Target-Directed Approaches for Screening Small Molecules against RNA Targets

Selective small molecule targeting of a triple helix encoded by the long non-coding RNA, MALAT1

(2019) Fardokht A Abulwerdi et al.   ACS Chemical Biology

Protein-slaying drugs could be the next blockbuster therapies

(2019) Megan Scudellari   NATURE

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 Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin

(2019) Matthew G. Costales et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unveiling the druggable RNA targets and small molecule therapeutics

(2019) Joanna Sztuba-Solinska et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Using SHAPE-MaP to probe small molecule-RNA interactions

(2019) Sarah Martin et al.   METHODS

Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA

(2019) Sarah L. Wicks et al.   METHODS

Fluorescence-based investigations of RNA-small molecule interactions

(2019) Kayleigh R. McGovern-Gooch et al.   METHODS

RNA-ALIS: Methodology for screening soluble RNAs as small molecule targets using ALIS affinity-selection mass spectrometry

(2019) Noreen F. Rizvi et al.   METHODS

The role of RNA G‐quadruplexes in human diseases and therapeutic strategies

(2019) Prakash Kharel et al.   Wiley Interdisciplinary Reviews-RNA

Long Non-coding RNAs as Functional and Structural Chromatin Modulators in Acute Myeloid Leukemia

(2019) Alexander A. Wurm et al.   Frontiers in Oncology

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

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

The role of long noncoding RNA in major human disease

(2019) Xiaoli Zhang et al.   BIOORGANIC CHEMISTRY

Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry

(2018) Noreen F. Rizvi et al.   ACS Chemical Biology

Measuring RNA–Ligand Interactions with Microscale Thermophoresis

(2018) Michelle H. Moon et al.   BIOCHEMISTRY

RNA-Targeted Therapeutics

(2018) Stanley T. Crooke et al.   Cell Metabolism

Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy

(2018) Walter Becker et al.   CHEMPHYSCHEM

Therapeutic Potential of Small Activating RNAs (saRNAs) in Human cancers

(2018) Sorah Yoon et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

MS methods to study macromolecule-ligand interaction: Applications in drug discovery

(2018) Federico Riccardi Sirtori et al.   METHODS

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

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

Tapping the RNA world for therapeutics

(2018) Judy Lieberman   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanistic studies of a small-molecule modulator of SMN2 splicing

(2018) Jingxin Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation

(2018) Carin K. Ingemarsdotter et al.   Retrovirology

Expansion of cat-ELCCA for the Discovery of Small Molecule Inhibitors of the Pre-let-7–Lin28 RNA–Protein Interaction

(2018) Daniel A. Lorenz et al.   ACS Medicinal Chemistry Letters

Selective Small Molecule Recognition of RNA Base Pairs

(2018) Hafeez S. Haniff et al.   ACS Combinatorial Science

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

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

Tapping the RNA world for therapeutics

(2018) Judy Lieberman   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modulation of oncogenic miRNA biogenesis using functionalized polyamines

(2018) Cathy Staedel et al.   Scientific Reports

Target deconvolution from phenotype-based drug discovery by using chemical proteomics approaches

(2018) Kazuishi Kubota et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

A Massively Parallel Selection of Small Molecule-RNA Motif Binding Partners Informs Design of an Antiviral from Sequence

(2018) Jessica L. Childs-Disney et al.   Chem

Precise Small Molecule Degradation of a Noncoding RNA Identifies Cellular Binding Sites and Modulates an Oncogenic Phenotype

(2018) Yue Li et al.   ACS Chemical Biology

Development of MTL-CEBPA: Small Activating RNA Drug for Hepatocellular Carcinoma

(2018) Ryan L. Setten et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA)

(2018) Atwood K. Cheung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small Molecule Inhibition of microRNA-210 Reprograms an Oncogenic Hypoxic Circuit

(2017) Matthew G. Costales et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FDA-Approved Oligonucleotide Therapies in 2017

(2017) Cy A. Stein et al.   MOLECULAR THERAPY

Antisense oligonucleotides: the next frontier for treatment of neurological disorders

(2017) Carlo Rinaldi et al.   Nature Reviews Neurology

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR

(2017) Neeraj N. Patwardhan et al.   MedChemComm

Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

(2017) Anders Foller Füchtbauer et al.   Scientific Reports

Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

(2017) Sai Pradeep Velagapudi et al.   ACS Central Science

Protein-ligand binding affinity determination by the waterLOGSY method: An optimised approach considering ligand rebinding

(2017) Renjie Huang et al.   Scientific Reports

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

Discovery of Inhibitors of MicroRNA-21 Processing Using Small Molecule Microarrays

(2016) Colleen M. Connelly et al.   ACS Chemical Biology

Small Molecule Recognition and Tools to Study Modulation of r(CGG)exp in Fragile X-Associated Tremor Ataxia Syndrome

(2016) Wang-Yong Yang et al.   ACS Chemical Biology

Development of pharmacophore models for small molecules targeting RNA: Application to the RNA repeat expansion in myotonic dystrophy type 1

