DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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http://dx.doi.org/10.1002/cbic.202100685 | DOI Listing |
Biochem Biophys Res Commun
June 2022
Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan. Electronic address:
Interleukin-5 (IL-5) is a type 2 cytokine involved in various allergic diseases, including severe eosinophilic asthma. In this study, we performed directed evolution against human IL-5 using systematic evolution of ligands by exponential enrichment (SELEX) from multiple mRNA-displayed peptide libraries. Peptide libraries were prepared with Escherichia coli-based reconstituted cell-free transcription and translation coupling system (PURE system) and spontaneously cyclized using multiple intramolecularly thiol-reactive benzoic acid-derived linkers, which were ribosomally incorporated through genetic code expansion.
View Article and Find Full Text PDFChem Commun (Camb)
April 2022
Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, Yamanashi 400-8510, Japan.
We report novel, ribosomally incorporatable, and intramolecularly cysteine-reactive fluorobenzoic acid-derived linkers for SELEX of mRNA-displayed unnatural peptides, which spontaneously cyclized intramolecular nucleophilic aromatic substitutions forming thioethers. With this strategy we identified several novel PCSK9-binding peptides.
View Article and Find Full Text PDFOrg Biomol Chem
April 2022
Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, The Netherlands.
Thiols are a functional group commonly used for selective reactions in a biochemical setting because of their high nucleophilicity. Phosphorus nucleophiles can undergo some similar reactions to thiols, but remain underexploited in this setting. In this work we show that phosphine nucleophiles react cleanly and quickly with a dehydroalanine electrophile, itself generated from cysteine, to give a stable adduct in a peptide context.
View Article and Find Full Text PDFChembiochem
June 2022
Department of Chemistry and Pharmaceutical Sciences, VU Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries.
View Article and Find Full Text PDFJ Pharm Pharmacol
March 2021
Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, Guangzhou, Guangdong Province, China.
Objectives: We aimed to characterize diurnal rhythms in CES1 expression and activity in mouse intestine, and to investigate a potential role of the core clock gene Bmal1 in generating diurnal rhythms.
Methods: The regulatory effects of intestinal Bmal1 on diurnal CES1 expression were assessed using intestine-specific Bmal1 knockout (Bmal1iKO) mice and colon cancer cells. The relative mRNA and protein levels were determined by qPCR and Western blotting, respectively.
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