Engineering covalent small molecule–RNA complexes in living cells

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

Abstract Covalent labeling of RNA in living cells poses many challenges. Here we describe a structure-guided approach to engineer covalent aptamer–ligand complexes. The key is modify the cognate ligand with an electrophilic handle that allows it react guanine at binding site. We illustrate this for preQ 1 -I riboswitch, vitro and vivo. Further, demonstrate versatility fluorescent light-up aptamer. coPepper system maintains strong fluorescence live-cell imaging even after washing, can be used super-resolution microscopy and, most notably, uniquely suited recovery photobleaching monitor intracellular dynamics. In addition, have generated Pepper second bioorthogonal chemistry allow easily traceable pull-down covalently linked target RNA. Finally, provide evidence suitability tethering strategy drug targeting.

Language: Английский

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Photoaffinity labelling with small molecules

Nature Reviews Methods Primers, Journal Year: 2024, Volume and Issue: 4(1)

Published: May 2, 2024

Language: Английский

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Chemical Synthesis of Modified RNA

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(22)

Published: March 26, 2024

Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA controlled manner-both vitro and vivo-are thus essential evaluate understand biology at the molecular mechanistic levels. The diversity modifications, combined with size uniformity (made up only 4 nucleotides) makes its site-specific modification challenging task that needs be addressed by complementary approaches. One such approach is solid-phase synthesis. We discuss recent developments this field, starting new protection concepts ongoing effort overcome current limitations. continue selected modifications have posed significant challenges for incorporation into RNA. These include deazapurine bases required atomic mutagenesis elucidate aspects catalytic RNAs, containing xanthosine, N

Language: Английский

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Aminothiazolone Inhibitors Disrupt the Protein–RNA Interaction of METTL16 and Modulate the m⁶A RNA Modification

JACS Au, Journal Year: 2024, Volume and Issue: 4(4), P. 1436 - 1449

Published: March 21, 2024

Targeting RNA-binding and modifying proteins via small molecules to modulate post-transcriptional modifications have emerged as a new frontier for chemical biology therapeutic research. One such protein that regulates the most prevalent eukaryotic RNA modification, N6-methyladenosine (m6A), is methyltransferase-like 16 (METTL16), which plays an oncogenic role in cancers by cofunctioning with other nucleic acid-binding proteins. To date, no potent small-molecule inhibitor of METTL16 or modulator interfering METTL16–RNA interaction has been reported validated, highlighting unmet need develop investigate METTL16-involved regulatory network. Herein, we described identification series first-in-class aminothiazolone inhibitors discovery pipeline started fluorescence-polarization (FP)-based screening. Structural optimization initial hit yielded inhibitors, compound 45, showed single-digit micromolar inhibition activity against METTL16-RNA binding. The identified can be useful probes elucidate biological function upon perturbation evaluate potential at level.

Language: Английский

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The Role of MicroRNAs in HIV Infection

Genes, Journal Year: 2024, Volume and Issue: 15(5), P. 574 - 574

Published: April 29, 2024

MicroRNAs (miRNAs), a class of small, non-coding RNAs, play pivotal role in regulating gene expression at the post-transcriptional level. These regulatory molecules are integral to many biological processes and have been implicated pathogenesis various diseases, including Human Immunodeficiency Virus (HIV) infection. This review aims cover current understanding multifaceted roles miRNAs assume context HIV infection pathogenesis. The discourse is structured around three primary focal points: (i) elucidation mechanisms through which regulate replication, encompassing both direct targeting viral transcripts indirect modulation host factors critical for replication; (ii) examination miRNA by HIV, mediated either proteins or activation cellular pathways consequent infection; (iii) assessment impact on immune response progression disease HIV-infected individuals. Further, this delves into potential utility as biomarkers therapeutic agents infection, underscoring challenges prospects inherent line inquiry. synthesis evidence positions significant modulators host-virus interplay, offering promising avenues enhancing diagnosis, treatment, prevention

Language: Английский

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Live Cell Screening to Identify RNA-Binding Small Molecule Inhibitors of the pre-let-7-Lin28 RNA-Protein Interaction

RSC Medicinal Chemistry, Journal Year: 2024, Volume and Issue: 15(5), P. 1539 - 1546

Published: Jan. 1, 2024

Dysregulation of the networking RNA-binding proteins (RBPs) and RNAs drives many human diseases, including cancers, targeting RNA–protein interactions (RPIs) has emerged as an exciting area RNA-targeted drug discovery.

Language: Английский

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ATOM-1: A Foundation Model for RNA Structure and Function Built on Chemical Mapping Data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 14, 2023

Abstract RNA-based medicines and RNA-targeting drugs are emerging as promising new approaches for treating disease. Optimizing these therapeutics by naive experimental screening is a time-consuming expensive process, while rational design requires an accurate understanding of the structure function RNA. To address this challenge, we present ATOM-1, first RNA foundation model trained on chemical mapping data, enabled data collection strategies purposely developed machine learning training. Using small probe neural networks top ATOM-1 embeddings, demonstrate that has rich internal representations Trained limited amounts additional achieve state-of-the-art accuracy key prediction tasks, suggesting approach can enable therapies across landscape.

Language: Английский

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RNA modulation

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

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Mapping small molecule–RNA binding sites via Chem-CLIP synergized with capillary electrophoresis and nanopore sequencing

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(6)

Published: March 20, 2025

Abstract Target validation and identification of binding sites are keys to the development bioactive small molecules that target RNA. Herein, we describe optimized protocols profile molecule–RNA interactions define in RNAs using covalent chemistry. Various reactive modules appended an RNA-binding molecule were studied for cross-linking RNA target. Electrophilic modules, whether N-chloroethyl aniline or diazirine, have profiles consistent with induced proximity; however, probes more specific than those a diazirine moiety. Depending upon identity module, adducts different nucleotides proximal molecule’s site formed. The where occurred elucidated by two platforms: (i) automated capillary electrophoresis identified impeding reverse transcriptase, “RT stops”; (ii) nanopore sequencing cross-link produces mutations corresponding complementary DNA formed transcriptase-polymerase chain reaction amplification cross-linked These approaches broadly applicable aid advancement chemical targeting RNA, including identifying chemistry screen high throughput format.

Language: Английский

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Advanced strategies for screening and identifying RNA-targeted small molecules: Bridging therapeutic potential and innovation

Results in Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 102305 - 102305

Published: April 1, 2025

Language: Английский

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