Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies
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Title
Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies
Authors
Keywords
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Journal
Expert Opinion on Drug Discovery
Volume -, Issue -, Pages -
Publisher
Informa UK Limited
Online
2022-11-03
DOI
10.1080/17460441.2022.2134852
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Note: Only part of the references are listed.- DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor
- (2022) Raphael I. Benhamou et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Targeting Xist with compounds that disrupt RNA structure and X inactivation
- (2022) Rodrigo Aguilar et al. NATURE
- Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly
- (2022) Di Liu et al. NATURE METHODS
- Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA
- (2022) Qiuxia Chen et al. NUCLEIC ACIDS RESEARCH
- Thoughts on how to think (and talk) about RNA structure
- (2022) Quentin Vicens et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion
- (2022) Caroline Gubser Keller et al. Nature Communications
- 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
- Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq
- (2022) Alec N. Sexton et al. METHODS
- Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model
- (2021) Tomonori Shibata et al. Nature Communications
- Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase
- (2021) Eunhye Lee et al. Nature Communications
- Fragment‐Based Drug Discovery for RNA Targets
- (2021) Kasper P. Lundquist et al. ChemMedChem
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes
- (2021) Wayne K. Dawson et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Quantum Mechanics Helps Uncover Atypical Recognition Features in the Flavin Mononucleotide Riboswitch
- (2021) Indrajit Deb et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Reprogramming of Protein-Targeted Small-Molecule Medicines to RNA by Ribonuclease Recruitment
- (2021) Peiyuan Zhang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies
- (2021) Lukasz T. Olenginski et al. MOLECULES
- Geometric deep learning of RNA structure
- (2021) Raphael J. L. Townshend et al. SCIENCE
- Fragment molecular orbital calculations for biomolecules
- (2021) Kaori Fukuzawa et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids
- (2021) Bei Liu et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR
- (2020) Mihajlo Novakovic et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
- (2020) Kalli Kappel et al. NATURE METHODS
- PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions
- (2020) Herschel Mukherjee et al. ACS Chemical Biology
- IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex
- (2020) Jesse Davila-Calderon et al. Nature Communications
- 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
- Targeted design and identification of AC1NOD4Q to block activity of HOTAIR by abrogating the scaffold interaction with EZH2
- (2019) Yu Ren et al. Clinical Epigenetics
- 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
- Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery
- (2019) Sai Shashank Chavali et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Biosensor-surface plasmon resonance: A strategy to help establish a new generation RNA-specific small molecules
- (2019) Tam Vo et al. METHODS
- Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA
- (2019) Sarah L. Wicks et al. METHODS
- NMR Characterization of RNA Small Molecule Interactions
- (2019) Rhese D. Thompson 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
- Mechanisms and functions of ribosome-associated protein quality control
- (2019) Claudio A. P. Joazeiro NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Evidence for ligandable sites in structured RNA throughout the Protein Data Bank
- (2019) William M. Hewitt et al. BIOORGANIC & MEDICINAL CHEMISTRY
- Exploring the Potential of Small Molecule-Based Therapeutic Approaches for Targeting Trinucleotide Repeat Disorders
- (2019) Arun Kumar Verma et al. MOLECULAR NEUROBIOLOGY
- RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
- (2019) Jaswinder Singh et al. Nature Communications
- Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space
- (2019) Noreen F. Rizvi et al. SLAS Discovery
- Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution
- (2019) Kaiming Zhang et al. Nature Communications
- 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 Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
- (2018) Jiří Šponer et al. CHEMICAL REVIEWS
- Principles for targeting RNA with drug-like small molecules
- (2018) Katherine Deigan Warner et al. NATURE REVIEWS DRUG DISCOVERY
- Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
- (2018) Amparo Garcia-Lopez et al. Nature Communications
- Structure–Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch
- (2018) Quentin Vicens et al. ACS Chemical Biology
- 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
- Small molecules that target group II introns are potent antifungal agents
- (2018) Olga Fedorova et al. Nature Chemical Biology
- De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes
- (2018) Kalli Kappel et al. NATURE METHODS
- Drugging the RNA World
- (2018) Matthew D. Disney et al. Cold Spring Harbor Perspectives in Biology
- ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
- (2018) Ryan J. Andrews et al. PeerJ
- Small Molecule Inhibition of microRNA-210 Reprograms an Oncogenic Hypoxic Circuit
- (2017) Matthew G. Costales et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography
- (2017) J. R. Stagno et al. NATURE
- In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models
- (2017) Àlex L. González et al. PLoS One
- Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2
- (2017) Steven Busan et al. RNA
- Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers
- (2017) Manaswini Sivaramakrishnan et al. Nature Communications
- Viral internal ribosomal entry sites: four classes for one goal
- (2017) Justine Mailliot et al. Wiley Interdisciplinary Reviews-RNA
- 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
- 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
- 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
