Search Results (2,313)

The inactivation of thrombin by antithrombin is highly enhanced by the presence of heparin chains forming “bridges” between the two proteins. X-ray structures for such ternary complexes have been published, but the molecular background of the lower efficiency of smaller heparinoids on thrombin inhibition remains poorly understood. Antithrombin-resistant prothrombin mutants (mutations affecting Arg596 in prothrombin) have been reported that cause severe thrombophilia. Our aim was to study the interactions in the antithrombin–thrombin Michaelis complex both in the presence and the absence of a heparinoid chain and in the presence of pentasaccharide by using molecular dynamics. We also intended to study the complexes of thrombin mutants as well as a known alternative antithrombin conformation at the “hinge” region built using docking. The binding between the proteins was investigated by Gaussian Accelerated Molecular Dynamics (GaMD). We compared the contribution of several amino acids at the binding “exosites” between AT and the wild type and mutant thrombins and between systems containing or not containing a heparinoid. In the docking-based simulations, several of the analyzed amino acid pairs no longer contributed to the interaction, suggesting that the open “hinge” conformation has limited biological relevance. We could identify multiple conformational types using clustering, revealing high flexibility in mutants and systems without heparinoid, probably indicating lower stability. We were also able to detect the allosteric effects of the ligands on the bound thrombin. In summary, we were able to obtain conformations using GaMD that can explain the better protein–protein interactions in the ternary complexes and the impaired AT binding of the thrombin Arg596 mutants at an atomic level. Full article

The cluster of differentiation 44 (CD44) is a member of the hyaluronic acid (HA) receptor family of cell adhesion molecules. Besides HA, this transmembrane protein also serves as a receptor for other components of the extracellular matrix (ECM), including fibronectin, collagen, and osteopontin (OPN). The CD44-HA axis is involved in a wide range of physiological and cancer-related processes, particularly in cell adhesion and migration, lymphocyte activation, as well as tumour progression and metastasis. The possibility of modulating the CD44-HA interaction with a pharmacological inhibitor has therefore been recognized as an emerging anti-cancer strategy. With its expression in a wide variety, CD44 has also become the most common surface biomarker of cancer stem cells. Due to the rapid progress of research on this crucial receptor, some published and deposited variants were often poorly described or lacked accession numbers in the available protein databases, which created confusion and hindered relevant research. In this work, we attempted to examine the protein sequences of the known CD44 variants and match them between the two UniProt and the National Centre for Biotechnology Information (NCBI) Protein databases. The deposited sequences were aligned to the CD44 canonical sequence and grouped based on the observed differences. Analysis of CD44–ligand experimental structures available in the Protein Data Bank (PDB) was also performed to identify the most promising small-molecule inhibitors of the CD44-HA interaction. Full article

Galectins, a family of glycan-binding proteins, play crucial roles in various cellular functions, acting at both intracellular and extracellular levels. Among them, Galectin-3 (Gal-3) stands out as a unique member, possessing an intrinsically unstructured N-terminal oligomerization domain and a canonical carbohydrate-recognition domain (CRD). Gal-3 binding to glycosylated plasma membrane cargo leads to its oligomerization and membrane bending, ultimately resulting in the formation of endocytic invaginations. An interactomic assay using proteomic analysis of endogenous Gal-3 immunoprecipitates identified the orphan G protein-coupled receptor GPRC5A as a novel binding partner of Gal-3. GPRC5A, also known as Retinoic Acid-Induced protein 3 (RAI3), is transcriptionally induced by retinoic acid. Our results further demonstrate that extracellular recombinant Gal-3 stimulates GPRC5A internalization. In SW480 colorectal cancer cells, glycosylated GPRC5A interacts with Gal-3. Interestingly, while GPRC5A expression was upregulated by the addition of all-trans retinoic acid (ATRA), its endogenous internalization in SW480 cells was specifically triggered by extracellular Gal-3, but not by ATRA. This study provides new insights into the endocytic mechanisms of GPRC5A, for which no specific ligand has been identified to date. Further research may uncover additional Gal-3-mediated functions in GPRC5A cellular signaling and contribute to the development of innovative therapeutic strategies. Full article

The widespread use of neonicotinoid insecticides has led to increasing resistance in non-target organisms, including the egg parasitoid Trichogramma dendrolimi, a crucial biological control agent. Film-residue bioassays on 17 geographic strains revealed striking inter-strain variability in susceptibility to imidacloprid, with mortality at a discriminating dose of 0.1 mg/L ranging from 25.7% to 87%. The most tolerant (FS) and least tolerant (HA) strains were subsequently selected for evaluation of biological parameters and comparative transcriptomics. Tolerant strains (FS) showed adaptive trade-offs: extended longevity (5.47 ± 0.57 d) and emergence (93.6 ± 1.9%), but reduced fecundity (54.6 ± 4.9 eggs) compared to HA. Transcriptome analysis revealed 2115 differentially expressed genes, with GO enrichment highlighting metabolic and detoxification pathways. KEGG analysis the most enriched pathways were “Protein digestion and absorption” and “Neuroactive ligand-receptor interaction”. RT-qPCR confirmed overexpression of CYP4C1, CYP6K1, and GstS1 in FS, indicating their potential roles in metabolic resistance if present. This study presents preliminary evidence of potential fitness trade-offs and molecular mechanisms that could underly imidacloprid resistance in T. dendrolimi, which may lead to important insights for resistance monitoring and more sustainable integrated pest management strategies. Full article

The novel data show that the Hsp70 protein is a potent activator of the immune system. Using limited trypsinolisis, we have identified the epitopes of Hsp70 responsible for TREM-1-dependent and TREM-1-independent cytotoxicity. The 11aa N9 peptide (AMTKDNNLLGR) contains nine amino acids that correspond to the amino acid sequence of the known TKD peptide. Also, like TKD, this peptide does not interact with the TREM-1 receptor but activates CD94+ NK cells that kill tumor cells by secreting granzymes and inducing apoptosis. The 16aa peptide N7 (SDNQPGVLIQVYEGEK) interacts with the TREM-1 receptor and induces the activation of NK cells and cytotoxic T lymphocytes at different time points. T-lymphocytes activated by this peptide induce two alternative processes of cell death in HLA-negative tumor cells, apoptosis and necroptosis, through the interaction of the FasL lymphocyte with the Fas receptor of the tumor cell. A shortened fragment of this peptide, N7.1 (SDNQPGVL), has been identified that inhibits the interaction of TREM-1 with its ligands. This peptide has shown protective effects in the development of sepsis in mice. The results obtained can be used in antitumor and anti-inflammation therapy. Full article

Background/Objectives: Hypertension is a global health challenge. Zhengan Xifeng Decoction (ZXD), a classical traditional Chinese medicine, has shown clinical efficacy against hypertension. This study aimed to identify the bioactive constituents of ZXD and elucidate its antihypertensive mechanisms by integrating plasma UPLC–MS (ultra-performance liquid chromatography–mass spectrometry) analysis, network pharmacology, and molecular dynamics (MD) simulations. Methods: ZXD constituents and plasma-absorbed compounds were characterized by UPLC–MS. Putative targets (TCMSP, SwissTargetPrediction) were cross-referenced with hypertension targets (GeneCards, OMIM) and analyzed in a STRING protein–protein interaction network (Cytoscape) to define hub targets, followed by GO/KEGG enrichment. Selected protein–ligand complexes underwent docking, Prime MM-GBSA calculation, and MD validation. Results: A total of 72 absorbed components were identified, including 14 prototype compounds and 58 metabolites. Network pharmacology identified ten key bioactive compounds (e.g., liquiritigenin, isoliquiritigenin, and caffeic acid), 149 hypertension-related targets, and ten core targets such as SRC, PIK3CA, PIK3CB, EGFR, and IGF1R. Functional enrichment implicated cardiovascular, metabolic, and stress-response pathways in the antihypertensive effects of ZXD. Molecular docking demonstrated strong interactions between key compounds, including liquiritigenin, caffeic acid, and isoliquiritigenin, and core targets, supported by the MM-GBSA binding free energy estimation. Subsequent MD simulations confirmed the docking poses and validated the stability of the protein–ligand complexes over time. Conclusions: These findings provide mechanistic insights into the multi-component, multi-target, and multi-pathway therapeutic effects of ZXD, offering a scientific basis for its clinical use and potential guidance for future drug development in hypertension management. Full article

