CADD522 is a small molecule that inhibits the DNA binding of RUNX2. It negatively regulated transcription of RUNX2 target genes such as matrix metalloproteinase-13, vascular endothelial growth factor and glucose transporter-1, but upregulated RUNX2 expression by increasing RUNX2 stability. CADD522 may represent a potential antitumor drug.

Muramyl dipeptide, a synthetic immunoreactive peptide, is an inducer of bone formation through induction of Runx2. Muramyl dipeptide directly enhances osteoblast differentiation by up-regulating Runx2 gene expression through MAPK pathways. Muramyl dipeptide indirectly attenuates osteoclast differentiation through a decreased RANKL/OPG ratio.

AI-10-47是一种小分子抑制剂，能够干扰 CBFβ 与 RUNX 蛋白的结合，IC₅₀ 值为 3.2 μM。通过抑制这种结合，AI-10-47 可阻止 RUNX 驱动的癌症，如急性髓性白血病 (AML) 中的细胞增殖。