High Affinity Binding Research Articles

Utilizing HPLC-DAD, multivariate analysis, molecular docking, and in vitro validation methods to investigate phenolic compounds with potential antidiabetic properties in Fraxinus mandshurica

This comprehensive study utilized response surface methodology (RSM) to optimize extraction conditions for total flavonoids and phenols from F. mandshurica. Optimal conditions for flavonoids were 75 % ethanol, 63 °C, and 84 min, yielding 14.98 ± 0.13 mg/g. For phenols, it was 70 % ethanol, 66 °C, and 87 min, resulting in 26.04 ± 0.22 mg/g. UPLC-Q-TOF-MS/MS identified 68 constituents in F. mandshurica, categorized into groups. HPLC-DAD established a method for quantitative analysis of 12 target compounds. Geographical distribution analysis highlighted the northeast region as the main production area. Fingerprinting of 30 samples and multivariate analysis identified five active compounds. Hierarchical cluster analysis (HCA) showed differences in active compounds based on origin. In vitro antidiabetic evaluation demonstrated α-glucosidase inhibitory effects. Molecular docking studies were conducted between 12 active compounds and the antidiabetic-related protein 8A27. Esculetin had the highest binding affinity. The study examined extraction methods, analyzed samples, and explored antidiabetic effects, providing data support and insights for F. mandshurica as a natural industrial product and for extracts and active compounds as antidiabetic sources.

Maeruines A−E, elusive indole alkaloids from stems of Maerua siamensis and their inhibitory effects on cyclooxygenases and HT-29 colorectal cancer cell proliferation

Five previously undescribed indole alkaloids, maeruines A−E (1−5), bearing imino-2H-thieno[2,3-b]indol-3(8H)-one skeleton, were obtained from the stems of Maerua siamensis. Their chemical structures were elucidated using spectroscopic techniques [NMR, MS, IR, and UV], and single-crystal X-ray diffraction. Maeruine D (4) displayed selective cyclooxygenase-2 (COX-2) inhibitory activity in vitro with an IC50 of 29.72 ± 6.36 μM. Molecular dynamics simulations revealed that maeruine D could form a stable complex with human COX-2, predominantly driven by hydrophobic interactions. In addition, five amino-acid residues including Val349, Leu352, Leu384, Val523, and Ala527 were identified as hot-spot ones, which may lead to high binding affinity and selectivity. Furthermore, it exhibited cytotoxicity against HT-29 colorectal cancer cells with an IC50 of 29.32 ± 4.76 μM, and, at 0.1−10 μM, significantly inhibited their proliferation, induced by the proinflammatory cytokine interleukin-1β (IL-1β), in a dose-dependent manner.

Cellulase exhibited a therapeutic potential to inhibit Salmonella enterica serovar Typhi biofilm by targeting multiple regulatory proteins of biofilm

Biofilm-mediated Salmonella enterica serovar Typhi (Salmonella Ser. Typhi) infections are a growing global health issue due to the formation of antibiotic resistance. The study aimed to discover some of the druggable target proteins of Salmonella Ser. Typhi biofilm and antibiofilm enzyme to prevent Salmonella Ser. Typhi biofilm-mediated infection. Enzymatic therapy has demonstrated effective therapeutic results against bacterial infections due to its specificity and high binding capacity to the target. Therefore, this study focused on the computational interaction between the cellulase enzyme and Salmonella Ser. Typhi biofilm targets proteins with help of the various computational experiments such as ADMET (absorption, distribution, metabolism, excretion, and toxicity), protein-protein interactions, MMGBSA, etc. Further, in vitro validations of the typhoidal biofilm and cellulose presence in Salmonella Ser. Typhi biofilm was conducted using Scanning Electron Microscopy (SEM), Fourier transform infrared spectroscopy, and Raman analysis. Additionally, a minimum biofilm inhibitory concentration assay for cellulase was conducted and find out the optimized cellulase concentration which showed its inhibitory effect on the Salmonella Ser. Typhi. The cellulase antibiofilm effect was analyzed with the help of SEM analysis. Further, the cellulose content in Salmonella Ser. Typhi was quantified before and after treatment of cellulase enzyme. As a result, 58.82 % cellulose content was decreased due to cellulase treatment in Salmonella Ser. Typhi. From the seven selected typhoidal biofilm regulatory proteins of Salmonella Ser. Typhi, we identified only five potential druggable targets: BcsA, CsgE, OmpR, CsgF, and CsgD. The BcsA protein is responsible for cellulose production in Salmonella Ser. Typhi biofilm. Consequently, cellulose worked as a fascinating drug target in Salmonella Ser. Typhi biofilm. Therefore, we used cellulase as a potential antibiofilm enzyme for target-based disruption of biofilm. The cellulase showed a high binding affinity with all five identified target proteins [BcsA(-205.62 kcal/mol) > CsgE(-108.20 kcal/mol) > OmpR(-107.58 kcal/mol) > CsgF(-73.74 kcal/mol) > CsgD(-66.61 kcal/mol)] in the protein-protein interaction analysis. Our computational analysis suggests that the cellulase enzyme may be used as a potential antibiofilm enzyme against Salmonella Ser. Typhi biofilm.

