Cytotoxicity of emerging halophenylacetamide disinfection byproducts in drinking water: Mechanism and prediction

Halophenylacetamides (HPAcAms) have been identified as a new group of nitrogenous aromatic disinfection byproducts (DBPs) in drinking water, but the toxicity mechanisms associated with HPAcAms remain almost completely unknown. In this work, the cytotoxicity of HPAcAms in human hepatoma (HepG2) cells was evaluated, intracellular oxidative stress/damage levels were analyzed, their binding interactions with antioxidative enzyme were explored, and a quantitative structure-activity relationship (QSAR) model was established. Results indicated that the EC50 values of HPAcAms ranged from 2353 μM to 9780 μM, and the isomeric structure as well as the type and number of halogen substitutions could obviously induce the change in the cytotoxicity of HPAcAms. Upon exposure to 2-(3,4-dichlorophenyl)acetamide (3,4-DCPAcAm), various important biomarkers linked to oxidative stress and damage, such as reactive oxygen species, 8‑hydroxy-2-deoxyguanosine, and cell apoptosis, exhibited a significant increase in a dose-dependent manner. Moreover, 3,4-DCPAcAm could directly bind with Cu/Zn-superoxide dismutase and induce the alterations in the structure and activity, and the formation of complexes was predominantly influenced by the van der Waals force and hydrogen bonding. The QSAR model supported that the nucleophilic reactivity as well as the molecular compactness might be highly important in their cytotoxicity mechanisms in HepG2 cells, and 2-(2,4-dibromophenyl)acetamide and 2-(3,4-dibromophenyl)acetamide deserved particular attention in future studies due to the relatively higher predicted cytotoxicity. This study provided the first comprehensive investigation on the cytotoxicity mechanisms of HPAcAm DBPs.

Deciphering the binding behavior and interaction mechanism of apigenin and α-glucosidase based on multi-spectroscopic and molecular simulation studies

This study investigated the molecular mechanism underlying the binding interaction between apigenin (API) and α-glucosidase (α-glu) by a combination of experimental techniques and computational simulation strategies. The spontaneously formation of stable API-α-glu complex was mainly driven by hydrogen bonds and hydrophobic forces, leading to a static fluorescence quenching of α-glu. The binding of API induced secondary structure and conformation changes of α-glu, decreasing the surface hydrophobicity of protein. Computational simulation results demonstrated that API could bind into the active cavity of α-glu via its interaction with active residues at the binding site. The important roles of key residues responsible for the binding stability and affinity between API and α-glu were further revealed by MM/PBSA results. In addition, it can be found that the entrance of active site tended to close after API binding as a result of its interaction with gate keeping residues. Furthermore, the structural basis for the binding interaction behavior of API was revealed and visualized by weak interaction analysis. The findings of our study revealed atomic-level mechanism of the interaction between API, which might shed light on the development of better inhibitors.

Structural characterization and binding interaction of rice glutelin fibrils complexing with curcumin

The rice glutelin (RG), the separated retentate (RGFs) and filtrate (FGFs) fractions from total glutelin fibrils (TGFs) at pH 3.5 were used as carrier for curcumin in this test. The solubility and antioxidant activities of curcumin were improved after binding with protein and fibrils. Compared to other complexes, the RGFs-curcumin complex exhibited a highest curcumin solubility (48.05%) and a superior sustained release property, probably owing to the stable hydrogen bond between the surface groups of fibrils and hydroxyl groups of polyphenols. In addition, thermodynamic parameters revealed that the RG/TGFs/RGFs-curcumin complexes were stabilized by hydrogen bonds and van der Waals forces, whereas FGFs interacted with curcumin through specific electrostatic interaction. Besides, after interacting with curcumin, the fibrils gathered into coarsened and agglutinated fibrillar aggregates, relating to the increment of a-helix and β-sheet structure. These results suggested that RGFs could be a good alternative for curcumin delivery in food industry.

New mechanistic insights into halogen-dependent cytotoxic pattern of monohaloacetamide disinfection byproducts

As highly toxic nitrogenous disinfection byproducts (DBPs), monohaloacetamides (monoHAcAms) generally exhibited a cytotoxic rank order of iodoacetamide ˃ bromoacetamide ˃ chloroacetamide. However, the mechanisms underlying the halogen-dependent cytotoxic pattern remain largely veiled as yet. In this work, oxidative stress/damage levels in monoHAcAm-treated Chinese hamster ovary cells were thoroughly analyzed, and binding interactions between monoHAcAms and antioxidative enzyme Cu/Zn-superoxide dismutase (Cu/Zn-SOD) were investigated by multiple spectroscopic techniques and molecular docking. Upon exposure to monoHAcAms, the intracellular levels of key biomarkers associated with oxidative stress/damage, including reactive oxygen species, malondialdehyde, lactate dehydrogenase, 8-hydroxy-2-deoxyguanosine, cell apoptosis, and G1 cell cycle arrest, were all significantly increased in a dose-response manner with the same halogen-dependent rank order as their cytotoxicity. Moreover, this rank order was also determined to be applicable to the monoHAcAm-induced alterations in the conformation, secondary structure, and activity of Cu/Zn-SOD, the microenvironment surrounding aromatic amino acid residues in Cu/Zn-SOD, as well as the predicted binding energy of SOD-monoHAcAm interactions. Our results revealed that the halogen-dependent cytotoxic pattern of monoHAcAms was attributed to their differential capacity to induce oxidative stress/damage and their interaction with antioxidative enzyme, which contribute to a better understanding of the halogenated DBP-induced toxicological mechanisms.

Thiazolidine-2,4-dione derivatives as potential α-glucosidase inhibitors: Synthesis, inhibitory activity, binding interaction and hypoglycemic activity

In order to find effective α-glucosidase inhibitors, a series of thiazolidine-2,4-dione derivatives (C1 ∼ 36) were synthesized and evaluated for α-glucosidase inhibitory activity. Compared to positive control acarbose (IC50 = 654.35 ± 65.81 μM), all compounds (C1 ∼ 36) showed stronger α-glucosidase inhibitory activity with IC50 values of 0.52 ± 0.06 ∼ 9.31 ± 0.96 μM. Among them, C23 with the best anti-α-glucosidase activity was a reversible mixed-type inhibitor. Fluorescence quenching suggested the binding process of C23 with α-glucosidase in a static process. Fluorescence quenching, CD spectra, and 3D fluorescence spectra results also implied that the binding of C23 with α-glucosidase caused the conformational change of α-glucosidase to inhibit the activity. Molecular docking displayed the binding interaction of C23 with α-glucosidase. Compound C23 (8 ∼ 64 μM) showed no cytotoxicity against LO2 and 293 cells. Moreover, oral administration of C23 (50 mg/kg) could reduce blood glucose and improve glucose tolerance in mice.

Molecular insights on the binding of chlortetracycline to bovine casein and its effect on the thermostability of chlortetracycline

Bovine casein was selected as a model protein to evaluate the impact of food matrix on the thermal degradation of antibiotics. Fluorescence quenching and isothermal titration calorimetry experiments revealed that chlortetracycline (CTC) could spontaneously bind to casein via hydrogen bonding and hydrophobic interactions. The amino acid residues forming the binding pocket were further identified using molecular docking, while saturation transfer difference NMR deciphered that the binding of CTC engages its -N(CH3)2 group. Moreover, the degradation behavior of free CTC versus that bound in casein-CTC complex was compared during thermal treatment. Compared with free CTC, a lower first-order rate constant was observed in the presence of casein. Removal of casein shortened the half-life of CTC by at least 48.1% at low concentrations. Elucidating that the formation of protein-antibiotic complexes alters the amenability of antibiotics to degradative reactions, which could help eliminate residual antibiotics and guarantee the safety of dairy products.

