Specific binding and inhibition of 6-benzylaminopurine to catalase: multiple spectroscopic methods combined with molecular docking study

Thermodynamics of benzoquinone-induced conformational changes in nucleic acids and human serum albumin

Biological macromolecules such as proteins, nucleic acids, carbohydrates and lipids, play a crucial role in biochemical and molecular processes. Thus, the study of the structure-function relationship of biomolecules in presence of ligands is an important aspect of structural biology. The current communication describes the chemico-biological interaction between benzene metabolite para-benzoquinone (BQ) with B-form of nucleic acids (B-DNA) and human serum albumin (HSA). The binding ability of HSA towards bromocresol green (BCG) was significantly suppressed when exposed to increasing concentrations of BQ in the presence of various physiological buffers. Further, the native fluorescence of HSA was drastically reduced and the secondary structures of HSA were significantly compromised with increasing concentrations of BQ. In vitro and in silico studies also revealed that BQ binds to domains I and II of HSA and thus altering the conformation of HSA which may potentially affect plasma osmotic pressure, as well as the binding and transport of numerous endogenous and exogenous molecules. Similarly, BQ interacts directly to the GC region of B-DNA particularly in the minor groove which was also assessed by computational docking studies. Isothermal titration calorimetry data suggest higher binding affinity of BQ towards DNA than HSA. Various spectroscopic observations also suggest that BQ binds to DNA preferably in the minor grooves. Thus, the results revealed that BQ may play a key role in inducing mutagenicity, either by formation of adducts on GC regions or by accelerating oxidative damage to biomacromolecules through chemico-biological interactions.

Spectroscopic studies and molecular docking on the interaction of delphinidin-3-O-galactoside with tyrosinase

The inhibitory effects of delphinidin-3-O-galactoside (DG) on the activities of tyrosinase (EC 1.14.18.1) (TY) from the edible Agaricus bisporus mushroom were investigated by enzyme kinetics, multispectroscopic methods, and molecular docking. As a result, DG showed strong inhibition on TY with the IC₅₀ of 34.14 × 10^-6  mol L^-1 . The inhibition mode of DG against TY was mixed type with α values of 5.09. The binding constant K_a and related thermodynamic parameters at the three different temperatures showed that the fluorescence quenching of TY by DG was static quenching. Synchronous fluorescence, three-dimensional fluorescence, ultraviolet-visible spectroscopy, and circular dichroism spectroscopies confirmed that the conformation or microenvironment of the TY protein were changed after binding with DG. Molecular docking revealed that DG had strong binding affinity to TY through hydrogen bonding and van der Waals force, and the results were consistent with the fluorescence data. Our findings suggested that DG may be potential TY inhibitor.

Structural and kinetic insights into HIV-1 reverse transcriptase inhibition by farnesiferol C

Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is the key enzyme for the virus gene replication and the most important target for antiviral therapy. Toxicity, drug resistance and side effects have led to search for new antiviral agents. Farnesiferol C (FC) is a well-known biologically active sesquiterpene coumarin derivative from genus Ferula. The current study was designed to examine the impacts of FC on the structure and function of HIV-1 RT, using some theoretical and experimental methods. FC inhibited HIV-1RT activity via mixed inhibition mechanism (IC₅₀ = 30 μM). Spectroscopic data showed some conformational changes in the secondary as well as tertiary structure of HIV-1RT following the interaction with FC. Results showed that FC could quench the intrinsic fluorescence emission of HIV-1RT through static quenching mechanism. Thermodynamic parameters revealed that hydrogen bondings and van der Waals forces are the major forces in the binding reaction and the low equilibrium constants (K_D) value obtained from surface plasmon resonance data, confirmed the high affinity of FC for HIV-1RT. Molecular docking studies indicated that FC interacts with enzyme through hydrophobic pocket. Taken together, the outcomes of this research revealed that, sesquiterpene coumarines can be used to design natural remedies as anti-HIV agents.

Surface plasmon resonance, fluorescence, and molecular docking studies of bovine serum albumin interactions with natural coumarin diversin

In the present study the binding of diversin (DIV), a prenylated coumarin isolated from Ferula diversivittata, to bovine serum albumin (BSA) was investigated using surface plasmon resonance (SPR), spectrofluorimetry, and molecular docking approaches. Following the activation of carboxylic groups, via NHS/EDC, BSA was immobilized on the carboxymethyl dextran (CMD) hydrogel coated Au sensor, and was used for real-time monitoring of the interactions between DIV and BSA. K_D value of DIV binding to BSA increased with increasing temperature, confirmed that the affinity between BSA and DIV decreases with rising temperature. In addition, the fluorescence and synchronous fluorescence spectroscopic data revealed that the intrinsic emission intensity of BSA was quenched via a dynamic mechanism. In addition, the micro-region around BSA tyrosine residue was changed upon interaction with DIV. The thermodynamic parameter findings suggested that the hydrophobic interactions were dominant in the binding and formation of the BSA and DIV complex. The molecular docking outputs indicated that there is only one binding site on BSA for DIV, in agreement with experimental data, and DIV bind BSA in subdomain IB.

Bioactive supra decorated thiazolidine-4-carboxylic acid derivatives attenuate cellular oxidative stress by enhancing catalase activity

Bioactive (2S,4R)-3-(tert-butoxycarbonyl)-2-(2-hydroxyphenyl)thiazolidine-4-carboxylic acid molecules restructure enzymes through complexation, allowing enhancing their activity to protect cells from oxidative stress.

