In silico docking of methyl isocyanate (MIC) and its hydrolytic product (1, 3-dimethylurea) shows significant interaction with DNA Methyltransferase 1 suggests cancer risk in Bhopal-Gas-Tragedy survivors

  • Khan, Inbesat (School of Biotechnology, Rajiv Gandhi Technological University) ;
  • Senthilkumar, Chinnu Sugavanam (Clinical Cytogenetics Laboratory, Department of Research, Jawaharlal Nehru Cancer Hospital & Research Centre) ;
  • Upadhyay, Nisha (School of Biotechnology, Rajiv Gandhi Technological University) ;
  • Singh, Hemant (School of Biotechnology, Rajiv Gandhi Technological University) ;
  • Sachdeva, Meenu (School of Biotechnology, Rajiv Gandhi Technological University) ;
  • Jatawa, Suresh Kumar (School of Biotechnology, Rajiv Gandhi Technological University) ;
  • Tiwari, Archana (School of Biotechnology, Rajiv Gandhi Technological University)
  • Published : 2015.12.03


DNA methyltransferase 1 (DNMT1) is a relatively large protein family responsible for maintenance of normal methylation, cell growth and survival in mammals. Toxic industrial chemical exposure associated methylation misregulation has been shown to have epigenetic influence. Such misregulation could effectively contribute to cancer development and progression. Methyl isocyanate (MIC) is a noxious industrial chemical used extensively in the production of carbamate pesticides. We here applied an in silico molecular docking approach to study the interaction of MIC with diverse domains of DNMT1, to predict cancer risk in the Bhopal population exposed to MIC during 1984. For the first time, we investigated the interaction of MIC and its hydrolytic product (1,3-dimethylurea) with DNMT1 interacting (such as DMAP1, RFTS, and CXXC) and catalytic (SAM, SAH, and Sinefungin) domains using computer simulations. The results of the present study showed a potential interaction of MIC and 1,3-dimethylurea with these domains. Obviously, strong binding of MIC with DNMT1 interrupting normal methylation will lead to epigenetic alterations in the exposed humans. We suggest therefore that the MIC-exposed individuals surviving after 1984 disaster have excess risk of cancer, which can be attributed to alterations in their epigenome. Our findings will help in better understanding the underlying epigenetic mechanisms in humans exposed to MIC.


Molecular docking;in silico interaction;methyl isocyanate (MIC);1,3-dimethylurea;DNMT1


  1. Baccarelli A, Bollati V (2009). Epigenetics and environmental chemicals. Current Opinion Pedia, 21, 243.
  2. Bashtrykov P, Jankevicius G, Smarandache A, et al (2012). Specificity of Dnmt1 for methylation of hemimethylated CpG sites resides in its catalytic domain. Chemistry & Biol, 19, 572-8.
  3. Baur X, Marek W, Ammon J, et al (1994). Respiratory and other hazards of isocyanates. Int Arch Occ Env health, 66, 141-152.
  4. Bezek S, Ujhazy E, Mach M, et al (2008). Developmental origin of chronic diseases: toxicological implication. Interdiscipli Toxicol, 1, 29-31.
  5. Bucher JR, Uraih L (1989). Carcinogenicity and pulmonary pathology associated with a single 2-hour inhalation exposure of laboratory rodents to methyl isocyanate. J Nat Cancer Inst, 81, 1586-7.
  6. Chen T, Li E (2006). Establishment and maintenance of DNA methylation patterns in mammals. DNA Methylation: Basic Mechanisms. Springer, 179-201.
  7. Clements EG, Mohammad HP, Leadem BR, et al (2012). DNMT1 modulates gene expression without its catalytic activity partially through its interactions with histonemodifying enzymes. Nucleic Acids Res, 40, 4334-46.
  8. Conner M, Rubinson H, Ferguson J, et al (1987). Evaluation of sister chromatid exchange and cytotoxicity in murine tissues in vivo and lymphocytes in vitro following methyl isocyanate exposure. Environ Health Perspectives, 72, 177.
  9. Dante R, Dante-Paire J, Rigal D, et al (1991). Methylation patterns of long interspersed repeated DNA and alphoid repetitive DNA from human cell lines and tumors. Anticancer res, 12, 559-63.
  10. De S (2012). Retrospective analysis of lung function abnormalities of Bhopal gas tragedy affected population. Indian J Med Res, 135, 193.
