Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia

pyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS

The pyGROMODS, an easy-to-use cross-platform python-based package, with a graphical user interface, for the generation of molecular dynamic (MD) input files and running MD simulation (MDS) of proteins, peptides, and protein-ligand complex using GROMACS, is here presented. Four routes, with underlining Python scripts, are implemented in pyGROMODS for the generation of MD input files. They are 'RLmulti' for processing multi-ligand protein complex, 'RLmany' for processing multiple ligands against a single protein target, 'RLsingle' for processing multiple pairs of proteins and ligands, and 'PPmore' for processing peptides or proteins without ligands or non-standard residues. In addition, using the package, the generated input files or appropriate input files from other sources can be uploaded to run MDS with GROMACS. The pyGROMODS is implemented with a unique ability to search the host machine systems for the installation of the required software, update and/or install required Python packages, allow the user to pre-define working directory, and generate unique workflow organization with well-defined folders and files in a well-organized manner. The pyGROMODS, which is released under the MIT License, is freely available for download via the GitHub (https://github.com/Dankem/pyGROMODS) and Zenodo (https://doi.org/10.5281/zenodo.7912747) repositories. The precompiled executables can also be downloaded from Zenodo (https://doi.org/10.5281/zenodo.8087090), and a video tutorial can be downloaded from https://youtu.be/I4OKc6uVx1M.Communicated by Ramaswamy H. Sarma.

Elucidating the anti-hypertensive mechanisms of Uncaria rhynchophylla-Alisma plantago-aquatica L: an integrated network pharmacology, cluster analysis, and molecular docking approach

Background: With the increasing global prevalence of hypertension, a condition that can severely affect multiple organs, there is a growing need for effective treatment options. Uncaria rhynchophylla-Alisma plantago-aquatica L. (UR-AP) is a traditional drug pair used for treating hypertension based on the liver-kidney synergy concept. However, the detailed molecular mechanisms underlying its efficacy remain unclear. Methods: This study utilized an integrative approach combining network pharmacology, cluster analysis, and molecular docking to uncover the bioactive components and targets of UR-AP in the treatment of hypertension. Initially, we extracted data from public databases to identify these components and targets. A Protein-Protein Interaction (PPI) network was constructed, followed by enrichment analysis to pinpoint the bioactive components, core targets, and pivotal pathways. Cluster analysis helped in identifying key sub-networks and hypothesizing primary targets. Furthermore, molecular docking was conducted to validate the interaction between the core targets and major bioactive components, thus confirming their potential efficacy in hypertension treatment. Results: Network pharmacological analysis identified 58 bioactive compounds in UR-AP, notably quercetin, kaempferol, beta-sitosterol (from Uncaria rhynchophylla), and Alisol B, alisol B 23-acetate (from Alisma plantago-aquatica L.), as pivotal bioactives. We pinpointed 143 targets common to both UR-AP and hypertension, highlighting MAPK1, IL6, AKT1, VEGFA, EGFR, and TP53 as central targets involved in key pathways like diastolic and endothelial function, anti-atherosclerosis, AGE-RAGE signaling, and calcium signaling. Cluster analysis emphasized IL6, TNF, AKT1, and VEGFA's roles in atherosclerosis and inflammation. Molecular docking confirmed strong interactions between these targets and UR-AP's main bioactives, underscoring their therapeutic potential. Conclusion: This research delineates UR-AP's pharmacological profile in hypertension treatment, linking traditional medicine with modern pharmacology. It highlights key bioactive components and their interactions with principal targets, suggesting UR-AP's potential as a novel therapeutic option for hypertension. The evidence from molecular docking studies supports these interactions, indicating the relevance of these components in affecting hypertension pathways. However, the study acknowledges its limitations, including the reliance on in silico analyses and the need for in vivo validation. These findings pave the way for future clinical research, aiming to integrate traditional medicine insights with contemporary scientific approaches for developing innovative hypertension therapies.

