viral myocarditis are reviewed systematically. In particular, the immune system in myocarditis is dissected with respect to infective viral and non-infective, ICI-induced myocarditis. EXPERT OPINION Vaccination is an excellent emerging preventative strategy for viral myocarditis, but most vaccines still require further development. Anti-viral treatments that inhibit viral replication need to be considered following viral infection in host myocardium, as lower viral load reduces inflammation severity. Understanding how the immune system continues to damage the heart even after viral clearance will define novel therapeutic targets/strategies. We propose that viral myocarditis can be best treated using a combination of antiviral agents and immunotherapies that control cytotoxic T cell activity.
Collapse
Affiliation(s)
- Tin Kyaw
- Inflammation and Cardiovascular Disease Laboratory, Baker Heart and Diabetes Institute
- Centre for Inflammatory Diseases, Monash Medical Centre, Monash University, Melbourne, Australia
- Department of Cardiometabolic Health, University of Melbourne Melbourne Australia
| | - Grant Drummond
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University Melbourne Australia
- Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Australia
| | - Alex Bobik
- Inflammation and Cardiovascular Disease Laboratory, Baker Heart and Diabetes Institute
- Centre for Inflammatory Diseases, Monash Medical Centre, Monash University, Melbourne, Australia
- Department of Cardiometabolic Health, University of Melbourne Melbourne Australia
- Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Australia
- Heart Centre, Alfred Hospital, Melbourne, Australia
| | - Karlheinz Peter
- Inflammation and Cardiovascular Disease Laboratory, Baker Heart and Diabetes Institute
- Department of Cardiometabolic Health, University of Melbourne Melbourne Australia
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University Melbourne Australia
- Heart Centre, Alfred Hospital, Melbourne, Australia
- Department of Immunology, Monash University Melbourne Australia
| |
Collapse
|
4
|
Ren M, Zhou Y, Tu T, Jiang D, Pang M, Li Y, Luo Y, Yao X, Yang Z, Wang Y. RVG Peptide-Functionalized Favipiravir Nanoparticle Delivery System Facilitates Antiviral Therapy of Neurotropic Virus Infection in a Mouse Model. Int J Mol Sci 2023; 24:ijms24065851. [PMID: 36982925 PMCID: PMC10058582 DOI: 10.3390/ijms24065851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Neurotropic viruses severely damage the central nervous system (CNS) and human health. Common neurotropic viruses include rabies virus (RABV), Zika virus, and poliovirus. When treating neurotropic virus infection, obstruction of the blood-brain barrier (BBB) reduces the efficiency of drug delivery to the CNS. An efficient intracerebral delivery system can significantly increase intracerebral delivery efficiency and facilitate antiviral therapy. In this study, a rabies virus glycopeptide (RVG) functionalized mesoporous silica nanoparticle (MSN) packaging favipiravir (T-705) was developed to generate T-705@MSN-RVG. It was further evaluated for drug delivery and antiviral treatment in a VSV-infected mouse model. The RVG, a polypeptide consisting of 29 amino acids, was conjugated on the nanoparticle to enhance CNS delivery. The T-705@MSN-RVG caused a significant decrease in virus titers and virus proliferation without inducing substantial cell damage in vitro. By releasing T-705, the nanoparticle promoted viral inhibition in the brain during infection. At 21 days post-infection (dpi), a significantly enhanced survival ratio (77%) was observed in the group inoculated with nanoparticle compared with the non-treated group (23%). The viral RNA levels were also decreased in the therapy group at 4 and 6 dpi compared with that of the control group. The T-705@MSN-RVG could be considered a promising system for CNS delivery for treating neurotropic virus infection.
Collapse
Affiliation(s)
- Meishen Ren
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - You Zhou
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Teng Tu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Dike Jiang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Maonan Pang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanwei Li
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Luo
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xueping Yao
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zexiao Yang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
5
|
Figueiredo-Nunes I, Trigueiro-Louro J, Rebelo-de-Andrade H. Exploring new antiviral targets for influenza and COVID-19: Mapping promising hot spots in viral RNA polymerases. Virology 2023; 578:45-60. [PMID: 36463618 PMCID: PMC9674405 DOI: 10.1016/j.virol.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Influenza and COVID-19 are infectious respiratory diseases that represent a major concern to public health with social and economic impact worldwide, for which the available therapeutic options are not satisfactory. The RdRp has a central role in viral replication and thus represents a major target for the development of antiviral approaches. In this study, we focused on Influenza A virus PB1 polymerase protein and the betacoronaviruses nsp12 polymerase protein, considering their functional and structural similarities. We have performed conservation and druggability analysis to map conserved druggable regions, that may have functional or structural importance in these proteins. We disclosed the most promising and new targeting regions for the discovery of new potential polymerase inhibitors. Conserved druggable regions of putative interaction with favipiravir and molnupiravir were also mapped. We have also compared and integrated the current findings with previous research.
Collapse
Affiliation(s)
- Inês Figueiredo-Nunes
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal
| | - João Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| |
Collapse
|
6
|
Abstract
The virus-encoded RNA-dependent RNA polymerase (RdRp) is responsible for viral replication, and its fidelity is closely related to viral diversity, pathogenesis, virulence, and fitness. Hepatitis C virus (HCV) and the second human pegivirus (HPgV-2) belong to the family Flaviviridae and share some features, including similar viral genome structure. Unlike HCV, HPgV-2 preserves a highly conserved genome sequence and low intrahost variation. However, the underlying mechanism remains to be elucidated. In this study, we evaluated the fidelity of HPgV-2 and HCV RdRp in an in vitro RNA polymerase reaction system. The results showed higher fidelity of HPgV-2 RdRp than HCV NS5B with respect to the misincorporation rate due to their difference in recognizing nucleoside triphosphate (NTP) substrates. Furthermore, HPgV-2 RdRp showed lower sensitivity than HCV to sofosbuvir, a nucleotide inhibitor against HCV RdRp, which explained the insusceptibility of HPgV-2 to direct-acting antiviral (DAA) therapy against HCV infection. Our results indicate that HPgV-2 could be an excellent model for studying the mechanisms involved in viral polymerase fidelity as well as RNA virus diversity and evolution. IMPORTANCE RNA viruses represent the most important pathogens for humans and animals and exhibit rapid evolution and high adaptive capacity, which is due to the high mutation rates for using the error-prone RNA-dependent RNA polymerase (RdRp) during replication. The fidelity of RdRp is closely associated with viral diversity, fitness, and pathogenesis. Previous studies have shown that the second human pegivirus (HPgV-2) exhibits a highly conserved genome sequence and low intrahost variation, which might be due to the fidelity of HPgV-2 RdRp. In this work, we used a series of in vitro RNA polymerase assays to evaluate the in vitro fidelity of HPgV-2 RdRp and compared it with that of HCV RdRp. The results indicated that HPgV-2 RdRp preserves significantly higher fidelity than HCV RdRp, which might contribute to the conservation of the HPgV-2 genome. The unique feature of HPgV-2 RdRp fidelity provides a new model for investigation of viral RdRp fidelity.
Collapse
|
7
|
Komeno T, Furuta Y, Nakajima N, Tani H, Morinaga Y. Analysis of the responsible site for favipiravir resistance in RNA-dependent RNA polymerase of influenza virus A/PR/8/34 (H1N1) using site-directed mutagenesis. Antiviral Res 2022; 205:105387. [PMID: 35931138 DOI: 10.1016/j.antiviral.2022.105387] [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: 03/18/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/02/2022]
Abstract
Favipiravir (T-705, 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) selectively and strongly inhibits the replication of influenza virus in vitro and in vivo. Favipiravir is converted to favipiravir-4-ribofuranosyl-5-triphosphate (favipiravir RTP) by intracellular enzymes and functions as a nucleotide analog to selectively inhibit RNA-dependent RNA polymerase (RdRP) of influenza virus. Our previous experiments failed in an attempt to obtain a favipiravir-resistant influenza virus in vitro using influenza virus A/PR/8/34(H1N1). Conversely, Goldhill et al. reported a favipiravir-resistant influenza virus generated by in vitro passage of influenza virus A/England/195/2009 (H1N1), an early isolate from the 2009 H1N1 pandemic (pdm09), in the presence of favipiravir with K229R mutation in PB1. This study focused on K229R mutation near the NTP cross-linked region in PB1 based on the above conflicting findings to confirm whether K229R mutation brings favipiravir resistance to influenza virus A/PR/8/34. Thirty PB1 mutants generated by site-directed mutagenesis of the NTP cross-linked region were evaluated using an influenza virus A/PR/8/34 replicon system. Among the 30 mutants, 10 possessed but 20 lost replicon activity. When susceptibility to favipiravir in 10 mutants was further assessed, the PB1 E491D mutant was five times more sensitive than the wild-type (WT), while only the PB1 K229R mutant was resistant to favipiravir. Results suggested that the evaluated region was essential for polymerase activity, and K229 mutation was responsible for polymerase inhibition of favipiravir in the influenza virus A/PR/8/34. Interestingly, the tested K229X series mutants entirely lost replicon activity, except for K229R. This suggested that the amino acid at position 229 in PB1 of influenza virus may play a pivotal role in polymerase activity. Moreover, this lysine residue is highly conserved among positive- and negative-sense single-stranded RNA viruses, in which favipiravir showed potent activity, suggesting that this mutation may determine the characterization of the in vitro broad-spectrum activity of favipiravir. Additionally, this mutation acquisition greatly influences the viral replication and the susceptibility to favipiravir.
Collapse
Affiliation(s)
- Takashi Komeno
- Toyama Pharmaceutical Research Department, FUJIFILM Toyama Chemical Co., Ltd., Toyama, Japan; Department of Microbiology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.
| | - Yousuke Furuta
- Toyama Pharmaceutical Research Department, FUJIFILM Toyama Chemical Co., Ltd., Toyama, Japan
| | - Nozomi Nakajima
- Toyama Pharmaceutical Research Department, FUJIFILM Toyama Chemical Co., Ltd., Toyama, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.
| |
Collapse
|
8
|
Borrego B, Moreno S, López-Valiñas Á, de la Losa N, Weber F, Núñez JI, Brun A. Identification of Single Amino Acid Changes in the Rift Valley Fever Virus Polymerase Core Domain Contributing to Virus Attenuation In Vivo. Front Cell Infect Microbiol 2022; 12:875539. [PMID: 35573791 PMCID: PMC9096444 DOI: 10.3389/fcimb.2022.875539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
Rift Valley fever (RVF) is an arboviral zoonotic disease affecting many African countries with the potential to spread to other geographical areas. RVF affects sheep, goats, cattle and camels, causing a high rate of abortions and death of newborn lambs. Also, humans can be infected, developing a usually self-limiting disease that can turn into a more severe illness in a low percentage of cases. Although different veterinary vaccines are available in endemic areas in Africa, to date no human vaccine has been licensed. In previous works, we described the selection and characterization of a favipiravir-mutagenized RVFV variant, termed 40Fp8, with potential as a RVF vaccine candidate due to the strong attenuation shown in immunocompromised animal models. Compared to the parental South African 56/74 viral strain, 40Fp8 displayed 7 amino acid substitutions in the L-protein, three of them located in the central region corresponding to the catalytic core of the RNA-dependent RNA polymerase (RdRp). In this work, by means of a reverse genetics system, we have analyzed the effect on virulence of these amino acid changes, alone or combined, both in vitro and in vivo. We found that the simultaneous introduction of two changes (G924S and A1303T) in the heterologous ZH548-RVFV Egyptian strain conferred attenuated phenotypes to the rescued viruses as shown in infected mice without affecting virus immunogenicity. Our results suggest that both changes induce resistance to favipiravir likely associated to some fitness cost that could be the basis for the observed attenuation in vivo. Conversely, the third change, I1050V, appears to be a compensatory mutation increasing viral fitness. Altogether, these results provide relevant information for the safety improvement of novel live attenuated RVFV vaccines.
Collapse
Affiliation(s)
- Belén Borrego
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
- *Correspondence: Belén Borrego, ; Alejandro Brun,
| | - Sandra Moreno
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
| | - Álvaro López-Valiñas
- Centre de Recerca en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA) Institut de Recerca en Tecnologies Agroalimentàries (IRTA), Barcelona, Spain
| | - Nuria de la Losa
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
| | - Friedemann Weber
- Institut für Virologie, FB10-Veterinary Medicine, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - José Ignacio Núñez
- Centre de Recerca en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA) Institut de Recerca en Tecnologies Agroalimentàries (IRTA), Barcelona, Spain
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
- *Correspondence: Belén Borrego, ; Alejandro Brun,
| |
Collapse
|
9
|
Repurposing drugs targeting epidemic viruses. Drug Discov Today 2022; 27:1874-1894. [DOI: 10.1016/j.drudis.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023]
|
10
|
Konstantinova ID, L.Andronova V, Fateev IV, Esipov RS. Favipiravir and Its Structural Analogs: Antiviral Activity and Synthesis Methods. Acta Naturae 2022; 14:16-38. [PMID: 35923566 PMCID: PMC9307979 DOI: 10.32607/actanaturae.11652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/27/2022] [Indexed: 01/18/2023] Open
Abstract
1,4-Pyrazine-3-carboxamide-based antiviral compounds have been under intensive study for the last 20 years. One of these compounds, favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, T-705), is approved for use against the influenza infection in a number of countries. Now, favipiravir is being actively used against COVID-19. This review describes the in vivo metabolism of favipiravir, the mechanism of its antiviral activity, clinical findings, toxic properties, and the chemical synthesis routes for its production. We provide data on the synthesis and antiviral activity of structural analogs of favipiravir, including nucleosides and nucleotides based on them.
Collapse
Affiliation(s)
- I. D. Konstantinova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - V. L.Andronova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia, Moscow, 123098 Russia
| | - I. V. Fateev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - R. S. Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| |
Collapse
|
11
|
Repurposing Probenecid to Inhibit SARS-CoV-2, Influenza Virus, and Respiratory Syncytial Virus (RSV) Replication. Viruses 2022; 14:v14030612. [PMID: 35337018 PMCID: PMC8955960 DOI: 10.3390/v14030612] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 12/02/2022] Open
Abstract
Viral replication and transmissibility are the principal causes of endemic and pandemic disease threats. There remains a need for broad-spectrum antiviral agents. The most common respiratory viruses are endemic agents such as coronaviruses, respiratory syncytial viruses, and influenza viruses. Although vaccines are available for SARS-CoV-2 and some influenza viruses, there is a paucity of effective antiviral drugs, while for RSV there is no vaccine available, and therapeutic treatments are very limited. We have previously shown that probenecid is safe and effective in limiting influenza A virus replication and SARS-CoV-2 replication, along with strong evidence showing inhibition of RSV replication in vitro and in vivo. This review article will describe the antiviral activity profile of probenecid against these three viruses.
Collapse
|
12
|
Ratajczak F, Joblin M, Ringsquandl M, Hildebrandt M. Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. BMC Bioinformatics 2022; 23:84. [PMID: 35246025 PMCID: PMC8894843 DOI: 10.1186/s12859-022-04608-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background Drug repurposing aims at finding new targets for already developed drugs. It becomes more relevant as the cost of discovering new drugs steadily increases. To find new potential targets for a drug, an abundance of methods and existing biomedical knowledge from different domains can be leveraged. Recently, knowledge graphs have emerged in the biomedical domain that integrate information about genes, drugs, diseases and other biological domains. Knowledge graphs can be used to predict new connections between compounds and diseases, leveraging the interconnected biomedical data around them. While real world use cases such as drug repurposing are only interested in one specific relation type, widely used knowledge graph embedding models simultaneously optimize over all relation types in the graph. This can lead the models to underfit the data that is most relevant for the desired relation type. For example, if we want to learn embeddings to predict links between compounds and diseases but almost the entirety of relations in the graph is incident to other pairs of entity types, then the resulting embeddings are likely not optimised to predict links between compounds and diseases. We propose a method that leverages domain knowledge in the form of metapaths and use them to filter two biomedical knowledge graphs (Hetionet and DRKG) for the purpose of improving performance on the prediction task of drug repurposing while simultaneously increasing computational efficiency. Results We find that our method reduces the number of entities by 60% on Hetionet and 26% on DRKG, while leading to an improvement in prediction performance of up to 40.8% on Hetionet and 14.2% on DRKG, with an average improvement of 20.6% on Hetionet and 8.9% on DRKG. Additionally, prioritization of antiviral compounds for SARS CoV-2 improves after task-driven filtering is applied. Conclusion Knowledge graphs contain facts that are counter productive for specific tasks, in our case drug repurposing. We also demonstrate that these facts can be removed, resulting in an improved performance in that task and a more efficient learning process. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04608-y.
Collapse
Affiliation(s)
- Florin Ratajczak
- Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Munich, Germany. .,Digital Technology and Innovation, Siemens Healthineers, Erlangen, Germany.
| | | | | | | |
Collapse
|
13
|
Smyk JM, Majewska A. Favipiravir in the Battle with Respiratory Viruses. Mini Rev Med Chem 2022; 22:2224-2236. [DOI: 10.2174/1389557522666220218122744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/12/2021] [Accepted: 01/13/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Among antiviral drugs, the vast majority targets only one or two related viruses. The conventional model, one virus - one drug, significantly limits therapeutic options. Therefore, in the strategy of controlling viral infections, there is a necessity to develop compounds with pleiotropic effects. Favipiravir (FPV) emerged as a strong candidate to become such a drug. The aim of the study is to present up-to-date information on the role of favipiravir in the treatment of viral respiratory infections. The anti-influenza activity of favipiravir has been confirmed in cell culture experiments, animal models and clinical trials. Thoroughly different - from the previously registered drugs - mechanism of action suggests that FVP can be used as a countermeasure for the novel or re-emerging influenza virus infections.
In recent months, favipiravir has been broadly investigated due to its potential efficacy in the treatment of Covid-19. Based on preclinical and clinical studies and a recently published meta-analysis it seems that favipiravir may be a promising antiviral drug in the treatment of patients with Covid-19.
FPV is also effective against other RNA respiratory viruses and may be a candidate for the treatment of serious infections caused by human rhinovirus, respiratory syncytial virus, metapneumovirus, parainfluenza viruses and hantavirus pulmonary syndrome.
Collapse
Affiliation(s)
- Julia M. Smyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland
| | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland
| |
Collapse
|
14
|
Detailed Analyses of Molecular Interactions between Favipiravir and RNA Viruses In Silico. Viruses 2022; 14:v14020338. [PMID: 35215932 PMCID: PMC8879546 DOI: 10.3390/v14020338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 02/05/2023] Open
Abstract
There are currently no antiviral agents for human metapneumovirus (HMPV), respiratory syncytial virus (RSV), mumps virus (MuV), or measles virus (MeV). Favipiravir has been developed as an anti-influenza agent, and this agent may be effective against these viruses in vitro. However, the molecular mechanisms through which the agent affects virus replication remain to be fully elucidated. Thus, to clarify the detailed molecular interactions between favipiravir and the RNA-dependent RNA polymerase (RdRp) of HMPV, RSV, MuV, MeV, and influenza virus, we performed in silico studies using authentic bioinformatics technologies. As a result, we found that the active form of favipiravir (favipiravir ribofuranosyl-5′-triphosphate [F-RTP]) can bind to the RdRp active sites of HMPV, RSV, MuV, and MeV. The aspartic acid residue of RdRp active sites was involved in the interaction. Moreover, F-RTP was incorporated into the growing viral RNA chain in the presence of nucleotide triphosphate and magnesium ions. The results suggested that favipiravir shows two distinct mechanisms in various viruses: RdRp active site inhibition and/or genome replication inhibition.
Collapse
|
15
|
Zhao J, Liu Q, Yi D, Li Q, Guo S, Ma L, Zhang Y, Dong D, Guo F, Liu Z, Wei T, Li X, Cen S. 5-Iodotubercidin inhibits SARS-CoV-2 RNA synthesis. Antiviral Res 2022; 198:105254. [PMID: 35101534 PMCID: PMC8800165 DOI: 10.1016/j.antiviral.2022.105254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a newly emerged infectious disease caused by a novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid global emergence of SARS-CoV-2 highlights the importance and urgency for potential drugs to control the pandemic. The functional importance of RNA-dependent RNA polymerase (RdRp) in the viral life cycle, combined with structural conservation and absence of closely related homologs in humans, makes it an attractive target for designing antiviral drugs. Nucleos(t)ide analogs (NAs) are still the most promising broad-spectrum class of viral RdRp inhibitors. In this study, using our previously developed cell-based SARS-CoV-2 RdRp report system, we screened 134 compounds in the Selleckchemicals NAs library. Four candidate compounds, Fludarabine Phosphate, Fludarabine, 6-Thio-20-Deoxyguanosine (6-Thio-dG), and 5-Iodotubercidin, exhibit remarkable potency in inhibiting SARS-CoV-2 RdRp. Among these four compounds, 5-Iodotubercidin exhibited the strongest inhibition upon SARS-CoV-2 RdRp, and was resistant to viral exoribonuclease activity, thus presenting the best antiviral activity against coronavirus from a different genus. Further study showed that the RdRp inhibitory activity of 5-Iodotubercidin is closely related to its capacity to inhibit adenosine kinase (ADK).
Collapse
|
16
|
DFT and MD simulation investigation of favipiravir as an emerging antiviral option against viral protease (3CL pro) of SARS-CoV-2. J Mol Struct 2021; 1246:131253. [PMID: 34376872 PMCID: PMC8342190 DOI: 10.1016/j.molstruc.2021.131253] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/18/2023]
Abstract
As per date, around 20 million COVID-19 cases reported from across the globe due to a tiny 125 nm sized virus: SARS-CoV-2 which has created a pandemic and left an unforgettable impact on our world. Besides vaccine, medical community is in a race to identify an effective drug, which can fight against this disease effectively. Favipiravir (F) has recently attracted too much attention as an effective repurposed drug against COVID-19. In the present study, the pertinency of F has been tested as an antiviral option against viral protease (3CLpro) of SARS-CoV-2 with the help of density functional theory (DFT) and MD Simulation. Different electronic properties of F such as atomic charges, molecular electrostatic properties (MEP), chemical reactivity and absorption analysis have been studied by DFT. In order to understand the interaction and stability of inhibitor F against viral protease, molecular docking and MD simulation have been performed. Various output like interaction energies, number of intermolecular hydrogen bonding, binding energy etc. have established the elucidate role of F for the management of CoV-2 virus for which there is no approved therapies till now. Our findings highlighted the need to further evaluate F as a potential antiviral against SARS-CoV-2.
Collapse
|
17
|
Janissen R, Woodman A, Shengjuler D, Vallet T, Lee KM, Kuijpers L, Moustafa IM, Fitzgerald F, Huang PN, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih SR, Vignuzzi M, Cameron CE, Dekker NH. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 2021; 81:4467-4480.e7. [PMID: 34687604 PMCID: PMC8628313 DOI: 10.1016/j.molcel.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022]
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.
Collapse
Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Louis Kuijpers
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Fiona Fitzgerald
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Angela L Perkins
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands.
| |
Collapse
|
18
|
Mravinec M, Bajc G, Butala M. Surface plasmon resonance approach to study drug interactions with SARS-CoV-2 RNA-dependent RNA polymerase highlights treatment potential of suramin. J Virol Methods 2021; 298:114283. [PMID: 34534610 PMCID: PMC8439102 DOI: 10.1016/j.jviromet.2021.114283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is essential for virus replication, therefore it is a promising drug target. Here we present a surface plasmon resonance approach to study the interaction of RdRp with drugs in real time. We monitored the effect of favipiravir, ribavirin, sofosbuvir triphosphate PSI-7409 and suramin on RdRp binding to RNA immobilized on the chip. Suramin precluded interaction of RdRp with RNA and even displaced RdRp from RNA.
