Spectroscopy and molecular simulation on the interaction of Nano-Kaempferol prepared by oil-in-water with two carrier proteins: An investigation of protein-protein interaction

Spectroscopy to study the interaction of magnetic deep eutectic solvents with bovine serum albumin

Deep eutectic solvents (DESs) were well known as new solvents because of their unique properties. Green DESs could be used as green, efficient, and economical extractants for the separation and purification of bovine serum albumin (BSA). In this study, FeCl3·6H2O was used as a reactant to prepare four types of magnetic deep eutectic solvents (MDESs). In these MDESs, FeCl3·6H2O was a hydrogen bond acceptor, while lactic acid, citric acid, acetic acid, and glycerol were hydrogen bond donors. Under simulated physiological conditions, the interactions between MDESs and BSA were investigated. Through fluorescence spectroscopy and series of calculations, the fluorescence quenching constants of the interaction between MDESs and BSA at different temperatures were analyzed, and the type of fluorescence quenching was determined to be static quenching; the binding sites were calculated, confirming that the 1:1 complexes were formed between MDESs and BSA; the thermodynamic parameters were calculated to clarify that the forces between them included hydrogen bonds, van der Waals forces, and electrostatic attraction; the binding rates of the MDESs-BSA system at different temperatures were calculated, and the ideal MDESs extractant for protein separation and purification was screened out. The results of circular dichroism spectroscopy measurement and calculation proved that after the addition of MDESs, the α-helix structure in BSA still dominates, further verifying that MDESs were extractants for protein separation and purification.

Electrochemical and computational studies on the interaction between calf-thymus DNA and skin whitening agent arbutin

The interaction between double-stranded calf thymus DNA (ctDNA) and the skin whitening agent arbutin (AR) examined by applying electrochemical and computational methods for the first time in literature. A single-use pencil graphite electrode via cyclic (CV) and differential pulse voltammetry (DPV) techniques were applied to determine the kinetic and thermodynamic parameters in the absence and presence of ctDNA. To examine the interaction process, oxidation peak currents and potentials of AR were observed prior to the addition of various ctDNA concentrations. The binding constants (KAR-DNA) and Gibbs free energy (ΔG°) values for the AR-DNA complex were determined as 1.82 × 104L/mol and -24.30 kJ/mol at 298 K, respectively. Temperature evaluation of the interaction was examined using thermodynamic parameters (ΔH°: -30.30 kJ/mol and ΔS°: -0.00197 kJ/mol) applying the Van't Hoff equation. The local interaction sites in the molecule structure were determined by applying Fukui functions and second-order perturbation theory in view of potential hydrogen binding centers. The optimized structure of AR was applied with a DNA structure revealing the binding position for AR-DNA complex. Experimental and computational examinations suggested that AR-DNA binds to ctDNA through a minor groove mode via conventional hydrogen bonds, hydrophobic interactions and van der Waals forces.

Ponceau 4R induces aggregation in human serum albumin and morin acts as an anti-aggregating agent against dye induced aggregates

Aggregation of proteins occurs because of improper protein folding and is responsible for the development of multiple severe maladies such as Type II diabetes mellitus, Parkison's, Huntington's, and spongiform encephalopathy. In the current work, the interaction and aggregation of human serum albumin (HSA) in the presence of the food colorant Ponceau 4R at pH 2.0 was evaluated using multiple in-silico and multi-spectroscopic approaches. The UV-visible spectroscopy and steady state fluorescence spectroscopy confirmed the complex formation between Ponceau 4R and HSA. The binding of HSA to Ponceau 4R favored static mode of fluorescence quenching. The values of KSV and Kb were found to be 1.905 × 105 M-1 and 1.43 × 105 M-1 respectively. Ponceau 4R leads to modification of HSA microenvironment, as proven by three-dimensional fluorescence spectroscopy. Ponceau 4R in the concentration range (60-200 µM) triggered the aggregation of HSA at pH 2.0 as confirmed by turbidity and Rayleigh light scattering (RLS). The secondary structure alteration of human serum albumin (α-helical structure to cross-β conformation) induced by 140 µM Ponceau 4R was evaluated utilizing far-UV CD spectroscopy. This concentration of Ponceau 4R (140 µM) will now be further used in aggregation inhibition studies. The production of β-rich aggregates of HSA is further established by a red shift in the absorption maxima of the Congo red spectra. The scanning electron microscopy (SEM) results showed that HSA aggregates induced by Ponceau 4R were amorphous in nature. Molecular docking analysis showed that electrostatic interactions, hydrophobic interactions and hydrogen bonding were responsible for the Ponceau 4R-induced aggregation of HSA. Furthermore, morin further inhibits the Ponceau 4R-induced aggregation of HSA. The results from turbidity, RLS, and SEM analysis confirmed that aggregates of HSA induced by 140 µM Ponceau 4R became soluble when human serum albumin was pre-incubated with various amounts of morin (0-600 µM). Thus, we conclude that Ponceau 4R triggers the aggregation of human serum albumin, whereas morin is responsible for the inhibition of aggregation of protein.

β-Lactoglobulin and sorghum phenolic compounds molecular binding: Interaction mechanism and thermal stability impact

The mechanism of molecular interaction between β-lactoglobulin (β-lg) and sorghum bran phenolic compounds from 4 genotypes was studied. Catechin (CA) and ferulic acid (FA) were used as model systems. Higher affinity for β-lg:FA interaction (Ksv ≈ 105 M-1) compared with β-lg:CA interaction (Ksv ≈ 104 M-1) was revealed, with different preferable binding sites identified through molecular docking. Nevertheless, regarding the molecular interaction between the proteins and the complex extracts of phenolic compounds, Ksv in the magnitude order of 104 M-1 were observed. Antioxidant capacity progressively increased after protein-phenolic interaction, indicating a potential synergistic effect. Concerning the thermal stability of the phenolic compounds, epimerization as the primary response of CA to thermal treatment (90 °C / 10 min) was identified, but the addition of β-lg exerted a protective effect against CA degradation (-7 % in β-lg:CA complexes); however, proteins were not able to protect complex phenolic matrices (e.g. sorghum extracts).

Biophysical and structural insights into Azamethiphos-DNA interactions

Azamethiphos (AZA), an organophosphate pesticide, is well-known for its cholinesterase inhibition and associated toxic risks to non-target organisms. Its high-water solubility facilitates environmental contamination and persistence, increasing the risk of human exposure through bioaccumulation in agricultural products. This study investigates AZA's DNA-binding potential and underlying interaction mechanisms. Using in silico techniques, we analyzed AZA's interactions with DNA, revealing that hydrogen bonding plays a crucial role in stabilizing the AZA-DNA complex. The study found that AZA preferentially binds to AT-rich regions of Ct-DNA, suggesting it acts as a groove binder by fitting into the grooves of the DNA double helix Additionally, fluorescence spectroscopy studies of AZA with DNA were conducted at three temperatures (288 K, 298 K, and 308 K). These experiments demonstrated that AZA binds to Ct-DNA with a moderate binding affinity (3.868, 2.238 and 0.0061 x 104 LM-1 at 288, 298 and 308 K respectively). Thermodynamic analysis confirmed the binding process is spontaneous (ΔG < 0), enthalpy driven (ΔH < 0, ΔS < 0) and facilitated by the presence of hydrogen bonds and van der Waals. These findings provide molecular-level insights into AZA's interactions with Ct-DNA, emphasizing its potential effects on genetic material. Understanding these interactions is crucial for assessing AZA's biological risks.

Nanocomplex of selachyl alcohol and sodium caseinate: Preparation, physicochemical properties, and interaction mechanism

Selachyl alcohol (SA), a naturally occurring 1-O-alkylglycerol, has garnered significant attention due to its wide biological activities. To enhance its aqueous solubility, the complexation with sodium caseinate (NaCas) was investigated. Results showed the SA-NaCas complex, optimally formed at a 1:4 mass ratio, yielded a nanoscale dispersion with enhanced surface hydrophobicity, reduced dynamic surface tension, and superior emulsifying indices compared to NaCas alone. Fluorescence spectroscopy elucidated the interaction between SA and NaCas as a spontaneous process, mainly driven by hydrophobic forces. The binding constant and Gibbs free energy change were 1.17 × 103 L/mol and - 18.09 kJ/mol at 308 K. Molecular docking revealed that hydrophobic and hydrogen bonding interactions were the main forces driving the binding of SA to the α- and β-casein components of NaCas. The SA-NaCas nanocomplex not only enhances SA's water solubility, but also can be used as an effective nano-delivery system with better physicochemical properties than NaCas.

