Experimental, computational and chemometrics studies of BSA-vitamin B6 interaction by UV–Vis, FT-IR, fluorescence spectroscopy, molecular dynamics simulation and hard-soft modeling methods

DNA and hemoglobin binding activities: Investigation of coumarin-thiosemicarbazone hybrids

Coumarin and coumarin-thiosemicarbazone hybrids were synthesized and characterized by various techniques such as FT-IR, 1H NMR, 13C NMR, MALDI-TOF-MS spectroscopy, and single crystal X-Ray diffractometer (XRD). The photochemical and photophysical properties of the compounds, such as solvatochromism, solubility, and chemical reactivity, were analyzed using UV-vis spectroscopy in different solvents. Due to the potential biological activities of the synthesized compounds, their binding affinity and mechanisms with calf thymus DNA (ct-DNA) and bovine hemoglobin (BHb) were determined using several useful spectrophotometric and theoretical approaches such as UV-vis absorption and fluorescence spectroscopy, molecular docking, and density functional theory (DFT). The experimental results showed that the compounds exhibited strong binding interactions with DNA and BHb. Additionally, the compounds demonstrated predominantly binding modes, such as intercalation and groove binding with DNA and π-π stacking interactions with BHb.To better understand the thermodynamics of these interactions, quenching constants, binding constants, and Gibbs free energy changes (ΔG°) were calculated. Molecular docking and DFT results supported the experimental data regarding the binding affinity and mechanisms of the compounds to DNA and BHb. Overall, this comprehensive study on coumarin and coumarin-thiosemicarbazone hybrids provides valuable insights into their interaction mechanisms with critical biomolecules, highlighting their potential in therapeutic applications as multifunctional agents.

Comprehensive views toward the biomolecular recognition of an anticancer drug, leflunomide with human serum albumin

Biomolecular association of an anticancer drug, leflunomide (LEF) with human serum albumin (HSA), the leading ligands carrier in human circulation was characterized using biophysical (i.e., fluorescence, absorption and voltammetric) methods and computational (i.e., molecular docking and molecular dynamics simulation) techniques. Evaluations of fluorescence, absorption and voltammetric findings endorsed the complex formation between LEF and HSA. An inverse relationship of Stern-Volmer constant-temperature and hyperchromic shift of the protein's absorption signal with addition of LEF confirmed the LEF quenched the HSA fluorescence through static process. Moderate nature of binding strength (binding constant = 2.76-4.77 × 104 M-1) was detected towards the LEF-HSA complexation, while the association process was naturally driven via hydrophobic interactions, van der Waals interactions and hydrogen bonds, as evident from changes in entropy (ΔS= + 19.91 J mol-1 K-1) and enthalpy (ΔH = - 20.09 kJ mol-1), and molecular docking assessments. Spectral analyses of synchronous and three-dimensional fluorescence validated microenvironmental fluctuations near Trp and Tyr residues upon LEF binding to the protein. LEF association with HSA significantly defended temperature-induced destabilization of the protein. Although LEF was found to attach to HSA at Sudlow's sites I and II, but exhibited greater preference toward its site I, as detected by the investigations of competitive site-marker displacement. Molecular dynamics simulation assessment revealed that the complex attained equilibrium throughout simulations, showing the LEF-HSA complex constancy.Communicated by Ramaswamy H. Sarma.

Binding characteristics and conformational changes in alpha-2-macroglobulin by the dietary flavanone naringenin: biophysical and computational approach

In the present study, we investigated the interaction of alpha-2-macroglobulin (α2M) with naringenin using multi-spectroscopic, molecular docking, and molecular simulation approaches to identify the functional changes and structural variations in the α2M structure. Our study suggests that naringenin compromised α2M anti-proteinase activity. The results of absorption spectroscopy and fluorescence measurement showed that naringenin-α2M formed a complex with a binding constant of (kb)∼104, indicative of moderate binding. The value of ΔG° in the binding indicates the process to be spontaneous and the major force responsible to be hydrophobic interaction. The findings of FRET reveal the binding distance between naringenin and the amino acids of α2M was 2.82 nm. The secondary structural analysis of α2M with naringenin using multi-spectroscopic methods like synchronous fluorescence, red-edge excitation shift (REES), FTIR, and CD spectra further confirmed the significant conformational alterations in the protein. Molecular docking approach reveals the interactions between naringenin and α2M to be hydrogen bonds, van der Waals forces, and pi interactions, which considerably favour and stabilise the binding. Molecular dynamics modelling simulations also supported the steady binding with the least RMSD deviations. Our study suggests that naringenin interacts with α2M to alter its confirmation and compromise its activity.Communicated by Ramaswamy H. Sarma.

