Plant Chemical Biology -- Copyright -- Contents -- Preface -- Contributors -- Part One Introduction -- 1.1 From Herbal Remedies to Cutting-Edge Science: A Historical Perspective of Plant Chemical Biology -- 1.1.1 Herbal Remedies and Pharmacology in the Ancient World -- 1.1.2 Alchemy, Chemistry, and the Isolation of the Bioactive Metabolites -- 1.1.3 The Discovery of Phytohormones and the Foundation of Modern Plant Chemical Biology -- 1.1.4 The Dawn of Plant Synthetic Chemistry -- 1.1.5 Serendipity Versus Rational Design of Chemical Libraries -- 1.1.6 The Development of Combinatorial Chemistry -- 1.1.7 Plant Chemical Biology in the -Omics Era -- 1.1.8 Introduction of Bioinformatics and Cheminformatics -- 1.1.9 Unique Challenges in the Field of Chemical Genomic Research -- 1.1.10 Concluding Remarks -- Acknowledgments -- References -- Part Two Sources of Small Molecules -- 2.1 Compound Collections -- 2.1.1 Introduction -- 2.1.2 Commercial Sources -- 2.1.3 Companies Providing Nonproprietary, Nonparallel Synthesized Libraries Sourced Externally to the Company -- 2.1.4 Companies Providing In-House Designed, Parallel Synthesized Libraries -- 2.1.5 Results of Database Analysis -- 2.1.6 Compound Selection and Database Filtering -- 2.1.7 Substructure Similarity/Dissimilarity -- 2.1.8 Cluster Analysis -- 2.1.9 Pharmacophore Analysis -- 2.1.10 Compound Acquisition Format and Storage -- Acknowledgments -- References -- 2.2 Combinatorial Chemistry Library Design -- 2.2.1 Introduction -- 2.2.2 Bioavailability -- 2.2.3 Chemical Space -- 2.2.4 Privileged Structures -- 2.2.5 Fragment-Based Design -- 2.2.6 Ligand-Based Design -- 2.2.7 Structure-Based Design -- 2.2.8 Conclusion and Summary -- References -- 2.3 Natural Product-Based Libraries -- 2.3.1 Introduction -- 2.3.2 Plant-Based Collections -- 2.3.3 Microbial-Derived Samples -- 2.3.4 Samples of Marine Origin.

2.3.5 Future Perspectives -- 2.3.6 Concluding Remarks -- References -- Part Three Identification of New Chemical Tools by High-Throughput Screening -- 3.1 Assay Design for High-Throughput Screening -- 3.1.1 Introduction -- 3.1.2 Approaching Assay Development -- 3.1.3 Assay Development -- 3.1.4 Assay Types and Considerations -- 3.1.5 Automation Adaptation and Validation -- 3.1.6 Closing -- Acknowledgment -- References -- Part Four Use of Chemical Biology to study Plant Physiology -- 4.1 Use of Chemical Biology to Understand Auxin Metabolism, Signaling, and Polar Transport -- 4.1.1 Introduction -- 4.1.2 Naturally Occurring Auxins -- 4.1.3 Auxin Biosynthesis -- 4.1.4 Auxin Conjugation and Release by Hydrolysis -- 4.1.5 Synthetic Auxins -- 4.1.6 Polar Auxin Transport -- 4.1.7 Current Models of Auxin Signaling -- 4.1.8 Application of Auxin-Related Molecules in Chemical Genetic Approach -- 4.1.9 Chemical Probes on Auxin Signaling from Chemical Library and Natural Sources -- 4.1.10 Rational Design of Auxin Antagonist on the Basis of TIR1 Structure -- 4.1.11 Chemical Probes on Auxin Transport from Chemical Library and Natural Sources -- 4.1.12 Concluding Remarks -- References -- 4.2 Brassinosteroids Signaling and Biosynthesis -- 4.2.1 Brassinosteroid Research Moves into the Era of Chemical Biology -- 4.2.2 Brassinosteroid Regulators -- 4.2.3 Brassinosteroid Receptors -- 4.2.4 Chemical Biology Research by Genetic Techniques Utilizing Brassinosteroid Biosynthesis Inhibitors: Chemical Genetics -- 4.2.5 Chemical Biology Research by Plant Physiological Techniques Utilizing Brassinosteroid Biosynthesis Inhibitors -- 4.2.6 Chemical Biology Research by Utilization of Brassinosteroid Biosynthesis Inhibitor in Cell Imaging and Biochemical Studies.

