BIOLOGY

By F. LIMIL

Section 1: Synthetic Approaches to Enable Small-molecule Probe Discovery Chapter 1 Synthetic Tools for the Elucidation of Biological Mechanisms 3 11 Context 3 12 Synthetic Approaches to Enable Small-molecule Probe Discovery 4 13 Synthetic Approaches to Classes of Modified Biomolecule 5 14 Summary 6 References 6 Chapter 2 The Application of Diversity-oriented Synthesis in Chemical Biology 8 21 Introduction 8 211 Small Molecule Screening Collections 9 212 Sources of Complex and Diverse Libraries 12 213 Synthetic Strategies for the Construction of Complex and Diverse Libraries: Diversityoriented Synthesis 14 22 Application of Diversity-oriented Synthesis for the Identification of Small Molecule Modulators 18 221 Structural Diversity and Phenotypic Screening 18 222 The Role of DOS in Target Validation through the Discovery of New Chemical Probes 25 23 Conclusions and Outlook 37 Acknowledgements 38 References 38 Chapter 3 Biology-oriented Synthesis 45 31 Introduction 45 32 Structural Classification of Natural Products, Protein Structure Similarity Clustering and Scaffold Hunter 47 33 Implications and Opportunities for Biology-oriented Synthesis 50 34 Applications of Biology-oriented Synthesis 52 341 Chemical-structure- and Bioactivity-guided Approaches 52 342 Protein-structure-clustering-guided Approaches 57 343 Natural-product-derived-fragment-based Approaches 61 35 Conclusions and Outlook 68 References 69 Chapter 4 Lead- and Fragment-oriented Synthesis 74 41 Introduction 74 411 Introduction to Lead-oriented Synthesis 75 412 Introduction to Fragment-oriented Synthesis 77 42 Lead-oriented Synthesis 79 421 Diverse and Novel Scaffolds for Lead-oriented Synthesis 79 422 New Synthetic Methods for Lead-oriented Synthesis 87 423 Natural Products as Inspiration for Lead-like Libraries 91 424 The European Lead Factory 93 43 Fragment-oriented Synthesis 94 44 Conclusions 107 References 108 Chapter 5 Principles and Applications of Fragment-based Drug Discovery for Chemical Probes 114 51 Introduction 114 511 What Is a Chemical Probe? 114 512 Chemical Probe Characteristics 115 513 Fragment Library Design 116 514 Screening Methods/Fragment Elaboration 116 52 Case Studies 117 521 A-1155463 (BCL-XL) 117 522 CCT244747 (CHK1) 118 523 GSK2334470 (PDK1) 120 524 PFI-3 (SMARCA2/4 and PB1) 123 525 BI-9564 (BRD9) 125 526 Astex DDR1 Kinase Inhibitor (DDR1/DDR2) 128 53 Outlook 129 Abbreviations 130 References 131 Chapter 6 Function-driven Discovery of Bioactive Small Molecules 138 61 Context 138 611 Chemical Approaches That Underpin Bioactive Small-molecule Discovery 139 612 Evolution of Biosynthetic Pathways to Natural Products 139 613 Scope of This Chapter 140 62 Synthetic Fermentation 140 621 Discovery of a Protease Inhibitor 141 622 Conclusion 141 63 Activity-directed Synthesis 144 631 Discovery of Androgen Receptor Agonists Using Intramolecular Reactions 145 632 Discovery of Androgen Receptor Agonists Using Intermolecular Reactions 148 633 Conclusion 151 64 Outlook 151 References 151 Chapter 7 DNA-encoded Library Technology (ELT) 153 71 Introduction 153 72 Overview of the ELT Process 154 73 DEL Design and on-DNA Reaction Development 156 731 On-DNA Reaction Development 156 732 DEL Design and Production 161 74 ELT Selections and Data Analysis 164 75 Post Selection Chemistry (PSC) 167 76 Examples of Probes Derived from DELs 172 761 Protein Arginine Deiminase 4-Inhibitor 172 762 Allosteric Wip1 Phosphatase Inhibitor 174 763 PDE12 Inhibitor 176 764 RIP3 Kinase Inhibitor 176 765 BACTm Inhibitor 177 References 177 Chapter 8 Engineering Chemistry to Enable Bioactive Small Molecule Discovery 184 81 Preamble 184 82 Technologies for Machine-assisted Synthesis 186 821 Machine Vision 186 822 Process Analytical Technology (PAT) 188 83 Integration of Synthesis with Biological Evaluation 194 84 Technologies for the Automated Synthesis of Bioactive Compounds 196 841 Immobilized Systems 197 842 Flow Chemistry 200 85 Advanced Automation 207 86 Future Outlook 214 References 214 Section 2: Synthetic Approaches to Classes of Modified Biomolecule Chapter 9 Genetically Encoded Cyclic Peptide Libraries 221 91 Introduction 221 92 SICLOPPS 223 921 SICLOPPS in Prokaryotic Cells 226 922 SICLOPPS in Eukaryotic Cells 228 93 Phage Display 229 931 Applications of Phage Display in Drug Discovery 231 94 mRNA Display 235 95 Concluding Remarks 239 References 239 Chapter 10 Modern Methods for the Synthesis of Carbohydrates 243 101 Introduction 243 102 Glycosylation: The Basics 244 103 Stereoselectivity in Glycosylation Reactions 244 104 Solvent and Protecting Group Strategies for Controlling Stereoselective Glycosylation 248 105 Organocatalyst-mediated Glycosylations 250 106 Automated Oligosaccharide Synthesis 254 107 Pushing the Limits of Solution-phase Synthesis 262 108 Conclusion 269 References 269 Chapter 11 Precursor-directed Biosynthesis and Semi-synthesis of Natural Products 275 111 Introduction 275 112 Strategies for Coupling of Biosynthesis and Chemical Synthesis 276 1121 Combinatorial Biosynthesis 278 1122 Precursor-directed Biosynthesis 278 1123 Mutasynthesis 278 1124 Semi-synthesis 278 113 Leveraging Assembly Line Biosynthetic Systems for Polyketide and Non-ribosomal Peptide Diversification 279 1131 Overview of Assembly Line Biosynthesis 279 1132 A Model for Biosynthetic Engineering: 6-Deoxyerythronolide B Synthase (DEBS) 281 1133 Precursor-directed Biosynthesis and Mutasynthesis of Unnatural Complex Polyketides 284 1134 Semi-synthesis of Complex Unnatural Polyketides 288 1135 Precursor-directed Biosynthesis and Mutasynthesis of Unnatural Nonribosomal Peptides 290 114 Leveraging Non-templated Biosynthetic Systems for Natural Product Diversification 291 1141 Overview of Non-templated Biosynthesis of Natural Products 291 1142 Unnatural Aromatic Polyketides via Type III PKSs 294 1143 Diversification of RiPPs 295 1144 Terpene Diversification 297 1145 Alkaloid Diversification 299 1146 Diversification of Natural Product Glycosides 300 115 Summary and Outlook 301 Acknowledgements 302 References 302 Chapter 12 Site-specific Protein Modification and Bio-orthogonal Chemistry 313 121 Modification of Native Amino Acids 313 1211 Modification of Lysine, Serine and Threonine 314 1212 Modification of Cysteine 317 1213 Modification of Tyrosine, Tryptophan and Methionine 322 122 Bio-orthogonal Chemistry 324 1221 Staudinger Ligation and CuAAC 324 1222 SPAAC and SPANC 327 1223 Inverse Electron-demand Diels–Alder Reactions (IEDDA) and Photoclick 327 123 Strategies to Incorporate Amino-acids Containing Reactive Groups 328 1231 Metabolite Suppression 328 1232 Amber Suppression 329 124 Enzymatic Protein Modification 330 1241 Modification Using Post-Translational Modification Enzymes 330 1242 Post-translational Modification 331 1243 Modification Using Transpeptidases 342 1244 Other Ligating Enzymes 346 125 Conclusions 346 References 347 Chapter 13 Chemical Protein Synthesis: Strategies and Biological Applications 357 131 Introduction 357 132 Overview of Chemical Protein Synthesis 358 1321 Bottom Up: Solid-phase Peptide Synthesis 358 1322 Convergent Protein Synthesis with Native Chemical Ligation 360 1323 Semi-synthesis: Coupling Chemical Synthesis with Recombinant Technology 365 133 General Applications of Synthetic Protein Chemistry 369 1331 Precise Installation of Probes 369 1332 Access to Post-translationally Modified Proteins 371 1333 Synthesis of Unusual and Artificial Structures 374 134 Case Studies: Biological Insights Through Synthetic Protein Chemistry 376 1341 HIV Protease—Probing Structure, Mechanism and Asymmetry 376 1342 Erythropoietin: Understanding and Manipulating Protein Serum Lifetime 378 1343 GTPases: Mechanism of Membrane Attachment of Molecular Address Tags 381 1344 Regulation of Regulators: Synthesis of Phosphorylated Kinases and Phosphatases 383 1345 Histones: The Geometry of Positivefeedback Loops 387 135 Concluding Remarks 389 Acknowledgements 390 References 390