Interaction of chromium(III) or chromium(VI) with catalase and its effect on the structure and function of catalase: An in vitro study

Heavy metal chromium (Cr) poses a severe health risk to humans via food chain contamination. In this study, the interactions of either trivalent chromium (Cr(III)) or hexavalent chromium (Cr(VI)) with catalase (CAT) were investigated via multi-spectroscopic studies and computational simulations. The fluorescence analysis showed that Cr(III) and Cr(VI) quenched the fluorescence of CAT through a dynamic and a static quenching mechanism, respectively. The binding constant of Cr(VI) with CAT was 3.44×10⁴lmol^-1 at 298K. Other detailed binding characterizations of the Cr(VI)-CAT complex were also obtained using spectra analysis and molecular docking. Synchronous fluorescence, UV-vis and circular dichroism (CD) spectral studies showed that either Cr(III) or Cr(VI) induced conformational changes of CAT, but the degree of influence was different. The response of CAT activity to Cr(III) or Cr(VI) was found to be variable depending on their valence states and concentrations.

Effects of Resveratrol on the Structure and Catalytic Function of Bovine Liver catalase (BLC): Spectroscopic and Theoretical Studies

Purpose: The study on the interaction between various compounds and macromolecules such as enzymes has been very important for monitoring the alteration of structural and functional properties of them. Resveratrol (3, 5, 4-trihydroxy-stilbene; RES) is a biologically active phytoallexin found in grapes and other food products. This article shows an interaction of native bovine liver catalase (BLC) with natural antioxidant product, trans resveratrol (tRES) using multispectroscopic methods.

Methods: The interaction between BLC and tRES is performed using UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy and molecular docking study.

Results: In vitro kinetic studies indicated that tRES can decrease BLC activity through uncompetitive inhibition. The results of spectroscopic methods represented that the binding of tRES with BLC can change the micro-region around aromatic amino acids (tryptophan (Trp) and tyrosine (Tyr)) and quench intrinsic fluorescence of BLC by a static mechanism. According to fluorescence quenching data analysis, it was revealed that tRES has one binding site on BLC. The thermodynamic parameters were obtained, which demonstrated that tRES can bind to BLC by van der Waals forces and hydrogen bonds. Molecular docking results indicated that tRES binds to BLC away from heme group and near to the Tyr 324 and Phe 265. These results are in agreement with the experimental results.

Conclusion: The inhibitory effect of tRES on BLC demonstrated that excessive consumption of the antioxidants could be resulted in hazardous effects.

Investigation of the binding mechanism and inhibition of bovine liver catalase by quercetin: Multi-spectroscopic and computational study

Introduction: The study on the side effects of various drugs and compounds on enzymes is a main issue for monitoring the conformational and functional changes of them. Quercetin (3,5,7,3',4'-pentahydroxyflavone, QUE), a polyphenolic flavonoid, widely found in fruits, vegetables and it is used as an ingredient in foods and beverages. The interaction of bovine liver catalase (BLC) with QUE has been studied in this research by using different spectroscopic methods. Methods: In this work, the interaction of QUE with BLC was investigated using different spectroscopic methods including ultraviolet-visible (UV-vis) absorption, circular dichroism (CD) and fluorescence spectroscopy and molecular docking studies. Results: Fluorescence data at different temperatures, synchronous fluorescence and CD studies revealed conformational changes in the BLC structure in the presence of different concentration of QUE. Also, the fluorescence quenching data showed that QUE can form a non-fluorescent complex with BLC and quench its intrinsic emission by a static process. The binding constant (Ka) for the interaction was 104, and the number of binding site was obtained ~1. The ∆H, ∆S and ∆G changes were obtained, indicating that hydrophobic interactions play a main role in the complex formation. In vitro kinetic studies revealed that QUE can inhibit BLC activity through non-competitive manner. Molecular docking study results were in good agreement with experimental data, confirming only one binding site on BLC for QUE at a cavity among the wrapping domain, threating arm and β-barrel. Conclusion: Inhibition of BLC activity upon interaction with QUE demonstrated that in addition to their beneficial effects, they should not be overlooked for their side effects.

6-Benzylaminopurine inhibits growth of Monilinia fructicola and induces defense-related mechanism in peach fruit

This study demonstrated the inhibitory effect of 6-benzylaminopurine (BAP), the first generation synthetic cytokinin, on the invasion of Monilinia fructicola in peach fruit and the possible mechanism involved for the first time. Our results suggested that BAP treatment had a 63% lower disease incidence and approximately 10 times lower lesion diameter compared to the control throughout the incubation period. In vitro BAP showed a direct inhibitory effect on M. fructicola spore germination. BAP could prevent fruit texture deterioration and protect the cell membrane from oxidative stress, while no adverse effects were observed on fruit quality maintenance. Analysis of defense-related enzymes activities indicated that the use of BAP induced higher specific polyphenol oxidase and peroxidase activities which triggered stronger host defensive responses. Thus, our results verified the proposed mechanism of BAP in controlling M. fructicola by direct inhibitory effect, delay peach senescence and activation of defensive enzymes.

Molecular interaction of inorganic mercury(ii) with catalase: a spectroscopic study in combination with molecular docking

Interaction of inorganic mercury(ii) with catalase was investigated using spectroscopic methods. Moreover, molecular docking was used to distinguish the interactions between different species of inorganic mercury(ii) and catalase.