Get access

Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined

Authors

  • Joseph M. Hayes,

    Corresponding author
    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    • Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
    Search for more papers by this author
  • Vicky T. Skamnaki,

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    2. Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
    Search for more papers by this author
  • Georgios Archontis,

    1. Department of Physics, University of Cyprus, CY1678 Nicosia, Cyprus
    Search for more papers by this author
  • Christos Lamprakis,

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    Search for more papers by this author
  • Josephine Sarrou,

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    Search for more papers by this author
  • Nicolas Bischler,

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    Search for more papers by this author
  • Alexios-Leandros Skaltsounis,

    1. Division of Pharmacognosy, Department of Pharmacy, University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
    Search for more papers by this author
  • Spyros E. Zographos,

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    Search for more papers by this author
  • Nikos G. Oikonomakos

    1. Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
    Search for more papers by this author
    • Deceased on August 31, 2008.


Abstract

With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC50 > 50 μM), indirubin-3′-oxime (IC50 = 144 nM), KT5720 (Ki = 18.4 nM) and staurosporine (Ki = 0.37 nM) as phosphorylase kinase (PhKγtrnc) ATP-binding site inhibitors, with the latter two revealed as potent inhibitors in the low nM range. Because of lack of structural information, we have exploited information from homologous kinase complexes to direct in silico calculations (docking, molecular dynamics, and MM-GBSA) to predict the binding characteristics of the four ligands. All inhibitors are predicted to bind in the same active site area as the ATP adenine ring, with binding dominated by hinge region hydrogen bonds to Asp104:O and Met106:O (all four ligands) and also Met106:NH (for the indirubins). The PhKγtrnc-staurosporine complex has the greatest number of receptor-ligand hydrogen bonds, while for the indirubin-3′-oxime and KT5720 complexes there is an important network of interchanging water molecules bridging inhibitor-enzyme contacts. The MM-GBSA results revealed the source of staurosporine's low nM potency to be favorable electrostatic interactions, while KT5720 has strong van der Waals contributions. KT5720 interacts with the greatest number of protein residues either by direct or 1-water bridged hydrogen bond interactions, and the potential for more selective PhK inhibition based on a KT5720 analogue has been established. Including receptor flexibility in Schrödinger induced-fit docking calculations in most cases correctly predicted the binding modes as compared with the molecular dynamics structures; the algorithm was less effective when there were key structural waters bridging receptor-ligand contacts. Proteins 2011. © 2010 Wiley-Liss, Inc.

Get access to the full text of this article

Ancillary