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Volumn 90, Issue 1, 2018, Pages 13-18

Molecular dynamics simulation revealed binding of nucleotide inhibitors to ZIKV polymerase over 444 nanoseconds

Author keywords

guanosine inhibitors; molecular docking; molecular dynamics simulation; polymerase; protein ligand docking; Zika virus

Indexed keywords

GUANOSINE; GUANOSINE TRIPHOSPHATE; IDX 184; MERICITABINE; MK 0608; NONSTRUCTURAL PROTEIN 5; NONSTRUCTURAL PROTEIN 5B; NUCLEOTIDYLTRANSFERASE INHIBITOR; RIBAVIRIN; RNA DIRECTED RNA POLYMERASE INHIBITOR; SOFOSBUVIR; UNCLASSIFIED DRUG; VIRUS ENZYME; VIRUS RNA; ANTIVIRUS AGENT; NUCLEOTIDE; RNA DIRECTED RNA POLYMERASE;

EID: 85030096112     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.24934     Document Type: Article
Times cited : (43)

References (50)
  • 2
    • 49749137527 scopus 로고
    • Zika virus: a report on three cases of human infection during an epidemic of jaundice in Nigeria
    • MacNamara FN. Zika virus: a report on three cases of human infection during an epidemic of jaundice in Nigeria. Trans R Soc Trop Med Hyg. 1954; 48:139–145.
    • (1954) Trans R Soc Trop Med Hyg , vol.48 , pp. 139-145
    • MacNamara, F.N.1
  • 3
    • 67149088928 scopus 로고    scopus 로고
    • Zika virus outbreak on Yap island, federated states of Micronesia
    • Duffy MR, Chen T-H, Hancock WT, et al. Zika virus outbreak on Yap island, federated states of Micronesia. N Eng J Med. 2009; 360:2536–2543.
    • (2009) N Eng J Med , vol.360 , pp. 2536-2543
    • Duffy, M.R.1    Chen, T.-H.2    Hancock, W.T.3
  • 4
    • 33947379655 scopus 로고    scopus 로고
    • Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses
    • Kuno G, Chang GJ. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch Virol. 2007; 152:687–696.
    • (2007) Arch Virol , vol.152 , pp. 687-696
    • Kuno, G.1    Chang, G.J.2
  • 6
    • 49749156769 scopus 로고
    • A simple technique for infection of mosquitoes with viruses transmission of Zika virus
    • Boorman JPT, Porterfield JS. A simple technique for infection of mosquitoes with viruses transmission of Zika virus. Trans R Soc Trop Med Hyg. 1956; 50:238–242.
    • (1956) Trans R Soc Trop Med Hyg , vol.50 , pp. 238-242
    • Boorman, J.P.T.1    Porterfield, J.S.2
  • 7
    • 48749131500 scopus 로고
    • Twelve isolations of Zika virus from Aedes (Stegomyla) africanus (Theobald) taken in and above a Uganda forest
    • Haddow AJW, Williams MC, Woodall JP, Simpson DIH, Goma LKH. Twelve isolations of Zika virus from Aedes (Stegomyla) africanus (Theobald) taken in and above a Uganda forest. Bull Wid Health Org. 1964; 31:69.
    • (1964) Bull Wid Health Org , vol.31 , pp. 69
    • Haddow, A.J.W.1    Williams, M.C.2    Woodall, J.P.3    Simpson, D.I.H.4    Goma, L.K.H.5
  • 8
    • 0018616782 scopus 로고
    • Zika virus infections in Nigeria: virological and seroepidemiological investigations in Oyo State
    • Fagbami AH. Zika virus infections in Nigeria: virological and seroepidemiological investigations in Oyo State. Epidemiol Infect. 1979; 83:213–219.
    • (1979) Epidemiol Infect , vol.83 , pp. 213-219
    • Fagbami, A.H.1
  • 9
    • 84993991632 scopus 로고    scopus 로고
    • Potential use of saliva samples to diagnose Zika virus infection
    • Tauro LB, Bandeira AC, Ribeiro GS, et al. Potential use of saliva samples to diagnose Zika virus infection. J Med Virol. 2017; 89:1–2.
    • (2017) J Med Virol , vol.89 , pp. 1-2
    • Tauro, L.B.1    Bandeira, A.C.2    Ribeiro, G.S.3
  • 10
    • 85024132534 scopus 로고    scopus 로고
    • Molecular detection of Zika virus in blood and RNA load determination during the French Polynesian outbreak
    • Musso D, Rouault E, Teissier A, et al. Molecular detection of Zika virus in blood and RNA load determination during the French Polynesian outbreak. J Med Virol. 2016; 89:1505–1510.
    • (2016) J Med Virol , vol.89 , pp. 1505-1510
    • Musso, D.1    Rouault, E.2    Teissier, A.3
  • 11
    • 84961114834 scopus 로고    scopus 로고
    • Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally
    • Zumla A, Goodfellow I, Kasolo F, et al. Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally. Int J Infect Dis. 2016; 45:92–94.
    • (2016) Int J Infect Dis , vol.45 , pp. 92-94
