Binding Of Complex Research Articles

Improved Rapid Equilibrium Dialysis-Mass Spectrometry (RED-MS) Method for Measuring Small Molecule-Protein Complex Binding Affinities in Solution.

Rapid equilibrium dialysis (RED) is predominantly used for the characterization of drug absorption, distribution, metabolism, and excretion (ADME) properties in plasma and biological fluids. We describe herein improvements in the use of RED in conjunction with mass spectrometry (RED-MS) to enable robust binding affinity measurements of small molecules for recombinant proteins and complexes from a single dialysis data set. The affinities calculated from RED-MS correlated well with measurements by both surface plasmon resonance (SPR) and affinity selection mass spectrometry (AS-MS). The method was particularly useful for quantifying the binding of small molecules to large protein complexes that were not amendable by common biophysical characterization techniques. Compound pooling and integration with automated liquid handling increased assay throughput and enabled the analysis of hundreds of measurements per week. RED-MS offers a viable option for measuring compound binding in solution and may facilitate small molecule affinity optimization toward difficult-to-drug protein complexes.

Genomic Variants Associated with Haematological Parameters and T Lymphocyte Subpopulations in a Large White and Min Pig Intercross Population

The breeding of disease-resistant pigs has consistently been a topic of significant interest and concern within the pig farming industry. The study of pig blood indicators has the potential to confer economic benefits upon the pig farming industry, whilst simultaneously providing valuable insights that can inform the study of human diseases. In this study, an F2 resource population of 489 individuals was generated through the intercrossing of Large White boars and Min pig sows. A total of 17 haematological parameters and T lymphocyte subpopulations were measured, including white blood cell count (WBC), lymphocyte count (LYM), lymphocyte count percentage (LYM%), monocyte count (MID), monocyte count percentage (MID%), neutrophilic granulocyte count (GRN), percentage of neutrophils (GRN%), mean platelet volume (MPV), platelet distribution width (PDW), platelet count (PLT), CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, CD4−CD8+CD3+, CD4−CD8−CD3+, and CD3+. The Illumina PorcineSNP60 Genotyping BeadChip was obtained for all of the F2 animals. Subsequently, a genome-wide association study (GWAS) was conducted using the TASSEL 5.0 software to identify associated variants and candidate genes for the 17 traits. Significant association signals were identified for PCT and PLT on SSC7, with 1 and 11 significant SNP loci, respectively. A single nucleotide polymorphism (SNP) on SSC12 was identified as a significant predictor of the white blood cell (WBC) trait. Significant association signals were detected for the T lymphocyte subpopulations, namely CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, and CD4−CD8+CD3+, with the majority of these signals observed on SSC7. The genes CLIC5, TRIM15, and SLC17A4 were identified as potential candidates for influencing CD4+/CD8+ and CD4−CD8+CD3+. A missense variant, c.2707 G>A, in the SLC17A4 gene has been demonstrated to be significantly associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Three missense variants (c.425 A>C, c.500 C>T, and c.733 A>G) have been identified in the TRIM15 gene as being linked to the CD4+/CD8+ trait. Nevertheless, only c.425 A>C has been demonstrated to be significantly associated with CD4-CD8+CD3+. In the CLIC5 gene, one missense variant (c.957 T>C) has been identified as being associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Additionally, significant association signals were observed for CD4+CD8+CD3+ and CD4+CD8−CD3+ on SSC2 and 5, respectively. Subsequently, a gene ontology (GO) enrichment analysis was conducted on all genes within the quantitative trait loci (QTL) intervals of platelet count, CD4+/CD8+, and CD4−CD8+CD3+. The MHC class II protein complex binding pathway was identified as the most significant pathway among the three immune traits. These results provide guidance for further research in the field of breeding disease-resistant pigs.

