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

Sahar Shahidi, Seyed Sadegh Shahraeini, Yekta Farmahini Farahani, Soroush Sardari
2020 Turk biyokimya dergisi = Turkish journal of biochemistry  
AbstractObjectivesThe 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
more » ... ichiacoli.MethodsFirst, 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).ResultsIn 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.ConclusionsOne possible mechanism involved in the action of nalidixic acid in inhibiting the E. coli growth is to influence thi-box riboswitch.
doi:10.1515/tjb-2020-0168 fatcat:xir2uf5hd5ee3nc2cnzy3qf52q