Search Results (160)

γ-Aminobutyric acid type A receptors (GABA_ARs) are pentameric ligand-gated ion channels mediating fast inhibitory neurotransmission in the mammalian brain. Although recent structural and kinetic studies have advanced understandings regarding their activation mechanisms, the molecular determinants coupling agonist binding to channel gating remain unclear. We investigated the contribution of the β₂E153 residue, located on loop B of the extracellular domain, to the activation of α₁β₂γ₂ GABA_ARs. Macroscopic and single-channel patch clamp recordings were used to characterize two β₂E153-mutants: charge reversal (β₂E153K) and hydrophobic substitution (β₂E153A). Both substitutions disrupted normal receptor kinetics, with β₂E153K selectively accelerating deactivation and β₂E153A affecting both deactivation and desensitization. Single-channel analysis showed that β₂E153A reduced open probability and mean open times, consistent with altered gating transitions inferred from kinetic modeling. Structural inspection suggested that β₂E153 forms electrostatic interactions with β₂K196 and β₂R207 to stabilize loop C and maintain the agonist-bound conformation. The disruption of this interaction likely destabilizes loop C, leading to weakened agonist binding and modified gating. Overall, our results identify β₂E153 as a key element in the long-range allosteric network linking the binding site to the channel gate in GABA_ARs. Full article

The cannabinoid receptor type 2 (CB₂) is increasingly recognized as a crucial regulator of neuroimmune balance in the brain. In addition to its well-established role in immunity, the CB₂ receptor has been identified in specific populations of neurons and glial cells throughout various brain regions, and its expression is dynamically increased during inflammatory and neuropathological conditions, positioning it as a potential non-psychoactive target for modifying neurological diseases. The expression of the CB₂ gene (CNR2) is finely tuned by epigenetic processes, including promoter CpG methylation, histone modifications, and non-coding RNAs, which regulate receptor availability and signaling preferences in response to stress, inflammation, and environmental factors. CB₂ signaling interacts with TRP channels (such as TRPV1), nuclear receptors (PPARγ), and orphan G Protein-Coupled Receptors (GPCRs, including GPR55 and GPR18) within the endocannabinoidome (eCBome), influencing microglial characteristics, cytokine production, and synaptic activity. We review how these interconnected mechanisms affect neurodegenerative and neuropsychiatric disorders, underscore the species- and cell-type-specificities that pose challenges for translation, and explore emerging strategies, including selective agonists, positive allosteric modulators, and biased ligands, that leverage the signaling adaptability of the CB₂ receptor while reducing central effects mediated by the CB₁ receptor. This focus on the neuro-centric perspective repositions the CB₂ receptor as an epigenetically informed, context-dependent hub within the eCBome, making it a promising candidate for precision therapies in conditions featuring neuroinflammation. Full article

Inhibition of agonist-induced M₂ muscarinic receptor (M₂R) activation by functional anti-M₂R autoantibodies has been associated with cardiac parasympathetic dysfunction in patients with chronic Chagas disease (CD). This study explored the allosteric nature of that inhibitory effect by assessing the ability of serum IgG from patients with CD and dysautonomia (DCD IgG) to modulate the interaction between M₂R and β-arrestins in HEK 293T cells using bioluminescence resonance energy transfer. DCD IgG alone did not stimulate arrestin-2 or arrestin-3 recruitment. When cells were preincubated with DCD IgG and then treated with carbachol, arrestin-2 translocation decreased in a concentration-dependent manner, while arrestin-3 recruitment remained unaffected. Inhibition curve analysis showed a submaximal inhibitory effect (68.1 ± 2.4%) and a Hill slope less than −1 (−4.03 ± 0.39). Carbachol concentration–response assays after preincubation with DCD IgG revealed a noncompetitive inhibition of arrestin-2 recruitment, with no change in arrestin-3 translocation. Unlikely, simultaneous exposure to DCD IgG and carbachol potentiated agonist-induced Arr-2 recruitment. We conclude that anti-M₂R autoantibodies selectively inhibit agonist-induced arrestin-2 recruitment, acting as negative allosteric modulators of agonist efficacy. The direction of autoantibody-induced allosteric modulation depends on the timing of IgG application relative to the agonist and the duration of receptor exposure to autoantibodies. Full article

