Genomes to hits In Silico - A country path today, a highway tomorrow: A case study of Chikungunya

Current Pharmaceutical Design

Volumn 19, Issue 26, 2013, Pages 4687-4700

  Soni, Anjali ^a   Pandey, Khushhali M ^b   Ray, Pratima ^c   Jayaram, B ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

^b MAULANA AZAD NATIONAL INSTITUTE OF TECHNOLOGY   (India)

^c ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

CHIKV; Docking and scoring; Genome annotation; Lead molecule; Protein folding

Indexed keywords

ACETYLSALICYLIC ACID; CHLOROQUINE; GLYCOPROTEIN E1; GLYCOPROTEIN E2; IBUPROFEN; NAPROXEN; PARACETAMOL; PREDNISOLONE; PROTEOME; RIBAVIRIN;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BINDING SITE; BIOINFORMATICS; BODY FAT; CASE STUDY; CHIKUNGUNYA; CHIKUNGUNYA ALPHAVIRUS; COMPETITIVE INHIBITION; COMPUTER MODEL; CONFORMATIONAL TRANSITION; DATA BASE; DNA SEQUENCE; DRUG DESIGN; ENDOCYTOSIS; GENE STRUCTURE; GENOME ANALYSIS; HUMAN; HYDROGEN BOND; LIGAND BINDING; MACHINE LEARNING; MOLECULAR DOCKING; NERVOUS TISSUE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN SECONDARY STRUCTURE; PROTEIN TARGETING; PROTEIN TERTIARY STRUCTURE; SALIVARY GLAND; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STOP CODON; VIRION; VIRUS ENVELOPE;

ANTIVIRAL AGENTS; CHIKUNGUNYA VIRUS; COMPUTER SIMULATION; GENOME, VIRAL; PROTEIN STRUCTURE, TERTIARY; VIRAL PROTEINS;

EID: 84881330917     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/13816128113199990379     Document Type: Article

References (181)

1. Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-402.
2. Li Y, Chia N, Lauria M, Bundschuh R. A performance enhanced PSI-BLAST based on hybrid alignment. Bioinformatics 2011; 27: 31-7.
3. Standley DM, Toh H, Nakamura H. Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan. Proteins 2008; 72: 1333-51.
4. Khandelwal G, Jayaram B. A phenomenological model for predicting melting temperatures of DNA sequences. PLoS ONE 2010; 5: e12433.
5. Dutta S, Singhal P, Agrawal P, et al. A physicochemical model for analyzing DNA sequences. J Chem Inf Model 2006; 46: 78-85.
6. Singhal P, Jayaram B, Dixit SB, Beveridge DL. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 2008; 94: 4173-83.
7. Khandelwal G, Jayaram B. DNA-water interactions distinguish messenger RNA genes from transfer RNA genes. J. Am. Chem. Soc 2012; 134: 8814-16.
8. Khandelwal G, Gupta J, Jayaram B. DNA energetics based analyses suggest additional genes in prokaryotes. J Bio Sc 2012; 37: 433-44.
9. Shenoy SR, Jayaram B. Proteins: Sequence to Structure and Function-Current Status. Curr Protein Pept Sci 2010; 11: 498-514.
10. Jayaram B, Dhingra P. Towards creating complete proteomic structural databases of whole organisms. Curr Bioinform 2012; 7: 424-35.
11. Leopold PE, Montal M, Onuchic JN. Protein Folding Funnels-a Kinetic Approach to the Sequence Structure Relationship. Proc Natl Acad Sci USA 1992; 89: 8721.25.
12. Jayaram B, Dhingra P, Lakhani B, Shekhar S. Bhageerath-targeting the near impossible: pushing the frontiers of atomic models for protein tertiary structure prediction. J Chem Sci 2012; 124: 83-91. doi:10.1007/s12039-011-0189-x
13. Narang P, Bhushan K, Bose S, Jayaram B. A computational pathway for bracketing native-like structures for small alpha helical globular proteins. Phys Chem Chem Phys 2005; 7: 2364-75.
14. Narang P, Bhushan K, Bose S, Jayaram B. Protein structure evaluation using an all-atom energy based empirical scoring function. J Biomol Struct Dyn 2006; 23: 385-406.
15. Arora N, Jayaram B. The Strength of Hydrogen Bonds in Alpha Helices. J Comput Chem 1997; 18: 1245-52.
16. Surjit B. Dixit, R. Bhasin, E. Rajasekaran and B. Jayaram. Solvation Thermodynamics of Amino Acids: Assessment of the Electrostatic Contribution and Force Field Dependence. J. Chem. Soc. Farad. Trans 1997; 93: 1105-13.
