Computer-Aided Drug Design Methods.

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TitleComputer-Aided Drug Design Methods.
Publication TypeJournal Article
Year of Publication2017
AuthorsYu, W, Mackerell, AD
JournalMethods Mol Biol
Volume1520
Pagination85-106
Date Published2017
ISSN1940-6029
Abstract

Computational approaches are useful tools to interpret and guide experiments to expedite the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) are the two general types of computer-aided drug design (CADD) approaches in existence. SBDD methods analyze macromolecular target 3-dimensional structural information, typically of proteins or RNA, to identify key sites and interactions that are important for their respective biological functions. Such information can then be utilized to design antibiotic drugs that can compete with essential interactions involving the target and thus interrupt the biological pathways essential for survival of the microorganism(s). LBDD methods focus on known antibiotic ligands for a target to establish a relationship between their physiochemical properties and antibiotic activities, referred to as a structure-activity relationship (SAR), information that can be used for optimization of known drugs or guide the design of new drugs with improved activity. In this chapter, standard CADD protocols for both SBDD and LBDD will be presented with a special focus on methodologies and targets routinely studied in our laboratory for antibiotic drug discoveries.

DOI10.1007/978-1-4939-6634-9_5
Alternate JournalMethods Mol. Biol.
PubMed ID27873247
PubMed Central IDPMC5248982
Grant ListR01 CA107331 / CA / NCI NIH HHS / United States