Comparison of the conformational stability of the non-native α-helical intermediate of thiol-modified β-lactoglobulin upon interaction with sodium n-alkyl sulfates at two different pH

Effects of myricetin and its derivatives on nonenzymatic glycation: A mechanism study based on proteomic modification and fluorescence spectroscopy analysis

Myricetin and its derivatives, myricitrin and dihydromyricetin, are flavonoids widely presented in foods and phytomedicine that possess tremendous health potential. In this study, we compared the antiglycation activity of myricetin and its derivatives, then investigated the underlying mechanism using proteomic modification and fluorescence spectroscopy analysis. All three compounds exhibited thorough inhibition on nonenzymatic glycation process, with the inhibitory effects on AGEs reaching 85% at 40 μmol/L. They effectively protected bovine serum albumin (BSA) structure by inhibiting protein oxidation, preventing the conversion from α-helix to β-sheet, and reducing amyloid-like cross-β structure formation. Among the three compounds, myricetin showed a predominant antiglycation activity. Proteomic analysis identified the early glycated sites that were protected by myricetin, including lysine K235, 256, 336, 421, 420, 489, etc. Additionally, fluorescence spectroscopy revealed spontaneous interactions between BSA and myricetin. Overall, myricetin holds promise as an antiglycation agent in both the food and drug industries.

Investigating the impact of common migration substances found in milk packaging on proteases: A multispectral and molecular docking approach

The effects of common migration substances in milk packaging on digestive protease were studied. We choose the common migrants found in eight types of multi-layer composite milk packaging. Enzyme activity experiments revealed that pepsin activity decreased by approximately 18 % at 500 μg/mL of stearic acid and stearamide treatment, while trypsin activity decreased by approximately 18 % only by stearic acid treatment (500 μg/mL). Subsequently, fluorescence spectroscopy, circular dichroism spectroscopy, and molecular docking technology were employed to investigate the inhibition mechanism of protease activity by migrating substances in three systems: stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin. Results showed that the inhibitory effect of stearic acid on trypsin is a reversible mixed inhibition, whereas the inhibitory effects of stearic acid and stearamide on pepsin are non-competitive. In all three systems, ΔH < 0, ΔS < 0, and ΔG < 0, indicating the binding process between the migrant and the protease is a spontaneous exothermic process primarily driven by hydrogen bonding and van der Waals forces. In addition, their binding constants are all around 104 L/moL, indicating that there are moderate binding affinities exist between migrants and proteases. The binding process results in the quenching of the protease's endogenous fluorescence and induces alterations in the enzyme's secondary structure. Synchronized fluorescence spectroscopy showed that stearic acid enhanced the hydrophobicity near the Tyr residue of trypsin. The molecular docking results indicated that the binding affinity of stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin was -22.51 kJ/mol, -12.35 kJ/mol, -19.28 kJ/mol respectively, which consistent with the trend in the enzyme activity results. This study can provide references for the selection of milk packaging materials and the use of processing additives, ensuring food health and safety.

Doxorubicin as a Drug Repurposing for Disruption of α-Chymotrypsinogen-A Aggregates

Protein conformation is affected by interaction of several small molecules resulting either stabilization or disruption depending on the nature of the molecules. In our earlier communication, Hg2+ was known to disrupt the native structure of α-Cgn A leading to aggregation (Ansari, N.K., Rais, A. & Naeem, A. Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A. Protein J (2024). https://doi.org/10.1007/s10930-024-10187-z ). Accumulation of β-rich aggregates in the living system is found to be linked with copious number of disorders. Here, we have investigated the effect of varying concentration of doxorubicin (DOX) i.e. 0-100 µM on the preformed aggregates of α-Cgn A upon incubation with 120 µM Hg2+. The decrease in the intrinsic fluorescence and enzyme activity with respect to increase in the Hg2+ concentration substantiate the formation of aggregates. The DOX showed the dose dependent decrease in the ThT fluorescence, turbidity and RLS measurements endorsing the dissolution of aggregates which were consistent with red shift in ANS, confirming the breakdown of aggregates. The α-Cgn A has 30% α-helical content which decreases to 3% in presence of Hg2+. DOX increased the α-helicity to 28% confirming its anti-aggregatory potential. The SEM validates the formation of aggregates with Hg2+ and their dissolution upon incubation with the DOX. Hemolysis assay checked the cytotoxicity of α-Cgn A aggregates. Docking revealed that the DOX interacted Lys203, Cys201, Cys136, Ser159, Leu10, Trp207, Val137 and Thr134 of α-Cgn A through hydrophobic interactions and Gly133, Thr135 and Lys202 forms hydrogen bonds.