17. Mittal A, Jayaram B, Shenoy S, Bawa TS. A Stoichiometry driven universal spatial organization of backbones of folded proteins: Are there Chargaff's rules for protein folding?. J Biomol Struct Dyn 2010; 28: 133-42.
18. Mittal A, Jayaram B. Backbones of folded proteins reveal novel invariant amino-acid neighborhoods. J Biomol Struct Dyn 2011; 28: 443-54.
19. Mittal A, Jayaram B. The Newest View on Protein Folding: Stoichiometric and Spatial Unity in Structural and Functional Diversity. J Biomol Struct Dyn 2011; 28: 669-74.
20. Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Curr Opin Struct Biol 2007; 17: 342.6.
21. Kim DE, Blum B, Bradley P, Baker D. Sampling Bottlenecks in De novo Protein Structure Prediction. J Mol Bio 2009; 393: 249.60.
22. Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol 1997; 4: 10.19.
23. Lindorff-Larsen K, Piana S, Palmo K, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010; 78: 1950-8.
24. Berka K, Laskowski RA, Hobza P, Vondrasek J. Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. J. Chem. Theory Comput 2010; 6: 2191.203.
25. Cooper S, Khatib F, Treuille A, et al. Predicting protein structures with a multiplayer online game. Nature 2010; 466: 756.60.
26. Faver JC, Benson ML, He X, et al. The energy computation paradox and ab initio protein folding. PLoS One 2011; 6: e18868.
27. Jayaram B, Bhushan K, Shenoy SR, et al. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Nucleic Acids Res 2006; 34: 6195-204.
28. Dhingra P, Mishra A, Rao S, Jayaram B. Bhageerath-H: A Homology ab initio Hybrid Webserver for Protein Tertiary Structure Prediction (Manuscript in preparation).
29. Mishra A, Rao S, Mittal A, Jayaram B. Capturing native protein structures with a physico-chemical metric (pcSM), BBA-Proteins & proteomics, 2013, under revision.
30. Dhingra P, Lakhani B, Jayaram B. Genarating native-like structures of soluble monomeric proteins via Bhageerath-H-a homology/ab initio hybrid method. J Comput Chem 2013 Under revision.
31. Lipinski CA. Lead-and drug-like compounds: the rule-of-five revolution. Drug Discov Today: Tech 2004; 1: 337-41.
32. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 1997; 46: 3-26.
33. Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 2000; 44: 235-49.
34. Shaikh SA, Jain T, Sandhu G, Latha N, Jayaram B. From drug target to leads-sketching a physicochemical pathway for lead molecule design in Silico. Curr Pharm Des 2007; 13: 3454-70.
35. Shaikh SA, Jain T, Sandhu G, Soni A, Jayaram B. From drug target to leads-sketching a physicochemical pathway for lead molecule design in Silico. Frontiers in Medicinal Chemistry, 2012, 6, 324-360. Eds: Atta ur Rahman, Allen B. Reitz and M. Iqbal Choudhary, Bentham Publishers. doi:10.2174/97816080546401120601
36. Jayaram B, Dhingra P, Mukherjee G, Perumal V. "Genomes to Hits: The Emerging Assembly Line In Silico", Proceedings of the Ranbaxy Science Foundation 17th Annual Symposium on "New Frontiers in Drug Design, Discovery and Development", 2012, Chapter 3, pages 13-35.
37. Das A, Kalra P, Latha N, Jayaram B. In Silico Trends in Thermodynamics and Kinetics of Binding-New Tools for De Novo Drug Design, in Recent Trends in Chemistry, Editors, Dr. M. M. Srivastava, Shalini Srivastava, 2002 Chapter-15, pp 218-234.
38. Gupta A, Gandhimathi A, Sharma P, Jayaram B. ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes. Protein Pept Lett 2007; 14: 632-46.
39. Jain T, Jayaram B. An all atom energy based computational protocol for predicting binding affinities of protein. ligand complexes. FEBS Lett 2005; 579: 6659-66.
40. Jain T, Jayaram B. Computational Protocol for Predicting the Binding Affinities of Zinc Containing Metalloprotein-Ligand Complexes. Proteins 2007; 67: 1167-78.
41. Singh T, Biswas D, Jayaram B. AADS-an automated active site identification, docking and scoring protocol for protein targets based on physico-chemical descriptors. J Chem Inf Model 2011; 51: 2515-27.
