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In Silico Drug Designing against DNA Topoisomerase 1 for Brain Cancer Treatment

Sasikumar P, Pandieswari S, Samundeeswari S and Vanitha M

Drug designing is the approach of finding drugs by design, based on their biological targets. Typically a drug target is a key molecule involved in a particular metabolic or signaling pathway that is specific to a disease condition or pathology, or to the infectivity or survival of a microbial pathogen. The structure of the drug molecule that can specifically interact with the biomolecules can be modeled using computational tools. These tools can allow a drug molecule to be constructed within the biomolecule using knowledge of its structure and the nature of its active site. Construction of the drug molecule can be made inside out or outside in depending on whether the core or the R-groups are chosen first. However many of these approaches are plagued by the practical problems of synthesis. One of the computational tools used in drug designing is “chemsketch”, which works with 65% accuracy. The drug structure was downloaded from the drug database and the structure is modified by introducing alcohol, methyl, sodium hydroxide etc. onto the functional groups of the drug. The new drugs obtained undergo various molecular modeling and dynamics to reduce their energy levels. Docking is performed using geometrically optimized molecules as ligands and protein DNA topoisomerase I as protein, converting their chemsketch forms into PDB format using SPDB viewer. HEX software is used for this purpose.