Evaluation of the binding behavior of olmutinib (HM61713) with model transport protein: Insights from spectroscopic and molecular docking studies

Impact of casein binding on thermal degradation of oxytetracycline: kinetics, products, and their toxicity

This work systematically investigated the effect of casein on the thermal transformation behavior of oxytetracycline (OTC). Fluorescence quenching and isothermal titration calorimetry experiments confirmed that OTC binds spontaneously to casein via non-covalent interactions. The -N(CH3)2 group in OTC was identified as the primary binding site. Casein-bound OTC was prepared using a combination of dialysis and ultrafiltration. During thermal treatment, the degradation of free OTC followed zero-order kinetics, whereas casein-bound OTC adhered to first-order kinetics. Seven identical thermal transformation products were identified, but the quantities of these products varied significantly depending on the existing form of OTC molecule. The binding of casein weakened the reactivity of the -N(CH3)2 group while enhancing the reactivity of degradation sites on the adjacent ring, resulting in decreased production of three lower-toxic products and increased production of four higher-toxicity products. Cytotoxicity assays revealed that heating increased the overall toxicity of OTC, particularly in its bound form.

Deciphering the molecular interaction between Vitamin D3 and pepsin by in vitro and in silico perspectives

The current study explored the molecular interaction between Vitamin D3 (Vit D3) and pepsin using multi-spectroscopic, molecular dynamic simulation (MDS), and molecular docking. The fluorescence emission spectra discovered Vit D3 interacted with pepsin in a static quenching manner due to the formation of the steady-state complex. Thermodynamic data revealed the spontaneous binding of Vit D3 on pepsin. The formation of the Pepsin-Vit D3 complex was also validated by circular dichroism (CD) spectroscopy. The fluorescence and CD spectroscopy results revealed Vit D3 altered the tertiary and secondary structure of pepsin, respectively. Meanwhile, FTIR spectroscopy results revealed a hypochromic shift in the amide I and II peaks. Kinetic parameters showed Vit D3 inhibited the activity of pepsin by the uncompetitive process. Applied spectroscopic methods disclosed that Vit D3 binding to pepsin caused microenvironmental modifications around the aromatic residues of protein and changed its structure and function. Moreover, MD simulation and molecular docking were done to analyze the formation of Pepsin-Vit D3 complexes. Molecular docking findings demonstrated the interaction of Vit D3 with pepsin mainly involved van der Waals forces and hydrogen bonds that were in good agreement with the fluorescence results. Finally, MDS findings including RMSD, RMSF, and RG confirmed all the experimental data.

Study on behavior intermolecular force and binding mechanism interaction between bovine hemoglobin and cyanocobalamin by using of spectroscopic and molecular docking methods

In this study, fluorescence, synchronous fluorescence, fluorescence resonance energy transfer (FRET), Fourier transform infrared (FT-IR) and molecular docking methods were employed to investigate the binding mechanism between bovine hemoglobin (BHb) and vitamin B12 (cyanocobalamin). Since BHb shares 90% sequence similarity with human hemoglobin investigating its interactions with small molecules is highly relevant. Fluorescence data analysis under varying temperatures indicated that the complex formation between vitamin B12 and BHb is stationary with ground-state complex formation. Thermodynamic investigation indicated hydrogen bonding and hydrophobic interactions in negative changes in enthalpy and entropy during the process of binding. Förster resonance energy transfer analysis determined the binding distance of vitamin B12 with BHb tryptophan residues as 3.11 nm. FT-IR spectroscopy, synchronous fluorescence and UV-visible examinations revealed that vitamin B12 may induce structural modification in BHb. Additionally, molecular docking simulations provided information about binding interactions and validated the spectroscopic findings.

Spectroscopic and molecular docking investigation on the interaction of a water-soluble Cu(II) complex containing diethanolamine and dipicolinic acid ligands with human serum albumin

Under physiological conditions, spectroscopic techniques as well as molecular docking simulation have been used to investigate the binding interaction mechanism between Cu(II) complex containing Pyridine-2,6-dicarboxylic acid (PDCA) and Diethanolamine (DEA) ligands, [Cu(DEA)(PDCA)] and human serum albumin (HSA). UV spectral changes of protein in the presence of the Cu(II) complex suggested the formation of a Protein-Cu(II) complex conjugate with specific new structure. The Cu(II) complex quenches the intrinsic fluorescence of the HSA via a static mechanism in which van der Waals interactions along with hydrogen bonds are fundamental binding forces. Displacement experiments performed by warfarin and ibuprofen site probes predict that the Cu(II) complex is located in subdomain IIA, Sudlow site 1 of HSA. Molecular docking results showed close resemblance with experimental data.

In vitro anticancer effects in hepatocellular carcinoma (HCC) and protein interaction study of xanthoangelol

Xanthoangelol (C25H28O4), a natural flavonoid derived from chalcones, has shown potential pharmacological activities. However, its primary interaction mechanism with proteins and cells is not well understood. In the present study, we focus on the anticancer effects of xanthoangelol against hepatocellular carcinoma (HCC) as well as its binding affinity with a plasma drug carrier protein, α2-macroglobulin. The anticancer effects of xanthoangelol on human HCC cell line HepG2 cells were assayed using MTT, LDH, qPCR, and caspase activity assays. Efficient binding of the xanthoangelol with α2-macroglobulin was established by experimental and molecular docking studies. It was found that xanthoangelol significantly mitigates cell viability through upregulating intrinsic (Bax/Bcl-2, caspase-9) and extrinsic (caspase-8) apoptotic pathways. Moreover, it was detected that xanthoangelol induces ER stress through the upregulation of CHOP in HepG2 cells. Fluorescence spectra show that xanthoangelol strongly interacts with α2-macroglobulin mediated by a static quenching mechanism and Trp1237 and Tyr1323 residues were exposed to the solvent with the addition of xanthoangelol. Meanwhile, both experimental and theoretical studies display that hydrophilic forces play a key role in the formation of xanthoangelol-α2-macroglobulin complex, leading to a slight conformational change in α2-macroglobulin. In conclusion, our findings suggest that xanthoangelol, which has a high binding affinity for a plasma carrier protein, may inhibit the viability of HCC by inducing apoptosis and ER stress.

Synthesis, characterization, and biological activities of novel organometallic compounds of rhenium(I) with 2-(2-benzylidenehydrazinyl) benzothiazole Schiff-base derivatives: Molecular docking, ADME, and DFT studies

A series of substituted 2-(2-benzylidenehydrazinyl)benzothiazole Schiff-base derivatives and complexes containing Re(I) were synthesized and analyzed using various characterization techniques, including elemental analysis, conductance measurement, 1H-NMR, FT-IR, and LC-MS. The biological activities of the compounds were evaluated. Binding affinity between the complexes and calf thymus DNA (CT-DNA) was conducted using UV-visible spectroscopy, viscosity measurement, fluorescence spectroscopy, and molecular docking studies, indicating intercalation binding mode. The broth dilution method evaluated antibacterial activity against two Gram-positive and three Gram-negative bacteria. The results demonstrated the effectiveness of each complex against the tested pathogens. The MTT assay examined cytotoxic qualities on MCF-7 cell lines, demonstrating strong cytotoxic effects. The lethality of brine prawn assay was employed to assess the toxicity of the compounds. The Schiff base was optimized using the 6-31 G (d, p) basis set and B3LYP techniques. Density functional theory calculations were performed to compare the bond angles and lengths of the synthesized compounds with experimental values, showing good agreement, and to calculate the related orbital energies. The therapeutic qualities were evaluated using an in silico ADMET model, which verified that the synthesized compounds have qualities similar to those of drugs.

