Ligand-receptor Binding Research Articles

Mitochondria Express Functional Signaling Ligand-Binding Receptors that Regulate their Biological Responses - the Novel Role of Mitochondria as Stress-Response Sentinels.

Evidence accumulated mitochondria, as the "powerplants of the cell," express several functional receptors for external ligands that modify their function and regulate cell biology. This review sheds new light on the role of these organelles in sensing external stimuli to facilitate energy production for cellular needs. This is possible because mitochondria express some receptors on their membranes that are responsible for their autonomous responses. This is not surprising given the widely accepted hypothesis that these intracellular organelles originated from prokaryotic ancestors that fused with eukaryotic cells during early evolution. It has been reported that mitochondria express functional estrogen, androgen, glucocorticoid, 5-hydroxytryptamine, melatonin, and cannabinoid receptors. What is intriguing is recent evidence showing that mitochondria could also be directly regulated by active mediators of intracellular complement (complosome) and intrinsic mediators of purinergic signaling. Accordingly, they express receptors for intracellular complement cleavage fragments (C5a and C3a) as well as for adenosine triphosphate (ATP), which, besides its crucial role in transferring energy in the cells, is also an important signaling molecule interacting with P2X7 receptor expressed not only on the cell surface but also on the mitochondria membrane. Based on this, intrinsic complosome and purinergic signaling mediators emerge as important cooperating regulators of reactive oxygen species (ROS) release from mitochondria and activators of intracellular pattern recognition receptor Nlrp3 inflammasome. This activation within the beneficial "hormetic zone response" regulates cell metabolism, proliferation, migration, and adaptation to the surrounding challenges of the microenvironment in a favorable way.

Therapeutic potential of rutin in premenstrual depression: evidence from in vivo and in vitro studies.

Premenstrual dysphoric disorder (PMDD) is a cyclical mood disorder that severely affects the daily life of women of reproductive age. Most of the medications being used clinically have limitations such as low efficacy, side effects, and high cost, so there is an urgent need to discover safer and more effective medications. Rutin is a natural flavonol glycoside with various pharmacological properties including antidepressant. The study of the efficacy and mechanism of action of rutin in PMDD-depressed subtype model rats plays an important role in the discovery of new drugs for the treatment of PMDD. Binding of rutin to gamma-aminobutyric acid type A receptors (GABAA receptors) was probed using molecular docking, microscale thermophoresis, radioactive receptor ligand binding assay and cell membrane clamp experiment. Behavioral tests in mice were performed to screen the optimal dose of rutin. Behavioral tests were performed to evaluate the effects of rutin on depressed mood, memory impairment, and social impairment in PMDD-depressed subtype model rats. HE staining and Golgi staining were performed to observe the neuronal damage in rat hippocampus. UHPLC-MS/MS targeted metabolomics was performed to detect the changes of neurotransmitter content in rat hippocampus. PCR array to detect the effect of rutin on mRNA expression of GABAA receptor partial subunits in rat hippocampus. The docking score of rutin with the GABAA receptor benzodiazepine site was -11.442 and the gliding score was -11.470. The Kd of rutin with the GABAA receptor (α1β2γ2) was 1.17 ± 0.89μM. Rutin competed with [H3]-flunitrazepam for the GABAA receptor benzodiazepine site and inhibited the inward flow of chloride ions (P < 0.05). In PMDD-depressed subtype rats, rutin alleviated depressed mood, memory impairment and social impairment, ameliorated hippocampal neuronal damage and reduces gamma-aminobutyric acid (GABA) and acetylcholine (ACh) levels (P < 0.05). Moreover, we found that rutin did not affect the relative mRNA expression of GABAA receptor subunits in rat hippocampus. Overall, rutin alleviated depressed mood, memory impairment and social impairment in PMDD-depressed subtype rats, which may be related to binding to GABAA receptor benzodiazepine sites, inhibiting chloride ions inward flow, ameliorating hippocampal neuronal damage and reducing GABA and ACh levels. The results of this study provide an experimental basis and scientific evidence for the development of new drugs for the treatment of PMDD.

Protein CREATE enables closed-loop design of de novo synthetic protein binders.