Elucidating the interaction mechanism of rutin with β-casein and β-lactoglobulin: A comprehensive analysis using multi-spectroscopy, molecular docking, and molecular dynamic simulations

Polyphenol-protein interactions are crucial for food processing, nutrition, and functional properties. This study investigates the interaction between rutin and β-casein (β-CAS) or β-lactoglobulin (β-LG) using multispectral analysis, molecular docking, and molecular dynamics (MD) simulations. Fluorescence spectroscopy reveals that rutin binds spontaneously (ΔG < 0) to β-CAS and β-LG, forming complexes with binding constants (Ka) at 298 K of 42.500 × 103 and 2.101 × 103 L·mol-1, respectively, and at 308 K of 5.814 × 103 and 4.350 × 103 L·mol-1. Multispectral analysis and microscopy reveal complex formation and changes in the proteins' secondary, crystalline, and microstructures. Molecular docking and MD simulations verify complex stability, showing heightened binding affinity between rutin and β-CAS. These results validate hydrophobic interactions and hydrogen bonding as the main forces between rutin and the two proteins. These findings offer insights for using milk proteins as rutin carriers and support potential food industry application.

Beyond DNA interactions: Insights into idarubicin's binding dynamics with tRNA using spectroscopic and computational approaches

Idarubicin (4-demethoxydaunomycin), a structural analogue of daunomycin derived from Streptomyces peucetius, exhibits enhanced anticancer efficacy due to the substitution of a methoxy group with a hydrogen atom. This study investigates the binding interactions of idarubicin with RNA using a multifaceted approach, including infrared (IR) spectroscopy, absorption spectroscopy, circular dichroism (CD), molecular docking, and molecular dynamics (MD) simulations. The IR results demonstrate significant binding to guanine and uracil, indicated by spectral shifts, while MD simulations reveal additional interactions with adenine, highlighting a flexible binding mechanism. The binding constant of the idarubicin-RNA complex was calculated to be K = 2.1 × 103 M-1, reflecting a strong affinity and stable interaction. Thermodynamic analysis shows that the negative Gibbs free energy (ΔG ∼ -4.57 kcal/mol) signifies spontaneous binding under physiological conditions. The binding free energy estimation was carried out to check the binding affinity, stability and interactions of the complex which was assessed through molecular dynamics simulations. The stability of the idarubicin-RNA complex is further supported by a hyperchromic effect observed in absorption spectroscopy, suggesting effective intercalation that enhances base exposure. The binding is driven by hydrogen bonding, π-π stacking interactions, and electrostatic forces, which collectively stabilize the complex. Notably, the conformational integrity of RNA is largely preserved, with key structural features remaining unchanged in both IR and CD analyses. Comparatively, idarubicin's interactions with RNA differ from those with DNA, where the latter shows more substantial conformational perturbations. These findings enhance our understanding of anthracycline functionality and provide valuable insights for developing novel analogues with improved efficacy and reduced side effects, informing future therapeutic strategies targeting RNA in cancer treatment.

The interface hydrophilic-hydrophobic integration of fluorinated defective graphene towards biomedical applications

In biomedical fields, rational design of novel two-dimensional (2D) biomedical nanomaterials aims to precisely manipulate biomolecules, including efficient capture, structural-functional transformation, directional movement, and self-assembly. In this work, we innovatively proposed new graphene nanosheets and selected two representative proteins to explore their binding mechanisms, structural-functional transformation of proteins, and biological effects of the materials. Fluorinated defective graphene (FDG) exhibited highly efficient capture and structural-functional transformation for the receptor binding domain (RBD), and we observed its collapse phenomenon in 2D materials for the first time. For the main protease (Mpro), FDG achieved an optimal balance between efficient capture, immobilization, and structural disruption. Further studies showed that fluorination on oxygen-containing defect graphene significantly enhanced variances in water distribution, surface properties, and hydrogen bond networks on the material surface. This allowed amino acids to be confined to specific areas, achieving efficient capture and directional movement. Additionally, the adsorption behavior and interaction strength of peptides and deoxynucleotides on FDG further validated the possibility of self-assembly. In summary, we highlight FDG as an excellent biomedical material with hydrophilic-hydrophobic integration.

Elucidation of the interaction between apo-transferrin and indisulam via multi-spectroscopic techniques and molecular modeling

Apo-transferrin (apo-TRF) is a vital protein for maintaining iron balance in the body, which is produced by the liver. Indisulam (IDM) has been extensively used to treat cancer in clinical study and has been identified as a molecular glue. Iron imbalances in the body are believed to encourage the growth and spread of cancer cells. Thus, understanding the interactions between apo-TRF and IDM may serve as a foundation for identifying novel therapeutic strategies for cancer associated with iron imbalances. In this study, multi-spectroscopic methods and computer simulations were employed to explore the binding mode between apo-TRF and IDM, as well as to investigate IDM's impact on the biological functions of apo-TRF. Multi-spectroscopic studies indicated that IDM and apo-TRF formed binary complexes with Ka of 1.274 × 104 M-1 at 298 K. The H-bonds and van der Waals forces were the dominant interaction forces based on an analysis of the thermodynamic parameters (ΔHθ = -37.565 kJ/mol, ΔSθ = -46.665 J mol-1 K-1). Three-dimensional (3D) and circular dichroism (CD) spectra revealed the conformational of apo-TRF changed by IDM, resulting in a looser and more unfolded structure. With escalating concentrations of IDM, a notable reduction in the binding affinity between apo-TRF and Fe3+ was observed, indicating that IDM could potentially alter iron transfer mediated by apo-TRF. Molecular docking analysis indicated that IDM docked in the apo-TRF iron-binding pocket. After in-depth analysis of the molecular dynamic results, it was found that Asp392 played an important role in this interaction. In addition, accessible surface area (ASA) values of key residues (Tyrosine, Aspartate, and Histidine) for iron transfer were altered, which could be a possible reason for the change in iron transport.

New insights into the interactions between the antibiotic enrofloxacin and fish protein by spectroscopic, thermodynamic, and theoretical simulation approaches

In this study, myofibrillar proteins (MPs) from crucian carp were utilized as a model to investigate the binding mechanism between fish proteins and antibiotic residues. Fluorescence quenching confirmed the static quenching (Ksv = 1.89 × 104 M-1 s-1, Kq = 1.89 × 1012 M-1 s-1) and effective binding (Kb = 5.66 × 106 M-1) of Enrofloxacin (ENRO) to MPs. Fourier-transform infrared spectroscopy and circular dichroism spectroscopy revealed that ENRO binding altered the secondary structure of MPs. The interaction mechanism, primarily driven by hydrogen bonding, electrostatic, and hydrophobic interactions (ΔH0 < 0, ΔS0 > 0), was elucidated using isothermal titration calorimetry. The ΔH0, -TΔS0 and ΔG0 values of the binding reaction between MPs and ENRO were -5.98 kJ/mol, -32.57 kJ/mol and -38.55kJ/mol. Molecular docking further verified the interaction forces, identifying key amino acid residues (Phe-40, His-93, and Lys-42) involved in ENRO binding. Additionally, protein carbonylation results demonstrated that even at maximum residue limits, ENRO accelerated MPs oxidation, further confirming the binding of the two. This study can provide theoretical support for the research of the dissipation fate of bound state residues in aquatic products.

Assessing the role of Berberine as an inhibitor of advanced glycation end products (AGEs) formation using in vitro and molecular interaction studies

Glycation leads to the formation of protein aggregates and advanced glycation end products (AGEs) by non-enzymatic reaction. AGEs have been linked to several pathological conditions such as diabetes, cardiovascular disorders, Alzheimer's etc. Our research objective is understanding how methylglyoxal triggers AGEs and protein aggregate formation in human serum albumin (HSA) and how the phytochemical berberine protects it. Employing various biochemical and biophysical techniques, we explored how berberine alters human serum albumin's biochemical properties and structure during multiple glycation stages. HSA was incubated with methylglyoxal at varying concentrations of berberine for 7-14 days at a temperature range of 35-37 degrees C. Methylglyoxal induced the formation of AGEs, fibrillar aggregates and hydrophobic protein patches in HSA as demonstrated by AGEs fluorescence, Thioflavin T (ThT) fluorescence and 1-anilinonaphthalene-8-sulphonic acid (ANS) fluorescence studies. The secondary structure of HSA was also disrupted as demonstrated by CD spectroscopy. All the parameters were nearly reverted back to native HSA formed in the glycated HSA + berberine samples. Molecular docking was utilized to identify the essential HSA residues involved in the HSA-berberine complex interaction and to ascertain the spontaneous binding of berberine to the HSA subdomain, hence favouring thermodynamic binding. The binding energy of HSA-berberine was determined to be -9.1 kcal/mol. The binding of berberine to lysine and arginine residues might be linked to its anti-glycation potential, as these amino acids play an important role in the glycation of proteins. However, further research is required to validate this assertion. Therefore, our study identifies AGEs and aggregates of the clinically significant protein HSA.

