Advanced network pharmacology study reveals multi-pathway and multi-gene regulatory molecular mechanism of Bacopa monnieri in liver cancer based on data mining, molecular modeling, and microarray data analysis

Active components unveiling and pharmacodynamic research on Valeriana jatamansi jones for ameliorating ulcerative colitis based on pharmacokinetics and network pharmacology

ETHNOPHARMACOLOGICAL RELEVANCE

Valeriana jatamansi Jones (V. jatamansi), a traditional Chinese medicine, is widely used in the treatment of gastrointestinal disorders, such as ulcerative colitis (UC). However, the active components of V. jatamansi with protective effect on the intestinal barrier remains elusive.

AIM OF THE STUDY

This investigation was conducted to confirm the efficacy of V. jatamansi ethanol extract for the treatment of UC and to identify the active compounds in ethanol extract of V. jatamansi that have a protective effect against intestinal barrier damage.

MATERIALS AND METHODS

The role of V. jatamansi extract was assessed on dextrose sodium sulfate (DSS) induced colitis in vivo. The wound healing, apoptosis and epithelial barrier permeability of intestinal epithelial cells (NCM460 cells) were evaluated in vitro. UHPLC-MS method was used to determine the pharmacokinetic characteristics of V. jatamansi extract after oral administration. The effect of absorbed compounds on the intestinal barrier was assessed on NCM460 cells. Fuzzy matter-element analysis was used to explore the main compounds, and the results were verified by FITC-dextran assay. Network pharmacology was used to predict the potential mechanisms and western blotting was used to validate the results.

RESULTS

The ethanol extract ofV. jatamansi relieves symptoms, inflammatory response and intestinal barrier damage in DSS-induced UC. It effectively alleviated DSS-induced epithelial barrier damage in NCM460 cells. Pharmacokinetic analyses indicated that the five components (chlorogenic acid, hesperidin, valerosidate, isochlorogenic acid B and cryptochlorogenic acid) were quickly absorbed into the blood after oral administration of ethanol extract. The fuzzy matter-element analysis and FITC-dextran assay demonstrated that valerosidate and chlorogenic acid played an important role in the protection of the intestinal barrier damage. Network pharmacological analyses and western blotting analyses showed that the ethanol extract of and absorbed components significantly inhibited the Bcl-2/Bax/Caspase-3 signaling pathway, and suppressed DSS-induced apoptosis in NCM460 cells.

CONCLUSION

The ethanol extract of V. jatamansi ameliorates intestinal barrier injury in UC mice through multi-components. Valerosidate and chlorogenic acid were identified as anti-colitis compounds. These provided new insights into finding the active components for the treatment of UC and contribute to the clinical application of V. jatamansi.

Quercetin inhibits mitophagy-mediated apoptosis and inflammatory response by targeting the PPARγ/PGC-1α/NF-κB axis to improve acute liver failure

BACKGROUND

Reactive oxygen species (ROS) from mitochondrial dysfunction are critical in triggering apoptosis and inflammation in acute liver failure (ALF). Quercetin (QUE), an antioxidant, is renowned for its therapeutic effects onliverdiseases. There are no studies on whether QUE regulates mitophagy level in hepatocytes to inhibit ALF.

OBJECTIVE

This study investigates QUE's protective effects on ALF and elucidates the mechanisms involved.

METHODS

The ALF and hepatocyte inflammatory injury model was established using LPS and D-Galn. To predict potential targets and mechanisms of QUE in ALF treatment, transcriptomics, network pharmacology, molecular docking techniques, and ChIP were employed. The expression level related to mitophagy, apoptosis, and signaling pathways were detected by CCK8, IHC, IF staining, TUNEL, RT-qPCR, TEM, Western blotting, ELISA, and flow cytometry.

RESULTS

Network pharmacology and transcriptomics revealed common targets between QUE and ALF. Enrichment analysis showed that the anti-ALF targets of QUE were significantly associated with mitochondria and NF-κB-related pathways. Subsequent experiments showed that QUE pretreatment significantly alleviated the loss of hepatocyte viability, enhanced mitochondrial membrane potential, activated mitophagy, and promoted the clearance of damaged mitochondria, thereby reducing ROS accumulation, significantly reducing cell apoptosis and inflammatory responses, reducing ALT and AST levels, and improving liver tissue pathology. Mechanistically, molecular docking, DARTS, and CETSA analyses confirmed that QUE directly binds to the PPARγ molecule, which reduced binding to IκB and significantly inhibit the NF-κB pathway to exert its protective effects.

