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179 results on '"Itkin, Zina"'

1. A landscape of response to drug combinations in non-small cell lung cancer

Author

Nair, Nishanth Ulhas, Greninger, Patricia, Zhang, Xiaohu, Friedman, Adam A., Amzallag, Arnaud, Cortez, Eliane, Sahu, Avinash Das, Lee, Joo Sang, Dastur, Anahita, Egan, Regina K., Murchie, Ellen, Ceribelli, Michele, Crowther, Giovanna S., Beck, Erin, McClanaghan, Joseph, Klump-Thomas, Carleen, Boisvert, Jessica L., Damon, Leah J., Wilson, Kelli M., Ho, Jeffrey, Tam, Angela, McKnight, Crystal, Michael, Sam, Itkin, Zina, Garnett, Mathew J., Engelman, Jeffrey A., Haber, Daniel A., Thomas, Craig J., Ruppin, Eytan, and Benes, Cyril H.

Published
2023
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2. Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex

Author

Sun, Yilun, Baechler, Simone A., Zhang, Xiaohu, Kumar, Suresh, Factor, Valentina M., Arakawa, Yasuhiro, Chau, Cindy H., Okamoto, Kanako, Parikh, Anup, Walker, Bob, Su, Yijun P., Chen, Jiji, Ting, Tabitha, Huang, Shar-yin N., Beck, Erin, Itkin, Zina, McKnight, Crystal, Xie, Changqing, Roper, Nitin, Nijhawan, Deepak, Figg, William Douglas, Meltzer, Paul S., Yang, James C., Thomas, Craig J., and Pommier, Yves

Published
2023
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3. High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

Author

Lang, Martin, Schmidt, Laura S., Wilson, Kelli M., Ricketts, Christopher J., Sourbier, Carole, Vocke, Cathy D., Wei, Darmood, Crooks, Daniel R., Yang, Youfeng, Gibbs, Benjamin K., Zhang, Xiaohu, Klumpp-Thomas, Carleen, Chen, Lu, Guha, Rajarshi, Ferrer, Marc, McKnight, Crystal, Itkin, Zina, Wangsa, Darawalee, Wangsa, Danny, James, Amy, Difilippantonio, Simone, Karim, Baktir, Morís, Francisco, Ried, Thomas, Merino, Maria J., Srinivasan, Ramaprasad, Thomas, Craig J., and Linehan, W. Marston

Published
2023
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4. Drug combinations identified by high-throughput screening promote cell cycle transition and upregulate Smad pathways in myeloma

Author

Peat, Tyler J., Gaikwad, Snehal M., Dubois, Wendy, Gyabaah-Kessie, Nana, Zhang, Shuling, Gorjifard, Sayeh, Phyo, Zaw, Andres, Megan, Hughitt, V. Keith, Simpson, R. Mark, Miller, Margaret A., Girvin, Andrew T., Taylor, Andrew, Williams, Daniel, D'Antonio, Nelson, Zhang, Yong, Rajagopalan, Adhithi, Flietner, Evan, Wilson, Kelli, Zhang, Xiaohu, Shinn, Paul, Klumpp-Thomas, Carleen, McKnight, Crystal, Itkin, Zina, Chen, Lu, Kazandijian, Dickran, Zhang, Jing, Michalowski, Aleksandra M., Simmons, John K., Keats, Jonathan, Thomas, Craig J., and Mock, Beverly A.

Published
2023
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6. Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space.

