Molecular mechanism of Ferula asafoetida for the treatment of asthma: Network pharmacology and molecular docking approach

Experimental validation of the molecular mechanism of phlorizin in the treatment of diabetic retinopathy

This study conducted an experiment to scrutinize the effect of phlorizin (Phl) on diabetic retinopathy (DR) and to delve into the related molecular mechanisms. Within this investigation, DR was induced in rats with diabetes mellitus (DM) by subjecting them to a regimen involving a high-fat and high-sugar diet, coupled with intraperitoneal administration of streptozotocin (STZ) at a dosage of 45 mg/kg. Retinal damage in DR rats was assessed by means of hematoxylin and eosin (HE) staining. The serum levels of inflammatory and angiogenic factors were also measured. Additionally, the levels of tight junction proteins, angiogenic proteins, and inflammatory proteins in the retinas of DR model rats were assessed using Western blot (WB),immunohistochemistry(IHC) and immunofluorescence(IF). Moreover, bioinformatics and network pharmacology methodologies were utilized to pinpoint intersecting genes linked to DR and to elucidate the mechanism of action of Phl. This involved screening with Venny, conducting Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)analyses, constructing a Protein-Protein Interaction (PPI) network, and performing molecular docking analysis. The results of this study demonstrated that Phl significantly normalized fasting glucose levels and reduced body weight, thereby alleviating obesity in DR rats after 12 weeks. Furthermore, the serum levels of inflammatory and angiogenic factors were considerably reduced in the drug-treated rats. WB, IHC and IF revealed increased expression of the tight junction proteins zonula occludens-1(ZO-1) and occludin in the retinas of drug-treated DR rats, validating the observed findings. Molecular biology validation experiments based on the predictions by network pharmacology indicated a substantial decrease in the expression levels of vascular endothelial growth factor (VEGF), notch homolog 1 (Notch1), and hypoxia inducible factor-1 (HIF-1α) in the retina upon treatment with Phl. This reduction resulted in the inhibition of neovascularization. Furthermore, Phl exhibited inhibitory effects on inflammatory pathways, leading to a decrease in cytokine release. The overexpression of VEGF was identified as a factor diminishing brain-derived neurotrophic factor(BDNF) expression while increasing the expression levels of inflammatory proteins. Therefore, the results of this research demonstrate that Phl has the potential to protect the retina of DR rats by inhibiting VEGF expression. This protective effect may be associated with the modulation of the VEGF/BDNF/NF-κB signaling pathway.

A Review of the Protective Effects of Ferula asafoetida on the Liver, Kidney, and Testes Against Formaldehyde-Induced Damage

Formaldehyde, a pervasive environmental toxin, has well-documented deleterious effects on critical organ systems. This review examines the therapeutic potential of Ferula asafoetida (FA) root extracts in protecting the testes, kidneys, and liver against formaldehyde-induced toxicity in rodent models. The literature reveals that FA's active constituents, known for their potent antioxidant and anti-inflammatory activities, may counteract oxidative stress and cellular damage caused by formaldehyde exposure. The review explores formaldehyde-induced pathophysiological mechanisms and FA's protective effects, including mitigation of oxidative damage, inflammation, and apoptosis. By analyzing empirical evidence, it compares the efficacy of various extract preparations, dosage regimens, and treatment durations. The review also addresses methodological heterogeneity and challenges in extrapolating findings to humans. It concludes with a call for rigorous, controlled clinical trials to validate FA's therapeutic viability, offering hope for those affected by formaldehyde toxicity.

The hemostatic molecular mechanism of Sanguisorbae Radix's pharmacological active components based on HSA: Spectroscopic investigations, molecular docking and dynamics simulation

The interactions between human serum albumin (HSA) and the hemostatic components of the Chinese medicine Sanguisorbae Radix (SR), specifically phenolic acid compounds such as caffeic acid (CA), ferulic acid (FA) and their 1:1 mixture (1:1) were studied to investigate the molecular mechanism underlying the hemostatic effect of SR. Network pharmacology combined with the experimental and computational data revealed that HSA is one of the hemostatic targets to SR phenolic acids. SDS-PAGE and multi-spectroscopy demonstrated that the phenolic acids bind to the Sudlow site I on HSA, altering its structure and influencing its migration velocity. There is an observed synergistic effect upon the mixture of CA and FA. Quantum chemistry, molecular docking, and molecular dynamics simulations indicate that the binding of phenolic acids to HSA is stable, and variations in binding efficiency are associated with the hydrophobicity of the substituent at the C3 position of the side chain, and also, the key amino acids and functional groups for hemostasis of SR were identified, along with the active sites that contribute to the synergistic enhancement by phenolic acids.