Bioactive compounds as potential alternative treatments to prevent cancer therapy-induced male infertility

About 8-12% of couples experience infertility, with male infertility being the cause in 50% of cases. Several congenital and acquired conditions, including chronic diseases and their treatments, can contribute to male infertility. Prostate cancer incidence increases annually by roughly 3%, leading to an increment in cancer treatments that have adverse effects on male fertility. To preserve male fertility post-cancer survival, conventional cancer treatments use sperm cryopreservation and hormone stimulation. However, these techniques are invasive, expensive, and unsuitable in prepubertal patients lacking mature sperm cells. Alternatively, nutritional therapies enriched with bioactive compounds are highlighted as non-invasive approaches to prevent male infertility that are easily implementable and cost-effective. In fact, curcumin and resveratrol are two examples of bioactive compounds with chemo-preventive effects at the testicular level. In this article, we summarize and discuss the literature regarding bioactive compounds and their mechanisms in preventing cancer treatment-induced male infertility. This information may lead to novel opportunities for future interventions.

Unraveling the Therapeutic Mechanism of Saussurea involucrata against Rheumatoid Arthritis: A Network Pharmacology and Molecular Modeling-Based Investigation

Rheumatoid arthritis (RA) is a chronic autoimmune disease with a global prevalence of approximately 0.46%, causing significant impairments in patients' quality of life and an economic burden. Saussurea involucrata (SI) has long been used in traditional medicine to treat RA, but its underlying mechanism remains unclear. This study utilized network pharmacology and molecular docking to explore the potential pharmacological effects of bioactive compounds in SI on RA. A total of 27 active compounds were identified, along with 665 corresponding targets. Additionally, 593 disease-related targets were obtained from multiple databases, with 119 common targets shared with SI. The high-ranking targets mainly belong to the MAPK family and NF-κB pathway, including MAPK14, MAPK1, RELA, TNF, and MAPK8, all of which are associated with inflammation and joint destruction in RA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed significant pathways related to IL-17 signaling, Th17 cell differentiation, and osteoclast differentiation. Molecular docking and dynamic simulations demonstrated strong interactions between several flavonoids and RA-related targets. Xuelianlactone, Involucratin, and Flazin exhibit outstanding binding efficacy with targets such as MAPK1, MAPK8, and TNF. These findings provide valuable insights into the therapeutic potential of SI for RA and offer directions for further drug development.

Fermented Gynochthodes officinalis (F.C.How) Razafim. & B.Bremer alleviates diabetic erectile dysfunction by attenuating oxidative stress and regulating PI3K/Akt/eNOS pathway

ETHNOPHARMACOLOGICAL RELEVANCE

As a traditional Chinese medicine, Gynochthodes officinalis (F.C.How) Razafim. & B.Bremer (G. officinalis) has been historically as tonics to treat impotence. Fermentation is an ancient processing method for traditional Chinese medicine. Whether fermentation affects the therapeutic effects of G. officinalis on diabetic erectile dysfunction has so far remained unknown.

AIMS OF THE STUDY

In this research, we aim to determine the effect of fermented or unfermented G. officinalis root extract on diabetes mellitus-induced erectile dysfunction (DMED) and the potential mechanisms.

MATERIALS AND METHODS

Candida sp. B5, Lactobacillus sp. Y5 and Lactobacillus sp. R2 are applied for the fermentation of G. officinalis. The optimum fermentation conditions of G. officinalis are investigated. Sprague-Dawley rats were used to establish a diabetic erectile dysfunction model, treated with different concentrations of fermented or unfermented G. officinalis, to compare the effect of fermented or unfermented G. officinalis on DMED and explore underlying mechanisms by assessment of intracavernous pressure, ELISA, Western blot, Masson's trichrome staining, and immunofluorescence. The corpus cavernosum smooth muscle cells (CCSMCs) and Schwann cells were isolated and used to investigate the effect of fermented or unfermented G. officinalis on hydrogen peroxide (H₂O₂)-induced apoptosis.

