Mass-based encoding and qualitative analysis of combinatorial libraries

Abstract

The insertion of isotopically labeled portions into solid state combinatorial synthesis constructs followed by mass spectrometer, mass-based nuclear magnetic resonance spectrometry or mass-based infrared spectrometry analysis allows for the physical, non-chemical encoding of large numbers of combinatorial synthesis products.

What is claimed is:  
     
         1 . A mass-based, non-chemical method for recording the reaction of at least a portion of a reaction series on each of a plurality of unique solid supports, said method comprising: 
 (a) preparing a plurality of agents each having a unique defined mass;    (b) preparing a group of solid supports;    (c) reacting each solid support group with a different chemical reagent under a controlled reaction condition;    (d) mixing the product groups of step (c) together and then dividing said mixture of unique solid supports into a plurality of groups for a second intermediate or final stage;    (e) repeating said reacting with a chemical reagent under a controlled reaction condition at least once to provide a plurality of final products, having different products on the different individual unique solid supports;    each of said unique defined mass agents being reacted with either: each of a group of unique solid supports; each of a group of first chemical reagents in a reaction series; each of a group of second chemical reagents in a reaction series; or each of a group of subsequently added chemical reagents in a reaction series; such that each of said group of unique solid supports, group of first chemical reagents, group of second chemical reagents or group of subsequent chemical reagents has been reacted with an agent having a defined mass that is different from any other defined mass agent reacted with any other of said groups;    said unique defined mass agents being capable of being analyzed and wherein said analysis defines the choice of a first chemical reagent, reaction condition under which said first chemical reagent was added, second chemical reagent, reaction condition under which said second chemical reagent was added, subsequent chemical reagent, or reaction condition under which said subsequent chemical reagent was added.    
     
     
         2 . A mass-based, non-chemical method for recording the reaction history of a reaction series on each of a plurality of unique solid supports, said method comprising: 
 (a) reacting, at a mass block insertion stage, a plurality of agents each having a unique defined mass with each of a group of said unique solid supports, such that each of said group of unique solid supports has been reacted with an agent having a defined mass that is different from any other agent reacted with any other of said groups of said unique solid supports;    (b) reacting each solid support group having a different defined mass agent with a different chemical reagent;    (c) mixing said groups together and then dividing said plurality of unique solid supports into a plurality of groups for a second intermediate or final stage;    (d) repeating said reacting with a chemical reagent at least once to provide a plurality of final products, having different products on the different individual unique solid supports;    said unique defined mass agents being capable of being analyzed and wherein said analysis defines the choice of a first chemical reagent.    
     
     
         3 . The method as claimed in  claim 1 , wherein said defined mass agents are analyzed by mass spectroscopy.  
     
     
         4 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each generate a unique single mass peak when analyzed by mass spectroscopy.  
     
     
         5 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each generate a unique double mass peak when analyzed by mass spectroscopy.  
     
     
         6 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each generate a unique pair of single mass peaks when analyzed by mass spectroscopy.  
     
     
         7 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each generate a unique pair of double mass peaks when analyzed by mass spectroscopy.  
     
     
         8 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each generate a unique pattern of one or more mass peaks.  
     
     
         9 . The method as claimed in  claim 8 , wherein said unique peak patterns for each of said defined mass agents can be expressed as a machine-readable pattern.  
     
     
         10 . The method as claimed in  claim 9 , wherein said machine readable patterns are bar codes.  
     
     
         11 . The method as claimed in  claim 3 , wherein said defined mass agents are selected so as to each independantly generate a unique mass spectrometry mass peak pattern selected from the group consisting of unique single mass peaks, unique double mass peaks, unique pairs of single mass peaks, unique pairs of double mass peaks, and unique peak patterns that are capable of being expressed as machine-readable patterns.  
     
     
         12 . The method as claimed in  claim 1 , wherein said defined mass agent is analyzed by nuclear magnetic resonance spectroscopy.  
     
     
         13 . The method as claimed in  claim 12 , wherein said defined mass agents are selected so as to each generate a unique pattern of one or more nuclear magnetic resonance peaks.  
     
     
         14 . The method as claimed in  claim 13 , wherein said unique peak patterns for each of said defined mass agents can be expressed as a machine-readable pattern.  
     
     
         15 . The method as claimed in  claim 14 , wherein said machine readable patterns are bar codes.  
     