    • Zumla, A.1    Goodfellow, I.2    Kasolo, F.3
  • 12
    • 84959283609 scopus 로고    scopus 로고
    • Zika virus associated with microcephaly
    • Mlakar J, Korva M, Tul N, et al. Zika virus associated with microcephaly. N Engl J Med. 2016; 374:951–958.
    • (2016) N Engl J Med , vol.374 , pp. 951-958
    • Mlakar, J.1    Korva, M.2    Tul, N.3
  • 13
    • 85016141754 scopus 로고    scopus 로고
    • The structure of Zika virus NS5 reveals a conserved domain conformation
    • Wang B, Tan X-F, Thurmond S, et al. The structure of Zika virus NS5 reveals a conserved domain conformation. Nat Commun. 2017; 8:14763.
    • (2017) Nat Commun , vol.8 , pp. 14763
    • Wang, B.1    Tan, X.-F.2    Thurmond, S.3
  • 14
    • 85015344807 scopus 로고    scopus 로고
    • Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5
    • Upadhyay AK, Cyr M, Longenecker K, Tripathi R, Sun C, Kempf DJ. Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5. Acta Crystallogr F Struct Biol Commun. 2017; 73:116–122.
    • (2017) Acta Crystallogr F Struct Biol Commun , vol.73 , pp. 116-122
    • Upadhyay, A.K.1    Cyr, M.2    Longenecker, K.3    Tripathi, R.4    Sun, C.5    Kempf, D.J.6
  • 15
    • 85013276209 scopus 로고    scopus 로고
    • Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses
    • Elfiky AA, Mahdy SM, Elshemey WM. Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses. J Med Virol. 2017; 89:1040–1047.
    • (2017) J Med Virol , vol.89 , pp. 1040-1047
    • Elfiky, A.A.1    Mahdy, S.M.2    Elshemey, W.M.3
  • 16
    • 84872683113 scopus 로고    scopus 로고
    • Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes
    • Elfiky AA, Elshemey WM, Gawad WA, Desoky OS. Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. Protein J. 2013; 32:75–80.
    • (2013) Protein J , vol.32 , pp. 75-80
    • Elfiky, A.A.1    Elshemey, W.M.2    Gawad, W.A.3    Desoky, O.S.4
  • 17
    • 84941038188 scopus 로고    scopus 로고
    • RNA-dependent RNA polymerases of picornaviruses: from the structure to regulatory mechanisms
    • Ferrer-Orta C, Ferrero D, Verdaguer N. RNA-dependent RNA polymerases of picornaviruses: from the structure to regulatory mechanisms. Viruses. 2015; 7:4438–4460.
    • (2015) Viruses , vol.7 , pp. 4438-4460
    • Ferrer-Orta, C.1    Ferrero, D.2    Verdaguer, N.3
  • 18
    • 85015416301 scopus 로고    scopus 로고
    • Applications of computer-aided approaches in the development of hepatitis C antiviral agents
    • Ganesan A, Barakat K. Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Expert Opin Drug Discov. 2017; 12:407–425.
    • (2017) Expert Opin Drug Discov , vol.12 , pp. 407-425
    • Ganesan, A.1    Barakat, K.2
  • 19
    • 84960158342 scopus 로고    scopus 로고
    • IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study
    • Elfiky AA, Elshemey WM. IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study. Med Chem Res. 2016; 25:1005–1008.
    • (2016) Med Chem Res , vol.25 , pp. 1005-1008
    • Elfiky, A.A.1    Elshemey, W.M.2
  • 20
    • 84925270533 scopus 로고    scopus 로고
    • 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
    • Elfiky AA, Elshemey WM, Gawad WA. 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 Theoretical Nanosci. 2015; 12:376–386.
    • (2015) J Comput Theoretical Nanosci , vol.12 , pp. 376-386
    • Elfiky, A.A.1    Elshemey, W.M.2    Gawad, W.A.3
  • 21
    • 84904756999 scopus 로고    scopus 로고
    • Daclatasvir plus sofosbuvir for HCV infection: an oral combination therapy with high antiviral efficacy
    • Asselah T. Daclatasvir plus sofosbuvir for HCV infection: an oral combination therapy with high antiviral efficacy. J Hepatol. 2014; 61:435–438.
    • (2014) J Hepatol , vol.61 , pp. 435-438
    • Asselah, T.1
  • 22
    • 85024487104 scopus 로고    scopus 로고
    • Hepatitis C viral polymerase inhibition using directly acting antivirals, a computational approach
    • In, A M, ed., Jersey city, NJ, USA, Austin Publishing group
    • Elfiky AA, Gawad WA, Elshemey WM. Hepatitis C viral polymerase inhibition using directly acting antivirals, a computational approach. In: A M, ed. Software and Techniques for Bio-Molecular Modeling. Jersey city, NJ, USA: Austin Publishing group; 2016: 197.
    • (2016) Software and Techniques for Bio-Molecular Modeling , pp. 197
