Deciphering the binding of carbendazim (fungicide) with human serum albumin: A multi-spectroscopic and molecular modelling studies

Interaction mechanism of a pesticide, Azoxystrobin with bovine serum albumin: Assessments through fluorescence, UV-Vis absorption, electrochemical and molecular docking simulation techniques

The current study's objective was to investigate how an antifungal pesticide Azoxystrobin (AZO) interacts with bovine serum albumin (BSA) under conditions that simulate a physiological medium (pH 7.4). This investigation was carried out using various experimental (UV-Vis absorption, steady-state fluorescence and 3-D fluorescence spectroscopies, and electrochemical) and theoretical (molecular docking and molecular dynamics simulations) methods. The fluorescence quenching data demonstrated that AZO caused fluorescence quenching in BSA, and this quenching process was attributed to the static quenching mechanism. By examining the fluorescence quenching of BSA at three different temperatures, it was determined that the binding constants for the AZO-BSA complexes were approximately 104 M-1 in magnitude, while the same magnitude of the binding constant was found by the electrochemical method. This indicates that the interaction between AZO and BSA was of moderate strength. This was further validated by the changes observed in the UV-Vis spectrum of BSA following the addition of AZO. The thermodynamic information, including ΔH and ΔS, revealed that the interaction forces primarily involved van der Waals forces as well as hydrogen bonds. The negative Gibbs free energy indicated that the reaction is spontaneous. In the theoretical investigation, the comparison highlights a remarkable consistency in how AZO interacts with the BSA active site over various time points. Hydrogen bonding and hydrophobic interactions consistently play a role in ensuring the stable and specific binding of the ligand. Moreover, the 3-D fluorescence spectral findings revealed alterations in the surrounding microenvironment of protein fluorophores when AZO binds. Upon analyzing the electrochemical data, it was observed that there was a consistent decrease in the peak currents of AZO when BSA was added to solutions containing AZO. The primary cause of this decrease in the peak currents was the reduction in the equilibrium concentration of AZO due to the addition of BSA. Furthermore, the formation of a non-electroactive complex between BSA and AZO, which impedes electron transport between AZO and the working electrode, accounts for these decreases. As a result, it can be said that the understanding of how AZO binds to BSA offers valuable insights that can be applied in the food, human health, and environment sectors.

Alleviation of carbendazim toxicity effect by Moringa oleifera oil and Linum usitatissimum L. oil on testes of male rats: Physiological, histological and in silico study

Carbendazim (CBZ) is a widely used fungicide that is used to control the unwanted growth of fungi on fruits and vegetables. Sixty male rats were divided into six groups, each having ten. Group one served as control, animals belonging to group two were exposed to CBZ in the measure of 200 mg/kg body weight (BW). In the third and fourth groups, rats were administered 800 mg/kg BW of Moringa oleifera (moringa oil) and Linum usitatissimum L. (flaxseed oil), plus CBZ with the same dose given to group two. Groups five and six were administered with moringa and flaxseed oils respectively for six weeks. A marked decline was seen in oxidative stress markers, reduced glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), and a rise in malondialdehyde (MDA) level in group two with severe histological disruptions. Moringa oil and flaxseed oil were used to alleviate these changes. In addition, a biocomputational molecular docking analysis of three proteins found in male rats was performed. In relation to CBZ (CID:10584007) the screened proteins namely testis-expressed protein (TX101_RAT), EPPI_RAT, and glutathione peroxidase 5 (GPX5_RAT) were docked, and their docking score were obtained (-5.9 kcal/mol), (-5.8 kcal/mol) and (-5.6 kcal/mol) respectively. By examining these interactions in 2D and 3D structures, a detailed understanding of the unique and specific binding affinity, hydrogen bonds, hydrophobic interactions, ionic bonds, and water bonds were obtained. Structure-based virtual screening (SBVS) molecular docking analysis showed that protein interaction with CBZ causes reproductive complications in protein expression and functions by hampering their normal function and blocking active sites.