The investigation of the interaction of warangalone with transferrin as a therapeutic biological macromolecule and the formation of a protein-ligand nanocomplex with superior anticancer activity against lung cancer cells

Though warangalone has shown anticancer properties against breast cancer cells, its colloidal stability and therapeutic index ought to be improved using a potential strategy, especially via protein-based (nano)carriers. In this research, transferrin was used as a plasma protein for the development of the warangalone-transferrin NPs. To investigate the mechanism underlying the formation of this complex, the interaction between warangalone and transferrin, as well as transferrin NPs, was analyzed using spectroscopic methods. The anticancer properties of warangalone and warangalone-transferrin NPs in lung cancer were subsequently evaluated. The findings showed that the hydrodynamic size, PDI, and zeta potential values of transferrin NPs were 122.4 ± 12.38 nm, 0.210, and -23.40 ± 3.28 mV, respectively. The association between warangalone and transferrin NP showed a strong binding strength (log Kb = 5.44 ± 0.07), while this affinity was reduced for the warangalone and the transferrin protein (log Kb = 4.88 ± 0.04). Theoretical research indicated that hydrophobic interactions serve as the main driving forces for the interaction of warangalone and transferrin. Cellular assays showed that the warangalone-transferrin NPs significantly affected cell death in lung cancer cells. This research, by offering promising data, could be highly beneficial for advancing warangalone-transferrin NPs as a promising anticancer platform.

Multifunctional copper-glutathione clusters with superior p-nitrophenol degradation and horseradish peroxidase-like activity

Copper nanoclusters (Cu NCs) are emerging as highly promising nanomaterials due to their unique physicochemical properties, making them an ideal platform for catalysis, sensing, and environmental remediation. This study explores the development of ultrasmall, water-soluble copper-glutathione (Cu-SG) nanoclusters, focusing on their catalytic capacity for the degradation of p-nitrophenol (p-NP), horseradish peroxidase (HRP)-like activity, and hydrogen peroxide (H2O2) detection. During synthesis, a combination of one-pot synthesis and acid-etching strategy was employed. The acid-etching approach was specifically utilized as an essential method to precisely regulate the structural properties of the clusters. The water-soluble ultrasmall Cu-SG nanoclusters show superior catalytic efficiency, achieving 98% conversion of p-NP to p-aminophenol (p-AP) within six minutes. The reaction followed first-order kinetics with a rate constant of 0.44 min-1, consistent with the Langmuir-Hinshelwood model. Notably, the Cu-SG retained catalytic efficiency across multiple reaction cycles, highlighting their recyclability and long-term stability. Additionally, Cu-SG exhibited excellent sensitivity and selectivity for rapid colorimetric H2O2 detection due to the strong HRP-like activity, achieving a detection limit of 6.03 μM with high resistance to interference from other ions and compounds. Thermodynamic analysis demonstrates an enthalpy driven spontaneous reduction of p-NP with Cu-SG, wherein the van der Waals and hydrogen bonding interactions are predominant. By contrast, the interaction of Cu-SG with H2O2 is an entropy-driven, spontaneous process, and the dominating hydrophobic forces drive the HRP-like catalytic mechanism. This study demonstrates the potential of the Cu-SG as an efficient, stable, and recyclable water-soluble copper nanocatalyst for pollutant degradation and as a sensitive sensor for reactive species.

The interaction of isoquinoline alkaloid crebanine with immunoglobulin G and cytotoxic effects toward MCF-7 breast cancer cell line

In this study, the interaction of crebanine, an isoquinoline alkaloid, with immunoglobulin G (IgG) was evaluated. Subsequently, the anticancer effects of crebanine in MCF-7 breast cancer cells were assessed. The results demonstrate that static quenching plays a key role in the fluorescence quenching of the IgG by crebanine, and some embedded hydrophobic patches of the IgG are exposed upon interaction with crebanine, while the characteristic β-sheet conformation of the IgG was almost preserved. Theoretical studies also show that several hydrophilic and hydrophobic residues play a crucial role in the formation of hydrogen bonds between crebanine and IgG, along with the stability of the complex. Cellular studies indicate that crebanine induces selective anticancer effects in MCF-7 cells (IC50: 36.76 μM) compared to human embryonic kidney cells (HEK-293, IC50: 723.77 μM) through the inhibition of colony formation, induction of oxidative stress and lipid peroxidation, upregulation of the Bax/Bcl-2 ratio, and cytochrome c release, which are indicative of the intrinsic apoptosis pathway. In conclusion, this study provides valuable information regarding the protein binding affinity and anticancer activity of crebanine, which are essential factors for determining the pharmacological activity of small molecules as drug candidates.

Electric field-induced conformational dynamics of CA9: a potential biomarker for glioblastoma multiforme

GBM, a malignant brain tumor prevalent in adults, can be treated using Electric field (EF) therapy. However, the underlying mechanism of EF-based GBM therapy is not well understood. In this study, we used bioinformatics and MD analysis to explore CA9 in EF therapy for GBM. CA9 was identified as a differentially expressed gene (DEG) sensitive to EF stimulation in GBM using GEO and TCGA for integrated analysis. Elevated CA9 expression was associated with reduced overall survival in GBM patients, indicating that CA9 was an adverse prognostic factor. Single-cell data demonstrated that CA9 expression was significantly higher in GBM cells than in normal cells, suggesting that CA9 could be an EF-sensitive biomarker for GBM. GSVA analysis suggested that CA9 was related to hypoxia and glucose metabolism in glioblastoma. MD simulations were employed to examine the impact of EF (0 V/nm ≤ E ≤ 0.5 V/nm) on the conformation of the CA9 protein, including RMSF, RMSD, Rg, secondary structure, and dipole moment. The CA9 protein structure was altered with different EF intensities, affecting the motion of protein atoms in an EF intensity-dependent manner. The number of hydrogen bonds was significantly reduced as the EF intensity increased, indicating that EF disrupted the hydrogen bonds. Additionally, the EF intensity affected the dipole moment and characteristic time. Besides, the CA9 gene family analysis suggested that this gene family was highly conserved. Overall, CA9 showed potential as a GBM biomarker sensitive to EF, presenting a prospective target for therapeutic interventions in EF-mediated GBM treatment.

Unraveling the Role of Polyoxometalates-Based Superchaotropes on the Photophysics of Organic Molecules and Modulation of Water Dynamics in a Hydrophilic Block Copolymer Solution

Polyoxometalates (POMs) are composed of nanometric metal-oxide anions and have rich solution chemistry. In this class, Keggin POMs have been identified as the most influential inorganic additives for aqueous nonionic soft matter systems. POMs being at the borderline of classical ions and charged colloids possess fascinating solution properties; the present work aims to delve deeper into the interactions between nanoions and nonionic soft matters from a spectroscopic point of view. Our studies reveal that although of the same structural makeup, silicotungstic acid hydrate (SiW) and phosphotungstic acid hydrate (PW) affect the photophysics of Coumarin-480 (C-480) in poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) ((PEO)76-(PPO)30-(PEO)76, F-68) copolymeric media in a dissimilar manner. From time-resolved studies, we find a preference for SiW toward the intramolecular charge transfer state of C-480, whereas PW favors the locally emissive state of the probe. Further, from rotational relaxation studies, it appears that SiW renders a rigid environment around the probe molecule, while PW relaxes the copolymeric environment. Finally, the dynamic quenching mechanism of the added nanoions was unraveled, which showed a straightforward Förster mechanism for SiW but a short-range interaction was operative for PW. From Fourier transform infrared and 1H NMR, it can be concluded that both the nanoions interacted with the PPO moiety of the copolymer; yet, their contrasting effect on the photophysics has been rationalized as a consequence of charge density on the ions.

Exploring the effects of whey protein components on the interaction and stability of cyanidin-3-O-glucoside

BACKGROUND

Anthocyanins are susceptible to degradation due to external factors. Despite the potential for improved anthocyanin stability with whey protein isolate (WPI), the specific effects of individual components within WPI on the stability of anthocyanins have yet to be studied extensively. This study investigated the interaction of WPI, β-lactoglobulin (β-Lg), bovine serum albumin (BSA), and lactoferrin (LF) with cyanidin-3-O-glucoside (C3G), and also considered their effects on stability.

RESULTS

Fluorescence analysis revealed static quenching effects between C3G and WPI, β-Lg, BSA, and LF. The binding constants were 1.923 × 103 L · mol⁻¹ for WPI, 24.55 × 103 L · mol⁻¹ for β-Lg, 57.25 × 103 L · mol⁻¹ for BSA, and 1.280 × 103 L · mol⁻¹ for LF. Hydrogen bonds, van der Waals forces, and electrostatic attraction were the predominant forces in the interactions between C3G and WPI and between C3G and BSA. Hydrophobic interaction was the main binding force in the interaction between C3G and β-Lg and between C3G and LF. The binding of C3G with WPI, β-Lg, BSA, and LF was driven by different thermodynamic parameters. Enthalpy changes (∆H) were -38.76 kJ · mol⁻¹ for WPI, -17.59 kJ · mol⁻¹ for β-Lg, -16.09 kJ · mol⁻¹ for BSA, and 39.50 kJ · mol⁻¹ for LF. Entropy changes (∆S) were -67.21 J · mol⁻¹·K⁻¹ for WPI, 3.72 J · mol⁻¹·K⁻¹ for β-Lg, 37.09 J · mol⁻¹·K⁻¹ for BSA, and 192.04 J · mol⁻¹·K⁻¹ for LF. The addition of C3G influenced the secondary structure of the proteins. The decrease in the α-helix content suggested a disruption and loosening of the hydrogen bond network structure. The presence of proteins enhanced the light stability and thermal stability (stability in the presence of light and heat) of C3G. In vitro simulated digestion experiments demonstrated that the addition of proteins led to a delayed degradation of C3G and to improved antioxidant capacity.

