Molecular docking revealed the binding of nucleotide/side inhibitors to Zika viral polymerase solved structures

SAR and QSAR in Environmental Research

Volumn 29, Issue 5, 2018, Pages 409-418

  Elfiky, A A ^a,b,c   Ismail, A M ^a,d  

^a CAIRO UNIVERSITY   (Egypt)

^b ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

^c UNIVERSITY OF ALBERTA   (Canada)

^d UNIVERSITY OF ALBERTA   (Canada)

Author keywords

drug protein interaction; molecular docking; NS5 solved structure; RNA dependent RNA polymerase; Zika virus

Indexed keywords

MOLECULAR MODELING; NUCLEOTIDES; RNA; VIRUSES;

AUTODOCK VINAS; BINDING AFFINITIES; DRUG-PROTEIN INTERACTIONS; HEPATITIS C VIRUS; MOLECULAR DOCKING; NS5 SOLVED STRUCTURE; RNA-DEPENDENT RNA POLYMERASE; VIRUS INFECTION; WORLD HEALTH ORGANIZATION; ZIKA VIRUS;

BINDING ENERGY;

ANTIVIRUS AGENT; NUCLEOSIDE; NUCLEOTIDE; RIBAVIRIN; RNA DIRECTED RNA POLYMERASE; SOFOSBUVIR; TENOFOVIR;

ANTAGONISTS AND INHIBITORS; CHEMISTRY; DRUG DESIGN; DRUG EFFECT; MOLECULAR DOCKING; MOLECULAR MODEL; ZIKA VIRUS;

ANTIVIRAL AGENTS; DRUG DESIGN; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; NUCLEOSIDES; NUCLEOTIDES; RIBAVIRIN; RNA REPLICASE; SOFOSBUVIR; TENOFOVIR; ZIKA VIRUS;

EID: 85045524506     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936x.2018.1454981     Document Type: Article

References (53)