Enzyme Inhibition-Based Assay to Estimate the Contribution of Formulants to the Effect of Commercial Pesticide Formulations

Pesticides can affect the health of individual organisms and the function of the entire ecosystem. Therefore, thorough assessment of the risks associated with the use of pesticides is a high-priority task. An enzyme inhibition-based assay is used in this study as a convenient and quick tool to study the effects of pesticides at the molecular level. The contribution of formulants to toxicological properties of the pesticide formulations has been studied by analyzing effects of 7 active ingredients of pesticides (AIas) and 10 commercial formulations based on them (AIfs) on the function of a wide range of enzyme assay systems differing in complexity (single-, coupled, and three-enzyme assay systems). Results have been compared with the effects of AIas and AIfs on bioluminescence of the luminous bacterium Photobacterium phosphoreum. Mostly, AIfs produce a considerably stronger inhibitory effect on the activity of enzyme assay systems and bioluminescence of the luminous bacterium than AIas, which confirms the contribution of formulants to toxicological properties of the pesticide formulation. Results of the current study demonstrate that "inert" ingredients are not ecotoxicologically safe and can considerably augment the inhibitory effect of pesticide formulations; therefore, their use should be controlled more strictly. Circular dichroism and fluorescence spectra of the enzymes used for assays do not show any changes in the protein structure in the presence of commercial pesticide formulations during the assay procedure. This finding suggests that pesticides produce the inhibitory effect on enzymes through other mechanisms.

Exploring the binding mechanism and adverse toxic effects of chiral phenothrin to human serum albumin: Based on multi-spectroscopy, biochemical and computational approach

To understand the binding mechanism of a mixture of chiral phenothrin with human serum albumin (HSA), we used multi-spectroscopy, including steady-state fluorescence spectroscopic titration, three-dimensional fluorescence spectroscopy, circular dichroism, and FTIR spectra to explore the precise interactions between the complex. Based on the modified Stern-Volmer equation, the binding constant (K_a) was calculated under three temperatures, which revealed that phenothrin interacts with HSA through a static quenching mechanism. The thermodynamic parameters including enthalpy change (ΔH) and entropy change (ΔS) were determined by fitting the experimental data with van't Hoff equation, which indicates that electrostatic force and hydrogen bonds dominate the interplay in the phenothrin-HSA complex. Circular dichroism and FTIR showed the addition of phenothrin changed the secondary structure of proteins, in which the α-helicity decreased from 52.37% in free HSA to 50.02%. The esterase-like activity was reduced with the increase of phenothrin concentration, which may be attributed to the perturbated senior structure of HSA. Competitive displacement experiments confirmed that phenothrin inserted into the subdomain IIA (site I) of HSA. Several computational approaches such as molecular docking, frontier molecular orbital analysis, and electrostatic potential analysis were utilized to probe into the binding mode of the phenothrin-HSA complex. The binding behaviors of the chiral phenothrin mixture differed during the complexation. In conclusion, both the experimental and theoretical investigations provide useful information for better understanding and reducing the potential deleterious effects of the chiral phenothrin mixture on human long-term physio-pathological status.

Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry

Atrazine (ATR), one of the most used herbicides worldwide, causes persistent contamination of water and soil due to its high resistance to degradation. ATR is associated with low fertility and increased risk of prostate cancer in humans, as well as birth defects, low birth weight and premature delivery. Describing ATR binding to human serum albumin (HSA) is clinically relevant to future studies about pharmacokinetics, pharmacodynamics and toxicity of ATR, as albumin is the most abundant carrier protein in plasma and binds important small biological molecules. In this work we characterize, for the first time, the binding of ATR to HSA by using fluorescence spectroscopy and performing simulations using molecular docking, classical molecular dynamics and quantum biochemistry based on density functional theory (DFT). We determine the most likely binding sites of ATR to HSA, highlighting the fatty acid binding site FA8 (located between subdomains IA-IB-IIA and IIB-IIIA-IIIB) as the most important one, and evaluate each nearby amino acid residue contribution to the binding interactions explaining the fluorescence quenching due to ATR complexation with HSA. The stabilization of the ATR/FA8 complex was also aided by the interaction between the atrazine ring and SER454 (hydrogen bond) and LEU481(alkyl interaction).

