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

Forced intercalation-induced light-up peptides as fluorogenic indicators for the HIV-1 TAR RNA-ligand assay

En Ting Tabitha Lee, Yusuke Sato, Akunna F. Ujuagu and Seiichi Nishizawa

Analyst, 2024, 149, 4179
DOI: 10.1039/D4AN00530A

Development of 2-deoxystreptamine–nucleobase conjugates for the inhibition of oncogenic miRNA production

Thi Phuong Anh Tran, Sylvain Poulet, Mélanie Pernak, Anita Rayar, Stéphane Azoulay, Audrey Di Giorgio and Maria Duca

RSC Med. Chem., 2022, 13, 311
DOI: 10.1039/D1MD00345C

Cyclic peptides targeting the SARS-CoV-2 programmed ribosomal frameshifting RNA from a multiplexed phage display library

Jacob A. Iannuzzelli, Rachel Bonn, Andrew S. Hong, Abhijith Saseendran Anitha, Jermaine L. Jenkins, Joseph E. Wedekind and Rudi Fasan

Chem. Sci., 2024, 15, 19520
DOI: 10.1039/D4SC04026K

Unveiling the promise of peptide nucleic acids as functional linkers for an RNA imaging platform

Aleksandra J. Wierzba, Erin M. Richards, Shelby R. Lennon, Robert T. Batey and Amy E. Palmer

RSC Chem. Biol., 2025, 6, 249
DOI: 10.1039/D4CB00274A

Chemotranscriptomic profiling with a thiamine monophosphate photoaffinity probe

Stefan Crielaard, Casper F. M. Peters, Alexandar Slivkov, Daphne A. L. van den Homberg and Willem A. Velema

Chem. Sci., 2025, 16, 4725
DOI: 10.1039/D4SC06189F

New perspectives in cancer drug development: computational advances with an eye to design

Matteo Castelli, Stefano A. Serapian, Filippo Marchetti, Alice Triveri, Valentina Pirota, Luca Torielli, Simona Collina, Filippo Doria, Mauro Freccero and Giorgio Colombo

RSC Med. Chem., 2021, 12, 1491
DOI: 10.1039/D1MD00192B

Three- and four-stranded nucleic acid structures and their ligands

Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi and Daisuke Miyoshi

RSC Chem. Biol., 2025, 6, 466
DOI: 10.1039/D4CB00287C

Nucleic acids as templates and catalysts in chemical reactions: target-guided dynamic combinatorial chemistry and in situ click chemistry and DNA/RNA induced enantioselective reactions

Puja Saha, Deepanjan Panda and Jyotirmayee Dash

Chem. Soc. Rev., 2023, 52, 4248
DOI: 10.1039/D3CS00166K

Fluorescent indicator displacement assay for the discovery of UGGAA repeat-targeted small molecules

Tomonori Shibata, Yasumasa Matsumoto, Akiko Iihara, Kazunori Yamada, Hiroshi Ochiai, Ryo Saito, Shinichi Kusaka and Toshiyuki Kume

Chem. Commun., 2023, 59, 5071
DOI: 10.1039/D3CC00837A

Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system

Elisabeth Kallert, Laura Almena Rodriguez, Jan-Åke Husmann, Kathrin Blatt and Christian Kersten

RSC Med. Chem., 2024, 15, 1527
DOI: 10.1039/D3MD00696D

Guanidine modification improves functions of natural RNA-targeting alkaloids

Tamaki Endoh, Sagar Satpathi, Yutong Chen, Saki Matsumoto, Tatsuya Ohyama, Peter Podbevšek, Janez Plavec, Kazumitsu Onizuka, Fumi Nagatsugi and Naoki Sugimoto

New J. Chem., 2024, 48, 8529
DOI: 10.1039/D3NJ05833F

Graphene family in cancer therapy: recent progress in cancer gene/drug delivery applications

Negin Borzooee Moghadam, Manizheh Avatefi, Mahnaz Karimi and Matin Mahmoudifard

J. Mater. Chem. B, 2023, 11, 2568
DOI: 10.1039/D2TB01858F

Protein-Based Virtual Screening Tools Applied for RNA–Ligand Docking Identify New Binders of the preQ1-Riboswitch

Elisabeth Kallert, Tim R. Fischer, Simon Schneider, Maike Grimm, Mark Helm and Christian Kersten

J. Chem. Inf. Model., 2022, 62, 4134
DOI: 10.1021/acs.jcim.2c00751

Stimulus-activated ribonuclease targeting chimeras for tumor microenvironment activated cancer therapy

Yuqi Zhang, Jinfeng Zhu, Ling Qiu, Zhengzhong Lv, Zhongsheng Zhao, Xingxiang Ren, Yirui Guo, Yan Chen, Miao Li, Yurong Fan, Zhixin Han, Yiming Feng and Haibin Shi

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-56691-3

NIR Light‐Mediated Mitochondrial RNA Modification for Cancer RNA Interference Therapeutics

Yali Feng, Jing Fang, Yan Zhao, Shuyue Ye, Anna Wang, Yuqi Zhang, Jinfeng Zhu, Jiachen Li, Zhengzhong Lv, Zhongsheng Zhao and Haibin Shi

Angewandte Chemie, 2023, 135
DOI: 10.1002/ange.202218969

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

High Throughput FISH Screening Identifies Small Molecules That Modulate Oncogenic lncRNA MALAT1 via GSK3B and hnRNPs

Nina Zablowsky, Lydia Farack, Sven Rofall, Jan Kramer, Hanna Meyer, Duy Nguyen, Alexander K. C. Ulrich, Benjamin Bader and Patrick Steigemann

ncRNA, 2023, 9, 2
DOI: 10.3390/ncrna9010002

Discovery of Macrocyclic Peptide Binders, Covalent Modifiers, and Degraders of a Structured RNA by mRNA Display

Xiyuan Yao, Kanokpol Aphicho, Shubhashree Pani, Anuchit Rupanya, Tong Lan and Bryan C. Dickinson

J. Am. Chem. Soc., 2025, 147, 34256
DOI: 10.1021/jacs.5c05540

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Willem A. Velema and Zhipeng Lu

JACS Au, 2023, 3, 316
DOI: 10.1021/jacsau.2c00625

Prediction and analysis of functional RNA structures within the integrative genomics viewer

Warren B Rouse, Ryan J Andrews, Nicholas J Booher, Jibo Wang, Michael E Woodman, Ernst R Dow, Theodore C Jessop and Walter N Moss

NAR Genomics and Bioinformatics, 2022, 4
DOI: 10.1093/nargab/lqab127

Aptamer-engineered NIR-II Ru-doped carbon quantum dot nanozyme for photoacoustic imaging-guided synergistic photothermal and catalytic cancer therapy

Yumin Hao, Zihan Wang, Yihong Chen, Chenxing Li, Huiping Wang, Chuan Dong, Shaomin Shuang, Ding Ding and Xiaojuan Gong