Activation of the Innate Immune System in Brain-Dead Donors Can Be Reduced by Luminal Intestinal Preservation During Organ Procurement Surgery - A Porcine Model

Organs obtained from brain dead donors can have suboptimal outcomes. Activation of the innate immune system and translocation of intestinal bacteria could be causative. Thirty two pigs were assigned to control, brain death (BD), BD + luminal intestinal polyethylene glycol (PEG), and BD + luminal intestinal University of Wisconsin solution (UW) groups. Animals were observed for 360 min after BD before organ retrieval. 2,000 mL luminal intestinal preservation solution was instilled into the duodenum at the start of organ procurement. Repeated measurements of plasma C3a, Terminal Complement Complex (TCC), IL-8, TNF, and lipopolysaccharide binding protein were analysed by immunoassays. C3a was significantly higher in the BD groups compared to controls at 480 min after brain death. TCC was significantly higher in BD and BD + UW, but not BD + PEG, compared to controls at 480 min. TNF was significantly higher in the BD group compared to all other groups at 480 min. LPS binding protein increased following BD in all groups except BD + PEG, which at 480 min was significantly lower compared with all other groups. Brain death induced innate immune system activation was decreased by luminal preservation using PEG during organ procurement, possibly due to reduced bacterial translocation.

Charge Transfer Interaction Dynamics between 2-Methyl-8-hydroxyquinoline and 2,4-Dinitrophenol: Synthesis, Spectroscopic Characterization, DNA Binding and DFT Studies

A novel charge transfer (CT) complex was formed by combining the electron-acceptor 2,4-dinitrophenol (DNP) with the electron-donor 2-methyl-8-hydroxyquinoline (MHQ). The complex obtained was further characterized using both experimental and theoretical methods. The Benesi-Hildebrand equation can be utilized to determine various spectroscopic physical measurements such as the molar absorptivity (εCT) and formation constant (KCT). The CT complex has a stoichiometry of 1:1. Multiple spectroscopic methods were employed to investigate the resultant solid compound. The existence of charge and proton transfer in the resultant complex was confirmed by FT-IR, 1H NMR, SEM-EDX and powder-XRD studies. An electron absorption spectroscopy examination was done to analyze the complex DNA binding capability. The resulting complex was determined to have an intercalative binding mechanism, with an intrinsic binding constant (Kb) value of 4.2 × 106 M-1. The experimental results were corroborated by performing theoretical calculations using DFT using a CAM-B3LYP/6-31G(d,p) basis set. The geometrical parameters, electrostatic potential maps (MEPs) and Mullikan charges were computed and examined in agreement with the experimental observations. In addition to electron transmission, the stability of the complex is influenced by the presence of a hydrogen bond.

Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations.

Peptide drugs play an essential role in modern therapeutics, but the computational design of these molecules is hindered by several challenges. Traditional methods like molecular docking and molecular dynamics (MD) simulation, as well as recent deep learning approaches, often face limitations related to computational resource demands, complex binding affinity assessments, extensive data requirements, and poor model interpretability. Here, we introduce PepHiRe, an innovative methodology that utilizes the hierarchical structural information in peptide sequences and employs a novel strategy called Ladderpath, rooted in algorithmic information theory, to rapidly generate and enhance the efficiency and clarity of novel peptide design. We applied PepHiRe to develop BH3-like peptide inhibitors targeting myeloid cell leukemia-1, a protein associated with various cancers. By analyzing just eight known bioactive BH3 peptide sequences, PepHiRe effectively derived a hierarchy of subsequences used to create new BH3-like peptides. These peptides underwent screening through MD simulations, leading to the selection of five candidates for synthesis and subsequent in vitro testing. Experimental results demonstrated that these five peptides possess high inhibitory activity, with IC50 values ranging from 28.13 ± 7.93 to 167.42 ± 22.15 nM. Our study explores a white-box model driven technique and a structured screening pipeline for identifying and generating novel peptides with potential bioactivity.

