Spermine as a possible endogenous allosteric activator of carboxypeptidase A: multispectroscopic and molecular simulation studies

Revealing the interaction between alpha-chymotrypsin and eugenol: An integrated multi-spectral and dynamic simulation approach

The study aims to explore the effects of Eugenol (EUG) as an antioxidant on α-Chymotrypsin (α-Chy) and its interaction mechanism, with potential implications for new therapy development. The interaction between EUG and α-Chy was demonstrated through ultraviolet (UV) spectroscopy, which resulted in a shift in absorption with docking energies of -22.76 kJ/mol. An increase in fluorescence intensity indicated that the Trp residues moved to a less polar environment, which is consistent with the changes in accessible surface area (ASA) values. The presence of EUG led to a decrease in α-helix, β-turn, and random coil structures as shown by circular dichroism (CD) and Fourier-transform infrared (FTIR) analysis. Additionally, there was a slight increase in β-sheet structures, indicating a decrease in enzyme stability. However, tests for thermal stability showed a decrease in folding upon the introduction of EUG, which contradicted the results obtained from molecular dynamics (MD) simulations. The docking studies revealed that EUG forms hydrogen bonds and van der Waals forces with the enzyme, indicating the interaction mechanism. Kinetic studies confirmed that EUG acts as a mixed inhibitor. However, further research involving live organisms is necessary to fully understand its potential.

Interaction between the antioxidant compound safranal and α-chymotrypsin in spectroscopic fields and molecular modeling approaches

Among various herbal plants, saffron has been the subject of study in various medical and food fields. Among the compounds of saffron, safranal is one of them. Safranal is a monoterpene aldehyde. The precursor of safranal is called picrocrocin, whose hydrolysis leads to the production of safranal. picrocrocin has two sugar components and aglycone. sugar component was separated during the drying process of saffron and safranal is produced. Saffron is the cause of the saffron aroma. Previous studies have shown that safranal offers many benefits such as antioxidants, blood pressure regulation and anti-tumor qualities. On the other hand, α-Chy is an enzyme secreted by the pancreas into the intestine and then acts as an efficient protease. In this study, various methods, such as molecular dynamics (MD) simulation and molecular binding, and different spectroscopic techniques, as well as protein stability techniques, were used to investigate the possible interactions between safranal and α-Chy. UV spectroscopic studies were showing that the existence of safranal decreased α-Chy absorption intensity. safranal caused the intrinsic fluorescence of α-Chy to be quenched too. According to the Stern-Volmer equation, the interaction between safranal and α-Chy was of the static type. In thermodynamic calculations, the interaction between safranal and α-Chy was stabilized by hydrophobic forces. And it was found that this interaction continued spontaneously. These results were, thus, consistent with the Docking data simulation (with the negative ΔG° number and positive changes in enthalpy and entropy). The thermal stability of α-Chy was also measured, showing that its melting point was shifted to a higher threshold as a result of the interaction. also, MD simulation indicated that α-Chy became more stable in the presence of safranal. In this paper, all the results of the laboratory techniques were confirmed by molecular dynamic simulations, so the correctness of the results was confirmed. From this research, we hope to carefully observe the possible changes in the behavior and structure of the enzyme in the presence of safranal.Communicated by Ramaswamy H. Sarma.

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.

Synthesis of 4-sulfamoyl phenyl diazocarboxylic acid derivatives as novel non-classical inhibitors of human carbonic anhydrase II activity: an in vitro study