Author

Kearney, Sara E, Zahoránszky-Kőhalmi, Gergely, Brimacombe, Kyle R, Henderson, Mark J, Lynch, Caitlin, Zhao, Tongan, Wan, Kanny K, Itkin, Zina, Dillon, Christopher, Shen, Min, Cheff, Dorian M, Lee, Tobie D, Bougie, Danielle, Cheng, Ken, Coussens, Nathan P, Dorjsuren, Dorjbal, Eastman, Richard T, Huang, Ruili, Iannotti, Michael J, Karavadhi, Surendra, Klumpp-Thomas, Carleen, Roth, Jacob S, Sakamuru, Srilatha, Sun, Wei, Titus, Steven A, Yasgar, Adam, Zhang, Ya-Qin, Zhao, Jinghua, Andrade, Rodrigo B, Brown, M Kevin, Burns, Noah Z, Cha, Jin K, Mevers, Emily E, Clardy, Jon, Clement, Jason A, Crooks, Peter A, Cuny, Gregory D, Ganor, Jake, Moreno, Jesus, Morrill, Lucas A, Picazo, Elias, Susick, Robert B, Garg, Neil K, Goess, Brian C, Grossman, Robert B, Hughes, Chambers C, Johnston, Jeffrey N, Joullie, Madeleine M, Kinghorn, A Douglas, Kingston, David GI, Krische, Michael J, Kwon, Ohyun, Maimone, Thomas J, Majumdar, Susruta, Maloney, Katherine N, Mohamed, Enas, Murphy, Brian T, Nagorny, Pavel, Olson, David E, Overman, Larry E, Brown, Lauren E, Snyder, John K, Porco, John A, Rivas, Fatima, Ross, Samir A, Sarpong, Richmond, Sharma, Indrajeet, Shaw, Jared T, Xu, Zhengren, Shen, Ben, Shi, Wei, Stephenson, Corey RJ, Verano, Alyssa L, Tan, Derek S, Tang, Yi, Taylor, Richard E, Thomson, Regan J, Vosburg, David A, Wu, Jimmy, Wuest, William M, Zakarian, Armen, Zhang, Yufeng, Ren, Tianjing, Zuo, Zhong, Inglese, James, Michael, Sam, Simeonov, Anton, Zheng, Wei, Shinn, Paul, Jadhav, Ajit, Boxer, Matthew B, Hall, Matthew D, Xia, Menghang, Guha, Rajarshi, and Rohde, Jason M

Subjects
Chemical Sciences
Abstract

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (-)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening.

Published
2018

11. FIGURE 3 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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12. Supplementary Table S1 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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13. Supplementary Figure S6 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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14. Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, additional, Kumar, Suresh, additional, Sun, Nai-Yun, additional, Elloumi, Fathi, additional, Thomas, Anish, additional, Roper, Nitin, additional, Varghese, Diana Grace, additional, Takebe, Naoko, additional, Zhang, Xiaohu, additional, Ceribelli, Michele, additional, Holland, David O., additional, Beck, Erin, additional, Itkin, Zina, additional, McKnight, Crystal, additional, Wilson, Kelli M., additional, Travers, Jameson, additional, Klumpp-Thomas, Carleen, additional, Thomas, Craig J., additional, Hoang, Chuong D., additional, Hernandez, Jonathan M., additional, Del Rivero, Jaydira, additional, and Pommier, Yves, additional

Published
2024
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15. FIGURE 6 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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16. FIGURE 5 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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17. FIGURE 4 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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18. FIGURE 8 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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19. FIGURE 7 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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20. FIGURE 2 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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21. FIGURE 1 from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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22. Data from Activity of the Ubiquitin-activating Enzyme Inhibitor TAK-243 in Adrenocortical Carcinoma Cell Lines, Patient-derived Organoids, and Murine Xenografts

Author

Arakawa, Yasuhiro, primary, Jo, Ukhyun, primary, Kumar, Suresh, primary, Sun, Nai-Yun, primary, Elloumi, Fathi, primary, Thomas, Anish, primary, Roper, Nitin, primary, Varghese, Diana Grace, primary, Takebe, Naoko, primary, Zhang, Xiaohu, primary, Ceribelli, Michele, primary, Holland, David O., primary, Beck, Erin, primary, Itkin, Zina, primary, McKnight, Crystal, primary, Wilson, Kelli M., primary, Travers, Jameson, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Hoang, Chuong D., primary, Hernandez, Jonathan M., primary, Del Rivero, Jaydira, primary, and Pommier, Yves, primary

