Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers

M Sigal, S Matsumoto, A Beattie, T Katoh… - Chemical …, 2024 - ACS Publications
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by
transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 …

Genome Mining for New Enzyme Chemistry

DT Nguyen, DA Mitchell, WA van der Donk - ACS catalysis, 2024 - ACS Publications
A revolution in the field of biocatalysis has enabled scalable access to compounds of high
societal values using enzymes. The construction of biocatalytic routes relies on the reservoir …

PepExplainer: An explainable deep learning model for selection-based macrocyclic peptide bioactivity prediction and optimization

S Zhai, Y Tan, C Zhu, C Zhang, Y Gao, Q Mao… - European Journal of …, 2024 - Elsevier
Macrocyclic peptides possess unique features, making them highly promising as a drug
modality. However, evaluating their bioactivity through wet lab experiments is generally …

A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides

AA Vinogradov, Y Zhang, K Hamada… - Journal of the …, 2024 - ACS Publications
Thiopeptides make up a group of structurally complex peptidic natural products holding
promise in bioengineering applications. The previously established thiopeptide/mRNA …

Illuminating Substrate Preferences of Promiscuous F420H2-Dependent Dehydroamino Acid Reductases with 4-Track mRNA Display

AA Vinogradov, G Bashiri, H Suga - Journal of the American …, 2024 - ACS Publications
Stereoselective reduction of dehydroamino acids is a common biosynthetic strategy to
introduce d-amino acids into peptidic natural products. The reduction, often observed during …

De Novo Discovery of a Noncovalent Cell-Penetrating Bicyclic Peptide Inhibitor Targeting SARS-CoV-2 Main Protease

Y Tan, J Yang, M Wang, Q Peng, Y Li, L Fu… - Journal of Medicinal …, 2024 - ACS Publications
Macrocyclic peptides have garnered significant attention as promising drug candidates.
However, they typically face challenges in achieving and enhancing cell permeability for …

Kinetic Analysis of Cyclization by the Substrate-Tolerant Lanthipeptide Synthetase ProcM

EK Desormeaux, GJ Barksdale, WA van der Donk - ACS catalysis, 2024 - ACS Publications
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides
(RiPPs) characterized by the presence of thioether cross-links called lanthionine and …

[HTML][HTML] Novel types of RiPP-modifying enzymes

D Richter, J Piel - Current Opinion in Chemical Biology, 2024 - Elsevier
Novel discoveries in natural product biosynthesis reveal hidden bioactive compounds and
expand our knowledge in enzymology. Ribosomally synthesized and post-translationally …

Expression and Subcellular Localization of Lanthipeptides in Human Cells

SM Eslami, C Padhi, IR Rahman… - ACS synthetic …, 2024 - ACS Publications
Cyclic peptides, such as most ribosomally synthesized and post-translationally modified
peptides (RiPPs), represent a burgeoning area of interest in therapeutic and …

Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning

JD Clark, X Mi, DA Mitchell, D Shukla - Digital Discovery, 2025 - pubs.rsc.org
Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic
enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple …