Natural Products Analysis: Instrumentation, Methods, and Applications -- Copyright -- Contents -- Preface -- Contributors -- Chapter 1 Natural Products Analysis: Instrumentation, Methods, and Applications -- 1.1 Book Motivation -- 1.2 The Broad Field of Natural Products -- 1.3 Discovery Phases -- 1.4 Absolute Structure -- 1.5 Mass Spectral Applications in Concert -- 1.6 Complex Structures and Complex Mixtures -- References -- Chapter 2 The Need for New Antifungal and Antimalarial Compounds -- 2.1 Introduction -- 2.2 Fungal Infections -- 2.2.1 Fungal Diseases -- 2.2.2 Antifungal Therapy -- 2.2.3 Fluoropyrimidines -- 2.2.4 Azoles -- 2.2.5 Echinocandins -- 2.2.6 Other Peptides -- 2.2.7 Polyenes -- 2.2.8 Miscellaneous Antifungals -- 2.3 Malaria -- 2.3.1 The Disease -- 2.3.2 Quinine -- 2.3.3 Artemisinin -- 2.3.4 Tetracyclines -- 2.3.5 Clindamycin -- 2.3.6 Combinations of Drugs -- 2.4 Conclusions -- References -- Chapter 3 Emerging Instrumental Methods for Antimicrobial Resistance and Virulence Testing -- 3.1 Introduction -- 3.2 Mass Spectrometry -- 3.3 Nucleic Acid Amplification and Sequencing -- 3.4 Perspective -- Acknowledgment -- References -- Chapter 4 Plant and Marine Sources: Biological Activity of Natural Products and Therapeutic Use -- 4.1 Introduction -- 4.2 Significance of Plant Sources -- 4.2.1 Methods Used in Chemistry of Plant-Derived Products -- 4.2.2 Chemistry and the Modes of Action of Plant Metabolites -- 4.3 Impact of Marine Natural Products -- 4.3.1 Marine Chemical Biology -- 4.4 Natural Products and Diseases -- 4.4.1 Endocrine System-Diabetes -- 4.4.2 Cardiovascular Ailments -- 4.4.3 Antiplatelet and Antisclerotic Drugs -- 4.4.4 Diseases Correlated with Problems of the Central Nervous System (CNS) -- 4.4.5 Plants Used Against the Respiratory Disorders -- 4.4.6 Infectious Diseases and the Use of Plant- or Marine-Derived Drugs.

4.4.7 Anticancer Drugs from Plants and Marine Sources -- 4.5 Conclusions -- References -- Chapter 5 Emerging Trends for Stimulating the Discovery of Natural Products -- 5.1 Mass Spectrometry-Based Metabolomics -- 5.2 Metagenomics and Symbiosis -- 5.3 Bioinformatic Annotation of Biosynthetic Pathways and Structure Prediction -- 5.4 New Tools For Absolute Configuration Determination -- References -- Chapter 6 Advances and Challenges in Optical Molecular Spectroscopy Including Surface Plasmon Resonance-Based Methods for Bioanalysis -- 6.1 Introduction to Principles and Analytical Aspects of Optical Spectroscopy -- 6.1.1 Description of Electromagnetic Radiation and Its Propagation -- 6.1.2 Light Absorption and the Beer-Lambert-Bouguer Law -- 6.1.3 Deviations from the Beer-Lambert-Bouguer Law -- 6.1.4 Calibration Methods in Optical Spectroscopy -- 6.1.5 Multivariate Quantitative Models -- 6.1.6 Multivariate Classification Models -- 6.2 Molecular Spectroscopy and Its Instrumentation -- 6.2.1 Types of Molecular Optical Spectroscopic Methods -- 6.2.2 General Types of Instrumentation -- 6.2.3 Electronic States and Electronic Spectroscopy -- 6.2.4 Vibrational States and Methods of Vibrational Spectroscopy -- 6.2.5 Terahertz Spectroscopy -- 6.2.6 Microwave Spectroscopy -- 6.3 Surface Plasmon Resonance -- 6.3.1 Kinetic and Thermodynamic Aspects of SPR -- 6.3.2 Instrumentation of SPR -- 6.3.3 Development of SPR Sensing -- 6.4 Surface-Enhanced Vibrational Spectroscopic Techniques -- 6.4.1 Surface-Enhanced Raman Scattering Spectroscopy -- 6.4.2 Surface-Enhanced Infrared Absorption -- 6.5 Chiroptical Methods -- 6.5.1 Introduction to Chiroptical Techniques -- 6.5.2 Chiroptical Experiments -- 6.5.3 Theory and Calculations -- 6.5.4 Examples of Applications -- 6.6 General Perspectives and Trends -- Acknowledgments -- References.

