Exploring c‐Met kinase flexibility by sampling and clustering its conformational space

Abstract

It is now widely recognized that the flexibility of both partners has to be considered in molecular docking studies. However, the question how to handle the best the huge computational complexity of exploring the protein binding site landscape is still a matter of debate. Here we investigate the flexibility of c-Met kinase as a test case for comparing several simulation methods. The c-Met kinase catalytic site is an interesting target for anticancer drug design. In particular, it harbors an unusual plasticity compared with other kinases ATP binding sites. Exploiting this feature may eventually lead to the discovery of new anticancer agents with exquisite specificity. We present in this article an extensive investigation of c-Met kinase conformational space using large-scale computational simulations in order to extend the knowledge already gathered from available X-ray structures. In the process, we compare the relevance of different strategies for modeling and injecting receptor flexibility information into early stage in silico structure-based drug discovery pipeline. The results presented here are currently being exploited in on-going virtual screening investigations on c-Met.

Large-Scale Virtual Screening Against the MET Kinase Domain Identifies a New Putative Inhibitor Type

“…Concerning MET conformational flexibility, our previous exploration by molecular dynamics and normal mode simulations [22] was limited to the 26 PDB structures available at that time ( Table 2). We have now extended this analysis by considering all the X-ray structures available for the wild-type MET in the PDB [53] deposited after 2012.…”

“…These results obtained thanks to the Dali server [55] clearly illustrate how MET 3D structures used here are organized into several families covering most of the protein conformational space presently known. To be in accordance with the 26 conformers coming from our previous work [22], the 19 added crystal structures were prepared and cleaned following the same protocol: missing residues, side chains, and hydrogens were added when necessary; unnecessary water molecules, ions, and additives were removed; basic and acidic side chains were ionized according to a pH set to 7. To consider possible binding sites fluctuations, short molecular dynamics (MD) simulations were undertaken for each of these 19 structures.…”

“…For that purpose, these structures were placed in a solvent box of 80 Å and counter ions were added for electrostatic neutrality. NAMD [57] molecular dynamics program was used with the same CHARMM36 force field and same protocol as previously described [22]. After minimization and equilibrium steps (64,000 conjugate gradients and 1 ns MD, respectively), 10 ns of MD were recorded, with a frame length of 1 ps.…”

“…In the present work, we carried out a virtual screening campaign in order to identify innovative compounds able to become new hits for further lead development. As MET plasticity upon ligand binding had been previously highlighted [22,23], we took into account this aspect for the molecular docking simulations. Indeed, MET can accommodate several distinct ligand binding modes and associated receptor conformations, a feature that is particular to the kinase family [24].…”

Sampling of Conformational Ensemble for Virtual Screening Using Molecular Dynamics Simulations and Normal Mode Analysis

“…Critical reviews on current approaches for generation of receptor conformational ensemble (RCE) have been reported [32,33]. Usually protein receptor conformations are identified using MD simulations [34][35][36][37][38][39][40]. McCammon and co-workers pioneered the Relaxed Complex Scheme (RCS), which is based on MD simulations to account for protein flexibility prior to ligand docking and VS [41,42].…”