Investigations on the interactions of DiAmsar with serum albumins: Insights from spectroscopic and molecular docking techniques

Diamine‐sarcophagine (DiAmsar) binding to human serum albumin (HSA) and bovine serum albumin (BSA) was investigated under simulative physiological conditions. Fluorescence spectra in combination with Fourier transform infrared (FT‐IR), UV‐visible (UV–vis) spectroscopy, cyclic voltammetry (CV), and molecular docking method were used in the present work. Experimental results revealed that DiAmsar had an ability to quench the HSA and BSA intrinsic fluorescence through a static quenching mechanism. The Stern–Volmer quenching rate constant (K_sv) was calculated as 0.372 × 10³ M^‐1 and 0.640 × 10³ M^‐1 for HSA and BSA, respectively. Moreover, binding constants (K_a), number of binding sites (n) at different temperatures, binding distance (r), and thermodynamic parameters (?H°, ?S°, and ?G°) between DiAmsar and HSA (or BSA) were calculated. DiAmsar exhibited good binding propensity to HSA and BSA with relatively high binding constant values. The positive ?H° and ?S° values indicated that the hydrophobic interaction is main force in the binding of the DiAmsar to HSA (or BSA). Furthermore, molecular docking results revealed the possible binding site and the microenvironment around the bond. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular interactions of thymol with bovine serum albumin: Spectroscopic and molecular docking studies

Thymol is the main monoterpene phenol present in the essential oils which is used in the food industry as flavoring and preservative agent. In this study, the interaction of thymol with the concentration range of 1 to 6 μM and bovine serum albumin (BSA) at fixed concentration of 1 μM was investigated by fluorescence, UV‐vis, and molecular docking methods under physiological‐like condition. Fluorescence experiments were performed at 5 different temperatures, and the results showed that the fluorescence quenching of BSA by thymol was because of a static quenching mechanism. The obtained binding parameters, K, were in the order of 10⁴ M^?1, and the binding number, n, was approximately equal to unity indicating that there is 1 binding site for thymol on BSA. Calculated thermodynamic parameters for enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) showed that the reaction was spontaneous and hydrophobic interactions were the main forces in the binding of thymol to BSA. The results of UV‐vis spectroscopy and Arrhenius' theory showed the complex formation in the interaction of thymol and BSA. Negligible conformational changes in BSA by thymol were observed in fluorescence experiments, and the same results were also obtained from UV‐vis studies. Results of molecular docking indicated that the subdomain IA of BSA was the binding site for thymol.     

Spectroscopic and molecular docking studies on the interaction between N‐acetyl cysteine and bovine serum albumin

The interaction between N‐acetyl cysteine (NAC) and bovine serum albumin (BSA) was investigated by UV–vis, fluorescence spectroscopy, and molecular docking methods. Fluorescence study at three different temperatures indicated that the fluorescence intensity of BSA was reduced upon the addition of NAC by the static quenching mechanism. Binding constant (K_b) and the number of binding sites (n) were determined. The binding constant for the interaction of NAC and BSA was in the order of 10³ M^?1, and the number of binding sites was obtained to be equal to 1. Enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) as thermodynamic values were also achieved by van't Hoff equation. Hydrogen bonding and van der Waals force were the major intermolecular forces in the interaction process and it was spontaneous. Finally, the binding mode and the binding sites were clarified using molecular docking which were in good agreement with the results of spectroscopy experiments. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 638–645, 2015.     

Probing the behavior of bovine serum albumin upon binding to atenolol: insights from spectroscopic and molecular docking approaches

Molecular interaction of atenolol, a selective β₁ receptor antagonist with the major carrier protein, bovine serum albumin (BSA), was investigated under imitated physiological conditions (pH 7.4) by means of fluorescence spectroscopy, UV absorption spectroscopy, Fourier transform infrared spectroscopy (FT-IR), and molecular modeling studies. The steady-state fluorescence spectra manifested that static type, due to formation of the atenolol-BSA complex, was the dominant mechanism for fluorescence quenching. The characteristic information about the binding interaction of atenolol with BSA in terms of binding constant (K_b) were determined by the UV–vis absorption titration, and were found to be in the order of 10³ M^?1 at different temperatures, indicating the existence of a weak binding in this system. Thermodynamic analysis revealed that the binding process was primarily mediated by van der Waals force and hydrogen bonds due to the negative sign for enthalpy change (ΔH⁰), entropy change (ΔS⁰). The molecular docking results elucidated that atenolol preferred binding on the site II of BSA according to the findings observed in competitive binding experiments. Moreover, via alterations in synchronous fluorescence, three-dimensional fluorescence and FT-IR spectral properties, it was concluded that atenolol could arouse slight configurational and micro-environmental changes of BSA.     

Interaction of cyproheptadine hydrochloride with human serum albumin using spectroscopy and molecular modeling methods

The interaction between cyproheptadine hydrochloride (CYP) and human serum albumin (HSA) was investigated by fluorescence spectroscopy, UV–vis absorption spectroscopy, Fourier transform infrared spectroscopy (FT‐IR) and molecular modeling at a physiological pH (7.40). Fluorescence of HSA was quenched remarkably by CYP and the quenching mechanism was considered as static quenching since it formed a complex. The association constants K_a and number of binding sites n were calculated at different temperatures. According to Förster's theory of non‐radiation energy transfer, the distance r between donor (human serum albumin) and acceptor (cyproheptadine hydrochloride) was obtained. The effect of common ions on the binding constant was also investigated. The effect of CYP on the conformation of HSA was analyzed using FT‐IR, synchronous fluorescence spectroscopy and 3D fluorescence spectra. The thermodynamic parameters ΔH and ΔS were calculated to be ?14.37 kJ mol^?1 and 38.03 J mol^?1 K^?1, respectively, which suggested that hydrophobic forces played a major role in stabilizing the HSA‐CYP complex. In addition, examination of molecular modeling indicated that CYP could bind to site I of HSA and that hydrophobic interaction was the major acting force, which was in agreement with binding mode studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Exploration of interaction of canthaxanthin with human serum albumin by spectroscopic and molecular simulation methods

The interaction between the food colorant canthaxanthin (CA) and human serum albumin (HSA) in aqueous solution was explored by using fluorescence spectroscopy, three‐dimensional fluorescence spectra, synchronous fluorescence spectra, UV–vis absorbance spectroscopy, circular dichroism (CD) spectra and molecular docking methods. The thermodynamic parameters calculated from fluorescence spectra data showed that CA could result in the HSA fluorescence quenching. From the K_SV change with the temperature dependence, it was concluded that HSA fluorescence quenching triggered by CA is the static quenching and the number of binding sites is one. Furthermore, the secondary structure of HSA was changed with the addition of CA based on the results of synchronous fluorescence, three‐dimensional fluorescence and CD spectra. Hydrogen bonds and van der Waals forces played key roles in the binding process of CA with HSA, which can be obtained from negative standard enthalpy (ΔH) and negative standard entropy (ΔS). Furthermore, the conclusions were certified by molecular docking studies and the binding mode was further analyzed with Discovery Studio. These conclusions can highlight the potential of the interaction mechanism of food additives and HSA.     

2-Amino-5-substituted-1,3,4-oxadiazole as chemosensor for Ni(II) ion detection: antifungal,antioxidant, DNA binding,and molecular docking studies

An oxadiazole derivative 2 was prepared by condensation reaction through cyclization of semicarbazone in the presence of bromine; the structural confirmation was supported by ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy, Fourier transform-infrared spectroscopy, and liquid chromatography-mass spectrometry. Its sensing ability towards Ni²⁺ ion was examined showing a binding constant of 1.04 × 10⁵ compared with other suitable metal cations (Ca²⁺, Co²⁺, Cr³⁺, Ag⁺, Pb²⁺, Fe³⁺, Mg²⁺, and K⁺) using ultraviolet–visible (UV–vis) and fluorescence spectroscopic studies. The minimum concentration of Ni²⁺ ions and limit of detection was found to be 9.4 μM. A job's plot gave the binding stoichiometry ratio of oxadiazole derivative 2 vs Ni²⁺ ions as 2:1. Furthermore, the intercalative binding mode of oxadiazole derivative 2 with calf thymus DNA was supported by ultraviolet–visible (UV–vis) and fluorescent light, viscosity, cyclic voltammetry, time-resolved fluorescence, and circular dichroism measurements. The molecular docking result gave the binding score for oxadiazole derivative 2 as −6.5 kcal/mol, which further confirmed the intercalative interaction. In addition, the antifungal activity of oxadiazole derivative 2 was also screened against several fungal strains (C. albicans, C. glabrata, and C. tropicalis) by broth dilution and disc diffusion methods. In antioxidant studies, the oxadiazole derivative 2 showed potential scavenging activity against 2,2-diphenyl-1-picrylhydrazyl and H₂O₂ free radicals.     

Characterization of the binding of paylean and DNA by fluorescence,UV spectroscopy and molecular docking techniques

The interaction of paylean (PL) with calf thymus DNA (ctDNA) was investigated using fluorescence spectroscopy, UV absorption, melting studies, ionic strength, viscosity experiments and molecular docking under simulated physiological conditions. Values for the binding constant K_a between PL and DNA were 5.11 × 10³, 2.74 × 10³ and 1.74 × 10³ L mol^–1 at 19, 29 and 39°C respectively. DNA quenched the intrinsic fluorescence of PL via a static quenching procedure as shown from Stern–Volmer plots. The relative viscosity and the melting temperature of DNA were basically unchanged in the presence of PL. The fluorescence intensity of PL–DNA decreased with increasing ionic strength. The value of K_a for PL with double‐stranded DNA (dsDNA) was larger than that for PL with single‐stranded DNA (ssDNA). All the results revealed that the binding mode was groove binding, and molecular docking further indicated that PL was preferentially bonded to A–T‐rich regions of DNA. The values for ΔH, ΔS and ΔG suggested that van der Waals forces or hydrogen bonding might be the main acting forces between PL and DNA. The binding distance was determined to be 3.37 nm based on the theory of Förster energy transference, which indicated that a non‐radiation energy transfer process occurred. Copyright © 2015 John Wiley & Sons, Ltd.     

Characterizing the interaction between pyrogallol and human serum albumin by spectroscopic and molecular docking methods

In the present study, the interaction of Pyrogallol (PG) with human serum albumin (HSA) was investigated by UV, fluorescence, Circular dichroism (CD), and molecular docking methods. The results of fluorescence experiments showed that the quenching of intrinsic fluorescence of HSA by PG was due to a static quenching. The calculated binding constants (K) for PG-HSA at different temperatures were in the order of 10⁴?M ^?1, and the corresponding numbers of binding sites, n were approximately equal to unity. The thermodynamic parameters, ΔH and ΔS were calculated to be negative, which indicated that the interaction of PG with HSA was driven mainly by van der Waals forces and hydrogen bonds. The negative value was obtained for ΔG showed that the reaction was spontaneous. In addition, the effect of PG on the secondary structure of HSA was analyzed by performing UV–vis, synchronous fluorescence, and CD experiments. The results indicated that PG induced conformational changes in the structure of HSA. According to Förster no-radiation energy transfer theory, the binding distance of HSA to PG was calculated to be 1.93?nm. The results of molecular docking calculations clarified the binding mode and the binding sites which were in good agreement with the results of experiments.

Communicated by Ramaswamy H. Sarma     

Biophysical and computational comparison on the binding affinity of three important nutrients to β-lactoglobulin: folic acid,ascorbic acid and vitamin K3

Small globular protein, β-lactoglobulin (βLG), which has significant affinity toward many drugs, is the most abundant whey protein in milk. In this study, the interaction of βLG with three important nutrients, ascorbic acid (ASC), folic acid (FOL), and vitamin K3 (VK3) was investigated by spectroscopic methods (UV–visible and fluorescence) along with molecular docking technique. The results of fluorescence measurements showed that studied nutrients strongly quenched βLG fluorescence in static (FOL and ACS) or static–dynamic combined quenching (VK3) mode. The values of binding constants (K_βLG-ASC ~ 4.34 × 10⁴ M^?1, K_βLG-FOL ~ 1.67 × 10⁴ M^?1and K_βLG-VK3 ~ 13.49 × 10⁴ M^?1 at 310 K) suggested that VK3 and FOL had stronger binding affinity toward βLG than ASC. Thermodynamic analysis indicated that hydrophobic interactions are the major forces in the stability of FOL–βLG complex with enthalpy- and entropy-driving mode while, hydrogen bonds and van der Waals interactions play a major role for βLG–ASC and βLG–VK3 associations. The results of 3D fluorescence FT-IR and UV–Visible measurements indicated that the binding of above nutrients to βLG may induce conformational and micro-environmental changes of protein. Also, there is a reciprocal complement between spectroscopic techniques and molecular docking modeling. The docking results indicate that the ASC, FOL, and VK3 bind to residues located in the subdomain B of βLG. Finally, this report suggests that βLG could be used as an effective carrier of above nutrients in functional foods.     

Multispectroscopic exploration and molecular docking analysis on interaction of eriocitrin with bovine serum albumin

Eriocitrin is a flavanone glycoside, which exists in lemon or lime citrus fruits. It possesses antioxidant, anticancer, and anti‐allergy activities. In order to investigate the pharmacokinetics and pharmacological mechanisms of eriocitrin in vivo, the interaction between eriocitrin and bovine serum albumin (BSA) was studied under the simulated physiological conditions by multispectroscopic and molecular docking methods. The results well indicated that eriocitrin and BSA formed a new eriocitrin‐BSA complex because of intermolecular interactions, which was demonstrated by the results of ultraviolet‐visible (UV‐vis) absorption spectra. The intrinsic fluorescence of BSA was quenched by eriocitrin, and static quenching was the quenching mechanism. The number of binding sites (n) and binding constant (K_b) at 310 K were 1.22 and 2.84 × 10⁶ L mol^?1, respectively. The values of thermodynamic parameters revealed that the binding process was spontaneous, and the main forces were the hydrophobic interaction. The binding distance between eriocitrin and BSA was 3.43 nm. In addition, eriocitrin changed the conformation of BSA, which was proved by synchronous fluorescence and circular dichroism (CD) spectra. The results of site marker competitive experiments suggested that eriocitrin was more likely to be inserted into the subdomain IIA (site I), which was further certified by molecular docking studies.     

Assessment of the interaction procedure between Pt(IV) prodrug [Pt(5,5′-dmbpy)Cl4 and human serum albumin: Combination of spectroscopic and molecular modeling technique

In this study, a cytotoxic Pt(IV) complex [Pt(5,5′-dmbpy)Cl₄ (5,5′-dmbpy is 5,5′-dimethyl-2,2′-bipyridine) was selected to investigate its affinity to human serum albumin (HSA) by spectroscopy and molecular docking methods. This complex has a bidentate nitrogen donor ligand with four chloride anions attached to a Pt(IV) metal in a distorted octahedral environment. The ?uorescence data showed this complex quench the intrinsic ?uorescence of HSA through a static quenching mechanism. The binding constant (K_b) and the number of binding sites (n) were obtained based on the results of fluorescence measurements. UV–vis, circular dichroism spectroscopy, and three-dimensional fluorescence spectroscopy proved that the Pt(IV) complex could slightly change the secondary structure of protein. Thermodynamic parameters show that the Pt(IV) complex binds to HSA through electrostatic and Vander Waals interactions with one binding site. The molecular docking results confirmed the spectroscopic results and showed that Pt(IV) complex is embedded into subdomain IIA of protein. The aim of this study is to describe the performance of effective anti-cancer drugs when faced with proteins such as HSA.     

The interaction of beta-lactoglobulin with ciprofloxacin and kanamycin; a spectroscopic and molecular modeling approach

A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibiotics. Spectroscopic techniques (Fluorescence, UV–vis, Circular Dichroism) combined with molecular docking were used to determine the binding mechanism of these drugs. Fluorescence studies showed moderate binding affinity with the calculated binding constants K_Cip = 60.1 (±0.2)?×?10³ M^?1 and K_kana = 2.5 (±0.6)?×?10³ M^?1 with the order of Cip > Kana. Results of UV–vis were consistent with fluorescence measurements and demonstrated a stronger complexation for Cip rather than Kana. The secondary structure of β-LG was preserved upon interaction with Kana; however, a reduction in β-sheet content from 39.1 to 31.9% was convoyed with an increase in α-helix from 12.8 to 20.5% due to complexation of Cip. Molecular docking studies demonstrated that preferred binding sites of these drugs are not the same and several amino acids are involved in stabilizing the interaction. Based on the achieved results, Kana and Cip can spontaneously bind to β-LG and this protein may serve as their transport vehicle.     

Spectroscopic analysis on the interaction of ferulic acid and tetramethylpyrazine with trypsin

The interaction of trypsin with tetramethylpyrazine (TMP) and ferulic acid (FA) was studied using fluorescence, synchronous fluorescence, UV–vis absorption, circular dichroism (CD) and three‐dimensional (3D) fluorescence spectra techniques. Using fluorescence quenching calculations, the bimolecular quenching constant (k_q), apparent quenching constant (K_SV), effective binding constant (K_a) and binding site number (n) were obtained. The distance r between donor and acceptor was found to be 2.049 and 1.281 nm for TMP–trypsin and FA–trypsin complexes. TMP and FA can quench the fluorescence intensity of trypsin by a static quenching procedure. Thermodynamic parameters calculated on the basis of different temperatures revealed that the binding of trypsin to TMP/FA mainly depended on van der Waals' forces and hydrogen bonds. The effect of TMP and FA on the conformation of trypsin was analyzed using synchronous fluorescence, CD, 3D fluorescence spectra and molecular docking studies. Copyright © 2013 John Wiley & Sons, Ltd.     

Insight into the interaction of benzothiazole tethered triazole analogues with human serum albumin: Spectroscopy and molecular docking approaches

The interaction of four benzothiazole tethered triazole analogues (MS43, MS70, MS71, and MS78) with human serum albumin (HSA) was investigated using various spectroscopic techniques (ultraviolet–visible (UV–vis) light absorption, fluorescence, circular dichroism (CD), molecular docking and density functional theory (DFT) studies). Fluorescence quenching constants (~10¹²) revealed a static mode of quenching and binding constants (K_b ~10⁴) indicating the strong affinity of these analogues for HSA. Further alteration in the secondary structure of HSA in the presence of these analogues was also confirmed by far UV–CD spectroscopy. The intensity loss in CD studied at 222 nm indicated an increase in random coil/β‐sheet conformations in the protein. Binding energy values (MS71 (?9.3 kcal mol^?1), MS78 (?8.02 kcal mol^?1), MS70 (?7.16 kcal mol^?1) and MS43 (?6.81 kcal mol^?1)) obtained from molecular docking revealed binding of these analogues with HSA. Molecular docking and DFT studies validated the experimental results, as these four analogues bind with HSA at site II through hydrogen bonding and hydrophobic interactions.     

Binding of caffeine with caffeic acid and chlorogenic acid using fluorescence quenching,UV/vis and FTIR spectroscopic techniques

The interactions of caffeine (CF) with chlorogenic acid (CGA) and caffeic acid (CFA) were investigated by fluorescence quenching, UV/vis and Fourier transform infrared (FTIR) spectroscopic techniques. The results of the study indicated that the fluorescence quenching between caffeine and hydroxycinnamic acids could be rationalized in terms of static quenching or the formation of non‐fluorescent CF–CFA and CF–CGA complexes. From fluorescence quenching spectral analysis, the quenching constant (K_SV), quenching rate constant (k_q), number of binding sites (n), thermodynamic properties and conformational changes of the interaction were determined. The quenching constants (K_SV) between CF and CGA, CFA are 1.84 × 10⁴ and 1.04 × 10⁴ L/mol at 298 K and their binding site n is ~ 1. Thermodynamic parameters determined using the Van't Hoff equation indicated that hydrogen bonds and van der Waal's forces have a major role in the reaction of caffeine with caffeic acid and chlorogenic acid. The 3D fluorescence, UV/vis and FTIR spectra also showed that the binding of CF with CFA and CGA induces conformational changes in CFA and CGA. Copyright © 2015 John Wiley & Sons, Ltd.     

Interaction of human serum albumin with novel imidazole derivatives studied by spectroscopy and molecular docking

This study was a detailed characterization of the interaction of a series of imidazole derivatives with a model transport protein, human serum albumin (HSA). Fluorescence and time‐resolved fluorescence results showed the existence of a static quenching mode for the HSA–imidazole derivative interaction. The binding constant at 296 K was in the order of 10⁴ M^–1, showing high affinity between the imidazole derivatives and HSA. A site marker competition study combined with molecular docking revealed that the imidazole derivatives bound to subdomain IIA of HSA (Sudlow's site I). Furthermore, the results of synchronous, 3D, Fourier transform infrared, circular dichroism and UV–vis spectroscopy demonstrated that the secondary structure of HSA was altered in the presence of the imidazole derivatives. The specific binding distance, r, between the donor and acceptor was obtained according to fluorescence resonance energy transfer. Copyright © 2015 John Wiley & Sons, Ltd.     

Multi-spectroscopic,thermodynamic and molecular docking studies to investigate the interaction of eplerenone with human serum albumin

The binding of small molecular drugs with human serum albumin (HSA) has a crucial influence on their pharmacokinetics. The binding interaction between the antihypertensive eplerenone (EPL) and HSA was investigated using multi-spectroscopic techniques for the first time. These techniques include ultraviolet-visible (UV-vis) spectroscopy, Fourier-transform infrared (FTIR), native fluorescence spectroscopy, synchronous fluorescence spectroscopy and molecular docking approach. The fluorescence spectroscopic study showed that EPL quenched HSA inherent fluorescence. The mechanism for quenching of HSA by EPL has been determined to be static in nature and confirmed by UV absorption and fluorescence spectroscopy. The modified Stern–Volmer equation was used to estimate the binding constant (K_b) as well as the number of bindings (n). The results indicated that the binding occurs at a single site (K_b = 2.238 × 10³ L mol⁻¹at 298 K). The enthalpy and entropy changes (∆H and ∆S) were 58.061 and 0.258 K J mol⁻¹, respectively, illustrating that the principal intermolecular interactions stabilizing the EPL–HSA system are hydrophobic forces. Synchronous fluorescence spectroscopy revealed that EPL binding to HSA occurred around the tyrosine (Tyr) residue and this agreed with the molecular docking study. The Förster resonance energy transfer (FRET) analysis confirmed the static quenching mechanism. The esterase enzyme activity of HSA was also evaluated showing its decrease in the presence of EPL. Furthermore, docking analysis and site-specific markers experiment revealed that EPL binds with HSA at subdomain IB (site III).     

Cobalt (II) complex with novel unsymmetrical tetradentate Schiff base (ON) ligand: in vitro cytotoxicity studies of complex,interaction with DNA/protein,molecular docking studies,and antibacterial activity

[C₂₀H₁₇N₃O₂] and cobalt (II) complex [Co(L²)(MeOH)₂].ClO₄, (L² = 4-((E)-1-((2-(((E)-pyridin-2-ylmethylene) amino) phenyl) imino) ethyl) benzene-1, 3-diol) novel Schiff base has been synthesiszed and chracterized by Fourier transform infrared, UV–vis, ¹H-NMR spectroscopy, and elemental analysis techniques. The interaction of Co(II) complex with DNA and BSA was investigated by electronic absorption spectroscopy, fluorescence spectroscopy, circular dichroism, and thermal denaturation studies. Our experiments indicate that this complex could strongly bind to CT-DNA via minor groove mechanism. In addition, fluorescence spectrometry of BSA with the complex showed that the fluorescence quenching mechanism of BSA was of static type. The complex exhibited significant in vitro cytotoxicity against three human cancer cell lines (JURKAT, SKOV3, and U87). The molecular docking experiment effectively proved the binding of complex to DNA and BSA. Finally, antibacterial assay over gram-positive and gram-negative pathogenic bacterial strains was studied.