Co(II), Ni(II), and Cu(II) Ternary Complexes With 2,6‐Pyridinedicarboxylic Acid and 2,2′‐Bipyridyl: Synthesis, Characterization, DNA Binding, Photo‐Cleavage, and Antimicrobial Studies

ABSTRACTThe interaction of 2,6‐pyridinedicarboxylicacid (PDA) and 2,2′‐bipyridyl (Bipy) with Co(II), Ni(II), and Cu(II) ions produced new ternary complexes [M (PDA)(Bipy)(H2O)] (M = Co(II), Ni(II), and Cu(II)), which were studied by elemental, spectral (FT‐IR, Mass, UV–Vis), and thermal analysis, and their interaction with Ct‐DNA was thoroughly studied using various methods, including absorption spectroscopy, fluorescence spectroscopy, and viscosity measurements. Spectrophotometric titration and viscosity measurements indicated that all the complexes bind to DNA via the groove mode of binding. The salt‐dependent binding of ternary metal complexes to Ct‐DNA has been studied by a UV–Vis spectrophotometric titration experiment. Furthermore, photocleavage studies were used to examine how the metal complexes interacted with the pBR322 DNA, and the results proved that these compounds have obvious photo cleavage properties. The biological effects were studied by antibacterial activity.

Combinatory Effect of Gemcitabine and 5‐Fluorouracil Investigated Through Chemoinformatics and Molecular Dynamics Simulation Against Breast Cancer

ABSTRACTCo‐delivering FDA‐approved drugs can be less harmful and boost biological activity by targeting different protein mechanism at same time. Gemcitabine and 5‐Fluorouracil (GE5F) adduct work together to destroy cancer cells and increase the efficacy in the fight against breast cancer. The basis set B3LYP/6‐311 G was utilized in this investigation to improve the structure of GE5F adduct. The natural bond analysis exhibited the intermolecular interactions of the GE5F adduct. Electronic transitions were seen to be π → π*, and theoretical calculations were performed for the ultraviolet to visible spectrum. The energy gap between HOMO and LUMO was used to study the GE5F adduct's structural stability and reactivity; the computed energy gap (ΔE) was 3.912 eV. The Mulliken charge population was assessed and the complex structure's electrostatic potential was established. Weak interactions of the GE5F were assessed using RDG analysis, and topological aspects were investigated using LOL and ELF analysis. Investigating the GE5F adduct's adsorption, distribution, metabolism, excretion, and toxicity properties, the results confirmed that GE5F adduct comes under the safety parameters being a drug‐likeness molecule. Molecular docking experiments were conducted using target proteins for breast cancer. The complex molecule had a higher binding affinity as indicated by the docking scores, which validated the better combinatorial interaction between gemcitabine and 5‐Fluorouracil. With − 9.4 kcal/mol, the complex molecule's strongest binding capacity was against PARP protein, and stable confirmation was observed through molecular dynamic simulation for 100 ns with four hydrogen bond interactions. These in silico finding will pave a way for in vitro and in vivo experiments with better enhancement of FDA approved drugs.

Laser-induced multi-doped graphene extended-gate field-effect transistor sensor for enhanced detection of cystatin C

In this study, we amplified the capabilities of laser-induced graphene (LIG) by developing a multi-doped LIG extended-gated field-effect transistor (EG-FET) sensor. This sensor integrates a multi-doped LIG EG electrode array as a disposable sensing component with a standard MOSFET for reusable transduction. The multi-doped LIG was synthesized using a dual-approach: initially, by using a MnCl2-doped polyimide (MnCl2-PI) film through precursor compounding, and subsequently, by employing a CO2 laser to respectively in situ generate MnO2 nanoparticles and gold nanoparticles (Au NPs) via direct laser conversion. By incorporating the resultant multi-doped LIG (Au NPs/MnO2/LIG) as the EG electrode, we boosted its electrical efficiency and provided ideal sites for the papain immobilization. This facilitated the selective binding of protein complexes with cystatin C (Cys C), allowing for precise measurement. Notably, the sensor exhibited a robust linear correlation across a concentration range from 50 ag/μL to 0.25 ng/μL and achieved a detection limit of 50 ag/μL. These advancements not only address traditional limitations of LIG applications but also highlight the potential of LIG-based EG-FET portable devices for accurate and early screening of chronic kidney disease (CKD).

