Atom-based 3D-QSAR, induced fit docking, and molecular dynamics simulations study of thieno[2,3-b]pyridines negative allosteric modulators of mGluR5

Abstract

Atom-based three dimensional-quantitative structure–activity relationship (3D-QSAR) model was developed on the basis of 5-point pharmacophore hypothesis (AARRR) with two hydrogen bond acceptors (A) and three aromatic rings for the derivatives of thieno[2,3-b]pyridine, which modulates the activity to inhibit the mGluR5 receptor. Generation of a highly predictive 3D-QSAR model was performed using the alignment of predicted pharmacophore hypothesis for the training set (R² = 0.84, SD = 0.26, F = 45.8, N = 29) and test set (Q² = 0.74, RMSE = 0.235, Pearson-R = 0.94, N = 9). The best pharmacophore hypothesis AARRR was selected, and developed three dimensional-quantitative structure activity relationship (3D-QSAR) model also supported the outcome of this study by means of favorable and unfavorable electron withdrawing group and hydrophobic regions of most active compound 42d and least active compound 18b. Following, induced fit docking and binding free energy calculations reveals the reliable binding orientation of the compounds. Finally, molecular dynamics simulations for 100 ns were performed to depict the protein–ligand stability. We anticipate that the resulted outcome could be supportive to discover potent negative allosteric modulators for metabotropic glutamate receptor 5 (mGluR5).

Keywords:

• Pharmacophore
• 3D-QSAR
• central nervous system
• mGluR5
• thieno[2,3-b]pyridines
• negative allosteric modulators

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors would like to thank Department of Biotechnology, Government of India for Research fellowship and financial support (project no: BT/502/NE/TBP/2013 and BT/PR8138/BID/7/458/2013).