Intrinsic mechanisms for the inhibition effect of graphene oxide on the catalysis activity of alpha amylase

Comprehending the interactions between graphene oxide (GO) and enzymes is critical for understanding the toxicities of GO. In this study, the inherent interactions of GO with α-amylase as a typical enzyme, and the impacts of GO on the conformation and biological activities of α-amylase were systematically investigated. The results reveal that GO formed ground-state complex with α-amylase primarily via hydrogen bonding and van der Waals interactions, thus quenching the intrinsic fluorescence of the protein statically. Particularly, the strong interactions altered the microenvironment of tyrosine and tryptophan residues, caused rearrangement of polypeptide structure, and reduced the contents of α-helices and β-sheets, thus changing the conformational structure of α-amylase. According to molecular docking results, GO binds with the amino acid residues (i.e., His299, Asp300, and His305) of α-amylase mainly through hydrogen bonding, which is in accordance with in vitro incubation experiments. As a consequence, the ability of α-amylase to catalyze starch hydrolysis into glucose was depressed by GO, suggesting that GO might cause dysfunction of α-amylase. This study discloses the intrinsic binding mechanisms of GO with α-amylase and provides novel insights into the adverse effects of GO as it enters organisms.

Identification of differential volatile and non-volatile compounds in coffee leaves prepared from different tea processing steps using HS-SPME/GC-MS and HPLC-Orbitrap-MS/MS and investigation of the binding mechanism of key phytochemicals with olfactory and taste receptors using molecular docking

Tea processing steps affected the proximate composition, enzyme activity and bioactivity of coffee leaves; however, the effects of different tea processing steps on the volatiles, non-volatiles, color, and sensory characteristics of coffee leaves have yet been demonstrated. Here the dynamic changes of volatile and non-volatile compounds in different tea processing steps were investigated using HS-SPME/GC-MS and HPLC-Orbitrap-MS/MS, respectively. A total of 53 differential volatiles (alcohol, aldehyde, ester, hydrocarbon, ketone, oxygen heterocyclic compounds, phenol, and sulfur compounds) and 50 differential non-volatiles (xanthone, flavonoid, organic acid, amino acid, organic amine, alkaloid, aldehyde, and purine et al.) were identified in coffee leaves prepared from different processing steps. Kill-green, fermentation, and drying steps significantly influenced the volatiles; however, kill-green, rolling, and drying steps significantly affected the color of coffee leaves and their hot water infusion. The coffee leaf tea that was prepared without the kill-green process was found to have a more pleasant taste as compared to the tea that was prepared with the kill-green process. This can be attributed to the fact that the former contained lower levels of flavonoids, chlorogenic acid, and epicatechin, but had higher levels of floral, sweet, and rose-like aroma compounds. The binding interactions between the key differential volatile and non-volatile compounds and the olfactory and taste receptors were also investigated. The key differential volatiles, pentadecanal and methyl salicylate generate fresh and floral odors by activating olfactory receptors, OR5M3 and OR1G1, respectively. Epicatechin showed a high affinity to the bitter receptors, including T2R16, T2R14, and T2R46. Since the specific content of differential compounds in different samples varies greatly, the dose-effect and structure-function relationships of these key compounds and the molecular mechanism of the odor and taste of coffee leaf tea need to be further studied.

Interaction of barley β-glucan with food dye molecules - An insight from pulse dipolar EPR spectroscopy

The interactions between dietary fibers (DFs) and small molecules are of great interest to food chemistry and nutrition science. However, the corresponding interaction mechanisms and structural rearrangements of DFs at the molecular level are still opaque due to the usually weak binding and the lack of appropriate techniques to determine details of conformational distributions in such weakly organized systems. By combining our previously established methodology on stochastic spin-labelling of DFs with the appropriately revised set of pulse electron paramagnetic resonance techniques, we present here a toolkit to determine the interactions between DFs and small molecules, using barley β-glucan as an example for neutral DF and a selection of food dye molecules as examples for small molecules. The proposed here methodology allowed us to observe subtle conformational changes of β-glucan by detecting multiple details of the local environment of the spin labels. Substantial variations of binding propensities were detected for different food dyes.

Performance of wild, tailed, humidity-robust phage on a surface-scanning magnetoelastic biosensor for Salmonella Typhimurium detection

A wild, tailed phage (TST) was compared with a genetically modified, filamentous phage (FST) for S. Typhimurium (ST) detection. When both phages were introduced into oppositely charged MUA and MUAM sensors, the RU values of TST showed an obvious increase on the MUAM sensor. The sensitivity of TST [54.78 ΔRU/(log PFU/mL)] was greater than that of FST [48.05 ΔRU/(log PFU/mL)]. The binding affinity (K_D = 1.75 × 10^-13 M) of TST on MUAM sensor was greater than that of FST. Both phages were specific to only ST, and TST exhibited a persistent binding capability at 50 % RH. When each phage-immobilized sensor was employed on chili pepper, the sensitivity [880.80 Hz/(log CFU/mL)] and detection limit (1.31 ± 0.27 log CFU/mL) of TST were significantly greater than those of FST. The orientation of TST on sensor promoted the uniform capture of bacteria and enhanced the reliable performance of a surface-scanning magnetoelastic biosensor.

Characterizing the binding interactions between virgin/aged microplastics and catalase in vitro

Microplastics (MPs) undergo physical, chemical, and biological aging in the environment, leading to changes in their physicochemical properties, affecting migration characteristics and toxicity. Oxidative stress effects induced by MPs in vivo have been extensively studied, but the toxicity difference between virgin and aged MPs and the interactions between antioxidant enzymes and MPs in vitro have not been reported yet. This study investigated the structural and functional changes of catalase (CAT) induced by virgin and aged PVC-MPs. It was shown that light irradiation aged the PVC-MPs, and the aging mechanism was photooxidation, resulting in a rough surface and appearing holes and pits. Because of the changes in physicochemical properties, aged MPs had more binding sites than virgin MPs. Fluorescence and synchronous fluorescence spectra results suggested that MPs quenched the endogenous fluorescence of CAT and interacted with tryptophane and tyrosine residues. The virgin MPs had no significant effect on the skeleton of CAT, while the skeleton and the polypeptide chains of CAT became loosened and unfolded after binding with the aged MPs. Moreover, the interactions of CAT with virgin/aged MPs increased the α-helix and decreased the β-sheet contents, destroyed the solvent shell, and resulted in a dispersion of CAT. Due to the large size, MPs cannot enter the interior of CAT and have no effects on the heme groups and activity of CAT. The interaction mechanism between MPs and CAT may be that MPs adsorb CAT to form the protein corona, and aged MPs had more binding sites. This study is the first comprehensive investigation of the effect of aging on the interaction between MPs and biomacromolecules and highlights the potential negative effects of MPs on antioxidant enzymes.

