Study on the binding mechanism of thiamethoxam with three model proteins:spectroscopic studies and theoretical simulations

Effect of the insecticide clothianidin on the photosynthetic electron transport chain in pea

Clothianidin (CL) is a neonicotinoid insecticide widely used in crop protection against insect pests. However, its effects on photosynthesis remain largely unknown. Here, by investigating the influence of CL at the concentrations of 22 and 110 μg/L on the primary processes of photosynthesis, membrane fluidity and structural changes of pea chloroplasts, we located several primary binding sites of this pesticide. Similar dynamics were observed for both concentrations. However, statistically significant differences were only found at 110 μg/L for all methods used. The light saturated rate of linear electron flow decreased mainly due to the disturbance of electron flow on the acceptor side of photosystem II (PSII) associated with the appearance of QB-nonreducing centers and empty QB binding sites of PSII. The functioning of the donor side of PSII, the activity of photosystem I (PSI) and the maximum quantum yield of PSII photochemistry (Fv/Fm) were not found to be significantly altered. Increased membrane fluidity and structural alterations of the thylakoid membrane led to a decrease in the development of the proton gradient ΔрН and membrane energization processes.

Design, synthesis and characterization of tetra substituted 2,3-dihydrothiazole derivatives as DNA and BSA targeting agents: advantages of the visible-light-induced multicomponent approach

This report describes the visible-light-induced one-pot multicomponent regioselective synthesis of a series of 5-aroyl-3-((arylidene)amino)-2-((arylidene)hydrazono)-4-methyl-2,3-dihydrothiazoles as DNA and BSA targeting agents. The multicomponent condensation of thiocarbohydrazide and aldehydes with α-bromo-1,3-diketones, generated in situ by the bromination of unsymmetrical 1,3-diketones with NBS using white LED light as an environmental friendly source in the presence of EtOAc solvent furnished the titled 2,3-dihydrothiazole derivatives in excellent yields. The exact regioisomeric structure was identified unambiguously by employing multinuclear 2D-NMR spectroscopy [1H-13C] HMBC; [1H-13C] HMQC and [1H-15N] HMBC. Furthermore, the binding characteristics of the synthesized 2,3-dihydrothiazole derivatives were assessed with double-stranded calf-thymus DNA duplex (ct-DNA) and bovine serum albumin (BSA). Initial screening of all the synthesized 2,3-dihydrothiazole derivatives using various in silico techniques including molecular reactivity analysis, Lipinski rule and molecular docking, concluded 5-(4'-chlorobenzoyl)-3-((4''-methoxybenzylidene)amino)-2-(4'''-methoxybenzylidene)hydrazono)-4-methyl-2,3-dihydrothiazole derivative 6a as the most suitable compound for studying binding interaction with DNA and BSA. Additionally, to illustrate the ex vivo binding mode of 6a with DNA and BSA, several spectroscopic techniques viz. UV-visible, circular dichroism (CD), steady-state fluorescence and competitive displacement assays were carried out.

Delineating the cascade of molecular events in protein aggregation triggered by Glyphosate, aminomethylphosphonic acid, and Roundup in serum albumins

The molecular basis of protein unfolding on exposure to the widely used herbicide, Glyphosate (GLY), its metabolite aminomethylphosphonic acid (AMPA), and the commercial formulation Roundup have been probed using human and bovine serum albumins (HSA and BSA). Protein solutions were exposed to chemical stress at set experimental conditions. The study proceeds with spectroscopic and imaging tools. Steady-state and time-resolved fluorescence (TRF) measurements indicated polarity changes with the possibility of forming a ground-state complex. Atomic force microscopy imaging results revealed the formation of fibrils from BSA and dimer, trimer, and tetramer forms of oligomers from HSA under the chemical stress of GLY. In the presence of AMPA, serum albumins (SAs) form a compact network of oligomers. The compact network of oligomers was transformed into fibrils for HSA with increasing concentrations of AMPA. In contrast, Roundup triggered the formation of amorphous aggregates from SAs. Analysis of the Raman amide I band of all aggregates showed a significant increase in antiparallel β-sheet fractions at the expense of α-helix. The highest percentage, 24.6%, of antiparallel β-sheet fractions was present in amorphous aggregate formed from HSA under the influence of Roundup. These results demonstrated protein unfolding, which led to the formation of oligomers and fibrils.

