Drug discovery methods

Abstract

Methods for identifying disease-related pathways that can be used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.

1 - 53 . (canceled) 
     
     
         54 . A method for identifying a new use for a known therapy comprising the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts; generating subsets of genomics information from the database wherein the subsets include disease-related pathways comprising a known therapy target; selecting at least one of such disease-related pathways wherein the known therapy target is also comprised within a second disease-related pathway; and identifying a treatment of the second disease as a new use for the known therapy. 
     
     
         55 . A method for prioritizing candidate development compounds for further development that comprises the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts; generating one or more subsets of genomics information from the database; and querying the one or more subsets to identify all pathways associated with the target of each candidate development compound and assigning higher priority to development compounds on the basis of whether or not they are likely to result in an undesirable effect based on their involvement in other biological pathways. 
     
     
         56 . A method for identifying disease-related pathways wherein the disease is a side effect of drug therapy that comprises the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts; identifying a disease-related pathway affected by a drug or drug discovery target; generating one or more subsets of genomics information from the database relating to the disease-related pathway; and querying the one or more subsets to identify alternative pathways that are also affected by the drug or the drug discovery target and that result in the undesirable phenotype. 
     
     
         57 . A method for identifying or validating a genotypic marker for a disease state that comprises providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts; generating one or more subsets of genomics information from the database; and querying the one or more subsets to identify a genotypic marker that is associated with the disease state. 
     
     
         58 . (canceled) 
     
     
         59 . A method of conducting business that comprises receiving compensation from a customer in return for identifying to the customer a drug discovery target discovered by querying a computer system to identify a disease-related pathway and identifying the biological interactions and actor concepts in the disease-related pathway whereby each of the actor concepts involved in each such reaction is a drug discovery target and wherein the computer system comprises a means for accessing genomics information in a database, generating subsets of genomics information from the database, and a means for computational analysis of biological relationships among the concepts represented in the subsets. 
     
     
         60 . (canceled) 
     
     
         61 . A method of drug discovery that comprises:
 (a) identifying a drug discovery target discovered by querying a computer system to identify a disease-related pathway and identifying the biological interactions and actor concepts in the disease-related pathway whereby one or more of the actor concepts involved in each such reaction is a drug discovery target and wherein the computer system comprises a means for computing subsets of genomics information specific to one or more target diseases using a database of genomics information, and a means for computational analysis of biological relationships among the concepts included within the subsets; and   (b) screening compounds against a drug discovery target to identify drug candidates.   
     
     
         62 . (canceled)