Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study

Growth factor receptor-bound protein 2 (Grb2) plays an essential role in the Ras-MAPK signalling pathway which is an important target for anti-cancer drug design. The precise mechanisms by which effective and selective ligands can bind to the Src homology 2 (SH2) domain of Grb2 and interrupt the signalling pathway are not fully understood. We report in this paper the results of molecular dynamics simulations of the Grb2 SH2 domain structure derived from X-ray in water solution and without constraints. The protein was complexed with two reference molecules: one is a potent and extensively studied inhibitor, while the other was shown to have no affinity for the Grb2 SH2 domain, in contradiction with previously performed in vacuo simulations. Analysis of the MD trajectories for the two complexes reveals interesting features which may explain the stability of the complex obtained for the first molecule versus the poor binding of the other ligand. It is shown that water most probably plays a critical role in the stability of these complexes, and it is proposed to consider this solvent behavior in forthcoming structure-based drug design strategies. In this respect structural details are given concerning water molecules reported to be stabilized between the active ligand and the protein receptor. We have also identified which residues from Grb2 SH2 and the two ligands could be involved in destabilizing interactions with bulk solvent. Finally, we propose guidelines for optimizing both ligands by preventing such unwanted effects.