RESULTS

The results reveal the optimum fermentation conditions of G. officinalis using Lactobacillus sp. Y5 were determined to be 35 °C, the ratio of solid to liquid 1:10, and six days of fermentation. The fermentation increases the abundance of major active ingredients within G. officinalis. After fermented or unfermented G. officinalis treatment for eight weeks by oral gavage at a dose of 100 mg kg^-1 or 300 mg kg^-1, the results show that the fermentation enhances the effect of G. officinalis on diabetic erectile dysfunction detected by intracavernous pressure. The protein expressions of the PI3K/Akt/eNOS pathway were upregulated in diabetic rats after fermented or unfermented G. officinalis treatment, while the level of oxidative stress was significantly reduced. Meanwhile, Masson's trichrome staining also displayed an improvement in the ratio of smooth muscle to collagen. In vitro experiments confirmed that fermented or unfermented G. officinalis protected CCSMCs and Schwann cells from apoptosis. In contrast, fermented G. officinalis showed a fortified protective effect over unfermented G. officinalis.

CONCLUSION

Our findings suggest that fermentation can increase the composition of main active ingredients in G. officinalis and enhance its role in diabetic erectile dysfunction. It augurs the potential therapeutic application of fermented G. officinalis well for treating diabetic erectile dysfunction.

Yangjing capsule improves oligoasthenozoospermia by promoting nitric oxide production through PLCγ1/AKT/eNOS pathway

Background: Oligoasthenozoospermia is an important factor leading to male infertility. Yangjing capsule (YC), a traditional Chinese preparation, displays beneficial effects on male infertility. However, whether YC could improve oligoasthenozoospermia remains unclear. Methods: In this study, we aimed to explore the effect of YC in the treatment of oligoasthenozoospermia. Male Sprague-Dawley (SD) rats were treated with 800 mg/kg ornidazole once daily for 30 days to induce in vivo oligoasthenozoospermia; primary Sertoli cells were treated with 400 μg/mL ornidazole for 24 h to induce in vitro oligoasthenozoospermia. Results: We found that YC improved the testicle and epididymis weight, sperm concentration, sperm progressive motility, serum testosterone, fertility rate and testis morphology in ornidazole-exposed rats and enhanced cell survival in ornidazole-stimulated primary Sertoli cells. YC also inhibited the ornidazole-caused decrease in nitric oxide (NO) generation and the phosphorylation of phospholipase C γ1 (PLCγ1), AKT, and eNOS in vivo and in vitro in oligoasthenozoospermia. Furthermore, the knockdown of PLCγ1 blunted the beneficial effects of YC in vitro. Conclusion: Collectively, our data suggested that YC protected against oligoasthenozoospermia by promoting NO levels through the PLCγ1/AKT/eNOS pathway.

Morinda officinalis extract exhibits protective effects against atopic dermatitis by regulating the MALAT1/miR-590-5p/CCR7 axis

BACKGROUND

Atopic dermatitis (AD) is a chronic inflammatory skin disease with a genetic predisposition, and the traditional Chinese medicine Morinda officinalis and its roots are characterized with anti-inflammatory effects and have been used for the treatment of various disease. However, it is still largely unknown whether Morinda officinalis extract (MOE) can be used for the treatment of AD.

OBJECTIVES

In our study we aimed to determine whether MOE could ameliorate 2,4-dinitrochlorobenzene (DNCB)-induced AD and elucidate molecular mechanisms.

METHODS

We established an AD mouse model by using DNCB. Skin pathological analysis and ELISA assay were used to detect the effect of MOE on the inflammation of AD model mouse skin and the expression changes of inflammatory factors, and further functional verification was performed in TNF-α/IFN-γ-induced HaCaT cells.

RESULTS

Our in vivo experiments confirmed that MOE remarkably reduced DNCB-induced AD lesions and symptoms, such as epidermal and dermal thickness and mast cell infiltration and inflammatory cytokines secretion in the mice models. In addition, the underlying mechanisms by which MOE ameliorated AD had been uncovered, and we verified that MOE inhibited MALAT1 expression in AD, resulting in attenuated expression of C-C chemokine receptor type 7 (CCR7) regulated by MALAT1-sponge miR-590-5p in a competing endogenous RNA (ceRNA) mechanisms-dependent manner, thereby inhibiting TNF-α/IFN-γ-induced cellular proliferation and inflammation.

The crucial role of LncRNA MIR210HG involved in the regulation of human cancer and other disease

Long noncoding RNAs (lncRNAs) have evoked considerable interest in recent years due to their critical functions in the regulation of disease processes. Abnormal expression of lncRNAs is found in multiple diseases, and lncRNAs have been exploited for diverse medical applications. The lncRNA MIR210HG is a recently discovered lncRNA that is widely dysregulated in human disease. MIR210HG was described to have biological functions with potential roles in disease development, including cell proliferation, invasion, migration, and energy metabolism. And MIR210HG dysregulation was confirmed to have promising clinical values in disease diagnosis, treatment, and prognosis. In this review, we systematically summarize the expression profiles, roles, underlying mechanisms, and clinical applications of MIR210HG in human disease.

Network Pharmacology and Molecular Docking Analysis Explores the Mechanisms of Cordyceps sinensis in the Treatment of Oral Lichen Planus

Objective

Oral lichen planus (OLP) is the most common potentially malignant disorder of the oral cavity. This study aimed to investigate the mechanism of action of Cordyceps sinensis in the treatment of OLP and provides a theoretical support for improving current treatment regimens for OLP.

Methods

The active components and therapeutic targets of Cordyceps sinensis were predicted and screened using the TCMSP, SymMap, PubMed, HIT 2.0, and PharmMapper databases, while the relevant OLP targets were predicted and screened using the DisGeNET and GeneCards databases. Protein-protein interactions (PPI) were examined using the String database, and Cytoscape was used to combine and illustrate the findings. GO and KEGG pathway enrichment analyses were carried out using RStudio, and AutoDock Vina and Pymol were used for molecular docking and visualization, respectively.

Results

A total of 404 potential target genes were discovered after evaluating 21 active compounds from Cordyceps sinensis. Potential therapeutic targets included 67 targets that matched and overlapped with OLP, including TNF, IL-6, CD4, EGFR, and IL1B. Key targets were predominantly engaged in the PI3K-Akt signaling pathway and the MAPK signaling pathway, according to the GO and KEGG analyses. These targets have a connection to biological processes including apoptosis signaling pathway regulation, T cell activation, and oxidative stress response. The molecular docking results showed that TNF, IL-6, CD4, EGFR, and IL1B could bind to their corresponding active components.

Conclusions

Cordyceps sinensis contains multiple components and acts on multiple targets and multiple pathways. Particularly, Cordyceps sinensis targets TNF, IL-6, CD4, EGFR, and IL1B, regulates PI3K-Akt and MAPK signaling pathways, as well as takes part in biological processes including apoptosis, T cell activation, and oxidative stress. Cordyceps sinensis could be a crucial choice in the therapy of OLP.

Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing

The pandemic of SARS-CoV-2 infections is a severe threat to human life and the world economic condition. Although vaccination has reduced the outspread, but still the situation is not under control because of the instability of RNA sequence patterns of SARS-CoV-2, which requires effective drugs. Several studies have suggested that the SARS-CoV-2 infection causing hub differentially expressed genes (Hub-DEGs). However, we observed that there was not any common hub gene (Hub-DEGs) in our analyses. Therefore, it may be difficult to take a common treatment plan against SARS-CoV-2 infections globally. The goal of this study was to examine if more representative Hub-DEGs from published studies by means of hub of Hub-DEGs (hHub-DEGs) and associated potential candidate drugs. In this study, we reviewed 41 articles on transcriptomic data analysis of SARS-CoV-2 and found 370 unique hub genes or studied genes in total. Then, we selected 14 more representative Hub-DEGs (AKT1, APP, CXCL8, EGFR, IL6, INS, JUN, MAPK1, STAT3, TNF, TP53, UBA52, UBC, VEGFA) as hHub-DEGs by their protein-protein interaction analysis. Their associated biological functional processes, transcriptional, and post-transcriptional regulatory factors. Then we detected hHub-DEGs guided top-ranked nine candidate drug agents (Digoxin, Avermectin, Simeprevir, Nelfinavir Mesylate, Proscillaridin, Linifanib, Withaferin, Amuvatinib, Atazanavir) by molecular docking and cross-validation for treatment of SARS-CoV-2 infections. Therefore, the findings of this study could be useful in formulating a common treatment plan against SARS-CoV-2 infections globally.

Network Pharmacology and Molecular Docking Elucidate the Underlying Pharmacological Mechanisms of the Herb Houttuynia cordata in Treating Pneumonia Caused by SARS-CoV-2

Used in Asian countries, including China, Japan, and Thailand, Houttuynia cordata Thumb (H. cordata; Saururaceae, HC) is a traditional herbal medicine that possesses favorable antiviral properties. As a potent folk therapy used to treat pulmonary infections, further research is required to fully elucidate the mechanisms of its pharmacological activities and explore its therapeutic potential for treating pneumonia caused by SARS-CoV-2. This study explores the pharmacological mechanism of HC on pneumonia using a network pharmacological approach combined with reprocessing expression profiling by high-throughput sequencing to demonstrate the therapeutic mechanisms of HC for treating pneumonia at a systemic level. The integration of these analyses suggested that target factors are involved in four signaling pathways, including PI3K-Akt, Jak-STAT, MAPK, and NF-kB. Molecular docking and molecular dynamics simulation were applied to verify these results, indicating a stable combination between four metabolites (Afzelin, Apigenin, Kaempferol, Quercetin) and six targets (DPP4, ELANE, HSP90AA1, IL6, MAPK1, SERPINE1). These natural metabolites have also been reported to bind with ACE2 and 3CLpro of SARS-CoV-2, respectively. The data suggest that HC exerts collective therapeutic effects against pneumonia caused by SARS-CoV-2 and provides a theoretical basis for further study of the active drug-like ingredients and mechanism of HC in treating pneumonia.

Lycium barbarum (Goji) as functional food: a review of its nutrition, phytochemical structure, biological features, and food industry prospects

Lycium genus (Goji berry) is recognized as a good source of homology of medicine and food, with various nutrients and phytochemicals. Lately, numerous studies have focused on the chemical constituents and biological functions of the L. barbarum L., covering phytochemical and pharmacological aspects. We aim to provide exclusive data on the nutrients of L. barbarum L. fruits and phytochemicals, including their structural characterization, the evolution of extraction, and purification processes of different phytochemicals of L. barbarum L. fruit while placing greater emphasis on their wide-ranging health effects. This review also profitably offers innovative approaches for the food industry and industrial applications of L. barbarum L. and addresses some current situations and problems in the development of L. barbarum L. in deep processing products, which can provide clues for the sustainable development of L. barbarum L. industry.

