Computer aided drug discovery has been broadly used in the pharmaceutical industry to determine new compounds that show significant inhibitory activity against a biological target. In this context, the 3D structure of COX 2 (prostaglandin G/H synthase 2) protein was modeled using homology modeling method by Discovery Studio. Ru(II)/Co(III) polypyridyl complexes of [Ru(phen)2dmbip]2+ (1), [Ru(bpy)2dmbip]2+(2), [Co(phen)2dmbip]3+ (3), [Co(phen)2dmbip]3+ (4), [Ru(phen)2fyip]2+ (5), [Ru(bpy)2fyip]2+(6), [Co(phen)2fyip]3+(7) and [Co(phen)2fyip]3+(8) were docked into the active site pocket of COX 2 and CDK2 (Cyclin-dependent kinase-2) proteins using LibDock algorithm in Discovery Studio 2.1. Results indicated that Ru(II)/Co(III) polypyridyl complexes interacted with both the proteins COX 2 and CDK2. Among all, the complex 1 exhibited highest binding affinity with both proteins than all other complexes.