Exploring the interactions between bovine serum albumin and sodium propionate through multi-spectroscopic and molecular docking analyses

To investigate the influence of sodium propionate (SP) on bovine serum albumin (BSA), it is important to study its thermodynamic properties, binding mode, and its impact on the conformation of it. Herein, the interactions between BSA and SP were examined using various spectroscopic methods and molecular docking analyses. The Stern-Volmer plot revealed that the SP can efficiently quench the BSA intensity through a mechanism of hybrid quenching. Fluorescence quenching of BSA emission intensity in existence of SP implies that the microenvironment around the fluorophores (Trp residues) is altered. The calculated thermodynamic parameters suggests that the SP interacts with BSA through hydrogen bonds and van der Waals interactions. According to the results, the most significant change in synchronous fluorescence of BSA occurred in the vicinity of the Trp microenvironment residues rather than the Tyr residues. The results of site-competitive replacement studies determined that SP can be bound to site I and II in the BSA molecule. FT-IR spectroscopy results showed that the secondary structure of the BSA undergoes changes after interacting with SP. Using molecular docking analysis, the binding energy of SP toward BSA was -6.26 kJ mol-1, indicating a favorable binding affinity to the protein.

Unraveling binding interactions between methasterone and bovine serum albumin (BSA): A spectroscopic and computational study

In this study, binding interactions between methasterone and bovine serum albumin (BSA) were analyzed using spectroscopic techniques and molecular docking. UV absorption spectroscopy showed the formation of a ground-state complex between methasterone and bovine serum albumin (BSA). Thermodynamic parameters from fluorometric analysis indicated that the hydrogen bonding and van der Waal forces were the main interacting forces between the complex and the reaction was found to be spontaneous. Molecular docking further validated it. Nano differential scanning fluorimetry showed the protein was found to be more thermally stable in the presence of methasterone. Circular dichroism spectroscopy revealed slight reduction in the helicity after binding with methasterone suggesting conformational changes to promote binding. As no prior information exists on the binding interactions between methasterone and BSA, this study provides insights into methasterone-BSA interactions, which can serve as a foundation for future investigations into its pharmacological properties.

Enzymatic Hydrolysates of κ-Carrageenan by κ-Carrageenase-Based Magnetic Cross-Linked Nanoflowers Confers Pancreatic Lipase Inhibition Activity

The immobilized κ-carrageenase MCNF was developed by synergistic integration of κ-carrageenase, calcium phosphate crystals, and magnetic nanoparticles. MCNF outperformed free κ-carrageenase in terms of optimal temperature, thermostability (45-55 °C), stability (pH 6.0 and 12.0), and storage stability. Furthermore, MCNF was extremely reusable and easy to separate from the reaction system. MCNF's enzymatic breakdown of κ-carrageenan resulted in a tetrasaccharide that competitively inhibited pancreatic lipase (PL). Fluorescence titration experiments showed that κ-carrageenan tetrasaccharide altered the microenvironment of PL by causing static bursting of its intrinsic fluorescence. The circular dichroism experiment demonstrated that adding κ-carrageenan tetrasaccharide reduced α-helix content and increased β-sheet content in PL's secondary structure. Molecular docking and dynamics simulation research suggested that the κ-carrageenan tetrasaccharide could form a stable complex with PL, entering its hydrophobic cavity and occupying its active site, reducing PL's catalytic activity. κ-Carrageenan tetrasaccharide could inhibit PL, making it a promising therapeutic agent for obesity prevention and treatment.

Probing the interactions of genistein with HMGB1 through multi-spectroscopic and in-silico approaches

Functional regulation of proteins by ligand-protein interactions plays a crucial role in understanding biological processes and identifying potential drugs. High mobility group box 1 (HMGB1) plays a pivotal role in sterile inflammation as a key immunomodulatory protein. Genistein, a well-known isoflavone compound, has been shown to have neuroprotective effects. In this study, we investigated the genistein-HMGB1 interactions using experimental and computational approaches. Our results revealed that genistein binds to HMGB1 with a KD value of 6.06 × 10-5 M. The addition of genistein significantly quenched the fluorescence of HMGB1. Thermodynamic analyses demonstrated that hydrogen bonds and hydrophobic forces are the primary forces during the binding process. Furthermore, the interaction between genistein and HMGB1 led to changes in the microenvironment of protein chromogenic amino acids and subtle alterations in the protein secondary structure. Molecular modeling results indicate that Pro95, Pro98, and Lys154 are the major amino acid residues for genistein binding to HMGB1. Meanwhile, at the cellular level, an inhibitory effect of genistein on HMGB1-induced NO release from microglia was observed, demonstrating an inhibition rate of 42.1 %. Our studies demonstrated that genistein could be applied in treating neurological diseases through its interaction with HMGB1.

Exploring the binding characteristics between lorlatinib and human alpha-1-acid glycoprotein: Multispectral and molecular modeling techniques

Approval in 2019 was granted for the highly selective, targeted agent lorlatinib, which primary target is ROS1 and ALK. The purpose of this work was to examine the binding mechanism between lorlatinib (LOR) and HAG employing multispectral and molecular modeling techniques. Fluorescence data demonstrated that LOR quenched HAG fluorescence as a static quenching, interecalated into the hydrophobic cavity of HAG with a moderate affinity. Thermodynamic and competitive experiments pointed out that LOR bound with HAG primarily through hydrogen bonding, hydrophobic, and van der Waals forces. Circular dichroism, three-dimensional and synchronous fluorescence spectroscopic studies noted that the secondary structure of HAG and microenvironments around tyrosine (Tyr) and tryptophan (Trp) residues were altered due to binding with LOR. The contribution of each energy involved in binding process of LOR and HAG has been analyzed by molecular simulation techniques. Besides, the environmental conditions with metal ions have also been studied. The present study is expected to provide a theoretical basis for further studying the metabolism of LOR in vivo, which may help to gain a deeper understanding of the general pharmacological activity of the drug.

Photophysical Properties, Fluorescence Quenching of Metformin Hydrochloride by Caffeine, and its Docking with the AMP-activated protein kinase receptor

In this research, the photophysical properties of metformin hydrochloride (MF-HCl) were studied using spectroscopic and molecular docking techniques. The interaction between metformin hydrochloride and caffeine is essential for understanding the pharmacokinetics of metformin, particularly in populations with high caffeine consumption. Metformin is a first-line medication for managing type 2 diabetes, while caffeine is a widely consumed dietary stimulant. Knowing how caffeine may affect the action of metformin is crucial for effective diabetes management. The spectroscopic techniques results showed that the photophysical properties (fluorescence quantum yields, lifetime, radiative, and non-radiative decay) of the drug are influenced by solvent polarity and drug concentration. The binding mechanism of metformin hydrochloride-caffeine (MF-HCl-CAF) was identified through the fluorescence quenching method. The quenching of drugs induced by caffeine is due to ground state complex formation. The binding occurs due to hydrogen bonds and Van der Waals forces in the reaction. The förster resonance energy transfer (FRET) between metformin hydrochloride and caffeine was also calculated using flourtools.com software. The threshold distance (R0), for 50% energy transfer from metformin hydrochloride to caffeine is 1.81 nm and the binding distance (r), between caffeine and the amino acid residue in metformin hydrochloride is 1.55 nm. Dynamic light scattering (DLS), Zeta potential, and Fourier transform infrared (FTIR) spectroscopy confirm the conformational change of the drugs, as the caffeine molecule binds to metformin hydrochloride molecules. The molecular docking of metformin hydrochloride with the amp-activated protein kinase receptor (PDB Id: 1z0n) is analyzed. Again the docking of both metformin hydrochloride and caffeine (two ligands) with the protein receptor (PDB Id: 1z0n) was also analyzed and the results agreed with the fluorescence quenching techniques.

Insights into the Binding of Metadoxine with Bovine Serum Albumin: A Multi-Spectroscopic Investigation Combined with Molecular Docking

BACKGROUND

Metadoxine, also known as pyruvate dehydrogenase activator, is a small molecule drug that has been used in the treatment of various medical conditions. Bovine serum albumin is a commonly studied protein that serves as a plasmatic for understanding protein-drug interactions due to its abundance.

OBJECTIVE

This research suggests that metadoxine can bind to bovine serum albumin with moderate affinity, leading to an alteration in the secondary structure of the protein, which may also influence the protein's stability and function, which could provide a comprehensive understanding of the interaction at a molecular level. In this study, a variety of methodologies wereused to determine various thermodynamic parameters.

METHODS

The study uses UV-visible, Fluorescence, Fourier-transform infrared, Circular dichroism spectroscopy, and Molecular docking to analyze the interaction between bovine serum albumin and metadoxine, providing thermodynamic parameters for understanding the protein structure and its binding.

