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Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach

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In the absence of three-dimensional (3D) structures of potential drug targets, ligand-based drug design is one of the popular approaches for drug discovery and lead optimization. 3D structure-activity relationships (3D QSAR) and pharmacophore modeling are the most important and widely used tools in ligand-based drug design that can provide crucial insights into the nature of the interactions between drug target and ligand molecule and provide predictive models suitable for lead compound optimization. This review article will briefly discuss the features and potential application of recent advances in ligand-based drug design, with emphasis on a detailed description of a novel 3D QSAR method based on the conformationally sample pharmacophore (CSP) approach (denoted CSP-SAR). In addition, data from a published study are used to compare the CSP-SAR approach to the Catalyst method, emphasizing the utility of the CSP approach for ligand-based model development.

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Keywords: AIC values; AMBER; Accelrys; Akaike information criteria; Aliphatic hydrophobic moieties; Apical Sodium-dependent Bile acid Transporter or ASBT; Aromatic hydrophobic moieties; Aromatic ring; Bayesian regularized artificial neural network (BRANN); CA; CATALYST; CHARMM; CSP; CoMFA; CoMSIA; DAT/SERT; Generalized Born Continuum Solvent Model GBMV; Hansch/Free- Wilson method; Hydrogen-bond acceptor; Hydrogen-bond donor; Ligand-Based Drug Design; MATLAB; MMFF; Monte Carlo (MC) simulations; Multivariable linear regression analysis (MLR); NG-OA distance; Negatively charged group (acidic); OA-NG-CG angles; Partial least square analysis (PLS); Positively charges group (basic); Principal component analysis (PCA); RMSD; SAR method; SHELL; San Diego; computer-aided drug design; conformationally-sampled pharmacophore (CSP); drug discovery; external validation; hASBT; internal validation; k-fold cross; lead optimization; molecular dynamics (MD); molecular mechanics; nonpeptidic opioids; opioid ligands; pharmacophore; quantum mechanical (QM); quantum mechanical methods; replica-exchange MD simulations; silico chemical alteration

Document Type: Research Article

Publication date: March 1, 2011

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  • Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
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