Paper of the Month

Interesting publications on protein-protein interactions

  1. Hong, S. H., Yoo, D.Y., Conway, L., Richards-Corke, K.C., Parker, C.G. and Arora, P.S. (2021) A Sos proteomimetic as a pan-Ras inhibitor. Proc. Natl. Acad. Sci. U. S. A. 118, e2101027118, doi:10.1073/pnas.2101027118.
  2. 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,
  3. Chang, D., Feng, S., Girik, V., Riezman, H. & Winssinger, N. (2021) Luciferase Controlled Protein Interactions. J. Am. Chem. Soc. 143, 10, 3665–3670,
  4. 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
  5. 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.
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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.,
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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:
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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
  29. 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
  30. 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.
  31. 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
  32. 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
  33. 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
  34. Kumar, S. & Hamilton, A.D. (2017) Alpha-Helix Mimetics as Modulators of Alpha-Beta Self-Assembly. J. Am. Chem. Soc. 139 (16), 5744-5755
  35. 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.
  36. 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.
  37. Spencer-Smith et al. (2017). Inhibition of RAS function through targeting an allosteric regulatory site. Nature Chemical Biology 13, 62-68 .
  38. Kotchy et al. (2016). The Mcl-1 inhibitor S63845 is tolerable and effective in diverse cancer models. Nature 538, 477-482.
  39. 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.
  40. 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
  41. 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.
  42. 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.
  43. Lessene, G., Czabotar P.E., et al. (2013). Structure-guided design of a selective BCL-XL inhibitor. Nat Chem Biol 9 (6), 390-397.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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
  49. 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
  50. Wanner J., Fry D.C., Peng Z. & Roberts J. (2011) Druggability assessment of protein-protein interfaces. Future Med Chem. 16, 2021-38.
  51. 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
  52. 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
  53. 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
  54. 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
  55. Wells J.A. & McClendon C.L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450, 1001-1009
  56. 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