Efficient Generation of Protein Pockets with PocketGen.

Designing small-molecule-binding proteins, such as enzymes and biosensors, is crucial in protein biology and bioengineering. Generating high-fidelity protein pockets areas where proteins interact with ligand molecules, is challenging due to complex interactions between ligand molecules and proteins, flexibility of ligand molecules and amino acid side chains, and complex sequence-structure dependencies. Here, we introduce PocketGen, a deep generative method for generating the residue sequence and the full-atom structure within the protein pocket region that leverages sequence structure consistency. PocketGen consists of a bilevel graph transformer for structural encoding and a sequence refinement module that uses a protein language model (pLM) for sequence prediction. The bilevel graph transformer captures interactions at multiple granularities (atom-level and residue/ligand-level) and aspects (intra-protein and protein-ligand) with bilevel attention mechanisms. For sequence refinement, a structural adapter using cross-attention is integrated into a pLM to ensure structure-sequence consistency. During training, only the adapter is fine-tuned, while the other layers of the pLM remain unchanged. Experiments show that PocketGen can efficiently generate protein pockets with higher binding affinity and validity than state-of-the-art methods. PocketGen is ten times faster than physics-based methods and achieves a 95% success rate (percentage of generated pockets with higher binding affinity than reference pockets) with over 64% amino acid recovery rate.

Structural insight into the lead identification of a dual inhibitor of PDE1B and PDE10A: Integrating pharmacophore-based virtual screening, molecular docking, and structure-activity-relationship approaches

Schizophrenia is a chronic neuropsychiatric disorder affecting more than 1% of the world's population. Current antipsychotic treatments show inadequacy in mitigating the negative and cognitive symptoms of schizophrenia. In addition, these medications cause undesirable extrapyramidal side effects. According to the studies, inhibition of phosphodiesterase (PDE) 1B and PDE10A simultaneously can alleviate positive, negative, and cognitive symptoms of schizophrenia. Thus, this study aims to identify new dual inhibitors of PDE1B and PDE10A using ligand-based pharmacophore modelling, virtual screening, and molecular docking studies. Accordingly, the generated pharmacophore models of PDE1B and PDE10A comprised hydrogen bond acceptor, aromatic ring, and hydrophobic features. These features were essential for retrieving the active hits from the Universal Natural Product Database in the virtual screening. Additional filters were subsequently employed to identify potential hits that could be developed into central nervous system-active compounds. Hits meeting all the screening criteria were subjected to docking studies with PDE1B and PDE10A. Among these hits, UNPD167314 exhibited significant binding affinities for the target receptors. It occupied the P-clamp and displayed hydrophobic, aromatic, and hydrogen bond interactions with the active site residues of both receptors, thus selected as a lead compound for the design of potent and selective dual inhibitors. The structural modifications of UNPD167314 resulted in the design of 35 novel inhibitors. Out of 35, four compounds exhibited high and comparable binding affinities for both PDE1B and PDE10A, making them promising candidates for further evaluation and optimisation.

