Not Quite Folded: Challenges in Predicting the hNPS‐hNPSR‐Ile107 Complex With AlphaFold2 Multimer

Dual-site TAS2R14 binding by (-)-epicatechin gallate: A computational framework for neuroprotective drug repurposing.

Bitter taste receptors, particularly TAS2R14, are widely expressed in extraoral tissues, including the central nervous system, where they have been implicated in neuroinflammatory and neurodegenerative processes. Although numerous pharmacological and natural compounds have demonstrated therapeutic potential against neurodegenerative disorders, clinically effective disease-modifying therapies remain strikingly limited. TAS2R14 is a promising yet underexplored candidate target; however, its mechanistic role in neurodegenerative disorders remains poorly understood. Here, we conducted a structure-based virtual screening of 4138 FDA-approved drugs from the MedChemExpress database to identify potential TAS2R14 ligands for therapeutic repositioning. Top candidates were prioritized through a hierarchical molecular docking workflow and binding free-energy calculations (MM-GBSA), orthogonal GNINA validation, in silico ADMET assessment, followed by 500 ns molecular dynamics (MD) simulations to evaluate the persistence of predicted binding modes and ligand-associated conformational behavior at both extracellular and intracellular binding sites. The selected hits exhibited distinct predicted interaction profiles and conformational dynamics at the two independent binding sites. Among them, (-)-epicatechin gallate exhibited favorable interactions, persistent contact with key binding site residues, and comparatively limited conformational fluctuations at both sites, supporting its prioritization as a potential dual-site TAS2R14 binder. Furthermore, fexofenadine and ezetimibe showed favorable binding stability at the extracellular and intracellular sites, respectively. Hydrogen-bond analysis, principal component analysis, dynamic cross-correlation matrix analysis, and free-energy landscape mapping further revealed ligand-dependent differences in interaction networks and receptor conformational behavior. Notably, (-)-epicatechin gallate, fexofenadine, and ezetimibe exhibited greater predicted binding stability than the reference ligands flufenamic acid, cholesterol, and Comp28.1 throughout the 500 ns simulations. As this study is purely computational, experimental validation through receptor activation assays and relevant biological models will be required to determine whether the predicted binding interaction translates into functional modulation of TAS2R14 and therapeutic benefit. Nevertheless, these findings provide a computational foundation for prioritizing candidate TAS2R14 ligands and support future experimental studies to evaluate receptor activation, specificity, selectivity, and therapeutic efficacy, particularly for (-)-epicatechin gallate, in the context of TAS2R14-targeted neuroprotective drug repositioning.

Integrated In Silico Discovery of Thymoquinone Analogs Targeting the Keap1–Nrf2 Pathway for Amyotrophic Lateral Sclerosis Therapy

This study identifies structurally tractable TQ analogs with improved predicted potency and establishes a robust computational framework for neuroprotective discovery as redox‐modulating agents in ALS.

Distal conformational steering by N-terminal pyroglutamylation enables subtype-selective GPCR activation across Aplysia PRXamide and human Neuromedin U signaling

Post-translational modifications (PTMs) diversify neuropeptide function, yet how minimal modifications encode receptor specificity without direct contact remains a fundamental challenge in chemical biology. Pyroglutamylation (pQ), a prevalent N-terminal PTM in bioactive peptides, introduces a rigid cyclic constraint, yet its mechanistic role in receptor signaling is unclear. Here, using two newly identified endogenous Aplysia PRXamide receptors (ApPRXa R1 and ApPRXa-R2) as a model system, we find that the same ligand, MMG2-pDPb (pQPPLPRYamide), produces opposite functional outcomes: pQ suppresses ApPRXa-R1 activation while enhancing ApPRXa-R2 activation. In vitro and in silico analyses demonstrate that the N-terminal pQ/Q remains solvent-exposed and does not directly contact receptor residues. Instead, pQ reshapes the ligand conformational ensemble and redistributes interaction networks across shared receptor contact sites. Strikingly, this molecular logic extends to mammalian Neuromedin U (NmU) receptors, as canine NmU (pQFLFRPRNamide) similarly biases subtype preference of human NmU receptors. Both static and dynamic analyses further reveal that receptor pocket mechanics determine the direction of this modulation: a loose and permissive pocket better accommodates the rigid pQ-constrained ligand, whereas a more compact pocket favors the non-pyroglutamylated ligand. These findings define a “PTM distal steering” mechanism that bridges “lock-key” and “induced-fit” paradigms and establish a general principle by which a minimal, non-contacting modification encodes receptor preference through ligand conformational biasing and pocket-dependent permissiveness, providing a chemical framework for optimizing stable, conformation-biased neuropeptide analogs.

