Fluorescent delivery vehicle containing cobalt oxide-umbelliferone nanoconjugate: DNA/protein interaction studies and anticancer activity on MF7 cancer cell line

An in-depth study of clofarabine's binding mechanism to DNA: A thorough experimental and theoretical investigation

The interaction of medicinal compounds with nucleic acids is a critical challenge in drug development. This research focused on the binding dynamics of clofarabine (CLO), an antineoplastic agent, with fish sperm DNA (dsDNA) under conditions that simulate the physiological environment at a pH of 7.4. The investigations employed multiple techniques, including fluorescence and UV spectroscopy, thermal denaturation analysis, viscosity measurements, electrochemical assessments, and molecular docking studies to elucidate these binding interactions. The binding constant (Kb) for the interaction between CLO and dsDNA, as determined from the Benesi-Hildebrand plot, was found to be 2.74 × 104 at a temperature of 298 K. The entropy (∆S) and enthalpy (∆H) changes associated with this binding interaction were measured as + 43.08 J mol-1 K-1 and -12.44 kJ mol-1, respectively. These values indicate that the predominant forces driving the binding interaction are primarily due to hydrogen bonding. Studies using the ethidium bromide and the Hoechst probe showed that CLO does not bind to dsDNA intercalatively. Findings obtained through UV-Vis absorption spectroscopy, competitive binding assays, and viscosity assessments indicated that CLO associates with dsDNA by binding within the minor groove. Molecular docking analyses demonstrated that CLO is accommodated within the AT-rich segment of the minor groove, with significant hydrogen bonding interactions occurring between CLO and dsDNA. These findings may offer valuable perspectives for elucidating the mechanisms underlying the toxicity, resistance, and adverse effects associated with CLO.

ct-DNA compaction by nanoparticles formed by silica and gemini surfactants having hydroxyl group substituted spacers: In vitro, in vivo, and ex vivo gene uptake to cancer cells

Hybrid nanoparticles formed by Silica (SiO2) coated with cationic gemini surfactants with variable hydroxyl group substituted spacers, 12-4(OH)-12,2Br- and 12-4(OH)2-12,2Br- have shown a great extent of compaction of calf thymus DNA (ct-DNA) compared to conventional counterpart cationic surfactant, dodecyl trimethylammonium bromide (DTAB). Study shows not only the hydrophobicity of the spacer but also the hydrogen bonding interactions between the hydroxyl group substituted spacer and DNA have a great role in DNA compaction. 12-4(OH)2-12,2Br- is more efficient in compacting ct-DNA compared to 12-4(OH)-12,2Br- due to the stronger binding of the former with ct-DNA than the latter. While 12-4(OH)-12,2Br- makes 50 % ct-DNA compaction at its 0.63 μM concentration in the presence of SiO2 nanoparticles, the same % of compaction can be achieved at a concentration as low as 0.25 μM of 12-4(OH)2-12,2Br-. However, DTAB makes 50 % ct-DNA compaction at a concentration as high as 7.00 μM under the same condition. Therefore, the present systems address the very common challenge, i.e., cytotoxicity due to cationic surfactants. The system of 12-4(OH)2-12,2Br- coated SiO2 nanoparticles displays the maximum cell viability (≥90 %), causing the least cell death in the mouse fibroblast cells (NIH3T3) cell lines compared to the cell viability of ≤80 % for DTAB. 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system has presented excellent in vitro cellular uptake of genes on mouse mammary gland adenocarcinoma (4T1) cells after incubating for 3 h and 6 h. In vivo study shows that 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system takes the highest amount of ct-DNA in cells and tumors in a time-dependent manner. The ex vivo studies using different organs of the mice demonstrate that the tumor sites in the breast of the mice are most affected by these formulations. Cytotoxicity assays and cellular uptake studies suggest that the present systems can be used for potential applications for gene delivery and oncological therapies.

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs

DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.

Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review.

Graphical abstract

Biophysical binding profile with ct-DNA and cytotoxic studies of a modulated nanoconjugate of umbelliferone cobalt oxide loaded on graphene oxide (GO) as drug carrier

In an attempt to identify suitable nano-carriers for drug delivery, natural drug umbelliferone was chosen to synthesize new modulated nanoconjugate of umbelliferone cobalt oxide with cobalt (II) nitrate in one pot assembly in the presence of tannic acid. The synthesized nanoconjugate drug (NCD) was then loaded on graphene oxide (GO) as drug carrier by simple ultrasonication method and thoroughly characterized by various spectroscopic techniques (FT-IR, SEM, TEM, XRD, EPR and thermogravimetric analysis) which revealed the successful loading of the nanoconjugate drug on GO. The UV-visible, fluorescence and electrochemical studies suggested that strong π-π stacking interactions exist between nanoconjugate drug and GO. The binding studies of NCD-GO with ct-DNA were performed by various optical and biophysical methods viz., UV-visible, fluorescence, circular dichroism (CD) and cyclic voltammetry (CV) which indicated electrostatic mode of binding towards the ct-DNA. Furthermore, condensate of nanoconjugate drug-loaded GO (NCD-GO) with ct-DNA was prepared and analyzed by scanning electron microscopy (SEM) which revealed that the interaction of NCD-GO with ct-DNA had occurred. Cleavage activity of NCD-GO with pBR322 was evaluated by gel electrophoresis and it was found that NCD-GO cleave DNA through hydrolytic pathway involving hydroxyl radical (OH). The cytotoxicity of NCD-GO was evaluated against human liver carcinoma (Huh-7), prostate cancer (Du-145) cell lines along with normal cell line (PNT 2). The results obtained showed selective cytotoxic activity of NCD-GO against Du-145 cell lines. The intracellular uptake was visualized by confocal microscopy which revealed the significant cellular uptake and internalization of nanoparticles by cells. Moreover, the adsorption of cobalt oxide umbelliferone on GO was studied by density functional theory. The process of adsorption was found exothermic in nature and the optimized geometry structure is quite stable. Communicated by Ramaswamy H. Sarma.

Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches

β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 10³ M^-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.