Study of the Binding of Cuminaldehyde with Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

Ali, Mohd Sajid; Rehman, Md Tabish; Al-Lohedan, Hamad A.; Alajmi, Mohamed F.

doi:https://doi.org/10.1155/2023/4191046

Journal of Spectroscopy

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Abstract Introduction Materials and Methods Results Conclusions Abbreviations Data Availability Conflicts of Interest Acknowledgments Supplementary Materials References Copyright Related Articles

Research Article | Open Access

Volume 2023 | Article ID 4191046 | https://doi.org/10.1155/2023/4191046

Study of the Binding of Cuminaldehyde with Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

Mohd Sajid Ali,¹Md Tabish Rehman,²Hamad A. Al-Lohedan,¹and Mohamed F. Alajmi²

Academic Editor: Artem E. Masunov

Received12 May 2022

Revised20 Oct 2022

Accepted23 Mar 2023

Published14 Apr 2023

Abstract

Here, we investigated the interaction of cuminaldehyde with a model carrier protein, bovine serum albumin (BSA). The formation of the BSA–cuminaldehyde complex was confirmed through ultraviolet–visible (UV–Vis) spectroscopy and further proven by detailed intrinsic fluorescence spectroscopic measurements. As observed, cuminaldehyde quenched the intrinsic tryptophanyl fluorescence of BSA. The fluorescence data, before the analyses, were corrected for the inner filter effect (IFE) because of the significant absorption of cuminaldehyde at the excitation wavelength that was employed in the measurements. The typical Stern–Volmer plots were slightly nonlinear; they exhibited negative deviation toward the x-axis, a typical phenomenon that is observed with proteins possessing more than one tryptophan residue. Thus, the modified Stern–Volmer equation was employed to analyze the data. The analyzed data revealed that the interaction of cuminaldehyde with BSA proceeded via a static quenching mechanism and that there was a fair 1 : 1 binding between them. The interaction was strengthened by hydrophobic forces and hydrogen bonding. A lowered concentration of cuminaldehyde did not affect the secondary structure of BSA, although an increased one partially exposed the protein by decreasing its α-helical contents. The molecular dockings and simulations of BSA and cuminaldehyde further confirmed the formation of the stable BSA–cuminaldehyde complex. The in silico results also revealed that the contributions of the hydrophobic interaction and hydrogen bonding were the driving forces that imparted the stability.

1. Introduction

Since its existence, humankind has consumed spices, herbs, and other products that are obtained from plants and animals. Spices are good antioxidant sources, which have also been utilized as food additives (to add flavor, color, aroma, taste, etc.) for more than 2000 years [1]. Cumin, which is an essential ingredient in many cuisines, is among the most popular spices. Its utilization as a food additive to add flavor is very common, particularly in the South Asian and Middle Eastern regions. Furthermore, cumin is employed to prepare traditional medicines. In the Ayurvedic medicine system, cumin seeds are employed to treat several digestive disorders, including chronic diarrhea and dyspepsia [2]. Additionally, its oil is also employed as carminative and astringent medicines.

It has been reported that cumin seed oil possesses many medicinal and pharmacological properties, such as antibacterial, antifungal, antibiofilm and quorum-sensing inhibition, antiviral, hypoglycemic, and anticancer activities [3]. It has also been demonstrated that cumin seed oil could enhance the drug bioavailability of an antibiotic drug, rifampicin [4]. Moreover, cumin oil is a good wound-healing and antioxidant agent, which has been reported to exhibit insecticidal properties [3].

