Search Results (1,260)

Cognitive impairment in schizophrenia remains insufficiently addressed by existing treatments. Current FDA-approved therapies primarily modulate neurotransmitter systems, resulting in incomplete symptom control and substantial adverse effects. There is therefore a critical need for therapeutic strategies that more directly address the intracellular signaling mechanisms underlying synaptic dysfunction and cognitive deficits in schizophrenia. Protein phosphatases represent an essential but historically underexplored class of signaling enzymes that regulate phosphorylation-dependent control of synaptic receptor trafficking, plasticity, and neuronal circuit function. Although multiple phosphatases have been implicated in schizophrenia through genetic, post-mortem, and functional studies, their therapeutic targeting has been limited by challenges related to selectivity, cellular permeability, and pleiotropy. Here, we review the etiology of schizophrenia and limitations of current pharmacological approaches, synthesize evidence linking specific protein phosphatases to schizophrenia pathophysiology, and discuss emerging strategies, including allosteric modulation and targeted protein degradation, that may enable selective intervention in phosphatase-driven signaling pathways. We highlight the striatal-enriched tyrosine phosphatase STEP (PTPN5) as a case study illustrating how selective phosphatase modulation can restore synaptic signaling in schizophrenia-relevant models. Full article

The progression of prostate cancer to castration-resistant disease (CRPC) remains a clinical challenge in which oxidative stress intersects with the PI3K/AKT–androgen receptor (AR) axis. Quercetin (QRC) is a redox-active dietary flavonol, yet its mechanistic impact on CRPC is incompletely defined. Here, we tested whether QRC suppresses AR output by directly modulating AKT. C4-2B and 22Rv1 CRPC cell lines were treated with increasing QRC concentrations, with or without enzalutamide (Enz). Proliferation and viability were monitored by IncuCyte imaging and SYTOX Green incorporation. AKT phosphorylation (S473), AR phosphorylation (S210/213), AR abundance and localization, and prostate-specific antigen (PSA) secretion were assessed by immunoblotting, immunofluorescence, and dot blot, respectively. Docking and molecular dynamic simulations were performed to identify and evaluate a putative QRC-binding site on AKT. QRC produced a dose-dependent cytostatic effect (IC₅₀ 24.37 μM in C4-2B; 21.54 μM in 22Rv1) without marked cell death, reduced pAKT(S473) by up to 80%, decreased pAR(S210/213), and diminished nuclear AR and PSA secretion. Simulations suggested a putative druggable allosteric pocket in the AKT1 N-lobe, with G159 emerging as a potential anchor residue. Enz cotreatment with QRC did not produce additive effects, consistent with a model in which QRC acts upstream of ligand-driven AR activation and thereby limits the incremental benefit of AR antagonism under these conditions. These data support QRC as an AKT–AR axis modulator in CRPC and provide a target engagement framework beyond simple ROS scavenging. Full article

Background/Objectives: The emergence of antimicrobial resistance necessitates the development of new and effective antimicrobial agents. In this study, three different series of imidazole-based chalcones (IBC1-25) were designed and synthesised using a sustainable approach, with the aim of identifying compounds with enhanced antimicrobial activity. Methods: A series of monoalkoxy, dialkoxy, and trialkoxy imidazole-based chalcones (IBC1–25) were synthesised and evaluated for their antimicrobial and antifungal activities against a range of microbial strains. Structure-activity relationships were analysed, and molecular docking studies were performed to investigate potential binding interactions with biofilm-associated regulatory proteins. In addition, ADME properties were predicted to assess drug-likeness. Results: Among the monoalkoxy derivatives (IBC1-14), IBC5 exhibited the broadest spectrum of activity, particularly against S. epidermidis. Several dialkoxy analogues (IBC17-21) demonstrated improved potency, with IBC20 showing notably high activity. While IBC22 and IBC25 were largely ineffective, IBC23 and IBC24 displayed significant antibacterial and antifungal activities. Overall, dialkoxy and trialkoxy derivatives exhibited enhanced efficacy, whereas monoalkoxy compounds with bulky or long-chain substituents were generally less active. The presence of multiple alkoxy substituents, such as methoxy and ethoxy groups, on the phenyl ring significantly improved activity, particularly against fungi and Gram-positive bacteria. Molecular docking studies revealed that IBC20 and IBC23 showed favourable binding to the biofilm-associated regulator TcaR, suggesting a potential allosteric inhibition mechanism, while weak interactions were observed with TagF. ADME predictions indicated good oral absorption and compliance with key drug-likeness criteria. Conclusions: The results demonstrate that both the number and type of alkoxy substituents play a critical role in antimicrobial activity. In particular, IBC20 and IBC23 emerge as promising candidates for further development as antimicrobial agents targeting biofilm-associated pathways. Full article

