Network pharmacology identifies IL6 as an important hub and target of tibolone for drug repurposing in traumatic brain injury

Gonadal hormone deprivation regulates response to tibolone in neurodegenerative pathways

Gonadal hormone deprivation (GHD) and decline such as menopause and bilateral oophorectomy are associated with an increased risk of neurodegeneration. Yet, hormone therapies (HTs) show varying efficacy, influenced by factors such as sex, drug type, and timing of treatment relative to hormone decline. We hypothesize that the molecular environment of the brain undergoes a transition following GHD, impacting the effectiveness of HTs. Using a GHD model in mice treated with Tibolone, we conducted proteomic analysis and identified a reprogrammed response to Tibolone, a compound that stimulates estrogenic, progestogenic, and androgenic pathways. Through a comprehensive network pharmacological workflow, we identified a reprogrammed response to Tibolone, particularly within "Pathways of Neurodegeneration", as well as interconnected pathways including "cellular respiration", "carbon metabolism", and "cellular homeostasis". Analysis revealed 23 proteins whose Tibolone response depended on GHD and/or sex, implicating critical processes like oxidative phosphorylation and calcium signalling. Our findings suggest the therapeutic efficacy of HTs may depend on these variables, suggesting a need for greater precision medicine considerations whilst highlighting the need to uncover underlying mechanisms.

A Novel Network Pharmacology Strategy Based on the Universal Effectiveness-Common Mechanism of Medical Herbs Uncovers Therapeutic Targets in Traumatic Brain Injury

Purpose

Many herbs can promote neurological recovery following traumatic brain injury (TBI). There must lie a shared mechanism behind the common effectiveness. We aimed to explore the key therapeutic targets for TBI based on the common effectiveness of the medicinal plants.

Material and methods

The TBI-effective herbs were retrieved from the literature as imputes of network pharmacology. Then, the active ingredients in at least two herbs were screened out as common components. The hub targets of all active compounds were identified through Cytohubba. Next, AutoDock vina was used to rank the common compound-hub target interactions by molecular docking. A highly scored compound-target pair was selected for in vivo validation.

Results

We enrolled sixteen TBI-effective medicinal herbs and screened out twenty-one common compounds, such as luteolin. Ten hub targets were recognized according to the topology of the protein-protein interaction network of targets, including epidermal growth factor receptor (EGFR). Molecular docking analysis suggested that luteolin could bind strongly to the active pocket of EGFR. Administration of luteolin or the selective EGFR inhibitor AZD3759 to TBI mice promoted the recovery of body weight and neurological function, reduced astrocyte activation and EGFR expression, decreased chondroitin sulfate proteoglycans deposition, and upregulated GAP43 levels in the cortex. The effects were similar to those when treated with the selective EGFR inhibitor.

Conclusion

The common effectiveness-based, common target screening strategy suggests that inhibition of EGFR can be an effective therapy for TBI. This strategy can be applied to discover core targets and therapeutic compounds in other diseases.

Colloidal therapeutics in the management of traumatic brain injury: Portray of biomarkers and drug-targets, preclinical and clinical pieces of evidence and future prospects

Complexity associated with the aberrant physiology of traumatic brain injury (TBI) makes its therapeutic targeting vulnerable. The underlying mechanisms of pathophysiology of TBI are yet to be completely illustrated. Primary injury in TBI is associated with contusions and axonal shearing whereas excitotoxicity, mitochondrial dysfunction, free radicals generation, and neuroinflammation are considered under secondary injury. MicroRNAs, proinflammatory cytokines, and Glial fibrillary acidic protein (GFAP) recently emerged as biomarkers in TBI. In addition, several approved therapeutic entities have been explored to target existing and newly identified drug-targets in TBI. However, drug delivery in TBI is hampered due to disruption of blood-brain barrier (BBB) in secondary TBI, as well as inadequate drug-targeting and retention effect. Colloidal therapeutics appeared helpful in providing enhanced drug availability to the brain owing to definite targeting strategies. Moreover, immense efforts have been put together to achieve increased bioavailability of therapeutics to TBI by devising effective targeting strategies. The potential of colloidal therapeutics to efficiently deliver drugs at the site of injury and down-regulate the mediators of TBI are serving as novel policies in the management of TBI. Therefore, in present manuscript, we have illuminated a myriad of molecular-targets currently identified and recognized in TBI. Moreover, particular emphasis is given to frame armamentarium of repurpose drugs which could be utilized to block molecular targets in TBI in addition to drug delivery barriers. The critical role of colloidal therapeutics such as liposomes, nanoparticles, dendrimers, and exosomes in drug delivery to TBI through invasive and non-invasive routes has also been highlighted.