    • Elfiky, A.A.1    Gawad, W.A.2    Elshemey, W.M.3
  • 23
    • 84890757693 scopus 로고    scopus 로고
    • Sofosbuvir for the treatment of hepatitis C virus
    • Asselah T. Sofosbuvir for the treatment of hepatitis C virus. Expert Opin Pharmacother. 2014; 15:121–130.
    • (2014) Expert Opin Pharmacother , vol.15 , pp. 121-130
    • Asselah, T.1
  • 24
    • 85000415085 scopus 로고    scopus 로고
    • The FDA-approved drug sofosbuvir inhibits Zika virus infection
    • Bullard-Feibelman KM, Govero J, Zhu Z, et al. The FDA-approved drug sofosbuvir inhibits Zika virus infection. Antivir Res. 2017; 137:134–140.
    • (2017) Antivir Res , vol.137 , pp. 134-140
    • Bullard-Feibelman, K.M.1    Govero, J.2    Zhu, Z.3
  • 25
    • 84988421322 scopus 로고    scopus 로고
    • Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials
    • Elfiky AA. Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials. J Med Virol. 2016; 88:2044–2051.
    • (2016) J Med Virol , vol.88 , pp. 2044-2051
    • Elfiky, A.A.1
  • 26
    • 85010023391 scopus 로고    scopus 로고
    • The clinically approved antiviral drug sofosbuvir impairs Brazilian Zika virus replication
    • Article 40920
    • Sacramento CQ, de Melo GR, Rocha N, et al. The clinically approved antiviral drug sofosbuvir impairs Brazilian Zika virus replication. bioRxiv. 2016; 7:1–12. Article no. 40920.
    • (2016) bioRxiv , vol.7 , pp. 1-12
    • Sacramento, C.Q.1    de Melo, G.R.2    Rocha, N.3
  • 27
    • 85024475880 scopus 로고    scopus 로고
    • Molecular modeling and docking revealed superiority of IDX-184 as HCV polymerase inhibitor
    • Elfiky AA, Ismail AM. Molecular modeling and docking revealed superiority of IDX-184 as HCV polymerase inhibitor. Future Virol. 2017; 12:339–347.
    • (2017) Future Virol , vol.12 , pp. 339-347
    • Elfiky, A.A.1    Ismail, A.M.2
  • 28
    • 0003653899 scopus 로고    scopus 로고
    • Molecular dynamics simulation methods
    • 2nd ed, England, Prentice Hall
    • Leach A. 2001. Molecular dynamics simulation methods. 2nd ed. Molecular Modelling: Principles and Applications. England: Prentice Hall; 353–406.
    • (2001) Molecular Modelling: Principles and Applications , pp. 353-406
    • Leach, A.1
  • 30
    • 84892405001 scopus 로고    scopus 로고
    • The electronic and quantitative structure activity relationship properties of modified telaprevir compounds as HCV NS3 protease inhibitors
    • Saleh NA, Elfiky AA, Ezat AA, Elshemey WM, Ibrahim M. The electronic and quantitative structure activity relationship properties of modified telaprevir compounds as HCV NS3 protease inhibitors. J Comput Theoretical Nanosci. 2014; 11:544–548.
    • (2014) J Comput Theoretical Nanosci , vol.11 , pp. 544-548
    • Saleh, N.A.1    Elfiky, A.A.2    Ezat, A.A.3    Elshemey, W.M.4    Ibrahim, M.5
  • 31
    • 73749087546 scopus 로고    scopus 로고
    • Structural and electronic properties of new fullerene derivatives and their possible application as HIV-1 protease inhibitors
    • Ibrahim M, Saleh NA, Hameed AJ, Elshemey WM, Elsayed AA. Structural and electronic properties of new fullerene derivatives and their possible application as HIV-1 protease inhibitors. Spectrochim Acta A Mol Biomol Spectrosc. 2010; 75:702–709.
    • (2010) Spectrochim Acta A Mol Biomol Spectrosc , vol.75 , pp. 702-709
    • Ibrahim, M.1    Saleh, N.A.2    Hameed, A.J.3    Elshemey, W.M.4    Elsayed, A.A.5
  • 32
    • 84912061839 scopus 로고    scopus 로고
    • The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors
    • Saleh NA. The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors. Spectrochim Acta A Mol Biomol Spectrosc. 2014; 136PC:1523–1529.
    • (2014) Spectrochim Acta A Mol Biomol Spectrosc , vol.136 PC , pp. 1523-1529
    • Saleh, N.A.1
  • 33
    • 84865738386 scopus 로고    scopus 로고
    • Hexapeptide functionality of cellulose as NS3 protease inhibitors
    • Ibrahim M, Saleh NA, Elshemey WM, Elsayed AA. Hexapeptide functionality of cellulose as NS3 protease inhibitors. Med Chem. 2012; 8:826–830.
    • (2012) Med Chem , vol.8 , pp. 826-830
    • Ibrahim, M.1    Saleh, N.A.2    Elshemey, W.M.3    Elsayed, A.A.4
  • 34
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005; 26:1781–1802.
    • (2005) J Comput Chem , vol.26 , pp. 1781-1802
