Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel–Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7
Open accessAbstract
Developing PROTACs to redirect the ubiquitination activity of E3 ligases and potently degrade a target protein within cells can be a lengthy and unpredictable process, and it remains unclear whether any combination of E3 and target might be productive for degradation. We describe a probe-quality degrader for a ligase–target pair deemed unsuitable: the von Hippel–Lindau (VHL) and BRD9, a bromodomain-containing subunit of the SWI/SNF chromatin remodeling complex BAF. VHL-based degraders could be optimized from suboptimal compounds in two rounds by systematically varying conjugation patterns and linkers and monitoring cellular degradation activities, kinetic profiles, and ubiquitination, as well as ternary complex formation thermodynamics. The emerged structure–activity relationships guided the discovery of VZ185, a potent, fast, and selective degrader of BRD9 and of its close homolog BRD7. Our findings qualify a new chemical tool for BRD7/9 knockdown and provide a roadmap for PROTAC development against seemingly incompatible target–ligase combinations.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
VZ185 is more effective than corresponding inhibitor in reducing viability of EOL-1 acute myeloid eosinophilic leukemia cells and A-204 malignant rhabdoid tumor cells.
“Subsequently, Ciulli’s group reported a VHL-based dual BRD7 and BRD9 degrader, VZ185, which was found to be more effective than the corresponding inhibitor in reducing the viability of EOL-1 acute myeloid eosinophilic leukemia cells and A-204 malignant rhabdoid tumor cells [181].”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [181]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
1 retracted
Niu, W., Luo, Y., Wang, X., Zhou, Y., Li, H., Wang, H., Fu, Y., Liu, S., Yin, S., Li, J., et al. (2018) · Cell Death and Disease · doi:10.1038/s41419-018-0536-7 · Cited by 26 · see citing works
Retracted<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463 · see citing works
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,671 · see citing works
<i>MolProbity</i> : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115 · see citing works
Overview of the <i>CCP</i> 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353 · see citing works
PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
Schüttelkopf, A. W., & van Aalten, D. M. F. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904011679 · Cited by 4,815 · see citing works
MOLREP : an Automated Program for Molecular Replacement
Vagin, A. A., & Teplyakov, A. (1997) · Journal of Applied Crystallography · doi:10.1107/s0021889897006766 · Cited by 4,791 · see citing works
Why Do Cancers Have High Aerobic Glycolysis?
Gatenby, R. A., & Gillies, R. J. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1478 · Cited by 4,784 · see citing works
Scaling and assessment of data quality
Evans, P. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905036693 · Cited by 4,391 · see citing works
Sakamoto, K. M., Kim, K. B., Kumagai, A., Mercurio, F., Crews, C. M., & Deshaies, R. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.141230798 · Cited by 2,609 · see citing works
Function and regulation of cullin–RING ubiquitin ligases
Petroski, M. D., & Deshaies, R. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1547 · Cited by 2,148 · see citing works
An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer
Soucy, T. A., Smith, P. G., Milhollen, M. A., Berger, A. J., Gavin, J. M., Adhikari, S., Brownell, J. E., Burke, K. E., Cardin, D. P., Critchley, S., et al. (2009) · Nature · doi:10.1038/nature07884 · Cited by 1,990 · see citing works
Phthalimide conjugation as a strategy for in vivo target protein degradation
Winter, G. E., Buckley, D. L., Paulk, J., Roberts, J. M., Souza, A., Dhe-Paganon, S., & Bradner, J. E. (2015) · Science · doi:10.1126/science.aab1433 · Cited by 1,760 · see citing works
