Caflisch - UZH | Computational Structural Biology

Dr. Danzhi Huang was a member of the Caflisch group from ~2002 - 09/2021 (interrupted).

(2024)

Corbeski, I., Vargas-Rosales, P.A., Bedi, R.K., Deng, J., Coelho, D., Braud, E., Iannazzo, L., Li, Y., Huang, D., Ethève-Quelquejeu, M., Cui, Q., Caflisch, A.
The catalytic mechanism of the RNA methyltransferase METTL3
eLife 12 RP92537 (2024) DOI | Full Text | Supp Info

(2023)

Bedi, R.K., Huang, D., Li, Y., Caflisch, A.
Structure-Based Design of inhibitors of the m6A‑RNA writer enzyme METTL3
ACS Bio. Med. Chem. Au 3 (4) 359–370 (2023) DOI | Full Text | Supp Info
Reimann, R.R., Puzio, M., Rosati, A., Emmenegger, M., Schneider, B.L., Valdés, P., Huang, D., Caflisch, A., Aguzzi, A.
Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity
Brain Pathol. 33 (2) e13130 (2023) DOI | Full Text | Supp Info

(2022)

Li, Y., Bedi, R.K., Nai, F., von Roten, V., Dolbois, A., Zálešák, F., Nachawati, R., Huang, D., Caflisch, A.
Structure-based design of ligands of the m6A-RNA reader YTHDC1
Eur. J. Med. Chem. Rep. 5 100057 (2022) DOI | Full Text

(2021)

Dolbois, A., Bedi, R.K., Bochenkova, E., Müller, A., Moroz-Omori, E.V., Huang, D., Caflisch, A.
1,4,9-Triazaspiro[5.5]undecan-2-one derivatives as potent and selective METTL3 inhibitors
J. Med. Chem. 64 (17) 12738-12760 (2021) DOI | Full Text | Supp Info
Moroz-Omori, E.V., Huang, D., Bedi, R.K., Cheriyamkunnel, S.J., Bochenkova, E., Dolbois, A., Rzeczkowski, M.D., Li, Y., Wiedmer, L., Caflisch, A.
METTL3 inhibitors for epitranscriptomic modulation of cellular processes
ChemMedChem 16 (19) 3035-3043 (2021) DOI | Full Text
Li, Y., Bedi, R.K., Wiedmer, L., Sun, X., Huang, D., Caflisch, A.
Atomistic and thermodynamic analysis of N6-methyladenosine (mA) recognition by the reader domain of YTHDC1
J. Chem. Theory Comput. 17 (2) 1240-1249 (2021) DOI | Full Text | Supp Info

(2020)

Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brütsch, M., Huang, D., Deerain, N., Spiliotopoulos, D., Cheng-Sánchez, I., Laul, E., Nevado, C., Śledź, P., Caflisch, A.
Hitting a moving target: simulation and crystallography study of ATAD2 bromodomain blockers
ACS Med. Chem. Lett. 11 (8) 1573-1580 (2020) DOI | Full Text
Bedi, R.K., Huang, D., Eberle, S.A., Wiedmer, L., Śledź, P., Caflisch, A.
Small-molecule inhibitors of METTL3, the major human epitranscriptomic writer
ChemMedChem 15 (9) 744-748 (2020) DOI | Full Text | Supp Info
Bedi, R.K., Huang, D., Wiedmer, L., Li, Y., Dolbois, A., Wojdyla, J.A., Sharpe, M.E., Caflisch, A., Śledź, P.
Selectively disrupting m6A-dependent protein-RNA interactions with fragments
ACS Chem. Biol. 15 (3) 618-625 (2020) DOI | Full Text | Supp Info

(2019)

Li, Y., Bedi, R.K., Wiedmer, L., Huang, D., Śledź, P., Caflisch, A.
Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif
J. Chem. Theory Comput. 15 (12) 7004-7014 (2019) DOI | Full Text | Supp Info

(2015)

Huang, D., Caflisch, A.
The roles of the conserved tyrosine in the β2-α2 loop of the prion protein
Prion 9 (6) 412-419 (2015) DOI | Full Text
Herrmann, U.S., Schütz, A.K., Shirani, H., Huang, D., Saban, D., Nuvolone, M., Li, B., Ballmer, B., Åslund, A.K.O., Mason, J.J., Rushing, E., Budka, H., Nyström, S., Hammarström, P., Böckmann, A., Caflisch, A., Meier, B.H., Nilsson, K.P.R., Hornemann, S., Aguzzi, A.
Structure-based drug design identifies polythiophenes as antiprion compounds
Sci. Transl. Med. 7 (299) 299ra123 (2015) DOI | Full Text
Huang, D., Caflisch, A.
Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein
J. Am. Chem. Soc. 137 (8) 2948-2957 (2015) DOI | Full Text | Supp Info
Dong, J., Zhao, H., Zhou, T., Spiliotopoulos, D., Rajendran, C., Li, X.D., Huang, D., Caflisch, A.
Structural analysis of the binding of type I, I1/2, and II inhibitors to eph tyrosine kinases
ACS Med. Chem. Lett. 6 (1) 79-83 (2015) DOI | Full Text | Supp Info

(2010)

Messner, S., Altmeyer, M., Zhao, H., Pozivil, A., Roschitzki, B., Gehrig, P., Rutishauser, D., Huang, D., Caflisch, A., Hottiger, M.O.
PARP1 ADP-ribosylates lysine residues of the core histone tails
Nucleic Acids Res. 38 (19) 6350-6362 (2010) DOI | Full Text | Supp Info
Huang, D., Caflisch, A.
Library screening by fragment-based docking
J. Mol. Recognit. 23 (2) 183-193 (2010) DOI | Full Text
Huang, D., Zhou, T., Lafleur, K., Nevado, C., Caflisch, A.
Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis
Bioinformatics 26 (2) 198-204 (2010) DOI | Full Text | Supp Info
Zhou, T., Huang, D., Caflisch, A.
Quantum mechanical methods for drug design
Curr. Top. Med. Chem. 10 (1) 33-45 (2010) DOI | Full Text

(2009)

Bodenreider, C., Beer, D., Keller, T.H., Sonntag, S., Wen, D., Yap, L., Yau, Y.H., Shochat, S.G., Huang, D., Zhou, T., Caflisch, A., Su, X.C., Ozawa, K., Otting, G., Vasudevan, S.G., Lescar, J., Lim, S.P.
A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease
Anal. Biochem. 395 (2) 195-204 (2009) DOI | Full Text | Supp Info
Lafleur, K., Huang, D., Zhou, T., Caflisch, A., Nevado, C.
Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4)
J. Med. Chem. 52 (20) 6433-6446 (2009) DOI | Full Text | Supp Info
Ekonomiuk, D., Su, X.C., Ozawa, K., Bodenreider, C., Lim, S.P., Otting, G., Huang, D., Caflisch, A.
Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics
J. Med. Chem. 52 (15) 4860-4868 (2009) DOI | Full Text | Supp Info
Su, X.C., Ozawa, K., Yagi, H., Lim, S.P., Wen, D., Ekonomiuk, D., Huang, D., Keller, T.H., Sonntag, S., Caflisch, A., Vasudevan, S.G., Otting, G.
NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease
FEBS J. 276 (15) 4244-4255 (2009) DOI | Full Text | Supp Info
Ekonomiuk, D., Su, X.C., Ozawa, K., Bodenreider, C., Lim, S.P., Yin, Z., Keller, T.H., Beer, D., Patel, V., Otting, G., Caflisch, A., Huang, D.
Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking
PLoS Negl. Trop. Dis. 3 (1) e356 (2009) DOI | Full Text | Supp Info

(2008)

Kolb, P., Kipouros, C.B., Huang, D., Caflisch, A.
Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors
Proteins 73 (1) 11-18 (2008) DOI | Full Text | Supp Info
Zhou, T., Huang, D., Caflisch, A.
Is quantum mechanics necessary for predicting binding free energy?
J. Med. Chem. 51 (14) 4280-4288 (2008) DOI | Full Text | Supp Info
Kolb, P., Huang, D., Dey, F., Caflisch, A.
Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model
J. Med. Chem. 51 (5) 1179-1188 (2008) DOI | Full Text | Supp Info

(2006)

Huang, D., Lüthi, U., Kolb, P., Cecchini, M., Barberis, A., Caflisch, A.
In silico discovery of beta-secretase inhibitors
J. Am. Chem. Soc. 128 (16) 5436-5443 (2006) DOI | Full Text | Supp Info

(2005)

Kolb, P., Cecchini, M., Huang, D., Caflisch, A.
Fragment-based high-throughput docking
349-378 (2005) | Full Text
Huang, D., Lüthi, U., Kolb, P., Edler, K., Cecchini, M., Audetat, S., Barberis, A., Caflisch, A.
Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations
J. Med. Chem. 48 (16) 5108-5111 (2005) DOI | Full Text | Supp Info

(2004)

Huang, D., Caflisch, A.
Efficient evaluation of binding free energy using continuum electrostatics solvation
J. Med. Chem. 47 (23) 5791-5797 (2004) DOI | Full Text

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