Blind docking predicts binding interactions between two molecular entities without prior knowledge of the binding site. This approach is essential because it explores the entire surface of the receptor to identify potential interaction sites. Blind docking widely works for both protein–protein and ligand–protein interaction studies. In protein–protein blind docking, the method aims to predict the correct orientation and interface of two proteins forming a complex. Protein blind docking is particularly valuable in studying transient interactions, protein–protein recognition, signaling pathways, tentative and significant biomolecular assemblies where structural data is limited. Ligand–protein blind docking discovers potential binding pockets across the entire protein surface. It is frequently applied in early-stage drug discovery, especially for novel or poorly characterized targets. The method helps identify allosteric sites or novel binding regions that are not evident from known structures. Overall, blind docking provides a versatile and powerful tool for studying molecular interactions, enabling discovery even in the absence of detailed structural information. In this scenario, we reported a timeline of attempts to improve this kind of computational approach with ML and hybrid approaches to obtain more reliable predictions. We dedicate two main sections to protein–protein and protein-ligand blind docking, presenting the reliability and caveats for each approach and outlining potential future directions. Full article

Background and Objectives: Neuroinflammation plays a significant role in liver and neurological disorders via its disruption of neurotransmission, which alters cerebral function, resulting in cognitive and motor impairment, fatigue, anxiety, and depression. A key interaction exists between GABAergic neurotransmission and neuroinflammation, whereby excessive GABA_A receptor activation exacerbates cognitive and behavioural impairment. Golexanolone, a novel GABA_A-receptor-modulating steroid antagonist (GAMSA), primarily attenuates GABAergic potentiation via GABA_A-positive steroid allosteric receptor modulators such as allopregnanolone. This review aims to summarize new evidence showing that golexanolone improves peripheral inflammation, neuroinflammation, and neurological alterations in animal models of different neurological pathologies. We provide an overview of the first clinical trial using this novel compound. Results: In rat models of hyperammonemia and minimal hepatic encephalopathy (MHE), peripheral inflammation induces microglia and astrocyte activation and neuroinflammation, altering GABAergic neurotransmission and resulting in cognitive and motor impairment. Golexanolone’s unique dual action reduces peripheral inflammation and glial activation, thus normalizing neurotransmission and cognitive and motor function. Furthermore, a phase II study in cirrhotic patients with MHE shows that golexanolone is well tolerated and improves cognition. Similarly, in a model of primary biliary cholangitis (PBC) involving bile-duct ligation, peripheral inflammation, neuroinflammation, and altered neurotransmission—associated with fatigue, impaired memory, and locomotor gait and motor incoordination—were reversed by the dual action of golexanolone. In the Parkinson’s disease (PD) rat model induced by neurotoxin 6-OHDA, rats exhibited fatigue, anhedonia, impaired memory, and locomotor gait and motor incoordination, which were associated with microglia and astrocyte activation in the substantia nigra and striatum, in addition to tyrosine hydroxylase (TH) loss. Golexanolone reduces microglia and astrocyte activation, partially reduces TH loss, and improves fatigue, anhedonia, memory, locomotor gait, and motor incoordination. Golexanolone also normalizes elevated levels of α-synuclein. Conclusions: These findings suggest that golexanolone has beneficial therapeutic effects for treating fatigue, depression, motor, and cognitive impairment across diverse neuroinflammatory conditions, including synucleinopathies. Full article

Understanding the atomistic basis of multi-layer mechanisms employed by broadly reactive neutralizing antibodies of the SARS-CoV-2 spike protein without directly blocking receptor engagement remains an important challenge in coronavirus immunology. Class 4 antibodies represent an intriguing case: they target a deeply conserved, cryptic epitope on the receptor-binding domain yet exhibit variable neutralization potency across subgroups F1 (CR3022, EY6A, COVA1-16), F2 (DH1047), and F3 (S2X259). The molecular basis for this variability is not fully understood. Here, we employed a multi-modal computational approach integrating atomistic and coarse-grained molecular dynamics simulations, binding free energy calculations, mutational scanning, and dynamic network analysis to elucidate how these antibodies engage the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and influence its function. Our results reveal that neutralization efficacy arises from the interplay of direct interfacial interactions and allosteric effects. Group F1 antibodies (CR3022, EY6A, COVA1-16) primarily operate via classic allostery, modulating flexibility in RBD loop regions to indirectly interfere with the ACE2 receptor binding through long-range effects. Group F2 antibody DH1047 represents an intermediate mechanism, combining partial steric hindrance—through engagement of ACE2-critical residues T376, R408, V503, and Y508—with significant allosteric influence, facilitated by localized communication pathways linking the epitope to the receptor interface. Group F3 antibody S2X259 achieves potent neutralization through a synergistic mechanism involving direct competition with ACE2 and localized allosteric stabilization, albeit with potentially increased escape vulnerability. Dynamic network analysis identified a conserved “allosteric ring” within the RBD core that serves as a structural scaffold for long-range signal propagation, with antibody-specific extensions modulating communication to the ACE2 interface. These findings support a model where Class 4 neutralization strategies evolve through the refinement of peripheral allosteric connections rather than epitope redesign. This study establishes a robust computational framework for understanding the atomistic basis of neutralization activity and immune escape for Class 4 antibodies, highlighting how the interplay of binding energetics, conformational dynamics, and allosteric modulation governs their effectiveness against SARS-CoV-2. Full article

