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PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.

Daniel Zaidman1, Jaime Prilusky2, Nir London1

  • 1Department of Organic Chemistry, The Weizmann Institute of Science, 76100, Rehovot, Israel.

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|September 25, 2020
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Summary
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We developed PRosettaC, a computational tool to model ternary complexes crucial for proteolysis-targeting chimera (PROTAC) drug design. This method accurately predicts complex structures, aiding the development of new targeted protein degradation therapies.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality that harness the ubiquitin-proteasome system for targeted protein degradation.
  • Successful PROTAC function relies on the formation of a ternary complex comprising the target protein, E3 ligase, and PROTAC molecule.
  • Limited availability of experimental structures for these ternary complexes hinders rational PROTAC design.

Purpose of the Study:

  • To develop a computational protocol for modeling PROTAC-induced ternary complexes.
  • To provide a tool that aids in the rational design and optimization of PROTACs.

Main Methods:

  • Developed a computational protocol, PRosettaC, that alternates sampling between protein-protein interactions and PROTAC conformational space.
  • Applied the PRosettaC protocol to a benchmark set of known PROTAC ternary complexes.
  • Validated the protocol by modeling a CRBN/BTK complex, comparing results with experimental data.

Main Results:

  • PRosettaC achieved near-native predictions for ternary complex structures, often with atomic accuracy for protein and PROTAC components.
  • The protocol successfully modeled a CRBN/BTK complex, aligning with experimental observations for various PROTACs.
  • Generated models can guide the design of novel PROTACs and improve existing ones.

Conclusions:

  • The PRosettaC protocol offers a reliable method for modeling PROTAC-induced ternary complexes.
  • This tool can accelerate the development of targeted protein degradation therapies by reducing design and synthesis efforts.
  • PRosettaC is accessible via a web server for broader scientific community use.