Molecular Mechanism of Cynodon dactylon Phytosterols Targeting MAPK3 and PARP1 to Combat Epithelial Ovarian Cancer: A Multifaceted Computational Approach

Epithelial Ovarian Cancer (EOC) presents a global health concern, necessitating the development of innovative therapeutic strategies to combat its impact. This study was employed to investigate the unexplored therapeutic efficacy of Cynodon dactylon phytochemicals against EOC using a multifaceted computational approach. A total of 19 out of 89 rigorously curated phytochemicals were assessed as potential drug targets via ADMET profiling, while protein-protein interaction analysis scrutinized the top 20 hub genes among 264 disease targets, revealing their involvement in cancer-related pathways and underscoring their significance in EOC pathogenesis. In molecular docking, Stigmasterol acetate showed the highest binding affinity (-10.9 kcal/mol) with Poly [ADP-ribose] polymerase-1 (PDB: 1UK1), while Arundoin and Beta-Sitosterol exhibited strong affinities (-10.4 kcal/mol and -10.1 kcal/mol, respectively); additionally, Beta-Sitosterol interacting with Mitogen-activated protein kinase 3 (PDB: 4QTB) showed a binding affinity of -10.1 kcal/mol, forming 2 hydrogen bonds and a total of 10 bonds with 10 residues. Molecular dynamics simulations exhibited the significant structural stability of the Beta-Sitosterol-4QTB complex with superior binding free energy (-36.61 kcal/mol) among the three complexes. This study identified C. dactylon phytosterols, particularly Beta-Sitosterol, as effective in targeting MAPK3 and PARP1 to combat EOC, laying the groundwork for further experimental validation and drug development efforts.

Utilizing network pharmacology, molecular docking, and animal models to explore the therapeutic potential of the WenYang FuYuan recipe for cerebral ischemia-reperfusion injury through AGE-RAGE and NF-κB/p38MAPK signaling pathway modulation

BACKGROUND

Stroke is a debilitating condition with high morbidity, disability, and mortality that significantly affects the quality of life of patients. In China, the WenYang FuYuan recipe is widely used to treat ischemic stroke. However, the underlying mechanism remains unknown, so exploring the potential mechanism of action of this formula is of great practical significance for stroke treatment.

OBJECTIVE

This study employed network pharmacology, molecular docking, and in vivo experiments to clarify the active ingredients, potential targets, and molecular mechanisms of the WenYang FuYuan recipe in cerebral ischemia-reperfusion injury, with a view to providing a solid scientific foundation for the subsequent study of this recipe.

MATERIALS AND METHODS

Active ingredients of the WenYang FuYuan recipe were screened using the traditional Chinese medicine systems pharmacology database and analysis platform. Network pharmacology approaches were used to explore the potential targets and mechanisms of action of the WenYang FuYuan recipe for the treatment of cerebral ischemia-reperfusion injury. The Middle Cerebral Artery Occlusion/Reperfusion 2 h Sprague Dawley rat model was prepared, and TTC staining and modified neurological severity score were applied to examine the neurological deficits in rats. HE staining and Nissl staining were applied to examine the pathological changes in rats. Immunofluorescence labeling and Elisa assay were applied to examine the expression levels of certain proteins and associated factors, while qRT-PCR and Western blotting were applied to examine the expression levels of linked proteins and mRNAs in disease-related signaling pathways.

RESULTS

We identified 62 key active ingredients in the WenYang FuYuan recipe, with 222 highly significant I/R targets, forming 138 pairs of medication components and component-targets, with the top five being Quercetin, Kaempferol, Luteolin, β-sitosterol, and Stigmasterol. The key targets included TP53, RELA, TNF, STAT1, and MAPK14 (p38MAPK). Targets related to cerebral ischemia-reperfusion injury were enriched in chemical responses, enzyme binding, endomembrane system, while enriched pathways included lipid and atherosclerosis, fluid shear stress and atherosclerosis, AGE-RAGE signaling in diabetic complications. In addition, the main five active ingredients and targets in the WenYang FuYuan recipe showed high binding affinity (e.g. Stigmasterol and MAPK14, total energy <-10.5 Kcal/mol). In animal experiments, the WenYang FuYuan recipe reduced brain tissue damage, increased the number of surviving neurons, and down-regulated S100β and RAGE protein expression. Moreover, the relative expression levels of key targets such as TP53, RELA and p38MAPK mRNA were significantly down-regulated in the WenYang FuYuan recipe group, and serum IL-6 and TNF-a factor levels were reduced. After WenYang FuYuan recipe treatment, the AGE-RAGE signaling pathway and downstream NF-kB/p38MAPK signaling pathway-related proteins were significantly modulated.