Dynamic Observation of the Membrane Interaction Processes of β-Lactoglobulin by Time-Resolved Vacuum-Ultraviolet Circular Dichroism

The elucidation of protein-membrane interactions is pivotal for comprehending the mechanisms underlying diverse biological phenomena and membrane-related diseases. In this investigation, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy, utilizing synchrotron radiation (SR), was employed to dynamically observe membrane interaction processes involving water-soluble proteins at the secondary-structure level. The study utilized a time-resolved (TR) T-shaped microfluidic cell, facilitating the rapid and efficient mixing of protein and membrane solutions. This system was instrumental in acquiring measurements of the time-resolved circular dichroism (TRCD) spectra of β-lactoglobulin (bLG) during its interaction with lysoDMPG micelles. The results indicate that bLG undergoes a β-α conformation change, leading to the formation of the membrane-interacting state (M-state), with structural alterations occurring in more than two steps. Global fitting analysis, employing biexponential functions with all of the TRCD spectral data sets, yielded two distinct rate constants (0.18 ± 0.01 and 0.06 ± 0.003/s) and revealed a unique spectrum corresponding to an intermediate state (I-state). Secondary-structure analysis of bLG in its native (N-, I-, and M-states) highlighted that structural changes from the N- to I-states predominantly occurred in the N- and C-terminal regions, which were prominently exposed to the membrane. Meanwhile, transitions from the I- to M-states extended into the inner barrel regions of bLG. Further examination of the physical properties of α-helical segments, such as effective charge and hydrophobicity, revealed that the N- to I- and I- to M-state transitions, which are ascribed to first- and second-rate constants, respectively, are primarily driven by electrostatic and hydrophobic interactions, respectively. These findings underscore the capability of the TR-VUVCD system as a robust tool for characterizing protein-membrane interactions at the molecular level.

Interfacial Interactions between Nanoplastics and Biological Systems: toward an Atomic and Molecular Understanding of Plastics-Driven Biological Dyshomeostasis

Micro- and nano-plastics (NPs) are found in human milk, blood, tissues, and organs and associate with aberrant health outcomes including inflammation, genotoxicity, developmental disorders, onset of chronic diseases, and autoimmune disorders. Yet, interfacial interactions between plastics and biomolecular systems remain underexplored. Here, we have examined experimentally, in vitro, in vivo, and by computation, the impact of polystyrene (PS) NPs on a host of biomolecular systems and assemblies. Our results reveal that PS NPs essentially abolished the helix-content of the milk protein β-lactoglobulin (BLG) in a dose-dependent manner. Helix loss is corelated with the near stoichiometric formation of β-sheet elements in the protein. Structural alterations in BLG are also likely responsible for the nanoparticle-dependent attrition in binding affinity and weaker on-rate constant of retinol, its physiological ligand (compromising its nutritional role). PS NP-driven helix-to-sheet conversion was also observed in the amyloid-forming trajectory of hen egg-white lysozyme (accelerated fibril formation and reduced helical content in fibrils). Caenorhabditis elegans exposed to PS NPs exhibited a decrease in the fluorescence of green fluorescent protein-tagged dopaminergic neurons and locomotory deficits (akin to the neurotoxin paraquat exposure). Finally, in silico analyses revealed that the most favorable PS/BLG docking score and binding energies corresponded to a pose near the hydrophobic ligand binding pocket (calyx) of the protein where the NP fragment was found to make nonpolar contacts with side-chain residues via the hydrophobic effect and van der Waals forces, compromising side chain/retinol contacts. Binding energetics indicate that PS/BLG interactions destabilize the binding of retinol to the protein and can potentially displace retinol from the calyx region of BLG, thereby impairing its biological function. Collectively, the experimental and high-resolution in silico data provide new insights into the mechanism(s) by which PS NPs corrupt the bimolecular structure and function, induce amyloidosis and onset neuronal injury, and drive aberrant physiological and behavioral outcomes.

Evidence for paraquat-pepsin interaction: In vitro and silico study

The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.

An Eco-friendly Strategy for the Synthesis of Spiro-benzimidazoquinazolinone and Spiro-benzothiazoloquinazolinone Derivatives using β-cyclodextrin as a Supramolecular Catalyst

BACKGROUND

Cyclodextrins selectively bind with reactants and facilitate chemical reactions through supramolecular catalysis, similar to the mechanisms employed by enzymes. In this paper, β-cyclodextrin was used as a supramolecular catalyst in water as a green, reusable, and ecofriendly solvent system to synthesize spiro-benzimidazoquinazolinones and spiro-benzothiazoloquinazolinones.