Interactions of three berberine mid-chain fatty acid salts with bovine serum albumin (BSA): Spectroscopic analysis and molecular docking

In this paper, the interaction of three berberine mid-chain fatty acid salts ([BBR][FAs]), viz. berberine caproate ([BBR][CAP]), berberine heptylate ([BBR][HEP]) and berberine octoate ([BBR][OCT]), with bovine serum albumin (BSA) was studied by means of UV-visible absorption spectroscopy, fluorescence spectroscopy, fourier transform infrared spectroscopy (FT-IR) and molecular docking techniques. Fluorescence experiments revealed that three berberine salts quench the fluorescence of BSA by static quenching mechanism resulted from a stable [BBR][FAs]-BSA complex formation. The stoichiometric numbers of [BBR][FAs]-BSA complexes were found to be 1:1. Synchronous and three-dimensional fluorescence spectra as well as FT-IR demonstrated that the binding of [BBR][FAs] altered the microenvironment and conformation of BSA. The binding average distance from [BBR][FAs] to BSA (3.2-3.5 nm) was determined according to Förster energy transfer theory. Site probe investigation showed that [BBR][FAs] bound to BSA active site I (sub-domain IIA). The binding promotes the esterase-like activity of BSA. The molecular docking results confirmed the fluorescence competition findings and provided the type of binding forces. Furthermore, the relationship between the anionic chain length of [BBR][FAs] and the interaction was explored, and the positive correlation was found.

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

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

Distinguishing the responsive mechanisms of fluorescent probes to hydrogen peroxide, proteins, and DNA/RNA

The responsive mechanisms of cationic quinolinium-vinyl-N,N-dimethylaniline boronate (QVD-B) derivative probes to hydrogen peroxide (H2O2), proteins and DNA/RNA are theoretically investigated in this study. The potential energy curves of QVD-B scanned on a dihedral angle (N+-C-CC) in the first singlet (S1) state exhibit large torsional energy barriers. Additionally, the energy of the lowest unoccupied molecular orbital (LUMO) of an acceptor moiety (-3.14 eV) is lower than that of a donor moiety (-1.13 eV) in QVD-B. This demonstrates that photoinduced electron transfer (PET) quenches the fluorescence of QVD-B, as opposed to the previous report of intramolecular single-bond rotation. After reacting with H2O2, the reaction product of quinoline-vinyl-N,N-dimethylaniline (QVD) turns off the PET pathway and turns on the fluorescence at 550 nm, which is consistent with the experimental results (580 nm). Among the possible configurations of QVD-B that forms with proteins and DNA, the calculated fluorescence values of corresponding twisted QVD-B-P (638 nm) and QVD-B-D (686 nm) are consistent with the experimental results (632 and 688 nm). The frontier molecular orbital and electron-hole analysis show that the charge transfer distance follows the order of QVD (1.88 Å) < QVD-B-P (4.49 Å) < QVD-B-D (6.39 Å), which induces the fluorescence red-shifts of QVD-B-P and QVD-B-D compared to that of QVD. The multi-detection mechanism of the fluorescent probe QVD-B is attributed to PET progress and different degrees of local charge transfer after photoexcitation.

