Targeted Protein Degradation: Methods and Protocols

ISBN-13: 9781071616673 / Angielski / Miękka / 2021

Cacace, Angela M.

Opis

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. 

Spis treści

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

1.       Protein Ligand Interactions Using Surface Plasmon Resonance

Nichole O’Connell

 

2.       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, and Mark J. Henderson

 

3.       Proteins and their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3

Danielle Allison Brackenridge and Liam James McGuffin

 

4.       Evaluating ligands for ubiquitin ligases using affinity beads

Jennifer Dobrodziej, Hanqing Dong, Kurt Zimmermann, and Christopher M. Hickey

Part II              Approaches to Study Ligase:Degrader:Target Ternary Complexes.

5.       Mechanistic and Structural Features of PROTAC Ternary Complexes

Ryan Casement, Adam Bond, Conner Craigon, and Alessio Ciulli

 

6.       MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding In Drug Development

Tanja Bortoschik, Andreas Zoephel, Klaus Rumpel, Alessio Ciulli, and Charles Heffern

 

7.       An in vitro Pull-down Assay of the E3 ligase:PROTAC:Substrate Ternary Complex to Identify Effective PROTACs

Daniel P. Bondeson, Blake E. Smith, and Alexandru D. Buhimschi

 

8.       Kinetic detection of E3: PROTAC: Target Ternary Complexes using NanoBRET technology in Live Cells

Sarah D. Mahan, Kristin M. Riching, Marjeta Urh, and Danette L. Daniels

Part III             Approaches and Tools to Understand Ubiquitylation and Proteasomal Degradation

9.       Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy

Kamaldeep S. Dhami and XiaoDong Huang

 

10.    Methodological Versatility of Tandem Ubiquitin Binding Entities (TUBEs) for Understanding Poly-ubiquitination and its Various Chains

Katie J. Sheets, Patrick H. Gross, Myra J. Zerr, and Dahmane Ouazia, and Karteek Kadimisetty

 

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

Alissa J. Nelson, Yiying Zhu, Jian Min Ren, and Matthew P. Stokes

 

12.    Determination of Proteasomal Unfolding Ability

by Christina M. Hurley and Daniel A. Kraut

Part IV            Methods for Evaluating Protein Degrader Function

13.    Methods for Quantitative Assessment of Protein Degradation

Radosław P. Nowak, Hong Yue, Emily Y. Park, and Eric S. Fischer

 

14.    A High Throughput method to prioritize PROTAC intracellular target engagement and cell permeability using NanoBRET

by James D. Vasta, Cesear R. Corona, and Matthew B. Robers

 

15.    Profiling CELMoD Mediated Degradation of Cereblon Neosubstrates

by Joel W. Thompson, Thomas Clayton, Gody Khambatta, Leslie A. Bateman, Christopher W. Carroll, Philip P. Chamberlain, and Mary E. Matyskiela

 

16.    Global Proteome Profiling to Assess Changes in Protein Abundance using Isobaric Labeling and Liquid Chromatography Tandem Mass Spectrometry

by Anthony P. Possemato, Kathryn Abell, and Matthew P. Stokes

 

17.    PHOTACs Enable Optical Control of Protein Degradation

by Martin Reynders and Dirk Trauner

 

18.    Protocols for synthesis of SNIPERs and the methods to evaluate the anti-cancer affects

by Yoshinori Tsukumo, Genichiro Tsuji, Hidetomo Yokoo,Norihito Shibata, Nobumichi Ohoka, Yosuke Demizu, and Mikihiko Naito