An insight into the interaction between malachite green oxalate with human serum albumin: Molecular dynamic simulation and spectroscopic approaches

Spontaneous interactions between typical antibiotics and soil enzyme: Insights from multi-spectroscopic approaches, XPS technology, molecular modeling, and joint toxic actions

A large amount of antibiotics enters the soil environment and accumulates therein as individuals and mixtures, threatening the soil safety. However, there is little information regarding the influence of single and mixed antibiotics on key soil proteins at molecular level. In this study, setting sulfadiazine (SD) and tetracycline hydrochloride (TC) as the representative antibiotics, the interactions between these agents and α-amylase (an important hydrolase in soil carbon cycle) were investigated through multi-spectroscopic approaches, X-ray photoelectron spectrometry, and molecular modeling. It was found that both SD and TC spontaneously bound to α-amylase with 1:1 stoichiometry mainly via forming stable chemical bonds. The interactions altered the polarity of aromatic amino acids, protein backbone, secondary structure, hydrophobicity and activity of α-amylase. The SD-TC mixtures were designed based on the direct equipartition ray to comprehensively characterize the possible concentration distribution, and interactive effects indicated that the mixtures antagonistically impacted α-amylase. These findings reveal the binding characteristics between α-amylase and typical antibiotics, which probably influence the ecological functions of α-amylase in soil. This study clarifies the potential harm of antibiotics on soil functional enzyme, which is significant for the environmental risk assessment of antibiotics and their mixtures.

The mechanism of interaction between tri-para-cresyl phosphate and human serum protein: A multispectroscopic and in-silico study

Organophosphate flame retardants (OPFRs) pose the significant risks to the environment and human health and have become a serious public health issue. Tricresyl phosphates (TCPs), a group of aryl OPFRs, exhibit neurotoxicity and endocrine disrupting toxicity. However, the binding mechanisms between TCPs and human serum albumin (HSA) remain unknown. In this study, through fluorescence and ultraviolet-visible (UV-vis) absorption spectroscopy, molecular docking and molecular dynamics (MD), tri-para-cresyl phosphate (TpCP) was selected to explore potential interactions between HSA and TCPs. The results of the fluorescence spectroscopy demonstrated that a decrease in the fluorescence intensity of HSA and a blue shift were observed with the increasing concentrations of TpCP. The binding constant (Ka) was 2.575 × 104 L/mol, 4.701 × 104 L/mol, 5.684 × 104 L/mol and 9.482 × 104 L/mol at 293 K, 298 K, 303 K, and 310 K, respectively. The fluorescence process between HSA and TpCP involved a mix of static and dynamic quenching mechanism. The gibbs free energy (ΔG0) of HSA-TpCP system was -24.452 kJ/mol, -25.907 kJ/mol, -27.363 kJ/mol, and - 29.401 kJ/mol at 293 K, 298 K, 303 K, and 310 K, respectively, suggesting that the HSA-TpCP reaction was spontaneous. The enthalpy change (ΔH0) and thermodynamic entropy change (ΔS0) of the HSA-TpCP system were 60.83 kJ/mol and 291.08 J/(mol·>k), respectively, indicating that hydrophobic force was the major driving force in the HSA-TpCP complex. Furthermore, multispectral analysis also revealed that TpCP could alter the microenvironment of tryptophan residue and the secondary structure of HSA and bind with the active site I of HSA. Molecular docking and MD simulations confirmed that TpCP could spontaneously form a stable complex with HSA, which was consistent with the fluorescence experimental results. This study provides novel insights into the mechanisms of underlying the transportation and distribution of OPFRs in humans.

The size-dependent effects of nanoplastics in mouse primary hepatocytes from cells to molecules

Nanoplastics (NPs) are easily ingested by organisms and their major accumulation organ was determined to be liver. To date, the size-dependent cytotoxicity of NPs on mammalian hepatocytes remains unclear. This study utilized mouse primary hepatocytes and catalase (CAT) as specific receptors to investigate the toxicity of NPs from cells to molecules, focusing on size-dependent effects. Results showed that the larger the particle size of NP at low doses (≤50 mg/L), the most pronounced inhibitory effect on hepatocyte viability. 20 nm NPs significantly inhibit cell viability only at high doses (100 mg/L). Larger NP particles (500 nm and 1000 nm) resulted in a massive release of lactate dehydrogenase (LDH) from the cell (cell membrane damage). Reactive oxygen species (ROS), superoxide dismutase (SOD) and CAT tests suggest that NPs disturbed the cellular antioxidant system. 20 nm NPs show great strength in oxidizing lipids and disrupting mitochondrial function compared to NPs of other particle sizes. The degree of inhibition of CAT activity by different sized NPs was coherent at the cellular and molecular levels, and NP-500 had the most impact. This suggests that the structure and microenvironment of the polypeptide chain in the vicinity of the CAT active site is more susceptible to proximity and alteration by NP-500. In addition, the smaller NPs are capable of inducing relaxation of CAT backbone, disruption of H-bonding and reduction of α-helix content, whereas the larger NPs cause contraction of CAT backbone and increase in α-helix content. All NPs induce CAT fluorescence sensitization and make the chromophore microenvironment hydrophobic. This study provides new insights for NP risk assessment and applications.

