9F01

Complex between D-SH2 domain of ABL with monobody 'DAM21

This is a non-PDB format compatible entry.

Summary for 9F01

• Entry DOI: 10.2210/pdb9f01/pdb
• Descriptor: synthetic D-SH2 domain NS1-10, nanobody DAM21.3, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: complex, nanobody, sh2 domain, mirror-image phage display, d-protein, protein binding
• Biological source: synthetic construct; More
• Total number of polymer chains: 8
• Total formula weight: 86533.08

Authors

Essen, L.-O.,Hantschel, O.,Schmidt, N.,Korf, L. (deposition date: 2024-04-14, release date: 2024-12-25, Last modification date: 2025-01-22)

Primary citation

Schmidt, N.,Kumar, A.,Korf, L.,Dinh-Fricke, A.V.,Abendroth, F.,Koide, A.,Linne, U.,Rakwalska-Bange, M.,Koide, S.,Essen, L.O.,Vazquez, O.,Hantschel, O.
Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase.
Nat Commun, 15:10724-10724, 2024

PubMed Abstract: Mirror-image proteins, composed of D-amino acids, are an attractive therapeutic modality, as they exhibit high metabolic stability and lack immunogenicity. Development of mirror-image binding proteins is achieved through chemical synthesis of D-target proteins, phage display library selection of L-binders and chemical synthesis of (mirror-image) D-binders that consequently bind the physiological L-targets. Monobodies are well-established synthetic (L-)binding proteins and their small size (~90 residues) and lack of endogenous cysteine residues make them particularly accessible to chemical synthesis. Here, we develop monobodies with nanomolar binding affinities against the D-SH2 domain of the leukemic tyrosine kinase BCR::ABL1. Two crystal structures of heterochiral monobody-SH2 complexes reveal targeting of the pY binding pocket by an unconventional binding mode. We then prepare potent D-monobodies by either ligating two chemically synthesized D-peptides or by self-assembly without ligation. Their proper folding and stability are determined and high-affinity binding to the L-target is shown. D-monobodies are protease-resistant, show long-term plasma stability, inhibit BCR::ABL1 kinase activity and bind BCR::ABL1 in cell lysates and permeabilized cells. Hence, we demonstrate that functional D-monobodies can be developed readily. Our work represents an important step towards possible future therapeutic use of D-monobodies when combined with emerging methods to enable cytoplasmic delivery of monobodies.

PubMed: 39715735
DOI: 10.1038/s41467-024-54901-y

Experimental method

X-RAY DIFFRACTION (2.73 Å)