(2016) Alicia J. Angelbello et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A Rapid and Versatile Assay for Ago2-Mediated Cleavage by Using Branched Rolling Circle Amplification

(2016) Marlen Hesse et al.   CHEMBIOCHEM

Microarray-based technologies for the discovery of selective, RNA-binding molecules

(2016) Fardokht A. Abulwerdi et al.   METHODS

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

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

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

(2016) Chun Kit Kwok et al.   NATURE METHODS

Twenty years on: the impact of fragments on drug discovery

(2016) Daniel A. Erlanson et al.   NATURE REVIEWS DRUG DISCOVERY

A comprehensive map of molecular drug targets

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

Non-coding RNAs as regulators in epigenetics

(2016) Jian-Wei Wei et al.   ONCOLOGY REPORTS

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

Structure of a low-population binding intermediate in protein-RNA recognition

(2016) Aditi N. Borkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

(2016) Subodh Kumar Mishra et al.   Database-The Journal of Biological Databases and Curation

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

Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy

(2015) Suzanne G. Rzuczek et al.   ACS Chemical Biology

Small molecule compounds targeting miRNAs for cancer therapy

(2015) Paloma del C. Monroig et al.   ADVANCED DRUG DELIVERY REVIEWS

Differential Scanning Fluorimetry for Monitoring RNA Stability

(2015) Robert Silvers et al.   CHEMBIOCHEM

Rationally designed molecular beacons for bioanalytical and biomedical applications

(2015) Jing Zheng et al.   CHEMICAL SOCIETY REVIEWS

The resurgence of phenotypic screening in drug discovery and development

(2015) Bridget K. Wagner   Expert Opinion on Drug Discovery

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

(2015) GuanQun Liu et al.   JOURNAL OF VIROLOGY

Conformational flexibility of viral RNA switches studied by FRET

(2015) Mark A. Boerneke et al.   METHODS

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

(2015) James Palacino et al.   Nature Chemical Biology

Rapid RNA–ligand interaction analysis through high-information content conformational and stability landscapes

(2015) Nathan J. Baird et al.   Nature Communications

Discovery of Selective Ligands for Telomeric RNA G-quadruplexes (TERRA) through 19F-NMR Based Fragment Screening

(2014) Miguel Garavís et al.   ACS Chemical Biology

Solution-Based Indirect Affinity Selection Mass Spectrometry—A General Tool For High-Throughput Screening Of Pharmaceutical Compound Libraries

(2014) Thomas N. O’Connell et al.   ANALYTICAL CHEMISTRY

Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor

(2014) Sai Pradeep Velagapudi et al.   CHEMICAL COMMUNICATIONS

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically

(2014) Katherine Deigan Warner et al.   CHEMISTRY & BIOLOGY

Elucidation of Nucleic Acid–Drug Interactions by Tandem Mass Spectrometry

(2014) Yvonne Hari et al.   CHIMIA

Comparison of the sensitivities of WaterLOGSY and saturation transfer difference NMR experiments

(2014) Aleksandar Antanasijevic et al.   JOURNAL OF BIOMOLECULAR NMR

MicroScale Thermophoresis: Interaction analysis and beyond

(2014) Moran Jerabek-Willemsen et al.   JOURNAL OF MOLECULAR STRUCTURE

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

mRNA-based therapeutics — developing a new class of drugs

(2014) Ugur Sahin et al.   NATURE REVIEWS DRUG DISCOVERY

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional conservation despite structural divergence in ligand-responsive RNA switches

(2014) Mark A. Boerneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis

(2014) Ece Cazibe Gaffarogullari et al.   RNA Biology

SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy

(2014) N. A. Naryshkin et al.   SCIENCE

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

A Molecular-Beacon-Based Screen for Small Molecule Inhibitors of miRNA Maturation

(2013) Debojit Bose et al.   ACS Chemical Biology

Structure of the Myotonic Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity

(2013) Jessica L. Childs-Disney et al.   ACS Chemical Biology

Targeting the Production of Oncogenic MicroRNAs with Multimodal Synthetic Small Molecules

(2013) Duc Duy Vo et al.   ACS Chemical Biology

Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

(2013) Neil M. Bell et al.   BIOCHEMISTRY

Learning from our mistakes: The ‘unknown knowns’ in fragment screening

(2013) Ben J. Davis et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication

(2013) Mi-Kyung Lee et al.   CHEMICAL COMMUNICATIONS

Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function

(2013) Arun A. Tanpure et al.   ISRAEL JOURNAL OF CHEMISTRY

Fragment-based drug discovery using NMR spectroscopy

(2013) Mary J. Harner et al.   JOURNAL OF BIOMOLECULAR NMR

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SMMRNA: a database of small molecule modulators of RNA

(2013) Ankita Mehta et al.   NUCLEIC ACIDS RESEARCH

LigandRNA: computational predictor of RNA-ligand interactions

(2013) A. Philips et al.   RNA

Two high-throughput screening assays for aberrant RNA–protein interactions in myotonic dystrophy type 1