Induced protein degradation: an emerging drug discovery paradigm
Lai, A. C., & Crews, C. M. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.211 · Cited by 1,486 · see citing works
Kadoch, C., Hargreaves, D. C., Hodges, H. C., Elias, L., Ho, L., Ranish, J. A., & Crabtree, G. R. (2013) · Nature Genetics · doi:10.1038/ng.2628 · Cited by 1,443 · see citing works
Catalytic in vivo protein knockdown by small-molecule PROTACs
Bondeson, D. P., Mares, A., Smith, I. E. D., Ko, E., Campos, S., Miah, A. H., Mulholland, K. E., Routly, N., Buckley, D. L., Gustafson, J. L., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1858 · Cited by 1,356 · see citing works
Structural basis of PROTAC cooperative recognition for selective protein degradation
Gadd, M. S., Testa, A., Lucas, X., Chan, K.-H., Chen, W., Lamont, D. J., Zengerle, M., & Ciulli, A. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2329 · Cited by 1,242 · see citing works
Self-citationStructure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide
Fischer, E. S., Böhm, K., Lydeard, J. R., Yang, H., Stadler, M. B., Cavadini, S., Nagel, J., Serluca, F., Acker, V., Lingaraju, G. M., et al. (2014) · Nature · doi:10.1038/nature13527 · Cited by 1,141 · see citing works
Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target BRD4
Lu, J., Qian, Y., Altieri, M., Dong, H., Wang, J., Raina, K., Hines, J., Winkler, J. D., Crew, A. P., Coleman, K., et al. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.05.009 · Cited by 1,140 · see citing works
Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4
Zengerle, M., Chan, K.-H., & Ciulli, A. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00216 · Cited by 1,056 · see citing works
Self-citationLessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead
Bondeson, D. P., Smith, B. E., Burslem, G. M., Buhimschi, A. D., Hines, J., Jaime-Figueroa, S., Wang, J., Hamman, B. D., Ishchenko, A., & Crews, C. M. (2018) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.09.010 · Cited by 923 · see citing works
PROTAC-induced BET protein degradation as a therapy for castration-resistant prostate cancer
Raina, K., Lu, J., Qian, Y., Altieri, M., Gordon, D., Rossi, A. M. K., Wang, J., Chen, X., Dong, H., Siu, K., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521738113 · Cited by 852 · see citing works
A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing
Pan, D., Kobayashi, A., Jiang, P., Ferrari de Andrade, L., Tay, R. E., Luoma, A. M., Tsoucas, D., Qiu, X., Lim, K., Rao, P., et al. (2018) · Science · doi:10.1126/science.aao1710 · Cited by 852 · see citing works
Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15
Han, T., Goralski, M., Gaskill, N., Capota, E., Kim, J., Ting, T. C., Xie, Y., Williams, N. S., & Nijhawan, D. (2017) · Science · doi:10.1126/science.aal3755 · Cited by 762 · see citing works
Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes
Narlikar, G. J., Sundaramoorthy, R., & Owen‐Hughes, T. (2013) · Cell · doi:10.1016/j.cell.2013.07.011 · Cited by 659 · see citing works
Modular PROTAC design for the degradation of oncogenic BCR-ABL
Lai, A. C., Toure, M., Hellerschmied, D., Salami, J., Jaime‐Figueroa, S., Ko, E., Hines, J., & Crews, C. M. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201507634 · Cited by 618 · see citing works
Plasticity in binding confers selectivity in ligand-induced protein degradation
Nowak, R. P., DeAngelo, S. L., Buckley, D., He, Z., Donovan, K. A., An, J., Safaee, N., Jedrychowski, M. P., Ponthier, C. M., Ishoey, M., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0055-y · Cited by 615 · see citing works
Cereblon expression is required for the antimyeloma activity of lenalidomide and pomalidomide
Zhu, Y. X., Braggio, E., Shi, C.-X., Bruins, L. A., Schmidt, J. E., Van Wier, S., Chang, X.-B., Bjorklund, C. C., Fonseca, R., Bergsagel, P. L., et al. (2011) · Blood · doi:10.1182/blood-2011-05-356063 · Cited by 607 · see citing works
Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation
Olson, C. M., Jiang, B., Erb, M. A., Liang, Y., Doctor, Z. M., Zhang, Z., Zhang, T., Kwiatkowski, N., Boukhali, M., Green, J. L., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2538 · Cited by 552 · see citing works
HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins
Buckley, D. L., Raina, K., Darricarrere, N., Hines, J., Gustafson, J. L., Smith, I. E., Miah, A. H., Harling, J. D., & Crews, C. M. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00442 · Cited by 488 · see citing works
The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation
Fischer, E. S., Scrima, A., Böhm, K., Matsumoto, S., Lingaraju, G. M., Faty, M., Yasuda, T., Cavadini, S., Wakasugi, M., Hanaoka, F., et al. (2011) · Cell · doi:10.1016/j.cell.2011.10.035 · Cited by 460 · see citing works
A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader
Huang, H.-T., Dobrovolsky, D., Paulk, J., Yang, G., Weisberg, E. L., Doctor, Z. M., Buckley, D. L., Cho, J.-H., Ko, E., Jang, J., et al. (2018) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.10.005 · Cited by 437 · see citing works
Drugging the undruggables: exploring the ubiquitin system for drug development
Huang, X., & Dixit, V. M. (2016) · Cell Research · doi:10.1038/cr.2016.31 · Cited by 427 · see citing works
Galdeano, C., Gadd, M. S., Soares, P., Scaffidi, S., Molle, I. V., Birced, I., Hewitt, S. H., Dias, D. M. G., & Ciulli, A. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5011258 · Cited by 424 · see citing works
Self-citationDelineating the role of cooperativity in the design of potent PROTACs for BTK
Zorba, A., Nguyen, C., Xu, Y., Starr, J., Borzilleri, K., Smith, J., Zhu, H., Farley, K. A., Ding, W., Schiemer, J., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803662115 · Cited by 419 · see citing works
Selective degradation of splicing factor CAPERα by anticancer sulfonamides
Uehara, T., Minoshima, Y., Sagane, K., Sugi, N. H., Mitsuhashi, K. O., Yamamoto, N., Kamiyama, H., Takahashi, K., Kotake, Y., Uesugi, M., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2363 · Cited by 396 · see citing works
Zhou, B. N., Hu, J., Xu, F., Chen, Z., Bai, L., Fernández‐Salas, E., Lin, M., Liu, L., Yang, C., Zhao, Y., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b01816 · Cited by 373 · see citing works
Salami, J., Alabi, S., Willard, R. R., Vitale, N. J., Wang, J., Dong, H., Jin, M., McDonnell, D. P., Crew, A. P., Neklesa, T. K., et al. (2018) · Communications Biology · doi:10.1038/s42003-018-0105-8 · Cited by 349 · see citing works
Quantitative Live-Cell Kinetic Degradation and Mechanistic Profiling of PROTAC Mode of Action
Riching, K. M., Mahan, S. D., Corona, C. R., McDougall, M. G., Vasta, J. D., Robers, M. B., Urh, M., & Daniels, D. L. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00692 · Cited by 307 · see citing works
Self-citationDegradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands
Remillard, D., Buckley, D. L., Paulk, J., Brien, G. L., Sonnett, M., Seo, H., Dastjerdi, S., Wühr, M., Dhe‐Paganon, S., Armstrong, S. A., et al. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201611281 · Cited by 294 · see citing works
Qin, C., Hu, Y., Zhou, B., Fernandez-Salas, E., Yang, C.-Y., Liu, L., McEachern, D., Przybranowski, S., Wang, M., Stuckey, J., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00506 · Cited by 281 · see citing works
Schiedel, M., Herp, D., Hammelmann, S., Swyter, S., Lehotzky, A., Robaa, D., Oláh, J., Ovádi, J., Sippl, W., & Jung, M. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b01872 · Cited by 275 · see citing works
Crew, A. P., Raina, K., Dong, H., Qian, Y., Wang, J., Vigil, D., Serebrenik, Y. V., Hamman, B. D., Morgan, A., Ferraro, C., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00635 · Cited by 257 · see citing works
Maniaci, C., Hughes, S. J., Testa, A., Chen, W., Lamont, D. J., Rocha, S., Alessi, D. R., Romeo, R., & Ciulli, A. (2017) · Nature Communications · doi:10.1038/s41467-017-00954-1 · Cited by 245 · see citing works
Self-citationFrost, J., Galdeano, C., Soares, P., Gadd, M. S., Grzes, K. M., Ellis, L. C. J., Epemolu, O., Shimamura, S., Bantscheff, M., Grandi, P., et al. (2016) · Nature Communications · doi:10.1038/ncomms13312 · Cited by 242 · see citing works
Self-citationTheodoulou, N. H., Bamborough, P., Bannister, A. J., Becher, I., Bit, R. A., Che, K. H., Chung, C., Dittmann, A., Drewes, G., Drewry, D. H., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00256 · Cited by 240 · see citing works
Hughes, S. J., & Ciulli, A. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170041 · Cited by 240 · see citing works
Self-citationBulatov, E., & Ciulli, A. (2015) · Biochemical Journal · doi:10.1042/bj20141450 · Cited by 237 · see citing works
Self-citationKaeser, M. D., Aslanian, A., Dong, M., Yates, J. R., & Emerson, B. M. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m806061200 · Cited by 237 · see citing works
Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor
Martin, L. J., Koegl, M., Bader, G., Cockcroft, X. F., Fedorov, O., Fiegen, D., Gerstberger, T., Hofmann, M. H., Hohmann, A. F., Kessler, D., et al. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b01865 · Cited by 228 · see citing works
Self-citationProteolysis-Targeting Chimeras: Induced Protein Degradation as a Therapeutic Strategy
Ottis, P., & Crews, C. M. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.6b01068 · Cited by 227 · see citing works
Proteolysis Targeting Chimeras (PROTACs) of Anaplastic Lymphoma Kinase (ALK)
Zhang, C., Han, X.-R., Yang, X., Jiang, B., Liu, J., Xiong, Y., & Jin, J. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.03.071 · Cited by 226 · see citing works
Chan, K.-H., Zengerle, M., Testa, A., & Ciulli, A. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b01912 · Cited by 222 · see citing works
Self-citationFunctional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands
Gechijian, L. N., Buckley, D. L., Lawlor, M. A., Reyes, J. M., Paulk, J., Ott, C. J., Winter, G. E., Erb, M. A., Scott, T. G., Xu, M., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0010-y · Cited by 222 · see citing works
Chemically induced degradation of CDK9 by a proteolysis targeting chimera (PROTAC)
Robb, C. M., Contreras, J. I., Kour, S., Taylor, M., Abid, M., Sonawane, Y. A., Zahid, M., Murry, D. J., Natarajan, A., & Rana, S. (2017) · Chemical Communications · doi:10.1039/c7cc03879h · Cited by 221 · see citing works
BRD7 is a candidate tumour suppressor gene required for p53 function
Drost, J., Mantovani, F., Tocco, F., Elkon, R., Comel, A., Holstege, H. H., Kerkhoven, R. M., Jonkers, J., Voorhoeve, P. M., Agami, R., et al. (2010) · Nature Cell Biology · doi:10.1038/ncb2038 · Cited by 199 · see citing works
Molle, I. V., Thomann, A., Buckley, D. L., So, E. C., Lang, S., Crews, C. M., & Ciulli, A. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.08.015 · Cited by 198 · see citing works
Self-citationA rationale to target the SWI/SNF complex for cancer therapy
Hohmann, A. F., & Vakoc, C. R. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.05.001 · Cited by 186 · see citing works
Modulating PCAF/GCN5 Immune Cell Function through a PROTAC Approach
Bassi, Z. I., Fillmore, M. C., Miah, A. H., Chapman, T. D., Maller, C., Roberts, E. J., Davis, L. C., Lewis, D. E., Galwey, N. W., Waddington, K. E., et al. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00705 · Cited by 186 · see citing works
Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition
Hohmann, A. F., Martin, L. J., Minder, J. L., Roe, J., Shi, J., Steurer, S., Bader, G., McConnell, D. B., Pearson, M. A., Gerstberger, T., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2115 · Cited by 184 · see citing works
Self-citationKang, J. U., Koo, S. H., Kwon, K. C., Park, J. W., & Kim, J. (2008) · Cancer Genetics and Cytogenetics · doi:10.1016/j.cancergencyto.2007.12.004 · Cited by 180 · see citing works
Soares, P., Gadd, M. S., Frost, J., Galdeano, C., Ellis, L. C. J., Epemolu, O., Rocha, S., Read, K. D., & Ciulli, A. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00675 · Cited by 180 · see citing works
