NMR 1H,19F-based screening of the four stem-looped structure 5_SL1–SL4 located in the 5′-untranslated region of SARS-CoV 2 RNA

Daniel Hymon, Jason Martins, Christian Richter, Sridhar Sreeramulu, Anna Wacker, Jan Ferner, Neeraj N. Patwardhan, Amanda E. Hargrove and Harald Schwalbe

RSC Med. Chem., 2024, 15, 165
DOI: 10.1039/D3MD00322A

Small molecule recognition of disease-relevant RNA structures

Samantha M. Meyer, Christopher C. Williams, Yoshihiro Akahori, Toru Tanaka, Haruo Aikawa, Yuquan Tong, Jessica L. Childs-Disney and Matthew D. Disney

Chem. Soc. Rev., 2020, 49, 7167
DOI: 10.1039/D0CS00560F

Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy

Daria V. Berdnikova

Chem. Commun., 2021, 57, 10819
DOI: 10.1039/D1CC04241F

Energy-resolved mass spectrometry to investigate nucleobase triplexes – a study applied to triplex-forming artificial nucleobases

Mauro Safir Filho, Lionel Massi, Antoine Millet, Dylan Michel, Wafa Moussa, Cyril Ronco and Rachid Benhida

New J. Chem., 2022, 46, 8112
DOI: 10.1039/D2NJ00665K

In silicostudy of the binding of daunomycin and phenylalanine transfer RNA: probe molecular recognition for structure-based drug design

Gonghao Wu, Jipeng Li, Jianxin Yang and Xingqing Xiao

Mol. Syst. Des. Eng., 2023, 8, 786
DOI: 10.1039/D2ME00236A

Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives

Aixiao Li, Ahmed Bouhss, Marie-Jeanne Clément, Cyril Bauvais, J. Paul Taylor, Guillaume Bollot and David Pastré

Front. Mol. Biosci., 2023, 10
DOI: 10.3389/fmolb.2023.1298441

Small molecule approaches to targeting RNA

Sandra Kovachka, Marc Panosetti, Benedetto Grimaldi, Stéphane Azoulay, Audrey Di Giorgio and Maria Duca

Nat Rev Chem, 2024, 8, 120
DOI: 10.1038/s41570-023-00569-9

RNA-Activatable Near-Infrared Photosensitizer for Cancer Therapy

Yin Jiang, Shumei Huang, Haiying Ma, Jintao Weng, Xiaomeng Du, Zhenxin Lin, Jaewon Kim, Wenhui You, Huatang Zhang, Dongqing Wang, Jong Seung Kim and Hongyan Sun

J. Am. Chem. Soc., 2024, 146, 25270
DOI: 10.1021/jacs.4c09470

Docking and scoring for nucleic acid–ligand interactions: Principles and current status

Yuyu Feng, Yumeng Yan, Jiahua He, Huanyu Tao, Qilong Wu and Sheng-You Huang

Drug Discovery Today, 2022, 27, 838
DOI: 10.1016/j.drudis.2021.10.013

DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites

Illimar Hugo Rekand and Ruth Brenk

J. Chem. Inf. Model., 2021, 61, 4068
DOI: 10.1021/acs.jcim.1c00155

Docking and Molecular Dynamics Simulation‐Based Analysis of Advanced Small‐Molecule Kinase Inhibitors Identified pre‐let‐7 miRNA Binders

Soma Roy, Yang Liu and Peng Wu

ChemBioChem, 2025
DOI: 10.1002/cbic.202500421

Inhibition of SARS-CoV-2 by Targeting Conserved Viral RNA Structures and Sequences

Shalakha Hegde, Zhichao Tang, Junxing Zhao and Jingxin Wang

Front. Chem., 2021, 9
DOI: 10.3389/fchem.2021.802766

Quantitative Microscopic Observation of Base–Ligand Interactions via Hydrogen Bonds by Single-Molecule Counting

Yusuke Takashima, Yuki Komoto, Takahito Ohshiro, Kazuhiko Nakatani and Masateru Taniguchi

J. Am. Chem. Soc., 2023, 145, 1310
DOI: 10.1021/jacs.2c11260

Chromenopyrazole−Peptide Conjugates as Small‐Molecule Based Inhibitors Disrupting the Protein−RNA Interaction of LIN28‐let‐7

