Interactions of pyrene and/or 1-hydroxypyrene with bovine serum albumin based on EEM-PARAFAC combined with molecular docking

Molecular spectra and docking simulations investigated the binding mechanisms of tetracycline onto E. coli extracellular polymeric substances

Extracellular polymeric substances (EPS), which were an important fraction of natural organic matter (NOM), played an important role in various environmental processes. However, the heterogeneity, complexity, and dynamics of EPS make their interactions with antibiotics elusive. Using advanced multispectral technology, this study examined how EPS interacts with different concentrations of tetracycline (TC) in the soil system. Our results demonstrated that protein-like (C1), fulvic-like (C2), and humic-like (C3) fractions were identified from EPS. Two-dimensional synchronous correlation spectroscopy (2D-SF-COS) indicated that the protein-like fraction gave faster responses than the fulvic-like fraction during the TC binding process. The sequence of structural changes in EPS due to TC binding was revealed by two-dimensional Fourier Transformation Infrared correlation spectroscopy (2D-FTIR-COS) as follows: 1550 > 1660 > 1395 > 1240 > 1087 cm-1. It is noteworthy that the sensitivity of the amide group to TC has been preserved, with its intensity gradually increasing to become the primary binding site for TC. The integration of hetero-2DCOS maps with moving window 2D correlation spectroscopy (MW2DCOS) provided a unique insight into understanding the correlation between EPS fractions and functional groups during the TC binding process. Moreover, molecular docking (MD) discovered that the extracellular proteins would provide plenty of binding sites with TC through salt bridges, hydrogen bonds, and π-π base-stacking forces. With these results, systematic investigations of the dynamic changes in EPS components under different concentrations of antibiotic exposure demonstrated the advanced capabilities of multispectral technology in examining intricate interactions with EPS in the soil environment.

Solid-phase fluorescence: Reproducibility and comparison with the solution states

Solid-phase fluorescence excitation-emission matrix (SPF-EEM) spectroscopy has potential for non-extractive, non-destructive, and non-contact analytical measurements of powder and solid-state samples, as well as front-face EEM spectroscopy for suspensions of high optical density. However, as there is no unified measurement method for SPF spectroscopy, comparing samples measured in different research fields is difficult. Therefore, this study designs a cell that can be created by a 3D printer and examines reproducibility on measuring fluorescent powders. The developed cell is applied to proteins (ovalbumin, BSA, gliadin, gluten, powdered collagen, casein), amino acids (tryptophan, tyrosine, and phenylalanine), soybean ingredients (daidzein, and genistein), and fluorescent chemicals (rhodamine B, fluorescein sodium salt, pyrene, and quinine sulfate dihydrate) and their spectra are compared with those in the solution states. When samples are refilled into the cell three times, the cell exhibits high reproducibility in terms of fluorescence peak wavelength and intensity. The solid proteins exhibit peaks attributed to the fluorescent amino acid residues, and broad peaks which are not detected for the proteins in the solution states. Powdered rhodamine B and fluorescein sodium salt do not exhibit fluorescence, possibly due to the inner-filter effect (IFE). Some non-colored molecules also exhibit loss of fluorescence or a remarkable difference between the solid and solution states, possibly due to the interaction of the fluorescent structure with the surrounding local environment, similar to the solvent effect, which is possibly affected by the molecular proximity, three-dimensional structure, and moisture absorption capacity.

Horizontal comparison of "red or blue shift" and binding energy of six fluoroquinolones: Fluorescence quenching mechanism, theoretical calculation and molecular modeling method

In this article, the interaction between six fluoroquinolones (FQs) and bovine serum albumin (BSA) was initially studied at 298 K, 303 K and 310 K respectively under simulated physiological conditions by fluorescence spectroscopy. At the same time, the sub-structural domains on BSA that may bind to FQs were investigated by molecular docking simulation technique. A combination of quantitative and qualitative approaches was used in the analysis of the binding constants, binding sites and corresponding thermodynamic parameters in the interaction system, it was found that FQs forms a complex with BSA and undergoes static quenching, which is the main cause of fluorescence quenching. The results indicated that hydrogen bonds, Van der Waals force and electrostatic interaction were the main binding forces between the complexes, it also showed that these six fluoroquinolones mainly bound to the IIA and IIIA structural domains of BSA, while DANO and SARA may be more toxic than other antibiotics. Based on Foster's non-radiative energy transfer theory, the binding distance between FQs and BSA was calculated to be less than 7 nm, indicating the existence of energy transfer between small molecule drugs and proteins. Synchronous fluorescence and UV-Vis absorption spectroscopy further confirmed that FQs can alter the secondary conformational change of BSA. Lomefloxacin has a different effect from the other five fluoroquinolone antibiotics because it causes a decrease in polarity and an increase in hydrophobicity around tryptophan residues, while the other five FQs have the opposite effect. Together, the study of FQs-BSA is of great significance to elucidate the pharmacokinetics and pharmacodynamics of FQs.

