Study on the interaction of paeoniflorin with human serum albumin (HSA) by spectroscopic and molecular docking techniques
© The Author(s) 2017
Received: 25 May 2017
Accepted: 10 November 2017
Published: 17 November 2017
The interaction of paeoniflorin with human serum albumin (HSA) was investigated using fluorescence, UV–vis absorption, circular dichroism (CD) spectra and molecular docking techniques under simulative physiological conditions. The results clarified that the fluorescence quenching of HSA by paeoniflorin was a static quenching process and energy transfer as a result of a newly formed complex (1:1). Paeoniflorin spontaneously bound to HSA in site I (subdomain IIA), which was primarily driven by hydrophobic forces and hydrogen bonds (ΔH° = − 9.98 kJ mol−1, ΔS° = 28.18 J mol−1 K−1). The binding constant was calculated to be 1.909 × 103 L mol−1 at 288 K and it decreased with the increase of the temperature. The binding distance was estimated to be 1.74 nm at 288 K, showing the occurrence of fluorescence energy transfer. The results of CD and three-dimensional fluorescence spectra showed that paeoniflorin induced the conformational changes of HSA. Meanwhile, the study of molecular docking also indicated that paeoniflorin could bind to the site I of HSA mainly by hydrophobic and hydrogen bond interactions.
Protein is an important chemical substance in our life and one of the main targets of all medicines in organism. Human serum albumin (HSA) is the most studied serum albumin because its primary structure is well known and it can interact with many endogenous and exogenous substances . It is a single-chain, non-glycosylated globular protein consisting of 585 amino acid residues, and 17 disulfide bridges assist in maintaining its familiar heart-like shape . Crystallographic data show that HSA contains three homologous a-helical domains (I, II, and III): I (residues 1–195), II (196–383), and III (384–585), each of which includes 10 helices that are divided into six-helix and four-helix subdomains (A and B) . The principal regions of ligand binding sites in HSA are located in hydrophobic cavities in subdomains IIA and IIIA, called site I and site II, respectively . These multiple binding sites underline the exceptional ability of HSA to act as a major depot and transport protein which is capable of binding, transporting and delivering an extraordinarily diverse range of endogenous and exogenous compounds in the bloodstream to their target organs . The binding affinity between serum albumin and many bioactive compounds is closely linked with the distribution and metabolism of these active ingredients [12–14]. Therefore, investigation of the binding of drug to HSA is of great importance to understand its effect on protein function during the blood transportation process and its biological activity in vivo.
HSA and BSA, two of the most extensively studied serum albumins, are homologous proteins. However, there are still some differences between them . HSA contains a single tryptophan (Trp-214) , while BSA has two tryptophan residues that possess intrinsic fluorescence: Trp-212 is located within a hydrophobic binding pocket of the protein and Trp-134 is located on the surface of the molecule . Therefore, the experimental results of the interaction between drugs and BSA cannot be completely identical with those of HSA. Although some spectroscopic studies on the interaction between paeoniflorin and bovine serum albumin (BSA) have been published [17–20], to our knowledge, a series of accurate and full basic data for clarifying the binding mechanisms of paeoniflorin to HSA remain unclear. Consequently, the binding characteristics of paeoniflorin with HSA including the quenching mechanism, quenching and binding constants were investigated in this study, by using fluorescence quenching method through the thermodynamic analysis. In addition, the conformational changes of HSA induced by paeoniflorin were also investigated by means of circular dichroism (CD) and three-dimensional fluorescence measurements. Finally, paeoniflorin molecule has been docked into the 3D structure of HSA in order to envisage a connection between the experimental and theoretical results. By comparing our results with those of previous studies, we can investigate the similarities and differences between paeoniflorin and two kinds of serum albumin.
Commercially prepared human serum albumin (HSA, purity > 99.0%) was purchased from Sigma-Aldrich Co. (USA), and stored in refrigerator at 4.0 °C. Paeoniflorin, ibuprofen and warfarin were purchased from the National Institute for the Control of Pharmaceutical and Products (China). Samples were weighed accurately on a microbalance (Sartorius BP211D, Germany) with a resolution of 0.01 mg. The stock solutions of paeoniflorin, warfarin and ibuprofen (each 1.25 × 10−3 mol L−1) were prepared with 0.05 mol L−1 Tris–HCl buffer containing NaCl (0.05 mol L−1, pH 7.4). The HSA stock solution was dissolved and diluted to 1.0 × 10−5 mol L−1 with the same buffer, then was stored in the dark at 4 °C before fluorescence and UV–vis absorption essay. In the analysis of CD spectra, HSA stock solution (1.0 × 10−6 mol L−1) was prepared with phosphate buffer (0.05 mol L−1, pH 7.4). All other reagents were all of analytical reagent grade and were used as purchased without further purification. Double distilled water was used for all solution preparation.
UV–vis absorption spectra
The UV–vis absorption spectra were recorded on a UV-2550 spectrophotometer (Shimadzu Co., Japan) over a wavelength range of 200–700 nm in a pH 7.4 Tris–HCl buffer at 298 K. Spectra of free paeoniflorin and paeoniflorin with 2.5 mL HSA solution were both measured. The concentrations of paeoniflorin varied from 0 to 5.0 × 10−5 mol L−1 at 1.0 × 10−5 mol L−1 intervals.
Binding competitive experiment
Two classical site probes, warfarin and ibuprofen, were selected as the markers of site I and site II separately. The concentrations of HSA and paeoniflorin were both fixed at 1.0 × 10−5 mol L−1, while the concentrations of the probes varied from 0 to 2.5 × 10−5 mol L−1 at 5.0 × 10−6 mol L−1 intervals. The experiment was carried out at room temperature. The wavelength range and the excitation wavelength remained unchanged .
Circular dichroism (CD) spectra
The CD spectra were measured on a J-810 automatic recording spectropolarimeter (Jasco Co., Japan) in the spectral range 200–240 nm under constant nitrogen flush. The solutions of HSA (1.0 × 10−6 mol L−1) and paeoniflorin (2.5 × 10−5 mol L−1) were both prepared with phosphate buffer.
The molecular docking studies were performed to explore the interaction between paeoniflorin and HSA by using AutoDock program version 220.127.116.11 and AutoDockTools version 1.5.6, which is the graphical user interface of AutoDock supplied by MGL Tools . The 3D structure of ligand (paeoniflorin) was constructed by ChemDraw. The default root, rotatable bonds and torsions of the ligand were set by AutoDockTools. The crystal structure of the Human Serum Albumin (PDB ID: 1AO6) was downloaded from the protein data bank (http://www.rcsb.org/pdb). All bound waters were removed from the protein using Pymol version 18.104.22.168. Polar hydrogen atoms were added, and AutoDock 4 atom types and Geisteger charges were assigned to the receptor protein using AutoDockTools. The docking site for the ligands on HSA was defined at the active site with grid box size of 60 × 60 × 60, spacing of 0.375 Å, and grid centre of 33.175, 30.604, and 34.136. The AutoGrid4 utility in AutoDock program was used to calculate the electrostatic map and atomic interaction maps for all atom types of the ligand molecule. The Lamarckian Genetic Algorithm (LGA) was selected with the population size of 150 individuals and with a maximum number of generations and energy evaluations of 27,000 and 2.5 million, respectively. During the docking procedure, the ligand was treated as flexible molecule and the receptor was kept rigid. Finally, 100 possible binding conformations were generated by AutoDock run. The best confirmation with least binding energy was visualized and analyzed by using PyMOl version 22.214.171.124 and Ligplot+ version 1.4.5 .
Results and discussion
Binding interaction of paeoniflorin with HSA
F0 and F represent the fluorescence intensities of paeoniflorin in the absence and presence of the quencher, respectively. [Q] denotes the concentration of the quencher. KSV, Kq, τ0 are the Stern–Volmer dynamic quenching constant, the quenching rate constant of the biomolecule (Kq = KSV/τ0), and the average lifetime of the fluorophore in the absence of quencher (τ0 = 6.0×10−9 s) , orderly.
Quenching constants (KSV and Kq), stability constants (Ka), correlation coefficients (R) and binding site numbers (n) and thermodynamic parameters calculated according to Stern–Volmer plots and double logarithm plots of HSA + paeoniflorin system at three temperatures
HSA + paeoniflorin (K)
KSV (L mol−1)
Kq (L mol−1 s−1)
KA (L mol−1)
∆G0 (kJ mol−1)
∆H0 (kJ mol−1)
∆S0 (J mol−1 K−1)
0.569 × 104
0.9483 × 1012
1.909 × 103
0.545 × 104
0.9083 × 1012
1.680 × 103
0.521 × 104
0.8683 × 1012
1.421 × 103
Binding constants and the number of binding sites
A linear plot based on lg [(F0 − F)/F] versus lg [Q] is expected, and n and Ka can be estimated from the slope and intercept.
Thermodynamics of the HSA–paeoniflorin interactions
ΔH° and ΔS° are the enthalpy change and the entropy change, respectively, both of which can be evaluated from the slope and intercept of the linear plot of ln Ka against 1/T. Ka is the binding constant at different temperature. R and T represent the gas constant and temperature, respectively.
