7SJQ

Ex silico engineering of cystine-dense peptides yielding a potent bispecific T-cell engager

Summary for 7SJQ

• Entry DOI: 10.2210/pdb7sjq/pdb
• Descriptor: Programmed cell death 1 ligand 1, Cystine-dense peptide, GLYCEROL, ... (7 entities in total)
• Functional Keywords: pdl1 binder, antitumor protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 19642.37

Authors

Rupert, P.B.,Strong, R. (deposition date: 2021-10-18, release date: 2022-06-08, Last modification date: 2023-10-18)

Primary citation

Crook, Z.R.,Girard, E.J.,Sevilla, G.P.,Brusniak, M.Y.,Rupert, P.B.,Friend, D.J.,Gewe, M.M.,Clarke, M.,Lin, I.,Ruff, R.,Pakiam, F.,Phi, T.D.,Bandaranayake, A.,Correnti, C.E.,Mhyre, A.J.,Nairn, N.W.,Strong, R.K.,Olson, J.M.
Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager.
Sci Transl Med, 14:eabn0402-eabn0402, 2022

PubMed Abstract: Cystine-dense peptides (CDPs) are a miniprotein class that can drug difficult targets with high affinity and low immunogenicity. Tools for their design, however, are not as developed as those for small-molecule and antibody drugs. CDPs have diverse taxonomic origins, but structural characterization is lacking. Here, we adapted Iterative Threading ASSEmbly Refinement (I-TASSER) and Rosetta protein modeling software for structural prediction of 4298 CDP scaffolds and performed in silico prescreening for CDP binders to targets of interest. Mammalian display screening of a library of docking-enriched, methionine and tyrosine scanned (DEMYS) CDPs against PD-L1 yielded binders from four distinct CDP scaffolds. One was affinity-matured, and cocrystallography yielded a high-affinity ( = 202 pM) PD-L1-binding CDP that competes with PD-1 for PD-L1 binding. Its subsequent incorporation into a CD3-binding bispecific T cell engager produced a molecule with pM-range in vitro T cell killing potency and which substantially extends survival in two different xenograft tumor-bearing mouse models. Both in vitro and in vivo, the CDP-incorporating bispecific molecule outperformed a comparator antibody-based molecule. This CDP modeling and DEMYS technique can accelerate CDP therapeutic development.

PubMed: 35584229
DOI: 10.1126/scitranslmed.abn0402

Experimental method

X-RAY DIFFRACTION (2 Å)