Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

Life Sciences

Volumn 248, Issue , 2020, Pages

  Elfiky, Abdo A ^a,b  

^a CAIRO UNIVERSITY   (Egypt)

^b JOUF UNIVERSITY   (Saudi Arabia)

Author keywords

COVID 19; Docking; Nucleotide inhibitors; RdRp; Sofosbuvir; Structural bioinformatics; Wuhan coronavirus

Indexed keywords

ANTIVIRUS AGENT; GUANOSINE TRIPHOSPHATE; HEPATITIS C ANTIBODY; IDX 184; REMIDISVIR; RIBAVIRIN; RNA DIRECTED RNA POLYMERASE; SOFOSBUVIR; UNCLASSIFIED DRUG; ADENOSINE PHOSPHATE; ALANINE; GUANOSINE PHOSPHATE; PROTEIN BINDING; REMDESIVIR; URIDINE TRIPHOSPHATE; VIRAL PROTEIN;

ARTICLE; BINDING AFFINITY; CHINA; COMPUTER MODEL; CONTROLLED STUDY; CORONAVIRUS DISEASE 2019; CORONAVIRUS INFECTION; DRUG EFFICACY; DRUG REPOSITIONING; DRUG STRUCTURE; ENZYME ACTIVE SITE; HUMAN; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; MOLECULAR DOCKING; NONHUMAN; SARS CORONAVIRUS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2; STRUCTURAL BIOINFORMATICS; VIRUS TRANSMISSION; ALPHA HELIX; ALPHACORONAVIRUS; AMINO ACID SEQUENCE; BETA SHEET; BETACORONAVIRUS; BIOLOGY; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; PROCEDURES; PROTEIN DOMAIN; SEQUENCE HOMOLOGY; THERMODYNAMICS; VIROLOGY; VIRUS PNEUMONIA;

ADENOSINE MONOPHOSPHATE; ALANINE; ALPHACORONAVIRUS; AMINO ACID SEQUENCE; ANTIVIRAL AGENTS; BETACORONAVIRUS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; CORONAVIRUS INFECTIONS; DRUG REPOSITIONING; GUANOSINE MONOPHOSPHATE; GUANOSINE TRIPHOSPHATE; HUMANS; MOLECULAR DOCKING SIMULATION; PNEUMONIA, VIRAL; PROTEIN BINDING; PROTEIN CONFORMATION, ALPHA-HELICAL; PROTEIN CONFORMATION, BETA-STRAND; PROTEIN INTERACTION DOMAINS AND MOTIFS; RIBAVIRIN; RNA REPLICASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFOSBUVIR; THERMODYNAMICS; URIDINE TRIPHOSPHATE; VIRAL PROTEINS;

EID: 85080998230     PISSN: 00243205     EISSN: 18790631     Source Type: Journal    
DOI: 10.1016/j.lfs.2020.117477     Document Type: Article

References (63)

