The combination of docking and molecular dynamics simulation is used to explain the isoform-specific selectivity between PI3Kalpha and PI3Kgamma, which are two lipid kinases in the class I PI3Ks. The protein flexibility is incorporated in docking the ligands to the ensemble of representative structures extracted from a clustering analysis of the molecular dynamics simulation in explicit aqueous...

Visual haptic-based biomolecular docking systems could be used for both research and e-learning in research intensive disciplines such as biology, physical chemistry, molecular medicine, biophysics, structural biology, bioinformatics, etc. The assembly of molecules in a three-dimensional space or molecular docking is used for rational drug design where a ligand docks onto a receptor. The comput...

  Objective(s): Recently we reported that the soybean 15-lipoxygenase (SLO) inhibitory activity of pyrimido[4,5-b][l,4]benzothiazines largely depends on the orientation of sulfur atom of thiazine core towards FeIII-OH in the active site pocket of the enzyme with subsequent oxidation of sulfur to sulfoxide. In this paper the results of a comparative study on the SLO inhibitory activities of the ...

Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells. The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high affinity adenosine triphosphate (ATP) binding site and analyzed absorption, distribution, metabolism, excretion and toxicity (ADME-toxicity). The molecular docking analysis reveal...

In this study, a new molecular docking method is presented to improve the docking accuracy. We introduce to docking design a concept of residue groups based on induced-fit and use K Score (a kind of PMF scoring function) to score the docking position. Genetic algorithm with the multi-population evolution and entropy-based searching technique with narrowing down space is used to solve the optimi...

The present research article relates to the discovery of the novel drugs based on Zonisamide to treatment of autism disease. In first step, the electronic properties, reactivity and stability of the said compound are discussed. To attain these properties, the said molecular structure is optimized using B3LYP/6-311++G(d,p) level of theory at room temperature. The frontier molecular orbitals (FMO...

Phytochemical investigation of the aerial parts of Euphorbia erythradenia Bioss. (Euphorbiaceae), one of Iranian endemic Euphorbias, with particular attention to triterpene constituents, using methanol solvent extraction was carried out. Five known triterpenes, including four cycloartanes and oleanolic acid, were isolated for the first time and identified using NMR and Mass techniques. Anti HIV...

Four prenylated flavonoids including isosophoranone, sophoraflavanone G, alopecurone J, alopecurone P and a resveratrol derivative HPD (2-(4-hydroxyphenyl)-2,3-dihydrobenzo[b] furan-3,4,6-triol), were isolated from the roots of Sophora pachycarpa. The cytotoxic activity of obtained compounds was evaluated against A2780, A549, HeLa, and HCT116 human cancer cell lines. We also evaluated their his...