Network pharmacology and topological analysis on tibolone metabolites and their molecular mechanisms in traumatic brain injury

Traumatic brain injury (TBI) is a pathology of great social impact, affecting millions of people worldwide. Despite the scientific advances to improve the management of TBI in recent years, we still do not have a specific treatment that controls the inflammatory process after mechanical trauma. The discovery and implementation of new treatments is a long and expensive process, making the repurpose of approved drugs for other pathologies a clinical interest. Tibolone is a drug in use for the treatment of symptoms associated with menopause and has been shown to have a broad spectrum of actions by regulating estrogen, androgen and progesterone receptors, whose activation exerts potent anti-inflammatory and antioxidant effects. In the present study, we aimed to investigate the therapeutic potential of the tibolone metabolites 3α-Hydroxytibolone, 3β-Hydroxytibolone, and Δ4-Tibolone as a possible therapy in TBI using network pharmacology and network topology analysis. Our results demonstrate that the estrogenic component mediated by the α and β metabolites can regulate synaptic transmission and cell metabolism, while the Δ metabolite may be involved in modulating the post-TBI inflammatory process. We identified several molecular targets, including KDR, ESR2, AR, NR3C1, PPARD, and PPARA, which are known to play critical roles in the pathogenesis of TBI. Tibolone metabolites were predicted to regulate the expression of key genes involved in oxidative stress, inflammation, and apoptosis. Overall, the repurposing of tibolone as a neuroprotective treatment for TBI holds promise for future clinical trials. However, further studies are needed to confirm its efficacy and safety in TBI patients.

Repurposing of Tibolone in Alzheimer's Disease

Alzheimer's disease (AD) is a debilitating neurodegenerative disease characterised by the accumulation of amyloid-beta and tau in the brain, leading to the progressive loss of memory and cognition. The causes of its pathogenesis are still not fully understood, but some risk factors, such as age, genetics, and hormones, may play a crucial role. Studies show that postmenopausal women have a higher risk of developing AD, possibly due to the decrease in hormone levels, especially oestrogen, which may be directly related to a reduction in the activity of oestrogen receptors, especially beta (ERβ), which favours a more hostile cellular environment, leading to mitochondrial dysfunction, mainly affecting key processes related to transport, metabolism, and oxidative phosphorylation. Given the influence of hormones on biological processes at the mitochondrial level, hormone therapies are of clinical interest to reduce the risk or delay the onset of symptoms associated with AD. One drug with such potential is tibolone, which is used in clinics to treat menopause-related symptoms. It can reduce amyloid burden and have benefits on mitochondrial integrity and dynamics. Many of its protective effects are mediated through steroid receptors and may also be related to neuroglobin, whose elevated levels have been shown to protect against neurological diseases. Its importance has increased exponentially due to its implication in the pathogenesis of AD. In this review, we discuss recent advances in tibolone, focusing on its mitochondrial-protective effects, and highlight how valuable this compound could be as a therapeutic alternative to mitigate the molecular pathways characteristic of AD.

Network pharmacology and molecular docking analysis on potential molecular targets and mechanism of action of BRAF inhibitors for application in wound healing

Topical application of BRAF inhibitors has been shown to accelerate wound healing in murine models, which can be extrapolated into clinical applications. The aim of the study was to identify suitable pharmacological targets of BRAF inhibitors and elucidate their mechanisms of action for therapeutic applicability in wound healing, by employing bioinformatics tools including network pharmacology and molecular docking. The potential targets for BRAF inhibitors were obtained from SwissTargetPrediction, DrugBank, CTD, Therapeutic Target Database, and Binding Database. Targets of wound healing were obtained using online databases DisGeNET and OMIM (Online Mendelian Inheritance in Man). Common targets were found by using the online GeneVenn tool. Common targets were then imported to STRING to construct interaction networks. Topological parameters were assessed using Cytoscape and core targets were identified. FunRich was employed to uncover the signaling pathways, cellular components, molecular functions, and biological processes in which the core targets participate. Finally, molecular docking was performed using MOE software. Key targets for the therapeutic application of BRAF inhibitors for wound healing are peroxisome proliferator-activated receptor γ, matrix metalloproteinase 9, AKT serine/threonine kinase 1, mammalian target of rapamycin, and Ki-ras2 Kirsten rat sarcoma viral oncogene homolog. The most potent BRAF inhibitors that can be exploited for their paradoxical activity for wound healing applications are Encorafenib and Dabrafenib. By using network pharmacology and molecular docking, it can be predicted that the paradoxical activity of BRAF inhibitors can be used for their potential application in wound healing.

