Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: a biophysical and molecular docking approaches

Abstract

Nalidixic acid is a bacterial DNA gyrase inhibitor and the first member of the synthetic quinolone antibiotics. It is used in the treatment of various infectious diseases like urinary tract infections, respiratory infections, sexually transmitted diseases, acute bronchitis, and sinusitis. Interactions studies are of great significance as it will be beneficial for designing new therapeutic molecules with preferable plasma solubility and its efficacy. In this paper, we have aim to ascertain the binding mode of nalidixic acid with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) through various biophysical and in silico method. UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with ct-DNA. The binding constant is in the range of 10³ M⁻¹, indicating the groove binding mode between ct-DNA and nalidixic acid. Groove binding mode was also validated by competitive displacement assay, potassium iodide quenching experiment, circular dichroism, DNA melting studies. In the case of BSA, UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with BSA. The value of a binding constant in the case of BSA was found to be 1.517 × 10⁵ M⁻¹. The site marker displacement experiment revealed the binding location of nalidixic acid to a site I in BSA. Secondary structural and microenvironmental changes also studied through circular dichroism and three-dimensional fluorescence. Furthermore, the synchronous fluorescence spectra of BSA with nalidixic acid showed that there were changes in the microenvironment around tryptophan residues. In silico molecular docking further confirmed the binding of nalidixic acid to site I in BSA and the minor groove of DNA.

Communicated by Ramaswamy H. Sarma

Keywords:

• Calf thymus DNA
• bovine serum albumin
• nalidixic acid
• multi-spectroscopic
• interaction

Acknowledgements

We are thankful to DST, New Delhi for providing INSPIRE-SRF to SS and to CSIR, New Delhi for providing SRF to FA. We are also thankful to the UGC-DRS-SAP, DST-FIST and DBT-PURSE for generous funding to the department of biochemistry, faculty of life sciences.

Disclosure statement

The authors declare that there is no conflict of interest in this work.