J Nanobiotechnol, 2025, 24
DOI: 10.1186/s12951-025-03919-5

RNA-targeting therapeutics: drugging the undruggable

Poonam Mundlia, Suraj Pratap Singh, Aayush Kaushal, Mary Chatterjee, Pavitra Ranawat, Ankur Pandey, Gurpal Singh and Ravi Pratap Barnwal

Future Medicinal Chemistry, 2025, 17, 1213
DOI: 10.1080/17568919.2025.2520152

Chemical Synthesis of Modified RNA

Laurin Flemmich, Raphael Bereiter and Ronald Micura

Angew Chem Int Ed, 2024, 63
DOI: 10.1002/anie.202403063

Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein–Ligand to RNA-Ligand Binding

Eleonora Serra, Alessia Ghidini, Riccardo Aguti, Mattia Bernetti, Sergio Decherchi and Andrea Cavalli

J. Chem. Inf. Model., 2025, 65, 6057
DOI: 10.1021/acs.jcim.5c00452

Small molecule targeting CELF1 RNA-binding activity to control HSC activation and liver fibrosis

Yang Tan, Xueqing Sun, Yizhu Xu, Bingjie Tang, Shuaiqi Xu, Dong Lu, Yan Ye, Xiaomin Luo, Xu Diao, Fulong Li, Tianyi Wang, Jiayu Chen, Qiang Xu and Xingxin Wu

Nucleic Acids Research, 2022, 50, 2440
DOI: 10.1093/nar/gkac139

Enabling In-Silico Hit Discovery Workflows Targeting RNA with Small Molecules

Nikita Chopra, Ara M. Abramyan, Zeineb Si Chaib, Wei Chen, Yeyue Xiong, Anna Bochicchio, David Rinaldo, Steven V. Jerome and Yuqi Zhang

J. Chem. Inf. Model., 2025, 65, 7393
DOI: 10.1021/acs.jcim.5c00814

Precision cardiovascular medicine: shifting the innovation paradigm

Masanori Aikawa, Abhijeet R. Sonawane, Sarvesh Chelvanambi, Takaharu Asano, Arda Halu, Joan T. Matamalas, Sasha A. Singh, Shizuka Uchida, Elena Aikawa, Alex Arenas, Jean-Luc Balligand, Chiara Giannarelli, Calum A. MacRae, Neil V. Morgan, Cécile Oury, Hendrik Tevaearai Stahel and Joseph Loscalzo

Front Sci, 2025, 3
DOI: 10.3389/fsci.2025.1474469

RNA-Targeting Techniques: A Comparative Analysis of Modern Approaches for RNA Manipulation in Cancer Research and Therapeutics

Michaela A. Boti, Marios A. Diamantopoulos and Andreas Scorilas

Genes, 2025, 16, 1168
DOI: 10.3390/genes16101168

Recent advances in the molecular design and applications of viral RNA-targeting antiviral modalities

Jiaojiao Dai, Xiangyi Jiang, Edeildo Ferreira da Silva-Júnior, Shaoqing Du, Xinyong Liu and Peng Zhan

Drug Discovery Today, 2024, 29, 104074
DOI: 10.1016/j.drudis.2024.104074

RNA-based therapies in hepatocellular carcinoma: state of the art and clinical perspectives

Le Xing, Zhen-Kai Wang, Dong-Mei Li, Jing Li and Ming Liu

Hepatoma Res, 2024
DOI: 10.20517/2394-5079.2024.25

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

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

Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy

Hao-Che Peng, Gabrielle L. Castro, Varshini Karthikeyan, Alina Jarrett, Melanie A. Katz, James A. Hargrove, David Hoang, Stefan Hilber, Wenting Meng, Lu Wang, Robert J. Fick, Jung-Mo Ahn, Christoph Kreutz and Allison L. Stelling

J. Phys. Chem. Lett., 2023, 14, 4313
DOI: 10.1021/acs.jpclett.3c00178

Computational methods for binding site prediction on macromolecules

Igor Kozlovskii and Petr Popov

Quart. Rev. Biophys., 2025, 58
DOI: 10.1017/S003358352500006X

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

Development of RNA G-quadruplex (rG4)-targeting l-RNA aptamers by rG4-SELEX

Mubarak I. Umar, Chun-Yin Chan and Chun Kit Kwok

Nat Protoc, 2022, 17, 1385
DOI: 10.1038/s41596-022-00679-6

Development of a specific and potent IGF2BP1 inhibitor: A promising therapeutic agent for IGF2BP1-expressing cancers

Amandeep Singh, Vikash Singh, Nadav Wallis, Giancarlo Abis, Froma Oberman, Tyler Wood, Mayura Dhamdhere, Tehila Gershon, Andres Ramos, Joel Yisraeli, Vladimir S. Spiegelman and Arun K. Sharma

European Journal of Medicinal Chemistry, 2024, 263, 115940
DOI: 10.1016/j.ejmech.2023.115940

Novel Perspectives towards RNA-Based Nano-Theranostic Approaches for Cancer Management

Rabia Arshad, Iqra Fatima, Saman Sargazi, Abbas Rahdar, Milad Karamzadeh-Jahromi, Sadanand Pandey, Ana M. Díez-Pascual and Muhammad Bilal

Nanomaterials, 2021, 11, 3330
DOI: 10.3390/nano11123330

NIR Light‐Mediated Mitochondrial RNA Modification for Cancer RNA Interference Therapeutics

Yali Feng, Jing Fang, Yan Zhao, Shuyue Ye, Anna Wang, Yuqi Zhang, Jinfeng Zhu, Jiachen Li, Zhengzhong Lv, Zhongsheng Zhao and Haibin Shi

Angew Chem Int Ed, 2023, 62
DOI: 10.1002/anie.202218969

Machine Learning Informs RNA‐Binding Chemical Space**

Kamyar Yazdani, Deondre Jordan, Mo Yang, Christopher R. Fullenkamp, David R. Calabrese, Robert Boer, Thomas Hilimire, Timothy E. H. Allen, Rabia T. Khan and John S. Schneekloth

Angew Chem Int Ed, 2023, 62
DOI: 10.1002/anie.202211358

Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication

Maclean Bassett, Marco Salemi and Brittany Rife Magalis

Microbiol Mol Biol Rev, 2022, 86
DOI: 10.1128/mmbr.00057-21

Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA

Greta Bagnolini, TinTin B. Luu and Amanda E. Hargrove

RNA, 2023, 29, 473
DOI: 10.1261/rna.079497.122

Computational advances in RNA-small molecule binding site prediction

Lang Yang, Zou Yan, Yanhui Liu and Yuyu Feng

Progress in Biophysics and Molecular Biology, 2026, 199, 267
DOI: 10.1016/j.pbiomolbio.2026.02.003

Inverse In Vitro Selection Enables Comprehensive Analysis of Cross‐Chiral L‐Aptamer Interactions

Alexander T. Piwko, Xuan Han, Adam M. Kabza, Sougata Dey and Jonathan T. Sczepanski

ChemBioChem, 2022, 23
DOI: 10.1002/cbic.202200520

Alkyne Activation in the Diversity Oriented Synthesis of sp2‐Rich Scaffolds: A Biased Library Approach for Targeting Polynucleotides (DNA/RNA)