CONCLUSION

In short, our results provide the first evidence that QUE improves acute liver failure by promoting mitophagy through regulating the PPARγ/PGC-1α/NF-κB axis and inhibiting apoptosis and inflammatory responses mediated by mitochondrial dysfunction, which provides evidence for the potential of QUE in the treatment of ALF.

Exploration of Bioactive Umami Peptides from Wheat Gluten: Umami Mechanism, Antioxidant Activity, and Potential Disease Target Sites

Umami peptides have the ability to enhance food flavours and have potential health benefits. The objective of this study was to conduct a comprehensive investigation into the umami intensity, taste mechanism, and antioxidant activity of six umami peptides derived from wheat gluten hydrolysates (WGHs) and fermented WGHs. The e-tongue analysis demonstrated that the peptides exhibited a direct proportionality in terms of umami value and concentration, and were capable of enhancing the umami of commercially available condiments. The molecular dynamics simulations demonstrated that the peptides interacted with T1R1/T1R3 receptors via hydrogen bonds, hydrophobic interactions, ionic interactions, and water bridges, thereby producing umami. Furthermore, the DPPH, ABTS, hydroxyl radical-scavenging, and FRAP assays demonstrated that the six peptides exhibited antioxidant activity in vitro. Ultimately, the network pharmacology and molecular docking results indicated that AKT1, JUN, and CASP3 may serve as the core targets for the peptides in the treatment of oxidative diseases. In conclusion, this work offers novel insights into the use of bioactive umami peptides, emphasising their prospective applications in the food and health supplement industries.

Evaluation of the inhibitory mechanism of Pennisetum glaucum (pearl millet) bioactive compounds for rheumatoid arthritis: an in vitro and computational approach

Introduction

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial infiltration and pannus formation, and its rising incidence is significantly contributing to the global disability rate. Despite advances in biological drugs, no treatment has successfully cured or averted its progression. Consequently, natural drugs are being explored as alternative therapeutic strategies.

Objective

This study aims to evaluate the therapeutic potential of Pennisetum glaucum (pearl millet) and to identify its bioactive compounds to assess their effectiveness against RA targets.

Methods

The therapeutic potential of P. glaucum extracts was evaluated by antioxidant and anti-inflammatory assays. Gas chromatography-mass spectrometry (GC-MS) was utilized to identify the compounds in P. glaucum extract. The pharmacokinetics and safety profile of these compounds were studied by absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Network pharmacology, molecular docking, and molecular dynamic (MD) simulation were employed to identify the active compounds and their therapeutic targets in P. glaucum for RA treatment.

Results

Acidified methanol (AM) extract of P. glaucum showed the highest phenolic (213 ± 0.008 mg GAE/g DW) and flavonoid content (138.1 ± 0.03 mg RE/g DW), demonstrating significant antioxidant and anti-inflammatory potential. GC-MS of AM extract identified 223 compounds. Lipinski and toxicity parameters screened out 17 compounds. Protein-protein interaction (PPI) analysis shortlisted 20 key targets in RA pathways, nine of which were upregulated in five microarray datasets. Molecular docking and MD simulations revealed that compound-7 (benzenesulfonamide, 2-nitro-N-phenyl-) and compound-9 (Pregnane-3,20-diamine, (3.beta.,5.alpha.,20S)-) bind strongly with MMP9, JAK2, PTGS2, and HIF1a compared to the reference, predicting stable interaction with these upregulated genes. Finally, PASS (prediction of activity spectra for biological active substances) analysis further validated the anti-arthritic potential of these compounds based on their chemical structure.

Conclusion

This study uncovered a therapeutic drug candidate against HIF1a, MMP9, JAK2, and PTGS2 for RA from P. glaucum active compounds, laying the groundwork for future research.