Proteins have proven to be useful agents in a variety of fields, from serving as potent therapeutics to enabling complex catalysis for chemical manufacture. However, they remain difficult to design and are instead typically selected for using extensive screens or directed evolution. Recent developments in protein large language models have enabled fast generation of diverse protein sequences in unexplored regions of protein space predicted to fold into varied structures, bind relevant targets, and catalyze novel reactions. Nevertheless, we lack methods to characterize these proteins experimentally at scale and update generative models based on those results. We describe Protein CREATE (Computational Redesign via an Experiment-Augmented Training Engine), an integrated computational and experimental pipeline that incorporates an experimental workflow leveraging next generation sequencing and phage display with single-molecule readouts to collect vast amounts of quantitative binding data for updating protein large language models. We use Protein CREATE to generate and assay thousands of designed binders to IL-7 receptor α and insulin receptor with parallel positive and negative selections to identify on-target binders. We discover not only individual novel binders but also features of ligand-receptor binding, including preservation of the IL7Rα - ligand hydrophobic interface specifically and existence of multiple approaches to contact the insulin receptor. We also demonstrate the importance of structural features, such as the lack of unpaired cysteine residues, toward design fidelity and find computational pre-screening metrics, such as interchain predicted TM scoring (iPTM), while useful, are imperfect predictors as they neither guarantee experimental binding nor rule it out. We use the data collected from Protein CREATE to score designs from the initial generative models. Globally, Protein CREATE will power future closed-loop design-build-test cycles to enable fine-grained design of protein binders.

Physiologic and structural characterization of desisobutyryl-ciclesonide, a selective glucocorticoid receptor modulator in newborn rats.

Bronchopulmonary dysplasia, the most prevalent chronic lung disease of prematurity, is often treated with glucocorticoids (GCs) such as dexamethasone (DEX), but their use is encumbered with several adverse somatic, metabolic, and neurologic effects. We previously reported that systemic delivery of the GC prodrug ciclesonide (CIC) in neonatal rats activated glucocorticoid receptor (GR) transcriptional responses in lung but did not trigger multiple adverse effects caused by DEX. To determine whether limited systemic metabolism of CIC was solely responsible for its enhanced safety profile, we treated neonatal rats with its active metabolite desisobutyryl-ciclesonide (Des-CIC). DEX but not Des-CIC caused a reduction in body weight as well as reduced insulin-like growth factor-1 serum levels and chronic hyperglycemia in neonatal rats. However, Des-CIC was as effective as DEX in reducing the expression of various bleomycin-induced proinflammatory cytokine mRNAs. In vitro studies with various cell types demonstrate the potent GR transactivation and transrepression activity of Des-CIC, although genome-wide transcriptomic analyses reveal differences in DEX vs. Des-CIC responses in neonatal rat lung and liver tissue. Des-CIC is a GR super-agonist as revealed by an in vitro coregulator peptide binding assay. In addition, molecular dynamics simulations revealed unique Des-CIC-dependent allosteric signaling pathways between specific residues in the GR ligand-binding domain and receptor surfaces interacting with coregulator peptides. Thus, Des-CIC is a potential novel selective GR modulator that could impart a favorable therapeutic index for CIC use for even modest durations of GC exposure which could have long-lasting adverse somatic, metabolic, or neurologic effects.

In Silico Analgesic and Toxicity Analysis of Modified Paracetamol on COX-2 Receptor (PDB ID: 3LN1)

Background: Paracetamol is often used as the main analgesic in Indonesia. The use of more than 4 g/day or a single dose above 10 g can cause hepatotoxicity. This can be overcome by modifying the structure through a computer-aided drug design (CADD) approach, particularly molecular docking, which aims to produce compounds with greater potency and fewer side effects. Objective: This study aimed to determine the analgesic activity and toxicity of paracetamol derivatives modified using the Topliss method. Methods: Analgesic activity was tested by molecular docking of the COX-2 receptor (PDB ID 3LN1) using AutoDock Tool 4.2 and toxicity testing using pkCSM and Protox Online Tool. Results: The results of docking showed that the free binding energy values ​​for test compounds 1 to 5 are -10.59 kcal/mol, -10.17 kcal/mol, -8.79 kcal/mol, -10.01 kcal/mol, and -9.32 kcal/mol, respectively, with corresponding inhibition constants of 17.29 nM, 35.21 nM, 360.88 nM, 46.36 nM, and 146.65 nM. These values are lower than paracetamol, which has a free binding energy of -6.21 kcal/mol and an inhibition constant of 28,043 nM. The results showed that the test compound was more stable in ligand-receptor binding. Toxicity tests showed that all the test compounds and paracetamol belonged to toxicity class IV. The test compound had an LD50 value of 1551 mg/kg, which was higher than that of paracetamol (338 mg/kg), indicating better effectiveness. Conclusions: Compound 2 was predicted to have the best biological activity and potential as an alternative to paracetamol.

