Selection of releveant publications from TargetRNA consortium members

(1) Kovachka, S.; Panosetti, M.; Grimaldi, B.; Azoulay, S.; Di Giorgio, A.; Duca, M. Small Molecule Approaches to Targeting RNA. Nat Rev Chem 2024, 8 (2), 120–135. https://doi.org/10.1038/s41570-023-00569-9.

(2) Silvestri, I.; Manigrasso, J.; Andreani, A.; Brindani, N.; Mas, C.; Reiser, J.-B.; Vidossich, P.; Martino, G.; McCarthy, A. A.; De Vivo, M.; Marcia, M. Targeting the Conserved Active Site of Splicing Machines with Specific and Selective Small Molecule Modulators. Nat Commun 2024, 15 (1), 4980. https://doi.org/10.1038/s41467-024-48697-0.

(3) Bains, J. K.; Qureshi, N. S.; Ceylan, B.; Wacker, A.; Schwalbe, H. Cell-Free Transcription-Translation System: A Dual Read-out Assay to Characterize Riboswitch Function. Nucleic Acids Res 2023, 51 (15), e82. https://doi.org/10.1093/nar/gkad574.

(4) Müller, J.; Klein, R.; Tarkhanova, O.; Gryniukova, A.; Borysko, P.; Merkl, S.; Ruf, M.; Neumann, A.; Gastreich, M.; Moroz, Y. S.; Klebe, G.; Glinca, S. Magnet for the Needle in Haystack: “Crystal Structure First” Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces. J. Med. Chem. 2022. https://doi.org/10.1021/acs.jmedchem.2c00813.

(5) Martin, C.; Bonnet, M.; Patino, N.; Azoulay, S.; Di Giorgio, A.; Duca, M. Design, Synthesis, and Evaluation of Neomycin-Imidazole Conjugates for RNA Cleavage. Chempluschem 2022, 87 (11), e202200250. https://doi.org/10.1002/cplu.202200250.

(6) He, J.; Nittinger, E.; Tyrchan, C.; Czechtizky, W.; Patronov, A.; Bjerrum, E. J.; Engkvist, O. Transformer-Based Molecular Optimization beyond Matched Molecular Pairs. Journal of Cheminformatics 2022, 14 (1), 18. https://doi.org/10.1186/s13321-022-00599-3.

(7) Hamway, Y.; Zimmermann, K.; Blommers, M. J. J.; Sousa, M. V.; Häberli, C.; Kulkarni, S.; Skalicky, S.; Hackl, M.; Götte, M.; Keiser, J.; da Costa, C. P.; Spangenberg, T.; Azzaoui, K. Modulation of Host–Parasite Interactions with Small Molecules Targeting Schistosoma Mansoni microRNAs. ACS Infect. Dis. 2022, 8 (10), 2028–2034. https://doi.org/10.1021/acsinfecdis.2c00360.

(8) Sreeramulu, S.; Richter, C.; Berg, H.; Wirtz Martin, M. A.; Ceylan, B.; Matzel, T.; Adam, J.; Altincekic, N.; Azzaoui, K.; Bains, J. K.; Blommers, M. J. J.; Ferner, J.; Fürtig, B.; Göbel, M.; Grün, J. T.; Hengesbach, M.; Hohmann, K. F.; Hymon, D.; Knezic, B.; Martins, J.; Mertinkus, K. R.; Niesteruk, A.; Peter, S. A.; Pyper, D. J.; Qureshi, N. S.; Scheffer, U.; Schlundt, A.; Schnieders, R.; Stirnal, E.; Sudakov, A.; Tröster, A.; Vögele, J.; Wacker, A.; Weigand, J. E.; Wirmer-Bartoschek, J.; Wöhnert, J.; Schwalbe, H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021. https://doi.org/10.1002/anie.202103693.

(9) Rekand, I. H.; Brenk, R. DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. J. Chem. Inf. Model. 2021, 61 (8), 4068–4081. https://doi.org/10.1021/acs.jcim.1c00155.

(10) Panchal, V.; Brenk, R. Riboswitches as Drug Targets for Antibiotics. Antibiotics 2021, 10 (1), 45. https://doi.org/10.3390/antibiotics10010045.

(11) Maucort, C.; Vo, D. D.; Aouad, S.; Charrat, C.; Azoulay, S.; Di Giorgio, A.; Duca, M. Design and Implementation of Synthetic RNA Binders for the Inhibition of miR-21 Biogenesis. ACS Med Chem Lett 2021, 12 (6), 899–906. https://doi.org/10.1021/acsmedchemlett.0c00682.

(12) Marcia, M.; Manigrasso, J.; De Vivo, M. Finding the Ion in the RNA-Stack: Can Computational Models Accurately Predict Key Functional Elements in Large Macromolecular Complexes? J. Chem. Inf. Model. 2021, 61 (6), 2511–2515. https://doi.org/10.1021/acs.jcim.1c00572.