A cobalt coordination complex binds on a unique binding site between domain-I and domain-III of serum albumin

Serum albumin binding influences physiological effects and pharmacokinetics of drugs. Major binding sites in serum albumin are sudlow sites I and II, located on domains IIA and IIIA, respectively. However, groove between domain I and III as a binding site is not well studied. In this work, we studied the binding of a cobalt coordination complex (DCoP) with bovine serum albumin (BSA) using multi-spectroscopic methods and molecular docking. DCoP strongly interacts with BSA with association constant of ∼7 × 105M−1. The binding was found to significantly alter protein's conformation and unfolding pathway. Results of this study shows that DCoP binds at the groove formed between domains III and I. We conclude that the groove is a rare binding site for large molecules and coordination complexes. The knowledge of unique binding site of serum albumin enlightens the comprehensive role of protein as a carrier biomacromolecule.

Functional genomics screens reveal a role for TBC1D24 and SV2B in antibody-dependent enhancement of dengue virus infection.

Under some conditions, dengue virus (DENV) can hijack IgG antibodies to facilitate its uptake into target cells expressing Fc gamma receptors (FcgR)-a process known as antibody-dependent enhancement (ADE) of infection. Beyond a requirement for FcgR, host dependency factors for this unusual IgG-mediated infection route remain unknown. To identify cellular factors exclusively required for ADE, here, we performed CRISPR knockout (KO) screens in an in vitro system poorly permissive to infection in the absence of IgG antibodies. Validating our approach, a top hit was FcgRIIa, which facilitates the binding and internalization of IgG-bound DENV but is not required for canonical infection. Additionally, we identified host factors with no previously described role in DENV infection, including TBC1D24 and SV2B, which have known functions in regulated secretion. Using genetic knockout and trans-complemented cells, we validated a functional requirement for these host factors in ADE assays performed with monoclonal antibodies and polyclonal sera in multiple cell lines and using all four DENV serotypes. We show that knockout of TBC1D24 or SV2B impaired the binding of IgG-DENV complexes to cells without affecting FcgRIIa expression levels. Thus, we identify cellular factors beyond FcgR that promote efficient ADE of DENV infection. Our findings represent a first step toward advancing fundamental knowledge behind the biology of a non-canonical infection route implicated in disease.IMPORTANCEAntibodies can paradoxically enhance rather than inhibit dengue virus (DENV) infection in some cases. To advance knowledge of the functional requirements of antibody-dependent enhancement (ADE) of infection beyond existing descriptive studies, we performed a genome-scale CRISPR knockout (KO) screen in an optimized in vitro system permissive to efficient DENV infection only in the presence of IgG. In addition to FcgRIIa, a known receptor that facilitates IgG-mediated uptake of IgG-bound, but not naked DENV particles, our screens identified TBC1D24 and SV2B, cellular factors with no known role in DENV infection. We validated a functional role for TBC1D24 and SV2B in mediating ADE of all four DENV serotypes in different cell lines and using various antibodies. Thus, we identify cellular factors beyond Fc gamma receptors that promote ADE mechanisms. This study represents a first step toward advancing fundamental knowledge beyond a poorly understood non-canonical viral entry mechanism.

Sandwich-Type Electrochemical Aptasensor with Supramolecular Architecture for Prostate-Specific Antigen.

A novel sandwich-type electrochemical aptasensor based on supramolecularly immobilized affinity bioreceptor was prepared via host-guest interactions. This method utilizes an adamantane-modified, target-responsive hairpin DNA aptamer as a capture molecular receptor, along with a perthiolated β-cyclodextrin (CD) covalently attached to a gold-modified electrode surface as the transduction element. The proposed sensing strategy employed an enzyme-modified aptamer as the signalling element to develop a sandwich-type aptasensor for detecting prostate-specific antigen (PSA). To achieve this, screen-printed carbon electrodes (SPCEs) with electrodeposited reduced graphene oxide (RGO) and gold nanoferns (AuNFs) were modified with the CD derivative to subsequently anchor the adamantane-modified anti-PSA aptamer via supramolecular associations. The sensing mechanism involves the affinity recognition of PSA molecules on the aptamer-enriched electrode surface, followed by the binding of an anti-PSA aptamer-horseradish peroxidase complex as a labelling element. This sandwich-type arrangement produces an analytical signal upon the addition of H2O2 and hydroquinone as enzyme substrates. The aptasensor successfully detected the biomarker within a concentration range of 0.5 ng/mL to 50 ng/mL, exhibiting high selectivity and a detection limit of 0.11 ng/mL in PBS.