Enhanced Sampling with Suboptimal Collective Variables: Reconciling Accuracy and Convergence Speed.

We introduce an enhanced sampling algorithm to obtain converged free energy landscapes of molecular rare events, even when the collective variable (CV) used for biasing is not optimal. Our approach samples a time-dependent target distribution by combining the on-the-fly probability enhanced sampling and its exploratory variant, OPES Explore. This promotes more transitions between the relevant metastable states and accelerates the convergence speed of the free energy estimate. We demonstrate the successful application of this combined algorithm on the two-dimensional Wolfe-Quapp potential, millisecond time-scale ligand-receptor binding in the trypsin-benzamidine complex, and folding-unfolding transitions in chignolin mini-protein. Our proposed algorithm can compute accurate free energies at an affordable computational cost and is robust in terms of the choice of CVs, making it particularly promising for the simulation of complex biomolecular systems.

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding.

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structures in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.

Screening of the key genes and signaling pathways for schizophrenia using bioinformatics and next generation sequencing data analysis

Schizophrenia is thought to be the most prevalent chronic psychiatric disorder. Researchers have identified numerous proteins associated with the occurrence and development of schizophrenia. This study aimed to identify potential core genes and pathways involved in schizophrenia through exhaustive bioinformatics and next generation sequencing (NGS) data analyses using GSE106589 NGS data of neural progenitor cells and neurons obtained from healthy controls and patients with schizophrenia. The NGS data were downloaded from the Gene Expression Omnibus database. NGS data was processed by the DESeq2 package in R software, and the differentially expressed genes (DEGs) were identified. Gene ontology (GO) enrichment analysis and REACTOME pathway enrichment analysis were carried out to identify potential biological functions and pathways of the DEGs. Protein-protein interaction network, module, micro-RNA (miRNA)-hub gene regulatory network, transcription factor (TF)-hub gene regulatory network, and drug-hub gene interaction network analysis were performed to identify the hub genes, miRNA, TFs, and drug molecules. Potential hub genes were analyzed using receiver operating characteristic curves in the R package. In this investigation, an overall 955 DEGs were identified: 478 genes were remarkably upregulated and 477 genes were distinctly downregulated. These genes were enriched for GO terms and pathways mainly involved in the multicellular organismal process, G protein-coupled receptor ligand binding, regulation of cellular processes, and amine ligand-binding receptors. MYC, FN1, CDKN2A, EEF1G, CAV1, ONECUT1, SYK, MAPK13, TFAP2A, and BTK were considered the potential hub genes. The MiRNA-hub gene regulatory network, TF-hub gene regulatory network, and drug-hub gene interaction network were constructed successfully and predicted key miRNAs, TFs, and drug molecules for schizophrenia diagnosis and treatment. On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of schizophrenia and provide potential targets for further investigation.

More and more pleiotropy within the IL-6 family of cytokines.

Historically, cytokines belonging to the gp130 family bind to specific ligand-binding receptors that stimulate cell signaling through a receptor complex comprising gp130 or gp130 together with another structurally related signaling receptor. However, recent findings increasingly dispel these stereotypes and suggest that the receptor specificity of gp130-activating cytokines is less strict than originally assumed. Weitz etal. now provide the latest example of this pleiotropy and report that human interleukin-6 can bind and stimulate signaling via the interleukin-11 receptor. Possible biological and therapeutic consequences of these findings are discussed.

