Register by November 5^th and save up to $200!

Day 3: 
Cambridge Healthtech Institute’s Inaugural...
Analytical Methods for Metabolic Profiling
Solving Problems in Analysis
December 15, 2004 • Wyndham Palace Resort and Spa • Lake Buena Vista, Florida

Wednesday, December 15, 2004

This one day conference, following the Metabolic Profiling and In Vitro Screens in Drug Metabolism meetings, will explore the problems and challenges associated with the various analytical methodologies applied to metabolic profiling and discuss ways to overcome these challenges in order to enhance the value of the information returned. Researchers active in any of these areas should make plans to attend this meeting.

8:006:30    Registration and Morning Coffee

9:00    Welcome by Session Chairperson
Dr. Pedro Mendes, Virginia Bioinformatics Institute

9:15    A MALDI-MS Approach for Metabolomics
Dr. Royston Goodacre, Department of Chemistry, University of Manchester Institute of Science and Technology
There are currently severe technological bottlenecks within metabolomics which limit the use of this approach within functional analyses. Current MS strategies for metabolomics include GC-MS, LC-ESI-MS and flow injection ESI-MS. However GC-MS and LC-MS are relatively slow both for the chromatography itself (typical run times are 10-30 min per sample) and for the subsequent deconvolution steps. Whilst direct infusion of metabolite extracts into ESI-MS is relatively rapid, ion suppression effects lead to incomplete coverage of the metabolome. MALDI-MS has been extensively used for peptide mass fingerprinting and for proteome profiling from complex mixtures. However MALDI-MS uses a low molecular weight matrix in concentrations 103-104 times those of the determinands to effect desorption and ionization, and since the matrix is also desorbed and ionized and hence detected by ToF-MS, and has similar Mwt to metabolites, requires alternate strategies for applications in metabolic profiling. We have been developing such strategies to limit the formation of matrix ions and this technology development will be reported for analyzing low molecular weight species.

9:45    Bioinformatics Tools for Analysis of Metabolomics Data
Dr. Eberhard Voit, Medical University of South Carolina 

10:15    MS-MS Peak Detection and Tools for Large Scale Analysis of MSMS data
Dr. Paul Kearny, Director of Bioinformatics, Caprion Pharmaceuticals

10:45    Poster and Exhibit Viewing, Morning Coffee

11:15    Metabolomics Data Analysis: Beyond Correlation
Dr. Pedro Mendes, Research Associate Professor, Virginia Bioinformatics Institute

11:45    Maximum Entropy vs. Knowledge-based Inference: Real-time Quantitative Trawling of ESI-LC/MS Complex Mixtures
Dr. Peter Leopold, President, BioAnalyte

12:15    Panel Discussion: Mining the Data for Gold…Making Sense of the Overwhelming Amount of Metabolic Data

12:45    Luncheon

2:00    Comments by Session Chairperson
Dr. Natalie Serkova, University of Colorado Health Science Center

2:10    Strategies for Dealing with Metabolite Elucidation in Drug Discovery and Development
Dr. Ala F. Nassar Drug Metabolism, Vion Pharmaceuticals, Inc.
In recent years, significant efforts in drug discovery have been aimed at addressing metabolism issues at the earliest possible stage, specifically toward use of newer, more rapid and accurate technologies to improve metabolite identification. Structural information on metabolites can be a great help in enhancing as well as streamlining the process of developing new drug candidates. Metabolite identification can assist with chemical synthesis efforts to block or enhance metabolism for early discovery, prediction of metabolites likely to be formed in vivo, determination of metabolic differences between species, identification of potential pharmacologically-active or -toxic metabolites, comparison of human pathways, synthesis of metabolites for toxicology testing, and drug-drug interactions. This talk examines the relative merits of current and potential strategies for dealing with metabolite characterization in various stages of drug discovery and development which are illustrated by some recent examples. Such modern approaches to the generation and use of structural information on metabolites can accelerate the drug discovery and development process by eliminating potentially harmful candidates earlier in the process, as well as improve the safety of new drugs.