Revamped role for approved drug: integrative computational and biophysical analysis of saquinavir's peptidyl arginine deiminase 4 inhibition for rheumatoid arthritis.

The pursuit of novel therapeutics is a complex and resource-intensive endeavor marked by significant challenges, including high costs and low success rates. In response, drug repositioning strategies leverage existing FDA-approved compounds to predict their efficacy across diverse diseases. Peptidyl arginine deiminase 4 (PAD4) plays a pivotal role in protein citrullination, a process implicated in the autoimmune pathogenesis of rheumatoid arthritis (RA). Targeting PAD4 has thus emerged as a promising therapeutic approach. This study employs computational and enzyme inhibition strategies to identify potential PAD4-targeting compounds from a library of FDA-approved drugs. In silico docking analyses validated the binding interactions and orientations of screened compounds within PAD4's active site, with key residues such as ASP350, HIS471, ASP473, and CYS645 participating in crucial hydrogen bonding and van der Waals interactions. Molecular dynamics simulations further assessed the stability of top compounds exhibiting high binding affinities. Among these compounds, Saquinavir (SQV) emerged as a potent PAD4 inhibitor, demonstrating competitive inhibition with a low IC50 value of 1.21 ± 0.04 µM. In vitro assays, including enzyme kinetics and biophysical analyses, highlighted significant changes in PAD4 conformation upon SQV binding, as confirmed by circular dichroism spectroscopy. SQV induced localized alterations in PAD4 structure, effectively occupying the catalytic pocket and inhibiting enzymatic activity. These findings underscore SQV's potential as a therapeutic candidate for RA through PAD4 inhibition. Further validation through in vitro and in vivo studies is essential to confirm SQV's therapeutic benefits in autoimmune diseases associated with dysregulated citrullination.

Ultrasonic synthesis, characterization, DFT and molecular docking of a biocompatible Zn-based MOF as a potential antimicrobial, anti-inflammatory and antitumor agent

Zinc metal–organic frameworks have emerged as promising candidates, demonstrating excellent biological properties stemming from the unique characteristics of MOFs and zinc. In this study, we employed a facile method to synthesize a zinc metal–organic framework [Zn(IP)(H2O)] using ultrasound irradiation, with the linker being isophthalic acid (IPA) (1,3-benzene dicarboxylic acid). The parent Zn-MOF and two Ag/Zn-MOF samples prepared via loading and encapsulation methods were comprehensively characterized using various techniques, including FT-IR, XRD, SEM, TEM, N2 adsorption–desorption isotherm, UV–vis spectroscopy and TGA. The parent Zn-MOF and two Ag/Zn-MOF samples exhibited a broad spectrum of antibacterial effects. Remarkably, genomic DNA of P. aeruginosa was effectively degraded by Zn-MOF, further supporting its potent antibacterial results. The free radical inhibition assay demonstrated a 71.0% inhibition under the influence of Zn-MOF. In vitro cytotoxicity activity of Zn-MOF against HepG-2 and Caco-2 cell lines revealed differential cytotoxic effects, with higher cytotoxicity against Caco-2 as explored from the IC50 values. This cytotoxicity was supported by the high binding affinity of Zn-MOF to CT-DNA. Importantly, the non-toxic property of Zn-MOF was confirmed through its lack of cytotoxic effects against normal lung cell (Wi-38). The anti-inflammatory treatment of Zn-MOF achieved 75.0% efficiency relative to the standard Ibuprofen drug. DFT and docking provided insights into the geometric stability of Zn-MOF and its interaction with active amino acids within selected proteins associated with the investigated diseases. Finally, the synthesized Zn-MOF shows promise for applications in cancer treatment, chemoprevention, and particularly antibacterial purposes.