  11. De S (2013). Annual change in spirometric parameters among patients affected in Bhopal gas disaster: a retrospective observational study. Lung India, 30, 103.
  12. Dhe-Paganon S, Syeda F, Park L (2011). DNA methyl transferase 1: regulatory mechanisms and implications in health and disease. Int J Biochem Mol Biol, 2, 58.
  13. Dikshit RP, Kanhere S (1999). Cancer patterns of lung, oropharynx and oral cavity cancer in relation to gas exposure at Bhopal. Cancer Causes & Control, 10, 627-36.
  14. Ennever FK, Rosenkranz HS (1987). Evaluating the potential for genotoxic carcinogenicity of methyl isocyanate. Toxicol Appl Pharmacol, 91, 502-5.
  15. Finkelstein JD (1990). Methionine metabolism in mammals. J Nutri Biochem, 1, 228-237.
  16. Fraga MF, Ballestar E, Paz MF, et al (2005). Epigenetic differences arise during the lifetime of monozygotic twins. Pro Nat Aca Sci USA, 102, 10604-9.
  17. Friesner RA, Banks JL, Murphy RB, et al (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47, 1739-49.
  18. Friesner RA, Murphy RB, Repasky MP, et al (2006). Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem, 49, 6177-96.
  19. Gassert T, Mackenzie C, Muir KM, et al (1986). Long term pathology of lung, eye, and other organs following acute exposure of rats to methyl isocyanate. Lancet, 2, 1403.
  20. Greenwood JR, Calkins D, Sullivan AP, et al (2010). Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. J Computer-aided Mol Design, 24, 591-604.
  21. Guo JU, Su Y, Shin JH, et al (2014). Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nature Neurosci, 17, 215-222.
  22. Halgren TA, Murphy RB, Friesner RA, et al (2004). Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem, 47, 1750-9.
  23. Hariom P, Mishra PK (2011). Repercussion of isocyanates exposure on different cellular proteins in human pulmonary arterial endothelial cells. Int J Res Chem Env, 1, 95-100.
  24. Hariom P, Raghuram GV, Jain D, et al (2011). Cell cycle deregulation by methyl isocyanate: implications in liver carcinogenesis. Environ Toxicol, 1-14.
  25. Heard E, Martienssen RA (2014). Transgenerational epigenetic inheritance: myths and mechanisms. Cell, 157, 95-109.
  26. Hermann A, Goyal R, Jeltsch A (2004). The DNMT1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem, 279, 48350-9.
  27. Hou L, Zhang X, Wang D, et al (2011). Environmental chemical exposures and human epigenetics. Int J Epi, 154.
  28. HSFS (2002). Methyl isocyanate. RTK 1270, Department of Health and Senior Services, Hazardous substance fact sheet, New Jersey.
  29. Irwin JJ, Shoichet BK (2005). ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model, 45, 177-82.
  30. Jacobson MP, Pincus DL, Rapp CS, et al (2004). A hierarchical approach to all atom protein loop prediction. Proteins: Structure, Function, and Bioinformatics, 55, 351-67.
  31. Jeltsch A, Jurkowska RZ (2014). New concepts in DNA methylation. Trends Biochem Sci, 39, 310-8.
  32. Jiang Q, Yu YC, Ding XJ, et al (2014). Bioinformatics analysis reveals significant genes and pathways to target for oral squamous cell carcinoma. Asian Pac J Cancer Prev, 15, 2273-8.
  33. Jones PA, Martienssen R (2005). A blueprint for a human epigenome project: the AACR human epigenome workshop. Cancer Res, 65, 11241-6.
  34. Jurkowska RZ, Jurkowski TP, Jeltsch A (2011).Structure and function of mammalian DNA methyltransferases. Chembiochem, 12, 206-22.
  35. Karol MH, Taskar S, Gangal S, et al (1987). The antibody response to methyl isocyanate: experimental and clinical findings. Environ Health Perspectives, 72, 169.
  36. Khamkar T, Abhyankar M, Tendulkar G, et al (2013). In silico molecular docking of marine drugs against cancer proteins. Adv Chem Sci, 2, 24-28.
  37. Kilgore JA, Du X, Melito L, et al (2013). Identification of DNMT1 selective antagonists using a novel scintillation proximity assay. J Biol Chem, 288, 19673-84.