Shuqi Chen, Daniel L. Priebbenow, Julie Somkhit, Carmen V. Scullino, Keli Agama, Yves Pommier and Bernard L. Flynn

Chemistry A European J, 2022, 28
DOI: 10.1002/chem.202201925

The multiple molecular dimensions of long noncoding RNAs that regulate gene expression and tumorigenesis

Marco Marcia

Current Opinion in Oncology, 2022, 34, 141
DOI: 10.1097/CCO.0000000000000813

An Encodable Scaffold for Sequence‐Specific Recognition of Duplex RNA

Jonathan G. Kwok, Zhi Yuan and Paramjit S. Arora

Angewandte Chemie, 2023, 135
DOI: 10.1002/ange.202308650

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies

Yanping Hu, Yan Wang, Jaideep Singh, Ruirui Sun, Lilei Xu, Xiaolin Niu, Keyun Huang, Guangcan Bai, Guoquan Liu, Xiaobing Zuo, Chunlai Chen, Peter Z. Qin and Xianyang Fang

ACS Chem. Biol., 2022, 17, 2448
DOI: 10.1021/acschembio.2c00199

The Fetal-to-Adult Hemoglobin Switch — Mechanism and Therapy

Stuart H. Orkin

N Engl J Med, 2025, 392, 2135
DOI: 10.1056/NEJMra2405260

Molecular dynamics analysis of biomolecular systems including nucleic acids

Takeru Kameda, Akinori Awazu and Yuichi Togashi

BIOPHYSICS, 2022, 19, n/a
DOI: 10.2142/biophysico.bppb-v19.0027

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo and Narutoshi Kamiya

ACS Omega, 2024
DOI: 10.1021/acsomega.3c06826

GCNfold: A novel lightweight model with valid extractors for RNA secondary structure prediction

Enbin Yang, Hao Zhang, Zinan Zang, Zhiyong Zhou, Shuo Wang, Zhen Liu and Yuanning Liu

Computers in Biology and Medicine, 2023, 164, 107246
DOI: 10.1016/j.compbiomed.2023.107246

Design, Synthesis, and Evaluation of Neomycin‐Imidazole Conjugates for RNA Cleavage

Céline Martin, Maurinne Bonnet, Nadia Patino, Stéphane Azoulay, Audrey Di Giorgio and Maria Duca

ChemPlusChem, 2022, 87
DOI: 10.1002/cplu.202200250

Transforming Medicine: Advances in Gene Therapy, Immunotherapy, and Targeted Cures

Komal Gupta, Vikram Sharma and Tohfa Siddiqui

CPPS, 2025, 26, 436
DOI: 10.2174/0113892037336137250102104842

Rational Approach to Identify RNA Targets of Natural Products Enables Identification of Nocathiacin as an Inhibitor of an Oncogenic RNA

Fei Ye, Hafeez S. Haniff, Blessy M. Suresh, Dong Yang, Peiyuan Zhang, Gogce Crynen, Christiana N. Teijaro, Wei Yan, Daniel Abegg, Alexander Adibekian, Ben Shen and Matthew D. Disney

ACS Chem. Biol., 2022, 17, 474
DOI: 10.1021/acschembio.1c00952

Binding and stabilizing effects of ruthenium(II) polypyridyl complexes [Ru(bpy)2(6-L-dppz)]2+ (L = F and CH3) toward duplex RNA poly(A)·poly(U) under molecular crowding conditions

Keliang Wan, Zhiqiang Tan and Lifeng Tan

Inorganica Chimica Acta, 2025, 578, 122556
DOI: 10.1016/j.ica.2025.122556

Small-molecule modulators of protein–RNA interactions

Wan Gi Byun, Donghyun Lim and Seung Bum Park

Current Opinion in Chemical Biology, 2022, 68, 102149
DOI: 10.1016/j.cbpa.2022.102149

Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes

Andrea Dodaro, Matteo Pavan, Silvia Menin, Veronica Salmaso, Mattia Sturlese and Stefano Moro

Front. Mol. Biosci., 2023, 10
DOI: 10.3389/fmolb.2023.1294543

Aryl Guanyl Hydrazones: A Viable Strategy for Designing BBB-Permeable, Neuroactive Compounds?

Eleonora Colombo, Leonardo Maiorana, Greta Donati, Andrea Menegon, Nicoletta Collura, Luca Muzio, Eloise Mastrangelo, Mario Milani, Luciana Marinelli and Pierfausto Seneci

ACS Chem. Neurosci., 2025, 16, 2767
DOI: 10.1021/acschemneuro.5c00463

Decoding RNA therapeutics: Precision approaches in women's health

Nazanin Pazhouhesh Far, Hoda Nouri Boroujerdi, Mahshid Seyed Karimi, Payam Vezvaei, Mahsa Behfar, Roya Mirzaei, Reza Habibi, Mahsa Manafi Varkiani, Amir Reza Aref and Nasim Ebrahimi

European Journal of Pharmacology, 2025, 1008, 178275
DOI: 10.1016/j.ejphar.2025.178275

Acetamiprid in Rizhao green tea: Residue dynamics, degradation pathways, and ecological risks via integrated experimental and computational approaches

Changjian Li, Shujie Zhang, Chengcheng Han, Xiaolin Han, Jian Song, Jian Ju and Huimin Zhu

Journal of Hazardous Materials, 2025, 495, 138786
DOI: 10.1016/j.jhazmat.2025.138786

Designing Reversible Photoswitching Azobenzene-Modified Nucleotide for Controlling Biological Function

Juncheng Li, Jinxi Du, Weiwei He, Ibrahim O. Adelakun, Miao Zhong, Savia Boyer, Ya Ying Zheng, Qishan Lin, Serdal Kirmizialtin, Jia Sheng and Ting Wang

J. Am. Chem. Soc., 2025, 147, 21638
DOI: 10.1021/jacs.5c03252

Discovery of RNA‐Targeting Small Molecules: Challenges and Future Directions

Zhengguo Cai, Hongli Ma, Fengcan Ye, Dingwei Lei, Zhenfeng Deng, Yongge Li, Ruichu Gu and Han Wen

MedComm, 2025, 6
DOI: 10.1002/mco2.70342

RNA‐Based Therapeutics: Cutting‐Edge Advances in Clinical Research

Débora Ferreira and Ligia R. Rodrigues

Advanced Therapeutics, 2025, 8
DOI: 10.1002/adtp.202500082

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators

Ilaria Silvestri, Jacopo Manigrasso, Alessandro Andreani, Nicoletta Brindani, Caroline Mas, Jean-Baptiste Reiser, Pietro Vidossich, Gianfranco Martino, Andrew A. McCarthy, Marco De Vivo and Marco Marcia

Nat Commun, 2024, 15
DOI: 10.1038/s41467-024-48697-0

RNA adsorption onto iron oxide nanoparticle have stability from nuclease

Sonali Mohanty, Mandakini Singh, Sonali Jena, Santosh Kumar and Suman Jha

International Journal of Biological Macromolecules, 2025, 322, 146655
DOI: 10.1016/j.ijbiomac.2025.146655