Influence of milk fat on the physicochemical property of nanoencapsulated curcumin and enhancement of its biological properties thereof

Curcumin, bioactive from turmeric Curcuma longa, has been known for its therapeutic properties. However, its lipophilic nature and poor bioavailability are the constraints to harnessing its properties. Encapsulation in nano-size helps to alleviate the constraints and enhance its biological properties due to its higher surface area. The study aims to encapsulate curcumin in a nanometer size range by solubilizing in lipid (milk fat) and using milk protein as a water-soluble carrier. The lipid:curcumin ratio (1:0.05, 1:0.1, 1:0.2, 1.5:0.1, 1.5:0.2, 2.0:0.1 and 2:0.2% (w/w)) produced nanoemulsion with droplets sizes 30-200 nm. The sample containing lipid: curcumin, as 1.0:0.05 resulted in an encapsulation efficiency of 92.6%, and its binding interaction with the carrier, was KD = 4.7 µM. A high solubility of curcumin in milk fat and digestion during in vitro lipolysis increased its bioaccessibility. A simulated gastro-intestinal in vitro studies showed that cumulative release percentage of nanoencapsulated curcumin was 60% at pH 7.4 compared to 0.8% of native curcumin. The anti-microbial property of nanoencapsulated curcumin was more potent than native curcumin against food pathogenic organisms such as S. aureus, B. cereus, E. coli, B. subtilis, P. aeruginosa, P. aeruginosa, C. violaceum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05684-5.

Insights into the Binding Interaction of Catechol 1,2-Dioxygenase with Catechol in Achromobacter xylosoxidans DN002

Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme-substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His₂₂₆ had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.

The binding effect and photooxidation on oxytetracycline with algal extracellular polymeric substances and natural organic matter

Surface water contains a large amount of dissolved organic matter (DOM). Interactions between DOM and micropollutants have a significant impact on micropollutant degradation. In this study, algal extracellular polymeric substances (EPS) and natural organic matter (NOM) were selected as two DOM sources and oxytetracycline (OTC) as a representative micropollutant. EPS was mainly composed of tryptophan and protein-like organics, while NOM was mainly composed of fulvic acid-like, humic acid-like, and hydrophobic acid components. In addition, OTC degradation significantly decreased when bound with EPS and the C=O and C-H bonds of CH₂ or CH₃ groups may be involved in binding EPS and OTC, respectively, while -COOH may be involved in the binding of NOM and OTC. Furthermore, triplet intermediates were found to play a major role in OTC photodegradation in both EPS and NOM, with the contribution calculated as 49.96% and 44.61%, respectively. Steady-state concentrations of ³EPS* in EPS and ³NOM* in NOM were 3.59 × 10^-14 mol L^-1 and 5.54 × 10^-15 mol L^-1, respectively. These results provide new insights into the degradation of antibiotic-containing wastewater in the natural environment or engineering applications.

Investigation on detoxication effects of 2-hydroxypropyl-β-cyclodextrin over two halogenated aromatic DBPs 2,4,6-trichlorophenol and 2,4,6-tribromophenol binding with human serum albumin

The health effects of disinfection byproducts (DBPs) in drinking water drew great attention recently. Herein, by using in vitro (fluorescence quenching, UV absorbance, circular dichroism) and in silico (molecular docking) method, binding interactions of two halophenolic DBPs (2,4,6-trichlorophenol [TCP] and 2,4,6-tribromophenol [TBP]) with human serum albumin (HSA) and the influence of hydroxypropyl-beta-cyclodextrin (HPCD) on the interactions were investigated. TCP/TBP could form complexes with HSA mainly by hydrogen bonding, while changing its secondary structure, among which TBP showed more influential effect. Interestingly, the binding constants for halophenol-HSA complexes decreased obviously with the involvement of HPCD. Molecular docking results revealed that HPCD could include TCP/TBP into its cavity and change their original binding sites from subdomain IB to IIA, resulting in a more stable binding system. These findings are beneficial for understanding the toxicity of halophenols inside the human body and indicated that HPCD could be a promising detoxication agent for DBPs.

Different interactions driving the binding of soy proteins (7S/11S) and flavonoids (quercetin/rutin): Alterations in the conformational and functional properties of soy proteins

The purpose of this research was to comparatively investigate the interactions between bioactive flavonoids (quercetin and rutin) and two predominant soy proteins (β-conglycinin and glycinin), and the structural and functional properties of their complexes. The binding affinities of quercetin/rutin toward 7S/11S were structure-dependent, in that rutin had a higher binding affinity than that of quercetin, and 11S exhibited higher affinity toward quercetin/rutin than that of 7S. The interactions in the 7S/11S-quercetin complexes were driven by van der Waals forces and hydrogen-bonding interactions, whereas the 7S/11S-rutin complexes exhibited hydrophobic interactions. Binding to quercetin or rutin altered the secondary structures (decrease in the α-helix and random coil contents and increase in the β-sheet content), decreased the surface hydrophobicity and thermal stability, and enhanced the antioxidant capacity of 7S and 11S. These findings provide valuable information that can facilitate the design of custom-tailored protein-flavonoid macromolecules.

The interaction between bovine serum albumin and [6]-,[8]- and [10]-gingerol: An effective strategy to improve the solubility and stability of gingerol

In this study, the binding mechanism between bovine serum albumin (BSA) and three gingerols ([6]-, [8]- and [10]-gingerol) was evaluated to explore an effective strategy for improving solubility and stability of gingerols. The fluorescence analysis suggested gingerols could bind with BSA to form a stable BSA/gingerols complex and [10]-gingerol had the strongest binding affinity (K_a = 4.016 × 10⁴ L/mol) at 298 K. Thermodynamic parameters and molecular modeling validated that hydrophobic interaction and hydrogen bonds were the main driving force for the interaction of BSA/gingerols. Gingerols bound to BSA at site I (subdomain IIA) resulted in a conformational change of BSA with a structure shrinkage, which was responsible for the decrease of surface hydrophobicity. The formation of BSA/gingerols complexes promoted the solubility of [6]-, [8]- and [10]-gingerol increasing by 1.50, 6.04 and 23.50 times, respectively. In addition, the stability and antioxidant capacity of gingerols was significantly improved after binding with BSA.

Non-covalent binding interaction between phthalic acid esters and DNA

The interaction of phthalic acid esters (PAEs) with DNA is known to be responsible for the disruption of endocrine functions and the teratogenic and carcinogenic effects. However, the binding strength and mechanism of this important process has often been neglected. Here, we confirmed the binding interaction between PAEs and DNA via fluorescence titration quenching experiment. The linear fitting curve proved that PAEs could bind to DNA, and the binding constants (K_A) were 4.11 × 10⁵, 1.04 × 10⁵, 7.60 × 10⁴, 1.99 × 10⁴, and 1.42 × 10³ L/mol for diethyl phthalate (DEP), bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), dimethyl phthalate (DMP), and benzyl butyl phthalate (BBP), respectively. DNA melting point, UV-vis spectra and Fourier transform infrared spectroscopy (FTIR) analyses revealed that PAEs interact predominantly with thymines in the DNA minor groove. Quantum chemical calculations showed that hydrogen bonding and van der Waals force formation between PAEs and DNA bases dominated the binding interaction. However, PAEs-DNA binding did not induce any DNA conformation change since the circular dichroism and FTIR spectra of B-DNA were not change. The electrostatic surface potential (ESP) might act an important role in PAEs-DNA binding interaction. This work will broaden our understanding of the interaction between PAEs and genetic materials.