42. Mukherjee G, Jayaram B. A rapid scoring methodology based on physico-chemical descriptors of small molecules (RASPD) for identifying hits against a protein target. Phys Chem Chem Phys 2013; DOI:10.1039/C3CP44697B.
43. Shaikh SA, Ahmed SR, Jayaram B. A molecular thermodynamic view of DNA-drug interaction: A case study of 25 minor groove binders. Arch Biochem Biophys 2004; 429: 81-99.
44. Shaikh SA, Jayaram B. A Swift All-Atom Energy-Based Computational Protocol to Predict DNA-Ligand Binding Affinity and Tm. J Med Chem 2007; 50: 2240-4.
45. Jayaram B, Latha N, Jain T, Sharma P, Gandhimathi A, Pandey VS. Sanjeevini: A comprehensive active site directed lead design software. Indian J Chem A 2006; 45: 1834-37.
46. Jayaram B, Singh T, Mukherjee G, Mathur A, Shekhar S, and Shekhar V. Sanjeevini: A freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics 2012; 13: S7. doi:10.1186/1471-2105-13-S17-S7
47. Kalra P, Reddy TV, Jayaram B. Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease. Inhibitor Binding. J Med Chem 2001; 44: 4325-38.
48. Mukherjee G, Patra N, Barua P, Jayaram B. A Fast Empirical GAFF Compatible Partial Atomic Charge Assignment Scheme for Modeling Interactions of Small Molecules with Biomolecular Targets. J Comput Chem 2011; 32: 893-907.
49. Powers AM, Logue CH. Changing patterns of chikungunya virus: re-emergence of a zoonotic arbovirus. J Gen Virol 2007; 88: 2363.77.
50. Gubler DJ. Human arbovirus infections worldwide. Ann N Y Acad Sci 2001; 951: 13-24.
51. Thiboutot MM, Kannan S, Kawalekar OU, et al. Chikungunya: A Potentially Emerging Epidemic? PLoS Negl Trop Dis 2010; 4: e623.
52. Robinson MC. An epidemic of virus disease in Southern Province, Tanganyika Territory, in 1952.53. I. Clinical features. Trans R Soc Trop Med Hyg 1955; 49: 28.32.
53. Sumathy K, Ella KM. Genetic diversity of chikungunya virus, India 2006-2010: Evolutionary dynamics and serotype analyses. J Med Virol 2012; 84: 462-70.
54. Anyamba A, Linthicum KJ, Small JL et al. Climate teleconnections and recent patterns of human and animal disease outbreaks. PLoS Negl Trop Dis 2012; 6: e1465.
55. Ross RW. The Newala epidemic: III. The virus: isolation, pathogenic properties and relationship to the epidemic. J Hyg 1956; 54: 177-91.
56. Lumsden WH. An epidemic of virus disease in Southern Province, Tanganyika Territory, in 1952.53. II. General description and epidemiology. Trans R Soc Trop Med Hyg 1955; 49: 33.57.
57. Powers AM, Brault AC, Tesh RB, Weaver SC. Re-emergence of chikungunya and o. nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships. J Gen Virol 2000; 81: 471-9.
58. Arankalle VA, Shrivastava S, Cherian S, et al. Genetic divergence of Chikungunya viruses in India (1963-2006) with special reference to the 2005-2006 explosive epidemic. J Gen Virol 2007; 88: 1967-76.
59. Yergolkar PN, Tandale BV, Arankalle VA, et al. Chikungunya outbreaks caused by African genotype, India. Emerg Infect Dis 2006; 12:1580-3.
60. Ravi V. Re-emergence of chikungunya virus in India. Indian J Med Microbiol 2006; 24: 83-4.
61. Lahariya C, Pradhan SK. Emergence of chikungunya virus in Indian subcontinent after 32 years: A review. J Vector Borne Dis 2006; 43:151-60.
62. Tsetsarkin KA, McGee CE, Volk SM, Vanlandingham DL, Weaver SC, Higgs S. Epistatic roles of E2 glycoprotein mutations in adaption of chikungunya virus to Aedes albopictus and Ae. aegypti mosquitoes. PLoS One 2009; 4: e6835.
63. Sam IC, Chan YF, Chan SY, et al. Chikungunya virus of Asian and Central/East African genotypes in Malaysia. J Clin Virol 2009; 46:180-3.
64. Staples JE, Breiman RF, Powers AM. Chikungunya fever: an epidemiological review of a re-emerging infectious disease. Clin Infect Dis 2009; 49: 942-8.