(13) Manigrasso, J.; Marcia, M.; De Vivo, M. Computer-Aided Design of RNA-Targeted Small Molecules: A Growing Need in Drug Discovery. Chem 2021, 7 (11), 2965–2988. https://doi.org/10.1016/j.chempr.2021.05.021.

(14) Lundquist, K. P.; Panchal, V.; Gotfredsen, C. H.; Brenk, R.; Clausen, M. H. Fragment-Based Drug Discovery for RNA Targets. ChemMedChem 2021, 16 (17), 2588–2603. https://doi.org/10.1002/cmdc.202100324.

(15) He, J.; You, H.; Sandström, E.; Nittinger, E.; Bjerrum, E. J.; Tyrchan, C.; Czechtizky, W.; Engkvist, O. Molecular Optimization by Capturing Chemist’s Intuition Using Deep Neural Networks. Journal of Cheminformatics 2021, 13 (1), 26. https://doi.org/10.1186/s13321-021-00497-0.

(16) Troelsen, N. S.; Shanina, E.; Gonzalez-Romero, D.; Danková, D.; Jensen, I. S. A.; Śniady, K. J.; Nami, F.; Zhang, H.; Rademacher, C.; Cuenda, A.; Gotfredsen, C. H.; Clausen, M. H. The 3F Library: Fluorinated Fsp3-Rich Fragments for Expeditious 19F NMR Based Screening. Angewandte Chemie International Edition 2020, 59 (6), 2204–2210. https://doi.org/10.1002/anie.201913125.

(17) Manigrasso, J.; Chillón, I.; Genna, V.; Vidossich, P.; Somarowthu, S.; Pyle, A. M.; De Vivo, M.; Marcia, M. Visualizing Group II Intron Dynamics between the First and Second Steps of Splicing. Nat Commun 2020, 11 (1), 2837. https://doi.org/10.1038/s41467-020-16741-4.

(18) Blaschke, T.; Arús-Pous, J.; Chen, H.; Margreitter, C.; Tyrchan, C.; Engkvist, O.; Papadopoulos, K.; Patronov, A. REINVENT 2.0: An AI Tool for De Novo Drug Design. J. Chem. Inf. Model. 2020, 60 (12), 5918–5922. https://doi.org/10.1021/acs.jcim.0c00915.

(19) Binas, O.; de Jesus, V.; Landgraf, T.; Völklein, A. E.; Martins, J.; Hymon, D.; Berg, H.; Bains, J. K.; Biedenbänder, T.; Fürtig, B.; Gande, S. L.; Niesteruk, A.; Oxenfarth, A.; Qureshi, N. S.; Schamber, T.; Schnieders, R.; Tröster, A.; Wacker, A.; Wirmer-Bartoschek, J.; Martin, M. A. W.; Stirnal, E.; Azzaoui, K.; Blommers, M. J. J.; Richter, C.; Sreeramulu, S.; Schwalbe, H. 19F-NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens. Chembiochem 2020. https://doi.org/10.1002/cbic.202000476.

(20) Arús-Pous, J.; Patronov, A.; Bjerrum, E. J.; Tyrchan, C.; Reymond, J.-L.; Chen, H.; Engkvist, O. SMILES-Based Deep Generative Scaffold Decorator for de-Novo Drug Design. Journal of Cheminformatics 2020, 12 (1), 38. https://doi.org/10.1186/s13321-020-00441-8.

(21) Hansen, K. Ø.; Andersen, J. H.; Bayer, A.; Pandey, S. K.; Lorentzen, M.; Jørgensen, K. B.; Sydnes, M. O.; Guttormsen, Y.; Baumann, M.; Koch, U.; Klebl, B.; Eickhoff, J.; Haug, B. E.; Isaksson, J.; Hansen, E. H. Kinase Chemodiversity from the Arctic: The Breitfussins. J. Med. Chem. 2019, 62 (22), 10167–10181. https://doi.org/10.1021/acs.jmedchem.9b01006.

(22) Segler, M. H. S.; Kogej, T.; Tyrchan, C.; Waller, M. P. Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks. ACS Cent. Sci. 2018, 4 (1), 120–131. https://doi.org/10.1021/acscentsci.7b00512.

(23) Wehler, T.; Brenk, R. Structure-Based Discovery of Small Molecules Binding to RNA. In RNA Therapeutics; Topics in Medicinal Chemistry; Springer, Cham, 2017; pp 47–77. https://doi.org/10.1007/7355_2016_29.

(24) Wang, H.; Mann, P. A.; Xiao, L.; Gill, C.; Galgoci, A. M.; Howe, J. A.; Villafania, A.; Barbieri, C. M.; Malinverni, J. C.; Sher, X.; Mayhood, T.; McCurry, M. D.; Murgolo, N.; Flattery, A.; Mack, M.; Roemer, T. Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus Aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting. Cell Chemical Biology 2017, 24 (5), 576-588.e6. https://doi.org/10.1016/j.chembiol.2017.03.014.

