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Targeted Protein Degradation

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Angela M. Cacace

    1. Platform Biology, Arvinas, Inc., New Haven, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Christopher M. Hickey

    1. Platform Biology, Arvinas, Inc., New Haven, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Miklós Békés

    1. Platform Biology, Arvinas, Inc., New Haven, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible result
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2365)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Methods to Discover and Characterize Ligands for Targets and/or Ligases

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Protein Ligand Interactions Using Surface Plasmon Resonance

      • Nichole O’Connell
      Pages 3-20

    3. High-Throughput Detection of Ligand-Protein Binding Using a SplitLuc Cellular Thermal Shift Assay

      • Tino W. Sanchez, Ashley Owens, Natalia J. Martinez, Eric Wallgren, Anton Simeonov, Mark J. Henderson
      Pages 21-41

    4. Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods with a Focus on FunFOLD3

      • Danielle Allison Brackenridge, Liam James McGuffin
      Pages 43-58

    5. Evaluating Ligands for Ubiquitin Ligases Using Affinity Beads

      • Jennifer Dobrodziej, Hanqing Dong, Kurt Zimmermann, Christopher M. Hickey
      Pages 59-75

  3. Approaches to Study Ligase:Degrader:Target Ternary Complexes

    1. Front Matter

      Pages 77-77
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    2. Mechanistic and Structural Features of PROTAC Ternary Complexes

      • Ryan Casement, Adam Bond, Conner Craigon, Alessio Ciulli
      Pages 79-113

    3. MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding in Drug Development

      • Tanja Bartoschik, Andreas Zoephel, Klaus Rumpel, Alessio Ciulli, Charles Heffern
      Pages 115-133

    4. An In Vitro Pull-down Assay of the E3 Ligase:PROTAC:Substrate Ternary Complex to Identify Effective PROTACs

      • Daniel P. Bondeson, Blake E. Smith, Alexandru D. Buhimschi
      Pages 135-150

    5. Kinetic Detection of E3:PROTAC:Target Ternary Complexes Using NanoBRET Technology in Live Cells

      • Sarah D. Mahan, Kristin M. Riching, Marjeta Urh, Danette L. Daniels
      Pages 151-171

  4. Approaches and Tools to Understand Ubiquitylation and Proteasomal Degradation

    1. Front Matter

      Pages 173-173
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    2. Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy

      • Kamaldeep S. Dhami, XiaoDong Huang
      Pages 175-184

    3. Tandem Ubiquitin Binding Entities (TUBEs) as Tools to Explore Ubiquitin-Proteasome System and PROTAC Drug Discovery

      • Karteek Kadimisetty, Katie J. Sheets, Patrick H. Gross, Myra J. Zerr, Dahmane Ouazia
      Pages 185-202

    4. Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-ε-GG Remnant Antibody Enrichment

      • Alissa J. Nelson, Yiying Zhu, Jian Min Ren, Matthew P. Stokes
      Pages 203-216

    5. Determination of Proteasomal Unfolding Ability

      • Christina M. Hurley, Daniel A. Kraut
      Pages 217-244

  5. Methods for Evaluating Protein Degrader Function

    1. Front Matter

      Pages 245-245
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    2. Methods for Quantitative Assessment of Protein Degradation

      • Radosław P. Nowak, Hong Yue, Emily Y. Park, Eric S. Fischer
      Pages 247-263

    3. A High-Throughput Method to Prioritize PROTAC Intracellular Target Engagement and Cell Permeability Using NanoBRET

      • James D. Vasta, Cesear R. Corona, Matthew B. Robers
      Pages 265-282

    4. Profiling CELMoD-Mediated Degradation of Cereblon Neosubstrates

      • Joel W. Thompson, Thomas Clayton, Gody Khambatta, Leslie A. Bateman, Christopher W. Carroll, Philip P. Chamberlain et al.
      Pages 283-300
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Keywords

About this book

This volume contains a collection of innovative techniques for studying targeted protein degradation. Chapters guide readers through heterobifunctional proteolysis-targeting chimeras (PROTACs) approaches, E3 ligase, E3 ligase-induced ubiquitylation, proteomic approaches, novel degrader molecules, molecular glue, and stabilize binding interaction between a target and E3 ubiquitin ligase. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

 

Authoritative and cutting-edge, Targeted Protein Degradation: Methods and Protocols aims to ensure successful results in this emerging field of drug discovery.

 

Editors and Affiliations

  • Platform Biology, Arvinas, Inc., New Haven, USA

    Angela M. Cacace, Christopher M. Hickey, Miklós Békés

Bibliographic Information

  • Book Title: Targeted Protein Degradation

  • Book Subtitle: Methods and Protocols

  • Editors: Angela M. Cacace, Christopher M. Hickey, Miklós Békés

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1665-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1664-2Published: 26 August 2021

  • Softcover ISBN: 978-1-0716-1667-3Published: 26 August 2021

  • eBook ISBN: 978-1-0716-1665-9Published: 25 August 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 351

  • Number of Illustrations: 17 b/w illustrations, 50 illustrations in colour

  • Topics: Chemistry/Food Science, general, Pharmaceutical Sciences/Technology

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