Background: Neurodevelopmental disorders span a wide spectrum of deficits, often with a known or suspected genetic basis. While some genetic determinants may indicate treatment with selective compounds, more often both the molecular cause of the disorder and the mechanism of action for the therapeutic compound are more ambiguously matched. Due to the polypharmacological nature of most neuroactive compounds, measuring gene expression changes following drug perturbation could be an effective strategy to gain insight into shared therapeutic action downstream of diversity in receptor interaction. High-throughput drug discovery platforms have effectively measured changes in gene expression following drug perturbation in cell cultures, but unfortunately, these platforms often lack specificity for neuroactive compounds, fail to capture the developmental influence of cell–cell interactions, and do not accurately model drug metabolism in an intact system. Methods: In this study, we present a high-throughput, low-cost and cell-type-specific approach for capturing transcriptional changes in neural cell populations following neuroactive compound exposure through the combined use of transgenic zebrafish, cell sorting, and bulk RNA-seq. Results: Our system captures unique transcriptional profiles between neuronal and non-neuronal cell populations and demonstrates specific drug responsiveness within our neuronal cell population. We assessed two known positive allosteric modulators (PAMs) of γ-Aminobutyric acid sub-type A receptors (GABA_AR), ivermectin and propofol, as a case study to explore shared pathway and gene expression changes following drug exposure; these chemically distinct agents share a mechanistic signature that dampens the neuronal hyperexcitability characteristic of a broad spectrum of neurodevelopmental disorders. Two shared downregulated genes reflect a core expression module for modulating GABAergic tone: SRC proto-oncogene, non-receptor tyrosine kinase (SRC), and Glutamate decarboxylase 2 (GAD2). Conclusions: We provide this methodology and analysis as a framework for exploring shared changes in gene expression following neuroactive compound exposure in vivo, leading to a more complete and nuanced understanding of therapeutic effects on neurons that can aid in drug repurposing efforts for neurodevelopmental disorders. Full article

Polycystic ovary syndrome (PCOS) is associated with impaired ovarian steroidogenesis and ovulation, which necessitates the development of effective ovulation inducers for PCOS. The aim of the study was to evaluate the effects of allosteric luteinizing hormone receptor agonist TP03 and human chorionic gonadotropin (hCG) on ovarian steroidogenesis, as well as ovulation in prepubertal female rats with dehydroepiandrosterone(DHEA)-induced PCOS. Taking into account differences in progesterone levels, cohorts with high (PCOS(H)) and low (PCOS(L)) progesterone were formed and treated with Follimag and Cetrotide. After 48 h, TP03 (25 mg/kg) or hCG (25 IU/rat) were injected, and hormone levels, gene expression, and ovarian morphology were assessed. The PCOS(H)-cohort exhibited irregular estrous cycles, ovarian cysts, and increased ovarian mass and estradiol levels, but the number of corpora lutea (CL) was maintained. In the PCOS(L)-cohort, ovarian weight was increased, and Star, Cyp11a1, and Adamts1 gene expression as well as the CL number were decreased. In both cohorts, TP03 and hCG increased progesterone levels and the expression of steroidogenesis (Star, Cyp11a1) and ovulation (Cox2, Adamts1, Egr1) genes, as well as inducing CL formation. Thus, TP03, like hCG, stimulates steroidogenesis and ovulation in PCOS-rats with different progesterone levels, which provides the first evidence of the effectiveness of allosteric LHR agonists as ovulation triggers in PCOS. Full article

