Using extension-based mRNA display to design antibody-like proteinogenic peptides for human PD-L1.

Justin N Ong, Brian J Grindel, Scott A Rankin, Sarah H Naylon, Anupallavi Srinivasamani, Guillaume J Trusz, Xiaowen Liang, Md Nasir Uddin, Lauren Fuller, Michael Curran, Stephane P Roche, Terry T Takahashi, Richard W Roberts, Steven W Millward

Journal: Protein science : a publication of the Protein Society 2025;34(9):e70268

PMID: 40852896

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Abstract

Many peptide drugs rely on nonproteinogenic amino acids and chemical modifications for improved activity and proteolytic stability. However, these features also make drug production expensive and challenging to scale. Here, we engineered small, linear, proteinogenic peptides that bind human programmed death-ligand 1 (hPD-L1) with high affinity and stability using mRNA display affinity maturation. The resulting peptides, SPAM2 and SPAM3, have antibody-like affinities for hPD-L1 (dissociation constants between ~250 and 300 pM) and are selective for hPD-L1. Both SPAM2 and SPAM3 compete with hPD-L1 ligands known to interact with the programmed cell death protein 1 site and are stable in human serum. SPAM3 bound human glioma D423 cells with high affinity in flow cytometry experiments comparable to that of a clinical therapeutic antibody. These results support the use of affinity maturation selections to dramatically enhance the biophysical properties of linear, proteinogenic peptides for translational applications.

Address: Deparment of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, USA.; Deparment of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.; Department of Chemistry, University of Southern California, Los Angeles, California, USA.; Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida, USA.; Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.; Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.; Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida, USA.; Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida, USA.; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, USA.; Department of Chemistry, University of Southern California, Los Angeles, California, USA.; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA.

DOI: 10.1002/pro.70268

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MeSH Terms: Humans, B7-H1 Antigen, Peptides, RNA, Messenger, Cell Line, Tumor, Protein Engineering