Icariin targets p53 to protect against ceramide-induced neuronal senescence: Implication in Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is a leading cause of dementia. The aging brain is particularly vulnerable to various stressors, including increased levels of ceramide. However, the role of ceramide in neuronal cell senescence and AD progression and whether icariin, a natural flavonoid glucoside, could reverse neuronal senescence remain inadequately understood.

AIM

In this study, we explore the role of ceramide in neuronal senescence and AD, and whether icariin can counteract these effects.

METHODS

We pretreated HT-22 cells with icariin and then induced senescence with ceramide. Various assays were employed to assess cell senescence, such as reactive oxygen species (ROS) production, cell cycle progression, β-galactosidase staining, and expression of senescence-associated proteins. In vivo studies utilized APP/PS1 mice and C57BL/6J mice injected with ceramide to evaluate behavioral changes, histopathological alterations, and senescence-associated protein expression. Transcriptomics, molecular docking, molecular dynamics simulations, and cellular thermal shift assays were employed to verify the interaction between icariin and P53. The specificity of icariin targeting of P53 was further confirmed through rescue experiments utilizing the P53 activator Navtemadlin.

RESULTS

Our data demonstrated that ceramide could induce neuronal senescence and AD-related pathologies, which were reversed by icariin. Moreover, molecular studies revealed that icariin directly targeted P53, and its neuroprotective effects were attenuated by P53 activation, providing evidence for the role of P53 in icariin-mediated neuroprotection.

CONCLUSION

Icariin demonstrates a protective effect against ceramide-induced neuronal senescence by inhibiting the P53 pathway. This identifies a novel mechanism of action for icariin, offering a novel therapeutic approach for AD and other age-related neurodegenerative diseases.

An Investigation of the Effect of the Traditional Naxi Herbal Formula Against Liver Cancer Through Network Pharmacology, Molecular Docking, and In Vitro Experiments

Background/Objectives: The formula Chong-Lou-Yao-Fang (CLYF) is an herbal medicinal formulation developed by the indigenous Naxi people for treating liver cancer. This study was to reveal the biological activity, potential targets, and molecular mechanisms of CLYF for cancer treatment. Methods: Network pharmacology, microarray data analysis, survival analysis, and molecular docking were employed to predict potential compounds, targets, and pathways for the treatment of liver cancer. In vitro experiments and Western blot validation were conducted to confirm these predictions. Results: 35 key compounds and 20 core targets were screened from CLYF, involving signaling pathways for PI3K-Akt, MAPK, hepatitis B and C, which were effective for liver cancer treatment. Microarray data analysis and survival analysis indicated that EGFR and TP53 serve as promising biomarkers for diagnosis and prognosis in liver cancer. Molecular docking revealed stable binding between EGFR, TP53, and AKT1 with active ingredients. Cell experiments confirmed that CLYF-A suppressed cell proliferation, induced apoptosis, and caused cell cycle arrest in HepG2 cells, which were associated with a loss of mitochondrial membrane potential. Compared to the control group, the relative protein expression levels of EGFR and AKT1 significantly decreased following treatment with CLYF-A, while TP53 levels increased significantly. Conclusions: Verification of the anticancer activity of CLYF and its potential mechanisms may have important implications for anticancer therapies. Our results may provide a scientific basis for the clinical use of CLYF for cancer treatment and have important implications for developing pharmaceutical preparations, which also need more pharmacological experiments, clinical experiments, and in vivo experiments.

Unraveling Cordia myxa's anti-malarial potential: integrative insights from network pharmacology, molecular modeling, and machine learning

Malaria is a potentially fatal infective illness caused due to parasites that belong to the Plasmodium genus, which are transferred to humans with the help of the stings of affected female Anopheles mosquitoes, and it persists as a serious public wellness problem worldwide. Cordia myxa is a medicinal plant that possesses various medicinal characteristics like antimicrobial, anti-inflammation, antioxidant, and antidiabetic activities, which makes it an important natural resource for the therapy of different maladies in traditional medicine. In this investigation, a certain network pharmacology method has been utilized to identify the potent active components, possible targets as well as signaling pathways present in C. myxa in relation to malaria therapy. The active compounds were submitted to molecular docking approaches to validate their successful activity against the potential targets. The study concluded that three constituents named cosmosiin, stigmastanol, robinetin, and quercetin were highly active and could regulate the expression of Interleukin 6 (IL6) and Cysteine-aspartic acid protease 3 (CASP3), which may act as a potential therapeutic target for malaria treatment. These analyses are validated by molecular dynamics simulation which reflects on the overall structural stability of the intermolecular conformation and interactions. These results can also be witnessed in simulation-based trajectories binding free energies, which concluded the significant role of electrostatic and van der Waals energies in total intermolecular interactions. Finally, we utilized machine learning to predict the anti-malarial activity of C. myxa compounds, comparing them with approved drugs. Using the Chemprop model and MAIP predictions, we assessed ten compounds, revealing their potential as lead anti-malarial agents. This study establishes a groundwork for comprehending the function of the anti-malaria action of C. myxa.