OBJECTIVE

A supramolecular catalyst β-cyclodextrin (β-CD) is used to synthesize spiro- benzimidazoquinazolinones and spiro-benzothiazoloquinazolinones via multicomponent reaction involving the condensation of dimedone, isatin, and 2-aminobenzimidazole/2-aminobenzothiazole.

METHODS

In a 50 mL round bottom flask were added the respective mixture of substituted isatin (1 mmol), dimedone (1mmol), and 2-aminobenzimidazole/2-aminobenzothiazole (1 mmol) in water (5 ml) containing β-CD (113 mg, 10 mol. %) was stirred at 60oC for 30 min. The desired product was obtained with excellent yield. After completion of the reaction (monitored by TLC), the reaction mixture was quenched with water and extracted with ethyl acetate (4X5 ml). The combined organic layers were washed with brine solution, dried over anhydrous Na2SO4 and evaporated under reduced pressure. The crude product was purified by silica gel chromatography.

RESULTS

β-cyclodextrin catalyst showed very good efficiency in the synthesis of the desired compounds and can be easily recovered and reused at least five times with minimal deactivation in catalytic activity.

CONCLUSION

The catalyst demonstrated remarkable effectiveness in producing the target compounds and conducting the reaction with different initial substances, resulting in excellent yields of the products, thereby confirming the broad applicability and versatility of this method.

DLPF Targeted Repetitive Transcranial Magnetic Stimulation Improves Brain Glucose Metabolism Along with the Clinical and Electrophysiological Parameters in CBD Patients

BACKGROUND

Corticobasal Degeneration (CBD) is a rare neurological disease caused by the pathological accumulation of tau protein. The primary pathological features of CBD include progressive neurodegenerative processes resulting in remarkable frontoparietal and basal ganglia atrophy.

OBJECTIVE

Like in many other neurodegenerative disorders, there is still no effective disease-modifying drug therapy in CBD. Therefore, the development of new treatment methods is of great importance. In this study, we aimed to assess the stimulating effects of high-frequency DLPFC rTMS on the motor, cognitive and behavioral disturbances in four CBD patients.

METHODS

Four (three females, one male) CBD patients who had been diagnosed as CBD were enrolled in this study. Patients were evaluated before and after the rTMS procedure regarding the motor, neuropsychometric and behavioral tests. The results of statistical analysis of behavioral and neuropsychometric evaluation were assessed via SPSS 18.0 package program. Data are expressed as mean, standard deviation. Before and after values of the groups were compared with the Wilcoxon sign rank test, and p<0.05 was considered significant.

RESULTS

We have provided strong preliminary evidence that the improvement in clinical parameters was associated with the normalizations of the theta activity and glucose metabolism.

CONCLUSION

Our current results are consistent with some previous trials showing a strong association between DLPFC targeted rTMS and electrophysiological normalizations in the left DLPFC.

Factorial design-assisted spectroscopic determination of oxybutynin hydrochloride

In this study, we have developed two facile spectroscopic methods for quantifying oxybutynin (OBT) hydrochloride in its pure form and tablets using design of experiments (DOEs). The spectroscopic methods depended on the ion-pair complex formation between the tertiary amino group in the drug and eosin in 0.2 M acetate buffer of pH 4. Method I involves spectrophotometric measurement of the absorbance of the developed complex at 550 nm and showed linearity through 1.0-10.0 µg ml-1. Method II involves spectrofluorometric measurement of the quenching influence of OBT on the native fluorescence of eosin (λ excitation/λ emission of 304/548 nm) and showed linearity through 1.0-6.0 µg ml-1. Critical parameters were identified through preliminary trials and optimized using the DOE. Additionally, the quenching mechanism was investigated and the pathway of the reaction was postulated. The fluorescence quenching constant and thermodynamic parameters were explored using the Stern-Volmer plot and Van't Hoff graph, respectively. Assessments conducted via analytical ecoscale revealed the 'excellent-greenness' of the methodology. The two methods have the potentials of being green and fast compared with other reported methods.

Structural mechanism of the Tanford transition of bovine β-lactoglobulin through microsecond molecular dynamics simulations

X-ray analysis has provided structural data about a pH-driven conformational change in β-lactoglobulin (BLG) known as the Tanford transition, which occurs at around pH 7 and involves the EF loop, which acts as a lid closing the internal cavity of the protein below pH 7 and opening it above pH 7. NMR studies using wild-type BLG have encountered problems trying to explain the Tanford transition, however, they have provided important insight using a dimeric BLG mutant, revealing that the opening and closure of the EF loop consists of two types of motions in the microsecond and milliseconds timescales. This provides valuable information indicating that the dimeric state is a good model to study the Tanford transition, although the understanding of this structural change is still lacking at the atomic level. We performed microsecond molecular dynamics (MD) simulations starting from different conformations of BLG in the monomeric and dimeric state, with protonated and deprotonated E89, in order to explore the Tanford transition. Our results provide structural information for the transition from the closed to the open conformation in BLG and show it occurs in the dimeric state in the microsecond timescale, in line with the fast motion observed through NMR experiments. In addition, MD simulations coupled to MMGBSA approach indicated that the most populated conformer of BLG in the open state is able to bind ligands with similar affinity to that of BLG at neutral pH obtained through crystallographic experiments.Communicated by Ramaswamy H. Sarma.

Potentiality of using front face fluorescence spectroscopy for quantitative analysis of cow milk adulteration in buffalo milk

In current study, synchronous front-face fluorescence spectroscopy together with partial least squares regression (PLSR) is used to predict the adulteration of cow and buffalo milk quantitatively. Fresh (unprocessed milk) samples of cow and buffalo were collected from local dairy farms. Fluorescence emission from milk samples mixed in different concentrations, show intensity variations at wavelengths 370-380 nm, 410 nm, 442 nm and 520-560 nm. Among them, the emissions at band position of 442 nm and 525 nm are highly selective between the two species and could help in finding adulteration of cow milk in buffalo milk and vice versa. The emissions at these wavelength positions correspond to fat-soluble vitamin-A as well as β-carotene. PLS regression is used as a statistical prediction model, which is developed by training with the emission spectra of milk samples having known level of adulterations. The developed model predicts the unknown level of adulterations by means of their spectral data. The goodness of the model is determined by the correlation coefficient R-square (r²) value, which in our case is 0.99. Furthermore, the model root mean square error in cross validation (RMSECV) and in prediction (RMSECP) remains 1.16 and 6.24 respectively. This approach can effectively be applied to determine milk adulterations among other species as well as in detecting external agents (fraudulent) added into milk and other dairy products by further studies.

Formation of molten globule state in horse heart cytochrome c under physiological conditions: Importance of soft interactions and spectroscopic approach in crowded milieu

To understand protein folding problem under physiological condition, usually taken as dilute aqueous buffer at pH 7.0 and 25 °C, knowledge of properties of folding intermediates is important, such as molten globule (MG). We observed that polyethylene glycol 400 Da (PEG 400) induces molten globule state conformation in cytochrome c at pH 7.0 and 25 °C. This PEG-induced MG state has: (i) native tertiary structure partially perturbed, (ii) unperturbed native secondary structure, (iii) newly exposed hydrophobic patches, and (iv) has 1.58 times more hydrodynamic volume than that of the native protein. Isothermal titration calorimetry and docking studies showed specific binding between PEG 400 and cytochrome c. The study delineates that PEG-protein interactions are more complex than the excluded-volume. The soft interactions need to be seriously studied in crowding milieu that leads to destabilization of protein and overcome stabilizing exclusion volume effect. This study not only can help in unraveling the mystery of steps involved in the proper folding of proteins to solve the massively complicated problems of protein folding but also provides novel insights towards importance of structural change in proteins inside cell where intermediate states of protein import-export easily via membranes rather than native form of proteins.

Elucidating the Role of Val-Asn 95 and Arg-Gly 52 Mutations on Structure and Stability of Fibroblast Growth Factor Homologous Factor 2

Background:

Fibroblast growth Factor Homologous Factors (FHFs) belong to a subclass of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities with FGFs. However, despite these similarities, there are properties which set them apart from FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2. Unlike FGFs, FHFs are not able to bind to FGF Receptors (FGFRs) and instead have been implicated in binding to Voltage-Gated Sodium Channels (VGSCs), neuronal MAP kinase scaffold protein and islet-brain-2 (IB2). The two amino acids Arg-52 and Val95 are conserved in all FHFs and mutation of these residues lead to its inability to bind with VGSC/IB2. However, it is not clear whether the loss of binding is due to destabilization of the protein on mutation or due to involvement of Arg52 and Val95 in conferring functionality to FHFs.

Objective:

In the present study, we have mutated these two conserved residues of FHF2 with its corresponding FGF counterpart amino acids and studied the effects of the mutations on the structure and stability of the protein.

