Characterizing the Ligand-Binding Landscape of Zika NS3 Helicase-Promising Lead Compounds As Potential Inhibitors

References

• Sreedharan J . The Zika virus: a new threat from mosquito . Scientia11, 9 – 17 ( 2016 ).
   Google Scholar
• Haddow AD , SchuhAJ, YasudaCYet al. Genetic characterization of Zika virus strains: geographic expansion of the asian lineage . PLoS Negl. Trop. Dis.6 ( 2 ), 1 – 7 ( 2012 ).
   Web of Science ®Google Scholar
• Martínez de Salazar P , SuyA, Sánchez-MontalváAet al. Zika fever . Enferm. Infect. Microbiol. Clin.34 ( 4 ), 247 – 252 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Barrows NJ , CamposRK, PowellSTet al. A Screen of FDA-Approved Drugs for Inhibitors of Zika Virus Infection . Cell Host Microbe20, 2259 – 270 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Wikan N , SmithDR . Zika virus: history of a newly emerging arbovirus . Lancet Infect. Dis.16 ( 7 ), 119 – 126 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Chan JFW , ChoiGKY, YipCCY, ChengVCC, YuenKY . Zika fever and congenital Zika syndrome: an unexpected emerging arboviral disease . J. Infect.72 ( 5 ), 507 – 524 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Heang V , YasudaCY, SovannLet al. Zika virus infection, Cambodia, 2010 . Emerg. Infect. Dis.18 ( 2 ), 349 – 351 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Kutsuna S , KatoY, TakasakiTet al. Two cases of Zika fever imported from French Polynesia to Japan, December to January 2013 . Eurosurveillance19 ( 4 ), 1 – 4 ( 2014 ).
   Web of Science ®Google Scholar
• Hamel R , DejarnacO, WichitSet al. Biology of Zika virus infection in human skin cells . J. Virol.89 ( 17 ), 8880 – 8896 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Foy BD , KobylinskiKC, FoyJLCet al. Probable non-vector-borne transmission of Zika virus, Colorado, USA . Emerg. Infect. Dis.17 ( 5 ), 880 – 882 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Hayes EB . Zika virus outside Africa . Emerg. Infect. Dis.15 ( 9 ), 1347 – 1350 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Musso D , RocheC, RobinEet al. Potential sexual transmission of Zika virus . Emerg. Infect. Dis.21 ( 2 ), 359 – 361 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Besnard M , LastèreS, TeissierA, Cao-LormeauVM, MussoD . Evidence of perinatal transmission of Zika virus, French Polynesia, December 2013 and February 2014 . Eurosurveillance19 ( 13 ), 8 – 11 ( 2014 ).
   Web of Science ®Google Scholar
• Plourde AR , BlochEM . A literature review of Zika virus . Emerg. Infect. Dis.22 ( 7 ), 1 – 15 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Charrel RN , Leparc-GoffartI, PasSet al. State of knowledge on Zika virus for an adequate laboratory response . Bull. World Heal. Organ.1 – 29 ( 2016 ).
   Google Scholar
• Cao-Lormeau VM , BlakeA, MonsSet al. Guillain–Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: a case–control study . Lancet387 ( 10027 ), 1531 – 1539 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Baharuddin A , HassanAA, ShengGCet al. Current approaches in antiviral drug discovery against the Flaviviridae family . Curr. Pharm. Des.20 ( 21 ), 3428 – 3444 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Malet H , MasséN, SeliskoBet al. The Flavivirus polymerase as a target for drug discovery . Antiviral Res.80 ( 1 ), 23 – 35 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Tian H , JiX, YangXet al. The crystal structure of Zika virus helicase: basis for antiviral drug design . Protein Cell7 ( 6 ), 450 – 454 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Jain R , ColomaJ, Garcia-SastreA, AggarwalAK . Structure of the NS3 helicase from Zika virus . Nat. Struct. Mol. Biol.23 ( 8 ), 752 – 754 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Incicco JJ , GebhardLG, González-LebreroRM, GamarnikAV, KaufmanSB . Steady-state NTPase activity of dengue virus NS3: number of catalytic sites, nucleotide specificity and activation by ssRNA . PLoS ONE8 ( 3 ), 1 – 8 ( 2013 ).
   Web of Science ®Google Scholar
• Pearlman DA , CaseDA, CaldwellJWet al. AMBER, a package of computer programs for applyingmolecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules . Comput. Phys. Commun.91, 1 – 41 ( 1995 ).
   Web of Science ®Google Scholar
• Miao Y , FeixasF, EunC, McCammonJA . Accelerated molecular dynamics simulations of protein folding . J. Comput. Chem.36 ( 20 ), 1536 – 1549 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Lindert S , BucherD, EastmanP, PandeV, MccammonJA . Accelerated molecular dynamics simulations with the AMOEBA polarizable force field on graphics processing units . J. Chem. Theory Comput.9, 1 – 2 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Pettersen EF , GoddardTD, HuangCCet al. UCSF Chimera – a visualization system for exploratory research and analysis . J. Comput. Chem.25 ( 13 ), 1605 – 1612 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Windows MMV, X MOS. Molegro Molecular Viewer User Manual. Molegro ApSC, Aarhus, Denmark ( 2011 ).
   Google Scholar
• Da Costa ECB , AmorimR, Da SilvaFCet al. Synthetic 1,4-pyran naphthoquinones are potent inhibitors of Dengue virus replication . PLoS ONE8 ( 12 ), 1 – 11 ( 2013 ).