The proposed physiological roles of bile acids have expanded beyond the digestion of fats to encompass cell signaling via the activation of a variety of nuclear and plasma membrane receptors in multiple organ systems. The current in silico study was inspired by previous observations from our group and others that bile acids interact functionally with cardiac, pulmonary, and gastrointestinal muscarinic receptors and more recent work demonstrating allosteric binding of cholesterol, the parent molecule for bile acid synthesis, to M₁ muscarinic receptors (M₁R). Here, we computationally tested the hypothesis that bile acids can allosterically bind to M₁R and thereby modulate receptor activation. Utilizing de novo site identification by the ligand competitive saturation (SILCS) method, putative novel allosteric binding sites of bile acid targeting M₁R were identified. Molecular dynamics simulations were used to uncover the molecular details of the activation mechanism of M₁R due to agonist binding along with allosteric modulation of bile acids on M₁R activation. Allosteric binding of bile acids and their glycine and taurine conjugates to M₁R negatively impacts the activation process, findings consistent with recent reports that M₁R expression and activation inhibit colon cancer cell proliferation. Thus, bile acids may augment colon cancer risk by inhibiting the tumor suppressor actions of M₁R. When validated experimentally, these findings are anticipated to shed light on our understanding of how bile acids in the membrane microenvironment can allosterically modulate the function of M₁R and possibly other G protein-coupled receptors. Full article

The corticotropin-releasing factor (CRF) and its type 1 receptor (CRF₁R) play a key role in the regulation of the hypothalamic–pituitary–adrenal (HPA) axis. Dysregulation of the HPA axis is associated with congenital adrenal hyperplasia (CAH) and depression. Non-peptide CRF₁R-selective antagonists displayed antidepressant effects on animal models and are used for the management of CAH. To develop novel non-peptide CRF₁R antagonists, we have previously designed and synthesized a series of substituted pyrimidines. Among these analogs, molecule 43 (M43) binds to CRF₁R with the highest affinity. Based on this finding, we selected M43 for further pharmacological characterization in the present study. The results suggest that M43 is a potent CRF₁R antagonist, blocking the ability of the CRF-related agonist, Tyr⁰-sauvagine, to stimulate (1) cAMP accumulation in HEK 293 cells expressing CRF₁R and (2) the proliferation rate of RAW 264.7 macrophages. Computational studies suggest that the antagonist properties of M43 are mostly attributed to its ability to interact with residues in the allosteric pocket of CRF₁R, comprised of the third, fifth, and sixth transmembrane domain residues, which block activation-associated structural rearrangements of the receptor. Our data will be used to design novel non-peptide CRF₁R antagonists for clinical use. Full article

Background: Understanding how aroma compounds enhance monosodium glutamate (MSG) umami perception remains a critical challenge in flavor science. Methods: The umami-enhancing effects of meaty flavorings were investigated using nasal clip sensory evaluation (orthonasal blockage). Active aroma compounds were subsequently identified using gas chromatography-mass spectrometry (GC-MS). The three-dimensional structure of the umami receptor T1R1/T1R3 was constructed by homology modeling. The interaction mechanism was deciphered using molecular dynamics (MD) simulations. Results: Seafood essence S demonstrated the most potent umami enhancement. Five key compounds significantly intensified the MSG umami intensity: methional, dimethyl sulfide (DMS), D-limonene (DLE), 2,3-dimethylpyrazine, and dimethyl trisulfide. Notably, this enhancement persisted even under nasal clip conditions, revealing a novel mechanism independent of cross-modal interactions. Sulfur-containing compounds consistently demonstrated umami-enhancing effects across the evaluation conditions. MD simulations showed that aroma compounds induced allosteric remodeling of T1R1/T1R3, strengthening MSG-receptor hydrogen bonding (1.8–2.6-fold increase), reducing receptor flexibility, and stabilizing the ternary complex. Binding affinity was highest for DMS, followed by DLE and methional. Conclusion: This study provides the first receptor-level evidence that aroma compounds directly modulate MSG-taste receptor interactions through allosteric regulation, offering a novel theoretical framework for odor–taste interactions with significant implications for umami enhancer design and flavor research. Full article