- The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures
- (2016) Gopinatha Suresh Kumar et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- SwiSpot: modeling riboswitches by spotting out switching sequences
- (2016) Marco Barsacchi et al. BIOINFORMATICS
- Precise small-molecule recognition of a toxic CUG RNA repeat expansion
- (2016) Suzanne G Rzuczek et al. Nature Chemical Biology
- DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo
- (2016) Meghan Zubradt et al. NATURE METHODS
- Automated screening for small organic ligands using DNA-encoded chemical libraries
- (2016) Willy Decurtins et al. Nature Protocols
- Non-coding RNAs as drug targets
- (2016) Masayuki Matsui et al. NATURE REVIEWS DRUG DISCOVERY
- 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
- 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
- Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA
- (2015) Wang-Yong Yang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- 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
- SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice
- (2015) James Palacino et al. Nature Chemical Biology
- Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis
- (2015) Matthew J Smola et al. Nature Protocols
- Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure
- (2015) Ryan T. Fuchs et al. PLoS One
- Discovery of Selective Ligands for Telomeric RNA G-quadruplexes (TERRA) through 19F-NMR Based Fragment Screening
- (2014) Miguel Garavís et al. ACS Chemical Biology
- Evaluating bias-reducing protocols for RNA sequencing library preparation
- (2014) Thomas J Jackson et al. BMC GENOMICS
- 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
- 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
- RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
- (2014) Nathan A Siegfried et al. NATURE METHODS
- 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
- 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
- Structure-Based Design of an RNA-Bindingp-Terphenylene Scaffold that Inhibits HIV-1 Rev Protein Function
- (2013) Luis González-Bulnes et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Covalent Small-Molecule-RNA Complex Formation Enables Cellular Profiling of Small-Molecule-RNA Interactions
- (2013) Lirui Guan et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle
- (2013) Neil M. Bell et al. BIOCHEMISTRY
- A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication
- (2013) Mi-Kyung Lee et al. CHEMICAL COMMUNICATIONS
- 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
- 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
- Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures
- (2012) Samuel Bleckley et al. PLoS One
- Identification of novel ligands for thiamine pyrophosphate (TPP) riboswitches
- (2011) Elena Cressina et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
- (2011) Kengo Sato et al. BIOINFORMATICS
- Ensemble of Secondary Structures for Encapsidated Satellite Tobacco Mosaic Virus RNA Consistent with Chemical Probing and Crystallography Constraints
- (2011) Susan J. Schroeder et al. BIOPHYSICAL JOURNAL
- Cellular IRES-mediated translation
- (2011) Anton A Komar et al. CELL CYCLE
- Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking
- (2011) Peter Daldrop et al. CHEMISTRY & BIOLOGY
- Rich Parameterization Improves RNA Structure Prediction
- (2011) Shay Zakov et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Identification of RNA Pseudoknot-Binding Ligand That Inhibits the −1 Ribosomal Frameshifting of SARS-Coronavirus by Structure-Based Virtual Screening
- (2011) So-Jung Park et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble
- (2011) Andrew C Stelzer et al. Nature Chemical Biology
- Expanded GGGGCC Hexanucleotide Repeat in Noncoding Region of C9ORF72 Causes Chromosome 9p-Linked FTD and ALS
- (2011) Mariely DeJesus-Hernandez et al. NEURON
- A Fragment-Based Approach to Identifying Ligands for Riboswitches
- (2010) Liuhong Chen et al. ACS Chemical Biology
- PHENIX: a comprehensive Python-based system for macromolecular structure solution
- (2010) Paul D. Adams et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs
- (2010) Adrian R. Ferré-D’Amaré METHODS
- CyloFold: secondary structure prediction including pseudoknots
- (2010) E. Bindewald et al. NUCLEIC ACIDS RESEARCH
- A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes
- (2010) Wanjun Gu et al. PLoS Computational Biology
- Predictions of RNA secondary structure by combining homologous sequence information
- (2009) Michiaki Hamada et al. BIOINFORMATICS
- Fpocket: An open source platform for ligand pocket detection
- (2009) Vincent Le Guilloux et al. BMC BIOINFORMATICS
- Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution
- (2009) Daniel A. Pomeranz Krummel et al. NATURE
- Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
- (2009) Alexander Serganov et al. NATURE
- Design, synthesis and selection of DNA-encoded small-molecule libraries
- (2009) Matthew A Clark et al. Nature Chemical Biology
- Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template
- (2009) Smadar Cohen-Chalamish et al. Nature Chemical Biology
- CENTROIDFOLD: a web server for RNA secondary structure prediction
- (2009) K. Sato et al. NUCLEIC ACIDS RESEARCH
- NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
- (2009) Douglas H. Turner et al. NUCLEIC ACIDS RESEARCH
- DOCK 6: Combining techniques to model RNA-small molecule complexes
- (2009) P. T. Lang et al. RNA
- Adaptive Ligand Binding by the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs
- (2009) Sunny D. Gilbert et al. STRUCTURE
- Prediction of RNA secondary structure using generalized centroid estimators
- (2008) Michiaki Hamada et al. BIOINFORMATICS
- SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing
- (2008) Herbert H. Tsang et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- 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
- Two-Dimensional Combinatorial Screening Identifies Specific Aminoglycoside−RNA Internal Loop Partners
- (2008) Matthew D. Disney et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
- (2008) Marc Parisien et al. NATURE
- The Vienna RNA Websuite
- (2008) A. R. Gruber et al. NUCLEIC ACIDS RESEARCH
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