1. Bogoch, I.I., Watts, A., Thomas-Bachli, A., Huber, C., Kraemer, M.U.G., Khan, K., Pneumonia of unknown etiology in Wuhan, China: potential for international spread via commercial air travel. Journal of Travel Medicine, 2020.
2. Hui, D.S., Azhar, I.E., Madani, T.A., Ntoumi, F., Kock, R., Dar, O., et al. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health—the latest 2019 novel coronavirus outbreak in Wuhan, China. International Journal of Infectious Diseases 91 (2020), 264–266.
3. Organization WH, Surveillance Case Definitions for Human Infection With Novel Coronavirus (nCoV): Interim Guidance v1, January 2020. 2020, World Health Organization.
4. Organization WH, Infection Prevention and Control during Health Care When Novel Coronavirus (nCoV) Infection Is Suspected: Interim Guidance, January 2020. 2020, World Health Organization.
5. Organization WH, Laboratory Testing of Human Suspected Cases of Novel Coronavirus (nCoV) Infection: Interim Guidance, 10 January 2020. 2020, World Health Organization.
6. Parr, J., Pneumonia in China: Lack of Information Raises Concerns Among Hong Kong Health Workers. 2020, British Medical Journal Publishing Group.
7. Elfiky, A.A.I., N. S, Anti-SARS and Anti-HCV Drugs Repurposing Against the Papain-like Protease of the Newly Emerged Coronavirus (2019-nCoV). preprint, 2020.
8. Ibrahim, I.M.A., Elshahat, D.H., Elfiky, M.M., Abdo, A., COVID-19 Spike-host Cell Receptor GRP78 Binding Site Prediction. preprint, 2020.
9. Yang, L., China Confirms Human-to-Human Transmission of Coronavirus. 2020.
10. Chan, J.F., Lau, S.K., To, K.K., Cheng, V.C., Woo, P.C., Yuen, K.-Y., Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin. Microbiol. Rev. 28 (2015), 465–522.
11. Elfiky, A.A., Mahdy, S.M., Elshemey, W.M., Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses. J. Med. Virol. 89 (2017), 1040–1047.
12. WHO, Middle East Respiratory Syndrome Coronavirus (MERS-CoV). 2016, WHO.
13. Báez-Santos, Y.M., Mielech, A.M., Deng, X., Baker, S., Mesecar, A.D., Catalytic function and substrate specificity of the papain-like protease domain of nsp3 from the Middle East respiratory syndrome coronavirus. J. Virol. 88 (2014), 12511–12527.
14. Hemida, M.G., Alnaeem, A., Some one health based control strategies for the Middle East respiratory syndrome coronavirus. One Health., 8, 2019, 100102.
15. Organization WH, Clinical Management of Severe Acute Respiratory Infection When Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection Is Suspected: Interim Guidance. 2019, World Health Organization.
16. Elfiky, A.A., Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials. J. Med. Virol. 88 (2016), 2044–2051.
17. Elfiky, A.A., Zika virus: novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase. Futur. Virol. 12 (2017), 721–728.
18. Elfiky, A.A., Novel guanosine derivatives as anti-HCV NS5b polymerase: a QSAR and molecular docking study. Med. Chem. 15 (2019), 130–137.
19. Elfiky, A.A., Elshemey, W.M., IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study. Med. Chem. Res. 25 (2016), 1005–1008.
20. Elfiky, A.A., Elshemey, W.M., Molecular dynamics simulation revealed binding of nucleotide inhibitors to ZIKV polymerase over 444 nanoseconds. J. Med. Virol. 90 (2018), 13–18.
21. Elfiky, A.A., Elshemey, W.M., Gawad, W.A., Desoky, O.S., Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. Protein J. 32 (2013), 75–80.
22. Elfiky, A.A., Ismail, A., Molecular dynamics and docking reveal the potency of novel GTP derivatives against RNA dependent RNA polymerase of genotype 4a HCV. Life Sci., 238, 2019, 116958.
23. Elfiky, A.A., Ismail, A.M., Molecular modeling and docking revealed superiority of IDX-184 as HCV polymerase inhibitor. Futur. Virol. 12 (2017), 339–347.
24. Ganesan, A., Barakat, K., Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Expert Opin. Drug Discovery 12 (2017), 407–425.
25. Doublie, S., Ellenberger, T., The mechanism of action of T7 DNA polymerase. Curr. Opin. Struct. Biol. 8 (1998), 704–712.
26. Elfiky, A.A., Ismail, A.M., Molecular docking revealed the binding of nucleotide/side inhibitors to Zika viral polymerase solved structures. SAR QSAR Environ. Res. 29 (2018), 409–418.
27. Ezat, A.A., Elfiky, A.A., Elshemey, W.M., Saleh, N.A., Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study. VirusDisease. 30:2 (2019), 207–213.
28. Yang, P.L., Gao, M., Lin, K., Liu, Q., Villareal, V.A., Anti-HCV drugs in the pipeline. Curr Opin Virol. 1 (2011), 607–616.
29. Markland, W., McQuaid, T., Jain, J., Kwong, A., Broad-spectrum antiviral activity of the IMP dehydrogenase inhibitor VX-497: a comparison with ribavirin and demonstration of antiviral additivity with alpha interferon. Antimicrob. Agents Chemother. 44 (2000), 859–866.
30. Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res., 2020, 1–3.
31. McQuaid, T., Savini, C., Seyedkazemi, S., Sofosbuvir, a significant paradigm change in HCV treatment. J Clin Transl Hepatol. 3 (2015), 27–35.
32. Berman, H., Henrick, K., Nakamura, H., Announcing the worldwide Protein Data Bank. Nat Struct Mol Biol., 10, 2003 980–.
