Molecular glues for protein-protein interactions: Progressing toward a new dream.

Markella Konstantinidou, Michelle R Arkin
Author Information
  1. Markella Konstantinidou: Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
  2. Michelle R Arkin: Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: michelle.arkin@ucsf.edu.

Abstract

The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.

Keywords

References

  1. Cell Rep. 2021 Jul 20;36(3):109394 [PMID: 34289372]
  2. Nature. 2020 Sep;585(7824):293-297 [PMID: 32494016]
  3. ACS Med Chem Lett. 2015 Apr 14;6(5):489-90 [PMID: 26005519]
  4. Cell. 2019 Jun 27;178(1):152-159.e11 [PMID: 31178121]
  5. Nat Commun. 2022 Jan 25;13(1):486 [PMID: 35078985]
  6. J Am Chem Soc. 2021 Jun 9;143(22):8454-8464 [PMID: 34047554]
  7. Expert Opin Ther Pat. 2018 Sep;28(9):665-678 [PMID: 30107136]
  8. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):E7285-E7292 [PMID: 30012605]
  9. Cell. 1995 Aug 11;82(3):507-22 [PMID: 7543369]
  10. Nature. 2010 Nov 18;468(7322):400-5 [PMID: 20927106]
  11. J Med Chem. 2019 May 9;62(9):4703-4715 [PMID: 30964291]
  12. Clin Pharmacol Ther. 2013 Apr;93(4):299-301 [PMID: 23511784]
  13. Nature. 2014 Aug 7;512(7512):49-53 [PMID: 25043012]
  14. Birth Defects Res C Embryo Today. 2015 Jun;105(2):140-56 [PMID: 26043938]
  15. Nat Rev Drug Discov. 2022 Mar;21(3):181-200 [PMID: 35042991]
  16. Elife. 2015 Apr 15;4:e07314 [PMID: 25875391]
  17. Nat Commun. 2022 Feb 10;13(1):815 [PMID: 35145136]
  18. Adv Exp Med Biol. 2020;1248:33-59 [PMID: 32185706]
  19. Science. 1996 Jul 12;273(5272):239-42 [PMID: 8662507]
  20. Nat Chem Biol. 2020 Oct;16(10):1105-1110 [PMID: 32690941]
  21. J Mol Biol. 2012 Aug 10;421(2-3):185-203 [PMID: 22244854]
  22. ACS Chem Biol. 2022 Nov 18;17(11):2972-2978 [PMID: 36255265]
  23. Curr Opin Chem Biol. 2022 Apr;67:102107 [PMID: 35033823]
  24. Nat Rev Drug Discov. 2017 Feb;16(2):101-114 [PMID: 27885283]
  25. Nat Rev Drug Discov. 2004 Apr;3(4):301-17 [PMID: 15060526]
  26. Nat Chem Biol. 2021 Feb;17(2):152-160 [PMID: 33199914]
  27. Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12037-42 [PMID: 12218175]
  28. J Med Chem. 2021 Nov 25;64(22):16687-16702 [PMID: 34761679]
  29. Biochem J. 2020 Apr 17;477(7):1219-1225 [PMID: 32271882]
  30. ChemMedChem. 2016 Apr 19;11(8):870-80 [PMID: 26789650]
  31. J Med Chem. 2021 Jun 10;64(11):7390-7403 [PMID: 34056906]
  32. Expert Opin Ther Pat. 2022 May;32(5):575-589 [PMID: 35272536]
  33. Chem Soc Rev. 2022 Jul 4;51(13):5498-5517 [PMID: 35723413]
  34. ACS Chem Biol. 2020 Dec 18;15(12):3143-3148 [PMID: 33196173]
  35. J Med Chem. 2021 Jun 24;64(12):8391-8409 [PMID: 34115499]
  36. Chem Sci. 2019 Jan 25;10(10):2869-2874 [PMID: 30996864]
  37. ACS Chem Biol. 2013 Sep 20;8(9):1869-75 [PMID: 23808890]
  38. Immunity. 2018 Mar 20;48(3):434-452 [PMID: 29562194]
  39. Angew Chem Int Ed Engl. 2023 Sep 11;62(37):e202308004 [PMID: 37455289]
  40. J Biol Chem. 2012 Dec 7;287(50):41914-21 [PMID: 23086940]
  41. Nature. 2019 Nov;575(7783):545-550 [PMID: 31581174]
  42. Nat Chem Biol. 2017 Jun;13(6):675-680 [PMID: 28437394]
  43. Science. 2017 Apr 28;356(6336): [PMID: 28302793]
  44. Science. 2014 Jan 17;343(6168):301-5 [PMID: 24292625]
  45. Expert Opin Ther Pat. 2016 Sep;26(9):973-7 [PMID: 27367741]
  46. Science. 2015 May 29;348(6238):1027-30 [PMID: 25858979]
  47. Drug Discov Today. 2009 Feb;14(3-4):155-61 [PMID: 19041415]
  48. Elife. 2013 May 28;2:e00498 [PMID: 23741617]
  49. Nature. 2001 Nov 15;414(6861):271-6 [PMID: 11713520]
  50. Science. 2022 Nov 4;378(6619):549-553 [PMID: 36378961]
  51. J Med Chem. 2017 Oct 12;60(19):8183-8191 [PMID: 28933844]
  52. Proc Natl Acad Sci U S A. 2013 May 28;110(22):8894-9 [PMID: 23676274]
  53. Nat Commun. 2020 Aug 7;11(1):3954 [PMID: 32770072]
  54. Cell Rep. 2017 Sep 19;20(12):2860-2875 [PMID: 28930682]
  55. Nat Chem Biol. 2020 Jan;16(1):7-14 [PMID: 31686031]
  56. J Med Chem. 2020 Apr 23;63(8):4047-4068 [PMID: 32275432]
  57. Nat Chem Biol. 2018 Jul;14(7):706-714 [PMID: 29892083]
  58. Br J Haematol. 2014 Mar;164(6):811-21 [PMID: 24328678]
  59. Oncotarget. 2016 May 24;7(21):30323-35 [PMID: 27083005]
  60. ACS Cent Sci. 2023 Apr 18;9(5):937-946 [PMID: 37252362]
  61. Cell Chem Biol. 2021 Jul 15;28(7):1032-1047 [PMID: 33930325]
  62. Mol Cell. 2021 Jan 7;81(1):88-103.e6 [PMID: 33220178]
  63. Nature. 2016 Jun 22;535(7611):252-7 [PMID: 27338790]
  64. RSC Chem Biol. 2023 Jan 3;4(3):192-215 [PMID: 36908699]
  65. Blood. 2021 Feb 4;137(5):661-677 [PMID: 33197925]
  66. Nature. 2022 Apr;604(7906):557-562 [PMID: 35388221]
  67. J Med Chem. 2022 Mar 10;65(5):3879-3893 [PMID: 35188766]
  68. Cell. 2021 Jan 7;184(1):3-9 [PMID: 33417864]
  69. Nat Chem Biol. 2020 Nov;16(11):1189-1198 [PMID: 32572277]
  70. J Mol Biol. 2023 Mar 15;435(6):167989 [PMID: 36736888]
  71. Nat Chem Biol. 2024 Jan;20(1):93-102 [PMID: 37679459]
  72. J Biol Chem. 2016 May 13;291(20):10515-27 [PMID: 26984404]
  73. J Am Chem Soc. 2023 Sep 20;145(37):20328-20343 [PMID: 37676236]
  74. Elife. 2018 Aug 01;7: [PMID: 30067223]
  75. J Med Chem. 2020 Mar 26;63(6):3131-3141 [PMID: 32105468]
  76. Semin Cancer Biol. 2006 Jun;16(3):162-72 [PMID: 16678438]
  77. Elife. 2020 Aug 17;9: [PMID: 32804079]
  78. Angew Chem Int Ed Engl. 2020 Nov 23;59(48):21520-21524 [PMID: 32816380]
  79. ACS Med Chem Lett. 2021 Apr 28;12(5):768-773 [PMID: 34055224]
  80. Oncoimmunology. 2020 Oct 14;9(1):1831153 [PMID: 33110706]
  81. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8554-9 [PMID: 11438690]
  82. Nat Chem Biol. 2020 Nov;16(11):1199-1207 [PMID: 32747809]
  83. Nature. 2020 Dec;588(7838):509-514 [PMID: 32927473]
  84. J Med Chem. 2022 Dec 22;65(24):16589-16621 [PMID: 36455032]
  85. Cell Chem Biol. 2021 Apr 15;28(4):559-566.e15 [PMID: 33513350]
  86. Nature. 2015 Jul 9;523(7559):183-188 [PMID: 26131937]
  87. Nat Commun. 2019 Mar 29;10(1):1402 [PMID: 30926793]
  88. J Med Chem. 2022 Jul 14;65(13):8881-8896 [PMID: 35749742]
  89. ACS Cent Sci. 2023 Jul 14;9(7):1269-1284 [PMID: 37521793]
  90. SLAS Discov. 2018 Feb;23(2):183-192 [PMID: 28945980]
  91. Science. 2023 Aug 18;381(6659):794-799 [PMID: 37590355]
  92. Nat Commun. 2020 Sep 14;11(1):4578 [PMID: 32929090]
  93. ACS Chem Biol. 2023 Feb 17;18(2):331-339 [PMID: 36656921]
  94. Nat Struct Mol Biol. 2020 Apr;27(4):319-322 [PMID: 32251415]
  95. Nat Chem Biol. 2017 May;13(5):514-521 [PMID: 28288108]
  96. J Am Chem Soc. 2019 Feb 27;141(8):3524-3531 [PMID: 30707565]
  97. J Med Chem. 2021 Jun 10;64(11):7646-7666 [PMID: 34037385]
  98. Science. 2019 Oct 4;366(6461):109-115 [PMID: 31604311]
  99. Nat Chem Biol. 2020 Jan;16(1):15-23 [PMID: 31819272]
  100. Nature. 2016 Apr 7;532(7597):127-30 [PMID: 26909574]
  101. J Cancer. 2021 Mar 5;12(9):2735-2746 [PMID: 33854633]
  102. Biochem Soc Trans. 2015 Dec;43(6):1234-40 [PMID: 26614666]
  103. Cell Chem Biol. 2023 Apr 20;30(4):394-402.e9 [PMID: 36898369]
  104. J Med Chem. 2020 Jul 9;63(13):6648-6676 [PMID: 32130004]
  105. J Med Chem. 2021 Aug 12;64(15):11614-11636 [PMID: 34313116]
  106. Angew Chem Int Ed Engl. 2010 Jun 1;49(24):4129-32 [PMID: 20437433]
  107. Clin Pharmacol Ther. 2023 Sep;114(3):558-568 [PMID: 37399310]
  108. Chem Biol. 2014 Sep 18;21(9):1102-14 [PMID: 25237857]
  109. Nature. 2007 Apr 5;446(7136):640-5 [PMID: 17410169]
  110. Science. 2018 Mar 30;359(6383): [PMID: 29599213]
  111. RSC Med Chem. 2021 Aug 2;12(9):1555-1564 [PMID: 34667951]
  112. J Med Chem. 2018 Jan 25;61(2):535-542 [PMID: 28425720]
  113. Science. 2014 Jan 17;343(6168):305-9 [PMID: 24292623]
  114. Nat Struct Mol Biol. 2014 Sep;21(9):803-9 [PMID: 25108355]
  115. ACS Chem Biol. 2020 Oct 16;15(10):2722-2730 [PMID: 32865967]
  116. Structure. 2019 Nov 5;27(11):1625-1633.e3 [PMID: 31693911]
  117. Nature. 2024 Mar;627(8002):204-211 [PMID: 38383787]
  118. Science. 2010 Mar 12;327(5971):1345-50 [PMID: 20223979]
  119. Biochemistry. 2014 Jun 3;53(21):3432-45 [PMID: 24811713]
  120. Nat Chem Biol. 2024 Mar;20(3):365-372 [PMID: 37828400]
  121. Mol Cell. 2022 Sep 15;82(18):3438-3452.e8 [PMID: 36055235]
  122. Nat Commun. 2023 Jul 13;14(1):4177 [PMID: 37443112]
  123. Oncotarget. 2017 Aug 7;8(42):72167-72181 [PMID: 29069777]
  124. ACS Chem Biol. 2020 Dec 18;15(12):3149-3158 [PMID: 33206504]
  125. Biochemistry. 2023 Feb 7;62(3):601-623 [PMID: 35856839]
  126. Nature. 2020 Dec;588(7836):164-168 [PMID: 33208943]
  127. Science. 2018 Nov 2;362(6414): [PMID: 30385546]
  128. Elife. 2021 Mar 10;10: [PMID: 33688831]
  129. J Med Chem. 2020 Jul 9;63(13):6694-6707 [PMID: 32501690]

Grants

  1. R01 GM147696/NIGMS NIH HHS

MeSH Term

Protein Binding
Proteins
Humans
Small Molecule Libraries
Drug Discovery

Chemicals

Proteins
Small Molecule Libraries

Word Cloud

Created with Highcharts 10.0.0interactionsmolecularMGsgluesprotein-proteinsmallmoleculesinduceproximitynativeneomorphicPPIstabilizersrecognitionmodulationonerapidlydevelopingareasdrugdiscoveryreviewdiscussadvancespastdecade2014-2023focusing-monovalenteitherstabilizinginducingincludeserendipitousrationaldiscoveriesdescribedifferentapproachesusedidentifyclassifycompoundsthreemaincategories:degradativenon-degradativeself-associationDiverseillustrativeexamplesstructuraldatadescribeddetailemphasizingelementscooperativebindinginterfacefundamentalMGmechanismactionMolecularinteractions:Progressingtowardnewdreamcooperativitycovalentdegradersternarycomplex

Similar Articles

Cited By