Current Computer - Aided Drug Design - Volume 2, Issue 1, 2006

The huge data sets produced by high-throughput screening (HTS) technologies have created a tremendous challenge for the drug discovery industry. Rapid processing of HTS data and identification of hits are essential in order to accelerate the discovery of quality lead compounds. In addition to finding active compounds among those screened, it is useful to identify the molecular features associated with the activity. To Read More

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are promising compounds in the search for potent and selective drugs for the treatment of AIDS. Although they are structurally diverse, the NNRTIs exhibit a striking similarity in their mode of action on the reverse transcriptase (RT) hydrophobic pocket. Several quantitative structure-activity relationship (QSAR) studies have been devoted to the HEPT and TIBO derivati Read More

This review focuses on both physicochemical and theoretical QSAR methods for the prediction of drug transport across the blood-brain barrier (BBB). Special emphasis is given to the recent progress that has been made in the modeling of BBB penetration, with a particular focus on the models based on kinetic parameters of BBB permeability dataset. Physicochemical models based on partition coefficients and chromato Read More

This work is concerned with rational drug design at the atomic level. Some fundamental stages of rational drug design are addressed, namely the atomic level understanding on disease-related enzymatic mechanisms and inhibition, which is a pre-requisite to any attempt to rationally design new, better inhibitors; the rational optimization of a lead compound, through chemical modifications that increase its affinity and/or spec Read More

In this review we describe progress in docking and especially high-throughput docking (HTD) for applications in drug design and in silico screening. Computational methods that are used in HTD to assist drug design involve two steps: docking and scoring. Several current docking programs have the ability to generate protein-ligand configurations that are close to the correct structure, as revealed by X-ray crystallography, in man Read More