Pharmacophore modeling, 3D-QSAR and docking study of 2-phenylpyrimidine analogues as selective PDE4B inhibitors. 2016

Naga Srinivas Tripuraneni, and Mohammed Afzal Azam
Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, Udhagamandalam 643001, Tamil Nadu, India; Constituent College of JSS University, Mysore, India.

Pharmacophore modeling, molecular docking, and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 2-phenylpyrimidine series as PDE4B selective inhibitors. A five point pharmacophore model was developed using 87 molecules having pIC50 ranging from 8.52 to 5.07. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2)=0.918), cross validation coefficient (Q(2)=0.852), and F value (175) at 4 component PLS factor. The external validation indicated that our QSAR model possessed high predictive power (R(2)=0.70). The generated model was further validated by enrichment studies using the decoy test. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviation. A 10ns molecular dynamics simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Further, similar orientation was observed between the superposition of the conformations of 85 after MD simulation and best XP-docking pose; MD simulation and 3D-QSAR pose; best XP-docking and 3D-QSAR poses. Outcomes of the present study provide insight in designing novel molecules with better PDE4B selective inhibitory activity.

UI MeSH Term Description Entries
D011743 Pyrimidines A family of 6-membered heterocyclic compounds occurring in nature in a wide variety of forms. They include several nucleic acid constituents (CYTOSINE; THYMINE; and URACIL) and form the basic structure of the barbiturates.
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D016018 Least-Squares Analysis A principle of estimation in which the estimates of a set of parameters in a statistical model are those quantities minimizing the sum of squared differences between the observed values of a dependent variable and the values predicted by the model. Rietveld Refinement,Analysis, Least-Squares,Least Squares,Analyses, Least-Squares,Analysis, Least Squares,Least Squares Analysis,Least-Squares Analyses,Refinement, Rietveld
D054703 Cyclic Nucleotide Phosphodiesterases, Type 4 A cyclic nucleotide phosphodiesterase subfamily that is found predominantly in inflammatory cells and may play a role in the regulation of CELL-MEDIATED IMMUNITY. The enzyme family includes over twenty different variants that occur due to multiple ALTERNATIVE SPLICING of the mRNA of at least four different genes. Cyclic Nucleotide Phosphodiesterase PDE4 Family,Cyclic Nucleotide Phosphodiesterases, Type 4A,Cyclic Nucleotide Phosphodiesterases, Type 4A5,Cyclic Nucleotide Phosphodiesterases, Type 4B,Cyclic Nucleotide Phosphodiesterases, Type 4C,Cyclic Nucleotide Phosphodiesterases, Type 4D,Cyclic Nucleotide Phosphodiesterases, Type 4D3,PDE4 Phosphodiesterases,PDE4D3 Phosphodiesterase,Phosphodiesterase 4,Phosphodiesterase 4A,Phosphodiesterase 4B,Phosphodiesterase 4C,Phosphodiesterase 4D,Phosphodiesterase IV,Phosphodiesterase-4,Type 4 Cyclic Nucleotide Phosphodiesterase,cAMP-Specific Phosphodiesterase 4A5,Phosphodiesterase 4A5, cAMP-Specific,Phosphodiesterase, PDE4D3,Phosphodiesterases, PDE4,cAMP Specific Phosphodiesterase 4A5
D056004 Molecular Dynamics Simulation A computer simulation developed to study the motion of molecules over a period of time. Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics
D058988 Phosphodiesterase 4 Inhibitors Compounds that specifically inhibit PHOSPHODIESTERASE 4. PDE-4 Inhibitor,PDE4 Inhibitor,Phosphodiesterase 4 Inhibitor,Phosphodiesterase Type 4 Inhibitor,PDE-4 Inhibitors,PDE4 Inhibitors,Phosphodiesterase Type 4 Inhibitors,4 Inhibitor, Phosphodiesterase,Inhibitor, PDE-4,Inhibitor, PDE4,Inhibitor, Phosphodiesterase 4,Inhibitors, PDE-4,Inhibitors, PDE4,Inhibitors, Phosphodiesterase 4,PDE 4 Inhibitor,PDE 4 Inhibitors
D062105 Molecular Docking Simulation A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein. Molecular Docking,Molecular Docking Simulations,Molecular Docking Analysis,Analysis, Molecular Docking,Docking Analysis, Molecular,Docking Simulation, Molecular,Docking, Molecular,Molecular Docking Analyses,Molecular Dockings,Simulation, Molecular Docking
D021281 Quantitative Structure-Activity Relationship A quantitative prediction of the biological, ecotoxicological or pharmaceutical activity of a molecule. It is based upon structure and activity information gathered from a series of similar compounds. Structure Activity Relationship, Quantitative,3D-QSAR,QSAR,QSPR Modeling,Quantitative Structure Property Relationship,3D QSAR,3D-QSARs,Modeling, QSPR,Quantitative Structure Activity Relationship,Quantitative Structure-Activity Relationships,Relationship, Quantitative Structure-Activity,Relationships, Quantitative Structure-Activity,Structure-Activity Relationship, Quantitative,Structure-Activity Relationships, Quantitative

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