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Research Article

A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers

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Received 11 Aug 2023, Accepted 14 Jan 2024, Published online: 29 Jan 2024

References

  • Babina, I. S., & Turner, N. C. (2017). Advances and challenges in targeting FGFR signalling in cancer. Nature Reviews Cancer, 17(5), 318–332. https://doi.org/10.1038/nrc.2017.8
  • Bai, N., Miller, S. A., Andrianov, G. V., Yates, M., Kirubakaran, P., & Karanicolas, J. (2021). Rationalizing PROTAC-mediated ternary complex formation using Rosetta. Journal of Chemical Information and Modeling, 61(3), 1368–1382. https://doi.org/10.1021/acs.jcim.0c01451
  • Békés, M., Langley, D. R., & Crews, C. M. (2022). PROTAC targeted protein degraders: The past is prologue. Nature Reviews Drug Discovery, 21(3), 181–200. https://doi.org/10.1038/s41573-021-00371-6
  • 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). Lessons in PROTAC design from selective degradation with a promiscuous warhead. Cell Chemical Biology, 25(1), 78–87. e5. https://doi.org/10.1016/j.chembiol.2017.09.010
  • 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). Targeting the C481S ibrutinib-resistance mutation in Bruton’s tyrosine kinase using PROTAC-mediated degradation. Biochemistry, 57(26), 3564–3575. https://doi.org/10.1021/acs.biochem.8b00391
  • Buschbeck, M. (2006). Strategies to overcome resistance to targeted protein kinase inhibitors in the treatment of cancer. Drugs in R&D, 7(2), 73–86. https://doi.org/10.2165/00126839-200607020-00002
  • Camidge, D. R., Pao, W., & Sequist, L. V. (2014). Acquired resistance to TKIs in solid tumours: Learning from lung cancer. Nature Reviews Clinical Oncology, 11(8), 473–481. https://doi.org/10.1038/nrclinonc.2014.104
  • Chan, K.-H., Zengerle, M., Testa, A., & Ciulli, A. (2018). 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. Journal of Medicinal Chemistry, 61(2), 504–513. https://doi.org/10.1021/acs.jmedchem.6b01912
  • Che, Y., Gilbert, A. M., Shanmugasundaram, V., & Noe, M. C. (2018). Inducing protein-protein interactions with molecular glues. Bioorganic & Medicinal Chemistry Letters, 28(15), 2585–2592. https://doi.org/10.1016/j.bmcl.2018.04.046
  • Crew, A. P., Raina, K., Dong, H., Qian, Y., Wang, J., Vigil, D., Serebrenik, Y. V., Hamman, B. D., Morgan, A., Ferraro, C., Siu, K., Neklesa, T. K., Winkler, J. D., Coleman, K. G., & Crews, C. M. (2018). Identification and characterization of Von Hippel-Lindau-recruiting proteolysis targeting chimeras (PROTACs) of TANK-binding kinase 1. Journal of Medicinal Chemistry, 61(2), 583–598. https://doi.org/10.1021/acs.jmedchem.7b00635
  • Cromm, P. M., & Crews, C. M. (2017). Targeted protein degradation: From chemical biology to drug discovery. Cell Chemical Biology, 24(9), 1181–1190. https://doi.org/10.1016/j.chembiol.2017.05.024
  • Drummond, M. L., & Williams, C. I. (2019). In silico modeling of PROTAC-mediated ternary complexes: Validation and application. Journal of Chemical Information and Modeling, 59(4), 1634–1644. https://doi.org/10.1021/acs.jcim.8b00872
  • Han, X., & Sun, Y. (2022). Strategies for the discovery of oral PROTAC degraders aimed at cancer therapy. Cell Reports Physical Science, 3(10), 101062. https://doi.org/10.1016/j.xcrp.2022.101062
  • Holohan, C., Van Schaeybroeck, S., Longley, D. B., & Johnston, P. G. (2013). Cancer drug resistance: An evolving paradigm. Nature Reviews. Cancer, 13(10), 714–726. https://doi.org/10.1038/nrc3599
  • Hwang, H., Pierce, B., Mintseris, J., Janin, J., & Weng, Z. (2008). Protein–protein docking benchmark version 3.0. Proteins, 73(3), 705–709. https://doi.org/10.1002/prot.22106
