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Platform Technologies in Drug Discovery and Validation

Copyright

Contents

Contributors

Preface

Chapter One: DNA-Encoded Library Technology: A Brief Guide to Its Evolution and Impact on Drug Discovery

1. Introduction to DELT

1.1. The Basic DELT Concept

1.2. Evolution of DELT

1.3. Different DNA-Encoding and -Directing Formats

2. Reported Hits Found With DELT as Example of the Potential to Deliver Drug-Like Molecules

2.1. Application of DELT to Cellular Selections

3. Evolutionary Directions for DNA-Encoded Platforms

4. Conclusion

References

Chapter Two: The Chemistry of Oligonucleotide Delivery

1. Introduction

2. Mechanisms of Action

2.1. Gene Expression Can Be Decreased by Inhibiting Transcription, Increasing mRNA Degradation, or Inhibiting Translation

2.2. Increased mRNA Translation (miRNA Antagonists, i.e., Antagomirs) and Increased mRNA Transcription (Oligonucleotides ...

2.3. Use of Oligonucleotides to Create New Products of Translation (Splice Blocking, mRNA, and CRISPR)

2.4. Nucleic Acids Can Be Used as Traditional Agonist/Antagonist and Bind Selectively to Receptors (Toll Receptor and Tel ...

3. Requirements of Nucleic Acid Delivery Vehicle

3.1. Have Pharmacological Activity

3.2. Be Nuclease Resistant

3.3. Be Sufficiently Long Circulating

3.4. Be Targeted to a Tissue or Cell Type

3.5. Ability to Access Target

4. Types of Delivery Vectors

4.1. Naked Oligonucleotides

4.1.1. Nucleotides That Replace Phosphodiester Group

4.2. Nucleoside Analogues That Alter the Structure of Ribose

4.3. 1 Position: The Base

4.4. 2 Modifications

4.5. 4 and 5 Modifications

4.6. Bicyclic 2′-4′ Modifications

4.7. Modification Patterns: Gapmer Overall Design

4.8. Conjugated Oligonucleotides

4.8.1. Delivery Vehicles Based Upon Complexation of Nucleic Acid

4.8.2. Strategies for Cytoplasmic Delivery

4.9. Liposomal Delivery Systems

4.9.1. Mechanism of Transfection

4.10. Polymer-Based Delivery Vehicles

4.10.1. Conclusion: Summary and Future of Delivery Vehicles

References

Chapter Three: CRISPR-Cas9 for Drug Discovery in Oncology

1. Introduction

2. Gene Editing Using CRISPR-Cas9

2.1. Mechanism of Gene Editing

2.2. Off-Target Activity of CRISPR-Cas9

2.3. Different CRISPR-Cas9 Systems

3. Use of Gene Editing in Drug Discovery

3.1. Target Identification and Validation

3.2. CRISPR-Cas9 for Assay Development

3.2.1. Protein Tagging and Protein Detection Systems

3.2.2. Reporter Systems

3.2.3. Chromatin Dynamics and Transcription Factors

3.3. Target Deconvolution and Selectivity Profiling

3.4. Synthesis of Synthetic Drugs and Biopharmaceuticals

3.5. Building Disease Models to Assess Drug Efficacy

3.6. Detecting Drug Resistance

3.7. Identifying Patient Selection

3.8. Assessment of Drug Disposition

3.9. Safety Assessment

4. Conclusions

References

Chapter Four: Recent Advances of Microfluidics Technologies in the Field of Medicinal Chemistry

1. Introduction

1.1. Application Areas in the Pharmaceutical Industry

1.2. Key Drivers for Adoption

1.3. Scientific Activity on Microfluidics-Driven Synthetic Chemistry

2. Flow Chemistry in the Path for Continuous Manufacturing

2.1. Solution-Phase Chemistry

2.2. Applying Supported Catalysts in API Synthesis

2.3. Applying Flow Photochemistry in API Synthesis

2.4. Integrated Approaches in API Synthesis

3. Application of Microfluidics Technology to Formulate Leads and Development Candidates With Poor Solubility and Bioavai ...