A network pharmacology approach to determine the underlying mechanisms of action of Yishen Tongluo formula for the treatment of oligoasthenozoospermia

Oligoasthenozoospermia is a complex disease caused by a variety of factors, and its incidence is increasing yearly worldwide. Yishen Tongluo formula (YSTLF), created by Professor Sun Zixue, has been used to treat oligoasthenozoospermia in clinical practice for several decades with a good therapeutic effect. However, the chemical and pharmacological profiles of YSTLF remain unclear and need to be elucidated. In this study, a network pharmacology approach was applied to explore the potential mechanisms of YSTLF in oligoasthenozoospermia treatment. All of the compounds in YSTLF were retrieved from the corresponding databases, and the bioactive ingredients were screened according to their oral bioavailability (OB) and drug-likeness (DL). The potential proteins of YSTLF were obtained from the traditional Chinese medicine systems pharmacology (TCMSP) database and the Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM) database, while the potential genes of oligoasthenozoospermia were obtained from the GeneCards database and the DisGeNET database. The STRING database was used to construct an interaction network according to the common targets identified by the online tool Venny for YSTLF and oligoasthenozoospermia. The topological characteristics of nodes were visualized and analyzed through Cytoscape. Biological functions and significant pathways were determined and analyzed using the Gene Ontology (GO) knowledgebase, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Metascape. Finally, the disease-formula-compound-target-pathway network was constructed by Cytoscape. A total of 106 bioactive ingredients and 134 potential targets from YSTLF were associated with oligoasthenozoospermia or considered to be therapeutically relevant. Pathway analysis indicated that the PI3K/Akt, MAPK and apoptosis signaling pathways were significant pathways involved in oligoasthenozoospermia. In conclusion, the current study expounded the pharmacological actions and molecular mechanisms of YSTLF in treating oligoasthenozoospermia from a holistic viewpoint. The potential molecular mechanisms were closely related to antioxidative stress, antiapoptosis and anti-inflammation, with TNF, CCND1, ESR1, NFKBIA, NR3C1, MAPK8, and IL6 being possible targets. This network pharmacology prediction may offer a helpful tool to illustrate the molecular mechanisms of the Chinese herbal compound YSTLF in oligoasthenozoospermia treatment.

Network pharmacology-based analysis for unraveling potential cancer-related molecular targets of Egyptian propolis phytoconstituents accompanied with molecular docking and in vitro studies

Cancer is one of the predominant causes of death worldwide. The new trend nowadays is to exploit natural products with the hope of developing new anticancer agents with fewer side effects. Propolis is one of these natural products which showed effectiveness in cancer treatment. The aim of this study is to understand the multi-level mechanism of action of propolis constituents in cancer treatment using an integrated approach of network pharmacology-based analysis, molecular docking and in vitro cytotoxicity testing. An inhouse database of chemical constituents from Egyptian propolis was compiled and assessed for its ADME properties using the QikProp module in the Schrodinger software. STITCH, UniProt, STRING, KEGG and DAVID databases were used for construction of constituent-target gene, gene-pathway, and constituent-target gene-pathway networks with the aid of Cytoscape 3.8.2. The network pharmacology-based analysis showed that the hit propolis constituents related to cancer targets were genistein, luteolin, benzoic acid, quercetin and vanillic acid, whereas the main cancer-associated targets were CYP1A1, CYP19A1, ESR1, NOS3, CASP3 and AKT1. Twenty-four cancer-related pathways were recognized where the most enriched ones were pathways in cancer and estrogen signaling pathway. The most enriched biological processes involved in the mechanism of action of propolis constituents in cancer treatment were negative regulation of the apoptotic process and the metabolic process and negative regulation of cellular glucuronidation. Molecular docking analysis of the top hit compounds against the most enriched target proteins in the constructed networks was carried out using the Maestro interface of the Schrodinger software. Among hit compounds, quercetin and genistein exhibited the most stabilized interaction. Finally, confirmation of the potential anticancer activity of propolis was assured by in vitro cytotoxicity testing of propolis extract on human prostate cancer (DU-145), breast adenocarcinoma (MCF-7) and colorectal adenocarcinoma (Caco-2) cell lines. This study presents deeper insights about propolis molecular mechanisms of action in cancer for the first time using an integrated approach of network pharmacology, molecular docking and in vitro testing.