Possible Rapid Therapeutics for SARS Coronavirus 2 RNA-dependent RNA polymerase: A Systematic Review Possible Rapid Therapeutics for SARS Coronavirus 2 …
Iranian Journal of Pharmaceutical Sciences,
Vol. 18 No. 3 (2022),
1 July 2022
,
Page 253-264
https://doi.org/10.22037/ijps.v18.42672
Abstract
Research confirms that viral polymerases play a key role in viral genome replication and transcription. Hence, they are essential for the multiplication and survival of viral particles. Our review is limited to original papers in the English language from 2019 to 2020 using various databases, including PubMed, Scopus, Google Scholar, and Science direct. Out of 159 papers, 27 drugs may effectively prevent RNA-dependent RNA polymerase (RdRP), of COVID-19, agreed in order of drug discovery years and paper publication, respectively. In this paper, we realized that the structure comparison and sequence alignment suggest that the mode of substrate RdRP is highly conserved in diverse RNA viruses, providing a foundation for designing broad-spectrum antiviral drugs based on nucleotide analogs.
Keywords:
- Conservative
- RNA viruses
- RNA polymerase
How to Cite
Asghariazar, V. ., Mazloum Jalali, K. ., Aghebati-Maleki, A. ., Biparva Haghighi, S. ., Balar, N., Peeri-Dogaheh, H., & Karami, C. . (2022). Possible Rapid Therapeutics for SARS Coronavirus 2 RNA-dependent RNA polymerase: A Systematic Review: Possible Rapid Therapeutics for SARS Coronavirus 2 …. Iranian Journal of Pharmaceutical Sciences, 18(3), 253–264. https://doi.org/10.22037/ijps.v18.42672
References
[1] Adedeji AO, Marchand B, te Velthuis AJ, Snijder EJ, Weiss S, et al. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PloS one. (2012) 7 (5).
[2] Ahn D-G, Choi J-K, Taylor DR,Oh J-W. Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates. Archives of virology. (2012) 157 (11): 2095-104.
[3] Adedeji AO, Marchand B, Te Velthuis AJ, Snijder EJ, Weiss S, et al. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PloS one. (2012) 7 (5): e36521.
[4] Bressanelli S, Tomei L, Roussel A, Incitti I, Vitale RL, et al. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proceedings of the National Academy of Sciences. (1999) 96 (23): 13034-9.
[5] Agostini ML, Andres EL, Sims AC, Graham RL, Sheahan TP, et al. Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. MBio. (2018) 9 (2).
[6] Venkataraman S, Prasad BV,Selvarajan R. RNA dependent RNA polymerases: insights from structure, function and evolution. Viruses. (2018) 10 (2): 76.
[7] Campagnola G, Gong P,Peersen OB. High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors. Antiviral research. (2011) 91 (3): 241-51.
[8] Li G,De Clercq E. Therapeutic options for the 2019 novel coronavirus (2019-nCoV). In: Nature Publishing Group. (2020).
[9] Furuta Y, Komeno T,Nakamura T. Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proceedings of the Japan Academy, Series B. (2017) 93 (7): 449-63.
[10] Kiso M, Takahashi K, Sakai-Tagawa Y, Shinya K, Sakabe S, et al. T-705 (favipiravir) activity against lethal H5N1 influenza A viruses. Proceedings of the National Academy of Sciences. (2010) 107 (2): 882-7.
[11] Tchesnokov EP, Feng JY, Porter DP,Götte M. Mechanism of inhibition of Ebola virus RNA-dependent RNA polymerase by remdesivir. Viruses. (2019) 11 (4): 326.
[12] Sheahan TP, Sims AC, Graham RL, Menachery VD, Gralinski LE, et al. Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science translational medicine. (2017) 9 (396).
[13] Gordon CJ, Tchesnokov EP, Woolner E, Perry JK, Feng JY, et al. Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. Journal of Biological Chemistry. (2020) 295 (20): 6785-97.
[14] Amirian ES,Levy JK. Current knowledge about the antivirals remdesivir (GS-5734) and GS-441524 as therapeutic options for coronaviruses. One Health. (2020): 100128.
[15] Warren TK, Wells J, Panchal RG, Stuthman KS, Garza NL, et al. Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430. Nature. (2014) 508 (7496): 402-5.
