A World of Probabilities: An sMD/MSM Approach for Rational Design of Allosteric Modulators
Adele Hardie1, Ben Cossins2, Silvia Lovera3 and Julien Michel1
1EaStChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, EH9 3FJ, UK
2UCB Pharma, 208 Bath Road, Slough, Berkshire, SL1 3WE.
3UCB Pharma, Chemin du Foriest 1, 1420 Braine-l’Alleud, Belgium
Currently it is challenging to predict whether ligands binding to an orthosteric site could be elaborated into allosteric modulators, as in these cases binding does not necessarily translate into a functional effect. We propose a workflow using steered molecular dynamics simulations (sMD) together with Markov State Models (MSM), to assess the allosteric effect of known binders. Steered MD simulations are employed to sample protein conformational space inaccessible to routine equilibrium MD timescales. Protein conformations sampled by sMD provide starting points for “seeded” molecular dynamics simulations, which are used to build an ensemble of MSMs. State probabilities computed from these MSMs may be used to predict the effect of ligand binding on protein function.
The potential and challenges of applying this methodology is illustrated using case studies with Protein Tyrosine Phosphatase 1B (PTP1B) and Exchange Factor Directly Activated by cAMP (EPAC) proteins. We show that the sMD/MSM protocol correctly captures the inhibition by experimentally validated inhibitors of PTP1B and the activation of EPAC by cAMP. Additionally, nuance in defining protein “states” is discussed. These examples confirm the workflow can be used for progressing hits towards lead molecules in computer-aided drug design campaigns.