A Novel Fluorescent Probe for the Detection of Cyanide Ions in Solutions and Studies on Its Biophysical Interactions with ctDNA and Proteases

A new cationic indolium based styryl dye (Ci) as a fluorescent probe was synthesized and its anions selectivity/sensitivity properties/molecular interactions with protease enzymes (pepsin/trypsin) and ctDNA has been studied by spectroscopic and computational methods. The fluorescence measurements at different temperatures indicated that quenching mechanism of enzymes by Ci was static. ΔH and ΔS data pointed out electrostatic/hydrophobic interactions with pepsin, and also hydrogen bonds/van der Waals forces with trypsin of Ci. According to Förster's non-radiative energy transfer, binding distances (r) were calculated as 3.53/3.27 nm for pepsin/trypsin. It was also investigated that groove binding is effective in interaction with ctDNA. The results were supported with molecular docking analyzes which have same tendency. Ci has been demonstrated hypsochromic effect with a decrease in polarity of solvents and it showed highly selective colorimetric and fluorometric sensing behavior for cyanide in organic solvent and in aqueous solution. ¹H NMR titration was performed to examine the interaction mechanism between Ci and cyanide. The LOD values of cyanide ion were reported as 4.87 × 10^-9 M and 9.70 × 10^-7 M in DMSO and DMSO/H₂O binary mixture, respectively. In addition, sensitivity of Ci as a chemosensor to cyanide was investigated in bitter almond samples.

A new method for predicting the acute toxicity of carbamate pesticides based on the perspective of binding information with carrier protein

Toxicity is one of the most important factors limiting the success of new drug development. In this paper, we built a fast and convenient new method (Carrier protein binding information-toxicity relationship, CPBITR) for predicting drug acute toxicity based on the perspective of binding information with carrier protein. First, we studied the binding information between carbamate pesticides and human serum albumin (HSA) through various spectroscopic methods and molecular docking. Then a total of 16 models were established to clarify the relationship between binding information with HSA and drug toxicity. The results showed that the binding information was related to toxicity. Finally we obtained the effective toxicity prediction model for carbamate pesticides. And the "Platform for Predicting Drug Toxicity Based on the Information of Binding with Carrier Protein" was established with the Back-propagation neural network model. We proposed and proved that it was feasible to predict drug toxicity from this new perspective: binding with carrier protein. According to this new perspective, toxicity prediction model of other drugs can also be established. This new method has the advantages of convenience and fast, and can be used to screen out low-toxic drugs quickly in the early stage. It is helpful for drug research and development.

A simple method for obtaining human albumin and its use for in vitro interaction assays with indole-thiazole and indole-thiazolidinone derivatives

This work aimed to develop a simple and low-cost method to obtain human serum albumin (HSA) and its consequent application for in vitro drug interaction assays. The HSA was purified by classic principles of plasma precipitation and thermocoagulation, using a multiple-stage fractionation. The quality of the final product was assessed by electrophoresis, protein dosage by the Lowry method and the pharmacopeial thermal stability. At the end, an isotonic solution of HSA with a total protein concentration of 2.7 mg·mL^-1 was obtained, which was visualized as a single band corresponding to the molecular weight of 66 kDa. After the thermal stability test, there was no indication of turbidity or color change of the solution. Finally, the HSA was useful for interaction assays with indole-thiazole and indole-thiazolidinone derivatives through UV-vis absorption and fluorescence spectroscopic studies, as well as by docking molecular analysis. Derivatives quenched the intrinsic fluorescence of HSA, disrupted the tryptophan residues microenvironment, and probably bind at Sudlow's site I. Therefore, the simplified methodology developed in this work proved to be effective in obtaining HSA that can be applied to research goals including drug interaction assays.