   Web of Science ®Google Scholar
• Borowski P , LangM, HaagAet al. Characterization of imidazo [4, 5-d] pyridazine nucleosides as modulators of unwinding reaction mediated by West Nile virus nucleoside triphosphatase/helicase: evidence for activity on the level of substrate and/or enzyme . Antimicrob. Agents Chemother.46 ( 5 ), 1231 – 1239 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Briguglio I , PirasS, CoronaP, CartaA . Inhibition of RNA helicases of ssRNA(+) virus belonging to Flaviviridae, Coronaviridae and Picornaviridae families . Int. J. Med. Chem.2011, 1 – 22 ( 2011 ).
   Google Scholar
• Mastrangelo E , PezzulloM, De burghgraeveTet al. Ivermectin is a potent inhibitor of Flavivirus replication specifically targeting NS3 helicase activity: new prospects for an old drug . J. Antimicrob. Chemother.67 ( 8 ), 1884 – 1894 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Kim S , ThiessenPA, BoltonEEet al. PubChem substance and compound databases . Nucleic Acids Res.44 ( 1 ), 1202 – 1213 ( 2016 ).
   Google Scholar
• Steffen C , ThomasK, HuniarUet al. TmoleX-a graphical user interface for TURBOMOLE . J. Comput. Chem.31, 2967 – 2970 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Case DA , CheathamTE, DardenTet al. The Amber bimolecular simulation programs . J. Comput. Chem.26 ( 16 ), 1668 – 1688 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Cornell WD , CieplakP, BaylyCIet al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules . J. Am. Chem. Soc.117 ( 19 ), 5179 – 5197 ( 1995 ).
   Web of Science ®Google Scholar
• Wang J , WolfRM, CaldwellJW, KollmanPA, CaseDA . Development and testing of a general Amber force field . J. Comput. Chem.25 ( 9 ), 1157 – 1174 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Goetz AW , WilliamsonMJ, XuD, PooleD, GrandSL, WalkerRC . Routine microsecond molecular dynamics simulations with amber – Part I: generalized born . J. Chem. Theory Comput.8, 1542 – 1555 . ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Jorgensen WL , ChandrasekharJ, MaduraJD, ImpeyRW, KleinML . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys.79 ( 2 ), 926 ( 1983 ).
   Web of Science ®Google Scholar
• Seifert E . OriginPro 9.1: scientific data analysis and graphing software – software review . J. Chem. Inf. Model.54 ( 5 ), 1552 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Greenidge PA , KramerC, MozziconacciJC, WolfRM . MM/GBSA binding energy prediction on the PDB bind data set: successes, failures, and directions for further improvement . J. Chem. Inf. Model.53 ( 1 ), 201 – 209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Godschalk F , GenhedenS, SöderhjelmP, RydeU . Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations . Phys. Chem.15 ( 20 ), 7731 – 7739 ( 2013 ).
   Google Scholar
• Tsui V , CaseDA . Theory and applications of the generalized born solvation model in macromolecular simulations . Biopolymers56 ( 4 ), 275 – 291 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Kollman PA , MassovaI, ReyesCet al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models . Acc. Chem. Res.33 ( 12 ), 889 – 897 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Meng XY , ZhangHX, MezeiM, CuiM . Molecular docking: a powerful approach for structure-based drug discovery . Curr. Comput. Aided Drug Des.7 ( 2 ), 146 – 157 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Ferreira LG , Dos SantosRN, OlivaG, AndricopuloAD . Molecular docking and structure-based drug design strategies . Molecules20 ( 7 ), 13384 – 13421 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• De Oliveira AS , Da SilvaML, FláviaAet al. NS3 and NS5 proteins: important targets for anti-dengue drug design . J. Braz. Chem. Soc.25 ( 10 ), 1759 – 1769 ( 2014 ).
   Web of Science ®Google Scholar
• Salsbury FR Jr . Molecular dynamics simulations of protein dynamics and their relevance to drug discovery . Curr. Opin. Pharmacol.10 ( 6 ), 738 – 744 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Arodola OA , SolimanMES . Could the FDA-approved anti-HIV PR inhibitors be promising anticancer agents? An answer from enhanced docking approach and molecular dynamics analyses . Drug Des. Devel. Ther.9, 6055 – 6065 ( 2015 ).
   PubMedGoogle Scholar
• Sing A Soliman ME . Understanding the cross-resistance of oseltamivir to HINI and H5NI influenza A neuraminidase mutation using multidimensional computational analyses . Drug Des. Devel Ther.9, 1 – 18 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Appiah-Kubi P , SolimanMES . Dual anti-inflammatory and selective inhibition mechanism of leukotriene A4 hydrolase/aminopeptidase: insights from comparative molecular dynamics and binding free energy analyses . J. Biomol. Struct. Dyn.1102, 1 – 16 ( 2016 ).
   Google Scholar
• Karubiu W , BhakatS, SolimanMES . Compensatory role of double mutation N348I/M184V on nevirapine binding landscape: insight from molecular dynamics simulation . Protein J.33 ( 5 ), 432 – 446 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Kumalo HM , SolimanME . Per-residue energy footprints-based pharmacophore modeling as an enhanced in silico approach in drug discovery: a case study on the identification of novel secretase1 (BACE1) inhibitors as anti-Alzheimer agents . Cell. Mol. Bioeng.9 ( 1 ), 175 – 189 ( 2016 ).
   Web of Science ®Google Scholar
• Mahfuz M , KhanA, MahmudH Alet al. In silico modeling and immunoinformatics probing disclose the epitope based peptide vaccine against Zika virus envelope glycoprotein . Indian J. Pharm. Biol. Res.2 ( 4 ), 44 – 57 ( 2014 ).
   Google Scholar
• CHIP: Centre for high performance computing . http://www.chpc.ac.za
   Google Scholar