Natural product biosynthesis: chemical logic and enzymatic machinery
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| Main Authors: | , |
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| Format: | Book |
| Language: | English |
| Published: |
London
Royal Society of Chemistry
[2017]
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xx, 765 Seiten Illustrationen, Diagramme 24 cm |
| ISBN: | 9781788010764 |
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| adam_text | Titel: Natural product biosynthesis
Autor: Walsh, Christopher T
Jahr: 2017
Natural Product Biosynthesis Chemical Logic and Enzymatic Machinery Christopher T. Walsh Chem-H, Stanford University, USA Email: cwalsh2@stanford.edu and Yi Tang Chemical and Biomolecular Engineering, Chemistry and Biochemistry, UCLA, USA Email: yitang@ucla.edu ROYAL SOCIETY OF CHEMISTRY THE QUEEN S AWARDS FOR ENTERPRISE: INTERNATIONAL TRADE
Contents Section I: Introduction to Natural Products 1 Major Classes of Natural Product Scaffolds and Enzymatic Biosynthetic Machinery 7 1.1 Introduction 7 1.2 Primary Metabolites vs. Secondary Metabolites 11 1.3 Polyketide Natural Products 14 1.4 Peptide Based Natural Products 16 1.5 Isoprenoid/Terpenoid Natural Products 19 1.6 Alkaloids 26 1.7 Purine and Pyrimidine Natural Products 27 1.8 Phenylpropanoid Scaffolds 29 1.9 Glycosylated Natural Products 32 1.10 Natural Product Scaffold Diversity From a Limited Set of Building Blocks and a Limited Set of Enzyme Families 37 1.11 Some Notable and Unusual Transformations in Secondary Pathways 38 1.12 Oxygenases are Pervasive in Natural Product Biosynthetic Pathways 39 1.13 Carbon-Carbon Bonds in Natural Product Biosynthesis 42 1.14 Testing Biosynthetic Hypotheses by Feeding Isotopically Labeled Building Blocks 46 Natural Product Biosynthesis: Chemical Logic and Enzymatic Machinery By Christopher T. Walsh and Yi Tang © Christopher T. Walsh and Yi Tang 2017 Published by the Royal Society of Chemistry, www.rsc.org xiii
xiv Contents 1.15 Historical and Contemporary Approaches to the Detection and Characterization of Natural Products 49 1.16 Summary: Distinct Assembly Logic for Different Classes of Natural Products 52 1.17 Approach of This Volume 53 References 54 Section II: Six Natural Product Classes * 2 Polyketide Natural Products 63 2.1 Introduction 63 2.2 Polyketides Have Diverse Scaffolds and Therapeutic Utilities 65 2.3 Acetyl-CoA, Malonyl-CoA and Malonyl-S-Acyl Carrier Proteins as Building Blocks for Fatty Acids and Polyketides 67 2.4 The Logic and Enzymatic Machinery of Fatty Acid Synthesis is Adapted by Polyketide Synthases 70 2.5 Polyketide Synthases (PKS) 74 2.6 Biosynthesis of Major Polyketide Structural Classes 80 2.7 Polyketides with Ring-forming [4 + 2] Cyclizations on or After PKS Assembly Lines: Concerted or Stepwise? 89 2.8 The Polyene Subclass of Polyketides 102 2.9 Polyketide to Polyether Metabolites 106 2.10 Convergence of Polyketide and Other Natural Product Pathways 111 2.11 Post-assembly Line Tailoring Enzymes 115 References 117 3 Peptide Derived Natural Products 3.1 Introduction 3.2 Ribosomal vs. Nonribosomal Amino Acid Oligomerization Characteristics 3.3 Posttranslational Modifications That Convert Nascent Proteins into Morphed, Compact Scaffolds: RIPPs 3.4 Nonribosomal Peptide Synthetase Assembly Lines: Alternative Routes to Highly Morphed Peptide Scaffolds 127 127 130 133 154
Contents xv 3.5 Nonproteinogenic Amino Acid Building Blocks 155 3.6 NRPS Assembly Line Logic: Priming, Initiation, Elongation, Termination 160 3.7 Different Chain Release Fates in the NRPS Termination Step 165 3.8 Structural Considerations of NRPS Assembly Lines 169 3.9 Pre-assembly Line vs. On-assembly Line vs. Post-assembly Line Tailoring of Peptidyl Chains 171 3.10 NRP-PK Hybrids: Machinery and Examples 174 3.11 Summary 186 References 187 4 Isoprenoids/Terpenes 195 4.1 Isoprene-based Scaffolds Comprise the Most Abundant Class of Natural Products 195 4.2 A 2 - and A 3 -Isopentenyl Diphosphates are the Biological Isoprenyl Building Blocks for Head to Tail Alkylative Chain Elongations 