Antitumor and antioxidant activities of purple potato ethanolic extract and its interaction with liposomes, albumin and plasmid DNA

The aim of the study was to broadly determine the biological activities of purple potato ethanolic extract of the Blue Congo variety (BCE). The antioxidant activity of BCE was determined in relation to liposome membranes, and peroxidation was induced by UVB and AAPH. To clarify the antioxidant activity of BCE, we investigated its interactions with hydrophilic and hydrophobic regions of a membrane using fluorimetric and FTIR methods. Next, we investigated the cytotoxicity and pro-apoptotic activities of BCE in two human colon cancer cell lines (HT-29 and Caco-2) and in normal cells (IPEC-J2). In addition, the ability to inhibit enzymes that are involved in pro-inflammatory reactions was examined. Furthermore, BCE interactions with serum albumin and plasmid DNA were investigated using steady state fluorescence spectroscopy and a single molecule fluorescence technique (TCSPC-FCS). We proved that BCE effectively protects lipid membranes against the process of peroxidation and successfully inhibits the cyclooxygenase and lipoxygenase enzymes. Furthermore, it interacts with the hydrophilic and hydrophobic parts of lipid membranes as well as with albumin and plasmid DNA. It was observed that BCE is more cytotoxic against colon cancer cell lines than normal IPEC-J2 cells; it also induces apoptosis in cancer cell lines, but does not induce cell death in normal cells.

Biophysical insight into the binding mechanism of doxofylline to bovine serum albumin: An in vitro and in silico approach

Insight into the mechanistic binding of bovine serum albumin (BSA) with doxofylline can layout pivotal enlightenment with relevance to pharmacokinetics and pharmacodynamics properties. Herein, many spectroscopic techniques and computational methods had been employed to interpret the structural and binding dynamics of BSA-doxofylline interaction. Doxofylline quenched the intrinsic fluorescence of BSA by static quenching. The stoichiometry and the binding constant of the BSA-doxofylline complex were 1:1 and in the order of 10³ M^-1. It was also concluded that the binding process was spontaneous and exothermic, primarily based on the thermodynamic study. Circular dichroism and three-dimensional excitation-emission matrix fluorescence results concluded pronounced conformational and microenvironmental changes in BSA structure on binding with doxofylline. The influence of metal ions and vitamins on the binding affinity of the BSA-doxofylline system were also explored. The in vitro findings were further supported by in silico analysis. With a score value of -6.25 kcal/mol, molecular docking showed strong interactions. Molecular dynamics simulation interpretation also suggested the stable binding with lower deviation in the values of RMSD and RMSF obtained by uninterrupted long simulation run. These studies will propose the optimum potency of distribution of the doxofylline into the bloodstream for asthma treatment.

Investigation on the binding interaction of rhodamine B with human serum albumin: effect of metal ions

The binding of rhodamine B (RB) to human serum albumin (HSA) in the absence and presence of Cu²⁺ or Fe³⁺ under simulated physiological conditions was studied by using various biophysical methods for the first time. The results showed that the interaction between HSA and RB could spontaneously result in the formation of HSA-RB complex (namely, static quenching mechanism) through hydrophobic interactions and hydrogen bonds irrespective of the absence or presence of metal ions. The presence of metal ions led to the reduction of binding affinity of RB to HSA compared with no metal ions, which might result from the conformational change of HSA caused by the binding of metal ions. Furthermore, the analysis of UV-vis absorption, circular dichroism, synchronous fluorescence and three-dimensional fluorescence experiments demonstrated that the addition of RB induced conformational and microenvironmental changes of HSA without and with metal ions. In short, this work will be helpful to in-depth understand the transport mechanism and biological effect of RB and the effect of metal ions on the interaction of HSA-RB in vivo.

Interaction of piroxicam with bovine serum albumin investigated by spectroscopic, calorimetric and computational molecular methods

The binding of drugs to serum proteins is governed by weak non-covalent forces. In this study, the nature and magnitude of the interactions between piroxicam (PRX) and bovine serum albumin (BSA) was assessed using spectroscopic, calorimetric and computational molecular methods. The fluorescence data revealed an atypical behavior during PRX and BSA interaction. The quenching process of tryptophan (Trp) by PRX is a dual one (approximately equal static and dynamic quenched components). The FRET results indicate that a non-radiative transfer of energy occurred. The association constant and the number of binding sites indicate moderate PRX and BSA binding. The competitive binding study indicates that PRX is bound to site I from the hydrophobic pocket of subdomain IIA of BSA. The synchronous spectra showed that the microenvironment around the BSA fluorophores and protein conformation do not change considerably. The Trp lifetimes revealed that PRX mainly quenches the fluorescence of Trp-213 situated in the hydrophobic domain. The CD and DSC investigation show that addition of PRX stabilizes the protein structure. ITC results revealed that BSA-PRX binding involves a combination of electrostatic, hydrophobic and hydrogen interactions. The analysis of the computational data is consistent with the experimental results. This thorough investigation of the PRX-BSA binding may provide support for other studies concerning moderate affinity drugs with serum protein.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization and biological evaluation of novel benzimidazole derivatives