The volatile oil of cumin contains several classes of compounds, including terpenes, alcohols, phenols, and aldehydes. The major constituents of cumin oil are cuminaldehyde, eugenol, and β-pinene, along with several other compounds, which are obtained in a low yield [3]. Cuminaldehyde (Figure 1) is an oxidized monoterpene aldehyde, which is most abundantly present in essential oil (EO) that is obtained from cumin. Cuminaldehyde also accounts for the characteristic aroma of the spice [5]. Similar to its source, cuminaldehyde possesses several therapeutic properties, including antidiabetic, antitumor, neuroprotective, anti-inflammatory, antimicrobial, and antifungal activities [6]. It was reported that it reduced the elevated blood glucose levels and enhanced insulin secretion more than the clinically utilized oral hypoglycemic agent, glibenclamide [7, 8] in diabetic rats. Lowered concentrations of cuminaldehyde can effectively reduce the synthesis of melanin by mouse melanoma cell lines. However, a high concentration range of cuminaldehyde was very cytotoxic [9]. Additionally, cuminaldehyde inhibits the fibrillation of α‐synuclein, which is a critical process in the pathophysiology of several neurodegenerative diseases, especially Parkinson’s disease [10].

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These broad therapeutic values of cuminaldehyde motivated us to consider its binding to the abundant plasma protein, serum albumin, which is also a carrier protein for several exogenous and endogenous substances, such as, fatty acids, bilirubin, and a wide variety of drugs [11–15]. The binding efficacy of a drug to serum albumin is pivotal to its therapeutic property since every drug possesses a different albumin-binding profile, which ranges from very strong to very weak binding. A strong binding efficacy of a drug may increase its stay in the human body, thus increasing the probabilities of many unwanted side effects. Conversely, a weak binding efficacy of a drug may be associated with a shorter half-life and early excretion from the body, thus making it less-effective owing to its shortage at the desired site of action. Moreover, the binding of substances, which are obtained from natural sources (plants), to serum albumin has greatly captivated the interests of researchers [16–25]. Recently, the bindings of several natural products that were obtained from different sources, including Red sea sponge, mountain thyme, cuminol, and saffron, to serum albumins were investigated, and it was observed that these compounds interacted differently with serum albumin and exerted different effects on the structure of the latter [26–29]. Thus, it is very valuable to elucidate the mechanism of a therapeutic agent using serum albumin.

In this study, bovine serum albumin (BSA) was employed as a model protein because of its >76% similarity to human serum albumin [30], and its interaction with cuminaldehyde was investigated via spectroscopic and computational methods.

2. Materials and Methods

BSA (≥98%, A7030) and cuminaldehyde (≥98.0%, 135178) were purchased from Sigma. A 20 mM tris buffer of pH 7.4 was employed as the medium for the study. The ultraviolet–visible UV–Vis spectroscopic measurements were conducted on a Perkin-Elmer Lambda 45 spectrophotometer utilizing a 1 cm quartz cell. Measurements of fluorescence intensity were carried out on a Hitachi F-7000 spectrofluorometer equipped with a Peltier system to maintain the desired temperature. The slit widths for excitation and emission were set at 5 nm, and the photomultiplier tube (PMT) voltage was set to 500 V. The protein was excited at 295 nm, and the fluorescence emission spectra were recorded in 300–500 nm range. A Jasco J-815 circular dichroism (CD) spectropolarimeter was employed to conduct the far-UV CD measurements in the range of 200–250 nm utilizing a 2 mm quartz cuvette to keep the high-tension voltages below 600 V. Molecular docking and molecular dynamics (MD) simulations were performed employing Schrodinger’s Glide and Desmond modules, as described previously [31]. Briefly, the three-dimensional structure of BSA was downloaded from RCSB-PDB database. The structure of protein was refined using protein preparation wizard of Glide by removing nonessential water molecules, adding any missing hydrogen atoms, assigning bond orders, creating zero bond order to disulfide bonds, and deleting any hetero atoms. A hydrogen bond network was generated. Finally, OPLS-2005 (Optimized Potentials for Liquid Simulations-2005) forcefield was utilized to minimize the energy of the system. Similarly, the structure of cuminaldehyde was drawn in the 2D sketcher platform of Schrodinger and optimized for docking by allocating proper bond order and angles in the LigPrep module of Schrodinger. Different ionization states of cuminaldehyde were generated at pH using Epik module, and their energies were minimized by the OPLS-2005 forcefield. The binding site of BSA was predicted using the SiteMap module, and the standard precision (SP) molecular docking was performed inside a box of , placed at . The docked BSA-cuminaldehyde complex was used as the starting point for MD simulation by placing it inside an orthorhombic simulation box at least 10 Å away from the walls of the box. The box was solvated with TIP3P water molecules and neutralized by adding Na + or Cl-ions. In addition, 0.15 M NaCl was added to mimic the physiological conditions. The whole system was minimized using the OPLS-2005 forcefield and the production run was conducted with an NPT ensemble at 330 K temperature and 1.013 bar pressure. Maestro was utilized for the visualization and analysis of the results. The binding affinity (K_d) of cuminaldehyde toward BSA was evaluated using the following relation between docking free energy and binding affinity [32]:where R and T are the Boltzmann gas constant (1.987 cal/mol/K) and temperature (298 K), respectively.

