Noncovalent interactions between Quinoline yellow and trypsin: In vitro and in silico methods

Assessment on malvidin-3-glucoside interaction with TLR4 via multi-spectroscopic analysis and molecular docking

As one innate immune pattern recognition receptor, Toll-like receptor 4 (TLR4) recently has been considered as a critical player in glucolipid metabolism. Blueberries contain high level of anthocyanins, especially malvidin-3-glucoside (Mv-3-glc), which contribute the anti-inflammatory, hypoglycemic, and hypolipidemic effects. It is speculated that Mv-3-glc is able to possess these functions by binding to TLR4. Here, the noncovalent interactions of Mv-3-glc and TLR4 was explored through multi-techniques including fluorescence and ultraviolet-visible (UV-Vis) absorption spectroscopy, as well as molecular docking. The results demonstrated that Mv-3-glc was able to quench TLR4 intrinsic fluorescence effectively. A stable complex was formed spontaneously and the reaction was exothermic. The degree of binding of Mv-3-glc to TLR4 showed a strong dependence on the chemical concentration, temperature, and pH values. The negative signs for enthalpy (ΔH = -69.1 ± 10.8 kJ/mol) and entropy (ΔS = -105.0 ± 12.3 J/mol/K) from the interaction of the Mv-3-glc and TLR4 shows that the major driving forces are the hydrogen bonding and van der Waals' force, which is consistent with the molecular docking results. In addition, molecular docking predicted that the active center with specific amino acid residues, Phe126, Ser127, Leu54, Ile153, and Tyr131 was responsible for the site of Mv-3-glc binding to TLR4/myeloid differentiation protein-2 (MD-2). These findings confirmed that Mv-3-glc could bind to TLR4, which would be beneficial to understand the target therapeutic effects of blueberry anthocyanins on TLR4 in regulating glucolipid metabolism.

Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation

Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.

Effect of glycation-induced concentration-dependent change in albumin structure and alteration in its binding capacity

Reducing sugars causes confirmatory alterations in albumin structure by the nonenzymatic glycation of the amino group of serum albumin. In this study, glucose and its hazardous metabolic products like glyoxal and methylglyoxal were incubated with bovine serum albumin (BSA). The confirmational changes in BSA molecule's structure by glycating substances was investigated using a variety of spectroscopic methods, including deconvolutionFourier Transform Infra-red (FT-IR) spectroscopy, fluorescence spectroscopy, UV spectroscopy and circular dichroism (CD) spectroscopy. Dynamic fluorescence quenching was observed in the case of glucose, while static quenching was observed in the case of methyl glyoxal and glyoxal. Similarly, employing deconvolution FT-IR spectroscopy and CD spectroscopy for determination of change in secondary structures in terms signature of α-helix, β-turn, β-sheet and random coil modifications. Destabilization or unfolding of the albumin structure, due to the disruption of the hydrogen bonding pattern that stabilizes the albumin manifold, causes a 25-50% reduction in α-helix and a 2-fold increase in β-sheet and turns in glycated BSA. The competitive displacement interaction studies with warfarin were performed using the ultrafiltration technique and quantitative determination of free drug in ultrafiltrate using LC-MS/MS. The binding of carbamazepine (CBZ) or its active metabolite to proteins was unaffected by the glycation of BSA with glucose and methyl glyoxal. Nevertheless, with glyoxal-modified BSA, it changed the binding of selected analytes significantly. Based on in vitro observations and results, it could be anticipated that the serum CBZ concentration variation may be worsened in uncontrolled diabetes circumstances, with an overall variance of 30-40% possible.Communicated by Ramaswamy H. Sarma.

Molecular interaction studies of P3CL on bovine serum albumin through biophysical approach

In the fields of pharmacology and life sciences, it is essential to study how prescribed drugs interact with carrier proteins in human serum albumin. The current study has evaluated the binding properties of rhodanine derivative; (z)-2-(4-(5-((3-(3-chlorophenyl)-1-phenyl-1H-pyrazol-4-oxo-2-thioxothiazolidin-3-yl)benzamido)acetic acid (P3CL) on bovine serum albumin (BSA) by biophysical approach. BSA is a homology model of Human serum albumin. Due to the cost-effectiveness of Human Serum Albumin (HSA) we have studied the binding properties of rhodanine derivative (P3CL) on BSA. The BSA-P3CL interactions were investigated by fluorescence spectroscopy and revealed the presence of a static quenching mechanism. P3CL possesses good binding affinity on BSA with binding constant KP3CL = 5.36330 × 1013 M-1 binding free energy. We have calculated the binding free energy, the number of binding sites, and the binding constants. The establishment of hydrogen bonds and the active participation of amino acids in drug binding were confirmed by molecular docking studies. As conventional processes for the investigation of pharmacological drugs, therapeutic combinations, and coordinated drug intake, the offered strategies are simple to comprehend, accurate, and rapid to put into practice. Our findings will support an additional investigation into ligand's pharmacological activity.Communicated by Ramaswamy H. Sarma.