Influence of para-substituted benzaldehyde derivatives with different push/pull electron strength groups on the conformation of human serum albumin and toxicological effects in zebrafish

Excessive intake of benzaldehyde and its derivatives can cause irreversible damage to living organisms. Hence, benzaldehyde derivatives with different para-substitutions of push/pull electronic groups were chosen to investigate the effect of different substituent properties on the structure of human serum albumin (HSA). The binding constants, number of binding sites, major interaction forces, protein structural changes, and binding sites of benzaldehyde (BzH) and its derivatives (4-BzHD) with HSA in serum proteins were obtained based on multispectral and molecular docking techniques. The mechanism of BzH/4-BzHD interaction on HSA is mainly static quenching and is accompanied by the formation of a ground state complex. BzH/4-BzHD is bound to HSA in a 1:1 stoichiometric ratio. The interaction forces for the binding of BzH/4-BzHD to HSA are mainly hydrogen bonding and hydrophobic interaction, which are also accompanied by a small amount of electrostatic interactions. The effect of BzH/4-BzHD on HSA conformation follows: 4-Diethylaminobenzaldehyde (4-DBzH) > 4-Nitrobenzaldehyde (4-NBzH) > 4-Hydroxybenzaldehyde (4-HBzH) > 4-Acetaminobenzaldehyde (4-ABzH) > BzH, which means that the stronger push/pull electronic strength of the para-substituted benzaldehyde derivatives has a greater effect on HSA conformation. Furthermore, the concentration-lethality curves of different concentrations for BzH/4-BzHD on zebrafish verified above conclusion. This work provides a scientific basis for the risk assessment of benzaldehyde and its derivatives to the ecological environment and human health and for the environmental toxicological studies of benzaldehyde derivatives with different strengths of push/pull electron substitution.

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.

Multiple spectroscopic and computational studies on binding interaction of 2-phenylamino-4-phenoxyquinoline derivatives with bovine serum albumin

Binding characteristics of potent non-nucleoside HIV-1 reverse transcriptase inhibitors, 4-(2',6'-dimethyl-4'-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (1) and 4-(2',6'-dimethyl-4'-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (2), to bovine serum albumin (BSA) under simulative physiological conditions were investigated by multiple spectroscopic and computational methods. The experimental results demonstrated that (1) and (2) bound to BSA at site III (subdomain IB), and quenched BSA fluorescence through a static quenching process. The binding interaction of (1) or (2) to BSA forms stable complexes with the binding constants (Kb) at the level of 104 L/mol and the number of binding site was determined to be 1 for both systems, indicating that new synthesized compounds occupied one site in BSA with moderate binding affinities. Based on the analysis of the thermodynamic parameters, it can be indicated that the main binding forces for interaction between BSA and both compounds were hydrogen bonding and van der Waals force. Synchronous fluorescence results revealed that the interaction of two compounds with BSA led to modifications in the microenvironment surrounding tryptophan residue of BSA. Circular dichroism spectra demonstrated alterations in the secondary structure of BSA induced by (1) and (2). Moreover, the experimental data of molecular docking and molecular dynamics (MD) simulations supported the results obtained from multiple spectroscopic techniques, confirming the binding interactions between both compounds and BSA.

Analysis of the binding mechanism for a water-soluble Pd(II) complex containing β-amino alcohols with HSA applying experimental and computational methods

In the study ahead, the binding interactions of the [Pd (HEAC) Cl2] complex with human serum albumin (HSA) protein have been assayed in vitro (pH= 7.40) utilizing computational and experimental procedures. The mentioned complex was synthesized as a water-soluble complex from {2-((2-((2-hydroxyethyl)amino)ethyl)amino) cyclohexanol} ligand = HEAC. The results of electronic absorption and circular dichroism investigations illustrated that the hydrophobicity of the Tryptophan microenvironment in HSA undergoes the changes by binding to the Pd(II) complex without substantial perturbations on the protein secondary structure. The fluorescence emission spectroscopy analysis revealed that with rising temperature, the quenching constant (Ksv) in the Stern-Volmer's relation decreases; so, it can be said that the interaction process is along with a static quenching mechanism. The values of 2.88 × 105 M-1, and 1.26 represent the binding constant (Kb) and the number of the binding sites (n), respectively. The Job graph showed the maximum point at χ = 0.5, which means organizing a new set with 1:1 stoichiometry. Thermodynamic profile (ΔH < 0, ΔS < 0, and ΔG < 0) has affirmed that van der Waals forces and hydrogen bonds have a basic function in the Pd(II) complex-albumin bindings. The ligand-competitive displacement studies utilizing warfarin and ibuprofen have represented that Pd(II) complex interacts with albumin by site II (subdomain IIIA). The computational molecular docking theory approved the results of the site-competitive tests; also, it indicated the existence of hydrogen bonds and van der Waals forces in Pd(II) complex-albumin interactions.Communicated by Ramaswamy H. Sarma.