Study on the anti-colon cancer effect of Renshen Yangrong Decoction based on network pharmacology, molecular docking, and in vivo and in vitro experiments

Renshen Yangrong Decoction (RSYRD) is a traditional Chinese medicinal compound widely used as an adjuvant in colon cancer treatment. However, the specific role of RSYRD in anti-colon cancer remains unclear. This study aimed to investigate the anti-colon cancer effects of RSYRD using network pharmacology, molecular docking, and in vitro and in vivo experiments. The active ingredients and targets of RSYRD were identified utilizing databases, and RSYRD-ingredient-target and protein-protein interaction (PPI) networks were constructed. Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the anti-colon cancer targets of RSYRD, followed by molecular docking using AutoDockTools 1.5.6. In vitro and in vivo experiments were conducted to explore the mechanism of RSYRD and evaluate its inhibitory efficacy on colon cancer. A total of 233 active ingredients and 88 colon cancer-related targets were identified, including 9 core targets. GO functional analysis revealed that RSYRD exerts anti-tumor effects through processes such as oxidative reactions, closely associated with intracellular reactive oxygen species (ROS). KEGG enrichment analysis indicated that the anti-tumor effect of RSYRD involved the interaction of cancer-related and viral disease-associated pathways, as well as the IL-17, TNF, and PI3K-AKT signaling pathways. Molecular docking showed stable ligand-receptor binding, with binding energies below −5.0 kcal/mol. In vitro experiments demonstrated that RSYRD increased ROS levels, reduced mitochondrial membrane potential (MMP), and promoted apoptosis in SW620 cells, thereby inhibiting cell proliferation and migration. In vivo experiments showed that RSYRD significantly suppressed colon cancer proliferation. This study identified Quercetin, Kaempferol, 7-Methoxy-2-methyl-isoflavone, Licochalcone-a, and Isorhamnetin as core ingredients in RSYRD, likely exerting anti-colon cancer effects by inhibiting proteins such as ESR1, HSP90AA1, NCOA2, and MAPK14, and suppressing the PI3K-AKT signaling pathway, thereby regulating tumor cell proliferation, migration, and apoptosis.

Design, Synthesis and Biological Evaluation of 4,6-Substituted 2-Styrylquinoline Derivatives: Potential Antimicrobial and Anticancer Agents

A series of novel 4,6-substituted 2-styrylquinoline derivatives (3a-h) was designed and synthesized based on the substitution in quinoline scaffolds (with Br, H, NO2 at C6 position) as well as the substitution in the styryl moeity (at C4' position). The target compounds were investigated for their antimicrobial activity against Gram-positive Staphylococcus aureus (ATCC 25923), Enterococcus faecalis (ATCC 29212) and Gram-negative bacterium Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 27853) and Candida albicans (ATCC 10231) and anticancer activity against human colon adenocarcinoma HT29 cells. Compared to standard drug ciprofloxacin, compounds 3e, 3b and 3c showed significant antibacterial activity against Staphylococcus aureus, Enterococcus faecalis and Escherichia coli. Additionally, synthesized compound 3e had significant activity against Candida albicans with MIC value of 8 µg/mL. In anticancer study, the maximum cell death rate was found in compounds 3e, 3b and 3c at the dose of 100 µM i.e., 72.9%., 44.01% and 35.46%, respectively and the measured IC50 were 58.84, 114.53 and 130 µM. The cytotoxic potential of compound 3e was confirmed by AO-EtBr dual staining assay in which red fluorescence of necrotic cells lost their membrane integrity due to toxicity induced by compound 3e. This growth inhibition and apoptotic activity of compound 3e was dose-dependent when the colour changed from green to red. Furthermore, in silico studies were conducted on the synthesized compounds to elucidate the potential mechanisms of action against dihydrofolate reductase (DHFR) from E. coli, DNA gyrase from P. aeruginosa, DHFR from S. aureus, acetolactate synthase from K. pneumoniae and DHFR from C. albicans. The derivatives also exhibited the strongest ligand-receptor binding affinity. Additionally, ADME analysis was performed to predict the pharmacokinetic profiles of the compounds, indicating good oral drug-like properties.

Ovarian expression of MerTK and its ligand Pros1 in non-pregnant estrus and pregnant mice.