3. Results and Discussions

The UV−Vis spectrum of cuminaldehyde is shown in Figure 1(a). The UV−Vis spectra of BSA without and with cuminaldehyde are shown in Figure 1(b). BSA exhibited two peaks: one strong peak around 210 nm is due to the absorption of polypeptide chains, and the other at 280 nm which was due to the presence of aromatic amino acids (tryptophan, tyrosine, and phenylalanine) [33–35]. Since cuminaldehyde exhibited strong absorption near this wavelength, its contribution was subtracted from the cumulative spectrum of the complex; thus, it was called the difference spectrum [36, 37]. The UV–Vis absorption profile of BSA changed slightly in the presence of cuminaldehyde because of the formation of a complex between them [38].

The interactions of biomolecules, particularly proteins, can be easily studied by fluorescence spectroscopy owing to the intrinsic fluorescence properties of most proteins, which are revealed when one or more fluorophore-like tryptophans or tyrosines are present therein. BSA contains two tryptophan residues, which are typically designated as TRP-134 and TRP-212, and ∼20 tyrosine residues that are distributed throughout the protein domain [30]. Tyrosine is more fluorescent than tryptophan when they are isolated. However, when they are together, the maximum fluorescence is an outcome of tryptophan emission that is due to the efficient energy transfer from tyrosine to tryptophan [39]. When the protein solution is excited at 280 nm, it exhibits the emissions of the tryptophan and tyrosine residues with an emission maximum at around 340 nm, while tryptophan exclusively emitted fluorescence when the excitation wavelength was 295 nm. The observed fluorescence emission profiles of BSA without and with cuminaldehyde at an excitation wavelength of 295 nm and various temperatures are shown in Figures S1–S4. Figure 1(a) shows that cuminaldehyde exhibits considerable absorption at 295 nm. Hence, the fluorescence data must be corrected for the inner filter effect (IFE; a factor that greatly influences the fluorescence quenching profiles of the protein by a ligand, which exhibits significant absorption at the excitation and emission wavelengths) [28, 37]. Thus, IFE was corrected by equation (S1). The corrected fluorescence spectra of BSA with and without cuminaldehyde at a 295 nm excitation and various temperatures are shown in Figures 2(a)–2(d), and the difference between the observed and corrected spectra could be elucidated by simple visual inspection.

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When cuminaldehyde is added to the BSA, the fluorescence intensity of the latter decreases (quenching) because of interaction between these two which changes the microenvironment of the fluorophore. The Stern–Volmer quenching constant (K_SV) is a measure of the efficacy of the quenching of the fluorophore by a quencher, which can be expressed by the following equation:where F₀ and F indicate the emission intensities of BSA without and with cuminaldehyde, respectively, and [Q] is the concentration of the quencher (cuminaldehyde) [40]. Moreover, the K_SV factor is related to the biomolecular quenching rate constant (K_q) via the following relation:where τ₀ is the average lifetime of the fluorophore without the quencher [41].

The plots of vs. with an intercept of 1 can be employed to obtain the values of K_SV as their slopes. The plots are shown in Figure 3(a), and the values of and , which were obtained from equation (1), are presented in Table 1. The figure shows that the plots deviated from the linearity and exhibited a downward curvature toward the x-axis, and this is a usual phenomenon that is associated with the presence of more than one tryptophan residue with different accessibilities to the quencher [39].

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As discussed, the downward curvature in the Stern–Volmer plots was due to the presence of two or more tryptophan residues, which are located in different environments and possess different accessibilities to the quencher, in the protein. The modified Stern–Volmer equation can be applied to calculate , the quenching constant of the accessible fraction by the following equation [42, 43]:where is the fraction of the initial fluorescence that was accessible to the quencher. Hence, the values of K_a were graphically determined by equation (3), and the plot of vs. yielded and as the intercept and slope, respectively. The values of K_a and f_a are presented in Table 2.

Fluorescence quenching is categorized as static or dynamic, although a combination of both in the interaction of a quencher and a fluorophore, which is mainly characterized by the upward curvature in the Stern–Volmer plots, has also been observed [33, 34, 39, 44]. Generally, static quenching is associated with moderate to strong interactions, while a weak interaction proceeds via a dynamic quenching mechanism [37, 39], which can be understood according to the values of K_q as follows: the quenching is said to be static if the K_q values are sufficiently higher than the diffusion-controlled limit [39]. Contrarily, the mechanism is dynamic if the values of K_q are near or lower than the diffusion-controlled limit. Further, the static and dynamic types of quenching can be differentiated by their opposite dependencies on temperature. A high temperature facilitates dynamic quenching, while a low one favors static quenching. Thus, an assessment of the quenching constants at different temperatures could elucidate the type of quenching that was involved in the interaction. The values of K_SV and K_q at different temperatures (Table 1) and those of K_a (Table 2) indicated that an increase in the temperature reduced quenching constants, and the values of K_q were much higher than the diffusion-controlled limit; thus, it was deduced here that the binding of BSA to cuminaldehyde proceeded via static quenching mechanism.

The binding constant (K_b) and number of binding sites (n) can be calculated by using the following equation [45]:where [P]₀ is the total concentration of BSA and [D]₀ is the total concentration of cuminaldehyde. The fluorescence data were treated using equation (5) by the successive approximation method, and the plots of log against were shown in Figure 3(c).

The values of K_b and n, which were obtained from the plots of vs. are listed in Table 3. There was a fair 1 : 1 binding between BSA and cuminaldehyde. Utilizing the values of K_b, which were obtained here, the thermodynamic parameters were calculated by the Van’t Hoff equations (equations S2 and S3). The van’t Hoff plot (lnK_b vs. 1/T) for the BSA–cuminaldehyde interaction is shown in Figure 4(a). The values of the enthalpy (ΔH) and entropy () changes were calculated by those of the slopes and intercepts of the van’t Hoff plot, respectively, as listed in Table 3. These values were further applied to calculate the values of at different temperatures (equation S3). The values of the thermodynamic parameters indicated that the binding was spontaneous and exothermic, with an increased entropy of the system. These thermodynamic parameters, particularly and , can also be applied to determine the binding forces (the hydrogen bonding, hydrophobic, Van der Waals, and electrostatic forces) that are involved in the interaction [46]. Hydrophobic interactions are dominant when the values of and are positive. Conversely, the negative values of these parameters could be obtained when the interaction is supported mainly by hydrogen bonding and Van der Waals forces. The calculated values of ΔH (negative) and ΔS (positive) revealed that hydrogen bonding and the hydrophobic forces were pivotal to the binding of cuminaldehyde to BSA.

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The far-UV CD is a valuable technique for qualitatively and quantitatively elucidating the secondary structure components. The information about the secondary structure components, such as the α-helix, β-sheets, β-turns, and random coils, could be obtained by far-UV CD measurements in the range of 200–250 nm. The α-helical proteins were characterized by two negative bands at 208 and 222 nm, while the β-sheet protein exhibited only one negative band at 218 nm. Thus, the changes in the secondary structure of a protein and the structural alterations could be monitored by CD spectroscopy. BSA is an α-helical protein with an α-helical content of ∼67% [30]. The far-UV CD spectra of BSA without and with cuminaldehyde, which exhibited the two negative peaks at 208 and 222 nm, are shown in Figure 4(b). A low concentration of cuminaldehyde exerted a very slight effect on the secondary structure of BSA. However, some significant decreases in α-helicity were observed by increasing the concentration of cuminaldehyde.

The % α-helix of a protein was calculated by the following equation [47]:where the mean residue ellipticity (MRE) was calculated using the following equation:where is the observed ellipticity (millidegrees), C is the concentration of the protein (molar), n is the number of amino acid residues, and l is the path length (centimeters). From the relations demonstrated above, the % α-helical contents of BSA without and with cuminaldehyde were calculated. It was observed that the α-helical content of native BSA was 68.5%, and this value is in good agreement with a previously observed one. Moreover, there was no visible change in the CD spectrum of BSA with 20 μM BSA (data are not shown), although the α-helicity decreased slightly to 67.7% when 40 μM cuminaldehyde was added. %α-helices of BSA further decreased to 65.1% and 63.8% when the concentrations of cuminaldehyde were further increased to 60 and 100 μM, respectively. Thus, it was concluded that an increased concentration of cuminaldehyde could partially unfold BSA.

3.1. Analysis of Molecular Docking and MD Simulation

The binding site of cuminaldehyde on BSA and the nature of the interaction between them were elucidated by molecular docking. An initial analysis of the structure of BSA revealed that it contained two primary binding sites, namely, Sudlow’s site I and II that are located at subdomains IIA and IIIA, respectively. A new binding site at subdomain IB, which is known as site IB or the digitoxin site, was also reported for the binding of bile salts [48]. Blind docking of cuminaldehyde with BSA revealed that it was bound at an intersection between Sudlow’s sites I and II, thus engaging residues from subdomains IIA and IIIA (Figures 5(a)), respectively. Cuminaldehyde formed two hydrogen bonds with Ser-279 and Leu-280 and formed hydrophobic interactions with Phe-205, Ala-209, Ala-212, Leu-326, Leu-330, Leu-346, Ala-349, and Val-481 (Figure 5(b)). Some charged residues, such as Arg-208, Lys-350, and Glu353 also contributed to the stability of BSA–cuminaldehyde. The docking energy in the standard precision (SP) mode was estimated as −5.8480 kcal mol⁻¹, which corresponded to a K_d value of .

The stability and dynamics of the BSA–cuminaldehyde complex were evaluated by MD simulation for 100 ns. The root-mean-square deviation (RMSD) measures the deviation in the structure of the protein alone or in complex with a ligand based on its initial form. RMSDs were measured across the Cα atoms of BSA without and with cuminaldehyde. Only the RMSD of BSA fluctuated in the 1.6–3.2 Å range for most of the simulation time (Figure 6(a)). Conversely, the RMSD of the BSA–cuminaldehyde complex fluctuated subsequently during 0–20 ns simulation, after which it attained a stable value within an acceptable limit of 2 Å for the rest of the simulation time. The obtained average RMSD values of BSA without and with cuminaldehyde were 2.58 and 2.32 Å, respectively. The results confirmed the formation of a stable BSA–cuminaldehyde complex. Further, the root-mean-square fluctuation (RMSF) measures the flexibilities of the side chains of the protein because of ligand binding. In this study, RMSFs of the Cα atoms of BSA were measured with cuminaldehyde and compared with the B-factor (this was experimentally determined by X-ray crystallography). The vertical green lines represent the positions of the amino acid residues that interacted with cuminaldehyde (Figure 6(b)). Overall, the results confirmed that cuminaldehyde formed a stable complex with BSA. Further, an analysis of the change in the secondary structure elements (SSEs) of BSA, which was caused by the binding of cuminaldehyde, was ascertained as a function of the simulation time (Figure 7(a)). It was observed that the SSE of BSA in the BSA–cuminaldehyde complex was constant at 66.0% throughout the simulation, thereby indicating that the binding of cuminaldehyde did not affect the secondary structure of BSA. Furthermore, the stabilities of BSA and cuminaldehyde were determined by monitoring the formation of a total number of contacts between BSA and cuminaldehyde during the simulation. We confirmed that the number of contacts between cuminaldehyde and BSA was in the range of 0–5 with an average of around two contacts (Figure 7(b)). These results agree well with the molecular docking results, thus indicating that cuminaldehyde formed two hydrogen bonds with BSA.