Ni(II)-selenosemicarbazones complexes as promising anticancer and anti-tubercular agents: Synthesis, characterization, molecular docking and binding studies with HSA and ct-DNA

Reaction of nickel(II) acetate with selenosemicarbazones (2-HOxsesc, 3-MeHOxsesc, 6-ClHOxsesc, 3-HIndsesc, 3-AcHIndsesc, 9-HAnsesc, 1-HNapsesc, 2-HNapsesc) in 1:2 (M:L) molar ratio yielded complexes of formula, [Ni(sesc)2] 1–8 (sesc = 2-Oxsesc 1, 3-MeOxsesc 2, 6-ClOxsesc 3, 3-Indsesc 4, 3-AcIndsesc 5, 9-Ansesc 6, 1-Napsesc 7, 2-Napsesc 8).Complexes are characterized using elemental analysis, FTIR, NMR (1H and 13C) spectroscopy and Mass spectrometry. The full optimized energy for 2-HOxsesc and its complex was found through Density Functional Theory calculation using B3LYP level and predicted geometry parameters are compared with literature. Selenosemicarbazones and their complexes were tested for their anti-tuberculosis activity against M. tuberculosis H37RV strain and anticancer activity against PA-1 and DU145cell lines. The anti-TB activity of 3-AcHIndsesc (MIC = 25 μg/mL) got exceptionally enhanced on complexation with Ni(II) (complex 5, MIC = 0.8 μg/mL). Anticancer activity of ligands have got enhanced on complexation with Ni(II) metal ion and best results were obtained in case of complex 5 (PA-1, IC50 =1.28; DU145, IC50 =3.83). The binding constant of 6.5 × 103M-1 and 3 × 104M−1 obtained from absorption spectroscopy (UV–Vis) indicates strong binding of complex 5 with HSA and ct-DNA. The molecular interaction of 3-AcHIndsesc and complex 5 with mycobacterium tuberculosis enoyl reductase and DNA (PDB ID: 1BNA) were checked with docking studies. The docking studies with mycobacterium tuberculosis enoyl reductase and DNA (PDB ID: 1BNA) gave minimum binding energy of -8.9 Kcal/mol and -7.5 Kcal/mol respectively for complex 5. The docking results are in well agreement with experimental data.

Development of a novel papain gel formulation: Exploring different concentrations for smear-layer deproteinization and enhanced dentin bonding

BackgroundThe self-etch adhesive system modifies but does not completely remove the smear layer, leading to the weakening of the bond strength due to the formation of a hybridized layer. Smear-layer deproteinization with papain enzyme partially removes the smear layer, and increases the bond strength with self-etch adhesive. The aim was to develop a deproteinizing agent with a high papain enzyme concentration to enhance dentin bonding with self-etch adhesives. MethodsPapain enzyme gel formulations (15 and 30 IU/g) were prepared and tested for physical stability, viscosity, pH, homogeneity, and organoleptic properties. Moreover, 64 teeth were used to test the deproteinization efficiency of the formed gel. Fourier transform infrared was used to calculate the ratio of organic to inorganic components of smear-layer after deproteinization with 15 and 30 IU/g papain gel and a 6 IU/g commercial papain gel. Moreover, tensile bond strength was measured after deproteinization and dentin bonding with self-etching adhesive for the same groups. A molecular modeling simulation was also performed to evaluate the protein-protein binding interaction, predict the conformational/orientation patterns, and estimate the binding energies of papain with collagen target protein. ResultsBoth 15 and 30 IU/g gels exhibited similar viscosity, pH, homogeneity, and organoleptic properties. However, after 60 s, the 15 IU/g gel was solid, while the 30 IU/g gel was half-solid. All tested groups decreased the amide:phosphate ratio and increased tensile bond strength. Binding complexes between papain and three deposited collagen-1 structures formed strong binding energies with high negative values and residue-wise binding patterns. ConclusionsThe production of the papain enzyme gel with a concentration of 15 IU/g was successful. In addition, it demonstrated promising results when used as a smear-layer deproteinization agent. Clinical significanceEnzymatic smear-layer deproteinization may improve dentin adhesion, and high concertation papain enzyme gels may improve dentin adhesion with the use of self-etch adhesive