RESULT

The binding of metadoxine with bovine serum albumin, causes a hyperchromic shift. In fluorescence spectroscopy, the value of the Stern Volmer increases constantly with an increase in temperature, suggesting a stronger interaction between the Metadoxine and the Bovine serum albumin, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism indicated a reduction in the secondary structure of Bovine serum albumin.

CONCLUSION

The interactions between metadoxine and bovine serum albumin, cause hyperchromic shift revealed by UV-visible spectroscopy, whereas in Fluorescence spectroscopy, the value of the Stern Volmer constant increases with an increase in temperature, suggesting a stronger interaction between the MD and the BSA, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism spectroscopy indicated a reduction in the secondary structure of the protein, as evidenced by the shifting of the amide II band and leading to a slight decrease in the α- helix content. The molecular docking shows that metadoxine was docked in the subdomain IIA binding pocket of BSA.

Probing the Biomolecular Interactions of DNA/HSA with the New Sn(IV) Complex and Computational Perspectives: Design, Synthesis, Characterization, Anticancer Activity, and Molecular Modeling Approach

The ligands 2,2'-bipyridyl and indole-3-carboxylic acid were used to create a Sn(IV) complex, which was then synthesized and carefully characterized using elemental analysis and spectroscopic techniques (UV-vis, IR, 1H, 13C, and 119Sn NMR, and ESI-MS) and RXPD. Utilizing biophysical techniques such as UV-vis, fluorescence titrations, circular dichroism, FTIR (for HSA), and cleavage activity (for DNA), in vitro binding studies of Sn(IV) complex and DNA/HSA were satisfied with the strong electrostatic binding interaction of the Sn(IV) complex via the phosphate backbone of the DNA helix as well as in the subdomain IIA of HSA. The observed trend in the binding interactions and computational studies of the Sn(IV) complex was attributed to the nature of the ligands bound to the Sn(IV) center that influences their in vitro activities. The Sn(IV) complex showed sufficient effectiveness to be considered a viable candidate for the creation of anticancer medications.

Probing the binding mode and interactions of proteinase K and glutathione: molecular simulation and experiments

Proteinase K, a serine protease from Tritirachium album Limber, is crucial in research due to its potent proteolytic activity, which relies on conformational stability and substrate affinity. Glutathione (GSH), an essential intracellular antioxidant, regulates various physiological processes by interacting with proteins, influencing their stability and function. Despite the importance of both proteinase K and GSH, their potential interaction remains unexplored. Understanding this interaction could uncover new regulatory mechanisms affecting proteinase K, with significant implications for research and therapeutic applications. In this study, we systematically investigated the binding of GSH to proteinase K using a comprehensive approach in which theoretical and experimental methods mutually validate each other. Molecular docking determined the binding mode and the interaction mechanism of proteinase K and GSH. Molecular dynamics (MD) simulations revealed that GSH binding significantly improved the stability of proteinase K, affirming the binding process was spontaneous, with hydrogen bonds and van der Waals forces emerging as the predominant contributors throughout the interaction. At the same time, the fluorescence spectrum and circular dichroism spectrum confirmed the interaction mechanism between GSH and proteinase K, as well as the conformational changes of proteinase K induced by GSH binding. We believe this study could offer valuable insights for future research into the structure and binding dynamics of other protein-ligand complexes under physiological conditions.

The presence of NSAIDs may affect the binding capacity of serum albumin to the natural products hymecromone and umbelliferone

The natural products 7-hydroxycoumarin (7HC) and 7-hydroxy-4-methylcoumarin (7H4MC), known as umbelliferone and hymecromone, respectively, are one of the simplest structural examples from coumarin's family, showing several biological activities. Bovine serum albumin (BSA) is the main model protein used in laboratory experiments to characterize the biophysical capacity of potential drugs to be carried until the target in the bloodstream. Thus, the interaction BSA:7HC and BSA:7H4MC was biophysically characterized by circular dichroism (CD), steady-state, and time-resolved fluorescence techniques combined with molecular docking calculations via cross-docking approach to better correlate with the biological medium. There is a ground-state association BSA:7HC/7H4MC, and the presence of the methyl group in the coumarin core did not change the binding affinity and trend to BSA significantly. However, comparing the obtained data with those reported to benzo-α-pyrone there is evidence that the incorporation of the hydroxyl group in the aromatic ring A of the coumarin core improves the binding affinity to albumin around 10-folds and changes the binding site from subdomain IIA to IIIA or IB. In addition, the presence of other drugs, e.g., naproxen or ketoprofen, might interfere with the binding capacity of 7HC and 7H4MC, resulting in perturbations on the residence time of some clinically used drugs in the bloodstream.

68Ga labeled Olmutinib: Design, synthesis, and evaluation of a novel PET EGFR probe

Radiolabeled tyrosine kinase inhibitors (TKIs) offer a promising approach for molecular imaging of EGFR-positive cancers. Despite the development of various EGFR small-molecule probes, none of the 68Ga-labeled small-molecule probes based on the chelator DOTA have shown tumor-specific uptake. To address this challenge, we selected Olmutinib, a third-generation EGFR covalent inhibitor, as a PET imaging tracer for EGFR-positive tumors. We synthesized the precursor DOTA-Olmutinib through a five-step process and subsequently radiolabeled it with 68Ga to prepare 68Ga-DOTA-Olmutinib. 68Ga-DOTA-Olmutinib displayed moderate lipophilicity (log P = 0.85) and exhibited high stability in vitro and in vivo. Western blot analysis was used to detect the level of EGFR in multiple tumor cells. In cell uptake experiments, 68Ga-DOTA-Olmutinib exhibited enhanced uptake specifically in tumor cells with a higher level of EGFR supporting it as an EGFR-specific tracer. Additionally, PET/CT imaging with 68Ga-DOTA-Olmutinib showed significant tumor uptake at 60 min with 4 % ID/g post-injection, marking a breakthrough, though the uptake is not yet ideal. Overall, our results suggest that 68Ga-labeled Olmutinib holds promise as a potential PET tracer for detecting EGFR-positive cancers.

Multispectral and molecular simulation of the interaction of human α1-acid glycoprotein with palbociclib

Palbociclib, a selective CDK4/6 inhibitor with potent anti-tumor effects, was investigated for its interaction with human α1-acid glycoprotein (HAG). Spectral analysis revealed that palbociclib forms a ground state complex with HAG, exhibiting binding constant (Kb) of 104 M-1 at the used temperature range. The interaction between the two was determined to be driven mainly by hydrogen bonding and hydrophobic forces. Multispectral studies indicated that the bound palbociclib altered the secondary structure of HAG and reduced polarity around Trp and Tyr amino acids. And, molecular docking and dynamics simulations verified the experimental findings. Finally, most of the metal ions present in plasma, such as K+, Cu2+, Ca2+, Mg2+, Ni2+, Fe3+, and Co2+, are detrimental to the binding of palbociclib to HAG, with the exception of Zn2+, which is favorable.

Binding of a Drug (Colchicine) to L-Asparaginase Enzyme Using Multispectroscopic, Thermodynamics, and Simulation Studies: Possible Implication in Acute Lymphoblastic Leukemia Treatment

The research aims to elucidate how drug interactions affect the activity of L-asparaginase (L-ASNase), an essential enzyme in cancer treatment, especially for acute lymphoblastic leukemia (ALL). Understanding these interactions is crucial for optimizing treatment effectiveness and reducing adverse effects. This study explores the intricate molecular interactions and structural dynamics of L-ASNase upon binding with colchicine. Fluorescence quenching experiments were conducted at various temperatures (298, 303, and 310 K), revealing notable interactions between L-ASNase and colchicine. These interactions were characterized by a reduction in fluorescence intensity and a blue shift in emission maxima. Additional analyses, including the determination of Stern-Volmer quenching constants (KSV), bimolecular quenching rate constants (kq), and thermodynamic parameters, indicated a static quenching mechanism with moderate binding affinities (Ka: 1.40-2.71 × 104 M-1) across different temperatures. Thermodynamic study suggested positive enthalpy and entropy changes (ΔH° = -10.26 kcal mol-1; ΔS° = -14.19 cal mol-1 K-1), suggesting a spontaneous reaction with negative ΔG° values (-5.86 to -6.03 kcal mol-1). FRET measurements supported optimal distances (r and Ro) for FRET occurrence, reinforcing the static quenching mechanism. Molecular docking further supported these findings, revealing a 1:1 stoichiometric binding ratio for L-ASNase:colchicine and elucidating specific binding orientations and interactions critical for complex stability. Subsequent molecular dynamics simulations spanning 100 ns underscored the stability of the L-ASNase-colchicine complex, with minimal deviations observed in key structural parameters such as RMSD, RMSF, Rg, and SASA. Additionally, spectroscopic analyses, including circular dichroism (CD), synchronous fluorescence, and 3D fluorescence provided insights into the conformational changes and alterations in the microenvironment of aromatic amino acid residues in L-ASNase upon colchicine binding. Moreover, L-ASNase activity was slightly reduced by 25% in the presence of colchicine. This comprehensive investigation sheds light on the molecular intricacies of the L-ASNase-colchicine complex, advancing our understanding of drug-target interactions and offering potential avenues for therapeutic applications.

Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Cancer: Current Use and Future Prospects

Tyrosine kinase inhibitors (TKIs) have emerged as a leading targeted cancer therapy, reducing the side effects often seen with non-targeted treatments, especially the damage to healthy cells. To tackle resistance, typically caused by epidermal growth factor receptor (EGFR) mutations, four generations of TKIs have been developed. Each generation has shown improved effectiveness and fewer side effects, resulting in better patient outcomes. For example, patients on gefitinib, a first-generation TKI, experienced a progression-free survival (PFS) of 10 months compared to 5 months with conventional chemotherapy. Second-generation TKI afatinib outperformed erlotinib and extended PFS to 11.1 months compared to 6.9 months with cisplatin. Third-generation TKIs further increased survival to 38.6 months, compared to 31.8 months with first-generation TKIs. This progress demonstrates the ability of newer TKIs to overcome resistance, particularly the T790M mutation, while reducing adverse effects. Ongoing research focuses on overcoming resistance from newer mutations like C797S to further improve patient survival. These developments highlight the significant progress in TKI therapy and the continued effort to refine cancer treatment. Recent research in South Korea shows that third-generation TKIs are ineffective against non-small cell lung cancer (NSCLC) with the C797S mutation. Several trials have started showing promising in vitro and in vivo results, but more trials are needed before clinical approval. This review underscores notable advancements in the field of EGFR TKIs, offering a comprehensive analysis of their mechanisms of action and the progression of various TKI generations in response to resistance.

Exploring the binding characteristics of bovine serum albumin with CDK4/6 inhibitors Ribociclib: Multi-spectral analysis and molecular simulation studies

Ribociclib (RIB), a tyrosine kinase inhibitor, exhibits promising antitumor efficacy and controlled toxicity in HR+/HER2- breast cancer patients, which is closely related to the binding with plasma proteins. This study utilized a combination of spectroscopic techniques including UV spectroscopy, fluorescence spectroscopy, and circular dichroism (CD) as well as molecular docking and molecular dynamic simulation to clarify the binding mechanism between bovine serum albumin (BSA) and RIB. The findings demonstrated that RIB produced a 1:1 stoichiometric complex with BSA, which quenched BSA's fluorescence in the manner of the static quenching mechanism. Site labelling experiments pinpointed Site III on BSA as the primary binding site for RIB, a finding validated by molecular docking. Van der Waals forces and hydrogen bonding interactions as key drivers in the formation of RIB-BSA complexes, a conclusion supported by molecular docking. Molecular simulation studies suggested that the insertion of RIB into the hydrophobic cavity (Site III) of BSA induced subtle conformational changes in the BSA protein, and CD measurements confirmed alterations in BSA secondary structure content. Synchronous and three-dimensional fluorescence spectroscopy further demonstrated that RIB decreased the hydrophobicity of the microenvironment surrounding tyrosine and tryptophan residues. These findings offer valuable insights into the pharmacokinetics and structural modifications of RIB.

Exploring the binding behaviors between nisoldipine and bovine serum albumin as a model protein by the aid of multi-spectroscopic approaches and in silico

Bovine serum albumin (BSA), a model protein was used to evaluate the binding behavior of nisoldipine and human serum albumin by a series of experiments and in silico in this article. The outcomes suggested that nisoldipine and BSA formed the nisoldipine-BSA complex with a molar ratio of 1:1, caused the fluorescence quenching of BSA, which quenching mechanism was attributable to static quenching. The binding constant of the nisoldipine-BSA complex was (1.3-3.0) × 104 M-1 at 298-310 K, indicating that nisoldipine on BSA protein had a moderate affinity. During the complexation of nisoldipine with BSA, nisoldipine can spontaneously insert into the site II (subdomain III A) of BSA and the distance of energy transfer from donor group in protein to acceptor group in nisoldipine was 3.21 nm, which led to the change in the hydrophobicity of the microenvironment surrounding Trp residues and in the secondary structure of BSA. Additionally, the findings also confirmed that the hydrogen bond and van der Waals force were responsible for forming the nisoldipine-BSA complex and the complexation process was a spontaneous exothermic process.Communicated by Ramaswamy H. Sarma.

Interactions of three berberine mid-chain fatty acid salts with bovine serum albumin (BSA): Spectroscopic analysis and molecular docking

In this paper, the interaction of three berberine mid-chain fatty acid salts ([BBR][FAs]), viz. berberine caproate ([BBR][CAP]), berberine heptylate ([BBR][HEP]) and berberine octoate ([BBR][OCT]), with bovine serum albumin (BSA) was studied by means of UV-visible absorption spectroscopy, fluorescence spectroscopy, fourier transform infrared spectroscopy (FT-IR) and molecular docking techniques. Fluorescence experiments revealed that three berberine salts quench the fluorescence of BSA by static quenching mechanism resulted from a stable [BBR][FAs]-BSA complex formation. The stoichiometric numbers of [BBR][FAs]-BSA complexes were found to be 1:1. Synchronous and three-dimensional fluorescence spectra as well as FT-IR demonstrated that the binding of [BBR][FAs] altered the microenvironment and conformation of BSA. The binding average distance from [BBR][FAs] to BSA (3.2-3.5 nm) was determined according to Förster energy transfer theory. Site probe investigation showed that [BBR][FAs] bound to BSA active site I (sub-domain IIA). The binding promotes the esterase-like activity of BSA. The molecular docking results confirmed the fluorescence competition findings and provided the type of binding forces. Furthermore, the relationship between the anionic chain length of [BBR][FAs] and the interaction was explored, and the positive correlation was found.

Structural and functional impacts of neonicotinoids analogues on Apis mellifera's chemosensory protein: Insights from spectroscopic and molecular modeling investigations

In the intricate web of ecological relationships, pollinators such as the Italian honeybee (Apis mellifera) play a crucial role in maintaining biodiversity and agricultural productivity. This study focuses on the interactions between three neonicotinoid compounds and the honeybee's chemosensory protein 3 (CSP3), a key player in their olfactory system. Employing advanced spectroscopic techniques and molecular modeling, we explore the binding dynamics and conformational changes in CSP3 upon exposure to these pesticides. The research reveals that all three neonicotinoids considerably quench CSP3's fluorescence through a dynamic and static mixing mechanism, indicating a strong binding affinity, predominantly driven by hydrophobic interactions. UV-visible absorption, synchronous fluorescence, and 3D fluorescence spectra support slight changes in the microenvironment around the aromatic amino acids of CSP3. Circular dichroism spectra indicate a reduction in CSP3's α-helix content, suggesting structural alterations. Molecular docking and dynamics simulations further elucidate the binding modes and stability of these interactions, highlighting the role of specific amino acids in CSP3's binding cavity. Findings provide critical insights into molecular mechanisms by which neonicotinoids may impair honeybee chemosensory function, offering implications for designing safer pesticides and understanding the broader ecological impact of these chemicals on pollinator health.

