Publications of the Caflisch Group

ZORA Publication List

Publications

• 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
  • Zhang, S., Liu, S., Lai, H.-F., Bender, K. W., Kim, G., Caflisch, A., & Zipfel, C. (2025). Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes Nature Plants, 11, 1642–1657. https://doi.org/10.1038/s41477-025-02050-5
  • Gosselé, Katherine A; Latino, Irene; Laul, Eleen; Kirillova, Mariia S; Pascanu, Vlad; Carloni, Emanuele; Bedi, Rajiv K; Pizzichetti, Chiara; Caflisch, Amedeo; González, Santiago F; Nevado, Cristina (2025). Selective CBP/EP300 Bromodomain Inhibitors: Novel Epigenetic Tools to Counter TNF-α-Driven Inflammation JACS Au, 5(6):2491-2499.
  • Vitalis, Andreas; Parker, David; Radler, Fabian; Vargas-Rosales, Pablo Andrés; Zhang, Yang; Marchand, Jean-Rémy; Caflisch, Amedeo (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening Journal of Computational Chemistry, 46(7):e70074.
  • Vitalis, Andreas; Winkler, Steffen; Zhang, Yang; Widmer, Julian; Caflisch, Amedeo (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories Journal of Chemical Information and Modeling, 65(5):2443-2455.
  • Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2025). The physics-AI dialogue in drug design RSC Medicinal Chemistry, 16(4):1499-1515.

• 2024

  • Widmer, Julian; Vitalis, Andreas; Caflisch, Amedeo (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains Journal of Biological Chemistry, 300(12):107998.
  • Tarullo, Marco; Fernandez Rodriguez, Guillermo; Iaiza, Alessia; Venezia, Sara; Macone, Alberto; Incocciati, Alessio; Masciarelli, Silvia; Marchioni, Marcella; Giorgis, Marta; Lolli, Marco Lucio; Fornaseri, Federico; Proietti, Ludovica; Grebien, Florian; Rosignoli, Serena; Paiardini, Alessandro; Rotili, Dante; Mai, Antonello; Bochenkova, Elena; Caflisch, Amedeo; Fazi, Francesco; Fatica, Alessandro (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(12):4096-4111.
  • Cazzanelli, Giulia; Dalle Vedove, Andrea; Sbardellati, Nicolo; Valer, Luca; Caflisch, Amedeo; Lolli, Graziano (2024). Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors Protein Science, 33(11):e5191.
  • Hwang, Wonmuk; Austin, Steven L; Blondel, Arnaud; Boittier, Eric D; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F; Gao, Jiali; Glowacki, David R; Gonzales, James E; Hamaneh, Mehdi Bagerhi; Harder, Edward D; Hayes, Ryan L; Huang, Jing; Huang, Yandong; Hudson, Phillip S; Im, Wonpil; Islam, Shahidul M; et al (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed Journal of Physical Chemistry B, 128(41):9976-10042.
  • Cheng-Sánchez, Iván; Gosselé, Katherine; Palaferri, Leonardo; Laul, Eleen; Riccabella, Gionata; Bedi, Rajiv K; Li, Yaozong; Müller, Anna; Corbeski, Ivan; Caflisch, Amedeo; Nevado, Cristina (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity JACS Au, 4(9):3466-3474.
  • Zhou, Jiangtao; Assenza, Salvatore; Tatli, Meltem; Tian, Jiawen; Ilie, Ioana M; Starostin, Eugene L; Caflisch, Amedeo; Knowles, Tuomas P J; Dietler, Giovanni; Ruggeri, Francesco S; Stahlberg, Henning; Sekatskii, Sergey K; Mezzenga, Raffaele (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs Advanced Science, 11(32):e2402740.
  • Zálešák, František; Nai, Francesco; Herok, Marcin; Bochenkova, Elena; Bedi, Rajiv K; Li, Yaozong; Errani, Francesco; Caflisch, Amedeo (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand Journal of Medicinal Chemistry, 67(11):9516-9535.
  • Nai, Francesco; Flores Espinoza, Maria Paula; Invernizzi, Annalisa; Vargas-Rosales, Pablo Andrés; Bobileva, Olga; Herok, Marcin; Caflisch, Amedeo (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1 ACS Bio & Med Chem Au, 4(2):100-110.
  • Corbeski, Ivan; Vargas-Rosales, Pablo Andrés; Bedi, Rajiv Kumar; Deng, Jiahua; Coelho, Dylan; Braud, Emmanuelle; Iannazzo, Laura; Li, Yaozong; Huang, Danzhi; Ethève-Quelquejeu, Mélanie; Cui, Qiang; Caflisch, Amedeo (2024). The catalytic mechanism of the RNA methyltransferase METTL3 eLife, 12:RP92537.
  • Errani, Francesco; Invernizzi, Annalisa; Herok, Marcin; Bochenkova, Elena; Stamm, Fiona; Corbeski, Ivan; Romanucci, Valeria; Di Fabio, Giovanni; Zálešák, František; Caflisch, Amedeo (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase JACS Au, 4(2):713-729.

• 2023

  • Bobrovs, Raitis; Drunka, Laura; Kanepe, Iveta; Jirgensons, Aigars; Caflisch, Amedeo; Salvalaglio, Matteo; Jaudzems, Kristaps (2023). Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors Journal of Chemical Information and Modeling, 63(21):6890-6899.
  • Cazzanelli, Giulia; Dalle Vedove, Andrea; Parolin, Eleonora; D'Agostino, Vito Giuseppe; Unzue, Andrea; Nevado, Cristina; Caflisch, Amedeo; Lolli, Graziano (2023). Reevaluation of bromodomain ligands targeting BAZ2A Protein Science, 32(9):e4752.
  • Vargas-Rosales, Pablo Andrés; D'Addio, Alessio; Zhang, Yang; Caflisch, Amedeo (2023). Disrupting Dimeric β-Amyloid by Electric Fields ACS Physical Chemistry Au, 3(5):456-466.

Pagination