1. F.N., Macnamara, Zika virus: A report on three cases of human infection during an epidemic of jaundice in Nigeria, Trans. R Soc. Trop. Med. Hyg. 48 (1954), pp. 139–145.
2. M., Gelfand, A study of cirrhosis of the liver in (A) adult and (B) juvenile Africans, Trans. R Soc. Trop. Med. Hyg. 58 (1964), pp. 339–348.
3. G., Kuno and G.J., Chang, Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses, Arch. Virol. 152 (2007), pp. 687–696.
4. A., Zumla, I., Goodfellow, F., Kasolo, F., Ntoumi, P., Buchy, M., Bates, E.I., Azhar, M., Cotton, and E., Petersen, Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally, Int. J. Infect. Dis. 45 (2016), pp. 92–94.
5. WHO, Zika strategic response framework and joint operations plan, January–June 2016, WHO, Switzerland, Geneva, 2016.
6. D., Musso, E., Rouault, A., Teissier, M.C., Lanteri, K., Zisou, J., Broult, E., Grange, T.X., Nhan, and M., Aubry, Molecular detection of Zika virus in blood and RNA load determination during the French Polynesian outbreak, J. Med. Virol. 89 (2017), pp. 1505–1510.
7. J.P.T., Boorman and J.S., Porterfield, A simple technique for infection of mosquitoes with viruses transmission of Zika virus, Trans. R Soc. Trop. Med. Hyg. 50 (1956), pp. 238–242.
8. A.J., Haddow, M.C., Williams, J.P., Woodal, D.I.H., Simpson, and L.K.H., Goma, Twelve isolations of Zika virus from Aedes (Stegomyla) africanus (Theobald) taken in and above a Uganda forest, Bull. World Health. Organ. 31 (1964), pp. 57–69.
9. A.H., Fagbami, Zika virus infections in Nigeria: Virological and seroepidemiological investigations in Oyo State, J. Hyg. (Lond) 83 (1979), pp. 213–219.
10. J.G., Olson and T.G., Ksiazek, Suhandiman, and Triwibowo, Zika virus, a cause of fever in Central Java, Indonesia, Trans. R. Soc. Trop. Med. Hyg. 75 (1981), pp. 389–393.
11. L.B., Tauro, A.C., Bandeira, G.S., Ribeiro, M.G., Reis, C.P.R.M., Pizarro, K.A., Araujo, A.P., Castro, J.M., Queiroz, S.S., Simon, G., Menezes, G.S., Campos, and S., Sardi, Potential use of saliva samples to diagnose Zika virus infection, J. Med. Virol. 89 (2017), pp. 1–2.
12. J., Mlakar, M., Korva, N., Tul, M., Popovic, M., Poljsak-Prijatelj, J., Mraz, M., Kolenc, K., Resman Rus, T., Vesnaver Vipotnik, V., Fabjan Vodusek, A., Vizjak, J., Pizem, M., Petrovec, and T., Avsic Zupanc, Zika virus associated with microcephaly, N. Engl. J. Med. 374 (2016), pp. 951–958.
13. W., Duan, H., Song, H., Wang, Y., Chai, C., Su, J., Qi, Y., Shi, and G.F., Gao, The crystal structure of Zika virus NS5 reveals conserved drug targets, EMBO J. 36 (2017), pp. 919–933.
14. V.M., Cao-Lormeau, C., Roche, A., Teissier, E., Robin, A.L., Berry, H.P., Mallet, A.A., Sall, D., Musso, Zika virus, French polynesia, South pacific 2003, Emerg, Infect Dis. 20 (2014), pp. 1085–1086.
15. G., Grard, M., Caron, I.M., Mombo, D., Nkoghe, S., Mboui Ondo, D., Jiolle, D., Fontenille, C., Paupy, and E.M., Leroy, Zika virus in Gabon (Central Africa)—2007: A new threat from Aedes albopictus? PLoS Negl. Trop. Dis. 8 (2014), p. e2681.
16. D., Musso, E.J., Nilles, and V.M., Cao-Lormeau, Rapid spread of emerging Zika virus in the Pacific area, Clin. Microbiol. Infect. 20 (2014), pp. 595–596.
17. A.K., Upadhyay, M., Cyr, K., Longenecker, R., Tripathi, C., Sun, and D.J., Kempf, Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5, Acta Crystallogr. F. Struct. Biol. Commun. 73 (2017), pp. 116–122.
18. A.A., Elfiky, S.M., Mahdy, and W.M., Elshemey, 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), pp. 1040–1047.
19. A., Ganesan and K., Barakat, Applications of computer-aided approaches in the development of hepatitis C antiviral agents, Expert Opin. Drug. Discov. 12 (2017), pp. 407–425.
20. A.A., Elfiky, W.A., Gawad, and W.M., Elshemey, Hepatitis C viral polymerase inhibition using directly acting antivirals, a computational approach, in Software and Techniques for Bio-Molecular Modeling, A., Mukhametov, ed., Gercy City, Austin Publishing Group, 2016, pp. 197–209.
21. R., Jácome, A., Becerra, S., Ponce De León, and A., Lazcano, Structural analysis of monomeric RNA-dependent polymerases: Evolutionary and therapeutic implications, PLOS ONE. 10 (2015), pp. e0139001.
22. C., Ferrer-Orta, D., Ferrero, and N., Verdaguer, RNA-dependent RNA polymerases of picornaviruses: From the structure to regulatory mechanisms, Viruses 7 (2015), pp. 4438–4460.
23. A.A., Elfiky, W.M., Elshemey, and W.A., Gawad, 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. Nanos. 12 (2015), pp. 376–386.
24. T., Asselah, Daclatasvir plus sofosbuvir for HCV infection: An oral combination therapy with high antiviral efficacy, J. Hepatol. 61 (2014), pp. 435–438.
25. A.S., Mayhoub, Hepatitis C RNA-dependent RNA polymerase inhibitors: A review of structure–activity and resistance relationships; Different scaffolds and mutations, Bioorg. Med. Chem. 20 (2012), pp. 3150–3161.
