| Literature DB >> 36046748 |
Xiaofeng Yin1, Jinchuan Li1, Zheng Hao1, Rui Ding1, Yanan Qiao2.
Abstract
Hepatocellular carcinoma (HCC) is a serious global health problem, and hepatitis B virus (HBV) infection remains the leading cause of HCC. It is standard care to administer antiviral treatment for HBV-related HCC patients with concurrent anti-cancer therapy. However, a drug with repressive effects on both HBV infection and HCC has not been discovered yet. In addition, drug resistance and side effects have made existing therapeutic regimens suboptimal. Traditional Chinese medicine (TCM) has multi-ingredient and multi-target advantages in dealing with multifactorial HBV infection and HCC. TCM has long been served as a valuable source and inspiration for discovering new drugs. In present study, a target-driven reverse network pharmacology was applied for the first time to systematically study the therapeutic potential of TCM in treating HBV-related HCC. Firstly, 47 shared targets between HBV and HCC were screened as HBV-related HCC targets. Next, starting from 47 targets, the relevant chemical components and herbs were matched. A network containing 47 targets, 913 chemical components and 469 herbs was established. Then, the validated results showed that almost 80% of the herbs listed in chronic hepatitis B guidelines and primary liver cancer guidelines were included in the 469 herbs. Furthermore, functional analysis was conducted to understand the biological processes and pathways regulated by these 47 targets. The docking results indicated that the top 50 chemical components bound well to targets. Finally, the frequency statistical analysis results showed the 469 herbs against HBV-related HCC were mainly warm in property, bitter in taste, and distributed to the liver meridians. Taken together, a small library of 913 chemical components and 469 herbs against HBV-related HCC were obtained with a target-driven approach, thus paving the way for the development of therapeutic modalities to treat HBV-related HCC.Entities:
Keywords: a systematic study; hepatitis B virus-related hepatocellular carcinoma; reverse network pharmacology; target-driven; traditional Chinese medicine
Mesh:
Year: 2022 PMID: 36046748 PMCID: PMC9420877 DOI: 10.3389/fcimb.2022.964469
Source DB: PubMed Journal: Front Cell Infect Microbiol ISSN: 2235-2988 Impact factor: 6.073
Figure 1Workflow of this study.
The PDB IDs for 46 targets.
| Gene symbol | PDB ID | Gene symbol | PDB ID | Gene symbol | PDB ID |
|---|---|---|---|---|---|
| AR | 4OHA | JUN | 6Y3V | CTNNB1 | 3FQN |
| ESR1 | 7BAA | CASP8 | 4JJ7 | ERBB2 | 5MY6 |
| RXRA | 6LB4 | FOS | 1S9K | NFKB1 | 7LFC |
| MAPK14 | 3LFF | IL2 | 5LQB | PPARA | 6KAX |
| RELA | 6NV2 | HIF1A | 4H6J | TGFB1 | 6OM2 |
| CASP3 | 4QUJ | EGFR | 5UG9 | EGF | 1NQL |
| TNF | 5UUI | STAT3 | 6NJS | ITGB3 | 3T3P |
| TP53 | 3D06 | STAT1 | 3wwt | SMAD3 | 5OD6 |
| AKT1 | 4GV1 | CREB1 | 5ZK1 | CDKN1B | 6ATH |
| IL6 | 1ALU | RB1 | 2R7G | CXCL12 | 4UAI |
| VEGFA | 4GLS | MYC | 6G6K | EP300 | 3BIY |
| IL1B | 5R8Q | PTEN | 7PC7 | ITGB1 | 4WK0 |
| MAPK1 | 4ZZN | HSP90AA1 | 5J2X | KRAS | 6P0Z |
| IL4 | 4YDY | MAPK3 | 4QTB | RHOA | 6V6U |
| NFKBIA | 6Y1J | MAPK8 | 2XRW | – | – |
| CCND1 | 2W96 | PTK2 | 6YOJ | – | – |
Figure 2Procedure of searching and screening for HBV-associated HCC targets, which were derived by taking the intersection of HBV targets and HCC targets. Protein-protein interactions amongst the 47 targets were in the dashed box section.
