Publications of the Caflisch Group

ZORA Publication List

Publications

• 2021

  • Moroz-Omori, E. V., Huang, D., Kumar Bedi, R., Cheriyamkunnel, S. J., Bochenkova, E., Dolbois, A., Rzeczkowski, M. D., Li, Y., Wiedmer, L., & Caflisch, A. (2021). METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes ChemMedChem, 16, 3035–3043. https://doi.org/10.1002/cmdc.202100291
  • Dolbois, A., Bedi, R. K., Bochenkova, E., Müller, A., Moroz-Omori, E. V., Huang, D., & Caflisch, A. (2021). 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors Journal of Medicinal Chemistry, 64, 12738–12760. https://doi.org/10.1021/acs.jmedchem.1c00773
  • Lee, J.-H., Wang, R., Xiong, F., Krakowiak, J., Liao, Z., Nguyen, P. T., Moroz-Omori, E. V., Shao, J., Zhu, X., Bolt, M. J., Wu, H., Singh, P. K., Bi, M., Shi, C. J., Jamal, N., Li, G., Mistry, R., Jung, S. Y., Tsai, K.-L., … Li, W. (2021). Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation Molecular Cell, 81, 3368-3385.e9. https://doi.org/10.1016/j.molcel.2021.07.024
  • Pohl, M. O., Busnadiego, I., Marrafino, F., Wiedmer, L., Hunziker, A., Fernbach, S., Glas, I., Moroz-Omori, E. V., Hale, B. G., Caflisch, A., & Stertz, S. (2021). Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir Journal of General Virology, 102, 001625. https://doi.org/10.1099/jgv.0.001625
  • Milardi, D., Gazit, E., Radford, S. E., Xu, Y., Gallardo, R. U., Caflisch, A., Westermark, G. T., Westermark, P., Rosa, C. L., & Ramamoorthy, A. (2021). Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes Chemical Reviews, 121, 1845–1893. https://doi.org/10.1021/acs.chemrev.0c00981
  • Li, Y., Bedi, R. K., Wiedmer, L., Sun, X., Huang, D., & Caflisch, A. (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, 1240–1249. https://doi.org/10.1021/acs.jctc.0c01136
  • Cappelletti, V., Hauser, T., Piazza, I., Pepelnjak, M., Malinovska, L., Fuhrer, T., Li, Y., Dörig, C., Boersema, P., Gillet, L., Grossbach, J., Dugourd, A., Saez-Rodriguez, J., Beyer, A., Zamboni, N., Caflisch, A., de Souza, N., & Picotti, P. (2021). Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ Cell, 184, 545-559.e22. https://doi.org/10.1016/j.cell.2020.12.021
  • Mallona, I., Ilie, I. M., Karemaker, I. D., Butz, S., Manzo, M., Caflisch, A., & Baubec, T. (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome Nucleic Acids Research, 49, 145–157. https://doi.org/10.1093/nar/gkaa1168

• 2020

  • Li, Y., Bedi, R. K., Moroz-Omori, E. V., & Caflisch, A. (2020). Structural and Dynamic Insights into Redundant Function of YTHDF Proteins Journal of Chemical Information and Modeling, 60, 5932–5935. https://doi.org/10.1021/acs.jcim.0c01029
  • Marchand, J.-R., Knehans, T., Caflisch, A., & Vitalis, A. (2020). An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules Journal of Chemical Information and Modeling, 60, 5188–5202. https://doi.org/10.1021/acs.jcim.0c00558
  • Goossens, K., Wroblowski, B., Langini, C., van Vlijmen, H., Caflisch, A., & De Winter, H. (2020). Assessment of the fragment docking program SEED Journal of Chemical Information and Modeling, 60, 4881–4893. https://doi.org/10.1021/acs.jcim.0c00556
  • Cocina, F., Vitalis, A., & Caflisch, A. (2020). Sapphire-based clustering Journal of Chemical Theory and Computation, 16, 6383–6396. https://doi.org/10.1021/acs.jctc.0c00604
  • Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brütsch, M., Huang, D., Deerain, N. M., Spiliotopoulos, D., Cheng-Sánchez, I., Laul, E., Nevado, C., Śledź, P., & Caflisch, A. (2020). Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers ACS Medicinal Chemistry Letters, 11, 1573–1580. https://doi.org/10.1021/acsmedchemlett.0c00080
  • Bedi, R. K., Huang, D., Eberle, S. A., Wiedmer, L., Śledź, P., & Caflisch, A. (2020). Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer ChemMedChem, 15, 744–748. https://doi.org/10.1002/cmdc.202000011
  • Pretze, M., Neuber, C., Kinski, E., Belter, B., Köckerling, M., Caflisch, A., Steinbach, J., Pietzsch, J., & Mamat, C. (2020). Synthesis, radiolabelling and initial biological characterisation of $^{18}$F-labelled xanthine derivatives for PET imaging of Eph receptors Organic & Biomolecular Chemistry, 18, 3104–3116. https://doi.org/10.1039/d0ob00391c
  • Bedi, R. K., Huang, D., Wiedmer, L., Li, Y., Dolbois, A., Wojdyla, J. A., Sharpe, M. E., Caflisch, A., & Sledz, P. (2020). Selectively Disrupting m$^{6}$A-Dependent Protein-RNA Interactions with Fragments ACS Chemical Biology, 15, 618–625. https://doi.org/10.1021/acschembio.9b00894
  • Caflisch, A. (2020). Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer’s Disease. ACS Chemical Neuroscience, 11, 103–104. https://doi.org/10.1021/acschemneuro.9b00676
  • Salutari, I., Martin, R., & Caflisch, A. (2020). The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide Proteins, 88, 31–46. https://doi.org/10.1002/prot.25764
  • Unzue, A., Jessen-Trefzer, C., Spiliotopoulos, D., Gaudio, E., Tarantelli, C., Dong, J., Zhao, H., Pachmayr, J., Zahler, S., Bernasconi, E., Sartori, G., Cascione, L., Bertoni, F., Śledź, P., Caflisch, A., & Nevado, C. (2020). Understanding the mechanism of action of pyrrolo[3,2-b]quinoxaline-derivatives as kinase inhibitors RSC Medicinal Chemistry, 11, 665–675. https://doi.org/10.1039/d0md00049c

• 2019

  • Li, Y., Bedi, R. K., Wiedmer, L., Huang, D., Śledź, P., & Caflisch, A. (2019). Flexible binding of m$^{6}$A reader protein YTHDC1 to its preferred RNA motif Journal of Chemical Theory and Computation, 15, 7004–7014. https://doi.org/10.1021/acs.jctc.9b00987

Pagination