Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches

Abstract

Matrix metalloproteinase-9 (MMP-9) is a significant target for the development of drugs for the treatment of arthritis, CNS disorders, and cancer metastasis. The structure-based and ligand-based methods were used for the virtual screening (VS) of database compounds to obtain potent and selective MMP-9 inhibitors. Experimentally known MMP-9 inhibitors were used to grow up ligand-based three pharmacophore models utilizing Schrodinger suite. The X-ray crystallographic structures of MMP-9 with different inhibitors were used to develop five energy-optimized structure-based (e-pharmacophore) models. All developed pharmacophores were validated and applied to screen the Zinc database. Pharmacophore matched compounds were subjected to molecular docking to retrieve hits with novel scaffolds. The molecules with diverse structures, high docking scores and low binding energies for various crystal structures of MMP-9, were selected as final hits. The Induced fit docking (IFD) analysis provided significant information about the driving of inhibitor to approve a suitable bioactive conformational position in the active site of protein. Since charge transfer reaction occurs during receptor–ligand interaction, therefore, electronic features of hits (ligands) are interesting parameters to explain the binding interactions. Density functional theory (DFT) at B3LYP/6-31G* level was utilized to explore electronic features of hits. The docking study of hits using AutoDock was helpful to establish the binding interactions. The study illustrates that the combined pharmacophore approach is advantageous to identify diverse hits which have better binding affinity to the active site of the enzyme for all possible bioactive conformations. The approach used in the study is worthy to design drugs for other targets.

Keywords:

• 3D-QSAR
• MMP-9
• IFD
• DFT
• e-Pharmacophore

Abbreviations:

• MMP, Matrix metalloproteinase
• 3D-QSAR, 3-dimensional-quantitative structure activity relationship
• ADME, absorption, distribution, metabolism, and excretion
• HOMO, high occupied molecular orbital
• LUMO, low unoccupied molecular orbital

Acknowledgments

The authors are grateful to Department of Biotechnology, Ministry of Science & Technology, New Delhi, India (BT/PR9624/MED/30/1253/2013 dated-29/11/2014), for the financial support. We would like to thank Dr Ozair Alam, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, India, for his assistance and support. SJ would like to thank Ministry of Human Resource Development (MHRD), New Delhi, India, for the award of senior research fellowship to her.