Reversing the Hypoxic Adaptive Response in Breast Cancer Cells through Small-Molecule Inhibition of Oncogenic MicroRNA-210

Marc Panosetti, Donatella Vecchio, Chloé Maucort, Vera Mongiardini, Audrey Di Giorgio, Benedetto Grimaldi and Maria Duca

J. Med. Chem., 2026, 69, 2814
DOI: 10.1021/acs.jmedchem.5c02728

Eurycomalactone switched hepatocellular carcinoma cells into quiescence through 5’tRFAla/DVL/β-catenin pathway inhibition

Zhipeng Zhang, Yanmei Wu, Wenqiang Liang, Zhifang Liao, Hongbo Liao, Xingxing Xing, Wenxin Yi, Zixuan Liu, Yicheng Li, Mengya Shi, Dongling Lin, Ting Gu, Biao Wu, Mingzhi Zou, Huilai Miao and Xin Wu

Sci Rep, 2025, 15
DOI: 10.1038/s41598-025-86888-x

Editorial: Machine learning-based methods for RNA data analysis—Volume II

Lihong Peng, Jialiang Yang, Minxian Wang and Liqian Zhou

Front. Genet., 2022, 13
DOI: 10.3389/fgene.2022.1010089

Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design

Christian Kersten, Philippe Archambault and Luca P. Köhler

J. Chem. Inf. Model., 2024, 64, 4485
DOI: 10.1021/acs.jcim.4c00520

Targeting the SARS-CoV-2 RNA Translation Initiation Element SL1 by Molecules of Low Molecular Weight

Sabrina Toews, Francesca Donà, Marco Keller, Jürgen Krauß, Franz Bracher, Úrsula López-García, Jörg Pabel, Daniel Merk, Marcel J. J. Blommers, Jan Ferner, Anna Wacker, Christian Richter and Harald Schwalbe

J. Am. Chem. Soc., 2025, 147, 28783
DOI: 10.1021/jacs.5c05264

Small molecule based targeting of the CssA RNA thermometer: insights from computational and biophysical approaches

Akanksha Sharma, Priyanka Gopi, Rimjhim Trivedi, Dinesh Kumar, Janeka Gartia, Adukamparai Rajukrishnan Suresh Babu, Prateek Pandya, Gurpal Singh and Ravi Pratap Barnwal

Biochimie, 2025, 237, 110
DOI: 10.1016/j.biochi.2025.07.017

Design of deep-red emissive forced intercalation-induced light-up peptide as an indicator for the HIV-1 TAR RNA-ligand assay: integration of benzo[c,d]indole-quinoline (BIQ) cyanine dye into Tat peptide

Akunna Francess Ujuagu, Yusuke Sato, En Ting Tabitha Lee and Seiichi Nishizawa

ANAL. SCI., 2024, 40, 2089
DOI: 10.1007/s44211-024-00642-3

2-Deoxystreptamine as a platform to design original inhibitors of oncogenic miRNA biogenesis

Thi Phuong Anh Tran, Nadia Patino, Audrey Di Giorgio and Maria Duca

Comptes Rendus. Chimie, 2025, 28, 911
DOI: 10.5802/crchim.426

Chemical pulldown of Prenylated-Adenosine-Incorporated RNA via sequential Fluorination-Azidation and a click reaction targeting prenyl functionality

Xiaoqian Chen, Youfang Gan, Yuyang Guo, Yuanyuan Li, Hongling Zhou and Rui Wang

Tetrahedron Letters, 2024, 134, 154856
DOI: 10.1016/j.tetlet.2023.154856

Deciphering the regulatory landscape of enhancer RNAs in health and disease

Qian Wang, Peter ten Dijke and Chuannan Fan

Sig Transduct Target Ther, 2026, 11
DOI: 10.1038/s41392-025-02436-z

Intronic RNA secondary structural information captured for the human MYC pre-mRNA

Taylor O Eich, Collin A O’Leary and Walter N Moss

NAR Genomics and Bioinformatics, 2024, 6
DOI: 10.1093/nargab/lqae143

MicroRNA-specific targets for neuronal plasticity, neurotransmitters, neurotrophic factors, and gut microbes in the pathogenesis and therapeutics of depression

Cong-Ya Chen, Yu-Fei Wang, Lan Lei and Yi Zhang

Progress in Neuro-Psychopharmacology and Biological Psychiatry, 2025, 136, 111186
DOI: 10.1016/j.pnpbp.2024.111186

Hepatitis B Virus Epsilon (ε) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target

Lukasz T. Olenginski, Solomon K. Attionu, Erica N. Henninger, Regan M. LeBlanc, Andrew P. Longhini and Theodore K. Dayie

Viruses, 2023, 15, 1913
DOI: 10.3390/v15091913

NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes

Yuyu Feng, Keqiong Zhang, Qilong Wu and Sheng-You Huang

J. Chem. Inf. Model., 2021, 61, 4771
DOI: 10.1021/acs.jcim.1c00341

Programmable technologies to manipulate gene expression at the RNA level

Huachun Liu, Simone Rauch and Bryan C. Dickinson

Current Opinion in Chemical Biology, 2021, 64, 27
DOI: 10.1016/j.cbpa.2021.03.004

Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations

Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo and Narutoshi Kamiya

J. Chem. Theory Comput., 2025, 21, 11259
DOI: 10.1021/acs.jctc.5c01114

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

Synthetic antibodies for accelerated RNA crystallography

Saurja DasGupta

WIREs RNA, 2024, 15
DOI: 10.1002/wrna.1869

Identification of novel DYRK1A inhibitors as treatment options for alzheimer’s disease through comprehensive in silico approaches

Ibrahim Akindeji Makinde, Sheriffdeen Oladimeji Hammed, Neeraj Kumar, Najwa Ahmad Kuthi, Haruna Isiyaku Umar, Temitayo Abidat Hassan, Idayat Oyinkansola Kehinde, Ridwan Opeyemi Bello, Abdullahi Tunde Aborode, Tajudeen Ogundare Jimoh, Al-Djazouli O. Mahamat, Mohammad Khalid and Omar A. Almohammed

Sci Rep, 2025, 15
DOI: 10.1038/s41598-025-23431-y

Autism Spectrum Disorder: Neurodevelopmental Risk Factors, Biological Mechanism, and Precision Therapy

Ling Wang, Binquan Wang, Chunyan Wu, Jie Wang and Mingkuan Sun

IJMS, 2023, 24, 1819
DOI: 10.3390/ijms24031819

Structure-informed design of an ultrabright RNA-activated fluorophore

Mo Yang, Peri R. Prestwood, Luiz F. M. Passalacqua, Sumirtha Balaratnam, Christopher R. Fullenkamp, J. Winston Arney, Kevin M. Weeks, Adrian Ferre-D’Amare and John S. Schneekloth

Nat. Chem., 2025, 17, 1188
DOI: 10.1038/s41557-025-01832-w

Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG)exp Degrader in Myotonic Dystrophy