Forty-seven HBV-associated HCC targets .
| Gene symbol | Uniprot ID | Protein name |
|---|---|---|
| AR | P10275 | Androgen receptor |
| ESR1 | P03372 | Estrogen receptor |
| RXRA | P19793 | Retinoic acid receptor RXR-alpha |
| MAPK14 | Q16539 | Mitogen-activated protein kinase 14 |
| RELA | Q04206 | Transcription factor p65 |
| CASP3 | P42574 | Caspase-3 |
| TNF | P01375 | Tumor necrosis factor |
| TP53 | P04637 | Cellular tumor antigen p53 |
| AKT1 | P31749 | RAC-alpha serine/threonine-protein kinase |
| IL6 | P05231 | Interleukin-6 |
| VEGFA | P15692 | Vascular endothelial growth factor A |
| IL1B | P01584 | Interleukin-1 beta |
| MAPK1 | P28482 | Mitogen-activated protein kinase 1 |
| IL4 | P05112 | Interleukin-4 |
| NFKBIA | P25963 | NF-kappa-B inhibitor alpha |
| CCND1 | P24385 | G1/S-specific cyclin-D1 |
| JUN | P05412 | Transcription factor AP-1 |
| CASP8 | Q14790 | Caspase-8 |
| FOS | P01100 | Proto-oncogene c-Fos |
| IL2 | P60568 | Interleukin-2 |
| HIF1A | Q16665 | Hypoxia-inducible factor 1-alpha |
| EGFR | P00533 | Epidermal growth factor receptor |
| STAT3 | P40763 | Signal transducer and activator of transcription 3 |
| STAT1 | P42224 | Signal transducer and activator of transcription 1-alpha/beta |
| CREB1 | P16220 | Cyclic AMP-responsive element-binding protein 1 |
| RB1 | P06400 | Retinoblastoma-associated protein |
| MYC | P01106 | Myc proto-oncogene protein |
| PTEN | P60484 | Phosphatidylinositol 3 |
| CAV1 | Q03135 | Caveolin-1 |
| HSP90AA1 | P07900 | Heat shock protein HSP 90-alpha |
| MAPK3 | P27361 | Mitogen-activated protein kinase 3 |
| MAPK8 | P45983 | Mitogen-activated protein kinase 8 |
| PTK2 | Q05397 | Focal adhesion kinase 1 |
| CTNNB1 | P35222 | Catenin beta-1 |
| ERBB2 | P04626 | Receptor tyrosine-protein kinase erbB-2 |
| NFKB1 | P19838 | Nuclear factor NF-kappa-B p105 subunit |
| PPARA | Q07869 | Peroxisome proliferator-activated receptor alpha |
| TGFB1 | P01137 | Transforming growth factor beta-1 proprotein |
| EGF | P01133 | Pro-epidermal growth factor |
| ITGB3 | P05106 | Integrin beta-3 |
| SMAD3 | P84022 | Mothers against decapentaplegic homolog 3 |
| CDKN1B | P46527 | Cyclin-dependent kinase inhibitor 1B |
| CXCL12 | P48061 | Stromal cell-derived factor 1 |
| EP300 | Q09472 | Histone acetyltransferase p300 |
| ITGB1 | P05556 | Integrin beta-1 |
| KRAS | P01116 | GTPase KRas |
| RHOA | P61586 | Transforming protein RhoA |
The targets are sorted in decreasing order of degree value.
Figure 3The 47 HBV-associated HCC targets-913 chemical components network. Orange nodes represented the targets, while green nodes represented chemical components. The edges indicated the interaction between targets and chemical components.
Figure 4The 47 targets-913 chemical components-469 herbs network. Orange, green, and blue nodes represented the targets, chemical components, and herbs, respectively.
Figure 5The functional enrichment analysis of 47 targets. (A) The top 20 KEGG pathways by p value. The bubble size indicated the number of targets clustered, and the color indicated the p value of the enrichment analysis. (B) The GO terms were sorted according to p value, with the most significantly enriched terms at the top. BP, biological processes. MF, molecular functions. The length of each bar indicated the number of targets clustered, and the color indicated the p value of the enrichment analysis.
Figure 6The binding scores between 46 targets (x axis) and the top 50 chemical components ranked by node degree value (y axis). Colors indicated different scores. (red, higher than 4.0; blue, less than 4.0).
Figure 7The hydrogen bonding plots of (A) AKT1-hesperidin, (B) CXCL12-hesperidi, and (C) AKT1-rutin. All ligands were depicted in a capped stick representation, while the interacting residues were shown as lines. The hydrogen bonds were yellow dashed lines.
Figure 8(A) Properties, (B) tastes, and (C) meridian tropism of herbs against HBV-associated HCC.