Software and resources for computational medicinal chemistry

Chenzhong Liao, Markus Sitzmann, Angelo Pugliese, Marc C Nicklaus
2011 Future Medicinal Chemistry  
Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on
more » ... ased drug design, ligand-based drug design, chemical databases and chemoinformatics tools. Drug discovery and development is a very costly and time-consuming process in which every available discipline, including computer-aided drug design (CADD), is utilized in order to achieve the desired results. CADD provides valuable insights into experimental findings and mechanism of action, new suggestions for molecular structures to synthesize, and can help make cost-effective decisions before expensive synthesis is started. Numerous compounds that were discovered and/or optimized using CADD methods have reached the level of clinical studies or have even gained US FDA approval [1, 2] . Many CADD techniques are used at various stages of a drug-discovery project, and one cannot designate a single 'best' computational drug-design technique in general. Hence, computational medicinal chemists should be aware of and willing to take advantage of all kinds of software and resources related to CADD during their routine work, although individually they may focus on, and subsequently become an expert in, the use of just one or a few specific techniques. Ligands (be they inhibitors, activators, agonists, antagonists or substrate analogs) can be identified using conventional hit-identifying methods such as high-throughput screening (HTS) assays or employing various CADD techniques. Because of their respective strengths and weaknesses for drug discovery, HTS and CADD techniques are often seen as complementary to each other [3] . HTS has been used in combination with, or substituted by, CADD techniques, the latter being generally faster, more economical and easier to set up than HTS. In addition, by using CADD techniques, one can attempt to optimize ligands to imbue them with high-binding affinity and good selectivity, as well as acceptable pharmacokinetic properties, the latter not usually being within the scope of HTS.
doi:10.4155/fmc.11.63 pmid:21707404 pmcid:PMC3413324 fatcat:csjirmoxcfhntfhgirqdm3hjae