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

Zhang, Kaiming; Horikoshi, Naoki; Li, Shanshan; Powers, Alexander S.; Hameedi, Mikhail A.; Pintilie, Grigore D.; Chae, Hee-Don; Khan, Yousuf A.; Suomivuori, Carl-Mikael; Dror, Ron O.; Sakamoto, Kathleen M.; Chiu, Wah; Wakatsuki, Soichi

doi:10.1021/acscentsci.1c01090

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

Journal Article · 07 February 2022 · ACS Central Science

DOI: https://doi.org/10.1021/acscentsci.1c01090 · OSTI ID:1872761

^[1]; Horikoshi, Naoki ^[2]; Li, Shanshan ^[3]; Powers, Alexander S. ^[1]; Hameedi, Mikhail A. ^[4]; Pintilie, Grigore D. ^[1]; Chae, Hee-Don ^[5];

^[6]; Suomivuori, Carl-Mikael ^[1];

^[1]; Sakamoto, Kathleen M. ^[1];

^[4];

^[4]

Stanford Univ., CA (United States)
Stanford Univ., CA (United States); Univ. of Tsukuba (Japan)
Univ. of Science and Technology of China, Hefei (China); Stanford Univ., CA (United States)
Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
Stanford Univ., CA (United States). School of Medicine
Stanford Univ., CA (United States); Stanford Univ., CA (United States). School of Medicine

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

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Stanford Maternal Child Health Research Institute; Stanford SPARK program; Leukemia and Lymphoma Society; National Natural Science Foundation of China; University of Science and Technology of China

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1872761

Journal Information:: ACS Central Science, Journal Name: ACS Central Science Journal Issue: 2 Vol. 8; ISSN 2374-7943

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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