CONCLUSION

The presence of WPI and its components enhanced the thermal stability, light stability, and oxidation stability of C3G. Preheated proteins exhibited a more pronounced effect than unheated proteins. These findings highlight the potential of preheating protein at appropriate temperatures to preserve C3G stability and bioactivity during food processing. © 2024 Society of Chemical Industry.

POU4F1 enhances lung cancer gemcitabine resistance by regulating METTL3-dependent TWF1 mRNA N6 adenosine methylation

This study aimed to investigate the role of POU Class 4 Homeobox 1 (POU4F1) in regulating gemcitabine (GEM) resistance in lung cancer cells. The mRNA and protein expressions were assessed using RT-qPCR, western blot, immunofluorescence, and immunohistochemistry. Cell viability and proliferation were assessed by CCK-8 assay and EdU assay. TUNEL staining and flow cytometry were employed to detect cell apoptosis. The m6A modification of TWF1 was detected using MeRIP assay. The interactions between molecules were validated using dual luciferase reporter gene, ChIP, and RIP assays. POU4F1 knockdown inhibited GEM resistance and autophagy in lung cancer cells. Mechanistically, POU4F1 transcriptionally activated methyltransferase-like protein 3 (METTL3) in GEM-resistant cells by binding to the METTL3 promoter. METTL3 promoted the N6-methyladenosine (m6A) modification and expression level of twinfilin-1 (TWF1). Overexpression of METTL3 and TWF1 weakened the effects of POU4F1 knockdown on GEM resistance and autophagy. Moreover, knockdown POU4F1 also enhanced GEM anti-tumor sensitivity in vivo. In conclusion, POU4F1 upregulation promoted GEM resistance in lung cancer cells by promoting autophagy through increasing METTL3-mediated TWF1 m6A modification.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04161-w.

Molecular dynamics of transferrin receptor binder peptides: unlocking blood-brain barrier for enhanced CNS drug delivery

A cystine-dense peptide (CDP) named TfRB1 was identified for its ability to bind to the transferrin receptor (TfR). CDPs are stabilized by their disulfide bonds, and variants of TfRB1 - specifically TfRB1G1, TfRB1G2, and TfRB1G3 - are explored for their potential to transport molecules across the blood-brain barrier (BBB) into the central nervous system (CNS). This study employed molecular modeling and dynamics simulations to characterize the interactions between these TfRB1 variants and TfR. Binding free energy calculations showed a strong correlation with experimental binding affinities of -10.99 kcal/mol for TfRB1G2 and -13.18 kcal/mol for TfRB1G3, with a relative error of 1.98%. The key forces driving these interactions include electrostatic and van der Waals forces, with mutations in TfRB1G3 (T9M and A13D) enhancing its binding affinity through improved interactions with residues such as Arg633. The free energy landscape analysis revealed that TfRB1G3 maintains the N-terminal residues of TfR in an α-helical conformation, unlike TfRB1G2. Per-residue free energy decomposition identified key residues - Leu619, Arg629, Tyr643, and Phe650 - as crucial for TfR binding, underscoring their competitive nature with transferrin. Additionally, Glu612, which is favorable for binding in TfRB1G2, becomes unfavorable in TfRB1G3. Conversely, Arg633 shifts from unfavorable in TfRB1G2 to favorable in TfRB1G3, compensating for the loss of favorable interaction with Glu612. These findings provide valuable molecular insights into the TfRB1 peptides' potential as drug carriers, highlighting their capability to deliver molecules to the CNS and compete with transferrin for BBB transport.

Mechanistic Insights into the interaction between aldehyde aroma compounds and β-Casein through Multi-Spectroscopy and molecular dynamics

The interaction between proteins and aroma compounds significantly impacts cheese flavor retention during processing. However, it is still unknown how cheese proteins and the aldehyde aroma compounds (AACs) interact. This study aims to clarify the interaction mechanisms between the AACs (benzaldehyde, 2-methylpropanal, 2-methylbutanal and 3-methylbutanal) and β-casein (β-CN) using SPME-GC/MS, multi-spectroscopy techniques, and molecular dynamics simulations. The results reveal notable variations in the binding abilities of the four AACs and β-CN, with the strongest binding observed for 3-methylbutanal. Specifically, the binding affinity (Ka) values between β-casein and benzaldehyde, 2-methylpropanal, 2-methylbutanal, and 3-methylbutanal are 2.26 × 103, 1.78 × 103, 2.03 × 103, and 2.52 × 103 M-1, respectively, indicating moderate binding affinity. Additionally, the quenching rate constants (Kq) for interactions with these compounds are 2.57 × 1011, 2.92 × 1011, 3.74 × 1011, and 4.81 × 1011 M-1s-1, significantly exceeding the collisional quenching limit, suggesting specific interactions. The interactions between the four AACs and β-CN occur through irreversible covalent bonding, primarily involving hydrogen bonds and hydrophobic interactions. The quenching mechanism of β-CN and the four AACs is static, which leads to changes in the secondary structure and microenvironment of β-CN. Molecular docking and dynamics simulations confirm that hydrogen bonds and hydrophobic interactions are the key driving forces for the binding of β-CN with the four AACs, and contribute to the stability of the composite system.

Sodium dodecyl sulfate rearranges the conformation of transferrin and attenuates its iron-binding capacity

Sodium dodecyl sulfate (SDS), an anionic surfactant used in many cleaning and hygiene products, is known for its dermal and respiratory toxicity. However, how this surfactant influences the iron dynamics within the body and the mechanism is unknown. We explored the interaction between SDS and human transferrin (HTF), focusing on the effects on iron-binding capacity and structural changes. Results revealed that SDS exposure led to a significant release of iron from HTF in a dose-dependent manner, changing its structure and reducing the iron-binding ability. Spectroscopic analyses showed that the protein secondary structure and skeleton, as well as the micro-environment of aromatic amino acids of HTF, were destroyed after SDS binding. Isothermal titration calorimetry (ITC) results (ΔG, ΔS, and ΔH were -40.1 kcal·mol-1, 0.16 kcal·mol-1·K-1, and 10.1 kcal·mol-1, respectively) indicated a spontaneous and hydrophobic interaction with one strong binding site. Molecular docking identified the preferred binding sites, emphasizing hydrophobic forces (with the hydrophobic tail) and hydrogen bonds (with the hydrophilic head) as the primary driving forces, which aligns with the ITC results. Overall, this comprehensive analysis sheds light on the intricate interplay between SDS and HTF, providing insights into potential health risks associated with SDS exposure.

Spectroscopic study on volasertib: Highly stable complexes with albumin and encapsulation into alginate/montmorillonite bionanocomposites

In the present work, we study different physicochemical properties related to LADME processes of volasertib, a Polo-like kinase 1 inhibitor in advanced clinical trials. Firstly, the protonation equilibria, the extent of ionization at the physiological pH and pKa values of this drug are studied combining spectroscopic techniques and computational calculations. Secondly, the binding process of volasertib to the human serum albumin (HSA) protein is analyzed by fluorescence spectroscopy. We report a high binding constant to HSA (Ka = 4.10 × 106 M-1) and their pharmacokinetic implications are discussed accordingly. The negative enthalpy and entropy (ΔH0 = -54.49 kJ/mol; ΔS0 = -58.90 J K-1 mol-1) determined for the binding process suggests the implication of hydrogen bonds and van der Waals interactions in the formation of the HSA-volasertib complex. Additionally, volasertib is encapsulated in an alginate/montmorillonite bionanocomposite as a proof of concept for an oral delivery nanocarrier. The physical properties of that nanocomposite as well as volasertib delivery kinetics are analyzed.

The inhibitory effects of free and bound phenolics from Phyllanthus emblica Linn. on α-amylase: a comparison study

BACKGROUND

Phyllanthus emblica Linn. (PE) is rich in polyphenols, which can be categorized into free and bound phenolics (PEFP and PEBP). This study evaluated the inhibitory effect of PEFB and PEBP on α-amylase for the first time. The mechanism of the inhibition effect of PEFP and PEBP on α-amylase was investigated by enzyme inhibition kinetics, multispectral analysis, thermodynamics, and molecular docking.

RESULTS

Free and bound phenolics inhibited α-amylase activity effectively in a mixed type of inhibition. Fluorescence quenching and thermodynamic analyses showed that the binding of PEFP and PEBP to α-amylase occurred through a static quenching process (Kq = 6.94 × 10¹² and 5.74 × 10¹² L mol-1 s-1), which was accompanied by a redshift (λem from 343 to 347 nm), leading to a change in the microenvironment. This process was found to be a spontaneous exothermic reaction (ΔG < 0). Circular dichroism (CD) analysis confirms that the secondary structure of α-amylase was altered, in particular a decrease in α-helixes and an increase in random coils. Molecular docking studies showed that PEFP and PEBP interacted with α-amylase through hydrogen bonding and hydrophobic interactions.