2:40    Metabolic Signature of Small Molecule Tyrosine Kinase Inhibitors by MRS - from Efficacy to Resistance Development
Dr. Natalie Serkova, Assistant Professor, Dept. Anesthesiology; Director, Biomedical MRS/MRI, University of Colorado Health Science Center
Tumor cells are known to have dramatically altered cellular metabolism. Impaired mitochondrial function of the cancer cell results in decreased mitochondrial metabolism and energy production with a subsequent increase in anaerobic glycolysis (the Warburg effect). Highly increased proliferation rates metabolically result in increased phospholipids turnover (phosphocholine). Magnetic resonance spectroscopy (MRS) allows for simultaneous evaluation of metabolic pathways involved in carcinogenesis, efficacy of novel anti-cancer drugs, as well as resistance development. Our MRS based data show that, unlike classic chemotherapeutics, novel TKIs, without cytocidal activity, reverse the Warburg effect with a subsequent decrease in glucose uptake and decrease phosphocholine level. In contrast to sensitive tumors, resistant cells fail to improve their mitochondrial metabolism and maintain high phosphocholine concentrations. MRS represents a novel metabolic approach for evaluation of drug efficacy from a single cell up to the human, which could be very useful in the development of novel targeted therapies, where therapeutic success is dependent on biological, rather than toxicological effects. 

3:10 Quantitative Determination of TCA Cycle and Glycolytic Intermediates by Stable Isotope Dilution Capillary Electrophoresis-Electrospray Ionization Mass Spectrometry
Dr. Robert Pawlosky, Staff Scientist, Laboratory of Metabolic Control, National Institute on Alcohol Abuse and Alcoholism-National Institutes of Health
This work will present a quantitative methodology for the determination of TCA cycle intermediates generated from the oxidation of glucose and fats in the mitochondria of cells in eukaryotic organisms. The analysis is based on capillary electrophoresis-mass spectrometry and uses stable isotopically labeled compounds to quantify intermediates, such as, succinic, lactic, and malic acids and ATP and reduced nucleotides. Application of the method to the determination of these and other analytes in mammalian liver, heart and blood will be demonstrated. The method may also be suitable for determining flux through the TCA and glycolytic pathways under various metabolic conditions.

3:45    Refreshment Break, Poster and Exhibit Viewing

4:10    Automated Analysis and Quality Control of Metabolic Data
Dr. Jim Samuelsson, Scientific Consulting, Genedata
In this talk we present methods and algorithms for automated metabolic data analysis. We show how probability based scoring algorithms operating at the peak list level, supported by quality control of the underlying raw spectra, if available, provide an efficient means of building up metabolic spectral libraries/databases of high quality. By using reference spectra of known compounds sampled under known conditions, the libraries/databases can be made highly specific. If, in addition, intensity values representing molecular abundances are available, quantitative methods can be employed to give information about condition-specific signatures (biomarkers) in the mass spectra. The automated algorithms and methods presented are suitable for implementing into computer software, freeing researchers from much tedious work, and enabling them to focus on the core biological issues.

4:30    New Advances to the SRI BioCyc Databases and Pathway Tools Software Suite
Dr. John Bashkin, Director, Business Development, SRI International
SRI's BioCyc collection of highly annotated metabolic pathway and genome databases encompasses more than 21 organisms, including Escherichia coli, Arabidopsis thaliana, and Homo sapiens while the MetaCyc collection contains metabolic pathway information from 160 organisms (www biocyc.org). The databases assist in metabolic profiling studies by allowing users to paint metabolomic data, including gene expression data, onto a one-screen display of a metabolic pathway map to aid in interpretation. In addition, users may visualize the layout of genes within a chromosome, an individual biochemical reaction, or a complete biochemical pathway with an interface supports a variety of queries. BioCyc may be also used as a reference source to look up individual facts or support computational studies of metabolism. Recent advances to the databases and associated Pathway Tools software suite will be described as will our academic and commercial licensing programs.

4:50 In Silico Metabolic Profiling by Systems Literature Analysis
Dr. Aris Persidis, President, Biovista
Metabolic profiling and modeling can be greatly assisted by efficient, value-adding and reliable methods that are in silico. Systems Literature Analysis (SLA) is a major emerging method in this area and is the in silico version of systems biology. It treats the literature as a system of millions of interconnected research parameters (animal models, cell lines, genes, networks, pathways, metabolites, diseases, reagents, experiments etc.) and uses advanced data mining to extract relationships and connections. With SLA, it is possible to conduct metabolic network profiling experiments in silico, thus helping to filter and prioritize animal model or cell line metabolic network experiments done in labs.

5:10    Conclusion of Analytical Methods for Metabolic Profiling Conference