Collapse
Affiliation(s)
- Martina Mravinec
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia.
| |
Collapse
|
19
|
Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PPH, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Res 2021; 49:8796-8810. [PMID: 34379778 PMCID: PMC8421151 DOI: 10.1093/nar/gkab660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.
Collapse
Affiliation(s)
- Xinzhou Xu
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julie Tung Sem Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alex Wing Hong Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Zixi Dai
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, Li Ka Shing Medical Sciences Building, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| |
Collapse
|
20
|
Battisti V, Urban E, Langer T. Antivirals against the Chikungunya Virus. Viruses 2021; 13:1307. [PMID: 34372513 PMCID: PMC8310245 DOI: 10.3390/v13071307] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/20/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has re-emerged in recent decades, causing large-scale epidemics in many parts of the world. CHIKV infection leads to a febrile disease known as chikungunya fever (CHIKF), which is characterised by severe joint pain and myalgia. As many patients develop a painful chronic stage and neither antiviral drugs nor vaccines are available, the development of a potent CHIKV inhibiting drug is crucial for CHIKF treatment. A comprehensive summary of current antiviral research and development of small-molecule inhibitor against CHIKV is presented in this review. We highlight different approaches used for the identification of such compounds and further discuss the identification and application of promising viral and host targets.
Collapse
Affiliation(s)
| | | | - Thierry Langer
- Department of Pharmaceutical Sciences, Pharmaceutical Chemistry Division, University of Vienna, A-1090 Vienna, Austria; (V.B.); (E.U.)
| |
Collapse
|
21
|
Rabie AM. Cyanorona-20: The first potent anti-SARS-CoV-2 agent. Int Immunopharmacol 2021; 98:107831. [PMID: 34247016 PMCID: PMC8164343 DOI: 10.1016/j.intimp.2021.107831] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 01/18/2023]
Abstract
Explicit hindrance and blockade of the viral RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is considered one of the most promising and efficient approaches for developing highly potent remedies for COVID-19. However, almost all of the reported viral RdRp inhibitors (either repurposed or new antiviral drugs) lack specific selectivity against the novel coronaviral RdRp and still at a beginning phase of advancement. Herein, I discovered and introduce a new pyrazine derivative, (E)-N-(4-cyanobenzylidene)-6-fluoro-3-hydroxypyrazine-2-carboxamide (cyanorona-20), as the first potent SARS-CoV-2 RdRp inhibitor with very high selectivity (209- and 45-fold more potent than favipiravir and remdesivir, respectively). This promising selective specific anti-COVID-19 compound is also deemed to be the first distinctive derivative of favipiravir. Cyanorona-20, the unprecedented nucleoside/nucleotide analog, was designed, synthesized, characterized, computationally studied, and biologically evaluated for its anti-COVID-19 actions (through a precise in vitro anti-COVID-19 assay). The results of the biological assay displayed that cyanorona-20 surprisingly exhibited very high and largely significant anti-COVID-19 activities (anti-SARS-CoV-2 EC50 = 0.45 μM), and, in addition, it could be also a very promising guide and lead compound for the design and synthesis of new anti-SARS-CoV-2 and anti-COVID-19 agents through structural modifications and further computational studies. Further appraisal for the improvement of cyanorona-20 medication is a prerequisite requirement in the coming days. In a word, the ascent of the second member (cyanorona-20 “Corona Antidote”) of the novel and promising class of anti-COVID-19 pyrazine derivatives would drastically make a medical uprising in the pharmacotherapeutic treatment regimens and protocols of the recently-emerged SARS-CoV-2 infection and its accompanying COVID-19.
Collapse
Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura, Egypt.
| |
Collapse
|
22
|
Discovery of ( E)- N-(4-cyanobenzylidene)- 6-fluoro- 3-hydroxypyrazine-2 -carboxamide (cyanorona-20): the first potent and specific anti-COVID-19 drug. CHEMICAL PAPERS 2021; 75:4669-4685. [PMID: 34025012 PMCID: PMC8126404 DOI: 10.1007/s11696-021-01640-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/02/2021] [Indexed: 01/18/2023]
Abstract
Abstract Specific inhibition of the viral RNA-dependent RNA polymerase (RdRp) of the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a very promising strategy for developing highly potent medicines for coronavirus disease 2019 (COVID-19). However, almost all of the reported viral RdRp inhibitors (either repurposed drugs or new antiviral agents) lack selectivity against the SARS-CoV-2 RdRp. Herein, I discovered a new favipiravir derivative, (E)-N-(4-cyanobenzylidene)-6-fluoro-3-hydroxypyrazine-2-carboxamide (cyanorona-20), as the first potent SARS-CoV-2 inhibitor with very high selectivity (209- and 45-fold more potent than favipiravir and remdesivir, respectively). Based on the significant reduction in the in vitro SARS-CoV-2 replication/copies, strong computational cyanorona-20 ligand-RdRp protein interactions, and anti-RdRp activity of the parent favipiravir drug, SARS-CoV-2 inhibition is thought to be mediated through the coronaviral-2 RdRp inhibition. This promising selective anti-COVID-19 compound is also, to the best of our knowledge, the first bioactive derivative of favipiravir, the known antiinfluenza and antiviral drug. This new nucleoside analog was designed, synthesized, characterized, computationally studied (through pharmacokinetic calculations along with computational molecular modeling and prediction), and biologically evaluated for its anti-COVID-19 activities (through a validated in vitro anti-COVID-19 assay). The results of the biological assay showed that cyanorona-20 surprisingly exhibited very significant anti-COVID-19 activity (anti-SARS-CoV-2 EC50 = 0.45 μM), and, in addition, it could be also a very promising lead compound for the design of new anti-COVID-19 agents. Cyanorona-20 is a new favipiravir derivative with promise for the treatment of SARS-CoV-2 infection. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01640-9.
Collapse
|
23
|
Zhirnov OP, Chernyshova AI. Favipiravir: the hidden threat of mutagenic action. JOURNAL OF MICROBIOLOGY, EPIDEMIOLOGY AND IMMUNOBIOLOGY 2021. [DOI: 10.36233/0372-9311-114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The antiviral drug favipiravir (FVP), which is a structural analogue of guanosine, undergoes chemical transformation in infected cells by cellular enzymes into a nucleotide form — favipiravir ribose triphosphate (FVPRTP). FVP-RTP is able to bind to viral RNA-dependent RNA polymerase and integrate into the viral RNA chain, causing a significant mutagenic effect through G→A and С→U transitions in the viral RNA genome. Besides the virus inhibiting effect, the increased synthesis of mutant virions under the action of FPV possess a threat of the emergence of novel threatening viral strains with high pathogenicity for humans and animals and acquired resistance to chemotherapeutic compound. There are three ways to minimize this mutagenic effect of FP. (1) Synthesis of new FPV modifications lacking the ability to integrate into the synthesized viral RNA molecule. (2) The combined use of FPV with antiviral chemotherapeutic drugs of a different mechanism of action directed at various viral and/or host cell targets. (3) Permanent application of high therapeutic doses of FPV under the strict medical control to enhance the lethal mutagenic effect on an infectious virus in the recipient organism to prevent the multiplication of its mutant forms.
