Albumin-induced circular dichroism in Congo red: Applications for studies of amyloid-like fibril aggregates and binding sites

Role for Carboxylic Acid Moiety in NSAIDs: Favoring the Binding at Site II of Bovine Serum Albumin

The molecular structures of nonsteroidal anti-inflammatory drugs (NSAIDs) vary, but most contain a carboxylic acid functional group (RCOOH). This functional group is known to be related to the mechanism of cyclooxygenase inhibition and also causes side effects, such as gastrointestinal bleeding. This study proposes a new role for RCOOH in NSAIDs: facilitating the interaction at the binding site II of serum albumins. We used bovine serum albumin (BSA) as a model to investigate the interactions with ligands at site II. Using dansyl-proline (DP) as a fluorescent site II marker, we demonstrated that only negatively charged NSAIDs such as ibuprofen (IBP), naproxen (NPX), diflunisal (DFS), and ketoprofen (KTP) can efficiently displace DP from the albumin binding site. We confirmed the importance of RCOO by neutralizing IBP and NPX through esterification, which reduced the displacement of DP. The competition was also monitored by stopped-flow experiments. While IBP and NPX displaced DP in less than 1 s, the ester derivatives were ineffective. We also observed a higher affinity of negatively charged NSAIDs using DFS as a probe and ultrafiltration experiments. Molecular docking simulations showed an essential salt bridge between the positively charged residues Arg409 and Lys413 with RCOO-, consistent with the experimental findings. We performed a ligand dissociation pathway and corresponding energy analysis by applying molecular dynamics. The dissociation of NPX showed a higher free energy barrier than its ester. Apart from BSA, we conducted some experimental studies with human serum albumin, and similar results were obtained, suggesting a general effect for other mammalian serum albumins. Our findings support that the RCOOH moiety affects not only the mechanism of action and side effects but also the pharmacokinetics of NSAIDs.

Circular dichroism spectrum of (R)-(+)-3,3'-dibromo-1,1'-bi-2-naphthol in albumin: Alterations caused by complexation-Experimental and in silico investigation

This study describes the interaction of human serum albumin (HSA) with the binol derivative (R)-(+)-3,3'-dibromo-1,1'-bi-2-naphthol (R-BrB), which has its optical activity based on the prohibitive energetic barrier for conversion into the enantiomer (S)-(+)-3,3'-dibromo-1,1'-bi-2-naphthol (S-BrB). The objective was to assess the ability of HSA to differentiate axial enantiomers based on their binding efficiency and their impact on the CD spectra. We discovered that both enantiomers were effective ligands, and the CD signal disappeared when equimolar amounts of R-BrB and S-BrB were simultaneously added, indicating no preference for either enantiomer. The complexation resulted in a significant signal increase at 250 nm and a bathochromic effect at 370 nm. Molecular docking simulations were performed, and the lower energy pose of R-BrB was selected for DFT calculations. The theoretical CD spectra of free and complexed R-BrB were obtained and showed alterations corroborating the experimental results. By comparing the difference spectrum (HSA:R-BrB minus HSA) with the spectrum of free RBrB in water or ethyl alcohol, we concluded that the CD signal intensification was due to the increased solubilization of R-BrB upon binding to HSA.

Diagnostics of preeclampsia based on Congo red binding to urinary components: Rationales and limitations

