Publications Caflisch Group

ZORA Publication List

Publications

• 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.
  • 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.
  • Widmer, Julian; Langini, Cassiano; Vitalis, Andreas; Caflisch, Amedeo (2023). Optimized reaction coordinates for analysis of enhanced sampling. Journal of Chemical Physics, 159(1):015101.
  • Bedi, Rajiv Kumar; Huang, Danzhi; Li, Yaozong; Caflisch, Amedeo (2023). Structure-Based Design of Inhibitors of the m$^{6}$A-RNA Writer Enzyme METTL3. ACS Bio & Med Chem Au, 3(4):359-370.
  • Ilie, Ioana M; Ehrhardt, Claus; Caflisch, Amedeo; Weitz-Schmidt, Gabriele (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12):3878-3891.
  • Reimann, Regina R; Puzio, Martina; Rosati, Antonella; Emmenegger, Marc; Schneider, Bernard L; Valdés, Pamela; Huang, Danzhi; Caflisch, Amedeo; Aguzzi, Adriano (2023). Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathology, 33(2):e13130.
  • Xiang, Yusen; Zhai, Guanglei; Li, Yaozong; Wang, Mengge; Chen, Xixiang; Wang, Ruyu; Xie, Hang; Zhang, Weidong; Ge, Guangbo; Zhang, Qian; Xu, Yechun; Caflisch, Amedeo; Xu, Jianrong; Chen, Hongzhuan; Chen, Lili (2023). Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. International journal of biological macromolecules, 226:780-792.

• 2022

  • Ilie, Ioana M; Caflisch, Amedeo (2022). Antibody binding increases the flexibility of the prion protein. BBA - Proteins and Proteomics, 1870(11-12):140827.
  • Dehabadi, Maryam Haji; Caflisch, Amedeo; Ilie, Ioana M; Firouzi, Rohoullah (2022). Interactions of Curcumin's Degradation Products with the Aβ$_{42}$ Dimer: A Computational Study. Journal of Physical Chemistry B, 126(39):7627-7637.
  • Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2022). Domino Effect in Allosteric Signaling of Peptide Binding. Journal of Molecular Biology, 434(17):167661.
  • Nai, Francesco; Nachawati, Raed; Zálešák, František; Wang, Xiang; Li, Yaozong; Caflisch, Amedeo (2022). Fragment Ligands of the m$^{6}$A-RNA Reader YTHDF2. ACS Medicinal Chemistry Letters, 13(9):1500-1509.
  • Dalle Vedove, Andrea; Cazzanelli, Giulia; Batiste, Laurent; Marchand, Jean-Rémy; Spiliotopoulos, Dimitrios; Corsi, Jessica; D'Agostino, Vito Giuseppe; Caflisch, Amedeo; Lolli, Graziano (2022). Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Medicinal Chemistry Letters, 13(9):1434-1443.
  • Ilie, Ioana M; Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein.. Biophysical Journal, 121(14):2813-2825.
  • García-Viñuales, Sara; Ilie, Ioana M; Santoro, Anna Maria; Romanucci, Valeria; Zarrelli, Armando; Di Fabio, Giovanni; Caflisch, Amedeo; Milardi, Danilo (2022). Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. BBA - Proteins and Proteomics, 1870(5):140772.
  • Nass, Karol J; Ilie, Ioana M; Saller, Manfred J; Driessen, Arnold J M; Caflisch, Amedeo; Kammerer, Richard A; Li, Xiaodan (2022). The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochimica et biophysica acta. Biomembranes, 1864(3):183825.
  • Salutari, Ilaria; Caflisch, Amedeo (2022). Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. Journal of Chemical Information and Modeling, 62(4):1014-1024.
  • Schilling, Johannes; Jost, Christian; Ilie, Ioana Mariuca; Schnabl, Joachim; Buechi, Oralea; Eapen, Rohan S; Truffer, Rafaela; Caflisch, Amedeo; Forrer, Patrik (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Journal of Biological Chemistry, 298(1):101403.
  • Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2022). Spiking burstiness and working memory in the human medial temporal lobe. Cerebral Cortex Communications, 3(4):tgac039.
  • Giordano, Deborah; Langini, Cassiano; Caflisch, Amedeo; Marabotti, Anna; Facchiano, Angelo (2022). Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis. Computational and Structural Biotechnology Journal, 20:3924-3934.

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