195 4.3 Long Chain Prenyl-PP Scaffolds 198 4.4 Two Routes to the IPP Isomers: Classical and Nonclassical Pathways 201 4.5 Self-condensation of Two A 2 -IPPs to Chrysanthemyl Cyclopropyl Framework 205 4.6 Cation-driven Scaffold Rearrangements: and Quenching 205 4.7 Head to Head vs. Head to Tail Alkylative Couplings: C 30 and C 40 Terpene Compounds 217 4.8 Squalene-2,3-Oxide and Cyclized Triterpenes 220 4.9 Phytoene to Carotenes and Vitamin A 239 4.10 Reaction of Isoprenes with Other Natural Product Classes 245 4.11 Geranyl-PP to Secologanin: Entryway to Strictosidine and a Thousand Alkaloids 249 References 254 5 Alkaloids 261 5.1 Introduction 261 5.2 Alkaloid Family Classifications 263
xvi Contents 5.3 Common Enzymatic Reactions in Alkaloid Biosynthetic Pathways 264 5.4 Three Aromatic Amino Acids as Alkaloid Building Blocks 271 5.5 Tryptophan as a Building Block for Alkaloids 285 5.6 Anthranilate as a Starter and Extender Unit for Fungal Peptidyl Alkaloids of Substantial Complexity 295 5.7 Tryptophan to Indolocarbazole Alkaloids 303 5.8 Tryptophan Oxidative Dimerization to Terrequinone 309 5.9 Additional Alkaloids: Steroidal Alkaloids 311 5.10 # Summary 314 ?References 315 6 Purine- and Pyrimidine-derived Natural Products 321 6.1 Introduction 321 6.2 Pairing of Specific Purines and Pyrimidines in RNA and DNA 322 6.3 Remnants of an RNA World? 325 6.4 Canonical Biosynthetic Routes to Purines and Pyrimidines 328 6.5 Caffeine, Theobromine and Theophylline 330 6.6 Plant Isopentenyl Adenine Cytokinins 331 6.7 Maturation of Ribonucleotides to Modified Purine and Pyrimidine Natural Products 333 6.8 Peptidyl Nucleosides 342 6.9 Summary 351 References 352 7 Phenylpropanoid Natural Product Biosynthesis 357 7.1 Introduction 357 7.2 Phenylalanine to para-Coumaryl-CoA 360 7.3 Monolignol, Lignan and Lignin Biosynthesis 365 7.4 para-Coumaryl-CoA to All the Other Classes of Phenylpropanoids 377 7.5 Chalcone to Flavanones and Beyond 383
Contents xvii 7.6 Cinnamate Derived Phenylpropanoids 395 7.7 A Closing Look at a Different Phenylpropanoid Route: Tyrosine as Precursor to Plastoquinines and Tocopherols 400 7.8 Summary 404 References 405 8 Indole Terpenes: Alkaloids II 413 8.1 Introduction 413 8.2 Two Routes to Tricyclic Scaffolds from Trp: P-Carbolines and Pyrroloindoles 414 8.3 Trp-Xaa Diketopiperazine NRPS Assembly Line Products as Substrates for Regioselective Prénylations 416 8.4 Seven Nucleophilic Sites on the Indole Ring: A Cornucopia of Possibilities 420 8.5 Fungal Generation of Tryptophan Derived Alkaloids from DKP 425 8.6 Bacterial Generation of Pentacyclic Indolecarbazoles 431 8.7 Vinca Alkaloids: Strictosidine to Tabersonine to Vindoline 434 8.8 Lyngbyatoxin: One- and Two-electron Reaction Manifolds in Indole in a Single Biosynthetic Pathway 437 8.9 Tryptophan to Cyclopiazonic Acid 440 8.10 Summary 445 References 445 Section III: Key Enzymes in Natural Product Biosynthetic Pathways 9 Carbon-based Radicals in C-C Bond Formations in Natural Products A. Oxygenases B. Oxygen-dependent Halogenases 457 9.1 Introduction 457 9.2 Oxygenases in Primary vs. Secondary Metabolism 460
xviii Contents 9.3 Oxidases vs. Oxygenases 464 9.4 Organic vs. Inorganic Cofactors for Oxygenase Catalysis 468 9.5 Scope and Mechanism of Oxygenations Catalyzed by Iron-based vs. Flavin-based Oxygenases 470 9.6 Oxygenases in Specific Natural Product Pathways 479 9.7 Uncoupling of Carbon Radicals from OH Capture: Sidelight or Central Purpose of Natural Product Biosynthetic Iron Enzymes? 493 9.8 Oxygen-dependent Halogenases 503 9.9 Fluorination of Substrates by a Nonoxidative Route: ‘•Fluorinase 511 9.10 Summary: The Chemical Versatility of Ferryl (High Valent Oxo-iron) Reaction Intermediates 515 References 516 10 S-Adenosyl Methionine: One Electron and Two Electron Reaction Manifolds in Biosyntheses 525 10.1 Introduction 525 10.2 Aerobic Radical Chemistry for SAM 529 10.3 Anaerobic Radical Chemistry for SAM 535 10.4 Scope of Reactions of Radical SAM Enzymes 540 10.5 SAM as Coenzyme 543 10.6 SAM as Consumable Substrate: No Methyl Transfers 546 10.7 Méthylations at Unactivated Carbon Centers: Consumption of Two SAMs to Two Distinct Sets of Products 556 10.8 Summary on SAM reactivity and utility 563 References 564 11 Natural Product Oligosaccharides and Glycosides 571 11.1 Introduction 571 11.2 Glucose is the Predominant Hexose in Primary Metabolism 580