  38. Leonhardt H, Page AW, Weier H-U, et al (1992). A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell, 71, 865-73.
  39. Li E, Bestor TH, Jaenisch R (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell, 69, 915-26.
  40. Lu SC (2000). S-adenosylmethionine. Int J Biochem Cell Biol, 32, 391-5.
  41. Mahdavi M, Mohabatkar H, Keyhanfar M, et al (2012). Linear and conformational B cell epitope prediction of the HER 2 ECD-Subdomain III by in silico methods. Asian Pac J Cancer Prev, 13, 3053-9.
  42. Malla TM, Senthilkumar CS, Sharma NC, et al (2011). Chromosome instability among Bhopal gas tragedy survivors. Am Eur J Toxicol Sci, 3, 245-9.
  43. Miller OJ, Schnedl W, Allen J, et al (1974). 5-Methylcytosine localised in mammalian constitutive heterochromatin. Nature, 251, 636-7.
  44. Mishra PK, Bhargava A, Raghuram GV, et al (2009a). Inflammatory response to isocyanates and onset of genomic instability in cultured human lung fibroblasts. Genet Molecul Res, 8, 129-43.
  45. Mishra PK, Bhargava A, Raghuram GV, et al (2009b). Induction of genomic instability in cultured human colon epithelial cells following exposure to isocyanates. Cell Biol Int, 33, 675-83.
  46. Mishra PK, Raghuram GV, Panwar H, et al (2009c). Mitochondrial oxidative stress elicits chromosomal instability after exposure to isocyanates in human kidney epithelial cells. Free Radic Res, 43, 718-28.
  47. Mortusewicz O, Schermelleh L, Walter J, et al (2005). Recruitment of DNA methyltransferase I to DNA repair sites. Pro Nat Aca Sci USA, 102, 8905-9.
  48. NOAAS (2015). METHYL ISOCYANATE. Chemical Datasheet. Office of Response and Restoration, NOAA's Ocean Service, National Oceanic and Atmospheric Administration, USA. gov. Available from URL: chemical/1112. Assessed on 27.7.15
  49. Okano M, Bell DW, Haber DA, et al (1999). DNA methyltransferases DNMT3A and DNMT3B are essential for de novo methylation and mammalian development. Cell, 99, 247-57.
  50. PDB (2014a) 3PTA. Protein Data Bank. Available at http:// Assessed on 16. 9. 2014.
  51. PDB (2014b) 3SWR. Protein Data Bank. Available at Assessed on 21. 9. 2014.
  52. PDB (2014c) 3EPZ. Protein Data Bank. Available at Assessed on 10.10.2014
  53. PDB (2014d) 4IEJ. Protein Data Bank. Available at Assessed on 21. 10. 2014
  54. Pradhan M, Esteve P-O, Chin HG, et al (2008). CXXC domain of human DNMT1 is essential for enzymatic activity. Biochem, 47, 10000-9.
  55. Qin W, Leonhardt H, Spada F (2011). Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1. J Cell Biochem, 112, 439-444.
  56. Raghuram GV, Pathak N, Jain D, et al (2010). Molecular mechanisms of isocyanate induced oncogenic transformation in ovarian epithelial cells. Reproduct Toxicol, 30, 377-86.
  57. Risner LE, Kuntimaddi A, Lokken AA, et al (2013). Functional specificity of CpG DNA-binding CXXC domains in mixed lineage leukemia. J Biol Chem, 288, 29901-10.
  58. Robertson KD (2005). DNA methylation and human disease. Nature Rev Genetics, 6, 597-610.
  59. Rountree MR, Bachman KE, Baylin SB (2000). DNMT1 binds HDAC2 and a new corepressor, DMAP1, to form a complex at replication foci. Nature genetics, 25, 269-77.
  60. Sastry GM, Adzhigirey M, Day T, et al (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Computer-aided Mol Design, 27, 221-34.
  61. Schluckebier G, Kozak M, Bleimling N, et al (1997). Differential binding of Sadenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M. TaqI. J Mol Biol, 265, 56-67.
  62. Schwetz B, Adkins Jr B, Harris M, et al (1987). Methyl isocyanate: reproductive and developmental toxicology studies in Swiss mice. Environ Health Perspectives, 72, 149.