Exploiting macrocyclic polylactam for sensing V-series nerve agents: A computational study

The nerve agents are organophosphorus compounds (OPs) developed as chemical warfare agents (CWAs) that inhibit acetylcholinesterase (AChE) and lead to impeding neurological signals in mammals. Therefore, detecting such nerve agents is important, and efforts to study the fundamental interactions of host systems with CWAs are scarce in the literature. In this report, the cyclic 18-membered tetralactam [Ⅰ] as a host molecule has been chosen to sense V-series nerve agents. The DFT calculated results reveal that VM, VG, and VX, bind strongly with the core unit of the host molecule tetralactam [Ⅰ] with a preference for VM. The remarkably higher binding affinity of VM is governed by more hydrogen bonding interactions with the core of the cyclic 18-membered tetralactam [Ⅰ]. The nerve agent Russian VX has been found to bind weakly with the receptor molecule. The hydrogen bonding interactions of these nerve agents have further been analyzed with non-covalent interactions (NCI) and atoms in molecule (AIM) calculations. The tetralactam moiety exhibits the binding with V-series nerve agents and the absorption spectral results can be used as diagnostic signatures for sensing of such nerve agents in useful applications.

Exploring flavonoids as potential inhibitors for Enterococcus faecium nicotinate nucleotide adenylyltransferase: An integration of in silico with empirical studies

Nicotinate nucleotide adenylyltransferase (NNAT) emerges as a promising target for drug development, given its pivotal role in the nicotinate nucleotide biosynthesis pathway crucial for bacterial survival. Using computational modelling and fluorescence methods, this study screened a library of 1427 compounds from MedChemExpress as potential inhibitors against Enterococcus faecium NNAT (EfNNAT). We employed Maestro's Glide HTVS, SP, and XP docking protocols to identify compounds with high binding affinity. The screening utilised two models of the EfNNAT crystal structure: energy-minimised and 100-ns MD-simulated model, hypothesising conformational change that may influence ligand selectivity in the HTVS study. Our findings revealed variations between the minimised versus MD-simulated models, impacting ligand selectivity by each model post-HTVS. However, quercetin 3-O-beta-d-glucose-7-O-beta-d-gentiobioside (QGG) appeared to be the top inhibitor selected by both models after more rigorous docking using Maestro-implemented SP and XP. A 500-ns all-atom MD simulation of the EfNNAT:ligand complex revealed that the compound interacts mainly through hydrogen bonding and water bridges. Validation of the in-silico studies via molecular spectroscopy confirmed QGG's binding to EfNNAT by displacing the fluorescent probes from the protein binding site. Although the binding demonstrated minimal impact on the thermal stability of EfNNAT as deduced from the thermal shift assay, ITC showed that QGG exhibits moderate binding affinity for EfNNAT, with the interaction being spontaneous and thermodynamically favourable. Insights gleaned from this study offer a mechanistic basis that could be leveraged to develop new leads. Expansion of the compound library holds promise for identifying inhibitors with enhanced affinity for EfNNAT.

A novel brominated chalcone derivative as a promising multi-target inhibitor against multidrug-resistant Listeria monocytogenes

Foodborne pathogens continue to challenge public health due to their ability to cause severe illness and their increasing resistance to current antimicrobial treatments. Listeria monocytogenes is a resilient foodborne pathogen that poses significant risks to vulnerable populations, leading to severe infections and high hospitalization rates. The emergence of antimicrobial-resistant (AMR) strains of L. monocytogenes underscores the need for novel therapeutic strategies. In this study, we investigated the antimicrobial efficacy of the (2E)-3-(3,5-dibromo-2-hydroxylphenyl)-1-(5-methylfuran-2-yl) prop-2-en-1-one (DK06) against multidrug-resistant L. monocytogenes. DK06 exhibited a significant dose-dependent inhibition of L. monocytogenes growth, achieving a maximum inhibition of 92.9 % at 320 μM. Molecular docking and dynamics simulations revealed high binding affinities for key virulence proteins PlcB and ArgA, with stable protein-ligand interactions. DK06 also disrupted biofilm formation at sub-MIC levels, reducing extracellular polymeric substances (EPS) and biofilm mass, as observed by scanning electron microscopy (SEM) analysis. Furthermore, DK06 downregulated the expression of virulence genes (plcB, argA, and hly) and decreased hemolytic activity. In vivo zebrafish studies confirmed the safety of DK06 up to 80 μM, demonstrating its efficacy in reducing mortality and oxidative stress associated with L. monocytogenes infection. DK06 also attenuated inflammation by downregulating key inflammatory markers (tnfa, il1b, il6, and nfkb). These findings indicate that DK06 is a promising multi-target inhibitor with potential application in treating infections and combating antimicrobial resistance.