Computational drug repurposing identifies flavoxate as a novel NLRP3 inflammasome inhibitor for Alzheimer’s disease therapy

Design and evaluation of a novel peptide-EV complex for targeted Alzheimer's disease therapy.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that involves the formation of amyloid-β (Aβ) aggregates, and the development of targeted therapeutic strategies is needed. In the current work, we report the rational design of H102-CP05, a 22-residue chimeric peptide that integrates the β-sheet breaker peptide H102 with the CD63-targeting anchor CP05 to enable extracellular vesicle (EV)-mediated delivery of an Aβ-inhibitory payload. Computational analysis confirmed favorable physicochemical properties and a non-allergenic profile. In silico immunogenicity assessment and C-IMMSIM simulation demonstrated a low risk of anti-drug antibody formation under chronic dosing conditions. Homology modelling and HADDOCK docking (score: -147.2 ± 4.6) predicted a computationally favourable CD63 binding configuration, while 100 ns molecular dynamics simulations confirmed structural stability in both aqueous and EV-mimetic lipid bilayer environments. In vitro cytotoxicity against HEK-293 cells revealed no significant toxicity (10-100 µM). Zebrafish embryo studies indicated acceptable developmental safety at lower concentrations, with concentration-dependent bradycardia observed at higher doses warranting further cardiovascular evaluation. Thioflavin T fluorescence assays demonstrated dose-dependent inhibition of Aβ fibrillation, with near-complete suppression at 100 µM. These findings collectively support H102-CP05 as a promising EV-displayed therapeutic candidate for AD.

Cannabidiol as a Promising Anti-Inflammatory Agent Targeting TYK2: Molecular Docking and Dynamic Simulation Approaches for Therapeutic Applications in Multiple Sclerosis.

INTRODUCTION Multiple sclerosis (MS) involves chronic inflammation driven by dysregulation of the JAK-STAT pathway. This study aimed to evaluate the potential interaction of natural cannabinoids with TYK2, with a focus on cannabidiol (CBD), using computational in silico approaches. METHODS A combined molecular docking and molecular dynamics (MD) workflow was used. Cannabinoid ligands and the TYK2 structure (JH2 domain) were prepared and docked in MOE, followed by 20 ns MD simulations under NVT and NPT conditions in GROMACS. Complex stability and ligand-protein interactions were analysed. RESULTS CBD showed a competitive docking score (-7.31 kcal/mol) and a refined RMSD of 0.9198 Å. MD simulations revealed a stable CBD-TYK2 complex, with RMSD fluctuations of 0.15-0.20 nm, which were lower than those observed for the reference inhibitor, deucravacitinib. RMSF analysis revealed a slight increase in local flexibility in specific regions without affecting the overall stability of the protein. The radius of gyration remained stable throughout the simulation, indicating that the protein's compactness was preserved. Hydrogen bond analysis showed fewer but transient interactions for CBD, consistent with a binding mode dominated by hydrophobic interactions. DISCUSSION These computational results suggest that CBD interacts stably with TYK2 through a distinct binding mode compared to the reference inhibitor, deucravacitinib, while maintaining the structural integrity of the protein. CONCLUSION CBD showed a stable predicted interaction with TYK2, supporting its potential as a candidate for further in vitro and in vivo studies in the context of MS-related inflammation.