Integrating Network Pharmacology, Brain Spatial Transcriptomics, In Silico Target Perturbation, and Virtual Screening Reveals Multi-Target Mechanisms of Baihe Dihuang Decoction in Sleep Disorders
Author: Y. X. Yang
Affiliation: Department of Anesthesiology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
This repository contains the complete computational pipeline, processed data, and manuscript for a five-layer integrative framework investigating the multi-target mechanisms of Baihe Dihuang Decoction (BHD) in sleep disorders.
- Network Pharmacology — STRING PPI network construction, GO/KEGG enrichment analysis
- Brain Spatial Transcriptomics — Allen Human Brain Atlas mapping across 104 sleep-relevant brain regions
- In Silico Target Perturbation — Single-target and cascade virtual knockout on real PPI network
- Virtual Screening — AutoDock Vina molecular docking (54 runs) against MAPK1 & AKT1
- Molecular Dynamics Simulation — OpenMM GPU-accelerated MD (128 ns) with MM-GBSA binding free energy
- 45 intersection targets between BHD compounds and sleep disorder genes
- PTGS2 (COX-2) and IL1B identified as most vulnerable network nodes
- Agomelatine predicted as a potential drug repurposing candidate
- Spatial transcriptomics reveals sleep-region-specific expression patterns
- Three-cellular-niche model integrating spatial, network, and pharmacological evidence
. ├── paper/ # Manuscript & publication materials │ ├── main.tex # LaTeX source │ ├── main.docx # Word manuscript │ ├── main_frontiers.pdf # Compiled PDF │ ├── Figure1-8_*.png # Main figures (8) │ ├── Graphical_Abstract.png # Graphical abstract │ ├── cover_letter_*.md # Cover letters │ └── supplementary/ # Supplementary materials (36 files) │ ├── TableS1-S11_*.csv # Supplementary tables │ ├── FigS1-S8_*.png # Supplementary figures │ └── README.md # Supplementary documentation ├── scripts/ # Analysis scripts ├── data/ # Processed & intermediate data └── README.md
All processed data are provided in the paper/supplementary/ directory. Raw data sources are publicly accessible:
| Source | URL |
|---|---|
| TCMSP | https://tcmspw.com |
| STRING Database | https://string-db.org |
| Allen Human Brain Atlas | https://human.brain-map.org |
| Protein Data Bank | https://www.rcsb.org (4QTB, 4GV1) |
| ADMETlab 2.0 | https://admetmesh.scbdd.com |
| Human Protein Atlas | https://www.proteinatlas.org |
| GeneCards | https://www.genecards.org |
| DisGeNET | https://www.disgenet.org |
| OMIM | https://www.omim.org |
- Network Analysis: NetworkX v3.2, Cytoscape v3.10
- Docking: AutoDock Vina 1.2.5, Meeko
- MD Simulation: OpenMM 8.5.2, AMBER14SB (protein), GAFF2 (ligand), NVIDIA RTX 3090
- MM-GBSA: GB^OBC implicit solvent model
- Statistics: Python 3.x (NumPy, SciPy, pandas, statsmodels)
- Visualization: Matplotlib, Seaborn
All tools are open-source or freely available for academic use.
If you use this work in your research, please cite:
�ibtex @article{yang2025bhd, title={Integrating Network Pharmacology, Brain Spatial Transcriptomics, In Silico Target Perturbation, and Virtual Screening Reveals Multi-Target Mechanisms of Baihe Dihuang Decoction in Sleep Disorders}, author={Yang, Y. X.}, journal={Journal of Biomolecular Structure and Dynamics}, year={2025}, note={Under review} }
This project is licensed under the MIT License — see the LICENSE file for details.
AI-assisted tools (Claude Code, Anthropic) were used for computational workflow orchestration, code development, and manuscript formatting. The author assumes full responsibility for all content.