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(b)

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Furthermore, the radius of gyration (rGyr) is an essential parameter for measuring the overall compactness of a protein that is bound to a ligand. Here, we have monitored rGyr of BSA with cuminaldehyde during the simulation (Figure 8(a)). An analysis of rGyr revealed that it possessed an average value of 2.67 Å, although it fluctuated between 2.60 and 2.73 Å throughout the simulation. Similarly, the variations in the molecular surface area (MolSA), solvent-accessible surface area (SASA), and polar surface area (PSA) of BSA in the BSA–cuminaldehyde complex were measured to determine the exposure of the amino acid residues to the solvent owing to their binding to the ligand (Figures 8(b)––8(d)). MolSA and PSA of the BSA–cuminaldehyde complex fluctuated in the ranges of 172–179 Å² and 42–46 Å² with average values of 175.7 and 43.8 Å², respectively. Moreover, SASA of BSA remained constant throughout the simulation at 39 Å² except at 50–60 ns and 95–100 ns, respectively.

4. Conclusions

Cumin, as well as its EO, is a popular spice, which possesses several medicinal properties. Like other spices and herbs, it also contains a variety of secondary metabolites, which account for its flavor and medicinal values. The interaction of cuminaldehyde (the major component of EO of cumin) with a model carrier protein (BSA) was studied in this work. Cuminaldehyde exhibited a reasonable 1 : 1 interaction with BSA, which decreased with increasing temperature. This corresponded to a static quenching mechanism, and hydrogen bonding and hydrophobic forces were the major forces that accounted for the interaction. The interaction also decreased the α-helical contents of BSA.

Abbreviations

ΔG:	Free energy change
ΔH:	Enthalpy change
ΔS:	Entropy change
BSA:	Bovine serum albumin
CD:	Circular dichroism
EO:	Essential oil
IFE:	Inner filter effect
K _a:	Modified Stern–Volmer quenching constant
K _b:	Binding constant
K _d:	Binding affinity
K _SV:	The Stern–Volmer quenching constant
K _q:	Quenching rate constant
MolSA:	Molecular surface area
MD:	Molecular dynamics
n:	Number of binding sites
PMT:	Photomultiplier tube
PSA:	Polar surface area
rGyr:	Radius of gyration
RMSD:	Root-mean-square deviation
RMSF:	Root-mean-square fluctuation
SASA:	Solvent-accessible surface area
SSE:	Secondary structure element
UV–Vis:	Ultraviolet–visible.

Data Availability

The data used to support the findings of this study are available from the corresponding author upon request.

Conflicts of Interest

The authors declare that they have no conflicts of interest.

Acknowledgments

“Authors acknowledge the generous support from the Researchers Supporting Project number (RSP 2023R122), King Saud University, Riyadh, Saudi Arabia.”

Supplementary Materials

Detailed procedure for experiments and computational studies. Equation (S1): Equation to correct inner filter effect, equations (S2) and (S3): van’t Hoff equations, Figures S1–S4. Observed fluorescence spectra at 25, 35, 45 and 55°C. (Supplementary Materials)

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Copyright © 2023 Mohd Sajid Ali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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