Collapse
Affiliation(s)
- O. P. Zhirnov
- The Russian-German Academy of Medico-Social and Biotechnological Sciences;
The D.I. Ivanovsky Institute of Virology, The N.F. Gamaleya National Research Center of Epidemiology and Microbiology
| | - A. I. Chernyshova
- The D.I. Ivanovsky Institute of Virology, The N.F. Gamaleya National Research Center of Epidemiology and Microbiology;
The I.M. Sechenov First Moscow State Medical University (Sechenov University)
| |
Collapse
|
24
|
Favipiravir Does Not Inhibit Chikungunya Virus Replication in Mosquito Cells and Aedes aegypti Mosquitoes. Microorganisms 2021; 9:microorganisms9050944. [PMID: 33925738 PMCID: PMC8145424 DOI: 10.3390/microorganisms9050944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Favipiravir (T-705) is a broad-spectrum antiviral drug that inhibits RNA viruses after intracellular conversion into its active form, T-705 ribofuranosyl 5'-triphosphate. We previously showed that T-705 is able to significantly inhibit the replication of chikungunya virus (CHIKV), an arbovirus transmitted by Aedes mosquitoes, in mammalian cells and in mouse models. In contrast, the effect of T-705 on CHIKV infection and replication in the mosquito vector is unknown. Since the antiviral activity of T-705 has been shown to be cell line-dependent, we studied here its antiviral efficacy in Aedes-derived mosquito cells and in Aedes aegypti mosquitoes. Interestingly, T-705 was devoid of anti-CHIKV activity in mosquito cells, despite being effective against CHIKV in Vero cells. By investigating the metabolic activation profile, we showed that, unlike Vero cells, mosquito cells were not able to convert T-705 into its active form. To explore whether alternative metabolization pathways might exist in vivo, Aedes aegypti mosquitoes were infected with CHIKV and administered T-705 via an artificial blood meal. Virus titrations of whole mosquitoes showed that T-705 was not able to reduce CHIKV infection in mosquitoes. Combined, these in vitro and in vivo data indicate that T-705 lacks antiviral activity in mosquitoes due to inadequate metabolic activation in this animal species.
Collapse
|
25
|
Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Löwe J, Barford D, Russo CJ. Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proc Natl Acad Sci U S A 2021; 118:e2021946118. [PMID: 33526596 PMCID: PMC7896311 DOI: 10.1073/pnas.2021946118] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.
Collapse
Affiliation(s)
- Katerina Naydenova
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kyle W Muir
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Long-Fei Wu
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ziguo Zhang
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Francesca Coscia
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mathew J Peet
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kyle Dent
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Dari Kimanius
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - John D Sutherland
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - David Barford
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Christopher J Russo
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| |
Collapse
|
26
|
Lem FF, Opook F, Lee DJH, Chee FT, Lawson FP, Chin SN. Molecular Mechanism of Action of Repurposed Drugs and Traditional Chinese Medicine Used for the Treatment of Patients Infected With COVID-19: A Systematic Scoping Review. Front Pharmacol 2021; 11:585331. [PMID: 33746739 PMCID: PMC7970521 DOI: 10.3389/fphar.2020.585331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background: The emergence of COVID-19 as a pandemic has resulted in the need for urgent development of vaccines and drugs and the conduction of clinical trials to fight the outbreak. Because of the time constraints associated with the development of vaccines and effective drugs, drug repurposing and other alternative treatment methods have been used to treat patients that have been infected by the SARS-CoV-2 virus and have acquired COVID-19. Objective: The objective of this systematic scoping review is to provide an overview of the molecular mechanism of action of repurposed drugs or alternative treatment medicines used to attenuate COVID-19 disease. Method: The research articles or gray literature, including theses, government reports, and official news online, were identified from four databases and one search engine. The full content of a total of 160 articles that fulfilled our inclusion criteria was analyzed and information about six drugs (ritonavir, lopinavir, oseltamivir, remdesivir, favipiravir, and chloroquine) and four Traditional Chinese Medicines (Shuang Huang Lian Kou Fu Ye, TCM combination of Bu Huan Jin Zheng Qi San and Da Yuan Yin, Xue Bi Jing Injection, and Qing Fei Pai Du Tang) was extracted. Results: All of the repurposed drugs and complementary medicine that have been used for the treatment of COVID-19 depend on the ability of the drug to inhibit the proliferation of the SARS-CoV-2 virus by binding to enzyme active sites, viral chain termination, or triggering of the molecular pathway, whereas Traditional Chinese Medicine plays a pivotal role in triggering the inflammation pathway, such as the neuraminidase blocker, to fight the SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Fui Fui Lem
- Clinical Research Centre, Hospital Queen Elizabeth, Ministry of Health Malaysia, Kota Kinabalu, Malaysia
| | - Fernandes Opook
- Wildlife Health, Genetic and Forensic Laboratory, Kota Kinabalu, Malaysia
| | | | - Fong Tyng Chee
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Sandakan, Malaysia
| | - Fahcina P. Lawson
- School of Medicine, The Johns Hopkins University, Baltimore, MD, United States
| | - Su Na Chin
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| |
Collapse
|
27
|
Borrego B, Brun A. A Hyper-Attenuated Variant of Rift Valley Fever Virus Generated by a Mutagenic Drug (Favipiravir) Unveils Potential Virulence Markers. Front Microbiol 2021; 11:621463. [PMID: 33633696 PMCID: PMC7900410 DOI: 10.3389/fmicb.2020.621463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus that causes Rift Valley fever (RVF), a zoonotic disease of wild and domestic ruminants, causing serious economic losses and a threat to human health that could be controlled by vaccination. Though RVF vaccines are available for livestock, no RVF vaccines have been licensed for veterinary use in non-endemic countries nor for human populations in RVF risk areas. In a recent work, we showed that favipiravir, a promising drug with antiviral activity against a number of RNA viruses, led to the extinction of RVFV from infected cell cultures. Nevertheless, certain drug concentrations allowed the recovery of a virus variant showing increased resistance to favipiravir. In this work, we characterized this novel resistant variant both at genomic and phenotypic level in vitro and in vivo. Interestingly, the resistant virus displayed reduced growth rates in C6/36 insect cells but not in mammalian cell lines, and was highly attenuated but still immunogenic in vivo. Some amino acid substitutions were identified in the viral RNA-dependent RNA-polymerase (RdRp) gene and in the virus encoded type I-interferon (IFN-I) antagonist NSs gene, in catalytic core motifs and nuclear localization associated positions, respectively. These data may help to characterize novel potential virulence markers, offering additional strategies for further safety improvements of RVF live attenuated vaccine candidates.
Collapse
Affiliation(s)
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| |
Collapse
|
28
|
Łagocka R, Dziedziejko V, Kłos P, Pawlik A. Favipiravir in Therapy of Viral Infections. J Clin Med 2021; 10:E273. [PMID: 33451007 PMCID: PMC7828521 DOI: 10.3390/jcm10020273] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 02/07/2023] Open
Abstract
Favipiravir (FPV) is a novel antiviral drug acting as a competitive inhibitor of RNA-dependent RNA polymerase (RdRp), preventing viral transcription and replication. FPV was approved in Japan in 2014 for therapy of influenza unresponsive to standard antiviral therapies. FPV was also used in the therapy of Ebola virus disease (EVD) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In this review, we discuss the mechanisms of action, pharmacokinetic parameters, toxicity, and adverse effects of FPV, as well as clinical studies evaluating the use of FPV in the therapy of influenza virus (IV) infection, EVD, and SARS-CoV-2 infection, along with its effectiveness in treating other human RNA infections.
Collapse
Affiliation(s)
- Ryta Łagocka
- Department of Conservative Dentistry and Endodontics, Pomeranian Medical University, 70-204 Szczecin, Poland;
| | - Violetta Dziedziejko
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-204 Szczecin, Poland; (V.D.); (P.K.)
| | - Patrycja Kłos
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-204 Szczecin, Poland; (V.D.); (P.K.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-204 Szczecin, Poland
| |
Collapse
|
29
|
Jia X, Ganter B, Meier C. Improving properties of the nucleobase analogs T-705/T-1105 as potential antiviral. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2021; 57:1-47. [PMID: 34728864 PMCID: PMC8553380 DOI: 10.1016/bs.armc.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this minireview we describe our work on the improvement of the nucleobase analogs Favipiravir (T-705) und its non-fluorinated derivative T-1105 as influenza and SARS-CoV-2 active compounds. Both nucleobases were converted into nucleotides and then included in our nucleotide prodrugs technologies cycloSal-monophosphates, DiPPro-nucleoside diphosphates and TriPPPro-nucleoside triphosphates. Particularly the DiPPro-derivatives of T-1105-RDP proved to be very active against influenza viruses. T-1105-derivatives in general were found to be more antivirally active as compared to their T-705 counterpart. This may be due to the low chemical stability of all ribosylated derivatives of T-705. The ribosyltriphosphate derivative of T-1105 was studied for the potential to act as a inhibitor of the SARS-CoV-2 RdRp and was found to be an extremely potent compound causing lethal mutagenesis. The pronucleotide technologies, the chemical synthesis, the biophysical properties and the biological effects of the compounds will be addressed as well.
