Small molecule docking to protein targets was developed as a drug discovery tool at a time when drug discovery was focused predominantly on enzyme active sites rather than allosteric sites. However, as early as 1963, Monod and coworkers astutely pointed out that protein function can be regulated allosterically by small molecules that need not be structurally related to a protein’s target (e.g. substrate) because they bind somewhere other than the active site . Some allosteric sites are similar to active sites, which are often located in deep grooves, somewhat buried in the protein structure, and contain a limited set of residues that provide a well defined binding site. Other allosteric sites are more like protein-protein interfaces (PPIs), which have less rigid binding requirements, frequently have species-specific variations in composition, and have overall greater structural flexibility.
Application of computational docking to allosteric sites or PPIs has been done successfully [2–5] despite the fact that most related software has been developed and benchmarked with active sites in mind . Oftentimes targeting PPIs is undertaken to find small molecules that will interfere with oligomer assembly. Alternatively, one can target a specific cleft formed at a PPI with the notion of stabilizing a particular assembly. We have undertaken a series of docking studies that address allosteric sites that occur at PPIs where small molecule binding modulates an equilibrium of functionally distinct alternate quaternary structure assemblies [4, 5]. Proteins with such assemblies have been called morpheeins and the equilibrium can be illustrated using a morphing dice schematic (Fig. 1). The distinguishing characteristic of proteins that function as morpheeins is that there exist alternate assemblies and each oligomeric assembly may have surface clefts that are assembly-specific. These clefts do not have the evolutionary requirement for conservation that is characteristic of active sites. The utility of docking to clefts in PPIs has been established [7, 8]. Oligomer-stabilizing, small molecule binding to one oli-gomeric form of a morpheein equilibrium can be schematically represented in the dice analogy by a tetramer-specific wedge whose binding draws the equilibrium toward that oligomer (Fig. 1).