Preeclampsia is a disorder that can occur during pregnancy and is one of the leading causes of death among pregnant women. This disorder occurs after the 20th week of pregnancy and is characterized by arterial hypertension, proteinuria, fetoplacental, and multiple organ dysfunctions. Despite the long history of studying preeclampsia, its etiology and pathogenesis remain poorly understood, and therapy is symptomatic. One of the factors of the disorder is believed to be misfolded proteins that are prone to form amyloid aggregates. The CRD tests, utilizing the binding of the amyloid-specific dye Congo red to urine components, demonstrate high efficiency in diagnosing preeclampsia. However, these tests have also been found to be positive in other disorders with proteinuria, presumably associated with concomitant amyloidosis. To assess the limitations of the CRD tests, we examined urine congophilia and protein components mediating Congo red positivity in patients with proteinuria, including preeclampsia, amyloid and non-amyloid nephropathies. We stained the urine samples and calculated congophilia levels. We also assessed the contribution of large protein aggregates to congophilia values using ultracentrifugation and determined the molecular weights of congophilic urinary proteins using centrifugal concentrators. All proteinuric groups demonstrate positive results in the CRD tests and congophilia levels were more than two times higher compared with the control non-proteinuric groups (p <0.01). There was a strong correlation between urine protein excretion and congophilia in amyloid nephropathy (rs = 0.76), non-amyloid nephropathies (rs = 0.90), and preeclampsia (rs = 0.90). Removal of large aggregates from urine did not affect the congophilia levels. Separation of urine protein fractions revealed congophilic components in the range of 30-100 kDa, including monomeric serum albumin. Our results indicate limitations of CRD tests in preeclampsia diagnostics in women with renal disorders and underscore the need for further research on the mechanisms of Congo red binding with urine components.

pH-dependent effect of Congo Red on the growth of Aspergillus nidulans and Aspergillus niger

The azo dye Congo Red (CR) is frequently used as an agent to elicit cell wall integrity stress in fungi. This highly toxic aromatic, heterocyclic compound contains two azo bonds as chromophore, which are responsible for protonation under acidic conditions, leading to changes in the molecular structure of the dye and the color of the solution. The investigation of how CR affects the growth of Aspergillus nidulans and Aspergillus niger on surface cultures provided us with evidence about its pH-dependent toxicity. Reducing the starting pH of the media from 7 to 3 decreased both the toxicity of CR and the dose-dependence of its toxicity substantially. These changes can be explained by the pH-dependent structural changes of CR and its precipitation at low pH. The pH also depended on the fungi; they could induce a decrease or even an increase, which could be important in the loss of dose-dependence. Our experiments led to the conclusion that in studies to evaluate the antifungal effect of CR, properly buffered solutions with pH values adjusted to above 5 are highly recommended to achieve a well-detectable and dose-dependent antifungal effect. However, for decolorization of CR solutions, lower pH is suggested where the decreased toxicity and solubility of CR could help this process.

Complementary spectroscopy studies and potential activities of levan-type fructan produced by Bacillus paralicheniformis ND2

This study aimed at the production of marine bacterial exopolysaccharides (EPS) as biodegradable and nontoxic biopolymers, competing the synthetic derivatives, with detailed structural and conformational analyses using spectroscopy techniques. Twelve marine bacterial bacilli were isolated from the seawater of Mediterranean Sea, Egypt, then screened for EPS production. The most potent isolate was identified genetically as Bacillus paralicheniformis ND2 by16S rRNA gene sequence of ~99 % similarity. Plackett-Burman (PB) design identified the optimization conditions of EPS production, which yielded the maximum EPS (14.57 g L^-1) with 1.26-fold increase when compared to the basal conditions. Two purified EPSs namely NRF1 and NRF2 with average molecular weights (Mw¯) of 15.98 and 9.70 kDa, respectively, were obtained and subjected for subsequent analyses. FTIR and UV-Vis reflected their purity and high carbohydrate contents while EDX emphasized their neutral type. NMR identified the EPSs as levan-type fructan composed of β-(2-6)-glycosidic linkage as a main backbone, and HPLC explained that the EPSs composed of fructose. Circular dichroism (CD) suggested that NRF1 and NRF2 had identical structuration with a little variation from the EPS-NR. The EPS-NR showed antibacterial activity with the maximum inhibition against S. aureus ATCC 25923. Furthermore, all the EPSs revealed a proinflammatory action through dose-dependent increment of expression of proinflammatory cytokine mRNAs, IL-6, IL-1β and TNFα.

