Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus

Journal of Molecular Modeling

Volumn 20, Issue 5, 2014, Pages

  Nguyen, Phuong T V ^a   Yu, Haibo ^a   Keller, Paul A ^a  

^a UNIVERSITY OF WOLLONGONG   (Australia)

Author keywords

Chikungunya virus; Molecular docking; Molecular dynamics simulations; nsP3 macro domain; Virtual screening

Indexed keywords

NONSTRUCTURAL PROTEIN 3; ADENOSINE DIPHOSPHATE RIBOSE; ANTIVIRUS AGENT; ENZYME INHIBITOR; NSP3 PROTEIN, VIRUS; PROTEIN BINDING; VIRUS PROTEIN;

ARTICLE; CHIKUNGUNYA ALPHAVIRUS; COMPUTER MODEL; DATA BASE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DOMAIN; SCREENING; VIRTUAL REALITY; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; CHIKUNGUNYA VIRUS; COMPUTER AIDED DESIGN; DRUG DATABASE; DRUG DESIGN; DRUG EFFECTS; ENZYME ACTIVE SITE; ENZYME STABILITY; ENZYMOLOGY; HYDROGEN BOND; METABOLISM; MOLECULARLY TARGETED THERAPY; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; REPRODUCIBILITY; STRUCTURE ACTIVITY RELATION; VALIDATION STUDY;

CHIKUNGUNYA VIRUS;

ADENOSINE DIPHOSPHATE RIBOSE; ANTIVIRAL AGENTS; BINDING SITES; CATALYTIC DOMAIN; CHIKUNGUNYA VIRUS; COMPUTER-AIDED DESIGN; DATABASES, PHARMACEUTICAL; DRUG DESIGN; ENZYME INHIBITORS; ENZYME STABILITY; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; MOLECULAR TARGETED THERAPY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; REPRODUCIBILITY OF RESULTS; STRUCTURE-ACTIVITY RELATIONSHIP; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84901581130     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2216-6     Document Type: Article

References (37)

