Publications

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Journal Article
Torres, S. Vázquez, J Y Leung, P., Venkatesh, P., Lutz, I. D., Hink, F., Huynh, H. - H., Becker, J., Yeh, A. Hsien- Wei, Juergens, D., Bennett, N. R., Hoofnagle, A. N., Huang, E., MacCoss, M. J., Expòsit, M., Lee, G. Rie, Bera, A. K., Kang, A., De La Cruz, J., Levine, P. M., Li, X., Lamb, M., Gerben, S. R., Murray, A., Heine, P., Korkmaz, E. Nihal, Nivala, J., Stewart, L., Watson, J. L., Rogers, J. M., and Baker, D. (2023) De novo design of high-affinity binders of bioactive helical peptides. Nature. 10.1038/s41586-023-06953-1
Kim, D. E., Jensen, D. R., Feldman, D., Tischer, D., Saleem, A., Chow, C. M., Li, X., Carter, L., Milles, L., Nguyen, H., Kang, A., Bera, A. K., Peterson, F. C., Volkman, B. F., Ovchinnikov, S., and Baker, D. (2023) De novo design of small beta barrel proteins. Proc Natl Acad Sci U S A. 120, e2207974120
Vorobieva, A. A., White, P., Liang, B., Horne, J. E., Bera, A. K., Chow, C. M., Gerben, S., Marx, S., Kang, A., Stiving, A. Q., Harvey, S. R., Marx, D. C., G Khan, N., Fleming, K. G., Wysocki, V. H., Brockwell, D. J., Tamm, L. K., Radford, S. E., and Baker, D. (2021) De novo design of transmembrane β barrels.. Science. 10.1126/science.abc8182
de Haas, R. J., Tas, R. P., van den Broek, D., Zheng, C., Nguyen, H., Kang, A., Bera, A. K., King, N. P., Voets, I. K., and de Vries, R. (2023) De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A. 120, e2220380120
Park, H. Ho, Logette, E., Raunser, S., Cuenin, S., Walz, T., Tschopp, J., and Wu, H. (2007) Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell. 128, 533-46
Ketcham, J. M., Haling, J., Khare, S., Bowcut, V., Briere, D. M., Burns, A. C., Gunn, R. J., Ivetac, A., Kuehler, J., Kulyk, S., Laguer, J., J Lawson, D., Moya, K., Nguyen, N., Rahbaek, L., Saechao, B., Smith, C. R., Sudhakar, N., Thomas, N. C., Vegar, L., Vanderpool, D., Wang, X., Yan, L., Olson, P., Christensen, J. G., and Marx, M. A. (2022) Design and Discovery of MRTX0902, a Potent, Selective, Brain-Penetrant, and Orally Bioavailable Inhibitor of the SOS1:KRAS Protein-Protein Interaction. J Med Chem. 65, 9678-9690
Hymel, D., Tsuji, K., Grant, R. A., Chingle, R. M., Kunciw, D. L., Yaffe, M. B., and Burke, T. R. (2021) Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain - binding peptide macrocycles. Org Biomol Chem. 19, 7843-7854
Wittlinger, F., Heppner, D. E., To, C., Günther, M., Shin, B. Hee, Rana, J. K., Schmoker, A. M., Beyett, T. S., Berger, L. M., Berger, B. - T., Bauer, N., Vasta, J. D., Corona, C. R., Robers, M. B., Knapp, S., Jänne, P. A., Eck, M. J., and Laufer, S. A. (2021) Design of a "Two-in-One" Mutant-Selective Epidermal Growth Factor Receptor Inhibitor That Spans the Orthosteric and Allosteric Sites. J Med Chem. 10.1021/acs.jmedchem.1c00848
Hsia, Y., Mout, R., Sheffler, W., Edman, N. I., Vulovic, I., Park, Y. - J., Redler, R. L., Bick, M. J., Bera, A. K., Courbet, A., Kang, A., Brunette, T. J., Nattermann, U., Tsai, E., Saleem, A., Chow, C. M., Ekiert, D., Bhabha, G., Veesler, D., and Baker, D. (2021) Design of multi-scale protein complexes by hierarchical building block fusion. Nat Commun. 12, 2294
Rugel, A., Tarpley, R. S., Lopez, A., Menard, T., Guzman, M. A., Taylor, A. B., Cao, X., Kovalskyy, D., Chevalier, F. D., Anderson, T. J. C., P Hart, J., LoVerde, P. T., and McHardy, S. F. (2018) Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents. ACS Med Chem Lett. 9, 967-973
Rugel, A., Tarpley, R. S., Lopez, A., Menard, T., Guzman, M. A., Taylor, A. B., Cao, X., Kovalskyy, D., Chevalier, F. D., Anderson, T. J. C., P Hart, J., LoVerde, P. T., and McHardy, S. F. (2018) Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents. ACS Med Chem Lett. 9, 967-973
Stille, J. K., Tjutrins, J., Wang, G., Venegas, F. A., Hennecker, C., Rueda, A. M., Sharon, I., Blaine, N., Miron, C. E., Pinus, S., Labarre, A., Plescia, J., Patrascu, M. Burai, Zhang, X., Wahba, A. S., Vlaho, D., Huot, M. J., T Schmeing, M., Mittermaier, A. K., and Moitessier, N. (2022) Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL covalent inhibitors.. Eur J Med Chem. 229, 114046
Tago, N., Katolik, A., Clark, N. E., Montemayor, E. J., Seio, K., Sekine, M., P Hart, J., and Damha, M. J. (2015) Design, Synthesis, and Properties of Phosphoramidate 2',5'-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme. J Org Chem. 80, 10108-18
Mandal, K., Pentelute, B. L., Bang, D., Gates, Z. P., Torbeev, V. Yu, and Kent, S. B. H. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angew Chem Int Ed Engl. 51, 1481-6
Soragni, A., Janzen, D. M., Johnson, L. M., Lindgren, A. G., Nguyen, A. Thai- Quynh, Tiourin, E., Soriaga, A. B., Lu, J., Jiang, L., Faull, K. F., Pellegrini, M., Memarzadeh, S., and Eisenberg, D. S. (2016) A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 29, 90-103
Banigan, J. R., Mandal, K., Sawaya, M. R., Thammavongsa, V., Hendrickx, A. P. A., Schneewind, O., Yeates, T. O., and Kent, S. B. H. (2010) Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography. Protein Sci. 19, 1840-9
Phelps, G. A., Cheramie, M. N., Fernando, D. M., Selchow, P., Meyer, C. J., Waidyarachchi, S. L., Dharuman, S., Liu, J., Meuli, M., Dal Molin, M., Killam, B. Y., Murphy, P. A., Reeve, S. M., Wilt, L. A., Anderson, S. M., Yang, L., Lee, R. B., Temrikar, Z. H., Lukka, P. B., Meibohm, B., Polikanov, Y. S., Hobbie, S. N., Böttger, E. C., Sander, P., and Lee, R. E. (2024) Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in abscessus. Proc Natl Acad Sci U S A. 121, e2314101120
Sinatra, L., Vogelmann, A., Friedrich, F., Tararina, M. A., Neuwirt, E., Colcerasa, A., König, P., Toy, L., Yesiloglu, T. Z., Hilscher, S., Gaitzsch, L., Papenkordt, N., Zhai, S., Zhang, L., Romier, C., Einsle, O., Sippl, W., Schutkowski, M., Gross, O., Bendas, G., Christianson, D. W., Hansen, F. K., Jung, M., and Schiedel, M. (2023) Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem. 66, 14787-14814
Sinatra, L., Vogelmann, A., Friedrich, F., Tararina, M. A., Neuwirt, E., Colcerasa, A., König, P., Toy, L., Yesiloglu, T. Z., Hilscher, S., Gaitzsch, L., Papenkordt, N., Zhai, S., Zhang, L., Romier, C., Einsle, O., Sippl, W., Schutkowski, M., Gross, O., Bendas, G., Christianson, D. W., Hansen, F. K., Jung, M., and Schiedel, M. (2023) Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem. 66, 14787-14814
Lama, L., Adura, C., Xie, W., Tomita, D., Kamei, T., Kuryavyi, V., Gogakos, T., Steinberg, J. I., Miller, M., Ramos-Espiritu, L., Asano, Y., Hashizume, S., Aida, J., Imaeda, T., Okamoto, R., Jennings, A. J., Michino, M., Kuroita, T., Stamford, A., Gao, P., Meinke, P., J Glickman, F., Patel, D. J., and Tuschl, T. (2019) Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression. Nat Commun. 10, 2261
Lama, L., Adura, C., Xie, W., Tomita, D., Kamei, T., Kuryavyi, V., Gogakos, T., Steinberg, J. I., Miller, M., Ramos-Espiritu, L., Asano, Y., Hashizume, S., Aida, J., Imaeda, T., Okamoto, R., Jennings, A. J., Michino, M., Kuroita, T., Stamford, A., Gao, P., Meinke, P., J Glickman, F., Patel, D. J., and Tuschl, T. (2019) Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression. Nat Commun. 10, 2261
Ye, G., Gallant, J., Zheng, J., Massey, C., Shi, K., Tai, W., Odle, A., Vickers, M., Shang, J., Wan, Y., Du, L., Aihara, H., Perlman, S., LeBeau, A., and Li, F. (2021) The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates. Elife. 10.7554/eLife.64815
Liu, H., Iketani, S., Zask, A., Khanizeman, N., Bednarova, E., Forouhar, F., Fowler, B., Hong, S. Jung, Mohri, H., Nair, M. S., Huang, Y., Tay, N. E. S., Lee, S., Karan, C., Resnick, S. J., Quinn, C., Li, W., Shion, H., Xia, X., Daniels, J. D., Bartolo-Cruz, M., Farina, M., Rajbhandari, P., Jurtschenko, C., Lauber, M. A., McDonald, T., Stokes, M. E., Hurst, B. L., Rovis, T., Chavez, A., Ho, D. D., and Stockwell, B. R. (2022) Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nat Commun. 13, 1891
Serafim, R. A. M., Gama, F. H. de Souza, Dutra, L. A., Reis, C. V. Dos, Vasconcelos, S. N. S., Santiago, Ada Silva, Takarada, J. E., Di Pillo, F., Azevedo, H., Mascarello, A., Elkins, J. M., Massirer, K. B., Gileadi, O., Guimarães, C. R. W., and Couñago, R. M. (2019) Development of Pyridine-based Inhibitors for the Human Vaccinia-related Kinases 1 and 2. ACS Med Chem Lett. 10, 1266-1271
Tan, L., Akahane, K., McNally, R., Reyskens, K. M. S. E., Ficarro, S. B., Liu, S., Herter-Sprie, G. S., Koyama, S., Pattison, M. J., Labella, K., Johannessen, iv, L., Akbay, E. A., Wong, K. - K., Frank, D. A., Marto, J. A., Look, T. A., J Arthur, S. C., Eck, M. J., and Gray, N. S. (2015) Development of Selective Covalent Janus Kinase 3 Inhibitors. J Med Chem. 58, 6589-606

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