26. S., Doublie and T., Ellenberger, The mechanism of action of T7 DNA polymerase, Curr. Opin. Struct. Biol. 8 (1998), pp. 704–712.
27. A.A., Elfiky, W.M., Elshemey, W.A., Gawad, and O.S., Desoky, Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes, Protein J. 32 (2013), pp. 75–80.
28. A.A., Elfiky and W.M., Elshemey, IDX-184 is a superior HCV direct-acting antiviral drug: A QSAR study, Med. Chem. Res. 25 (2016), pp. 1005–1008.
29. P., Ramharack and M.E.S., Soliman, Zika virus drug targets: A missing link in drug design and discovery–A route map to fill the gap, RSC Advances 6 (2016), pp. 68719–68731.
30. A., Pattnaik, N., Palermo, B.R., Sahoo, Z., Yuan, D., Hu, A.S., Annamalai, H.L.X., Vu, I., Correas, P.K., Prathipati, C.J., Destache, Q., Li, F.A., Osorio, A.K., Pattnaik, and S.H., Xiang, Discovery of a non-nucleoside RNA polymerase inhibitor for blocking Zika virus replication through in silico screening, Antivir. Res. 151 (2018), pp. 78–86.
31. A.A., Elfiky, Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials, J. Med. Virol. 88 (2016), pp. 2044–2051.
32. K.M., Bullard-Feibelman, J., Govero, Z., Zhu, V., Salazar, M., Veselinovic, M.S., Diamond, and B.J., Geiss, The FDA-approved drug sofosbuvir inhibits Zika virus infection, Antivir. Res. 137 (2017), pp. 134–140.
33. K., Hercík, J., Kozak, M., Šála, M., Dejmek, H., Hřebabecký, E., Zborníková, M., Smola, D., Ruzek, R., Nencka, and E., Boura, Adenosine triphosphate analogs can efficiently inhibit the Zika virus RNA-dependent RNA polymerase, Antivir. Res. 137 (2017), pp. 131–133.
34. A., Singh and N.K., Jana, Discovery of potential Zika virus RNA polymerase inhibitors by docking-based virtual screening, Comput. Biol. Chem. 71 (2017), pp. 144–151.
35. B., Wang, X.F., Tan, S., Thurmond, Z.M., Zhang, A., Lin, R., Hai, and J., Song, The structure of Zika virus NS5 reveals a conserved domain conformation, Nat. Commun. 8 (2017), p. 14763.
36. A.S., Godoy, G.M.A., Lima, K.I.Z., Oliveira, N.U., Torres, F.V., Maluf, R.V.C., Guido, and G., Oliva, Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase, Nat. Commun. 8 (2017), p. 14764.
37. H., Berman, K., Henrick, and H., Nakamura, Announcing the worldwide Protein Data Bank, Nat. Struct. Mol. Biol. 10 (2003), p. 980.
38. Structural Analysis and Verification Server, Molecular Biology Institute, Universtiy of California, Los Angeles, USA, 2018; software available at https://services.mbi.ucla.edu/SAVES/.
39. W.M., Elshemey, A.A., Elfiky, and W.A., Gawad, Correlation to protein conformation of wide-angle X-ray scatter parameters, Protein J. 29 (2010), pp. 545–550.
40. L.A., Kelley, S., Mezulis, C.M., Yates, M.N., Wass, and M.J.E., Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protocols 10 (2015), pp. 845–858.
41. A.A., Elfiky and W.M., Elshemey, Molecular dynamics simulation revealed binding of nucleotide inhibitors to ZIKV polymerase over 444 nanoseconds, J. Med. Virol. 90 (2018), pp. 13–18.
42. W., Humphrey, A., Dalke, and K., Schulten, VMD: Visual molecular dynamics, J. Molec. Graph. 14 (1996), pp. 33–38.
43. M.H., Powdrill, J.A., Bernatchez, and M., Götte, Inhibitors of the hepatitis C virus RNA-dependent RNA polymerase NS5B, Viruses 2 (2010), pp. 2169–2195.
44. W., Xue, P., Jiao, H., Liu, and X., Yao, Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598, Antivir. Res. 104 (2014), pp. 40–51.
45. N.L., Mallalieu, M.H., Rahimy, C.A., Crowley, J.R., Appleman, P.F., Smith, and J.L., Freddo, Pharmacokinetics and pharmacodynamics of setrobuvir, an orally administered hepatitis C virus non-nucleoside analogue inhibitor, Clin. Ther. 36 (2014), pp. 2047–2063.
46. E., Murakami, T., Tolstykh, H., Bao, C., Niu, H.M., Steuer, D., Bao, W., Chang, C., Espiritu, S., Bansal, A.M., Lam, M.J., Otto, M.J., Sofia, and P.A., Furman, Mechanism of activation of PSI-7851 and its diastereoisomer PSI-7977, J. Biol. Chem. 285 (2010), pp. 34337–34347.
47. A.D., Becke, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys. 98 (1993), pp. 5648–5652.
48. A., Leach, Molecular Modelling: Principles and Applications, 2nd ed., Prentice Hall, Harlow, 2001.
49. O., Trott and A.J., Olson, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem. 31 (2010), pp. 455–461.
50. G.M., Morris, R., Huey, W., Lindstrom, M.F., Sanner, R.K., Belew, D.S., Goodsell, and A.J., Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, J. Comput. Chem. 30 (2009), pp. 2785–2791.
51. The PyMOL Molecular Graphics System, Version 2.0, Schrödinger, LLC.
52. Maestro, Schrödinger, LLC, New York, NY.
53. A.A., Elfiky, Zika virus: Novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase, Future Virol. 12 (2017), pp. 721–728.