Determining the value of early measurement of interleukin-10 in predicting the absence of brain lesions in CT scans of patients with mild traumatic brain injury

Blood-based biomarkers were recently proposed as predictors of traumatic brain injury (TBI) outcomes. This would be a critical step forward since the majority of TBI events are mild and structural brain damage in this group may be missed by current brain imaging methods. We sought to determine the performance of early measurement of interleukin-10 (IL-10) to distinguish computed tomography (CT)-positive from negative patients with mild TBI. We designed a single-center prospective observational study, which enrolled consecutive patients classed with mild TBI according to Glasgow Coma Scale [GCS] scores and appearance of at least one clinical symptom. Serum IL-10 levels were measured <3 h post hospital admission. The performance of IL-10 levels in correctly classifying patients was evaluated. IL-10 levels were significantly higher in the group with positive CT scans (p < 0.001). With sensitivity set at 100%, the specificity of IL-10 was only 38.1%. However, the specificities of IL-10 for prediction of negative and positive cases increased to 59% and 49%, respectively, when both parameters were assessed within 90 min of admission. For mild TBI patients between 36 and 66 years, classification performance increased significantly at the 100% sensitivity level with a specificity of 93%. Our results suggest that IL-10 may be an easily accessible clinically useful diagnostic biomarker that can distinguish between mild TBI patients with and without structural brain damage with higher effectiveness when lower times of blood sampling are employed and patients are between 36 and 66 years of age.

The prognostic value of neutrophil-to-lymphocyte ratio in patients with traumatic brain injury: A systematic review

Traumatic brain injury (TBI) places a heavy load on healthcare systems worldwide. Despite significant advancements in care, the TBI-related mortality is 30–50% and in most cases involves adolescents or young adults. Previous literature has suggested that neutrophil-to-lymphocyte ratio (NLR) may serve as a sensitive biomarker in predicting clinical outcomes following TBI. With conclusive evidence in this regard lacking, this study aimed to systematically review all original studies reporting the effectiveness of NLR as a predictor of TBI outcomes. A systematic search of eight databases was conducted according to the Preferred Reporting Items for Systematic Review and Meta-Analyses statement (PRISMA) recommendations. The risk of bias was assessed using the Quality in Prognostic Studies (QUIPS) tool. Eight studies were ultimately included in the study. In most of the studies interrogated, severity outcomes were successfully predicted by NLR in both univariate and multivariate prediction models, in different follow-up durations up to 6 months. A high NLR at 24 and 48 h after TBI in pediatric patients was associated with worse clinical outcomes. On pooling the NLR values within studies assessing its association with the outcome severity (favorable or not), patients with favorable outcomes had 37% lower NLR values than those with unfavorable ones (RoM= 0.63; 95% CI = 0.44–0.88; p = 0.007). However, there were considerable heterogeneity in effect estimates (I² = 99%; p < 0.001). Moreover, NLR was a useful indicator of mortality at both 6-month and 1-year intervals. In conjunction with clinical and radiographic parameters, NLR might be a useful, inexpensive marker in predicting clinical outcomes in patients with TBI. However, the considerable heterogeneity in current literature keeps it under investigation with further studies are warranted to confirm the reliability of NLR in predicting TBI outcomes.