Induced circular dichroism as a tool to monitor the displacement of ligands between albumins

The induction of chirality in a ligand can be a powerful analytical tool for studying protein-ligand interactions. Here, we advanced by applying the technique to monitor the inversion of the induced circular dichroism (ICD) spectrum when ligands move between human and bovine serum albumin proteins (HSA and BSA). ICD experiments were performed using dimers of methyl vanillate (DVT) and vanillin (DVN). The sign and spectra shape were dependent on the albumin type. DVN presented a positive maximum in 312 nm when complexed with HSA and a negative one in BSA. It was possible to induce and follow the time-dependent displacement of the ligand from BSA (2.2 × 10⁶ M^-1) to HSA (6.6 × 10⁵ M^-1) via ICD inversion. The Molecular Mechanics Generalized Born Surface Area approach was used to calculate the binding free energy of the conformers, and a dissociation pathway for each system was proposed using Umbrella Sampling calculations. Four energy minima dihedral angle conformers were identified, and the corresponding CD spectra were calculated using the quantum chemistry approach. Then, weighted spectra for the conformationally accessible conformers were obtained based on each conformer's Boltzmann probability distribution. In conclusion, the methodology described in the manuscript might be helpful in monitoring the movement of ligands between proteins that they bind.

4-Chloro-1,2-phenylenediamine induced structural perturbation and genotoxic aggregation in human serum albumin

4-Chloro-1,2-phenylenediamine (4-Cl-OPD) is a halogenated aromatic diamine used as a precursor in permanent hair color production. Despite its well-documented mutagenic and carcinogenic effects in various in vitro and in vivo models, its role in fibrillar aggregate formation and their genotoxic effect in therapeutic proteins has received less attention. The significance of human serum albumin (HSA) arises from its involvement in bio-regulatory and transport processes. HSA misfolding and aggregation are responsible for some of the most frequent neurodegenerative disorders. We used various complementary approaches to track the formation of amyloid fibrils and their genotoxic effect. Molecular dynamics study demonstrated the complex stability. The impact of 4-Cl-OPD on the structural dynamics of HSA was confirmed by Raman spectroscopy, X-ray diffraction, HPLC and SDS-PAGE. Fibrilllar aggregates were investigated using Congo red assay, DLS, and SEM. The genotoxic nature of 4-Cl-OPD was confirmed using plasmid nicking assay and DAPI staining, which revealed DNA damage and cell apoptosis. 4-Cl-OPD provides a model system for studying fibrillar aggregation and their genotoxic potential in the current investigation. Future studies should investigate the inhibition of the aggregation/fibrillation process, which may yield valuable clinical insights.

Concomitant binding of two fluorescent probes at site-I of human serum albumin: The protein acting as a scaffold enabling fluorescence resonance energy transfer

Human serum albumin (HSA) is the primary drug carrier in the blood plasma. Here, I aimed to show that two ligands can be accommodated simultaneously in the binding site-I of HSA. To do so, I studied the interaction inside the protein among site-I ligands of HSA via fluorescence resonance energy transfer (FRET), synchronous fluorescence, red edge excitation shift (REES), and induced circular dichroism (ICD). Warfarin (WAR), coumarin-153 (C153), 6-(p-toluidino)-2-naphthalenesulfonic acid sodium salt (TNS), dansylglycine (DGY), and 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM) were enrolled in the investigation. I found that WAR can transfer energy to C153 only in the presence of the protein. In addition, the presence of WAR at site-I altered the protein microenvironment felt by C153. The alteration was detected by measuring the synchronous fluorescence, REES, and ICD in C153. The findings were validated by measuring the energy transfer from TNS to DCM and the alteration in synchronous fluorescence and REES. FRET was not observed using WAR as donor and DGY as acceptor. The result is consistent, as DGY is a site-II ligand at a higher WAR distance. In all studied cases, the effects were only observed in the presence of HSA. In conclusion, the protein acted as a scaffold approximating the ligands. These findings prove that more than one ligand can simultaneously be complex at site-I of HSA.