Methods:

Several biophysical methods like isothermal equilibrium denaturation study, ANS fluorescence, intrinsic fluorescence, acrylamide quenching, circular dichroism studies as well as using computational approaches were employed.

Results:

The single mutations were found to affect the overall stability, conformation and functionality of the protein.

Conclusion:

Thus, the studies throw light on the role of specific amino acids in deciding the stability, structure and functionality of proteins and will be useful for development of therapeutically engineered proteins.

Evaluation of the toxicity of 5-fluorouracil on three digestive enzymes from the view of side effects

Among the side effects of 5-fluorouracil (5-FU), the performance of the gastrointestinal reactions is faster and more obvious than others. In this work, the effects of 5-FU on the activities and conformational structures of the important digestive enzymes including α-amylase, pepsin and trypsin were studied to analyze the mechanism of the gastrointestinal adverse effects causing by 5-FU binding. The results showed that the enzymatic activity of pepsin was obviously reduced by the presence of 5-FU that bound directly to the enzyme activity cavity site. The molecular modeling and fluorescence quenching data indicated that the hydrophobic, polar and hydrogen bonding forces were involved in the ground state complex formation between proteases and 5-FU. In addition, 5-FU changed the tertiary structures of α-amylase, pepsin, and trypsin.

Curious Results in the Prospective Binding Interactions of the Food Additive Tartrazine with β-Lactoglobulin

The detailed characterizations of the binding interactions between food additive tartrazine (TZ) and β-lactoglobulin (β-LG) have been investigated through spectroscopic techniques combined with a molecular modeling study. A series of analyses, such as hyperchromic change in the UV-visible spectra, temperature-dependent quenching constant, time-resolved fluorescence, and Rayleigh scattering measurements, show that quenching of β-LG proceeds by a static quenching mechanism. TZ specifically binds with β-LG in a stoichiometry ratio of 1:1, and the observed binding constants (10⁴, K) are 7.64, 9.13, 9.72, and 10.79 at 293, 298, 303, and 308 K, respectively. However, the curious results of binding constants (K) with temperature, encountered in the static quenching, have been well explained on the basis of Le Chatelier's principle. Thermodynamic data and pH-dependent studies along with the surface hydrophobicity binding displacement assay reveal that the durable mode of binding is chiefly entropy-driven, revealing noteworthy interactions of such ionic molecules with the hydrophobic part of β-LG. The modulation of protein conformation has been investigated through steady-state absorption spectroscopy, synchronous emission spectroscopy, circular dichroism, and dynamic light scattering studies. TZ acts as a potential inhibitor in fibrillogenesis. Furthermore, the molecular docking study offers accurate insights about the binding of TZ with β-LG, in consistence with the experimental results. This study would be helpful in pharmaceutical, food, and industrial engineering chemistry research.

Utility of Europium ion characteristic peak for quantitation of Fenoterol hydrobromide and Salmeterol xinafoate in different matrices; application to stability studies

A simple selective luminescent dependent approach was established for quantitation of two selective β₂ agonists namely; Fenoterol hydrobromide (FEN) and Salmeterol xinafoate (SAL). This approach utilizes the capability of the cited drugs to undergo a complexation reaction with Europium ion (Eu³⁺) in the presence of 1,10-phenanthroline as a co-ligand. The resultant complex leads to a hypersensitive transition and enhancement of the Eu³⁺ emission peak at 615nm (279nm excitation). Under the optimized conditions, the rectilinear concentration plots of both drugs were (70-1500ngmL^-1) and (100-2000ngmL^-1) with limit of quantitation 51.3 and 84.4ngmL^-1 for FEN and SAL, respectively. The luminescence properties of the complex and its optimum formation conditions were carefully investigated according to the regulations of ICH and the method was successfully applied in plasma. The good accuracy and selectivity of the suggested method allowed extending the proposed protocol into stability study of the cited drugs.