[16] Westover JB, Mathis A, Taylor R, Wandersee L, Bailey KW, et al. Galidesivir limits Rift Valley fever virus infection and disease in Syrian golden hamsters. Antiviral research. (2018) 156: 38-45.
[17] Trang TP, Whalen M, Hilts‐Horeczko A, Doernberg SB,Liu C. Comparative effectiveness of aerosolized versus oral ribavirin for the treatment of respiratory syncytial virus infections: a single‐center retrospective cohort study and review of the literature. Transplant Infectious Disease. (2018) 20 (2): e12844.
[18] Cameron CE,Castro C. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase. Current opinion in infectious diseases. (2001) 14 (6): 757-64.
[19] Te HS, Randall G,Jensen DM. Mechanism of action of ribavirin in the treatment of chronic hepatitis C. Gastroenterology & hepatology. (2007) 3 (3): 218.
[20] Elfiky AA. SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics. (2020): 1-9.
[21] Jang JH, Kim JW, Jeong SH, Myung HJ, Kim H, et al. Clevudine for chronic hepatitis B: antiviral response, predictors of response, and development of myopathy. Journal of viral hepatitis. (2011) 18 (2): 84-90.
[22] Jones SA, Murakami E, Delaney W, Furman P,Hu J. Noncompetitive inhibition of hepatitis B virus reverse transcriptase protein priming and DNA synthesis by the nucleoside analog clevudine. Antimicrobial agents and chemotherapy. (2013) 57 (9): 4181-9.
[23] Frampton JE,Perry CM. Emtricitabine. Drugs. (2005) 65 (10): 1427-48.
[24] Murphy RA,Valentovic MA. Factors contributing to the antiviral effectiveness of tenofovir. Journal of Pharmacology and Experimental Therapeutics. (2017) 363 (2): 156-63.
[25] Copertino Jr DC, Lima B, Duarte R, Wilkin T, Gulick R, et al. Antiretroviral Drug Activity and Potential for Pre-Exposure Prophylaxis Against COVID-19 and HIV Infection. (2020).
[26] Birkus G, Bam RA, Willkom M, Frey CR, Tsai L, et al. Intracellular activation of tenofovir alafenamide and the effect of viral and host protease inhibitors. Antimicrobial agents and chemotherapy. (2016) 60 (1): 316-22.
[27] Sheahan TP, Sims AC, Zhou S, Graham RL, Pruijssers AJ, et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice. Science translational medicine. (2020) 12 (541).
[28] Merat S, Poustchi H, Hemming K, Jafari E, RADMARD AR, et al. polypill for prevention of cardiovascular disease in an urban iranian population with special focus on nonalcoholic steatohepatitis: a pragmatic randomized controlled trial within a cohort (polyiran-liver)–study protocol (study protocol). (2015).
[29] Beck BR, Shin B, Choi Y, Park S,Kang K. Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Computational and structural biotechnology journal. (2020).
[30] Mantry PS,Pathak L. Dasabuvir (ABT333) for the treatment of chronic HCV genotype I: a new face of cure, an expert review. Expert review of anti-infective therapy. (2016) 14 (2): 157-65.
[31] Dutta K, Shityakov S, Morozova O, Khalifa I, Zhang J, et al. Beclabuvir can inhibit the RNA-dependent RNA polymerase of newly emerged novel coronavirus (SARS-CoV-2). (2020).
[32] Clark MP, Ledeboer MW, Davies I, Byrn RA, Jones SM, et al. Discovery of a novel, first-in-class, orally bioavailable azaindole inhibitor (VX-787) of influenza PB2. Journal of medicinal chemistry. (2014) 57 (15): 6668-78.
[33] Yoshino R, Yasuo N,Sekijima M. Molecular dynamics simulation reveals the mechanism by which the influenza cap-dependent endonuclease acquires resistance against baloxavir marboxil. Scientific reports. (2019) 9 (1): 1-8.
[34] Noshi T, Kitano M, Taniguchi K, Yamamoto A, Omoto S, et al. In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Antiviral research. (2018) 160: 109-17.
[35] Lou Y, Liu L,Qiu Y. Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: an Exploratory Randomized, Controlled Trial. medRxiv. (2020).
[36] Ahlquist P. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nature Reviews Microbiology. (2006) 4 (5): 371-82.
[37] Wu C, Liu Y, Yang Y, Zhang P, Zhong W, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B. (2020).