Quentin M. R. Gibaut, Jessica A. Bush, Yuquan Tong, Jared T. Baisden, Amirhossein Taghavi, Hailey Olafson, Xiyuan Yao, Jessica L. Childs-Disney, Eric T. Wang and Matthew D. Disney

ACS Cent. Sci., 2023, 9, 1342
DOI: 10.1021/acscentsci.2c01223

Fragment‐Based Drug Discovery for RNA Targets

Kasper P. Lundquist, Vipul Panchal, Charlotte H. Gotfredsen, Ruth Brenk and Mads H. Clausen

ChemMedChem, 2021, 16, 2588
DOI: 10.1002/cmdc.202100324

Advanced strategies for screening and identifying RNA-targeted small molecules: Bridging therapeutic potential and innovation

Zukela Ruzi, Daxiong Han and Kailibinuer Aierken

Results in Chemistry, 2025, 15, 102305
DOI: 10.1016/j.rechem.2025.102305

Structure-based deep learning for binding site detection in nucleic acid macromolecules

Igor Kozlovskii and Petr Popov

NAR Genomics and Bioinformatics, 2021, 3
DOI: 10.1093/nargab/lqab111

Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders

Dávid Bajusz, Anita Rácz, Janusz M Bujnicki and Filip Stefaniak

Briefings in Bioinformatics, 2025, 26
DOI: 10.1093/bib/bbaf620

Chemical Synthesis of Modified RNA

Laurin Flemmich, Raphael Bereiter and Ronald Micura

Angewandte Chemie, 2024, 136
DOI: 10.1002/ange.202403063

RNA modification-mediated aberrant alternative splicing: An underlying driver of disease pathogenesis

Jin Zeng, Li-Ting Diao, Shu-Juan Xie and Zhen-Dong Xiao

Cell Investigation, 2025, 1, 100047
DOI: 10.1016/j.clnves.2025.100047

RNA as an off-target for FDA-approved drugs

Christopher R. Fullenkamp and John S. Schneekloth

Nat. Chem., 2023, 15, 1329
DOI: 10.1038/s41557-023-01330-x

RNA Dünyasından Kliniğe: Madde Kullanım Bozuklukları için RNA Terapötikleri

Süheyla Ayfer ALKAÇ and Selda MERCAN

OSMANGAZİ JOURNAL OF MEDICINE, 2023
DOI: 10.20515/otd.1379032

Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

F. P. Panei, P. Gkeka and M. Bonomi

Nat Commun, 2024, 15
DOI: 10.1038/s41467-024-49638-7

The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development

Xin Li, Abhjeet S. Bhullar, Daniel W. Binzel and Peixuan Guo

Advanced Drug Delivery Reviews, 2022, 186, 114316
DOI: 10.1016/j.addr.2022.114316

Design and Implementation of Synthetic RNA Binders for the Inhibition of miR-21 Biogenesis

Chloé Maucort, Duc Duy Vo, Samy Aouad, Coralie Charrat, Stéphane Azoulay, Audrey Di Giorgio and Maria Duca

ACS Med. Chem. Lett., 2021, 12, 899
DOI: 10.1021/acsmedchemlett.0c00682

Computer-aided design of RNA-targeted small molecules: A growing need in drug discovery

Jacopo Manigrasso, Marco Marcia and Marco De Vivo

Chem, 2021, 7, 2965
DOI: 10.1016/j.chempr.2021.05.021

Structural conservation of antibiotic interaction with ribosomes

Helge Paternoga, Caillan Crowe-McAuliffe, Lars V. Bock, Timm O. Koller, Martino Morici, Bertrand Beckert, Alexander G. Myasnikov, Helmut Grubmüller, Jiří Nováček and Daniel N. Wilson

Nat Struct Mol Biol, 2023, 30, 1380
DOI: 10.1038/s41594-023-01047-y

X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences

Edwin N. Ogbonna, Ananya Paul, Abdelbasset A. Farahat, J. Ross Terrell, Ekaterina Mineva, Victor Ogbonna, David W Boykin and W. David Wilson

ACS Bio Med Chem Au, 2023, 3, 335
DOI: 10.1021/acsbiomedchemau.3c00002

DeepRNA-DTI: a deep learning approach for RNA-compound interaction prediction with binding site interpretability

Haelee Bae and Hojung Nam

J Cheminform, 2025, 18
DOI: 10.1186/s13321-025-01132-y

Pivotal role of long non-coding RNA in the development of new therapeutic approaches for plural mesothelioma

Caroline Joseph Kiriacos, Dina M. Elkahwagy and Manar Mansour

Discov Onc, 2026
DOI: 10.1007/s12672-026-04677-y

Small Molecule RNA Degraders

Javier Bonet‐Aleta, Tomoaki Maehara, Benjamin A. Craig and Gonçalo J. L. Bernardes

Angew Chem Int Ed, 2024, 63
DOI: 10.1002/anie.202412925

RNet: a network strategy to predict RNA binding preferences

Haoquan Liu, Yiren Jian, Jinxuan Hou, Chen Zeng and Yunjie Zhao

Briefings in Bioinformatics, 2023, 25
DOI: 10.1093/bib/bbad482

Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy

Eric W Ottesen, Natalia N Singh, Diou Luo, Bailey Kaas, Benjamin J Gillette, Joonbae Seo, Hannah J Jorgensen and Ravindra N Singh

Nucleic Acids Research, 2023, 51, 5948
DOI: 10.1093/nar/gkad259

Site‐Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting

Phillip Yesley, Georgia Poulladofonou, Danny Incarnato and Willem A. Velema

Angewandte Chemie, 2026, 138
DOI: 10.1002/ange.202517243

Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch

Stefan Crielaard, Rick Maassen, Tess Vosman, Ivy Rempkens and Willem A. Velema

J. Am. Chem. Soc., 2022, 144, 10462
DOI: 10.1021/jacs.2c02685

Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging

Zhe Ma, Kulsoom and Fu Wang

Chemical & Biomedical Imaging, 2026, 4, 130
DOI: 10.1021/cbmi.5c00068

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning

Juan G. Carvajal-Patiño, Vincent Mallet, David Becerra, Luis Fernando Niño Vasquez, Carlos Oliver and Jérôme Waldispühl

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-57852-0

RNA-based therapeutics: an overview and prospectus

Yiran Zhu, Liyuan Zhu, Xian Wang and Hongchuan Jin

Cell Death Dis, 2022, 13
DOI: 10.1038/s41419-022-05075-2

De‐Novo Design of pre‐miR‐21 Maturation Inhibitors: Synthesis and Activity Assessment

Iryna Shcheholeva, Daniel Fernández‐Remacha, Roger Estrada‐Tejedor, Maria Duca and Véronique Michelet

Chemistry A European J, 2023, 29
DOI: 10.1002/chem.202300825

Synthetic RNA Modulators in Drug Discovery

Farzad Zamani and Takayoshi Suzuki

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

Exploring the RNA‐Binding Potential of Three‐Dimensional Cyanines Derived From [2.2]Paracyclophane: A Structure–Property Relationship

Rongyu Sun, Cristian Siretanu, Georgina Ilieska, Simon Felder, Erica Benedetti and Laurent Micouin

