Exploring Kinetics and Drug Residence Time in Biological Systems through Molecular Simulations

Abstract

Characterizing thermodynamics and kinetics of molecular systems is the ultimate goal of biophysics. In drug discovery, this information becomes essential. Understanding local and global rearrangements, how formation and disruption of biomolecular complexes occur, the molecular determinants involved and the preferred pathways followed, contribute to forming a solid ground for the development of new drugs. Quantifying specific kinetic parameters, such as off rates and the closely related residence time, is increasingly being incorporated in the drug optimization phase. Several experimental techniques established to study and quantify kinetic features. Conversely, the computational counterpart still faces severe challenges, such as accessing the time scales at which these slow events occur, while acquiring acceptable statistics. During this PhD program, we explored current, state-of-the-art computational methods, and combination thereof, to study kinetic properties of pharmaceutically relevant biomolecules. In particular, we applied different protocols to three test systems. In the first case, we reconstructed the free energy surface of an intrinsically disordered protein and calculated interconversion rates between the differently folded states identified. In the second application, Markov State Models were employed to identify relevant states along the protein-ligand binding pathway. Using these states as a template, a putative pathway on which computing the free energy profile associated with the binding process was determined. As for the third test case, we performed unbinding simulations on a series of ligands and prioritized them according to their average computational unbinding time. The obtained ranking was subsequently confirmed by performing experimental assays. Despite clear limitations, the picture arising from the studies was encouraging. Computer simulations emerged undoubtedly as a valuable instrument for assessing kinetic properties of biomolecular systems. Therefore, in light of the rapid advances in computer power expected from the upcoming years, their role as effective tools to assist the discovery of novel drug-like molecules is extremely promising.