Comprehending the pharmacological mechanism of marine phenolic acids in bladder cancer therapy against matrix metalloproteinase 9 protein by integrated network pharmacology and in-silico approaches

Bladder cancer (BC) is the 10th most common tumour with a high incidence and recurrence rate worldwide; however, the current therapies present limitations as, regularly, not all patients benefit from treatment. Therefore, the search for new, active marine phenolic acids with anti-tumour properties is imperative. In this study, we subjected marine phenolic acids to in silico investigations such as network pharmacology, molecular docking, and molecular dynamics simulation (MD) to identify a plausible pathway and the lead compound that inhibits BC. According to the network pharmacology analysis, eight hub genes (PLAU, MMP2, ITGB3, MAPK1, PTPN11, ESR1, TLR4, MMP9) were found and linked to the enrichment of hsa05205: proteoglycans in cancer, and four hub genes (MMP1, MMP2, MAPK1, MMP9) were involved in the enrichment of hsa05219: BC. Subsequently, molecular docking studies showed that the marine phenolic acids exhibit a strong binding affinity for the target protein, matrix metalloproteinase-9 (MPP9). Among these 14 marine phenolic acids, chicoric acid showed the highest binding affinity of -67.1445 kcal/mol and formed hydrogen bonds with the residues of Ala189, Gln227, Leu188, His226, Ala242, Arg249, Ala191, and Gly186 in the active site of the MPP9 protein. Then, molecular dynamics simulation revealed that chicoric acid formed a stable protein-ligand complex with RMSD and RMSF values of 0.72 nm and 0.53 nm, respectively. Furthermore, the PCA method was employed to understand the dynamical behaviour in the conformational space of MPP9 protein bound to chicoric acid, and the results showed the good conformational space behaviour of MPP9 protein. Moreover, chicoric acid showed a free binding energy value of -32.62 kcal/mol, which indicated it could be a BC inhibitor. Overall, chicoric acid demonstrated potential anti-BC activity through MPP9 protein inhibition.

Investigating the mechanism of tricyclic decyl benzoxazole -induced apoptosis in liver Cancer cells through p300-mediated FOXO3 activation

OBJECTIVE

To investigate whether tricyclic decylbenzoxazole (TDB) regulates liver cancer cell proliferation and apoptosis through p300-mediated FOXO acetylation.

METHODS

Sequencing, adenovirus, and lentivirus transfection were performed in human liver cancer cell line SMMC-7721 and apoptosis was detected by Tunel, Hoechst, and flow cytometry. TEM for mitochondrial morphology, MTT for cell proliferation ability, Western blot, and PCR were used to detect protein levels and mRNA changes.

RESULTS

Sequencing analysis and cell experiments confirmed that TDB can promote the up-regulation of FOXO3 expression. TDB induced FOXO3 up-regulation in a dose-dependent manner, promoted the expression of p300 and Bim, and enhanced the acetylation and dephosphorylation of FOXO3, thus promoting apoptosis. p300 promotes apoptosis of cancer cells through Bim and other proteins, while HAT enhances the phosphorylation of FOXO3 and inhibits apoptosis. Overexpression of FOXO3 can increase the expression of exo-apoptotic pathways (FasL, TRAIL), endo-apoptotic pathways (Bim), and acetylation at the protein level and inhibit cell proliferation and apoptotic ability, while FOXO3 silencing or p300 mutation can partially reverse apoptosis. In tumor tissues with overexpression of FOXO3, TDB intervention can further increase the expression of p53 and caspase-9 proteins in tumor cells, resulting in loss of mitochondrial membrane integrity during apoptosis, the release of cytoplasm during signal transduction, activation of caspase-9 and synergistic inhibition of growth.

CONCLUSION

TDB induces proliferation inhibition and promotes apoptosis of SMMC-7721 cells by activating p300-mediated FOXO3 acetylation.

Generation of a medicine food homology formula and its likely mechanism in treatment of microvascular angina

Microvascular angina (MVA) is the most common cause of cardiac ischemic chest pain in patients without obstructive coronary artery disease (CAD) and lacks of effective treatment means. Medicine food homology (MFH) involves substances with both nutritional and medicinal qualities that have the potential to improve MVA symptoms as medicines, dietary supplements. However, research on MFH formula (MFHF) for MVA is not available. The study aims to generate a core MFHF for MVA through data mining and offer scientific backing for the utilization of edible medications in the prevention and alleviation of MVA. 11 databases were utilized to construct a database of MFH drugs, and the MFHF was generated through frequency analysis, association rule analysis, and clustering analysis. The composition of the formula is Codonopsis Radix, Astragali Radix, Platycodonis Radix, Persicae Semen, Glycyrrhizae Radix Et Rhizoma, Angelicae Sinensis Radix, and Allii Macrostemonis Bulbus. Through network pharmacology and molecular docking, we identified five major active components of MFHF: Adenosine, Nonanoic Acid, Lauric Acid, Caprylic Acid, and Enanthic Acid, along with nine core targets (NFKB1, ALB, AKT1, ACTB, TNF, IL6, ESR1, CASP3, and PTGS) for the improvement of MVA. These 5 active components have various biological activities, such as reducing oxidative stress, anti-inflammation, analgesia effect, inhibiting platelet aggregation, vasodilatation, vascular endothelial protection, and cardio-protection. GO and KEGG enrichment analyses revealed that MFHF mainly acted on the response to xenobiotic stimulus, integrative component of the plasma membrane, RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding, pathways in cancer, lipid and atherosclerosis, human cytomegalovirus infection, and the PI3K-Akt signaling pathway, which are the main pathogenesis of MVA.

The role of artificial intelligence in the development of anticancer therapeutics from natural polyphenols: Current advances and future prospects

Natural polyphenols, abundant in the human diet, are derived from a wide variety of sources. Numerous preclinical studies have demonstrated their significant anticancer properties against various malignancies, making them valuable resources for drug development. However, traditional experimental methods for developing anticancer therapies from natural polyphenols are time-consuming and labor-intensive. Recently, artificial intelligence has shown promising advancements in drug discovery. Integrating AI technologies into the development process for natural polyphenols can substantially reduce development time and enhance efficiency. In this study, we review the crucial roles of natural polyphenols in anticancer treatment and explore the potential of AI technologies to aid in drug development. Specifically, we discuss the application of AI in key stages such as drug structure prediction, virtual drug screening, prediction of biological activity, and drug-target protein interaction, highlighting the potential to revolutionize the development of natural polyphenol-based anticancer therapies.

Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Analysis Reveal Insights into the Molecular Mechanism of Cordia myxa in the Treatment of Liver Cancer

Traditional treatments of cancer have faced various challenges, including toxicity, medication resistance, and financial burdens. On the other hand, bioactive phytochemicals employed in complementary alternative medicine have recently gained interest due to their ability to control a wide range of molecular pathways while being less harmful. As a result, we used a network pharmacology approach to study the possible regulatory mechanisms of active constituents of Cordia myxa for the treatment of liver cancer (LC). Active constituents were retrieved from the IMPPAT database and the literature review, and their targets were retrieved from the STITCH and Swiss Target Prediction databases. LC-related targets were retrieved from expression datasets (GSE39791, GSE76427, GSE22058, GSE87630, and GSE112790) through gene expression omnibus (GEO). The DAVID Gene Ontology (GO) database was used to annotate target proteins, while the Kyoto Encyclopedia and Genome Database (KEGG) was used to analyze signaling pathway enrichment. STRING and Cytoscape were used to create protein-protein interaction networks (PPI), while the degree scoring algorithm of CytoHubba was used to identify hub genes. The GEPIA2 server was used for survival analysis, and PyRx was used for molecular docking analysis. Survival and network analysis revealed that five genes named heat shot protein 90 AA1 (HSP90AA1), estrogen receptor 1 (ESR1), cytochrome P450 3A4 (CYP3A4), cyclin-dependent kinase 1 (CDK1), and matrix metalloproteinase-9 (MMP9) are linked with the survival of LC patients. Finally, we conclude that four extremely active ingredients, namely cosmosiin, rosmarinic acid, quercetin, and rubinin influence the expression of HSP90AA1, which may serve as a potential therapeutic target for LC. These results were further validated by molecular dynamics simulation analysis, which predicted the complexes with highly stable dynamics. The residues of the targeted protein showed a highly stable nature except for the N-terminal domain without affecting the drug binding. An integrated network pharmacology and docking study demonstrated that C. myxa had a promising preventative effect on LC by working on cancer-related signaling pathways.