ChemBioChem, 2026, 27
DOI: 10.1002/cbic.202500835

Noncoding RNA therapeutics for substance use disorder

Seyed Afshin Seyednejad and Gregory C. Sartor

Adv. Drug Alcohol Res., 2022, 2
DOI: 10.3389/adar.2022.10807

RNA‐Targeting Carbon Dots for Live‐Cell Imaging of Granule Dynamics

Lei Jiang, Hao Cai, Wanwan Zhou, Zijian Li, Liang Zhang and Hong Bi

Advanced Materials, 2023, 35
DOI: 10.1002/adma.202210776

Introduction to a review series on RNA therapeutics in hematology

Jason Gotlib

Blood, 2023, 142, 1577
DOI: 10.1182/blood.2023020910

Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA

Natalia A Szulc, Zuzanna Mackiewicz, Janusz M Bujnicki and Filip Stefaniak

Briefings in Bioinformatics, 2023, 24
DOI: 10.1093/bib/bbad187

Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward

Asimina Zisi, Jiri Bartek and Mikael S. Lindström

Cancers, 2022, 14, 2126
DOI: 10.3390/cancers14092126

Machine Learning Informs RNA‐Binding Chemical Space**

Kamyar Yazdani, Deondre Jordan, Mo Yang, Christopher R. Fullenkamp, David R. Calabrese, Robert Boer, Thomas Hilimire, Timothy E. H. Allen, Rabia T. Khan and John S. Schneekloth

Angewandte Chemie, 2023, 135
DOI: 10.1002/ange.202211358

MicroRNA-based therapeutics for inflammatory disorders of the microbiota-gut-brain axis

Neha Datta, Charlotte Johnson, Dina Kao, Pratik Gurnani, Cameron Alexander, Christos Polytarchou and Tanya M. Monaghan

Pharmacological Research, 2023, 194, 106870
DOI: 10.1016/j.phrs.2023.106870

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning

Sowmya Ramaswamy Krishnan, Arijit Roy, Limsoon Wong and M Michael Gromiha

Nucleic Acids Research, 2025, 53
DOI: 10.1093/nar/gkaf239

Generative AI for computational chemistry: A roadmap to predicting emergent phenomena

Pratyush Tiwary, Lukas Herron, Richard John, Suemin Lee, Disha Sanwal and Ruiyu Wang

Proc. Natl. Acad. Sci. U.S.A., 2025, 122
DOI: 10.1073/pnas.2415655121

Non-coding RNAs in renal cell carcinoma: Implications for drug resistance

Yiqi Liu, Hu Zhang, Yuan Fang, Dongshan Tang and Zhigang Luo

Biomedicine & Pharmacotherapy, 2023, 164, 115001
DOI: 10.1016/j.biopha.2023.115001

Tumor Diagnosis and Therapy Mediated by Metal Phosphorus‐Based Nanomaterials

Yang Liu, Yinghui Wang, Shuyan Song and Hongjie Zhang

Advanced Materials, 2021, 33
DOI: 10.1002/adma.202103936

Riboswitch Dynamics and Their Expanding Biotechnological Applications

Dian Chen and Yu Liu

HM, 2025
DOI: 10.53941/hm.2025.100027

Small-molecule RNA ligands: a patent review (2018–2024)

Elia Ravegnini, Andrea Trabocchi and Elena Lenci

Expert Opinion on Therapeutic Patents, 2025, 35, 675
DOI: 10.1080/13543776.2025.2492759

Small Molecule RNA Degraders

Javier Bonet‐Aleta, Tomoaki Maehara, Benjamin A. Craig and Gonçalo J. L. Bernardes

Angewandte Chemie, 2024, 136
DOI: 10.1002/ange.202412925

Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion

James P. Falese, Emily J. McFadden, Christopher A. D'Inzeo and Amanda E. Hargrove

RNA, 2025, 31, 1260
DOI: 10.1261/rna.080488.125

RNA therapeutics in hematology

Prakas Kumar Mandal

JHAS, 2024, 3, 79
DOI: 10.25259/JHAS_5_2024

Advances and Mechanisms of RNA–Ligand Interaction Predictions

Chen Zhuo, Chengwei Zeng, Haoquan Liu, Huiwen Wang, Yunhui Peng and Yunjie Zhao

Life, 2025, 15, 104
DOI: 10.3390/life15010104

Unveiling RNA ligands: Harnessing NMR for hit generation

Alexandra Gaspar and Jorge M.P.J. Garrido

European Journal of Medicinal Chemistry, 2026, 304, 118495
DOI: 10.1016/j.ejmech.2025.118495

Identification of Selective Small Molecule Modulators of mRNA Processing Using a Multiplexed QuantiGene High-Throughput Screening Platform

Sarah Sirin, Nirodhini S. Siriwardana, Michael Wood, James Mills, Dominic J. Reynolds and Frédéric H. Vaillancourt

ASSAY and Drug Development Technologies, 2026, 24, 138
DOI: 10.1177/1540658X251366782

Stefano Bosio, Mattia Bernetti, Walter Rocchia and Matteo Masetti

J. Chem. Inf. Model., 2024, 64, 4570
DOI: 10.1021/acs.jcim.4c00420

A blood–brain penetrant RNA-targeted small molecule triggers elimination of r(G 4 C 2 ) exp in c9ALS/FTD via the nuclear RNA exosome

Jessica A. Bush, Samantha M. Meyer, Rita Fuerst, Yuquan Tong, Yue Li, Raphael I. Benhamou, Haruo Aikawa, Patrick R. A. Zanon, Quentin M. R. Gibaut, Alicia J. Angelbello, Tania F. Gendron, Yong-Jie Zhang, Leonard Petrucelli, Torben Heick Jensen, Jessica L. Childs-Disney and Matthew D. Disney

Proc. Natl. Acad. Sci. U.S.A., 2022, 119
DOI: 10.1073/pnas.2210532119

Small Molecule‐Driven Organic Electrochemical Transistors for Rapid, Ultrasensitive and Amplification‐Free Detection of RNA Biomarkers

Jiacheng Yu, Qitong Feng, Jintao Zheng, Han Liu, Hui Liu, Runzhi Zhou, Xiaohong Jiang, Haoyang Yan, Zheng Liang, Mingxi Chen, Omer Yehezkeli, Haifeng Dong, Lin Li, Bo Peng, Nicolas H. Voelcker, Jiacan Su and Keying Guo

Advanced Materials, 2026, 38
DOI: 10.1002/adma.202515338

An Encodable Scaffold for Sequence‐Specific Recognition of Duplex RNA

Jonathan G. Kwok, Zhi Yuan and Paramjit S. Arora

Angew Chem Int Ed, 2023, 62
DOI: 10.1002/anie.202308650

Mutation of novel ethanol‐responsive lncRNAGm41261 impacts ethanol‐related behavioral responses in mice

S. L. Plasil, S. P. Farris, Y. Blednov, R. D. Mayfield, R. A. Mangieri, U. J. Nwokeji, H. C. Aziz, P. S. Lambeth, R. A. Harris and G. E. Homanics