Spectroscopic probing of the refolding of an unfolded protein through the formation of mixed-micelles

We report the unfolding of the globular protein, Bovine Serum Albumin (BSA) induced by anionic surfactant sodium dodecyl sulfate (SDS) and subsequently monitored the refolding of this denatured BSA using triblock copolymers F127 and P123 through the formation of mixed micelles. Our study exclusively represents the reversibility of this unfolding-refolding process using pluronic triblock copolymers F127/P123 as refolding agents. We confirm the recovery of its native state from its denatured state estimating the α-helical structure of the denatured protein from the CD data which support our steady state fluorescence spectra monitoring the fluorescence of the intrinsic Trp molecules present in BSA. Time resolved study also corroborates the stepwise recovery of the denatured BSA as well as the reversibility of the processes. Isothermal Titration Calorimetry (ITC) data explain the negligible interactions between the triblock copolymers and the native state of BSA. The high binding constant of SDS and triblock copolymers probably play the crucial role in the stepwise recovery of the unfolded BSA followed by reversibility of the refolding processes through the formation of the mixed micelles. The mechanism of mixed-micelle formation has been substantiated by the fact that the Guanidine Hydrochloride denatured BSA does not react with F127/P123 whereby no recovery of the protein was observed.

Two novel rhodamine-based fluorescent probes for the rapid and sensitive detection of Fe3+: Experimental and DFT calculations

Fe³⁺ ions play an important role in both biological and environmental field. In this work, two novel rhodamine-based colorimetric and fluorescent probes (RBA2 and RBA3) were designed and synthesized for the efficient detection of Fe³⁺. Upon the addition of Fe³⁺, the fluorescence intensity of RBA2 and RBA3 enhanced 108-fold and 222-fold, respectively. RBA2 and RBA3 exhibited a low detection limit which could achieve 12.8 nM and 11.0 nM. In addition, the binding modes of RBA2 and RBA3 with Fe³⁺ were proved to be 1:1 stoichiometry in the complexes by Job's plot, ESI-MS and ¹H NMR results. The complexing ability of RBA3 with Fe³⁺ excessed to that of RBA2 that was determined by the binding association constants, and highly consistent with DFT calculations results. Furthermore, RBA2 and RBA3 were further utilized to detect Fe³⁺ in living cells and real water samples, indicating their promising prospects in biological and environmental field.

A combined experimental and theoretical investigation of ruthenium(II)-hydrazone complex with DNA: Spectroscopic, nuclease activity, topoisomerase inhibition and molecular docking

A new Dichlorotetra(4-hydroxy-N'-(pyridin-4-ylmethylene)benzohydrazone)Ru(II) complex 1 has been synthesized and characterized using spectroscopic techniques. The structure of complex 1 has been optimized through ORCA computational programme package using B3LYP functionals. The complex binds efficiently with calf thymus DNA (CT-DNA) as monitored by UV-visible titrations (K_b = 4.8 × 10⁵), ethidium bromide displacement studies (K_sv = 1.39) as well as Circular Dichroism (CD) titrations. The complex intercalates with DNA base pairs. It shows cleavage of supercoiled (SC) DNA into nicked circular (NC) DNA efficiently via oxidative pathway. Complex 1 also inhibits Topoisomerase I (Topo I) relaxation activity at concentration < 20 μM. The molecular docking studies support that Topo I inhibition occur via blocking religation of G11 hydroxyl group.

Streptozocin; a GLUT2 binding drug, interacts with human serum albumin at loci h6DOM3-h7DOM3

Streptozocin (STZ) is a broad range antibiotic, highly genotoxic, antineoplastic and hyperglycemic. HSA is the most abundant protein in physiology and it binds to almost all exogenic and endogenic ligands, including drugs. STZ-induced fluorescence quenching of HSA has been done at pH 7.4, pH 3.5 and at pH 7.4 with 4.5 M urea at temperatures 286 K, 291 K, and 306 K. K_sv found to be 10³ M^-1, binding constant 1.5X10³M^-1 and binding sites ~1. But, K_sv for HSA and glucopyranose interaction was found lesser than that of HSA-STZ binding. Binding of STZ/glucopyranose on HSA seems to result in complex formation as calculated K_q > 10¹⁰ M^-1 s^-1. The number of binding sites, binding constants, and binding energies were increased with temperature. The ΔG⁰, ΔH⁰, and ΔS⁰ for HSA-STZ interaction were found to be -17.7 × 10³ J·mol^-1; 2.34 × 10⁵ J·mol^-1 and 841 JK^-1 mol^-1 respectively at pH 7.4 and 291 K. The comparative bindings of N, F and I states of HSA with STZ and their molecular docking analyses indicate that IIIA-B junction (i.e., inter-helix h6_DOM3-h7_DOM3) is the probable binding site, a locus close to fatty acid binding site-5. These results could be useful for therapeutic and analytical exploitation of STZ, as albumin used as the vehicle for drug delivery.