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

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

Probing the binding of morin with alpha-2-macroglobulin using multi-spectroscopic and molecular docking approach : Interaction of morin with α2M

Alpha-2-macroglobulin (α2M) is an essential antiproteinase that is widely distributed in human plasma. The present study was aimed at investigating the binding of a potential therapeutic dietary flavonol, morin, with human α2M using a multi-spectroscopic and molecular docking approach. Recently, flavonoid-protein interaction has gained significant attention, because a majority of dietary bioactive components interact with proteins, thereby altering their structure and function. The results of the activity assay exhibited a 48% reduction in the antiproteolytic potential of α2M upon interaction with morin. Fluorescence quenching tests unequivocally confirmed quenching in the fluorescence of α2M in the presence of morin, conforming complex formation and demonstrating that the binding mechanism involves a dynamic mode of interaction. Synchronous fluorescence spectra of α2M with morin showed perturbation in the microenvironment around tryptophan residues. Furthermore, structural changes were observed through CD and FT-IR, showing alterations in the secondary structure of α2M induced by morin. FRET further supports the results of the dynamic mode of quenching. Moderate interaction is shown by binding constant values using Stern-Volmer's fluorescence spectroscopy. Morin binds to α2M at 298 K with a binding constant of 2.7 × 104 M-1, indicating the strength of the association. The α2M-morin system was found to have negative ΔG values, which suggests that the binding process was spontaneous. Molecular docking also reveals the different amino acid residues involved in this binding process, revealing that the binding energy is -8.1 kcal/mol.

Spectrofluorometric and computational approaches for the interaction studies of aclonifen and bifenox with human serum albumin

Interaction of two broadly used herbicides, aclonifen (ACF) and bifenox (BIF) with the major transporter in human circulation, human serum albumin (HSA) were examined using fluorescence and absorption spectral measurements combined with in silico analyses. Assessment of the fluorescence and absorption spectral results affirmed the complexation between ACF/BIF and HSA. Increase in the K_SV value with temperature characterized the ACF/BIF-induced quenching of the protein fluorescence as dynamic quenching. The moderate binding affinities (K_f = 1.74×10⁴ - 1.95×10⁶ M^-1 for ACF-HSA complex; K_f = 2.00×10³ - 1.02×10⁶ M^-1 for BIF-HSA complex) were pointed out between ACF/BIF and HSA, showing a relatively higher binding constant values with increasing temperatures. Quantitative evaluation of thermodynamic data (ΔS = +0.86 kJ mol^-1 K^-1 and ΔH = +225.43 kJ mol^-1 for ACF-HSA complex; ΔS = +1.11 kJ mol^-1 K^-1 and ΔH = +304.63 kJ mol^-1 for BIF-HSA complex) predicted the contribution of hydrophobic interactions in the ACF-HSA and BIF-HSA association processes, which were well supported by our molecular docking results. In silico analyses were made to acquire insight details into the ACF and BIF binding to HSA at the binding sites and suggested the locations of ACF and BIF binding sites as both subdomain IIA (site I) and subdomain IIIA (site II) of HSA, showing more preference toward site I.

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.

Analysis of reaction between vitamin B6 and bovine serum albumin based on a terahertz metamaterial sensor

A four-peak terahertz metamaterial sensor was used to detect the reaction between different concentrations of vitamin B₆ (VB₆) and bovine serum albumin (BSA), which achieves a concentration range (0.015-0.125 mg/µl) of VB₆ and a maximum binding concentration (0.05 mg/µl) of VB₆ and 0.0875 mg/µl BSA. To understand the combination of VB₆ and BSA, the reactants between VB (VB₁, VB₃, and VB₅) with the same concentration (0.05 mg/µl) and a BSA solution with a concentration of 0.0875 mg/µl were carried on the surface of the sensor. Experimental results show that the reactants cause the four resonance peaks of the sensor to produce the coincident redshift, which is the same as the order of their binding coefficients determined by the fluorescence method. The experimental process indicates that it is feasible to use terahertz metamaterials to detect the reaction process of organic matter.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

A Component Content Measurement Method Modified Using Indirect Hard Modeling for Polymer Blends Based on Raman Spectroscopy

