A collaborative research team led by the Guangzhou Institutes of Biomedicine and Health (GIBH) of the Chinese Academy of Sciences (CAS), in partnership with Johns Hopkins University and the Hangzhou Institute for Advanced Study, has introduced a new class of DNA methyltransferase 1 (DNMT1) inhibitors featuring a 7-azaindole core scaffold. Among these compounds, DMI46 demonstrated potent therapeutic activity in models of hypomethylating agent (HMA)-resistant acute myeloid leukemia (AML), highlighting its potential as a candidate therapy for refractory AML.

The study was recently published in Proceedings of the National Academy of Sciences (PNAS).

Promoter DNA hypermethylation, a hallmark of human cancer, can silence key tumor suppressor genes (TSGs) and serves as a major epigenetic driver of tumor initiation and progression. Reversing aberrant DNA methylation to restore TSG expression through DNMT1 inhibition has emerged as an important therapeutic strategy.

Currently, the nucleoside HMAs decitabine and azacitidine are approved as frontline therapies for hematologic malignancies such as AML. However, these agents must be incorporated into DNA to form DNMT1-DNA adducts—highly cytotoxic DNA lesions that cause dose-limiting toxicities and limit the clinical benefit of first-generation HMAs. Overall response rates remain at approximately 40%, and most initial responders develop drug resistance and experience relapse within two years. There is therefore an urgent need for DNMT1 inhibitors (DNMT1i) with improved safety profiles and the ability to overcome resistance to nucleoside HMAs.

The team previously reported that conformational transitions of the DNMT1 catalytic domain between open and closed states are essential for methyltransferase activity, suggesting the feasibility of developing non-nucleoside DNMT1i that block these transitions.

In this study, the researchers combined structure-guided scaffold hopping with chemical optimization to target this conformational regulatory region. Using their sensitive cell-based screening platform for HMAs, they identified a series of DNMT1i with a bicyclic 7-azaindole scaffold. Among these, DMI46 effectively reversed cancer-specific DNA hypermethylation, reactivated numerous epigenetically silenced TSGs, and exhibited strong anti-AML activity. Unlike decitabine, DMI46 induces minimal DNA damage and exhibits an improved safety profile with a wider therapeutic window.

Furthermore, cryoelectron microscopy (cryo-EM) analyses revealed that the 7-azaindole scaffold not only forms key contacts with DNMT1 but also intercalates into DNA through enhanced π-π stacking, thereby anchoring the compound within the DNMT1-DNA complex. This configuration enables the extension of the phenyl substituents toward the catalytic loop and DNA-recognition helix, locking DNMT1 in an open, inactive conformation and preventing its conformational transitions. These structural features underpin the sustained on-target DNMT1 inhibition and robust antiproliferative activity of DMI46 in AML models resistant to either non-nucleoside or nucleoside HMAs.

Beyond its effects on tumor cells, pharmacologic modulation of DNA methylation can also influence immune and hematopoietic cells, indicating broader translational potential for 7-azaindole-based DNMT1i. Such applications include chemical reprogramming approaches for adoptive immune cell therapies and combination strategies with immune checkpoint blockade to enhance antitumor efficacy in solid tumors.

Additionally, the team found that DMI46 selectively induces DNA demethylation and fetal hemoglobin activation, promotes erythroid maturation, and alleviates the progression of β-thalassemia—supporting its potential utility in treating this highly prevalent genetic disorder in southern China.

This research was supported by the National Key R&D Program of China, the CAS Strategic Priority Research Program, and other funding sources.

DMI46 traps DNMT1 in an open, inactive conformation and confers robust therapeutic activity in AML models resistant to current HMAs. (Image by GIBH)