Self-citationIshoey, M., Chorn, S., Singh, N., Jaeger, M. G., Brand, M., Paulk, J., Bauer, S., Erb, M. A., Parapatics, K., Müller, A. C., et al. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00969 · Cited by 177 · see citing works
Lin, Y. A., Chalker, J. M., & Davis, B. G. (2010) · Journal of the American Chemical Society · doi:10.1021/ja104994d · Cited by 171 · see citing works
LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor
Clark, P. G. K., Vieira, L. C. C., Tallant, C., Fedorov, O., Singleton, D. C., Rogers, C. M., Monteiro, O., Bennett, J. M., Baronio, R., Müller, S., et al. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201501394 · Cited by 167 · see citing works
Self-citationHomo-PROTACs for the Chemical Knockdown of Cereblon
Steinebach, C., Lindner, S., Udeshi, N. D., Mani, D. R., Kehm, H., Köpff, S., Carr, S. A., Gütschow, M., & Krönke, J. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00693 · Cited by 160 · see citing works
Wang, X., Sansam, C. G., Thom, C. S., METZGER, D., Evans, J. A., Nguyen, P. T. L., & Roberts, C. W. M. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-0733 · Cited by 153 · see citing works
Shibata, N., Nagai, K., Morita, Y., Ujikawa, O., Ohoka, N., Hattori, T., Koyama, R., Sano, O., Imaeda, Y., Nara, H., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00168 · Cited by 147 · see citing works
Mechanisms by which SMARCB1 loss drives rhabdoid tumor growth
Kim, K. H., & Roberts, C. (2014) · Cancer Genetics · doi:10.1016/j.cancergen.2014.04.004 · Cited by 142 · see citing works
Collins, I., Wang, H., Caldwell, J., & Chopra, R. (2017) · Biochemical Journal · doi:10.1042/bcj20160762 · Cited by 135 · see citing works
Scotto, L., Narayan, G., Nandula, S. V., et al. (2008) · Molecular Cancer · doi:10.1186/1476-4598-7-58 · Cited by 123 · see citing works
LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor
Clark, P. G. K., Vieira, L. C. C., Tallant, C., Fedorov, O., Singleton, D. C., Rogers, C. M., Monteiro, O., Bennett, J. M., Baronio, R., Müller, S., et al. (2015) · Angewandte Chemie · doi:10.1002/ange.201501394 · Cited by 123 · see citing works
Self-citationHarte, M. T., O'Brien, G. J., Ryan, N., Gorski, J. J., Savage, K. I., Crawford, N., Mullan, P. B., & Harkin, D. P. (2010) · Cancer Research · doi:10.1158/0008-5472.can-09-2089 · Cited by 120 · see citing works
Evidence that Swi/Snf directly represses transcription in S. cerevisiaePreprint
Martens, J. A., & Winston, F. (2002) · Genes & Development · doi:10.1101/gad.1009902 · Cited by 110 · see citing works
Target Engagement in Lead Generation
Durham, T. B., & Blanco, M.-J. (2015) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2014.12.076 · Cited by 99 · see citing works
Lucas, X., & Ciulli, A. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.12.015 · Cited by 92 · see citing works
Self-citationCyrus, K., Wehenkel, M., Choi, E., Lee, H., Swanson, H. I., & Kim, K. (2010) · ChemMedChem · doi:10.1002/cmdc.201000146 · Cited by 91 · see citing works
BRD7, a Tumor Suppressor, Interacts with p85α and Regulates PI3K Activity
Chiu, Y., Lee, J. Y., & Cantley, L. C. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.016 · Cited by 78 · see citing works
Park, S. W., Herrema, H., Salazar, M., Çakır, I., Cabi, S., Sahin, F. B., Chiu, Y., Cantley, L. C., & Özcan, U. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.04.006 · Cited by 76 · see citing works
Evidence for a Stereoelectronic Effect in Human Oxygen Sensing
Loenarz, C., Mecinović, J., Chowdhury, R., McNeill, L. A., Flashman, E., & Schofield, C. J. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200805427 · Cited by 68 · see citing works
Design and synthesis of potent and selective inhibitors of BRD7 and BRD9 bromodomains
Hay, D. A., Rogers, C. M., Fedorov, O., et al. (2015) · MedChemComm · doi:10.1039/c5md00152h · Cited by 66 · see citing works
BRD7: a novel tumor suppressor gene in different cancers.