In Silico Prediction of New Inhibitors for Kirsten Rat Sarcoma G12D Cancer Drug Target Using Machine Learning-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulation Approaches

Single-point mutations in the Kirsten rat sarcoma (KRAS) viral proto-oncogene are the most common cause of human cancer. In humans, oncogenic KRAS mutations are responsible for about 30% of lung, pancreatic, and colon cancers. One of the predominant mutant KRAS G12D variants is responsible for pancreatic cancer and is an attractive drug target. At the time of writing, no Food and Drug Administration (FDA) approved drugs are available for the KRAS G12D mutant. So, there is a need to develop an effective drug for KRAS G12D. The process of finding new drugs is expensive and time-consuming. On the other hand, in silico drug designing methodologies are cost-effective and less time-consuming. Herein, we employed machine learning algorithms such as K-nearest neighbor (KNN), support vector machine (SVM), and random forest (RF) for the identification of new inhibitors against the KRAS G12D mutant. A total of 82 hits were predicted as active against the KRAS G12D mutant. The active hits were docked into the active site of the KRAS G12D mutant. Furthermore, to evaluate the stability of the compounds with a good docking score, the top two complexes and the standard complex (MRTX-1133) were subjected to 200 ns MD simulation. The top two hits revealed high stability as compared to the standard compound. The binding energy of the top two hits was good as compared to the standard compound. Our identified hits have the potential to inhibit the KRAS G12D mutation and can help combat cancer. To the best of our knowledge, this is the first study in which machine-learning-based virtual screening, molecular docking, and molecular dynamics simulation were carried out for the identification of new promising inhibitors for the KRAS G12D mutant.

Elucidating the anti-cancer potential of Cinnamomum tamala essential oil against non-small cell lung cancer: A multifaceted approach involving GC-MS profiling, network pharmacology, and molecular dynamics simulations

Cinnamomum tamala (Buch.-Ham.) T.Nees & Eberm., or Indian Bay Leaf, is a well-known traditional ayurvedic medicine used to treat various ailments. However, the molecular mechanism of action of Cinnamomum tamala essential oil (CTEO) against non-small cell lung cancer (NSCLC) remains elusive. The present study aims to decipher the molecular targets and mechanism of CTEO in treating NSCLC. GC-MS analysis detected 49 constituents; 44 successfully passed the drug-likeness screening and were identified as active compounds. A total of 3961 CTEO targets and 4588 anti-NSCLC-related targets were acquired. JUN, P53, IL6, MAPK3, HIF1A, and CASP3 were determined as hub genes, while cinnamaldehyde, ethyl cinnamate and acetophenone were identified as core compounds. Enrichment analysis revealed that targets were mainly involved in apoptosis, TNF, IL17, pathways in cancer and MAPK signalling pathways. mRNA expression, pathological stage, survival analysis, immune infiltrate correlation and genetic alteration analysis of the core hub genes were carried out. Kaplan-Meier overall survival (OS) curve revealed that HIF1A and CASP3 are linked to worse overall survival in Lung Adenocarcinoma (LUAD) cancer patients compared to normal patients. Ethyl cinnamate and cinnamaldehyde showed high binding energy with the MAPK3 and formed stable interactions with MAPK3 during the molecular dynamic simulations for 100 ns. The MM/PBSA analysis revealed that van der Waals (VdW) contributions predominantly account for a significant portion of the compound interactions within the binding pocket of MAPK3. Density functional theory analysis showed cinnamaldehyde as the most reactive and least stable compound. CTEO exhibited selective cytotoxicity by inhibiting the proliferation of A549 cells while sparing normal HEK293 cells. CTEO triggered apoptosis by arresting the cell cycle, increasing ROS accumulation, causing mitochondrial depolarisation, and elevating caspase-3, caspase-8 and caspase-9 levels in A549 cells. The above study provides insights into the pharmacological mechanisms of action of Cinnamomum tamala essential oil against non-small cell lung cancer treatment, suggesting its potential as an adjuvant therapy.

