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.
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http://dx.doi.org/10.1039/d2cc00584k | DOI Listing |
Org Biomol Chem
January 2025
Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune-411008, India.
We report the stereoselective total synthesis of kavaratamide A, a linear lipodepsipeptide from the cyanobacterium (collected in Kavaratti, India), and its unnatural C25-epimer. The convergent approach employs Keck asymmetric allylation to construct the chiral β-hydroxy carboxylic acid fragment [(3)-HDA; 3-hydroxydecanoic acid], while the peptide unit was assembled from L-Val, -Me-L-Ala, ()-Hiva, and ()-Pr--Me-pyr using well-orchestrated coupling methods to prevent racemization. Modifications to the Keck allylation conditions enabled the synthesis of the C25-epimer with good yield.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States.
Macrocyclization or stapling is an important strategy for increasing the conformational stability and target-binding affinity of peptides and proteins, especially in therapeutic contexts. Atomistic simulations of such stapled peptides and proteins could help rationalize existing experimental data and provide predictive tools for the design of new stapled peptides and proteins. Standard approaches exist for incorporating nonstandard amino acids and functional groups into the force fields required for MD simulations and have been used in the context of stapling for more than a decade.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.
Language modeling applied to biological data has significantly advanced the prediction of membrane penetration for small-molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or noncanonical amino acids, and cyclizations.
View Article and Find Full Text PDFBioorg Chem
January 2025
Department of Chemistry, University of Richmond, Gottwald Science Center, B-100 138 UR Drive, Richmond, VA 23173, United States. Electronic address:
We report the development of a new electron-rich aniline (ERA)-based cleavable linker. Anilines can be incorporated into peptides during SPPS and are stable to most reaction conditions. ERA-containing peptides can be cleaved rapidly in the presence of oxidants, such as DDQ, CAN, and NaIO, in 30 min at room temperature.
View Article and Find Full Text PDFToxins (Basel)
December 2024
Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria.
Recently, the use of click chemistry for localization of chemically modified cyanopeptides has been introduced, i.e., taking advantage of promiscuous adenylation (A) domains in non-ribosomal peptide synthesis (NRPS), allowing for the incorporation of clickable non-natural amino acids (non-AAs) into their peptide products.
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