(2012) Catherine Z. Chen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Label-Free Microscale Thermophoresis Discriminates Sites and Affinity of Protein-Ligand Binding

(2012) Susanne A. I. Seidel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of novel telomeric G-quadruplex-targeting chemical scaffolds through screening of three NCI libraries

(2012) Khondaker M. Rahman et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Expanding the Number of ‘Druggable’ Targets: Non-Enzymes and Protein-Protein Interactions

(2012) Leah N. Makley et al.   Chemical Biology & Drug Design

Formation of telomeric repeat-containing RNA (TERRA) foci in highly proliferating mouse cerebellar neuronal progenitors and medulloblastoma

(2012) Z. Deng et al.   JOURNAL OF CELL SCIENCE

Design of a Bioactive Small Molecule That Targets the Myotonic Dystrophy Type 1 RNA via an RNA Motif–Ligand Database and Chemical Similarity Searching

(2012) Raman Parkesh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reporter assays for studying quadruplex nucleic acids

(2012) Kangkan Halder et al.   METHODS

From dynamic combinatorial ‘hit’ to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy

(2012) Leslie O. Ofori et al.   NUCLEIC ACIDS RESEARCH

Fluorescent intercalator displacement replacement (FIDR) assay: determination of relative thermodynamic and kinetic parameters in triplex formation—a case study using triplex-forming LNAs

(2012) Sujay P. Sau et al.   NUCLEIC ACIDS RESEARCH

A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis

(2012) Danielle Biscaro Pedrolli et al.   NUCLEIC ACIDS RESEARCH

G4LDB: a database for discovering and studying G-quadruplex ligands

(2012) Qian Li et al.   NUCLEIC ACIDS RESEARCH

Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches

(2012) S. M. Dibrov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Tuan Tran et al.   Nature Communications

Molecular Interaction Studies Using Microscale Thermophoresis

(2011) Moran Jerabek-Willemsen et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Identification of Novel Quadruplex Ligands from Small Molecule Libraries by FRET-Based High-Throughput Screening

(2011) Armin Benz et al.   CHEMBIOCHEM

Ternary resin-bound dynamic combinatorial chemistry

(2011) Anna V. Gromova et al.   CHEMICAL COMMUNICATIONS

Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

(2011) Peter Daldrop et al.   CHEMISTRY & BIOLOGY

Identification of Ligands for the Tau Exon 10 Splicing Regulatory Element RNA by Using Dynamic Combinatorial Chemistry

(2011) Paula López-Senín et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

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

Trends in the exploitation of novel drug targets

(2011) Mathias Rask-Andersen et al.   NATURE REVIEWS DRUG DISCOVERY

Impact of high-throughput screening in biomedical research

(2011) Ricardo Macarron et al.   NATURE REVIEWS DRUG DISCOVERY

Identification of oncogenic microRNA-17-92/ZBTB4/specificity protein axis in breast cancer

(2011) K Kim et al.   ONCOGENE

Molecular docking for virtual screening of natural product databases

(2011) Dik-Lung Ma et al.   Chemical Science

A modified fluorescent intercalator displacement assay for RNA ligand discovery

(2010) Papa Nii Asare-Okai et al.   ANALYTICAL BIOCHEMISTRY

Fluorescence Polarization/Anisotropy in Diagnostics and Imaging

(2010) David M. Jameson et al.   CHEMICAL REVIEWS

Fluorescent Indicator Displacement Assay for Ligand−RNA Interactions

(2010) Jinhua Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fragment screening against the thiamine pyrophosphate riboswitchthiM

(2010) Elena Cressina et al.   Chemical Science

An effective docking strategy for virtual screening based on multi-objective optimization algorithm

(2009) Honglin Li et al.   BMC BIOINFORMATICS

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

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

(2009) P. T. Lang et al.   RNA

Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay

(2008) Malathy Krishnamurthy et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Targeting RNA with Small Molecules

(2008) Jason R. Thomas et al.   CHEMICAL REVIEWS

Affinity Selection-Mass Spectrometry and its Emerging Application to the High Throughput Screening of G Protein-Coupled Receptors

(2008) Charles Whitehurst et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

RNA in motion

(2008) Kathleen B Hall   CURRENT OPINION IN CHEMICAL BIOLOGY

RNA dynamics: it is about time

(2008) Hashim M Al-Hashimi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Estimating Protein−Ligand Binding Affinity Using High-Throughput Screening by NMR

(2008) Matthew D. Shortridge et al.   JOURNAL OF COMBINATORIAL CHEMISTRY

Discovery of Ligands for a Novel Target, the Human Telomerase RNA, Based on Flexible-Target Virtual Screening and NMR

(2008) Irene Gómez Pinto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Dynamic Combinatorial Selection of Molecules Capable of Inhibiting the (CUG) Repeat RNA−MBNL1 Interaction In Vitro: Discovery of Lead Compounds Targeting Myotonic Dystrophy (DM1)

(2008) Peter C. Gareiss et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization

(2008) Markus Hafner et al.   Nature Protocols