Computational and in vitro analyses of the antibacterial effect of the ethanolic extract of Pluchea indica L. leaves.

The most common gram-negative, Escherichia coli, and gram-positive bacteria, Bacillus spp., have evolved different mechanisms that have caused the emergence of multi-drug resistance. As a result, drugs that block the bacterial growth cycle are needed. Here, in silico and in vitro studies were performed to assess compounds in the Pluchea indica leaf extract, a medicinal plant, that can inhibit bacterial proteins. Briefly, P. indica leaves were extracted using ethanol. The crude extract was then subjected to gas chromatography-mass spectrometry for metabolite screening. Molecular docking simulations with rhomboid protease (Rpro) (Protein data bank ID number: 3ZMI from E. coli and filamenting temperature-sensitive mutant Z (FtsZ) protein data bank ID number: 2VAM from Bacillus subtilis were performed. Moreover, the well diffusion method was used to confirm the antibacterial activity of P. indica leaf extract. A total of 10 compounds were identified in the P. indica extract and used for computational analysis. Based on drug-likeness prediction, P. indica compounds may be drug-like molecules. Binding affinity tests indicated that 10,10-Dimethyl-2,6-dimethylenebicyclo(7.2.0)undecan-5.β.-ol and 11,11-Dimethyl-4,8-dimethylenebicyclo(7.2.0)undecan-3-ol had the most negative values. Accordingly, these compounds may be potential ligands that bind to bacterial proteins. The root mean square fluctuation values was <2 Å, indicating stable fluctuation binding for the ligand-protein complex. According to in vitro antibacterial assays, a high concentration (50%) of the P. indica extract markedly inhibited E. coli and B. subtilis, with inhibitory zone diameters of 31.86±1.63 and 21.09±0.09 mm, respectively. Overall, the compounds in the P. indica leaf extract were identified as functional inhibitors of E. coli and B. subtilis proteins via in silico analysis. This may facilitate development of antibacterial agents.

Anisole-Water and Anisole-Ammonia Complexes in Ground and Excited (S1) States: A Multiconfigurational Symmetry-Adapted Perturbation Theory (SAPT) Study.

Binary complexes of anisole have long been considered paradigm systems for studying microsolvation in both the ground and electronically excited states. We report a symmetry-adapted perturbation theory (SAPT) analysis of intermolecular interactions in anisole-water and anisole-ammonia complexes within the framework of the multireference SAPT(CAS) method. Upon the S1 ← S0 electronic transition, the hydrogen bond in the anisole-water dimer is weakened, which SAPT(CAS) shows to be determined by changes in the electrostatic energy. As a result, the water complex becomes less stable in the relaxed S1 state despite decreased Pauli repulsion. Stronger binding of the anisole-ammonia complex following electronic excitation is more nuanced and results from counteracting shifts in the repulsive (exchange) and attractive (electrostatic, induction and dispersion) forces. In particular, we show that the formation of additional binding N-H···π contacts in the relaxed S1 geometry is possible due to reduced Pauli repulsion in the excited state. The SAPT(CAS) interaction energies have been validated against the coupled cluster (CC) results and experimentally determined shifts of the S1 ← S0 anisole band. While for the hydrogen-bonded anisole-water dimer SAPT(CAS) and CC shifts are in excellent agreement, for ammonia SAPT(CAS) is only qualitatively correct.

