Molecular docking and molecular dynamic simulations of apoptosis proteins with potential anticancer compounds present in Clinacanthus nutans extract using gas chromatography-mass spectrometry

Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski's rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound 211 exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of -8.95 kcal/mol, -8.60 kcal/mol, -10.33 kcal/mol, and -9.90 kcal/mol, respectively. During MD simulation, compound 211 and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.

Curcumin attenuates ulcerative colitis via regulation of Sphingosine kinases 1/NF-κB signaling pathway

Curcumin, a compound from Curcuma longa L., has significant anti-inflammatory properties. However, the mechanisms underlying its anti-inflammatory activity in dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) remain inadequately understood. This study aimed to further elucidate the molecular mechanisms of curcumin DSS-induced UC mice. Our data showed that curcumin alleviated DSS-induced colitis by reducing intestinal damage and inflammation, increasing goblet cells in colon tissues. Enzyme-linked immunosorbent assay revealed that curcumin reduced the expression of inflammatory cytokines (tumor necrosis factor-alpha, interleukin-1β, and interleukin-8) in serum and myeloperoxidase in colon tissues. A comprehensive analysis integrating network pharmacology and RNA sequencing (RNA-seq) revealed significant enrichment of the nuclear factor kappa B (NF-κB) signaling pathways. Notably, RNA-seq analysis demonstrated that curcumin significantly downregulated the mRNA expression of sphingosine kinase 1 (SphK1). Furthermore, molecular docking analysis showed that curcumin can bind to SphK1 and NF-κB. Additionally, curcumin was found to inhibit the activation of the SphK1/NF-κB signaling pathway in DSS-induced UC colon tissue. This study addresses pharmacologic and mechanistic perspectives of curcumin that ameliorates DSS-induced UC and inflammatory response.

In Vitro and In Silico Studies of the Biological Activities of Some Secondary Metabolites Belonging to Ficus sur Forssk (Moraceae): Towards Optimization of Wighteone Metabolite

Based on ethnomedicinal and chemotaxonomic records of Ficus plants, Ficus sur Forssk was studied in the search for bioactive compounds. Eleven known compounds including mixture α -amyrin acetate and β -amyrin acetate (1 and 2), lupeol (3), 3β-acetoxy-olean-12-en-11-one (4), lupenyl acetate (5), taraxastan-3,20-diol (6), 3'- (3-methylbut-2-enyl) biochanin A (7), derrone (8), quercetin (9), stigmasterol (10), and stigmasterol glycoside (11) were isolated from stem barks of Ficus sur Forssk. Their structures were obtained through analysis of spectroscopic data 1D and 2D NMR), mass spectrometry, and by comparison of these data with the literature. Nine isolated compounds (1-7, 10, 11) were tested as the active wighteone metabolite previously isolated from the roots of this plant against the human HepG2 hepatocellular carcinoma cells and a small panel of sensitive microbial strains for structure- activity relationship purpose. The compounds didn't show any activity. With the aim of understanding the impact of the structural difference between wighteone metabolite and its analogs, the former were cross-docked to evaluate their anticancer properties via the apoptosis pathway. Wighteone metabolite proved to be the best ligand confirming its previous bioassay result. Thus, the current study lays the framework for the further optimization of wighteone metabolite regarding its anticancer activity.

Tri-chalcone suppressed breast cancer cell proliferation and induced apoptosis through intrinsic and extrinsic pathways

Breast cancer development depends critically on antiproliferative and apoptotic mechanisms. However, the mechanisms underlying the antiproliferative and apoptosis effects of breast cancer treated with tri-chalcone remain unclear. Tri-chalcones have been demonstrated in prior studies to inhibit the proliferation of breast cancer cells (MCF-7). Following the discovery, this study seeks to investigate the effect of tri-chalcone compounds on targets involved in antiproliferative and apoptosis mechanisms. In this study, we employed bioinformatics analysis along with in vitro evaluation using tri-chalcone-treated MCF-7 cells to determine the responses of antiproliferative and apoptosis mechanisms. The analysis revealed that the compounds interact with six apoptosis target receptors: TNFα, Bak, Bcl-2, caspase-9, and caspase-8. Tri-chalcone S1-2 exhibited the strongest binding affinities for TNFα (-7.39 kcal/mol), caspase-8 (-8.43 kcal/mol), caspase-9 (-8.53 kcal/mol), Bcl-2 (-8.51 kcal/mol), and Bak (-7.15 kcal/mol). The tri-chalcone S1-2 paired with the corresponding proteins showed minor flexibility and extremely small changes of less than 0.25 nm during the MD simulation. Additionally, tri-chalcone S1-2 had a significant inhibitory effect on the proliferation of MCF-7 cells (5.31 ± 0.26 µg/mL) compared to other compounds. S1-2 also induced apoptosis, affecting nearly half (43.80%) of the total early and late apoptosis in MCF-7 cells. S1-2-treated MCF-7 cells also demonstrated upregulations of genes TNFα (1.50), Bak (1.42), caspase-8 (1.24), and caspase-9 (1.61), accompanied by a downregulation of gene Bcl-2 (0.71). The discovery gives us a better understanding of how tri-chalcone S1-2 suppressed MCF-7 cell proliferation and induced apoptosis through intrinsic and extrinsic pathways.