Discovering potential asthma therapeutics targeting hematopoietic prostaglandin D2 synthase: An integrated computational approach

Allergic asthma, a chronic inflammatory illness that affects millions worldwide, has serious economic and health consequences. Despite advances in therapy, contemporary treatments have poor efficacy and negative effects. This study investigates hematopoietic prostaglandin D2 synthase (HPGDS) as a potential target for novel asthma therapies. Targeting HPGDS may provide innovative treatment methods. A library of phytochemicals was used to find putative HPGDS inhibitors by structure-based and ligand-based virtual screening. Among the 2295 compounds screened, four compounds (ZINC208828240, ZINC95627530, ZINC14727536, and ZINC14711790) demonstrated strong binding affinities of −10.4, −10.3, −9.2, −9.1 kcal/mol respectively with key residues, suggesting their potential as a highly effective HPGDS inhibitor. Molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) computations were further performed to evaluate the stability and binding affinity of the complexes. MD simulations and MMPBSA confirmed that compound ZINC14711790 showed high stability and binding affinity (binding energy −31.52 kcal/mol) than other compounds, including HQL-79, suggesting that this compound might be used as promising inhibitors to treat asthma. RMSD and RMSF analysis also revealed that ZINC14711790 exhibited strong dynamic stability. The findings of this study show the efficacy of ZINC14711790 as HPGDS inhibitors with high binding affinity, dynamic stability, and appropriate ADMET profile.

ITIH4 in Rheumatoid Arthritis Pathogenesis: Network Pharmacology and Molecular Docking Analysis Identify CXCR4 as a Potential Receptor.

Elevated levels of Inter-alpha-trypsin-inhibitor heavy chain 4 (ITIH4) have grabbed attention in rheumatoid arthritis (RA) pathogenesis, though its precise mechanisms remain unexplored. To elucidate these mechanisms, a comprehensive strategy employing network pharmacology and molecular docking was utilized. RA targets were sourced from the DisGeNET Database while interacting targets of ITIH4 were retrieved from the STRING and Literature databases. Venny 2.1 was used to identify overlapping genes, followed by Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) through Cytoscape 3.10.2 software, and molecular docking was performed in the ClusPro server. The study identified 18 interacting proteins of ITIH4 associated with RA, demonstrating their major involvement in the chemokine signaling pathway by enrichment analysis. Molecular docking of ITIH4 with the 18 proteins revealed that C-X-C chemokine-receptor type 4 (CXCR4), a major protein associated with chemokine signaling, has the highest binding affinity with ITIH4 with energy -1705.7 kcal/mol forming 3 Hydrogen bonds in the active site pocket of ITIH4 with His441, Arg288, Asp443 amino acids. The effect of ITIH4 on CXCR4 was analyzed via knockdown studies in rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS), demonstrating the significant downregulation of CXCR4 protein expression validated by Western blot in RA-FLS. In conclusion, it was speculated that CXCR4 might serve as a potential receptor for ITIH4 to activate the chemokine signaling, exacerbating RA pathogenesis.

Negative Charges, Not Necessary Phosphorylation, are Required for Ligand Recognition by 14-3-3 Proteins.

Protein-protein interactions involving 14-3-3 proteins regulate various cellular activities in normal and pathological conditions. These interactions have mostly been reported to be phosphorylation-dependent, but the 14-3-3 proteins also interact with unphosphorylated proteins. In this work, we investigated whether phosphorylation is required, or, alternatively, whether negative charges are sufficient for 14-3-3ε binding. We substituted the pThr residue of pT(502-510) peptide by residues with varying number of negative charges, and investigated binding of the peptides to 14-3-3ε using MD simulations and biophysical methods. We demonstrated that at least one negative charge is required for the peptides to bind 14-3-3ε while phosphorylation is not necessary, and that two negative charges are preferable for high affinity binding.