65. Vassil St. Georgiev. Emerging and Re-emerging Infectious Diseases. National Institute of Allergy and Infectious Diseases, NIH Infectious Disease, 2009, Part I, 23-28, DOI: 10.1007/978-1-60327-297-1_4.
66. Department of Health and Human Services; Centers for Disease Control and Prevention; National Institutes of Health. Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th Edition. Washington DC: US Government Printing Office; 2007. Arboviruses and Related Zoonotic Viruses.
67. World Health Organization. Communicable Diseases Branch. Chikungunya fever, laboratory diagnosis of Chikungunya fevers. Geneva: World Health Organization 2007.
68. Rezza G. Re-emergence of Chikungunya and other scourges: the role of globalization and climate change. Ann Ist Super Sanita 2008; 44: 315-8.
69. Epstein PR. Chikungunya fever resurgence and global warming. Am J Trop Med Hyg 2007; 76: 403-4.
70. Tabachnick WJ. Challenges in predicting climate and environmental effects on vector-borne disease episystems in a changing world. J Exp Biol 2010; 213: 946-54.
71. Stock I. Chikungunya fever--expanded distribution of a reemerging tropical infectious disease. Med Monatsschr Pharm 2009; 32: 17-26.
72. Gould EA, Gallian P, De Lamballerie X, Charrel RN. First cases of autochthonous dengue fever and chikungunya fever in France: from bad dream to reality! Clin Microbiol Infect 2010; 16: 1702-4.
73. Weaver SC, Reisen WK. Present and future arboviral threats. Antiviral Res 2010; 85: 328-45.
74. Moulay D, Aziz-Alaoui MA, Cadivel M. The chikungunya disease: modeling, vector and transmission global dynamics. Math Biosci 2011; 229: 50-63.
75. Lam SK, Chua KB, Hooi PS et al. Chikungunya infection-emerging disease in Malaysia. Southeast Asian J Trop Med Public Health 2001; 32: 447.51.
76. Laras K, Sukri NC, Larasati RP, et al. Tracking the re-emergence of epidemic chikungunya virus in Indonesia. Trans R Soc Trop Med Hyg 2005; 99: 128.41.
77. Mathew T, Tiruvengadam KV. Further studies on the isolate of Chikungunya from the Indian repatriates of Burma. Indian J Med Res 1973; 61: 517-20.
78. Pastorino B, Muyembe-Tamfum JJ, Bessaud M, et al. Epidemic resurgence of Chikungunya virus in Democratic Republic of the Congo: identification of a new central African strain. J Med Virol 2004; 74: 277-82.
79. Rezza G, Nicoletti L, Angelini K, et al. Infection with chikungunya virus in Italy: an outbreak in a temperate region. Lancet 2007; 370: 1840-6.
80. Borgherini G, Poubeau P, Staikowsky F, et al. Outbreak of chikungunya on Reunion Island: early clinical and laboratory features in 157 adult patients. Clin Infect Dis 2007; 44: 1401-7.
81. Lemant J, Boisson V, Winer A, et al. Serious acute chikungunya virus infection requiring intensive care during the Reunion Island outbreak in 2005.2006. Crit Care Med 2008; 36: 2536-41.
82. Selvavinayagam TS. Chikungunya fever outbreak in Vellore, South India. Indian J Community Med 2007; 32: 286-7.
83. Dwibedi B, Sabat J, Mahapatra N, Kar SK, Kerketta AS, et al. Rapid spread of chikungunya virus infection in Orissa: India. Indian J Med Res 2011; 133: 316.21.
84. Dutta P, Khan SA, Khan AM, Borah J, Chowdhury P, Mahanta J. First evidence of chikungunya virus infection in Assam, Northeast India. Trans R Soc Trop Med Hyg 2011; 105: 355.7.
85. Reiter P, Fontenille D, Paupy C. Aedes albopictus as an epidemic vector of chikungunya virus: another emerging problem? Lancet Infect Dis 2006; 6: 463-4.
86. H. Townson, M.B. Nathan. Resurgence of Chikungunya. Trans R Soc Trop Med Hyg 2008; 102: 308-9.
87. Srikanth P, Sarangan G, Mallilankaraman K, et al. Molecular characterization of Chikungunya virus during an outbreak in South India. Indian J Med Microbiol 2010; 28: 299-302.
88. Santhosh SR, Dash PK, Parida M, Khan M, Rao PV. Appearance of E1: A226V mutant Chikungunya virus in coastal Karnataka, India during 2008 outbreak. Virol J 2009; 6: 172.