Pascal Hommen, Jimin Hwang, Fubao Huang, Lydia Borgelt, Lisa Hohnen and Peng Wu

ChemBioChem, 2023, 24
DOI: 10.1002/cbic.202300376

Synthetic RNA Modulators in Drug Discovery

Farzad Zamani and Takayoshi Suzuki

J. Med. Chem., 2021, 64, 7110
DOI: 10.1021/acs.jmedchem.1c00154

RNA-Targeting Splicing Modifiers: Drug Development and Screening Assays

Zhichao Tang, Junxing Zhao, Zach J. Pearson, Zarko V. Boskovic and Jingxin Wang

Molecules, 2021, 26, 2263
DOI: 10.3390/molecules26082263

Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery

Meredith J. Zeller, Ashok Nuthanakanti, Kelin Li, Jeffrey Aubé, Alexander Serganov and Kevin M. Weeks

ACS Chem. Biol., 2022, 17, 438
DOI: 10.1021/acschembio.1c00880

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA

Jianbo Zhao, Scott D. Kennedy and Douglas H. Turner

J. Chem. Theory Comput., 2022, 18, 1241
DOI: 10.1021/acs.jctc.1c00643

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery

Kengo Sato and Michiaki Hamada

Briefings in Bioinformatics, 2023, 24
DOI: 10.1093/bib/bbad186

Recognition of Noncanonical RNA Base Pairs Using Triplex-Forming Peptide Nucleic Acids

Sara Farshineh Saei, Vladislavs Baskevics, Martins Katkevics and Eriks Rozners

ACS Chem. Biol., 2025, 20, 179
DOI: 10.1021/acschembio.4c00662

Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis

Jake M. Peterson, Collin A. O'Leary, Evelyn C. Coppenbarger, Van S. Tompkins and Walter N. Moss

MethodsX, 2023, 11, 102275
DOI: 10.1016/j.mex.2023.102275

The Emergence of Oligonucleotide Building Blocks in the Multispecific Proximity-Inducing Drug Toolbox of Destruction

Kevin Xiao Tong Zhou and Katherine E. Bujold

ACS Chem. Biol., 2025, 20, 3
DOI: 10.1021/acschembio.4c00311

MicroRNAs modulate neuroinflammation after intracerebral hemorrhage: Prospects for new therapy

Siqi Xia, Yonghe Zheng, Feng Yan and Gao Chen

Front. Immunol., 2022, 13
DOI: 10.3389/fimmu.2022.945860

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Eric Largy, Alexander König, Anirban Ghosh, Debasmita Ghosh, Sanae Benabou, Frédéric Rosu and Valérie Gabelica

Chem. Rev., 2022, 122, 7720
DOI: 10.1021/acs.chemrev.1c00386

A Chemical Biology Perspective to Therapeutic Regulation of RNA Splicing in Spinal Muscular Atrophy (SMA)

Lei Zhang, Frank Abendroth and Olalla Vázquez

ACS Chem. Biol., 2022, 17, 1293
DOI: 10.1021/acschembio.2c00161

Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases

Kazuhiko NAKATANI

Proc. Jpn. Acad., Ser. B, 2022, 98, 30
DOI: 10.2183/pjab.98.003

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

Yang Liu, Georg L. Goebel, Laurin Kanis, Oguz Hastürk, Claus Kemker and Peng Wu

JACS Au, 2024, 4, 1436
DOI: 10.1021/jacsau.3c00832

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Shalakha Hegde, Sana Akhter, Zhichao Tang, Chang Qi, Chenguang Yu, Anna Lewicka, Yu Liu, Kushal Koirala, Mikhail Reibarkh, Kevin P Battaile, Anne Cooper, Scott Lovell, Erik D Holmstrom, Xiao Wang, Joseph A Piccirilli, Qi Gao, Yinglong Miao and Jingxin Wang

Nucleic Acids Research, 2025, 53
DOI: 10.1093/nar/gkaf559

Exploiting functional regions in the viral RNA genome as druggable entities

Dehua Luo, Yingge Zheng, Zhiyuan Huang, Zi Wen, Lijun Guo, Yingxiang Deng, Qingling Li, Yuqing Bai, Shozeb Haider and Dengguo Wei

eLife, 2025, 13
DOI: 10.7554/eLife.103923.3

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Daria V. Berdnikova, Paolo Carloni, Sybille Krauß and Giulia Rossetti