Interactions between hydroxylated polycyclic aromatic hydrocarbons and serum albumins: Multispectral and molecular docking analyses

Hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) can bind to serum albumin and influence their distribution and elimination in organisms. Herein, multispectral analysis and molecular docking methods were used to investigate the binding mechanism of two OH-PAHs, 1-hydroxyphenanthrene (1-OHPhe) and 9-hydroxyphenanthrene (9-OHPhe), with two homologous serum albumins, human serum albumin (HSA) and bovine serum albumin (BSA). The quenching constants of HSA with 1-OHPhe and 9-OHPhe were much larger than those for BSA. Energy transfer from the tryptophan (Trp) residues in HSA to 1-OHPhe and 9-OHPhe was more probable than from Trp in BSA. The interactions of 1-OHPhe and 9-OHPhe with Trp in HSA and BSA altered the microenvironment of Trp. Molecular docking results revealed that the binding modes and binding forces of 1-OHPhe and 9-OHPhe with HSA and BSA were different. The two OH-PAHs were used as fluorescent probes to analyze the microenvironmental hydrophobicities of HSA and BSA, which were distinctly different. The structural difference between HSA and BSA induced significant variations in their binding behavior with 1-OHPhe and 9-OHPhe. Moreover, HSA was more susceptible to 1-OHPhe and 9-OHPhe than BSA. This work suggests that the differences between the two serum albumins should be considered in related studies.

A mutispectroscopic study on the structure-affinity relationship of the interactions of bisphenol analogues with bovine serum albumin

Bisphenol A (BPA) is a recognized endocrine-disrupting chemical (EDC), and its analogues also exert negative effects on health. The structure-affinity relationship between the structures of nine bisphenol (BP) analogues and the conformational changes of bovine serum albumin (BSA) was studied by various characterization methods and molecular docking. BPs including BPA and its analogues, bisphenol B (BPB), bisphenol C (BPC), bisphenol AP (BPAP), bisphenol M (BPM), bisphenol P (BPP), bisphenol Z (BPZ), diethylstilbestrol (DES) and dienestrol (DS) interacted with BSA. At the concentration of 3.85 × 10^-5 mol l^-1, DS was found to lead to 64% quenching, while BPAP, BPM and DES quenched 60%, 59% and 55% of BSA fluorescence, respectively. The values of ΔH (-19.31-135.42 kJ mol^-1) and ΔS (12.52-495.63 J mol^-1 K^-1) indicated that hydrophobic interactions and hydrogen bonds played important roles in the binding process. The binding constants of DS (8.87 × 10⁴ l mol^-1), DES (3.05 × 10⁴ l mol^-1), BPAP (1.52 × 10⁴ l mol^-1), BPC (1.16 × 10⁴ l mol^-1) and BPM (1.10 × 10⁴ l mol^-1) to BSA were greater than that of BPA (1.18 × 10³ l mol^-1) to BSA, indicating that they may exert more negative effects than BPA. The molecular structure differences of these BPs partly affected their ability to bind to BSA. The binding constants of BPB/BPP to BSA were smaller due to the steric hindrance of ethyl and benzene ring. BPs with conjugated double bond structures (DS and DES) and benzene ring structures (BPM, BPP, BPAP) had a greater influence on the conformation of BSA.