Effective protein immobilization is a critical step in biosensor development, as it ensures the stability, functionality, and orientation of biomolecules on the sensor surface. Here, we present a novel affinity-based terpolymer coating designed to enhance protein immobilization for biosensor applications. The novelty lies in the incorporation of nitrilotriacetic acid (NTA) ligands directly into the polymeric chains, facilitating histidine-tagged protein oriented binding through a robust metal-chelating interaction. To validate the system, magnetic microbeads coated with the polymer were tested for their ability to bind native and His-tagged proteins. The results demonstrated the superior binding capacity, enhanced stability, and reversibility of the interactions compared to traditional coatings, which immobilize proteins through nucleophile reactions with amine residues. Moreover, enzyme immobilization tests confirmed that the polymer preserves enzymatic activity, highlighting its potential for biosensor applications requiring functional biomolecules. This innovative polymeric coating offers a fast, versatile, and scalable solution for next-generation biosensor platforms, paving the way for improved sensitivity, reliability, and accessibility in diagnostic and analytical technologies. Full article

TGR5 has emerged as a promising therapeutic target for obesity and metabolic disorders due to its regulatory roles in energy expenditure, glucose homeostasis, thermogenesis, and gut hormone secretion. This review summarizes the structural mechanisms of TGR5 activation, focusing on orthosteric and allosteric ligand interactions, toggle switch dynamics, and G protein coupling based on cryo-EM and docking-based models. A wide range of bioactive natural compounds including oleanolic acid, curcumin, betulinic acid, ursolic acid, quinovic acid, obacunone, nomilin, and 5β-scymnol are examined for their ability to modulate TGR5 signaling and elicit favorable metabolic effects. Molecular docking simulations using CB-Dock2 and PDB ID 7BW0 revealed key interactions within the orthosteric pocket, supporting their mechanistic potential as TGR5 agonists. Emerging strategies in TGR5-directed drug development are also discussed, including gut-restricted agonism to minimize gallbladder-related side effects, biased and allosteric modulation to fine-tune signaling specificity, and AI-guided optimization of natural product scaffolds. These integrated insights provide a structural and pharmacological framework for the rational design of safe and effective TGR5-targeted therapeutics. Full article

Background/Objectives: Orofacial clefts (OFCs) are among the most common birth defects globally, sometimes exacerbated by adverse drug reactions (ADRs) from corticosteroids and antiepileptics. Comprehending the pharmacogenomic and pharmacogenetic elements that lead to ADRs is essential for enhancing precision medicine and clinical outcomes. This study examines rare genetic variants in drug-metabolizing and drug-transporting genes among Ghanaian and Nigerian families with a history of OFCs, intending to assess their pathogenicity and functional implications. Methods: We recruited 104 Ghanaian families and 26 Nigerian families, generating whole-genome sequencing (WGS) data from 390 individuals (130 case-parent trios). DNA isolated from saliva and buccal swab samples underwent WGS, and subsequent WGS data were analyzed through extensive bioinformatics analyses. Variants were called and annotated using the GATK workflow. The HOPE in silico modeling tool evaluated the structural impact of genetic variants on encoded proteins, while molecular docking using PyRx examined alterations in ligand binding affinity. Results: Our study revealed pathogenic variants in vital genes associated with drug metabolism and transport, specifically CYP1A2, CYP2C18, CYP27A1, CYP2B6, SLC6A2, and ABCC3. Structural modeling research demonstrated substantial size, charge, conformation, and hydrophobicity variations between wildtype and mutant proteins. Variants positioned near conserved regions or within functional domains were anticipated to be deleterious, potentially compromising protein function and ligand interactions. Molecular docking studies verified changes in binding affinities between wildtype and mutant proteins for common ligands. The identified variations were linked to the metabolism of frequently used pharmaceuticals in Africa, such as caffeine, ketoconazole, efavirenz, carbamazepine, and artemether. Conclusions: These findings highlight the need for pharmacogenetic screening to inform personalized medicine, diminish ADRs, and enhance the clinical care of OFCs in Sub-Saharan Africa. Full article