CONCLUSION

This study utilized network pharmacology, molecular docking, and animal experiments to identify the potential mechanism of the WenYang FuYuan recipe, which may be associated with the regulation of the AGE-RAGE signaling pathway and the inhibition of target proteins and mRNAs in the downstream NF-kB/p38MAPK pathway.

A comprehensive review of the molecular and genetic mechanisms underlying gum and resin synthesis in Ferula species

Ferula spp. are plants that produce oleo-gum-resins (OGRs), which are plant exudates with various colors. These OGRs have various industrial applications in pharmacology, perfumery, and food. The main constituents of these OGRs are terpenoids, a diverse group of organic compounds with different structures and functions. The biosynthesis of OGRs in Ferula spp., particularly galbanum, holds considerable economic and ecological importance. However, the molecular and genetic underpinnings of this biosynthetic pathway remain largely enigmatic. This review provides an overview of the current state of knowledge on the biosynthesis of OGRs in Ferula spp., highlighting the major enzymes, genes, and pathways involved in the synthesis of different terpenoid classes, such as monoterpenes, sesquiterpenes, and triterpenes. It also examines the potential of using omics techniques, such as transcriptomics and metabolomics, and genome editing tools, such as CRISPR/Cas, to increase the yield and quality of Ferula OGRs, as well as to create novel bioactive compounds with enhanced properties. Moreover, this review addresses the current challenges and opportunities of applying gene editing in Ferula spp., and suggests some directions for future research and development.

Study on the Pharmacological Mechanism of Icariin for the Treatment of Alzheimer's Disease Based on Network Pharmacology and Molecular Docking Techniques

The purpose of this study is to explore the pharmacological mechanism of icariin (ICA) in the treatment of Alzheimer's disease (AD) based on network pharmacology and network molecular docking technology. In order to investigate the regulatory effect of ICA on the expression level of AD pathological phosphorylation regulatory proteins, this study further explored the possible molecular mechanism of ICA regulating AD autophagy through network pharmacology. Macromolecular docking network was verified by Autodock Vina 1.1.2 software. The main active ingredients of ICA, the physicochemical properties, and pharmacokinetic information of ICA were predicted using online databases and relevant information. The results showed that the targets of MAPK3, AKT1, HSP90AA1, ESR1, and HSP90AA1 were more critical in the treatment of AD. Autophagy, apoptosis, senescence factors, phosphatidylinositide 3-kinase/protein kinase B (P13K/AKT) signaling pathway, MAKP, mTOR, and other pathways were significantly associated with AD. Docking of ICA with HIF-1, BNIP3, PINK1, and Parkin pathway molecules showed that the key targets of the signaling pathway were more stably bound to ICA, which may provide a better pathway for ICA to regulate autophagy by providing a better pathway. ICA can improve AD, and its mechanism may be related to the P13K/AKT, MAKP, and mTOR signaling pathways, thereby regulating autophagy-related proteins.

From seeds to survival rates: investigating Linum usitatissimum's potential against ovarian cancer through network pharmacology

Ovarian cancer is a malignant tumor that primarily forms in the ovaries. It often goes undetected until it has spread to the pelvis and abdomen, making it more challenging to treat and often fatal. Historically, natural products and their structural analogues have played a pivotal role in pharmacotherapy, especially for cancer. Numerous studies have demonstrated the therapeutic potential of Linum usitatissimum against ovarian cancer, but the specific molecular mechanisms remain elusive. This study combines data mining, network pharmacology, and molecular docking analysis to pioneer an innovative approach for ovarian cancer treatment by identifying potent phytochemicals. Findings of current study revealed that Apigenin, Vitamin E, Palmitic acid, Riboflavin, Isolariciresinol, 5-Dehydro-avenasterol, Cholesterol, Pantothenic acid, Nicotinic acid, Campesterol, Beta-Sitosterol, Stigmasterol, Daucosterol, and Vitexin suppress tumor growth by influencing AKT1, JUN, EGFR, and VEGFA. Kaplan-Meier survival analysis spotlighted AKT1, JUN, EGFR, and VEGFA as potential diagnostic and prognostic biomarkers for ovarian cancer. However, it is imperative to conduct in vivo and in vitro examinations to ascertain the pharmacokinetics and biosafety profiles, bolstering the candidacy of L. usitatissimum in ovarian cancer therapeutics.