CONCLUSION

The present study provides valuable insights into the mechanism of action of PEFP and PEBP on α-amylase, which will provide a theoretical basis for their possible use as novel natural α-amylase inhibitors. © 2024 Society of Chemical Industry.

Binding characteristics of the major kratom alkaloid, mitragynine, towards serum albumin: Spectroscopic, calorimetric, microscopic, and computational investigations

Mitragynine (MTG) is a prominent indole alkaloid that is present abundantly in Mitragyna speciosa, commonly referred to as kratom. MTG has garnered significant attention due to its selective agonistic characteristics towards opioid receptors and related analgesic effects. In the circulatory system, the in vivo efficacy of MTG is dictated by its interaction with plasma proteins, primarily human serum albumin (HSA). In the present study, we utilized a broad methodology that included spectroscopic, calorimetric, microscopic, and in silico approaches to characterize the interaction between MTG and HSA. Alterations in the UV absorption spectrum of HSA by the presence of MTG demonstrated a ground-state complexation between the protein and the ligand. The Ka values obtained for the MTG-HSA interaction were in the range 103-104 M-1 based on analysis of fluorescence and ITC data, respectively, indicating an intermediate binding affinity. The binding reaction was thermodynamically favorable as revealed by ΔH, ΔS, and ΔG values of -16.42 kJ mol-1, 39.97 J mol-1 K-1, and -28.34 kJ mol-1, respectively. Furthermore, CD spectroscopy results suggested MTG binding induced minimal effects on the structural integrity of HSA, supported by computational methods. Changes in the dimensions of HSA particles due to aggregation, as observed using atomic force microscopy in the presence of MTG. Competitive drug displacement results seemingly suggested site III of HSA located at subdomain IB as the preferred binding site of MTG, but were in inconclusive. However, docking results showed the clear preference of MTG to bind to site III, facilitated by hydrophobic (alkyl and pi-alkyl) and van der Waals forces, together with carbon hydrogen bonds. Additionally, the MTG-HSA complexation was demonstrated to be stable based on molecular dynamics analysis. The outcomes of this study shed light on the therapeutic potential of MTG and can help in the design of more effective derivatives of the compound.

Tracing sulfate sources in a tropical agricultural catchment with a stable isotope Bayesian mixing model

Sulfate (SO42-) is an essential anion in drinking water and a vital macronutrient for plant growth. However, elevated sulfate levels can impact ecosystem or human health and could be an important indicator of acid rock drainage or pollution. Therefore, monitoring SO42- sources and transport is important for water quality assessments. This study focused on exploring the sources and transformations of SO42- as well as estimating the proportional contribution of the potential SO42- pollutant sources to groundwater and surface water in a tropical river basin, the Densu River Basin. The study used major ions combined with stable sulfur and oxygen isotope compositions and a Bayesian isotope mixing model, MixSIAR. The major ion characteristics indicate that SO42- concentrations remain stable throughout the rainy and dry seasons but originate from diverse sources. The multi-isotope model (δ34SSO4, δ18OSO4) identified four potential SO42- sources: detergent, precipitation, sewage, and sulfate fertilizer. However, the δ34SSO4 and δ18OSO4 values of the fertilizer source signatures overlapped with those of precipitation and sewage. Nevertheless, the contributions from each source were disentangled using the MixSIAR model, which revealed sewage as the most dominant SO42- pollutant in the Densu Basin, accounting for ~47 % of sulfate in groundwater and ~ 56 % of sulfate in surface water. Sulfate fertilizer (~33 %) was the second most important source after sewage for groundwater, while detergent (~23 %) was the second most important source for surface water. The redox processes of bacterial sulfate reduction and sulfide oxidation were determined to have a minimal impact on the sulfur isotope fractionation within the basin. This study highlights the benefits of combining major ions, sulfur isotopes and the MixSIAR model for identifying sources of sulfate. This approach accounts for uncertainties in source contributions which allows for more robust and reliable apportionment of sulfate sources. The study emphasizes the need for effective waste management and pollution control measures to protect water quality and provides vital guidelines on how to partition sulfate sources on a large catchment scale and evidence for making pollution management decisions on water resources.

Multispectral and molecular simulation of the interaction of human α1-acid glycoprotein with palbociclib

Palbociclib, a selective CDK4/6 inhibitor with potent anti-tumor effects, was investigated for its interaction with human α1-acid glycoprotein (HAG). Spectral analysis revealed that palbociclib forms a ground state complex with HAG, exhibiting binding constant (Kb) of 104 M-1 at the used temperature range. The interaction between the two was determined to be driven mainly by hydrogen bonding and hydrophobic forces. Multispectral studies indicated that the bound palbociclib altered the secondary structure of HAG and reduced polarity around Trp and Tyr amino acids. And, molecular docking and dynamics simulations verified the experimental findings. Finally, most of the metal ions present in plasma, such as K+, Cu2+, Ca2+, Mg2+, Ni2+, Fe3+, and Co2+, are detrimental to the binding of palbociclib to HAG, with the exception of Zn2+, which is favorable.

Computational Analysis of Interactions Between Drugs and Human Serum Albumin

Drug molecules exist as complexed with serum proteins such as human serum albumin (HSA) and/or unbound free form in the blood circulation. Drugs can be effective only when they are free. Thus, it is important to understand aspects that are important for interaction between drugs and interacting proteins. In this study, interactions among 2990 FDA approved drugs and HSA were computational analyzed to unravel principles that are critical for drug-HSA interactions. Docking results showed that drugs have higher affinity toward cavity-1 (C1) than cavity-2 (C2). A total of 1131 drug molecules have docking score greater than 60 while 768 molecules have docking score greater than 60 when they are docked in C2. In addition, three solvent channels have potential to direct solvent to C1 cavity while C2 does not have any effective channel. The post MD analyses demonstrated that drugs are making polar interactions with basic amino acids in the binding cavities. Verbscoside and ceftazidime both have stable low RMSD values throughout MD simulation with 2 Å on average in C1 cavity. The ligand RMSD shows less stability for verbscoside, which is around 4 Å when it is in complex with HSA in C1. The individual contribution of the residues K192, K196, R215, and R254 to ceftazidime are -1.92 ± 0.18, -3.09 ± 0.09, -2.17 ± 0.17, and - 2.32 ± 0.098, respectively. These residues contribute the binding energy of the verbscoside by -6.06 ± 0.08, -2.10 ± 0.06, and - 1.57 ± 0.03 kcal/mol individually in C1 cavity. C2 is making polar interactions with drug via R469, K472, and K488 residues and their contribution to the two drugs are -3.13 ± 0.21 kcal/mol for R469, -1.94 ± 0.18 kcal/mol for K472, and -1.96 ± 0.11 kcal/mol for K488 to total binding energy of ceftazidime. The binding energy of verbscoside is 57.17 ± 7.00 kcal/mol and Arg-407 has the highest contribution this bind energy individually with -4.29 ± 0.12 kcal/mol. Drugs with hydrogen bond donor/acceptor chemical adducts such as verbscoside involve higher hydrogen bond formation in C1 pocket. Ceftazidime makes interaction with HSA toward hydrophobic residues, L384, L404, L487, and L488 in the C2 cavity.

Deciphering the interactions between altertoxins and glutenin based on molecular dynamic simulation: inspiration from detection

BACKGROUND

Mycotoxin contamination of food has been gaining increasing attention. Hidden mycotoxins that interact with biological macromolecules in food could make the detection of mycotoxins less accurate, potentially leading to the underestimation of the total exposure risk. Interactions of the mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) with high-molecular glutenin were explored in this study.

RESULTS

The recovery rates of AOH and AME (1, 2, and 10 μg kg-1) in three types of grains (rice, corn, and wheat) were relatively low. Molecular dynamics (MD) simulations indicated that AOH and AME bound to glutenin spontaneously. Hydrogen bonds and π-π stacking were the primary interaction forces at the binding sites. Alternariol with one additional hydroxyl group exhibited stronger binding affinity to glutenin than AME when analyzing average local ionization energy. The average interaction energy between AOH and glutenin was -80.68 KJ mol-1, whereas that of AME was -67.11 KJ mol-1.

CONCLUSION

This study revealed the mechanisms of the interactions between AOH (or AME) and high-molecular glutenin using MD and molecular docking. This could be useful in the development of effective methods to detect pollution levels. These results could also play an important role in the evaluation of the toxicological properties of bound altertoxins. © 2024 Society of Chemical Industry.

Molecular docking and molecular dynamics simulation of wheat gluten-derived antioxidant peptides acting through the Keap1-Nrf2 pathway

BACKGROUND

In our previous study, we successfully identified five peptides from wheat gluten: Ala-Pro-Ser-Tyr (APSY), Leu-Tyr (LY), Pro-Tyr (PY), Arg-Gly-Gly-Tyr (RGGY) and Tyr-Gln (YQ). Molecular docking and molecular dynamics simulation methods were employed to investigate the interaction between these antioxidant peptides and the Kelch-like ECH-associated protein 1 (Keap1 protein), revealing the molecular mechanism of their non-competitive binding. In addition, the total antioxidant capacity of the five peptides was determined using the 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) method.

