Computational pharmacology profiling of borapetoside C against melanoma

Investigation of alpha amylase inhibitors from Bidens pilosa L. by in silico and in vitro studies

Bidens pilosa L. has been traditionally used as an anti-diabetic herbal medicine; however, its mechanism of action remains elusive. In this study, the potential role of B. pilosa compounds on alpha-amylase inhibition and regulation of multiple pathways was investigated via computational and experimental studies. The phytocompounds were retrieved from plant databases and published literature. The druggability profile of these compounds was predicted using MolSoft. The probable targets of these phytocompounds were predicted using BindingDB (similarity index ≥ 0.7). Further, compound-gene set-pathway and functional enrichment analysis were performed using STRING and KEGG pathway databases. The network between compound-protein-pathway was constructed using Cytoscape. Molecular docking was performed using AutoDock Vina, executed through the POAP pipeline. The stability of the best docked complex was subjected to all-atom molecular dynamics (MD) simulation for 100 ns to investigate their structural stabilities and intermolecular interactions using GROMACS software. Finally, B. pilosa hydroalcoholic extract was subjected to LC-MS and tested for dose- and time-dependent alpha-amylase inhibitory activity. Out of 31 bioactive compounds, 13 were predicted to modulate the human pancreatic alpha-amylase (AMY2A) and 12 pathways associated with diabetes mellitus. PI3K-Akt signaling pathway (hsa04151) scored the lowest false discovery rate by triggering 15 genes. Further intermolecular interaction analysis of the docked complex revealed that Brassidin had the highest active site interaction and lowest binding energy compared to standard acarbose, and MD reveals the formation of a stable complex throughout 100 ns production run. LC-MS analysis revealed the presence of 13 compounds (targeting AMY2A) in B. pilosa hydroalcoholic extract, which showed potent AMY2A inhibition by in vitro studies that corroborate in silico findings for its anti-diabetic activity. Based on these findings, enriched fractions/pure compounds inhibitory activity that can be performed in future for drug discovery.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00187-9.

Synergistic effects of Momordica charantia, Nigella sativa, and Anethum graveolens on metabolic syndrome targets: In vitro enzyme inhibition and in silico analyses

Momordica charantia, Nigella sativa, and Anethum graveolens are established medicinal plants possessing noted anti-diabetic and anti-obesity properties. However, the molecular mechanisms underscoring their inhibitory effects on pancreatic lipase, α-glucosidase, and HMG-CoA reductase remain unexplored. This study aimed to elucidate the efficacy of various NS, MC, and AG blends in modulating the enzymatic activity of pancreatic lipase, HMG-CoA reductase, and a-glucosidase, utilizing an integrative approach combining in vitro assessments and molecular modeling techniques. A factorial design matrix generated eight distinct concentration combinations of NS, MC, and AG, subsequently subjected to in vitro enzyme inhibition assays. Molecular docking analyses using AutoDock Vina, molecular dynamics simulations, MMPBSA calculations, and principal component analysis, were executed with Gromacs to discern the interaction dynamics between the compounds and target enzymes. A formulation comprising NS:MC:AG at a 215:50:35 μg/mL ratio yielded significant inhibition of pancreatic lipase (IC50: 74.26 ± 4.27 μg/mL). Moreover, a concentration combination of 215:80:35 μg/mL effectively inhibited both α-glucosidase (IC50: 66.09 ± 3.98 μg/mL) and HMGCR (IC50: 129.03 μg/mL). Notably, MC-derived compounds exhibited superior binding affinity towards all three enzymes, compared to their reference molecules, with diosgenin, Momordicoside I, and diosgenin displaying binding affinities of -11.0, -8.8, and -7.9 kcal/mol with active site residues of pancreatic lipase, α-glucosidase, and HMGCR, respectively. Further, 100 ns molecular dynamics simulations revealed the formation and stabilization of non-bonded interactions between the compounds and the enzymes' active site residues. Through a synergistic application of in vitro and molecular modeling methodologies, this study substantiated the potent inhibitory activity of the NS:MC:AG blend (at a ratio of 215:80:35 μg/mL) and specific MC compounds against pancreatic lipase, α-glucosidase, and HMGCR. These findings provide invaluable insights into the molecular underpinnings of these medicinal plants' anti-diabetic and anti-obesity effects and may guide future therapeutic development.

Integration of network pharmacology, molecular docking, and simulations to evaluate phytochemicals from Drymaria cordata against cervical cancer

Introduction: Cervical cancer is prevalent among women worldwide. It is a type of cancer that occurs in the cells of the cervix, the lower part of the uterus. Mostly, it is observed in developing nations due to limited access to screening tools. Natural products with anticancer properties and fewer side effects have gained attention. Therefore, this study evaluates the potential of Drymaria cordata as a natural source for treating cervical cancer. Methodology: Phytocompounds present in Drymaria cordata were screened for their molecular properties and drug-likeness. The selected compounds were studied using systems biology tools such as network pharmacology, molecular docking, and molecular dynamics simulations, including MMGBSA studies. Results: Through network pharmacology, molecular docking, and molecular dynamics simulations, quercetin 3-O-β-d-glucopyranosyl-(1→2)-rhamnopyranoside was identified as a hit compound targeting HRAS and VEGFA proteins. These proteins were found to be responsible for the maximum number of pathway modulations in cervical cancer. Conclusion: Drymaria cordata exhibits potential for treating cervical cancer due to the presence of quercetin 3-O-β-d-glucopyranosyl-(1→2)-rhamnopyranoside. Further validation of these findings through in vitro and in vivo studies is required.

The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology

Delta-9-tetrahydrocannabinol, a component of marijuana, interacts with cannabinoid receptors in brain involved in memory, cognition, and emotional control. However, marijuana use and schizophrenia development is a complicated and contentious topic. As a result, more investigation is needed to understand this relationship. Through the functional enrichment analysis, we report the delta-9-tetrahydrocannabinol to manipulate the homeostatic biological process and molecular function of different macromolecules. Additionally, using molecular docking and subsequent processing for molecular simulations, we assessed the binding ability of delta-9-tetrahydrocannabinol with the estrogen-related protein, dopamine receptor 5, and hyaluronidase. It was found that delta-9-tetrahydrocannabinol may have an impact on the brain's endocannabinoid system and may trigger the schizophrenia progression in vulnerable people. Delta-9-tetrahydrocannabinol may interfere with the biological function of 18 proteins linked to schizophrenia and disrupt the synaptic transmission (dopamine, glutamine, and gamma-aminobutyric acid). It was discovered that it may affect lipid homeostasis, which is closely related to membrane integrity and synaptic plasticity. The negative control of cellular and metabolic processes, fatty acids binding /activity, and the manipulated endocannabinoid system (targeting cannabinoid receptors) were also concerned with delta-9-tetrahydrocannabinol. Hence, this may alter neurotransmitter signaling involved in memory, cognition, and emotional control, showing its direct impact on brain physiological processes. This may be one of the risk factors for schizophrenia development which is also closely tied to some other variables such as frequency, genetic vulnerability, dosage, and individual susceptibility.