Methods for drug discovery, disease treatment, and diagnosis using metabolomics

Abstract

The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.

1 . A method for metabolomically facilitating the diagnosis of a disease state of a subject, comprising:
 obtaining a small molecule profile from a subject suspected of having and/or having a disease state; and   comparing the small molecule profile from the subject to a standard small molecule profile, thereby diagnosing the disease state.   
     
     
         2 . A method for metabolomically predicting whether a subject is predisposed to having a disease state, comprising:
 obtaining a small molecule profile from the subject; and   comparing the small molecule profile from the subject to a standard small molecule profile, thereby predicting whether a subject is predisposed to having a disease state.   
     
     
         3 . A method for metabolomically predicting a subject's response to a therapeutic agent, comprising:
 obtaining a small molecule profile from the subject;   comparing the small molecule profile of the subject to a known standard established for the therapeutic agent as an indication of whether the subject would benefit from treatment with the therapeutic agent, thereby predicting a subject's response to said therapeutic agent.   
     
     
         4 . A method for metabolomically monitoring the effectiveness of a therapeutic agent in clinical trials, comprising:
 obtaining a small molecule profile from a subject in a clinical trial being treated with a therapeutic agent; and   monitoring changes in the small molecule profile of the subject as an indication of the effectiveness of the therapeutic agent in the subject, thereby monitoring the effectiveness of said therapeutic agent.   
     
     
         5 . A method for identifying small molecules regulated, modulated, or associated with a gene, comprising:
 obtaining a small molecule profile of a cellular compartment from a genetically modified source; and   comparing the small molecule profile to a standard small molecule profile, thus identifying the small molecules regulated, modulated or associated with the gene.   
     
     
         6 . The method of  claim 5 , wherein said cellular compartment is a cell. 
     
     
         7 . The method of  claim 5 , wherein said genetic modification is an expression vector. 
     
     
         8 . The method of  claim 5 , wherein said expression vector is a portion of the human genome. 
     
     
         9 . The method of  claim 5 , wherein said expression vector is associated with a particular disease state. 
     
     
         10 . A method for identifying potential drug targets, comprising:
 contacting a labeled disease relevant small molecule with cellular components; and   identifying interactions between said cell components and the labeled disease-relevant small molecule, thus identifying potential drug targets.   
     
     
         11 . The method of  claim 10 , wherein said cellular components are a nucleic acid array. 
     
     
         12 . The method of  claim 11 , wherein said cellular components are a protein array. 
     
     
         13 . A method for identifying small molecules relevant to disease resistance in a plant comprising:
 obtaining a small molecule profile of a plant resistant to said disease; and   comparing the small molecule profile of said plant to a standard small molecule profile;   thereby, identifying small molecules relevant to disease resistance in said plant.   
     
     
         14 . A method for identifying small molecules modulated by an insecticide, a pesticide, an herbicide or a fertilizer, comprising:
 obtaining a small molecule profile of a subject treated with said insecticide, pesticide, herbicide or fertilizer; and   comparing the small molecule profile of said test compound to a standard small molecule profile, thus identifying small molecules modulated by said insecticide, pesticide, herbicide or fertilizer.   
     
     
         15 . A method for metabolomically determining whether a subject can be administered an agent to effectively treat a disease or disorder associated with an aberrant small molecule profile, comprising:
 obtaining a small molecule profile from the subject; and   comparing the small molecule profile from the subject to a standard small molecule profile, thereby predicting whether a subject can be administered an agent to treat a disease or disorder associated with an aberrant small molecule profile.   
     
     
         16 . A method for identifying small molecules regulated, modulated, or associated with a gene, comprising:
 obtaining a small molecule profile from a genetically modified source, wherein said genetically modified source is modified with respect to said gene; and   comparing the small molecule profile to a standard small molecule profile, thus identifying the small molecules regulated, modulated or associated with the gene.   
     
     
         17 . A method for identifying small molecules regulated by a gene in a subject, comprising:
 removing or functionally disrupting said gene; and   comparing the small molecule profile to a standard small molecule profile, thus identifying the small molecules regulated by said gene.   
     
     
         18 . A method for identifying small molecules regulated by a gene in a cell, comprising:
 removing or functionally disrupting said gene; and   comparing the small molecule profile to a standard small molecule profile, thus identifying the small molecules regulated by said gene.