     
         16 . The method as claimed in  claim 1 , wherein said defined mass agent is analyzed by infrared spectroscopy or by Raman spectroscopy.  
     
     
         17 . The method as claimed in  claim 16 , wherein said defined mass agents are selected so as to each generate a unique pattern of one or more infrared spectroscopy or Raman spectroscopy peaks.  
     
     
         18 . The method as claimed in  claim 17 , wherein said unique peak patterns for each of said defined mass agents can be expressed as a machine-readable pattern.  
     
     
         19 . The method as claimed in  claim 18 , wherein said machine readable patterns are bar codes.  
     
     
         20 . The method as claimed in  claim 1 , wherein said first, second or subsequent reagent is a substrate for the determination of binding specificity to a chemical compound of interest.  
     
     
         21 . The method as claimed in  claim 3 , wherein said mass spectroscopy analysis provides mass peaks capable of being recognized as representing encoded reagents.  
     
     
         22 . The method as claimed in  claim 1 , wherein additional mass peaks are generated that serve as signature peaks for positive identification of relevant mass peaks.  
     
     
         23 . The method as claimed in  claim 1 , wherein said plurality of defined mass agents are molecular entities that differ from one another by having at least one of their atoms substituted by a different isotope of that atom, provided that the chemical structural formula of said defined mass agents is the same.  
     
     
         24 . The method as claimed in  claim 23 , wherein said plurality of defined mass agents are molecular entities that differ from one another by having at least one isotopic substitution at different atomic positions within the molecule provided that the chemical structural formula of said defined mass agents is the same.  
     
     
         25 . The method as claimed in  claim 1 , wherein said plurality of defined mass agents are regularly repeating molecular entities that differ from one another by an integral number of said repeating molecular entities.  
     
     
         26 . The method as claimed in  claim 1 , wherein at least two groups of said unique solid supports are employed in each said reacting.  
     
     
         27 . The method as claimed in  claim 1 , comprising the additional step of screening said final products on said unique solid supports for a characteristic of interest and identifying the reaction history of at least one final product having said characteristic of interest.  
     
     
         28 . The method as claimed in  claim 1 , comprising the additional step of cleaving said final products from said solid supports and screening said final products.  
     
     
         29 . The method as claimed in  claim 1 , wherein said analysis is automated.  
     
     
         30 . The method as claimed in  claim 10 , wherein said reaction steps are automated.  
     
     
         31 . A kit for encoding the reaction history of a plurality of reaction series, comprising a plurality of different isotopically distinguishable organic compounds, each of the compounds characterized by having distinguishable masses but having the same chemical composition and the same chemical properties, each compound encoding at least one bit of different physical information which can be determined by a physical measurement.  
     
     
         32 . A kit as claimed in  claim 31 , wherein said compounds are mixed with one another in a plurality of discrete ratios to produce a plurality of isotope mixtures that are physically distinguishable from each other.  
     
     
         33 . A kit as claimed in  claim 32 , wherein said compounds are mixed with one another in a series of regularly repeating increasing increments.  
     
     
         34 . A kit as claimed in  claim 31 , wherein said compounds are of the formula:  
       R—C 
       where R is a suitable solid support which allows for attachment and detachment of a molecular moiety of choice; and C is an isotopically doped linker which allows for attachment and detachment from said solid supprt.  
     
     
         35 . A kit as claimed in  claim 31 , wherein said compounds are of the formula:  
       L 1 -C-L 2    
         
       where L 1  is a covalent bond or an organic moiety; C is an isotopically doped linker; and L 2  is a covalent bond or an organic moiety.  
     
     
         36 . A kit as claimed in  claim 35 , wherein L 1  and L 2  are the same.  
     
     
         37 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       R-L 1 -C-L 2    
       where R is a suitable solid support which allows for attachment and detachment of a molecular moiety of choice; L 1  is a covalent bond or an organic moiety; C is an isotopically doped linker; and L 2  is a covalent bond or an organic moiety.  
     
     
         38 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       (L) n1 -(C) n2    
       where n1 is an integer of from one to ten, n2 is an integer of from one to ten, L an organic moiety or a covalent bond when n1 is one, and C is an isotopically doped linker.  
     
     
         39 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       R-L-C  
       where R is a suitable solid support which allows for attachment and detachment of a plurality of molecular moiety of choice; L is a covalent bond or an organic moiety; and C is an isotopically doped linker.  
     