4. Microfluidics Techniques to Support ADME Studies

4.1. Microfluidics in Biological Media

4.2. Electrosynthetic Methods

5. Integrated Microfluidics-Based Synthesis and Screening

6. Microfluidics Chemistry in Hit-to-Lead and Lead Optimization

6.1. Continuous-Flow Hydrogenation

6.2. Multistep and Library Synthesis Under Flow Condition

7. Other Applications of Microfluidics Technologies to Support Drug Discovery

7.1. Microfluidics in DNA-Encoded Library Technologies

7.2. New Building Block, Reagent, and Natural Product Synthesis

8. Conclusion and Future Directions

References

Chapter Five: High-Throughput Screening

1. Introduction—A Brief History of High-Throughput Screening

1.1. HTS: Process, Timelines, Expectations, and Terminology

1.1.1. Assays

1.1.2. Compound Libraries

1.1.3. Process

2. HTS Platforms and Technologies: Automation, Liquid Handling, Detection

2.1. Automation

2.2. Plate Storage

2.3. Robotic Arms

2.4. Liquid Handling

2.5. Air and Positive Displacement

2.6. Pin Tools

2.7. Acoustic Transfer

2.8. Peristaltic Pumps

2.9. Solenoid Syringe and Solenoid Pressure Bottle Systems

2.10. Piezo-Actuator-Based Liquid Handling

3. Detection Technologies

3.1. Absorbance

3.2. Fluorescence

3.3. Luminescence

3.4. Radiometric

3.5. Plate Readers

3.6. PMT-Based Detectors

3.7. CCD-Based Detectors

3.8. Radiometric Detectors

3.9. Whole Plate Kinetic Imaging

4. Analysis and Quality Control

4.1. Screening Informatics

5. Current and Future Trends

6. Changing Landscape of Screening in Big Pharma

7. Current HTS Strategies

8. Integrated Screening Approaches

8.1. Fragment-Based Lead Discovery

8.2. Affinity-Based Technologies

9. Physiologically Relevant Cells

10. Screening at Academic Institutions and CROs

11. Conclusion and Future Directions

Acknowledgments

References

Further Reading

Chapter Six: Kinase-Centric Computational Drug Development

1. Introduction: Kinases in a Nutshell

1.1. The Structure of Protein Kinases

1.2. FDA-Approved Kinase Inhibitors

1.3. Obstacles in Kinase Research

1.4. Outlook of the Chapter

2. Databases, Resources, and Tools

2.1. Bioactivity and Profiling Resources

2.1.1. Databases

2.1.2. Profiling Datasets in Literature

2.2. Disease-Associated Kinase Resources

2.3. Sequence-Based Kinase Resources

2.4. Structure-Based Kinase Resources

2.4.1. Databases and Collections

2.4.2. Kinase-Specific Visualization Resources

3. Structure- and Ligand-Based Applications for Kinase Drug Design

3.1. Structure-Based Target Assessment

3.1.1. Protein Structure Preprocessing

3.1.2. Binding Site Detection

3.1.3. Structure-Based Druggability

3.1.4. Application: Identifying Novel and Druggable Pockets

3.2. Protein-Ligand Interactions and Binding Site Comparisons

3.2.1. Interaction Fingerprints

3.2.2. Binding Site Comparison

3.2.3. Application: Explaining Bioactivity Profiles

3.3. Computational Approaches to Tackle Obstacles in Kinase Research

3.3.1. The Pocketome of Human Kinases

3.3.2. Detection of Selectivity Pockets

3.3.3. Profiling Data for Activity/Selectivity Prediction

4. Summary and Outlook

References

Chapter Seven: Free Energy Calculation Guided Virtual Screening of Synthetically Feasible Ligand R-Group and Scaffold Mod ...