Genes Brain and Behavior, 2024, 23
DOI: 10.1111/gbb.12886

lncRNA-miRNA/RBP-mRNA Network Involved in Human Triple-Negative Breast Cancer: An Integrated Approach

Wen Yun, Yao Li, Jianyuan Huang and Yuan Yuan

J Environ Pathol Toxicol Oncol, 2025, 44, 75
DOI: 10.1615/JEnvironPatholToxicolOncol.2024056566

Small Molecule Drugs Targeting Non-Coding RNAs as Treatments for Alzheimer’s Disease and Related Dementias

Lien D. Nguyen, Rachel K. Chau and Anna M. Krichevsky

Genes, 2021, 12, 2005
DOI: 10.3390/genes12122005

G-Quadruplex mRNAs Silencing with Inducible Ribonuclease Targeting Chimera for Precision Tumor Therapy

Yuan Zhang, Lingyan Wang, Fenglin Wang, Xia Chu and Jian-Hui Jiang

J. Am. Chem. Soc., 2024, 146, 15815
DOI: 10.1021/jacs.4c02091

Inhibition of DDX5-Mediated G-Quadruplex Unwinding in the β-Catenin 5′-UTR by Magnesium Isoglycyrrhizinate Alleviates Chemotherapy-Induced Intestinal Injury

Ying Zhang, Wenqiang Fu, Yaohui Wang, Anyuan Wu, Zhenzhen Zhu, Xunkai Yin, Yan Li, Yongdi Sun, Wenpu Shi, Jianming Cheng, Lihong Hu, Jian Liu and Jian Cui

Research, 2026, 9
DOI: 10.34133/research.1044

Recent advances in the analysis of the evolutionary RNA based therapeutics; a review

Hadeel A. Khalil, Nehal W. El-Sayed, Rowan M. Elmoslhy and Amira F. El-Yazbi

International Journal of Biological Macromolecules, 2026, 344, 150466
DOI: 10.1016/j.ijbiomac.2026.150466

Application of Antisense Oligonucleotides as an Alternative Approach for Gene Expression Control and Functional Studies

Amelia Szukowska, Magdalena Żuk, Julia Sztompke, Bartosz Bednarz and Urszula Kaźmierczak

IJMS, 2025, 26, 10524
DOI: 10.3390/ijms262110524

Solid Phase Synthesis and TAR RNA-Binding Activity of Nucleopeptides Containing Nucleobases Linked to the Side Chains via 1,4-Linked-1,2,3-triazole

Piotr Mucha, Małgorzata Pieszko, Irena Bylińska, Wiesław Wiczk, Jarosław Ruczyński, Katarzyna Prochera and Piotr Rekowski

Biomedicines, 2024, 12, 570
DOI: 10.3390/biomedicines12030570

Computational drug discovery under RNA times

Mattia Bernetti, Riccardo Aguti, Stefano Bosio, Maurizio Recanatini, Matteo Masetti and Andrea Cavalli

QRB Discovery, 2022, 3
DOI: 10.1017/qrd.2022.20

Ru(II) Complex-Mediated Phase Separation Amplifies Photocatalytic RNA Damage to Stimulate RIG-I Immunotherapy

Xiao-Xiao Chen, Xia Mu, Zhi-Yuan Li, Kun Peng, Qing-Hua Shen, Yue-Bin Zhang and Cai-Ping Tan

JACS Au, 2025, 5, 4547
DOI: 10.1021/jacsau.5c00867

Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development

Martina Traykovska, Katya B. Popova and Robert Penchovsky

ACS Synth. Biol., 2021, 10, 3167
DOI: 10.1021/acssynbio.1c00443

RNA–Small-Molecule Interaction: Challenging the “Undruggable” Tag

Jaskirat Kaur, Akanksha Sharma, Poonam Mundlia, Vikas Sood, Ankur Pandey, Gurpal Singh and Ravi Pratap Barnwal

J. Med. Chem., 2024, 67, 4259
DOI: 10.1021/acs.jmedchem.3c01354

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

RNA-targeted small-molecule drug discoveries: a machine-learning perspective

Huan Xiao, Xin Yang, Yihao Zhang, Zongkang Zhang, Ge Zhang and Bao-Ting Zhang

RNA Biology, 2023, 20, 384
DOI: 10.1080/15476286.2023.2223498

Metabolic disorders affecting the liver and heart: Therapeutic efficacy of miRNA-based therapies?

Lucia La Sala, Valentina Carlini, Caterina Conte, Maria Belen Macas-Granizo, Elham Afzalpour, Jimmy Martin-Delgado, Marco D’Anzeo, Roberto F.E. Pedretti, Angelo Naselli, Antonio E. Pontiroli and Riccardo Cappato

Pharmacological Research, 2024, 201, 107083
DOI: 10.1016/j.phrs.2024.107083

Binding of a Tricationic meso-Substituted Porphyrin to poly(A)⋅poly(U): an Experimental Study

Olga Ryazanova, Igor Voloshin, Igor Dubey, Larysa Dubey and Victor Karachevtsev

J Fluoresc, 2024, 35, 6491
DOI: 10.1007/s10895-024-04000-4

Harnessing RNA‐Protein Interactions for Therapeutic Interventions

Khushboo Goel and Ishu Saraogi

Chemistry An Asian Journal, 2025, 20
DOI: 10.1002/asia.202401117

RNA chemistry and therapeutics

Siyu Wang, Drew Weissman and Yizhou Dong

Nat Rev Drug Discov, 2025, 24, 828
DOI: 10.1038/s41573-025-01237-x

Small-Molecule 3D Ligand for RNA Recognition: Tuning Selectivity through Scaffold Hopping

Simon Felder, Corinne Sagné, Erica Benedetti and Laurent Micouin

ACS Chem. Biol., 2022, 17, 3069
DOI: 10.1021/acschembio.2c00171

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 Newly Identified Peripheral Duplex Anchors and Stabilizes the MALAT1 Triplex

Mary N. Mwangi, Michael J. Yonkunas, Abeer A. Ageeli, Kayleigh R. McGovern-Gooch, Sevde Yilmaz and Nathan J. Baird

Biochemistry, 2024, 63, 2280
DOI: 10.1021/acs.biochem.4c00156

Design, synthesis, and screening of an RNA optimized fluorinated fragment library

Kasper P. Lundquist, Isabella Romeo, Raffaele B. Puglielli, Maëlle Pestalozzi, Marie L. Gram, Emily S. Hudson, Ofri Levi, Yoav S. Arava, Charlotte H. Gotfredsen and Mads H. Clausen

SLAS Discovery, 2025, 31, 100215
DOI: 10.1016/j.slasd.2025.100215

NMR analysis of interaction between RNA structure elements and small molecules

Megumi Tomemori, Rika Ichijo, Yoko Shinohara, Kaori Hatta, Kazuhiko Nakatani and Gota Kawai

The Journal of Biochemistry, 2025, 178, 1
DOI: 10.1093/jb/mvaf020

Targeting RNA-protein interactions with small molecules: promise and therapeutic potential