Spectroscopic investigation on the binding interactions between graphene quantum dots and carbonic anhydrase

As a new member of the nanomaterials family, ultrasmall graphene quantum dots (GQDs) have shown broad application prospects in the field of biomedicine, but the analysis of their biological effects at the molecular level is yet limited. Herein, carbonic anhydrase (CA) was selected as a model protein to assess the interactions between GQDs and biomacromolecules. A range of spectroscopic techniques were employed to systematically investigate the binding interactions between GQDs and CA and the catalytic function of CA in the presence of GQDs was evaluated. Experimental results showed that GQDs could quench the intrinsic fluorescence of CA and the concentration dependent quenching efficiency exhibited an obvious deviation from the linear plot, indicating a static binding mode. Further investigation suggested that van der Waal interactions and hydrogen bonding were the main driving forces. Additionally, circular dichroism measurement showed that the binding of GQDs induced slight conformational changes of CA. The catalytic capability assessment proved that these binding interactions resulted in the reduction of the biological functions of CA. This comprehensive study provided important insight into the interaction of GQDs with biomacromolecules, which would be crucial for the further applications of GQDs and other nanomaterials in the biomedical field.

Interaction of graphene oxide with lysozyme:Insights from conformational structure and surface charge investigations

Lysozyme (Lyz) is an important antibacterial protein that exists widely in nature. In recent years, the application of graphene oxide (GO) in the field of biotechnology electronics, optics, chemistry and energy storage has been extensively studied. However, due to the unique properties of GO, the mechanism of its interaction with biomacromolecule proteins is very complex. To further explore the interaction between GO and proteins we explore the influence of different pH and heat treatment conditions on the interaction between GO and Lyz, the GO (0-20 μg/mL) was added at a fixed Lyz concentration (0.143 mg/mL) under different pHs. The structure and surface charge changes of Lyz were measured by spectroscopic analysis and zeta potential. The results showed that the interaction between GO and Lyz depends on temperature and pH, significant changes have taken place in its tertiary and secondary structures. By analyzing the UV absorption spectrum, it was found that lysozyme and GO formed a stable complex, and the conformation of the enzyme was changed. In acidic pH conditions (i.e., pH < pI), a high density of Lyz were found to adsorb on the GO surface, whereas an increase in pH resulted in a progressive decrease in the density of the adsorbed Lyz. This pH-dependent adsorption is ascribed to the electrostatic interactions between the negatively charged GO surface and the tunable ionization of the Lyz molecules. The secondary structure of Lyz adsorbed on GO was also found to be highly dependent on the pH. In this paper, we investigated the exact mechanism of pH-influenced GO binding to lysozyme, which has important guidance significance for the potential toxicity of GO biology and its applications in biomedical fields such as structure-based drug design.

Epigallocatechin gallate (EGCG) attenuates staphylococcal alpha-hemolysin (Hla)-induced NLRP3 inflammasome activation via ROS-MAPK pathways and EGCG-Hla interactions

Alpha-hemolysin (Hla), the virulence factor secreted by Staphylococcus aureus (S. aureus), plays a critical role in infection and inflammation, which is a severe health burden worldwide. Therefore, it is necessary to develop a drug against Hla. Epigallocatechin gallate (EGCG), a polyphenol extracted from green tea, has excellent anti-inflammatory activity. In this study, we investigated the inhibitory effect of EGCG on Hla-induced NLRP3 inflammasome activation in vitro and in vivo and elucidated the potential molecular mechanism. We found that EGCG attenuated the hemolysis of Hla by inhibiting its secretion. Besides, EGCG significantly decreased overproduction of ROS and activation of MAPK signaling pathway induced by Hla, thereby markedly attenuating the expression of NLRP3 inflammasome-related proteins in THP-1 cells. Notably, EGCG could spontaneously bind to Hla with affinity constant of 1.71 × 10-4 M, thus blocking the formation of the Hla heptamer. Moreover, Hla-induced expression of NLRP3, ASC and caspase-1 protein and generation of IL-1β and IL-18 in the damaged liver tissue of mice were also significantly suppressed by EGCG in a dose-dependent manner. Collectively, EGCG could be a promising candidate for alleviating Hla-induced the activation of NLRP3 inflammasome, depending on ROS mediated MAPK signaling pathway, and inhibition of Hla secretion and heptamer formation. These findings will enlighten the applications of EGCG to reduce the S. aureus infection by targeting Hla in food and related pharmaceutical fields.

Advance in dietary polyphenols as dipeptidyl peptidase-IV inhibitors to alleviate type 2 diabetes mellitus: aspects from structure-activity relationship and characterization methods

Dietary polyphenols with great antidiabetic effects are the most abundant components in edible products. Dietary polyphenols have attracted attention as dipeptidyl peptidase-IV (DPP-IV) inhibitors and indirectly improve insulin secretion. The DPP-IV inhibitory activities of dietary polyphenols depend on their structural diversity. Screening methods that can be used to rapidly and accurately identify potential polyphenol DPP-IV inhibitors are urgently needed. This review focuses on the relationship between the structures of dietary polyphenols and their DPP-IV inhibitory effects. Different characterization methods used for polyphenols as DPP-IV inhibitors have been summarized and compared. We conclude that the position and number of hydroxyl groups, methoxy groups, glycosylated groups, and the extent of conjugation influence the efficiency of inhibition of DPP-IV. Various combinations of methods, such as in-vitro enzymatic inhibition, ex-vivo/in-vivo enzymatic inhibition, cell-based in situ, and in-silico virtual screening, are used to evaluate the DPP-IV inhibitory effects of dietary polyphenols. Further investigations of polyphenol DPP-IV inhibitors will improve the bioaccessibility and bioavailability of these bioactive compounds. Exploration of (i) dietary polyphenols derived from multiple targets, that can prevent diabetes, and (ii) actual binding interactions via multispectral analysis, to understand the binding interactions in the complexes, is required.

Insight into the role of binding interaction in the transformation of tetracycline and toxicity distribution

The transformation of free state organic micro-pollutants (MPs) has been widely studied; however, few studies have focused on mixed and bound states MPs, even though numerous ionizable organic MPs process a strong tendency to combine with dissolved organic matters in aquatic environments. This study systemically investigated the distribution and toxicity assessment of tetracycline (TET) transformation products in free, mixed and bound states during UV, UV/H₂O₂, UV/PS and CNTs/PS processes. A total of 33 major transformation products were identified by UPLC-Q-TOF-MSMS analysis, combining the double bond equivalence and aromaticity index calculations. The binding interaction would weaken the attack on the dimethylamino (-N(CH₃)₂) group and induce the direct destruction of rings A and B of TET through the analysis of 2D Kernel Density changes and density functional theory (DFT) calculations. Toxicity assessment and statistics revealed that the intermediate products with medium molecular weight (230≤ m/z ≤ 380) exhibited higher toxicity, which was closely related to the number of the rings in molecular structures (followed as 2»3 > 1≈4). A predicted toxicity accumulation model (PTAM) was established to evaluate the overall toxicity changes during various oxidation processes. This finding provides new insight into the fate of bound MPs during various oxidation processes in the natural water matrix.

The interaction of folate-modified Bletilla striata polysaccharide-based micelle with bovine serum albumin

We fabricated an amphiphilic folate-modified Bletilla striata polysaccharide (FA-BSP-SA) copolymer that exhibited good biocompatibility and superior antitumor effects. This study investigated the affinity between FA-BSP-SA and bovine serum albumin (BSA) via multispetroscopic approaches. Changes in the morphology and particle size showed that FA-BSP-SA formed a blurry "protein corona". Stern-Volmer equation demonstrated that FA-BSP-SA micelles decreased the fluorescence of BSA via static quenching. The measurement results of thermodynamic parameters (entropy change, enthalpy change, and Gibbs free energy) suggested that the binding between FA-BSP-SA and BSA was spontaneous in which Van der Waals forces and hydrogen bonding played major roles. The results from synchronous fluorescence, circular dichroism, and UV spectra also revealed that BSA conformation was slightly altered by decreasing α-helical contents. In addition, the antitumor effects in vitro of Dox@FA-BSP-SA micelles and the cellular uptake behavior of micelles in 4T1 cells were decreased after incubating with BSA.