The first class of carbonic anhydrase inhibitors (CAIs) discovered was sulfonamides, but their clinical use is limited due to side effects caused by their inhibition of multiple CA isoforms. To overcome this, researchers have focused on developing isoform-selective CAIs. This study involved the synthesis and characterization of novel carboxylic acid/sulfonamide derivatives. We investigated the interaction between these compounds and the human carbonic anhydrase II (hCA II) isoform using spectroscopic and computational methods. The synthesized compounds were evaluated based on their IC50, Kd and Ki values, and it was found that the inhibitory potency and binding affinity of the compounds increased with the number of carboxylic acids zinc binding groups. Specifically, the compound C4, with three carboxylic acid groups, showed the strongest inhibitory potency. Fluorescence measurements revealed that all compounds quenched the intrinsic fluorescence of hCA II through a dynamic quenching process, and each compound had one binding site in the hCA II structure. Thermodynamic analysis indicated hydrogen bonds and van der Waals interactions played key roles in the binding of these compounds to hCA II. Docking studies showed that the carboxylic acid groups directly attached to the zinc ion in the active site, displacing water/hydroxide ions and causing steric hindrance. Overall, the strengthening of inhibitory activity and the binding power of these carboxylic acid derivatives for the hCA II makes these compounds interesting for designing novel hCA II inhibitors.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.

Elucidating binding mechanisms of naringenin by alpha-chymotrypsin: Insights into non-binding interactions and complex formation

As an inevitable parameter in the description of enzyme properties, the investigation of enzyme-ligand interactions has attracted a lot of attention. Alpha-Chymotrypsin (α-Chy) is essential for protein digestion and plays an important role in human health. Naringenin (NAG) as a potent antioxidant has recently been applied in the pharmaceutical industry. Using multispectral methods and computational simulation techniques, the binding strength of NAG to α-Chy was investigated in this research. UV-vis and fluorescence quenching data showed significant spectral changes upon binding of NAG to α-Chy. As demonstrated by fluorescence techniques, NAG could employ a static quenching process to decrease the intrinsic fluorescence of α-Chy. Both circular dichroism (CD) and FTIR spectroscopic analyses revealed that binding of NAG to α-Chy caused more flexible conformation. The slight increases in RMSD (0.06 nm) were observed for the NAG-(α-Chy) compound was supported by the results of thermal stability data. Docking computation confirmed that hydrogen and Van der Waals interactions are the important forces, which is in exact agreement with thermodynamics studies. Kinetic analysis of the enzyme showed an increase in activity, which was consistent, with the MD simulation results. The findings from the in-silico studies were in complete agreement with the experimental results.

Structural changes and anti-hepatocellular carcinoma activity of interferon-γ after interaction with sinensetin

Exploring the interaction of small molecules with therapeutic proteins can provide useful information about development of ligand-protein complexes as synergistically therapeutic platforms. In this study, the interaction of sinensetin with human interferon gamma (IFNγ) was evaluated experimentally and theoretically. Also, the synergistic effects of IFNγ- sinensetin complex on the inhibition of hepatocellular carcinoma HepG2 cell proliferation were assessed by cell viability and quantitative real time PCR assays. It was realized that sinensetin interacts with IFNγ through a static quenching mechanism and hydrophobic forces mediated by presence of Lys55 and Lys58 amino acid residues in the binding site were the main contributing forces in the spontaneous formation of IFNγ-sinensetin complex. Also, the interaction of sinensetin with IFNγ did not induce a significant change in the secondary and tertiary structure of the protein. Cellular assays revealed a synergistic effect of sinensetin on IFNγ -triggered anticancer action in HepG2 cells through overexpression of caspase-3 mRNA and protein. In conclusion, this study may hold great promise for the development of potential ligand- protein complexes for therapeutic purposes.

Effect of polysaccharides on conformational changes and functional properties of protein-polyphenol binary complexes: A comparative study

