Paper Citing NAMD - Abstract
Bhunia, Shome S.; Singh, Supriya; Saxena, Shruti; Saxena, Anil K.
Pharmacophore Modeling, Docking and Molecular Dynamics Studies on Caspase-3 Activators Binding at beta-Tubulin Site
CURRENT COMPUTER-AIDED DRUG DESIGN, 11:72-83, 2015
Induction of apoptosis by the activation of caspase 3 makes it a promising target for designing anticancer drugs hence an investigation for the essential structural features mandatory for caspase 3 activation has been carried out using a dataset comprising of caspase 3 activator candidate drug Azixa in phase II clinical trial and its analogs using DS2.0. A training set of 40 compounds was selected for the purpose of model generation from 76 molecules with an activity range spanning from 0.002 mu M to 6.9 mu M. Among the generated pharmacophore models, the best model Hypo1 constituted by two hydrophobic aliphatic (Hal), two hydrophobic aromatic (Har), and one hydrogen bond acceptor (HBA) features with a correlation coefficient of 0.85, and a cost difference (null cost - total cost) of 46 bits well predicted the test set of 36 compounds (R-pred = 0.8). The key mechanism conferring caspase 3 activation is due to binding of Azixa at beta-tubulin site that is located close to or at same site as colchicine. In the absence of co-crystal structure we have proposed a binding mode of Azixa at the tubulin site by performing docking studies and performed molecular dynamics simulation to ascertain the temporal changes of the protein-ligand complex.
