Paper of the Month

Interesting publications on protein-protein interactions

  1. Ekanayake, A. I., Sobze, L., Kelich, P., Youk, J. Bennett, N.J. et al. (2021) Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. J. Am. Chem. Soc. 143, 5497-5507, https://doi.org/10.1021/jacs.1c01186
  2. Chang, D., Feng, S., Girik, V., Riezman, H. & Winssinger, N. (2021) Luciferase Controlled Protein Interactions J. Am. Chem. Soc. 143, 10, 3665–3670, https://doi.org/10.1021/jacs.0c11016
  3. de Vries, R. M. J. M., Meijer, F. A., Doveston, R. G., Leijten-van de Gevel, I. A. & Brunsveld, L. (2021) Cooperativity between the orthosteric and allosteric ligand binding sites of RORγt Proc. Natl. Acad. Sci. U. S. A. 118, doi:10.1073/pnas.2021287118
  4. Bartling, C. R. O., Jensen, T.M.T., Henry, S.M., Colliander, A.L., Sereikaite, V. et al. (2021) Targeting the APP-Mint2 Protein–Protein Interaction with a Peptide-Based Inhibitor Reduces Amyloid-β Formation. JACS. https://doi.org/10.1021/jacs.0c10696
  5. Słabicki, M., Yoon, H., Koeppel, J., Nitsch, L., Roy Burman, S.S. et al. (2020) Small-molecule-induced polymerization triggers degradation of BCL6. Nature 588164–168 https://doi.org/10.1038/s41586-020-2925-1
  6. Henley, M. J., Linhares, B.M., Morgan, B.S., Cierpicki, T., Fierke, C.A. & Mapp, A.K. (2020) Unexpected specificity within dynamic transcriptional protein–protein complexes. Proc. Natl. Acad. Sci. 117, 27346-27353, doi:10.1073/pnas.2013244117
  7. Wolter, M., Valenti, D., Cossar, P.J., Levy, L.M., Hristeva, S., et al. (2020) Fragment‐Based Stabilizers of Protein-Protein Interactions through Imine‐Based Tethering. Angew. Chem. Int. Ed., doi:10.1002/anie.202008585
  8. Curran P.R., Radoux C.J., Smilova M.D., Sykes R.A., Higueruelo A.P., et al. (2020) Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design. J. Chem. Inf. Model., 60, 4, 1911–1916 https://pubs.acs.org/doi/10.1021/acs.jcim.9b00996
  9. Bosc N., Muller C., Hoffer L., Lagorce D., Bourg S., et al. (2020) Fr-PPIChem: An Academic Compound Library Dedicated to Protein–Protein Interactions. ACS Chem. Biol., https://doi.org/10.1021/acschembio.0c00179
  10. Sadek J., Wuo M.G., Rooklin D., Hauenstein A., Hong S.H. et al. (2020) Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat. Commun., 11, 1786 https://doi.org/10.1038/s41467-020-15576-3
  11. Guéret S.M., Thavam S., Carbajo R.J., Potowski M., Larsson N., et al. (2020) Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. J. Am. Chem. Soc., 142, 4904-4915 https://pubs.acs.org/doi/pdf/10.1021/jacs.0c00269
  12. Testa A., Hughes S. J., Wright J. E., Ciulli A. (2020) Structure-Based Design of a Macrocyclic PROTAC. Angew. Chem. Int. Ed., 59, 1727-1734 https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201914396
  13. O’Connell J., Porter J., Kroeplien B., Norman T., Rapecki S., et al. (2019) Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer. Nature Commun., 10, 5795 https://doi.org/10.1038/s41467-019-13616-1
  14. Jeganathan S., Wendt M., Kiehstaller S., Brancaccio D., Kuepper A., et al. (2019) Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Angew. Chem. Int. Ed. 58, 17351-17358 https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201907901
  15. Rimbault C., Maruthi K., Breillat C., Genuer C., Crespillo S., et al. (2019) Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules. Nature Commun, 10, 4521  https://www.nature.com/articles/s41467-019-12528-4
  16. Achala N. D., Hewage P., Yao H., Nammalwar B., Gnanasekaran K.K., et al. (2019) Small Molecule Inhibitors of the BfrB–Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J. Am. Chem. Soc. 141: https://pubs.acs.org/doi/10.1021/jacs.9b00394