Network pharmacology and molecular dynamic simulation integrated strategy for the screening of active components and mechanisms of phytochemicals from Datura innoxia on Alzheimer and cognitive decline

Alzheimer's disease (AD) ranks as the most prevalent neurodegenerative disorder with dementia and it accounts for more than 70% of all cases. Despite extensive reporting on the experimental investigation of Datura innoxia (DI) and its phytochemical components in the treatment of AD, the urgent need for elucidation of the principle of multi-mechanism and multi-level treatment of AD remains. In this research, molecular docking and network pharmacology were used to evaluate active compounds and molecular targets of DI for the treatment of AD. The phytochemical compounds of DI were obtained from the Indian Medicinal Plants, Phytochemistry, and Therapeutics (IMPPAT) as well as the Traditional Chinese Medicine System Pharmacology (TCMSP) databases. The screening includes the 28 most abundant components of DI and the Swiss Target Prediction database was used to predict targets of these compounds. The GeneCards database was used to collect AD-related genes. Both DI and AD targets were imported into a Venn diagram, and the 28 overlapped genes were identified as potential DI anti-AD targets. The results showed that Dinoxin B, Meteloidine, Scopoline, and Tropic acid had no effect on AD-related genes. Furthermore, the GO enrichment analysis indicates that DI influences molecular functions and biological processes such as learning or memory and modulation of chemical synaptic transmission as well as the membrane raft and membrane microdomain. The KEGG pathway analysis revealed that the key pathways implicated in DI's anti-AD actions include serotonergic synapse, IL-17 signaling pathway, and AGE-RAGE signaling pathway in diabetic complications. Based on the STRING and Cytoscape network-analysis platforms, the top ten anti-AD core targets include APP, CASP3, IL6, BACE1, IL1B, ACE, PSEN1, GAPDH, GSK3B and ACHE. The molecular docking and molecular dynamic simulation of the top two molecules against the top three target proteins confirmed the strong binding affinity and stability at the docked site. Overall, our findings pave the path for further research into the development and optimization of potential anti-AD agents from DI.Communicated by Ramaswamy H. Sarma.

Identification of novel inhibitors against VP40 protein of Marburg virus by integrating molecular modeling and dynamics approaches

Marburg virus (MV) is a highly etiological agent of haemorrhagic fever in humans and has spread across the world. Its outbreaks caused a 23-90% human death rate. However, there are currently no authorized preventive or curative measures yet. VP40 is the MV matrix protein, which builds protein shell underneath the viral envelope and confers hallmark filamentous. VP40 alone is able to induce assembly and budding of filamentous virus-like particles (VLPs), which resemble authentic virions. As a result, this research is credited with clarifying the function of VP40 and leading to the discovery of new therapeutic targets effective in combating MV disease (MVD). Virtual screening, molecular docking and molecular dynamics (MD) simulation were used to find the putative active chemicals based on a 3D pharmacophore model of the protein's active site cavity. Initially, andrographidine-C, a potent inhibitor was selected for the development of the pharmacophore model. Later, a library of 30,000 compounds along with the andrographidine-C was docked against VP40 protein. Three best hits including avanafil, diuvaretin and macrourone were subjected to further MD simulation analysis, as these compounds had better binding affinities as compared to andrographidine-C. Furthermore, throughout the 100 ns simulations, the back bone of VP40 protein in presence of avanafil, diuvaretin and macrourone remained stable which was further validated by MM-PBSA analysis. Additionally, all of these compounds depict maximum drug-like properties. The predicted drugs based on the ligand, avanafil, diuvaretin and macrourone could be exploited and developed as an alternative or complementary therapy for the treatment of MVD.Communicated by Ramaswamy H. Sarma.

