A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites

An expanding repertoire of “allosteric” drugs is revealing that structure-based drug design (SBDD) is not restricted to the “active site” of the target protein. Such compounds have been shown to bind distant regions of the protein topography, potentially providing higher levels of target specificity, reduced toxicity and access to new regions of chemical space. Unfortunately, the location of such allosteric pockets is not obvious in the absence of a bound crystal structure and the ability to predict their presence would be useful in the discovery of novel therapies. Here, we describe a method for the prediction of “druggable” binding sites that takes protein flexibility into account through the use of molecular dynamics (MD) simulation. By using a dynamic representation of the target, we are able to sample multiple protein conformations that may expose new drug-binding surfaces. We perform a fragment-based mapping analysis of individual structures in the MD ensemble using the FTMAP algorithm and then rank the most prolific probe-binding protein residues to determine potential “hot-spots” for further examination. This approach has recently been applied to a pair of human G-protein-coupled receptors (GPCRs), resulting in the detection of five potential allosteric sites.