HDAC-IN-98 is a HDAC1, HDAC2, HDAC3 inhibitor (one of the most selective class I HDAC inhibitors) with human IC50 values of 41.2 nM, 52.5 nM, and 74.3 nM respectively. HDAC-IN-98 induces H3K9 acetylation, p21 upregulation, G2/M arrest, cell apoptosis, has strong antiproliferative effects in colorectal cancer cells, low toxicity in healthy colon epithelium, modulates short-term in vitro effects via autophagy, and shows strong antitumor efficacy in vivo in the chorioallantoic membrane model (CAM) assay. HDAC-IN-98 can be used for the research of colorectal cancer [1].
In Vitro, HDAC-IN-98 (compound 5d) selectively inhibits class I HDAC enzymes (HDAC1, HDAC2, HDAC3) with sub-nanomolar to low-nanomolar IC50 values and weak or no activity against other HDAC isoforms (IC50: HDAC1 = 41.2 nM, HDAC2 = 52.5 nM, HDAC3 = 74.3 nM, HDAC10 = 4261 nM, HDAC5/8/11 >10000 nM)[1]. HDAC-IN-98 (1 μM; up to 60 min) inhibits total HDAC activity in a complex nuclear extract system[1]. HDAC-IN-98 (0.1-100 μM; 48 h) selectively reduces viability of CRC cells with IC50 values ranging from 14 μM and minimal toxicity to normal colon cells (IC50: HCT116 = 1 μM, HT29 = 4 μM, DLD1 = 4 μM, HCEC >100 μM)[1]. HDAC-IN-98 (1-4 μM; 48 h) modulates epigenetic markers (H3K9 acetylation) and apoptotic pathways (PARP cleavage) in CRC cells without inhibiting class II HDACs[1]. HDAC-IN-98 (1-4 μM; 48 h) disrupts cell cycle progression, inducing subG1 accumulation (apoptosis) in HCT116 and G1 arrest in HT29/DLD1 cells[1]. HDAC-IN-98 (1-4 μM; 48 h) triggers apoptosis selectively in HCT116 cells without inducing necrosis[1]. HDAC-IN-98 (up to 10 μM) shows minimal hERG liability at concentrations relevant to its anticancer activity[1]. HDAC-IN-98 (1 μM; in vitro pretreatment; 48 h) exhibits potent antitumor efficacy in chicken embryos with colorectal cancer chorioallantoic membrane model (CAM) models independent of p21 status. In the HCT116 p21 wildtype CAM model, HDAC-IN-98 confirmes a robust upregulation of p21. In the HCT116 p21−/− CAM model, HDAC-IN-98 significantly reduces the vessel area, the vessel length, and the number of branching points whereas the vessel thickness is not affected[1].
References:
[1]. Carullo G, et al. Targeting Class I Histone Deacetylases Triggers Antitumor Responses in Colorectal Cancer In Vitro and In Vivo. J Med Chem. 2026;69(2):1049-1074.
In Vitro, HDAC-IN-98 (compound 5d) selectively inhibits class I HDAC enzymes (HDAC1, HDAC2, HDAC3) with sub-nanomolar to low-nanomolar IC50 values and weak or no activity against other HDAC isoforms (IC50: HDAC1 = 41.2 nM, HDAC2 = 52.5 nM, HDAC3 = 74.3 nM, HDAC10 = 4261 nM, HDAC5/8/11 >10000 nM)[1]. HDAC-IN-98 (1 μM; up to 60 min) inhibits total HDAC activity in a complex nuclear extract system[1]. HDAC-IN-98 (0.1-100 μM; 48 h) selectively reduces viability of CRC cells with IC50 values ranging from 14 μM and minimal toxicity to normal colon cells (IC50: HCT116 = 1 μM, HT29 = 4 μM, DLD1 = 4 μM, HCEC >100 μM)[1]. HDAC-IN-98 (1-4 μM; 48 h) modulates epigenetic markers (H3K9 acetylation) and apoptotic pathways (PARP cleavage) in CRC cells without inhibiting class II HDACs[1]. HDAC-IN-98 (1-4 μM; 48 h) disrupts cell cycle progression, inducing subG1 accumulation (apoptosis) in HCT116 and G1 arrest in HT29/DLD1 cells[1]. HDAC-IN-98 (1-4 μM; 48 h) triggers apoptosis selectively in HCT116 cells without inducing necrosis[1]. HDAC-IN-98 (up to 10 μM) shows minimal hERG liability at concentrations relevant to its anticancer activity[1]. HDAC-IN-98 (1 μM; in vitro pretreatment; 48 h) exhibits potent antitumor efficacy in chicken embryos with colorectal cancer chorioallantoic membrane model (CAM) models independent of p21 status. In the HCT116 p21 wildtype CAM model, HDAC-IN-98 confirmes a robust upregulation of p21. In the HCT116 p21−/− CAM model, HDAC-IN-98 significantly reduces the vessel area, the vessel length, and the number of branching points whereas the vessel thickness is not affected[1].
References:
[1]. Carullo G, et al. Targeting Class I Histone Deacetylases Triggers Antitumor Responses in Colorectal Cancer In Vitro and In Vivo. J Med Chem. 2026;69(2):1049-1074.