Probing the interaction between 7-geranyloxycoumarin and bovine serum albumin: Spectroscopic analyzing and molecular docking study

Insight into the interaction and binding mechanism of a natural nonnutritive sweetener mogroside V with soybean protein isolates based on multi-spectroscopic techniques and computational simulations

As a natural low-calorie sweetener, Mogroside V (Mog-V) has gradually become one of the alternatives to sucrose with superior health attributes. However, Mog-V will bring unpleasant aftertastes when exceeding a threshold concentration. To investigate the possibility of soy protein isolates (SPIs), namely β-conglycinin (7S), and glycinin (11S) as flavor-improving agents of Mog-V, the binding mechanism between Mog-V and SPIs was explored through multi-spectroscopy, particle size, zeta potential, and computational simulation. The results of the multi-spectroscopic experiments indicated that Mog-V enhanced the fluorescence of 7S/11S protein in a static mode. The binding affinity of 7S-Mog-V was greater compared with 11S-Mog-V. Particle size and zeta potential analysis revealed that the interaction could promote aggregation of 7S/11S protein with different stability. Furthermore, computational simulations further confirmed that Mog-V could interact with the 7S/11S protein in different ways. This research provides a theoretical foundation for the development and application of SPI to improve the flavor of Mog-V, opening a new avenue for further expanding the market demand for Mog-V.

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.

Binding and displacement study of gentamicin, 5-fluorouracil, oxytetracycline and rolitetracycline with (BSA: Drug2) complex using spectroscopic and calorimetric techniques: Biophysical approach

Understanding of energetics of interactions between drug and protein is essential in pharmacokinetics and pharmacodynamics study. The binding affinity (K) helps in investigating how tightly or loosely drug is bound to protein. The binding, displacement, conformational change and stability study of drugs- gentamicin (GM), 5-fluorouracil (5FU), oxytetracycline (OTC) and rolitetracycline (RTC) with bovine serum albumin (BSA) has been carried out in presence of each other drug by fluorescence, UV-visible spectroscopy, molecular docking, circular dichroism techniques and thermal denaturation method. The site marker study and docking methods have confirmed that 5FU and GM are able to bind at site 1 and OTC and RTC at site II of BSA. The order of their binding affinities with BSA for the binary system were as GM <5FU < OTC < RTC with the order of 102 < 103 < 105 < 105-6 M-1. The displacement study has shown that higher affinity drug decreases the equilibrium constant of another drug already in bound state with BSA if both these drugs are having the same binding site. Therefore 5FU, GM (binding site 1) drugs were not able to displace OTC and RTC (binding site 2) and vice-versa as they are binding at two different sites. The binding constant values were found to be decreasing with increasing temperature for all the systems involved which suggests static or mixed type of quenching, however can only confirmed with the help of TCSPC technique. The ΔG0 (binding energy) obtained from docking method were in accordance with the ITC method. From molecular docking we have determined the amino acid residues involved in binding process for binary and ternary systems by considering first rank minimum binding energy confirmation. From CD it has been observed that RTC causes most conformational change in secondary and tertiary structure of BSA due to the presence of pyrrole ring. OTC-RTC with higher affinity showed highest melting temperature Tm values while low affinity drugs in (5FU-GM) combination showed lowest Tm value. 5FU showed large endothermic denaturation enthalpy ΔHd0 due to the presence of highly electronegative fluorine atom in the pyridine analogue.

Spectroscopic investigation and structural simulation in human serum albumin with hydroxychloroquine/Silybum marianum and a possible potential COVID-19 drug candidate

In this study, the interaction between human serum albumin (HSA) and the hydroxychloroquine/Silybum marianum (HCQ/SM) mixture was investigated using various techniques. The observed high binding constant (Kb) and Stern-Volmer quenching constant (KSV) indicate a strong binding affinity between the HCQ/SM mixture and HSA. The circular dichroism (CD) analysis revealed that HCQ/SM induced conformational changes in the secondary structure of HSA, leading to a decrease in the α-helical content. UV-Vis analysis exhibited a slight redshift, indicating that the HCQ/SM mixture could adapt to the flexible structure of HSA. The experimental results demonstrated the significant conformational changes in HSA upon binding with HCQ/SM. Theoretical studies were carried out using molecular dynamics simulation via the Gromacs simulation package to explore insights into the drug interaction with HSA-binding sites. Furthermore, molecular docking studies demonstrated that HCQ/SM-HSA exhibited favorable docking scores with the receptor (5FUZ), suggesting a potential therapeutic relevance in combating COVID-19 with a value of -6.24 kcal mol-1. HCQ/SM exhibited stronger interaction with both SARS-CoV-2 virus main proteases compared to favipiravir. Ultimately, the experimental data and molecular docking analysis presented in this research offer valuable insights into the pharmaceutical and biological properties of HCQ/SM mixtures when interacting with serum albumin.

Turn-On Fluorescent Probe for BSA Detection Constructed by Supramolecular Assembly

The fluorescent probe method has attracted significant research attention due to its high sensitivity and reproducibility in detecting bovine serum albumin (BSA). In this study, we constructed a fluorescent probe for BSA detection by assembling an amphiphilic organic fluorescent molecule, termed 2-(2'-hydroxyphenyl) benzothiazole (HBT-11), with BSA. In an aqueous solution, HBT-11 exhibited a weak fluorescence emission at 501 nm. However, the addition of BSA substantially enhanced the fluorescence emission at 501 nm, indicating that the assembly was driven by electrostatic interactions between HBT-11 and BSA. HBT-11, serving as a fluorescent probe for BSA detection, demonstrated a limit of detection (LOD) as low as 3.92 nmol L-1, excellent photostability, high selectivity, and robust anti-interference capability. Notably, we successfully applied HBT-11 for detecting BSA in fetal bovine serum and selectively imaging BSA in HeLa cells.

New insights on the binding of butyl-paraben to trypsin: experimental and computational approaches

Butyl-paraben (BP) is one of the most widely used preservatives in numerous foodstuffs, skin care products, and a variety of drugs, and trypsin is the main digestive enzyme, the research on the binding between the two is essential for human health. In the present paper, the effect of BP on trypsin has been explored using experimental and computational techniques to evaluate BP toxicity at the protein level. The obtained results from molecular docking and kinetic assay revealed BP was embedded in the hydrophobic cavity-S1 binding pocket of the enzyme to inhibit its activity by a competitive model. Intrinsic fluorescence of trypsin after interaction with BP revealed the static mode of quenching. FRET indicated that the distance of the enzyme to BP is 1.89 nm with high energy efficiency. Thermodynamic results proved that BP spontaneously bound to trypsin in an enthalpy-driven manner, the van der Waals interactions and H-bonds serving as the predominant forces in binding processes. CD spectroscopy and molecular dynamics (MD) simulation revealed that the trypsin structure transformed from the β-Sheet structure to the unordered Coil structure upon interacting with BP. Resonance light scattering (RLS), synchronous fluorescence, and three-dimensional (3 D) spectroscopies further supported the alteration in the conformation of trypsin. Differential scanning calorimetry (DSC) showed that trypsin was somewhat destabilized in the presence of BP. Accordingly, all of the experimental data were confirmed by MD simulation.Communicated by Ramaswamy H. Sarma.

Comparison of the Effects on Bovine Serum Albumin Induced by Different Forms of Vanadium

Various forms of vanadium coexist in vivo, and the behavior mechanism is different. An investigation of the separate and simultaneous binding of three vanadium forms with bovine serum albumin (BSA) was performed. VO(acac)₂/NaVO₃/VOSO₄ bound to site I of BSA, and their binding constants were 4.26 × 10⁵, 9.18 × 10³, and 4.31 × 10² L mol^-1 at 298 K, respectively. VO(acac)₂ had the strongest binding ability to BSA and had the most influence on the secondary structure of BSA and the microenvironment of around amino acid residues. The effect of NaVO₃ and VOSO₄ coexistence on the binding of VO(acac)₂ to BSA was therefore further investigated. Both NaVO₃ and VOSO₄ had an effect on the binding of VO(acac)₂ and BSA, with NaVO₃ having the most noticeable effect. NaVO₃ interfered with the binding process of VO(acac)₂ and BSA, increased the binding constant, and changed the binding forces between them. Competition and allosteric effect may be responsible for the change of binding process between VO(acac)₂ and BSA in the presence of NaVO₃/VOSO₄.

Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.

Exploration of binding mechanism of apigenin to pepsin: Spectroscopic analysis, molecular docking, enzyme activity and antioxidant assays

Pepsin plays an important role in nutrient metabolism. Apigenin (AP) is a beneficial polyphenol to human health. To enhance the bioavailability of AP and elucidate the inhibitory effect of AP on pepsin, the interaction mechanism of AP with pepsin was investigated using spectroscopic analysis and molecular docking, and the activity of pepsin and antioxidant activity of AP was also evaluated. Specifically, AP performed static quenching of pepsin and had only one binding site on pepsin. More interestingly, the interaction between AP and pepsin was spontaneous, while hydrogen bonds and van der Waals forces were the main binding forces. Generally, synchronous and three-dimensional fluorescence confirmed that AP induced the conformational changes of pepsin, and molecular docking proved the above results and illustrated the specific binding patterns. Specifically, AP inhibited the activity of pepsin, while pepsin decreased the antioxidant activity of AP. These results provided useful information for elucidating the interactions between AP and pepsin.

Exploring the interaction of myricetin with human alpha-2-macroglobulin: biophysical and in-silico analysis

Myricetin (MYR) is a bioactive secondary metabolite found in plants that is recognized for its nutraceutical value and is an essential constituent of various foods and beverages. It is reported to exhibit a plethora of activities, including antioxidant, antimicrobial, antidiabetic, anticancer, and anti-inflammatory. Alpha-2-macroglobulin (α2M) is a major plasma anti-proteinase that can inhibit proteinases of both human and non-human origin, regardless of their specificity and catalytic mechanism. Here, we explored the interaction of MYR-α2M using various biochemical and biophysical techniques. It was found that the interaction of MYR brings subtle change in its anti-proteolytic potential and thereby alters its structure and function, as can be seen from absorbance and fluorescence spectroscopy. UV spectroscopy of α2M in presence of MYR indicated the occurrence of hyperchromism, suggesting complex formation. Fluorescence spectroscopy reveals that MYR reduces the fluorescence intensity of native α2M with a shift in the wavelength maxima. At 318.15 K, MYR binds to α2M with a binding constant of 2.4 × 10³ M^-1, which indicates significant binding. The ΔG value was found to be - 7.56 kcal mol^-1 at 298.15 K, suggesting the interaction to be spontaneous and thermodynamically favorable. The secondary structure of α2M does not involve any major change as was confirmed by CD analysis. The molecular docking indicates that Asp-146, Ser-172, Glu-174, and Tyr-180 were the key residues involved in α2M-MYR complex formation. This study contributes to our understanding of the function and mechanism of protein and flavonoid binding by providing a molecular basis of the interaction between MYR and α2M.

Molecular interactions between bovine serum albumin (BSA) and trihalophenol: Insights from spectroscopic, calorimetric and molecular modeling studies

The issue of disinfection byproducts (DBPs) in the water has received critical attention due to the health effects on humans. In the water environment, interactions between bovine serum albumins (BSA), the most abundant water-soluble protein, and DBPs unavoidably occur. In this study, comparative binding interactions of two aromatic DBPs - 2,4,6-trichlorophenol (TCP) and 2,4,6-tribromophenol (TBP) with BSA were investigated systematically utilizing fluorescence spectrometry, UV absorption spectrometry, isothermal titration calorimetry and molecular docking approach. The fluorescence quenching results indicated that TCP/TBP could quench the endogenous fluorescence of BSA through static quenching mechanisms, and TBP showed a more substantial quenching effect. The binding constants were determined for TCP-BSA (3.638 × 10⁵ L/mol, 303 K) and TBP-BSA (6.394 × 10⁵ L/mol, 303 K) complexes, with TBP showing higher binding affinity than TCP. The thermodynamic study and docking analysis suggested that hydrogen bonding and van der Waals forces were the primary interaction forces. Both of TCP and TBP were located in the subdomain IIIA of BSA, and TBP could form more stable complex than TCP. The results of the present study contributed valuable information on the environmental behaviors of halophenols in water environment from perspectives of binding with BSA.

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.