Chronic environmental level exposure to perfluorooctane sulfonate overshadows graphene oxide to induce apoptosis through activation of the ROS-p53-caspase pathway in marine medaka Oryzias melastigma

The widespread occurrence of perfluorooctane sulfonate (PFOS) and the mass production and application of graphene oxide (GO) lead to their inevitable release and interaction in the environment, which may enhance associated toxic impacts on aquatic organisms. This study elucidates the induction of apoptosis by 60-day chronic single and mixture exposures to environmentally relevant levels of PFOS (0.5 μg/L and 5 μg/L) and GO (1 mg/L) in adult marine medaka Oryzias melastigma. Results showed a significant increase (p < 0.05) in reactive oxygen species (ROS) levels, the apoptotic positive rate in livers, and activities of caspases 3, 8, and 9 in all treated groups compared to the control. PFOS individual and PFOS-GO combined exposures significantly impacted fish growth, upregulated expressions of six apoptosis-related genes including p53, apaf1, il1b, tnfa, bcl2l1, bax, as well as enriched cell cycle and p53 signaling pathways (transcriptomic analysis) related to apoptosis compared to control group. Besides higher ROS production, GO also had a higher binding affinity to proteins than PFOS, especially to caspase 8 as revealed by molecular docking. Overall, PFOS induced ROS-p53-caspase apoptosis pathway through multi-gene regulation during single or mixture exposure, while GO single exposure induced apoptosis through tissue damage and ROS-caspase pathway activation and direct docking with caspase 8 to activate the caspase cascade. Under co-exposure, the PFOS-induced apoptotic pathway overshadowed the GO-induced pathway, due to competition for limited active sites on caspases. These findings will contribute to a better understanding of the apoptosis mechanism and ecological risks of nanomaterials and per- and polyfluoroalkyl substances in marine ecosystems.

Designing of a chimeric multiepitope vaccine against bancroftian lymphatic filariasis through immunoinformatics approaches

The filarial worms of Wuchereria bancrofti are the primary cause of lymphatic filariasis (LF), a mosquito-borne disease among the neglected tropical parasitic diseases. Considering the global endemic consequences of the disease, there is a need to develop a successful vaccine candidate against LF. Using advanced immunoinformatics approaches, we designed two multiepitope vaccines targeting W. bancrofti’s glutathione S-transferase and thioredoxin. Therefore, we predicted several MHC-1, MHC-2, and B-cell epitopes from these proteins and mapped two vaccine candidates (V1 and V2). The vaccines were subsequently employed for physicochemical analysis, structural prediction and validation, docking and normal mode analysis, codon optimization, and immune simulation. The selected MHC-1, MHC-2, and B-cell epitopes were antigenic without allergenicity or toxicity. The designed vaccines were expected to be soluble, stable proteins under physiological conditions. Compared to V2, V1’s secondary and tertiary structures were simultaneously favorable, with Ramachandran plot analysis revealing 95.6% residues in favored areas. Subsequently, the molecular docking analysis indicated that the V1 had a high binding affinity for the TLR-2, TLR-4 and TLR-5, as suggested by the docking scores of -1248.7, -1038.5 and -1562.8, respectively. The NMA of these complexes further indicated their structural flexibility. Molecular dynamics simulations of V1-TLR complexes revealed V1-TLR-4 as the most stable, with the lowest free energy and minimal fluctuations, indicating the strongest binding affinity. The results of the codon optimization showed high levels of expression, with a favorable CAI score (&lt;1.0). A three-dose vaccination analysis showed significant and persistent immunological responses, including adaptive and innate immune responses. The findings emphasize the potential of the V1 against W. bancrofti, but further validation is required through in vitro, in vivo, and clinical trials.