This study aimed to investigate the effect of different polysaccharides on the binding behavior and functional properties of soybean protein isolate (SPI)-quercetin (Que) complex. The binding behavior was assessed using multi-spectral technique with the Stern-Volmer equation, which confirmed the presence of static fluorescence quenching in Que and SPI. The addition of sodium alginate (SA) resulted in a reduction of the binding affinity between SPI and Que, while dextran (DX) exhibited some promoting effect. A slight blue shift was observed in amide I and amide II bands, indicating the presence of hydrophobic and electrostatic interactions. Circular dichroism spectra revealed the ordered structures transformed into a more disordered state when polysaccharides were added, leading to an increase in random coils (SA: 18.5 %, DX: 15.4 %). Docking and dynamic simulations demonstrated that SA displayed greater stability within the hydrophobic compartments of SPI than DX, increased rigidity and stability of the SPI structure in SPI-Que-SA complexes. Electrostatic forces played a significant role between SPI and SA, while van der Waals forces were the main driving forces in SPI-DX complexes. Overall, the introduction of SA led to a looser and stable structure of SPI-Que complexes, resulting in an improvement of their emulsifying, foaming, and antioxidant properties.

Compound effect and mechanism of oxidative damage induced by nanoplastics and benzo [a] pyrene

Nanoplastics and polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in soil environments. In order to objectively evaluate the toxic interaction between polystyrene nanoplastics (PS NPs) and benzo [a] pyrene (BaP), oxidative damage at the level of earthworm cells and biomacromolecules was investigated by experiments combined with molecular dynamics simulation. Studies on cells reveal that PS NPs and BaP had synergistic toxicity when it came to causing oxidative stress. Cellular reactive oxygen species (ROS) levels under combined pollutant exposure were 24% and 19% higher, respectively than when PS NPs and BaP were exposed alone (compared to the blank group). In addition, BaP and PS NPs inhibited the ability of CAT to decompose H2O2 by affecting the structure of the proximal amino acid Tyr 357 in the active center of CAT, which exacerbated oxidative stress to a certain extent. Therefore, the synergistic toxic effect of BaP and PS NPs is due to the mutual complement of the two to the induction of protein structural looseness, and the strengthening of the stability of the conjugate (CAT-BaP-PS) under the weak interaction. This work provides a new perspective and approach on how to talk about the toxicity of combined pollutants.

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

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.

The interactions between Reactive Black 5 and human serum albumin: combined spectroscopic and molecular dynamics simulation approaches

Azo dyes are made in significant amounts annually and released into the environment after being employed in the industry. There are some reports about the toxic effects of these dyes on several organisms. Thus, the textile dye Reactive Black 5 (RB5) has been examined for its cytotoxic effects on the human serum albumin (HSA) structure. Molecular interaction between RB5 and HSA indicated the combination of docking methods, molecular dynamic simulation, and multi-spectroscopic approaches. HSA's intrinsic fluorescence was well quenched with enhancing RB5 level, confirming complex formation. Molecular dynamics (MD) simulation was done to study the cytotoxic effects of RB5 and HSA conformation. Molecular modeling revealed that the RB5-HSA complex was stabilized by hydrogen bonds and van der Waals interactions. The results of molecular docking revealed that the binding energy of RB5 to HSA was - 27.94 kJ/mol. The change in secondary structure causes the annihilation of hydrogen bonding networks and the reduction of biological activity. This research can indicate a suitable molecular modeling interaction of RB5 and HAS and broaden our knowledge for azo dye toxicity under natural conditions.

Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods

Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.

The effect of putrescine on the lysozyme activity and structure: Spectroscopic approaches and molecular dynamic simulation

The present research addressed the influence of polyamine (putrescine) on the compound as well as function of lysozyme; accordingly, UV- Visible, fluorescence spectroscopy and simulation method were applied to fulfill this goal. Lysozyme's structural variability was examined at various putrescine ‌concentrations; also, the putrescine binding to lysozyme was addressed using spectrofluorescence, circular dichroism (CD) and UV-Vis measurements. The obtained results indicated that with raising the putrescine concentration, the intrinsic quenching fluorescence of lysozyme was decreased based on the static mechanism. Analysis of thermodynamic parameters also indicated that van der Waals as well as hydrogen bond forces served a fundamental role in determining the resulting stability; this was in agreement with modeling studies. Measurement of UV absorption spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy also demonstrated that lysozyme's second and tertiary structures were altered in a putrescine concentration-dependent manner. Putrescine inhibited lysozyme's enzymatic activity, displaying its affinity with the lysozyme's active site. Further, molecular simulation conducted revealed that putrescine could have spontaneous binding to lysozyme, changing its structure, thus further emphasizing the experimental results.

