In silico 3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase

Abstract

Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and the ATP-binding site was characterized. We have collected five inhibitors of hMAK from the literature and docked into the ATP-binding site of the kinase domain. Solvated interaction energies (SIE) of inhibitor binding are calculated from the molecular dynamics simulations trajectories of protein–inhibitor complexes. The contribution from each active site residue in hMAK toward inhibitor binding revealed the nature and extent of interactions between inhibitors and individual residues. The main chain atoms of Met79 invariably form hydrogen bonds with all five inhibitors. The amino acids Leu7, Val15, and Leu129 stabilize the inhibitors via CH–pi interactions. The Asp140 in the active site and Glu77 in hinge region show characteristic hydrogen bonding interactions with inhibitors. From SIE, the residue-wise interactions revealed the nature of non-bonding contacts and modifications required to increase the inhibitor activity. Our work provides 3D model structure of hMAK and molecular basis for the mechanisms of hMAK inhibition at atomic level that aid in designing new potent inhibitors.

Keywords:

• human male germ cell-associated kinase
• prostate cancer
• protein structure modeling
• molecular docking
• molecular dynamics
• binding free energies
• solvated interaction energies

Acknowledgements

The authors thank the Centre or Development of Advanced Computing (CDAC), Pune, India, and the Centre for Modelling Simulation and Design (CMSD), University of Hyderabad, Hyderabad, for providing access to their computational facilities. LGP thanks CSIR for research funding. KT thanks UGC-Dr D.S. Kothari postdoctoral Fellowship, BAR thanks Ministry of Human resource Development for providing research fellowship.