Flavokawain B is an effective natural peroxisome proliferator-activated receptor γ-selective agonist with a strong glucose-lowering effect

Rosiglitazone, a full PPARγ agonist and a classical insulin sensitizer, was once used as a powerful weapon in the treatment of T2DM. However, its applications have been restricted recently because of its multiple side effects. Here, a natural compound, flavokawain B (FKB), which was screened in our previous experiments, was investigated for its potential as a preferable insulin sensitizer because it has no or few side effects. Using the surface plasmon resonance (SPR) technique, we confirmed that FKB is a natural ligand for PPARγ with high binding affinity. In in vitro experiments, FKB significantly increased 2-NBDG uptake in HepG2 and 3T3-L1 cells, which partially stimulated PPARγ transcriptional activity. Compared with rosiglitazone, FKB had little effect on the adipose differentiation of 3T3-L1 cells, and all of these features suggest that FKB is a selective modulator of PPARγ (SPPARγM). Moreover, FKB increased the mRNA expression levels of most genes related to insulin sensitivity and glucose metabolism but had no obvious effect on those related to adipose differentiation. In vivo experiments confirmed that FKB effectively decreased abnormal fasting blood glucose and postprandial blood glucose levels and reduced glycated hemoglobin levels, similar to rosiglitazone, in HFD-fed/STZ-treated and db/db mice, two T2DM animal models, but did not cause side effects, such as weight gain or liver or kidney damage. Further investigation revealed that FKB could inhibit PPARγ-Ser273 phosphorylation, which is the key mechanism involved in improving insulin resistance. Together, FKB is a well-performing SPPARγM that exerts a powerful glucose-lowering effect without causing the same side effects as rosiglitazone, and it may have great potential for development.

Synergistic effects of β-Cyclodextrin derivative inclusion complexes with favipiravir to enhance solubility and antiviral efficacy against Herpes Simplex virus type 1 (HSV-1)

In this study, the formation of β-cyclodextrin derivatives (β-Cyclodextrin; β-CD, Hydroxypropyl-β-Cyclodextrin; Hβ-CD, and Sulfobutylether-β-Cyclodextrin; Sβ-CD) inclusion complexes with favipiravir (FPR) was confirmed using various spectroscopic and analytical techniques. These complexes were shown to enhance FPR solubility and antiviral activity against herpes simplex virus type 1 (HSV-1). UV–visible and fluorescence spectroscopy revealed a continuous increase in FPR absorbance and fluorescence intensity with increasing β-CD concentrations, indicating the successful formation of 1:1 inclusion complexes. The prepared β-CD solid complexes were characterized using FTIR, XRD, FESEM, and TGA-DSC, which highlighted significant surface properties, morphological changes, and improved thermal stability. Phase solubility studies demonstrated enhanced FPR solubility in the presence of the β-CDs, with stability constants (Ks) following the order: Hβ-CD (694.8 M−1) > Sβ-CD (418.4 M−1) > β-CD (364.3 M−1). In-vitro release studies showed that the Hβ-CD complex achieved a higher cumulative release of 90.16 ± 1.94 % over 90 min compared to free FPR (25.32 ± 0.29 %), attributed to its greater solubility. Molecular docking provided insights into the interaction mechanisms, revealing higher binding affinities and stability for FPR with β-CD. In-vitro antiviral assays against HSV-1 demonstrated significant viral titer reductions for free FPR with β-CDs, with Hβ-CD outperforming others due to its rapid release profile after 96 h of incubation, confirming its potential for improved antiviral formulations. The cytotoxic effects of FPR and its β-CDs inclusion complexes were evaluated on Vero cells using an MTT assay over 96 h, showing reduced cytotoxicity for the inclusion complexes compared to free FPR. Additionally, cellular uptake studies revealed that β-CDs inclusion complexes conjugated with DAPI and FITC exhibited greater intensity within Vero cells compared to free FPR.