A comparative study of the interaction of naringenin with lysozyme by multi-spectroscopic methods, activity comparisons, and molecular modeling procedures

The present study applied steady-state fluorescence, UV-Vis spectrophotometry, molecular docking studies, and circular dichroism (CD) to investigate the interaction of naringenin with lysozyme in an aqueous medium. The UV-Vis measurement indicated the changes in lysozyme secondary and tertiary structure change as a function of the concentration of naringenin. Naringenin could be used to turn the static quenching mechanism into the intrinsic fluorescence of lysozyme. The negative amount of Gibbs free energy (ΔG°) suggested that the binding operation was spontaneous. Fluorescence studies also demonstrated the changes occurring in the Trp microenvironment upon the concatenation into lysozyme. Analysis of thermodynamic parameters also revealed that hydrophobic forces played a fundamental role in determining the complex stability; this was consistent with the previous modeling studies. Circular dichroism also suggested that the alpha-helicity of lysozyme was enhanced as ligand was bound. Naringenin inhibited lysozyme enzymatic activity, displaying its affinity with the lysozyme active site. Further, molecular docking studies demonstrated that naringenin could bind to both residues essential for catalytic activity in the proximity of Trp 62 and Trp 63.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

Design, synthesis, biological evaluation, common feature pharmacophore model and molecular dynamics simulation studies of ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate as Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors

SHP2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell death pathway (PD-1/PD-L1) and cell growth and differentiation pathway (MAPK). Moreover, mutations in SHP2 have been implicated in Leopard syndrome (LS), Noonan syndrome (NS), juvenile myelomonocytic leukemia (JMML) and several types of cancer and solid tumors. Thus, SHP2 inhibitors are much needed reagents for evaluation of SHP2 as a therapeutic target. A series of novel ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate derivatives were designed and synthesized, and their SHP2 inhibitory activities (IC₅₀) were determined. Among the desired compounds, 1d shares the highest inhibitory activity (IC₅₀ = 0.99 μM) against SHP2. Additionally, a common feature pharmacophore model was established to explain the structure activity relationship of the desired compounds. Finally, molecular dynamics simulation was carried out to explore the most likely binding mode of compound 1d with SHP2. In brief, the findings reported here may at least provide a new strategy or useful insights in discovering novel effective SHP2 inhibitors.Communicated by Ramaswamy H. Sarma.

The effect of putrescine on stability and structural properties of bovine serum albumin

Serum albumins are the abounding proteins in plasma. Their most important characteristic is that they act as carriers for a type of compound, for example, different drugs. Bovine Serum Albumin (BSA) is a single-chain polypeptide with 583 amino acids. Polyamines such as putrescine can interact with negatively charged molecules. The effect of putrescine on the structure of bovine serum albumin has been surveyed utilizing the method of UV-Vis spectroscopy, Thermal stability, fluorescence spectroscopy, and molecular docking at temperature 298 K and 308 K at pH 7.4 using Tris-HCl as a buffer. The complex formation between putrescine and bovine serum albumin was discovered as alter in the absorbance at 280 nm. The amount of absorption increases with the addition of putrescine. The adding of putrescine alters the bovine serum albumin and decrements the hydrophobicity of the micro-environment of the Trp residues in the inner hydrophobic zone. The static kind of quenching process was chiefly contained within the quenching of intrinsic emission of the protein. The fluorescence quenching details (K_sv) for complex bovine serum albumin-putrescine revealed one binding site for putrescine. The negative amount of Gibbs free energy change (ΔG°) suggested the binding operation was spontaneous.Communicated by Ramaswamy H. Sarma.