Molecules, 2021, 26, 3384
DOI: 10.3390/molecules26113384

Targeting MicroRNAs with Small Molecules

Kisanet Tadesse and Raphael I. Benhamou

ncRNA, 2024, 10, 17
DOI: 10.3390/ncrna10020017

RLsite: Integrating 3D-CNN and BiLSTM for RNA-ligand binding site prediction

Yan 艳 Zou 邹, Lang 浪 Yang 杨, Yanhui 艳辉 Liu 刘 and Yuyu 玉宇 Feng 冯

Chinese Phys. B, 2025, 34, 088709
DOI: 10.1088/1674-1056/adea9b

Analysis of key genes in Mycobacterium ulcerans reveals conserved RNA structural motifs and regions with apparent pressure to remain unstructured

Warren B. Rouse, Jessica Gart, Lauren Peysakhova and Walter N. Moss

Front. Trop. Dis, 2022, 3
DOI: 10.3389/fitd.2022.1009362

A map of the SARS-CoV-2 RNA structurome

Ryan J Andrews, Collin A O’Leary, Van S Tompkins, Jake M Peterson, Hafeez S Haniff, Christopher Williams, Matthew D Disney and Walter N Moss

NAR Genomics and Bioinformatics, 2021, 3
DOI: 10.1093/nargab/lqab043

Rethinking IRPs/IRE system in neurodegenerative disorders: Looking beyond iron metabolism

Zhengyang Yao, Lin Fu, Fengju Jia, Mingxia Bi, Qian Jiao, Xi Chen, Xixun Du and Hong Jiang

Ageing Research Reviews, 2022, 73, 101511
DOI: 10.1016/j.arr.2021.101511

MicroRNAs in the Regulation of Solute Carrier Proteins Behind Xenobiotic and Nutrient Transport in Cells

Colleen Yi and Ai-Ming Yu

Front. Mol. Biosci., 2022, 9
DOI: 10.3389/fmolb.2022.893846

Type I BODITh Photosensitizers with Twisted Conformation for Augmented Photodynamic Therapy and FOXO1-Involved Apoptosis

Tian Zhang, Jiahong Li, Jinjun Shao, Xiaorui Wang, Peng Chen, Huili Ma, Lulu Qu and Xiaochen Dong

Nano Lett., 2025, 25, 8379
DOI: 10.1021/acs.nanolett.5c01663

A commentary on the use of pharmacoenhancers in the pharmaceutical industry and the implication for DMPK drug discovery strategies

Vanessa Martins, Lynsey Fazal, Aram Oganesian, Alpesh Shah, Jessie Stow, Hugh Walton and Nicola Wilsher

Xenobiotica, 2022, 52, 786
DOI: 10.1080/00498254.2022.2130838

Rational guide RNA engineering for small-molecule control of CRISPR/Cas9 and gene editing

Xingyu Liu, Wei Xiong, Qianqian Qi, Yutong Zhang, Huimin Ji, Shuangyu Cui, Jing An, Xiaoming Sun, Hao Yin, Tian Tian and Xiang Zhou

Nucleic Acids Research, 2022, 50, 4769
DOI: 10.1093/nar/gkac255

Synthesis of Bleomycin-Inspired RNA Ligands Targeting the Biogenesis of Oncogenic miRNAs

Chloé Maucort, Maurinne Bonnet, Jean-Claude Ortuno, Gordon Tucker, Emie Quissac, Maïté Verreault, Stéphane Azoulay, Christophe Di Giorgio, Audrey Di Giorgio and Maria Duca

J. Med. Chem., 2023, 66, 10639
DOI: 10.1021/acs.jmedchem.3c00797

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

Anita Donlic, Emily G. Swanson, Liang-Yuan Chiu, Sarah L. Wicks, Aline Umuhire Juru, Zhengguo Cai, Kamillah Kassam, Chris Laudeman, Bilva G. Sanaba, Andrew Sugarman, Eunseong Han, Blanton S. Tolbert and Amanda E. Hargrove

ACS Chem. Biol., 2022, 17, 1556
DOI: 10.1021/acschembio.2c00224

Small molecules targeting microRNAs: new opportunities and challenges in precision cancer therapy

Ancuta Jurj, Beatrice Fontana, Gabriele Varani and George A. Calin

Trends in Cancer, 2024, 10, 809
DOI: 10.1016/j.trecan.2024.06.006