Over the last decade computational (in silico) methods have been applied to pharmacology hypothesis development and testing. In silico research in medicine is thought to have the potential to speed the rate of discovery of drugs while reducing the need for expensive laboratory works and clinical works.
Dr. Ignitius Kunjumon, Faculty at the department of Atmospheric Sciences, Cochin University of Science and Technology, addressed the students and faculty of Amrita School of Biotechnology on February 18th 2015. In his seminar titled “Design Your First Drug Using AutoDock Tools” Dr. Kunjumon discussed how to design and dock a new drug to a particular target protein using the computer software AutoDock.
AutoDock is a suit of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known three-dimensional structure. AutoDock is free, very fast, provides high quality predictions of ligand conformations and good correlation between predicted inhibition constants and experimental ones. It has also been shown to be useful in blind docking, where the location of binding is not known. The drug to be tested is designed using the software Ghemical. The respective three-dimensional structure of the target protein is downloaded from PDB. Both of the data (protein and drug) is entered in the AutoDock software and the result shown will contain the ligand binding to the appropriate site in the protein. Thus allowing us to know about the binding energy, binding site and specificity of the drug with which it can be taken to the next phase of the drug discovery process.
Dr. Kunjumon’s talk thus provided an interesting setting where students and faculty were given a chance to interact and ask questions about the process and the future of silico methods and their applications in the drug discovery process.