Biodegradation of malachite green by Pleurotus eryngii: a study on decolorization, mechanism, toxicity, and enzyme

The purpose of this study was to investigate the biodegradation of malachite green (MG) by Pleurotus eryngii via decolorization. This study also explored the possible mechanisms and toxicity. The results indicated that this fungus exhibited strong decolorizing potential. MG degradation based on UPLC-TOF-Triple-MS analysis revealed the formation of intermediates such as 4-(dimethylamino)benzophenone, 4-(methylamino)benzophenone, and 4-(dimethylamino)phenol. Furthermore, a significant reduction in the toxicity of the degradation products was observed using the zebrafish animal model. A newly discovered dye-decolorizing peroxidase (DyP-PE) from P. eryngii was amplified, cloned, and expressed. The purified 56.4 kDa DyP-PE strongly decolorized MG, suggesting potentially application in the bioremediation of MG pollution. Thus, the DyP-PE derived from P. eryngii may contribute to the degradation of MG.

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods

Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.

Inhibition mechanism of fisetin on acetylcholinesterase and its synergistic effect with galantamine

The search for acetylcholinesterase (AChE) inhibitors produced by natural sources is of great significance for the prevention and therapy of Alzheimer's disease and has been widely concerned. In this study, fisetin, a flavonoid compound of plant origin, displayed a mixed inhibition mode on AChE (IC50 = 8.88 ± 0.14 μM). Fluorescence spectra analysis revealed that fisetin statically quenched AChE fluorescence, and the ground state complex was formed by hydrogen bonds and hydrophobic interactions. Circular dichroism assays showed that fisetin induced AChE structure loosened with a decrease in α-helix structure (from 20.6 % to 19.5 %). Computer simulation exhibited that fisetin bound to both the peripheral anionic site (PAS) and the catalytic active site (CAS) and increased the stability of the AChE. Interestingly, the combination of fisetin and galantamine enhanced the binding affinity between AChE and galantamine and induced AChE structure further loosened, while the inhibition mode was still the mixed type. The heatmap analysis indicated that galantamine (0.2 μM) combined with fisetin (2.25 μM) had a significant synergy on AChE inhibition, probably because fisetin binding at the PAS-AChE induced conformation changes of the gorge and CAS, which enhanced galantamine binding affinity with CAS, and a further loose structure of AChE was induced by the mixture, so finally the interaction between the substrate and AChE was strongly affected. This work may offer a theoretical reference for the functional research of fisetin as a potential AChE inhibitor and an enhanced supplement for galantamine.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Delineating the cascade of molecular events in protein aggregation triggered by Glyphosate, aminomethylphosphonic acid, and Roundup in serum albumins

The molecular basis of protein unfolding on exposure to the widely used herbicide, Glyphosate (GLY), its metabolite aminomethylphosphonic acid (AMPA), and the commercial formulation Roundup have been probed using human and bovine serum albumins (HSA and BSA). Protein solutions were exposed to chemical stress at set experimental conditions. The study proceeds with spectroscopic and imaging tools. Steady-state and time-resolved fluorescence (TRF) measurements indicated polarity changes with the possibility of forming a ground-state complex. Atomic force microscopy imaging results revealed the formation of fibrils from BSA and dimer, trimer, and tetramer forms of oligomers from HSA under the chemical stress of GLY. In the presence of AMPA, serum albumins (SAs) form a compact network of oligomers. The compact network of oligomers was transformed into fibrils for HSA with increasing concentrations of AMPA. In contrast, Roundup triggered the formation of amorphous aggregates from SAs. Analysis of the Raman amide I band of all aggregates showed a significant increase in antiparallel β-sheet fractions at the expense of α-helix. The highest percentage, 24.6%, of antiparallel β-sheet fractions was present in amorphous aggregate formed from HSA under the influence of Roundup. These results demonstrated protein unfolding, which led to the formation of oligomers and fibrils.

Exploring the binding mechanism and adverse toxic effects of degradation metabolites of pyrethroid insecticides to human serum albumin: Multi-spectroscopy, calorimetric and molecular docking approaches

Pyrethroid insecticides (PIs), a class of structurally similar non-persistent organic pollutants, can be degraded and metabolized to more toxic, and longer half-life products. In this study, the binding interaction mechanisms between human serum albumin (HSA) and the main degradation metabolites of PIs, 3-phenoxybenzoic acid (3-PBA) and 4-fluoro-3-phenoxybenzoic acid (4-F-3-PBA), were studied by theoretical simulation and experimental verification. Steady state fluorescence spectra showed that the fluorescence quenching mechanism was static. According to the binding constant, 4-F-3-PBA (1.53 × 105 L mol-1) was bound more strongly to HSA than 3-PBA (1.42 × 105 L mol-1) in subdomain ⅡA (site I). It was found by isothermal titration calorimetry that the metabolites and HSA spontaneously combined mainly through hydrogen bond and van der Waals interaction. Ultraviolet absorption spectra and circular dichroism spectra showed that the metabolites caused slight changes in the microenvironment and conformation of HSA. The above results were proved by molecular docking. The toxicity properties of the metabolites were further analyzed by software, and 4-F-3-PBA was found to be more toxic than 3-PBA. Considering the high exposure level of these metabolites in food, the environment and human body, it is necessary to further explore the toxicity of PIs metabolites.