Contents xix 11.3 A Gallery of Glycosylated Natural Products 591 11.4 The Chemical Logic for Converting NDP-Glucose to NDP-Modified Hexoses 597 11.5 Balance of Gtfs and Glycosidases: Cyanogenic Glycosides and Glucosinolates 607 11.6 Aminoglycosides: Oligosaccharides without an Aglycone 615 11.7 Kanamycin, Tobramycin, Neomycin 615 11.8 Streptomycin 618 11.9 Moenomycins 620 11.10 Summary 624 References 624 Section IV: Genome-independent and Genome-dependent Detection of Natural Products 12 Natural Products Isolation and Characterization: Gene Independent Approaches 635 12.1 Introduction 635 12.2 Historic and Contemporary Isolation Protocols for Natural Products 635 12.3 Isolation and Characterizations of Specific Natural Products 639 12.4 Case Studies: Historical and Current 643 12.5 Five Plant Derived Natural Products 644 12.6 Three Microbial Metabolites 652 12.7 Expanding the Inventory of Natural Products 658 References 684 13 Natural Products in the Post Genomic Era 691 13.1 Introduction 691 13.2 Bioinformatic and Computational Predictions of Biosynthetic Gene Clusters 696 13.3 The Phosphonate Class of Natural Products: Can Genomics Define the Complete Set? 700
XX Contents 13.4 Overview of Heterologous Expression Systems 705 13.5 Selected Examples of Pathway Reconstitutions 707 13.6 Bioinformatics-based Natural Product Prospecting in Bacterial Genomes 720 13.7 Heterologous expression in E. coli 721 13.8 Metabolic Engineering for Diversity Generation 725 13.9 Plug and Play Approach to Cloning Transcriptionally Silent Gene Clusters of Unknown Function from Bacteria 728 13.10 Comparative Metabolomics in the Post Genomic Era 730 * References 734 Subject Index 741
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| spelling | Walsh, Christopher T. 1944-2023 Verfasser (DE-588)1133021670 aut Natural product biosynthesis chemical logic and enzymatic machinery Christopher T. Walsh (Chem-H, Stanford University, USA) and Yi Tang (Chemical and Biomolecular Engineering, Chemistry and Biochemistry, UCLA, USA) London Royal Society of Chemistry [2017] © 2017 xx, 765 Seiten Illustrationen, Diagramme 24 cm txt rdacontent n rdamedia nc rdacarrier Biosynthese (DE-588)4006902-3 gnd rswk-swf Natural products / Biotechnology Enzymology Biosynthese (DE-588)4006902-3 s DE-604 Tang, Yi Verfasser (DE-588)1133021891 aut Erscheint auch als Online-Ausgabe 978-1-78801-131-0 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029738948&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Natural product biosynthesis chemical logic and enzymatic machinery |
| title_auth | Natural product biosynthesis chemical logic and enzymatic machinery |
| title_exact_search | Natural product biosynthesis chemical logic and enzymatic machinery |
| title_full | Natural product biosynthesis chemical logic and enzymatic machinery Christopher T. Walsh (Chem-H, Stanford University, USA) and Yi Tang (Chemical and Biomolecular Engineering, Chemistry and Biochemistry, UCLA, USA) |
| title_fullStr | Natural product biosynthesis chemical logic and enzymatic machinery Christopher T. Walsh (Chem-H, Stanford University, USA) and Yi Tang (Chemical and Biomolecular Engineering, Chemistry and Biochemistry, UCLA, USA) |
| title_full_unstemmed | Natural product biosynthesis chemical logic and enzymatic machinery Christopher T. Walsh (Chem-H, Stanford University, USA) and Yi Tang (Chemical and Biomolecular Engineering, Chemistry and Biochemistry, UCLA, USA) |
| title_short | Natural product biosynthesis |
| title_sort | natural product biosynthesis chemical logic and enzymatic machinery |
| title_sub | chemical logic and enzymatic machinery |
| topic | Biosynthese (DE-588)4006902-3 gnd |
| topic_facet | Biosynthese |
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