High throughput screening methods : evolution and refinement / edited by Joshua A. Bittker, Nathan T. Ross.

Format:

Book

Author/Creator:

Joshua A Bittker

Contributor:

Bittker, Joshua A., editor.

Ross, Nathan T., editor.

Royal Society of Chemistry (Great Britain), issuing body.

Series:

Chemical Biology Series

Chemical Biology Series, 2055-1975 ; 1

Language:

English

Subjects (All):

High throughput screening (Drug development).

Physical Description:

1 online resource (417 pages) : illustrations (some color), tables.

Edition:

1st ed.

Place of Publication:

Cambridge, England : Royal Society of Chemistry, 2017.

Summary:

This book serves as a practical reference for the current state of the art in high throughput screening, which remains a key part of early stage drug and tool compound discovery.

Contents:

Cover

Contents

Foreword: Transforming Medicine by Innovating the Science of Therapeutics

Preface

Chapter 1 HTS Methods: Assay Design and Optimisation

1.1 Introduction

1.2 HTS at AstraZeneca

1.2.1 Criteria and Acceptance

1.2.2 Robustness/Reliability

1.2.3 Analysing Data to Define Robustness/Reliability

1.2.4 As Simple to Run as Possible

1.2.5 Assay Validation

1.3 Summary

References

Chapter 2 Considerations Related to Small-molecule Screening Collections

2.1 Introduction

2.2 General Considerations Related to HTS Compound Collections

2.2.1 Determination of Screening Objectives

2.2.2 Size of HTS Compound Collections

2.2.3 Chemical Diversity in Compound Collections

2.2.4 Quality of Compounds in Screening Collections

2.3 Sources of Compounds in Screening Collections

2.3.1 Natural Products in Screening Collections

2.3.2 Synthetic Drug-like Compounds

2.3.3 Diverse Collections

2.4 Performance of Compounds in Screening Collections

2.4.1 Background

2.4.2 Performance of Compounds from Different Sources

2.4.3 Performance Diversity of Compound Collections

2.4.4 Pan Assay Interference Compounds

2.4.5 Dark Chemical Matter

2.5 Conclusions and Discussion

Chapter 3 Combination Screening

3.1 Introduction

3.2 Measures of Synergy

3.2.1 Bliss Independence Model of Synergy

3.2.2 Loewe Additivity

3.2.3 Other Measures

3.2.4 Reconciling Measures of Synergy

3.3 Design of Combination Experiments

3.4 Statistical Inference of Combination Effects

3.4.1 The Error Distribution

3.4.2 Bootstrap Intervals

3.4.3 Intervals for Bliss Independence

3.4.4 Intervals for Loewe Additivity Interaction Index

3.5 Null Hypothesis Significance Testing

3.5.1 Significance Testing of Bliss

3.5.2 Significance Test of Loewe Additivity.

3.6 Concluding Remarks

Chapter 4 Modern Biophysical Methods for Screening and Drug Discovery

4.1 Introduction

4.2 Physicochemical Properties and High Concentration Screening

4.2.1 Physicochemical Properties of Chemical Libraries

4.2.2 High Concentration Screening

4.3 Differential Scanning Fluorimetry

4.4 Surface Plasmon Resonance

4.5 Mass Spectrometry Techniques

4.5.1 Affinity Selection MS

4.5.2 Affinity Chromatography Methods

4.5.3 Protein MS

4.6 NMR Spectroscopy

4.6.1 Protein NMR

4.6.2 Ligand Observed NMR

4.7 Calorimetric Methods

4.7.1 Differential Scanning Calorimetry

4.7.2 Isothermal Titration Calorimetry

4.8 X-Ray Crystallography

4.9 Newer Methods on the Horizon

4.10 Summary and Recommendations

Acknowledgments

Chapter 5 Genetic Perturbation Methods, from the 'Awesome Power' of Yeast Genetics to the CRISPR Revolution

5.1 Introduction

5.2 Genetic Methodologies

5.2.1 Random Mutagenesis

5.2.2 Targeted Genome-wide Deletions (Homozygous/Heterozygous)

5.2.3 Random Genome-wide Deletions (Homozygous/Heterozygous)

5.2.4 RNA Interference

5.2.5 CRISPR

5.2.6 Overexpression

5.2.7 Synthetic Biology

5.3 Concluding Remarks

Chapter 6 Understanding Luminescence Based Screens

6.1 Why Luminescence? An Introduction to Bioluminescent and Chemiluminescent Assays

6.1.1 Overview of Common Luminescent Enzymes Employed in Assays

6.1.2 Chemiluminescence in HTS Assays

6.2 Considerations and Applications of Bioluminescent Assays

6.2.1 Prevalence of Luciferase Inhibitors in Compound Libraries

6.2.2 Mechanisms of Luciferase Inhibition

6.2.3 Ligand Based Stabilization of Luciferases: Impact on RGA Results.

6.2.4 Methods to Mitigate Luciferase Inhibitors in RGAs: Counter-Screens and Orthogonal Assay Formats

6.2.5 Luciferases as Post-translational Sensors

6.2.6 Use of Luciferases in Biochemical Applications

6.3 Considerations and Applications of Amplified Luminescent Proximity Homogenous Assays: AlphaScreen and AlphaLISA

6.3.1 Example Protocols and Key Experiments

6.3.2 Interferences with ALPHA Technology

6.4 Conclusion

Chapter 7 High Throughput Screening Compatible Methods for Quantifying Protein Interactions in Living Cells

7.1 Introduction

7.2 Analysis of PPIs in Intact Cells

7.2.1 Two-hybrid Systems

7.2.2 Protein Fragment Complementation Technologies

7.2.3 FRET for Analysis of PPIs

7.3 Measuring Target Engagement in Cells

7.3.1 Target Engagement by Protein Stability Analysis

7.3.2 Real Time, Quantitative Analysis of Target Engagement via FRET

7.4 Outlook

Chapter 8 Approaches to High Content Imaging and Multi-feature Analysis

8.1 Introduction

8.2 Imaging Hardware

8.3 Image Analysis

8.4 Quality Control of Image Acquisition and Well Level Data

8.4.1 Quality Control of Image Acquisition

8.4.2 Quality Control of Well Level Data

8.5 Single Cell Analysis

8.6 Analysis of Multiparametric Data

8.6.1 Feature Selection and Dimensional Reduction

8.6.2 Distance and Similarity

8.7 Machine Learning: Supervised and Unsupervised Methods

8.7.1 Supervised Learning (Classification)

8.7.2 Unsupervised Learning (Clustering)

8.8 Conclusion

Chapter 9 Pharmacological and Genetic Screening of Molecularly Characterized Cell Lines

9.1 Introduction

9.2 Cell Lines

9.2.1 Applications in Cancer

9.2.2 Mistaken Identities

9.2.3 Authentication

9.2.4 Molecular Characterizations.

9.3 In vitro Drug Screening towards Precision Medicine

9.3.1 Drug Sensitivity Studies

9.3.2 Molecular Predictors of Drug Response

9.3.3 Datasets

9.3.4 Drug Perturbation Studies

9.3.5 Genetic Perturbation

9.4 Conclusions and Outlook

Chapter 10 Multidimensional Profile Based Screening: Understanding Biology through Cellular Response Signatures

10.1 Introduction

10.2 Multidimensional Profiling through Multi-feature Measurement in a Single System

10.2.1 LINCS Concept

10.2.2 Gene Expression Profiling: CMap

10.2.3 Proteomics Profiling and Other Measurements

10.2.4 Cell Morphology Profiling: Cell Painting

10.3 Multidimensional Profiling through Single Feature Measurement in Multiple Systems

10.3.1 Expanding on the NCI-60: Building a Comprehensive Cell Viability Profile Matrix

10.3.2 Current Logistical Constraints in Screening: Large Numbers of Cell Lines or Large Numbers of Compounds?

10.3.3 PRISM: Multiplexed Cancer Cell Line HTS

10.4 Analysis Approaches for using Cell Based Profiles to Identify Mechanism of Action

10.4.1 NCI-60 COMPARE

10.4.2 CMap: Computational Aspects

10.5 Comprehensive Cell Line Profiling Requires Comprehensive Reference Annotations

10.5.1 Importance of Compound Annotations

10.5.2 Importance of Cell Line Annotations and Quality Control

10.6 Summary and Needs for the Future

10.6.1 Increasing the Number of Cell Lines for Screening and Call for Common Quality Control

10.6.2 Increasing the Perturbagen Dimension to include Genetic Perturbagens

10.7 Conclusion

Chapter 11 3D Cell Culture and Dish Based Organogenesis: Optimizing In vitro Cellular Physiology

11.1 Introduction

11.2 3D Culture Gels, Scaffolds and Bioprinting

11.2.1 Hydrogels

11.2.2 Scaffolds

11.2.3 3D Bioprinting.

11.3 3D Culture and Drug Discovery

11.4 Organs-on-Chips

11.5 3D Cell Culture Limitations

11.6 Conclusion

Chapter 12 Small-molecule-mediated Targeted Protein Degradation for Drug Discovery

12.1 Introduction

12.2 E3-ligase-targeting Heterobifunctional Degraders

12.2.1 The State of the Art

12.2.2 CRBN-recruiting Heterobifunctional Degraders

12.2.3 VHL-recruiting Heterobifunctional Degraders

12.2.4 The Generality of the Bifunctional Degrader Approach

12.2.5 Towards the Mechanism of Action of Bifunctional Degraders

12.2.6 Towards a Therapeutic

12.2.7 Scope and Limitations

12.3 Alternative Approaches to Small-molecule-mediated Targeted Protein Degradation

12.3.1 Hydrophobic Tag

12.3.2 Chaperone Mediated Autophagy

12.3.3 Molecular Glue Degraders

12.4 Identifying Suitable Targets for Small-molecule-mediated Protein Degradation

12.5 Conclusion and Outlook

Chapter 13 Phenotypic Screens with Model Organisms

13.1 Introduction to Large-scale Screens

13.2 What Animal Models to Choose for a Screen?

13.3 Problems and Questions Addressed with Phenotypic Screens

13.3.1 Genetic Screens

13.3.2 Small Bioactive Molecule Screens

13.3.3 Genome Editing Assisted Targeted Screens

13.3.4 Summary

13.4 The Output of Large Scale Screens

13.4.1 Features of Different Screen Models

13.4.2 Behavioral Readout: Motion Index versus Complex Behavior

13.4.3 Physiological Readout: Electrophysiology and Imaging

13.5 Criteria, Sensitivity, Performance and Visualization of the Screen

13.5.1 Defining a ''Hit": Variance and Dimensionality

13.5.2 Assessing, Visualizing and Ranking Performance

13.5.3 Current Limitations and the Future

Chapter 14 Encoded Compound Libraries to Accelerate Small-molecule Therapeutic Discovery.

14.1 Introduction.

Notes:

Includes bibliographical references at the end of each chapters and index.

Description based on online resource; title from PDF title page (ebrary, viewed December 22, 2016).

Description based on publisher supplied metadata and other sources.

ISBN:

1-78262-677-8

OCLC:

965825566