4.2.7 Chemical Genetics with a Focus on the Regulatory Activity of Brassinosteroid Biosynthesis Inhibitors on the Chloroplast Function -- 4.2.8 Outlook for the Future -- References -- 4.3 Chemical Genetic Approaches on ABA Signal Transduction -- 4.3.1 Abscisic Acid Signal Transduction: Lessons from Exogenous ABA Treatment -- 4.3.2 Abscisic Acid Signal Transduction: Lessons from ABA Derivatives Treatment -- 4.3.3 Abscisic Acid Signal Transduction: New Insights from Chemical Genetics -- 4.3.4 Pyrabactin and Its Cellular Target PYR1 : Discovery of ABA Receptors, PYR / PYL /RCARS -- 4.3.5 ABA Antagonist DFPM : Mechanisms for Crosstalks Between Abiotic and Biotic Signaling Pathways -- 4.3.6 Summary -- References -- 4.4 Jasmonic Acid -- 4.4.1 Introduction: Jasmonic Acid and Related Bioactive Molecules -- 4.4.2 Jasmonate Biosynthesis Pathway -- 4.4.3 Metabolic Conversion and Structure-Activity Relationship of Jasmonates -- 4.4.4 (+)-7- iso -Jasmonoyl- L -Isoleucine Is the Natural Bioactive Jasmonate -- 4.4.5 Dissecting the JA Signaling Pathway -- 4.4.6 Receptor of the Native Bioactive Jasmonate, JA -ILE -- 4.4.7 Searching for Additional JA Signaling Pathways and Components -- 4.4.8 Conclusions -- Ackowledgment -- References -- 4.5 Chemical Genetics as a Tool to Study Ethylene Biology in Plants -- 4.5.1 Introduction -- 4.5.2 Small Molecules in Ethylene Biosynthesis and Signaling -- 4.5.3 Possible Screens and Recent Findings in Chemical Genetics of Ethylene -- 4.5.4 Chemical Genetics in Ethylene-Hormone Interaction Studies -- 4.5.5 Target Identification -- 4.5.6 Future Perspectives -- References -- Part Five Use of Chemical Biology to Study Plant Cellular Processes -- 5.1 The Use of Small Molecules to Dissect Cell Wall Biosynthesis and Manipulate the Cortical Cytoskeleton -- 5.1.1 Introduction.

5.1.2 The Power of Molecular Genetics in the Study of Cell Walls -- 5.1.3 Why Use Chemical Genetics to Study Plant Cell Walls? -- 5.1.4 The Use of Chemical Genetics in Cell Wall Research -- Acknowledgments -- References -- 5.2 The use of Chemical Biology to Study Plant Cellular Processes: Subcellular Trafficking -- 5.2.1 The Plant Endomembrane System, a Complex Network Essential for Diverse Developmental Functions -- 5.2.2 Chemical Genomics Strategies to Study the Plant Trafficking Network -- 5.2.3 The Identification of Novel Compounds Targeting the Plant Trafficking Network -- 5.2.4 Chemical Genomics Can Target Evolutionarily Conserved Pathways in Eukaryotes -- 5.2.5 Broadly Used Bioactive Natural Compounds to Investigate Vesicular Trafficking in Plants -- 5.2.6 Advantages of a Chemical Genomics Strategy to Dissect the Plant Endomembrane System -- 5.2.7 Concluding Remarks -- Acknowledgments -- References -- Part Six Target Identification -- 6.1 Target Identification of Biologically Active Small Molecules -- 6.1.1 Introduction -- 6.1.2 Affinity-Based Approaches to Identify Protein Targets -- 6.1.3 Variation on the Affinity Approach to Target Identification -- 6.1.4 Label-Free Approaches -- 6.1.5 Genetic Approaches for Identifying Targets or Pathways of Novel Compounds -- References -- Part Seven Translation of Plant Chemical Biology from the Lab to the Field -- 7.1 Prospects and Challenges for Translating Emerging Insights in Plant Chemical Biology into New Agrochemicals -- 7.1.1 Introduction -- 7.1.2 Plant Chemical Biology Toward Herbicide Discovery -- 7.1.3 Plant Chemical Biology Toward Agrochemicals for Plant Protection -- 7.1.4 Plant Chemical Biology Toward Agrochemicals for Plant Improvement and Yield -- 7.1.5 Chemical Probes Versus Agrochemical Lead -- 7.1.6 Conclusion -- References -- 7.2 In Vitro Propagation.

7.2.1 Plant Tissue Culture as a Historical Basis for the Discovery of Plant Growth Regulators -- 7.2.2 Cytokinins Used in Tissue Culture -- 7.2.3 Auxins Used in Tissue Culture -- 7.2.4 Hormones in Tissue Culture Applications -- 7.2.5 Concluding Remarks -- References -- Index -- Supplementary Images.