Antimicrobial potential of Hippocratea Indica Willd. Acetone Leaf fractions against Salmonella Typhi: an in vitro and in silico study

Salmonella Typhi is a major global concern in many low- and middle-income countries. In addition, the emergence and persistence of drug resistant strains has increased the impact of this disease. Plant metabolites have been explored traditionally and scientifically as antimicrobial agents. Thus, this study was designed to investigate the antimicrobial potential of acetone leaf fractions of H. indica against S. Typhi. Dried pulverized leaves of H. indica were extracted using cold maceration with acetone after defatting with n-hexane. The leaf extract was concentrated and subjected to column chromatography and eight bioactive fractions were identified. The fractions were characterized using gas chromatography-mass spectrometry. The fractions were evaluated for antibacterial activity against Salmonella Typhi in-vitro and in-silico. The lowest MIC was observed in fractions 20 and 21 (0.375 mg/mL) while the lowest MBC was observed in all fractions except 7, 17 and 18 (0.375 mg/mL). A ligand from fraction 8 had the highest binding affinity to Type I dehydroquinase (-3.4) and a ligand from fraction 7 had the highest binding affinity to Gyrase B (-11.2). This study concludes that the overall antimicrobial activity of the acetone leaf extract of H. indica provided evidence that it contains drug-like compounds that can be further explored as a drug candidate against S. Typhi.

Analysis of action of 1,4-naphthoquinone scaffold-derived compounds against acute myeloid leukemia based on network pharmacology, molecular docking and molecular dynamics simulation

1,4-Naphthoquinone scaffold-derived compounds has shown considerable pharmacological properties against cancer, including acute myeloid leukemia (AML) However, its impact and mechanisms in AML are uncertain. In this study, the mechanisms of 1,4-naphthoquinone scaffold-derived compounds against AML were investigated via network pharmacology, molecular docking and molecular dynamics simulation. ASINEX database was used to collect the 1,4-naphthoquinone scaffold-derived compounds, and compounds were extracted from the software to evaluate their drug similarity and toxicity. The potential targets of compounds were retrieved from the SwissTargetPrediction Database and the Similarity Ensemble Approach Database, while the potential targets of AML were obtained from the GeneCards databases and Gene Expression Omnibus. The STRING database was used to construct a protein-protein interaction (PPI) network, topologically and Cyto Hubb plugin of Cytoscape screen the central targets. After selecting the potential key targets, the gene ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the intersection targets, and a network map of "compounds-potential targets-pathway-disease" were constructed. Molecular docking of the compounds with the core target was performed, and core target with the strongest binding force and 1,4-naphthoquinone scaffold-derived compounds was selected for further molecular dynamics simulation and further molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) approach verification. In addition, the Bloodspot database was applied to perform the overall survival of core targets. A total of 19 1,4-naphthoquinone scaffold-derived compounds were chosen out, and then 836 targets of compounds, 96 intersection targets of AML were screened. Core targets include STAT3, TLR4, HSP90AA1, JUN, MMP9, PTPRC, JAK2, PTGS2, KIT and CSF1R. GO functional enrichment analysis revealed that 90 biological processes, 10 cell components and 12 molecular functions were enriched while KEGG pathway enrichment analysis revealed 34 enriched signaling pathways. Analysis of KEGG enrichment hinted that these 10 core genes were located in the pathways in cancer, suggesting that 1,4-naphthoquinone scaffold-derived compounds had potential activity against AML. Molecular docking analysis revealed that the binding energies between 1,4-naphthoquinone scaffold-derived compounds and the core proteins were all higher than - 6 kcal/mol, indicating that the 10 core targets all had strong binding ability with compounds. Moreover, a good binding capacity was inferred from molecular dynamics simulations between compound 7 and MMP9. The total binding free energy calculated using the MM/GBSA approach revealed values of - 6356.865 kcal/mol for the MMP9-7 complex. In addition, Bloodspot database results exhibited that HSP90AA1, MMP9 and PTPRC were associated with overall survival. The findings provide foundations for future studies into the interaction underlying the anti-AML potential of compounds with 1,4-naphthoquinone-based scaffold structures. Compounds with 1,4-naphthoquinone-based scaffold structures exhibits considerable potential in mitigating and treating AML through multiple targets and pathways.

Investigating the potential of mono-chalcone compounds in targeting breast cancer receptors through network pharmacology, molecular docking, molecular dynamics simulation, antiproliferative effects, and gene expressions

The study aims to investigate various aspects of synthesized mono-chalcone compounds 5 and 8 concerning breast cancer, including network pharmacology, molecular docking, molecular dynamics (MD) simulations, antiproliferative effects, and gene expressions. Initially, the compounds underwent a network pharmacology analysis targeting breast cancer-related targets, with MalaCards, SwissTargetPrediction, and PharmMapper identifying 70 breast cancer target receptors. Subsequently, protein-protein interaction (PPI) network analysis revealed two distinct target gene clusters. Survival analysis identified seven significant target genes following Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) evaluation. Molecular docking and MD simulations were conducted on these seven target genes (AKT2, BRAF, ESR1, FGFR1, IGF1, IGF1R, and KIT), revealing that compound 8 exhibited the highest binding affinities, as well as better stability and compactness when interacting with the targeted proteins. Next, the compounds underwent cell viability assay and gene expression analysis to validate the in silico findings. Both compounds demonstrated the ability to suppress breast cancer proliferation, with compound 8 showing increased selectivity in targeting breast cancer cells while causing minimal harm to normal breast cells. The suppression of breast cancer cell proliferation was attributed to decreased expression levels of AKT2, BRAF, FGFR1, IGF1, IGF1R, KIT, and ESR1. Hence, the results provide insights into the molecular interaction responsible for the anti-breast cancer capabilities of mono-chalcone compounds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03991-y.