Experimental and Theoretical Approaches to Monitor the Behavior of Bovine Liver Catalase in Interaction with a Binuclear Bismuth Complex

Here, the antioxidant potency of a binuclear Bi(III) complex {[Bi2(μ-ox)(dipic)2(H2O)2 (taa)2].H2O, where ox2- = oxalato, dipic2- = pyridine 2,6-dicarboxylato, and taa = thiourea} was evaluated using the •DPPH assay. It was demonstrated that the Bi complex exhibited a high ability to inhibit DPPH free radicals. The binding mechanism of the complex with bovine liver catalase (BLC) was also investigated, revealing structural and activity changes in the enzyme in the presence of the complex. The catalase activity in the decomposition of hydrogen peroxide increased in the presence of the Bi complex, reaching 39.8% higher than its initial activity at a concentration of 7.77 × 10-6 M. The complex exhibited a relatively high affinity for BLC, with K b values of 3.98, 0.13, and 0.09 × 105 M-1 at 303, 310, and 317 K, respectively. The mechanisms involved in the interaction were hydrogen bonding and van der Waals interactions, as validated through molecular docking simulations. Synchronous fluorescence showed that tryptophan was more affected by enzyme-complex interactions than tyrosine. In addition, a cell viability test using the MTT method revealed that at its highest concentration, the Bi complex caused a decrease in the number of cells below 50% compared to the control, while cisplatin showed negative effects at all concentrations. These findings suggest that the Bi complex has the potential to be developed as a promising candidate for BLC-related therapeutic target therapy.

Inquiry lipaseoring the mechanism of pancreatic lipase inhibition by isovitexin based on multispectral method and enzyme inhibition assay

Isovitexin is a main natural flavonoid component in various plants. Currently, the inhibitory effect of isovitexin on pancreatic lipase (PL) and its mechanism have not been elucidated yet. In the present study, we investigated the inhibitory effect of isovitexin on PL, as well as its interaction mechanism, using enzyme inhibition methods, spectroscopic analysis, and molecular simulations. Results showed that isovitexin possessed significant PL inhibitory activity, with IC50 values of 0.26 ± 0.02 mM. The interaction between isovitexin and PL was dominated by static quenching, and mainly through hydrogen bonding and hydrophobic interaction forces. Analysis of fluorescence spectroscopy confirmed that isovitexin binding altered the conformation of the PL. Circular dichroism (CD) spectrum indicated that isovitexin altered the secondary structure of PL by decreasing the α-helix content and increasing the β-fold content. Molecular simulations further characterize the conformational changes produced by the interaction between isovitexin with PL. The performed study may provide a new insight into the inhibitory mechanism of isovitexin as a novel PL inhibitor.

Bioinformatics-driven discovery of novel EGFR kinase inhibitors as anti-cancer therapeutics: In silico screening and in vitro evaluation

Epidermal growth factor receptor EGFR inhibitors are widely used as first line therapy for the treatment of non-small-cell lung cancer (NSCLC) in patients harboring EGFR mutation. However, the acquisition of a second-site mutation (T790 M) limited the efficacy and developed resistance. Therefore, discovery and development of specific drug target for this mutation is of urgent needs. In our study we used the ChemDiv diversity database for receptor-based virtual screening to secure EGFR-TK inhibitors chemotherapeutics. We identified four compounds that bind to the ATP-binding region of the EGFR-TK using AutoDock 4.0 and AutoDock Vina1.1.2 and post-docking investigations. The ligand showed hydrophobic interactions to the hydrophobic region of the binding site and engaged in hydrogen bonding with Met793. The ligands also explored π-cation interactions between the π-system of the ligand-phenyl ring and the positive amino group of Lys745. Molecular mechanics Poisson-Boltzmann surface area MM/PBSA per-residue energy decomposition analyses revealed that Val726, Leu792, Met793, Gly796, Cys797, Leu798, and Thr844 contributed the most to the binding energy. Biological evaluation of the retrieved hit compounds showed suppressing activity against EGFR auto phosphorylation and selective apoptosis-induced effects toward lung cancer cells harboring the EGFR L858R/T790M double mutation. Our work anticipated into novel and specific EGFR-TKIs and identified new compounds with therapeutic potential against lung cancer.

Synthesis, characterization, and BSA binding studies of newfangled 2-phenylacetohydrazide derivatives

Five 2-phenylacetohydrazide derivatives (BPAH = N'-benzylidene-2-phenylacetohydrazide, HBPAH = N'-(2-hydroxybenzylidene)-2-phenylacetohydrazide), PPAH = 2-phenyl-N'-3-phenylallylideneacetohydrazide, FMPAH = N'-(furan-2-ylmethylene)-2-phenylaceto hydrazide and EPAH = N'-ethylidene-2-phenylacetohydrazide were synthesized by the condensation of 2-phenylacetohydrazide with the corresponding aldehyde. The synthesized compounds were characterized by FTIR, 1D, and 2D NMR spectroscopy. The structure of the BPAH and PPAH were analyzed by single crystal X-ray diffraction analysis and in both crystallized compounds, the molecules adopted trans geometry around the -C[bond, double bond]N- (imine) functional group. To explore the pharmacological significance of these compounds, the binding ability of these compounds with Bovine Serum Albumin (BSA) was investigated using fluorescence spectroscopy. BPAH and PPAH showed the highest binding ability while EPAH, HBPAH, and FMPAH had lower binding ability to BSA molecules. Thermodynamic parameters ΔG, ΔH°, and ΔS° demonstrated that interactions of BSA with compounds BPAH, EPAH, FMAH, and HBPAH were exothermic while for PPAH it was endothermic. The negative enthalpy and entropy of the compounds BPAH, EPAH, FMAH, and HBPAH indicated that van der Waals' forces and hydrogen bonding played a major role in stabilizing the BSA binding with the molecules. Hydrophobic interactions were predominant in the binding of PPAH with BSA tends to interact with two sets of BSA binding sites with an increase in temperature.

Photophysical Properties of Sinapic Acid and Ferulic Acid and Their Binding Mechanism with Caffeine

Sinapic acid (SA) and ferulic acid (FA) are bioactive compounds used in the food, pharmaceutical, and cosmetic industries due to their antioxidant properties. In this work, we studied the photophysical properties of SA and FA in different solvents and concentrations and their interactions with caffeine (CF), using ultraviolet-visible (UV-Vis), fluorescence spectroscopy and Fourier transform infrared (FTIR) spectroscopy. The findings show that the quantum yield, fluorescence lifetime, radiative decay rates, and non-radiative decay rates of SA and FA are influenced by the concentrations and solvent polarity. The interaction between SA and FA with CF was also studied using UV-Vis and fluorescence spectroscopy. The results indicate that the CF quenched the fluorescence intensity of SA and FA by static quenching due to the formation of a non-fluorescent complex. The van't Hoff equation suggests that the van der Waals forces and hydrogen bonds force were responsible for the interaction between SA and CF, as indicated by a negative change in enthalpy (Δ H o  < 0) and a negative change in entropy (Δ S o  < 0). On the other hand, the interaction between FA and CF was primarily controlled by electrostatic force, as indicated by a negative change in enthalpy (Δ H o < 0) and a positive change in entropy (Δ S o > 0). The negative change in Gibbs free energy (Δ G o ) indicates that both compounds underwent a spontaneous binding process.

Increasing the polarity of β-lapachone does not affect its binding capacity with bovine plasma protein

Despite ortho-quinones showing several biological and pharmacological activities, there is still a lack of biophysical characterization of their interaction with albumin - the main carrier of different endogenous and exogenous compounds in the bloodstream. Thus, the interactive profile between bovine serum albumin (BSA) with β-lapachone (1) and its corresponding synthetic 3-sulfonic acid (2, under physiological pH in the sulphonate form) was performed. There is one main binding site of albumin for both β-lapachones (n ≈ 1) and a static fluorescence quenching mechanism was proposed. The Stern-Volmer constant (KSV) values are 104 M-1, indicating a moderate binding affinity. The enthalpy (-3.41 ± 0.45 and - 8.47 ± 0.37 kJ mol-1, for BSA:1 and BSA:2, respectively) and the corresponding entropy (0.0707 ± 0.0015 and 0.0542 ± 0.0012 kJ mol-1 K-1) values indicate an enthalpically and entropically binding driven. Hydrophobic interactions and hydrogen bonding are the main binding forces. The differences in the polarity of 1 and 2 did not change significantly the affinity to albumin. In addition, the 1,2-naphthoquinones showed a similar binding trend compared with 1,4-naphthoquinones.

