Journal Article

Nucleic acid binding affinity and antioxidant activity of N-m-Tolyl-4-Chlorophenoxyacetohydroxamicacid

Chauhan, Sohilkhan, Tripathi, Mamta, Alqahtani, Mohammed S., Shahid, Mudassar, Pande, Rama, Syed, Rabbani, Das, Devashish, Khilari, Rubi, Sarkar, Avijit

2024

Overview

Hydroxamic acids represent a group of weak organic acids, both naturally occurring and synthetically derived, characterized by the general formula RC(= O)N(R’OH). In this study, we investigated the binding behavior of N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) through a combination of techniques including UV–visible spectroscopy, fluorescence emission analysis, viscometry, and computational simulations using AutoDock4 software. Our findings reveal that the mode of binding between the compound and the nucleic acids is consistent with intercalation. Competitive binding experiments demonstrated that the complex competes effectively with ethidium bromide (EB) for binding to ct-DNA/t-RNA, displacing EB from its binding sites. Additionally, the introduction of the compound into the DNA-EB system resulted in a quenching of fluorescence emission peaks. Analysis of absorption spectra indicated a red shift and hypochromic shift when the compound interacted with DNA, further supporting the intercalative binding mode. The calculated binding constant (K b ) value for the compound is 6.62 × 10 4  M −1 and 5.40 × 10 3  M −1 indicating a strong interaction with ct-DNA and t-RNA respectively. We determined the Stern–Volmer constants for ct-DNA and t-RNA as 9.96 × 10 4  M −1 and 8.13 × 10 5  M −1 , respectively. The binding free energy values for ct-DNA/t-RNA were calculated to be − 3.741 × 10 7 and − 5.425 × 10 8  kcal/mol, respectively. Viscometric studies corroborated the UV results, showing a continuous increase in relative viscosity of ct-DNA/t-RNA solutions with the addition of the optimal hydroxamic acid concentration. Furthermore, we assessed the antioxidant activity of the compound using DPPH-radical scavenging and β-carotene linoleic acid assays. Gel electrophoresis results demonstrated the compound's remarkable efficacy in preventing DNA damage. Collectively, all experimental evidence supports the conclusion that N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid binds to ct-DNA/t-RNA through an intercalative mechanism, which is consistent with our molecular docking simulations.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/154 / 631/1647 / 631/45 / 631/92 / Acids / Animals / Antioxidants / Antioxidants - chemistry / Antioxidants - metabolism / Antioxidants - pharmacology / Binding / Binding Sites / Binding, Competitive / Calf thymus / Cattle / Ct-DNA /t-RNA / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - metabolism / DNA damage / Emissions / Ethidium - chemistry / Ethidium - metabolism / Ethidium bromide / Fluorescence / Free energy / Humanities and Social Sciences / Hydroxamic acid / Hydroxamic Acids - chemistry / Hydroxamic Acids - metabolism / Hydroxamic Acids - pharmacology / Interaction / Linoleic acid / Molecular Docking Simulation / multidisciplinary / Nucleic acids / Organic acids / Ribonucleic acid / RNA / RNA, Fungal - chemistry / RNA, Fungal - metabolism / Science / Science (multidisciplinary) / Spectrometry, Fluorescence / Spectroscopy / Spectrum analysis / Viscometry / Yeast / β-Carotene