Structural insights into inhibition of the bivalent menin-MLL interaction by small molecules in leukemia

Abstract

Menin functions as a critical oncogenic cofactor of mixed lineage leukemia (MLL) fusion proteins in the development of acute leukemias, and inhibition of the menin interaction with MLL fusion proteins represents a very promising strategy to reverse their oncogenic activity. MLL interacts with menin in a bivalent mode involving 2 N-terminal fragments of MLL. In the present study, we reveal the first high-resolution crystal structure of human menin in complex with a smallmolecule inhibitor of the menin-MLL interaction, MI-2. The structure shows that the compound binds to the MLL pocket in menin and mimics the key interactions of MLL with menin. Based on the menin-MI-2 structure, we developed MI-2-2, a compound that binds to menin with low nanomolar affinity (K d ‫؍‬ IntroductionTranslocations of the MLL (mixed lineage leukemia) gene frequently occur in aggressive human acute myeloid and lymphoid leukemias in both children and adults. 1 Fusion of MLL with 1 of more than 60 different genes results in chimeric MLL fusion proteins that enhance proliferation and block hematopoietic differentiation, ultimately leading to acute leukemia. 2 Patients with leukemias harboring MLL translocations have very unfavorable prognoses and respond poorly to currently available treatments. 2,3 The relapse risk is very high using conventional chemotherapy and stem cell transplantation, 2 leading to an overall 5-year survival rate of only approximately 35%. 4 All MLL fusion proteins preserve an N-terminal MLL fragment approximately 1400 amino acids in length fused in-frame with the C-terminus of the fusion partner. 3,[5][6][7] Two regions in this fragment of MLL have been shown to be indispensable for leukemogenic transformation: the N-terminal region, which binds to menin 8 and to lens epithelium-derived growth factor (LEDGF), 9 and the conserved region encompassing the CXXC domain, which mediates binding to nonmethylated CpG DNA [10][11][12] and interacts with the polymerase associated factor complex (PAFc). 13,14 Targeting these interactions provides new opportunities for the development of new therapeutic agents for the MLL leukemias. 15 Menin is a tumor-suppressor protein encoded by the MEN1 (multiple endocrine neoplasia 1) gene. 16 Mutations of MEN1 are associated with tumors of the parathyroid glands, pancreatic islet cells, and anterior pituitary gland. 17 Menin is also a highly specific binding partner for MLL and MLL fusion proteins and is required to regulate the expression of MLL target genes, including HOXA9 and MEIS1. 8 Loss of the ability to bind menin abolishes the oncogenic potential of MLL fusion proteins both in vitro and in vivo. 8 Disruption of the interaction between menin and MLL fusion proteins using genetic methods blocks the development of acute leukemia in mice, 8 indicating that menin functions as a critical oncogenic cofactor of MLL fusion proteins and is required for their leukemogenic activity. The menin-MLL interaction represents an attractive therapeutic target for the development of novel drugs for acut...

Cooperative gene activation by AF4 and DOT1L drives MLL-rearranged leukemia

“…Because AF4 recruitment appears to be primarily dependent on MLL-ENL ( Figure 3) and target recognition by MLL fusion proteins requires MENIN (4, 5), we hypothesized that MI-2-2, a MENIN-MLL interaction inhibitor (42), would inhibit AF4 recruitment to the MLL target chromatin in MLL-AEP leukemia cells. Indeed, MI-2-2 impaired the expression of HOXA9 and MEIS1 in NODAL modulator 1 (NOMO-1) cells, which express MLL-AF9 endogenously ( Figure 7, A and B).…”

Reprogramming of histone methylation controls the differentiation of monocytes into macrophages

“…Menin, the product of the MEN1 gene, is a highly specific partner for the MLL complex, and it links the MLL complex to target gene promoters [14]. Thus, the disruption of menin/MLL interactions by specific compounds results in the failure to regulate HOXA expression and suppresses MLL-AFs fusion protein-induced leukemogenesis in vitro and in vivo [15][16][17]. Currently, a genomewide understanding of the mechanistic and functional importance of TrxG partners in the regulation of MP differentiation is lacking.…”

“…The mixed-lineage leukemia proteins (MLL) are orthologs of TrxG genes that functionally antagonize PcG [8]. The MLL SET domain specifically catalyzes H3K4me3 and leads to the activation of genes, such as HOX [8,[14][15][16][17]. Menin, the product of the MEN1 gene, is a highly specific partner for the MLL complex, and it links the MLL complex to target gene promoters [14].…”

Small molecule inhibitors for acute myeloid leukemia: where is the field heading?

“…Small molecule inhibition of this protein-protein interaction (PPI) has been shown to reverse MLL-fusion protein oncogenic activity [15]. Shi et al described the identification of a potent small molecule inhibitor of the menin-MLL PPI named MI-2-2 ( Figure 1) [16]. This compound displayed an IC 50 = 46 nM and provided significant cytotoxicity (50% growth inhibition [GI 50 While MLL mutation occurs only in approximately 10% of all adult AML cases, in infants this mutation is detected in >70% of cases.…”