A spectroscopic study of the interaction of the antioxidant naringin with bovine serum albumin

The interaction of naringin with bovine serum albumin has been performed using fluorescence, circular dichroism and fourier transform infrared spectroscopy in 20 mM phosphate buffer of pH 7.0 as well as molecular docking studies. The changes in enthalpy (ΔH°) and entropy (ΔS°) of the interaction were found to be +18.73 kJ/mol and +143.64 J mol-1 K-1 respectively, indicating that the interaction of naringin with bovine serum albumin occurred mainly through hydrophobic interactions. Negative values of free energy change (ΔG°) at different temperatures point toward the spontaneity of the interaction. Circular dichroism studies reveal that the helical content of bovine serum albumin decreased after interaction with naringin. According to the Förster non-radiative energy transfer theory the distance between Trp 213 residue and naringin was found to be 3.25 nm. Displacement studies suggest that naringin binds to site 1 (subdomain IIA) of bovine serum albumin (BSA) which was also substantiated by molecular docking studies

A comparative study of interaction of tetracycline with several proteins using time resolved anisotropy, phosphorescence, docking and FRET

A comparative study of the interaction of an antibiotic Tetracycline hydrochloride (TC) with two albumins, Human serum albumin (HSA) and Bovine serum albumin (BSA) along with Escherichia Coli Alkaline Phosphatase (AP) has been presented exploiting the enhanced emission and anisotropy of the bound drug. The association constant at 298 K is found to be two orders of magnitude lower in BSA/HSA compared to that in AP with number of binding site being one in each case. Fluorescence resonance energy transfer (FRET) and molecular docking studies have been employed for the systems containing HSA and BSA to find out the particular tryptophan (Trp) residue and the other residues in the proteins involved in the binding process. Rotational correlation time (θc) of the bound TC obtained from time resolved anisotropy of TC in all the protein-TC complexes has been compared to understand the binding mechanism. Low temperature (77 K) phosphorescence (LTP) spectra of Trp residues in the free proteins (HSA/BSA) and in the complexes of HSA/BSA have been used to specify the role of Trp residues in FRET and in the binding process. The results have been compared with those obtained for the complex of AP with TC. The photophysical behaviour (viz., emission maximum, quantum yield, lifetime and θc) of TC in various protic and aprotic polar solvents has been determined to address the nature of the microenvironment of TC in the protein-drug complexes

Naturally Occurring Anthraquinones as Potential Inhibitors of SARS-CoV-2 Main Protease: A Molecular Docking Study

Background: The novel coronavirus (COVID-19) has quickly spread throughout the globe, affecting millions of people. The World Health Organization (WHO) has recently declared this infectious disease as a pandemic. At present, several clinical trials are going on to identify possible drugs for treating this infection. SARS-CoV-2 Mpro is one of the most critical drug targets for the blockage of viral replication. Method: The blind molecular docking analyses of natural anthraquinones with SARS-CoV-2 Mpro were carried out in an online server, SWISSDOCK, which is based on EADock DSS docking software. Results: Blind molecular docking studies indicated that several natural antiviral anthraquinones could prove to be effective inhibitors for SARS-CoV-2 Mpro of COVID-19 as they bind near the active site having the catalytic dyad, HIS41 and CYS145 through non-covalent forces. The anthraquinones showed less inhibitory potential as compared to the FDA approved drug, remdesivir. Conclusion: Among the natural anthraquinones, alterporriol Q could be the most potential inhibitor of SARS-CoV-2 Mpro among the natural anthraquinones studied here, as its ∆G value differed from that of remdesivir only by 0.51 kcal/ mol. The uses of these alternate compounds might be favorable for the treatment of the COVID-19.</p

Glycation of human serum albumin alters its binding efficacy towards the dietary polyphenols: a comparative approach

Diabetes is a major problem in the world. The proteins became modified during glycation after reacting with the reducing sugars (e.g. D-glucose) via non-enzymatic pathways. The glycated analogue of human serum albumin (HSA) has been characterized with the help of multi-spectroscopic methods. It has been observed that six glucose molecules can bind covalently to HSA under experimental condition. The binding affinity of the modified HSA towards the dietary polyphenols has been estimated using UV–vis and fluorescence spectroscopic techniques. The binding constant values of the ligands were found to decrease after the modification of HSA. The binding affinities (K_b) of the polyphenols decreased towards human serum albumin after its structural modification with D-glucose. Highest percentage decrease in the binding is observed for quercetin among all the polyphenols

Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies

We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin using multi-spectroscopic and molecular docking methods. The binding constants were found to be in the order of 104 M−1 and the number of binding sites was determined as one. MALDI-TOF analyses showed that one fisetin molecule binds to a single bovine serum albumin (BSA) molecule which is also supported by fluorescence quenching studies. The negative Gibbs free energy change (∆G°) values point to a spontaneous binding process which occurs through the presence of electrostatic forces with hydrophobic association that results in a positive entropy change (+51.69 ± 1.18 J mol−1 K−1). The unfolding and refolding of BSA in urea have been studied in absence and presence of fisetin using steady-state fluorescence and lifetime measurements. Urea denaturation studies indicate that fisetin is gradually released from its binding site on the protein. In the absence of urea, an increase in temperature that causes denaturation of the protein results in the release of fisetin from its bound state indicating that fisetin binds only to the native state of the protein. The circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopic studies showed an increase in % α-helix content of BSA after binding with fisetin. Site marker displacement studies in accordance with the molecular docking results suggested that fisetin binds in close proximity of the hydrophobic cavity in site 1 (subdomain IIA) of the protein. The PEARLS (Program of Energetic Analysis of Receptor Ligand System) has been used to estimate the interaction energy of fisetin with BSA and the results are in good correlation with the experimental findings

An investigation into the altered binding mode of green tea polyphenols with human serum albumin on complexation with copper

Green tea is rich in several polyphenols, such as (−)-epicatechin-3-gallate (ECG), (−)-epigallocatechin (EGC), and (−)-epigallocatechin-3-gallate (EGCG). The biological importance of these polyphenols led us to study the major polyphenol EGCG with human serum albumin (HSA) in an earlier study. In this report, we have compared the binding of ECG, EGC, and EGCG and the Cu(II) complexes of EGCG and ECG with HSA. We observe that the gallate moiety of the polyphenols plays a crucial role in determining the mode of interaction with HSA. The binding constants obtained for the different systems are 5.86 ± 0.72 × 10⁴ M⁻¹ (K _ECG-HSA), 4.22 ± 0.15 × 10⁴ M⁻¹ (K _{ECG-Cu(II)-HSA}), and 9.51 ± 0.31 × 10⁴ M⁻¹ (K _{EGCG-Cu(II)-HSA}) at 293 K. Thermodynamic parameters thus obtained suggest that apart from an initial hydrophobic association, van der Waals interactions and hydrogen bonding are the major interactions which held together the polyphenols and HSA. However, thermodynamic parameters obtained from the interactions of the copper complexes with HSA are indicative of the involvement of the hydrophobic forces. Circular dichroism and the Fourier transform infrared spectroscopic measurements reveal changes in α-helical content of HSA after binding with the ligands. Data obtained by fluorescence spectroscopy, displacement experiments along with the docking studies suggested that the ligands bind to the residues located in site 1 (subdomains IIA), whereas EGC, that lacks the gallate moiety, binds to the other hydrophobic site 2 (subdomain IIIA) of the protein

In Silico Screening of Naturally Occurring Coumarin Derivatives for the Inhibition of the Main Protease of SARS-CoV-2

The dissemination of a novel corona virus, SARS-CoV-2, through rapid human to human transmission has led to a global health emergency. The lack of a vaccine or medication for effective treatment of this disease has made it imperative for developing novel drug discovery approaches. Repurposing of drugs is one such method currently being used to tackle the viral infection. The genome of SARS-CoV-2 replicates due to the functioning of a main protease called Mpro. By targeting the active site of Mpro with potential inhibitors, this could prevent viral replication from taking place. Blind docking technique was used to investigate the interactions between 29 naturally occurring coumarin compounds and SARS-CoV-2 main protease, Mpro, out of which 17 coumarin compounds were seen to bind to the active site through the interaction with the catalytic dyad, His41 and Cys145, along with other neighbouring residues. On comparing the ΔG values of the coumarins bound to the active site of Mpro, corymbocoumarin belonging to the class pyranocoumarins, methylgalbanate belonging to the class simple coumarins and heraclenol belonging to the class furanocoumarins, displayed best binding efficiency and could be considered as potential Mpro protease inhibitors. Preliminary screening of these naturally occurring coumarin compounds as potential SARS-CoV-2 replication inhibitors acts as a stepping stone for further in vitro and in vivo experimental investigation and analytical validation. </p

