Small molecule printing

Abstract

The present invention provides compositions and methods to facilitate the identification of compounds that are capable of interacting with a biological macromolecule of interest. In one aspect, a composition is provided that comprises an array of one or more types of chemical compounds attached to a solid support, wherein the density of the array of compounds is at least 1000 spots per cm 2 . In particularly preferred embodiments, these compounds are attached to the solid support through a covalent interaction. In general, these inventive arrays are generated by: (1) providing a solid support, wherein said solid support is functionalized with a selected chemical moiety capable of interacting with a desired chemical compound to form an attachment; (2) providing one or more solutions of one or more types of compounds to be attached to the solid support; and (3) delivering said one or more types of compounds to the solid support, whereby an array is formed and the array of compounds has a density of at least 1000 spots per cm 2 . In another aspect, the present invention provides methods for utilizing these arrays to identify small molecule partners for biological macromolecules of interest comprising: (1) providing an array of compounds, wherein the array has a density of at least 1000 spots per cm 2 ; (2) contacting the array with one of more types of biological macromolecules of interest; and (3) determining the interaction of specific small molecule-biological macromolecule partners.

1 . An array comprising:
 a plurality of more than one type of small molecule, having a molecular weight of less than 1500 g/mol, attached to a solid support through a benzylidene linker, wherein the solid support is a substantially flat surface, wherein the small molecules become attached to the support through reaction with diazobenzylidene moieties, wherein attachment of the small molecules to the support is robust enough so that the small molecules are not inadvertently cleaved during subsequent assaying steps, and wherein the density of said array of small molecules is at least 1000 spots per cm 2 .   
     
     
         2 . (canceled) 
     
     
         3 . The array of  claim 1 , wherein said array of small molecules comprises an array of non-oligomeric small molecules. 
     
     
         4 . The array of  claim 1 , wherein said array of small molecules comprises an array of non-peptidic and non-oligomeric small molecules. 
     
     
         5 . The array of  claim 1 , wherein said attachment is characterized in that the benzylidene linkage is robust enough so that the small molecules are (1) not inadvertently cleaved during subsequent manipulation steps and (2) inert so that the functionalities employed do not interfere with subsequent manipulation steps. 
     
     
         6 . The array of  claim 1 , wherein each of said small molecules in said array is attached to the solid support through a linkage generated by a nucleophilic displacement reaction. 
     
     
         7 . The array of  claim 1 , wherein each of said small molecules in said array is attached to the solid support through a linkage generated by a nucleophilic displacement of N 2  by a heteroatom. 
     
     
         8 . (canceled) 
     
     
         9 . The array of  claim 1 , wherein the benzylidene linker attaching small molecule to glass slide is as shown below: 
       
         
           
           
               
               
           
         
         wherein Y is hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; 
         cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety; and 
         X is a heteroatom selected from the group consisting of O, S, and N, of an attached small molecule R. 
       
     
     
         10 . The array of  claim 1 , wherein the benzylidene linker attaching small molecule to glass slide is as shown below: 
       
         
           
           
               
               
           
         
       
       wherein X is a heteroatom selected from the group consisting of O, S, and N, of an attached small molecule R. 
     
     
         11 . The array of  claim 1 , wherein the benzylidene linker attaching small molecule to glass slide is as shown below: 
       
         
           
           
               
               
           
         
       
       wherein
 n is an integer ranging from 1 to 12; 
 Y is hydrogen; halogen; hydroxyl, alkyloxy; thiol; 
 alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety; and 
 X is a heteroatom selected from the group consisting of O, S, and N, of an attached small molecule R. 
 
     
     
         12 . The array of  claim 1 , wherein the benzylidene linker attaching small molecule to glass slide is as shown below: 
       
         
           
           
               
               
           
         
       
       wherein
 n is an integer ranging from 1 to 12; 
 Y is hydrogen; halogen; hydroxyl, alkyloxy; thiol; 
 alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety; and 
 X is a heteroatom selected from the group consisting of O, S, and N, of an attached small molecule R. 
 
     
     
         13 . The array of  claim 1 , wherein the solid support is glass. 
     
