mRNA-based therapeutics: powerful and versatile tools to combat diseases

S Qin, X Tang, Y Chen, K Chen, N Fan… - Signal transduction and …, 2022 - nature.com
The therapeutic use of messenger RNA (mRNA) has fueled great hope to combat a wide
range of incurable diseases. Recent rapid advances in biotechnology and molecular …

Intelligent biomaterialomics: molecular design, manufacturing, and biomedical applications

Y Yi, HW An, H Wang - Advanced Materials, 2024 - Wiley Online Library
Materialomics integrates experiment, theory, and computation in a high‐throughput manner,
and has changed the paradigm for the research and development of new functional …

De novo discovery of thiopeptide pseudo-natural products acting as potent and selective TNIK kinase inhibitors

AA Vinogradov, Y Zhang, K Hamada… - Journal of the …, 2022 - ACS Publications
Bioengineering of ribosomally synthesized and post-translationally modified peptides
(RiPPs) is an emerging approach to explore the diversity of pseudo-natural product …

Deep Learning-Driven Library Design for the De Novo Discovery of Bioactive Thiopeptides

JS Chang, AA Vinogradov, Y Zhang, Y Goto… - ACS Central …, 2023 - ACS Publications
Broad substrate tolerance of ribosomally synthesized and post-translationally modified
peptide (RiPP) biosynthetic enzymes has allowed numerous strategies for RiPP …

Discovery of Thioether-Cyclized Macrocyclic Covalent Inhibitors by mRNA Display

T Lan, C Peng, X Yao, RST Chan, T Wei… - Journal of the …, 2024 - ACS Publications
Macrocyclic peptides are promising scaffolds for the covalent ligand discovery. However,
platforms enabling the direct identification of covalent macrocyclic ligands in a high …

Large-scale analysis of mRNA sequences localized near the start and amber codons and their impact on the diversity of mRNA display libraries

S Umemoto, T Kondo, T Fujino, G Hayashi… - Nucleic Acids …, 2023 - academic.oup.com
Extremely diverse libraries are essential for effectively selecting functional peptides or
proteins, and mRNA display technology is a powerful tool for generating such libraries with …

Accurate models of substrate preferences of post-translational modification enzymes from a combination of mRNA display and deep learning

AA Vinogradov, JS Chang, H Onaka, Y Goto… - ACS Central …, 2022 - ACS Publications
Promiscuous post-translational modification (PTM) enzymes often display nonobvious
substrate preferences by acting on diverse yet well-defined sets of peptides and/or proteins …

Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning

T Ito, TD Nguyen, Y Saito, Y Kurumida, H Nakazawa… - MAbs, 2023 - Taylor & Francis
Despite the advances in surface-display systems for directed evolution, variants with high
affinity are not always enriched due to undesirable biases that increase target-unrelated …

Natural and man-made cyclic peptide-based antibiotics

S Lai, Q Zhang, L Jin - Antibiotics, 2022 - mdpi.com
In recent years, an increasing number of drug-resistant bacterial strains have been identified
due to the abuse of antibiotics, which seriously threatens human and animal health …

Directed evolution of PD-L1-targeted affibodies by mRNA display

BJ Grindel, BJ Engel, JN Ong… - ACS chemical …, 2022 - ACS Publications
Therapeutic monoclonal antibodies directed against PD-L1 (eg, atezolizumab) disrupt PD-
L1: PD-1 signaling and reactivate exhausted cytotoxic T-cells in the tumor compartment …