Discovery of BTC-86, a Novel Second-Generation Menin-MLL Inhibitor to Overcome the Acquired Resistance in MEN1 for R/R Acute Leukemia

The menin-MLL1 interaction is essential for acute leukemias driven by MLL rearrangements (MLLr) or mutations in the nucleophosmin 1 gene (NPM1c). Menin-MLL inhibitor SNDX-5613 (revumenib) has demonstrated robust clinical responses in the clinical trial. However, somatic MEN1 mutations were found at residues M327, G331 or T349 at the revumenib-menin interface in the patients with acquired resistance to menin inhibition and post a major challenge to the management of acute leukemias driven by MLLr or NPM1c. Therefore, developing second-generation inhibitors that block MLL1 binding while having activity against those MEN1 mutations becomes an important strategy to combat acquired resistance to the first -generation menin-MLL inhibitors.

The MMPT (Matched Molecular Pair Transformation) process is used to develop menin-MLL inhibitors. Fluorescence polarization assay is used to assess the impact of BTC-86 on the binding of MLL to wild-type (WT) or mutated menin proteins. Using the MMPT process, we have discovered a novel second-generation menin-MLL inhibitor BTC-86 that has similar binding activity against wild-type menin protein and MEN1 resistance mutations. SNDX-5613 shows notable steric hinderance in the binding pocket of M327I mutant versus that of wild-type menin. Based on the modeling study, BTC-86 can adopt a novel binding mode, which shows little change in its bound position to M327I mutant compared to that of wild-type menin. BTC-86 is the most potent one in inhibition of menin-MLL1 binding against all the MEN1 acquired mutations among all five clinical molecules, including SNDX-5613, JnJ-75276617, and KO-539.

Furthermore, BTC-86 is a potent and highly selective menin-MLL inhibitor in cell viability of multiple leukemia cell lines. BTC-86 shows anti-tumor efficacies in multiple tumor mouse models carrying MLLr or NPM1c, which are correlated with in vivo on-target activity (inhibition of MEIS1 gene expression) and excellent pharmacokinetic properties.

BTC-86 has lower risk in QTc prolongation (IC₅₀ of hERG greater than 30 µM), and has better human metabolic stability than the first-generation menin-MLL inhibitor. Moreover, it is well tolerated in an exploratory rat toxicology study.

In conclusion, BTC-86 is a potent second-generation menin-MLL inhibitor that blocks MLL1 binding while having similar activity against wild-type and mutant MEN1 proteins. IND-enabling study of BTC-86 is in progress. Further studies in clinical setting are warranted to confirm BTC-86 as a second-generation menin-MLL inhibitor for overcoming acquired resistance in MEN1.