Publications Caflisch Group

ZORA Publication List

Publications

• 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.

• 2021

  • Dalle Vedove, Andrea; Cazzanelli, Giulia; Corsi, Jessica; Sedykh, Maria; D’Agostino, Vito Giuseppe; Caflisch, Amedeo; Lolli, Graziano (2021). Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining. ACS Bio & Med Chem Au, 1(1):5-10.
  • Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2021). Unsupervised Methods for Detection of Neural States: Case Study of Hippocampal-Amygdala Interactions. eNeuro, 8(6):0484-20.
  • Moroz-Omori, Elena V; Huang, Danzhi; Kumar Bedi, Rajiv; Cheriyamkunnel, Sherry J; Bochenkova, Elena; Dolbois, Aymeric; Rzeczkowski, Maciej D; Li, Yaozong; Wiedmer, Lars; Caflisch, Amedeo (2021). METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes. ChemMedChem, 16(19):3035-3043.
  • Dolbois, Aymeric; Bedi, Rajiv K; Bochenkova, Elena; Müller, Anna; Moroz-Omori, Elena V; Huang, Danzhi; Caflisch, Amedeo (2021). 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. Journal of Medicinal Chemistry, 64(17):12738-12760.
  • Lee, Joo-Hyung; Wang, Ruoyu; Xiong, Feng; Krakowiak, Joanna; Liao, Zian; Nguyen, Phuoc T; Moroz-Omori, Elena V; Shao, Jiaofang; Zhu, Xiaoyu; Bolt, Michael J; Wu, Haoyi; Singh, Pankaj K; Bi, Mingjun; Shi, Caleb J; Jamal, Naadir; Li, Guojie; Mistry, Ragini; Jung, Sung Yun; Tsai, Kuang-Lei; Ferreon, Josephine C; Stossi, Fabio; Caflisch, Amedeo; Liu, Zhijie; Mancini, Michael A; Li, Wenbo (2021). Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Molecular Cell, 81(16):3368-3385.e9.
  • Pohl, Marie O; Busnadiego, Idoia; Marrafino, Francesco; Wiedmer, Lars; Hunziker, Annika; Fernbach, Sonja; Glas, Irina; Moroz-Omori, Elena V; Hale, Benjamin G; Caflisch, Amedeo; Stertz, Silke (2021). Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. Journal of General Virology, 102(7):001625.
  • Milardi, Danilo; Gazit, Ehud; Radford, Sheena E; Xu, Yong; Gallardo, Rodrigo U; Caflisch, Amedeo; Westermark, Gunilla T; Westermark, Per; Rosa, Carmelo La; Ramamoorthy, Ayyalusamy (2021). Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chemical Reviews, 121(3):1845-1893.
  • Li, Yaozong; Bedi, Rajiv Kumar; Wiedmer, Lars; Sun, Xianqiang; Huang, Danzhi; Caflisch, Amedeo (2021). Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation, 17(2):1240-1249.
  • Cappelletti, Valentina; Hauser, Thomas; Piazza, Ilaria; Pepelnjak, Monika; Malinovska, Liliana; Fuhrer, Tobias; Li, Yaozong; Dörig, Christian; Boersema, Paul; Gillet, Ludovic; Grossbach, Jan; Dugourd, Aurelien; Saez-Rodriguez, Julio; Beyer, Andreas; Zamboni, Nicola; Caflisch, Amedeo; de Souza, Natalie; Picotti, Paola (2021). Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell, 184(2):545-559.e22.
  • Mallona, Izaskun; Ilie, Ioana Mariuca; Karemaker, Ino Dominiek; Butz, Stefan; Manzo, Massimiliano; Caflisch, Amedeo; Baubec, Tuncay (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1):145-157.

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