In silico identification of novel antagonists and binding insights by structural and functional analyses of guanylate kinase of Leishmania donovani and interaction with inhibitors

Abstract

Guanylate kinase (GK; EC 2.7.4.8) is an important enzyme which catalyzed the ATP-dependent phosphorylation of GMP (guanosine monophosphate) into GDP (guanosine diphosphate) for survival of parasites; this suggests that it is a good target for design inhibitor(s). Knowledge of 3D structure of GKLdv is essential for elucidating interaction studies with the inhibitors and compared with substrate binding pattern in both the built model and template structures. The final reliable model of GKLdv has revealed α/β type protein with a G-X2-G-X-G-K that has a catalytic conserved domain in both template and model structure. The core domain consists of a central five-stranded parallel β-sheet (β5, β6, β3 and β4) whereas model has both α1-α10 and β1-β9 and active sites consist of flexible loop (FL1 to FL3). The superimposition structure of main-chain atoms of the GK model with closely homologue of GK (1EX7, chain A), has revealed better alignment and its root mean square deviation (RMSD) (43% similarity) is 0.602Ǻ. The virtual screening result has suggested that the binding pocket interacts with 5GP (5′-guanylic acid) with exhibited higher score in both GOLD and LigandFit scores and involve in amino acid interaction (H-bonding) are Arg40, Try80, Tyr52, Ser36, Glu71, and Asp102. The reported antileishmanial diospyrin (IC₅₀-7.2μM) has also exhibited higher binding activities (Dock score - 49.314 and Fitness score - 52.69) with frequently involved amino acids are Arg45, Glu102, Tyr35, Tyr54, Ser38, Tyr82, Ile103, Asp104, Lys106, Lys18, Pro13 and Ser14. The sigma pi interaction between Ile103 with diospyrin ring has revealed greater stable complex after molecular dynamic simulation studies. The best scoring compounds need for further validation in-vitro test.