    • Phillips, J.C.1    Braun, R.2    Wang, W.3
  • 35
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: introducing water into the modelling of biomolecular complexes
    • van Dijk AD, Bonvin AM. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics. 2006; 22:2340–2347.
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • van Dijk, A.D.1    Bonvin, A.M.2
  • 36
    • 84856679087 scopus 로고    scopus 로고
    • Molecular dynamics studies of human?-Glucuronidase
    • Noorbatcha IA, Khan AM, Salleh HM. Molecular dynamics studies of human?-Glucuronidase. Am J Appl Sci. 2010; 7:823–828.
    • (2010) Am J Appl Sci , vol.7 , pp. 823-828
    • Noorbatcha, I.A.1    Khan, A.M.2    Salleh, H.M.3
  • 37
    • 84978375335 scopus 로고    scopus 로고
    • Water determines the structure and dynamics of proteins
    • Bellissent-Funel M-C, Hassanali A, Havenith M, et al. Water determines the structure and dynamics of proteins. Chem Rev. 2016; 116:7673–7697.
    • (2016) Chem Rev , vol.116 , pp. 7673-7697
    • Bellissent-Funel, M.-C.1    Hassanali, A.2    Havenith, M.3
  • 39
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the web: a case study using the Phyre server
    • Kelley LA, Sternberg MJ. Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc. 2009; 4:363–371.
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 41
    • 0024804228 scopus 로고
    • Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals’ potentials and crystal data for aliphatic and aromatic hydrocarbons
    • Lii JH, Allinger NL. 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. 1989; 111:8576–8582.
    • (1989) J Am Chem Soc , vol.111 , pp. 8576-8582
    • Lii, J.H.1    Allinger, N.L.2
  • 42
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys. 1993; 98:5648–5652.
    • (1993) J Chem Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 43
    • 85034063406 scopus 로고    scopus 로고
    • Zika virus: novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase
    • In press
    • Elfiky AA. Zika virus: novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase. Future Virol. 2017; In press.
    • (2017) Future Virol
    • Elfiky, A.A.1
  • 44
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010; 31:455–461.
    • (2010) J Comput Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 45
    • 85011602101 scopus 로고    scopus 로고
    • A structural view of the RNA-dependent RNA polymerases from the Flavivirus genus
    • Lu G, Gong P. A structural view of the RNA-dependent RNA polymerases from the Flavivirus genus. Virus Res. 2017; 234:34–43.
    • (2017) Virus Res , vol.234 , pp. 34-43
    • Lu, G.1    Gong, P.2
  • 46
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • 27–38
    • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996; 14:33–38, 27–38.
    • (1996) J Mol Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 47
    • 67849109995 scopus 로고    scopus 로고
    • Solvent accessible surface area approximations for rapid and accurate protein structure prediction
    • Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J. Solvent accessible surface area approximations for rapid and accurate protein structure prediction. J Mol Model. 2009; 15:1093–1108.
    • (2009) J Mol Model , vol.15 , pp. 1093-1108
    • Durham, E.1    Dorr, B.2    Woetzel, N.3    Staritzbichler, R.4    Meiler, J.5
  • 48
    • 85034049549 scopus 로고    scopus 로고
    • IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study
    • Elfiky AA, Elshemey WM. IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study. Med Chem Res. 2016;90:1–4.
    • (2016) Med Chem Res , vol.90 , pp. 1-4
    • Elfiky, A.A.1    Elshemey, W.M.2
  • 49
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega
    • Sievers F, Wilm A, Dineen D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol. 2011; 7:539.
    • (2011) Mol Syst Biol , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3
  • 50
    • 84904790793 scopus 로고    scopus 로고
    • Deciphering key features in protein structures with the new ENDscript server
    • Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014; 42:W320–W324.
    • (2014) Nucleic Acids Res , vol.42 , pp. W320-W324
    • Robert, X.1    Gouet, P.2


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