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

Methods Mol Biol. 2015;1215:425-44. doi: 10.1007/978-1-4939-1465-4_19.

Abstract

The availability of 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 a simple approach that can be used to identify both drug leads and drug targets using two popular Web-accessible databases: (1) DrugBank and (2) The Human Metabolome Database. First, it is illustrated 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. The second part illustrates how putative drug targets and drug leads for endogenous diseases (i.e., noninfectious 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.

MeSH terms

  • Amino Acid Sequence
  • Antineoplastic Agents / analysis
  • Antineoplastic Agents / therapeutic use
  • Antiviral Agents / analysis
  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • Databases as Topic
  • Drug Delivery Systems*
  • Drug Design*
  • Drug Evaluation, Preclinical*
  • HIV Protease / chemistry
  • Humans
  • Male
  • Metabolome
  • Molecular Docking Simulation*
  • Molecular Sequence Data
  • Prostatic Neoplasms / drug therapy
  • User-Computer Interface*

Substances

  • Antineoplastic Agents
  • Antiviral Agents
  • HIV Protease
  • p16 protease, Human immunodeficiency virus 1