Identifying putative drug targets and potential drug leads: Starting points for virtual screening and docking

Abstract

The availability of three-dimensional (3D) models of both drug leads (small molecule ligands) and drug targets (proteins) is essential to molecular docking and computational drug discovery. This chapter describes an emerging methodology that can be used to identify both drug leads and drug targets using three newly developed web-accessible databases: 1) DrugBank; 2) The Human Metabolome Database; and 3) PubChem. Specifically, it illustrates how putative drug targets and drug leads for exogenous diseases (i.e., infectious diseases) can be readily identified and their 3D structures selected using only the genomic sequences from pathogenic bacteria or viruses as input. It also illustrates how putative drug targets and drug leads for endogenous diseases (i.e., non-infectious diseases or chronic conditions) can be identified using similar databases and similar sequence input. This chapter is intended to illustrate how bioinformatics and cheminformatics can work synergistically to help provide the necessary inputs for computer-aided drug design. © 2008 Humana Press.