Collapse
|
30
|
Hossain MJ, Rahman SMA. Repurposing therapeutic agents against SARS-CoV-2 infection: most promising and neoteric progress. Expert Rev Anti Infect Ther 2020; 19:1009-1027. [PMID: 33355520 DOI: 10.1080/14787210.2021.1864327] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION The pathogenic and highly transmissible etiological agent, SARS-CoV-2, has caused a serious threat COVID-19 pandemic. WHO has declared the epidemic a public health emergency of international concern owing to its high contagiosity, mortality rate, and morbidity. Till now, there is no approved vaccine or drug to combat the COVID-19 and avert this global crisis. AREAS COVERED In this narrative review, we summarized the updated results (January to August 2020) of the most promising repurposing therapeutic candidates to treat the SARS-CoV-2 viral infection. The repurposed drugs classified under four headlines like antivirals, anti-parasitic, immune-modulating, and miscellaneous drugs were discussed with their in vitro efficacy to recent clinical advancements against COVID-19. EXPERT OPINION Currently, palliative care, ranging from outpatient management to intensive care, including oxygen administration, ventilator support, intravenous fluids therapy, with some repurposed drugs, are the primary weapons to fight against COVID-19. Until a safe and effective vaccine is developed, an evidence-based drug repurposing strategy might be the wisest option to save people from this catastrophe. Several existing drugs are now under clinical trials, and some of them are approved in different places of the world for emergency use or as adjuvant therapy in COVID-19 with standard of care.
Collapse
Affiliation(s)
- Md Jamal Hossain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka-1000, Bangladesh
| | - S M Abdur Rahman
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka-1000, Bangladesh
| |
Collapse
|
31
|
Hucke FIL, Bugert JJ. Current and Promising Antivirals Against Chikungunya Virus. Front Public Health 2020; 8:618624. [PMID: 33384981 PMCID: PMC7769948 DOI: 10.3389/fpubh.2020.618624] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/21/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever (CHIKF) and is categorized as a(n) (re)emerging arbovirus. CHIKV has repeatedly been responsible for outbreaks that caused serious economic and public health problems in the affected countries. To date, no vaccine or specific antiviral therapies are available. This review gives a summary on current antivirals that have been investigated as potential therapeutics against CHIKF. The mode of action as well as possible compound targets (viral and host targets) are being addressed. This review hopes to provide critical information on the in vitro efficacies of various compounds and might help researchers in their considerations for future experiments.
Collapse
|
32
|
Parveen RS, Hegde S, Nayak V. Investigational Drugs for the COVID 19 Pandemic – A Concise Review. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Reena Sherin Parveen
- Department of Pharmacology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal , Karnataka, -576104, India
| | - Sherya Hegde
- Department of Pharmacology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal , Karnataka, -576104, India
| | - Veena Nayak
- Department of Pharmacology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal , Karnataka, -576104, India
| |
Collapse
|
33
|
Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution 2020; 74:2549-2559. [PMID: 33047822 PMCID: PMC7993354 DOI: 10.1111/evo.14107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Following widespread infections of the most recent coronavirus known to infect humans, SARS‐CoV‐2, attention has turned to potential therapeutic options. With no drug or vaccine yet approved, one focal point of research is to evaluate the potential value of repurposing existing antiviral treatments, with the logical strategy being to identify at least a short‐term intervention to prevent within‐patient progression, while long‐term vaccine strategies unfold. Here, we offer an evolutionary/population‐genetic perspective on one approach that may overwhelm the capacity for pathogen defense (i.e., adaptation) – induced mutational meltdown – providing an overview of key concepts, review of previous theoretical and experimental work of relevance, and guidance for future research. Applied with appropriate care, including target specificity, induced mutational meltdown may provide a general, rapidly implemented approach for the within‐patient eradication of a wide range of pathogens or other undesirable microorganisms.
Collapse
Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Ryan A Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, 01655
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| |
Collapse
|
34
|
Lou Y, Liu L, Yao H, Hu X, Su J, Xu K, Luo R, Yang X, He L, Lu X, Zhao Q, Liang T, Qiu Y. Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial. Eur J Pharm Sci 2020; 157:105631. [PMID: 33115675 PMCID: PMC7585719 DOI: 10.1016/j.ejps.2020.105631] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND Effective antiviral drugs for COVID-19 are still lacking. This study aims to evaluate the clinical outcomes and plasma concentrations of baloxavir acid and favipiravir in COVID-19 patients. METHODS Favipiravir and baloxavir acid were evaluated for their antiviral activity against SARS-CoV-2 in vitro before the trial initiation. We conducted an exploratory trial with 3 arms involving hospitalized adult patients with COVID-19. Patients were randomized assigned in a 1:1:1 ratio into baloxavir marboxil group, favipiravir group, and control group. The primary outcome was the percentage of subjects with viral negative by Day 14 and the time from randomization to clinical improvement. Virus load reduction, blood drug concentration and clinical presentation were also observed. The trial was registered with Chinese Clinical Trial Registry (ChiCTR 2000029544). RESULTS Baloxavir acid showed antiviral activity in vitro with the half-maximal effective concentration (EC50) of 5.48 μM comparable to arbidol and lopinavir, but favipiravir didn't demonstrate significant antiviral activity up to 100 μM. Thirty patients were enrolled. The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir marboxil, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. One reason for the lack of virological effect and clinical benefits may be due to insufficient concentrations of these drugs relative to their antiviral activities. One of the limitations of this study is the time from symptom onset to randomization, especially in the baloxavir marboxil and control groups, which is higher than the favipiravir group. CONCLUSIONS Our findings could not prove a benefit of addition of either baloxavir marboxil or favipiravir under the trial dosages to the existing standard treatment.
Collapse
Affiliation(s)
- Yan Lou
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Lin Liu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hangping Yao
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xingjiang Hu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Junwei Su
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Kaijin Xu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Rui Luo
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xi Yang
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Lingjuan He
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xiaoyang Lu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Qingwei Zhao
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Tingbo Liang
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Yunqing Qiu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| |
Collapse
|
35
|
Shannon A, Selisko B, Le NTT, Huchting J, Touret F, Piorkowski G, Fattorini V, Ferron F, Decroly E, Meier C, Coutard B, Peersen O, Canard B. Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis. Nat Commun 2020; 11:4682. [PMID: 32943628 PMCID: PMC7499305 DOI: 10.1038/s41467-020-18463-z] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.
Collapse
Affiliation(s)
- Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Barbara Selisko
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Nhung-Thi-Tuyet Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Johanna Huchting
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Véronique Fattorini
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Chris Meier
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Olve Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA.