Binding mechanism of five typical sweeteners with bovine serum albumin

In this work, the interactions between bovine serum albumin (BSA) and five sweeteners including aspartame (APM), acesulfame (AK), sucralose (TGS), sodium cyclamate (SC), and rebaudioside-A (REB-A) have been studied by multispectroscopic techniques, and molecular simulation in order to provide much useful information for the application of new and safer artificial sweeteners. Fluorescence quenching assays indicated that the formation of complexes between sweeteners and BSA mainly induced the fluorescence quenching of protein and the binding site number were about 1 indicting that there is one mainly binding site of APM, AK, TGS, SC, or REB-A in domain of BSA with relatively weak interactions. Molecular modeling results indicated that hydrogen bonding interactions were the mainly binding forces of sweeteners with BSA. Circular dichroism spectra indicated that APM and REB-A obviously induced the secondary structure changes of BSA. The presence of APM increased the fraction of α-Helix of BSA from 65.4% to 73.8%, while the presence of REB-A resulted in decreasing the fraction of α-helix of BSA from 65.4% to 51.2%. The melting temperature studies showed that these five sweeteners except REB-A act as stabilizers to increase the thermal stability of BSA during the thermal denaturation process. In addition, AK, TGS, and SC obviously increased the esterase-like activity of BSA, and such loss of activity of BSA induced by APM and REB-A.

Use of spectroscopic and zeta potential techniques to study the interaction between lysozyme and curcumin in the presence of silver nanoparticles at different sizes

This article describes, for the first time, the effect of three different sizes of silver nanoparticles on the binding of curcumin to lysozyme as examined by spectroscopic and zeta potential techniques at physiological conditions. The binding constants of curcumin to lysozyme in the presence of silver nanoparticles were measured. Based on the results of synchronous fluorescence and three-dimensional fluorescence spectroscopy, the presence of the different sizes of silver nanoparticles caused conformational changes in lysozyme during the binding of curcumin. Such changes were also observed when increasing the curcumin concentration. The results of fluorescence resonance energy transfer theory indicated that different sizes of silver nanoparticles could change the binding distance between curcumin and lysozyme. Based on the red edge excitation shift approach, we concluded that the limited mobility around the Trp residues decreased in the presence of silver nanoparticles with bigger size. Under resonance light scattering, the aggregation of curcumin on lysozyme in the presence of silver nanoparticles can play a major role in functional proteins. Communicated by Ramaswamy H. Sarma.

Interaction of promethazine and adiphenine to human hemoglobin: A comparative spectroscopic and computational analysis

The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra. The UV-Vis spectroscopy suggested ground state complex formation. The activation energy (E_a) was observed more in the case of Hb-ADP than Hb-PMT interaction system. The FRET result indicates the high probability of energy transfer from β Trp37 residue of Hb to the PMT (r=2.02nm) and ADP (r=2.33nm). The thermodynamic data reveal that binding of PMT with Hb are exothermic in nature involving hydrogen bonding and van der Waal interaction whereas in the case of ADP hydrophobic forces play the major role and binding process is endothermic in nature. The CD results show that both PMT and ADP, induced secondary structural changes of Hb and unfold the protein by losing a large helical content while the effect is more pronounced with ADP. Additionally, we also utilized computational approaches for deep insight into the binding of these drugs with Hb and the results are well matched with our experimental results.

Dynamics of Ionic Liquid-Assisted Refolding of Denatured Cytochrome c: A Study of Preferential Interactions toward Renaturation

In vitro refolding of denatured protein and the influence of the alkyl chain on the refolding of a protein were tested using long chain imidazolium chloride salts, 1-methyl-3-octylimidazolium chloride [C₈mim][Cl], and 1-decyl-3-methylimidazolium chloride [C₁₀mim][Cl]. The horse heart cytochrome c (h-cyt c) was denatured by urea and guanidinium hydrochloride (GdnHCl), as well as by base-induced denaturation at pH 13, to provide a broad overview of the overall refolding behavior. The variation in the alkyl chain of the ionic liquids (ILs) showed a profound effect on the refolding of denatured h-cyt c. The ligand-induced refolding was correlated to understand the mechanism of the conformational stability of proteins in aqueous solutions of ILs. The results showed that the long chain ILs having the [C₈mim]⁺ and [C₁₀mim]⁺ cations promote the refolding of alkali-denatured h-cyt c. The IL having the [C₁₀mim]⁺ cation efficiently refolded the alkali-denatured h-cyt c with the formation of the MG state, whereas the IL having the [C₈mim]⁺ cation, which is known to be compatible for protein stability, shows slight refolding and forms a different transition state. The lifetime results show successful refolding of alkaline-denatured h-cyt c by both of the ILs, however, more refolding was observed in the case of [C₁₀mim][Cl], and this was correlated with the fast and medium lifetimes (τ₁ and τ₂) obtained, which show an increase accompanied by an increase in secondary structure. The hydrophobic interactions plays an important role in the refolding of chemically and alkali-denatured h-cyt c by long chain imidazolium ILs. The formation of the MG state by [C₁₀mim][Cl] was also confirmed, as some regular structure exists far below the CMC of IL. The overall results suggested that the [C₁₀mim]⁺ cation bound to the unfolded h-cyt c triggers its refolding by electrostatic and hydrophobic interactions that stabilize the MG state.

