title: A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors.
abstract: Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.
authors.affiliation: a Department of Pharmaceutical Chemistry , J.S.S. College of Pharmacy (Constituent College of JSS University, Mysore) , Ooty, Udhagamandalam 643001 Tamil Nadu , India.
authors.forename: Naga Srinivas
authors.initials: NS
authors.lastname: Tripuraneni
authors.affiliation: a Department of Pharmaceutical Chemistry , J.S.S. College of Pharmacy (Constituent College of JSS University, Mysore) , Ooty, Udhagamandalam 643001 Tamil Nadu , India.
authors.forename: Mohammed Afzal
authors.initials: MA
authors.lastname: Azam
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4 / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D058988:Phosphodiesterase 4 Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D021281:Quantitative Structure-Activity Relationship; D015203:Reproducibility of Results
chemical_list: D008024:Ligands; D058988:Phosphodiesterase 4 Inhibitors; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4
keywords: docking; molecular dynamics; pharmacophore hypotheses; phosphodiesterases 4; pyrazolopyridines