Source 1primary paper2026MED
Toolkit/Maestro Schrodinger suite
Maestro Schrodinger suite
Also known as: Maestro Schrödinger suite
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Molecular docking and protein-ligand interaction analysis of the 27 phytochemicals with each of the 10 hub genes were performed using the Maestro Schrodinger suite.
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Objective: Elucidate molecular mechanisms underlying the therapeutic effects of Product Nkabinde phytochemicals in HIV treatment using network pharmacology and molecular docking.
Why it works: The workflow narrows from PN phytochemicals and HIV-related genes to intersecting genes, then to a PPI-derived hub-gene set, then to enriched pathways and docked phytochemical-target pairs, allowing computational prioritization of plausible anti-HIV mechanisms.
immune regulationmetabolic modulationinflammation-related pathwaysoxidative stress regulationapoptotic signallingtranscription regulationgene-set intersectionprotein-protein interaction network analysishub-gene prioritizationGO enrichment analysisKEGG enrichment analysismolecular dockingprotein-ligand interaction analysis
Stages
- 1.Intersect PN phytochemical targets with HIV-related genes(in_silico_filter)
This stage reduces the search space to genes shared between PN phytochemical associations and HIV, creating a focused target set for downstream network analysis.
Selection: common genes between the 27 PN phytochemicals and HIV were computed on a Venn diagram
- 2.PPI network construction and hub-gene prioritization(hit_picking)
This stage prioritizes a smaller set of hub genes from the intersecting gene network for functional interpretation and docking.
Selection: protein-protein interaction network of intersecting genes was plotted using STRING and hub genes were computed
- 3.Functional enrichment of hub genes(functional_characterization)
This stage assigns biological meaning to the prioritized hub genes before or alongside docking-based target interaction analysis.
Selection: GO and KEGG enrichment analysis using ShinyGO
- 4.Docking of PN phytochemicals against prioritized hub genes(secondary_characterization)
This stage evaluates which PN phytochemicals may interact strongly with prioritized HIV-relevant hub targets.
Selection: molecular docking and protein-ligand interaction analysis of 27 phytochemicals with each of the 10 hub genes using the Maestro Schrodinger suite
Steps
- 1.Compute common genes between PN phytochemicals and HIVformulation under analysis
Identify shared genes linking PN phytochemicals to HIV-related biology.
This first step defines the candidate target space before network and enrichment analyses.
- 2.Plot PPI network of intersecting genes using STRINGPPI analysis tool
Organize intersecting genes into an interaction network for hub-gene identification.
The network must be built after the intersecting genes are defined and before hub genes can be computed.
- 3.Compute 10 hub genes from the PPI network
Prioritize a smaller set of central genes for downstream enrichment and docking.
Hub-gene prioritization follows network construction and narrows the candidate set before more detailed interpretation.
- 4.Analyze hub genes for GO and KEGG enrichment using ShinyGOenrichment analysis tool
Interpret the biological processes and pathways represented by the prioritized hub genes.
Enrichment analysis is performed after hub-gene prioritization to assign functional meaning to the narrowed target set.
- 5.Perform molecular docking and protein-ligand interaction analysis of 27 phytochemicals against 10 hub genesphytochemical set and docking platform
Evaluate predicted binding interactions between PN phytochemicals and prioritized hub targets.
Docking is done after target prioritization so computational effort is focused on the most relevant hub genes.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Chemical
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Molecular docking identified several Product Nkabinde phytochemical-target complexes with reported binding energies, including rutin-HSP90AA1, catechin-JUN, quercetin-3-O-arabinoside-AKT1, rutin-EGFR, aloin-ESR1, and quercetin-3-0-β-D-(6'-galloyl)-glucopyranoside-BCL2.
Consequently, molecular docking unveils complexes with higher binding energies, such as rutin-HSP90AA1 (-10.578), catechin-JUN (-9.512), quercetin-3-O-arabinoside-AKT1 (-9.874), rutin-EGFR (-8.127), aloin-ESR1 (-8.585), and quercetin-3-0-β-D-(6'-galloyl)-glucopyranoside-BCL2 (-7.021 kcal/mol).
binding energy -10.578 kcal/molbinding energy -9.512 kcal/molbinding energy -9.874 kcal/molbinding energy -8.127 kcal/molbinding energy -8.585 kcal/molbinding energy -7.021 kcal/mol
GO analysis suggested that Product Nkabinde is associated with transcription regulation, miRNA-related processes, responses to hormones and endogenous stimuli, oxidative stress regulation, apoptotic signalling, kinase binding, protein kinase binding, transcription factor binding, and ubiquitin ligase binding pathways.
GO analysis further reveals that PN plays key roles in transcription regulation, such as miRNA, responses to hormones and endogenous stimuli, oxidative stress regulation, and apoptotic signalling, kinase binding, protein kinase binding, transcription factor binding, and ubiquitin ligase binding enriched pathways.
The study concludes that the results reveal pathways associated with HIV pathology and possible anti-HIV mechanisms of Product Nkabinde.
Overall, the results reveal pathways associated with HIV pathology and possible anti-HIV mechanisms of PN.
Pathway enrichment analysis indicated that the 10 hub genes regulated by Product Nkabinde are associated with immune regulation, metabolic modulation, viral comorbidity, carcinogenesis, and inflammation.
The pathway enrichments reveal that the 10 hub genes regulated by PN focus on immune regulation, metabolic modulation, viral comorbidity, carcinogenesis, and inflammation.
The study aimed to elucidate molecular mechanisms underlying the therapeutic effects of Product Nkabinde phytochemicals in HIV treatment using network pharmacology and molecular docking.
This study aims to elucidate the molecular mechanisms underlying the therapeutic effects of phytochemicals identified from PN in HIV treatment, utilizing network pharmacology and molecular docking.
Approval Evidence
1 source1 linked approval claimfirst-pass slug maestro-schrodinger-suite
Molecular docking and protein-ligand interaction analysis of the 27 phytochemicals with each of the 10 hub genes were performed using the Maestro Schrodinger suite.
Source:
docking resultsupports
Molecular docking identified several Product Nkabinde phytochemical-target complexes with reported binding energies, including rutin-HSP90AA1, catechin-JUN, quercetin-3-O-arabinoside-AKT1, rutin-EGFR, aloin-ESR1, and quercetin-3-0-β-D-(6'-galloyl)-glucopyranoside-BCL2.
Consequently, molecular docking unveils complexes with higher binding energies, such as rutin-HSP90AA1 (-10.578), catechin-JUN (-9.512), quercetin-3-O-arabinoside-AKT1 (-9.874), rutin-EGFR (-8.127), aloin-ESR1 (-8.585), and quercetin-3-0-β-D-(6'-galloyl)-glucopyranoside-BCL2 (-7.021 kcal/mol).
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.