Investigation on the interaction of aromatic organophosphate flame retardants with human serum albumin via computer simulations, multispectroscopic techniques and cytotoxicity assay

Organophosphate flame retardants (OPFRs) are newly emerging estrogenic environmental pollutants, which attracted widespread public interest owing to their potential threats to human. Here, the interaction between two typical aromatic OPFRs, TPHP/EHDPP and HSA was researched by different experiments. Experimental results indicated that TPHP/EHDPP can insert the site I of HSA and be encircled by several amino acid residues, Asp451, Glu292, Lys195, Trp214 and Arg218 played vital roles in this binding process. At 298 K, the Ka value of TPHP-HSA complex was 5.098 × 104 M-1, and the Ka value of EHDPP-HSA was 1.912 × 104 M-1. Except H-bonds and van der Waals forces, the π-electrons on the phenyl ring of aromatic-based OPFRs played a pivotal role in maintaining the stability of the complexes. The content alterations of HSA were observed in the present of TPHP/EHDPP. The IC50 values of TPHP and EHDPP were 157.9 μM and 31.14 μM to GC-2spd cells, respectively. And the existence of HSA has a regulatory effect on the reproductive toxicity of TPHP/EHDPP. In addition, the results of present work implied Ka values of OPFRs and HSA are possible to be a useful parameter for evaluating their relative toxicity.

Impacts of Halogen Substitutions on Bisphenol A Compounds Interaction with Human Serum Albumin: Exploring from Spectroscopic Techniques and Computer Simulations

Bisphenol A (BPA) is an endocrine-disrupting compound, and the binding mechanism of BPA with carrier proteins has drawn widespread attention. Halogen substitutions can significantly impact the properties of BPA, resulting in various effects for human health. Here, we selected tetrabromobisphenol A (TBBPA) and tetrachlorobisphenol A (TCBPA) to investigate the interaction between different halogen-substituted BPAs and human serum albumin (HSA). TBBPA/TCBPA spontaneously occupied site I and formed stable binary complexes with HSA. Compared to TCBPA, TBBPA has higher binding affinity to HSA. The effect of different halogen substituents on the negatively charged surface area of BPA was an important reason for the higher binding affinity of TBBPA to HSA compared to TCBPA. Hydrogen bonds and van der Waals forces were crucial in the TCBPA-HSA complex, while the main driving factor for the formation of the TBBPA-HSA complex was hydrophobic interactions. Moreover, the presence of TBBPA/TCBPA changed the secondary structure of HSA. Amino acid residues such as Lys199, Lys195, Phe211, Arg218, His242, Leu481, and Trp214 were found to play crucial roles in the binding process between BPA compounds and HSA. Furthermore, the presence of halogen substituents facilitated the binding of BPA compounds with HSA.

Novel antiosteoporotic peptides purified from protein hydrolysates of taihe black-boned silky fowl: By larval zebrafish model and molecular docking

The black-boned silky fowl (BSF) muscle protein hydrolysate was gained by alcalase. The hydrolysate could stimulate MC3T3-E1 cell proliferation, as well as enhance alkaline phosphatas (ALP) activity and deposits of minerals. After isolation and purification, 55 peptide sequences with Mascot score over 40 were identified. Combined with molecular docking simulation and molecular dynamics analysis, two novel peptides (PASTGAAK and PGPPGTPF) were identified with the lowest binding energy of -4.99 kcal/mol and -3.07 kcal/mol with receptor BMPR1A of BMP-2/Smad pathway, showing the ability to increase BMPR1A stability. Moreover, both PASTGAAK and PGPPGTPF revealed strong anti-osteoporosis activities in the zebrafish model induced by dexamethasone. Additionally, the identified peptides could be beneficial for the differentiation of MC3T3-E1 cell for upregulating the expression of some osteoblast-related genes and proteins by stimulating BMP-2/Smad pathway. Overall, the two newly identified peptides could be the potential candidate to prevent osteoporosis.

Probing the toxic effect of quinoline to catalase and superoxide dismutase by multispectral method

Quinoline is a common nitrogen heterocyclic aromatic hydrocarbon with high water solubility. Studies have shown that quinoline can be teratogenic, carcinogenic and mutagenic. And Hepatocytes are the target cell of quinoline, which contain a large number of mitochondria and are related to cell function and the balance of reactive oxygen species (ROS). However, the research on the effect of quinoline on hepatocyte damage and anti-oxidation system is still unclear. Through the means of multispectral experiments, it is concluded that quinoline can affect the catalase (CAT) and superoxide dismutase (SOD), change their structure and affect their activity. The binding mode and binding site of quinoline to CAT/SOD were analyzed by isothermal calorimetric titration (ITC) and Molecular Operating Environment (MOE). In molecular docking simulation, the binding site of quinoline-CAT system is close to the active site, and affect the microenvironment of Tyr 357. This may be the reason why quinoline affects CAT activity and synchronous fluorescence (Δλ = 15 nm). This study demonstrated that quinoline has a great effect on CAT, which may affect the intracellular ROS balance and become a potential way to cause hepatocyte damage.

