Targeting RNA structures in diseases with small molecules

RNA therapeutics on the rise

(2020) Feng Wang et al.   NATURE REVIEWS DRUG DISCOVERY

Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans

(2018) Anthony M. Mustoe et al.   BIOCHEMISTRY

Management of the toxicities of common targeted therapeutics for gynecologic cancers

(2018) Camille C. Gunderson et al.   GYNECOLOGIC ONCOLOGY

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

(2018) Laura R. Ganser et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

(2018) Laura R. Ganser et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA Structure Design Improves Activity and Specificity of trans -Splicing-Triggered Cell Death in a Suicide Gene Therapy Approach

(2018) Sushmita Poddar et al.   Molecular Therapy-Nucleic Acids

Machine Learning for Drug-Target Interaction Prediction

(2018) Ruolan Chen et al.   MOLECULES

Challenges and Approaches to Predicting RNA with Multiple Functional Structures

(2018) Susan J Schroeder   RNA

Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity

(2018) Su Yang et al.   Cell Reports

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

(2017) Ali Ezzat et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression

(2017) Meredith Corley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slow molecular recognition by RNA

(2017) Kristin R. Gleitsman et al.   RNA

Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers

(2017) Manaswini Sivaramakrishnan et al.   Nature Communications

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

(2017) Meiling Piao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence

(2016) Matthew D. Disney et al.   ACCOUNTS OF CHEMICAL RESEARCH

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs

(2016) Matthew D. Disney et al.   ACS Chemical Biology

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm

(2016) Huimin Luo et al.   BIOINFORMATICS

Predicting drug target interactions using meta-path-based semantic network analysis

(2016) Gang Fu et al.   BMC BIOINFORMATICS

A click chemistry-based microRNA maturation assay optimized for high-throughput screening

(2016) Daniel A. Lorenz et al.   CHEMICAL COMMUNICATIONS

Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design

(2016) Fumiaki Yokokawa et al.   JOURNAL OF MEDICINAL CHEMISTRY

A comprehensive map of molecular drug targets

(2016) Rita Santos et al.   NATURE REVIEWS DRUG DISCOVERY

The P42 peptide and Peptide-based therapies for Huntington’s disease

(2016) Cecilia Marelli et al.   Orphanet Journal of Rare Diseases

Design of a small molecule against an oncogenic noncoding RNA

(2016) Sai Pradeep Velagapudi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Molecule Inhibition of miR-544 Biogenesis Disrupts Adaptive Responses to Hypoxia by Modulating ATM-mTOR Signaling

(2015) Christopher L. Haga et al.   ACS Chemical Biology

An overview of the clinical application of antisense oligonucleotides for RNA-targeting therapies

(2015) Graham McClorey et al.   CURRENT OPINION IN PHARMACOLOGY

Rationally Designed Small Molecules That Target Both the DNA and RNA Causing Myotonic Dystrophy Type 1

(2015) Lien Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice

(2015) James Palacino et al.   Nature Chemical Biology

RNA Structures as Mediators of Neurological Diseases and as Drug Targets

(2015) Viachaslau Bernat et al.   NEURON

The Expanding View of RNA and DNA Function

(2014) Ronald R. Breaker et al.   CHEMISTRY & BIOLOGY

Therapeutic potentials of gene silencing by RNA interference: Principles, challenges, and new strategies

(2014) Yan Deng et al.   GENE

Targeting Toxic RNAs that Cause Myotonic Dystrophy Type 1 (DM1) with a Bisamidinium Inhibitor

(2014) Chun-Ho Wong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification of Biologically Active, HIV TAR RNA-Binding Small Molecules Using Small Molecule Microarrays

(2014) Joanna Sztuba-Solinska et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sequence-based design of bioactive small molecules that target precursor microRNAs

(2014) Sai Pradeep Velagapudi et al.   Nature Chemical Biology

Discovery of a Biomarker and Lead Small Molecules to Target r(GGGGCC)-Associated Defects in c9FTD/ALS

(2014) Zhaoming Su et al.   NEURON

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Screening for inhibitors of the hepatitis C virus internal ribosome entry site RNA

(2013) Shou Zhou et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

Virtual Screening Strategies in Drug Discovery: A Critical Review

(2013) A. Lavecchia et al.   CURRENT MEDICINAL CHEMISTRY

LigandRNA: computational predictor of RNA-ligand interactions

(2013) A. Philips et al.   RNA

Fragment Based Drug Design: From Experimental to Computational Approaches

(2012) A. Kumar et al.   CURRENT MEDICINAL CHEMISTRY

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA-mediated regulation of gene expression is affected by disease-associated SNPs within the 3′-UTR via altered RNA structure

(2012) Ulrike Haas et al.   RNA Biology

Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations

(2012) Tuan Tran et al.   Nature Communications

Structure of the HIV-1 Frameshift Site RNA Bound to a Small Molecule Inhibitor of Viral Replication

(2011) Ryan J. Marcheschi et al.   ACS Chemical Biology

The Tuberculosis Drug Streptomycin as a Potential Cancer Therapeutic: Inhibition of miR-21 Function by Directly Targeting Its Precursor

(2011) Debojit Bose et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Strategies in the Rational Drug Design

(2011) T. Mavromoustakos et al.   CURRENT MEDICINAL CHEMISTRY

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

(2011) Andrew C Stelzer et al.   Nature Chemical Biology

How were new medicines discovered?

(2011) David C. Swinney et al.   NATURE REVIEWS DRUG DISCOVERY

A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD

(2011) Alan E. Renton et al.   NEURON

Structure-Activity Relationships through Sequencing (StARTS) Defines Optimal and Suboptimal RNA Motif Targets for Small Molecules

(2010) Sai Pradeep Velagapudi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Small Molecule Modifiers of MicroRNA miR-122 Function for the Treatment of Hepatitis C Virus Infection and Hepatocellular Carcinoma

(2010) Douglas D. Young et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Repeat expansion disease: progress and puzzles in disease pathogenesis

(2010) Albert R. La Spada et al.   NATURE REVIEWS GENETICS

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Rational drug design

(2009) Soma Mandal et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

FOG: Fragment Optimized Growth Algorithm for thede NovoGeneration of Molecules Occupying Druglike Chemical Space

(2009) Peter S. Kutchukian et al.   Journal of Chemical Information and Modeling

Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA

(2009) Jerod Parsons et al.   Nature Chemical Biology

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

(2009) J. F. Arambula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Role of RNA structure in regulating pre-mRNA splicing

(2009) M. Bryan Warf et al.   TRENDS IN BIOCHEMICAL SCIENCES

Small-Molecule Inhibitors of MicroRNA miR-21 Function

(2008) Kiranmai Gumireddy et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets

(2008) Christophe Guilbert et al.   Journal of Chemical Information and Modeling

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

CONFIRM: connecting fragments found in receptor molecules

(2008) David C. Thompson et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Two-Dimensional Combinatorial Screening Identifies Specific Aminoglycoside−RNA Internal Loop Partners

(2008) Matthew D. Disney et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

(2008) D. N. Wilson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA