Pharmacophore modeling: advances, limitations, and current utility in drug discovery

Pharmacophore modeling is a successful yet very diverse subfield of computer-aided drug design. The concept of the pharmacophore has been widely applied to the rational design of novel drugs. In this paper, we review the computational implementation of this concept and its common usage in the drug d...

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Bibliographic Details
Published in:Journal of receptor, ligand and channel research ligand and channel research, 2014-01, Vol.7, p.81
Main Authors: Qing, Xiaoyu, Lee, Xiao Yin, De Raeymaeker, Joren, Tame, Jeremy R.H, Zhang, Kam Y.J, De Maeyer, Marc, Voet, Arnout R.D
Format: Article
Language:English
Subjects:
ADME-tox
Analysis
Biological activity
Chemistry
computer-aided drug design
Design
Drug discovery
Informatics
Ligands
Methods
Pharmaceutical sciences
Pharmacology
pharmacophore fingerprint
protein design
Protein-protein interactions
Proteins
virtual screening
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Summary:Pharmacophore modeling is a successful yet very diverse subfield of computer-aided drug design. The concept of the pharmacophore has been widely applied to the rational design of novel drugs. In this paper, we review the computational implementation of this concept and its common usage in the drug discovery process. Pharmacophores can be used to represent and identify molecules on a 2D or 3D level by schematically depicting the key elements of molecular recognition. The most common application of pharmacophores is virtual screening, and different strategies are possible depending on the prior knowledge. However, the pharmacophore concept is also useful for ADME-tox modeling, side effect, and off-target prediction as well as target identification. Furthermore, pharmacophores are often combined with molecular docking simulations to improve virtual screening. We conclude this review by summarizing the new areas where significant progress may be expected through the application of pharmacophore modeling; these include protein-protein interaction inhibitors and protein design. Keywords: ADME-tox, computer-aided drug design, pharmacophore fingerprint, protein design, virtual screening
ISSN:1178-699X
1178-699X
DOI:10.2147/JRLCR.S46843