Yu, X., Li, Z., & Shen, J. (2016) · PubMed Central · Cited by 57 · see citing works
Crawford, T. D., Vartanian, S., Côté, A., Bellon, S. F., Duplessis, M., Flynn, E. M., Hewitt, M. C., Huang, H.-R., Kiefer, J. R., Murray, J. M., et al. (2017) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2017.05.063 · Cited by 43 · see citing works
Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands
Remillard, D., Buckley, D. L., Paulk, J., Brien, G. L., Sonnett, M., Seo, H., Dastjerdi, S., Wühr, M., Dhe‐Paganon, S., Armstrong, S. A., et al. (2017) · Angewandte Chemie · doi:10.1002/ange.201611281 · Cited by 23 · see citing works
Ihara, M., Suzuki, S., Taniguchi, N., et al. (1993) · Journal of the Chemical Society Perkin Transactions 1 · doi:10.1039/p19930002251 · Cited by 22 · see citing works
Greiner, R., Ziegler, D., Cibu, D., et al. (2017) · Organic Letters · doi:10.1021/acs.orglett.7b03242 · Cited by 22 · see citing works
Zhang, Q., Ren, H., & Baker, G. L. (2014) · The Journal of Organic Chemistry · doi:10.1021/jo5016135 · Cited by 16 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Targeted protein degradation: expanding the toolbox
Schapira, M., Calabrese, M. F., Bullock, A. N., & Crews, C. M. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0047-y · Cited by 960 · see citing works
BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design
Farnaby, W., Koegl, M., Roy, M. J., Whitworth, C., Diers, E., Trainor, N., Zollman, D., Steurer, S., Karolyi-Oezguer, J., Riedmueller, C., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0294-6 · Cited by 562 · see citing works
Self-citationDevelopment of targeted protein degradation therapeutics
Chamberlain, P. P., & Hamann, L. G. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0362-y · Cited by 489 · see citing works
Edmondson, S. D., Yang, B., & Fallan, C. (2019) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2019.04.030 · Cited by 422 · see citing works
Current strategies for the design of PROTAC linkers: a critical review
Troup, R. I., Fallan, C., & Baud, M. G. J. (2020) · Exploration of Targeted Anti-tumor Therapy · doi:10.37349/etat.2020.00018 · Cited by 424 · see citing works
SPR-measured dissociation kinetics of PROTAC ternary complexes influence target degradation rate
Roy, M. J., Winkler, S., Hughes, S. J., Whitworth, C., Galant, M., Farnaby, W., Rumpel, K., & Ciulli, A. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00092 · Cited by 386 · see citing works
Self-citationDegradation of proteins by PROTACs and other strategies
Wang, Y., Jiang, X., Feng, F., Liu, W., & Sun, H. (2020) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2019.08.001 · Cited by 335 · see citing works
PROTACs: great opportunities for academia and industry (an update from 2020 to 2021)
He, M., Cao, C., Ni, Z., Liu, Y., Song, P., Hao, S., He, Y., Sun, X., & Rao, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00999-9 · Cited by 283 · see citing works
PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics
Khan, S., He, Y., Zhang, X., Yuan, Y., Pu, S., Kong, Q., Zheng, G., & Zhou, D. (2020) · Oncogene · doi:10.1038/s41388-020-1336-y · Cited by 252 · see citing works
Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity
Imaide, S., Riching, K. M., Makukhin, N., Vetma, V., Whitworth, C., Hughes, S. J., Trainor, N., Mahan, S. D., Murphy, N., Cowan, A. D., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00878-4 · Cited by 251 · see citing works
Self-citationTargeted protein degradation via intramolecular bivalent glues
