Pervasive transcriptome interactions of protein-targeted drugs

Translational Modeling of Chloroquine and Hydroxychloroquine Dosimetry in Human Airways for Treating Viral Respiratory Infections

(2022) Aditya R. Kolli et al.   PHARMACEUTICAL RESEARCH

R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures

(2022) Anita Donlic et al.   ACS Chemical Biology

Quantitative Structure–Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure

(2022) Zhengguo Cai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ribosomal RNA 2′- O -methylations regulate translation by impacting ribosome dynamics

(2022) Sohail Khoshnevis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SHAPE-enabled fragment-based ligand discovery for RNA

(2022) Meredith J. Zeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-Wide Mapping of Small-Molecule RNA-Binding Sites in Cells Informs an Isoform-Specific Degrader of QSOX1 mRNA

(2022) Yuquan Tong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

G4Atlas: a comprehensive transcriptome-wide G-quadruplex database

(2022) Haopeng Yu et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Informs RNA‐Binding Chemical Space

(2022) Kamyar Yazdani et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A first-in-class clinical G-quadruplex-targeting drug. The bench-to-bedside translation of the fluoroquinolone QQ58 to CX-5461 (Pidnarulex)

(2022) Hong Xu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Reprogramming of Protein-Targeted Small-Molecule Medicines to RNA by Ribonuclease Recruitment

(2021) Peiyuan Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identifying transcriptional programs underlying cancer drug response with TraCe-seq

(2021) Matthew T. Chang et al.   NATURE BIOTECHNOLOGY

Drug repurposing: Misconceptions, challenges, and opportunities for academic researchers

(2021) C. Glenn Begley et al.   Science Translational Medicine

An Umbrella Review of Clinical Efficacy and Adverse Cardiac Events Associated with Hydroxychloroquine or Chloroquine with or Without Azithromycin in Patients with COVID-19

(2021) Kavous Shahsavarinia et al.   Anesthesiology and Pain Medicine

Regulation of translation by site-specific ribosomal RNA methylation

(2021) Martin D. Jansson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites

(2021) Sumirtha Balaratnam et al.   Nature Communications

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions

(2020) Herschel Mukherjee et al.   ACS Chemical Biology

A general fragment-based approach to identify and optimize bioactive ligands targeting RNA

(2020) Blessy M. Suresh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Perspectives on targeting RNA with small molecules to capture opportunities at the intersection of chemistry, biology, and medicine

(2019) Matthew D. Disney   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A cross-linking approach to map small molecule-RNA binding sites in cells

(2019) Sai Pradeep Velagapudi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing

(2019) Pui Yan Yeung et al.   Scientific Reports

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

(2019) Ann Lin et al.   Science Translational Medicine

R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes

(2019) Brittany S. Morgan et al.   ACS Chemical Biology

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

When antibiotics turn toxic

(2018) Jo Marchant   NATURE

Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA

(2018) Pu Guo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms

(2017) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

The Drug Repurposing Hub: a next-generation drug library and information resource

(2017) Steven M Corsello et al.   NATURE MEDICINE

Post-marketing withdrawal of 462 medicinal products because of adverse drug reactions: a systematic review of the world literature

(2016) Igho J. Onakpoya et al.   BMC Medicine

Precise small-molecule recognition of a toxic CUG RNA repeat expansion

(2016) Suzanne G Rzuczek et al.   Nature Chemical Biology

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

(2016) Ryan A Flynn et al.   Nature Protocols

Phase II and phase III failures: 2013–2015

(2016) Richard K. Harrison   NATURE REVIEWS DRUG DISCOVERY

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Diazirine-Containing RNA Photo-Cross-Linking Probes for Capturing microRNA Targets

(2014) Kosuke Nakamoto et al.   JOURNAL OF ORGANIC CHEMISTRY

Reprogramming the Mechanism of Action of Chlorambucil by Coupling to a G-Quadruplex Ligand

(2014) Marco Di Antonio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

Using transcriptome sequencing to identify mechanisms of drug action and resistance

(2012) Sarah A Wacker et al.   Nature Chemical Biology

RTL-P: a sensitive approach for detecting sites of 2′-O-methylation in RNA molecules

(2012) Zhi-Wei Dong et al.   NUCLEIC ACIDS RESEARCH

Cardiotoxicity of kinase inhibitors: the prediction and translation of preclinical models to clinical outcomes

(2011) Thomas Force et al.   NATURE REVIEWS DRUG DISCOVERY

ChemMine tools: an online service for analyzing and clustering small molecules

(2011) T. W. H. Backman et al.   NUCLEIC ACIDS RESEARCH

Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA

(2010) Luigi Warren et al.   Cell Stem Cell

RNA under attack: Cellular handling of RNA damage

(2008) Elisabeth J. Wurtmann et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A Diazirine-Based Nucleoside Analogue for Efficient DNA Interstrand Photocross-Linking

(2008) Zhihai Qiu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY