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.     

Fluorescence spectroscopic studies on the interaction of Gemini surfactant 14‐6‐14 with bovine serum albumin

The interaction of the cationic Gemini surfactant hexamethylene‐1,3‐bis (tetradecyldimethylammonium bromide) (14‐6‐14) with bovine serum albumin (BSA) has been investigated by fluorescence quenching spectra and three‐dimensional (3D) fluorescence spectra. The Stern–Volmer quenching constants K_SV and the corresponding thermodynamic parameters ΔH, ΔG and ΔS have been estimated by the fluorescence quenching method. The results indicated that hydrophobic forces were the predominant intermolecular forces between BSA and the surfactant. Competitive experiments and the number of binding sites calculation show that 14‐6‐14 can be inserted in site‐II (in subdomain IIIA) of BSA. The effect of 14‐6‐14 on the conformation of BSA was evaluated by synchronous fluorescence spectroscopy and 3D fluorescence spectral methods. The results show that the conformation of BSA was changed dramatically in the presence of 14‐6‐14, by binding to the Trp and Try residues of BSA. The investigation provides interaction between BSA and 14‐6‐14 as a model for molecular design and industrial research. Copyright © 2011 John Wiley & Sons, Ltd.     

Using resonance light scattering and UV/vis absorption spectroscopy to study the interaction between gliclazide and bovine serum albumin

At different temperatures (298, 310 and 318 K), the interaction between gliclazide and bovine serum albumin (BSA) was investigated using fluorescence quenching spectroscopy, resonance light scattering spectroscopy and UV/vis absorption spectroscopy. The first method studied changes in the fluorescence of BSA on addition of gliclazide, and the latter two methods studied the spectral change in gliclazide while BSA was being added. The results indicated that the quenching mechanism between BSA and gliclazide was static. The binding constant (K_a), number of binding sites (n), thermodynamic parameters, binding forces and Hill's coefficient were calculated at three temperatures. Values for the binding constant obtained using resonance light scattering and UV/vis absorption spectroscopy were much greater than those obtained from fluorescence quenching spectroscopy, indicating that methods monitoring gliclazide were more accurate and reasonable. In addition, the results suggest that other residues are involved in the reaction and the mode ‘point to surface’ existed in the interaction between BSA and gliclazide. Copyright © 2015 John Wiley & Sons, Ltd.     

Study on the interaction between anti‐tuberculosis drug ethambutol and bovine serum albumin: multispectroscopic and cyclic voltammetric approaches

The binding of bovine serum albumin (BSA) to ethambutol (EMB) was investigated using spectroscopic methods, viz., fluorescence, Fourier transform infrared (FTIR), ultraviolet (UV)/vis absorption and cyclic voltammetry techniques. Spectroscopic analysis of the emission quenching at different temperatures revealed that the quenching mechanism of serum albumin by EMB is static, which was also confirmed by lifetime measurements. The number of binding sites, n, and binding constant, K, were obtained at various temperatures. The distance, r, between EMB and the protein was evaluated according to the Förster energy transfer theory. Based on displacement experiments using site probes, viz., warfarin, ibuprofen and digitoxin, the site of binding of EMB in BSA was proposed to be Sudlow's site I. The effect of EMB on the conformation of BSA was analyzed by using synchronous fluorescence spectra (SFS) and 3D fluorescence spectra. The results of fluorescence, UV/vis absorption and FTIR spectra showed that the conformation of BSA was changed in the presence of EMB. The thermodynamic parameters including enthalpy change (ΔH⁰), entropy change (ΔS⁰) and free energy change (ΔG⁰) for BSA–EMB were calculated according to the van't Hoff equation and are discussed.     

Intermolecular interaction of fosinopril with bovine serum albumin (BSA): The multi‐spectroscopic and computational investigation

The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi‐spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, K_b, value was found to lie between 2.69 × 10³ and 9.55 × 10³ M^?1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub‐domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH⁰) and entropy change (ΔS⁰) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril‐BSA interaction, and 8‐anilino‐1‐naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic interactions. Moreover, spectroscopic results (synchronous fluorescence, 3‐dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril interaction.     

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.     

The interaction between cepharanthine and two serum albumins: multiple spectroscopic and chemometric investigations

The binding modes of cepharanthine (CEPT) with bovine serum albumin (BSA) and human serum albumin (HSA) have been established by reproducing physiological conditions, which is very important to understand the pharmacokinetics and toxicity of CEPT. These spectral data were further analyzed by the multivariate curve resolution‐alternating least squares method. Moreover, the concentration profiles and pure spectra of three species (BSA/HSA, CEPT and CEPT–BSA/HSA) and the apparent equilibrium constants K_app were evaluated. The experimental results showed that CEPT could quench the fluorescence intensity of BSA/HSA by a combined quenching (static and dynamic) procedure. The binding constant (K), the thermodynamic parameters (ΔG, ΔH and ΔS) and binding subdomain were measured, and indicated that CEPT could spontaneously bind to BSA/HSA on subdomain IIA through the hydrophobic interactions. The effect of CEPT on the secondary structure of proteins has been analyzed by circular dichroism, 3D fluorescence and Fourier transform infrared spectra. The binding distance between CEPT and tryptophan of BSA/HSA was 2.305/1.749 nm, which is based on the Förster resonance energy transfer theory. Copyright © 2013 John Wiley & Sons, Ltd.     

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.     

The effects of experimental conditions of fluorescence quenching on the binding parameters of apigenin to bovine serum albumin by response surface methods

A fluorescence quenching technique is often used to study interactions between small molecules and serum albumin. However, the results are quite different by using spectroscopic techniques on the same drug‐protein interaction research and they may be affected by different conditions (e.g. working solution of pH and ionic strength). In this research, using apigenin as an example, the effect of experimental conditions of fluorescence quenching on the binding parameters of drug to bovine serum albumin was investigated using a response surface method (RSM). The effect of pH, the concentration of NaCl and the concentration Mg²⁺ on the quenching constant (K_SV), the apparent association constant (K_a) and the number of binding sites (n) was studied by single‐factor experiments with pH, [NaCl] and [Mg²⁺] as independent variables and K_SV, K_a and n as response values. Prediction models were fit to a quadratic polynomial regression equation and the results showed that both K_SV and n displayed a second‐order model, whereas Ka displayed linear relation dependence on pH, [NaCl] and [Mg²⁺]. Under these experimental conditions, [NaCl] was the most significant (p < 0.05) impact factor on K_SV and K_a, whereas n was most affected by pH (p < 0.05). Copyright © 2013 John Wiley & Sons, Ltd.     

A study on the interaction between 3‐spiro‐piperidones and bovine serum albumin using spectroscopic approaches

The interaction between 3‐spiro‐2′‐pyrrolidine‐3′‐spiro‐3″‐piperidine‐2,3″‐dione (PPD) and bovine serum albumin (BSA) in aqueous solution was studied using fluorescence and UV–vis spectroscopy. Fluorescence emission data revealed that BSA (1.00 × 10^‐5 mol/L) fluorescence was statically quenched by PPD at various concentrations, which implies that a PPD–BSA complex was formed. The binding constant (K_A), the number of binding sites (n) and the specific binding site of the PPD with BSA were determined. Energy‐transfer efficiency parameters were determined and the mechanism of the interaction discussed. The thermodynamic parameters, ΔG, ΔH and ΔS, were obtained according to van't Hoff's equation, showing the involvement of hydrophobic forces in these interactions. The effect of PPD acting on the BSA conformation was detected by synchronous fluorescence. Copyright © 2012 John Wiley & Sons, Ltd.     

Combining time‐resolved fluorescence with synchronous fluorescence spectroscopy to study bovine serum albumin‐curcumin complex during unfolding and refolding processes

We investigated the complex interaction between bovine serum albumin (BSA) and curcumin by combining time‐resolved fluorescence and synchronous fluorescence spectroscopy. The interaction was significant and sensitive to fluorescence lifetime and synchronous fluorescence characteristics. Binding of curcumin significantly shortened the fluorescence lifetime of BSA with a bi‐molecular quenching rate constant of k_q = 3.17 × 10¹² M^‐1s^‐1. Denaturation by urea unfolded the protein molecule by quenching the fluorescence lifetime of BSA. The tyrosine synchronous fluorescence spectra were blue shifted whereas the position of tryptophan synchronous fluorescence spectra was red shifted during the unfolding process. However, denaturation of urea had little effect on the synchronous fluorescence peak of tyrosine in curcumin‐BSA complex except in the low concentration range; however, it shifted the peak to the red, indicating that curcumin shifted tryptophan moiety to a more polar environment in the unfolded state. Decreases in the time‐resolved fluorescence lifetime and curcumin‐BSA complex during unfolding were recovered during refolding of BSA by a dilution process, suggesting partial reversibility of the unfolding process for both BSA and curcumin‐BSA complex. Copyright © 2012 John Wiley & Sons, Ltd.     

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.     

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.     

Fluorescent bovine serum albumin interacting with the antitussive quencher dextromethorphan: a spectroscopic insight

The interaction of dextromethorphan hydrobromide (DXM) with bovine serum albumin (BSA) is studied by using fluorescence spectra, UV–vis absorption, synchronous fluorescence spectra (SFS), 3D fluorescence spectra, Fourier transform infrared (FTIR) spectroscopy and circular dichroism under simulated physiological conditions. DXM effectively quenched the intrinsic fluorescence of BSA. Values of the binding constant, K_A, are 7.159 × 10³, 9.398 × 10³ and 16.101 × 10³ L/mol; the number of binding sites, n, and the corresponding thermodynamic parameters ΔG°, ΔH° and ΔS° between DXM and BSA were calculated at different temperatures. The interaction between DXM and BSA occurs through dynamic quenching and the effect of DXM on the conformation of BSA was analyzed using SFS. The average binding distance, r, between the donor (BSA) and acceptor (DXM) was determined based on Förster's theory. The results of fluorescence spectra, UV–vis absorption spectra and SFS show that the secondary structure of the protein has been changed in the presence of DXM. Copyright © 2015 John Wiley & Sons, Ltd.     

Spectroscopic exploration and thermodynamic characterization of desvenlafaxine interacting with fluorescent bovine serum albumin

The mechanism of the interaction between bovine serum albumin (BSA) and desvenlafaxine was studied using fluorescence, ultraviolet absorption, 3‐dimensional fluorescence spectroscopy, circular dichroism, synchronous fluorescence spectroscopy, cyclic voltametry, differential scanning calorimetry, and attenuated total reflection–Fourier transform infrared spectroscopic techniques under physiological condition at pH 7.4. Stern‐Volmer calculations authenticate the fluorescence of BSA that was quenched by desvenlafaxine in a collision quenching mode. The fluorescence quenching method was used to evaluate number of binding sites “n” and binding constant K _A that were measured, and various thermodynamic parameters were evaluated at different temperatures by using the van't Hoff equation and differential scanning calorimetry technique, which indicated a spontaneous and hydrophobic interaction between BSA and desvenlafaxine. According to the Förster theory we calculate the distance between the donor, BSA and acceptor, desvenlafaxine molecules. Furthermore, circular dichroism and attenuated total reflection–Fourier transform infrared spectroscopy indicate nominal changes in the secondary structure of the protein.     

Study on the interactions of mapenterol with serum albumins using multi‐spectroscopy and molecular docking

The interactions of mapenterol with bovine serum albumin (BSA) and human serum albumin (HSA) have been investigated systematically using fluorescence spectroscopy, absorption spectroscopy, circular dichroism (CD) and molecular docking techniques. Mapenterol has a strong ability to quench the intrinsic fluorescence of BSA and HSA through static quenching procedures. At 291 K, the binding constants, K_a, were 1.93 × 10³ and 2.73 × 10³ L/mol for mapenterol–BSA and mapenterol–HAS, respectively. Electrostatic forces and hydrophobic interactions played important roles in stabilizing the mapenterol–BSA/has complex. Using site marker competitive studies, mapenterol was found to bind at Sudlow site I on BSA/HSA. There was little effect of K⁺, Ca²⁺, Cu²⁺, Zn²⁺ and Fe³⁺ on the binding. The conformation of BSA/HSA was changed by mapenterol, as seen from the synchronous fluorescence spectra. The CD spectra showed that the binding of mapenterol to BSA/HSA changed the secondary structure of BSA/HSA. Molecular docking further confirmed that mapenterol could bind to Sudlow site I of BSA/HSA. According to Förster non‐radiative energy transfer theory (FRET), the distances r₀ between the donor and acceptor were calculated as 3.18 and 2.75 nm for mapenterol–BSA and mapenterol–HAS, respectively. Copyright © 2015 John Wiley & Sons, Ltd.     

Study on the interaction of chromate with bovine serum albumin by spectroscopic method

The interaction between two chromates [sodium chromate (Na₂CrO₄) and potassium chromate K₂CrO₄)] and bovine serum albumin (BSA) in physiological buffer (pH 7.4) was investigated by the fluorescence quenching technique. The results of fluorescence titration revealed that two chromates could strongly quench the intrinsic fluorescence of BSA through a static quenching procedure. The apparent binding constants K and number of binding sites n of chromate with BSA were obtained by the fluorescence quenching method. The thermodynamic parameters enthalpy change (ΔH), entropy change (ΔS) were negative, indicating that the interaction of two chromates with BSA was driven mainly by van der Waals forces and hydrogen bonds. The process of binding was a spontaneous process in which Gibbs free energy change was negative. The distance r between donor (BSA) and acceptor (chromate) was calculated based on Forster’s non-radiative energy transfer theory. The results of UV–Vis absorption, synchronous fluorescence, three-dimensional fluorescence and circular dichroism (CD) spectra showed that two chromates induced conformational changes of BSA.     

A biophysical and computational study unraveling the molecular interaction mechanism of a new Janus kinase inhibitor Tofacitinib with bovine serum albumin

The interaction of a recently certified kinase inhibitor Tofacitinib (TFB) with bovine serum albumin (BSA) has been studied, by spectroscopic and molecular docking studies. Spectrofluorimetric measurements at 3 different temperatures (288, 298, and 310 K) showed that TFB quench the intrinsic fluorescence of BSA upon forming a nonfluorescent complex. The intrinsic fluorescence data showed that TFB binds to BSA with binding constant (K _b) of approximately 10⁴M⁻¹, affirming a significant affinity of TFB with BSA. The decrease in Stern‐Volmer quenching constant with increasing temperature exhibited the static mechanism of quenching. Negative value of ΔG (−6.94 ± 0.32 kcal·mol⁻¹), ΔH (−7.87 ± 0.52 kcal·mol⁻¹), and ΔS (−3.14 ± 0.42 cal·mol⁻¹·K⁻¹) at all 3 temperatures declared the reaction between BSA and TFB to be spontaneous and exothermic. Far‐UV circular dichroism spectroscopy results demonstrated an increase in helical content of BSA in the presence of TFB. Moreover, dynamic light scattering measurements showed that TFB resulted into a decrease in the hydrodynamic radii (from 3.6 ± 0.053 to 2.9 ± 0.02 nm) of BSA. Molecular docking studies confirmed that TFB binds near site II on BSA, hydrogen bonding, and hydrophobic interaction were involved in the BSA‐TFB complex formation. The present study characterizing the BSA‐TFB interaction could be significant towards gaining an insight into the drug pharmacokinetics and pharmacodynamics and also in the direction of rational drug designing with better competence, against emerging immune‐mediated diseases, ie, alopecia and rheumatoid arthritis.     

Different spectroscopic and molecular modeling studies on the interaction between cyanidin‐3‐O‐glucoside and bovine serum albumin

Anthocyanin is one of the flavonoid phytopigments that shows strong antioxidant activity. The cyanidin‐3‐O‐glucoside (C3G) is one of the principal types of anthocyanins. To understand the interaction between C3G and bovine serum albumin (BSA), fluorescence spectroscopy, ultraviolet–visible absorption, Fourier transform infrared spectroscopy, circular dichroism and molecular modeling techniques were used. Binding constant (K_a) and the number of binding sites (n) were calculated. The quenching mechanism of fluorescence of BSA by C3G was discussed. The results studied by Fourier transform infrared spectroscopy and circular dichroism experiments indicate that the secondary structures of the protein have been changed by the interaction of C3G with BSA. The result of molecular modeling confirmed that the C3G bound to the site I (sub‐domain IIA) of BSA, and that the hydroxyl groups in the B ring of C3G took part in the binding with BSA. Copyright © 2013 John Wiley & Sons, Ltd.     

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

The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV–Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized in terms of the static quenching mechanism. According to fluorescence quenching calculations, the bimolecular quenching constant (k_q), dynamic quenching (K_SV) and static quenching (K_LB) at 310 K were obtained. The efficiency of energy transfer and the distance between the donor (BSA) and the acceptor (VB6) were calculated by Foster’s non-radiative energy transfer theory and were equal to 41.1% and 2.11 nm.The collected UV–Vis and fluorescence spectra were combined into a row-and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS helped to estimate the stoichiometry of interactions, concentration profiles and pure spectra for three species (BSA, VB6 and VB6-BSA complex) existed in the interaction procedure. Based on the MCR-ALS results, using mass balance equations, a model was developed and binding constant of complex was calculated using non-linear least squares curve fitting. FT-IR spectra showed that the conformation of proteins was altered in presence of VB6. Finally, the combined docking and molecular dynamics (MD) simulations were used to estimate the binding affinity of VB6 to BSA. Five-nanosecond MD simulations were performed on bovine serum albumin (BSA) to study the conformational features of its ligand binding site. From MD results, eleven BSA snapshots were extracted, at every 0.5 ns, to explore the binding affinity (GOLD score) of VB6 using a docking procedure. MD simulations indicated that there is a considerable flexibility in the structure of protein that affected ligand recognition. Structural analyses and docking simulations indicated that VB6 binds to site I and GOLD score values depend on the conformations of both BSA and ligand. Molecular modeling results showed that VB6–BSA complex formed not only on the basis of electrostatic forces, but also on the basis of π–π staking and hydrogen bond. There was an excellent agreement between the experimental and computational results. The results presented in this paper, will offer a reference for detailed and systematic studies on the biological effects and action mechanism of small molecules with proteins.