Comprehending the intermolecular interaction of dacomitinib with bovine serum albumin: experimental and theoretical approaches

Dacomitinib (DAC), as a member of tyrosine kinase inhibitors is primarily used to treat non-small cell lung cancer. The intermolecular interaction between DAC and bovine serum albumin (BSA) was comprehended with the help of experiments and theoretical simulations. The outcomes indicated that DAC quenched the endogenous fluorescence of BSA through static quenching mode. In the binding process, DAC was preferentially inserted into the hydrophobic cavity of BSA subdomain IA (site III), and a fluorescence-free DAC-BSA complex with molar ratio of 1:1 was generated. The outcomes confirmed that DAC had a stronger affinity on BSA and the non-radiative energy transfer occurred in the combination process of two. And, it can be inferred from the outcomes of thermodynamic parameters and competition experiments with 8-aniline-1-naphthalenesulfonic acid (ANS) and D-(+)- sucrose that hydrogen bonds (H-bonds), van der Waals forces (vdW) and hydrophobic forces had a significant impact in inserting DAC into the hydrophobic cavity of BSA. The outcomes from multi-spectroscopic measurements that DAC could affect the secondary structure of BSA, that was, α-helix content decreased slightly from 51.0% to 49.7%. Moreover, the combination of DAC and BSA led to a reduction in the hydrophobicity of the microenvironment around tyrosine (Tyr) residues in BSA while had little influence on the microenvironment of around tryptophan (Trp) residues. The outcomes from molecular docking and molecular dynamics (MD) simulation further demonstrated the insertion of DAC into site III of BSA and hydrogen energy and van der Waals energy were the dominant energy of DAC-BSA stability. In addition, the influence of metal ions (Fe3+, Cu2+, Co2+, etc.) on the affinity of the system was explored.Communicated by Ramaswamy H. Sarma.

Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation

Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.

In silico elucidation for the identification of potential phytochemical against ACE-II inhibitors

CONTEXT

The present study aims to investigate the therapeutic potential of phytocompounds derived from Annona reticulata leaves for the treatment of hypertension, utilizing computational methodologies. Gaining a comprehensive understanding of the molecular interactions between neophytadiene and γ-sitosterol holds significant importance in the advancement of innovative therapeutic approaches. This study aims to examine the inhibitory effects of neophytadiene and γ-sitosterol using molecular docking and dynamics simulations. Additionally, we will evaluate their stability and predict their drug-like properties as well as their ADME/toxicity profiles. Neophytadiene and γ-sitosterol have a substantial binding affinity with 1O8A, as shown by the docking study. The stability of the complexes was confirmed through molecular dynamics simulations, while distinct clusters were identified using PCA. These findings suggest the presence of potential stabilizers. The drug-likeness and ADME/toxicity predictions revealed positive characteristics, such as efficient absorption rates, limited distribution volume and non-hazardous profiles. The neophytadiene and γ-sitosterol exhibit potential as hypertension medication options. Computational investigations reveal that these compounds exhibit high affinity for binding, stability and favourable pharmacokinetic properties. The results of this study lay the groundwork for additional experimental verification and highlight the promising prospects of utilizing natural compounds in the field of pharmaceutical research.

METHODS

Target proteins (1O8A) were used to perform molecular docking with representative molecules. Stability, conformational changes and binding energies were assessed through molecular dynamics simulations lasting 100 ns. Principal component analysis (PCA) was utilized to analyze molecular dynamics (MD) simulation data, to identify potential compounds that could stabilize the main protease. The safety and pharmacokinetic profiles of the compounds were evaluated through drug-likeness and ADME/toxicity predictions.

Evidence for paraquat-pepsin interaction: In vitro and silico study

The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.

Binding mechanism, photo-induced cleavage and computational studies of interaction cefepime drug with Human serum albumin

The binding interaction of cefepime to human serum albumin (HSA) in aqueous solution was investigated by molecular spectroscopy (UV spectra, fluorescence spectra and CD spectra), photo-cleavage and modeling studies under simulative physiological conditions. Spectrophotometric results are rationalized in terms of a static quenching process and binding constant (Kb) and the number of binding sites (n ≈ 1) were calculated using fluorescence quenching approaches at three temperature settings. Thermodynamic data of ΔG, ΔH and ΔS at different temperatures were evaluated. The results showed that the electrostatic and hydrogen bonding interactions play a major role in the binding of cefepime to HSA. The value of 3.4 nm for the distance r between the donor (HSA) and acceptor (cefepime) was derived from the fluorescence resonance energy transfer (FRET). FTIR and CD measurements has been reaffirmed HSA-cefepime association and demonstrated reduction in α-helical content of HSA. Furthermore, the study of molecular modeling also indicated that cefepime could strongly bind to the site I (subdomain IIA) of HSA. Additionally, cefepime shows efficient photo- cleavage of HSA cleavage. Our results may provide valuable information to understand the pharmacological profile of cefepime drug delivery in blood stream.Communicated by Ramaswamy H. Sarma.

Comprehending the intermolecular interaction of JAK inhibitor fedratinib with bovine serum albumin (BSA)/human alpha-1-acid glycoprotein (HAG): Multispectral methodologies and molecular simulation

The primary coverage of this paper is to investigate the molecular interaction of JAK2 inhibitor, fedratinib (FED) with BSA/HAG proteins through multispectral approaches and molecular docking as well as MD calculation. Arrival at a conclusion, the endogenous fluorescence of BSA/HAG protein was quenched separately in the form of static and mixed quenching. The FED-BSA and FED-HAG complexes with the stoichiometric ratio of 1:1 were formed in the interaction process. And, The Kb values of these complexes were of 104-105 M-1 and 105-106 M-1, respectively, representing that the FED-HAG complex exhibited a comparatively high affinity compared to the FED-BSA complex. It is confimed that FED inserted into the interface area between subdomain IIA and IIB of BSA (marked as site II') and the bucket-shaped hydrophobic cavity of HAG, respectively, resulting in the slight alteration in the secondary structure of BSA/HAG and the micro-environment round Tyr and Trp residues. The expetimental results also confirmed that van der Waals forces (VDW), hydrogen bonds and hydrophobic interaction played a dominant role in the formation of two stable complexes. The above experimental results were supplemented and verified through molecular docking and MD simulation. Meanwhile, the effects of common ions on affinity were explored. This study could shine a light on evaluating the pharmacological properties of the JAK inhibitor FED, understanding the distribution and operation of the drug in the body, and leading to the development of the creation of novel medication devise.

Transport proteins and their differential roles in the accumulation of phenanthrene in wheat

The study focuses on the uptake, accumulation, and translocation of polycyclic aromatic hydrocarbons (PAHs) in cereals, specifically exploring the role of peroxidase (UniProt accession: A0A3B5XXD0, abbreviation: PX1) and unidentified protein (UniProt accession: A0A3B6LUC6, abbreviation: UP1) in phenanthrene solubilization within wheat xylem sap. This research aims to clarify the interactions between these proteins and phenanthrene. Employing both in vitro and in vivo analyses, we evaluated the solubilization capabilities of recombinant transport proteins for phenanthrene and examined the relationship between protein expression and phenanthrene concentration. UP1 displayed greater transport efficiency, while PX1 excelled at lower concentrations. Elevated PX1 levels contributed to phenanthrene degradation, marginally diminishing its transport. Spectral analyses and molecular dynamics simulations validated the formation of stable protein-phenanthrene complexes. The study offers crucial insights into PAH-related health risks in crops by elucidating the mechanisms of PAH accumulation facilitated by transport proteins.

