Capture compounds, collections thereof and methods for analyzing the proteome and complex compositions

Abstract

Capture compounds and collections thereof and methods using the compounds for the analysis of biomolecules are provided. In particular, collections, compounds and methods are provided for analyzing complex protein mixtures, such as the proteome. The compounds are multifunctional reagents that provide for the separation and isolation of complex protein mixtures. Automated systems for performing the methods also are provided.

1 . A capture compound for assessing interactions of a molecule Y with targets and non-targets, wherein
 the capture compound has the formula:   
       
         
           
           
               
               
           
         
         
           Y is selected from among a pharmaceutical drug or fragment, intermediate, metabolite or prodrug thereof, an enzyme substrate, inhibitor or co-factor, a receptor ligand and an ATP analog; 
           X is an activatable group that, upon exposure to an activating condition, covalently binds to proteins; 
           Q is a sorting function for immobilizing or separating the capture compounds; 
           Z is a trifunctional group that is not cleavable by mass spectrometry 
         
       
     
     
         2 . The compound of  claim 1 , wherein Q is biotin or an oligonucleotide. 
     
     
         3 . The compound of  claim 1 , wherein Z is an amino acid. 
     
     
         4 . The compound of  claim 1 , wherein X is a group whose binding to proteins is activated by exposure to light, exposure to a change in pH or exposure to a change in temperature. 
     
     
         5 . The compound of  claim 4 , wherein X is a photoactivatable group. 
     
     
         6 . The compound of  claim 1 , wherein:
 X is selected from among an azide or a diazarine;   Z is an amino acid; and   Q is biotin or an oligonucleotide.   
     
     
         7 . The compound of  claim 6 , wherein Y is a pharmaceutical drug or fragment, intermediate, metabolite or prodrug thereof 
     
     
         8 . The compound of  claim 6 , wherein Y is an enzyme substrate, inhibitor or co-factor. 
     
     
         9 . The compound of  claim 6 , wherein Y is a ligand for a receptor. 
     
     
         10 . The compound of  claim 1 , wherein X is 
       
         
           
           
               
               
           
         
       
       or an arylazide; Z is selected from serine, threonine, lysine, tyrosine and cysteine; and Q is biotin or an oligonucleotide. 
     
     
         11 . The compound of  claim 7 , wherein X is 
       
         
           
           
               
               
           
         
       
       or an arylazide; Z is selected from serine, threonine, lysine, tyrosine and cysteine; and Q is biotin or an oligonucleotide. 
     
     
         12 . The compound of  claim 8 , wherein X is 
       
         
           
           
               
               
           
         
       
       or an arylazide; Z is selected from serine, threonine, lysine, tyrosine and cysteine; and Q is biotin or an oligonucleotide. 
     
     
         13 . The compound of  claim 9 , wherein X is 
       
         
           
           
               
               
           
         
       
       or an arylazide; Z is selected from serine, threonine, lysine, tyrosine and cysteine; and Q is biotin or an oligonucleotide. 
     
     
         14 . The compound of  claim 1  that is immobilized on a solid support. 
     
     
         15 . The compound of  claim 1 , wherein Q is an oligonucleotide or oligonucleotide analog. 
     
     
         16 . The compound of  claim 1 , wherein X is selected from among a diazirine, 3-trifluoromethyldiazirine and an azide; Z is an amino acid and Q is biotin. 
     
     
         17 . The compound of  claim 1 , wherein Z is selected from among serine, threonine, lysine, tyrosine and cysteine. 
     
     
         18 . The compound of  claim 1  that comprises a mass modifying tag linked to Z. 
     
     
         19 . The compound of  claim 1  that further comprising a solubility group W that influences the solubility properties of the capture compound. 
     
     
         20 . The method of  claim 1 , wherein Z has the formula:
   (S 1 ) t M(R 15 ) a (S 2 ) b , wherein:   S 1  and S 2  are spacer moieties;   t and b are each independently 0 or 1;   a is an integer from 0 to 4;   M is a central moiety possessing three or more points of attachment;   R 15  is a monovalent group independently selected from Y 2 R 18 ;   Y 2  is a divalent group independently having any combination of the following groups: a direct link, arylene, heteroarylene, cycloalkylene, >C(R 17 ) 2 , C(R 17 )═C(R 17 ), >C═C(R 23 )(R 24 ), >C(R 23 )(R 24 ), C≡C, O, >S(A) u , >P(D) v (R 17 ), >P(D) v (ER 17 ), >N(R 17 ), >N(COR 17 ), >N + (R 23 )(R 24 ), >Si(R 17 ) 2  and >C(E); wherein:   u is 0, 1 or 2;   v is 0, 1, 2 or 3;   A is O or NR 17 ;   D is S or O; and   E is S, O or NR 17 ;   R 17  and R 18  are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, SiR 27 R 28 R 25 , alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR 19 R 20 ;   R 19  and R 20  are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;   R 23  and R 24  are selected from (i) or (ii) as follows:   (i) R 23  and R 24  are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl; or   (ii) R 23  and R 24  together form alkylene, alkenylene or cycloalkylene;   R 25 , R 27  and R 28  are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR 19 R 20 ;   R 15 , R 17 , R 18 , R 19 , R 20 , R 23 , R 24 , R 25 , R 27  and R 28  can be substituted with one or more substituents each independently selected from Z 2 ; Z 2  is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy, S(O) h R 35 ; h is 0, 1 or 2, NR 35 R 36 , COOR 35 , COR 35 , CONR 35 R 36 , OC(O)NR 35 R 36 , N(R 35 )C(O)R 36 , alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxylaryl, halo, pseudohalo, haloalkyl and carboxamido; and   R 35  and R 36  are each independently selected from among hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino.   
     
     
         21 . The compound of  claim 1 , wherein Y is an ATP analog. 
     
     
         22 . A plurality of compounds of  claim 1 , wherein in each compound X, Y and Z are the same, but the moiety Y is linked to the moiety Z in different orientations via different points of attachments on the Y moiety. 
     
     
         23 . The compound of  claim 1  that comprises a label. 
     
     
         24 . The compound of  claim 23 , wherein the label is a radiolabel. 
     
     
         25 . The compound of  claim 1  that includes a fluorescent, chemiluminescent, bioluminescent, phosphorescent or colorimetric group. 
     
     
         26 . An addressable array, comprising a compound of  claim 1 .