Activating mutations in the epidermal growth factor receptor (EGFR) are key oncogenic drivers across multiple cancers, yet the structural mechanisms by which these mutations promote persistent receptor activation remain elusive. Here, we investigate how three clinically relevant mutations—T790M, L858R, and the T790M_L858R double mutant—reshape EGFR’s conformational ensemble and regulatory network architecture. Using multiscale molecular simulations and kinetic modeling, we show that these mutations, particularly in combination, enhance flexibility in the αC-helix and A-loop, favoring activation-competent states. Markov state modeling reveals a shift in equilibrium toward active macrostates and accelerated transitions between metastable conformations. To resolve the underlying coordination mechanism, we apply neural relational inference to reconstruct time-dependent interaction networks, uncovering the mutation-induced rewiring of allosteric pathways linking distant regulatory regions. This coupling of conformational redistribution with network remodeling provides a mechanistic rationale for sustained EGFR activation and suggests new opportunities for targeting dynamically organized allosteric circuits in therapeutic design. Full article

TRPA1 (Transient Receptor Potential Ankyrin 1), a cation channel predominantly expressed in sensory neurons, plays a critical role in detecting noxious stimuli and mediating pain signal transmission. As a key player in nociceptive signaling pathways, TRPA1 has emerged as a promising therapeutic target for the development of novel analgesics. Crotalphine (CRP), a 14-amino acid peptide, has been demonstrated to specifically activate TRPA1 and elicit potent analgesic effects. Previous cryo-EM (cryo-electron microscopy) studies have elucidated the structural mechanisms of TRPA1 activation by small-molecule agonists, such as iodoacetamide (IA), through covalent modification of N-terminal cysteine residues. However, the molecular interactions between TRPA1 and peptide ligands, including crotalphine, remain unclear. Here, we present the cryo-EM structure of ligand-free human TRPA1 consistent with the literature, as well as TRPA1 complexed with crotalphine, with resolutions of 3.1 Å and 3.8 Å, respectively. Through a combination of single-particle cryo-EM studies, patch-clamp electrophysiology, and microscale thermophoresis (MST), we have identified the cysteine residue at position 621 (Cys621) within the TRPA1 ion channel as the primary binding site for crotalphine. Upon binding to the reactive pocket containing C621, crotalphine induces rotational and translational movements of the transmembrane domain. This allosteric modulation coordinately dilates both the upper and lower gates, facilitating ion permeation. Full article

Valerian root extracts are widely used as mild sedatives to promote sleep, with clinical studies confirming their efficacy. Their sleep-promoting effects are associated with the adenosine A1 receptor (A1AR), a key regulator of sleep through neural activity inhibition. Adenosine, a neuromodulator that accumulates during wakefulness, activates A1ARs to facilitate sleep transitions. Using advanced analytics, we detected adenosine at 0.05% in the valerian extract Ze 911, supporting direct A1AR activation in vitro. Additionally, we explored A1ARs’ allosteric sites for modulatory activity. Valerenic acid and pinoresinol, key constituents of Ze 911, were identified as positive allosteric modulators (PAMs) of A1ARs. Valerenic acid exhibited strong PAM activity, with high cooperativity (αβ = 4.79 for adenosine and αβ = 23.38 for CPA) and intrinsic efficacy (τB = 5.98 for adenosine and τB = 3.14 for CPA). Pinoresinol displayed weaker PAM activity, with moderate cooperativity (αβ = 3.42 for adenosine and αβ = 0.79 for CPA) and limited efficacy (τB = 0.93 for adenosine and τB = 1.66 for CPA). The allosteric modulation observed in valerian extract Ze 911 suggests a mechanism of action in which valerenic acid and pinoresinol enhance receptor activation through allosteric interactions, potentially amplifying the effects of endogenous adenosine. By targeting A1ARs’ allosteric sites, valerian extract Ze 911 offers increased therapeutic selectivity and reduced off-target effects, emphasizing its potential for managing sleep disorders. Full article

SHP2, a non-receptor protein tyrosine phosphatase, plays a pivotal role in regulating intracellular signaling pathways, particularly the RAS/MAPK and PI3K/AKT cascades, which are critical for cellular proliferation, differentiation, and survival. Aberrant SHP2 activity, often driven by gain-of-function mutations, is implicated in oncogenesis and drug resistance, making it an attractive therapeutic target. Traditional inhibitors targeting SHP2’s catalytic site face limitations such as poor selectivity and low bioavailability. Recent advancements in allosteric inhibitors, specifically targeting SHP2’s tunnel site, offer improved specificity and pharmacokinetics. Natural products, especially saponins with their unique structural diversity, have emerged as promising candidates for SHP2 inhibition. This review explores the structural and functional dynamics of SHP2, highlights the potential of saponin-based inhibitors, and discusses their mechanisms of action, including their interactions with key residues in the tunnel site. The therapeutic potential of saponins is further emphasized by their ability to overcome the limitations of catalytic inhibitors and their applicability in combination therapies. Future directions include structural optimization to improve pharmacokinetics and the development of innovative strategies such as PROTACs to enhance the clinical utility of saponin-based SHP2 inhibitors. Full article