89. Kannan M, Rajendran R, Sunish IP, et al. A study on Chikungunya outbreak during 2007 in Kerala, South India. Indian J Med Res 2009; 129: 311-5.
90. Schuffenecker I, Iteman I, Michault A, et al. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 2006; 3: e263.
91. Manimunda SP, Sugunan AP, Rai SK, et al. Outbreak of Chikungunya Fever, Dakshina Kannada District, South India. Am J Trop Med Hyg 2010; 83: 751-54.
92. Ray P, Ratagiri VH, Kabra SK, et al. Chikungunya Infection in India: Results of a prospective hospital based multi-centric study. PLoS ONE 2012; 7(2): e30025. doi:10.1371/journal.pone.0030025.
93. Chem YK, Zainah S, Berendam SJ, Rogayah TA, Khairul AH, Chua KB. Molecular epidemiology of chikungunya virus in Malaysia since its first emergence in 1998. Med J Malaysia 2010; 65(1): 31-5.
94. M Naresh Kumar CV, Anthony Johnson AM, R Sai Gopal DV. Molecular characterization of chikungunya virus from Andhra Pradesh, India & phylogenetic relationship with Central African isolates. Indian J Med Res 2007; 126: 534-40.
95. Dash PK, Parida MM, Santhosh SR, et al. East Central South African genotype as the causative agent in reemergence of Chikungunya outbreak in India. Vector Borne Zoonotic Dis 2007; 7: 519-27.
96. Diallo M, Thonnon J, Traore-Lamizana M, Fontenille D. Vectors of Chikungunya virus in Senegal: current data and transmission cycles. Am J Trop Med Hyg 1999; 60: 281-6.
97. Tsetsarkin KA, Vanlandingham DL, McGee CE, Higgs S. A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog 2007; 3: e201.
98. Vazeille M, Moutailler S, Coudrier D, et al. Two chikungunya isolates from the outbreak of La Reunion (Indian Ocean) exhibit different patterns of infection in the mosquito, Aedes albopictus. PLoS One 2007; 2: e1168.
99. Mourya DT, Yadav P. Vector biology of dengue & chikungunya viruses. Indian J Med Res 2006; 124: 475.80.
100. Pages F, Peyrefitte CN, Mve MT, et al. Aedes albopictus mosquito: the main vector of the 2007 Chikungunya outbreak in Gabon. PLoS One 2009; 4:e4691.
101. Vazeille M, Martin E, Mousson L, Failloux AB. Chikungunya, a new threat propagated by the cosmopolite Aedes albopictus. BMC Proceedings 2011; 5: O8.
102. N. Pardigon. The biology of Chikungunya: a brief review of what we still do not know. Pathol Biol 2009; 57: 127.32.
103. Martin E, Moutailler S, Madec Y, Failloux A-B. Differential responses of the mosquito Aedes albopictus from the Indian Ocean region to two chikungunya isolates. BMC Ecology 2010; 10: 8.
104. Ng LC, Tan LK, Tan CH, et al. Entomologic and virologic investigation of Chikungunya, Singapore. Emerg Infect Dis 2009; 15:1243-9.
105. Tsetsarkin KA, McGee CE, Higgs S. Chikungunya virus adaptation to Aedes albopictus mosquitoes does not correlate with acquisition of cholesterol dependence or decreased pH threshold for fusion reaction. Virology 2011; 8: 376.
106. Tsetsarkin KA, Chen R, Leal G, et al. Chikungunya virus emergence is constrained in Asia by lineage-specific adaptive landscapes. Proc Natl Acad Sci USA 2011; 108: 7872-7.
107. Hapuarachchi HC, Bandara KB, Sumanadasa SD, Hapugoda MD, Lai YL, Lee KS. Re-emergence of chikungunya virus in Southeast Asia: virological evidence from Sri Lanka and Singapore. J Gen Virol 2010; 91: 1067-76.
108. Volk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. J Virol 2010; 84: 6497.504.
109. Chretien JP, Anyamba A, Bedno SA, et al. Drought-associated Chikungunya emergence along coastal East Africa. Am J Trop Med Hyg 2007; 76: 405-7.
110. Anish TS, Vijayakumar K, Leela Itty Amma KR. Domestic and environmental factors of chikungunya-affected families in Thiruvananthapuram (Rural) district of Kerala, India. J Global Infect Dis 2011; 3: 32-6.