Integrated virtual screening, molecular modeling and machine learning approaches revealed potential natural inhibitors for epilepsy

Epilepsy, a prevalent chronic disorder of the central nervous system, is typified by recurrent seizures. Present treatments predominantly offer symptomatic relief by managing seizures, yet fall short of influencing epileptogenesis. This study endeavored to identify novel phytochemicals with potential therapeutic efficacy against S100B, an influential protein in epileptogenesis, through an innovative application of machine learning-enabled virtual screening. Our study incorporated the use of multiple machine learning algorithms, including Support Vector Machine (SVM), k-Nearest Neighbors (kNN), Naive Bayes (NB), and Random Forest (RF). These algorithms were employed not only for virtual screening but also for essential feature extraction and selection, enhancing our ability to distinguish between active and inactive compounds. Among the tested machine learning algorithms, the RF model outshone the rest, delivering an impressive 93.43 % accuracy on both training and test datasets. This robust RF model was leveraged to sift through the library of 9,000 phytochemicals, culminating in the identification of 180 potential inhibitors of S100B. These 180 active compounds were than docked with the active site of S100B proteins. The results of our study highlighted that the 6-(3,12-dihydroxy-4,10,13-trimethyl-7,11-dioxo-2,3,4,5,6,12,14,15,16,17-decahydro-1H cyclopenta[a] phenanthren -17-yl)-2-methyl-3-methylideneheptanoic acid, rhinacanthin K, thiobinupharidine, scopadulcic acid, and maslinic acid form significant interactions within the binding pocket of S100B, resulting in stable complexes. This underscores their potential role as S100B antagonists, thereby presenting novel therapeutic possibilities for epilepsy management. To sum up, this study's deployment of machine learning in conjunction with virtual screening not only has the potential to unearth new epilepsy therapeutics but also underscores the transformative potential of these advanced computational techniques in streamlining and enhancing drug discovery processes.

Exploring the multi-gene regulatory molecular mechanism of Saudi Arabian flora against epilepsy based on data mining, network pharmacology and docking analysis

Epilepsy is a chronic neurological disorder marked by recurrent seizures, significantly affecting the population in Saudi Arabia across all age demographics. The global prevalence of active epilepsy is around 6.38/1,000 persons and in the Arabian region, the median prevalence of active epilepsy is 4.4/1,000 persons. However, over 75% of individuals are untreated. Consequently, the development of therapeutic strategies with increased efficacy and safety profiles is essential to improve the survival rate among epilepsy patients. The current study integrates network pharmacology along with Bioinformatics approaches to explore the potential molecular mechanisms of local flora of Saudi Arabia including Solanum incanum, Abrus precatorius, Withania somnifera, and Azadirachta indica in epilepsy treatment. In the preliminary phase, data related to the bioactive components of the local plants and the associated target genes of both these plants and epilepsy were gathered from scientific literature and open-source databases. This data was then analyzed to identify common targets between the plants and ovarian cancer. Based on these common targets, a protein-protein interaction (PPI) network was constructed utilizing the STRING database, which was subsequently incorporated into the Cytoscape software for identification of hub genes based on their degree of connectivity. Lastly, an interplay network depicting the associations between the compounds and the overlapping genes was formulated via Cytoscape, to study the potential network pharmacology implications of these active compounds in relation to ovarian cancer. Following that, a compound-target protein-pathway network was constructed which uncovered that namely abrectorin, genistin, (+)-catechin, precatorine, (+)-ascorbic acid, licoflavanone, skrofulein, stigmasterone, 5,7-Dihydroxy-4'-methoxy-8,3'-di-C-prenylflavanone could potentially be used as antagonists for the therapeutic management of epilepsy by targeting TNF and TP53 proteins. Furthermore, the implementation of molecular docking reinforces the binding affinity of the compound, indicating a robust stability of the forecasted compounds at the docked site. This research lays both a theoretical and experimental groundwork for more profound investigations and establishes a practical method for the strategic employment of active compounds in the development of anti-epileptic therapeutics.