Elucidation of binding dynamics of tyrosine kinase inhibitor tepotinib, to human serum albumin, using spectroscopic and computational approach

Tepotinib (TPT), an anticancer drug, is a fibroblast growth factor receptor inhibitor approved by the FDA for the chemotherapy of urothelial carcinoma. The binding of anticancer medicines to HSA can affect their pharmacokinetics and pharmacodynamics. The absorption, fluorescence emission, circular dichroism, molecular docking, and simulation studies were used to evaluate the binding relationship between TPT and HSA. The absorption spectra exhibited a hyperchromic effect upon the interaction of TPT with HSA. The Stern-Volmer and binding constant of the HSA-TPT complex demonstrates that fluorescence quenching is triggered by a static rather than a dynamic process. Further, the displacement assays and molecular docking results revealed that TPT preferred binding to site III of HSA. Circular dichroism spectroscopy confirmed that TPT binding to HSA induces conformational changes and reduces α-helical content. The thermal CD spectra reveal that tepotinib enhances protein's stability in the temperature range of 20 to 90 °C. The findings of MDS studies provide further evidence for the stability of the HSA-TPT complex. Consequently, the findings of the present investigation provide a clear picture of the impacts of TPT on HSA interaction. These interactions are thought to make the microenvironment around HSA more hydrophobic than in its native state.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

Triphenylmethane dye (C52H54N4O12) is potentially a hazardous substance in edible freshwater fish at trace level: toxicity, hematology, biochemistry, antioxidants, and molecular docking evaluation study

Malachite green (C₅₂H₅₄N₄O₁₂) is a synthetic dye that is used in textile industries as a colorant and in aquaculture sectors to contain microbial damage. Aquatic contamination of malachite green (MG) has been reported globally. Fish is the highest trophic organism among aquatic inhabitants, highly sensitive to waterborne contaminants (metals, coloring agents, etc.). Toxicity of waterborne chemicals on nontarget organisms can be determined by assessing biomarkers. Assessing blood parameters and tissue antioxidants (enzymatic and nonenzymatic) is useful to evaluate MG toxicity. To initiate the MG toxicity data for freshwater fish (Cyprinus carpio), the median lethal toxicity was primarily evaluated. Then, hematological, blood biochemical (glucose, protein, and cholesterol) and tissue biochemical (amino acids, lipids), and vital tissue (gills, liver, and kidney) antioxidant capacity (CAT, LPO, GST, GR, POxy, vitamin C, and GSH) of C. carpio were analyzed under acute (LC_50-96 h) and sublethal (Treatment I-1/10^th and Treatment II-1/5^th LC_50-96 h) exposure periods (28 days). Molecular docking for MG with hemoglobin was also obtained. Biomarkers examined were affected in the MG-treated groups with respect to the control group. Significant changes (p < 0.05) were observed in hematology (Hb, RBCs, and WBCs), glucose, proteins, lipids and tissue CAT, LPO, and GST activities under acute MG exposure. In sublethal treatment groups, biomarkers studied were significant (p < 0.05) throughout the study period. The potential for MG binding to hemoglobin was tested in this study. MG is potentially a multiorgan toxicant. Literally a chemical that is harmful to the aquatic environment if safety is concerned.

New Insights into the Inhibition of Hesperetin on Polyphenol Oxidase: Inhibitory Kinetics, Binding Characteristics, Conformational Change and Computational Simulation

The inhibitory activity of hesperetin on polyphenol oxidase (PPO) and their interaction characteristics were investigated using multiple spectroscopic methods and computational simulation. Hesperetin, a mixed inhibitor, reversibly inhibited PPO activity, and its half-maximum inhibitory concentration (IC₅₀) values on monophenolase and diphenolase were 80.8 ± 1.4 μM and 776.0 ± 15.5 μM, respectively. Multivariate curve resolution-alternate least squares (MCR-ALS) analysis suggested PPO interacted with hesperetin and formed PPO-hesperetin complex. Hesperetin statically quenched PPO's endogenous fluorescence, and hydrophobic interactions mainly drove their binding. Hesperetin affected the polarity of the microenvironment around the Trp residues in PPO, but had no effect on that around Tyr residues. Circular dichroism (CD) results showed that hesperetin increased α-helix content and decreased β-fold and random coil contents, thus tightening PPO's structure. Molecular docking showed that hesperetin entered the hydrophobic cavity of PPO, bound near the dinuclear copper active center, interacted with Val283, Phe264, His85, Asn260, Val248, and His263 via hydrophobic interactions, formed hydrogen bonds with Met280, His89, and His259 residues and also interacted with Phe292, His61, Phe90, Glu256, His244, Asn260, Phe264, and Gly281 via van der Waals forces. The molecular dynamics simulation results also demonstrated that the addition of hesperetin reduced the stability and hydrophobicity of PPO and increased PPO's structural denseness. Thus, the inhibition of hesperetin on PPO may be because hesperetin bound near the active center of PPO, interacted with the surrounding residues, occupied the binding site for substrate, and induced the changes in PPO's secondary structure, thus inhibiting the catalytic activity of PPO. This study may provide novel views for the inhibition of hesperetin on PPO and theoretical guidance for developing flavonoids as new and efficient PPO inhibitors.