Dopamine D2-like receptors, including D2, D3, and D4, are members of the aminergic G protein-coupled receptor (GPCR) family and are targets for neurological disorders. The development of subtype selective ligands is important for enhanced therapeutics and reduced side effects; however, it is challenging to design and develop selective ligands owing to the high degree of sequence homology among D2-like subtypes. To gain insight into the structural basis of subtype selectivity of piperazinylalkyl pyrazole/isoxazole analogs for D2-like dopamine receptors, we carried out 3D quantitative structure–activity relationship (3D-QSAR) and molecular docking studies. The 3D-QSAR models for the D2, D3, and D4 subtypes showed robust correlation coefficients (r²) of 0.960, 0.912, and 0.946, as well as reliable predictive values (Q²) of 0.511, 0.808, and 0.560, respectively. Contour map analysis revealed key structural determinants for ligand activity, highlighting the distinct steric and electrostatic requirements for each subtype. These findings were further rationalized by molecular docking studies, which confirmed that interactions with non-conserved residues modulate binding affinity. Crucially, our analysis identified a critical structural basis for D4 subtype selectivity. This selectivity is attributed to a spatial constraint within the hydrophobic pocket formed by TMs 3, 5, and 6. This constraint restricts the orientation of bulky substituents on the 4-phenylpiperazine moiety. These findings provide actionable structural insights for the rational design of next-generation subtype-selective antagonists for D2-like dopamine receptors. Full article

Background/Objectives: Whilst adoptive cell therapy (ACT) using chimeric antigen receptor-engineered T (CAR-T) cells represents an efficient approach for the treatment of patients suffering from several hematological malignancies, solid tumors have been shown to be far more challenging to tackle, mainly due to the hostile tumor microenvironment that inhibits optimal T cell functionality. As proven by the broad clinical success of immune checkpoint inhibitors, blocking the interaction of programmed cell death ligand 1 (PD-L1) expressed on tumor cells and the checkpoint receptor programmed cell death 1 (PD-1) expressed on activated T cells allows an intrinsic T cell-mediated anti-tumor response to be unleashed. We developed a cellular product (MDG1015) consisting of New York esophageal squamous cell carcinoma-1 (NY-ESO-1)/L antigen family member 1a (LAGE-1a)-specific CD8+ T cell receptor-transduced (TCR-)T cells co-expressing the costimulatory switch protein (CSP) PD1-41BB, which turns an inhibitory signal mediated by the PD-1:PD-L1 axis into positive T cell costimulation. Methods: In vitro co-cultures of MDG1015 and PD-L1-positive or -negative target cells were used to analyze TCR-T cell functionality, such as TCR-T (poly-)cytokine release, the killing of target cells, and TCR-T proliferation. The safety of MDG1015 was evaluated via different panels of antigen-negative cell lines or primary cells expressing or lacking PD-L1. Results: Preclinical analyses demonstrated TCR-gated activation of the CSP, leading to enhanced functionality of MDG1015 against antigen-expressing, PD-L1-positive tumor cells without any impact on antigen-negative target cells. Conclusions: The favorable, preclinical functionality and safety profile qualifies MDG1015 as a promising cellular therapy for explorative clinical testing in hard-to-treat solid tumor indications. Full article