1. Introduction to Virtual Screening

2. Detailed Statistical Analysis of a Recent R-Group Virtual Screening Campaign

3. Consideration of an Appropriate Null Model for the Evaluation of Affinity Scoring

4. Conclusions and Future Perspective

References

Chapter Eight: Phenotypic Screening

1. Introduction

2. Screening Technologies

3. Screening Endpoints

4. Options of Molecules and Modalities to Screen

5. Recent Example of a High-Throughput Phenotypic Screen

6. Reducing Library Size by Prioritizing Known Phenotypic Responses

7. Utilizing Natural Products/Natural Product-Like Libraries

8. Libraries Based on Biological Measurements of Diversity

9. Targeting Specific Pathways

10. Applying the Principles of Fragment-Based Screening

11. Utilization of Other Modalities

12. Inference Methods for Target Identification

13. Driving SAR Using the Primary Assay in the Absence of a Known Target

14. Conclusions

References

Chapter Nine: Targeted Protein Degradation

1. Introduction to the Ubiquitin Proteasome System (UPS)

1.1. Protein Homeostasis and UPS

1.2. Structures and Mechanisms of E3 Ligases

1.2.1. The HECT E3 Family

1.2.2. The RING E3 Family

1.2.3. The RING-in-Between-RING-RING (RBR) E3 Family

1.3. E3s and Human Diseases

2. Small Molecule-Driven Proteostasis

2.1. Proteasome Inhibitors

2.2. Molecular Glues

2.3. DUBs Inhibitors

2.4. Receptor Degraders

2.5. Hydrophobic Tagging-Mediated Degradation

3. Heterobifunctional Degraders: An Exciting New Therapeutic Modality

3.1. Mechanism of Action

3.2. History and Early Heterobifunctional Degraders

3.3. Recent Advances

4. Empirical vs Rational Design

References

Chapter Ten: Chemical Biology in Drug Discovery

1. Chemical Proteomics for Target Deconvolution and Mechanism of Action Studies

1.1. Affinity-Based Proteomics

1.2. Family Affinity Matrices

1.3. Activity-Based Protein Profiling (ABPP)

1.4. Cellular Photoaffinity Labelling

2. Target Identification by Computational Approaches

2.1. Chemical Similarity Searches

2.2. Data Mining/Machine Learning

2.3. Panel Docking

2.4. Bioactivity Spectra-Based Algorithms

3. Target Engagement

3.1. Cellular Thermal Shift Assay

3.2. Fluorescence Polarization, FRET, and nanoBRET

4. Target Validation

4.1. Target Validation by Protein Degradation Approaches

4.2. Target Validation by Genetic Methods

5. Conclusion and Future Directions in Chemical Biology

References

Chapter Eleven: Fragment-Based Lead Discovery

1. Introduction

2. History and Overview of FBLD

3. The FBLD Process

4. Fragment Libraries

4.1. Fragment Library Design

4.1.1. Commercially Available Fragment Libraries

4.2. Experimental Characterization of Fragment Libraries

4.3. Fragment-Based Screening

4.3.1. Summary of FBS Methods

4.3.1.1. Nuclear Magnetic Resonance

4.3.1.2. Protein-Observed NMR

4.3.1.3. Ligand-Observed NMR

Saturation Transfer Difference

Water-Ligand Observed Through Gradient Spectroscopy

Relaxation-Filtered Experiments (1H and 19F)