Response pathways of superoxide dismutase and catalase under the regulation of triclocarban-triggered oxidative stress in Eisenia foetida: Comprehensive mechanism analysis based on cytotoxicity and binding model

Triclocarban (TCC) is an emerging environmental contaminant, posing potential ecological risks. Displaying a high accumulation effect and 120-day half-life in the soil environment, the toxic effects of TCC to soil organisms have been widely reported. Previous studies have confirmed that TCC can induce the oxidative stress and changes in superoxide dismutase (SOD) and catalase (CAT) activities in earthworms, but the underlying mechanisms of oxidative stress and disorder in antioxidant enzyme activities induced by TCC have not yet been elucidated. Here, we explored the multiple response mechanisms of SOD and CAT under the regulation of oxidative stress induced by TCC. Results indicated that higher-dose (0-2.0 mg/L) TCC exposure triggered the overproduction of ROS in Eisenia foetida coelomocytes, causing oxidative damage and a decrease in cell viability that was response to ROS accumulation. The TCC-induced inhibition of intracellular SOD/CAT activity was found under the regulation of oxidative stress (SOD: 29.2 %; CAT: 18.5 %), and this effect was blunted by antioxidant melatonin. At the same time, the interaction between antioxidative enzymes and TCC driven by various forces (SOD: electrostatic interactions; CAT: van der Waals forces and hydrogen bonding) led to inhibited SOD activity (9.84 %) and enhanced CAT activity (17.5 %). Then, to elucidate the binding mode of TCC, we explored the changes in SOD and CAT structure (protein backbone and secondary structure), the microenvironment of aromatic amino acids, and aggregation behavior through multispectral techniques. Molecular docking results showed that TCC inhibited SOD activity in a substrate competitive manner and enhanced CAT activity by the stabilizing effects of TCC on the heme groups. Collectively, this study reveals the response mechanisms of SOD/CAT under the regulation of TCC-triggered oxidative stress and shed a new light on revealing the toxic pathways of exogenous pollutants on antioxidant-related proteins function.

Structural aspects of formetanate hydrochloride binding with human serum albumin using spectroscopic and molecular modeling techniques

Formetanate Hydrochloride (FMT), a highly potent chemical, acts as an insecticide, acaricide, and miticide to protect various fruits and vegetables. The widespread use elevates concern about its presence in the ecosystem, impact upon human health via interaction with biological receptors. Spectroscopic and molecular modeling techniques at different temperatures were used to investigate the binding of FMT with Human serum albumin (HSA) at the molecular level. The experimental and computational results have provided the binding affinity, binding mode, conformational flexibility, and thermodynamic profile of FMT-HSA complex. The FMT binding appears to be spontaneous, and entropy driven. Overall binding affinity of FMT falls within -7.29 to -4.67 Kcal M-1. FMT binds in domain I, subdomain IA of HSA and is stabilized by hydrophobic interactions. Molecular dynamics simulations of the FMT-HSA complex over 100 ns at 288 K, 298 K and 308 K indicated that FMT showed minor adjustments in conformation and placement within the binding site. While, MM/PBSA analysis of the complex provided individual contributions of energy terms. Quantum mechanical (QM) calculations were used to calculate absolute energy values of different poses of FMT which in turn showed minor variations in energy suggesting slight conformational variation in the bound form. The computational results are in agreement with experimental findings.

Band Structure Engineering within Two-Dimensional Borocarbonitride Nanosheets for Surface-Enhanced Raman Scattering

Herein, with two-dimensional (2D) borocarbonitride (BCN) as a metal- and plasmon-free surface-enhanced Raman scattering (SERS) platform, we demonstrate a band structure engineering strategy to facilitate the charge transfer process for an enhanced SERS response. Especially, when the conduction band of the BCN substrate is tuned to align with the LUMO of the target molecule, remarkable SERS performance is achieved, ascribed to the borrowing effect from the vibronic coupling of resonances through the Herzberg-Teller coupling term. Meanwhile, fluorescence quenching is achieved due to the efficient charge transfer between the BCN substrate and target molecule. Consequently, BCN can accurately detect 20 kinds of trace chemical and bioactive analytes. Moreover, BCN exhibits excellent thermal and chemical stability, which can not only withstand high-temperature (300 °C) heating in the air but also resist long-term corrosion in harsh acid (pH = 0, HCl) and base (pH = 14, NaOH). This work provides new insight into band structure engineering in promoting the SERS performance of plasmon- and metal-free semiconductor substrates.