Mechanism of Dual-Site Recognition in a Classic DNA Aptamer.

Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such as biosensing and targeted therapy. We herein utilized enhanced sampling molecular dynamics to address affinities of adenosine monophosphate (AMP) to the dual binding sites in the DNA aptamer, focusing on the dynamic recognition mechanism and pathways. The present results indicate that in addition to the widely known intermolecular interactions, inequivalence of chemical environments of the two binding sites leads to slightly higher stability of AMP binding to the site proximal to the aptamer terminus. In the presence of two AMPs captured by the two sites, each binding free energy is enhanced. In particular, an additional hydrogen bond of AMP to A10 is introduced in the dual-site binding complex, which increases the binding energy from -4.25 ± 0.47 to -9.48 ± 0.33 kcal mol-1 in the site close to the loop. For the dual-site recognition process, the free energy landscape and minimum free energy pathway calculations elucidate the crucial role of electrostatic interactions between the AMP phosphate groups and Na+ ions in positively cooperative binding mechanisms.

Synthesis and BSA binding study of the Cu(II) complex and applications of it to enhance catalytic activity for C(Sp2)-H bond functionalization and for the synthesis of polyhydroquinolines

Among the various copper-catalyzed coupling reactions, C–S and C–N bond-forming reactions have carried off plentiful recognition due to their demand in the synthesis of molecules having biological and pharmaceutical impact. Organo-copper complex has an incontestable supremacy over the other catalytic complex due to its low cost and the use of readily accessible and stable ligands. As a consequence and in continuation of our explorative studies in this direction, an efficient and novel organo-copper complex has been synthesized and characterized by spectroscopic (NMR, FT-IR) and single crystal X-ray diffraction (XRD) methods. The synthesized stable metal complex has fascinating physical, chemical, biological and catalytic properties. In the chemical exploration refer to protein-metal interactions; we have often used Bovine Serum Albumin (BSA) protein. The synthesized copper complex has the potential to form coordinate bonds with functional groups present in BSA, together with amino acid residues and the protein backbone. The binding of metal complexes to BSA has outstanding imputation in medicinal chemistry. For enhancement of the catalytic activity of the organo-copper complex, we have evaluated it in carbon-hetero bond formation reactions where it proffered an influential tool for the establishment of C–S and C–N bonds.

Confocal image of three oxoaporphine alkaloids in cancer cell lines and their interaction with DNA by multispectroscopic and molecular docking techniques

Dicentrinone (Di), liriodenine (Li) and lysicamine (Ly) are three natural oxoaporphine alkaloids (OAs), which revealed significant biological activity such as anticancer, anti-inflammatory and antimicrobial activities and were considered as potential lead compounds for the development of new clinical chemicals. In the present study, confocal laser scanning fluorescence microscopy observation demonstrated these three natural OAs could traverse inside of the nucleus and get an opportunity to interact with DNA. Their interaction properties with DNA were then investigated simultaneously by two spectral fluorescent probes of ethidium bromide (EB) and methyl green (MG), as well as UV–vis absorption and cyclic voltammetry measurements, and further verified by the molecular docking analysis. Results indicated Di and Li were distinctly classified as the intercalative molecules to DNA, however, Ly was confirmed with a mixed-mode binding of partial intercalation and groove affinity. Their binding ability was revealed as the follows: Di ≥ Li > Ly, which was correlated with their structural changes. Thermodynamic studies revealed the binding process of Li and Ly with ctDNA was all spontaneous, the hydrophobic interaction was the major binding force for Li-ctDNA complex, however, the interaction between Ly and ctDNA relied on both hydrophobic and hydrogen binding force. Molecular docking provided detailed computational interaction of Di, Li and Ly with DNA, which proved the intercalation binding of Li-DNA complex and Di-DNA complex stabilizing mainly by the π-π binding force, however, apart from a small quantity of π-π interaction, another binding force in the Ly-DNA complex mainly was supplied from the weaker Pi-Alkyl, hydrogen bond and Pi-Anion interactions.