Oligonucleotide nanoassemblies with allyl bromide scaffold-based small molecules

The development of oligonucleotide nanoassemblies with small molecules has shown great potential in bio-medical applications. However, the interaction of negatively charged oligonucleotides with halogenated small molecules represents a scientific challenge. Here, we introduced a distinct allyl bromide halogenated scaffold, which exhibits specific interaction with adenine nucleic bases of the oligonucleotides, thus leading to the formation of self-assembled nanostructures.

Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase-A Computational Study

Coproheme decarboxylase (ChdC) is an important enzyme in the coproporphyrin-dependent pathway (CPD) of Gram-positive bacteria that decarboxylates coproheme on two propionates at position 2 and position 4 sequentially to generate heme b by using H₂O₂ as an oxidant. This work focused on the ChdC from Geobacillus stearothermophilus (GsChdC) to elucidate the mechanism of its sequential two-step decarboxylation of coproheme. The models of GsChdC in a complex with substrate and reaction intermediate were built to investigate the reorienting mechanism of harderoheme. Targeted molecular dynamics simulations on these models validated that harderoheme is able to rotate in the active site of GsChdC with a 19.06-kcal·mol^-1 energy barrier after the first step of decarboxylation to bring the propionate at position 4 in proximity of Tyr145 to continue the second decarboxylation step. The harderoheme rotation mechanism is confirmed to be much easier than the release-rebinding mechanism. In the active site of GsChdC, Trp157 and Trp198 comprise a "gate" construction to regulate the clockwise rotation of the harderoheme. Lys149 plays a critical role in the rotation mechanism, which not only keeps the Trp157-Trp198 "gate" from being closed but also guides the propionate at position 4 through the gap between Trp157 and Trp198 through a salt bridge interaction.

Investigating binding dynamics of trans resveratrol to HSA for an efficient displacement of aflatoxin B1 using spectroscopy and molecular simulation

Resveratrol is a polyphenol belonging to the class stilbenes. The active and stable form of resveratrol is trans-resveratrol. This polyphenol is bestowed with numerous biological properties. Aflatoxin B₁ is a hepato-carcinogen and mutagen that is produced by Aspergillus species. In this study, the interaction of trans-resveratrol with HSA followed by competitive dislodging of AFB₁ from HSA by trans-resveratrol has been investigated using spectroscopic studies. The UV-absorption studies revealed ground state complex formation between HSA and trans-resveratrol. Trans-resveratrol binds strongly to HSA with the binding constant of ~ 10⁷ M⁻¹ to a single binding site (n = 1.58), at 298.15 K. The Stern–Volmer quenching constant was calculated as 7.83 × 10⁴ M⁻¹ at 298.15 K, suggesting strong fluorescence quenching ability of trans-resveratrol. Site markers displacement assay projected subdomain IIA as the binding site of trans-resveratrol to HSA. The molecular docking approach envisages the amino acid residues involved in the formation of the binding pocket. As confirmed from the site marker displacement assays, both trans-resveratrol and AFB₁ binds to HSA in the same binding site, subdomain IIA. The study explores the ability of trans-resveratrol to displace AFB₁ from the HSA-AFB₁ complex, thereby affecting the toxicokinetic behavior of AFB₁ associated with AFB₁ exposure.

Aflatoxin B1 Induced Structural and Conformational Changes in Bovine Serum Albumin: A Multispectroscopic and Circular Dichroism-Based Study

Aflatoxin B₁ (AFB₁) is a mutagen that has been categorized as a group 1 human carcinogen by the International Agency for Research on Cancer. It is produced as a secondary metabolite by soil fungi Aspergillus flavus and Aspergillus parasiticus . Here, in this study, the effect of AFB₁ on the structure and conformation of bovine serum albumin (BSA) using multispectroscopic tools like fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, and circular dichroism spectropolarimetry has been ascertained. Ultraviolet absorption spectroscopy revealed hyperchromicity in the absorption spectra of BSA in the presence of AFB₁. The binding constant was calculated in the range of 10⁴ M^-1, by fluorescence spectroscopy suggesting moderate binding of the toxin to BSA. The study also confirms the static nature of fluorescence quenching. The stoichiometry of binding sites was found to be unity. The competing capability of warfarin for AFB₁ was higher than ibuprofen as calculated from site marker displacement assay. Förster resonance energy transfer confirmed the high efficiency of energy transfer from BSA to AFB₁. Circular dichroism spectropolarimetry showed a decrease in the α-helix in BSA in the presence of AFB₁. The melting temperature of BSA underwent an increment in the presence of a mycotoxin from 62.5 to 70.3 °C. Molecular docking confirmed the binding of AFB₁ to subdomain IIA in BSA.