In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application

Selective inhibition of BET bromodomains

Filippakopoulos, P., Qi, J., Picaud, S., Shen, Y., Smith, W. B., Fedorov, O., Morse, E. M., Keates, T., Hickman, T. T., Felletar, I., et al. (2010) · Nature · doi:10.1038/nature09504 · Cited by 4,262 · see citing works

Protacs: Chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation

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

Identification of a Primary Target of Thalidomide Teratogenicity

Ito, T., Ando, H., Suzuki, T., Ogura, T., Hotta, K., Imamura, Y., Yamaguchi, Y., & Handa, H. (2010) · Science · doi:10.1126/science.1177319 · Cited by 2,136 · 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

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

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

Lessons 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

Cereblon is a direct protein target for immunomodulatory and antiproliferative activities of lenalidomide and pomalidomide

Lopez-Girona, A., Mendy, D., Ito, T., Miller, K., Gandhi, A. K., Kang, J., Karasawa, S., Carmel, G., Jackson, P., Abbasian, M., et al. (2012) · Leukemia · doi:10.1038/leu.2012.119 · Cited by 814 · see citing works

The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study

Burslem, G. M., Smith, B. E., Lai, A. C., Jaime-Figueroa, S., McQuaid, D. C., Bondeson, D. P., Toure, M., Dong, H., Qian, Y., Wang, J., et al. (2018) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.09.009 · Cited by 686 · 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

Targeted protein degradation by PROTACs

Neklesa, T. K., Winkler, J. D., & Crews, C. M. (2017) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2017.02.027 · Cited by 599 · see citing works

Protac-Induced Protein Degradation in Drug Discovery: Breaking the Rules or Just Making New Ones?

Churcher, I. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01272 · Cited by 491 · see citing works

Chemically induced proximity in biology and medicine

Stanton, B. Z., Chory, E. J., & Crabtree, G. R. (2018) · Science · doi:10.1126/science.aao5902 · Cited by 475 · see citing works

A Comprehensive Mathematical Model for Three-Body Binding Equilibria

Douglass, E. F., Miller, C. J., Sparer, G., Shapiro, H., & Spiegel, D. A. (2013) · Journal of the American Chemical Society · doi:10.1021/ja311795d · Cited by 472 · see citing works

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities

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

Delineating 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

Protein Degradation by In-Cell Self-Assembly of Proteolysis Targeting Chimeras

Lebraud, H., Wright, D. J., Johnson, C. N., & Heightman, T. D. (2016) · ACS Central Science · doi:10.1021/acscentsci.6b00280 · Cited by 413 · see citing works

Protein Knockdown Using Methyl Bestatin−Ligand Hybrid Molecules: Design and Synthesis of Inducers of Ubiquitination-Mediated Degradation of Cellular Retinoic Acid-Binding Proteins

Itoh, Y., Ishikawa, M., Naito, M., & Hashimoto, Y. (2010) · Journal of the American Chemical Society · doi:10.1021/ja100691p · Cited by 404 · see citing works

Targeting the C481S ibrutinib-resistance mutation in Bruton’s tyrosine kinase using PROTAC-mediated degradation

Buhimschi, A. D., Armstrong, H. A., Toure, M., Jaime-Figueroa, S., Chen, T. L., Lehman, A. M., Woyach, J. A., Johnson, A. J., Byrd, J. C., & Crews, C. M. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b00391 · Cited by 394 · see citing works

Beyond the Rule of 5: Lessons Learned from AbbVie’s Drugs and Compound Collection

DeGoey, D. A., Chen, H.-J., Cox, P. B., & Wendt, M. D. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00717 · Cited by 387 · 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

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 International Edition · doi:10.1002/anie.201611281 · Cited by 294 · see citing works

Discovery of QCA570 as an Exceptionally Potent and Efficacious Proteolysis Targeting Chimera (PROTAC) Degrader of the Bromodomain and Extra-Terminal (BET) Proteins Capable of Inducing Complete and Durable Tumor Regression

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

Chemically Induced Degradation of Sirtuin 2 (Sirt2) by a Proteolysis Targeting Chimera (PROTAC) Based on Sirtuin Rearranging Ligands (SirReals)

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

Identification and Characterization of Von Hippel-Lindau-Recruiting Proteolysis Targeting Chimeras (PROTACs) of TANK-Binding Kinase 1

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

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

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

Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders

Hughes, S. J., & Ciulli, A. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170041 · Cited by 240 · see citing works

Targeting Cullin–RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation

Bulatov, E., & Ciulli, A. (2015) · Biochemical Journal · doi:10.1042/bj20141450 · Cited by 237 · see citing works

Proteolysis-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

Impact of Target Warhead and Linkage Vector on Inducing Protein Degradation: Comparison of Bromodomain and Extra-Terminal (BET) Degraders Derived from Triazolodiazepine (JQ1) and Tetrahydroquinoline (I-BET726) BET Inhibitor Scaffolds

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

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

Assessing Different E3 Ligases for Small Molecule Induced Protein Ubiquitination and Degradation

Ottis, P., Toure, M., Cromm, P. M., Ko, E., Gustafson, J. L., & Crews, C. M. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00485 · Cited by 176 · see citing works

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

Huang, S. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.02.005 · Cited by 164 · see citing works

Small‐Molecule Control of Intracellular Protein Levels through Modulation of the Ubiquitin Proteasome System

Buckley, D. L., & Crews, C. M. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201307761 · Cited by 153 · see citing works

Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system

Guharoy, M., Bhowmick, P., Sallam, M., & Tompa, P. (2016) · Nature Communications · doi:10.1038/ncomms10239 · Cited by 145 · see citing works

Chemical approaches to targeted protein degradation through modulation of the ubiquitin–proteasome pathway

Collins, I., Wang, H., Caldwell, J., & Chopra, R. (2017) · Biochemical Journal · doi:10.1042/bcj20160762 · Cited by 135 · see citing works

Integrative computational modeling of protein interactions

Rodrigues, J., & Bonvin, A. M. J. J. (2014) · FEBS Journal · doi:10.1111/febs.12771 · Cited by 106 · see citing works

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

Huang, S. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.03.007 · Cited by 106 · see citing works

Jostling for Position: Optimizing Linker Location in the Design of Estrogen Receptor‐Targeting PROTACs

Cyrus, 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

Inducing protein-protein interactions with molecular glues

Che, Y., Gilbert, A. M., Shanmugasundaram, V., & Noe, M. C. (2018) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2018.04.046 · Cited by 71 · see citing works

Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase

Lucas, X., Molle, I. V., & Ciulli, A. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00842 · Cited by 44 · see citing works

Inducing Protein Degradation as a Therapeutic Strategy

Crews, C. M. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01333 · Cited by 43 · see citing works

Inducing Protein Degradation as a Therapeutic Strategy

Crews, C. M., Georg, G. I., & Wang, S. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b00735 · Cited by 38 · see citing works

Small molecule-mediated protein knockdown as a new approach to drug discovery

Tinworth, C. P., Lithgow, H., & Churcher, I. (2016) · MedChemComm · doi:10.1039/c6md00347h · Cited by 32 · see citing works

The size matters? A computational tool to design bivalent ligands

Pérez‐Benito, L., Henry, A., Matsoukas, M., Lopez, L., Pulido, D., Royo, M., Cordomí, A., Tresadern, G., & Pardo, L. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty422 · Cited by 28 · see citing works

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

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

Chemistries of bifunctional PROTAC degraders

Cao, C., He, M., Wang, L., He, Y., & Rao, Y. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00220e · Cited by 313 · see citing works

PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes

Zaidman, D., Prilusky, J., & London, N. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00589 · Cited by 224 · see citing works

Chasing molecular glue degraders: screening approaches

Domostegui, A., Nieto-Barrado, L., Perez-Lopez, C., & Mayor-Ruiz, C. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00197g · Cited by 200 · see citing works

Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation <i>via</i> New <i>In Silico</i> Methodologies

Drummond, M. L., Henry, A., Li, H., & Williams, C. I. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00897 · Cited by 166 · 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

Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders

Hanzl, A., Casement, R., Imrichova, H., Hughes, S. J., Barone, E., Testa, A., Bauer, S., Wright, J., Brand, M., Ciulli, A., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-022-01177-2 · Cited by 133 · see citing works

Integrative Modeling of PROTAC-Mediated Ternary Complexes

Weng, G., Li, D., Kang, Y., & Hou, T. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01576 · Cited by 130 · 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

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

Bai, N., Riching, K. M., Makaju, A., Wu, H., Acker, T. M., Ou, S.-C., Zhang, Y., Shen, X., Bulloch, D. N., Rui, H., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101653 · Cited by 77 · see citing works

Importance of Three-Body Problems and Protein–Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations

Li, W., Zhang, J., Guo, L., & Wang, Q. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01150 · Cited by 63 · see citing works

Structural Characterization of Degrader-Induced Ternary Complexes Using Hydrogen–Deuterium Exchange Mass Spectrometry and Computational Modeling: Implications for Structure-Based Design

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

Μέθοδοι βιοπληροφορικής, υπολογιστικής συστημικής βιολογίας και μηχανικής μάθησης, εφαρμοσμένες στην in silico ογκολογία

Ουζούνογλου, Ε. (2018) · doi:10.12681/eadd/43531

МУЛЬТИПЛИКАТИВНАЯ ФУНКЦИЯ ПРИНАДЛЕЖНОСТИ КАК МЕТРИКА ОЦЕНКИ IN SILICO КАРДИОТОКСИЧНОСТИ ХИМИЧЕСКИХ СОЕДИНЕНИЙ

Королева, А. Р., & Vasil’ev, P. M. (2020) · Сбор. мат. межд. науч.-практ. конф., посвященной 30-летнему юбилею Мед. института «Современная медицина новые подходы и актуальные исследования» · doi:10.36684/33-2020-1-443-448

IN SILICO ДОСЛІДЖЕННЯ МОЖЛИВИХ ШЛЯХІВ МЕТАБОЛІЗМУ АТРИСТАМІНУ В ОРГАНІЗМІ ЛЮДИНИ

Podolsky, I. M., & Shtrygol, S. Y. (2019) · Medical and Clinical Chemistry · doi:10.11603/mcch.2410-681x.2019.v.i3.10558

Large-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae

Förster, J., Famili, I., Palsson, B. Ø., & Nielsen, J. (2003) · OMICS A Journal of Integrative Biology · doi:10.1089/153623103322246584 · Cited by 140 · see citing works

Exploitation of in silico potential in prediction, validation and elucidation of mechanism of anti-angiogenesis by novel compounds: comparative correlation between wet lab and in silico data

Arif, J. M., Siddiqui, M. H., Akhtar, S., et al. (2013) · International Journal of Bioinformatics Research and Applications · doi:10.1504/ijbra.2013.054697 · Cited by 9 · see citing works