Peptide-surfactant interactions: A combined spectroscopic and molecular dynamics simulation approach

In the present contribution, we report a combined spectroscopic and computational approach aiming to unravel at atomic resolution the effect of the anionic SDS detergent on the structure of two model peptides, the α-helix TrpCage and the β-stranded TrpZip. A detailed characterization of the specific amino acids involved is performed. Monomeric (single molecules) and micellar SDS species differently interact with the α-helix and β-stranded peptides, emphasizing the different mechanisms occurring below and above the critical aggregation concentration (CAC). Below the CAC, the α-helix peptide is fully unfolded, losing its hydrophobic core and its Asp-Arg salt bridge, while the β-stranded peptide keeps its native structure with its four Trp well oriented. Above the CAC, the SDS micelles have the same effect on both peptides, that is, destabilizing the tertiary structure while keeping their secondary structure. Our studies will be helpful to deepen our understanding of the action of the denaturant SDS on peptides and proteins.

Ultrasound-assisted interaction between chlorin-e6 and human serum albumin: pH dependence, singlet oxygen production, and formulation effect

The interaction between chlorin e6 (Ce6) and human serum albumin (HSA) in the presence and absence of ultrasound have been investigated by ultraviolet-visible absorption spectroscopy and fluorescence spectroscopy. Ce6 is found to bind strongly to HSA at or near physiological pH conditions, but the strength of the binding is significantly weakened at lower pHs. The intrinsic fluorescence of HSA is incrementally quenched with increasing concentration of Ce6, and the quenching is enhanced after exposure to high-frequency ultrasound. Our experimental results suggest that Ce6-induced sonodynamic oxidation of HSA is mainly mediated by singlet oxygen. The formulation of Ce6 by high molecular weight polyvinylpyrrolidone (PVP) increased its stability in aqueous solutions and its quantum yield of singlet oxygen under ultrasound irradiation.

Study of binding interaction of rivaroxaban with bovine serum albumin using multi-spectroscopic and molecular docking approach

Background

Rivaroxaban is a direct inhibitor of coagulation factor Xa and is used for venous thromboembolic disorders. The rivaroxaban interaction with BSA was studied to understand its PK and PD (pharmacokinetics and pharmacokinetics) properties. Multi-spectroscopic studies were used to study the interaction which included UV spectrophotometric, spectrofluorometric and three dimensional spectrofluorometric studies. Further elucidation of data was done by molecular simulation studies to evaluate the interaction behavior between BSA and rivaroxaban.

Results

Rivaroxaban quenched the basic fluorescence of BSA molecule by the process of static quenching since rivaroxaban and BSA form a complex that results in shift of the absorption spectra of BSA molecule. A decline in the values of binding constants was detected with the increase of temperatures (298–308 K) and the binding constants were in range from 1.32 × 10⁵ to 4.3 × 10³ L mol⁻¹ indicating the instability of the BSA and rivaroxaban complex at higher temperatures. The data of number of binding sites showed uniformity. The site marker experiments indicated site I (sub-domain IIA) as the principal site for rivaroxaban binding. The thermodynamic study experiments were carried at the temperatures of 298/303/308 K. The ∆G⁰, ∆H⁰ and ∆S⁰ at these temperatures ranged between − 24.67 and − 21.27 kJ mol⁻¹ and the values for ∆H⁰ and ∆S⁰ were found to be − 126 kJ mol⁻¹ and ∆S − 340 J mol⁻¹ K⁻¹ The negative value of ∆G⁰ indicating spontaneous binding between the two molecules. The negative values in ∆H⁰ and ∆S⁰ indicated van der Waals interaction and hydrogen bonding were involved during the interaction between rivaroxaban and BSA.

Conclusions

The results of molecular docking were consistent with the results obtained from spectroscopic studies in establishing the principal binding site and type of bonds between rivaroxaban and BSA.