Published
2024
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23. Human Pluripotent Stem Cells for High-Throughput Drug Screening and Characterization of Small Molecules

Author

Ryu, Seungmi, primary, Chu, Pei-Hsuan, additional, Malley, Claire, additional, Braisted, John, additional, Ormanoglu, Pinar, additional, Huang, Ruili, additional, Itkin, Misha, additional, Itkin, Zina, additional, Shinn, Paul, additional, Klumpp-Thomas, Carleen, additional, Michael, Sam, additional, Tristan, Carlos A., additional, Simeonov, Anton, additional, and Singeç, Ilyas, additional

Published
2021
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24. Correction to: Human Pluripotent Stem Cells for High-Throughput Drug Screening and Characterization of Small Molecules

Author

Ryu, Seungmi, primary, Chu, Pei-Hsuan, additional, Malley, Claire, additional, Braisted, John, additional, Ormanoglu, Pinar, additional, Huang, Ruili, additional, Itkin, Misha, additional, Itkin, Zina, additional, Shinn, Paul, additional, Klumpp-Thomas, Carleen, additional, Michael, Sam, additional, Tristan, Carlos A., additional, Simeonov, Anton, additional, and Singeç, Ilyas, additional

Published
2021
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25. Preclinical Evaluation of the FGFR-Family Inhibitor Futibatinib for Pediatric Rhabdomyosarcoma

Author

Wu, Jerry T., primary, Cheuk, Adam, additional, Isanogle, Kristine, additional, Robinson, Christina, additional, Zhang, Xiaohu, additional, Ceribelli, Michele, additional, Beck, Erin, additional, Shinn, Paul, additional, Klumpp-Thomas, Carleen, additional, Wilson, Kelli M., additional, McKnight, Crystal, additional, Itkin, Zina, additional, Sotome, Hiroshi, additional, Hirai, Hiroshi, additional, Calleja, Elizabeth, additional, Wacheck, Volker, additional, Gouker, Brad, additional, Peer, Cody J., additional, Corvalan, Natalia, additional, Milewski, David, additional, Kim, Yong Y., additional, Figg, William D., additional, Edmondson, Elijah F., additional, Thomas, Craig J., additional, Difilippantonio, Simone, additional, Wei, Jun S., additional, and Khan, Javed, additional

Published
2023
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26. High-Throughput Screening for Drug Combinations

Author

Shinn, Paul, primary, Chen, Lu, additional, Ferrer, Marc, additional, Itkin, Zina, additional, Klumpp-Thomas, Carleen, additional, McKnight, Crystal, additional, Michael, Sam, additional, Mierzwa, Tim, additional, Thomas, Craig, additional, Wilson, Kelli, additional, and Guha, Rajarshi, additional

Published
2019
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27. Abstract LB315: Inhibition of FGFR4 with futibatinib combined with inhibition of IGF1R, Src family kinases, or AKT is synergistic against rhabdomyosarcoma

Author

Wu, Jerry, primary, Cheuk, Adam, additional, Wei, Jun S., additional, Kim, Yong, additional, Milewski, David, additional, Zhang, Xiaohu, additional, Ceribelli, Michele, additional, Beck, Erin, additional, Shinn, Paul, additional, Klump-Thomas, Carleen, additional, Wilson, Kelli M., additional, McKnight, Crystal, additional, Itkin, Zina, additional, Calleja, Elizabeth, additional, Wacheck, Volker, additional, Sotome, Hiroshi, additional, Hirai, Hiroshi, additional, Thomas, Craig, additional, and Khan, Javed, additional

Published
2023
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28. High-throughput Approaches to Uncover Synergistic Drug Combinations in Leukemia

Author

Chory, Emma J., primary, Wang, Meng, additional, Ceribelli, Michele, additional, Michalowska, Aleksandra M, additional, Golas, Stefan, additional, Beck, Erin, additional, Klumpp-Thomas, Carleen, additional, Chen, Lu, additional, McKnight, Crystal, additional, Itkin, Zina, additional, Wilson, Kelli M., additional, Holland, David, additional, Divakaran, Sanjay, additional, Bradner, James, additional, Khan, Javed, additional, Gryder, Berkley E., additional, Thomas, Craig J., additional, and Stanton, Benjamin Z., additional

Published
2023
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29. mTOR inhibition overcomes RSK3-mediated resistance to BET inhibitors in small cell lung cancer

Author

Kumari, Anju, primary, Gesumaria, Lisa, additional, Liu, Yan-Jin, additional, Hughitt, V. Keith, additional, Zhang, Xiaohu, additional, Ceribelli, Michele, additional, Wilson, Kelli M., additional, Klumpp-Thomas, Carleen, additional, Chen, Lu, additional, McKnight, Crystal, additional, Itkin, Zina, additional, Thomas, Craig J., additional, Mock, Beverly A., additional, Schrump, David S., additional, and Chen, Haobin, additional

Published
2023
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30. High-throughput Approaches to Uncover Synergistic Drug Combinations in Leukemia

Author

Chory, Emma J., primary, Wang, Meng, additional, Ceribelli, Michele, additional, Michalowska, Aleksandra M, additional, Golas, Stefan, additional, Beck, Erin, additional, Klumpp-Thomas, Carleen, additional, Chen, Lu, additional, McKnight, Crystal, additional, Itkin, Zina, additional, Divakaran, Sanjay, additional, Bradner, James, additional, Khan, Javed, additional, Gryder, Berkley E., additional, Thomas, Craig J., additional, and Stanton, Benjamin Z., additional

Published
2022
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32. Additional file 3 of High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

Author

Lang, Martin, Schmidt, Laura S., Wilson, Kelli M., Ricketts, Christopher J., Sourbier, Carole, Vocke, Cathy D., Wei, Darmood, Crooks, Daniel R., Yang, Youfeng, Gibbs, Benjamin K., Zhang, Xiaohu, Klumpp-Thomas, Carleen, Chen, Lu, Guha, Rajarshi, Ferrer, Marc, McKnight, Crystal, Itkin, Zina, Wangsa, Darawalee, Wangsa, Danny, James, Amy, Difilippantonio, Simone, Karim, Baktir, Morís, Francisco, Ried, Thomas, Merino, Maria J., Srinivasan, Ramaprasad, Thomas, Craig J., and Linehan, W. Marston

Abstract

Supplementary Material 3: Table S2

Published
2023
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33. Additional file 4 of High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

Author

Lang, Martin, Schmidt, Laura S., Wilson, Kelli M., Ricketts, Christopher J., Sourbier, Carole, Vocke, Cathy D., Wei, Darmood, Crooks, Daniel R., Yang, Youfeng, Gibbs, Benjamin K., Zhang, Xiaohu, Klumpp-Thomas, Carleen, Chen, Lu, Guha, Rajarshi, Ferrer, Marc, McKnight, Crystal, Itkin, Zina, Wangsa, Darawalee, Wangsa, Danny, James, Amy, Difilippantonio, Simone, Karim, Baktir, Morís, Francisco, Ried, Thomas, Merino, Maria J., Srinivasan, Ramaprasad, Thomas, Craig J., and Linehan, W. Marston

Abstract

Supplementary Material 4: Supplemental Methods

Published
2023
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34. Additional file 1 of High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

Author

Lang, Martin, Schmidt, Laura S., Wilson, Kelli M., Ricketts, Christopher J., Sourbier, Carole, Vocke, Cathy D., Wei, Darmood, Crooks, Daniel R., Yang, Youfeng, Gibbs, Benjamin K., Zhang, Xiaohu, Klumpp-Thomas, Carleen, Chen, Lu, Guha, Rajarshi, Ferrer, Marc, McKnight, Crystal, Itkin, Zina, Wangsa, Darawalee, Wangsa, Danny, James, Amy, Difilippantonio, Simone, Karim, Baktir, Morís, Francisco, Ried, Thomas, Merino, Maria J., Srinivasan, Ramaprasad, Thomas, Craig J., and Linehan, W. Marston

Abstract

Supplementary Material 1: Figures S1–S9

Published
2023
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35. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike

Author

Fu, Ying, primary, da Fonseca Rezende e Mello, Juliana, additional, Fleming, Bryan D., additional, Renn, Alex, additional, Chen, Catherine Z., additional, Hu, Xin, additional, Xu, Miao, additional, Gorshkov, Kirill, additional, Hanson, Quinlin, additional, Zheng, Wei, additional, Lee, Emily M., additional, Perera, Lalith, additional, Petrovich, Robert, additional, Pradhan, Manisha, additional, Eastman, Richard T., additional, Itkin, Zina, additional, Stanley, Thomas B., additional, Hsu, Allen, additional, Dandey, Venkata, additional, Sharma, Kedar, additional, Gillette, William, additional, Taylor, Troy, additional, Ramakrishnan, Nitya, additional, Perkins, Shelley, additional, Esposito, Dominic, additional, Oh, Eunkeu, additional, Susumu, Kimihiro, additional, Wolak, Mason, additional, Ferrer, Marc, additional, Hall, Matthew D., additional, Borgnia, Mario J., additional, and Simeonov, Anton, additional

Published
2022
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36. Suite of TMPRSS2 Assays for Screening Drug Repurposing Candidates as Potential Treatments of COVID-19

Author

Shrimp, Jonathan H., primary, Janiszewski, John, additional, Chen, Catherine Z., additional, Xu, Miao, additional, Wilson, Kelli M., additional, Kales, Stephen C., additional, Sanderson, Philip E., additional, Shinn, Paul, additional, Schneider, Rick, additional, Itkin, Zina, additional, Guo, Hui, additional, Shen, Min, additional, Klumpp-Thomas, Carleen, additional, Michael, Samuel G., additional, Zheng, Wei, additional, Simeonov, Anton, additional, and Hall, Matthew D., additional

Published
2022
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39. A Suite of TMPRSS2 Assays for Screening Drug Repurposing Candidates as Potential Treatments of COVID-19

Author

Shrimp, Jonathan H., primary, Janiszewski, John, additional, Chen, Catherine Z., additional, Xu, Miao, additional, Wilson, Kelli M., additional, Kales, Stephen C., additional, Sanderson, Philip E., additional, Shinn, Paul, additional, Itkin, Zina, additional, Guo, Hui, additional, Shen, Min, additional, Klumpp-Thomas, Carleen, additional, Michael, Samuel G., additional, Zheng, Wei, additional, Simeonov, Anton, additional, and Hall, Matthew D., additional

Published
2022
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40. mTOR Inhibition Overcomes RSK3-mediated Resistance to BET Inhibitors in Small Cell Lung Cancer

Author

Kumari, Anju, primary, Gesumaria, Lisa, additional, Liu, Yan-Jin, additional, Hughitt, V Keith, additional, Zhang, Xiaohu, additional, Ceribelli, Michele, additional, Wilson, Kelli M, additional, Klumpp-Thomas, Carleen, additional, Chen, Lu, additional, McKnight, Crystal, additional, Itkin, Zina, additional, Thomas, Craig, additional, Mock, Beverly A, additional, Schrump, David S, additional, and Chen, Haobin, additional

Published
2021
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42. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike

Author

Fu, Ying, primary, Rezende e Mello, Juliana da Fonseca, additional, Fleming, Bryan D., additional, Renn, Alex, additional, Chen, Catherine Z., additional, Hu, Xin, additional, Xu, Miao, additional, Gorshkov, Kirill, additional, Hanson, Quinlin, additional, Zheng, Wei, additional, Lee, Emily M., additional, Perera, Lalith, additional, Petrovich, Robert, additional, Pradhan, Manisha, additional, Eastman, Richard T., additional, Itkin, Zina, additional, Stanley, Thomas, additional, Hsu, Allen, additional, Dandey, Venkata, additional, Gillette, William, additional, Taylor, Troy, additional, Ramakrishnan, Nitya, additional, Perkins, Shelley, additional, Esposito, Dominic, additional, Oh, Eunkeu, additional, Susumu, Kimihiro, additional, Wolak, Mason, additional, Ferrer, Marc, additional, Hall, Matthew D., additional, Borgnia, Mario J., additional, and Simeonov, Anton, additional

Published
2021
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43. A high throughput screening assay for inhibitors of SARS-CoV-2 pseudotyped particle entry

Author

Xu, Miao, primary, Pradhan, Manisha, additional, Gorshkov, Kirill, additional, Petersen, Jennifer D., additional, Shen, Min, additional, Guo, Hui, additional, Zhu, Wei, additional, Klumpp-Thomas, Carleen, additional, Michael, Sam, additional, Itkin, Misha, additional, Itkin, Zina, additional, Straus, Marco R., additional, Zimmerberg, Joshua, additional, Zheng, Wei, additional, Whittaker, Gary R., additional, and Chen, Catherine Z., additional

Published
2021
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45. Inhibiting SARS‐CoV‐2 infection with lysosomal alkalizers

Author

Gorshkov, Kirill, primary, Chen, Catherine, additional, Bostwick, Robert, additional, Rasmussen, Lynn, additional, Tran, Bruce, additional, Cheng, Yu‐Shan, additional, Xu, Miao, additional, Pradhan, Manisha, additional, Henderson, Mark, additional, Zhu, Wei, additional, Oh, Eunkeu, additional, Susumu, Kimihiro, additional, Wolak, Mason, additional, Shamim, Khalida, additional, Huang, Wenwei, additional, Hu, Xin, additional, Shen, Min, additional, Klumpp‐Thomas, Carleen, additional, Itkin, Zina, additional, Shinn, Paul, additional, Torre, Juan Carlos, additional, Simeonov, Anton, additional, Michael, Samuel, additional, Hall, Matthew, additional, Lo, Donald, additional, and Zheng, Wei, additional

Published
2021
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46. Deep learning identifies synergistic drug combinations for treating COVID-19

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Synthetic Biology Center, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Jin, Wengong, Stokes, Jonathan, Eastman, Richard T., Itkin, Zina, Zakharov, Alexey V., Collins, James J., Jaakkola, Tommi S, Barzilay, Regina, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Synthetic Biology Center, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Jin, Wengong, Stokes, Jonathan, Eastman, Richard T., Itkin, Zina, Zakharov, Alexey V., Collins, James J., Jaakkola, Tommi S, and Barzilay, Regina

Abstract

Effective treatments for COVID-19 are urgently needed. However, discovering single-agent therapies with activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been challenging. Combination therapies play an important role in antiviral therapies, due to their improved efficacy and reduced toxicity. Recent approaches have applied deep learning to identify synergistic drug combinations for diseases with vast preexisting datasets, but these are not applicable to new diseases with limited combination data, such as COVID-19. Given that drug synergy often occurs through inhibition of discrete biological targets, here we propose a neural network architecture that jointly learns drug−target interaction and drug−drug synergy. The model consists of two parts: a drug−target interaction module and a target−disease association module. This design enables the model to utilize drug−target interaction data and single-agent antiviral activity data, in addition to available drug−drug combination datasets, which may be small in nature. By incorporating additional biological information, our model performs significantly better in synergy prediction accuracy than previous methods with limited drug combination training data. We empirically validated our model predictions and discovered two drug combinations, remdesivir and reserpine as well as remdesivir and IQ-1S, which display strong antiviral SARS-CoV-2 synergy in vitro. Our approach, which was applied here to address the urgent threat of COVID-19, can be readily extended to other diseases for which a dearth of chemical−chemical combination data exists.

Published
2021

47. Therapeutic targeting of ATR yields durable regressions in small cell lung cancers with high replication stress

Author

Thomas, Anish, primary, Takahashi, Nobuyuki, additional, Rajapakse, Vinodh N., additional, Zhang, Xiaohu, additional, Sun, Yilun, additional, Ceribelli, Michele, additional, Wilson, Kelli M., additional, Zhang, Yang, additional, Beck, Erin, additional, Sciuto, Linda, additional, Nichols, Samantha, additional, Elenbaas, Brian, additional, Puc, Janusz, additional, Dahmen, Heike, additional, Zimmermann, Astrid, additional, Varonin, Jillian, additional, Schultz, Christopher W., additional, Kim, Sehyun, additional, Shimellis, Hirity, additional, Desai, Parth, additional, Klumpp-Thomas, Carleen, additional, Chen, Lu, additional, Travers, Jameson, additional, McKnight, Crystal, additional, Michael, Sam, additional, Itkin, Zina, additional, Lee, Sunmin, additional, Yuno, Akira, additional, Lee, Min-Jung, additional, Redon, Christophe E., additional, Kindrick, Jessica D., additional, Peer, Cody J., additional, Wei, Jun S., additional, Aladjem, Mirit I., additional, Figg, William Douglas, additional, Steinberg, Seth M., additional, Trepel, Jane B., additional, Zenke, Frank T., additional, Pommier, Yves, additional, Khan, Javed, additional, and Thomas, Craig J., additional

Published
2021
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48. Synergistic and Antagonistic Drug Combinations against SARS-CoV-2

Author

Bobrowski, Tesia, primary, Chen, Lu, additional, Eastman, Richard T., additional, Itkin, Zina, additional, Shinn, Paul, additional, Chen, Catherine Z., additional, Guo, Hui, additional, Zheng, Wei, additional, Michael, Sam, additional, Simeonov, Anton, additional, Hall, Matthew D., additional, Zakharov, Alexey V., additional, and Muratov, Eugene N., additional

Published
2021
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49. Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2

Author

Chen, Catherine Z., primary, Shinn, Paul, additional, Itkin, Zina, additional, Eastman, Richard T., additional, Bostwick, Robert, additional, Rasmussen, Lynn, additional, Huang, Ruili, additional, Shen, Min, additional, Hu, Xin, additional, Wilson, Kelli M., additional, Brooks, Brianna M., additional, Guo, Hui, additional, Zhao, Tongan, additional, Klump-Thomas, Carleen, additional, Simeonov, Anton, additional, Michael, Samuel G., additional, Lo, Donald C., additional, Hall, Matthew D., additional, and Zheng, Wei, additional

Published
2021
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50. The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules

Author

Gorshkov, Kirill, primary, Chen, Catherine Z., additional, Bostwick, Robert, additional, Rasmussen, Lynn, additional, Tran, Bruce Nguyen, additional, Cheng, Yu-Shan, additional, Xu, Miao, additional, Pradhan, Manisha, additional, Henderson, Mark, additional, Zhu, Wei, additional, Oh, Eunkeu, additional, Susumu, Kimihiro, additional, Wolak, Mason, additional, Shamim, Khalida, additional, Huang, Wenwei, additional, Hu, Xin, additional, Shen, Min, additional, Klumpp-Thomas, Carleen, additional, Itkin, Zina, additional, Shinn, Paul, additional, Carlos de la Torre, Juan, additional, Simeonov, Anton, additional, Michael, Sam G., additional, Hall, Matthew D., additional, Lo, Donald C., additional, and Zheng, Wei, additional

Published
2020
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