Mesothelin- and nucleolin-specific T cells from combined short peptides effectively kill triple-negative breast cancer cells

BackgroundTriple-negative breast cancer (TNBC), known for its aggressiveness and limited treatment options, presents a significant challenge. Adoptive cell transfer, involving the ex vivo generation of antigen-specific T cells from peripheral blood mononuclear cells (PBMCs), emerges as a promising approach. The overexpression of mesothelin (MSLN) and nucleolin (NCL) in TNBC samples underscores their potential as targets for T cell therapy. This study explored the efficacy of multi-peptide pulsing of PBMCs to generate MSLN/NCL-specific T cells targeting MSLN+/NCL+ TNBC cells.MethodsTNBC patient samples were confirmed for both MSLN and NCL expression via immunohistochemistry. Synthesized MSLN and NCL peptides were combined and administered to activate PBMCs from healthy donors. The cancer-killing ability of the resultant T cells was assessed using crystal violet staining, and their subtypes and cytotoxic cytokines were characterized through flow cytometry and cytokine bead array.ResultsFindings showed that 85.3% (127/149) of TNBC cases were positive for either MSLN or NCL, or both; with single positivity rates for MSLN and NCL of 14.1% and 28.9%, respectively. MSLN and NCL peptides, with high binding affinity for HLA-A*02, were combined and introduced to activated PBMCs from healthy donors. The co-pulsed PBMCs significantly induced TEM and TEMRA CD3+/CD8+ T cells and IFN-γ production, compared to single-peptide pulsed or unpulsed conditions. Notably, MSLN/NCL-specific T cells successfully induced cell death in MSLN+/NCL+ MDA-MB-231 cells, releasing key cytotoxic factors such as perforin, granzymes A and B, Fas ligand, IFN-γ, and granulysin.ConclusionsThese findings serve as a proof-of-concept for using multiple immunogenic peptides as a novel therapeutic approach in TNBC patients.

Virtual Screening and Molecular Dynamics Simulation to Identify Inhibitors of the m6A-RNA Reader Protein YTHDC1

YTHDC1 (YTH domain containing 1), a crucial reader protein of N6-methyladenosine (m6A) mRNA, plays a critical role in various cellular functions and is considered a promising target for therapeutic intervention in acute myeloid leukemia and other cancers. In this study, we identified orthosteric small-molecule ligands for YTHDC1. Using a molecular docking approach, we screened the eMolecules database and recognized 15 top-ranked ligands. Subsequently, molecular dynamics simulations and MM/PBSA analysis were used to assess the stability and binding free energy of these potential hit compounds in complex with YTHDC1. Notably, five compounds with IDs of ZINC82121447, ZINC02170552, ZINC65274016, ZINC10763862, and ZINC02412146 exhibited high binding affinities and favorable binding free energies. The results also showed that these compounds formed strong hydrogen bonds with residues SER378, ASN363, and ASN367 and interacted with the aromatic cage of the YTHDC1 reader protein through TRP377, TRP428, and hydrophobic residue LEU439. To assess their viability as lead compounds, we conducted absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies to reveal promising features for these identified small molecules, shedding light on their pharmacokinetic and safety profiles.

In Silico Evaluation of HIV Protease and RNA Polymerase Inhibitors as Potential COVID-19 Therapeutics.

The COVID-19 coronavirus, also known as the acute respiratory syndrome coronavirus, emerged as a significant global health concern. First identified in Wuhan, China, in December 2019, the virus rapidly spread to over 187 countries due to its high transmissibility. Until an effective treatment or vaccine is developed, preventive measures remain the only mandatory strategy to curb person-to-person transmission. The study aimed to explore potential therapeutic options for COVID-19 by repurposing existing drugs. Specifically, the objective was to evaluate a library of clinically approved or investigational antiviral compounds through docking studies to identify candidates with high binding affinity to COVID-19 proteins. The study employed molecular docking techniques using the Maestro interface (Schrodinger Suite, LLC, NY) to assess the interaction of selected compounds with various COVID-19 protein targets. A total of 15 compounds were analyzed for their binding potential to multiple forms of the virus's proteins. The docking studies revealed that several compounds, particularly HIV protease inhibitors and RNA-dependent RNA polymerase inhibitors, demonstrated strong binding affinities to key COVID-19 enzymes. These interactions suggest their potential as therapeutic candidates for COVID-19 treatment. The findings from this drug repurposing study highlight the potential of certain existing antiviral agents in the treatment of COVID-19. The identified compounds could serve as promising candidates for further investigation in the ongoing battle against the coronavirus pandemic.