111. Chakkaravarthy VM, Vincent S, Ambrose T. Novel Approach of Geographic Information Systems on Recent Out-Breaks of Chikungunya in Tamil Nadu, India. J Environ Sci Technol 2011; 4: 387-94.
112. Lakshmi V, Neeraja M, Subbalaxmi MVS, et al. Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India. Clin Infect Dis 2008; 46: 1436-42.
113. Her Z, Kam YW, Lin RT, Ng LF. Chikungunya: a bending reality. Microbes Infect 2009; 11: 1165.76.
114. Kondekar S, Gogtay NJ. Why Chikungunya is called chikungunya. J Postgrad Med 2006; 52: 307.
115. Sudeep AB and Parashar D. Chikungunya: an overview. J Biosci 2008; 33: 443.9.
116. Yazdani R, Kaushik VV. Chikungunya fever. Rheumatology 2007; 46: 1214-15.
117. De Andrade DC, Jean S, Clavelou P, Dallel R, Bouhassira D. Chronic pain associated with the Chikungunya Fever: long lasting burden of an acute illness. BMC Infect Dis 2010; 10: 31-7.
118. Suhrbier A, La Linn M. Clinical and pathologic aspects of arthritis due to Ross River virus and other alphaviruses. Curr Opin Rheumatol 2004; 16: 374.9.
119. Dubrulle M, Mousson L, Moutailler S, Vazeille M, Failloux A-B. Chikungunya Virus and Aedes Mosquitoes: Saliva Is Infectious as soon as Two Days after Oral Infection. PLoS ONE 2009; 4: e5895.
120. Chamberlain RW. Epidemiology of arthropod-borne togaviruses: The role of arthropods as hosts and vectors and of vertebrate hosts in natural transmission cycles. In The Togaviruses: Biology, structure, replication. R.W. Schlesinger, ed. (Orlando: Academic), 1980; pp. 175-227.
121. Mourya DT, Ranadive SN, Gokhale MD, Barde PV, Padbidri VS, Banerjee K. Putative Chikungunya virus-specific receptor proteins on the midgut brush border membrane of Aedes aegypti mosquito. Indian J Med Res 1998; 107: 10.4.
122. Kielian M, Rey FA. Virus membrane-fusion proteins: more than one way to make a hairpin. Nat Rev Microbiol 2006; 4: 67.76.
123. Marsh M, Helenius A. Virus entry: open sesame. Cell 2006; 124: 729.40.
124. Lu YE, Cassese T, Kielian M. The cholesterol requirement for Sindbis virus entry and exit and characterization of a spike protein region involved in cholesterol dependence. J Virol 1999; 73: 4272-8.
125. Ahn A, Schoepp RJ, Sternberg D, Kielian M. Growth and stability of a cholesterol-independent Semliki Forest virus mutant in mosquitoes. Virology 1999; 262: 452-6.
126. Solignat M, Gay B, Higgs S, Briant L, Devaux C. Replication cycle of chikungunya: a re-emerging arbovirus. Virology; 393: 183-97.
127. Khan AH, Morita K, Parquet Md Mdel C, Hasebe F, Mathenge EG, Igarashi A. Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site. J Gen Virol 2002; 83: 3075-84.
128. Ou JH, Strauss EG, Strauss JH. Comparative studies of the 3.-terminal sequences of several alphavirus RNAs. Virology 1981; 109: 281-9.
129. Ou JH, Trent DW, Strauss JH. The 3.-noncoding regions of alphavirus RNAs contain repeating sequences. J Mol Biol 1982; 156: 719-30.
130. Ou JH, Strauss EG, Strauss JH. The 5.-terminal sequences of the genomic RNAs of several alphaviruses. J Mol Biol 1983; 168: 1-15.
131. Pfeffer M, Kinney RM, Kaaden OR. The alphavirus 3.-nontranslated region: size heterogeneity and arrangement of repeated sequence elements. Virology 1998; 240: 100-8.
132. Schwartz O, Albert ML. Biology and pathogenesis of chikungunya virus. Nat Rev Microbiol 2010; 8: 491-500.
133. Simizu B, Yamamoto K, Hashimoto K, Ogata T. Structural proteins of Chikungunya virus. J Virol 1984; 51: 254-58.
134. Weaver, S. C., Frey, T. K., Huang, H. V., Kinney, R. M., Rice, C. M., Roehrig, J. T., Shope, R. E. & Strauss, E. G. (2005). Togaviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 999.1008. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. Amsterdam: Elsevier Academic Press.
