Publications of the Caflisch Group

ZORA Publication List

Publications

• 2017

  • Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas (2017). Focused conformational sampling in proteins. Journal of Chemical Physics, 147(19):195102.
  • Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). Correction to: The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(46):19121.
  • Abplanalp, Jeannette; Leutert, Mario; Frugier, Emilie; Nowak, Kathrin; Feurer, Roxane; Kato, Jiro; Kistemaker, Hans V A; Filippov, Dmitri V; Moss, Joel; Caflisch, Amedeo; Hottiger, Michael O (2017). Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nature Communications, 8(1):2055.
  • Marchand, Jean-Rémy; Dalle Vedove, Andrea; Lolli, Graziano; Caflisch, Amedeo (2017). Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Journal of Chemical Information and Modeling, 57(10):2584-2597.
  • Spiliotopoulos, Dimitrios; Wamhoff, Eike-Christian; Lolli, Graziano; Rademacher, Christoph; Caflisch, Amedeo (2017). Discovery of BAZ2A bromodomain ligands. European journal of medicinal chemistry, 139:564-572.
  • Bacci, Marco; Vymětal, Jiří; Mihajlovic, Maja; Caflisch, Amedeo; Vitalis, Andreas (2017). Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. Journal of Chemical Theory and Computation, 13(10):5117-5130.
  • Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(40):16734-16745.
  • Peón, Antonio; Robles, Adrián; Blanco, Beatriz; Convertino, Marino; Thompson, Paul; Hawkins, Alastair R; Caflisch, Amedeo; González-Bello, Concepción (2017). Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem, 12(18):1512-1524.
  • Spiliotopoulos, Dimitrios; Zhu, Jian; Wamhoff, Eike-Christian; Deerain, Nicholas; Marchand, Jean-Rémy; Aretz, Jonas; Rademacher, Christoph; Caflisch, Amedeo (2017). Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorganic & Medicinal Chemistry Letters, 27(11):2472-2478.
  • Ghayor, Chafik; Gjoksi, Bebeka; Dong, Jing; Siegenthaler, Barbara; Caflisch, Amedeo; Weber, Franz E (2017). N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Scientific Reports, 7:42108.

• 2016

  • Marchand, Jean-Rémy; Lolli, Graziano; Caflisch, Amedeo (2016). Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation. Journal of Medicinal Chemistry, 59(21):9919-9927.
  • Zhu, Jian; Caflisch, Amedeo (2016). Twenty crystal structures of bromodomain and PHD finger containing protein 1 (BRPF1)/ligand complexes reveal conserved binding motifs and rare interactions. Journal of Medicinal Chemistry, 59(11):5555-5561.
  • Lolli, Graziano; Caflisch, Amedeo (2016). High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography. ACS Chemical Biology, 11(3):800-807.
  • Xu, Min; Caflisch, Amedeo; Hamm, Peter (2016). Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates. Journal of Chemical Theory and Computation, 12(3):1393-1399.
  • Ben Halima, Saoussen; Mishra, Sabyashachi; Raja, K Muruga Poopathi; Willem, Michael; Baici, Antonio; Simons, Kai; Brüstle, Oliver; Koch, Philipp; Haass, Christian; Caflisch, Amedeo; Rajendran, Lawrence (2016). Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein. Cell Reports, 14(9):2127-2141.
  • Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H (2016). Correction to concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry, 55(39):5647.
  • Roos, Martina; Pradère, Ugo; Ngondo, Richard P; Behera, Alok; Allegrini, Sara; Civenni, Gianluca; Zagalak, Julian A; Marchand, Jean-Rémy; Menzi, Mirjam; Towbin, Harry; Scheuermann, Jörg; Neri, Dario; Caflisch, Amedeo; Catapano, Carlo V; Ciaudo, Constance; Hall, Jonathan (2016). A Small-Molecule Inhibitor of Lin28. ACS Chemical Biology, 11(10):2773-2781.
  • Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2016). Fragment-based in silico screening of bromodomain ligands. Drug Discovery Today: Technologies, 19:81-90.
  • Arnon, Zohar A; Vitalis, Andreas; Levin, Aviad; Michaels, Thomas C T; Caflisch, Amedeo; Knowles, Tuomas P J; Adler-Abramovich, Lihi; Gazit, Ehud (2016). Dynamic microfluidic control of supramolecular peptide self-assembly. Nature Communications, 7:13190.
  • Reichen, Christian; Hansen, Simon; Forzani, Cristina; Honegger, Annemarie; Fleishman, Sarel J; Zhou, Ting; Parmeggiani, Fabio; Ernst, Patrick; Madhurantakam, Chaithanya; Ewald, Christina; Mittl, Peer R E; Zerbe, Oliver; Baker, David; Caflisch, Amedeo; Plückthun, Andreas (2016). Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. Journal of Molecular Biology, 428(22):4467-4489.
  • Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Christopher Fromme, J; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7:10882.
  • Unzue, Andrea; Zhao, Hongtao; Lolli, Graziano; Dong, Jing; Zhu, Jian; Zechner, Melanie; Dolbois, Aymeric; Caflisch, Amedeo; Nevado, Cristina (2016). The “Gatekeeper” residue influences the mode of binding of acetyl indoles to bromodomains. Journal of Medicinal Chemistry, 59(7):3087-3097.
  • Unzue, Andrea; Lafleur, Karine; Zhao, Hongtao; Zhou, Ting; Dong, Jing; Kolb, Peter; Liebl, Johanna; Zahler, Stefan; Caflisch, Amedeo; Nevado, Cristina (2016). Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation. European journal of medicinal chemistry, 112:347-366.
  • Unzue, Andrea; Xu, Ming; Dong, Jing; Wiedmer, Lars; Spiliotopoulos, Dimitrios; Caflisch, Amedeo; Nevado, Cristina (2016). Fragment-based design of selective nanomolar ligands of the crebbp bromodomain. Journal of Medicinal Chemistry, 59(4):1350-1356.