Hsia, O., Hinterndorfer, M., Cowan, A. D., Iso, K., Ishida, T., Sundaramoorthy, R., Nakasone, M. A., Imrichova, H., Schätz, C., Rukavina, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07089-6 · Cited by 222 · see citing works
Self-citationExtended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2
Mares, A., Miah, A. H., Smith, I. E. D., Rackham, M., Thawani, A. R., Cryan, J., Haile, P. A., Votta, B. J., Beal, A. M., Capriotti, C., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-0868-6 · Cited by 232 · see citing works
Recent Developments in PROTAC‐Mediated Protein Degradation: From Bench to Clinic
Hu, Z., & Crews, C. M. (2022) · ChemBioChem · doi:10.1002/cbic.202100270 · Cited by 231 · see citing works
PROTAC-DB: an online database of PROTACs
Weng, G., Shen, C., Cao, D., Gao, J., Dong, X., He, Q., Yang, B., Li, D., Wu, J., & Hou, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa807 · Cited by 219 · see citing works
RNA‐PROTACs: Degraders of RNA‐Binding Proteins
Ghidini, A., Cléry, A., Halloy, F., Allain, F. H. T., & Hall, J. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202012330 · Cited by 197 · see citing works
PROTACs: A novel strategy for cancer therapy
Liu, J., Ma, J., Liu, Y., Xia, J., Li, Y., Wang, Z. P., & Wei, W. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.02.006 · Cited by 186 · see citing works
Harnessing the Power of Proteolysis for Targeted Protein Inactivation
Verma, R., Mohl, D., & Deshaies, R. J. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.010 · Cited by 185 · see citing works
Discovery of SHP2-D26 as a First, Potent, and Effective PROTAC Degrader of SHP2 Protein
Wang, M., Lu, J., Wang, M., Yang, C.-Y., & Wang, S. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c00471 · Cited by 172 · see citing works
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta
Bai, N., Miller, S. A., Andrianov, G. V., Yates, M., Kirubakaran, P., & Karanicolas, J. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c01451 · Cited by 157 · see citing works
Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity
Klein, V. G., Bond, A. G., Craigon, C., Lokey, R. S., & Ciulli, A. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01496 · Cited by 152 · see citing works
Self-citationSteinebach, C., Ng, Y. L. D., Sosič, I., Lee, C.-S., Chen, S., Lindner, S., Vu, L. P., Bricelj, A., Haschemi, R., Monschke, M., et al. (2020) · Chemical Science · doi:10.1039/d0sc00167h · Cited by 148 · see citing works
Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies
He, Y., Khan, S., Huo, Z., Lv, D., Zhang, X., Liu, X., Yuan, Y., Hromas, R., Xu, M., Zheng, G., et al. (2020) · Journal of Hematology & Oncology · doi:10.1186/s13045-020-00924-z · Cited by 126 · see citing works
Zhang, X., Thummuri, D., Liu, X., Hu, W., Zhang, P., Khan, S., Yuan, Y., Zhou, D., & Zheng, G. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112186 · Cited by 123 · see citing works
Wang, Z., He, N., Guo, Z., Niu, C., Song, T., Guo, Y., Cao, K., Wang, A., Zhu, J., Zhang, X., et al. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b00919 · Cited by 120 · see citing works
Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes
Schiemer, J., Horst, R., Meng, Y., Montgomery, J. I., Xu, Y., Feng, X., Borzilleri, K., Uccello, D. P., Leverett, C., Brown, S., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00686-2 · Cited by 113 · see citing works
Bifunctional chemical probes inducing protein–protein interactions