Searching for Natural Products That Delay Nucleation Phase and Promote Elongation Phase of Amyloid β42 toward Alzheimer's Disease Therapeutics

Aggregation of amyloid β42 (Aβ42) is one of the hallmarks of Alzheimer's disease (AD). The mechanism of Aβ42 aggregation mainly consists of two phases, nucleation and elongation (including plateau region as a saturation phase). During the nucleation phase, the monomer gradually forms toxic oligomers. During the elongation phase, each nucleus acts as a template and associates with monomers to initiate less toxic fibrillization. We previously proposed a method of classifying compounds into nine groups based on their ability to modulate the nucleation and/or elongation phases. An orcein derivative (O4), which is a phenoxazine dye isolated from the lichen Roccella tinctoria and containing a 2,5-cyclohexadienone moiety, was reported to convert oligomers into relatively inert fibrils, resulting in the reduction of the neurotoxicity of Aβ42. Focusing on O4 in the pursuit of anti-AD drugs, we herein screened 480 natural products including NPDepo (RIKEN) for the compounds that delayed the nucleation phase and promoted the elongation phase. The signal intensities for Aβ42 treated with each of the 15 compounds that met these criteria were lowered in dot blotting using antioligomer antibody, and the fibril formation of Aβ42 in the presence of these compounds was observed in transmission electron microscopy. Among the 15 compounds, 12 compounds (80%) reduced the toxicity of Aβ42 against mouse neuroblastoma Neuro-2a cells. Some of these anticytotoxic compounds contain 2-pyrone and 4-pyrone that interacted with Aβ42, maybe by shifting the equilibrium of Aβ from toxic oligomer into inert fibrils.

Development of a caffeic acid–phthalimide hybrid compound for NADPH oxidase inhibition

NADPH oxidases are pharmacological targets for the treatment of inflammation-based diseases. This work presents the synthesis and study of a caffeic acid/phthalimide hybrid compound (C2) as a potential inhibitor of NADPH oxidases. Throughout the study, we have compared compound C2 with its precursor caffeic acid (C1). The redox properties were compared using three different antioxidant methodologies and showed that C2 was slightly less effective than C1, a well-established and robust antioxidant. However, C2 was three-fold more effective than albumin (used as a model protein). This chemical feature was decisive for the higher efficiency of C2 as an inhibitor of the release of superoxide anions by stimulated neutrophils and enzymatic activity of cell-free NADPH oxidase. Docking simulation studies were performed using the crystal structure of the recombinant dehydrogenase domain of the isoform NOX5 of C. stagnale, which retains the FAD cofactor (PDB: 5O0X). Considering that C2 could bind at the FAD redox site of NOX5, studies were conducted by comparing the interactions and binding energies of C1 and C2. The binding energies were −50.30 (C1) and −74.88 (C2) (kJ mol⁻¹), which is in agreement with the higher efficacy of the latter as an NADPH oxidase inhibitor. In conclusion, incorporating the phthalimide moiety into caffeic acid was decisive for its effectiveness as an NADPH oxidase inhibitor.

The incorporation of the phthalimide moiety into caffeic acid was decisive for its effectiveness as an NADPH oxidase inhibitor.

Induced CD of iron(ii) clathrochelates: sensing of the structural and conformational alterations of serum albumins

An ability of inherently achiral macrobicyclic metal complexes iron(ii) clathrochelates to acquire an induced CD (ICD) output in the visible spectral range upon interaction with bovine serum albumin (BSA) was recently discovered. In the present work, the CD-reporting properties of iron(ii) clathrochelates to proteins and the thermodynamic parameters of their binding to albumins are evaluated. It is shown that iron(ii) clathrochelates functionalized by six ribbed carboxyphenylsulfide groups are able to discriminate between serum albumins of relative structure (here human and bovine albumins) by giving distinct ICD spectra. Besides, by the variation of the shape and intensity of CD bands, these cage metal complexes reflect the pH-triggered alterations of the tertiary structure of albumins. The constitutional isomerism (ortho-, meta- or para-isomers) of terminal carboxyphenylsulfide groups of iron(ii) clathrochelates strongly affects both the character of their ICD output upon binding with proteins and the parameters of the formed guest-host associates. Using isothermal titration calorimetry, it was determined that cage metal complexes bearing meta- and ortho-isomers of carboxyphenylsulfide groups possess higher association constants (Ka ∼ 2 × 104 M-1) and clathrochelate-to-BSA binding ratios (n = 2) than the para-isomer (Ka ∼ 5 × 103 M-1, n = 1). The iron(ii) clathrochelates are suggested to be potential molecular three-dimensional scaffolds for the design of CD-sensitive reporters able to recognize specific elements of protein surfaces.

