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Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.

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Runcie AC, Zengerle M, Chan KH, Testa A, van Beurden L, Baud MGJ, Epemolu O, Ellis LCJ, Read KD, Coulthard V, Brien A, Ciulli A
OpenAccess logo Chem Sci 9 2452-2468 (2018)
Related entries: 5o38, 5o39, 5o3b, 5o3c, 5o3d, 5o3e, 5o3f, 5o3g, 5o3h, 5o3i

Cited: 14 times
EuropePMC logo PMID: 29732121

Abstract

Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins. The four BET (bromodomain & extra-terminal domain) proteins - BRD2, BRD3, BRD4 and BRDT bind acetylated chromatin via their bromodomains and regulate processes such as cell proliferation and inflammation. BET bromodomains are of particular interest, as they are attractive therapeutic targets but existing inhibitors are pan-selective. We previously established a bump-&-hole system for the BET bromodomains, pairing a leucine/alanine mutation with an ethyl-derived analogue of an established benzodiazepine scaffold. Here we optimize upon this system with the introduction of a more conservative and less disruptive leucine/valine mutation. Extensive structure-activity-relationships of diverse benzodiazepine analogues guided the development of potent, mutant-selective inhibitors with desirable physiochemical properties. The active enantiomer of our best compound - 9-ME-1 - shows ∼200 nM potency, >100-fold selectivity for the L/V mutant over wild-type and excellent DMPK properties. Through a variety of in vitro and cellular assays we validate the capabilities of our optimized system, and then utilize it to compare the relative importance of the first and second bromodomains to chromatin binding. These experiments confirm the primacy of the first bromodomain in all BET proteins, but also significant variation in the importance of the second bromodomain. We also show that, despite having a minor role in chromatin recognition, BRD4 BD2 is still essential for gene expression, likely through the recruitment of non-histone proteins. The disclosed inhibitor:mutant pair provides a powerful tool for future cellular and in vivo target validation studies.

Reviews citing this publication (7)

  1. Current strategies for the design of PROTAC linkers: a critical review. Troup RI, Fallan C, Baud MGJ. Explor Target Antitumor Ther 1 273-312 (2020)
  2. Inhibitors of bromodomain and extra-terminal proteins for treating multiple human diseases. Kulikowski E, Rakai BD, Wong NCW. Med Res Rev 41 223-245 (2021)
  3. The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Islam K. Cell Chem Biol 25 1171-1184 (2018)
  4. Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders. Diehl CJ, Ciulli A. Chem Soc Rev 51 8216-8257 (2022)
  5. Improved methods for targeting epigenetic reader domains of acetylated and methylated lysine. Engelberg IA, Foley CA, James LI, Frye SV. Curr Opin Chem Biol 63 132-144 (2021)
  6. Molecular Epigenetics: Chemical Biology Tools Come of Age. Bagert JD, Muir TW. Annu Rev Biochem 90 287-320 (2021)
  7. Recent progress and structural analyses of domain-selective BET inhibitors. Divakaran A, Harki DA, Pomerantz WCK. Med Res Rev 43 972-1018 (2023)

Articles citing this publication (7)

  1. Structure-Based Design of a Macrocyclic PROTAC. Testa A, Hughes SJ, Lucas X, Wright JE, Ciulli A. Angew Chem Int Ed Engl 59 1727-1734 (2020)
  2. Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity. Imaide S, Riching KM, Makukhin N, Vetma V, Whitworth C, Hughes SJ, Trainor N, Mahan SD, Murphy N, Cowan AD, Chan KH, Craigon C, Testa A, Maniaci C, Urh M, Daniels DL, Ciulli A. Nat Chem Biol 17 1157-1167 (2021)
  3. Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain Inhibitor. Divakaran A, Talluri SK, Ayoub AM, Mishra NK, Cui H, Widen JC, Berndt N, Zhu JY, Carlson AS, Topczewski JJ, Schonbrunn EK, Harki DA, Pomerantz WCK. J Med Chem 61 9316-9334 (2018)
  4. Development of BromoTag: A "Bump-and-Hole"-PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins. Bond AG, Craigon C, Chan KH, Testa A, Karapetsas A, Fasimoye R, Macartney T, Blow JJ, Alessi DR, Ciulli A. J Med Chem 64 15477-15502 (2021)
  5. Development of an N-Terminal BRD4 Bromodomain-Targeted Degrader. Divakaran A, Scholtz CR, Zahid H, Lin W, Griffith EC, Lee RE, Chen T, Harki DA, Pomerantz WCK. ACS Med Chem Lett 13 1621-1627 (2022)
  6. Alternative Mechanisms for DNA Engagement by BET Bromodomain-Containing Proteins. Kalra P, Zahid H, Ayoub A, Dou Y, Pomerantz WCK. Biochemistry 61 1260-1272 (2022)
  7. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation. Thomas AM, Serafini M, Grant EK, Coombs EAJ, Bluck JP, Schiedel M, McDonough MA, Reynolds JK, Lee B, Platt M, Sharlandjieva V, Biggin PC, Duarte F, Milne TA, Bush JT, Conway SJ. ACS Chem Biol 18 2405-2417 (2023)


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