Method for identifying validated target and assay combinations for drug development

Abstract

The invention comprises methods useful within a larger process for identifying compounds and/or designing further compounds with activity to produce a desired phenotype (for example, growth inhibition) in cells whose target cell component is the subject of certain studies to identify such compounds. The invention employs constructed cells comprising a regulable gene encoding a biomolecule which modulates (inhibits or activates) in vivo the function of a target component of the cell which can be an enzyme, for example, methionyl-tRNA synthetase of Staphylococcus aureus . The process incorporates methods for identifying biomolecules that bind to a chosen target cell component in vitro, methods for identifying biomolecules that also bind to the chosen target and modulate its function intracellularly, causing a phenotypic effect. The intracellular effect of a biomolecule can be tested in cell culture, or tested after introduction of the constructed cells into a host mammal in vivo, and methods for identifying compounds that compete with the biomolecules for sites on the target in competitive binding assays. Compounds identified by the series of steps in this process are candidates for drugs with the desired activity on the cell. Targets for which such compounds can be identified are validated as being essential to a phenotype of the cell.

What is claimed is:  
     
         1 . A method for identifying a biomolecule that produces a phenotypic effect on a cell, said method comprising: 
 a) in cells comprising a biomolecule and a target cell component, wherein the biomolecule is a biomolecular binder of the target cell component, and expression of an exogenous gene encoding the biomolecule is regulable, regulating expression of the gene, thereby producing the biomolecule; and    b) monitoring, for the phenotypic effect, the cells in culture relative to control cells, whereby, if a phenotypic effect is observed in the cells, compared to the control cells, then the biomolecule is a biomolecule that produces a phenotypic effect on the cell.    
     
     
         2 . The method of  claim 1  wherein the biomolecule is a peptide.  
     
     
         3 . The method of  claim 1  wherein the target cell component is a protein.  
     
     
         4 . The method of  claim 1  wherein the phenotypic effect is inhibition of growth.  
     
     
         5 . The method of  claim 1  wherein the phenotypic effect is inhibition of growth and wherein the cell is a pathogen cell.  
     
     
         6 . The method of  claim 1  wherein the phenotypic effect is inhibition of growth and wherein the cell is a mammalian cell.  
     
     
         7 . A method for determining whether a biomolecule produces a phenotypic effect on a first cell, comprising; 
 a) identifying a biomolecule which binds to an isolated target cell component of the first cell;    b) constructing a second cell comprising the target cell component and a regulable exogenous gene encoding the biomolecule;    c) testing the second cell for the phenotypic effect upon production of the biomolecule in the second cell;    whereby, if the second cell shows the phenotypic effect upon production of the biomolecule, the biomolecule produces a phenotypic effect on the first cell.    
     
     
         8 . The method of  claim 7  wherein the biomolecule is a peptide.  
     
     
         9 . The method of  claim 7  wherein the target cell component is a protein.  
     
     
         10 . The method of  claim 7  wherein the phenotypic effect is inhibition of growth.  
     
     
         11 . The method of  claim 7  wherein the phenotypic effect is inhibition of growth and wherein the first cell is a pathogen cell.  
     
     
         12 . The method of  claim 7  wherein the phenotypic effect is inhibition of growth and wherein the cell is a mammalian cell.  
     
     
         13 . A method for identifying a compound which is a functional analog of a biomolecule which produces a phenotypic effect on a cell, said method comprising: 
 a) testing, for the phenotypic effect, a cell which produces the biomolecule by regulable expression of an exogenous gene in the cell; and    b) identifying, if the biomolecule caused the phenotypic effect, one or more compounds that compete with the biomolecule for binding to a target cell component, whereby if a compound competes with the biomolecule for binding to the target cell component, then the compound is a functional analog of the biomolecule which produces a phenotypic effect on the cell.    
     
     
         14 . The method of  claim 13  wherein the biomolecule is a peptide.  
     
     
         15 . The method of  claim 13  wherein the target cell component is a protein.  
     
     
         16 . The method of  claim 13  wherein the phenotypic effect is inhibition of growth.  
     
     
         17 . The method of  claim 13  wherein the phenotypic effect is inhibition of growth and wherein the cell is a pathogen cell.  
     
     
         18 . The method of  claim 13  wherein the phenotypic effect is inhibition of growth and wherein the cell is a mammalian cell.