Spectroscopic and Small-angle X-ray scattering analysis of binding between Copper(II) -1-allylimidazole complex, a potential anti-tumor agent, and bovine serum albumin

Interactions between transport proteins and compounds with therapeutic potential are pharmacologically important. In this study, using fluorescence, circular dichroism (CD), and small-angle X-ray Scattering (SAXS), we investigated the interaction between bovine serum albumin (BSA) and a copper(II)-1-allylimidazole complex with potential anti-cancer properties. The results revealed dynamic fluorescence quenching of the model carrier protein BSA by the copper(II) complex. The enthalpy change (ΔH), free energy (ΔG), and entropy change (ΔS) were calculated to be 108 kJ/mol, -16.47 kJ/mol, and 419 J/mol K, respectively, according to the Van't Hoff equation. The reaction was an endothermic and spontaneous process, and hydrophobic interactions played a major role in binding. The results indicate a much lower affinity (K_b ∼ 10²-10³) for the metal complex compared with similar compounds (K_b ∼ 10³-10⁵). CD showed that the studied copper(II) complex does not change the secondary structure of the protein, while SAXS showed that the this compound may attach to the protein surface and stimulate interactions between proteins. The results suggest that the copper(II) complex with 1-allylimidazole binds weakly to BSA, leading to aggregation of albumin in solution, thereby altering its pharmacokinetic properties. The findings are pertinent to drug design.

Investigation on conformational variation and activity of trypsin affected by black phosphorus quantum dots via multi-spectroscopy and molecular modeling

Binding interaction between black phosphorus quantum dots (BPQDs) and trypsin was researched deeply to illustrate the variations on conformation and activity of trypsin affected by BPQDs via multi-spectroscopy and molecular modeling. Experimental results implied that inherent fluorescence of trypsin was quenched by BPQDs via static fluorescence quenching mode. BPQDs bound with trypsin to construct ground-state complex under the binding forces of van der Waal interaction and hydrophobic interaction, resulting in the conformational change of trypsin to be more hydrophilic and incompact. The result of molecular modeling indicated that BPQDs interacted with trypsin at its allosteric site and inhibited the activity of trypsin via non-competitive manner. Finally, BPQDs efficiently inhibited the digestion activity of trypsin on human serum albumin, human cervical carcinoma HeLa cells, and human lung adenocarcinoma A549 cells. This work not only explores the in-depth understanding on the influence of BPQDs on proteinases but also paves the way for further application of BPQDs on human beings for diseases treatments.

Binding and drug displacement study of colchicine and bovine serum albumin in presence of azithromycin using multispectroscopic techniques and molecular dynamic simulation

The binding and displacement interaction of colchicine and azithromycin to the model transport protein bovine serum albumin (BSA) was evaluated in this study. Azithromycin, a macrolide antibiotic, has antiviral properties and hence, has been used concomitantly with hydroxychloroquine against SARS-CoV-2. Colchicine, a natural plant product is used to treat and prevent acute gout flares. Some macrolide antibiotics are reported to have fatal drug-drug interactions with colchicine. The displacement interaction between colchicine and azithromycin on binding to BSA was evaluated using spectroscopic techniques, molecular docking and molecular dynamic simulation studies. The binding constant recorded for the binary system BSA-colchicine was 7.44 × 104 whereas, the binding constant for the ternary system BSA-colchicine in presence of azithromycin was 7.38 × 104 and were similar. Azithromycin didn't bind to BSA neither did it interfere in binding of colchicine. The results from molecular docking studies also led to a similar conclusion that azithromycin didn't interfere in the binding of colchicine to BSA. These findings are important since there is possibility of serious adverse event with co-administration of colchicine and azithromycin in patients with underlying gouty arthritis and these patients need to be continuously monitored for colchicine toxicity.

Salmon sperm DNA binding study to cabozantinib, a tyrosine kinase inhibitor: Multi-spectroscopic and molecular docking approaches

In the current work, the binding interaction of cabozantinib with salmon sperm DNA (SS-DNA) was studied under simulated physiological conditions (pH 7.4) using fluorescence emission spectroscopy, UV-Vis absorption spectroscopy, viscosity measurement, ionic strength measurement, FT-IR spectroscopy, and molecular modeling methods. The obtained experimental data demonstrated an apparent binding interaction of cabozantinib with SS-DNA. The binding constant (K_b) of cabozantinib with SS-DNA evaluated from the Benesi-Hildebrand plot was equal to 5.79 × 10⁵ at 298 K. The entropy and enthalpy changes (∆S⁰ and ∆H⁰) in the binding interaction of SS-DNA with cabozantinib were 44.13 J mol^-1 K^-1 and -19.72 KJ mol^-1, respectively, demonstrating that the basic binding interaction forces are hydrophobic and hydrogen bonding interactions. Results from UV-Vis absorption spectroscopy, competitive binding interaction with rhodamine B or ethidium bromide, and viscosity measurements revealed that cabozantinib binds to SS-DNA via minor groove binding. The molecular docking results revealed that cabozantinib fits into the AT-rich region of the B-DNA minor groove and the binding site of cabozantinib was 4 base pairs long. Moreover, cabozantinib has eight active torsions, implying a high degree of flexibility in its structure, which played a significant role in the formation of a stable cabozantinib-DNA complex.

Enhanced cytotoxicity and antioxidant capacity of kaempferol complexed with α-lactalbumin

As a dietary polyphenol, kaempferol exhibits numerous biological activities such as antioxidant and anticancer properties. However, its application is limited because of its poor solubility and low permeability. This work aims to investigate the interaction of kaempferol with α-lactalbumin. Multiple-spectroscopic techniques were used to prove the interaction between kaempferol and α-lactalbumin. UV-vis absorption spectra suggested that the conformation of α-lactalbumin could be changed via binding with kaempferol. The fluorescence quenching test showed that kaempferol significantly quenched the intrinsic fluorescence of α-lactalbumin. Circular dichroism spectroscopy showed that the percent helicity of α-lactalbumin secondary structure increased when combined with kaempferol. In addition, the α-lactalbumin-kaempferol complex showed stronger inhibition ability on the growth of HeLa cells compared with kaempferol alone. The complex also showed higher antioxidant capacity than kaempferol alone. Molecular docking provided three predicted binding sites of α-lactalbumin for kaempferol, as well as five predicted binding poses of kaempferol. The weak intermolecular interactions were the main forces to stabilize the α-lactalbumin-kaempferol complex. Besides, the binding stability between α-lactalbumin and kaempferol was explored by molecular dynamics simulation. In conclusion, this work provides a basis for the potential application of α-lactalbumin as a delivery carrier for kaempferol owing to its nontoxic and biocompatible properties.

