Identification of novel inhibitors of Daboia russelli phospholipase A2 using the combined pharmacophore modeling approach.
Crystal structures available for Daboia russelli venom PLA(2) confirm that it undergoes dimerization with asymmetry and hence difference in the conformation of active site of the two subunits. The active site of subunit A is open and that of subunit B is closed. Pharmacophore models were generated based on the interaction of different types of inhibitors with their preferred subsites in the active site of subunit A. Particularly, the features responsible for recognizing subsites 1-3 and those of subsites 4-6 were combined as these two are involving in inflammation and anticoagulation processes, respectively. Pharmacophore model was edited to make the geometry suitable for the active site of both the subunits A and B. Final model is validated and subjected for screening a library of druglike compounds. Eight compounds were shortlisted and subjected for molecular docking and dynamics simulation to assess their binding mode with both the subunits. Based on the hydrophobic interactions and binding free energy, four compounds were selected for further biochemical assay. The overall results suggest that two compounds can bind both the subunits of PLA(2) of Daboia russelli venom in spite of its aggregated form and other two inhibit structurally very similar Naja naja PLA(2).
Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai, 600025, India.
Chandrasekaran
C
Ramakrishnan
Vikram
V
Joshi
Joseph Mavelithuruthel
JM
Joseph
Bannikuppe S
BS
Vishwanath
Devadasan
D
Velmurugan
D000818:Animals; D001665:Binding Sites; D057927:Hydrophobic and Hydrophilic Interactions; D007213:Indomethacin / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D062105:Molecular Docking Simulation; D064801:Phospholipase A2 Inhibitors / Q000737:chemistry / Q000378:metabolism*; D054467:Phospholipases A2 / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D017819:Viperidae / Q000378:metabolism; D014810:Vitamin E / Q000737:chemistry / Q000378:metabolism
D008024:Ligands; D064801:Phospholipase A2 Inhibitors; D014810:Vitamin E; D054467:Phospholipases A2; D007213:Indomethacin
Daboia russelli PLA2; PLA2 inhibition assay; hydrophobicity; molecular dynamics simulation; pharmacophore modeling; phospholipase A2 inhibitors