The cell division cycle is controlled by cyclin-dependent kinases (cdk), wh
ich consist of a catalytic subunit (cdk1-cdk8) and a regulatory subunit (cy
clin A-H). Purine-like inhibitors of cyclin-dependent kinases have recently
been found to be of potential use as anticancer drugs. Rigid and flexible
docking techniques were used for analysis of binding mode and design of new
inhibitors. X-ray structures of three (ATP, olomoucine, roscovitine) cdk2
complexes were available at the beginning of the study and were used to opt
imize the docking parameters. The new potential inhibitors were then docked
into the cdk2 enzyme, and the enzyme/inhibitor interaction energies were c
alculated and tested against the assayed activities of cdk1 (37 compounds)
and cdk2 (9 compounds). A significant rank correlation between the activity
and the rigid docking interaction energy has been found. This implies that
(i) the rigid docking can be used as a tool for qualitative prediction of
activity and (ii) values obtained by the rigid docking technique into the c
dk2 active site can also be used for the prediction of cdk1 activity. While
the resulting geometries obtained by the rigid docking are in good agreeme
nt with the X-ray data, the flexible docking did not always produce the sam
e inhibitor conformation as that found in the crystal.