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

Cationic triarylmethane dyes such as malachite green are aromatic xenobiotic compounds causing environmental pollution. The affinity between hazardous materials and biomolecules makes it important to understand the properties of such compounds. Accordingly, in this study, the possible molecular interaction between this pollutant and the human serum albumin (HSA) was investigated using a combination of molecular docking, molecular dynamic simulation and multi-spectroscopic approaches. The docking results illustrated that malachite green oxalate (MGO) could bind to some of the HSA amino acids with the estimated free energy = -32.93 kJ/mol. Further, the results of the dynamic simulation revealed that MGO had a steady interaction with the protein though increasing flexibility and decreasing the HSA compactness. These results were, therefore, in agreement with those obtained by spectroscopic techniques. The MGO concentration of 0.0005 mM could quench the HSA's intrinsic fluorescence by %16.88. The protein structural changes also revealed that the binding interaction of MGO-HSA was accompanied by an increase in the α-helix and a decrease in the β-sheet of the protein. Overall, this study indicated the suitable molecular modeling interaction of MGO and HSA.

Influence of antioxidant flavonoids quercetin and rutin on the in-vitro binding of neratinib to human serum albumin

This study was designed to examine the interaction of neratinib (NRB) with human serum albumin (HSA) in presence of flavonoids quercetin and rutin. Both quercetin and rutin can compete with NRB to bind to HSA and displace NRB from its binding site. The interaction mechanism was studied with several spectroscopic techniques and molecular docking. Static fluorescence quenching mechanism was observed on interaction of HSA with NRB. van der Waals force and hydrogen bond were involved in the HSA-NRB interaction as per the results of thermodynamic parameters. Further, the conformational changes were observed in the HSA on its interaction with NRB. Interaction of NRB with HSA in presence of quercetin and rutin resulted in changes in the binding constants of HSA-NRB suggesting some impact on the binding of NRB in the presence of flavonoids.

Assessment of binding interaction dihydromyricetin and myricetin with bovine lactoferrin and effects on antioxidant activity

The binding interactions of bovine lactoferrin (BLF) with two flavonoids dihydromyricetin (DMY) and myricetin (MY) were investigated by the multi-spectroscopic, microscale thermophoresis (MST) techniques, molecular docking, and then their antioxidant activities were studied by detection of free radical scavenging activity against DPPH. Results of UV-vis and fluorescence spectroscopies showed that DMY/MY and BLF formed the ground state complex through the static quenching mechanism. Moreover, MY with more planar stereochemical structure had higher affinity for BLF than DMY with twisted stereochemical structure, according to the binding constant (K_b), free energy change (ΔG°), dissociation constant (K_d) and donor-acceptor distance (r). Thermodynamic parameters revealed that hydrogen bond and van der Waals force were major forces in the formation of BLF-DMY complex, while hydrophobic interactions played major roles in the formation of BLF-DMY complex. The circular dichroism (CD) study indicated that MY induced more conformational change in BLF than DMY. Furthermore, molecular modeling provided insights into the difference of binding interactions between BLF and two flavonoids. Finally, the radical scavenging activity assays indicated the presence of BLF delayed the decrease in antioxidant capacities of two flavonoids. These results were helpful to understand the binding mechanism and biological effects of non-covalent BLF-flavonoid interaction.

Phytochemical profile, antioxidant, α-amylase inhibition, binding interaction and docking studies of Justicia carnea bioactive compounds with α-amylase

The present study investigated the antioxidant and invitro antidiabetic capacities of Justicia carnea aqueous leaf extract (JCAE) using α-amylase inhibition model. α-Amylase binding-interaction with JCAE was also investigated using fluorescence spectroscopy and molecular docking. Phytochemical screening and Gas Chromatography-Mass Spectrometry (GC-MS) analysis indicated presence of bioactive compounds. Phenolic (132 mg GAE/g) and flavonoid contents (31.08 mg CE/g) were high. JCAE exhibited high antioxidant capacity and effectively inhibited α-amylase activity (IC₅₀, 671.43 ± 1.88 μg/mL), though lesser than acarbose effect (IC₅₀, 108.91 ± 0.61 μg/mL). α-Amylase intrinsic fluorescence was quenched in the presence of JCAE. Ultraviolet-visible and FT-IR spectroscopies affirmed mild changes in α-amylase conformation. Synchronous fluorescence analysis indicated alterations in the microenvironments of tryptophan residues near α-amylase active site. Molecular docking affirmed non-polar interactions of compounds 6 and 7 in JCAE with Asp-197 and Trp-58 residues of α-amylase, respectively. Overall, JCAE indicated potential to prevent postprandial hyperglycemia by slowing down carbohydrate hydrolysis.

Potential ability of different types of cyclodextrins to modulate the interaction between bovine serum albumin and 1-hydroxypyrene

Hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) can bind with functional biomacromolecules and thus cause toxic effects in vivo. Four types of cyclodextrins (CDs) were selected to explore their potential ability to regulate the bindings between 1-hydroxypyrene (1-OHPyr) and bovine serum albumin (BSA) using multi-spectroscopic methods combined with molecular docking. The results showed that the four CDs caused varied modulating effects on the binding of BSA with 1-OHPyr, and the effects of γ-CD and (2-hydroxypropyl)-β-CD (HPCD) are the most significant. Specifically, γ-CD and HPCD could significantly reduce the binding affinity between 1-OHPyr and BSA, inhibit the micro-environmental changes of tryptophan residues, and slightly recover the helicity of BSA. The interactions and inclusion behavior of CDs with 1-OHPyr was the main reason why CDs could affect the binding of 1-OHPyr to BSA. The results indicated that γ-CD and HPCD might have potential application value in regulating the toxic effects of OH-PAHs.

Binding interaction of allethrin with esterase: Bioremediation potential and mechanism

The main aim of this work was to study the allethrin binding interactions with esterase and its bioremediation potential using an isolated bacterial strain CW7, identified as Pseudomonas nitroreducens. The degradation conditions with strain CW7 were optimized using response surface methodology at pH 7.0, a temperature of 32 °C, and an inocula concentration of 150 mg·L^-1, with 96% allethrin degradation observed over 7 days. The kinetic parameters q_max, K_s, and K_i were calculated to be 0.512 day^-1, 4.97 mg·L^-1, and 317.13 mg·L^-1, respectively. Nine intermediate metabolites were identified after analysing the degradation products by gas chromatography-mass spectrometry. Strain CW7 effectively degraded a wide variety of pyrethroids as a carbon source. Molecular modeling, docking, and enzyme kinetics were used to investigate the binding pocket of the esterase containing amino acids such as alanine, arginine, valine, proline, cysteine, glycine, isoleucine, phenylalanine, serine, asparagine, and threonine, which play active roles in allethrin degradation.

NMR quantification of H-bond donating ability for bioactive functional groups and isosteres

The H-bond donating ability for 127 compounds including drug fragments and isosteres have been quantified using a simple and rapid method with ³¹P NMR spectroscopy. Functional groups important to medicinal chemistry were evaluated including carboxylic acids, alcohols, phenols, thioic acids and nitrogen group H-bond donors. ³¹P NMR shifts for binding to a phosphine oxide probe have a higher correlation with equilibrium constants for H-bonding (log K^H_A) than acidity (pK_a), indicating that these binding experiments are representative of H-bonding ability and not proton transfer. Additionally, ³¹P NMR binding data for carboxylic acid isosteres correlates with physicochemical properties such as lipophilicity, membrane permeability and plasma protein binding. This method has been used to evaluate the H-bond donating ability of small molecule drug compounds such as NSAIDs and antimicrobials.