33. NCBI, National Center of Biotechnology Informatics (NCBI) database website. http://www.ncbi.nlm.nih.gov/, 2020.
34. Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res., 42, 2014, W252-W8.
35. Kirchdoerfer, R.N., Ward, A.B., Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat. Commun., 10, 2019, 2342.
36. SAVES, Structural Analysis and Verification Server Website. 2020.
37. Williams, C.J., Headd, J.J., Moriarty, N.W., Prisant, M.G., Videau, L.L., Deis, L.N., et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27 (2018), 293–315.
38. Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R., Thornton, J.M., AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996), 477–486.
39. Eisenberg, D., Lüthy, R., Bowie, J.U., VERIFY3D: assessment of protein models with three-dimensional profiles. Methods in Enzymology: Elsevier, 1997, 396–404.
40. Pontius, J., JRaSJW, Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology 264 (1996), 121–136.
41. Hooft, R.W., Vriend, G., Sander, C., Abola, E.E., Errors in protein structures. Nature., 381, 1996, 272.
42. Elfiky, A.A., The antiviral Sofosbuvir against mucormycosis: an in silico perspective. Future Virology, 0, 2020 null.
43. Summers, K.L., Mahrok, A.K., Dryden, M.D., Stillman, M.J., Structural properties of metal-free apometallothioneins. Biochem. Biophys. Res. Commun. 425 (2012), 485–492.
44. Lii, J.H., Allinger, N.L., Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals’ potentials and crystal data for aliphatic and aromatic hydrocarbons. J. Am. Chem. Soc. 111 (1989), 8576–8582.
45. Trott, O., Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 (2010), 455–461.
46. Angela, M., Lam, C.E., Bansal, S., Micolochick Steuer, H.M., Niu, C., Zennou, V., Keilman, M., Zhu, Y., Lan, S., Otto, M.J., Furman, P.A., Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus. Antimicrob. Agents Chemother. 56 (2012), 3359–3368.
47. Elfiky, A.A., GW, A., EW, M., M, A., Hepatitis C viral polymerase inhibition using directly acting antivirals, a computational approach. Software and Techniques for Bio-Molecular Modeling, 2016, Austin Publishing Group, USA, 197.
48. Lam, M.J.O., Sofia, M.J., Espiritu, C., Bansal, S., Steuer, A.M., Bao, D., Chang, W., Bao, C.N., Micolochick Eisuke Murakami, H.M., Tolstykh, T., Furman, H.P.A., Mechanism of activation of PSI-7851 and its diastereoisomer PSI-7977. J. Biol. Chem. 285 (2010), 34337–34347.
49. Bullard-Feibelman, K.M., Govero, J., Zhu, Z., Salazar, V., Veselinovic, M., Diamond, M.S., et al. The FDA-approved drug sofosbuvir inhibits Zika virus infection. Antivir. Res. 137 (2017), 134–140.
50. Sacramento, C.Q., de Melo, G.R., Rocha, N., LVB, H., Mesquita, M., de Freitas, C.S., et al. The clinically approved antiviral drug sofosbuvir impairs Brazilian zika virus replication. Sci Rep., 7, 2017, 40920, 10.1038/srep40920.
51. Cretton-Scott, E., Perigaud, C., Peyrottes, S., Licklider, L., Camire, M., Larsson, M., et al. 588 in vitro antiviral activity and pharmacology of IDX184, a novel and potent inhibitor of HCV replication. J. Hepatol., 48, 2008, S220.
52. Elfiky, A.A., Elshemey, W.M., Gawad, W.A., 2′-Methylguanosine prodrug (IDX-184), phosphoramidate prodrug (Sofosbuvir), diisobutyryl prodrug (R7128) are better than their parent nucleotides and ribavirin in hepatitis C virus inhibition: a molecular modeling study. J. Comput. Theor. Nanosci. 12 (2015), 376–386.
53. Zhou, X.J., Pietropaolo, K., Chen, J., Khan, S., Sullivan-Bolyai, J., Mayers, D., Safety and pharmacokinetics of IDX184, a liver-targeted nucleotide polymerase inhibitor of hepatitis C virus, in healthy subjects. Antimicrob. Agents Chemother. 55 (2011), 76–81.
54. Gane, E.J., Stedman, C.A., Hyland, R.H., Ding, X., Svarovskaia, E., Symonds, W.T., et al. Nucleotide polymerase inhibitor sofosbuvir plus ribavirin for hepatitis C. N. Engl. J. Med. 368 (2013), 34–44.
55. Glue, P., The Clinical Pharmacology of Ribavirin. Seminars in Liver Disease. 1999, 17–24.
56. Manns, M.P., McHutchison, J.G., Gordon, S.C., Rustgi, V.K., Shiffman, M., Reindollar, R., et al. Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial. Lancet 358 (2001), 958–965.
57. Warren, T.K., Jordan, R., Lo, M.K., Ray, A.S., Mackman, R.L., Soloveva, V., et al. Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature. 531 (2016), 381–385.
58. Salentin, S., Schreiber, S., Haupt, V.J., Adasme, M.F., Schroeder, M., PLIP: fully automated protein–ligand interaction profiler. Nucleic Acids Res., 43, 2015, W443-W7.
59. Becke, A.D., Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98 (1993), 5648–5652.
60. Leach, A., Molecular Modelling: Principles and Applications. 2nd edition, 2001, Prentice Hall.
61. Stewart, J.J.P., Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J. Mol. Model. 13 (2007), 1173–1213.
62. Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30 (2009), 2785–2791.
63. Ibrahim, I., Abdelmalek, D., Elshahat, M., Elfiky, A., COVID-19 Spike-host cell receptor GRP78 binding site prediction. J. Infect., 2020 In press.