     
         40 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       L-C 1 A-B-D-C 2    
       L is a covalent bond or an organic moiety; C 1  is an isotopically doped linker; A is a first monomer in a reaction series, B is a second monomer in a reaction series, and D is a third monomer in a reaction series; and C 2  is a second isotopically doped linker that can physically be the same as or different from C 1 .  
     
     
         41 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       L-C 1 -A-B-C 2    
       L is a covalent bond or an organic moiety; C 1  is an isotopically doped linker; A is a first monomer in a reaction series, B is a second monomer in a reaction series; and C 2  is a second isotopically doped linker that can physically be the same as or different from C 1 .  
     
     
         42 . A kit as claimed in  claim 31 , wherein said compounds are of the formula  
       L-C 1 -A-C 2    
       L is a covalent bond or an organic moiety; C 1  is an isotopically doped linker; A is a first monomer in a reaction series; and C 2  is a second isotopically doped linker that can physically be the same as or different from C 1 .  
     
     
         43 . A kit as claimed in  claim 31 , wherein said components are isotopically doped suitable solid supports.  
     
     
         44 . A kit as claimed in  claim 31 , wherein said components are of the formula  
       
         
           
           
               
               
           
         
       
       where R is a suitable solid support; L is a covalent bond or an organic moiety; C is an isotopically doped moiety; and A is a first chemical reagent in a reaction series.  
     
     
         45 . A kit as claimed in  claim 31 , where said components are of the formula  
       
         
           
           
               
               
           
         
       
       where R is a suitable solid support; L is a covalent bond or an organic moiety; C is an isotopically doped moiety; and A is a first chemical reagent in a reaction series.  
     
     
         46 . A solid support characterized by having a unique defined mass agent and a ligand bound to the surface of said solid support.  
     
     
         47 . A solid support characterized by having up to 20 discrete unique defined mass agents bound to the surface of said solid support.  
     
     
         48 . A solid support as claimed in  claim 46 , wherein said ligand is an organic moiety.  
     
     
         49 . A solid support as claimed in  claim 46 , wherein said ligand is bound to said unique defined mass agent.  
     
     
         50 . A solid support as claimed in  claim 46 , wherein said ligand is a non-oligomer which is aliphatic, alicyclic, aromatic, heterocyclic or a combination thereof.  
     
     
         51 . A solid support as claimed in  claim 46 , wherein said ligand is an oligomer which is an oligopeptide, oligonucleotide, oligosaccharide, polylipid, polyester, polyamide, polyurethane, polyurea, polyether, polyphosphorus where phosphorus is a derivative taken from the group consisting of phosphate, phosphonate, phosphoramide, phosphonamide, phosphite, or phosfinamide, or polysulfur where sulfur is a derivative taken from the group consisting of sulfone, sulfonate, sulfite, sulfinamiide, or sulfenamide.  
     
     
         52 . A solid support as claimed in  claim 46 , wherein said support is a resin bead of about 1 to 10000 μm in diameter.  
     
     
         53 . A solid support as claimed in  claim 46 , wherein said support is a polystyrene resin bead of about 1 to 10000 μm in diameter.  
     
     
         54 . A solid support characterized by being isotopically doped.  
     
     
         55 . A solid support as claimed in  claim 54 , wherein said support is an isotopically doped resin bead.  
     
     
         56 . A solid support as claimed in  claim 55 , wherein said support is an isotopically doped polystyrene resin bead of about 10 to 2000 μm in diameter.  
     
     
         57 . A library comprising a plurality of solid supports as claimed in  claim 46 .  
     
     
         58 . A library comprising a plurality of solid supports as claimed in  claim 46 , wherein said final products have been cleaved from said solid supports.  
     
     
         59 . A process for identifying compounds having a characteristic of interest, which comprises screening a library as claimed in  claim 57 .  
     
     
         60 . A process as claimed in  claim 59 , wherein the compounds have been cleaved from the solid support.  
     
     
         61 . A process as claimed in  claim 60 , wherein said cleavage is between said solid support and said unique defined mass agent.  
     
