Structural basis of PROTAC cooperative recognition for selective protein degradation

Morgan Gadd, Andrea Testa, Xavier Lucas, Kwok Ho Chan, Wenzhang Chen, Douglas Lamont, Michael Zengerle, Alessio Ciulli (Lead / Corresponding author)

Research output: Contribution to journalArticle

133 Citations (Scopus)
294 Downloads (Pure)

Abstract

Inducing macromolecular interactions with small molecules to activate cellular signaling is a challenging goal. PROTACs (proteolysis-targeting chimaeras) are bifunctional molecules that recruit a target protein in proximity to an E3 ubiquitin ligase to trigger protein degradation. Structural elucidation of the key ternary species ligase:PROTAC:target and how this impacts target degradation selectivity remains elusive. We solved the crystal structure of Brd4-degrader MZ1 in complex with human VHL and the Brd4 bromodomain (Brd4BD2). The ligand folds into itself to allow formation of specific intermolecular interactions in the ternary complex. Isothermal titration calorimetry studies, supported by surface mutagenesis and proximity assays, are consistent with pronounced cooperative formation of ternary complexes with Brd4BD2. Structure-based designed compound AT1 exhibits highly selective depletion of Brd4 in cells. Our results elucidate how PROTAC-induced de novo contacts dictate preferential recruitment of a target protein into stable and cooperative complex with an E3 ligase for selective degradation.
Original languageEnglish
Pages (from-to)514-521
Number of pages11
JournalNature Chemical Biology
Volume13
Issue number5
Early online date13 Mar 2017
DOIs
Publication statusPublished - May 2017

Fingerprint

Proteolysis
Ubiquitin-Protein Ligases
Calorimetry
Ligases
Mutagenesis
Proteins
Ligands

Keywords

  • Biophysics
  • Pharmacology
  • Small molecules
  • X-ray crystallography

Cite this

Gadd, Morgan ; Testa, Andrea ; Lucas, Xavier ; Chan, Kwok Ho ; Chen, Wenzhang ; Lamont, Douglas ; Zengerle, Michael ; Ciulli, Alessio. / Structural basis of PROTAC cooperative recognition for selective protein degradation. In: Nature Chemical Biology. 2017 ; Vol. 13, No. 5. pp. 514-521.
@article{8ac28f6520cc469f8ba84dcca434cd0f,
title = "Structural basis of PROTAC cooperative recognition for selective protein degradation",
abstract = "Inducing macromolecular interactions with small molecules to activate cellular signaling is a challenging goal. PROTACs (proteolysis-targeting chimaeras) are bifunctional molecules that recruit a target protein in proximity to an E3 ubiquitin ligase to trigger protein degradation. Structural elucidation of the key ternary species ligase:PROTAC:target and how this impacts target degradation selectivity remains elusive. We solved the crystal structure of Brd4-degrader MZ1 in complex with human VHL and the Brd4 bromodomain (Brd4BD2). The ligand folds into itself to allow formation of specific intermolecular interactions in the ternary complex. Isothermal titration calorimetry studies, supported by surface mutagenesis and proximity assays, are consistent with pronounced cooperative formation of ternary complexes with Brd4BD2. Structure-based designed compound AT1 exhibits highly selective depletion of Brd4 in cells. Our results elucidate how PROTAC-induced de novo contacts dictate preferential recruitment of a target protein into stable and cooperative complex with an E3 ligase for selective degradation.",
keywords = "Biophysics , Pharmacology , Small molecules , X-ray crystallography",
author = "Morgan Gadd and Andrea Testa and Xavier Lucas and Chan, {Kwok Ho} and Wenzhang Chen and Douglas Lamont and Michael Zengerle and Alessio Ciulli",
note = "This work was supported by the European Research Council (ERC-2012-StG-311460 DrugE3CRLs Starting Grant to A.C.); the UK Biotechnology and Biological Sciences Research Council (BBSRC grant BB/J001201/2 to A.C.); the European Commission (H2020-MSCA-IF-2014-655516 Marie Skłodowska-Curie Actions Individual Fellowship to K H.C.,and H2020-MSCA-IF-2015-806323 Marie Skłodowska-Curie Actions Individual Fellowship to X.L.); and the Wellcome Trust (Strategic Awards 100476/Z/12/Z for biophysics and drug discovery and 094090/Z/10/Z for structural biology and X-ray crystallography to the Division of Biological Chemistry and Drug Discovery). We are thankful to P. Fyfe for support with the in-house X-ray facility; L. Finn for support with tissue culture facility (MRC-PPU); the Ferguson lab for access to LI-COR equipment; T. Cardote for the gift of full-length Cul2- Rbx1 and A. Knebel (MRC-PPU/DSTT) for the gift of E1 and E2 enzymes; the Division of Computational Biology for support with computational cluster; and to Diamond Light Source for beamtime (BAG proposal MX10071) and beamline support at beamline I04-1.",
year = "2017",
month = "5",
doi = "10.1038/nchembio.2329",
language = "English",
volume = "13",
pages = "514--521",
journal = "Nature Chemical Biology",
issn = "1552-4450",
publisher = "Nature Publishing Group",
number = "5",

}

Structural basis of PROTAC cooperative recognition for selective protein degradation. / Gadd, Morgan; Testa, Andrea; Lucas, Xavier; Chan, Kwok Ho; Chen, Wenzhang; Lamont, Douglas; Zengerle, Michael; Ciulli, Alessio (Lead / Corresponding author).

In: Nature Chemical Biology, Vol. 13, No. 5, 05.2017, p. 514-521.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Structural basis of PROTAC cooperative recognition for selective protein degradation

AU - Gadd, Morgan

AU - Testa, Andrea

AU - Lucas, Xavier

AU - Chan, Kwok Ho

AU - Chen, Wenzhang

AU - Lamont, Douglas

AU - Zengerle, Michael

AU - Ciulli, Alessio

N1 - This work was supported by the European Research Council (ERC-2012-StG-311460 DrugE3CRLs Starting Grant to A.C.); the UK Biotechnology and Biological Sciences Research Council (BBSRC grant BB/J001201/2 to A.C.); the European Commission (H2020-MSCA-IF-2014-655516 Marie Skłodowska-Curie Actions Individual Fellowship to K H.C.,and H2020-MSCA-IF-2015-806323 Marie Skłodowska-Curie Actions Individual Fellowship to X.L.); and the Wellcome Trust (Strategic Awards 100476/Z/12/Z for biophysics and drug discovery and 094090/Z/10/Z for structural biology and X-ray crystallography to the Division of Biological Chemistry and Drug Discovery). We are thankful to P. Fyfe for support with the in-house X-ray facility; L. Finn for support with tissue culture facility (MRC-PPU); the Ferguson lab for access to LI-COR equipment; T. Cardote for the gift of full-length Cul2- Rbx1 and A. Knebel (MRC-PPU/DSTT) for the gift of E1 and E2 enzymes; the Division of Computational Biology for support with computational cluster; and to Diamond Light Source for beamtime (BAG proposal MX10071) and beamline support at beamline I04-1.

PY - 2017/5

Y1 - 2017/5

N2 - Inducing macromolecular interactions with small molecules to activate cellular signaling is a challenging goal. PROTACs (proteolysis-targeting chimaeras) are bifunctional molecules that recruit a target protein in proximity to an E3 ubiquitin ligase to trigger protein degradation. Structural elucidation of the key ternary species ligase:PROTAC:target and how this impacts target degradation selectivity remains elusive. We solved the crystal structure of Brd4-degrader MZ1 in complex with human VHL and the Brd4 bromodomain (Brd4BD2). The ligand folds into itself to allow formation of specific intermolecular interactions in the ternary complex. Isothermal titration calorimetry studies, supported by surface mutagenesis and proximity assays, are consistent with pronounced cooperative formation of ternary complexes with Brd4BD2. Structure-based designed compound AT1 exhibits highly selective depletion of Brd4 in cells. Our results elucidate how PROTAC-induced de novo contacts dictate preferential recruitment of a target protein into stable and cooperative complex with an E3 ligase for selective degradation.

AB - Inducing macromolecular interactions with small molecules to activate cellular signaling is a challenging goal. PROTACs (proteolysis-targeting chimaeras) are bifunctional molecules that recruit a target protein in proximity to an E3 ubiquitin ligase to trigger protein degradation. Structural elucidation of the key ternary species ligase:PROTAC:target and how this impacts target degradation selectivity remains elusive. We solved the crystal structure of Brd4-degrader MZ1 in complex with human VHL and the Brd4 bromodomain (Brd4BD2). The ligand folds into itself to allow formation of specific intermolecular interactions in the ternary complex. Isothermal titration calorimetry studies, supported by surface mutagenesis and proximity assays, are consistent with pronounced cooperative formation of ternary complexes with Brd4BD2. Structure-based designed compound AT1 exhibits highly selective depletion of Brd4 in cells. Our results elucidate how PROTAC-induced de novo contacts dictate preferential recruitment of a target protein into stable and cooperative complex with an E3 ligase for selective degradation.

KW - Biophysics

KW - Pharmacology

KW - Small molecules

KW - X-ray crystallography

U2 - 10.1038/nchembio.2329

DO - 10.1038/nchembio.2329

M3 - Article

C2 - 28288108

VL - 13

SP - 514

EP - 521

JO - Nature Chemical Biology

JF - Nature Chemical Biology

SN - 1552-4450

IS - 5

ER -