The interaction of MerTK, which negatively regulates immune responses, with its ligand Pros1 contributes to the resolution of apoptosis and inflammation, participating in the healing process of tissues. The levels of MerTK and Pros1, intensely expressed in macrophages (Mϕs), are affected by sex hormones. The expression levels of these proteins in Mϕs, which have a role in corpus luteum (CL) development or regression and folliculogenesis, were investigated in this study since their expressions have not been evaluated in pregnant mouse ovaries. We analyzed mouse ovaries from non-pregnant mice at estrus and gestation days 5, 8, and 15 (each n:10). We used qPCR to evaluate Mertk and Pros1 mRNA levels and assessed their protein expression and localization using immunohistochemistry and double immunofluorescence staining for co-localization. Mertk and Pros1 mRNA and protein levels significantly increased in GD15. MerTK and Pros1 protein levels in mouse CL on GD15 were significantly higher than all other groups. MerTK and Pros1 positive Mϕs were observed in CL of GD15 by double immunofluorescence. MerTK protein levels were increased in granulosa cells GD15 of primary and growing follicles. Our study revealed for the first time that the expression of MerTK and Pros1 was significantly increased in CL at GD15 in mice. These results suggest that increased levels of MerTK andPros1 may enhance their interaction as receptor-ligand binding partners in CL potentially contributing to the balance of apoptosis and inflammation.

Characterization of novel small molecule inhibitors of estrogen receptor-activation function 2 (ER-AF2).

Up to 40% of patients with estrogen receptor (ER)-positive breast cancer will develop resistance against the majority of current ER-directed therapies. Resistance can arise through various mechanisms such as increased expression levels of coregulators, and key mutations acquired in the receptor's ligand binding domain rendering it constitutively active. To overcome these resistance mechanisms, we explored targeting the ER Activation Function 2 (AF2) site, which is essential for coactivator binding and activation. Using artificial intelligence and the deep docking methodology, we virtually screened > 1billion small molecules and identified 290 potential AF2 binders that were then characterized and validated through an iterative screening pipeline of cell-based and cell-free assays. We ranked the compounds based on their ability to reduce the transcriptional activity of the estrogen receptor and the viability of ER-positive breast cancer cells. We identified a lead compound, VPC-260724, which inhibits ER activity at low micromolar range. We confirmed its direct binding to the ER-AF2 site through a PGC1α peptide displacement experiment. Using proximity ligation assays, we showed that VPC-260724 disrupts the interaction between ER-AF2 and the coactivator SRC-3 and reduces the expression of ER target genes in various breast cancer models including the tamoxifen resistant cell line TamR3. In conclusion, we developed a novel ER-AF2 binder, VPC-260724, which shows antiproliferative activity in ER-positive breast cancer models. The use of an ER-AF2 inhibitor in combination with current treatments may provide a novel complementary therapeutic approach to target treatment resistance in ER-positive breast cancer.

Agonist activation to open the Gα subunit of the GPCR–G protein precoupled complex defines functional agonist activation of TAS2R5

G protein-coupled receptors (GPCRs) regulate multiple cellular responses and represent highly successful therapeutic targets. The mechanisms by which agonists activate the G protein are unclear for many GPCR families, including the bitter taste receptors (TAS2Rs). We ascertained TAS2R5 properties by live cell-based functional assays, direct binding affinity measurements using optical resonators, and atomistic molecular dynamics simulations. We focus on three agonists that exhibit a wide range of signal transduction in cells despite comparable ligand-receptor binding energies derived from direct experiment and computation. Metadynamics simulations revealed that the critical barrier to activation is ligand-induced opening of the G protein between the α-helical (AH) and Ras-like domains of Gα subunit from a precoupled TAS2R5-G protein state to the fully activated state. A moderate agonist opens the AH-Ras cleft from 22 Å to 31 Å with an energy gain of -4.8 kcal mol-1, making GDP water-exposed for signaling. A high-potency agonist had an energy gain of -11.1 kcal mol-1. The low-potency agonist is also exothermic for Gα opening, but with an energy gain of only -1.4 kcal mol-1. This demonstrates that TAS2R5 agonist-bound functional potencies are derived from energy gains in the transition from a precoupled complex at the level of Gα opening. Our experimental and computational study provides insights into the activation mechanism of signal transduction that provide a basis for rational design of new drugs.

Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism.

Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and their mechanism of peptidoglycan binding remains unexplored, for this is a challenging task experimentally. This research aimed to explore the binding mechanism of endolysins using computational approaches, namely molecular docking and bioinformatical tools, and analyze the performance of these approaches. The docking engine Autodock Vina 1.1.2 and the 3D-RISM module of AmberTools 24 were studied in the current work and used for receptor-ligand affinity and binding energy calculations, respectively. Two possible mechanisms of single-domain endolysin-ligand binding were predicted by Autodock Vina and verified by the 3D-RISM. As a result, the previously obtained experimental results on peptidoglycan binding of the isolated gamma phage endolysin PlyG enzymatically active domain were supported by molecular docking. Both methods predicted that single-domain endolysins are able to bind peptidoglycan, with Autodock Vina being able to give accurate numerical estimates of protein-ligand affinities and 3D-RISM providing comparative values.

ER export via SURF4 uses diverse mechanisms of both client and coat engagement.

Protein secretion is an essential process that drives cell growth and communication. Enrichment of soluble secretory proteins into ER-derived transport carriers occurs via transmembrane cargo receptors that connect lumenal cargo to the cytosolic COPII coat. Here, we find that the cargo receptor, SURF4, recruits different SEC24 cargo adaptor paralogs of the COPII coat to export different cargoes. The secreted protease, PCSK9, requires both SURF4 and a co-receptor, TMED10, for export via SEC24A. In contrast, secretion of Cab45 and NUCB1 requires SEC24C/D. We further show that ER export signals of Cab45 and NUCB1 bind co-translationally to SURF4 via a lumenal pocket, contrasting prevailing models of receptor engagement only upon protein folding/maturation. Bioinformatics analyses suggest that strong SURF4-binding motifs are features of proteases, receptor-binding ligands, and Ca2+-binding proteins. We propose that certain classes of proteins are fast-tracked for rapid export to protect the health of the ER lumen.

BIOM-49. PATIENT-CENTRIC INTEGRATED GRAPH DATABASE REVEALS CRITICAL BIOMARKERS IN THE RECURRENCE OF IDH WILD-TYPE GLIOMA

Abstract BACKGROUND IDH wild-type glioblastoma (GBM) represents a formidable therapeutic challenge due to its consistent recurrence and progression despite standard treatments. Understanding the molecular and cellular mechanisms driving GBM recurrence through data integration is crucial. This study employs a novel graph database strategy to uncover insights into these tumors and identify functional biomarkers through graph algorithms-based pathway enrichment analysis. METHOD We developed a stand-alone graph database using Neo4j for primary-recurrent paired GBMs, integrating clinical and gene expression data from the Glioma Longitudinal AnalySiS (GLASS) Consortium and internal MD Anderson cohort. Based on log2 fold-change, we used hierarchical trees for differentially expressed genes to decompose the expression profile. Nodes in the database represent patients with considerable absolute log2 values determined by hierarchical trees, while shared patients define the edges. We applied graph algorithms such as degree centrality and community detection to identify potential biomarkers and supplemented these analyses with pathway identification to refine the biomarker list. Further, we divided the data set into 80% training and 20% testing sets. We evaluated the predictive performance of these biomarkers using machine learning models, including logistic regression, random forest, SVM, and neural networks. RESULTS DEG analysis revealed 33 down-regulated and 418 up-regulated genes in recurrent tumors. The top enriched pathways included neuroactive ligand-receptor interaction and GPCR ligand binding. Our database approach implicated 35 out of 451 genes as significant drivers of recurrence in IDH wild-type GBM. The prediction performance of these biomarkers was comparable to features selected through methods such as mRMR and logistic lasso and target identification methods like WGCNA. CONCLUSION Our innovative systems biology approach reveals that ligand-receptor interactions are crucial in driving recurrence in IDH wild-type GBM. This method also yielded promising mechanistic targets for recurrence, prompting focused and therapeutically relevant functional analyses. Moreover, this methodology is not limited to our study but can be applied in other multi-omics settings, offering a robust tool for biomarker discovery and validation.