Structural alterations and inhibition of lysozyme activity upon binding interaction with rotenone: Insights from spectroscopic investigations and molecular dynamics simulation

The pervasive employment of pesticides such as rotenone on a global scale represents a substantial hazard to human health through direct exposure. Therefore, exploring the interactions between such compounds and body macromolecules such as proteins is crucial in comprehending the underlying mechanisms of their detrimental effects. The present study aims to delve into the molecular interaction between rotenone and lysozyme by employing spectroscopic techniques along with Molecular dynamics (MD) simulation in mimicked physiological conditions. The binding interaction resulted in a fluorescence quenching characterized by both dynamic and static mechanisms, with static quenching playing a prominent role in governing this phenomenon. The analysis of thermodynamic parameters indicated that hydrophobic interactions primarily governed the spontaneous bonding process. FT-IR and circular dichroism findings revealed structural alternations of lysozyme upon complexation with rotenone. Also, complexation with rotenone declined the biological activity of lysozyme, thus rotenone could be considered an enzyme inhibitor. Further, the binding interaction substantially decreased the thermal stability of lysozyme. Molecular docking studies showed the binding location and the key residues interacting with rotenone. The findings of the spectroscopic investigations were confirmed and accurately supported by MD simulation studies.

Insight into intermolecular binding mechanism of apatinib mesylate and human alpha-1-acid glycoprotein: combined multi-spectroscopic approaches with in silico

Apatinib mesylate (APM), an oral tyrosine kinase inhibitor, has a good anti-tumor activity in the treatment of various cancers, particularly in advanced non-small cell lung cancer. In this study, the intermolecular binding mechanism between APM and human alpha-1-acid glycoprotein (HAG) was investigated by combining multi-spectroscopic approaches with in silico techniques. The findings revealed that APM gave rise to the fluorescence quenching of HAG by forming a ground-state complex between APM and HAG with a stoichiometric ratio of 1:1, and APM has a moderate affinity for HAG as the binding constant of APM and HAG of approximately 105 M-1, which was larger than the APM-HAG complex. The findings from thermodynamic parameter analysis indicated that the dominant driving forces for the formation of the APM-HAG complex were van der Waals forces, hydrogen bonding and hydrophobic interactions, which were also verified with site-probe studies and molecular docking. The findings from in silico study indicated that APM inserted into the opening of the hydrophobic cavity of HAG, leads to a slight conformational change in the HAG, which was verified by circular dichroism (CD) measurements, that was, the beta sheet level of HAG decreased. Additionally, the results of synchronous and 3D fluorescence spectroscopies confirmed the decline in hydrophobicity of the microenvironment around Trp and Tyr residues. Moreover, some common metal ions such as Cu2+, Mg2+, Fe3+, Ca2+, and Zn2+ could cause the alteration in the binding constant of APM with HAG, leading to the change in the efficacy of APM. It will be expected that these study findings are to provide useful information for further understanding pharmacokinetic and structural modifications of APM.Communicated by Ramaswamy H. Sarma.

Structural changes and anti-hepatocellular carcinoma activity of interferon-γ after interaction with sinensetin

Exploring the interaction of small molecules with therapeutic proteins can provide useful information about development of ligand-protein complexes as synergistically therapeutic platforms. In this study, the interaction of sinensetin with human interferon gamma (IFNγ) was evaluated experimentally and theoretically. Also, the synergistic effects of IFNγ- sinensetin complex on the inhibition of hepatocellular carcinoma HepG2 cell proliferation were assessed by cell viability and quantitative real time PCR assays. It was realized that sinensetin interacts with IFNγ through a static quenching mechanism and hydrophobic forces mediated by presence of Lys55 and Lys58 amino acid residues in the binding site were the main contributing forces in the spontaneous formation of IFNγ-sinensetin complex. Also, the interaction of sinensetin with IFNγ did not induce a significant change in the secondary and tertiary structure of the protein. Cellular assays revealed a synergistic effect of sinensetin on IFNγ -triggered anticancer action in HepG2 cells through overexpression of caspase-3 mRNA and protein. In conclusion, this study may hold great promise for the development of potential ligand- protein complexes for therapeutic purposes.

In-silico and in-detail experimental interaction studies of new antitumor Zn(II) complex with CT-DNA and serum albumin

In this study, a novel Zn(II) complex with the formula [Zn(pyrr-ac)2] (pyrr-ac: pyrrolidineacetate) was synthesized and characterized through molar conductivity, elemental analysis, 1H Nuclear Magnetic Resonance (1H NMR), UV-Visible spectroscopy, and Fourier transform infrared (FT-IR) methods. B3LYP level of DFT method along with aug-cc-pVTZ-PP/6-311G(d,p) basis set was utilized to perform the geometry optimization and HOMO-LUMO analysis. In addition, MEP, NLO and NBO computations were also performed at the same level of theory. In vitro antitumor activity of the mentioned complex on leukemia cell line, K562, was investigated using the MTT assay which surprisingly revealed the effective antitumor activity of the studied zinc complex. Interaction of this compound with biological macromolecules viz., CT-DNA and BSA was studied via different spectroscopic methods. The results of fluorescence experiment displayed that the metal complex binds to both macromolecules through hydrogen bond (H-bond) and van der Waals (vdW) forces. UV-Vis tests indicated a decline in the absorption spectra of CT-DNA/BSA in the presence of the compound. The interaction was further corroborated for CT-DNA via gel electrophoresis, CD spectroscopy and viscosity experiments and for BSA using CD spectroscopy. Furthermore, molecular docking simulation was done to evaluate the nature of interaction between the aforementioned zinc complex and CT-DNA/BSA. These results were in agreement with experimental findings and demonstrated that the main interaction is hydrogen bonding. The above type of investigations may provide a pathway through which zinc complexes join the anticancer category.[Figure: see text]The in-silico and in-vitro results confirm that the newly made [Zn(pyrr-ac)2] complex interacts with CT-DNA than BSA.Communicated by Ramaswamy H. Sarma.

Assessment on binding characteristics of ethiprole and a model protein bovine serum albumin (BSA) through various spectroscopic techniques integrated with computer simulation

To investigate the binding characteristics of pesticide ethiprole (ETP) with serum albumin is of great significance for pathological analysis of pesticide poisoning, gene mutation, and clinical detection. In present work, the binding characteristics of ETP with a model protein BSA has been estimated by means of multi-spectroscopic approaches integrated with computer simulation. The outcomes testified that the intrinsic fluorescence of BSA was mainly quenched by ETP in a static quenching mode and the stable ETP-BSA complex with the stoichiometry of 1:1 and the binding constant of 6.81 × 103 M-1 (298 K) was produced. The outcomes revealed that ETP combined preferentially to the subdomain IIA (Site I) of BSA and caused the decline in the content of α-helix of BSA and the enhancement in the hydrophobicity of environment centered on Trp residues. The outcomes of experimental and theoretical studies provide the sufficient evidence about the driving forces for the complexation of ETP with BSA, which included van der Waals forces (vdW), hydrogen bonding (H-bonding) interaction, and hydrophobicity. Simultaneously, the theoretical calculation results also confirmed the existence of the significant changes in the physicochemical natures of ETP including molecular conformation, dipole moment, frontier orbital energy, and the atomic charge distribution, which was a responsible for the complexation with BSA.Communicated by Ramaswamy H. Sarma.

Molecular Recognition Study toward the Mitochondrial Electron Transport Chain Inhibitor Mubritinib and Human Serum Albumin

The ability to bind plasma proteins helps in comprehending relevant aspects related to the pharmacological properties of many drugs. Despite the vital role of the drug mubritinib (MUB) in the prophylaxis of various diseases, its interaction with carrier proteins still needs to be clarified. The present work focuses on the interaction between MUB and Human serum albumin (HSA), investigated by employing multispectroscopic, biochemical, and molecular docking approaches. The results reveal that MUB has quenched HSA intrinsic fluorescence (following a static mechanism) by attaching very close (r = 6.76 Å) and with moderate affinity (Kb ≈ 104 M-1) to the protein site I (mainly by H-bonds, hydrophobic and Van der Waals forces). On one side, the HSA-MUB interaction has been accompanied by a slight disturbance in the HSA chemical environment (around the Trp residue) and protein secondary structure modifications. On another side, MUB competitively inhibits HSA esterase-like activity, which is very similar to other Tyrosine kinase inhibitors, and evidence that protein functional alterations have been triggered by MUB interaction. In summary, all of the presented observations can shed light on diverse pharmacological factors associated with drug administration.