Exploring the interactions of acenaphthene with bovine serum albumin: Spectroscopic methods, molecular modeling and chemometric approaches

The interaction of acenaphthene (ACN), a widespread environmental pollutant, with bovine serum albumin (BSA) was explored using spectroscopic methods, molecular modeling and chemometric approaches. The multivariate curve resolution-alternating least squares (MCR-ALS) analysis decomposed the overlapped excitation-emission matrix (EEM) spectra of mixture of ACN and BSA successfully and extracted spectral profiles of pure BSA, ACN and BSA-ACN complex. Based on fluorescence quenching analysis, ACN quenched the inherent fluorescence of BSA remarkably via a static mechanism. The obtained value of binding constant (K_b = 3.82 × 10⁵ L mol^-1) revealed a high binding affinity of ACN to BSA which facilitates its distribution by blood circulation system. Furthermore, the binding parameters values revealed that one binding site in BSA was involved in BSA-ACN complex. FT-IR, UV-Vis and CD spectra showed that the conformation of BSA was altered in presence of ACN slightly. Molecular docking simulation suggested that ACN was located in the IA region of BSA and the main interactions between ACN and BSA, are van der Waals forces. The obtained results provide some insight into interactions between ACN and serum albumins at the molecular level.

The different interactions of two anticancer drugs with bovine serum albumin based on multi-spectrum method combined with molecular dynamics simulations

Paclitaxel is the best natural anticancer drug and artemisinin also has anticancer effect. In this study, the interactions between BSA and these two drugs were determined in PBS (pH 7.40) by multi-spectroscopic method and molecular dynamics (MD) simulations. The results showed that paclitaxel and artemisinin could statically quench the BSA fluorescence when the complexes were formed and the stoichiometric ratio of BSA-drugs was 1:1. Particularly, the BSA-paclitaxel complex was more stable than BSA-artemisinin complex. During the binding, the surroundings around Trp residue site was largely affected than Tyr site, especially Trp 214 to a more hydrophobic environment. In addition, the binding processes were mainly spontaneous through electrostatic force interaction. In summary, we concluded that the free drug of paclitaxel in blood was low and duration time of artemisinin was shorter.

Multi-spectroscopic and molecular docking studies of human serum albumin interactions with sulfametoxydiazine and sulfamonomethoxine

Sulfonamides are a kind of antibiotics which have been widely used as feed additives for livestock and poultry. However, sulfa drugs have raised worldwide concerns because of their adverse impact on human health. In this study, two sulfonamides, sulfametoxydiazine (SMD) and sulfamonomethoxine (SMM), were selected to explore the binding modes with human serum albumin (HSA). The spectroscopic approaches revealed that SMD or SMM could spontaneously enter into the binding site I of HSA through hydrogen bond interactions and van der Waals forces, and that SMD exhibited much stronger binding affinity toward HSA than SMM at different temperatures (p < 0.01, n = 3). The binding constants for SMD-HSA and SMM-HSA were determined to be (8.297 ± 0.010) × 10⁴ L·mol^-1 and (1.178 ± 0.008) × 10⁴ L·mol^-1 at 298 K, respectively. The interaction of SMD or SMM to HSA induced microenvironmental and conformational changes in HSA, where SMD had a greater effect on the α-helix content of HSA. Results from molecular docking implied that the amino acid residues of HSA, such as Arg222, Ala291 and Leu238, played key roles in the sulfonamide-HSA binding process. Meanwhile, hydrogen bonds might be a key factor contributing to the binding affinity of sulfa drugs and HSA. Additionally, the combined use of SMD and SMM led to an obvious variation in K_a values of binary systems (p < 0.01, n = 3). These findings might be helpful to understand the biological effects of sulfonamides in humans.

Investigation of the binding interactions between dimethyl phthalate and its metabolite with bovine serum albumin by multispectroscopy

