Publications of the Caflisch Group

ZORA Publication List

Publications

• 2026

  • Liu, B., Spalinger, M. R., Invernizzi, A., Gerdes, E., Steglich, B., Schwarzfischer, M., Machicote, A., Pelczar, P., Pöhlmann, D., Nawrocki, M., Böttcher, M., Aleko, A., Velasquez, L. N., Wende, S., Stallbaum, F., Neuendorff, J., Grosshauser, S., Muscate, F., Douilhet, G., … Caflisch, A. (2026). Indirect inhibition of the NLRP3-interleukin-1β axis contributes to the efficacy of JAK1 inhibitors in experimental colitis and human ulcerative colitis Nature Communications, Epub ahead of print. https://doi.org/10.1038/s41467-026-71808-y
  • Matter, C. M., & Caflisch, A. (2026). Fine-Tuning a Transformer Model for METTL3 Lead Optimization ACS Bio & Med Chem Au, 6, 160–167. https://doi.org/10.1021/acsbiomedchemau.5c00198
  • Corbeski, I., Bedi, R. K., Matter, C. M., Stamm, F., Bochenkova, E., Herok, M., Hartshorn, M. J., & Caflisch, A. (2026). Ligand-Induced Opening of a Cryptic Pocket in METTL14 ACS Bio & Med Chem Au, 6, 130–144. https://doi.org/10.1021/acsbiomedchemau.5c00184
  • Bedi, R. K., & Caflisch, A. (2026). A DNA-Based Binding Assay for the mA-RNA Reader Proteins Chembiochem, 27, e202500897. https://doi.org/10.1002/cbic.202500897

• 2025

  • Vargas-rosales Pablo Andrés, Giangreco, G., & Caflisch, A. (2025). Disrupting Amyloid Filaments of Tau by Means of Electric Fields Journal of Physical Chemistry B, 129, 9124–9137. https://doi.org/10.1021/acs.jpcb.5c04393
  • Invernizzi, A., Nai, F., Bedi Rajiv Kumar, Vargas-rosales Pablo Andrés, Li, Y., Bochenkova, E., Herok, M., Zálešák, F., & Caflisch, A. (2025). Discovery of YTHDF2 Ligands by Fragment-Based Design ACS Bio & Med Chem Au, 5, 753–765. https://doi.org/10.1021/acsbiomedchemau.5c00099
  • Gosselé, K. A., Latino, I., Laul, E., Kirillova, M. S., Pascanu, V., Carloni, E., Bedi, R. K., Pizzichetti, C., Caflisch, A., González, S. F., & Nevado, C. (2025). Selective CBP/EP300 Bromodomain Inhibitors: Novel Epigenetic Tools to Counter TNF-α-Driven Inflammation JACS Au, 5, 2491–2499. https://doi.org/10.1021/jacsau.5c00085
  • Vitalis, A., Parker, D., Radler, F., Vargas-Rosales, P. A., Zhang, Y., Marchand, J.-R., & Caflisch, A. (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening Journal of Computational Chemistry, 46, e70074. https://doi.org/10.1002/jcc.70074
  • Vitalis, A., Winkler, S., Zhang, Y., Widmer, J., & Caflisch, A. (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories Journal of Chemical Information and Modeling, 65, 2443–2455. https://doi.org/10.1021/acs.jcim.4c01301
  • Vargas-Rosales, P. A., & Caflisch, A. (2025). The physics-AI dialogue in drug design RSC Medicinal Chemistry, 16, 1499–1515. https://doi.org/10.1039/d4md00869c

• 2024

  • Widmer, J., Vitalis, A., & Caflisch, A. (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains Journal of Biological Chemistry, 300, 107998. https://doi.org/10.1016/j.jbc.2024.107998
  • Tarullo, M., Fernandez Rodriguez, G., Iaiza, A., Venezia, S., Macone, A., Incocciati, A., Masciarelli, S., Marchioni, M., Giorgis, M., Lolli, M. L., Fornaseri, F., Proietti, L., Grebien, F., Rosignoli, S., Paiardini, A., Rotili, D., Mai, A., Bochenkova, E., Caflisch, A., … Fatica, A. (2024). Off-Target Inhibition of Human Dihydroorotate Dehydrogenase (hDHODH) Highlights Challenges in the Development of Fat Mass and Obesity-Associated Protein (FTO) Inhibitors ACS Pharmacology & Translational Science, 7, 4096–4111. https://doi.org/10.1021/acsptsci.4c00533
  • Cazzanelli, G., Dalle Vedove, A., Sbardellati, N., Valer, L., Caflisch, A., & Lolli, G. (2024). Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors Protein Science, 33, e5191. https://doi.org/10.1002/pro.5191
  • Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., Choi, Y. K., Chu, J.-W., Crowley, M. F., Cui, Q., Damjanovic, A., Deng, Y., Devereux, M., Ding, X., Feig, M. F., … et al. (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed Journal of Physical Chemistry B, 128, 9976–10042. https://doi.org/10.1021/acs.jpcb.4c04100
  • Cheng-Sánchez, I., Gosselé, K., Palaferri, L., Laul, E., Riccabella, G., Bedi, R. K., Li, Y., Müller, A., Corbeski, I., Caflisch, A., & Nevado, C. (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity JACS Au, 4, 3466–3474. https://doi.org/10.1021/jacsau.4c00292
  • Zhou, J., Assenza, S., Tatli, M., Tian, J., Ilie, I. M., Starostin, E. L., Caflisch, A., Knowles, T. P. J., Dietler, G., Ruggeri, F. S., Stahlberg, H., Sekatskii, S. K., & Mezzenga, R. (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs Advanced Science, 11, e2402740. https://doi.org/10.1002/advs.202402740
  • Zálešák, F., Nai, F., Herok, M., Bochenkova, E., Bedi, R. K., Li, Y., Errani, F., & Caflisch, A. (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand Journal of Medicinal Chemistry, 67, 9516–9535. https://doi.org/10.1021/acs.jmedchem.4c00599
  • Nai, F., Flores Espinoza, M. P., Invernizzi, A., Vargas-Rosales, P. A., Bobileva, O., Herok, M., & Caflisch, A. (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1 ACS Bio & Med Chem Au, 4, 100–110. https://doi.org/10.1021/acsbiomedchemau.3c00030
  • Corbeski, I., Vargas-Rosales, P. A., Bedi, R. K., Deng, J., Coelho, D., Braud, E., Iannazzo, L., Li, Y., Huang, D., Ethève-Quelquejeu, M., Cui, Q., & Caflisch, A. (2024). The catalytic mechanism of the RNA methyltransferase METTL3 ELife, 12, RP92537. https://doi.org/10.7554/eLife.92537
  • Errani, F., Invernizzi, A., Herok, M., Bochenkova, E., Stamm, F., Corbeski, I., Romanucci, V., Di Fabio, G., Zálešák, F., & Caflisch, A. (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase JACS Au, 4, 713–729. https://doi.org/10.1021/jacsau.4c00040

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