Synthesis and computational studies of 1,3,4-thiadiazole and benzothiazole clubbed benzimidazole analogous as anti-tubercular and anti-protozoal agent

• The synthesis involves the preparation of N -Mannich bases of 2-(pyridine-4-yl)-1H-benzodimidazole by incorporating benzothiazole and 1,3,5-thiadiazole under microwave irradiation conditions. • The green synthesis method seeks to improve reaction efficiency and yield by utilizing microwave energy. • Studies using molecular dynamics (MD) simulations have validated the stability of the ligand-protein complex. • The newly synthesized compound shows greater potency against L. Mexicana . The present article discusses the synthesis of N -Mannich bases ( 2a-j ) of 2-(pyridine-4-yl)-1H-benzodimidazole, incorporating Benzothiazole ( 2a-e ) and 1,3,5-thiadiazole ( 2f-j ) under microwave irradiation. The synthesized compounds were well characterized using spectroscopic methods. We evaluated their in vitro Leishmanicidal, Trypanocidal, anti-mycobacterial, and anti-bacterial activities. The N -Mannich base with chloro-fluoro substituted 1,3,5-thiadiazole ( 2i ) demonstrated micromolar potency against L. mexicana (IC 50 = 1.35 µg/mL) and T. cruzi (IC 50 = 1.89 µg/mL). The penta-fluoro substituted 1,3,5-thiadiazole compound ( 2h ) exhibited activity against M. tuberculosis in primary screening (MIC = 6.25 µg/mL), comparable to Rifampicin. Compounds 2c and 2j were also found to be equipotent (MIC = 50 µg/mL) against gram-positive bacteria S. aureus MTCC 96. N -Mannich bases of Benzimidazole with 1,3,5-Thiadiazole showed greater potency than those with Benzothiazole in vitro biological evaluations. The compound 2h exhibited good binding energy in the active pocket of the receptor (PDB ID: 4cod ) with a docking score of -8.517. Molecular dynamics (MD) simulation studies conducted for the compound 2h have validated the stability of the ligand-protein complex. These studies have been meticulously carried out throughout 20.001 ns, providing detailed insights into the dynamic behavior and interactions of the complex within this time frame. In silico toxicity, predictions indicated that the active compounds are mildly toxic, with LD50 values ranging from 1000 to 2000 mg/kg of body weight. The newer hybrid derivatives of benzimidazole Mannich bases with 1,3,4-thiadiazole and benzothiazole were synthesized using microwave irradiation and evaluated for their antibacterial, antituberculosis and antiprotozoal potency. Comparative studies of molecular docking and MD simulation may reveal more insights of action of mechanism.