Effect of local anesthetic drug procaine hydrochloride on the conformational stability of bovine hemoglobin: Multi-spectroscopic and computational approaches

A spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of human hemoglobin with 2,4-dichlorophenoxyacetic acid

2,4-Dichlorophenoxyacetic acid (2,4-D) is a systemic herbicide widely used to control dicotyledonous weeds. The general population is routinely exposed to 2,4-D due to consumption of contaminated food and water. 2,4-D is known to damage cellular components in human erythrocytes. This study investigated in detail the interaction of 2,4-D with human hemoglobin (Hb), the major protein in erythrocytes (>95%), and characterized the binding properties utilizing multi-spectrometric and in silico techniques. The UV-visible spectra suggested that 2,4-D interacts with Hb. The fluorescence quenching studies at three different temperatures further showed the binding of 2,4-D to Hb and the formation of a ground-state complex. The results indicated that 2,4-D binds spontaneously to a single moderate-affinity binding site on Hb. Furthermore, the binding process involved van der Waals forces and hydrogen bonding. Circular dichroism and synchronous fluorescence spectra showed that the binding of 2,4-D altered the conformation of Hb and decreased the polarity around its tryptophan residues. 2,4-D binding inhibited the inherent esterase activity of Hb. Computational analysis demonstrated that the Hb-2,4-D complex was stable and identified the amino acid residues at the binding site. Thus, 2,4-D interacts with Hb, modifies the protein conformation and consequently impairs its functions.

Study on behavior intermolecular force and binding mechanism interaction between bovine hemoglobin and cyanocobalamin by using of spectroscopic and molecular docking methods

In this study, fluorescence, synchronous fluorescence, fluorescence resonance energy transfer (FRET), Fourier transform infrared (FT-IR) and molecular docking methods were employed to investigate the binding mechanism between bovine hemoglobin (BHb) and vitamin B12 (cyanocobalamin). Since BHb shares 90% sequence similarity with human hemoglobin investigating its interactions with small molecules is highly relevant. Fluorescence data analysis under varying temperatures indicated that the complex formation between vitamin B12 and BHb is stationary with ground-state complex formation. Thermodynamic investigation indicated hydrogen bonding and hydrophobic interactions in negative changes in enthalpy and entropy during the process of binding. Förster resonance energy transfer analysis determined the binding distance of vitamin B12 with BHb tryptophan residues as 3.11 nm. FT-IR spectroscopy, synchronous fluorescence and UV-visible examinations revealed that vitamin B12 may induce structural modification in BHb. Additionally, molecular docking simulations provided information about binding interactions and validated the spectroscopic findings.

Characterization of the binding interaction between bovine hemoglobin and riboflavin sodium phosphate: multi-spectroscopic analysis and molecular docking studies

Proteins are essential bimolecular substances that play a crucial role in the maintaining life and are closely associated with its the origin, evolution, and metabolism. Through the use of molecular docking, synchronous fluorescence spectroscopy, ultraviolet-visible absorption, fluorescence, and Fourier transform infrared (FT-IR) spectroscopy, this study sought to clarify the relationship between bovine hemoglobin (BHb) and riboflavin sodium phosphate (RSP) at the normal biological condition. The fluorescence quenching experiment indicated that RSP can cause a static quenching mechanism that quenches BHb's natural fluorescence. Thermodynamic measurements demonstrated that the hydrogen bonding molecular force and hydrophobic contacts caused negative enthalpy and entropy changes during RSP binding to BHb. Using Förster resonance energy transfer, the binding distance between RSP and the BHb tryptophan residues was determined to be 3.11 nm. Fourier transform infrared spectroscopy, synchronous fluorescence, and UV-visible studies revealed that the secondary structure of BHb was considerably altered due to interaction with RSP. The molecular docking simulation revealed that, in addition to hydrophobic interactions, the hydrogen bonds were involved in the interaction of BHb-RSP complex. This study aims to enhance our understanding of the molecular interactions between BHb and RSP, which is significant for elucidating the biochemical pathways involved in metabolic processes.