  17. Miles J.A., Hobor F., Taylor J., Tiede C., Rowell P.R., Trinh C. H., Jackson, B., Nadat F., Kyle H.F., Wicky B.I.M., Clarke J., Tomlinson D. C., Wilson A.J., Edwards T.A. et al. (2019) Selective Affirmers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs. BioRxiv 651364; doi: 10.1101/651364 https://www.biorxiv.org/content/10.1101/651364v1
  18. Wu Q., Heidenreich, D., Zhou, S., Ackloo, S., Krämer, A., Nakka, K., et al. (2019) A chemical toolbox for the study of bromodomains and epigenetic signaling. Nature Commun. 10: 1915  https://doi.org/10.1038/s41467-019-09672-2
  19. Cao Q., Shin W.S., Chan H., Vuong C.K., Dubois B., et al. (2018) Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat. Chem. 10, 1213-1221 https://doi.org/10.1038/s41557-018-0147-z
  20. Rogers J.M., Passioura T. & Suga H. (2018) Nonproteinogenic deep mutational scanning of linear and cyclic peptides. Proc. Natl. Acad. Sci. U. S. A. 115: 10959-10964 http://www.pnas.org/content/pnas/115/43/10959
  21. McArthur K., Whitehead L.W., Heddleston J.M., Li L., Padman B.S., at al. (2018) BAK/BAX macropores facilitate mitochondrial herniation and mtDNA efflux during apoptosis. Science, 359 (6378): eaao6047 http://science.sciencemag.org/content/359/6378/eaao6047.full
  22. Ramaswamy K., Forbes L., Minuesa G., Gindin, T.; Brown, F., et al. (2018) Peptidomimetic blockade of MYB in acute myeloid leukemia. Nature Commun, 9 (1): 11 https://doi.org/10.1038/s41467-017-02618-6
  23. Hosseinzadeh P., Bhardwaj, G., Mulligan, V.K., Shortridge, M. D., Craven, T. W., et al. (2017) Comprehensive computational design of ordered peptide macrocycles. Science, 358 (6369): 1461-1466. http://science.sciencemag.org/content/358/6369/1461
  24. Gerken P. A., Wolstenhulme J. R., Tumber A., Hatch S. B., Zhang Y. et al. (2017) Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew. Chem. Int. Ed., 56: 15555-15559. http://dx.doi.org/10.1002/anie.201706788
  25. Kategaya L., Di Lello P., Rougé L., Pastor R., Clark K.R., Drummond J., et al. (2017) USP7 small-molecule inhibitors interfere with ubiquitin binding. Nature, 550: 534. https://www.nature.com/articles/nature24006
  26. Lasko L.M., Jakob C.G., Edalji R.P., Qiu W., Montgomery D., Digiammarino E.L., et al. (2017) Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. Nature, 550(7674): 128-132.
  27. Bosc N., Kuenemann M.A., Becot J., Vavrusa M., Cerdan A.H., Sperandio O., (2017), Privileged substructures to modulat protein-protein interactions. J. Chem. Inf. Model. 10.1021/acs.jcim.7b00435
  28. Jiang H., Deng R., Yang X., Shang J., Lu S., Zhao Y., Song K., Liu X., Zhang Q., Chen Y., Chinn E., Wu G., Li J., Chen G., Yu J., & Zhang J. (2017) Peptidomimetic inhibitors of APC-Asef interactin block colorectal cancer migration. Nat. Chem. Biol. 13, 994-1001
  29. Grison C.M., Burslem G.M., Miles J.A., Pilsl L.K.A., Yeo D.J., Imani Z., Warriner S.L., Webb M.E. & Wilson A.J. (2017) Double quick, double click reversible peptide “stapling”. Chem. Sci., 8 (7): p. 5166-5171.
  30. McCoull, W., Abrams, RD., Anderson, E., Blades, K., Barton, P. et al. (2017) Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. Journal of Medicinal Chemistry 60 (10), 4386-4402
  31. Niu, X., Brahmbhatt, H., Mergenthaler, P., Zhang, Z., Sang, J., et al. (2017) A Small-Molecule Inhibitor of Bax and Bak Oligomerization Prevents Genotoxic Cell Death and Promotes Neuroprotection. Cell Chemical Biology 24, 493-506.e5
  32. Berlow, R. B., Dyson, H. J. & Wright, P. E. (2017) Hypersensitive termination of the hypoxic response by a disordered protein switch. Nature 543, 447-451
  33. Kumar, S. & Hamilton, A.D. (2017) Alpha-Helix Mimetics as Modulators of Alpha-Beta Self-Assembly. J. Am. Chem. Soc. 139 (16), 5744-5755
  34. Johannes, J. W., Bates, S., et al. (2017) Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors. ACS Med. Chem. Lett. 8, 239-244.