Patterns of corticosterone exposure affect the subcellular localisation of mineralocorticoid and glucocorticoid receptor complexes and gene expression

Mineralocorticoid (MR) and glucocorticoid receptors (GR) act as transcription factors and major mediators of glucocorticoid signalling, with pivotal roles in regulating the stress response and hormonal signalling, mood, cognition and memory. The MR and GR share many target genes, have a high degree of homology in their DNA binding (DBD) and ligand binding domain (LBD) but differ considerably in the N-terminal domain (NTD). Using Proximity Ligation Assay (PLA) we quantitatively assessed MR-GR complex subcellular localisation and transcriptional regulation in murine neuroblastoma (N2A) cells stimulated by constant or pulsatile corticosterone (CORT) patterns. We observe that continuous receptor activation by CORT caused localisation at the periphery of the cell nucleus. Truncation of the receptor Ligand Binding Domain (LBD) led to a stronger localisation of MR-GR complexes at the periphery of the cell nuclei. This was also observed for GR immunofluorescence (IF), while in cells expressing only MR or GR the mRNA response to pulsatile hormone treatment was substantially attenuated. However, there was no clearcut correlation between the spatial distribution of MR-GR complexes and the mRNA levels of target genes. Overall, our findings suggest that longer presence in the cell nucleus favors more peripheral nuclear localisation.

Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies

G protein-coupled receptors (GPCRs) control critical cell signaling. Their response to extracellular stimuli involves conformational changes to convey signals to intracellular effectors, among which the most important are G proteins and β-arrestins (βArrs). Biased activation of one pathway is a field of intense research in GPCR pharmacology. Combining NMR, site-directed mutagenesis, molecular pharmacology, and molecular dynamics (MD) simulations, we studied the conformational diversity of the vasopressin V2 receptor (V2R) bound to different types of ligands: the antagonist Tolvaptan, the endogenous unbiased agonist arginine-vasopressin, and MCF14, a partial Gs protein-biased agonist. A double-labeling NMR scheme was developed to study the receptor conformational changes and ligand binding: V2R was subjected to lysine 13CH3 methylation for complementary NMR studies, whereas the agonists were tagged with a paramagnetic probe. Paramagnetic relaxation enhancements and site-directed mutagenesis validated the ligand binding modes in the MD simulations. We found that the bias for the Gs protein over the βArr pathway involves interactions between the conserved NPxxY motif in the transmembrane helix 7 (TM7) and TM3, compacting helix 8 (H8) toward TM1 and likely inhibiting βArr signaling. A similar mechanism was elicited for the pathogenic mutation I130N, which constitutively activates the Gs proteins without concomitant βArr recruitment. The findings suggest common patterns of biased signaling in class A GPCRs, as well as a rationale for the design of G protein-biased V2R agonists.

Short Lysine-Containing Tripeptide as Analgesic Substance: The Possible Mechanism of Ligand–Receptor Binding to the Slow Sodium Channel

A possible molecular mechanism of the ligand–receptor binding of Ac-Lys-Lys-Lys-NH2 (Ac-KKK-NH2) to the NaV1.8 channel that is responsible for nociceptive signal coding in the peripheral nervous system is investigated by a number of experimental and theoretical techniques. Upon Ac-KKK-NH2 application at 100 nM, a significant decrease in the effective charge carried by the NaV1.8 channel activation gating system Zeff is demonstrated in the patch-clamp experiments. A strong Ac-KKK-NH2 analgesic effect at both the spinal and supraspinal levels is detected in vivo in the formalin test. The distances between the positively charged amino groups in the Ac-KKK-NH2 molecule upon binding to the NaV1.8 channel are 11–12 Å, as revealed by the conformational analysis. The blind docking with the NaV1.8 channel has made it possible to locate the Ac-KKK-NH2 binding site on the extracellular side of the voltage-sensing domain VSDI. The Ac-KKK-NH2 amino groups are shown to form ionic bonds with Asp151 and Glu157 and a hydrogen bond with Thr161, which affects the coordinated movement of the voltage sensor up and down, thus modulating the Zeff value. According to the results presented, Ac-KKK-NH2 is a promising candidate for the role of an analgesic medicinal substance that can be applied for pain relief in humans.