Raman spectroscopy has been proven to be useful for the component content measurement of polymer blends. However, the soft modeling methods commonly used in quantitative analysis of Raman spectroscopy require a large number of training samples, resulting in a waste of materials and time. This work adopted a modified indirect hard modeling (IHM) method to measure the component content of polymer blends based on Raman spectroscopy. The Raman spectra of polypropylene (PP)/polystyrene (PS) blends with different component content were collected and resolved into the sum of multiple Voigt peak functions. For a large number of peak parameters, the two-dimensional correlation spectroscopy was used to screen out the characteristic Voigt peaks highly correlated with component content to reduce the parameter dimensions and build the parameterized spectral models. The spectral model of the blend was expressed as the weighted sum of the pure component spectral models, during which the parameters of the pure component models were adjusted within a range. According to the relationship between the weight and content of the pure component, a linear regression model for component content prediction was established. The coefficient of determination (R²)/root mean squared error of the IHM component content prediction model was 0.9931/0.4367 wt%. Besides, two popular soft modeling methods, partial least squares and artificial neural network, were compared with the IHM method, which showed that the IHM model had higher prediction accuracy with fewer training samples.

Insight into the binding characteristics of rutin and alcohol dehydrogenase: Based on the biochemical method, spectroscopic experimental and molecular model

Alcohol dehydrogenase (ADH) is a crucial enzyme in the alcohol metabolism pathway. Its activity is associated with the development of alcohol-relative diseases. Rutin is a kind of widely distributed dietary flavonoids, which have the ability to resist alcohol-induced liver injury. Here, the role of rutin on alcohol metabolism was investigated via the methods of biochemistry, spectroscopy and computer simulation. The experiment results demonstrated that rutin entered into the position of coenzyme (NAD) on ADH and formed a binary complex, which of process activated the catalyze activity of ADH in a concentration dependent manner. The combination of rutin on ADH induced microenvironmental variations as well as secondary structural change of ADH, where the level of α-helix reduced yet β-sheet raised. The values of ∆H and ∆S suggested that H-bonds and van der Waals force occupied vital roles in the stabilization of ADH-rutin complex. Furthermore, molecular docking results further confirmed that the H-bonds between the hydroxyl groups on the benzene rings of rutin and surrounding amino acid were beneficial to maintain the stability of complex. Particularly, the van der Waals force and π-alkyl between rutin and Val residues may be the main reason for activation of ADH activity.

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.

Drug affinity responsive target stability (DARTS) accelerated small molecules target discovery: Principles and application

Drug affinity responsive target stability (DARTS) is a novel target discovery approach and is particularly adept at screening small molecule (SM) targets without requiring any structural modifications. The DARTS method is capable of revealing drug-target interactions from cells or tissues by tracking changes in the stability of proteins acting as receptors of bioactive SMs. Due to its simple operation and high efficiency, the DARTS method has been applied to uncover the drug-action mechanism. This review summarized analytical principles, protocols, validation approaches, applications, and challenges involved in the DARTS method. Due to the innate advantages of the DARTS method, it is expected to be a powerful tool to accelerate SM target discovery, especially for bioactive natural products with unknown mechanisms.

Investigation of the binding properties between levamlodipine and HSA based on MCR-ALS and computer modeling

Levamlodipine (LEE) is a drug commonly used for antihypertensive treatment in clinical therapy. The overlapping fluorescence spectra of LEE and human serum albumin (HSA) cause some trouble in analysis of interactions between them by using the classic fluorescence method. Here, the multivariate curve resolution-alternating least squares (MCR-ALS) approach was used to overcome this disadvantage. Meanwhile, the binding properties of LEE-HSA complex were then explored through computer modeling. The MCR-ALS results suggested that LEE-HSA complex was present in the mixture solution of LEE and HSA. This conclusion was then confirmed by the Stern-Volmer equation and time-resolved fluorescence experiment. The binding constant (K_a) was 2.139 × 10⁴ L·mol^-1 at 298 K. LEE was located close to the Trp-214 residue of HSA, with van der Waals forces and hydrogen bonding as main driving forces for this interaction. LEE can alter the conformation of HSA, in which the content of α-helix reduced from 57.2% to 52.3%. The Pi-Alkyl interactions contributed to maintaining the stability of the LEE-HSA complex. The results of molecular dynamics simulations showed that LEE-HSA complex was formed within 5 ns, and the particle size (R_g) of HSA was altered by the binding reaction. This study would promote better understanding of the transportation and distribution mechanisms of LEE in the human body.