Background: Alterations in the adrenergic system have been associated with the pathophysiology of Alzheimer’s disease (AD). A novel α_1A-adrenergic receptor (AR)-positive allosteric modulator (PAM), CCF219B, has been shown to outperform donepezil with rescue of AD cognition/memory deficits with a reduction in amyloid biomarkers and without cardiovascular side effects. Initial pharmacological analysis in transfected cell lines revealed a signal bias with increased efficacy (but not potency) of cAMP signaling and ligand selectivity for norepinephrine (NE). As most GPCR allosteric modulators change the potency of agonists, we hypothesized and now report that CCF219B induced additional aspects of its allosteric interactions with NE that may provide mechanistic insight. Methods: Using Rat-1 fibroblasts stably transfected with α_1A-AR, we determined the activation profile of pERK and p38 messengers by CCF219B in the presence of NE. Using membranes prepared from the stably transfected fibroblasts or from the brain of WT mice or the AD mouse model, hAPP(lon), equilibrium or kinetic radioligand-binding analyses were performed. Results: We identified p-ERK1/2 but not p38 as an additional signal pathway that is potentiated by CCF219B in the presence of NE. An analysis of binding studies of CCF219B in membranes derived from the brains of WT or hAPP(lon) mice revealed profiles that were time-dependent and resulted in an increase in α_1A-AR expression that was unaltered in the presence of cycloheximide or when performed at 37 °C. hAPP(lon) mice displayed a reduction in α_1A-AR-binding sites that were rescued upon prolonged incubation with CCF219B but also displayed a compensatory increase in α_1B/D-AR subtype expression. Binding kinetics reveal that CCF219B can decrease the association rate of ³H-NE but only in the presence of GTP. The association rate increased for the radiolabeled antagonist, ¹²⁵I-HEAT. There were no changes in the dissociation rate of either radiolabel. Conclusions: CCF219B affects the association but not the dissociation rate of NE and explains its ability to increase the active state of the receptor by promoting a pre-coupled conformation, consistent with increasing efficacy but not potency. Potentiation of pERK may contribute to CCF219B’s ability to confer neuroprotection and be pro-cognitive in AD. CCF219B’s ability to increase the expression of α_1A-AR provides a positive feedback loop and strengthens the hypothesis that α₁-AR subtypes may be involved in AD etiology and/or progression. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa in 2021, has become the dominant strain worldwide. It harbors approximately 50 mutations compared to the original strain, with 15 located in the receptor-binding domain (RBD) of the spike protein that facilitates viral entry via binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. How do these mutated residues modulate the intermolecular interactions and binding affinity between the RBD and ACE2? This is a question of great theoretical importance and practical implication. In this study, we employed quantum chemical calculations at the B2PLYP-D3/def2-TZVP level of theory to investigate the molecular determinants governing Omicron’s ACE2 interaction. Comparative analysis of the Omicron and wild-type RBD–ACE2 interfaces revealed that mutations including S477N, Q493R, Q498R, and N501Y enhance binding through the formation of bifurcated hydrogen bonds, π–π stacking, and cation–π interactions. These favorable interactions counterbalance such destabilizing mutations as K417N, G446S, G496S, and Y505H, which disrupt salt bridges and hydrogen bonds. Additionally, allosteric effects improve the contributions of non-mutated residues (notably A475, Y453, and F486) via structural realignment and novel hydrogen bonding with ACE2 residues such as S19, leading to an overall increase in the electrostatic and π-system interaction energy. In conclusion, our findings provide a mechanistic basis for Omicron’s increased infectivity and offer valuable insights for the development of targeted antiviral therapies. Moreover, from a methodological perspective, we directly calculated mutation-induced binding energy changes at the residue level using advanced quantum chemical methods rather than relying on the indirect decomposition schemes typical of molecular dynamics-based free energy analyses. The strong correlation between calculated energy differences and experimental deep mutational scanning (DMS) data underscores the robustness of the theoretical framework in predicting the effects of RBD mutations on ACE2 binding affinity. This demonstrates the potential of quantum chemical methods as predictive tools for studying mutation-induced changes in protein–protein interactions and guiding rational therapeutic design. Full article