Abstract
This Report will analyze the biochemical nature of metabolomics, the technologies behind metabolomics, metabonomics related approaches, and the appropriate market potentials. This Report highlights new developments in chemical network (biochemical pathways) technology and the analytical tools developed to facilitate drug discovery. The Report provides market trends and evaluates metabolonomic pertaining to the pharmaceutical industry and the potential of being applied in the areas of drug discovery and development, and preventive screening/diagnostics. In addition, this Report indicates target compound analysis by discussing methods that measure the quantification of specific metabolites. Profiles of the major players in the metabolomics/metabonomics and systems biology field are also included.
TABLE OF CONTENTS
Chapter 1: Executive Summary
Chapter 2: Definitions and Models
- Metabolomics and Metabonomics
- Metabonome Provides Real-World Information about Drug Toxicity, Gene Function, and Homeostasis
- The Metabolome
- Utility of the Metabolome and Metabolic Toxicology in Drug Discovery
- Beyond the Genome and the Proteome
- Metabonomic Intervention in the Drug Development Pipeline
- Glucoronidation and Metabonates
- The Complexity of Metabolome
- Metabolomics and Plants
- Metabonomics Needs Biologists, Computer Scientists, Chemists, Engineers, Mathematicians, and Physicists
- Systems Biology
- Metabolic Control Analysis (MCA)
- Historical Genesis of MCA
- Biochemical Considerations
- Mammal-Microbe-Xenobiotic Systems Interactions
- Gut Metabolic System
- Pattern Recognition Methodologies
- Global Metabolomic Analysis-Metabolomic Vector Analysis
- Predictive and Preventive Medicine
- Related "Omic" Disciplines and Drug Discovery Platforms
- Genomics and Transcriptomics
- Lipomics and Glycomics .
- The Immunome
- References
Chapter 3: Bioinformatics-Databases and Software .
- Databases for Metabolic Pathway Analysis
- Introduction to Pathway Analysis
- Bibliome
- Data Mining
- Information Technology in Life Sciences
- Bioinformatics in Molecular R&D
- Predicting Gene Function and Structure
- DNA Technologies
- Intranet and Internet
- Gene Mapping and Genome Sequencing
- Automation and Computerization of Biotech Research
- Algorithms
- Chemometrics
- University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
- Leading Database Resources
- PathDB Depiction
- Selective Target Evaluation in Microbes (STEM.)
- PseudoCyc, a Pathway/Genome Database for Pseudomonas Aeruginosa
- and MetaCyc Database
- Biomolecular Interaction Network Database (BIND)
- 123genomics
- GGOBI
- Plant Systems
- Platform Plant Metabolomics (PPM)
- Arabidopsis
- Medicago Trunculata
- International Rice Research Institute (IRRI)
- Natural Product Analysis
- Max Planck Institute (MPI) for Molecular Plant Physiology
- Databases Associated with Genomics and Proteomics
- National Center for Biological Information (NCBI)
- Databases and Software
- NCBI s Nucleotide and Genomic Database
- European Bioinformatics Institute, and the Wellcome Trust Genome
- ExPASy Molecular Biology Server
- Boehringer Mannheim Biochemical Pathways
- Biocarta s Proteomic Pathway Project
- Structural Classification of Proteins (SCOP)
- Protein Function and Biochemical Pathways (PFBP) Project
- BRENDA
- Software for Metabolic Pathway Analysis .
- Computer Simulation of Metabolism
- Compound, Organism, Reaction and Enzyme (CORE)
- Artificial Neural Nets (ANN)
- Quantification of Biotechnological Systems
- The GO Consortium
- FlyBase
- CellML and E-Cell.
- E-Cell Project .
- References
- On the representation of gene function in genetic databases.
Chapter 4: Techniques in Metabolomics and Metabonomics
- Analytical Techniques
- Overview of Spectroscopic Techniques
- Mass Spectrometry (MS)
- FTIR Spectroscopy
- Diffuse Reflectance-Absorbance FT-IR
- Dispersive Raman Spectroscopy
- Atomic Absorption Spectrophotometry
- Pyrolysis Mass Spectrometry
- Combination Strategies Including: GC/MS, FTIR-MS, Liquid Chromatography (LC)/MS, and LC/MS/MS
- Evaluation of Glycosylation Sites by MS/MS
- MS/MS Analysis Used For Flavonoid Identification and Determination .
- High Throughput Screening (HTS) LC-MS
- Analysis of Fingerprinting Methods
- Use of NMR in Biomedicine
- LC/NMR
- Gas Chromatography (GC)
- High Performance Liquid Chromatography (HPLC) .
- Lab-on-a-Chip
- Capillary Electrophoresis (CE)/MS of Plants
- Recent Examples of Drug Enantioseparations by Chiral CE
- Conclusions Technological overview of Spectroscopic Methodologies
Chapter 5: Metabolomics and Metabonomics: Markets, Applications, and Current Research .
- Market Value
- Innovative Enhancements to the MS Technologies
- 2D Gels
- Mass Spectroscopy
- SWOT Analysis for Metabolomic Technologies
- Applications and Research
- Main Metabolomic and Metabonomic Application Categories
- Unifying Research in Genomics and Proteomics
- Drug Discovery and Development
- Genomics to Metabolomics
- Metabolite Profiling Defines Metabotypes
- Bioarray Innovations
- Integrated Genomics
- Third Generation Proteomics
- Target Identification and Diagnostic Biomarkers
- Clinical End Point and Presence of Biomarker
- Target Validation .
- Lead Prioritization
- Preclinical and Clinical Studies
- Metabolomic Analyses to Assist With Toxicity Profiles
- Personalized Medicine and Nutrition
- Current Research on Pathway Analysis .
- Future Directions.
Chapter 6: Company Profiles
- Taxicogenomics-Icora (formerly Paradigm Genetics), Morphochem Inc
- Chemogenomics-Acadia Pharmaceuticals, Amorpha Discovery Corp, Neogenesis Pharmaceuticals, Vertex Pharmaceuticals
- Ribonomics-Biolog, Intradigm Corp., Ribonomics Inc, Sequitur .
- Phenomics-Mitokor Inc, Cellular Genomics Inc, Phenomenome Discoveries Inc, Organon
- Target Identification-Metabolon Inc, High Chem Ltd., Metabometrix, GeneGo
- COMET Network, Vion Pharmaceuticals, Pfizer
- PhysioLab Entelos
- Acadia Pharmaceuticals
- Accelyrs Inc
- Agilent Technologies, Inc
- Bruker BioSciences Corp.
- Caliper Life Sciences
- Icoria, Inc. (Paradigm Genetics)
- Sequenom