Inhibitory potential of N-acetylaspartate against protein glycation, AGEs formation and aggregation: Implication of brain osmolyte in glycation-related complications

Protein glycation and aggregation have a pivotal role in many diseases including diabetes and neurodegenerative disorders. N-acetyl aspartate (NAA), an osmolyte derived from L-aspartic acid, is one of the most abundant metabolites in the mammalian brain. Although NAA is supposed to be a substitute for a neuronal marker, its function is not fully elucidated. Herein, we have investigated the effect of NAA on glycation, AGEs formation and aggregation of irisin. AGE-specific fluorescence showed the strong inhibition of AGEs formation in the presence of NAA, demonstrating its anti-glycating property. The aggregates present in MG-modified irisin were also reduced by NAA, which was confirmed by Thioflavin T fluorescence and fluorescence microscopy. Further, for the explanation of the strong anti-glycating potential of NAA, the interaction between irisin and NAA was also examined. Interaction studies involving steady-state fluorescence and molecular docking demonstrated that hydrogen bonding and salt bridges by NAA stabilize the irisin. It was found that glycation-prone residues i.e., lysine and arginine are specifically involved in the interaction which might prevent them from getting modified during the process of glycation. This study for the first time reported the antiglycating potential of NAA which can be implicated in the therapeutic management of various glycation-related complications.

Enantioselective effect of chiral prothioconazole on the conformation of bovine serum albumin

As a typical chiral triazole fungicide, the enantioselective toxicity of prothioconazole to environmental organisms is of increasing concern. Herein, the binding mechanism of chiral PTCs to BSA was investigated by multi-spectral technique and molecular docking. Fluorescence titration and fluorescence lifetime experiments fully established that quenching BSA fluorescence by chiral PTCs is static quenching and could spontaneously bind to BSA. Hydrophobic interactions dominate the binding process of chiral PTCs to BSA. Differently, although both chiral PTCs and BSA have a primary binding site, the difference in chiral isomerism leads to a stronger binding ability of S-PTC than R-PTC. Both configurations of PTC can change the conformation of BSA and induce changes in the microenvironment around its amino acid residues, and the effect of S-PTC is more significant. Overall, S-PTC exhibited a more substantial effect on BSA structure relative to R-PTC. That is, S-PTC may lead to more potent potential toxicological effects on environmental organisms. This study provides a comprehensive assessment of the environmental behavior of chiral pesticides and their potential toxicity to environmental organisms at the molecular level and provides a theoretical basis for the screening of highly effective and biologically less toxic enantiomers of chiral pesticides.

Discovery of Novel EGFR Inhibitor Targeting Wild-Type and Mutant Forms of EGFR: In Silico and In Vitro Study

Targeting L858R/T790M and L858R/T790M/C797S mutant EGFR is a critical challenge in developing EGFR tyrosine kinase inhibitors to overcome drug resistance in non-small cell lung cancer (NSCLC). The discovery of next-generation EGFR tyrosine kinase inhibitors (TKIs) is therefore necessary. To this end, a series of furopyridine derivatives were evaluated for their EGFR-based inhibition and antiproliferative activities using computational and biological approaches. We found that several compounds derived from virtual screening based on a molecular docking and solvated interaction energy (SIE) method showed the potential to suppress wild-type and mutant EGFR. The most promising PD13 displayed strong inhibitory activity against wild-type (IC50 of 11.64 ± 1.30 nM), L858R/T790M (IC50 of 10.51 ± 0.71 nM), which are more significant than known drugs. In addition, PD13 revealed a potent cytotoxic effect on A549 and H1975 cell lines with IC50 values of 18.09 ± 1.57 and 33.87 ± 0.86 µM, respectively. The 500-ns MD simulations indicated that PD13 formed a hydrogen bond with Met793 at the hinge region, thus creating excellent EGFR inhibitory activity. Moreover, the binding of PD13 in the hinge region of EGFR was the major determining factor in stabilizing the interactions via hydrogen bonds and van der Waals (vdW). Altogether, PD13 is a promising novel EGFR inhibitor that could be further clinically developed as fourth-generation EGFR-TKIs.

A new strategy to alleviate the obesity induced by endocrine disruptors-A unique lysine metabolic pathway of nanoselenium Siraitia grosvenorii to repair gut microbiota and resist obesity

Obesity caused by endocrine disruptors (EDCs) has become a hot topic threatening human health. Recently, Nanoselenium Siraitia grosvenorii (NSG) has been shown to have potential health-modulating uses. Based on the results of 16S rRNA sequencing and metabolomics analysis, NSG has the unique function of improving gut microbiota and inhibiting obesity. Specifically, NSG can enhance gut microbiota diversity and change their composition. A significant positive correlation exists between the liver change in lysine and the high-importance dominant species ([Ruminococcus]_gnavus, Alistipes_finegoldii, etc.). NSG metabolites analysis showed that the lysine level increased by 44.45% and showed a significantly negatively correlated with (TG, TC, Leptin, etc.). Significantly, NSG reduces the degradation of lysine metabolism in the liver and inhibits fatty acid β-oxidation. In addition, NSG decreased Acetyl-CoA levels by 24% and regulated the downregulation of TCA genes (CS, Ogdh, Fh1, and Mdh2) and the upregulation of ketone body production genes (BDH1). NSG may have a positive effect on obesity by reducing the participation of Acetyl-CoA in the TCA cycle pathway and enhancing the ketogenic conversion of Acetyl-CoA. In conclusion, the results of this study may provide a new dietary intervention strategy for preventing endocrine disruptor-induced obesity.

Interaction between Chinese quince fruit proanthocyanidins and bovine serum albumin: Antioxidant activity, thermal stability and heterocyclic amine inhibition

Heterocyclic amines (HCAs) are carcinogenic and mutagenic substances produced in fried meat. Adding natural antioxidants (e.g., proanthocyanidins (PAs)) is a common method to reduce HCAs; however, the interaction between the PAs and protein can affect the inhibitory efficacy of PAs on the formation of HCAs. In this study, two PAs (F1 and F2) with different degrees of polymerization (DP) were extracted from Chinese quince fruits. These were combined with bovine serum albumin (BSA). The thermal stability, antioxidant capacity and HCAs inhibition of all four (F1, F2, F1-BSA, F2-BSA) were compared. The results showed that F1 and F2 interact with BSA to form complexes. Circular dichroism spectra indicate that complexes had fewer α-helices and more β-sheets, β-turns and random coils than BSA. Molecular docking studies indicated that hydrogen bonds and hydrophobic interactions are the forces holding the complexes together. The thermal stabilities of F1 and, particularly, F2 were stronger than those of F1-BSA and F2-BSA. Interestingly, F1-BSA and F2-BSA showed increased antioxidant activity with increasing temperature. F1-BSA's and F2-BSA's HCAs inhibition was stronger than F1 and F2, reaching 72.06 % and 76.3 %, respectively, for norharman. This suggests that PAs can be used as natural antioxidants for reducing the HCAs in fried foods.

A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling

Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein–ligand complex studies.

Investigation of the separate and simultaneous bindings of warfarin and fenofibrate to bovine serum albumin

Lipid-lowering drugs are often taken with anticoagulant drugs in hyperlipidemia patients. Fenofibrate (FNBT) and warfarin (WAR) are common clinical lipid-lowering drugs and anticoagulant drugs, respectively. A study of binding affinity, binding force, binding distance, and binding sites was performed to determine the interaction mechanism between drugs and carrier proteins (bovine serum albumin, BSA), as well as their effects on BSA conformation. Both FNBT and WAR can form complexes with BSA by van der Waals force and hydrogen bonds. WAR had a stronger fluorescence quenching effect on BSA, a stronger binding affinity, and greater effects on BSA conformation than FNBT. According to fluorescence spectroscopy and cyclic voltammetry, co-administration of drugs decreased one drug's binding constant to BSA and increased its binding distance. This suggested that each drug's binding to BSA was disturbed by each other, as well as each drug's binding ability to BSA was altered by the other. It was demonstrated that co-administration of drugs had greater effects on the secondary structure of BSA and microenvironment polarity surrounding amino acid residues, using multiple spectroscopy techniques, such as ultraviolet spectroscopy, Fourier transform infrared spectroscopy, and synchronous fluorescence spectroscopy.