135. Schlesinger, M. & Schlesinger, S. (1986). Formation and assembly of alphavirus glycoproteins. In The Togaviridae and Flaviviridae, pp. 121.148. Edited by S. Schelsinger & M. J. Schlesinger. New York: Plenum Publishing Corp.
136. Strauss EG, Strauss JH. (1986). Structure and replication of the alphavirus genome. In The Togaviridae and Flaviviridae, pp. 35-90. Edited by S. Schlesinger & M. J. Schlesinger. New York: Plenum Press.
137. Kääriäinen L, Takkinen K, Keränen S, Söderlund H. Replication of the genome of alphaviruses. J Cell Sci Suppl 1987; 7: 231-50.
138. Strauss JH, Strauss EG. The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 1994; 58: 491-562.
139. Ten Dam E, Flint M, Ryan MD. Virus-coded proteinases of the Togaviridae. J Gen Virol 1999; 80: 1879-88.
140. Lemm JA, Rümenapf T, Strauss EG, Strauss JH, Rice CM. Polypeptide requirements for assembly of functional Sindbis virus replication complexes: a model for the temporal regulation of minusand plus-strand RNA synthesis. EMBO J 1994; 13: 2925-34.
141. Voss JE, Vaney MC, Duquerroy S, et al. Glycoprotein organization of Chikungunya virusparticles revealed by X-ray crystallography. Nature 2010; 468:709-12.
142. Söderlund H, Ulmanen I. Transient association of Semliki Forest virus capsid protein with ribosomes. J Virol 1977; 24: 907-9.
143. Choi H-K, Tong L, Minor W, et al. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 1991; 354: 37-43.
144. Ulmanen, I., Söderlund, H., and Kääriäinen, L. Semliki Forest virus capsid protein associates with the 60 S ribosomal subunit in infected cells. J Virol 1976; 20: 203-10.
145. Garoff H, Simons K, Dobberstein B. Assembly of the Semliki Forest virus membrane glycoproteins in the membrane of the endoplasmic reticulum in vitro. J Mol Biol 1978; 124: 587-600.
146. Sariola M, Saraste J, Kuismanen E. Communication of post-Golgi elements with early endosytic pathway:regulation of endoproteolytic cleavage of Semliki Forest virus p62 precursor. J Cell Sci 1995; 108: 2465-75.
147. Wahlberg JM, Boere WAM, Garoff H. The heterodimeric association between the membrane proteins of Semliki Forest virus changes its sensitivity to low pH during virus maturation. J Virol 1989; 63: 4991-7.
148. Zhao H, Garoff H. Role of cell surface spikes in alphavirus budding. J Virol 1992; 66: 7089-95.
149. Suomalainen M, Liljeström P, Garoff H. Spike proteinnucleocapsid interactions drive the budding of alphaviruses. J Virol 1992; 66: 4737-47.
150. Queyriaux B, Simon F, Grandadam M, Michel R, Tolou H, Boutin JP. Clinical burden of chikungunya virus infection. Lancet Infect Dis 2008; 8: 2-3.
151. Mourya DT, Mishra AC. Chikungunya fever. Lancet 2006; 368: 186.7.
152. Mohan A, Kiran DHN, Manohar IC, Kumar DP. Epidemology, clinical manifestations and diagnosis of chikungunya fever: lessons learned from the re-emerging epidemic. Indian J Dermatol 2010; 55: 54.63.
153. Ali Ou Alla S, Combe B. Arthritis after infection with Chikungunya virus. Best Pract Res Clin Rheumatol 2011; 25: 337-46.
154. Brighton SW, Prozesky OW, De La Harpe AL. Chikungunya virus infection: a retrospective study of 107 cases. S Afr Med J 1982; 63: 313.15.
155. Vijayakumar KP, Anish TS, George B, Lawrence T, Muthukkutty SC, Ramachandran R. Clinical profile of chikungunya patients during the epidemic of 2007 in Kerala, India. J Global Infect Dis 2011; 3: 221-6.
156. Couderc T, Lecuit M. Focus on Chikungunya pathophysiology in human and animal models. Microbes Infect 2009; 11: 1197-1205.
157. Robin S, Ramful D, Le Seach' F, Jaffar-Bandjee MC, Rigou G, Alessandri JL. Neurologic manifestations of pediatric chikungunya infection. J Child Neurol 2008; 23: 1028-35.
158. Pakran J, George M, Riyaz N, et al. Purpuric macules with vesiculobullous lesions: a novel manifestation of chikungunya. Int J Dermatol 2011; 50: 61-9.
