Classical MD and metadynamics simulations on back-pocket binders of CDK2 and VEGFR2: a guidepost to design novel small-molecule dual inhibitors

Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores

Water confined within hydrophobic spaces can undergo cooperative dewetting transitions due to slight changes in water density and pressure that push water toward the vapor phase. Many transmembrane protein ion channels contain nanoscale hydrophobic pores that could undergo dewetting transitions, sometimes blocking the flow of ions without physical blockages. Standard molecular dynamics simulations have been extensively applied to study the behavior of water in nanoscale pores, but the large free energy barriers of dewetting often prevent direct sampling of both wet and dry states and quantitative studies of the hydration thermodynamics of biologically relevant pores. Here, we describe a metadynamics protocol that uses the number of waters within the pore as the collective variable to drive many reversible transitions between relevant hydration states and calculate well-converged free energy profiles of pore hydration. By creating model nanopore systems and changing their radius and morphology and including various cosolvents, we quantify how these pore properties and cosolvents affect the dewetting transition. The results reveal that the dewetting free energy of nanoscale pores is determined by two key thermodynamic parameters, namely, the effective surface tension coefficients of water-air and water-pore interfaces. Importantly, while the effect of salt can be fully captured in the water activity dependence, amphipathic cosolvents such as alcohols modify both dry and wet states of the pore and dramatically shift the wet-dry equilibrium. The metadynamics approach could be applied to studies of dewetting transitions within nanoscale pores of proteins and provide new insights into why different pore properties evolved in biological systems.