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Objectives The development of novel antibiotic compounds requires riboswitches; in fact, riboswitches are RNA elements present in the 5′ untranslated region of bacterial mRNA and have a metabolite-binding aptamer domain and an expression platform regulating the expression of vital genes. In the present research, one riboswitch, namely thi-box riboswitch with distinct regulatory mechanisms, was studied. It recognizes Thiamine Pyrophosphates (TPP) regulating TPP-biosynthesis genes in  Escherichia coli . Methods First, the compounds similar to riboswitch ligands were studied, and their binding with the riboswitch and nucleosides was investigated by molecular docking. Then, compounds containing high binding energy were chosen, and their minimum inhibitory concentration in  E. coli  was determined by the MIC test. Finally, the binding of compounds to nucleotides and RNA was investigated by measuring the absorbance spectrum through NanoDrop and circular dichroism (CD). Results In the thi-box riboswitch, nalidixic acid was found to have the best binding energy (−5.31 kJ/mol), and it inhibited  E. coli  growth at the minimum inhibitory concentration of 125 μg/mL, and it could bind to ribonucleosides and RNA  in vitro . Conclusions One possible mechanism involved in the action of nalidixic acid in inhibiting the  E. coli  growth is to influence thi-box riboswitch.

Thiamine pyrophosphate riboswitch regulation: a new possible mechanism involved in the action of nalidixic acid