     
         14 . The array of  claim 1 , wherein the solid support is derivatized glass. 
     
     
         15 . The array of  claim 1 , wherein the solid support is silylated glass. 
     
     
         16 . The array of  claim 1 , wherein the solid support is γ-aminopropylsilylated glass. 
     
     
         17 . The array of  claim 1 , wherein the solid support is a polymer. 
     
     
         18 . The array of  claim 1 , wherein the solid support is metal. 
     
     
         19 . The array of  claim 1 , wherein the solid support is a metal-coated surface. 
     
     
         20 . The array of  claim 1 , wherein the solid support is a gold-coated surface. 
     
     
         21 - 24 . (canceled) 
     
     
         25 . A method for forming the array of  claim 1 , the method comprising:
 providing a solid support, wherein said solid support is a substantially flat surface derivatized with diazobenzylidene moieties capable of interacting with more than one type of small molecule, having a molecular weight of less than 1500 g/mol, to form a covalent linkage;   providing one or more solutions of more than one type of small molecule to be attached to the solid support; and   delivering said one or more solutions of said more than one type of small molecule to the solid support, whereby each of said small molecules is attached to the solid support through a covalent interaction, wherein attachment of the small molecules to the support is robust enough so that the small molecules are not inadvertently cleaved during subsequent assaying steps, and wherein the array of small molecules has a density of at least 1000 spots per cm 2 .   
     
     
         26 . The method of  claim 25 , wherein said solid support comprises a glass slide. 
     
     
         27 . The method of  claim 25 , wherein providing a solution of one or more types of small molecules to be attached to the solid support comprises providing one or more solutions generated from a library of small molecules, wherein each member of said library is initially attached to a bead, placed in an individual well, then cleaved from the bead to provide the solution. 
     
     
         28 - 29 . (canceled) 
     
     
         30 . A method of identifying small molecule partners for biological macromolecules of interest comprising:
 providing the array of  claim 1 ;   contacting said array with one or more types of biological macromolecules of interest; and   determining the binding of specific small molecule-biological macromolecule partners.   
     
     
         31 . A method for identifying small molecule partners for a gene product comprising:
 providing the array of  claim 1 ;   contacting said array with a library of recombinant proteins; and   determining the binding of specific recombinant proteins with small molecule partner.   
     
     
         32 - 33 . (canceled) 
     
     
         34 . The array of  claim 1 , wherein the small molecule attached to the benzylidine linker attached to the solid support is as shown below: 
       
         
           
           
               
               
           
         
       
       wherein
 Y is hydrogen; halogen; hydroxyl; alkyloxy; thiol; alkyl thiol; amino; alkylamino; 
 dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety; and 
 X is a heteroatom selected from the group consisting of O, S, and N, of an attached small molecule R. 
 
     
     
         35 . A solid support comprising a substantially flat glass surface, wherein the glass surface is derivatized with diazobenzylidene moieties, and wherein the solid support has the structure: 
       
         
           
           
               
               
           
         
       
       wherein
 Y is hydrogen; halogen; hydroxyl; alkyloxy; thiol; alkyl thiol; amino; alkylamino; 
 dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety. 
 
     
     
         36 . A solid support comprising a substantially flat glass surface, wherein the glass surface is derivatized with diazobenzylidene moieties, and wherein the solid support has the structure: 
       
         
           
           
               
               
           
         
       
     
     
         37 . A solid support comprising a substantially flat glass surface, wherein the glass surface is derivatized with diazobenzylidene moieties, and wherein the solid support has the structure: 
       
         
           
           
               
               
           
         
       
       wherein
 Y is hydrogen; halogen; hydroxyl; alkyloxy; thiol; alkyl thiol; amino; alkylamino; 
 dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched aliphatic, heteroaliphatic, aryl, or heteroaryl, optionally substituted with one or more of hydrogen; halogen; hydroxyl, alkyloxy; thiol; alkyl thiol; amino, alkylamino; dialkylamino; acetyl; acyl; azido; nitrile; cyano; cyclic acetal; or cyclic or acyclic, linear or branched substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety; and 
 n is an integer ranging from 1 to 12.