  • Ignatov, M., Jindal, A., Kotelnikov, S., Beglov, D., Posternak, G., Tang, X., Maisonneuve, P., Poda, G., Batey, R. A., Sicheri, F., Whitty, A., Tonge, P. J., Vajda, S., & Kozakov, D. (2023). High Accuracy Prediction of PROTAC Complex Structures. Journal of the American Chemical Society, 145(13), 7123–7135. https://doi.org/10.1021/jacs.2c09387
  • Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006). PIPER: An FFT‐based protein docking program with pairwise potentials. Proteins, 65(2), 392–406. https://doi.org/10.1002/prot.21117
  • Lai, A. C., & Crews, C. M. (2017). Induced protein degradation: An emerging drug discovery paradigm. Nature Reviews Drug Discovery, 16(2), 101–114. https://doi.org/10.1038/nrd.2016.211
  • Lau, K. H., Tan, A. M., & Shi, Y. (2022). New and emerging targeted therapies for advanced breast cancer. International Journal of Molecular Sciences, 23(4), 2288. p. https://doi.org/10.3390/ijms23042288
  • Lensink, M. F., & Wodak, S. J. (2013). Docking, scoring, and affinity prediction in CAPRI. Proteins, 81(12), 2082–2095. https://doi.org/10.1002/prot.24428
  • Marin, J. J. G., Sanchez de Medina, F., Castaño, B., Bujanda, L., Romero, M. R., Martinez-Augustin, O., Moral-Avila, R. D., & Briz, O. (2012). Chemoprevention, chemotherapy, and chemoresistance in colorectal cancer. Drug Metabolism Reviews, 44(2), 148–172. https://doi.org/10.3109/03602532.2011.638303
  • Martin, T. A., & Jiang, W. G. (2010). Anti-Cancer agents in medicinal chemistry (Formerly current medicinal chemistry - Anti-cancer agents). Anti-Cancer Agents in Medicinal Chemistry, 10(1), 1.
  • Oxnard, G. R., Arcila, M. E., Chmielecki, J., Ladanyi, M., Miller, V. A., & Pao, W. (2011). New strategies in overcoming acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer. Clinical Cancer Research, 17(17), 5530–5537. https://doi.org/10.1158/1078-0432.CCR-10-2571
  • Schneekloth, A. R., Pucheault, M., Tae, H. S., & Crews, C. M. (2008). Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics. Bioorganic & Medicinal Chemistry Letters, 18(22), 5904–5908. https://doi.org/10.1016/j.bmcl.2008.07.114
  • Schrödinger Release 2020-3. (2020a). BioLuminate. Schrödinger, LLC.
  • Schrödinger Release 2020-3. (2020b). Protein preparation wizard. Epik Solutions.
  • Snyder, L. B., Flanagan, J. J., Qian, Y., Gough, S. M., Andreoli, M., Bookbinder, M., Cadelina, G., Bradley, J., Rousseau, E., Chandler, J., Willard, R., Pizzano, J., Crews, C. M., Crew, A. P., Houston, J., Moore, M. D., Peck, R., & Taylor, I. (2021). The discovery of ARV-471, an orally bioavailable estrogen receptor degrading PROTAC for the treatment of patients with breast cancer. Cancer Research, 81(13_Suppl), 44–44. https://doi.org/10.1158/1538-7445.AM2021-44
  • Sun, X., & Rao, Y. (2019). PROTACs as potential therapeutic agents for cancer drug resistance. Biochemistry, 59(3), 240–249. https://doi.org/10.1021/acs.biochem.9b00848
  • Troup, R. I., Fallan, C., & Baud, M. G. (2020). Current strategies for the design of PROTAC linkers: A critical review. Exploration of Targeted Anti-Tumor Therapy, 1(5), 273–312. https://doi.org/10.37349/etat.2020.00018
  • Vogel, V. (2011). Selective estrogen receptor modulators and aromatase inhibitors for breast cancer chemoprevention. Current Drug Targets, 12(13), 1874–1887.
  • Vakser, I. A. (2014). Protein-protein docking: From interaction to interactome. Biophysical Journal, 107(8), 1785–1793. https://doi.org/10.1016/j.bpj.2014.08.033
  • Wang, C., Zheng, C., Wang, H., Zhang, L., Liu, Z., & Xu, P. (2022). The state of the art of PROTAC technologies for drug discovery. European Journal of Medicinal Chemistry, 235, 114290. https://doi.org/10.1016/j.ejmech.2022.114290
  • Weerakoon, D., Carbajo, R. J., De Maria, L., Tyrchan, C., & Zhao, H. (2022). Impact of PROTAC linker plasticity on the solution conformations and dissociation of the ternary complex. Journal of Chemical Information and Modeling, 62(2), 340–349. https://doi.org/10.1021/acs.jcim.1c01036

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