Exploration of novel ligands to target C-C Motif Chemokine Receptor 2 (CCR2) as a promising pharmacological treatment against traumatic brain injury

It is widely reported that the overexpression of the C-C Motif Chemokine Receptor 2 (CCR2) has negative implications in neuroinflammatory diseases such as traumatic brain injury (TBI), although promising drugs to tackle this have been less forthcoming. As of 2016, only 2 drugs specifically targeting this receptor have made their way to market, with unsuccessful outcome unfortunately, suggesting that the search for more specific and precise ligands is utterly necessary. In this paper we hypothesized that by targeting Glu291, Met295, Trp98, Leu45 and Val189 amino acids, essential in the binding of CCR2 with C-C Motif Chemokine Ligand 2 (CCL2), the endogenous substrate, mitigates its activity in TBI. We used a pharmacophore model to screen for suitable ligands that may bind to CCR2, which returned 871 ligands. Docking and molecular dynamics results uncovered that two ligands (A102) and (A435) contained several of those important residues and showed a stability and compactness when in complex with CCR2, with these results confirmed by MMGBSA calculations with A102 recording a better interaction compared to A435. Finally, a PPI network was built to explore downstream signaling being regulated by both ligands in TBI, showing amyloid precursor protein (APP) as a key target and neuroactive-ligand receptor interaction (1.80E-27) the top functional annotated category. In conclusion, for the first time we report novel ligands A102 and A435 targeting CCR2 as a potential new pharmacological approach to target inflammation post-TBI.

Role of statins in regulating molecular pathways following traumatic brain injury: A system pharmacology study

Traumatic brain injury (TBI) is a serious disorder with debilitating physical and psychological complications. Previous studies have indicated that genetic factors have a critical role in modulating the secondary phase of injury in TBI. Statins have interesting pleiotropic properties such as antiapoptotic, antioxidative, and anti-inflammatory effects, which make them a suitable class of drugs for repurposing in TBI. In this study, we aimed to explore how statins modulate proteins and pathways involved in TBI using system pharmacology. We first explored the target associations with statins in two databases to discover critical clustering groups, candidate hub and critical hub genes in the network of TBI, and the possible connections of statins with TBI-related genes. Our results showed 1763 genes associated with TBI. Subsequently, the analysis of centralities in the PPI network displayed 55 candidate hub genes and 15 hub genes. Besides, MCODE analysis based on threshold score:10 determined four modular clusters. Intersection analysis of genes related to TBI and statins demonstrated 204 shared proteins, which suggested that statins influence 31 candidate hub and 9 hub genes. Moreover, statins had the highest interaction with MCODE1. The biological processes of the 31 shared proteins are related to gene expression, inflammation, antioxidant activity, and cell proliferation. Biological enriched pathways showed Programmed Cell Death proteins, AGE-RAGE signaling pathway, C-type lectin receptor signalling pathway, and MAPK signaling pathway as top clusters. In conclusion, statins could target several critical post-TBI genes mainly involved in inflammation and apoptosis, supporting the previous research results as a potential therapeutic agent.

Combination of multiple methods and views for recognition, transportation, and structure-guided modification of lysine-specific demethylase phenylcyclopropylamine inhibitor

Lysine-Specific Demethylase 1 (LSD1) is a typical histone-specific demethylase, which plays an important role in protein methylation modification. It is a member of the amine oxidase family (MAO) that specifically removes methyl groups from monomethylated H3K4, dimethylated H3K4 and H3K9 sites associated with tumorigenesis. Phenylcyclopropylamine derivatives are a class of specific LSD1 inhibitors, drawing attention due to their high efficiency. Here, extensive molecular dynamics (MD) simulations are combined with a three-dimensional quantitative structure-activity relationship (3D-QSAR) in order to design a new phenylcyclopropylamine inhibitor from multiple perspectives. In a ligand-oriented point of view, a 3D-QSAR model with comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) can be built based on the 55 phenylcyclopropylamine compounds targeting LSD1 obtained experimentally. The aromatic and piperazine rings are identified as the potential key groups regulating the activity of the compounds. In an interaction-oriented view, the representative compound is defined with the highest inhibitory efficiency. The binding and delivery mechanism and conformational dependence of activity, including channel and dynamic properties, are studied using RAMD and umbrella sampling technologies. The direct hydrogen bond and conjugated interactions are identified as a major driving force in this procedure. The dominant region of the phenylcyclopropylamine influences the free energy and detects the key residues in recognition and delivery. On the basis of both the ligand and interaction, a series of new inhibitor structures were designed, and two of them showed better efficiency. In order to select the inhibitor with a longer residence time, a comparison is conducted between the designed inhibitors and the experimentally obtained inhibitor from the perspective of static binding and dynamic delivery properties. This work creates new guidance for the phenylcyclopropylamine inhibitor design of LDS1 by combining the ligand and receptor, considering both static and dynamic properties. This scheme could be applied in other inhibitor design systems.

