Abstract:
A series of 12 novel 2-(substituted)-5,6-dimethyl/-5,6,7,8-tetrahydrobenzo[b]thieno[2,3-d]pyrimidine4-(3H)-one derivatives were designed to recognise their hypothetical binding motif required to bind with the enzyme cyclooxygenase-2 (COX-2). The novel compounds were designed based on in silico molecular docking studies by using the crystal structures of COX-1 (PDB ID: 3N8X) and COX-2 (PDB ID: 3LN1) isoenzymes respectively by employing the Glide (Schrodinger Inc.) software program. Docking studies revealed that nonselective non-steroidal anti-inflammatory drugs (NSAIDs) like indomethacin form a salt bridge with the amino acid residue Arg120 inside the binding pocket of COX-1/2 which gives a generalised anchoring point for all the classical NSAIDs (non-steroidal anti-inflammatory drugs) thus limiting their selectivity due to curtailed freedom of movement of the ligand. Interestingly all the designed compounds did not form any such salt bridge and predicted to be comparatively selective towards the COX-2 over the COX-1 isoenzyme. Further, these designed compounds were also found to be aligned with the reference standard drug celecoxib inside the binding pocket of COX-2 by forming significant hydrogen bonding interactions with all the crucial amino acid residues. The compounds which were predicted to have good binding affinity as well as selectivity towards COX-2 were further screened for their in silico pharmacokinetic properties (absorption, distribution, metabolism and excretion: ADME) to test their drug-likeness by using the QikProp (Schrodinger Inc.) software program. The predicted ADME properties of all the designed compounds were found to be in the ranges as predicted by QikProp for 95% of known oral drugs and also satisfy the Lipinski’s rule of five.
Two of the 12 designed compounds (compound 7 and 8) were synthesised, purified and characterised by following the appropriate synthetic scheme-1. An attempt was made to evaluate their in vitro COX-1/2 activity; the outcome of the assay is not yet conclusive due to technical error associated with the COX inhibition assay kit. The repetition of COX inhibition assay to confirm the inhibitory binding affinity and selectivity of all the newly synthesised compounds towards COX-2 over COX-1 will be the basis of the future research work.
Keywords: Thieno[2,3-d]pyrimidine, docking studies, in silico ADME prediction, COX-1/2 inhibition assay.
