Interaction of anthraquinone dyes with lysozyme: evidences from spectroscopic and docking studies

Preventive effects of thymoquinone on glyco-nitro-oxidized human fibrinogen: A comprehensive biophysical study projecting possible therapeutic role in diabetes and associated complications

Persistence of long-term hyperglycemia results in the glyco-oxidation of plasma proteins, which is considered to be a significant factor in metabolic dysfunction, linking hyperglycemia to the emergence of vascular complications. Methylglyoxal (MGO), a dicarbonyl species formed excessively under diabetes, elevates the oxidative stress, enhancing the generation of superoxide anion, which ultimately reacts with nitric oxide (NO•) to form peroxynitrite (PON). PON, being a powerful nitro-oxidizing agent distorts protein structure, hampering its function. This article describes the binding mechanism of thymoquinone (TQ) to fibrinogen (Fg) and its protective effects under simultaneous glyco-nitro-oxidation. Thermodynamic investigations revealed hydrogen bonding and Vander Waal interactions stabilise the complex, confirming its spontaneity and exothermic nature. TQ-induced micro-environmental and structural alterations in fibrinogen were observed by synchronous, 3-D fluorescence maps, and red edge excitation shift (REES). Molecular docking confirmed the wet lab experiments. Previous studies have shown that glycation, as well as nitro-oxidation, modifies the key residues of fibrinogen, leading to its aggregation. Our findings showed that TQ prevented MGO + PON-induced damage to fibrinogen. The current study analyzed the protective effects of TQ on glyco-nitro-oxidized fibrinogen using various biochemical, spectroscopic, and computational methods. NBT assay and carbonyl content revealed glyco-nitro-oxidation-mediated oxidative stress, which was effectively mitigated by TQ in a concentration-dependent manner. The secondary structural alterations in fibrinogen were prevented by TQ as observed by circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR). Moreover, multiple assays and electron microscopy confirmed structural perturbations leading to the development of fibrillar aggregates that were reduced in TQ treated samples. Our findings project TQ as a potent protective agent against hyperglycemia and related human complications.

Reversible and size-controlled assembly of reflectin proteins using a charged azobenzene photoswitch

Disordered proteins often undergo a stimuli-responsive, disorder-to-order transition which facilitates dynamic processes that modulate the physiological activities and material properties of cells, such as strength, chemical composition, and reflectance. It remains challenging to gain rapid and spatiotemporal control over such disorder-to-order transitions, which limits the incorporation of these proteins into novel materials. The reflectin protein is a cationic, disordered protein whose assembly is responsible for dynamic color camouflage in cephalopods. Stimuli-responsive control of reflectin's assembly would enable the design of biophotonic materials with tunable color. Herein, a novel, multivalent azobenzene photoswitch is shown to be an effective and non-invasive strategy for co-assembling with reflectin molecules and reversibly controlling assembly size. Photoisomerization between the trans and cis (E and Z) photoisomers promotes or reduces Coulombic interactions, respectively, with reflectin proteins to repeatedly cycle the sizes of the photoswitch-reflectin assemblies between 70 nm and 40 nm. The protein assemblies formed with the trans and cis isomers show differences in interaction stoichiometry and secondary structure, which indicate that photoisomerization modulates the photoswitch-protein interactions to change assembly size. Our results highlight the utility of photoswitchable interactions to control reflectin assembly and provide a tunable synthetic platform that can be adapted to the structure, assembly, and function of other disordered proteins.

In-Vitro Study of the Binding of Atorvastatin with Adenine using Multi-Spectroscopic Approaches

Atorvastatin-an oral lipid regulating drug is a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase), which is the rate determining enzyme for cholesterol synthesis. Adenine is a purine nucleobase that is found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) to generate genetic information. The binding mechanism of atorvastatin and adenine was studied for the first time utilizing various techniques, including UV-visible spectrophotometry, spectrofluorimetry, synchronous fluorescence spectroscopy (SF), Fourier transform infrared (FTIR), fluorescence resonance energy transfer (FRET), and metal ion complexation. The fluorescence spectra of the complex indicated that atorvastatin is bound to adenine via hydrophobic interaction through a spontaneous binding process, and the fluorescence quenching mechanism was found to be static quenching with a binding constant of 1.4893 × 104 Lmol-1 at 298 K. Various temperature settings were used to investigate thermodynamic characteristics, such as binding forces, binding constants, and the number of binding sites. The interaction parameters, including the standard enthalpy change (ΔHο) and standard entropy change (ΔSο) were calculated using Van't Hoff's equation to be 42.82 kJmol-1 and 208.9 Jmol-1K-1, respectively. The findings demonstrated that the adenine- atorvastatin binding was endothermic. Furthermore, the results of the experiments revealed that some metal ions (K+, Ca+2, Co+2, Cu+2, and Al+3) facilitate the binding interaction between atorvastatin and adenine. Slight changes are observed in the FTIR spectra of adenine, indicating the binding interaction between adenine and atorvastatin.

Insights into the interaction and inhibitory action of palmatine on lysozyme fibrillogenesis: Spectroscopic and computational studies

Interaction under amyloidogenic condition between naturally occurring protoberberine alkaloid palmatine and hen egg white lysozyme was executed by adopting spectrofluorometric and theoretical molecular docking and dynamic simulation analysis. In spetrofluorometric method, different types of experiments were performed to explore the overall mode and mechanism of interaction. Intrinsic fluorescence quenching of lysozyme (Trp residues) by palmatine showed effective binding interaction and also yielded different binding parameters like binding constant, quenching constant and number of binding sites. Synchronous fluorescence quenching and 3D fluorescence map revealed that palmatine was able to change the microenvironment of the interacting site. Fluorescence life time measurements strongly suggested that this interaction was basically static in nature. Molecular docking result matched with fluorimetric experimental data. Efficient drug like interaction of palmatine with lysozyme at low pH and high salt concentration prompted us to analyze its antifibrillation potential. Different assays and microscopic techniques were employed for detailed analysis of lysozyme amyloidosis.Thioflavin T(ThT) assay, Congo Red (CR) assay, 8-anilino-1-naphthalenesulfonic acid (ANS) assay, Nile Red (NR) assay, anisotropy and intrinsic fluorescence measurements confirmed that palmatine successfully retarded and reduced lysozyme fibrillation. Dynamic light scattering (DLS) and atomic force microscopy (AFM) further reiterated the excellent antiamyloidogenic potency of palmatine.

Invitro anti-biofilm activity and the artificial chaperone activity of quinoline-based ionic liquids

The maintenance of protein conformation under stressful conditions is one of the prevailing challenges. This has led to a rapid growth in the ingenious protein therapies, in the past few decades, prioritizing the investigation of the structure and function of proteins in novel environments. Ionic Liquids (ILs) are currently dominating the biomedical industry, by endowing great solubility and stability to bio-molecules, especially proteins. Recently, researchers have devoted their attention towards the artificial chaperone activity of several classes of ILs. Thus, comprehending the long-term as well as momentary stability of protein conformation in IL formulations is an absolute necessity. In this context, we present the activity of quinoline-based ionic liquids (ILs) as artificial cheperones against time-dependent, self induced fibril formation in Bovine Serum Albumin (BSA). Herein, a series of quinoline-based ILs were synthesized and characterized. The structural and morphological changes induced in BSA in the presence and absence of these ILs are corroborated using several spectroscopic measurements and in-silico studies. The anti-microbial and antibiofilm activity of these compounds demonstrating their medicinal properties is substantiated in this study. Furthermore, the present research also gives an account of the toxicity of these compounds under in vivo conditions, using C. elegans as the model organism.

Evaluation of the effect of phenylpropanoids on the binding of heparin to human serum albumin and glycosylated human serum albumin concerning anticoagulant activity: A comparison study

The nonenzymatic advanced glycation end products (AGEs) and the accumulation of AGEs are the two main factors associated with the long-term pathogenesis of diabetes. Human serum albumin (HSA) as the most abundant serum protein has a higher fortuity to be modified by nonenzymatic glycation. In this study, the interaction of three phenylpropanoids (caffeic acid (Caf), p-coumaric acid (Cou), and cinnamic acid (Cin)) toward HSA and glycosylated HSA (gHSA) was analyzed by multiple spectroscopic techniques combined with molecular docking. The formation of fibrils in HSA and gHSA was confirmed by the Thioflavin T (ThT) assay. The phenylpropanoids have shown anti-fibrillation properties in vitro. The obtained thermodynamic parameters indicated that hydrogen bonding and van der Waals forces are the main forces in the binding interaction, and the quenching mechanism of the protein fluorescence is static. Molecular docking results, as well as the in vitro results, showed that Caf, Cou, and Cin exhibit more stable interactions with HSA, respectively. In addition, molecular docking analysis showed that Caf and Cou interact well with K199. Given the critical role of K199 in HSA glycosylation in diabetic patients, this process inhibits the interaction of stabilizer compounds and thus accelerates gHSA aggregation.

The induction of tau aggregation is restricted by sulfamethoxazole and provides new information regarding the use of the drug

The aggregation of tau protein in the form of paired helical filament (PHF) leads to the breakdown of microtubule structure and the development of neurodegenerative disorders, such as Alzheimer's disease. Therefore, inhibiting tau protein aggregation is a potential strategy for preventing the progression of these disorders. In this study, sulfamethoxazole (SMZ), an antibiotic that easily crosses the blood-brain barrier and interacts with tau protein, was tested for its ability to inhibit tau aggregation in vitro. Various multi-spectroscopic techniques including XRD, LDH cytotoxicity colorimetric assay, and microscopic imaging were employed. The results showed that SMZ effectively interacts with tau protein through hydrogen and van der Waals interactions. It also effectively inhibited tau protein aggregation in vitro and significantly reduced toxicity in the SH-SY5Y neuroblastoma cell line. Molecular docking and MD simulation results suggested that SMZ may reduce tau protein aggregation by interacting with the PHF6 motif. Overall, these findings indicate that SMZ has therapeutic potential as a tau protein aggregation inhibitor, at least under in vitro conditions. These findings suggest that SMZ has potential as a treatment for neurodegenerative disorders involving tau protein aggregation. However, further research is needed to confirm these results and assess the effectiveness of SMZ in animal models and clinical trials.Communicated by Ramaswamy H. Sarma.

Insights on the in-vitro binding interaction between donepezil and bovine serum albumin

In this work, the binding mechanism between donepezil (DNP) and bovine serum albumin (BSA) was established using several techniques, including fluorimetry, UV- spectrophotometry, synchronous fluorimetry (SF), fourier transform infrared (FTIR), fluorescence resonance energy transfer (FRET) besides molecular docking study. The fluorescence quenching mechanism of DNP-BSA binding was a combined dynamic and static quenching. The thermodynamic parameters, binding forces, binding constant, and the number of binding sites were determined using a different range of temperature settings. Van't Hoff's equation was used to calculate the reaction parameters, including enthalpy change (ΔH^ο) and entropy change (ΔS^ο). The results pointed out that the DNP-BSA binding was endothermic. It was shown that the stability of the drug-protein system was predominantly due to the intermolecular hydrophobic forces. Additionally, the site probing method revealed that subdomain IIA (Site I) is where DNP and BSA's binding occurs. This was validated using a molecular docking study with the most stable DNP configuration. This study might help to understand DNP's pharmacokinetics profile and toxicity as well as provides crucial information for its safe use and avoiding its toxicity.

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

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

Molecular recognition of two bioactive coumarin derivatives 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin by hen egg white lysozyme: Exploring the binding mechanism, thermodynamic parameters and structural changes using multispectroscopic and computational approaches

Multispectroscopic and computational methods of exploring the interaction between a carrier protein and therapeutic compounds provide a preliminary investigation into establishing the efficacy of such compounds. Here, two coumarin derivatives, 7-hydroxycoumarin (7-HC) and 4-methyl-7-hydroxycoumarin (4-Me-7-HC), were selected to carry out numerous biophysical interaction studies with a model carrier protein, hen egg white lysozyme (HEWL). Fluorescence spectroscopy studies conducted between HEWL and 7-HC/4-Me-7-HC revealed the binding constants (K_b) were in the range of 10⁴ M^-1, indicating a moderate nature of binding. The quenching mechanism observed during complexation process was an unusual static quenching due to the effect of temperature on the rate constant. Thermodynamic parameters revealed a positive ΔH and ΔS for HEWL-7-HC/4-Me-7-HC, indicating hydrophobic forces played a dominant role in the interaction process. FRET studies suggested a possible non-radiative energy transfer from the donor (HEWL) to the acceptor (coumarins). Molecular docking studies revealed the interaction of 7-HC/4-Me-7-HC with intrinsic fluorophores, Trp63 and Trp108, Trp108 being an essential residue for binding as proven by molecular dynamic (MD) simulation. MD simulation studies also indicated conformational stability gained by HEWL upon interaction with 7-HC and 4-Me-7-HC. The microenvironment surrounding the Trp residues showed a significant Stoke's shift on carrying out 3-D fluorescence. CD studies revealed a decrease in the alpha helical content of HEWL upon interacting with the ligands. Enzymatic assay conducted for HEWL in the presence of 7-HC/4-Me-7-HC saw an increase in the activity of HEWL, suggesting a change in structural conformation and stability of the protein, altering its activity.Communicated by Ramaswamy H. Sarma.

Exploring the molecular interaction of mebendazole with bovine serum albumin using multi-spectroscopic approaches and molecular docking

This article presents the binding interaction between mebendazole (MBZ) and bovine serum albumin. The interaction has been studied using different techniques, such as fluorescence quenching spectroscopy, UV-visible spectroscopy, synchronous fluorescence spectroscopy, fourier transform infrared, and fluorescence resonance energy transfer in addition to molecular docking. Results from Stern Volmer equation stated that the quenching for MBZ-BSA binding was static. The fluorescence quenching spectroscopic study was performed at three temperature settings. The binding constant (kq), the number of binding sites (n), thermodynamic parameters (ΔHο, ΔSο and ΔGο), and binding forces were determined. The results exhibited that the interaction was endothermic. It was revealed that intermolecular hydrophobic forces led to the stabilization of the drug-protein system. Using the site marker technique, the binding between MBZ and BSA was found to be located at subdomain IIA (site I). This was furtherly approved using the molecular docking technique with the most stable MBZ configuration. This research may aid in understanding the pharmacokinetics and toxicity of MBZ and give fundamental data for its safe usage to avoid its toxicity.

Spectroscopic investigation of conformational changes in urease caused by interaction with humic acid

Urease in soil interacts with humic acid (HA), which results in a change of the enzymatic activity and stability. However, knowledge on the conformational change of urease in the presence of HA is still lacking. Therefore, the structure of urease (net zero charge at pH 5.2) interacting with HA and the microenvironments of the tyrosine (Tyr) and tryptophane (Trp) residues were investigated at pH 6.7 and 8.0 and 0.5 and 50 mmol L^-1 KCl using spectroscopic techniques. Fluorescence intensity of urease was progressively inhibited by HA with increasing mass ratio f of HA/urease. Moreover, quenching of urease fluorescence by HA was strongest at pH 6.7 (and 50 mmol L^-1 KCl) where the hydrophobic attraction was counteracted by only a weak electrostatic repulsion. HA exerted only a minor effect on the positions of the maximum excitation bands for Tyr and Trp residues, indicating insignificant changes in the microenvironment of these residues in the presence of HA. At pH 6.7, the amide I and amide II bands were inhibited by HA. Curve-fitting of the amide I band of urease in complexes indicated that the percentages of α-helix, β-sheet and β-turn were changed. At pH 8 HA had little effect on the circular dichroism and attenuated total reflectance Fourier transform infrared spectra of urease. At this pH the interaction between urease and HA was weak due to the relatively strong electrostatic repulsion and the conformational change was insignificant. The present results increase our understanding of negatively charged protein behavior in natural environments dominated by humic substances.

The effect of putrescine on the lysozyme activity and structure: Spectroscopic approaches and molecular dynamic simulation

The present research addressed the influence of polyamine (putrescine) on the compound as well as function of lysozyme; accordingly, UV- Visible, fluorescence spectroscopy and simulation method were applied to fulfill this goal. Lysozyme's structural variability was examined at various putrescine ‌concentrations; also, the putrescine binding to lysozyme was addressed using spectrofluorescence, circular dichroism (CD) and UV-Vis measurements. The obtained results indicated that with raising the putrescine concentration, the intrinsic quenching fluorescence of lysozyme was decreased based on the static mechanism. Analysis of thermodynamic parameters also indicated that van der Waals as well as hydrogen bond forces served a fundamental role in determining the resulting stability; this was in agreement with modeling studies. Measurement of UV absorption spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy also demonstrated that lysozyme's second and tertiary structures were altered in a putrescine concentration-dependent manner. Putrescine inhibited lysozyme's enzymatic activity, displaying its affinity with the lysozyme's active site. Further, molecular simulation conducted revealed that putrescine could have spontaneous binding to lysozyme, changing its structure, thus further emphasizing the experimental results.

Probing the Role of Cu(II) Ions on Protein Aggregation Using Two Model Proteins

Copper is an essential trace element for human biology where its metal dyshomeostasis accounts for an increased level of serum copper, which accelerates protein aggregation. Protein aggregation is a notable feature for many neurodegenerative disorders. Herein, we report an experimental study using two model proteins, bovine serum albumin (BSA) and human serum albumin (HSA), to elucidate the mechanistic pathway by which serum albumins get converted from a fully folded globular protein to a fibril and an amorphous aggregate upon interaction with copper. Steady-state fluorescence, time-resolved fluorescence studies, and Raman spectroscopy were used to monitor the unfolding of serum albumin with increasing copper concentrations. Steady-state fluorescence studies have revealed that the fluorescence quenching of BSA/HSA by Cu(II) has occurred through a static quenching mechanism, and we have evaluated both the quenching constants individually. The binding constants of BSA-Cu(II) and HSA-Cu(II) were found to be 2.42 × 104 and 0.05 × 104 M-1, respectively. Further nanoscale morphological changes of BSA mediated by oligomers to fibril and HSA to amorphous aggregate formation were studied using atomic force microscopy. This aggregation process correlates with the Stern-Volmer plots in the absence of discernible lag phase. Raman spectroscopy results obtained are in good agreement with the increase in antiparallel β-sheet structures formed during the aggregation of BSA in the presence of Cu(II) ions. However, an increase in α-helical fractions is observed for the amorphous aggregate formed from HSA.

Environmental stability and cytotoxicity of layered black phosphorus modified with Polyvinylpyrrolidone and Zeolitic Imidazolate Framework-67

Layered black phosphorus (LBP) is regarded as a promising two-dimensional nanomaterial in various application fields. As bare LBP is unstable in humid environment, many modification methods have been developed recently. However, environmental risks of modified LBP nanomaterials are largely unknown. Herein, by sonication and in-situ surface-confined synthesis, polyvinylpyrrolidone (PVP) coated LBP (LBP/PVP), and zeolitic imidazolate framework-67 (ZIF-67) modified LBP (LBP/PVP-ZIF-67) nanomaterials were synthesized. Environmental stability and toxicity of the modified nanomaterials were compared with bare LBP. Results show that LBP/PVP-ZIF-67 exhibits excellent photothermal performance, and higher potential in electrochemical hydrogen evolution than bare LBP or LBP/PVP. Characteristic visible light absorbance at 593 nm was introduced into the nanomaterial by ZIF-67. LBP/PVP has stability in aqueous environment or cytotoxicity similar to LBP. LBP/PVP-ZIF-67 is completely stable in water within 120 h, in contrast to over 30% degradation of LBP or LBP/PVP. More than 50% of LBP in the LBP/PVP-ZIF-67 can degrade to dissolvable phosphorus in oxygenated water after 17 days, indicating the nanomaterial will not be persistent in the environment. Moreover, modification with ZIF-67 can reduce cytotoxicity of LBP. Therefore, this study develops a safe strategy to modify LBP and provides basic information for ecological risk assessment of LBP based materials.

Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions

In this work we present a computational analysis together with experimental studies, focusing on the interaction between a benzothiazole (BTS) and lysozyme. Results obtained from isothermal titration calorimetry, UV-vis, and fluorescence were contrasted and complemented with molecular docking and machine learning techniques. The free energy values obtained both experimentally and theoretically showed excellent similarity. Calorimetry, UV-vis, and 3D/2D-lig-plot analysis revealed that the most relevant interactions between BTS and lysozyme are based on a predominance of aromatic, hydrophobic Van der Waals interactions, mainly aromatic edge-to-face (T-shaped) π-π stacking interactions between the benzene ring belonging to the 2-(methylthio)-benzothiazole moiety of BTS and the aromatic amino acid residue TRP108 of the lysozyme receptor. Next, conventional hydrogen bonding interactions contribute to the stability of the BTS-lysozyme coupling complex. In addition, mechanistic approaches performed using elastic network models revealed that the BTS ligand theoretically induces propagation of allosteric signals, suggesting non-physiological conformational flexing in large blocks of lysozyme affecting α-helices. Likewise, the BTS ligand interacts directly with allosteric residues, inducing perturbations in the conformational dynamics expressed as a moderate conformational softening in the α-helices H1, H2, and their corresponding β-loop in the lysozyme receptor, in contrast to the unbound state of lysozyme.

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.

Spectroscopic and Molecular Docking Study of the Interaction between Neutral Re(I) Tetrazolate Complexes and Bovine Serum Albumin

Re(I) complexes have potential in biomedical sciences as imaging agents, diagnostics and therapeutics. Thus, it is crucial to understand how Re(I) complexes interact with carrier proteins, like serum albumins. Here, two neutral Re(I) complexes were used (fac-[Re(CO)₃ (1,10-phenanthroline)L], in which L is either 4-cyanophenyltetrazolate (1) or 4-methoxycarbonylphenyltetrazole ester (2), to study the interactions with bovine serum albumin (BSA). Spectroscopic measurements, calculations of thermodynamic and Förster resonance energy transfer parameters, as well as molecular modelling, were performed to study differential binding between BSA and complex 1 and 2. Induced-fit docking combined with quantum-polarised ligand docking were employed in what is believed to be a first for a Re(I) complex as a ligand for BSA. Our findings provide a basis for other molecular interaction studies and suggest that subtle functional group alterations at the terminal region of the Re(I) complex have a significant impact on the ability of this class of compounds to interact with BSA.

Unveiling the interaction mechanism of alogliptin benzoate with human serum albumin: Insights from spectroscopy, microcalorimetry, and molecular docking and molecular dynamics analyses

The interaction between a DPP-4 inhibitor, alogliptin benzoate (AB), and human serum albumin (HSA) was systematically investigated via spectroscopy, microcalorimetry and molecular simulations. Steady-state fluorescence and time-resolved fluorescence spectrometry illustrated that the fluorescence quenching type of AB to HSA was static and caused by the formation of ground state AB-HSA complex. Isothermal titration calorimetry (ITC) combined with fluorescence spectra revealed that the affinity of AB to the subdomain IIA of HSA was moderate with a binding constant in the order of 10⁴. Molecular docking analysis and thermodynamic parameters demonstrated that this combination was maintained by hydrogen bonding along with van der Waals force and hydrophobic force. Circular dichroism and three-dimensional (3D) fluorescence showed that AB increased the hydrophobicity of Trp residue and the α-helix content of HSA by 1.99%. Microdifferential scanning calorimetry revealed that the addition of AB enhanced the thermal stability of HSA. The action forces, binding stability, binding sites, and protein structure of the AB-HSA system were evaluated via molecular dynamics analysis in the simulated environment. On the basis of molecular docking, MD simulation constructed a more reliable 3D model of the AB-HSA complex in terms of spatial structure.

Fabrication of graphene oxide and sliver nanoparticle hybrids for fluorescence quenching of DNA labeled by methylene blue

Since graphene oxide‑silver nanoparticles (GO-AgNPs) have special affinities to DNA, it become increasingly important in fields of biological analysis in which GO-AgNPs nanocomposites universally functioned as a quencher. In this paper, GO-AgNPs nanocomposites with different GO to AgNPs ratios were synthesized as a fluorescence quencher to interact with DNA labeled by methylene blue (MB). The results showed that the fluorescence intensity of DNA-MB system decreased with the increasing of GO-AgNPs nanocomposites concentration. The quenching phenomenon of DNA-MB by AgNPs and GO was not a simple additive effect but a synergistic effect. The quenching efficiency of synthesized GO-AgNPs nanocomposites with different ratios (1:1, 1:3, 1:5, 1:10) increased with the decrease of GO/Ag ratio. Thermodynamic analysis was employed to investigate the interaction of GO-AgNPs and DNA-MB, it can be concluded that the intermolecular force between GO-AgNPs and DNA-MB was hydrogen bonding. Our works will provide important theoretical and experimental bases for fluorescence sensing of DNA.

Toxicity assessment of Fluoranthene, Benz(a)anthracene and its mixed pollution in soil: Studies at the molecular and animal levels

An increasing amount of Fluoranthene (Fla) and Benz(a)anthracene (BaA) is being produced and used, eventually entering the soil sediments. The accumulation of Fla and BaA will cause poisoning to typical enzymes (α-Amylase) and organisms (Eisenia fetida) in soil. However, the studies about exploring and comparing the different effects of Fla, BaA and their joint effect at different levels are rarely reported. In this paper, the different effects of Fla, BaA and their mixed pollutant on α-Amylase were evaluated and compared at the molecular level, and the effect of Fla-BaA to the antioxidant system of earthworm (Eisenia fetida) was investigated from the aspects of concentration and exposure time at the animal level. The results showed that Fla-BaA had the greatest influence on the skeleton structure and the microenvironment of amino acid residue of α-Amylase compared to Fla and BaA, and in the mixed pollutant system, the joint effect mode was additive mode. The inhibitory effect of Fla-BaA on the activity of α-Amylase was also stronger than that of the system alone. The assays at the animal level showed that low concentrations (below 5 mg/kg) of Fla-BaA increased the activity of GSH-Px and SOD while high concentrations inhibited their activity. The POD that was activated throughout the experiment period suggested its key role in the earthworm antioxidant system. Changes in T-AOC and MDA showed that long-term and high-dose of Fla-BaA exposure inhibited the antioxidant capacity of Eisenia fetida, causing lipid peroxidation and damage to cells.

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4-15) and α3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P4₃2₁2 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P2₁2₁2₁) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.

Novel Albumin Nanoparticle Enhanced the Anti-Insulin-Resistant-Hepatoma Activity of Metformin

Introduction

Metformin is an ideal candidate to treat the liver tumor with insulin resistance because of its good performance in the treatment of type 2 diabetes and the advantage in cancer therapy. We aim to develop a delivery system with higher efficiency than free drug.

Methods

Metformin-bovine serum albumin (met-BSA) nanoparticles (NPs) were prepared using the anti-solvent precipitation method with a stabilizer of BSA for particle growth. The therapeutic effect of the drug was tested by the insulin-resistant HepG2 cells and C57BL/6J mice at a glucose starvation condition. The interaction mechanism of the drug and the protein during the formation of the NPs was tested using a series of spectroscopy.

Results

Metformin and BSA formed nonporous and spherical particles of about 200 nm with proper lognormal distribution and thermostability. The cellular uptake, as well as the anti-liver cancer activities of met-BSA, was enhanced dramatically compared with the free drug. The thermodynamic studies suggested that the weak binding of metformin to BSA was governed by hydrogen bonds and van der Waals forces. Moreover, the results of synchronous, circular dichroism (CD) and three-dimensional fluorescence demonstrated that the BSA skeleton and chromophore microenvironments were changed in the presence of metformin.

Conclusion

Therefore, met-BSA has been proved as a simple yet effective therapeutic agent for cancer with insulin resistance, promising for future clinic translations in cancer treatment.

Effects of carbendazim on catalase activity and related mechanism

The different techniques like spectroscopy and fluorescence quenching were used to study the interactive effect of carbendazim (CARB) and catalase (CAT) at the molecular level. The results showed that conditions were beneficial to the quenching mechanism at 25.0 °C, pH 7.0, while the binding constant k was 1.92 × 10⁵ L mol^-1 and the number of binding site was 1.0385. The thermodynamic parameters indicated that CARB could interact spontaneously with CAT to form a complex mainly by van der Waals' interactions and hydrogen bonds. The interaction mechanism between CARB and CAT was that the effects of CARB on CAT in soil were activated and then restore stability. However, the effects of CARB on simple CAT were activated and then inhibited.

Interactions of the cis and trans states of an azobenzene photoswitch with lysozyme induced by red and blue light

Exploring the interaction between an azobenzene-based photoswitch and natural protein can help elucidate how the photo-control of an optical molecule participates in the transmission and delivery of proteins, as well as the effects of azo-switch trans and cis states on protein configurations. In this study, fluorescence analysis, circular dichroism spectroscopy, molecular docking, and molecular dynamics simulations were used to study the interaction among different configurations of tetra-ortho-methoxy substituted azobenzene di-maleimide (toM-ABDM), a red light-induced optical azo-switch, and lysozyme (LYZ). Results showed that toM-ABDM caused the static quenching of LYZ. The cis toM-ABDM had stronger binding affinity than trans toM-ABDM. The noncovalent interaction, hydrogen bonds and van der Waals forces, could not regulate the conformation of LYZ in photo-control. A binding model of toM-ABDM and LYZ in different forms induced by red and blue light was further established by computer simulation.

Understanding the interaction of carbon quantum dots with CuO and Cu2O by fluorescence quenching

In spite copper oxide being one of the essential micronutrient, copper oxide in its nano size is found to be toxic in nature; this instigates for the detection of copper oxides in trace levels. In the present study, we demonstrate simple cost effective detection method for CuO/Cu₂O using carbon quantum dots (CQD) by fluorescence quenching technique. CuO/Cu₂O nanoparticles are synthesised by mere variation of fuel ratio by solution combustion technique. The resulting oxides are characterized by various analytical and spectroscopic techniques. Powder X- ray diffraction (PXRD) results reveals that samples prepared with oxidizer to fuel (O/F) ratios 1:1, 1:1.5 and 1:2 showed pure nano CuO, major CuO phase (minor Cu₂O) and major Cu₂O phase (minor CuO) respectively. Further, the samples prepared using 1:1 O/F ratio and calcinated at 700 °C showed highly crystalline CuO phase. In order to study the interaction of CuO/ Cu₂O with CQDs the fluorescence quenching method has been employed. The bimolecular quenching rate constants for the samples prepared with different O/F ratios have been measured. The interaction between CQDs and copper oxides, indicates fluorescence quenching greatly depends on the oxidation state of the copper oxide and can be a promising method for detecting CuO/Cu₂O through CQDs.

Mechanistic interaction study of 5,6-Dichloro-2-[2-(pyridin-2-yl)ethyl]isoindoline-1,3-dione with bovine serum albumin by spectroscopic and molecular docking approaches

A synthesized and promising biologically hypoglycemic compound 5,6-Dichloro-2-[2-(pyridin-2-yl)ethyl]isoindoline-1,3-dione (5e) was studied for its binding to a model protein (bovine serum albumin; BSA) by spectroscopic and molecular simulation approaches. Fluorescence studies revealed that 5e quenched BSA's intrinsic fluorescence by static quenching. The experiments were performed at three different temperatures and the quenching constants and binding constants were evaluated. Stern-Volmer constant (Ksv) values decreased from 1.36 × 104 to 1.20 × 104 as the temperature increased suggesting static quenching involvement in the interaction. Decreased binding constants from 1.70 × 104 to 4.57 × 103 at higher temperatures indicated instability of the complex at rising temperatures. Site I (subdomain IIA) of BSA was found to interact with 5e. The thermodynamic results showed the binding interaction was spontaneous and enthalpy driven. The secondary structure alterations in BSA due to interaction with 5e were studied by UV-visible, synchronous fluorescence, and three-dimensional fluorescence spectra. The results indicate the 5e binds effectively to the BSA and thus, this study can be useful in further exploring the pharmacokinetics and pharmacodynamics of 5e.

Light-Responsive Size of Self-Assembled Spiropyran-Lysozyme Nanoparticles with Enzymatic Function

Novel light-responsive nanoassemblies with switchable size and enzymatic activity are built from a protein and a water-soluble spiropyran. Assemblies are created by electrostatic self-assembly in aqueous solution such that the photochromic property of the spiropyran enables light responsiveness. Upon visible light exposure, the aggregate size increases from 200 to 400 nm. The enzyme retains its activity upon aggregation into the assembly, while it decreases through visible light irradiation. Fundamentally, we show how the two different spiropyran isomers, the open-ring merocyanine form and the closed-ring spiropyran form, bind differently to the protein, which triggers the assembly size and use of thermodynamic data to understand the binding process and the size response. Thus, as a proof of concept, a self-assembly driven light-tunable enzyme activity in conjunction with a triggerable assembly size is demonstrated for a model system. The concept bears future potential for various possible biological applications ranging from genetic control over vaccine applications to the detection of certain proteins.

The Importance of Anthraquinone and Its Analogues and Molecular Docking Calculation

In drug-delivery systems containing nano-drug structures, targeting the tumorous tissue by anthraquinone molecules with high biological activity, and reaching and destroying tumors by their tumor-killing effect reveals remarkable results for the treatment of tumors. The various biological activities of anthraquinones and their derivatives depend on molecular conformation; hence, their intra-cell interaction mechanisms including deoxyribonucleic acid (DNA), ribonucleic acid (RNA), enzymes, and hormones. Computer-based drug design plays an important role in the design of drugs and the determination of goals for them. Molecular docking has been widely used in structure-based drug design. The effects of anthraquinone analogues in tumor cells as a result of their interaction with DNA strand has increased the number of studies done on them, and they have been shown to have a wide range of applications in chemistry, medicine, pharmacy, materials, and especially in the field of biomolecules.

Effects of dietary dosage forms of copper supplementation on growth, antioxidant capacity, innate immunity enzyme activities and gene expressions for juvenile Litopenaeus vannamei

The experiment was conducted to evaluate the effects of different dietary dosage forms of copper supplementation on growth performance, hematological characteristics, antioxidant capacity, immune responses and gene expressions related to innate immune of juvenile Pacific white shrimp Litopenaeus vannamei. Three isonitrogenous and isolipidic diets were formulated to contain three dosage forms of copper: copper sulfate (Diet I-Cu), copper sulfate + copper amino acid complex (1: 1, Diet M-Cu) and copper amino acid complex from Availa^®Cu100 (Diet Availa-Cu), respectively. 360 Pacific white shrimp juveniles (initial weight 1.86 ± 0.03 g) were randomly allocated in 12 tanks corresponding to quadruplicate tanks of the three dietary treatments, and the 8-week feeding trail was conducted. The results indicated that percent weight gain (PWG) and specific growth rate (SGR) in shrimp fed M-Cu diet were significantly higher than that fed I-Cu diet. Survival, feed efficiency (FE), protein efficiency ratio (PER) of shrimp were not significantly different between all treatment groups. High contents of total protein (TP) and glucose (GLU) were found in shrimp fed the diet containing M-Cu, whereas contents of cholesterol (CHOL) and triacylglycerol (TAG) in shrimp fed M-Cu diet were significantly lower than that in I-Cu diet group. In hemolymph, shrimp fed M-Cu diet had high activities of phenoloxidase (PO), alkaline phosphatase (ALP) and acid phosphatase (ACP). While, Cu/Zn superoxide dismutase (Cu/Zn SOD), ceruloplasmin (CP) and lysozyme (LZM) in hemolymph were not significantly affected by different dietary dosage forms of copper. High activities of Cu/Zn SOD, ALP, ACP and LZM in hepatopancreas were observed in shrimp fed M-Cu diet. Shrimp fed diet supplemented with Availa-Cu showed a significantly higher gene expression levels of Cu/Zn sod, alp, acp and lzm in hepatopancreas than that fed I-Cu diet. This study indicated that copper amino acid complex was more effective than copper sulfate to improve growth performance and enhance antioxidant ability and innate immune system.

Probing the binding of phenolic aldehyde vanillin with bovine serum albumin: Evidence from spectroscopic and docking approach

The interactions of bovine serum albumin (BSA) with vanillin (VAN) were studied using UV-vis absorption, fluorescence, synchronous fluorescence, three dimensional fluorescence spectroscopy (3D), Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and molecular docking techniques. The results revealed that VAN causes the static quenching of BSA by forming BSA-VAN complex. The thermodynamic parameters obtained using isothermal titration calorimetry (ITC) showed that the interaction between BSA and VAN is spontaneous and hydrogen bonding, van der Waals forces are mainly involved in stabilizing the complex. The distance between the donor and the acceptor was analyzed using fluorescence resonance energy transfer (FRET) which showed Forster distance of 2.58 nm. Molecular docking technique was applied to study the modes of interaction between BSA-VAN system and it was found that VAN bound to the sub-domain IIA of BSA. Structural analysis using 3D, synchronous fluorescence FTIR, and CD showed that upon binding of VAN, BSA exhibits small micro-environmental changes around tryptophan amino acid residue.

Study on the interactions between toxic nitroanilines and lysozyme by spectroscopic approaches and molecular modeling

Being exogenous environmental pollutants, nitroanilines (NAs) are highly toxic and have mutagenic and carcinogenic activity. Being lack of studies on interactions between NAs and lysozyme at molecular level, the binding interactions of lysozyme with o-nitroaniline (oNA), m-nitroaniline (mNA) and p-nitroaniline (pNA) were investigated by means of steady-state fluorescence, synchronous fluorescence, UV-vis absorption spectroscopy, as well as molecular modeling. The experimental results revealed that the fluorescence of lysozyme is quenched by oNA and mNA through a static quenching, while the fluorescence quenching triggered by pNA is a combined dynamic and static quenching. The number of binding sites (n) and the binding constant (K_b) corresponding thermodynamic parameters ΔH^⊖, ΔS^⊖, ΔG^⊖ at different temperatures were calculated. The reactions between NAs and lysozyme were spontaneous and entropy driven and the binding of NAs to lysozyme induced conformation changes of lysozyme. The difference of the position of -NO₂ group affected the binding and the binding constants K_b decreased in the following pattern: K_b (pNA) >K_b (mNA) >K_b (oNA). Molecular docking studies were performed to reveal the most favorable binding sites of NAs on lysozyme. Our recently results could offer mechanistic insights into the nature of the binding interactions between NAs and lysozyme and provide information about the toxicity risk of NAs to human health.

Binding behavior of trelagliptin and human serum albumin: Molecular docking, dynamical simulation, and multi-spectroscopy

This study aims to investigate the interaction mechanism of a hypoglycemic agent, trelagliptin (TLP), and human serum albumin (HSA) through computer simulation and assisted spectroscopy methods. Computer simulation including molecular docking and molecular dynamics analysis was conducted under physiological conditions. Molecular docking results indicate that TLP bound to HSA at site I, and the binding behavior was mainly governed by hydrophobic force. Competitive experiments further verified the theoretical conclusion from molecular docking. Molecular dynamics simulation revealed that TLP indeed stably bound to site I of HSA in the hydrophobic subdomain IIA. Moreover, TLP presented a certain effect on the structural compactness of HSA. In molecular dynamics simulation, hydrogen bonds appeared, which suggested the reliability and stability of the combination. The binding energy of the stable phase is around -250 kJ/mol. Fluorescence quenching studies and time-resolved fluorescence analysis indicated that the evident fluorescence quenching phenomenon of HSA could be due to TLP binding initiated by static quenching mechanism. The binding constants (K_a) of the complex were found to be around 10⁴ via fluorescence data, and the calculated thermodynamic parameters indicated that hydrophobic force played major role in the binding of TLP to HSA. Synchronous fluorescence and three-dimensional fluorescence results demonstrated that TLP slightly disturbed the microenvironment of amino residues. Circular dichroism spectra showed that TLP affected the secondary structure of HSA. The theoretical and experimental results showed excellent agreement.