[38] Naqvi AAT, Fatima K, Mohammad T, Fatima U, Singh IK, et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease. (2020): 165878.
[39] Gao Y, Yan L, Huang Y, Liu F, Zhao Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. (2020) 368 (6492): 779-82.
[40] Ahmad J, Ikram S, Ahmad F, Rehman IU,Mushtaq M. SARS-CoV-2 RNA Dependent RNA polymerase (RdRp)–A drug repurposing study. Heliyon. (2020) 6 (7): e04502.
[41] Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, et al. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. Journal of translational medicine. (2020) 18 (1): 1-15.
[42] Janabi AHD. Effective Anti-SARS-CoV-2 RNA Dependent RNA Polymerase Drugs Based on Docking Methods: The Case of Milbemycin, Ivermectin, and Baloxavir Marboxil. Avicenna Journal of Medical Biotechnology. (2020) 12 (4): 246.
[2] Ahn D-G, Choi J-K, Taylor DR,Oh J-W. Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates. Archives of virology. (2012) 157 (11): 2095-104.
[3] Adedeji AO, Marchand B, Te Velthuis AJ, Snijder EJ, Weiss S, et al. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PloS one. (2012) 7 (5): e36521.
[4] Bressanelli S, Tomei L, Roussel A, Incitti I, Vitale RL, et al. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proceedings of the National Academy of Sciences. (1999) 96 (23): 13034-9.
[5] Agostini ML, Andres EL, Sims AC, Graham RL, Sheahan TP, et al. Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. MBio. (2018) 9 (2).
[6] Venkataraman S, Prasad BV,Selvarajan R. RNA dependent RNA polymerases: insights from structure, function and evolution. Viruses. (2018) 10 (2): 76.
[7] Campagnola G, Gong P,Peersen OB. High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors. Antiviral research. (2011) 91 (3): 241-51.
[8] Li G,De Clercq E. Therapeutic options for the 2019 novel coronavirus (2019-nCoV). In: Nature Publishing Group. (2020).
[9] Furuta Y, Komeno T,Nakamura T. Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proceedings of the Japan Academy, Series B. (2017) 93 (7): 449-63.
[10] Kiso M, Takahashi K, Sakai-Tagawa Y, Shinya K, Sakabe S, et al. T-705 (favipiravir) activity against lethal H5N1 influenza A viruses. Proceedings of the National Academy of Sciences. (2010) 107 (2): 882-7.
[11] Tchesnokov EP, Feng JY, Porter DP,Götte M. Mechanism of inhibition of Ebola virus RNA-dependent RNA polymerase by remdesivir. Viruses. (2019) 11 (4): 326.
[12] Sheahan TP, Sims AC, Graham RL, Menachery VD, Gralinski LE, et al. Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science translational medicine. (2017) 9 (396).
[13] Gordon CJ, Tchesnokov EP, Woolner E, Perry JK, Feng JY, et al. Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. Journal of Biological Chemistry. (2020) 295 (20): 6785-97.
[14] Amirian ES,Levy JK. Current knowledge about the antivirals remdesivir (GS-5734) and GS-441524 as therapeutic options for coronaviruses. One Health. (2020): 100128.
[15] Warren TK, Wells J, Panchal RG, Stuthman KS, Garza NL, et al. Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430. Nature. (2014) 508 (7496): 402-5.
[16] Westover JB, Mathis A, Taylor R, Wandersee L, Bailey KW, et al. Galidesivir limits Rift Valley fever virus infection and disease in Syrian golden hamsters. Antiviral research. (2018) 156: 38-45.
[17] Trang TP, Whalen M, Hilts‐Horeczko A, Doernberg SB,Liu C. Comparative effectiveness of aerosolized versus oral ribavirin for the treatment of respiratory syncytial virus infections: a single‐center retrospective cohort study and review of the literature. Transplant Infectious Disease. (2018) 20 (2): e12844.
[18] Cameron CE,Castro C. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase. Current opinion in infectious diseases. (2001) 14 (6): 757-64.
[19] Te HS, Randall G,Jensen DM. Mechanism of action of ribavirin in the treatment of chronic hepatitis C. Gastroenterology & hepatology. (2007) 3 (3): 218.
[20] Elfiky AA. SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics. (2020): 1-9.