The energy transfer of paeoniflorin with HSA
Energy transfer efficiency (E), critical binding distance (R), overlap integral (J) and binding distance (r) calculated according to Föster’s non-radioactive energy transfer theory
J (cm3 L mol−1)
HSA + paeoniflorin
0.729 × 10−16
F and F0 indicate the fluorescence intensities of HSA in the presence and absence of paeoniflorin, respectively. R and r denote the critical binding distance and binding distance between HSA and drug.
According to calculation, the values of E, R, J, r were 5.37%, 1.08 nm, 0.729 × 10−16 cm3 L mol−1 and 1.74 nm, respectively. The result of binding distance (r) below 8 nm and the fulfillment of the required condition 0.5 R < r < 2 R suggested that a high probability of the energy transfer occurred between paeoniflorin and HSA , which was reported for the first time.
In general, the conformation of HSA will change when it is bound to small molecules. In this part, three-dimensional fluorescence spectra, CD spectra and molecular modeling were introduced to investigate it.
Three-dimensional (3D) fluorescence spectra
Three-dimensional fluorescence spectral characteristic parameters of free HSA system, HSA + paeoniflorin systems
HSA + paeoniflorin
wherein MRE (mean residue ellipticity) is ellipse rate of the average residues; Cp is the mole fraction of protein; n is the number of amino acid residues; l is the light path of sample cell. According to the calculation result, the percentage of α-helix of HSA declined slightly from 54.2 to 53.4%, indicating that paeoniflorin induced a slight change of helical structure content of HSA [52, 53].
The thermodynamics study illustrated that the main forces among the HSA–paeoniflorin complex were hydrophobic forces and hydrogen bonding which were not completely identical with Han-Yan Wen’s work . Meanwhile, molecular docking was used to verify the theoretical calculations in this experiment.
In this paper, the interaction of paeoniflorin with HSA was investigated by fluorescence, UV–vis, CD and molecular docking techniques under simulated physiological conditions. In addition, our results compared with previous work were also discussed. The results demonstrated that the fluorescence of HSA would be quenched with the addition of paeoniflorin. This change was via static quenching and energy transfer. According to Stern–Volmer equation, the binding constant was calculated (1.909 × 103 L mol−1, 288 K). Besides, the study of thermodynamics parameters with negative value of ∆H°, ∆G°, and positive value of ∆S° indicated that the process was spontaneous and was mainly driven by hydrophobic interactions and hydrogen bonds. In accordance with the Förster’s non-radioactive energy transfer theory, the binding distance between paeoniflorin and HSA was evaluated as 1.74 nm. The results of the current study suggest that paeoniflorin can bind to HSA and form 1:1 complex. Analysis of molecular probes and molecular docking showed that the binding site located in Sudlow’s site I. Combined with paeoniflorin, the conformation of HSA changed according to the results of 3D, UV–vis and CD spectra. Additionally, paeoniflorin may induce conformational changes of HSA and affect its biological function as the carrier protein.
The conclusions are important in the field of pharmacology and biochemistry and are helpful for understanding the effect of paeoniflorin on protein function during the blood transportation process and its biological activity in vivo. The clear and quantitative information on the nature of paeoniflorin–HSA interaction may provide some information for its rational use in clinical practice.
The fluorescence spectroscopy, UV–vis absorption, fluorescence probe experiments, synchronous fluorescence, circular dichroism (CD) spectra and three-dimensional spectra study on interaction of paeoniflorin with human serum albumin (HSA) was accomplished by LX and YL together with their students YH and YL. The molecular docking study was accomplished by HL and HA together with their student LZ. LX and YL accomplished the writing of the article. YL and HL were the study designers and corresponding authors. All authors read and approved the final manuscript.
The authors greatly acknowledge the National Natural Science Foundation of China (81403177), the Science and Technology Planning Project of Shenyang Science and Technology Bureau (F12-277-1-14) and Innovation Team Project of the Education Department of Liaoning Province (LT2015011) for financial supports.
The authors declare that they have no competing interests.
Availability of data and materials
The dataset supporting the conclusions of this article is included within the article and its additional file.
Consent for publication
Ethics approval and consent to participate
The fluorescence spectroscopy, UV–vis absorption, fluorescence probe experiments, synchronous fluorescence, circular dichroism (CD) spectra and three-dimensional spectra study was funded by the National Natural Science Foundation of China (81403177) and the Science and Technology Planning Project of Shenyang Science and Technology Bureau (F12-277-1-14). The molecular docking study was funded by Innovation Team Project of the Education Department of Liaoning Province (LT2015011).
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