Virtual screening against the active site of cyclooxygenase-2 (COX-2) enzyme identified 3-ethyl-5-methyl-7- phenylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione (1) as a potential inhibitor. Biological evaluation revealed 1 possesses a moderate level of anti-inflammatory activity in the paw induced edema rat model (60% edema inhibition at a dose of 10 mg/kg). Docking studies highlighted the possibility of hydrogen bonding and hydrophobic interactions between 1 and the COX-2 acrive site. Using an approach based on molecular modeling-guided lead optimisation, new pyridopyrimidine analogues were designed. The designed pyrido[2,3-d]pyrimidine-1,4-dione derivatives were synthesized from the corresponding 6-aminouracil derivatives in a one-step simple reaction with very good to excellent yields. Anti-inflammatory results showed that some drivatives are more potent than indomethacin (relative potency of 105%, 106% and 109%). The ulecerogenic effect of selected derivatives was examined in vivo reavealing greater gastric safety than indomethacin and highlighting possible COX-2 selectivity for these compounds.