Binding pocket dynamics along the recovery stroke of human beta-cardiac myosin

摘要

The druggability of small-molecule binding sites can be significantly affected by protein motions and conformational changes. Ligand binding, protein dynamics and protein function have been shown to be closely interconnected in myosins. The breakthrough discovery of omecamtiv mecarbil (OM) has led to an increased interest in small molecules that can target myosin and modulate its function for therapeutic purposes (myosin modulators). In this work, we use a combination of computational methods, including steered molecular dynamics, umbrella sampling and binding pocket tracking tools, to follow the evolution of the OM binding site during the recovery stroke transition of human beta-cardiac myosin. We found that steering two internal coordinates of the motor domain can recapture the main features of the transition and in particular the rearrangements of the binding site, which shows significant changes in size, shape and composition. Possible intermediate conformations were also identified, in remarkable agreement with experimental findings. The differences in the binding site properties observed along the transition can be exploited for the future development of conformation-selective myosin modulators. Author summarySmall molecules, including drugs, tend to bind to crevices or pockets on the surface of proteins. The shape, size and composition of these binding sites can change as a result of the protein dynamics. This is particularly important if the motions that modulate the binding site are linked to the function of the protein, since molecules that can selectively target different binding site states will likely have different effects on the protein function. In this work we focus on beta-cardiac myosin, a key protein for heart contraction that has become the subject of intensive research in recent years because of the therapeutic potential of its small-molecule modulators. Using computational techniques, we show how the binding site of the first-in-class cardiac myosin activator omecamtiv mecarbil changes during the recovery stroke, one of the main functional motions of the protein. Importantly, we identify features in the shape, size and composition of the site that can be exploited for the development of drugs that can target different stages of the recovery stroke and thus have different types of biological effects.