Enzyme engineering of choline oxidase for improving stability

Functioning as a flavoprotein, choline oxidase facilitates the transformation of choline into glycine betaine. Notably, choline oxidase and its resultant product, glycine betaine, find extensive applications across various industries and fields of study. However, its high sensitivity and tendency to lose functional activity at high temperatures reduces its industrial usage. MD simulation and mutation studies have revealed the role of certain residues responsible for the enzyme's thermal instability. This study focuses on inducing thermal stability to choline oxidase of A. globiformis through computational approaches at a maximum temperature of 60 °C. MD simulation analysis showed that Trp 331, Val 464 and Ser 101 contribute to structural instability, leading to the instability at 60 °C. Mutation of these residues with phenylalanine residues and simulation of the mutated enzyme at 60 °C exhibited thermostability and insignificant residual fluctuation. The re-docking and MM/GBSA analyses further validated the mutated enzyme's binding affinity and catalytic activity.Communicated by Ramaswamy H. Sarma.

Investigating the effect of pH on the interaction of cypermethrin with human serum albumin: Insights from spectroscopic and molecular dynamics simulation studies

To efficiently combat the negative consequences of the utilization of pesticides and hazardous substances with biomolecules, it is crucial to comprehend the features of the corresponding compounds. In this study, interactions between cypermethrin (CYP) and HSA at neutral and acidic pH were investigated using a set of spectroscopic and computational tools, such as UV/VIS's absorption spectroscopy, fluorescence, Fourier-transform infrared (FTIR) spectroscopy, molecular docking, and molecular dynamics. Furthermore, the effect of CYP on the HSA thermal stability was investigated. The increase in the CYP concentration at acidic and neutral pH resulted in static HSA fluorescence quenching. In the interaction between HSA and CYP at both pH, increasing the temperature led to a decrease in the Stern-Volmer quenching constant and the binding constant. We also revealed that with increasing CYP concentration, the melting temperature of HSA increases at both pH values.

Evidence for paraquat-pepsin interaction: In vitro and silico study

The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.

Biophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase

Human Lymphatic filariasis is caused by parasitic nematodes Wuchereria bancrofti, Brugia malayi, and Brugia timori. Protein disulfide isomerase (PDI), a redox-active enzyme, helps to form and isomerize the disulfide bonds, thereby acting as a chaperone. Such activity is essential for activating many essential enzymes and functional proteins. Brugia malayi protein disulfide isomerase (BmPDI) is crucial for parasite survival and an important drug target. Here, we used a combination of spectroscopic and computational analysis to study the structural and functional changes in the BmPDI during unfolding. Tryptophan fluorescence data revealed two well-separated transitions during the unfolding process, suggesting that the unfolding of the BmPDI is non-cooperative. The binding of the fluorescence probe 8-anilino-1-naphthalene sulfonic acid dye (ANS) validated the results obtained by the pH unfolding. The dynamics of molecular simulation performed at different pH conditions revealed the structural basis of BmPDI unfolding. Detailed analysis suggested that under different pH, both the global structure and the conformational dynamics of the active site residues were differentially altered. Our multiparametric study reveals the differential dynamics and collective motions of BmPDI unfolding, providing insights into its structure-function relationship.Communicated by Ramaswamy H. Sarma.

Investigation on conformational variation and enzymatic activity of trypsin affected by Ti3C2 QDs via spectroscopic technique and molecular modeling

In this paper, Ti₃C₂ quantum dots (Ti₃C₂ QDs) were synthesized by simply treating Ti₃C₂ MXene powder with acid and base via hydrothermal method. Ti₃C₂ QDs exhibited superior fluorescence property and were used for the fluorescent imaging of living HeLa cells successfully. In order to evaluate the influence of Ti₃C₂ QDs on protease with specific biological functions, binding interaction of Ti₃C₂ QDs with trypsin was studied comprehensively and deeply through spectroscopic strategies and molecular modeling technique. The intrinsic fluorescence of trypsin was spontaneously quenched by Ti₃C₂ QDs through static quenching mode under van der Waals interaction force, and Ti₃C₂ QDs bound with the inactive residue domain of trypsin firmly with stoichiometric ratio of 1:1. Ti₃C₂ QDs induced the microenvironmental variation of the amino acid residues in trypsin, reducing the thermal stability of trypsin significantly. Gel electrophoresis experiments and microscopic imaging experiments demonstrated that Ti₃C₂ QDs inhibited the enzymatic activity of trypsin on the digestion of human serum albumin and HeLa cells obviously. These results revealed not only the deep interaction mechanism between Ti₃C₂ QDs and protease but also the influence of Ti₃C₂ QDs on the enzymatic activity of trypsin, paving the way for the safe biological application of Ti₃C₂ QDs in the diagnosis and the therapy of protease-related diseases.