Maniaci, C., & Ciulli, A. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.07.003 · Cited by 100 · see citing works
Self-citationPROTAC degraders as chemical probes for studying target biology and target validation
Němec, V., Schwalm, M. P., Müller, S., & Knapp, S. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00478j · Cited by 98 · see citing works
Wang, Y., Zhou, Y., Cao, S., Sun, Y., Dong, Z., Li, C., Wang, H., Yao, Y., Yu, H., Song, X., et al. (2021) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2021.104833 · Cited by 96 · see citing works
Zhang, X., Thummuri, D., He, Y., Liu, X., Zhang, P., Zhou, D., & Zheng, G. (2019) · Chemical Communications · doi:10.1039/c9cc07217a · Cited by 86 · see citing works
Development of selective small molecule MDM2 degraders based on nutlin
Wang, B., Wu, S., Liu, J., Yang, K., Xie, H., & Tang, W. (2019) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2019.05.046 · Cited by 77 · see citing works
Discovery of a Novel BCL-X<sub>L</sub> PROTAC Degrader with Enhanced BCL-2 Inhibition
Pal, P., Thummuri, D., Lv, D., Liu, X., Zhang, P., Hu, W., Poddar, S. K., Hua, N., Khan, S., Yuan, Y., et al. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c00517 · Cited by 60 · see citing works
Eron, S. J., Huang, H., Agafonov, R. V., Fitzgerald, M. E., Patel, J., Michael, R. E., Lee, T. D., Hart, A. A., Shaulsky, J., Nasveschuk, C. G., et al. (2021) · ACS Chemical Biology · doi:10.1021/acschembio.1c00376 · Cited by 57 · see citing works
Qi, Z., Yang, G., Deng, T., Wang, J., Zhou, H., Popov, S. A., Shults, E. E., & Wang, C. (2021) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2021.104901 · Cited by 39 · see citing works
Wang, Y., Deng, S., & Xu, J. (2020) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2020.0066 · Cited by 10 · see citing works
- Authors
- Zoppi, V., Hughes, S. J., Maniaci, C., Testa, A., Gmaschitz, T., Wieshofer, C., Koegl, M., Riching, K. M., Daniels, D. L., Spallarossa, A., & Ciulli, A.
- Affiliations
- University of Dundee (GB)
- Boehringer Ingelheim (Germany) (DE)
- Promega (United States) (US)
- University of Genoa (IT)
- Corresponding author
- Ciulli, Alessio
- ORCID
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-12-12
- Volume
- 62
- Issue
- 2
- Pages
- 699-726
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- PMC
- PMC6348446
- OpenAlex
- W2903964626
- Cited by
- 336
- References
- 88
- Citations by year
- 2026: 31 · 2025: 32 · 2024: 47 · 2023: 46 · 2022: 48 · 2021: 48 · 2020: 59 · 2019: 24 · 2014: 1
- FWCI
- 12.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Medicinal Chemistry (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion, cc-by)
- CINECA IRIS Institutial Research Information System (University of Genoa) (submittedVersion, other-oa)
- Funders
- Universit? degli Studi di Genova
- Wellcome Trust (094090/Z/10/Z, 100476/Z/12/Z)
- FP7 Ideas: European Research Council (311460)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- PROTACs, VHL, BRD9, BRD7, protein degraders, E3 ubiquitin ligase, SWI/SNF chromatin remodeling, SWI/SNF complex, bromodomain, structure-activity relationship, linkers, ternary complex formation, ubiquitination, iterative design
- MeSH terms
- Bromodomain Containing Proteins, Chromosomal Proteins, Non-Histone, HeLa Cells, Humans, Kinetics, Protein Binding, Structure-Activity Relationship, Thermodynamics, Transcription Factors, Drug Design, Proteome, Von Hippel-Lindau Tumor Suppressor Protein, Ubiquitination, Proteolysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review