Helical water-soluble NiII complexes with pyridoxal ligand derivatives: Structural evaluation and interaction with biomacromolecules

This article deals with the synthesis of Schiff-based bis-azomethine-based ligands derived from pyridoxal and aliphatic dihydrazides and the synthesis of nickel(II) complexes C1-C4. The synthesized complexes had their structures elucidated by monocrystal X-ray diffraction and were characterized by vibrational and absorption spectroscopy. The synthesized ligands have characteristics that allow the formation of self-assembly processes, thus, the flexibility or rigidity of the coordination of organic molecules added to the orbitals of the Ni^II cation leads to the formation of helical complexes with double helix and a dinucler nickel(II) complex. Moreover, compounds was their interactions with CT-DNA and HSA absorption and emission analysis and molecular docking calculations.

Evaluation of the interaction of novel tyrosine kinase inhibitor apatinib mesylate with bovine serum albumin using spectroscopies and theoretical calculation approaches

Apatinib mesylate (APM), a novel tyrosine kinase inhibitor, has been applied in treating various cancers. In the present study, the binding mechanism of APM with bovine serum albumin (BSA) was studied by making use of various spectroscopic and theoretical calculation approaches to provide theoretical support for further studying its pharmacokinetics and metabolism. The results from fluorescence experiments showed that the quenching mechanism of BSA induced by APM was static quenching and the APM-BSA complex with the stoichiometry of 1:1 was formed during binding reaction. Moreover, the findings also showed that the binding process of APM to BSA was spontaneous and enthalpy-driven, and the mainly driving forces were hydrogen bonding, van der Waals as well as hydrophobic interactions. From the outcomes of the competitive experiments, it can be found that the binding site was primarily nestled in sub-domain IIIA of BSA (site II) which was in line with the results of molecular docking. An appreciable decline in α-helix content of BSA can be observed from the FT-IR data, meaning that the conformational change of BSA occurred after binding with APM, this phenomenon can be corroborated by the results of UV-vis, synchronous fluorescence and 3D fluorescence studies. Furthermore, the effect of some metal ions (e.g. K⁺, Co²⁺, Ni²⁺, Fe³⁺) on the binding constant of APM to BSA was explored.Communicated by Ramaswamy H. Sarma.

Inhibitory mechanism of epicatechin gallate on tyrosinase: inhibitory interaction, conformational change and computational simulation

Epicatechin gallate can inhibit the activity of tyrosinase in a mixed-type manner.

A novel fluorescence method for the rapid and effective detection of Listeria monocytogenes using aptamer-conjugated magnetic nanoparticles and aggregation-induced emission dots

The sensitive and specific detection of L. monocytogenes through immunomagnetic separation and fluorescence response produced by recognition of IgG-coated TPE-OH@BSA nanoparticles.

Probing the binding mechanism of capecitabine to human serum albumin using spectrometric methods, molecular modeling, and chemometrics approach

Capecitabine as a prodrug of 5-Fluorouracil plays an important role in the treatment of breast and gastrointestinal cancers. Herein, in view of the importance of this drug in chemotherapy, interaction mechanism between Capecitabine (CAP) and human serum albumin (HSA) as a major transport protein in the blood circulatory system has been investigated by using a combination of spectroscopic and molecular modeling methods. The fluorescence spectroscopic results revealed that capecitabine could effectively quench the intrinsic fluorescence of HSA through a static quenching mechanism. Evaluation of the thermodynamic parameters suggested that the binding process was spontaneous while hydrogen bonds and van der Waals forces played a major role in this interaction. The value of the binding constant (K_b = 1.820 × 10⁴) suggested a moderate binding affinity between CAP and HSA which implies its easy diffusion from the circulatory system to the target tissue. The efficiency of energy transfer and the binding distance between the donor (HSA) and acceptor (CAP) were determined according to forster theory of nonradiation energy transfer as 0.410 and 4.135 nm, respectively. Furthermore, UV-Vis spectroscopic results confirmed that the interaction was occurred between HSA and CAP and caused conformational and micro-environmental changes of HSA during the interaction. Multivariate curve resolution-alternating least square (MCR-ALS) methodology as an efficient chemometric tool was used to separate the overlapped spectra of the species. The MCR-ALS result was exploited to estimate the stoichiometry of interaction and to provide concentration and structural information about HSA-CAP interactions. Molecular docking studies suggested that CAP binds mainly to the subdomain IIA of HSA, which were compatible with those obtained by experimental data. Finally, molecular dynamics simulation (MD) was performed on the best docked complex by considering the permanence and flexibility of HSA-CAP complex in the binding site. MD result showed that CAP could steadily bind to HSA in the site I based on the formation of hydrogen bond and π-π stacking interaction in addition to hydrophobic force.