Identification of difluorinated curcumin molecular targets linked to traumatic brain injury pathophysiology

Traumatic brain injury (TBI) affects approximately 50% of the world population at some point in their lifetime. To date, there are no effective treatments as most of the damage occurs due to secondary effects through a variety of pathophysiological pathways. The phytoceutical curcumin has been traditionally used as a natural remedy for numerous conditions including diabetes, inflammatory diseases, and neurological and neurodegenerative disorders. We have carried out a system pharmacology study to identify potential targets of a difluorinated curcumin analogue (CDF) that overlap with those involved in the pathophysiological mechanisms of TBI. This resulted in identification of 312 targets which are mostly involved in G protein-coupled receptor activity and cellular signalling. These include adrenergic, serotonergic, opioid and cannabinoid receptor families, which have been implicated in regulation of pain, inflammation, mood, learning and cognition pathways. We conclude that further studies should be performed to validate curcumin as a potential novel treatment to ameliorate the effects of TBI.

Identification of HMGCR, PPGARG and prohibitin as potential druggable targets of dihydrotestosterone for treatment against traumatic brain injury using system pharmacology

BACKGROUND

Traumatic Brain Injury (TBI) has long-term devastating effects for which there is no accurate and effective treatment for inflammation and chronic oxidative stress. As a disease that affects multiple signalling pathways, the search for a drug with a broader spectrum of pharmacological action is of clinical interest. The fact that endocrine disruption (e.g hypogonadism) has been observed in TBI patients suggests that endogenous therapy with testosterone, or its more androgenic derivative, dihydrotestosterone (DHT), may attenuate, at least in part, the TBI-induced inflammation, but the underlying molecular mechanisms by which this occurs are still not completely clear.

AIMS AND METHODS

In this study, the main aim was to investigate proteins that may be related to the pathophysiological mechanism of TBI and also be pharmacological targets of DHT in order to explore a possible therapy with this androgen using network pharmacology.

RESULTS AND CONCLUSIONS

We identified 2.700 proteins related to TBI and 1.567 that are potentially molecular targets of DHT. Functional enrichment analysis showed that steroid (p-value: 2.1-22), lipid metabolism (p-value: 2.8-21) and apoptotic processes (p-value: 5.2-21) are mainly altered in TBI. Furthermore, being mitochondrion an organelle involved on these molecular processes we next identified that out of 32 mitochondrial-related proteins 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR), peroxisome proliferator activated receptor gamma (PPGARG) and prohibitin are those found highly regulated in the network and potential targets of DHT in TBI. In conclusion, the identification of these cellular nodes may prove to be essential as targets of DHT for therapy against post-TBI inflammation.

Bio-informatics and in Vitro Experiments Reveal the Mechanism of Schisandrin A Against MDA-MB-231 cells

Schisandrin A (SchA) has been reported to have good anti-cancer effects. However, its anti-cancer mechanism in breast cancer remains unknown. This study aimed to explore the mechanism of SchA in breast cancer treatment using bio-informatics analysis and in vitro experiments. The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Gene Cards, and PharmMapper databases were used to screen the candidate targets of SchA against MDA-MB-231 cells selected as the tested cell line through MTT analysis. The functions and pathways of the targets were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and further analyzed using DAVID 6.8.1 database. Network pharmacology analysis revealed 77 candidate targets, 31 signal pathways, and 208 GO entries (P < 0.05). The targets regulated serine-type endopeptidase and protein tyrosine kinase activities, thereby promoting the migration and inhibiting the apoptosis of MDA-MB-231 cells. Comprehensive analysis of the ‘Protein–Protein Interaction’ (PPI) and ‘Component-Targets-Pathways’ (C-T-P) networks constructed using Cytoscape 3.7.1 software revealed four core targets: EGFR, PIK3R1, MMP9 and Caspase 3. Their docking scores with SchA were subsequently investigated through molecular docking. The wound healing, Hoechst 33342/PI, and western blot assays confirmed that SchA significantly down-regulated EGFR, PIK3R1, and MMP9, but up-regulated cleaved-caspase 3, thus inhibiting the migration and promoting the apoptosis of MDA-MB-231 cells. Reckoning the findings of the study, SchA is a potential adjuvant treatment for breast cancer.