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France.
| |
Collapse
|
36
|
Lawson B, Suppiah S, Rota PA, Hickman CJ, Latner DR. In vitro inhibition of mumps virus replication by favipiravir (T-705). Antiviral Res 2020; 180:104849. [PMID: 32553844 DOI: 10.1016/j.antiviral.2020.104849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/21/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
During the last decade multiple mumps outbreaks have occurred in the U.S. despite high two dose MMR coverage with most cases detected among two dose MMR vaccine recipients. Waning immunity, the evolution of wild-type virus strains, and settings with intense exposure have contributed to the resurgence of mumps. Typically, mumps virus infections resolve without serious clinical sequelae; however, serious complications may occur among unvaccinated or severely immunocompromised individuals. Favipiravir (T-705) has been shown to have in vitro anti-viral activity against a broad range of positive and negative strand RNA viruses. Here, we demonstrate that T-705 inhibits the growth of wildtype and vaccine strains of mumps virus in vitro at low micro-molar concentrations (EC50 8-10μM). We did not observe the development of resistance after five subsequent passages at low concentrations of drug. Both viral RNA and protein synthesis were selectively reduced compared to host mRNA and protein synthesis. Antiviral treatment options for mumps virus infection may be valuable, especially for areas with a high disease burden or for cases with severe complications. These results presented here suggest that further studies are warranted.
Collapse
Affiliation(s)
- Benton Lawson
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suganthi Suppiah
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul A Rota
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carole J Hickman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Donald R Latner
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| |
Collapse
|
37
|
Luo Z, Ang MJY, Chan SY, Yi Z, Goh YY, Yan S, Tao J, Liu K, Li X, Zhang H, Huang W, Liu X. Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community. RESEARCH (WASHINGTON, D.C.) 2020; 2020:6925296. [PMID: 32607499 PMCID: PMC7315394 DOI: 10.34133/2020/6925296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/08/2023]
Abstract
The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression.
Collapse
Affiliation(s)
- Zichao Luo
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Melgious Jin Yan Ang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Siew Yin Chan
- Frontiers Science Center for Flexible Electronics & Shaanxi Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zhigao Yi
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Yi Yiing Goh
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Shuangqian Yan
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Jun Tao
- Sports Medical Centre, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Chang Chun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xiaosong Li
- Department of Oncology, The Fourth Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100048, China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Chang Chun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics & Shaanxi Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an 710072, China
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Fuzhou 350807, China
| |
Collapse
|
38
|
Hoffman RM, Han Q. Oral Methioninase for Covid-19 Methionine-restriction Therapy. In Vivo 2020; 34:1593-1596. [PMID: 32503816 PMCID: PMC8378026 DOI: 10.21873/invivo.11948] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/21/2020] [Accepted: 05/23/2020] [Indexed: 11/10/2022]
Abstract
The Covid-19 pandemic is a world-wide crisis without an effective therapy. While most approaches to therapy are using repurposed drugs that were developed for other diseases, it is thought that targeting the biology of the SARS-CoV-2 virus, which causes Covid-19, can result in an effective therapeutic treatment. The coronavirus RNA cap structure is methylated by two viral methyltransferases that transfer methyl groups from S-adenosylmethionine (SAM). The proper methylation of the virus depends on the level of methionine in the host to form SAM. Herein, we propose to restrict methionine availability by treating the patient with oral recombinant methioninase, aiming to treat Covid-19. By restricting methionine we not only interdict viral replication, which depends on the viral RNA cap methyaltion, but also inhibit the proliferation of the infected cells, which have an increased requirement for methionine. Most importantly, the virally-induced T-cell- and macrophage-mediated cytokine storm, which seems to be a significant cause for Covid-19 deaths, can also be inhibited by restricting methionine, since T-cell and macrophrage activation greatly increases the methionine requirement for these cells. The evidence reviewed here suggests that oral recombinant methioninase could be a promising treatment for coronavirus patients.
Collapse
|
39
|
Shannon A, Selisko B, Le NTT, Huchting J, Touret F, Piorkowski G, Fattorini V, Ferron F, Decroly E, Meier C, Coutard B, Peersen O, Canard B. Favipiravir strikes the SARS-CoV-2 at its Achilles heel, the RNA polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.15.098731. [PMID: 32511380 PMCID: PMC7263509 DOI: 10.1101/2020.05.15.098731] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. Here we show that Favipiravir exerts an antiviral effect as a nucleotide analogue through a combination of chain termination, slowed RNA synthesis and lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.
Collapse
Affiliation(s)
- A. Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - B. Selisko
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - NTT Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - J. Huchting
- University of Hamburg, Faculty of Sciences, Department of Chemistry, Organic Chemistry, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - F. Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - G. Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - V. Fattorini
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - F. Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - E. Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - C Meier
- University of Hamburg, Faculty of Sciences, Department of Chemistry, Organic Chemistry, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - B. Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - O. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - B. Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| |
Collapse
|
40
|
Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs. Pathogens 2020; 9:pathogens9050320. [PMID: 32357471 PMCID: PMC7281371 DOI: 10.3390/pathogens9050320] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
Collapse
|
41
|
Shiraki K, Daikoku T. Favipiravir, an anti-influenza drug against life-threatening RNA virus infections. Pharmacol Ther 2020; 209:107512. [PMID: 32097670 PMCID: PMC7102570 DOI: 10.1016/j.pharmthera.2020.107512] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/14/2020] [Indexed: 12/16/2022]
Abstract
Favipiravir has been developed as an anti-influenza drug and licensed as an anti-influenza drug in Japan. Additionally, favipiravir is being stockpiled for 2 million people as a countermeasure for novel influenza strains. This drug functions as a chain terminator at the site of incorporation of the viral RNA and reduces the viral load. Favipiravir cures all mice in a lethal influenza infection model, while oseltamivir fails to cure the animals. Thus, favipiravir contributes to curing animals with lethal infection. In addition to influenza, favipiravir has a broad spectrum of anti-RNA virus activities in vitro and efficacies in animal models with lethal RNA viruses and has been used for treatment of human infection with life-threatening Ebola virus, Lassa virus, rabies, and severe fever with thrombocytopenia syndrome. The best feature of favipiravir as an antiviral agent is the apparent lack of generation of favipiravir-resistant viruses. Favipiravir alone maintains its therapeutic efficacy from the first to the last patient in an influenza pandemic or an epidemic lethal RNA virus infection. Favipiravir is expected to be an important therapeutic agent for severe influenza, the next pandemic influenza strain, and other severe RNA virus infections for which standard treatments are not available.
Collapse
Affiliation(s)
- Kimiyasu Shiraki
- Senri Kinran University and Department of Virology, University of Toyama, Japan.
| | - Tohru Daikoku
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Hokuriku University, Japan
| |
Collapse
|
42
|
Bugert JJ, Hucke F, Zanetta P, Bassetto M, Brancale A. Antivirals in medical biodefense. Virus Genes 2020; 56:150-167. [PMID: 32076918 PMCID: PMC7089181 DOI: 10.1007/s11262-020-01737-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
The viruses historically implicated or currently considered as candidates for misuse in bioterrorist events are poxviruses, filoviruses, bunyaviruses, orthomyxoviruses, paramyxoviruses and a number of arboviruses causing encephalitis, including alpha- and flaviviruses. All these viruses are of concern for public health services when they occur in natural outbreaks or emerge in unvaccinated populations. Recent events and intelligence reports point to a growing risk of dangerous biological agents being used for nefarious purposes. Public health responses effective in natural outbreaks of infectious disease may not be sufficient to deal with the severe consequences of a deliberate release of such agents. One important aspect of countermeasures against viral biothreat agents are the antiviral treatment options available for use in post-exposure prophylaxis. These issues were adressed by the organizers of the 16th Medical Biodefense Conference, held in Munich in 2018, in a special session on the development of drugs to treat infections with viruses currently perceived as a threat to societies or associated with a potential for misuse as biothreat agents. This review will outline the state-of-the-art methods in antivirals research discussed and provide an overview of antiviral compounds in the pipeline that are already approved for use or still under development.