1. Her Z, Kam Y-W, Lin RTP, Ng LFP (2009) Chikungunya: a bending reality. Microbes Infect 11(14-15):1165-1176. doi:10.1016/j.micinf.2009.09.004
2. Robinson MC (1955) An epidemic of virus disease in Southern Province, Tanganyika Territory, in 1952-53. I. Clinical features. Trans R Soc Trop Med Hyg 49(1):28. doi:10.1016/0035-9203(55) 90080-8
3. Powers AM, Logue CH (2007) Changing patterns of chikungunya virus: re-emergence of a zoonotic arbovirus. J Gen Virol 88(Pt 9): 2363-2377. doi:10.1099/vir.0.82858-0 (Pubitemid 47323881)
4. Schwartz O, Albert ML (2010) Biology and pathogenesis of chikungunya virus. Nat Rev Microbiol 8(7):491-500. doi:10.1038/nrmicro2368
5. Ziegler SA, Lu L, da Rosa AP, Xiao SY, Tesh RB (2008) An animal model for studying the pathogenesis of chikungunya virus infection. Am J Trop Med Hyg 79(1):133-139 (Pubitemid 351957217)
6. Queyriaux B, Simon F, Grandadam M, Michel R, Tolou H, Boutin J-P (2008) Clinical burden of chikungunya virus infection. Lancet Infect Dis 8(1):2 - 3. doi:10.1016/s1473-3099(07)70294-3
7. Santhosh SR, Dash PK, ParidaMM, KhanM, TiwariM, Lakshmana Rao PV (2008) Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates. Virus Res 135(1):36-41. doi:10.1016/j.virusres.2008. 02.004
8. Chandak NH, Kashyap RS, Kabra D, Karandikar P, Saha SS, Morey SH, Purohit HJ, Taori GM, Daginawala HF (2009) Neurological complications of Chikungunya virus infection. Neurol India 57(2): 177-180. doi:10.4103/0028-3886.51289
9. Singh SK, Unni SK (2011) Chikungunya virus: host pathogen interaction. Rev Med Virol 21(2):78-88. doi:10.1002/rmv.681
10. Sourisseau M, Fsihi H, Frenkiel M-P, Blanchet F, Afonso PV, Ceccaldi P-E, Ozden S, Gessain A, Schuffenecker I, Verhasselt B, Zamborlini A, Schilte C, Saïb A, Rey FA, Arenzana-Seisdedos F, Desprès P, Michault A, Albert ML, Schwartz O, Casartelli N, Trouillet C, Guivel-Benhassine F, Rudnicka D, Sol-Foulon N, Le Roux K, Prevost M-C (2007) Characterization of reemerging chikungunya virus. Plos Pathog 3(6):e89-e89. doi:10.1371/journal.ppat.0030089
11. Rashad AA, Mahalingam S, Keller PA (2014) Chikungunya virus: emerging targets and new opportunities for medicinal chemistry. J Med Chem 57:1147-1166. doi:10.1021/jm400460d
12. Rashad AA, Keller PA (2013) Structure based design towards the identification of novel binding sites and inhibitors for the chikungunya virus envelope proteins. J Mol Graph Model 44:241-252. doi:10.1016/j.jmgm.2013.07.001
13. Voss J, Vaney MC, Duquerroy S, Vonrhein C, Ginard-Blanc C, Crublet E, Thompson A, Bricogne G, Rey FA (2010) Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Nature 468(7324):709-712. doi:10.1038/nature09555
14. Singh KD, Kirubakaran P, Nagarajan S, Sakkiah S, Muthusamy K, Velmurgan D, Jeyakanthan J (2012) Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease. J Mol Model 18(1):39-51. doi:10.1007/s00894-011-1018-3
15. Gould EA, Delogu I, Forrester N, Khasnatinov M, Gritsun T, de Lamballerie X, Canard B, Coutard B, Malet H, Morin B, Jamal S, Weaver S, Gorbalenya A, Moureau G, Baronti C (2010) Understanding the alphaviruses: recent research on important emerging pathogens and progress towards their control. Antivir Res 87(2):111-124. doi:10.1016/j.antiviral.2009.07.007
16. Rungrotmongkol T, Nunthaboot N, Malaisree M, Kaiyawet N, Yotmanee P, Meeprasert A, Hannongbua S (2010) Molecular insight into the specific binding of ADP-ribose to the nsP3macro domains of chikungunya and venezuelan equine encephalitis viruses: molecular dynamics simulations and free energy calculations. J Mol Graph Model 29(3):347-353. doi:10.1016/j.jmgm.2010.09.010
17. Malet H, Lafitte D, Ferron F, Lescar J, Gorbalenya AE, de Lamballerie X, Canard B, Coutard B, Jamal S, Dutartre H, Papageorgiou N, Neuvonen M, Ahola T, Forrester N, Gould EA (2009) The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket. J Virol 83(13):6534. doi:10.1128/JVI.00189-09
18. LaStarza MW, Lemm JA, Rice CM (1994) Genetic analysis of the nsP3 region of Sindbis virus: evidence for roles in minusstrand and subgenomic RNA synthesis. J Virol 68(9):5781-5791 (Pubitemid 24258594)
19. Dé I, Fata-Hartley C, Sawicki SG, Sawicki DL (2003) Functional analysis of nsP3 phosphoprotein mutants of Sindbis virus. J Virol 77(24):13106-13116. doi:10.1128/jvi.77.24.13106-13116.2003 (Pubitemid 37494306)
20. Wang YF, Sawicki SG, Sawicki DL (1994) Alphavirus nsP3 functions to form replication complexes transcribing negative-strand RNA. J Virol 68(10):6466-6475 (Pubitemid 24294897)
21. Lastarza MW, Grakoui A, Rice CM (1994) Deletion and duplication mutations in the C-terminal nonconserved region of sindbis virus nsP3: effects on phosphorylation and on virus replication in vertebrate and invertebrate cells. Virology 202(1):224-232. doi:10.1006/viro.1994.1338 (Pubitemid 24241994)
22. Neuvonen M, Ahola T (2009) Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites. J Mol Biol 385(1):212-225. doi:10.1016/j.jmb.2008.10.045
23. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455-461. doi:10.1002/jcc.21334
24. Accelrys Software Inc. (2013) Discovery Studio modeling environment, 40th edn. Accelrys Software Inc., San Diego
25. Huang B (2009) MetaPocket: a meta approach to improve protein ligand binding site prediction. OMICS 13(4):325-330. doi:10.1089/omi.2009.0045
26. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46:3-26. doi:10.1016/s0169-409x(96)00423-1
27. Phillips JC, Schulten K, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781-1802. doi:10. 1002/jcc.20289
28. MacKerell AD, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Bashford D, ReiherWE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz- Kuczera J, Yin D, Karplus M, Bellott DRL, Evanseck JD, FieldMJ, Fischer S, Gao J, Guo H (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys ChemB 102(18):3586-3616. doi:10.1021/jp973084f (Pubitemid 128576688)
29. Case DA, Woods RJ, Cheatham RTE, Darden T, Gohlke H, Luo R, Merz JKM, Onufriev A, Simmerling C, Wang B (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668-1688. doi:10.1002/jcc.20290 (Pubitemid 43076180)
30. Ulrich E, Lalith P, Max LB, Tom D, Hsing L, Lee GP (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577-8593. doi:10.1063/1.470117
31. Brooks BR, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Brooks RCL, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Mackerell JAD, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545-1614. doi:10.1002/jcc.21287
32. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph Model 14(1):33 -38. doi:10.1016/02637855(96)00018-5
33. Trott O, Olson AJ (2010) Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455-461. doi:10.1002/jcc.21334
34. Badrinarayan P, Sastry GN (2011) Virtual high throughput screening in new lead identification. Comb Chem High Throughput Screen 14(10):840-860. doi:10.2174/138620711797537102
35. van Gunsteren WF, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A (2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed Engl 45(25):4064-4092. doi:10.1002/anie.200502655
36. Bruno A, Guadix AE, Costantino G (2009) Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions. J Chem Inf Model 49(6):1602-1616. doi:10.1021/ci900067g
37. Rajgaria R, McAllister SR, Floudas CA (2009) Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. Proteins 74(4):929-947. doi:10.1002/prot.22202