# PD0325901 alleviates thrombin-inhibited osteogenic differentiation through an IL-1β-activated feedback loop between MEK-Erk1/2 and NF-κB signal pathways: insights from bioinformatics and experimental verification

**Authors:** Yang-Shuo Ge, Chun-Meng Huang, Jun Shen, Ting-Ting Meng, Min-Jun Zhao, Jian-Li Yin, Xin-Hui Huang, Liao-Lin Chen, Jia-Hui Luo, Yu-Qing Zhai, Jia-Wei Du, Yi-Lin Wang, Xue-Zong Wang, Ping-Ping Sun, Dao-Fang Ding

PMC · DOI: 10.3389/fimmu.2026.1730337 · Frontiers in Immunology · 2026-03-09

## TL;DR

This study shows that PD0325901 can reverse thrombin's negative effects on bone cell development by targeting an inflammatory signaling loop involving IL-1β, MEK-Erk1/2, and NF-κB.

## Contribution

The novel finding is that PD0325901 inhibits a feedback loop between MEK-Erk1/2 and NF-κB pathways mediated by IL-1β, which is crucial for thrombin-induced suppression of bone formation.

## Key findings

- Thrombin inhibits osteogenic differentiation by activating MEK-Erk1/2 and NF-κB pathways through IL-1β.
- PD0325901 reverses thrombin's effects by suppressing IL-1β-dependent signaling and restoring osteogenic markers.
- MMP-9 is identified as a key downstream gene in the IL-1β-mediated feedback loop.

## Abstract

To elucidate the molecular mechanisms underlying thrombin-induced suppression of osteoblast differentiation, and to identify the MEK inhibitor PD0325901 (PD03) as a potential therapeutic candidate.

Following treatment of primary rat osteoblasts with thrombin (20 U/mL) and PD03 (0.1 μM) during osteogenic induction, the cells were harvested and subjected to RNA sequencing to identify differentially expressed genes (DEGs). The combination of network pharmacology and RNA sequencing was used to predict the targets of PD03 in thrombin-induced osteoblasts. Alkaline phosphatase (ALP) activity was assessed through staining and quantitative analysis; the expression of osteogenic genes was measured by quantitative PCR (qPCR) and western blot; mineralized nodule formation was evaluated by Alizarin Red S staining; the expression of signaling pathway-related proteins (p-Erk1/2, p-Stat3, p-p65, MMP-9, COX-2) and proliferation-related proteins (PCNA and MCM2) were examined by western blot; nuclear localization of NF-κB was observed by immunofluorescence (IF); intracellular calcium levels were quantified using a calcium assay and probe labeling; osteoblast proliferation was evaluated by EdU staining; IL-1β secretion in cell supernatants was detected by ELISA; the expression of IL-1RA was measured by western blot; the effects of MMP-9 knockdown and COX-2 overexpression on osteogenic differentiation were investigated.

Thrombin promoted osteoblast proliferation and inhibited osteogenic differentiation by upregulating inflammatory factors and activating inflammatory signaling pathways, including MEK-Erk1/2 and NF-κB, which in turn reduced ALP activity, calcium ion influx, expression of osteogenic markers (e.g., Col1α1, Runx2, OCN), and mineralized nodule formation. PD03 reverses these effects by suppressing thrombin-induced activation of IL-1β-dependent signaling pathway, in which the downstream gene MMP-9 plays a critical role.

PD03 inhibits thrombin-induced activation of the IL-1β-mediated feedback loop between the MEK-Erk1/2 and NF-κB pathways, thereby restoring bone formation and offering a promising therapeutic approach for mitigating bone loss in patients with elevated thrombin levels.

## Linked entities

- **Genes:** COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277], RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860], BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632], MMP9 (matrix metallopeptidase 9) [NCBI Gene 4318], COX2 (cytochrome c oxidase subunit II) [NCBI Gene 4513], PCNA (proliferating cell nuclear antigen) [NCBI Gene 5111], MCM2 (minichromosome maintenance complex component 2) [NCBI Gene 4171], IL1B (interleukin 1 beta) [NCBI Gene 3553], IL1R1 (interleukin 1 receptor type 1) [NCBI Gene 3554], PERK12 (Protein kinase superfamily protein) [NCBI Gene 838963], Lcp1 (lymphocyte cytosolic protein 1) [NCBI Gene 18826]
- **Proteins:** MMP9 (matrix metallopeptidase 9), COX2 (cytochrome c oxidase subunit II), PCNA (proliferating cell nuclear antigen), MCM2 (minichromosome maintenance complex component 2), IL1B (interleukin 1 beta), IL1R1 (interleukin 1 receptor type 1), PERK12 (Protein kinase superfamily protein), Lcp1 (lymphocyte cytosolic protein 1)
- **Chemicals:** PD0325901 (PubChem CID 9826528)
- **Species:** Rattus norvegicus (taxon 10116)

## Full-text entities

- **Genes:** COX2 (cytochrome c oxidase subunit II) [NCBI Gene 4513] {aka COII, MTCO2}, ALPP (alkaline phosphatase, placental) [NCBI Gene 250] {aka ALP, PALP, PLAP, PLAP-1}, STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774] {aka ADMIO, ADMIO1, APRF, HIES}, RELA (RELA proto-oncogene, NF-kB subunit) [NCBI Gene 5970] {aka AIF3BL3, CMCU, NFKB3, p65}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, F2 (coagulation factor II, thrombin) [NCBI Gene 2147] {aka PT, RPRGL2, THPH1}, PCNA (proliferating cell nuclear antigen) [NCBI Gene 5111] {aka ATLD2}, RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860] {aka AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, MCM2 (minichromosome maintenance complex component 2) [NCBI Gene 4171] {aka BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN}, MMP9 (matrix metallopeptidase 9) [NCBI Gene 4318] {aka CLG4B, GELB, MANDP2, MMP-9}, MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, IL1RN (interleukin 1 receptor antagonist) [NCBI Gene 3557] {aka CRMO2, DIRA, ICIL-1RA, IL-1RN, IL-1ra, IL-1ra3}
- **Diseases:** bone loss (MESH:D001847), inflammatory (MESH:D007249)
- **Chemicals:** PD03 (MESH:C506614), calcium (MESH:D002118), Alizarin Red S (MESH:C004468)
- **Species:** Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116]

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13006212/full.md

## References

54 references — full list in the complete paper: https://tomesphere.com/paper/PMC13006212/full.md

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Source: https://tomesphere.com/paper/PMC13006212