RESULTS

The affinities of APSY, LY, PY, RGGY and YQ were -8.9, -8.3, -8.5, -9.1 and - 7.9 kcal mol-1, respectively. The five peptides effectively bound to Keap1 protein through hydrogen, π-σ, π-alkyl and alkyl interactions. Significant roles were observed for the P1 pocket residue ARG-415 and the P3 pocket residue ALA-556 in the interactions of the Keap1-peptide complexes. Molecular dynamics simulations further elucidated the dynamic process of peptide binding to the Keap1 protein. All five peptides formed stable complexes with Keap1 protein, with van der Waals forces playing crucial roles in these complex systems, indicative of the peptides' strong binding ability to Keap1 protein. The van der Waals forces were -178.74, -123.11, -134.36, -132.59, and -121.44 kJ mol-1 for the Keap1-APSY, Keap1-LY, Keap1-PY, Keap1-RGGY and Keap1-YQ complexes, respectively. These peptides exhibited excellent antioxidant effects. Among them, the YQ peptide exhibited the highest total antioxidant capacity, with an activity value of 1.18 ± 0.06 mmol Trolox equivalent (TE) L-1 at a concentration of 0.10 mg mL-1. The RGGY, PY, LY and APSY peptides followed in descending order, with activity values of 0.91 ± 0.05, 0.72 ± 0.06, 0.62 ± 0.04 and 0.60 ± 0.05 mmol TE L-1, respectively.

CONCLUSION

These results unveiled the molecular mechanism by which the five antioxidant peptides act on active pockets through the Keap1-Nrf2 signaling pathway, providing a theoretical basis for the development of antioxidants. © 2024 Society of Chemical Industry.

Nucleic acid binding affinity and antioxidant activity of N-m-Tolyl-4-Chlorophenoxyacetohydroxamicacid

Hydroxamic acids represent a group of weak organic acids, both naturally occurring and synthetically derived, characterized by the general formula RC(= O)N(R'OH). In this study, we investigated the binding behavior of N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) through a combination of techniques including UV-visible spectroscopy, fluorescence emission analysis, viscometry, and computational simulations using AutoDock4 software. Our findings reveal that the mode of binding between the compound and the nucleic acids is consistent with intercalation. Competitive binding experiments demonstrated that the complex competes effectively with ethidium bromide (EB) for binding to ct-DNA/t-RNA, displacing EB from its binding sites. Additionally, the introduction of the compound into the DNA-EB system resulted in a quenching of fluorescence emission peaks. Analysis of absorption spectra indicated a red shift and hypochromic shift when the compound interacted with DNA, further supporting the intercalative binding mode. The calculated binding constant (Kb) value for the compound is 6.62 × 104 M-1 and 5.40 × 103 M-1 indicating a strong interaction with ct-DNA and t-RNA respectively. We determined the Stern-Volmer constants for ct-DNA and t-RNA as 9.96 × 104 M-1 and 8.13 × 105 M-1, respectively. The binding free energy values for ct-DNA/t-RNA were calculated to be - 3.741 × 107 and - 5.425 × 108 kcal/mol, respectively. Viscometric studies corroborated the UV results, showing a continuous increase in relative viscosity of ct-DNA/t-RNA solutions with the addition of the optimal hydroxamic acid concentration. Furthermore, we assessed the antioxidant activity of the compound using DPPH-radical scavenging and β-carotene linoleic acid assays. Gel electrophoresis results demonstrated the compound's remarkable efficacy in preventing DNA damage. Collectively, all experimental evidence supports the conclusion that N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid binds to ct-DNA/t-RNA through an intercalative mechanism, which is consistent with our molecular docking simulations.

Synergistic integration of deep learning with protein docking in cardiovascular disease treatment strategies

This research delves into the exploration of the potential of tocopherol-based nanoemulsion as a therapeutic agent for cardiovascular diseases (CVD) through an in-depth molecular docking analysis. The study focuses on elucidating the molecular interactions between tocopherol and seven key proteins (1O8a, 4YAY, 4DLI, 1HW9, 2YCW, 1BO9 and 1CX2) that play pivotal roles in CVD development. Through rigorous in silico docking investigations, assessment was conducted on the binding affinities, inhibitory potentials and interaction patterns of tocopherol with these target proteins. The findings revealed significant interactions, particularly with 4YAY, displaying a robust binding energy of -6.39 kcal/mol and a promising Ki value of 20.84 μM. Notable interactions were also observed with 1HW9, 4DLI, 2YCW and 1CX2, further indicating tocopherol's potential therapeutic relevance. In contrast, no interaction was observed with 1BO9. Furthermore, an examination of the common residues of 4YAY bound to tocopherol was carried out, highlighting key intermolecular hydrophobic bonds that contribute to the interaction's stability. Tocopherol complies with pharmacokinetics (Lipinski's and Veber's) rules for oral bioavailability and proves safety non-toxic and non-carcinogenic. Thus, deep learning-based protein language models ESM1-b and ProtT5 were leveraged for input encodings to predict interaction sites between the 4YAY protein and tocopherol. Hence, highly accurate predictions of these critical protein-ligand interactions were achieved. This study not only advances the understanding of these interactions but also highlights deep learning's immense potential in molecular biology and drug discovery. It underscores tocopherol's promise as a cardiovascular disease management candidate, shedding light on its molecular interactions and compatibility with biomolecule-like characteristics.

The effect of rice protein-polyphenols covalent and non-covalent interactions on the structure, functionality and in vitro digestion properties of rice protein

The characteristics of the crosslinking between rice protein (RP) and ferulic acid (FA), gallic acid (GA), or tannin acid (TA) by covalent binding of Laccase and non-covalent binding were evaluated. The RP-polyphenol complexes greatly improved the functionality of RP. The covalent effect with higher polyphenol binding equivalence showed higher emulsion activity than the non-covalent effect. The solubility, and antioxidant activity of covalent binding were higher than that of non-covalent binding in the RP-FA group, but there was a contrasting behavior in the RP-GA group. The RP-FA was most soluble in conjugates, while the RP-GA had the highest solubility in mixtures. It was found that the covalent complexes were more stable in the intestinal tract. The content of polyphenols in the RP-TA group was rapidly increased at the later intestinal digestion, which indicated the high polyphenol-protective effect in this group. Meanwhile, the RP-TA group showed high reducing power but low digestibility.

Construction of resveratrol and quercetin nanoparticles based on folic acid targeted Maillard products between Jiuzao glutelin isolate and carboxymethyl chitosan: Improved stability and function

Advanced targeted nanoparticles (NPs) were designed to enhance the targeted delivery of resveratrol (RES) and quercetin (QUE) by utilizing carboxymethyl chitosan (CTS) and Jiuzao glutelin isolate (JGI) conjugates. Briefly, RES and QUE were encapsuled within CTS-JGI-2 (CTS/JGI, m/m, 2:1). The carrier's targeting properties were further improved through the incorporation of folic acid (FA) and polyethylenimine (PEI). Moreover, the stability against digestion was enhanced by incorporating baker yeast cell walls (BYCWs) to construct RES-QUE/FA-PEI/CTS-JGI-2/MAT/BYCW NPs. The results demonstrated that FA-PEI/CTS-JGI-2/MAT/BYCW NPs could improve cellular uptake and targeting property of RES and QUE through endocytosis of folic acid receptors (FOLRs). Additionally, RES-QUE successfully alleviated LPS- and DSS-induced inflammation by regulating NF-κB/IkBa/AP-1 and AMPK/SIRT1signaling pathways and reducing the secretion of inflammatory mediators and factors. These findings indicate FA-PEI/CTS-JGI-2/MAT/BYCW NPs hold promise as an oral drug delivery system with targeted delivery capacities for functional substances prone to instability in dietary supplements.

Construction and validation of a ubiquitination-related prognostic risk score signature in breast cancer

Background

Breast cancer (BC) is a highly common form of cancer that occurs in many parts of the world. However, early -stage BC is curable. Many patients with BC have poor prognostic outcomes owing to ineffective diagnostic and therapeutic tools. The ubiquitination system and associated proteins were found influencing the outcome of individuals with cancer. Therefore, developing a biomarker associated with ubiquitination genes to forecast BC patient outcomes is a feasible strategy.

Objective

The primary goal of this work was to develop a novel risk score signature capable of accurately estimate the future outcome of patients with BC by targeting ubiquitinated genes.

Methods

Univariate Cox regression analysis was conducted utilizing the E1, E2, and E3 ubiquitination-related genes in the GSE20685 dataset. Genes with p < 0.01 were screened again using the Non-negative Matrix Factorization (NMF) algorithm, and the resulting hub genes were composed of a risk score signature. Patients were categorized into two risk groups, and the predictive effect was tested using Kaplan-Meier (KM) and Receiver Operating Characteristic (ROC) curves. This risk score signature was later validated using multiple external datasets, namely TCGA-BRAC, GSE1456, GSE16446, GSE20711, GSE58812 and GSE96058. Immuno-microenvironmental, single-cell, and microbial analyses were also performed.