Background: Fast excitatory transmission in the central nervous system is carried out by AMPA-type glutamate receptors. Neuronal hyperexcitability and epilepsy have been associated with the dysregulation of AMPA receptor function. Modulation of the gating kinetics of AMPA receptor function has been proposed to be a desirable target for therapy, especially when the modulation is transmembrane AMPA receptor regulatory protein (TARP)-dependent and AMPA receptor subunit composition-dependent. Methods: Eight dibenzobarrelene-based heterocycles were characterized for their effects on the human embryonic kidney cells expressing homomeric GluA1 and heteromeric GluA1/2 AMPA receptors, either alone or co-expressed with the TARPγ8 auxiliary subunit, using whole-cell patch-clamp electrophysiological recordings, and the current amplitude and kinetics of desensitization and deactivation were measured after rapid glutamate application. Results: Each chemical evaluated suppressed glutamate-induced currents via AMPA receptors and augmented both desensitization and deactivation, indicating a negative allosteric modulatory effect. The co-expression of TARPγ8 diminished, but did not eradicate, the inhibition and acceleration induced by the compounds. The observations indicate that the chemicals diminish agonist-bound open states and facilitate transitions to non-conducting states while maintaining effectiveness. Conclusions: The present study describes a specific kinetic mechanism by which dibenzobarrelene derivatives impair the function of the AMPA receptor and its dependence on auxiliary proteins. The present study provides a mechanistic understanding of AMPA receptor gating modulation and establishes a pharmacological framework for future investigations in more physiologically relevant systems. Full article

Allosteric modulation has emerged as a powerful strategy for achieving superior selectivity and safety in drug discovery and protein function regulation. Unlike highly conserved orthosteric sites, allosteric pockets are structurally diverse and less evolutionarily constrained, making them particularly suitable for modulation by designed miniproteins. Miniproteins can provide extended binding interfaces and high affinity for shallow, dynamic, or cryptic regulatory surfaces that are often inaccessible to small molecules. Recent advances in artificial intelligence (AI) are transforming this field through deep learning-based structure prediction and generative modeling. These AI-driven approaches enable the identification of allosteric hotspots, characterization of conformational ensembles, and de novo design of structured miniprotein binders. They are rapidly expanding the landscape for designing selective modulators across diverse allosteric targets, including GPCRs, receptor tyrosine kinases, nuclear receptors, ion channels, and other protein–protein interaction systems. This review summarizes state-of-the-art AI-driven computational methodologies for designing miniproteins as potential allosteric modulators and discusses their current challenges and future opportunities in allosteric drug discovery. Full article

