FLEXIBLE LIGAND DOCKING USING CONFORMATIONAL ENSEMBLES

Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK , is modified to allow it to rapidly fit multiple conformations of lig ands. Conformations of a given molecule are pre-calculated in the same frame of reference, so that each conformer shares a common rigid frag ment with all other conformations. The ligand conformers are then dock ed together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the sam e molecule. The algorithm was tested using three organic ligand protei n systems and two protein-protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method f ound conformations that resembled those determined in X-ray crystal st ructures (RMS values typically less than 1.5 Angstrom). To test the me thod's usefulness for inhibitor discovery, multi-compound and multi-co nformer databases were screened for compounds known to bind to dihydro folate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conf ormations resembling those observed experimentally. The ligand ensembl e method was 100-fold faster than docking a single conformation at a t ime and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation.