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Book Details
Abstract
Biophysical techniques are used in many key stages of the drug discovery process including in screening for new receptor ligands, in characterising drug mechanisms, and in validating data from biochemical and cellular assays.
This book provides an overview of the biophysical methods applied in drug discovery today, including traditional techniques and newer developments. Perspectives from academia and industry across a spectrum of techniques are brought together in a single volume. Small and biotherapeutic approaches are covered and strengths and limitations of each technique are presented. Case studies illustrate the application of each technique in real applied examples. Finally, the book covers recent developments in areas such as electron microscopy with discussions of their possible impact on future drug discovery.
This is a go-to volume for biophysicists, analytical chemists and medicinal chemists providing a broad overview of techniques of contemporary interest in drug discovery.
The techniques highlighted in this volume are introduced with concise theoretical background that prepares the reader for subsequent illustrative examples from the literature. The theoretical and methodological information is rather limited, but the reader is directed to useful references for further reading. This book will be helpful for medicinal, synthetic, and biophysical chemists urveying an array of tools for their specific drug discovery projects, especially to those who do not want to be inundated with theoretical details. Even though most chapters in this book are written in a manner suitable for an audience with intermediate to advance knowledge of biophysics, Chapter1 will pique the interest of beginners in the field, and is a nice introductory reading for medicinal chemistry graduate students, as it provides a historical perspective and overview of biophysical techniques used at various phases of the drug discovery workflow, namely, hit generation, validation, and drug structure optimization.
Professor Ian Mitchelle de Vera, Saint Louis University School of Medicine, USA
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| Preface | vii | ||
| Contents | ix | ||
| Chapter 1 Impact and Evolution of Biophysics in Medicinal Chemistry | 1 | ||
| 1.1 Introduction | 1 | ||
| 1.2 Evolution of Biophysics in Medicinal Chemistry | 3 | ||
| 1.2.1 Phenotypic Drug Discovery | 3 | ||
| 1.2.2 Targeted and Fragment-based Drug Discovery | 3 | ||
| 1.2.3 Phenotypic Drug Discovery 2.0 | 5 | ||
| 1.2.4 Evolving Compound Collections and Chemical Technologies | 5 | ||
| 1.3 Biophysical Screening Approaches | 7 | ||
| 1.3.1 Protein- and Ligand-based NMR | 7 | ||
| 1.3.2 Thermal Denaturation Techniques | 8 | ||
| 1.3.3 Surface Plasmon Resonance | 9 | ||
| 1.3.4 Affinity Selection and Size Exclusion Chromatography Mass Spectrometry | 10 | ||
| 1.4 Mechanism of Action and Determination of Kinetics and Thermodynamics | 12 | ||
| 1.4.1 Mechanism of Action-evading Nuisance Mechanisms | 12 | ||
| 1.4.2 Residence Time, Target Engagement and Kinetics | 13 | ||
| 1.4.3 Thermodynamics in Optimization | 16 | ||
| 1.5 Structural Biology of Complex Targets—Overcoming Challenges with Biophysics | 17 | ||
| 1.5.1 Introduction | 17 | ||
| 1.5.2 Protein Complexes | 18 | ||
| 1.6 Conclusion and Introduction to Book Chapters | 18 | ||
| Acknowledgments | 20 | ||
| References | 20 | ||
| Chapter 2 Ligand-detected NMR Methods in Drug Discovery | 23 | ||
| 2.1 Introduction | 23 | ||
| 2.2 NMR Methods | 24 | ||
| 2.2.1 Relaxation | 24 | ||
| 2.2.2 Transferred-NOESY experiments | 26 | ||
| 2.2.3 Saturation Transfer Difference | 26 | ||
| 2.2.4 Water-LOGSY | 28 | ||
| 2.2.5 Pseudo Contact Shift measurements | 28 | ||
| 2.3 Competitive NMR Experiments | 29 | ||
| 2.4 Binding Quantification | 30 | ||
| 2.5 NMR in Drug Discovery | 31 | ||
| 2.5.1 Screening | 31 | ||
| 2.5.2 Hit validation | 33 | ||
| 2.5.3 Structure-guided Hit Optimization | 33 | ||
| 2.6 Example of Application to Medicinal Chemistry Projects | 35 | ||
| 2.7 Conclusions and Future Perspectives | 38 | ||
| References | 39 | ||
| Chapter 3 Receptor-based NMR Techniques in Drug Discovery | 44 | ||
| 3.1 Introduction | 44 | ||
| 3.2 Protein-ligand Binding Understood as an Exchange Process | 45 | ||
| 3.3 Chemical Shift Perturbation Monitoring the Receptor | 48 | ||
| 3.3.1 General Considerations | 48 | ||
| 3.3.2 Expanding the Molecular Weight Available for a Protein Target | 50 | ||
| 3.3.3 Methyl TROSY-based Approaches | 51 | ||
| 3.4 Paramagnetic Spin-labels for Lead Discovery and Optimization | 53 | ||
| 3.4.1 General Considerations | 53 | ||
| 3.4.2 Accessorizing Proteins with Spin Labels | 54 | ||
| 3.4.3 The SLAPSTIC Experiment | 55 | ||
| 3.5 Residual Dipolar Couplings (RDCs) | 56 | ||
| 3.6 Structure-Activity Relationship (SAR) by NMR | 57 | ||
| 3.7 NMR-based Drug Discovery in Membrane Proteins | 59 | ||
| 3.7.1 Solution versus Solid State NMR | 60 | ||
| 3.7.2 Isotope Labeling in Membrane Proteins | 61 | ||
| 3.8 Concluding Remarks | 62 | ||
| References | 63 | ||
| Chapter 4 Molecular Mechanisms of Drug Action: X-ray Crystallography at the Basis of Structure-based and Ligand-based Drug Design | 67 | ||
| 4.1 Introduction | 67 | ||
| 4.2 Applications | 69 | ||
| 4.2.1 Structure/Dynamics/Affinity Relationships - Rational Drug-design | 69 | ||
| 4.2.2 Crystal Structures as an Input for In silico Drug-design: Docking and Scoring | 75 | ||
| 4.2.3 Rational Drug Design from a Ligand-based Approach Based on Properties Formulated in Chemical Reactivity Theory | 78 | ||
| 4.3 Future Perspectives | 79 | ||
| Acknowledgments | 81 | ||
| References | 81 | ||
| Chapter 5 Mass Spectrometry in Biophysics: from High Throughput Screening to Structural Biology | 87 | ||
| 5.1 Introduction | 87 | ||
| 5.2 Applications | 89 | ||
| 5.2.1 Native Mass Spectrometry of Biomolecules to Study Structure and Dynamics | 90 | ||
| 5.2.2 Covalent Approaches to Interrogate Proteins | 93 | ||
| 5.2.3 HDX-MS | 97 | ||
| 5.2.4 Mass Spectrometry Techniques for Drug Screening | 100 | ||
| 5.3 Perspectives | 106 | ||
| Acknowledgments | 107 | ||
| References | 107 | ||
| Chapter 6 Characterization of Pharmaceutical Solids Combining NMR, X-ray diffraction and Computer Modelling | 120 | ||
| 6.1 General Introduction | 120 | ||
| 6.2 Methods | 121 | ||
| 6.2.1 SSNMR Spectroscopy in Pharmaceutical Research | 121 | ||
| 6.2.2 Single-crystal X-ray Diffraction | 127 | ||
| 6.2.3 Powder X-ray Diffraction | 130 | ||
| 6.3 Application Case-Studies | 138 | ||
| 6.3.1 Polymorphism | 138 | ||
| 6.3.2 NMR and X-ray Approaches to Study \r\nAmorphous Systems | 142 | ||
| 6.3.3 Drug Delivery Systems | 146 | ||
| 6.3.4 Formulated Drugs | 147 | ||
| 6.3.5 From Crystal Packing Interactions to Crystal Structure Determination | 148 | ||
| 6.4 Future Perspectives | 160 | ||
| Acronyms | 161 | ||
| Acknowledgments | 162 | ||
| References | 162 | ||
| Chapter 7 Surface Plasmon Resonance for Identifying and Characterising Small Molecule Ligands | 170 | ||
| 7.1 Introduction and Perspectives | 170 | ||
| 7.1.1 Principles of SPR | 170 | ||
| 7.1.2 Overcoming the Challenges of SPR | 171 | ||
| 7.2 Applications of SPR | 177 | ||
| 7.2.1 SPR Considerations in the Different Phases of Drug Discovery | 177 | ||
| 7.2.2 Recent Applications of SPR in Drug Discovery | 194 | ||
| 7.2.3 Advances in Membrane Protein Capabilities for SPR | 196 | ||
| 7.2.4 SPR in Drug Metabolism and Pharmacokinetics | 198 | ||
| 7.2.5 Biomarker Characterization by SPR | 199 | ||
| 7.3 Future Perspectives | 199 | ||
| Acknowledgments | 204 | ||
| References | 204 | ||
| Chapter 8 Fluorescent Thermal Shift Assays for Identifying Small Molecule Ligands | 208 | ||
| 8.1 Introduction | 208 | ||
| 8.2 FTSA Principle | 209 | ||
| 8.3 Optimal Experimental Set-up | 211 | ||
| 8.3.1 Buffer | 211 | ||
| 8.3.2 Protein | 212 | ||
| 8.3.3 Dyes | 212 | ||
| 8.3.4 Compounds | 214 | ||
| 8.3.5 Controls | 214 | ||
| 8.3.6 Temperature | 214 | ||
| 8.3.7 Instrumentation | 215 | ||
| 8.4 Data Analysis | 215 | ||
| 8.4.1 Tm Determination | 215 | ||
| 8.4.2 Kd Determination | 216 | ||
| 8.5 Advantages | 218 | ||
| 8.6 Limitations | 219 | ||
| 8.7 FTSA in Drug Discovery | 222 | ||
| 8.7.1 Screening for Ligand Binding | 223 | ||
| 8.7.2 Screening for Fragment Binding | 224 | ||
| 8.7.3 Mechanism of Small Molecule Inhibition | 225 | ||
| 8.8 Successful Applications of FTSA for Ligand Binding Screens | 227 | ||
| 8.9 Other Uses of FTSA | 228 | ||
| 8.10 Non-fluorescent Dye Thermal Shift Assays | 229 | ||
| 8.11 Cellular Thermal Shift Assays | 230 | ||
| 8.11.1 CETSA | 231 | ||
| 8.11.2 Future Perspectives | 232 | ||
| Acknowledgments | 234 | ||
| References | 234 | ||
| Chapter 9 Fluorescent Probes in Medicinal Chemistry | 239 | ||
| 9.1 Introduction | 239 | ||
| 9.2 Types of Fluorophores | 240 | ||
| 9.3 Applications of Fluorescent Probes for the Study of Macromolecules | 242 | ||
| 9.3.1 Fluorescent Probes for the Study of Proteins | 242 | ||
| 9.3.2 Fluorescent Probes for the Study of Nucleic Acids | 249 | ||
| 9.4 Fluorescent Probes for the Study of Metabolites | 253 | ||
| 9.4.1 Detection of Metabolites Using Small Molecule Fluorophores | 253 | ||
| 9.4.2 FRET Biosensors for the Detection of Small Molecules | 254 | ||
| 9.4.3 Development of Cellular Organelle-targeting Fluorescent Probes | 255 | ||
| 9.5 Future Perspectives | 257 | ||
| Abbreviations | 258 | ||
| Acknowledgments | 258 | ||
| References | 258 | ||
| Chapter 10 Transmission Cryo-electron Microscopy in Drug Discovery | 263 | ||
| 10.1 Introduction | 263 | ||
| 10.2 Advances in Cryo-electron Microscopy | 264 | ||
| 10.3 Examples of High-resolution Cryo-EM Structures Suitable for Drug Discovery | 267 | ||
| 10.4 Future Perspectives | 272 | ||
| Acknowledgments | 274 | ||
| References | 274 | ||
| Chapter 11 Molecular Imaging | 277 | ||
| 11.1 Magnetic Resonance Imaging | 279 | ||
| 11.1.1 Hyperpolarization | 279 | ||
| 11.2 Modalities Based on Radioactive Isotopes | 283 | ||
| 11.2.1 Positron Emission Tomography: Principles and Applications | 284 | ||
| 11.2.2 Single-Photon Emission Computed Tomography: Principles and Applications | 289 | ||
| 11.3 Optical Molecular Imaging | 291 | ||
| 11.3.1 Bioluminescence Imaging (BLI) | 291 | ||
| 11.3.2 Fluorescence Imaging | 294 | ||
| 11.4 Multi-Spectral Optoacoustic Tomography | 296 | ||
| 11.5 Conclusions | 299 | ||
| Acknowledgments | 299 | ||
| References | 299 | ||
| Subject Index | 307 |