Synthesis, characterization, computational studies and in vitro antiparasitic activity of novel flavanoidal-1,2,4,5-tetrazinane-6'-thione

Keeping in view the growing resistance of conventional antiparasitic drugs, this study aimed to synthesize a series of six noble flavanoidal tetrazinane-6'-thione derivatives by employing a facile one pot reaction pathway. Structural characterizations of synthesized compounds were performed by using IR, 1HNMR, 13CNMR and LC-MS spectra. Molecular docking study showed that one of the newly synthesized compounds strongly bind with the amino residues of BSA with two hydrogen bonding interactions. Physiological properties, pharmacokinetic properties (ADME) and toxicity of all synthesized compounds was carried out using Molinspiration and pkCSM softwares. DFT calculations were performed for all synthesized compounds using B3LYP method to obtain various molecular properties. Using a previously established model for parasitic infections, Clinostomum complanatum we showed that the newly synthesized compounds have a very potent parasitic activity. To elucidate the possible mechanisms, we tested the exposed parasites and observed a perturbation in lipid peroxidation and the antioxidant enzyme superoxide dismutase. Implications of this are discussed in the light of development of these molecules as antiparasitic drugs. HIGHLIGHTSSix noble flavanoidal-1,2,4,5-tetrazinane-6'-thiones (7-12) were synthesized using flavanone derivatives and thiocarbohydrazide in acetic acid as a reagent in ethanol employing one-pot synthesis.Structural characterization of synthesized compounds was done using IR, 1HNMR, 13CNMR and LC-MS spectra.Physicochemical analysis determined that all synthesized compounds are efficiently absorbed and have good permeability.In silico ADME and Toxic properties were determined for all synthesized compounds.In vitro antiparasitic activity was performed for all synthesized compounds against Clinostomum complanatum.Molecular Docking studies demonstrated the binding interaction with BSA enzyme through hydrogen bonding.Density functional theory (DFT) have been performed to estimate the various molecular properties of the synthesized compounds.Communicated by Ramaswamy H. Sarma.

Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods

The ability of a therapeutic compound to bind to proteins is critical for characterizing its therapeutic impacts. We have selected quercetin (Qu), a most common flavonoid found in plants and vegetables among therapeutic molecules that are known to have anti-inflammatory, antioxidant, anti-genotoxic, and anti-cancer effects. The current study aimed to see how quercetin interacts with pepsin in an aqueous environment under physiological conditions. Absorbance and emission spectroscopy, circular dichroism (CD), and kinetic methods, as well as molecular dynamic (MD) simulation and docking, were applied to study the effects of Qu on the structure, dynamics, and kinetics of pepsin. Stern-Volmer (K_sv) constants were computed for the pepsin-quercetin complex at three temperatures, showing that Qu reduces enzyme emission spectra using a static quenching. With Qu binding, the V_max and the k_cat/K_m values decreased. UV-vis absorption spectra, fluorescence emission spectroscopy, and CD result indicated that Qu binding to pepsin leads to microenvironmental changes around the enzyme, which can alter the enzyme's secondary structure. Therefore, quercetin caused alterations in the function and structure of pepsin. Thermodynamic parameters, MD binding, and docking simulation analysis showed that non-covalent reactions, including the hydrophobic forces, played a key role in the interaction of Qu with pepsin. The findings conclude of spectroscopic experiments were supported by molecular dynamics simulations and molecular docking results.

Exploring the binding mode of ester-based cationic gemini surfactants with calf thymus DNA: A detailed physicochemical, spectroscopic and theoretical study

Gene therapy is a transfectant method for the treatment of hereditary disease, which transfers the gene mutation into the cells. In the view of the high prospects of utilization of cationic gemini surfactants as a non-viral vector for the gene transfection, we have made a comprehensive study on the interactions between a recently synthesized series of ester-functionalized cationic C_m-E2O-C_m gemini surfactants (m = 12, 14 and 16) with calf thymus deoxyribonucleic acid (ctDNA) utilizing various techniques. The micellization behavior of gemini surfactants has been altered in the presence of ctDNA. A series of measurements (fluorescence, UV-vis and time-resolved fluorescence) show that the quenching of ctDNA proceeds by a static mechanism. The competitive displacement studies (EB, AO and HO), KI quenching analysis, CD studies and viscosity measurements suggested intercalative binding mode in a stoichiometry ratio of 1:1 with the K_b (binding constant) order being: C₁₆-E2O-C₁₆ > C₁₄-E2O-C₁₄ > C₁₂-E2O-C₁₂. The thermodynamic parameters show that the geminis interacted with ctDNA spontaneously through ionic/electrostatic interactions. Furthermore, the theoretical approaches offer accurate insights about the binding of gemini surfactants with DNA, and are in consistence with the experimental results.