The berberine derivative 13-(2-methylbenzyl)-berberine (BED) has been shown to inhibit the MexXY-OprM efflux system of Pseudomonas aeruginosa (PA), a key contributor to aminoglycoside resistance, by interacting with the inner membrane protein MexY at an allosteric pocket (ALP). To enhance binding efficacy, this study aims to identify novel chemical scaffolds that target the MexY allosteric pocket through an integrated computational strategy. In this work, a ligand-based virtual screening (LBVS) approach was employed using a 2D/3D pharmacophore model derived from BED to perform in silico screening of an Enamine compound library, which encompasses a broad and diverse chemical space. A key objective was to compare the predictive performance of this pharmacophore-based workflow with a structure-based (SB) strategy incorporating molecular docking and molecular dynamics (MD) simulations. Notably, the top-ranked LBVS hits were consistently validated by docking and MD analyses, showing stable binding and interaction patterns comparable or superior to those of BED. This convergence between ligand-based (LB) and SB methods highlights the internal coherence of the workflow and supports the robustness of the pharmacophore hypothesis. The identified scaffolds generally displayed high hydrophobicity, consistent with the physicochemical nature of the binding site, but resulting in limited aqueous solubility and complicating their experimental evaluation. While these features confirm the importance of hydrophobic interactions in MexY recognition, with a particular focus on some few residues, such as Phe560, it also underscores the need for formulation strategies or rational scaffold modifications introducing moderate polarity without weakening key contacts. Overall, the integrated computational strategy not only yields promising lead chemical structures but also provides a solid basis for their future optimization, ultimately supporting the design of new efflux pump inhibitors (EPIs) capable of contributing to improved antibiotic susceptibility in multidrug-resistant PA strains. Full article

Peptidyl arginine deiminase 4 (PAD4) is a Ca²⁺-dependent enzyme that catalyzes histone citrullination and plays a central role in chromatin decondensation during neutrophil extracellular trap (NET) formation. Dysregulated PAD4-mediated NETosis contributes to the pathogenesis of diverse inflammatory and immune-related diseases, including autoimmune disorders, cancer, and thrombosis. Although several synthetic PAD4 inhibitors have been developed, their therapeutic application has been limited by issues related to selectivity, irreversible covalent reactivity, and suboptimal pharmacokinetic properties, prompting growing interest in natural products as alternative modulators of PAD4 activity and NETosis. This article presents a structural and mechanistic overview of natural products that target PAD4 and regulate NETosis. Based on enzyme kinetics, structural analyses, and functional validation, natural PAD4 modulators are classified into four categories: (i) active-site-directed inhibitors that bind within the U-shaped substrate tunnel, (ii) mixed and active-site-adjacent inhibitors that engage surface pockets flanking the catalytic site, (iii) allosteric and hybrid modulators that bind to regulatory regions distinct from the active site, and (iv) functionally validated PAD4 binders supported by biophysical and cellular evidence. Integration of structural, biochemical, and cellular data highlights that indirect or noncanonical modes of PAD4 regulation represent biologically coherent strategies for controlling pathological NETosis. Full article

Psoriasis is a chronic, immune-mediated inflammatory skin disease requiring effective long-term systemic treatment. Current options, including using conventional small molecules and biological therapies, are limited by adverse events, suboptimal efficacy, or poor adherence due to inconvenient administration. This highlights an unmet need for safe, convenient, and effective oral self-administered dosage form therapies aligned with patient preferences. This review evaluates the mechanism, safety, and efficacy of next-generation tyrosine kinase 2 (TYK2) inhibitors and compares them to currently available therapeutic options. The pathogenesis of psoriasis is driven by chronic systemic inflammation mediated by the interleukin-23 (IL-23)/Th17/interleukin-17 (IL-17) axis. Selective TYK2 inhibitors, such as deucravacitinib, envudeucitinib, and zasocitinib, act through a unique allosteric mechanism by binding to the regulatory pseudokinase domain (JH2) rather than the enzyme’s catalytic domain. This enables highly selective suppression of IL-23-mediated inflammation while mitigating systemic toxicity seen with nonselective Janus kinase (JAK) inhibitors. Clinical trials (POETYK PSO-1 and PSO-2) and long-term extension studies demonstrate that deucravacitinib provides superior efficacy compared to the first-generation oral small molecule apremilast, with high and sustained response rates. It maintains durable efficacy for up to four years in patients with moderate to severe plaque psoriasis and shows a stable long-term safety profile, with low incidence of major adverse cardiovascular events (MACEs), venous thromboembolism (VTE), serious infections, and malignancies. Selective TYK2 inhibition bridges the therapeutic gap, providing an optimal balance of efficacy and oral convenience. With the potential to improve patient adherence and quality of life, these agents represent a promising option to become a first-line oral systemic therapy for psoriasis. Full article

