Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT & GC hairpin duplex DNA

Raubasine-Induced Groove Binding in Salmon Testes DNA: Exploring the Structural Modulation, Antiglycation, and Antioxidant Properties

As one of nature's most fundamental blueprints and due to its critical role in life processes, DNA has naturally become the cornerstone of numerous research efforts. One particularly intriguing area of study is understanding how small molecules interact with nucleic acids. In this study, we investigated the interaction between the plant-derived indole alkaloid Raubasine (Ajmalicine; AJM) and Salmon Testes (ST) DNA using biophysical and computational techniques. A hyperchromic shift in the fluorescence intensity indicated the effective binding of AJM to ST DNA. The binding constant was in the order of 105 M-1 with a single preferential binding mode. Thermodynamic analysis revealed that exothermic binding was driven by positive entropy and negative enthalpy. The salt-dependent fluorescence analysis indicates the involvement of nonpolyelectrolytic forces in the interaction. Studies of iodide quenching, urea denaturation, dye displacement, and molecular docking further support that AJM binds to ST DNA through groove binding. Structural perturbation of DNA was evident from circular dichroism. The stability of the AJM-DNA complex was confirmed by molecular dynamics simulations. Prolonged elevated blood glucose levels induce nonenzymatic glycation of DNA, resulting in DNA-AGE (advanced glycation end-products) formation and free radical production, which disrupts the DNA structure. We explored ST-DNA glycation and its suppression by AJM. DNA-AGEs in vitro were characterized using UV-vis and fluorescence spectroscopy. The inhibition of glycation by AJM was assessed through changes in AGEs fluorescence intensity, gel electrophoresis patterns, and antioxidant activity, highlighting its ability to target glycated sites or neutralize free radicals generated during glycation. Our findings reveal AJM's potential to prevent the formation of AGEs, which may offer promising avenues for targeted therapies against glycation-related diseases such as diabetes, neurodegeneration, and cancer.

Entropically driven binding of Camptothecin in the minor groove of salmon testes DNA

The present study focuses on binding association of Camptothecin (CMT) towards natural deoxy-ribonucleic acid (salmon testes, ST) under physiological conditions of pH 7.4. Extensive spectroscopic and computational techniques have been employed to elucidate thermodynamics of the said interaction. UV and fluorescence analyses portrays significant intensity changes (hyper-chromic and hypsochromic) in the spectra, which confirms effective CMT binding to ST DNA. The McGhee-von Hipple method and Scatchard plot analyses estimated the binding affinities in 105 M-1 range. Associated thermodynamic data revealed spontaneous and exothermic nature of binding. Temperature-dependent fluorescence showed negative change in enthalpy and positive change in entropy, leading to the formation of a 1:1 adduct. Non-polyelectrolytic forces appeared to be the driving force of the ligand-DNA interaction, according to salt-dependent fluorescence. Dye displacement assay, viscosity study, DNA melting, iodide quenching, urea denaturation assay examined the minor groove nature of CMT. In silico docking study examined precise molecular representations of the minor groove binding mechanism that formed between the complex, and the study's findings were consistent with the experimental results. Simulation studies also validated the experimental analysis and docking data. These findings could expedite the process of creating new and improved CMT molecular derivatives and help in the creation of DNA-targeted medicines, which may be beneficial from a pharmaceutical point of view.

3-Amide-β-carbolines block the cell cycle by targeting CDK2 and DNA in tumor cells potentially as anti-mitotic agents

β-Carboline alkaloids are natural and synthetic products with outstanding antitumor activity. C3 substituted and dimerized β-carbolines exert excellent antitumor activity. In the present research, 37 β-carboline derivatives were synthesized and characterized. Their cytotoxicity, cell cycle, apoptosis, and CDK2- and DNA-binding affinity were evaluated. β-Carboline monomer M3 and dimer D4 showed selective activity and higher cytotoxicity in tumor cells than in normal cells. Structure-activity relationships (SAR) indicated that the amide group at C3 enhanced the antitumor activity. M3 blocked the A549 (IC50 = 1.44 ± 1.10 μM) cell cycle in the S phase and inhibited A549 cell migration, while D4 blocked the HepG2 (IC50 = 2.84 ± 0.73 μM) cell cycle in the G0/G1 phase, both of which ultimately induced apoptosis. Furthermore, associations of M3 and D4 with CDK2 and DNA were proven by network pharmacology analysis, molecular docking, and western blotting. The expression level of CDK2 was downregulated in M3-treated A549 cells and D4-treated HepG2 cells. Moreover, M3 and D4 interact with DNA and CDK2 at sub-micromolar concentrations in endothermic interactions caused by entropy-driven adsorption processes, which means that the favorable entropy change (ΔS > 0) overcomes the unfavorable enthalpy change (ΔH > 0) and drives the spontaneous reaction (ΔG < 0). Overall, these results clarified the antitumor mechanisms of M3 and D4 through disrupting the cell cycle by binding DNA and CDK2, which demonstrated the potential of M3 and D4 as novel antiproliferative drugs targeting mitosis.

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.

PROTEIN BINDING CHARACTERISTICS OF YOHIMBINE, A NATURAL INDOLE ALKALOID BASED DRUG FOR ERECTILE DYSFUNCTION

Even to this day, talking about sexual-dysfunctions largely remains a taboo. Hence less studies were recorded and fewer remedies given. Erectile dysfunction (ED) is one of the most commonly treated psychological disorders which leads to major distress, interpersonal limitation and reduces the quality of life & marriage. This study aimed to assess a plant-derived molecule, Yohimbine (Yoh, a β-carboline indole-alkaloid; often used for ED treatment) and its potential binding phenomenon with hemoglobin (Hb). Successful binding of the Yoh with Hb is evident from spectroscopic and molecular-docking results. Yoh quenched the fluorescence of Hb efficiently through static mode. The binding affinity was in the order of 10⁵ M^-1 with 1:1 stoichiometry. Thermodynamic analyses concluded that the protein-ligand association to be spontaneous and attributed by entropy-driven exothermic-binding. Non-polyelectrolytic factor was the core, dominating factor. The structural aspects have been deciphered through infra-red spectroscopy and computational-methods. The giant 3D-protein moiety was significantly perturbed through drug-binding. Hydrophobic forces and hydrogen bonding participation were stipulated by molecular modeling data. This study reveals the detailed interaction pattern and molecular mechanism of Hb-Yoh binding; correlating the structure-function relationship for the first time; therefore, holds enormous importance from the standpoint of rational and efficient drug-designing & development.