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

• Published in: Blood 2012-11, Vol.120 (23), p.4461-4469
• Main Authors: Shi, Aibin, Murai, Marcelo J., He, Shihan, Lund, George, Hartley, Thomas, Purohit, Trupta, Reddy, Gireesh, Chruszcz, Maksymilian, Grembecka, Jolanta, Cierpicki, Tomasz
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antineoplastic Agents - chemistry; Antineoplastic Agents - metabolism; Antineoplastic Agents - therapeutic use; Apoptosis - drug effects; Binding Sites - genetics; Biological and medical sciences; Cell Differentiation - drug effects; Cell Line, Tumor; Cell Proliferation - drug effects; Crystallography, X-Ray; Dose-Response Relationship, Drug; Drug Screening Assays, Antitumor; HEK293 Cells; Hematologic and hematopoietic diseases; Histone-Lysine N-Methyltransferase; Humans; Immunoblotting; Immunoprecipitation; Leukemia - drug therapy; Leukemia - pathology; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Medical sciences; Models, Molecular; Molecular Sequence Data; Mutation; Myeloid Neoplasia; Myeloid-Lymphoid Leukemia Protein - chemistry; Myeloid-Lymphoid Leukemia Protein - genetics; Myeloid-Lymphoid Leukemia Protein - metabolism; Plenary Paper; Protein Binding - drug effects; Protein Structure, Tertiary; Proto-Oncogene Proteins - chemistry; Proto-Oncogene Proteins - genetics; Proto-Oncogene Proteins - metabolism
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2012-05-429274

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 small-molecule 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 (Kd = 22nM) and very effectively disrupts the bivalent protein-protein interaction between menin and MLL. MI-2-2 demonstrated specific and very pronounced activity in MLL leukemia cells, including inhibition of cell proliferation, down-regulation of Hoxa9 expression, and differentiation. Our results provide the rational and essential structural basis to design next generation of inhibitors for effective targeting of the menin-MLL interaction in leukemia and demonstrate a proof of concept that inhibition of complex multivalent protein-protein interactions can be achieved by a small-molecule inhibitor.