The rapid spread of antibiotic resistance through plasmid-mediated conjugation remains a primary global health concern. Despite its critical role in horizontal gene transfer, no approved drugs currently target this process, leaving a critical therapeutic gap. Integration Host Factor (IHF), a DNA-binding protein essential for plasmid replication and mobilization, emerges as a promising yet underexplored target for anti-conjugation strategies. This work aimed to develop a predictive computational model and identify small molecules that disrupt IHF function, thereby reducing plasmid transfer and limiting resistance gene dissemination. A curated dataset of 65 compounds with reported anti-plasmid activity was analyzed using a 3D-QSAR model based on algebraic descriptors computed with QuBiLS-MIDAS. The model was validated through leave-one-out cross-validation (Q² = 0.82), Tropsha’s criteria, and Y-scrambling. Representative compounds were selected via pharmacophore clustering and evaluated through molecular docking at both the DNA-binding site and a predicted allosteric pocket of IHF. The most promising complexes underwent 200 ns molecular dynamics simulations to assess stability and interaction patterns. The QSAR model demonstrated strong predictive performance (R² = 0.90). Docking simulations revealed more favorable binding energies at the allosteric site (up to −12.15 kcal/mol) compared to the DNA-binding site. Molecular dynamics confirmed the stability of these interactions, with allosteric complexes showing lower RMSD fluctuations and consistent binding energy profiles. Dynamic cross-correlation analysis revealed that allosteric ligand binding induces conformational changes in key catalytic residues, including Pro65, Pro61, and Leu66. These alterations may compromise DNA recognition and disrupt the initiation of replication. To our knowledge, this is the first computational study proposing allosteric inhibition of IHF as an anti-conjugation strategy. These findings provide a foundation for experimental validation and the development of novel agents to prevent horizontal gene transfer, offering a promising approach to restoring antibiotic efficacy against multidrug-resistant pathogens. Full article

The role of adenylate kinase in regulating the glycolysis rate and the potential contribution of the adenylate kinase reaction to ATP production were examined using mathematical models of energy metabolism in human erythrocytes and resting anaerobic mammalian skeletal muscle. The adenylate kinase reaction was shown to play a critical role in the regulation of cellular energy metabolism. Through the action of adenylate kinase, small changes in intracellular [ATP] give rise to large changes in [AMP], a potent activator of glycolytic flux via the activation of phosphofructokinase (PFK). This mechanism ensures an increase in the glycolytic rate as [ATP] decreases within the physiological range of ATP concentrations. As a result, negative feedback regulation of glycolysis by [ATP] is established, allowing the rate of ATP production to adjust to the energy demands of the cell and thereby stabilizing [ATP] under varying rates of ATP consumption. Importantly, allosteric inhibition of PFK by ATP alone was insufficient to provide negative feedback regulation of glycolysis via [ATP]. The contribution of the adenylate kinase reaction to ATP production appears to be negligible. Also, due to the presence of adenylate kinase in cells, energy metabolism is regulated not by the absolute concentration of ATP, but by the energy charge or the ratio of [ATP] to the sum of [ATP], [ADP], and [AMP]. Full article