An Investigation into the Identification of Potential Inhibitors of SARS-CoV-2 Main Protease Using Molecular Docking Study

A new strain of a novel infectious disease affecting millions of people, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a pandemic by the World Health Organization (WHO). Currently, several clinical trials are underway to identify specific drugs for the treatment of this novel virus. The inhibition of the SARS-CoV-2 main protease is necessary for the blockage of the viral replication. Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. All the studied molecules could bind to the active site of the SARS-CoV-2 protease (PDB: 6Y84), out of which rutin (a natural compound) has the highest inhibitor efficiency among the 33 molecules studied, followed by ritonavir (control drug), emetine (anti-protozoal), hesperidin (a natural compound), lopinavir (control drug) and indinavir (anti-viral drug). All the molecules, studied out here could bind near the crucial catalytic residues, HIS41 and CYS145 of the main protease, and the molecules were surrounded by other active site residues like MET49, GLY143, HIS163, HIS164, GLU166, PRO168, and GLN189. As this study is based on molecular docking, hence being particular about the results obtained, requires extensive wet-lab experimentation and clinical trials under in vitro as well as in vivo conditions

Magnetic field effect corroborated with docking study to explore photoinduced electron transfer in drug-protein interaction

Conventional spectroscopic tools such as absorption, fluorescence, and circular dichroism spectroscopy used in the study of photoinduced drug−protein interactions can yield useful information about ground-state and excited-state phenomena. However, photoinduced electron transfer (PET) may be a possible phenomenon in the drug−protein interaction, which may go unnoticed if only conventional spectroscopic observations are taken into account. Laser flash photolysis coupled with an external magnetic field can be utilized to confirm the occurrence of PET and authenticate the spin states of the radicals/radical ions formed. In the study of interaction of the model protein human serum albumin (HSA) with acridine derivatives, acridine yellow (AY) and proflavin (PF+), conventional spectroscopic tools along with docking study have been used to decipher the binding mechanism, and laser flash photolysis technique with an associated magnetic field (MF) has been used to explore PET. The results of fluorescence study indicate that fluorescence resonance energy transfer takes place from the protein to the acridine-based drugs. Docking study unveils the crucial role of Ser 232 residue of HSA in explaining the differential behavior of the two drugs towards the model protein. Laser flash photolysis experiments help to identify the radicals/radical ions formed in the due course of PET (PF•, AY•−, TrpH•+, Trp•), and the application of an external MF has been used to characterize their initial spin-state. Owing to its distance dependence, MF effect gives an idea about the proximity of the radicals/radical ions during interaction in the system and also helps to elucidate the reaction mechanisms. A prominent MF effect is observed in homogeneous buffer medium owing to the pseudoconfinement of the radicals/radical ions provided by the complex structure of the protein

The influence of common metal ions on the interactions of the isoflavone genistein with bovine serum albumin

The interaction of genistein with bovine serum albumin (BSA) has been characterized via UV–vis, fluorescence spectroscopy and Circular Dichroism (CD) measurements under physiological conditions. In this study, we have investigated the effect of some common metal ions on the binding of genistein with BSA using fluorescence studies. The fluorescence data reveal that the binding affinity of genistein to BSA increases in presence of certain metal ions. The possibility of non-radiative energy transition from the donor tryptophan to the acceptor genistein has been observed in absence and presence of metal ions. The observed similarities in the values of efficiency of energy transfer (E) and the separation between the donor and acceptor (r) in both the cases may be correlated with the complexation between the genistein and metal ions, which is also observed from the UV–vis studies. The changes in enthalpy (ΔH°) and entropy (ΔS°) of the interaction were found to be −14.64 kJ mol−1 and +42.75 J mol−1 K−1 respectively. These values indicate the involvement of electrostatic interactions along with a hydrophobic association that results in a positive entropy change. CD analysis shows that there is a slight increase in the% α-helical content of BSA on binding with genistein at lower molar ratios. Warfarin and ibuprofen displacement studies in accordance with the molecular docking show that genistein binds to site I (subdomain IIA) of BSA