  63. Senthilkumar CS (2012) Bhopal methyl isocyanate affected population and cancer susceptibility: where do we stand now? Asian Pac J Cancer Prev, 13, 5323-5324.
  64. Senthilkumar CS, Akhter S, Malla TM, et al (2015). Increased micronucleus frequency in peripheral blood lymphocytes contributes to cancer risk in the methyl isocyanate-affected population of Bhopal. Asian Pac J Cancer Prev, 16, 4409-4419.
  65. Senthilkumar CS, Malla TM, Sah NK, et al (2013). Methyl isocyanate exposure and atypical lymphocytes. Int J Occ Environ Med, 4, 167-168.
  66. Senthilkumar CS, Malla TM, Sah NK, et al (2011). Cancer morbidity among methyl isocyanate exposed long-term survivors and their offspring: a hospital-based five year descriptive study (2006-2011) and future directions to predict cancer risk in the affected population. Asian Pac J Cancer Prev, 12, 3443-52.
  67. Senthilkumar CS, Sah NK, Ganesh N (2012). Methyl isocyanate and carcinogenesis: bridgeable gaps in scientific knowledge. Asian Pacific J Cancer Prev, 13, 2429-2435.
  68. Shelley JC, Cholleti A, Frye LL, et al (2007). Epik: a software program for pK a prediction and protonation state generation for drug-like molecules. J Computer-aided Mol Design, 21, 681-691.
  69. Shivakumar D, Williams J, Wu Y, et al (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput, 6, 1509-19.
  70. Shrivastava R, Punde RP, Deshpande S, et al (2010). Molecular characterization and bioinformatics approach of tuberculosis infection prevalent in methyl isocyanate affected population in Bhopal. Pharmacologyonline, 3, 757-767.
  71. Shrivastava R, Yasir M, Tripathi MK, et al (2013). In silico interaction of methyl isocyanate with immune protein responsible for Mycobacterium tuberculosis infection using molecular docking. Toxicol Ind Health, 0748233713498447.
  72. Song CQ, Zhang JH, Shi JC, et al (2014). Bioinformatic Prediction of SNPs within miRNA Binding Sites of Inflammatory Genes Associated with Gastric Cancer. Asian Pac J Cancer Prev, 15, 937-943.
  73. Song J, Teplova M, Ishibe-Murakami S, et al (2012). Structurebased mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science, 335, 709-712.
  74. Stringer R, Labunska I, Brigden K, et al (2002). Chemical stockpiles at union carbide india limited in bhopal: an investigation. greenpeace research laboratories. technical note 12/2002. november 2002. ISBN 90, 73361-80.
  75. Tice RR, Luke CA, Shelby MD (1987) Methyl isocyanate: an evaluation of in vivo cytogenetic activity. Environ mutagenesis, 9, 37-58.
  76. Tripathi MK, Yasir M, Gurjar VS, et al (2015). Insights from the molecular docking of hydrolytic products of methyl isocyanate (MIC) to inhibition of human immune proteins. Interdisciplinary Sciences: Computational Life Sciences, 1-8.
  77. Vandenplas O, Malo J-L, Saetta M, et al (1993). Occupational asthma and extrinsic alveolitis due to isocyanates: current status and perspectives. British J Ind Med, 50, 213.
  78. Wang DG, Chen G, Wen XY, et al (2015). Identification of Biomarkers for Diagnosis of Gastric Cancer by Bioinformatics. Asian Pac J Cancer Prev, 16, 1361-5.
  79. Wang Y, Yan L (2015). Analysis of molecular pathways in pancreatic ductal adenocarcinomas with a bioinformatics approach. Asian Pac J Cancer Prev, 16, 2561-7.
  80. Wu BL, Luo LW, Li CQ, et al (2013). Comprehensive bioinformation analysis of the MRNA profile of fascin knockdown in esophageal squamous cell carcinoma. Asian Pac J Cancer Prev, 14, 7221-27.
  81. Zhuo WL, Zhang L, Xie QC, et al (2014). Identifying Differentially Expressed Genes and Screening Small Molecule Drugs for Lapatinib-resistance of Breast Cancer by a Bioinformatics Strategy. Asian Pac J Cancer Prev, 15, 10847-53.

Cited by

  1. Identification of dual ligands targeting angiotensin II type 1 receptor and peroxisome proliferator-activated receptor-γ by core hopping of telmisartan vol.35, pp.12, 2017,