Molecular dynamics in drug design

TitleMolecular dynamics in drug design
Publication TypeJournal Article
Year of Publication2015
AuthorsZhao H., Caflisch A.
JournalEuropean Journal of Medicinal Chemistry
Volume91
Pagination4-14
Date PublishedFeb 16 2015
Type of ArticleReview Article
ISSN0223-5234
KeywordsAtomistic simulation, bromodomains, high-throughput docking, In silico screening, Proteases, Tyrosine kinases
Abstract

Abstract Molecular dynamics (MD) simulations are useful tools for structure-based drug design. We review recent publications in which explicit solvent MD was used at the initial or final stages of high-throughput docking campaigns. In some cases, MD simulations of the protein target have been carried out before docking to generate a conformer of the protein which differs from the available crystal structure(s). Furthermore, MD runs have been performed after docking to assess the predicted binding modes of the top ranking compounds as final filter in silico or to guide chemical synthesis for hit optimization. We present examples of in silico discoveries of tyrosine kinase inhibitors and bromodomain antagonists whose binding mode was predicted by automated docking and further corroborated by MD simulations with final validation by X-ray crystallography.

URLhttp://www.sciencedirect.com/science/article/pii/S0223523414007314
DOI10.1016/j.ejmech.2014.08.004
pubindex

0194

Alternate JournalEur. J. Med. Chem.
Highlight Role: 
Drug Design