Network pharmacology-based strategy for predicting therapy targets of Ecliptae Herba on breast cancer

Breast cancer is a prevalent malignancy affecting women globally, characterized by significant morbidity and mortality rates. Ecliptae Herba is a traditional herbal medicine commonly used in clinical practice, has recently been found to possess antitumor properties. In order to explore the underlying material basis and molecular mechanisms responsible for the anti-breast cancer effects of Ecliptae Herba, we used network pharmacology and experimental verification. UPLC-MS/MS was utilized to identify compounds present in Ecliptae Herba. The active components of Ecliptae Herba and its breast cancer targets were screened using public databases. Hub genes were identified using the STRING and Metascape database. The R software was utilized for visual analysis of GO and KEGG pathways. The affinity of the hub targets for the active ingredients was assessed by molecular docking analysis, which was verified by experimental assessment. A total of 178 targets were obtained from the 10 active components of Ecliptae Herba, while 3431 targets associated with breast cancer were screened. There were 144 intersecting targets between the components and the disease. Targets with a higher degree, namely EGFR and TGFB1, were identified through the hub subnetwork of PPI. GO and KEGG analyses revealed that Ecliptae Herba plays an important role in multiple cancer therapeutic mechanisms. Moreover, molecular docking results showed that the core components had good binding affinity with key targets. Finally, it was confirmed that TGF-β1 might be a potential crucial target of Ecliptae Herba in the treatment of breast cancer by cytological experiments, and the TGF-β1/Smad signaling pathway might be an important pathway for Ecliptae Herba to exert its therapeutic effects. This study elucidated the active ingredients, key targets, and molecular mechanisms of Ecliptae Herba in the treatment of breast cancer, providing a scientific foundation and therapeutic mechanism for the prevention and treatment of breast cancer with Traditional Chinese medicine.

Exploring therapeutic targets and drug candidates for obesity: a combined network pharmacology, bioinformatics approach

The remarkably high prevalence of obesity in Saudi Arabia reflects a global epidemic demanding urgent attention due to its associated health risks. The integration of traditional medicine, a vital cultural aspect, involves the use of medicinal plants to address various diseases, including obesity. This research merges network pharmacology (NP) and bioinformatics to innovate obesity treatment by identifying effective phytochemicals from native plants in the Taif valley. Focusing on six indigenous plants-Senna alexandrina, Capsicum annuum, Zingiber officinale, Curcuma longa, Trigonella foenum-graecum, and Foeniculum vulgare-we conducted preliminary screenings for potential bioactive compounds. We systematically compiled compound data from public databases and reviewed literature, revealing active compounds like apigenin, kaempferol, moupinamide, cyclocurcumin, chrysoeriol, isorhamnetin, rheinanthrone, cyclocurcumin, and riboflavin.Constructing a compound-target genes-obesity network unveiled their significant impact on metabolic regulation and fat accumulation, interacting notably with key proteins AKT1 and PTGS2. Molecular docking and 100 ns Molecular Dynamic (MD) simulations demonstrated robust binding affinity and stability at the docking site. Employing adipocytes as a cellular model, we gauged their viability and response to obesity-related stressors post-treatment with these native plant compounds.In conclusion, Saudi Arabia's indigenous plants hold promise as natural solutions for obesity treatment. This research opens new avenues in the battle against this pervasive health crisis by incorporating the potential of native botanicals.Communicated by Ramaswamy H. Sarma.