The metabolic control analysis (MCA) was applied to several subsystems selected from the model of human erythrocyte energy metabolism. These subsystems represent varying degrees of simplification of energy metabolism, from the simplest subsystem of the first three glycolytic reactions that determine the steady-state rate of glycolysis, to an expanded subsystem that includes all glycolytic reactions plus passive and active ion transport across the cell membrane. The control coefficients of enzyme activities for the rate of glycolysis are found to be very different in different subsystems. However, no specific trend is observed in changes in control coefficients as the subsystem becomes more complex. Thus, in subsystems containing only glycolysis, the control coefficients of hexokinase (HK) and phosphofructokinase (PFK) together amount to 0.99. When ATPases are added, this value decreases to 0.18 and below, and the maximum control coefficient goes to ATPase (0.82–1.00). It would seem that there is a natural decrease in the contribution of HK and PFK to the regulation of the rate of glycolysis as the dimension of the system increases. However, disabling the allosteric regulation of PFK by AMP completely changes the picture. In a subsystem containing only glycolysis, disabling this regulation does not affect the control coefficients. After adding ATPase to such a subsystem, the HK and PFK control coefficients increase, and the control coefficient of ATPase takes on a negative value. Thus, we found that in extended subsystems involving glycolysis and ATPase or transmembrane ion transport, information on the initial regulation of glycolysis may not be revealed in the MCA results. It appears that the MCA alone cannot reveal regulatory mechanisms of metabolic systems in the presence of strong allosteric and feedback regulation. Full article

Aldose Reductase (AR; AKR1B1) is an enzyme that plays a key role in the metabolism of glucose and other carbonyl compounds, and whose hyperactivity contributes to oxidative stress and vascular dysfunction. Despite decades of investigation into this enzyme, inhibitors have failed to translate into clinical application for Diabetic Retinopathy (DR). We argue that these failures might arise from non-selective inhibition, considering the dual roles of AR, which contribute not only to DR pathology but also support retinal health, as AR is an important detoxifying enzyme for aldehydes produced during oxidative stress. Here, we discuss missing structural information, despite more than one hundred crystal structures of AR in complex with inhibitors. Our review bridges this gap by discussing how recent advances in structural biology, e.g., fragment-based drug discovery and MicroED, provide novel ways to selectively modulate AR functions, offering advantages for the detection of weak, allosteric, or conformation-dependent binding events. Despite past challenges, we suggest that therapeutic targeting of AR to find new-generation inhibitors will become more effective once we have a clearer understanding of the requirements for selective inhibition of AR, blocking its pathological impact while preserving its physiological functions. By integrating fragment screening and structural biology, we outline a strategy to reinvigorate AR modulation as a viable retina-specific approach for managing DR, with potentially broader relevance toward multiple diabetic microvascular complications. Full article

This study investigated the α-glucosidase inhibitory potential of enzymatic/alkaline treatments from Palmaria palmata using different proteases and pairwise combinations thereof. Treatments prepared with Alcalase^®, Flavourzyme^®, and Formea^® Prime, alone or in combination, were evaluated for dose-dependent inhibitory activity. Alcalase^®-derived treatments exhibited the highest α-glucosidase inhibition, achieving an IC₅₀ of 2.48 mg·mL⁻¹, outperforming other treatments and combinations. Membrane fractionation of the Alcalase^®-derived treatment into >5 kDa, 3–5 kDa, 1–3 kDa, and <1 kDa fractions revealed a size-dependent trend, with the <1 kDa fraction showing the strongest inhibition (IC₅₀ of 1.94 mg·mL⁻¹). Three peptides, RADIPFRRA, DGIAEAWLG, and FWSQIFGVAF, from the <1 kDa fraction were identified as potential α-glucosidase inhibitors using the BIOPEP-UWM database and were further selected based on a Peptide Ranker score above 0.6 for in silico docking analyses. Docking revealed distinct binding modes: RADIPFRRA and DGIAEAWLG occupied the catalytic cleft, interacting with key residues (Asp518, Asp616, Trp481, Trp613) consistent with competitive inhibition, whereas FWSQIFGVAF bound to a peripheral site, suggesting potential allosteric modulation. Physicochemical analysis further highlighted differences in charge and isoelectric point correlating with their binding behavior. Together, these findings demonstrate that low-molecular-weight peptides derived from P. palmata proteins, particularly those generated by Alcalase^®, possess significant α-glucosidase inhibitory activity, and provide structural insights for the rational design of peptide-based modulators of carbohydrate metabolism. Full article