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Computational Intelligence and Pattern Analysis in Biological Informatics by Jason T. Wang, Sanghamitra Bandyopadhyay, Ujjwal Maulik

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CHAPTER 10

IN SILICO DRUG DESIGN USING A COMPUTATIONAL INTELLIGENCE TECHNIQUE

SOUMI SENGUPTA AND SANGHAMITRA BANDYOPADHYAY

10.1 INTRODUCTION

Discovery of novel lead molecules has always been a long, time consuming, and expensive process in traditional drug discovery. It involves searching a chemical space of >1018 compounds [1] to find a suitable small molecule that can act as a drug and is safe to be administered. Finding a suitable molecule with the desired chemical property from such a large search space is a very complex problem. With the advent of new technologies and the abundance of three-dimensional (3D) structures of proteins, the scientific fraternity can exploit this structural information in order to design novel ligands possessing high-binding affinity to selective target proteins. This approach of finding novel ligand molecules using the structure information of the receptor is usually referred to as structure-based drug design.

Several Lead molecules have been discovered using the structure-based drug design approach. A few of them are approved drugs and many others are under clinical trials. Prostaglandin D synthase inhibitors [2] and X-linked inhibitor of apoptosis protein inhibitors [2] are most recent examples of drug design using fragment-based Lead design. The success of this approach inspired the scientists to apply computational technologies to aid the drug discovery process. The main objectives of the computational methods was to reduce the time and expense ...

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