Investigations of conformational structure and enzymatic activity of trypsin after its binding interaction with graphene oxide

Herein, interaction between graphene oxide (GO) and trypsin was systematically characterized for deep investigations of conformational structure and enzymatic activity of trypsin affected by GO. Results indicated that GO bound with trypsin to form ground state complex with molar ratio of 1 to 1. Intrinsic fluorescence of trypsin was statically quenched by GO through van der Waal interaction, hydrophobic interaction, hydrogen bond, and electrostatic interaction. Both tertiary structure and secondary structure of trypsin were changed obviously after its binding with trypsin, resulting in the structure transformation of trypsin from the β-sheet structure to the α-helix structure. Since GO bound with the allosteric site of trypsin to inhibit its enzymatic activity via non-competitive manner, GO efficiently protected human serum albumin and human cervical carcinoma HeLa cells from the digestion of trypsin. These results explored the exact binding mechanism of GO with protease, which provides more important information for possible biological risk of GO on human beings.

Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view

This study aims to clarify the interaction mechanism of substrate with catechol 2,3-dioxygenase (C23O) through multi-technique combination. A novel C23O (named C23O-2G) was cloned, heterogeneously expressed, and identified as a new member in subfamily I.2 of extradiol dioxygenases. Based on the simulations of molecular docking and dynamics, the exact binding sites of catechol on C23O-2G were identified, and the catalytic mechanism mediated by key residues was proposed. The roles of the predicted residues during catalysis were confirmed by site-directed mutagenesis, and the mutation of Thr254 could significantly increase catalytic efficiency and substrate specificity of C23O-2G. The binding and thermodynamic parameters obtained from fluorescence spectra suggested that catechol could effectively quench the intrinsic fluorescence of C23O-2G via static and dynamic quenching mechanisms and spontaneously formed C23O-2G/catechol complex by the binding forces of hydrogen bond and van der Waals force. The results of UV-vis spectra, synchronous fluorescence, and CD spectra revealed obvious changes in the microenvironment and conformation of C23O-2G, especially for the secondary structure. The atomic force microscope images further demonstrated the changes from an appearance point of view. This study could improve our mechanistic understanding of representative dioxygenases involved in aromatic compound degradation.

Vaccine Design Against Leptospirosis Using an Immunoinformatic Approach

Vaccination is the best way to prevent the spread of emerging or reemerging infectious disease. Current research for vaccine development is mainly focused on recombinant-, subunit-, and peptide-based vaccine. At this point, immunoinformatics has been proven as a powerful method for identification of potential vaccine candidates, by analyzing immunodominat B- and T-cell epitopes. This method can reduce the time and cost of experiment to a great extent, by reducing the number of vaccine candidates for experimental testing for their efficacy. This chapter describes the use of immunoinformatics and molecular docking methods to screen potential vaccine candidates by taking Leptospira as a model.

Spectroscopic and molecular modeling investigation on inhibition effect of nitroaromatic compounds on acetylcholinesterase activity

Nitroaromatic compounds (NACs) are widely distributed in the environment and are considered toxic or carcinogenic. However, little attention has been paid to the binding interactions between NACs and biomacromolecules (e.g., proteins). Here we investigated the effects of three model NACs, nitrobenzene (NB), 1,3-dinitrobenzene (DNB), and 1,3,5-trinitrobenzene (TNB), on the activity of acetylcholinesterase (AChE). The presence of NACs (up to 0.5 mM) effectively suppressed the AChE-catalyzed hydrolysis of acetylthiocholine iodide, with the suppression effect increasing with the nitro-group substitution (TNB > DNB > NB). Consistently, the UV absorption of AChE at 206 nm arising from the skeleton structure decreased by the addition NACs, and the decrease exhibited the same compound sequence, reflecting the perturbing interactions with the skeleton enzyme structure. However, no changes were made on the secondary structure of AChE, as evidenced by the circular dichroism analysis. The fluorescence quenching analysis of AChE demonstrated that NB and DNB interacted with both tryptophan (Trp) and tyrosine (Tyr) residues, whereas TNB interacted only with Trp. The UV absorption and fluorescence quenching analyses both reflected that the interactions with the non-skeleton aromatic amino acids were weak. ¹H NMR analysis confirmed the strong π-π coupling interactions between TNB and model Trp. Molecular simulation indicated that the DNB or TNB molecule was sandwiched between Trp84 and Phe330 at the catalytic site via π-π coupling interactions. The findings highlight the importance of specific interactions of NACs with proteins to cause them to malfunction.

Physicochemical determinants of antibody-protein interactions

Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Although physicochemical rules cannot be generalized for every antibody-protein interaction, there are some features which should be taken into account during antibody development and engineering efforts. In this chapter, physicochemical analysis of antibody paratope-protein epitope interactions will be discussed to highlight important characteristics. First, paratope and non-paratope regions of antibodies will be described and important roles of these regions on binding and biophysical features of antibodies will be discussed. Then, general features of epitope regions of protein antigens will be introduced along with several computational/experimental tools to identify them. Lastly, a rising star of antibody biopharmaceuticals, nanobodies, will be described to show importance of next-generation antibody fragment based biopharmaceuticals in drug development.

Investigating the binding properties between antimony(V) and dissolved organic matter (DOM) under different pH conditions during the soil sorption process using fluorescence and FTIR spectroscopy

Antimony (Sb) is listed as a priority pollutant by European Union and U.S. Environmental Protection Agency. However, reports on its environmental behavior, particularly the sorption process in soil are still limited. In this paper, Sb(V) was selected as the sorbate and the black soil as the sorbent. The initial sorption rate (k₂q_e,cal²) was calculated to be 0.1254 mg g^-1∙min^-1 and the maximum sorption amount (q_m) 57.33 mg g^-1. Once the dissolved organic matter (DOM) was removed from the soil, the values of k₂q_e,cal² and q_m went down to 0.1066 mg g^-1∙min^-1 and 19.01 mg g^-1, respectively. These results suggested that the existence of DOM significantly influenced the mass transfer rate and sorption amount of Sb(V) in soil. In order to find out the reason why DOM exerted such an influence, the binding interaction mechanism between Sb(V) and DOM was investigated under different pH values. The protein-like and humic-like substances as well as the functional groups of CO, phenol hydroxyl, C-O, C-H, C-X and sulfur/phosphorus contributed to the formation of DOM-Sb(V)-complexes under pH of 7.0, in which the humic-like substance and the functional groups containing oxygen showed higher binding affinity for Sb(V) than protein-like substance and other functional groups, respectively. The protein-like substance and some functional groups disappeared under pH of 4.0 and 10.0. Alkaline condition resulted in a bigger impact on reducing the number of functional groups than acid condition. It can be concluded that the strongest binding interaction occurred at pH of 7.0 then followed by 4.0 and 10.0. This paper might be helpful to further studying the environmental behavior of Sb(V) in soil.

Comprehensive spectroscopic studies of synergism between Gadong starch based carbon dots and bovine serum albumin

Carbon dots (C-dots) were used to study the binding mechanisms with serum protein, bovine serum albumin (BSA) by using two notable binding systems known as non-covalent and covalent interaction. Interaction between C-dots and BSA were estimated by Stern-Volmer equation and Double Log Regression Model (DLRM). According to the fluorescent intensity, quenching of model carrier protein by C-dots was due to dynamic quenching for non-covalent and static quenching for covalent binding. The binding site constant, K_A and number of binding site, for covalent interaction is 1754.7L/mol and n≈1 (0.6922) were determined by DLRM on fluorescence quenching results. The blue shift of the fluorescence spectrum, from 450nm to 421nm (non-covalent) and 430nm (covalent) and suggested that both the microenvironment of C-dots and protein changed in relation to the protein concentration. The fluorescence intensity results show that protein structure has a significant role in Protein-C-dots interactions and type of binding influence physicochemical properties of C-dots differently. Understanding to this bio interface is important to utilize both quantum dots and biomolecules for biomedical field. It can be a useful guideline to design further applications in biomedical and bioimaging.