Chapter 7 Advanced Techniques for NMR Analysis of Complex Biological Mixtures-From Simple NMR to Hyphenated Techniques -- 7.1 Introduction -- 7.2 Sample Preparation -- 7.2.1 Biological Material Collection -- 7.2.2 Biological Material Storage -- 7.2.3 Extraction -- 7.2.4 Sample Preparation for NMR Analysis -- 7.3 NMR Analysis of Extracts -- 7.3.1 Multidimensional NMR -- 7.3.2 Virtual NMR Chromatography -- 7.3.3 LC-NMR -- 7.4 NMR-Based Metabolomics -- 7.4.1 NMR versus MS for Metabolomics -- 7.4.2 NMR Data Acquisition -- 7.4.3 Data Preprocessing -- 7.4.4 Statistical Data Analysis -- 7.5 Structure Identification of Metabolites in Mixtures Using Databases -- 7.6 Covariance NMR -- 7.7 Metabolite Quantitation -- 7.8 Application of NMR-Based Metabolomics to the Analysis of Food and Nutraceuticals -- 7.8.1 Food Analysis -- 7.8.2 Analysis of Plant Extracts -- 7.9 Conclusions -- Acknowledgment -- References -- Chapter 8 Advances in X-Ray Diffraction: Implications to the Pharmaceutical Industry -- 8.1 X-Ray Diffraction on Single Crystals -- 8.2 Structure Analysis From a Microcrystal -- 8.3 Methods for Absolute Structure Identification -- 8.4 Structure Analysis from Powder Samples -- 8.5 The Use of Alternative Type of Radiation for Analysis -- 8.6 Position of Diffraction Methods and their Contribution to the Structure Elucidation of Natural Compounds -- 8.7 Future Prospects of Diffraction Techniques -- References -- Chapter 9 Laser Ablation Inductively Coupled Plasma Mass Spectrometry as a Tool in Biological Sciences -- 9.1 Introducing Elemental Analysis of Biogenic Materials Containing Heteroelements -- 9.2 Laser Ablation Inductively Coupled Plasma Mass Spectrometry in Biological Sciences -- 9.2.1 Fundamental Aspects of Spot Analysis and Imaging via Laser Ablation-ICP-MS -- 9.2.2 LA-ICP-MS Setup and Its Influence on Analytical Outcomes.

9.2.3 Normalization of the Isotope Signal and Internal Reference Element -- 9.2.4 Quantification Approaches -- 9.2.5 Imaging via LA-ICP-MS -- 9.2.6 Comparison with Other Methods for Analysis of Solids -- 9.3 The Critical View of Utilization of LA-ICP-MS -- Acknowledgments -- References -- Chapter 10 Imaging Mass Spectrometry, Metabolism, and New Views of the Microbial World -- 10.1 Introduction -- 10.2 An Overview of Imaging Mass Spectrometry -- 10.2.1 Instrumentation -- 10.2.2 Experimental Considerations -- 10.3 Applications of Imaging Mass Spectrometry to Microbiology -- 10.3.1 Microbial Ecology -- 10.3.2 High-Resolution Chemical Snapshots with SIMS -- 10.3.3 Bioremediation -- 10.3.4 Intracellular Metabolism -- 10.3.5 Nutrient Exchanges Among Siblings -- 10.3.6 Nutrient Exchanges Among Symbionts -- 10.3.7 Localizing Metabolic Processes Within Species-Diverse Communities -- 10.3.8 Identification of Metabolically Active Cells Within Multispecies Communities -- 10.3.9 Deciphering Growth Dynamics Within Multispecies Communities -- 10.3.10 Adapting SIMS to Study Secondary Metabolism -- 10.3.11 The Study of Natural Products with MALDI Imaging Mass Spectrometry -- 10.3.12 Kinetic Resolution of Natural Product Production -- 10.3.13 Biosynthesis and Secretion of Natural Products -- 10.3.14 Imaging Bacterial Competition -- 10.3.15 Competitive Inhibition of Pathogenic Bacteria -- 10.3.16 Natural Product Resistance Through the Eyes of IMS -- 10.3.17 Deconstructing Metabolic Exchanges Between Competing Species -- 10.3.18 Antibiotics and Symbiotic Interactions -- 10.3.19 Imaging Diverse Microbial Communities -- 10.3.20 Peptidogenomics -- 10.3.21 Mass Spectral Molecular Networking -- 10.4 Future Developments -- 10.4.1 Pushing the Limits of Spatial Resolution -- 10.4.2 nanoDESI -- 10.4.3 Analysis of Proteins.

10.4.4 Ionization Enrichment by Derivatization and Labeling -- 10.5 Conclusion -- References -- Chapter 11 Structural Separations for Natural Product Characterization by Ion Mobility-Mass Spectrometry: Fundamental Theory to Emerging Applications -- 11.1 Introduction -- 11.1.1 Historical Perspective on Ion Mobility and Mass Spectrometry Technology -- 11.1.2 Ion Mobility-Mass Spectrometry: Correlation of Two Dimensions -- 11.1.3 Deriving Structural Information from IM-MS Measurements -- 11.2 Utilization of Conformation Space for Exploration of Primary and Secondary Metabolites -- 11.2.1 Leveraging Conformation Space for Primary Metabolites -- 11.2.2 Leveraging Conformation Space for Secondary Metabolites -- 11.3 Emerging Applications of Ion Mobility Separations to Secondary Metabolite Discovery -- 11.3.1 Prioritization and Dereplication of Secondary Metabolites -- 11.3.2 Untargeted Secondary Metabolite Discovery -- 11.3.3 Imaging Mass Spectrometry of Secondary Metabolites -- 11.3.4 Imaging Ion Mobility-Mass Spectrometry of Secondary Metabolites -- 11.4 Conclusions -- Acknowledgments -- References -- Chapter 12 High-Resolution Tandem Mass Spectrometry for Nonribosomal Peptide and Polyketide Analysis -- 12.1 Structural Characterization of Natural Products -- 12.1.1 The Biosynthesis of Nonribosomal Peptides and Polyketides -- 12.2 Mass Spectrometry-Based Strategies for the Elucidation of Biosynthetic Pathways -- 12.2.1 High-Resolution Mass Spectrometry -- 12.2.2 The Proteomics Approach -- 12.2.3 Characterization of Isolated Intermediates Along the Biosynthetic Pathway -- 12.3 High-Resolution Tandem Mass Spectrometry -- 12.4 Tandem Mass Spectrometry Analysis of Polyketides and Nonribosomal Peptides -- 12.4.1 Fragmentation of Erythromycin A Using CAD and EID -- 12.4.2 Structural Characterization of Actinomycin D by CAD and EID.

12.4.3 Fragmentation of Lasalocid A and iso-Lasalocid A.