Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis

Abstract

A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r2 coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r2 of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

Understanding Structure–Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations

“…Even in the two cases where these values differ by over 1.0 kcal/mol, it is worth noting the correct prediction on the qualitative impact of the modifications (i.e., whether they would improve or reduce potency). Therefore, the TI outcomes for cruzain agreed with other retrospective studies in which the error of the calculated free energy of binding was around 1–2 kcal/mol relative to the experimental data. − These results are especially encouraging when we consider that the determination of ligand protonation state was not trivial and most ligands contained halogen atoms for which the interactions are still challenging for force fields …”

Combined treatment of mitoxantrone sensitizes breast cancer cells to rapalogs through blocking eEF-2K-mediated activation of Akt and autophagy

“…According to the specific interaction pattern of mitoxantrone and eEF-2K, we found that there are five hydrogen-bond interactions (Arg140, Lys170, Ile232, Glu 233, and Gly 234) between them (Fig. 6C ), and four residues have been reported in the literatures 26 – 29 , which further demonstrated that mitoxantrone is likely to be a potent inhibitor of eEF-2K.

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Eukaryotic elongation factor 2 kinase as a drug target in cancer, and in cardiovascular and neurodegenerative diseases

“…There is clearly an acute need to identify better eEF2K inhibitors as tool compounds to explore the roles of eEF2K in normal cell physiology and in disease. Such efforts have been hindered by the lack of a 3-dimensional structure for eEF2K but will be aided by the development of a homology model of eEF2K based on the known structures of two other members of the α-kinase family [39] .…”