Background: Abnormal activation of Angiotensin II (Ang II) serves as a primary trigger for myocardial hypertrophy and cardiac injury. Isoquercitrin (IQ) and Quercetin (Que) possess anti-inflammatory and anti-apoptotic properties, but their protective effects against Ang II-induced cardiac injury remain unclear. This study aimed to investigate the mechanisms and therapeutic efficacy of IQ and Que in heart failure. Methods: Cytotoxic effects of IQ and Que on Ang II-induced H9c2 rat cardiomyocyte apoptosis models were assessed in vitro using the CCK-8 assay. Reactive Oxygen Species (ROS) generation and apoptotic fluorescence levels were measured. WB analysis examined protein expression in inflammatory and apoptotic pathways. In vivo heart failure model was established in mice, with cardioprotective effects of IQ and Que evaluated via echocardiography. Molecular docking was employed to analyze ligand–target interactions. Results: IQ outperformed Que in promoting cell viability and decreasing ROS. IQ exhibited a more potent inhibitory effect on apoptosis through regulating Bax, Caspase-3, CytoC, and Bcl-2 and demonstrated superior suppression of cardiac inflammation by inhibiting phosphorylation of ERK, JNK, and P38. Compared with Que, IQ more effectively attenuated Ang II-induced cardiac injury by ameliorating reductions in EF% and FS%, suppressing ST-segment elevation, and significantly reducing serum levels of CK-MB, LDH, ANP, BNP, and FFA in a heart failure model. Molecular docking verified stronger binding affinity of IQ for key targets. Conclusions: IQ demonstrates superior cardioprotection over Que by regulating MAPK signaling and mitochondrial apoptosis pathways, supporting its potential as a therapeutic candidate for heart failure. Full article

Class 1 phytoglobins (Pgbs) are known for their multifunctional roles in plant stress responses, with recent studies suggesting broader interactions involving metabolic and transcriptional regulation. Interestingly, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) moonlights in many roles in colocalized spaces during cellular stress that are strikingly suitable for supporting Pgb function. This study investigates the molecular interactions of class 1 Pgb from sugar beet (Beta vulgaris), BvPgb 1.2, and an alanine-substituted mutant (C86A), focusing on their ability to bind GAPDH and DNA. Using dual-emission isothermal spectral shift (SpS) analysis, we report strong binding interactions with GAPDH, with dissociation constants (K_D) of 260 ± 50 nM for the recombinant wild-type protein (rWT) and a significantly stronger affinity for C86A (120 ± 40 nM), suggesting that the cysteine residue limits the interaction. Remarkably strong DNA-binding affinities were also observed for both variants, displaying biphasic binding. This behavior is characteristic of hexacoordinated globins and reflects the presence of two distinct species: a fast-reacting open pentacoordinated form and a slow-reacting closed hexacoordinated form with high apparent affinity. Here, the K_D in the open configuration was 120 ± 50 nm and 50 ± 20 nM for rWT and C86A, respectively. In the closed configuration, however, the cysteine appears to support the interaction, as the K_D was measured at 100 ± 10 pM and 230 ± 60 pM for rWT and C86A, respectively. Protein–protein docking studies reinforced these findings, revealing electrostatically driven interactions between BvPgb 1.2 and GAPDH, characterized by a substantial buried surface area indicative of a stable, biologically relevant complex. Protein–DNA docking similarly confirmed energetically favorable binding near the heme pocket without obstructing ligand accessibility. Together, these findings indicate a potential regulatory role for BvPgb 1.2 through its interaction with GAPDH and DNA. Full article

Nucleic acid aptamers are single-stranded DNA or RNA molecules that can bind to a target with high specificity and affinity, as screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). In recent years, SELEX technologies have been significantly advanced for the screening of aptamers for a variety of target molecules, cells, and even bacteria and viruses. By integrating recent advances of emerging technologies with SELEX, novel screening technologies for nucleic acid aptamers have emerged with improved screening efficiency, reduced production costs and enhanced aptamer performance for a wide range of applications in medical diagnostics, drug delivery, and environmental monitoring. Aptasensors utilize aptamers to detect a wide range of analytes, allowing for the accurate identification and determination of small molecules, proteins, and even whole cells with remarkable specificity and sensitivity. Further optimization of the aptasensor can be achieved by aptamer truncation, which not only maintains the high specificity and affinity of the aptamer binding with the target analytes, but also reduces the manufacturing cost. Predictive models also demonstrate the powerful capability of determination of the minimal functional sequences by simulation of aptamer–target interaction processes, thus effectively shortening the aptamer screening procedure and reducing the production costs. This paper summarizes the research progress of protein-targeted aptamer screening in recent years, introduces several typical aptasensors at present, discusses the optimization methods of aptasensors by combining efficient SELEX with advanced predictive algorithms or post-SELEX processes, as well as the challenges and opportunities faced by aptasensors. Full article