Results

The selected gene signature comprising six ubiquitination-related genes (ATG5, FBXL20, DTX4, BIRC3, TRIM45, and WDR78) showed good prognostic power in patients with BC. It was validated using multiple externally validated datasets, with KM curves showing significant differences in survival (p < 0.05). The KM curves also demonstrated superior predictive ability compared to traditional clinical indicators. Single-cell analysis revealed that Vd2 gd T cells were less abundantin the low-risk group, whereas patients in the high-risk group lacked myeloid dendritic cells. Tumor microbiological analysis revealed a notable variation in microorganism diversity between the high- and low-risk groups.

Conclusion

This study established an risk score signature consisting of six ubiquitination genes, that can accurately forecast the outcome of patients with BC using multiple datasets. It can provide personalized and targeted assistance to provide the evaluation and therapy of individuals having BC.

Enhancing cisplatin drug sensitivity through PARP3 inhibition: The influence on PDGF and G-coupled signal pathways in cancer

Drug resistance poses a significant challenge in cancer treatment despite the clinical efficacy of cisplatin. Identifying and targeting biomarkers open new ways to improve therapeutic outcomes. In this study, comprehensive bioinformatic analyses were employed, including a comparative analysis of multiple datasets, to evaluate overall survival and mutation hotspots in 27 base excision repair (BER) genes of more than 7,500 tumors across 23 cancer types. By using various parameters influencing patient survival, revealing that the overexpression of 15 distinct BER genes, particularly PARP3, NEIL3, and TDG, consistently correlated with poorer survival across multiple factors such as race, gender, and metastasis. Single nucleotide polymorphism (SNP) analyses within protein-coding regions highlighted the potential deleterious effects of mutations on protein structure and function. The investigation of mutation hotspots in BER proteins identified PARP3 due to its high mutation frequency. Moving from bioinformatics to wet lab experiments, cytotoxic experiments demonstrated that the absence of PARP3 by CRISPR/Cas9-mediated knockdown in MDA-MB-231 breast cancer cells increased drug activity towards cisplatin, carboplatin, and doxorubicin. Pathway analyses indicated the impact of PARP3 absence on the platelet-derived growth factor (PDGF) and G-coupled signal pathways on cisplatin exposure. PDGF, a critical regulator of various cellular functions, was downregulated in the absence of PARP3, suggesting a role in cancer progression. Moreover, the influence of PARP3 knockdown on G protein-coupled receptors (GPCRs) affects their function in the presence of cisplatin. In conclusion, the study demonstrated a synthetic lethal interaction between GPCRs, PDGF signaling pathways, and PARP3 gene silencing. PARP3 emerged as a promising target.

The protection role of human growth hormone on skin cells following ultraviolet B exposure

BACKGROUND

Ultraviolet-B (UVB) radiation is the leading environmental cause of skin damage and photoaging. The epidermis and dermis layers of the skin mainly absorb UVB. UVB stimulates apoptosis, cell cycle arrest, generation of reactive oxygen species, and degradation of collagen and elastin fibers.

OBJECTIVE

This study investigated the potential of human growth hormone (hGH) in protecting the skin fibroblasts and keratinocytes (HFFF-2 and HaCaT cell lines) from UVB-induced damage.

METHODS

The MTT assay was performed to evaluate UVB-induced mitochondrial damage via assessing the mitochondrial dehydrogenase activity, and flow cytometry was carried out to investigate the effects of UVB and hGH on the cell cycle and apoptosis of UVB-irradiated cells. In addition, the fold change mRNA expression levels of Type I collagen and elastin in HFFF-2 cells were evaluated using the qRT-PCR method following UVB exposure.

RESULTS

We observed that treatment of cells with hGH before UVB exposure inhibited UVB-induced loss of mitochondrial dehydrogenase activity, apoptosis, and sub-G1 population formation in both cell lines. We also found that hGH-treated HFFF-2 cells showed up-regulated mRNA expression of Type I collagen, elastin, and IGF-1 in response to UVB irradiation.

CONCLUSION

These findings suggest hGH as a potential anti-UVB compound that can protect skin cells from UVB-induced damage. Our findings merit further investigation and can be used to better understand the role of hGH in skin photoaging.

The molecular and network mechanisms of antilipidemic potential effects of Ganfule capsules in nonalcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a common liver disorder characterized by hepatic steatosis, inflammation and fibrosis. Ganfule (GFL), a traditional Chinese medicine, has demonstrated therapeutic potential in the treatment of NAFLD but the mechanisms involved are not fully understood.To evaluate the biochemical mechanisms of GFL in treating NAFLD by examining its effects on biological networks, key therapeutic targets, histopathological changes and clinical implications.

METHODS

Chemical component screening, key target prediction, biological functional enrichment analysis, lipid profile localization analysis and complex network analysis were performed on GFL using multi-database mining, network analysis and molecular docking. An NAFLD rat model was then established and treated with different doses of GFL. Histopathological evaluation and western blotting were used to verify the expression levels of key target proteins in GFL-treated NAFLD rats.

RESULTS

Network analysis analysis identified 12 core targets, 12 core active ingredients and 7 core Chinese medicinal herbs in GFL potentially involved in the treatment of NAFLD. Biological functional enrichment analysis revealed the involvement of lipid metabolism, apoptosis and intracellular signaling pathways. Molecular docking confirmed a strong affinity between GFL's core compounds and certain target proteins. Histopathological examination of an NAFLD rat model showed reduced hepatocellular steatosis after GFL treatment. Western blotting revealed significant downregulation of PPARA and PPARD protein expression and upregulation of PIK3CG and PRKACA protein expression in NAFLD rats treated with lower doses of GFL.

CONCLUSIONS

Our results suggest that GFL modulates key proteins involved in lipid metabolism and apoptosis pathways. GFL improved the histopathological features of NAFLD rats by regulating lipid metabolism as well as reducing hepatocyte apoptosis and hepatocellular steatosis. These findings offer insights into the biochemical mechanism of action of GFL and support its use in the treatment for NAFLD.

Paraquat disrupts KIF5A-mediated axonal mitochondrial transport in midbrain neurons and its antagonism by melatonin

Paraquat (PQ) is a broad-spectrum herbicide used worldwide and is a hazardous chemical to human health. Cumulative evidence strengthens the association between PQ exposure and the development of Parkinson's disease (PD). However, the underlying mechanism and effective interventions against PQ-induced neurotoxicity remain unclear. In this study, C57BL/6 J mice were treated with PQ (i.p., 10 mg/kg, twice a week) and melatonin (i.g., 20 mg/kg, twice a week) for 8 weeks. Results showed that PQ-induced motor deficits and midbrain dopaminergic neuronal damage in C57BL/6 J mice were protected by melatonin pretreatment. In isolated primary midbrain neurons and SK-N-SH cells, reduction of cell viability, elevation of total ROS levels, axonal mitochondrial transport defects and mitochondrial dysfunction caused by PQ were attenuated by melatonin. After screening of expression of main motors driving axonal mitochondrial transport, data showed that PQ-decreased KIF5A expression in mice midbrain and in SK-N-SH cell was antagonized by melatonin. Using the in vitro KIF5A-overexpression model, it was found that KIF5A overexpression inhibited PQ-caused neurotoxicity and mitochondrial dysfunction in SK-N-SH cells. In addition, application of MTNR1B (MT2) receptor antagonist, 4-P-PDOT, significantly counteracted the protection of melatonin against PQ-induced neurotoxicity. Further, Kif5a-knockdown diminished melatonin-induced alleviation of motor deficits and neuronal damage against PQ in C57BL/6 J mice. The present study establishes a causal link between environmental neurotoxicants exposure and PD etiology and provides effective interventive targets in the pathogenesis of PD.

Insight into the interaction of 5,6 epoxy-cholesterols with human serum albumin

5,6-Epoxy-cholesterols has been recently revealed to control metabolic pathway in breast cancer, which makes investigating their binding interaction with human serum albumin (HSA) an attractive field of research. The main aim of this article is to examine the binding interaction of 5,6 α-epoxy-cholesterol (5,6 α EC) and 5,6 β-epoxy-cholesterol (5,6 β- EC) with HSA using different spectroscopic methods and molecular modeling. These compounds interact with HSA via hydrophobic interactions and hydrogen bonds with binding constants 6.3 × 105 M-1 for 5,6 α-epoxy-cholesterol and 6.9 × 105 M-1 for 5,6 β-epoxy-cholesterol besides, the mechanism of the interaction can be attributed to static quenching. Circular dichroism data indicated that the α-helical content of HSA increased from 50.5 to 59.8 and 61.1 % after the addition of 5,6 α-ECs and 5,6 β-EC, respectively, with a ratio of 1:2. Thermodynamic analysis revealed that binding between 5,6-epoxy-cholesterols and HSA is spontaneous and entropy-driven. The molecular docking and esterase-like activity experiments were performed to envision a link between the experimental and theoretical results. The optimal binding site of 5,6-epoxy-cholesterols with HSA was located in subdomain IIA. Moreover, theoretical calculations were performed using the B3LYP function with the 6-311++G (d,p) basis set, indicating the HOMO-LUMO energy gap of 7.874 eV for 5,6 α-epoxy-cholesterol and 7.873 eV for 5,6 β-epoxy-cholesterol. The obtained findings are assumed to provide basic data for understanding the binding interactions of HSA with oxysterol compounds, which could help explore the pharmacokinetics and pharmacodynamics of oxysterol compounds.

