Elucidation of the Mechanism of Partial Activation of EPAC1 Allosteric Modulators by Markov State Modelling

The development of selective modulators of exchange protein activated by cAMP (EPAC1/RAPGEF3), which preferentially bind its cAMP-binding site, would pave the way for novel therapeutic interventions in cardiac, metabolic, inflammatory, and oncologic disorders. Here we have applied a computational workflow using Markov State Models (MSMs) and steered molecular dynamics (sMD) to probe the allosteric activation of EPAC1 by both cAMP and pharmaceutical hit compound I942. sMD was used to examine the large-scale domain rearrangement EPAC1 undergoes during activation. Intermediate conformations accessed via sMD were then used as starting points for equilibrium MD simulations, which were pooled for the construction of MSMs. The resulting models capture the activation of wild-type (WT) EPAC1 by cAMP, and provide an explanation for the lack of response to cAMP shown by the L273W point mutant. sMD/MSM modelling also elucidated the structural basis for partial activation of EPAC1 by ligand I942 and revealed the crucial contribution of ligand interactions with EPAC1’s catalytic region to achieve full activation. The mechanistic insights from this study suggest a design strategy to guide the development of potent small-molecule EPAC1 activators.