Application of Ensemble Machine Learning Methods for QSAR Classification of Leukotriene A4 Hydrolase Inhibitors in Drug Discovery

Inflammatory diseases such as asthma, rheumatoid arthritis, and cardiovascular conditions are driven by overproduction of leukotriene B4 (LTB4), a potent inflammatory mediator. Leukotriene A4 hydrolase (LTA4H) plays a critical role in converting leukotriene A4 into LTB4, making it a prime target for drug discovery. Despite ongoing efforts, developing effective LTA4H inhibitors has been challenging due to the complex binding properties of the enzyme and the structural diversity of potential inhibitors. Traditional drug discovery methods, like high-throughput screening (HTS), are often time-consuming and inefficient, prompting the need for more advanced approaches. Quantitative Structure-Activity Relationship (QSAR) modeling, enhanced by ensemble machine learning techniques, provides a promising solution by enabling accurate prediction of compound bioactivity based on molecular descriptors. In this study, six ensemble machine learning methods—AdaBoost, Extra Trees, Gradient Boosting, LightGBM, Random Forest, and XGBoost—were employed to classify LTA4H inhibitors. The dataset, comprising 636 compounds labeled as active or inactive based on pIC50 values, was processed to extract 450 molecular descriptors after feature engineering. The results show that the LightGBM model achieved the highest classification accuracy (83.59%) and Area Under the Curve (AUC) value (0.901), outperforming other models. XGBoost and Random Forest also demonstrated strong performance, with AUC values of 0.890 and 0.895, respectively. The high sensitivity (95.24%) of the XGBoost model highlights its ability to accurately identify active compounds, though it exhibited slightly lower specificity (61.36%), indicating a higher false-positive rate. These findings suggest that ensemble machine learning models, particularly LightGBM, are highly effective in predicting bioactivity, offering valuable tools for early-stage drug discovery. The results indicate that ensemble methods significantly enhance QSAR model accuracy, making them viable for identifying promising LTA4H inhibitors, potentially accelerating the development of anti-inflammatory therapies.

FCGR2/3 polymorphisms are associated with susceptibility to Kawasaki disease but do not predict intravenous immunoglobulin resistance and coronary artery aneurysms.

Kawasaki disease (KD) is a pediatric vasculitis that can result in coronary artery aneurysm (CAA) formation, which is a dangerous complication. Treatment with intravenous immunoglobulin (IVIg) significantly decreases the risk of CAA, possibly through competitive binding to Fc-gamma receptors (FcγRs), which reduces the binding of pathological immune complexes. However, ~20% of children have recrudescence of fever and have an increased risk of CAA. Therefore, we aimed to identify genetic markers at the FCGR2/3 locus associated with susceptibility to KD, IVIg resistance, or CAA. We investigated the association of single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs) at the FCGR2/3 locus with KD susceptibility, IVIg resistance, and CAA risk using a family-based test (KD susceptibility) and case-control analyses (IVIg resistance and CAA risk) in different cohorts, adding up to a total of 1,167 KD cases. We performed a meta-analysis on IVIg resistance and CAA risk including all cohorts supplemented by previous studies identified through a systematic search. FCGR2A-p.166His was confirmed to be strongly associated with KD susceptibility (Z = 3.17, p = 0.0015). In case-control analyses, all of the investigated genetic variations at the FCGR2/3 locus were generally not associated with IVIg resistance or with CAA risk, apart from a possible association in a Polish cohort for the FCGR3B-NA2 haplotype (OR = 2.15, 95% CI = 1.15-4.01, p = 0.02). Meta-analyses of all available cohorts revealed no significant associations of the FCGR2/3 locus with IVIg resistance or CAA risk. FCGR2/3 polymorphisms are associated with susceptibility to KD but not with IVIg resistance and CAA formation. Currently known genetic variations at the FCGR2/3 locus are not useful in prediction models for IVIg resistance or CAA risk.