(25) Steinert, H.; Sochor, F.; Wacker, A.; Buck, J.; Helmling, C.; Hiller, F.; Keyhani, S.; Noeske, J.; Grimm, S.; Rudolph, M. M.; Keller, H.; Mooney, R. A.; Landick, R.; Suess, B.; Fürtig, B.; Wöhnert, J.; Schwalbe, H. Pausing Guides RNA Folding to Populate Transiently Stable RNA Structures for Riboswitch-Based Transcription Regulation. eLife 2017, 6, e21297. https://doi.org/10.7554/eLife.21297.

(26) Rekand, I.; Brenk, R. Design of Riboswitch Ligands, an Emerging Target Class for Novel Antibiotics. Fut. Med. Chem. 2017, 9 (14), 1649–1662.

(27) De Vivo, M.; Masetti, M.; Bottegoni, G.; Cavalli, A. Role of Molecular Dynamics and Related Methods in Drug Discovery. Journal of Medicinal Chemistry 2016, 59 (9), 4035–4061. https://doi.org/10.1021/acs.jmedchem.5b01684.

(28) Zhao, C.; Rajashankar, K. R.; Marcia, M.; Pyle, A. M. Crystal Structure of Group II Intron Domain 1 Reveals a Template for RNA Assembly. Nat Chem Biol 2015, 11 (12), 967–972. https://doi.org/10.1038/nchembio.1949.

(29) Tran, T. P. A.; Vo, D. D.; Di Giorgio, A.; Duca, M. Ribosome-Targeting Antibiotics as Inhibitors of Oncogenic microRNAs Biogenesis: Old Scaffolds for New Perspectives in RNA Targeting. Bioorganic & Medicinal Chemistry 2015, 23 (17), 5334–5344. https://doi.org/10.1016/j.bmc.2015.07.062.

(30) Pedrolli, D.; Langer, S.; Hobl, B.; Schwarz, J.; Hashimoto, M.; Mack, M. The ribB FMN Riboswitch from Escherichia Coli Operates at the Transcriptional and Translational Level and Regulates Riboflavin Biosynthesis. FEBS J. 2015, 282 (16), 3230–3242. https://doi.org/10.1111/febs.13226.

(31) Pedrolli, D. B.; Kühm, C.; Sévin, D. C.; Vockenhuber, M. P.; Sauer, U.; Suess, B.; Mack, M. A Dual Control Mechanism Synchronizes Riboflavin and Sulphur Metabolism in Bacillus Subtilis. Proc. Natl. Acad. Sci. U.S.A. 2015, 112 (45), 14054–14059. https://doi.org/10.1073/pnas.1515024112.

(32) Daldrop, P.; Brenk, R. Structure-Based Virtual Screening for the Identification of RNA-Binding Ligands. Methods Mol. Biol. 2014, 1103, 127–139.

(33) Reining, A.; Nozinovic, S.; Schlepckow, K.; Buhr, F.; Furtig, B.; Schwalbe, H. Three-State Mechanism Couples Ligand and Temperature Sensing in Riboswitches. Nature 2013, 499 (7458), 355–359. https://doi.org/10.1038/nature12378.

(34) Pedrolli, D. B.; Matern, A.; Wang, J.; Ester, M.; Siedler, K.; Breaker, R.; Mack, M. A Highly Specialized Flavin Mononucleotide Riboswitch Responds Differently to Similar Ligands and Confers Roseoflavin Resistance to Streptomyces Davawensis. Nucleic Acids Research 2012, 40 (17), 8662–8673. https://doi.org/10.1093/nar/gks616.

(35) Marcia, M.; Pyle, A. M. Visualizing Group II Intron Catalysis through the Stages of Splicing. Cell 2012, 151 (3), 497–507. https://doi.org/10.1016/j.cell.2012.09.033.

(36) Daldrop, P.; Reyes, F. E.; Robinson, D. A.; Hammond, C. M.; Lilley, D. M.; Batey, R. T.; Brenk, R. Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking. Chem. Biol. 2011, 18 (3), 324–335.

(37) Ott, E.; Stolz, J.; Lehmann, M.; Mack, M. The RFN Riboswitch of Bacillus Subtilis Is a Target for the Antibiotic Roseoflavin Produced by Streptomyces Davawensis. RNA Biol 2009, 6 (3), 276–280. https://doi.org/8342 [pii].

(38) Schwalbe, H.; Buck, J.; Furtig, B.; Noeske, J.; Wohnert, J. Structures of RNA Switches: Insight into Molecular Recognition and Tertiary Structure. Angewandte Chemie. International Edition in English 2007, 46 (8), 1212–1219.

(39) Jahnke, W.; Flörsheimer, A.; Blommers, M. J. J.; Paris, C. G.; Heim, J.; Nalin, C. M.; Perez, L. B. Second-Site NMR Screening and Linker Design. Curr Top Med Chem 2003, 3 (1), 69–80. https://doi.org/10.2174/1568026033392778.

(40) Gotfredsen, C. H.; Schultze, P.; Feigon, J. Solution Structure of an Intramolecular Pyrimidine−Purine−Pyrimidine Triplex Containing an RNA Third Strand. J. Am. Chem. Soc. 1998, 120 (18), 4281–4289. https://doi.org/10.1021/ja973221m.