Curran Rhodes, Sumirtha Balaratnam, Kamyar Yazdani, Srinath Seshadri and John S. Schneekloth

Med Chem Res, 2024, 33, 2050
DOI: 10.1007/s00044-024-03342-9

Noncoding RNAs Emerging as Drugs or Drug Targets: Their Chemical Modification, Bio-Conjugation and Intracellular Regulation

Jin Wang, Tian Tian, Xin Li and Yan Zhang

Molecules, 2022, 27, 6717
DOI: 10.3390/molecules27196717

Engineering covalent small molecule–RNA complexes in living cells

Raphael Bereiter, Laurin Flemmich, Kamila Nykiel, Sarah Heel, Stephan Geley, Malou Hanisch, Clemens Eichler, Kathrin Breuker, Alexandra Lusser and Ronald Micura

Nat Chem Biol, 2025, 21, 843
DOI: 10.1038/s41589-024-01801-3

Interrogating RNA–Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations

Yihang Wang, Shaifaly Parmar, John S. Schneekloth and Pratyush Tiwary

ACS Cent. Sci., 2022, 8, 741
DOI: 10.1021/acscentsci.2c00149

RNA‐Selective Small‐Molecule Ligands: Recent Advances in Live‐Cell Imaging and Drug Discovery

Ka Hin Chan, Yakun Wang, Bo‐Xin Zheng, Wei Long, Xinxin Feng and Wing‐Leung Wong

ChemMedChem, 2023, 18
DOI: 10.1002/cmdc.202300271

P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2

Franklin Ingrid Kamga Youmbi, Vianney Kengne Tchendji and Clémentin Tayou Djamegni

Computational Biology and Chemistry, 2023, 104, 107878
DOI: 10.1016/j.compbiolchem.2023.107878

Chemically Modified Platforms for Better RNA Therapeutics

Yesi Shi, Xueyan Zhen, Yiming Zhang, Yongjiang Li, Seyoung Koo, Qimanguli Saiding, Na Kong, Gang Liu, Wei Chen and Wei Tao

Chem. Rev., 2024, 124, 929
DOI: 10.1021/acs.chemrev.3c00611

The changing landscape of medicinal chemistry optimization

Anita Rácz, Levente M. Mihalovits, Maximilian Beckers, Nikolas Fechner, Nikolaus Stiefl, Finton Sirockin, William McCoull, Emma Evertsson, Malin Lemurell, Gergely Makara and György M. Keserű

Nat Rev Drug Discov, 2025, 24, 870
DOI: 10.1038/s41573-025-01225-1

Site‐Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting

Phillip Yesley, Georgia Poulladofonou, Danny Incarnato and Willem A. Velema

Angew Chem Int Ed, 2026, 65
DOI: 10.1002/anie.202517243

Novel Quinazoline Derivatives Inhibit Splicing of Fungal Group II Introns

Olga Fedorova, Michelle Luo, G. Erik Jagdmann, Michael C. Van Zandt, Luke Sisto and Anna Marie Pyle

ACS Chem. Biol., 2025, 20, 378
DOI: 10.1021/acschembio.4c00631

Chemical Design of Magnetic Nanomaterials for Imaging and Ferroptosis-Based Cancer Therapy

Wei Xu, Guoqiang Guan, Renye Yue, Zhe Dong, Lingling Lei, Heemin Kang and Guosheng Song

Chem. Rev., 2025, 125, 1897
DOI: 10.1021/acs.chemrev.4c00546

Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening

Kaichen Wang, Sean Xian Yu Lee, Chaitanya K. Jaladanki, Wei Shen Ho, Justin Jang Hann Chu, Hao Fan and Christina Li Lin Chai

J. Chem. Inf. Model., 2025, 65, 3010
DOI: 10.1021/acs.jcim.4c01903

RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals

Siyi Chen, Qi Mao, Hong Cheng and Wanyi Tai

J. Med. Chem., 2024, 67, 16002
DOI: 10.1021/acs.jmedchem.4c01330

Electrostatic Anchoring in RNA-Ligand Design─Dissecting the Effects of Positive Charges on Affinity, Selectivity, Binding Kinetics, and Thermodynamics

Laura Almena Rodriguez, Elisabeth Kallert, Jan-Åke Husmann, Kirsten Schaubruch, Katherina I. S. Meisel, Marvin Schwickert, Sabrina N. Hoba, Ralf Heermann and Christian Kersten

J. Med. Chem., 2025, 68, 8659
DOI: 10.1021/acs.jmedchem.5c00339

Molecular insights into de novo small-molecule recognition by an intron RNA structure

Tianshuo Liu, Ling Xu, Kevin Chung, Luke J. Sisto, Jimin Hwang, Chengxin Zhang, Michael C. Van Zandt and Anna Marie Pyle

Proc. Natl. Acad. Sci. U.S.A., 2025, 122
DOI: 10.1073/pnas.2502425122

Alkaline Phosphatase-Controllable and Red Light-Activated RNA Modification Approach for Precise Tumor Suppression

Jing Fang, Yali Feng, Yuqi Zhang, Anna Wang, Jiachen Li, Chaoxiang Cui, Yirui Guo, Jinfeng Zhu, Zhengzhong Lv, Zhongsheng Zhao, Chenjie Xu and Haibin Shi

J. Am. Chem. Soc., 2022, 144, 23061
DOI: 10.1021/jacs.2c10409

Targeted Degradation of Structured RNAs via Ribonuclease-Targeting Chimeras (RiboTacs)

Salma Haj-Yahia, Arijit Nandi and Raphael I. Benhamou

Expert Opinion on Drug Discovery, 2023, 18, 929
DOI: 10.1080/17460441.2023.2224960

Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40

Yuquan Tong, Jessica L. Childs‐Disney and Matthew D. Disney

British J Pharmacology, 2024, 181, 4152
DOI: 10.1111/bph.17308

Post-Docking Refinement of Peptide or Protein-RNA Complexes Using Thermal Titration Molecular Dynamics (TTMD): A Stability Insight

Andrea Dodaro, Gianluca Novello, Silvia Menin, Chiara Cavastracci Strascia, Mattia Sturlese, Veronica Salmaso and Stefano Moro

J. Chem. Inf. Model., 2025, 65, 1441
DOI: 10.1021/acs.jcim.4c01393

Physical mechanisms of exit dynamics in microchannels of nonequilibrium transport systems

Yu-Qing Wang, Da-Sen Wei, Li-Wen Zhang, Tun-Yu Zhang, Tian-Ze Li, Mo-Lin Fang, Kai-Chen Ouyang, Yu-Xuan He and Guan-Yu Chen

Int. J. Mod. Phys. B, 2024, 38
DOI: 10.1142/S0217979224501935

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

Targeting RNA splicing modulation: new perspectives for anticancer strategy?

Xuemei Lv, Xiaoyu Sun, Yang Gao, Xinyue Song, Xiaoyun Hu, Lang Gong, Li Han, Miao He and Minjie Wei

J Exp Clin Cancer Res, 2025, 44
DOI: 10.1186/s13046-025-03279-w