  35. Sarnowski, M. P., Kang, C. W., Elbatrawi, Y. M., Wojtas, L. & Del Valle, J. R. (2017) Peptide N-Amination Supports beta-Sheet Conformations. Angew. Chem. Int. Ed. 56, 2083-2086.
  36. Spencer-Smith et al. (2017). Inhibition of RAS function through targeting an allosteric regulatory site. Nature Chemical Biology 13, 62-68 .
  37. Kotchy et al. (2016). The Mcl-1 inhibitor S63845 is tolerable and effective in diverse cancer models. Nature 538, 477-482.
  38. Akcay, G., Belmonte, M.A., Aquila, B., Chuaqui, C. et al. (2016). ” Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain. ” Nat Chem Biol 12, 931-936.
  39. Sable, R., Durek, T., et al. (2016) Constrained Cyclic Peptides as Immunomodulatory Inhibitors of the CD2:CD58 Protein–Protein Interaction. ACS Chem. Biol. 11, 2366-2374
  40. Kim, W., Bird, G.H., et al. (2013). Targeted disruption of the EZH2–EED complex inhibits EZH2-dependent cancer. Nat Chem Biol 9 (10), 643-650.
  41. Patrone, J.D., Kennedy J.P., et al. (2013). Discovery of Protein–Protein Interaction Inhibitors of Replication Protein A. ACS Medicinal Chemistry Letters 4(7), 601-605.
  42. Lessene, G., Czabotar P.E., et al. (2013). Structure-guided design of a selective BCL-XL inhibitor. Nat Chem Biol 9 (6), 390-397.
  43. Karatas, H., E. C. Townsend, et al. (2012). High-Affinity, Small-Molecule Peptidomimetic Inhibitors of MLL1/WDR5 Protein–Protein Interaction. Journal of the American Chemical Society 135(2), 669-682.
  44. Ko, E., Raghuraman A., et al. (2012). Exploring Key Orientations at Protein–Protein Interfaces with Small Molecule Probes. Journal of the American Chemical Society 135(1), 167-173.
  45. Guo, Y. & Partch, C.L. et al. (2012). Regulating the ARNT/TACC3 Axis: Multiple Approaches to Manipulating Protein/Protein Interactions with Small Molecules. ACS Chemical Biology 8(3), 626-635.
  46. Thiel P., Kaiser M. & Ottmann C. (2012) Small-molecule stabilization of protein-protein interactions: an underestimated concept in drug discovery? Angew Chem 51 (9), 2012-8. doi: 10.1002/anie.201107616.
  47. Buckley, L.D., Van Molle, I., Gareiss, P.C., Tae, H.S., Michel J., et al. (2012) Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1? Interaction J. Am. Chem. Soc., DOI: 10.1021/ja209924v
  48. Surade S. & Blundell T.L. (2012) Structural Biology and Drug Discovery of Difficult Targets: The Limits of Ligandability. Chemistry & Biology 19 (1) Pages 42–50
  49. Wanner J., Fry D.C., Peng Z. & Roberts J. (2011) Druggability assessment of protein-protein interfaces. Future Med Chem. 16, 2021-38.
  50. Bullock B.N., Jochim A.L. & Arora P.S. (2011) Assessing Helical Protein Interfaces for Inhibitor Design. J. Am. Chem. Soc. DOI: 10.1021/ja206074j
  51. Morelli X., Bourgeas R. & Roche P. (2011) Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr. Opin. Chem. Biol. 15, 475-481
  52. Phillips C., Roberts L.R., et al. (2011) Design and Structure of Stapled Peptides Binding to Estrogen Receptors. Journal of the American Chemical Society 133:9696-9699
  53. Patgiri A., Yadav K.K., Arora P.S. & Bar-Sagi D. (2011) An orthosteric inhibitor of the Ras-Sos interaction. Nat. Chem. Biol. 7, 585-587
  54. Wells J.A. & McClendon C.L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450, 1001-1009
  55. Vassilev L.T., Vu B.T., Graves B., et al. (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303, 844-848