Synthesis, modelling, biological activity of new thiophene hybridized with pyrazole, and/or pyridine analogues as potential DNA <i>gyrase</i> and topoisomerase IV inhibitors

Promoted by the well-established, valuable biological activity of thiophene-based hybrids, the study displayed the synthesis of two series of thiophene-pyrazole hybrids, 7a-c and thiophene-pyridine hybrids 9a-c, via reacting arylhydrazone with halogenated reagents and nucleophilic addition of cyanoacetamide to the arylidene-malononitrile, respectively. The chemical structure of the produced hybrids was elucidated using reliable spectroscopic techniques, including Fourier transform infrared (FTIR), Nuclear magnetic resonance (NMR), and Mass spectra (MS). The density functional theory (DFT) modeling of the delivered conjugates disclosed comparable non-planar configurations and frontier molecular orbital (FMO) constructions, in which the benzoate junction and oxo-thienyl moiety performed as donor (highest occupied molecular orbital; HOMO) and acceptor (lowest unoccupied molecular orbital; LUMO) portions, respectively. Furthermore, the antimicrobial activity of the manufactured hybrids was evaluated, and analog 7a exhibited outstanding activity against both bacterial strains and C. albicans, with large inhibition zones (IZ = 41-43 mm). Meanwhile, the cytotoxicity efficacy of the synthesized derivatives was assessed against human breast cancer (MCF-7), normal kidney epithelial (Vero), and the normal cells (WI-38) cell lines. The series 7a-c was more active in general than the other conjugates; for example, derivative 7a was very selective towards MCF-7 (IC 50 = 14.39±0.26 μM). Furthermore, the hybrid’s inhibitory effect on the bacterial topoisomerases IV and DNA gyrase B was evaluated, where hybrid 7a presented the greatest action (IC 50 = 12.09±0.31 and 0.43±0.12 μM), respectively. Moreover, molecular docking performed against bacterial DNA gyrase B revealed that analogues 7a-c and 9a-c exhibited superior bindings; analogue 9c demonstrated the strongest binding energy (-7.9520 kcal/mol), proposing improved target arrangement. Finally, the Swiss absorption, distribution, metabolism and excretion (ADME) analysis highlighted the pharmacokinetic properties of the synthesized thiophene hybrids. Analogues with low molecular weight, 4 and 5 , exhibited optimal solubility and absorption, while bulkier analogues 6 , 7a-c, and 9a-c presented lower solubility due to increased topological polar surface area (TPSA) and lipophilicity.