Molecular insight on the binding of halogenated organic phosphate esters to human serum albumin and its effect on cytotoxicity of halogenated organic phosphate esters

Halogenated Organic Phosphate Esters (OPEs) are commonly found in plasticizers and flame retardants. However, they are one kind of persistent contaminants that can pose a significant threat to human health and ecosystem as new environmental estrogen. In this study, two representative halogenated OPEs, tris(1,3-dichloro-2-propyl) phosphate (TDCP) and tris(2,3-dibromopropyl) phosphate (TDBP), were selected as experimental subjects to investigate their interaction with human serum albumin (HSA). Despite having similar structures, the two ligands exhibited contrasting effects on enzyme activity of HSA, TDCP inhibiting enzyme activity and TDBP activating it. Furthermore, both TDCP and TDBP could bind to HSA at site I, interacted with Arg222 and other residues, and made the conformation of HSA unfolded. Thermodynamic parameters indicated the main driving forces between TDBP and HSA were hydrogen bonding and van der Waals forces, while TDCP was mainly hydrophobic force. Molecular simulations found that more hydrogen bonds of HSA-TDBP formed during the binding process, and the larger charge area of TDBP than TDCP could partially account for the differences observed in their binding abilities to HSA. Notably, the cytotoxicity of TDBP/TDCP was inversely proportional to their binding ability to HSA, implying a new method for determining the cytotoxicity of halogenated OPEs in vitro.

Probing the toxic effect of chlorpyrifos as an environmental pollutant on the structure and biological activity of lysozyme under physiological conditions

The pervasive use of pesticides like chlorpyrifos (CPY) has been associated with deleterious effects on biomolecules, posing significant risks to environmental integrity, public health, and overall ecosystem equilibrium. Accordingly, in this study, we investigated the potential binding interaction between the well-conserved enzyme, lysozyme (LSZ), and CPY through various spectroscopic techniques and molecular modeling. The UV-vis absorption and fluorescence experiments confirmed the complex formation and static quenching of the intrinsic fluorescence intensity. LSZ revealed a singular binding site for CPY, with binding constants around 105 M-1 across different temperature ranges. Analysis of thermodynamic parameters showed the spontaneous nature of the complexation process, while also revealing the pivotal role of hydrophobic interactions in stabilizing the LSZ-CPY system. According to circular dichroism and Fourier transform infrared studies, CPY binding changed the secondary structure of LSZ by boosting α-helix presence and reducing the levels of β-sheet and β-turn content. Further, CPY decreased the stability and activity of LSZ. Computational docking delineated the specific and highly preferred binding site of CPY within the structure of LSZ. Molecular dynamic simulation indicated the enduring stability of the LSZ/CPY complex and revealed structural modifications in the LSZ after binding with CPY. This research provides a detailed understanding of the intermolecular dynamics between CPY and LSZ, concurrently elucidating the molecular-level implications for the potential hazards of pesticides in the natural environment.

Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A

Protein aggregation is related to numerous pathological conditions like Alzheimer's and Parkinson's disease. In our study, we have shown that an already existing FDA-approved drug; methotrexate (MTX) can be reprofiled on preformed α-chymotrypsinogen A (α-Cgn A) aggregates. The zymogen showed formation of aggregates upon interaction with mercuric ions, with increasing concentration of Hg2Cl2 (0-150 µM). The hike in ThT and ANS fluorescence concomitant with blue shift, bathochromic shift and the hyperchromic effect in the CR absorbance, RLS and turbidity measurements, substantiate the zymogen β-rich aggregate formation. The secondary structural alterations of α- Cgn A as analyzed by CD measurements, FTIR and Raman spectra showed the transformation of native β-barrel conformation to β-inter-molecular rich aggregates. The native α- Cgn A have about 30% α-helical content which was found to be about 3% in presence of mercuric ions suggesting the formation of aggregates. The amorphous aggregates were visualized by SEM. On incubation of Hg2Cl2 treated α- Cgn A with increasing concentration of the MTX resulted in reversing aggregates to the native-like structure. These results were supported by remarkable decrease in ThT and ANS fluorescence intensities and CR absorbance and also consistent with CD, FTIR, and Raman spectroscopy data. MTX was found to increase the α-helical content of the zymogen from 3 to 15% proposing that drug is efficient in disrupting the β-inter-molecular rich aggregates and reverting it to native like structure. The SEM images are in accordance with CD data showing the disintegration of aggregates. The most effective concentration of the drug was found to be 120 µM. Molecular docking analysis showed that MTX molecule was surrounded by the hydrophobic residues including Phe39, His40, Arg145, Tyr146, Thr151, Gly193, Ser195, and Gly216 and conventional hydrogen bonds, including Gln73 (bond length: 2.67Å), Gly142 (2.59Å), Thr144 (2.81Å), Asn150 (2.73Å), Asp153 (2.71Å), and Cys191 (2.53Å). This investigation will help to find the use of already existing drugs to cure protein misfolding-related abnormalities.

Computational identification of potential modulators of heme-regulated inhibitor (HRI) for pharmacological intervention against sickle cell disease

Sickle cell disease (SCD) poses a significant health challenge and therapeutic approaches often target fetal hemoglobin (HbF) to ameliorate symptoms. Hydroxyurea, a current therapeutic option for SCD, has shown efficacy in increasing HbF levels. However, concerns about myelosuppression and thrombocytopenia necessitate the exploration of alternative compounds. Heme-regulated inhibitor (HRI) presents a promising target for pharmacological intervention in SCD due to its association with HbF modulation. This study screened compounds for their potential inhibitory functions against HRI. Small-molecule compounds from 17 folkloric plants were subjected to in silico screening against HRI. Molecular docking was performed, and free binding energy calculations were determined using molecular mechanics with generalized born and surface area (MMGBSA). Lead compounds were subjected to molecular dynamics simulation at 100 ns. Computational quantum mechanical modeling of the lead compounds was subsequently performed. We further examined the pharmacodynamics, pharmacokinetic and physiological properties of the identified compounds. Five potential HRI inhibitors, including kaempferol-3-(2G-glucosyrutinoside), epigallocatechin gallate, tiliroside, myricetin-3-O-glucoside and cannabiscitrin, with respective docking scores of -16.0, -12.17, -11.37, -11.56 and 11.07 kcal/mol, were identified. The MMGBSA analysis of the complexes yielded free-binding energies of -69.76, -71.17, -60.44, -53.55 and -55 kcal/mol, respectively. The identified leads were stable within HRI binding pocket for the duration of the 100 ns simulation. The study identified five phytoligands with potential inhibitory effects on HRI. This finding holds promise for advancing SCD treatment strategies. However, additional preclinical analyses are warranted to validate the chemotherapeutic properties of the lead compounds.

A Conserved Tryptophan (Trp10) at the Hydrophobic Core Modulates the Stability and Inhibitory Activity of Potato I Type Inhibitors

BACKGROUND

Different inhibitor families have their own conserved three-dimensional structures, but how these structures determine whether a protein can become an inhibitor is still unknown. The buckwheat trypsin inhibitor (BTI) pertains to the Potato I type inhibitor family, which is a simple and essential bio-molecule that serves as a model for the investigation of protease-inhibitor interaction.

OBJECTIVE

To study the effects of mutations at Trp10 and Ile25 in the hydrophobic cavity (scaffold) of rBTI on its inhibitory activity and stability.

METHODS

Site-directed mutagenesis and molecular modeling were performed using the sequence of BTI. The hydrogen bonds formed by all amino acids and conformational differences of Trp53 were analyzed in the tertiary structures of rBTI and mutants.

RESULTS

Mutant rBTI-W10A almost completely lost its inhibitory activity (retaining 10%), while rBTI-I25A retained about 50% of its inhibitory activity. Both rBTI-W10A and rBTI-I25A could be degraded by trypsin. The hydrogen bond analysis results showed that mutating Trp10 or Ile25 weakened the specific cohesion interactions in the hydrophobic core of rBTI, disrupting the tight hydrogen bond network in the cavity. This further led to difficulty in maintaining the binding loop conformation, ultimately causing the Trp53 to undergo conformational changes. It was also difficult for residues in the mutants to form hydrogen bonds with amino acids in bovine trypsin; thus, the mutants could not stably bind to trypsin.

CONCLUSION

Our findings suggest that the hydrophobic core is also an important factor in the maintenance of inhibitory activity and stability of rBTI.