Influence of protein configuration on aggregation kinetics of nanoplastics in aquatic environment

Aggregation kinetics of nanoplastics in aquatic environment are influenced by their interactions with proteins having different structures and properties. This study employed time-resolved dynamic light scattering (TR-DLS) to investigate the effects of 5 proteins (bovine hemoglobin (BHb), bovine (BSA) and human serum albumin (HSA), collagen type I (Col I), and bovine casein (CS)) on aggregation kinetics of polystyrene nanoplastics (PSNPs) under natural water conditions, which were simulated using various ionic strength (1-1000 mM NaCl and 0.01-100 mM CaCl₂), pH (3-9), and protein concentration (1-5 mg/L of total organic carbon). The results indicated that the interactions between proteins and PSNPs strongly depended on electrostatic properties, protein structures, and solution chemistries, which induced distinct aggregation behaviors in NaCl and CaCl₂ solutions. Electrostatic repulsion and steric hindrance dominated their interactions in NaCl solution by stabilizing PSNPs with the order of spherical BSA and disordered CS > heart-shaped HSA > fibrillar Col I; whereas positively charged BHb destabilized PSNPs with aggregation rate of 1.71 nm/s at 300 mM NaCl. In contrast, at CaCl₂ concentration below 20 mM, proteins destabilized PSNPs following the sequence of HSA > BHb > Col I > BSA depending on counterbalance among double layer compression, cation bridging, and steric hindrance; whereas CS stabilized PSNPs by precipitating Ca²⁺ that inhibited charge screening effect. Both protein concentration and solution pH affected protein corona formation, surface charge, and protein structure that altered stability of PSNPs. Characterizations using fluorescence spectroscopy, circular dichroism, and two-dimensional correlation analysis spectroscopy showed fluorescence quenching and ellipticity reduction of proteins, indicating strong adsorption affinity between PSNPs and proteins. The study provides insight to how protein configuration and water chemistry affect fate and transport of nanoplastics in aquatic environment.

Enhanced Removal of Malachite Green Using Calcium-Functionalized Magnetic Biochar

To efficiently remove malachite green (MG), a novel calcium-functionalized magnetic biochar (Ca/MBC) was fabricated via a two-step pyrolysis method. Iron-containing oxides endowed the target complexes with magnetic properties, especially the chemotactic binding ability with MG, and the addition of calcium significantly changed the morphology of the material and improved its adsorption performance, especially the chemotactic binding ability with MG, which could be confirmed through FTIR, XPS, and adsorption experiments. Electrostatic adsorption, ligand exchange, and hydrogen bonding acted as essential drivers for an enhanced adsorption process, and the maximum theoretical adsorption capacity was up to 12,187.57 mg/g. Ca/MBC maintained a higher adsorption capacity at pH = 4–12, and after five adsorption–desorption cycles, the adsorption capacity and adsorption rate of MG remained at 1424.2 mg/g and 71.21%, highlighting the advantages of Ca/MBC on adsorbing MG. This study suggests that biochar can be modified by a green synthesis approach to produce calcium-functionalized magnetic biochar with excellent MG removal capacity. The synthetic material can not only remove pollutants from water but also provide an efficient way for soil remediation.

Spectroscopic and in silico insight into the interaction between dicofol and human serum albumin

Dicofol, a broad-spectrum acaricide, has garnered considerable attention because of the potential harm to the environment and various organisms. Herein, this study applied spectroscopic and in silico methods to understand the interaction between human serum albumin (HSA) and dicofol. Fluorescence experiments demonstrated that dicofol formed a stable complex and the binding process occurred in Suldow's site I of HSA. Its binding constant was 2.26 × 10⁵ M^-1 at 298 K. Van der Waals forces and hydrogen bond were primarily facilitated the interaction between dicofol and HSA (ΔH < 0, ΔS < 0) according to thermodynamic experiments. Additionally, 3D fluorescence and circular dichroism (CD) spectra revealed a few conformational changes in HSA due to dicofol. Molecular docking analysis indicated that dicofol interacted with Ser192, Gln196, Leu481, Arg218, Leu238, and Phe211 via van der Waals forces and formed a hydrogen bond with His242. Molecular dynamics (MD) simulation showed that Lys195 and Arg218 residues contributed greater energy for forming the HSA-dicofol complex. MD simulation analysis also showed that dicofol can affect the HSA structure with a reduction in α-helix. This research is desired to facilitate a new perspective on the toxicity mechanism of dicofol in the human body.

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

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

Urolithin A alleviates advanced glycation end-product formation by altering protein structures, trapping methylglyoxal and forming complexes

Urolithin A (UroA) is a first-in-class natural compound derived from the gut microbiota-derived metabolites of ellagitannins. This research for the first time evaluates the mechanisms of UroA inhibiting advanced glycation end-product (AGE) formation by fluorescence spectroscopy, molecular docking, liquid chromatography (LC) and LC-Oribitrap tandem mass spectrometry. The results indicated that UroA exhibited a good suppression effect on the formation of AGEs in human serum albumin (HSA)-fructose and HSA-methylglyoxal (MGO) systems. Further mechanism analysis revealed that UroA alleviated AGE formation by changing the conformational structure of HSA, trapping reactive MGO to form mono-MGO-UroA complexes, promoting the exposure of chromophores to a more hydrophobic micro-environment, and forming stable UroA-HSA complexes. UroA bound with HSA in an equimolar manner, the binding was an exothermic spontaneous process, subdomain IIIA was the preferred binding pocket, and hydrogen bonding, hydrophobic interactions and van der Waals forces were the major interaction forces. The number of glycation sites detected in glycated HSA was reduced by 1 and 2, respectively, when 181.82 and 363.64 μM UroA was added. These could provide an insight into the mechanism of UroA inhibiting HSA glycation, and highlight its value as a promising glycation inhibitor in the prevention of diabetic complications.