In search of achieving less toxic and more potent chemotherapeutics, three novel heterocyclic benzimidazole derivatives: 2-(1H-benzo[d]imidazol-2-yl)-4-chlorophenol (BM1), 4-chloro-2-(6-methyl-1H-benzo[d]imidazol-2-yl)phenol (BM2) and 4-chloro-2-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (BM3) with DNA-targeting properties, were synthesized and fully characterized by important physicochemical techniques. The DNA binding properties of the compounds were investigated by UV-Visible absorption titrations and thermal denaturation experiments. These molecules exhibited a good binding propensity to fish sperm DNA (FS-DNA), as evident from the high binding constants (K_b) values: 1.9 × 10⁵, 1.39 × 10⁵ and 1.8 × 10⁴ M^‒1 for BM1, BM2 and BM3, respectively. Thermal melting studies of DNA further validated the absorption titration results and best interaction was manifested by BM1 with ΔT_m = 4.96 °C. The experimental DNA binding results were further validated theoretically by molecular docking study. It was confirmed that the molecules (BM1-BM3) bind to DNA via an intercalative and groove binding mode. The investigations showed a correlation between binding constants and energies obtained experimentally and through molecular docking, indicating a binding preference of benzimidazole derivatives with the minor groove of DNA. BM1 was the preferential candidate for DNA binding because of its flat structure, π-π interactions and less steric hindrance. To complement the DNA interaction, antimicrobial assays (antibacterial & antifungal) were performed. It was observed that compound BM2 showed promising activity against all bacterial strains (Micrococcus luteus, Staphylococcus aureus, Enterobacter aerogenes and Escherichia coli) and fungi (Aspergillus flavus, Aspergillus fumigatus and Fusarium solani), while rest of the compounds were active against selective strains. The MIC values of BM2 were found to be in the range of 12.5 ± 2.2-25 ± 1.5 µg/mL. Thus, the compound BM2 was found to be the effective DNA binding antimicrobial agent. Furthermore, the preliminary cytotoxic properties of synthesized compounds were evaluated by brine shrimps lethality assay to check their nontoxic nature towards healthy normal cells.Communicated by Ramaswamy H. Sarma.

Synthesis and characterization of heterobimetallic SnIV-CuII/ZnII complexes: DFT studies, cleavage potential and cytotoxic activity

Heterobimetallic complexes [Cu(L)Sn(CH₃)₂(H₂O)(Cl)] (3) and [Zn(L)Sn(CH₃)₂(H₂O)(Cl)] (4) have been synthesized from their monometallic analogs [Cu(L)(H₂O)(Cl)] (1) and [Zn(L)(H₂O)(Cl)] (2) of Schiff base ligand (L) which were characterized by various spectroscopic and analytical methods. DFT calculations were carried out to simulate the vibrational spectra to support the anticipated structures. The interaction studies of ligand (L) and complexes (1-4) with CT-DNA were performed by employing UV-vis, and fluorescence spectroscopic techniques which revealed that heterobimetallic complexes 3 and 4 showed higher affinity with DNA due to dual mode of action as compared to monometallic complexes 1 and 2. Further, validation of the interaction studies was accomplished by carrying out molecular docking studies with DNA. Gel assay displayed that both the complexes have ability to cleave DNA efficiently and are specific minor groove binders. Cu^II-Sn^IV complex 3 cleaved pBR322 DNA via oxidative mechanism, while Zn^II-Sn^IV complex 4 followed hydrolytic cleavage pathway. In vitro cytotoxicity evaluation of complex 3 was tested on a different cancer cell lines showing promising antitumor activity.Communicated by Ramaswamy H. Sarma.

Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase

The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q² of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q² of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.