Conductance Changes in Bovine Serum Albumin Caused by Drug-Binding Triggered Structural Transitions

Proteins, due to their binding selectivity, are promising candidates for fabricating nanoscale bio-sensors. However, the influence of structural change on protein conductance caused by specific protein-ligand interactions and disease-induced degeneration still remains unknown. Here, we excavated the relationship between circular dichroism (CD) spectroscopy and conductive atomic force microscopy (CAFM) to reveal the effect of the protein secondary structures changes on conductance. The secondary structure of bovine serum albumin (BSA) was altered by the binding of drugs, like amoxicillin (Amox), cephalexin (Cefa), and azithromycin (Azit). The CD spectroscopy shows that the α-helical and β-sheet content of BSA, which varied according to the molar ratio between the drug and BSA, changed by up to 6%. The conductance of BSA monolayers in varying drug concentrations was further characterized via CAFM. We found that BSA conductance has a monotonic relation with α-helical content. Moreover, BSA conductance seems to be in connection with the binding ability of drugs and proteins. This work elucidates that protein conductance variations caused by secondary structure transitions are triggered by drug-binding and indicate that electrical methods are of potential application in protein secondary structure analysis.

Investigation of the binding sites and orientation of Norfloxacin on bovine serum albumin by surface enhanced Raman scattering and molecular docking

Norfloxacin (NFX) is an antibacterial agent belonging to the fluoroquinolone family of drugs, known to bind bovine serum albumin (BSA). Surface-enhanced Raman scattering (SERS) and fluorescence spectroscopy in combination with molecular docking were explored to investigate the binding interaction between NFX with Bovine serum albumin (BSA) at a physiological condition. This study focused on identifying the binding site and relevant interaction mechanisms between NFX and BSA. Spectrophotometric titration with molecular docking results demonstrated that the binding site of NFX on BSA was located in sub-domain IIA. The principle binding site was identified within a hydrophobic cavity which is surrounded by the residues Leu 197, Arg 198, Ser 201, Ala 209, Trp 213, Ser 343, Leu 346, Lys 350, Ser 453, Leu 480, Val 481, and the binding force was mainly hydrophobic interaction and hydrogen bond interaction. In addition, the absorptive orientation of the NFX molecule on the colloidal surface underwent a set of changes during the process of NFX binding to BSA.

Phenylpropanoids and lignans from Prunus tomentosa seeds as efficient β-amyloid (Aβ) aggregation inhibitors

Alzheimer's disease (AD) is characterized by the progressive accumulation of extracellular β-amyloid (Aβ) aggregates. Recently, lignans and phenylpropanoids are attracting increasing attention to discovery useful agents of inhibition on Aβ aggregation. In the present study, to develop potential agents for slowing the progression of AD, Prunus tomentosa seeds were selected as a raw material for bioactive compounds, which led to the separation of two pairs of new enantiomeric lignans and phenylpropanoids using chiral HPLC. The planar structures of these compounds were elucidated by spectroscopic data analyses. And their absolute configurations were determined by comparing of experimental and calculated electronic circular dichroism (ECD). The biosynthesis pathway was also discussed. Additionally, the inhibitory activity on Aβ aggregation of all optical pure compounds was tested by thioflavin T (ThT) assay. The isolates (1a, 1b, 2a and 2b) showed more potent inhibitory activity than positive control curcumin with inhibitory rate of 73.89 ± 3.41% 78.69 ± 1.50%, 63.25 ± 2.68%, and 67.13 ± 0.90% at 20 μM, respectively. More importantly, the inhibition profiles were explained by molecular dynamics and docking simulation studies.

Investigation of the interaction of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase using inhibition kinetics, CD, FT-IR and molecular docking methods

Applying enzyme kinetics, spectroscopic, and molecular docking methods, the interaction properties of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase were systematically investigated. The α-glucosidase inhibitory activities (IC₅₀ = 0.40 mM) were significantly higher than that of acarbose (as control) and the spectrometric results revealed that 2,4-dimethoxy-6,7-dihydroxyphenanthrene inhibited α-glucosidase in a reversible and noncompetitive manner, which is that the inhibitor bind to the inactive region of α-glucosidase and could be separated from the bind sites. Hydrogen bond was the key interaction force obtained from the results of the molecular docking study, and the binding energy was -27.754 kJ/mol. The CD studies showed that the content of α-helix in α-glucosidase increased from 17.2% to 17.8% with the concentration varying of 2,4-dimethoxy-6,7-dihydroxyphenanthrene. The α-helix increasing trend (19.70% - 21.43%) of α-glucosidase secondary structure was further proved by Fourier transform infrared spectra (FT-IR) results and the FT-IR spectra of α-glucosidase resulted in obvious red shift with the addition of 2,4-dimethoxy-6,7-dihydroxyphenanthrene. All the measurements proved the interaction of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase and revealed the conformational change of α-glucosidase secondary structure.

A Chalcone-Based Potential Therapeutic Small Molecule That Binds to Subdomain IIA in HSA Precisely Controls the Rotamerization of Trp-214

The principal intent of this work is to explore whether the site-specific binding of a newly synthesized quinoline-appended anthracenyl chalcone, (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ), with an extracellular protein of the human circulatory system, human serum albumin (HSA), can control the rotamerization of its sole tryptophan residue, Trp-214. With this aim, we have systematically studied the binding affinity, interactions, and localization pattern of the title compound inside the specific binding domain of the transport protein and any conformation alteration caused therein. Multiple spectroscopic experiments substantiated by an in silico molecular modeling exercise provide evidence for the binding of the guest ADMQ in the hydrophobic domain of HSA, which is primarily constituted by residues Trp-214, Arg-218, Arg-222, Asp-451, and Tyr-452. Rotationally restricted ADMQ prefers to reside in Sudlow site I (subdomain IIA) of HSA in close proximity (2.45 nm) to the intrinsic fluorophore Trp-214 and is interestingly found to control its vital rotamerization process. The driving force for this rotational interconversion is predominantly found to be governed by the direct interaction of ADMQ with Trp-214. However, the role of induced conformational perturbation in the biomacromolecule itself upon ADMQ adoption cannot be ruled out completely, as indicated by circular dichroism, 3D fluorescence, root-mean-square deviation, root-mean-square fluctuation, and secondary structure element observations. The comprehensive spectroscopic study outlined herein provides important information on the biophysical interaction of a chalcone-based potential therapeutic candidate with a carrier protein, exemplifying its utility in having a regulatory effect on the microconformations of Trp-214.

Preparation of self-assembled nanoparticles of ε-polylysine-sodium alginate: A sustained-release carrier for antigen delivery

Low immunogenicity prohibits the widespread use of subunit vaccine against infectious diseases and cancers. Hence, a new generation of adjuvants and delivery systems is indispensable for more potent antigen-specific immune responses. Predominantly, nanoparticles formulated from biodegradable polymers are being widely explored as carriers of novel vaccines owing to their outstanding natural properties. We fabricated a model antigen - bovine serum albumin (BSA) encapsulated ε-polylysine (ε-PL) - sodium alginate (SA) nanoparticles (PSNPs), which were self-assembled by ionotropic complexation method, a very simple and mild process, as a result of the electrostatic interaction between oppositely charged polyelectrolyte complexes (PEC). After the preparation, various in vitro parameters were characterized. Scanning electron microscope and dynamic light scattering were employed to study the morphology, size, zeta potential and optimize formulation. Forming mechanism of PSNPS was analyzed and verified by infrared absorption spectra and thermal analysis. Delivery behavior of PSNPs was assessed via release study, cytotoxicity measurement and cellular uptake. BSA-PSNPs with a mean particle diameter 133.2 ± 0.5 nm, narrow size distribution and negatively charged surface had been synthesized successfully by this method. The results of in vitro studies demonstrated that the nanosuspension was able to prevent burst release of loaded BSA and presented sustained-release behavior. It was no cytotoxicity by the bio-assessment using macrophage cells, and was observed significantly higher uptake compared with BSA free solution. Herein, ε-polylysine - sodium alginate nanoparticles had been found to be a potential candidate for vaccine delivery.

Multiplex immunoassays using surface modification-mediated porous layer open tubular capillary

We proposed an innovative surface modification-mediated porous layer open tubular (PLOT) capillary, which was modified via an in situ biphasic reaction. This capillary comprised three-dimensional homogeneous and porous structures, which could increase the surface-area-to-volume ratio for antibody immobilization. The PLOT capillary was shown as an ideal immunoreaction base to enhance the sensitivity of immunoassays and shorten analysis time. By connecting two separate PLOT capillaries using a suitable sleeve tube, we can perform multiplex targets detection in the same sample. We developed a sensitive, rapid, and multiplex PLOT capillary-mediated immunosensor for the simultaneous identification of alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) in clinical serum samples with good accuracy. The detection sensitivity of the PLOT immunosensor improved by 10-fold compared with that of bare-capillary sensor, and the whole analysis could be completed within 1 h. This work suggest that suitable surface modification strategy is an effective tool to improve the analytical performance of conventional immunoassay and our study provided a feasible, sensitive, and multi-target assay for the detection of cancer biomarkers, which would be of valuable application in clinical diagnosis.

Hydrogen bonding and π-π stacking in nicotinamide/H2O mixtures

The interactions between nicotinamide (NA) and H₂O were studied using UV-visible spectra (UV-Vis), cyclic voltammetry (CV), nuclear magnetic resonance (NMR), density functional theory (DFT) and atoms in molecules (AIM) analysis. According to the changes of the UV-Vis spectra and the oxidation and reduction potentials in cyclic voltammograms of NA in aqueous solution, it was found that hydrogen bonding occurred between NA and H₂O molecules. Quantum chemistry calculations and AIM analysis further confirmed the existence of hydrogen bonding between H₂O molecules and the amide group, the nitrogen atom, and hydrogen atoms on the pyridine ring of NA molecules. In addition, the NMR results demonstrated that the π-π stacking between NA pyridine rings could be formed at higher concentrations.

Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation

Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.

Interaction of phenazinium-based photosensitizers with the 'N' and 'B' isoforms of human serum albumin: Effect of methyl substitution

The present work is focused on exploring the interaction of two phenazinium-based biological photosensitizers, phenosafranin (PSF) and safranin-O (SO), with human serum albumin (HSA), with particular emphasis on the physiologically significant NB conformational transition of the protein on the dye:HSA interaction. In addition, the presence of methyl substitution on the planar phenazinium ring in SO paves way for looking into the effect of simple chemical manipulation (that is, methyl substitution on the dye nucleus) on the dye:protein interaction behavior as a function of various (pH-induced) isoforms of HSA. Our results reveal a significantly stronger binding interaction of SO with the B isoform of HSA (at pH9.0) compared to that with the N isoform (at pH7.4). On the contrary, the PSF:HSA interaction is found to be reasonably insensitive to the aforesaid conformational transition of HSA. However, the probable binding location of both the dye molecules (PSF and SO) is found to be within the protein scaffolds (domain IB). This is further quantified from the modulation of fluorescence decay behavior of the dyes within the protein scaffolds. It is important to note that the rotational relaxation behavior of the protein-bound dyes reveals an unusual 'dip-rise-dip', an observation not reported earlier. Such unusual anisotropy decay is meticulously analyzed by an associated (or multicomponent) exponential decay model which emphasizes on the fractional contributions from differential classes of fluorophore populations characterized by the fast (due to unbound or solvent exposed part of the fluorophore) and slow (due to embedded or bound part) motions, in combination with their different local mobilities. Furthermore, the translational diffusion of the dye molecules in the presence of the protein in different isoforms (N-form or B-form) at a single molecule level is also measured by Fluorescence Correlation Spectroscopy (FCS).