Investigation of the binding behavior of bioactive 7-methoxyflavone to human serum albumin by coupling multi-spectroscopic with computational approaches

The natural flavonoids with bioactivity as secondary plant metabolites are mostly found in fruits, vegetables, tea and herbs, the distribution and bioavailability of which in vivo depends on the interaction and successive binding with carrier proteins in the systemic circulation. In this paper, the binding behavior of bioactive 7-methoxyflavone (7-MF) with human serum albumin (HSA) was studied with the aid of the combination of multi-spectroscopic methods, molecular docking and molecular dynamic simulation. The results of multi-spectroscopic experiments revealed that 7-MF interacted with HSA predominantly via fluorescence static quenching and the microenvironment around the fluorophore Trp residues in HSA became more hydrophilicity with the binding of 7-MF. Thermodynamic analysis demonstrated that hydrogen bonds and van der Waals forces played a dominant role in stabilizing the HSA-7-MF complex. Moreover, the docking experiment and molecular dynamic simulation further confirmed that 7-MF could enter the active cavity of HSA and caused more stable conformation and change of secondary structure of HSA through forming hydrogen bond. The exploration of the mechanism of 7-MF binding to HSA lights a new avenue to understand the stability, transport and distribution of 7-MF and 7-MF may hold great potential to be extended as a promising alternative of dietary supplements or pharmaceutical agents.

Probing the Interactions of Lamotrigine and Phenobarbital with Tau Protein: Experimental and Molecular Modeling Studies

Tau, as a small protein in neurons, plays a main role in stabilizing and assembling the internal microtubules. Here, the effects of antiepileptic drugs, including lamotrigine (LTG) and phenobarbital (PHB), on tau protein structure have been investigated by surface plasmon resonance (SPR), fluorescence spectroscopy along molecular modeling. Fluorescence data analysis revealed that both drugs quench the intrinsic emission intensity of tau protein via a static quenching mechanism. Analysis of SPR data at three different temperatures revealed that binding of LTG and PHB to tau protein leads to a decrease and increase in equilibrium constants (K_D) values with increasing temperature, respectively. Therefore, the affinity of LTG decreases and PHB increases with increasing temperature. In addition, molecular docking studies indicated that both LTG and PHB bind to the S1 pocket of tau protein. Our data demonstrated the preventive effect of two important antiepileptic pharmaceuticals on the aggregation of tau protein. Given that any damage to the tau protein possibly leads to neurodegenerative diseases, this study can provide useful and important information and a basis for further research and study to treat tauopathy.

Binding mechanism of lipase with Lentinus edodes mycelia polysaccharide by multi-spectroscopic methods

It is an effective strategy to avoid obesity by inhibiting the activity of lipase. In this study, the binding mechanism of lipase and Lentinus edodes mycelia polysaccharide (LMP) were explored with multi-spectral methods, for example, three-dimensional (3D) fluorescence, Fourier-transformed infrared (FT-IR), and Raman spectra. At 290 K, the binding constant was 2.44 × 10⁵  L/mol, there was only one binding site between LMP and lipase. Static quenching was the quenching mechanism. The major forces were hydrogen bonding and van der Waals force. The binding of LMP to lipase impacted the microenvironment around tyrosine and tryptophan residues. The polarity around these residues was decreased and hydrophobicity was enhanced. This study not only revealed the binding mechanism of LMP on lipase but also provided scientific evidence for expanding the application of LMP in functional food industries.

Investigation on the binding of cyanobacterial metabolite calothrixin A with human serum albumin for evaluating its potential toxicology

Calothrixin A (CLA), as a carbazole-1,4-quinone alkaloid with unique indolo [3,2-j] phenanthridine framework, is a natural metabolite from the Calothrix cyanobacteria. Since the interaction to the functional serum albumins may play an important role in estimating its potential physiological or toxicological effects in vivo, we here explored the binding information of CLA with human serum albumin (HSA) by multi-spectroscopic experiments and computational approaches. The molecular docking results showed that there was one binding site of CLA to the site I (subdomain IIA) of HSA, causing the spontaneous formation of the ground state complex of CLA-HSA through the integration of hydrogen bond, hydrophobic interaction, and electrostatic interaction. Moreover, CLA could effectively trigger the change of HSA's secondary structure because of an obvious decrease of α-helical content in HSA. Taking into consideration of the crucial role of HSA to transport extraneous functional small molecules in vivo, this study may provide a worthy theoretical basis to evaluate the in vivo toxicity of CLA, aiming to reduce/avoid the potential toxic side effects of CLA in the next hit-to-lead campaign.