Pakistan Journal of Biological Sciences1028-88801812-5735Asian Network for Scientific Information10.3923/pjbs.2012.121.131KIT Gene Encoding Receptor Tyrosine Kinase and its Interaction with Sunitinib and HDAC Inhibitors: An in silico Approach]]>VanajothiR. RajamanikandanS. SudhaA. SrinivasanP. 32012153KIT is a growth factor receptor, important for normal germ cell migration and development. The malfunction of KIT gene results in constitutive activation of the tyrosine kinase activity of c-KIT which is believed to be the major oncogenic event in stomach, small intestine mastocytosis, acute leukemias, melanomas and colon tumors. The genetics of these diseases could be better understood by knowing the functional relevance of their SNP variation. In this study, a computational analysis to detect the most deleterious non-synonymous SNPs of KIT gene was performed and investigated its binding affinity to native and predicted mutant protein structure (D816V) with sunitinib and HDAC (Trichostatin A and Panobinostat) inhibitors was investigated. Out of 1,288 SNPs retrieved from dbSNP database against KIT gene, 11 non-synonymous SNPs were detected to be damaging and deleterious by SIFT, PolyPhen and I-Mutant2.0 servers. Further, we modeled the mutant protein based on the deleterious nsSNP (rs121913507) and showed that the mutation from Aspartic acid to Valine at 816 position exhibit greatest impact on stability. The RMSD values of mutant and native structures are found to be 0.40 and 1.9 Å, respectively. Furthermore, the binding affinity of sunitinib and HDAC inhibitors were compared with native and mutant protein. 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