Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods

Platinum (II) complex of isopentyl glycine ligand: DNA binding, molecular dynamic, and anticancer activity against breast cancer

In this paper, we performed thorough experimental and theoretical calculations to examine the interaction between Pt derivative, as an anticancer, and ct-DNA. The mode of DNA binding with [Pt(NH3)2(Isopentylgly)]NO3, where Isopentylgly is Isopentyl glycine, was evaluated by various spectroscopic methods, docking, and molecular dynamics simulation studies. UV-Vis and fluorescence spectroscopic titration results and CD spectra of DNA-drug showed this interaction is via groove binding. Also, thermal stability studies or DNA melting temperature changes (ΔTm), as well as the quenching emissions monitoring proved it. Also, the thermodynamic parameter and binding constant displayed that complex-DNA formation is a spontaneous process, and H-binding and also groove binding were found to be the main forces. Theoretical studies stated [Pt(NH3)2(Isopentylgly)]NO3-DNA formation occurs on C-G center on DNA, along with rising DNA-compound stability. IC50 value against the human breast cell line probably is due to the Isopentyl glycine ligand in the structure of the Pt compound, and it was obtained more than cisplatin and less than carboplatin against the MCF7 cell.Communicated by Ramaswamy H. Sarma.

Deciphering the inhibitory mechanisms of betanin and phyllocactin from Hylocereus polyrhizus peel on protein glycation, with insights into their application in bread

Protein glycation closely intertwines with the pathogenesis of various diseases, sparking a growing interest in exploring natural antiglycation agents. Herein, high-purity betacyanins (betanin and phyllocactin) derived from Hylocereus polyrhizus peel were studied for their antiglycation potential using an in vitro bovine serum albumin (BSA)-glucose model. Notably, betacyanins outperformed aminoguanidine, a recognized antiglycation agent, in inhibiting glycation product formation across different stages, especially advanced glycation end-products (AGEs). Interestingly, phyllocactin displayed stronger antiglycation activity than betanin. Subsequent mechanistic studies employing molecular docking analysis and fluorescence quenching assay unveiled that betacyanins interact with BSA endothermically and spontaneously, with hydrophobic forces playing a dominant role. Remarkably, phyllocactin demonstrated higher binding affinity and stability to BSA than betanin. Furthermore, the incorporation of betacyanins into bread dose-dependently suppressed AGEs formation during baking and shows promise for inhibiting in vivo glycation process post-consumption. Overall, this study highlights the substantial potential of betacyanins as natural antiglycation agents.

Purification and characterization of betacyanin monomers from Hylocereus polyrhizus peel: A comparative study of their antioxidant and antidiabetic activities with mechanistic insights

Betacyanins have garnered escalating research interest for their promising bioactivities. However, substantial challenges in purification and separation have impeded a holistic comprehension of the distinct bioactivities of individual betacyanins and their underlying mechanisms. Herein, betanin and phyllocactin monomers with purity exceeding 95% were successfully obtained from Hylocereus polyrhizus peel using a feasible protocol. These monomers were subsequently employed for comparative bioactivity assessments to uncover underlying mechanisms and illuminate structure-activity relationships. Interestingly, phyllocactin exhibited superior antioxidant activities and 36.1% stronger inhibitory activity on α-glucosidase compared to betanin. Mechanistic studies have revealed that they function as mixed-type inhibitors of α-amylase and competitive inhibitors of α-glucosidase, with interactions predominantly driven by hydrogen bonding. Notably, phyllocactin demonstrated a greater binding affinity with enzymes than betanin, thereby substantiating its heightened inhibitory activity. Overall, our results highlight novel bioactivities of betacyanin monomers and provide profound insights into the intricate interplay between structures and properties.

Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid

In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.

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.