Unveiling the multi-target compounds of Rhazya stricta: Discovery and inhibition of novel target genes for the treatment of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a prevalent kidney malignancy with a pressing need for innovative therapeutic strategies. In this context, emerging research has focused on exploring the medicinal potential of plants such as Rhazya stricta. Nevertheless, the complex molecular mechanisms underlying its potential therapeutic efficacy remain largely elusive. Our study employed an integrative approach comprising data mining,network pharmacology,tissue cell type analysis, and molecular modelling approaches to identify potent phytochemicals from R. stricta, with potential relevance for ccRCC treatments. Initially, we collected data on R. stricta's phytochemical from public databases. Subsequently, we integrated this information with differentially expressed genes (DEGs) in ccRCC, which were derived from microarray datasets(GSE16441,GSE66270, and GSE76351). We identified potential intersections between R. stricta and ccRCC targets, which enabled us to construct a compound-genes-pathway network using Cytoscape software. This helped illuminate R. stricta's multi-target pharmacological effects on ccRCC. Moreover, tissue cell type analysis added another layer of insight into the cellular specificity of potential therapeutic targets in the kidney. Through further Kaplan-Meier survival analysis, we pinpointed MMP9,ACE,ERBB2, and HSP90AA1 as prospective diagnostic and prognostic biomarkers for ccRCC. Notably, our study underscores the potential of R. stricta derived compounds-namely quebrachamine,corynan-17-ol, stemmadenine,strictanol,rhazinilam, and rhazimolare-to impede ccRCC progression by modulating the activity of MMP9,ACE,ERBB2, and HSP90AA1 genes. Further, molecular docking and dynamic simulations confirmed the plausible binding affinities of these compounds. Despite these promising findings, we recognize the need for comprehensive in vivo and in vitro studies to further investigate the pharmacokinetics and biosafety profiles of these compounds.

Network pharmacology based anti-diabetic attributes of bioactive compounds from Ocimum gratissimum L. through computational approach

The present research was framed to determine the key compounds present in the plant Ocimum gratissimum L. targeting protein molecules of Diabetes Mellitus (DM) by employing In-silico approaches. Phytochemicals previously reported to be present in this herb were collated through literature survey and public phytochemical databases, and their probable targets were anticipated using BindingDB (p ≥ 0.7). STRING and KEGG pathway databases were employed for pathway enrichment analysis. Homology modelling was executed to elucidate the structures of therapeutic targets. Further, Phytocompounds from O. gratissimum were subjected for docking with four therapeutic targets of DM by using AutoDock vina through POAP pipeline implementation. 30 compounds were predicted to target 136 protein molecules including aldose reductase, DPP4, alpha-amylase, and alpha-glucosidase. Neuroactive ligand-receptor interaction, MAPK, PI3K-Akt, starch and insulin resistance were predicted to have potentially modulation by phytocompounds. Based on the phytocompound's binding score with the four targets of DM, Rutin scored the lowest binding energy (-11 kcal/mol) with Aldose reductase by forming 17 intermolecular interactions. In conclusion, based on the network and binding score, phytocompounds from O. gratissimum have a synergistic and considerable effect in the management of DM via multi-compound, multi-target, and multi-pathway mechanisms.

Therapeutic effects of Crataegus monogyna inhibitors against breast cancer

Breast cancer is a silent killer disorder among women and a serious economic burden in healthcare management. Every 19 s, a woman is diagnosed with breast cancer, and every 74 s, a woman worldwide passes away from the disease. Despite the increase in progressive research, advanced treatment approaches, and preventive measures, breast cancer rates continue to increase. This study provides a combination of data mining, network pharmacology, and docking analysis that surely could revolutionize cancer treatment by exploiting prestigious phytochemicals. Crataegus monogyna is a small, rounded deciduous tree with glossy, deeply lobed leaves and flat sprays of cream flowers, followed by dark red berries in autumn. Various studies demonstrated that C. monogyna is therapeutically effective against breast cancer. However, the particular molecular mechanism is still unknown. This study is credited for locating bioactive substances, metabolic pathways, and target genes for breast cancer treatment. According to the current investigation, which examined compound-target genes-pathway networks, it was found that the bioactive compounds of C. monogyna may operate as a viable solution against breast cancer by altering the target genes implicated in the disease pathogenesis. The expression level of target genes was analyzed using GSE36295 microarray data. Docking analysis and molecular dynamic simulation studies further strengthened the current findings by validating the effective activity of the bioactive compounds against putative target genes. In summary, we propose that six key compounds, luteolin, apigenin, quercetin, kaempferol, ursolic acid, and oleanolic acid, contributed to the development of breast cancer by affecting the MMP9 and PPARG proteins. Integration of network pharmacology and bioinformatics revealed C. monogyna's multitarget pharmacological mechanisms against breast cancer. This study provides convincing evidence that C. monogyna might partially alleviate breast cancer and ultimately lays a foundation for further experimental research on the anti-breast cancer activity of C. monogyna.