[21] Jang JH, Kim JW, Jeong SH, Myung HJ, Kim H, et al. Clevudine for chronic hepatitis B: antiviral response, predictors of response, and development of myopathy. Journal of viral hepatitis. (2011) 18 (2): 84-90.
[22] Jones SA, Murakami E, Delaney W, Furman P,Hu J. Noncompetitive inhibition of hepatitis B virus reverse transcriptase protein priming and DNA synthesis by the nucleoside analog clevudine. Antimicrobial agents and chemotherapy. (2013) 57 (9): 4181-9.
[23] Frampton JE,Perry CM. Emtricitabine. Drugs. (2005) 65 (10): 1427-48.
[24] Murphy RA,Valentovic MA. Factors contributing to the antiviral effectiveness of tenofovir. Journal of Pharmacology and Experimental Therapeutics. (2017) 363 (2): 156-63.
[25] Copertino Jr DC, Lima B, Duarte R, Wilkin T, Gulick R, et al. Antiretroviral Drug Activity and Potential for Pre-Exposure Prophylaxis Against COVID-19 and HIV Infection. (2020).
[26] Birkus G, Bam RA, Willkom M, Frey CR, Tsai L, et al. Intracellular activation of tenofovir alafenamide and the effect of viral and host protease inhibitors. Antimicrobial agents and chemotherapy. (2016) 60 (1): 316-22.
[27] Sheahan TP, Sims AC, Zhou S, Graham RL, Pruijssers AJ, et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice. Science translational medicine. (2020) 12 (541).
[28] Merat S, Poustchi H, Hemming K, Jafari E, RADMARD AR, et al. polypill for prevention of cardiovascular disease in an urban iranian population with special focus on nonalcoholic steatohepatitis: a pragmatic randomized controlled trial within a cohort (polyiran-liver)–study protocol (study protocol). (2015).
[29] Beck BR, Shin B, Choi Y, Park S,Kang K. Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Computational and structural biotechnology journal. (2020).
[30] Mantry PS,Pathak L. Dasabuvir (ABT333) for the treatment of chronic HCV genotype I: a new face of cure, an expert review. Expert review of anti-infective therapy. (2016) 14 (2): 157-65.
[31] Dutta K, Shityakov S, Morozova O, Khalifa I, Zhang J, et al. Beclabuvir can inhibit the RNA-dependent RNA polymerase of newly emerged novel coronavirus (SARS-CoV-2). (2020).
[32] Clark MP, Ledeboer MW, Davies I, Byrn RA, Jones SM, et al. Discovery of a novel, first-in-class, orally bioavailable azaindole inhibitor (VX-787) of influenza PB2. Journal of medicinal chemistry. (2014) 57 (15): 6668-78.
[33] Yoshino R, Yasuo N,Sekijima M. Molecular dynamics simulation reveals the mechanism by which the influenza cap-dependent endonuclease acquires resistance against baloxavir marboxil. Scientific reports. (2019) 9 (1): 1-8.
[34] Noshi T, Kitano M, Taniguchi K, Yamamoto A, Omoto S, et al. In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Antiviral research. (2018) 160: 109-17.
[35] Lou Y, Liu L,Qiu Y. Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: an Exploratory Randomized, Controlled Trial. medRxiv. (2020).
[36] Ahlquist P. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nature Reviews Microbiology. (2006) 4 (5): 371-82.
[37] Wu C, Liu Y, Yang Y, Zhang P, Zhong W, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B. (2020).
[38] Naqvi AAT, Fatima K, Mohammad T, Fatima U, Singh IK, et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease. (2020): 165878.
[39] Gao Y, Yan L, Huang Y, Liu F, Zhao Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. (2020) 368 (6492): 779-82.
[40] Ahmad J, Ikram S, Ahmad F, Rehman IU,Mushtaq M. SARS-CoV-2 RNA Dependent RNA polymerase (RdRp)–A drug repurposing study. Heliyon. (2020) 6 (7): e04502.
[41] Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, et al. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. Journal of translational medicine. (2020) 18 (1): 1-15.
[42] Janabi AHD. Effective Anti-SARS-CoV-2 RNA Dependent RNA Polymerase Drugs Based on Docking Methods: The Case of Milbemycin, Ivermectin, and Baloxavir Marboxil. Avicenna Journal of Medical Biotechnology. (2020) 12 (4): 246.
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