Effect of some amino acids on the binding of quercetin and rutin flavonoids with DNA

Evaluating binding behavior of quercetin to human serum albumin and calf thymus DNA: Insights from molecular dynamics, spectroscopy, and apoptotic pathway regulation

In this work, we sought to apprehend quercetin binding affinity and its interaction behavior in complex with human serum albumin (HSA) and calf thymus DNA (ctDNA) through multi spectroscopy and molecular dynamics and also evaluated its effects on colorectal cancer. The binding constants of ctDNA-quercetin and HSA-quercetin complexes at 298 K, which were calculated to be (2.67 ± 0.04) × 103 M-1 and (4.77 ± 0.05) × 104 M-1 respectively, denoted the strong binding of quercetin with ctDNA and HSA. The Ksv and Kb values decrease with increasing temperature, indicating that the quenching of HSA and ctDNA in the presence of quercetin is caused by the combined dynamic and static effects. The obtained thermodynamic parameters for the ctDNA-quercetin interaction represented the existence of electrostatic forces (ΔH0 < 0 and ΔS0 > 0), and the thermodynamic parameters of HSA-quercetin complex disclose the dominance of hydrogen bonds and van der Waals interactions (ΔH0 < 0 and ΔS0 < 0). Moreover, the interactions were exothermic, as evidenced by the negative ΔH0 value for both interactions. According to molecular docking and MD simulation data, quercetin was capable of placing into the site 1 of HSA and forming stable interaction plus this ligand tended to unwind DNA's strands as an intercalator ligand, which was confirmed by experimental results. The fluorescence competition studies between the two intercalator probes of ethidium bromide (EB) and acridine orange (AO), as well as the effect of ionic strength, proposed the strong tendency of quercetin to exist between the two strands of ctDNA as a sign of its intercalative property. Consequently, quercetin can be assumed as an efficient intercalator ligand carried by HSA with an anticancer property. We also conducted cell viability experiments on HT-29 and SW620 cell lines to validate the anticancer ability of quercetin, and observed its decreasing impact on the cell viability of these two cell lines. Additionally, the outcomes of Real-time qPCR proved its capability to reduce the CXCR4 expression and increase the NKD2 expression in Wnt signaling pathway. Therefore, these facts confirm the inhibiting ability of quercetin towards colorectal cancer growth via the prevention of Wnt pathway and approve its functionality as a potential anticancer agent for this cancer.

Comprehensive Investigations About the Binding Interactions of Sudan Dyes with DNA by Spectroscopy and Docking Methods

Sudan dyes are recognized as carcinogens, which are strictly determined whether there are them in food for food safety. Hence, in order to understand the mechanism at the molecular level, this work investigated the binding interactions of Sudan I-IV with calfthy mus DNA. The synchronous fluorescence and UV-vis spectral results suggested the complex formation between Sudan I-IV and ct-DNA. EB and Hoechst 33258 displacement experimental results confirmed the binding sites of Sudan I-IV in ct-DNA and the minor groove-binding mode of Sudan I-IV with ct-DNA. The molecular modeling computational method also proved binding mode, which is consistent with the spectral experiments. In addition, the aromatic rings of Sudan I-IV play important roles in binding with DNA. Compared to Sudan I and II, the increase of molecular conjugation system enhances the binding abilities of Sudan III and Sudan IV with DNA. Vdm + Hbond + desolv energies of them are the main contribution of their combined energies.

Non-covalent binding interaction of bioactive coumarin esculetin with calf thymus DNA and yeast transfer RNA: A detailed investigation to decipher the binding affinities, binding location, interacting forces and structural alterations at a molecular level

Esculetin is a well-known coumarin derivative found abundantly in nature possessing an extensive array of pharmacological and therapeutic properties. Consequently, to comprehend its molecular recognition mechanism, our objective is to conduct a complete investigation of its interactions with the nucleic acid, specifically ct-DNA, and t-RNA, using spectroscopic and computational techniques. The intrinsic fluorescence of esculetin is quenched when it interacts with ct-DNA and t-RNA, and this occurs through a static quenching mechanism. The thermodynamic parameters demonstrated that the interaction is influenced by hydrogen bonding and weak van der Waals forces. CD and FT-IR results revealed no conformational changes in ct-DNA and t-RNA structure on binding with esculetin. Furthermore, competitive displacement assay with ethidium bromide, melting temperature, viscosity measurement, and potassium iodide quenching experiments, reflected that esculetin probably binds to the minor groove of ct-DNA. The molecular docking results provided further confirmation for the spectroscopic findings, including the binding location of esculetin and binding energies of esculetin complexes with ct-DNA and t-RNA. Molecular dynamics simulation studies demonstrated the conformational stability and flexibility of nucleic acids.

C60 adduct with L-arginine as a promising nanomaterial for treating cerebral ischemic stroke

The work aimed to investigate the biocompatibility and biological activity of the water-soluble fullerene adduct C60-Arg. It was found that the material is haemocompatible, is not cyto- and genotoxic, possesses pronounced antioxidant activity. Additionally, this paper outlines the direction of application of water-soluble fullerene adducts in the creation of neuroprotectors. It has been suggested that a putative mechanism of the protective action of the C60-Arg adduct is associated with its antioxidant properties, the ability to penetrate the blood-brain barrier, and release nitrogen monoxide as a result of the catabolism of L-arginine residues, which promote vascular relaxation. The action of the C60-Arg adduct was compared with the action of such an antioxidant as Edaravone, which is approved in Japan for the treatment of ischemic and haemorrhagic strokes.