Binding interactions of Vildagliptin with pepsin: A multi-spectroscopic and in-silico approach and a comparative account with metformin

Vildagliptin (VDG) and Metformin (Met) belong to a class of dipeptidylpeptidase-4 (DPP-4) inhibitor and biguanide, respectively and used for the management of diabetes mellitus type II (DMTII). Both the drugs are orally available which leads to various side effects due to its oral ingestion. Occurrence of these side effects might be due to some interactions with pepsin at a molecular level. Therefore, in order to investigate these interactions, multi-spectroscopic and in-silico techniques have been extensively studied to identify the binding characteristics of VDG with pepsin. Fluorescence data suggested that the quenching is due to dynamic and static mechanism and static was dominant one. However, fluorescence and UV-Vis spectroscopic measurement analysis suggested that VDG tends to associate with pepsin, via ground-state complex formation. Fluorescence study revealed the binding-constant value which was found to be 0.559 × 103 M-1 at 298.15 K that is non-covalent in nature. VDG-pepsin complex shows exothermic and spontaneous binding as confirmed by the calculated values of ΔH, ΔS, and ΔG, are majorly caused by van der Waals forces and H-bonding interactions. CD spectra of pepsin in presence of VDG confirmed post binding conformational change. Enzyme-activity assay showed that activity of pepsin was decreased by upto 28 %. FRET analysis suggested that energy transfer efficiency is negligible for VDG-pepsin interaction. In-silico analysis reveals that H-bonding and electrostatic negative forces are the significant driving forces involved in the interaction of VDG and pepsin.

Structural alterations and inhibition of lysozyme activity upon binding interaction with rotenone: Insights from spectroscopic investigations and molecular dynamics simulation

The pervasive employment of pesticides such as rotenone on a global scale represents a substantial hazard to human health through direct exposure. Therefore, exploring the interactions between such compounds and body macromolecules such as proteins is crucial in comprehending the underlying mechanisms of their detrimental effects. The present study aims to delve into the molecular interaction between rotenone and lysozyme by employing spectroscopic techniques along with Molecular dynamics (MD) simulation in mimicked physiological conditions. The binding interaction resulted in a fluorescence quenching characterized by both dynamic and static mechanisms, with static quenching playing a prominent role in governing this phenomenon. The analysis of thermodynamic parameters indicated that hydrophobic interactions primarily governed the spontaneous bonding process. FT-IR and circular dichroism findings revealed structural alternations of lysozyme upon complexation with rotenone. Also, complexation with rotenone declined the biological activity of lysozyme, thus rotenone could be considered an enzyme inhibitor. Further, the binding interaction substantially decreased the thermal stability of lysozyme. Molecular docking studies showed the binding location and the key residues interacting with rotenone. The findings of the spectroscopic investigations were confirmed and accurately supported by MD simulation studies.

Interaction between a photoisomerizable azobenzene compound and alpha-lactalbumin: Spectroscopic and computational simulation studies

The combination of light and photoresponsive compounds provides a peculiar way of regulating biological systems. Azobenzene is a classical organic compound with photoisomerization properties. Exploring the interactions between azobenzene and proteins can deepen the biochemical applications of the azobenzene compounds. In this paper, the interaction of 4-[(2,6-dimethylphenyl)diazenyl]-3,5-dimethylphenol with alpha-lactalbumin was investigated by UV-Vis absorption spectra, multiple fluorescence spectra, computer simulations, and circular dichroism spectra. Most critically, the interaction differences between proteins and the trans- and cis-isomer of ligands have been analyzed and compared. Results showed that both isomers of ligands were bound to alpha-lactalbumin to form ground state complexes and statically quenched the steady-state fluorescence of alpha-lactalbumin. The van der Waals forces and hydrogen bonding dominated the binding; the difference is that the binding of the cis-isomer to alpha-lactalbumin is more rapidly stabilized, and the binding strength is greater than the trans-isomer. These binding differences were modeled and analyzed by molecular docking and kinetic simulations, and we found that both isomers bind through the hydrophobic aromatic cluster 2 of alpha-lactalbumin. However, the bent structure of the cis-isomer is more closely aligned with the construction of the aromatic cluster and may have contributed to the above differences.

