7SND image
Deposition Date 2021-10-27
Release Date 2022-08-03
Last Version Date 2024-11-06
Entry Detail
PDB ID:
7SND
Keywords:
Title:
Pacifastin related protease inhibitors
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.79 Å
R-Value Free:
0.20
R-Value Work:
0.13
R-Value Observed:
0.14
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Pacifastin-related peptide
Chain IDs:A, B, C, D
Chain Length:33
Number of Molecules:4
Biological Source:Coptotermes formosanus
Primary Citation

Abstact

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 (KD = 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.

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Primary Citation of related structures