This flexibility not only presents a challenge to to structure-based drug design approaches but also opportunities for the design of specific compounds with suitable kinetic properties.We are developing methods to model and simulate protein and ligand dynamics in order to identify transient binding pockets in proteins and to compute the kinetics of drug binding. To efficiently generate protein conformations that reveal transient pockets, we are developing two methods based on the Rotationally-induced perturbation (RIP) simulation method: L-RIP and RIPlig (Kokh et al., in prep).
Different searching algorithms for the prediction of optimal binding poses of ligands, which are the core engines of docking programs, are accounted for.
As Feynman eloquently put it, this is 'nature as she is - absurd' , in which a frozen, motionless receptor was thought to accommodate a small molecule without undergoing any conformational rearrangements, has been largely abandoned in favor of binding models that account not only for conformational changes, but also for the random jiggling of receptors and ligands [).
In contrast, crystal structures of large ACh R antagonists like snake α-neurotoxins bound to ACh BP reveal that this same loop is displaced by as much as 10 Å, producing an active site that is far more open (Figure ] proposed that the unbound ACh BP and ACh R are highly dynamic proteins that, in the absence of a ligand, sample many conformational states, both open and closed, that are selectively stabilized by the binding of agonists and antagonists.
Most notably, incorporating more protein flexibility improved the performance of the method.
The pharmacophore models successfully discriminate known inhibitors from drug-like non-inhibitors.