Interpretation of the binding interaction between bupropion hydrochloride with human serum albumin: A collective spectroscopic and computational approach

Bupropion hydrochloride (BPH) an antidepressant and widely used to treat addiction of nicotine. The actual protein existing in blood plasma for the vehicle of exogenous and endogenous substances is human serum albumin i.e. HSA. The interaction of BPH with HSA was examined by molecular docking, multiple spectroscopy's such as fluorescence (emission, synchronous and three-dimensional), UV-vis (ultraviolet-visible), FT-IR (Fourier transform infrared) and CD (circular dichroism) at physiological pH 7.40 at 286, 296 and 306 K. BPH was particularly bind to HSA through forces called hydrogen bonds and vander Waals at site I (IIA) which was confirmed from negative values of thermodynamics calculated by van't Hoff equation and docking studies in addition to site marker analysis. This interaction was spontaneous and exothermic process. Secondary structure including conformation of HSA changes after interaction with BPH was revealed from CD and FT-IR (Fourier self-deconvolution to curve fitting), UV-vis, 3D and synchronous florescence techniques. Forster's theory (non-radiation energy transfer) was applied to calculate the distance from tryptophan of HSA to BPH. This interaction involves static quenching (Stern-Volmer and Modified Stern-Volmer equations) with larger binding constant values were in the range 10⁵ confirming that strong interaction was exists between BPH and HSA. The interference of bio-active Mg²⁺, Cu²⁺, Zn²⁺, Ca²⁺ and Fe²⁺ metal ions on this interaction was also analysed.

A biophysical probe on the binding of 2-mercaptothioazoline to bovine hemoglobin

2-Mercaptothiazoline (MTZ) is broadly present in daily use as an antifungal reagent, a brightening agent, and a corrosion inhibitor. MTZ is potentially harmful for human health. Although the toxic effects of MTZ on experimental animals have been reported, the effects of MTZ on the proteins in the circulatory system at the molecular level have not been identified previously. Here, we explored the interaction of MTZ with bovine hemoglobin (BHb) in vitro using multiple spectroscopic techniques and molecular docking. In this study, the binding capacity, acting force, binding sites, molecular docking simulation, and conformational changes were investigated. MTZ quenched the intrinsic emission of BHb via the static quenching process and could spontaneously bind with BHb mainly through van der Waals forces and hydrogen bond. The computational docking visualized that MTZ bound to the β2 subunit of BHb, which further led to some changes of the skeleton and secondary structure of BHb. This research provides valuable information about the molecular mechanisms on BHb induced by MTZ and is beneficial for clarifying the toxicological actions of MTZ in blood.

A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR

The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn¹⁷⁹ and the high occurrence of π-π interactions involving Phe¹¹⁰. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed.

Interaction of a digestive protease, Candida rugosa lipase, with three surfactants investigated by spectroscopy, molecular docking and enzyme activity assay

The extensive use of surfactants in food, laundry products and agriculture has caused concern about their biosafety. However, few studies have been done on their potential effect on the lipase which has always been used with surfactants in food and laundry industry. Herein, we investigated the interaction of three surfactants (sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), sodium lauryl sulfonate (SLS)) with Candida rugosa lipase (CRL), which is a popular biocatalyst used regularly with surfactants. The effect of the three surfactants on the conformation and activity of CRL was evaluated by using multiple spectral methods, enzyme activity assay and molecular docking modeling. The results demonstrated that CRL interacted with SDS, SDBS and SLS primarily through hydrophobic forces, H-bonding and electrostatic forces, respectively. The binding constants (K_A) of SDBS with CRL varied with temperature: 1.99×10³mol/L at 298K and 4.13×10³mol/L at 318K. SDS and SDBS affected the secondary structure and skeleton of CRL, which changed the polarity of CRL and enhanced its activity. SLS also changed the secondary structure and activity of CRL moderately, but had little effect on its polarity and chromophore microenvironment. Accordingly, all three surfactants exhibited effect to CRL on the molecular level calling for more attention to pay on their biosafety. The work demonstrates that SDS, SDBS and SLS could cause negative effects to CRL from different angles and therefore are not bio-friendly detergents.

Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT)4 G-quadruplex aptamer

Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)₄ G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)₄ G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.

Binding interactions of perfluoroalkyl substances with thyroid hormone transport proteins and potential toxicological implications

Perfluoroalkyl substances (PFASs) have been shown to cause abnormal levels of thyroid hormones (THs) in experimental animals, but the molecular mechanism is poorly understood. Here, a fluorescence displacement assay was used to determine the binding affinities of 16 PFASs with two major TH transport proteins, transthyretin (TTR) and thyroxine-binding globulin (TBG). Most of the tested PFASs bound TTR with relative potency (RP) values of 3×10(-4) to 0.24 when compared with that of the natural ligand thyroxine, whereas fluorotelomer alcohols did not bind. Only perfluorotridecanoic acid and perfluorotetradecanoic acid bound TBG, with RP values of 2×10(-4) when compared with that of thyroxine. Based on these results, it was estimated that displacement of T4 from TTR by perfluorooctane sulfonate and perfluorooctanoic acids would be significant for the occupationally exposed workers but not the general population. Structure-binding analysis revealed that PFASs with a medium chain length and a sulfonate acid group are optimal for TTR binding, and PFASs with lengths longer than 12 carbons are optimal for TBG binding. Three mutant proteins were prepared to examine crucial residues involved in the binding of PFASs to TH transport proteins. TTR with a K15G mutation and TBG with either a R378G or R381G mutation showed decreased binding affinity to PFASs, indicating that these residues play key roles in the interaction with the compounds. Molecular docking showed that the PFASs bind to TTR with their acid group forming a hydrogen bond with K15 and the hydrophobic chain towards the interior. PFASs were modeled to bind TBG with their acid group forming a hydrogen bond with R381 and the hydrophobic chain extending towards R378. The findings aid our understanding of the behavior and toxicity of PFASs on the thyroid hormone system.

Spectroscopic analysis on the binding interaction of biologically active pyrimidine derivative with bovine serum albumin

A biologically active antibacterial reagent, 2-amino-6-hydroxy-4-(4-N, N-dimethylaminophenyl)-pyrimidine-5-carbonitrile (AHDMAPPC), was synthesized. It was employed to investigate the binding interaction with the bovine serum albumin (BSA) in detail using different spectroscopic methods. It exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus which are common food poisoning bacteria. The experimental results showed that the fluorescence quenching of model carrier protein BSA by AHDMAPPC was due to static quenching. The site binding constants and number of binding sites (n≈1) were determined at three different temperatures based on fluorescence quenching results. The thermodynamic parameters, enthalpy change (ΔH), free energy (ΔG) and entropy change (ΔS) for the reaction were calculated to be 15.15 kJ/mol, -36.11 kJ/mol and 51.26 J/mol K according to van't Hoff equation, respectively. The results indicated that the reaction was an endothermic and spontaneous process, and hydrophobic interactions played a major role in the binding between drug and BSA. The distance between donor and acceptor is 2.79 nm according to Förster's theory. The alterations of the BSA secondary structure in the presence of AHDMAPPC were confirmed by UV-visible, synchronous fluorescence, circular dichroism (CD) and three-dimensional fluorescence spectra. All these results indicated that AHDMAPPC can bind to BSA and be effectively transported and eliminated in the body. It can be a useful guideline for further drug design.