Spectroscopy and molecular dynamic study of the interaction of calf thymus DNA by anticancer Pt complex with butyl glycine ligand

Despite the past few decades since the discovery of anticancer drugs, there is still no definitive treatment for its treatment. Cisplatin is a chemotherapy medication used to treat some cancers. In this research, the DNA binding affinity of Pt complex with butyl glycine ligand was studied by various spectroscopy methods and simulation studies. Fluorescence and UV-Vis spectroscopic data showed groove binding in ct-DNA-[Pt(NH₃)₂(butylgly)]NO₃ complex formation by the spontaneous process. The results were also confirmed by small changes in CD spectra and thermal study (T_m), as well as the quenching emission of [Pt(NH₃)₂(butylgly)]NO₃ complex on DNA. Finally, thermodynamic and binding parameters displayed that hydrophobic forces are the main forces. Based on docking simulation, [Pt(NH₃)₂(butylgly)]NO₃ could bind to DNA and via minor groove binding on C-G center on DNA, formed a stable DNA complex.

Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.

Inactivation of Soybean Trypsin Inhibitor by Dielectric-Barrier Discharge Plasma and Its Safety Evaluation and Application

The trypsin inhibitor (TI) is one of the most important anti-nutritive elements in soybeans. As a new nonthermal technology, dielectric-barrier discharge (DBD) cold plasma has attracted increasing attention in food processing. In this research, we investigated the effect of dielectric-barrier discharge (DBD) plasma treatment on soybean trypsin inhibitor content and its structure, evaluated TI toxicity and the safety of its degradation products after treatment with DBD technology in vitro and in vivo, and applied the technology to soybean milk, which was analyzed for quality. Using the statistical analysis of Student’s t-test, the results demonstrated that DBD plasma treatment significantly decreased the content of TI (33.8 kV at 1, 3, or 5 min, p < 0.05, p < 0.01, p < 0.001) and destroyed the secondary and tertiary structures of TI. TI was toxic to Caco-2 cells and could inhibit body weight gain, damage liver and kidney functions, and cause moderate or severe lesions in mouse organ tissues, whereas these phenomena were alleviated in mice treated with degradation products of TI after DBD plasma treatment under the optimal condition (33.8 kV at 5 min). The content of TI in DBD-treated soymilk was also significantly reduced (p < 0.001), while the acidity, alkalinity, conductivity, color, and amino acid composition of soymilk were not affected, and there were no statistical differences (p > 0.05). In summary, DBD plasma is a promising non-thermal processing technology used to eliminate TI from soybean products.

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.

Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin

The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×10⁴, M^-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.

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.

Interaction between phloretin and insulin: a spectroscopic study

Diabetes is among the top ten deadly diseases in the world. It occurs either when the pancreas does not produce enough insulin (INS) or when the body cannot effectively use the insulin it produces. Phloretin (PHL) has a biological effect that can treat diabetes. A spectroscopic study was carried out to explore the interaction between phloretin and insulin. UV/Vis spectroscopy, fluorescence spectroscopy, and circular dichroism spectropolarimeter were used in the study. UV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The fluorescence analysis results showed that the excitation and emission occurred at 280-nm and 305-nm wavelengths, respectively. Temperature changes did not affect INS emissions. However, the interaction of PHL–INS caused a redshift at 305 to 317 nm. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and increased the binding site. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each had a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and hydrophobic interaction. The free energy (ΔG0) recorded was negative. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values were greater than KS. The higher the temperature, the less was KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter implies that phloretin could induce regional configuration changes in insulin. The addition of PHL has revealed that the proportion of α-helix in the insulin stabilizes its structure. Phloretin’s stabilization and enhancement of the α-helix structural configuration in insulin indicate that phloretin can improve insulin resistance.

Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach

Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the T_m was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.