Comprehensive Bioinformatics Analysis Combined with Wet-Lab Experiments to Find Target Proteins of Chinese Medicine Monomer.
Xiaohui XuYun-Yi ZhuChangling YueQianwen YangZhaohuan ZhangPublished in: Molecules (Basel, Switzerland) (2022)
How to use bioinformatics methods to quickly and accurately locate the effective targets of traditional Chinese medicine monomer (TCM) is still an urgent problem needing to be solved. Here, we used high-throughput sequencing to identify the genes that were up-regulated after cells were treated with TCM monomers and used bioinformatics methods to analyze which transcription factors activated these genes. Then, the binding proteins of these transcription factors were analyzed and cross-analyzed with the docking proteins predicted by small molecule reverse docking software to quickly and accurately determine the monomer's targets. Followeding this method, we predicted that the TCM monomer Daphnoretin (DT) directly binds to JAK2 with a binding energy of -5.43 kcal/mol, and activates the JAK2/STAT3 signaling transduction pathway. Subsequent Western blotting and in vitro binding and kinase experiments further validated our bioinformatics predictions. Our method provides a new approach for quickly and accurately locating the effective targets of TCM monomers, and we also have discovered for the first time that TCM monomer DT is an agonist of JAK2.
Keyphrases
- bioinformatics analysis
- transcription factor
- molecularly imprinted
- small molecule
- protein protein
- genome wide identification
- dna binding
- high throughput sequencing
- molecular dynamics
- molecular dynamics simulations
- induced apoptosis
- genome wide
- solid phase extraction
- cell cycle arrest
- gene expression
- tyrosine kinase
- cell proliferation
- endoplasmic reticulum stress
- high resolution
- signaling pathway
- cell death
- oxidative stress
- protein kinase