An Engineered Thermostable Laccase with Great Ability to Decolorize and Detoxify Malachite Green

Laccases can catalyze the remediation of hazardous synthetic dyes in an eco-friendly manner, and thermostable laccases are advantageous to treat high-temperature dyeing wastewater. A novel laccase from Geothermobacter hydrogeniphilus (Ghlac) was cloned and expressed in Escherichia coli. Ghlac containing 263 residues was characterized as a functional laccase of the DUF152 family. By structural and biochemical analyses, the conserved residues H78, C119, and H136 were identified to bind with one copper atom to fulfill the laccase activity. In order to make it more suitable for industrial use, Ghlac variant Mut2 with enhanced thermostability was designed. The half-lives of Mut2 at 50 °C and 60 °C were 80.6 h and 9.8 h, respectively. Mut2 was stable at pH values ranging from 4.0 to 8.0 and showed a high tolerance for organic solvents such as ethanol, acetone, and dimethyl sulfoxide. In addition, Mut2 decolorized approximately 100% of 100 mg/L of malachite green dye in 3 h at 70 °C. Furthermore, Mut2 eliminated the toxicity of malachite green to bacteria and Zea mays. In summary, the thermostable laccase Ghlac Mut2 could effectively decolorize and detoxify malachite green at high temperatures, showing great potential to remediate the dyeing wastewater.

Fe3+-citric acid/sodium alginate hydrogel: A photo-responsive platform for rapid water purification

As water pollution in human society becomes more and more serious, the demand for materials that can be used for wastewater treatment is increasing. Here, we reported a sodium alginate-based hydrogel (Fe³⁺-CA/SA hydrogel) that can efficiently photocatalyze the degradation of malachite green. The Fe³⁺-CA/SA hydrogel is composed of sodium alginate, citric acid, and Fe³⁺. The hydrogel has multi-leveled pore structure and photochromic ability. Benefiting from the unique microstructure and positive feedback chemical reaction process, the hydrogel has high photocatalytic efficiency. Under 365 nm UV light irradiation, the hydrogel can degrade around 95% of malachite green (20 mg/L) in about 4 min, and there is no need to add H₂O₂ in the degradation process. The work helps to expand the application of sodium alginate-based hydrogels in the field of water treatment. It also has exploratory significance for the principle of photocatalytic degradation of malachite green.

Synthesis of ZnO Nanoparticles Loaded on Biochar Derived from Spartina alterniflora with Superior Photocatalytic Degradation Performance

Spartina alterniflora is an invasive plant from coastal wetlands, and its use in applications has garnered much interest. In this study, a composite photocatalyst (ZnO@BC) was synthesized by preparing zinc oxide (ZnO) nanoparticles with S. alterniflora extracts, S. alterniflora, and one-step carbonization, which was characterized using scanning electron microscope (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), Raman, X-ray photoelectron spectroscopy, ultraviolet-visible spectroscopy (UV-vis DRS), photoluminescence (PL) and N₂ adsorption-desorption isotherm. The degradation capacity and mechanism of malachite green (MG) using ZnO@BC were analyzed under visible irradiation, and the degradation products of malachite green were detected by LC-MS. The results show that ZnO@BC has a larger surface area (83.2 m²/g) and various reactive groups, which enhance its photocatalytic efficiency, with the presence of oxygen vacancy further improving the photocatalytic activity. The total removal rate of malachite green (400 mg/L) using ZnO@BC is up to 98.38%. From the LC-MS analysis, it could be concluded that malachite green is degraded by demethylation, deamination, conjugate structure and benzene ring structure destruction. This study provides a novel idea for the high-value utilization of S. alterniflora.

Profiling the interaction of a novel toxic pyruvate dehydrogenase kinase inhibitor with human serum albumin

To discover novel pyruvate dehydrogenase kinase (PDK) inhibitors, a new compound 2,2-dichloro-1-(4-((4-isopropylphenyl)amino)-3-nitrophenyl)ethan-1-one, namely XB-1 was identified, which inhibited PDK activity with a half maximal inhibitory concentration (IC₅₀) value of 337.0 nM, and reduced A549 cell proliferation with a half maximal effective concentration (EC₅₀) value of 330.0 nM. However, the compound appears to exhibit a negligible selectivity between cancer cell and normal one, indicating a potential toxicity existed for the compound. Herein, the interaction of the toxic XB-1 to human serum albumin (HSA) was firstly explored by spectroscopic approaches with the aim to reduce/avoid the toxicity of PDK inhibitors in the next hit-to-lead campaign. In detail, it was found that the XB-1 could effectively bind to HSA mainly via hydrogen bond interaction in PBS buffer (pH = 7.4, 10.0 mM), resulting in the formation of HSA-XB-1 complex. The negative value of ΔG showed that the binding of XB-1 to HSA is a spontaneous process. The result from site-selective binding assay suggested that the XB-1 bound to the site I of HSA by competing with warfarin, which was perfect in agreement with the molecular docking method. The results of this paper may offer a valuable theoretical basis to study the toxicity of biofunctional molecules and may offer thoughts about how to avoid/reduce toxicity for a small molecule.

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.