Computational protocol: In silico screening for identification of novel β-1,3-glucan synthase inhibitors using pharmacophore and 3D-QSAR methodologies

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Protocol publication

[…] 2D structures were drawn using 2D sketcher of Maestro (Maestro ), the 3D structure conversion and minimizations of ligands were performed using LigPrep (LigPrep ). Various possible ionization states were generated at pH 7 ± 2.0. In order to develop a pharmacophore model, 3D realistic representations of the experimental molecular structures are necessary. Since most ligands were flexible, it is important to consider a range of thermally accessible conformational states to increase the chances of finding geometry close to the putative binding mode. PHASE provides two built-in approaches, both of which employ the MacroModel conformational search engine. Conformers were generated using ConfGen (Watts et al. ) followed by minimization of each generated structure using Merck Molecular Force Field (MMFF). [...] ADME properties were calculated using QikProp (). It calculates regression modeling-based 44 properties of physiochemical and pharmacokinetical relevance using the experimental results of over 710 compounds including about 500 drugs. Further, it also evaluates the acceptability of hits based on the Lipinski’s rule of five, provides ranges for comparing a particular molecule’s properties with those of 95 % of known drugs, and retrieve most similar drugs available. […]

Pipeline specifications

Software tools LigPrep, ConfGen, QikProp
Application Drug design
Chemicals Hydrogen