Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia

• DOI: 10.1021/acscentsci.1c01090
• Publication Date: 2022-02-07T20:12:31Z
• Authors: Kaiming Zhang; Naoki Horikoshi; Shanshan Li; Alexander S. Powers; Mikhail A. Hameedi; Grigore D. Pintilie; Hee-Don Chae; Yousuf A. Khan; Carl-Mikael Suomi...; Ron O. Dror; Kathleen M. Sakamoto; Wah Chiu; Soichi Wakatsuki
• Keywords: Helix (gastropod); Protein Engineering; CREB-binding protein

Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain CREB-binding protein (CBP), potential therapeutic target acute myeloid leukemia other cancers, is which defied structure-based inhibitor design. Here, we develop an experimental approach overcome the size limitation by engineering double-shell sandwich between apoferritin inner shell maltose-binding outer shell. To assist homogeneous orientations target, disulfide bonds introduced at target–apoferritin interface, resulting in cryo-EM structure 2.6 Å resolution. We used dynamics simulations design peptides block interaction CBP with intrinsically disordered pKID CREB. allows fluorescence polarization assays confirming binding these interacting peptides. Further analysis reveals helix–helix single helix best peptide, providing possible strategy developments next-generation inhibitors.