159. Parida MM, Santhosh SR, Dash PK, et al. Rapid and real-time detection of Chikungunya virus by reverse transcription loopmediated isothermal amplification assay. J Clin Microbiol 2007; 45: 351-7.
160. Yap G, Pok KY, Lai YL, et al. Evaluation of chikungunya diagnostic assays: differences in sensitivity of serology assays in two independent outbreaks. PLoS Negl Trop Dis 2010; 4: e753.
161. Edwards CJ, Welch SR, Chamberlain J, et al. Molecular diagnosis and analysis of Chikungunya virus. J Clin Virol 2007; 39: 271.5.
162. Mishra B, Sharma M, Pujhari SK, et al. Utility of multiplex reverse transcriptase-polymerase chain reaction for diagnosis and serotypic characterization of dengue and chikungunya viruses in clinical samples. Diagn Microbiol Infect Dis 2011; 71: 118-25.
163. Alphey L, Benedict M, Bellini R, et al. Sterile-Insect Methods for Control of Mosquito-Borne Diseases: An Analysis. Vector Borne Zoonotic Dis 2010; 10: 295-311.
164. Levitt NH, Ramsburg HH, Hasty SE, Repik PM, Cole FE Jr, Lupton HW. Development of an attenuated strain of Chikungunya virus for use in vaccine production. Vaccine 1986; 4: 157-62.
165. Harrison VR, Eckels KH, Bartelloni PJ, Hampton C. Production and valuation of a formalin killed chikungunya vaccine. J Immunol 1971; 107: 643-7.
166. Edelman R, Tacket CO, Wasserman SS, Bodison SA, Perry JG and Mangiafico JA. Phase II safety and immunogenicity study of live chikungunya virus Vaccine TSI-GSD-218. Am J Trop Med Hyg 2000; 62: 681-5.
167. Akahata W, Yang ZY, Andersen H, et al. A VLP vaccine for epidemic Chikungunya virus protects nonhuman primates against infection. Nat Med 2010; 16: 334-8.
168. Anbarasu K, Manisenthil KK, Ramachandran S. Antipyretic, antiinflammatory and analgesic properties of nilavembu kudineer choornam: a classical preparation used in the treatment of chikungunya fever. Asian Pac J Trop Med 2011; 4: 819-23.
169. Delogu I, Pastorino B, Baronti C, Nougairède A, Bonnet E, de Lamballerie X. In vitro antiviral activity of arbidol against Chikungunya virus and characteristics of a selected resistant mutant. Antiviral Res 2011; 90: 99-107.
170. Partidos CD, Weger J, Brewoo J, et al. Probing the attenuation and protective efficacy of a candidate chikungunya virus vaccine in mice with compromised interferon (IFN) signaling. Vaccine 2011; 29: 3067-73.
171. Wang D, Suhrbier A, Penn-Nicholson A, et al. A complex adenovirus vaccine against chikungunya virus provides complete protection against viraemia and arthritis. Vaccine 2011; 29: 2803-9.
172. De Lamballerie X, Ninove L, Charrel RN. Antiviral treatment of chikungunya virus infection. Infect Disord Drug Targets 2009; 9: 101-4.
173. Khan M, Santhosh SR, Tiwari M, Lakshmana Rao PV, Parida M. Assessment of in vitro prophylactic and therapeutic efficacy of chloroquine against Chikungunya virus in vero cells. J Med Virol 2010; 82: 817-24.
174. Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead Discovery Using Molecular Docking. Curr Opin Chem Biol 2002; 6: 439-46.
175. Cross JB, Thompson DC, Rai BK, et al. Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy. J Chem Inf Model 2009; 49: 1455-74.
176. Di L, Kerns EH, Carter GT. Drug-like property concepts in pharmaceutical design. Curr Pharm Des 2009; 15: 2184-94.
177. Wang J. Comprehensive assessment of ADMET risks in drug discovery. Curr Pharm Des 2009; 15: 2195-219.
178. Raunio H. In silico toxicology-non-testing methods. Front Pharmacol 2011; 2: 33.
179. Zhu F, Qin C, Tao L, et al. Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting. Proc Natl Acad Sci USA 2011; 108:12943-8.
180. Tang W, Lu AY. Drug metabolism and pharmacokinetics in support of drug design. Curr Pharm Des 2009; 15: 2170-83.
181. Férriz JM, Vinsová J. Prodrug design of phenolic drugs. Curr Pharm Des 2010; 16: 2033-52.