• 2015

  • Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas (2015). Weighted distance functions improve analysis of high-dimensional data: application to molecular dynamics simulations. Journal of Chemical Theory and Computation, 11(11):5481-5492.
  • Huang, Danzhi; Caflisch, Amedeo (2015). The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion, 9(6):412-419.
  • Herrmann, Uli S; Schütz, Anne K; Shirani, Hamid; Huang, Danzhi; Saban, Dino; Nuvolone, Mario; Li, Bei; Ballmer, Boris; Åslund, Andreas K O; Mason, Jeffrey J; Rushing, Elisabeth; Budka, Herbert; Nystrom, Sofie; Hammarstrom, Per; Böckmann, Anja; Caflisch, Amedeo; Meier, Beat H; Nilsson, K Peter R; Hornemann, Simone; Aguzzi, Adriano (2015). Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine, 7(299):299ra123.
  • Marchand, Jean-Rémy; Caflisch, Amedeo (2015). Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem, 10(8):1327-1333.
  • Zhao, Hongtao; Caflisch, Amedeo (2015). Current kinase inhibitors cover a tiny fraction of fragment space. Bioorganic & Medicinal Chemistry Letters, 25(11):2372-2376.
  • Blöchliger, Nicolas; Xu, Min; Caflisch, Amedeo (2015). Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophysical Journal, 108(9):2362-2370.
  • Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2015). A molecular simulation protocol to avoid sampling redundancy and discover new states. BBA - Biochimica et Biophysica Acta, 1850(5):889-902.
  • Ewald, Christina; Christen, Martin T; Watson, Randall P; Mihajlovic, Maja; Zhou, Ting; Honegger, Annemarie; Plückthun, Andreas; Caflisch, Amedeo; Zerbe, Oliver (2015). A combined NMR and computational approach to investigate peptide binding to a designed armadillo repeat protein. Journal of Molecular Biology, 427(10):1916-1933.
  • Huang, Danzhi; Caflisch, Amedeo (2015). Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society, 137(8):2948-2957.
  • Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H (2015). Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry, 54(3):711-721.
  • Dong, Jing; Zhao, Hongtao; Zhou, Ting; Spiliotopoulos, Dimitrios; Rajendran, Chitra; Li, Xiao-Dan; Huang, Danzhi; Caflisch, Amedeo (2015). Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Medicinal Chemistry Letters, 6(1):79-83.
  • Xu, Min; Unzue, Andrea; Dong, Jing; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo (2015). Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. Journal of Medicinal Chemistry:2487-2491.
  • Zhao, Hongtao; Caflisch, Amedeo (2015). Molecular dynamics in drug design. European journal of medicinal chemistry, 91:4-14.

Pagination