Combining Ligand-Observed NMR Experiments

Competition

4.3.1.4. X-Ray Crystallography

4.3.1.5. Surface Plasmon Resonance

4.3.1.6. Thermal Shift Assay

4.3.1.7. Biochemical Assays

4.3.1.8. Mass Spectrometry

4.3.1.9. Microscale Thermophoresis

4.3.1.10. Other Approaches

4.4. Fragment Validation

4.5. Fragment Characterization

5. Fragment Evolution

5.1. Fragment Optimization

5.2. Fragment Linking

5.3. Fragment Growing

5.4. Fragment Merging

5.5. Target-Templated Chemistry

5.5.1. Dynamic Combinatorial Chemistry

5.5.2. Click Chemistry

5.6. Evolving Fragments in the Absence of Structural Information

5.7. Factors to Consider During Fragment Evolution

5.7.1. Conserved (“Structural”) Waters

5.7.2. Binding Mode

5.7.3. Potency, Efficiency, and Metrics Thereof

5.8. Combined Approaches and Integration With Other Hit ID Methods

6. Future Challenges

7. Conclusions

References

Chapter Twelve: Antibody-Drug Conjugates

1. Introduction

2. mAbs Selection for ADC

2.1. General Overview of mAbs

2.1.1. Full-Length Antibodies

2.1.2. Antibody Fragments

2.2. Properties of Antibodies Used in ADCs

3. Drug Attachment and Release

3.1. Conjugation to Lysine

3.2. Conjugation to Cysteine

3.3. Conjugation to Sugars

3.4. Enzyme-Based Conjugation to Amino Acids

3.5. Click Conjugation

3.6. Chemically Labile Linkers

3.6.1. Acid-Labile Linkers (Hydrazones)

3.6.2. Disulfide Linkers

3.7. Enzymatically Cleavable Linkers

3.7.1. Peptide Linkers

3.7.2. β-Glucuronide Linkers

3.8. Noncleavable Linkers

4. Payloads for ADC

4.1. Tubulin Inhibitors

4.1.1. Auristatins

4.1.2. Maytansinoids

4.1.3. Tubulysins

4.1.4. Cryptophycins

4.2. DNA-Damaging Agents

4.2.1. Pyrrolobenzodiazepines

4.2.2. Doxorubicin

4.2.3. Duocarmycins

4.2.4. Calicheamicins

4.3. RNA Inhibitors

5. Analytical Characterization of ADCs

6. Therapeutic Index

6.1. Mechanism of ADC Therapeutic Action

6.2. Mechanisms of ADC Toxicities

6.2.1. On-Target Toxicity

6.2.2. Off-Target Toxicity

6.3. Therapeutic Index of ADCs in Clinical Development

7. Challenges and Perspective

References

Chapter Thirteen: Antibody-Recruiting Small Molecules: Synthetic Constructs as Immunotherapeutics

1. Introduction to the Immune System, Immunotherapy, and Antibody-Recruiting Small Molecules

1.1. Harnessing the Human Immune Response to Treating Diseases

1.2. Introduction and Evolution of ARMs

1.3. Features of ABTs and TBTs

2. Selected Application of ARMs to Cancer and Viral Infections

2.1. In Vivo Application of ARMs in Oncology

2.2. Application of ARMs to Viral Infections

3. Structure-Activity Relationship Studies for Optimizing TBTs

4. New Structural Modalities

4.1. Activity-Based and Metabolic Labeling as a Strategy to Target Bacterial Infections

4.2. New ARM Modalities

4.3. Beyond ARMs: Synthetic Bifunctional Constructs for Redirecting Immune Effector Cells

5. ARMs in the Clinic

6. Conclusions and Outlook: Expanding the Reach of ARMs to Identify New TBTs and ABTs

6.1. Applicability of ARMs

6.2. Identification of Novel Cell Surface Targets and TBT Ligands

6.3. Identification of Suitable ABTs to Maximize Endogenous Antibody Recruiting

References

Chapter Fourteen: A Decade of Deuteration in Medicinal Chemistry

1. Introduction

2. Deuteration as a Strategy to Increase Drug Exposure

3. A Deuterated Drug Gains Regulatory Approval

4. Clinical Compounds

4.1. Deuterated Versions of Previously Known Drugs

4.2. Deuterated Novel Drug Candidates

4.3. Deuterated Endogenous Metabolites

5. Can Deuterium-Containing Drugs Be Manufactured With Acceptable Costs?

6. Chemical Biology Tools

7. Deuterated PET Ligands

8. Conclusions

References

Chapter Fifteen: From Natural Peptides to Market

1. Introduction

2. Characteristics of Peptides in Nature

2.1. Distribution

2.2. Clearance and Half-Life

2.3. Potency and Selectivity

3. From Natural Peptides to Drugs

3.1. Safety

3.2. Clinical Efficacy: Agonists and Antagonists

3.3. Mode of Administration

3.4. Frequency of Administration

3.5. Delivery Device, Dose, and Stability

3.6. Cost of Goods

4. A Brief Look at the Peptides on the Market

5. A Promising Future

6. Scope and Opportunity for Peptide Therapeutics

References

Keyword Index, Volume 50

Cumulative Chapter Titles Keyword Index, Volume 1 - 50

Cumulative NCE Introduction Index, 1983-2017

Cumulative NCE Introduction Index, 1983-2017 (By Indication)

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