A NEW DOCKING PROGRAM (SANDOCK)1 IDENTIFIES LIGANDS WITH Kd VALUES UP TO 100nM AND BINDING MODES CONFIRMED BY X-RAY STRUCTURE ANALYSIS. By M.D. Walkinshaw# and P. Burkhard*, Department of Structural Biology, Biozentrum, University of Basel, Switzerland *, Department of Biochemistry, The University of Edinburgh, Scotland #
A new docking program (SANDOCK) was developed to screen large three dimensional databases of small ligand molecules for compounds which are complementary to the active site of a target protein. This program is very efficient as it can screen very large databases with up to a million compounds in a reasonable time and can successfully identify novel binding compounds.
It was possible to identify a series of ligands that bind to three different target proteins FKBP, cyclophilin and thrombin with dissociation constants which are in part as low as 100nM and with binding modes corresponding to that predicted by SANDOCK.
The dissociation constants were determined by applying fluorescence measurements. In addition, the binding of some selected compounds were also confirmed by NMR techniques, which show, that the ligands indeed bind to the predicted region of the protein.
Finally the x-ray structure of thrombin with the small ligand p-Aminobenzamidi-ne shows, that the predicted binding mode of the ligand is correct. The rms difference between the atoms of the docked ligand and the x-ray structure of the ligand is only 0.726 Å, in spite of some conformational changes of the protein upon ligand binding. All hydrogen bonds between the protein and the ligand predicted by SANDOCK are formed, and the predicted distances differ only very little from those found in the x-ray structure.
1) SANDOCK is a further development of Dock 1.0. [I.D. Kuntz et al. in J. Mol. Biol., 161, 269-288 (1983)]