Interaction between 1-pyrenesulfonic acid and albumin: Moving inside the protein

Due to the high sensitivity to alterations in microenvironment polarity of macromolecules, pyrene and its derivatives have long been applied in biosciences. Human serum albumin (HSA), besides its numerous physiological functions, is the main responsible by transport of endogenous and exogenous compounds in the circulatory system. Here, a comprehensive study was carry out to understand the interaction between HSA and the pyrene derivative 1-pyrenesulfonic acid (PMS), which showed a singular behaviour when bound to this protein. The complexation of PMS with HSA was studied by steady state, time-resolved and anisotropy fluorescence, induction of circular dichroism (ICD) and molecular docking. The fluorescence quenching of PMS by HSA was abnormal, being stronger at lower concentration of the quencher. Similar behaviour was obtained by measuring the ICD signal and fluorescence lifetime of PMS complexed in HSA. The displacement of PMS by site-specific drugs showed that this probe occupied both sites, but with higher affinity for site II. The movement of PMS between these main binding sites was responsible by the abnormal effect. Using the holo (PDB: ID 1A06) and apo (PDB: ID 1E7A) HSA structures, the experimental results were corroborated by molecular docking simulation. The abnormal spectroscopic behaviour of PMS is related to its binding in different regions in the protein. The movement of PMS into the protein can be traced by alteration in the spectroscopic signals. These findings bring a new point of view about the use of fluorescence quenching to characterize the interaction between albumin and ligands.

Inhibition of the formation of amyloid-like fibrils with spices, especially cloves

During the study of inhibition of amyloid fibril formation, α-chymotrypsin protein was developed in 55% ethanol at pH 7.0. We investigated the inhibitory effect of different spices on amyloid fibril formation using turbidity measurements and Congo red binding assays. We found that all spices except the black pepper and caraway seed prevented fibril formation. The highest inhibition was measured with the clove, which reduced the amount of aggregates by 90%. We studied the inhibitory effect of the cloves at different concentrations on aggregation, it was found that the inhibitory activity of clove is dependent on concentration. We have measured the total phenolic content of the spice extracts too. Based on all these findings we have come to the following conclusion: Our results indicate that spices can contain other compounds too - not only phenolic compounds - which influence the formation of amyloid fibrils, and the effectiveness of various phenolic compounds are different.

Induction of axial chirality in divanillin by interaction with bovine serum albumin

Vanillin is a plant secondary metabolite and has numerous beneficial health applications. Divanillin is the homodimer of vanillin and used as a taste enhancer compound and also a promissory anticancer drug. Here, divanillin was synthesized and studied in the context of its interaction with bovine serum albumin (BSA). We found that divanillin acquires axial chirality when complexed with BSA. This chiroptical property was demonstrated by a strong induced circular dichroism (ICD) signal. In agreement with this finding, the association constant between BSA and divanillin (3.3 x 105 mol-1L) was higher compared to its precursor vanillin (7.3 x 104 mol-1L). The ICD signal was used for evaluation of the association constant, demonstration of the reversibility of the interaction and determination of the binding site, revealing that divanillin has preference for Sudlow's site I in BSA. This property was confirmed by displacement of the fluorescent markers warfarin (site I) and dansyl-L-proline (site II). Molecular docking simulation confirmed the higher affinity of divanillin to site I. The highest scored conformation obtained by docking (dihedral angle 242°) was used for calculation of the circular dichroism spectrum of divanillin using Time-Dependent Density Functional Theory (TDDFT). The theoretical spectrum showed good similarity with the experimental ICD. In summary, we have demonstrated that by interacting with the chiral cavities in BSA, divanillin became a atropos biphenyl, i.e., the free rotation around the single bound that links the aromatic rings was impeded. This phenomenon can be explained considering the interactions of divanillin with amino acid residues in the binding site of the protein. This chiroptical property can be very useful for studying the effects of divanillin in biological systems. Considering the potential pharmacological application of divanillin, these findings will be helpful for researchers interested in the pharmacological properties of this compound.