Collapse
Affiliation(s)
- J J Bugert
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany.
| | - F Hucke
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany
| | - P Zanetta
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany
| | - M Bassetto
- Department of Chemistry, Swansea University, Swansea, SA2 8PP, UK
| | - A Brancale
- Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| |
Collapse
|
43
|
Sinigaglia A, Peta E, Riccetti S, Barzon L. New avenues for therapeutic discovery against West Nile virus. Expert Opin Drug Discov 2020; 15:333-348. [DOI: 10.1080/17460441.2020.1714586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Elektra Peta
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Silvia Riccetti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| |
Collapse
|
44
|
Ye C, Wang D, Liu H, Ma H, Dong Y, Yao M, Wang Y, Zhang H, Zhang L, Cheng L, Xu Z, Lei Y, Zhang F, Ye W. An Improved Enzyme-Linked Focus Formation Assay Revealed Baloxavir Acid as a Potential Antiviral Therapeutic Against Hantavirus Infection. Front Pharmacol 2019; 10:1203. [PMID: 31680975 PMCID: PMC6807675 DOI: 10.3389/fphar.2019.01203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
Hantaviruses, etiologic pathogens responsible for two severe human diseases, exist in areas ranging from Eurasia to America and remain global public health concerns. Conventionally, plaque formation assays have been used for hantavirus titering. However, hantaviruses replicate slowly within cells and produce minimal cytopathic effects, making this technique difficult to master. The improved enzyme-linked immunosorbent assay-based antigen detection method is easier to perform but is still time consuming. Here, we established an enzyme-linked focus formation assay (FFA) for Hantaan virus titering that is twice as fast as traditional assays. Moreover, using this method, we evaluated the effects of favipiravir (T-705) and another influenza virus drug, baloxavir acid (BXA), on hantavirus replication. We found that the endonuclease inhibitor BXA exerted similar anti-hantavirus effects as T-705. Overall, we developed a time-saving method for hantavirus titering and suggest BXA as a potential treatment choice for hantavirus-exposed individuals.
Collapse
Affiliation(s)
- Chuantao Ye
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China.,Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Dan Wang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - He Liu
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Hongwei Ma
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Yangchao Dong
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Min Yao
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Yuan Wang
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Hui Zhang
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Zhikai Xu
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| | - Wei Ye
- Department of Microbiology, School of Preclinical Medicine, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
45
|
Abstract
Selection of viral mutants resistant to compounds used in therapy is a major determinant of treatment failure, a problem akin to antibiotic resistance in bacteria. In this scenario, mutagenic base and nucleoside analogs have entered the picture because they increase the mutation rate of viral populations to levels incompatible with their survival. This antiviral strategy is termed lethal mutagenesis. It has found a major impulse with the observation that some antiviral agents, which initially were considered only inhibitors of virus multiplication, may in effect exert part of their antiviral activity through mutagenesis. Here, we review the conceptual basis of lethal mutagenesis, the evidence of virus extinction through mutagenic nucleotide analogs and prospects for application in antiviral designs.
Collapse
|
46
|
Abdelnabi R, Geraets JA, Ma Y, Mirabelli C, Flatt JW, Domanska A, Delang L, Jochmans D, Kumar TA, Jayaprakash V, Sinha BN, Leyssen P, Butcher SJ, Neyts J. A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses. PLoS Biol 2019; 17:e3000281. [PMID: 31185007 PMCID: PMC6559632 DOI: 10.1371/journal.pbio.3000281] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/08/2019] [Indexed: 12/22/2022] Open
Abstract
Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are "capsid binders" that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo-electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.
Collapse
Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - James A. Geraets
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Yipeng Ma
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Justin W. Flatt
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Aušra Domanska
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leen Delang
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Dirk Jochmans
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Timiri Ajay Kumar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Pieter Leyssen
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Sarah J. Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail: (JN); (SJB)
| | - Johan Neyts
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
- * E-mail: (JN); (SJB)
| |
Collapse
|
47
|
Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
Collapse
Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| |
Collapse
|
48
|
Ben Ouirane K, Boulard Y, Bressanelli S. The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif. J Biol Chem 2019; 294:7573-7587. [PMID: 30867194 DOI: 10.1074/jbc.ra118.005209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
RNA viruses synthesize new genomes in the infected host thanks to dedicated, virally-encoded RNA-dependent RNA polymerases (RdRps). As such, these enzymes are prime targets for antiviral therapy, as has recently been demonstrated for hepatitis C virus (HCV). However, peculiarities in the architecture and dynamics of RdRps raise fundamental questions about access to their active site during RNA polymerization. Here, we used molecular modeling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp. Tracing the possible passage of incoming UTP or GTP through the RdRp-specific entry tunnel, we found two successive checkpoints that regulate nucleotide traffic to the active site. We observed that a magnesium-bound nucleotide first binds next to the tunnel entry, and interactions with the triphosphate moiety orient it such that its base moiety enters first. Dynamics of RdRp motifs F1 + F3 then allow the nucleotide to interrogate the RNA template base prior to nucleotide insertion into the active site. These dynamics are finely regulated by a second magnesium dication, thus coordinating the entry of a magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. The findings of our work suggest that at least some of these features are general to viral RdRps and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses.
Collapse
Affiliation(s)
- Kaouther Ben Ouirane
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Yves Boulard
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Stéphane Bressanelli
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| |
Collapse
|
49
|
Abstract
Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections, in particular due to the apparent lack of emergence of resistance mutations against the drug in cell culture or animal studies. We demonstrate here that a mutation in a conserved region of the viral RNA polymerase confers resistance to favipiravir in vitro and in cell culture. The resistance mutation has a cost to viral fitness, but this can be restored by a compensatory mutation in the polymerase. Our findings support the development of favipiravir-resistance diagnostic and surveillance testing strategies and reinforce the importance of considering combinations of therapies to treat influenza infections. Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections. While emergence of resistance has been observed for many antiinfluenza drugs, to date, clinical trials and laboratory studies of favipiravir have not yielded resistant viruses. Here we show evolution of resistance to favipiravir in the pandemic H1N1 influenza A virus in a laboratory setting. We found that two mutations were required for robust resistance to favipiravir. We demonstrate that a K229R mutation in motif F of the PB1 subunit of the influenza virus RNA-dependent RNA polymerase (RdRP) confers resistance to favipiravir in vitro and in cell culture. This mutation has a cost to viral fitness, but fitness can be restored by a P653L mutation in the PA subunit of the polymerase. K229R also conferred favipiravir resistance to RNA polymerases of other influenza A virus strains, and its location within a highly conserved structural feature of the RdRP suggests that other RNA viruses might also acquire resistance through mutations in motif F. The mutations identified here could be used to screen influenza virus-infected patients treated with favipiravir for the emergence of resistance.
Collapse
|
50
|
Gregori J, Soria ME, Gallego I, Guerrero-Murillo M, Esteban JI, Quer J, Perales C, Domingo E. Rare haplotype load as marker for lethal mutagenesis. PLoS One 2018; 13:e0204877. [PMID: 30281674 PMCID: PMC6169937 DOI: 10.1371/journal.pone.0204877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/19/2018] [Indexed: 12/23/2022] Open
Abstract
RNA viruses replicate with a template-copying fidelity, which lies close to an extinction threshold. Increases of mutation rate by nucleotide analogues can drive viruses towards extinction. This transition is the basis of an antiviral strategy termed lethal mutagenesis. We have introduced a new diversity index, the rare haplotype load (RHL), to describe NS5B (polymerase) mutant spectra of hepatitis C virus (HCV) populations passaged in absence or presence of the mutagenic agents favipiravir or ribavirin. The increase in RHL is more prominent in mutant spectra whose expansions were due to nucleotide analogues than to multiple passages in absence of mutagens. Statistical tests for paired mutagenized versus non-mutagenized samples with 14 diversity indices show that RHL provides consistently the highest standardized effect of mutagenic treatment difference for ribavirin and favipiravir. The results indicate that the enrichment of viral quasispecies in very low frequency minority genomes can serve as a robust marker for lethal mutagenesis. The diagnostic value of RHL from deep sequencing data is relevant to experimental studies on enhanced mutagenesis of viruses, and to pharmacological evaluations of inhibitors suspected to have a mutagenic activity.
Collapse
Affiliation(s)
- Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L., Sant Cugat del Vallés, Barcelona, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Isabel Gallego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
- * E-mail: (CP); (JQ)
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- * E-mail: (CP); (JQ)
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| |
Collapse
|