To understand the behavior of dimethyl phthalate (DMP) and realize the effect of DMP and its metabolite, monomethyl phthalate (MMP), on the conformation changes of bovine serum albumin (BSA), the interaction mechanisms of DMP and MMP with BSA were investigated by multispectroscopy and molecular docking. The results of the fluorescence quenching experiment showed that the fluorescence quenching of BSA by DMP and MMP was due to the formation of a complex though static quenching, which was also confirmed by time-resolved fluorescence measurements. The binding constants were 8.06 × 10⁴ M^-1 and 4.74 × 10⁴ M^-1 for DMP-BSA and MMP-BSA, respectively, and the number of binding sites were 1.20 (DMP) and 1.18 (MMP). The thermodynamic parameters showed different binding forces for DMP and MMP with BSA. The binding of DMP to BSA was driven mainly by hydrophobic interactions and hydrogen bonding, and MMP bound to BSA by van der Waals forces and hydrogen bonding, which were in accordance with the results from the molecular docking. The conformation and structural alterations of BSA upon DMP or MMP binding were studied by UV-vis spectroscopy, circular dichroism spectroscopy and synchronous fluorescence spectroscopy. The presence of metabolite did not change the quenching mechanism but decreased the binding affinity of DMP toward BSA as well as shortened the binding distance, which may be attributed to the competition between DMP and MMP for binding to BSA. This study revealed the combined effects of DMP and its metabolite on BSA at the molecular level.

Biomolecular interaction of a platelet aggregation inhibitor, 3,4-methylenedioxy-β-nitrostyrene with human serum albumin: multi-spectral and computational characterization

Molecular interaction of the 3,4-methylenedioxy-β-nitrostyrene (MNS), an inhibitor of platelet aggregation with the main transport protein, albumin from human serum (HSA) was explored using absorption, fluorescence and circular dichroism (CD) spectroscopy in combination with in silico analyses. The MNS-HSA complexation was corroborated from the fluorescence and absorption spectral results. Implication of static quenching mechanism for MNS-HSA system was predicted from the Stern-Volmer constant, K_SV-temperature relationship as well as the bimolecular quenching rate constant, k_q values. Stabilization of the complex was affirmed by the value of the binding constant (K_a = 0.56-1.48 × 10⁴ M^-1). Thermodynamic data revealed that the MNS-HSA association was spontaneously driven mainly through hydrophobic interactions along with van der Waal's interaction and H-bonds. These results were well supported by in silico interpretations. Far-UV and near-UV CD spectral results manifested small variations in the protein's secondary and tertiary structures, respectively, while three-dimensional fluorescence spectra displayed microenvironmental fluctuations around protein's fluorophores, upon MNS binding. Significant improvement in the protein's thermostability was evident from the temperature-stability results of MNS-bound HSA. Binding locus of MNS, as identified by competitive drug displacement findings as well as in silico analysis, was found to be located in subdomain IIA (Sudlow's site I) of the protein.Communicated by Ramaswamy H. Sarma.

Different effects of Forsythia suspensa metabolites on bovine serum albumin (BSA)

Forsythia suspensa metabolites have many bioactivities, such as selective immuno suppression, antioxidation, anti-hepatic injury, etc. In the present study, the interactions of the three metabolites with BSA have been investigated in a buffer (pH 7.40) using multi-spectroscopic techniques in combination with molecular docking methods. Two isoformers, forsythoside A and forsythoside I can statically quench BSA intrinsic fluorescence by forming the complexes with BSA at stoichiometric ratio of 1:1 that is again proved by UV-visible absorption. During the binding, the proportion of α-helix in BSA increases, the microenvironment around Tryptophan 213 changes and FRET is one of the major factors to quench fluorescence. Forsythoside E forms BSA-forsythoside E complex (1:1) and thus enhances the intrinsic fluorescence of BSA. During the process, forsythoside E affects not only Tryptophan residues but also Tyrosine residues so that the conformation of BSA is consequently changed. All above binding processes are spontaneous mainly through hydrogen bonding and the hydrophobic force interaction, which is supported by docking analysis and thermodynamic parameters. In addition, three compounds do not induce BSA aggregation. These findings are beneficial to understand the detailed information of the interactions of Forsythia suspensa metabolites with BSA.

Data on the fluorescence quenching analysis of BSA induced by pyrene and/or 1-hydroxypyrene in binary and ternary systems

This article present data related to the publication entitled "Interactions of pyrene and/or 1-hydroxypyrene with bovine serum albumin based on EEM-PARAFAC combined with molecular docking" (Zhang et al., 2018) [1]. The excitation-emission matrix (EEM) fluorescence spectral parameters of pyrene, 1-hydroxypyrene, bovine serum albumin (BSA), and their mixtures were presented in this article. Combined EEM - parallel factor analysis with fluorescence quenching analysis, some data related to the binding affinity of pyrene and/or 1-hydroxypyrene with BSA in the binary and ternary systems were obtained.