     
         62 . A mass-based, non-chemical method for generating machine or human-recognizable patterns to record the reaction history of a reaction series on each of a plurality of unique solid supports, said method comprising: 
 (a) generating a set of agents each having a unique defined mass such that each agent differs from any other agent in the set by having a defined mass that is different from any other agent in the set;    (b) generating a recognition pattern for each agent in said set;    (c) reacting, at a mass block insertion stage, a plurality of agents each having a unique defined mass with each of a group of said unique solid supports, such that each of said group of unique solid supports has been reacted with an agent having a defined mass that is different from any other agent reacted with any other of said groups of said unique solid supports;    (d) reacting each solid support group having a different defined mass agent with a different first chemical reagent;    (e) mixing said groups together and then dividing said plurality of unique solid supports into a plurality of groups for a second intermediate or final stage;    (f) optionally repeating said reacting with a chemical reagent at least once to provide a plurality of final products, having different products on the different individual unique solid supports;    (g) analyzing said products for a characteristic of interest,    (h) further analyzing products found to have a characteristic of interest in step (g) by an analytical method that generates a like type of patterns as that type generated for the recognition patterns in step (b); and    (i) comparing the analytical patterns generated in step (h) to said recognition patterns.    
     
     
         63 . A mass-based, non-chemical method for generating machine-recognizable patterns to record the reaction history of a reaction series on each of a plurality of unique solid supports, said method comprising: 
 (a) generating a set of agents each having a unique defined mass such that each agent differs from any other agent in the set by having a defined mass that is different from any other agent in the set;    (b) generating a machine-recognizable recognition pattern for each agent in said set;    (c) reacting, at a mass block insertion stage, a plurality of agents each having a unique defined mass with each of a group of said unique solid supports, such that each of said group of unique solid supports has been reacted with an agent having a defined mass that is different from any other agent reacted with any other of said groups of said unique solid supports;    (d) reacting each solid support group having a different defined mass agent with a different first chemical reagent;    (e) mixing said groups together and then dividing said plurality of unique solid supports into a plurality of groups for a second intermediate or final stage;    (f) optionally repeating said reacting with a chemical reagent at least once to provide a plurality of final products, having different products on the different individual unique solid supports;    (g) analyzing said products for a characteristic of interest through the use of an analysis device;    (h) further analyzing products found to have a characteristic of interest in step (g) by an analytical method that generates a like type of patterns as that type generated for the recognition patterns in step (b); and    (i) comparing the analytical patterns generated in step (h) to said recognition patterns such that said unique defined mass agents are capable of being analyzed and identified.    
     
     
         64 . The method as claimed in  claim 63 , wherein said identification in step (i) leads to the -ready identification of said first chemical reagent.  
     
     
         65 . The method as claimed in  claim 63 , wherein said method steps are executed by suitable automation apparatus means and under the control of a suitable computer means.  
     
     
         66 . The method as claimed in  claim 63 , wherein said analysis device is selected from the group consisting of a flourescence activation cell scanner, a chromatography column or a chromatography plate.  
     
     
         67 . The method as claimed in  claim 63 , wherein said analytical method is selected from the group consisting of mass spectrometry, nuclear magnetic resonance spectroscopy, infrared spectroscopy or Raman spectroscopy.  
     
     
         68 . The method as claimed in  claim 63  wherein said analysis device is close coupled to said automation apparatus used in the method so as to be automated and under the control of a computer.  
     
     
         69 . The method as claimed in  claim 63 , wherein said analytical method is executed by a corresponding device that is close coupled to said automation apparatus used in the method so as to be automated and under the control of a computer.  
     
     
         70 . A database readily retrievable from a suitable data storage means comprised of the set of machine-readable patterns generated by the method as claimed in  claim 63 .  
     
     
         71 . A mass-based, non-chemical method for generating machine or human-recognizable patterns to record the reaction history of a reaction sequence of interest selected from a reaction series on each of a plurality of unique solid supports, said method comprising: 
 (a) generating a set of agents each having a unique defined mass such that each agent differs from any other agent in the set by having a defined mass that is different from any other agent in the set;    (b) generating a recognition pattern for each agent in said set;    (c) reacting, at a mass block insertion stage, a plurality of agents each having a unique defined mass with each of a group of said unique solid supports, such that each of said group of unique solid supports has been reacted with an agent having a defined mass that is different from any other agent reacted with any other of said groups of said unique solid supports;    (d) reacting each solid support group having a different defined mass agent with a different first chemical reagent;    (e) mixing said groups together and then dividing said plurality of unique solid supports into a plurality of groups for a second intermediate or final stage;    (f) optionally repeating said reacting with a chemical reagent at least once to provide a plurality of final products, having different products on the different individual unique solid supports;    (g) analyzing said products for a characteristic of interest;    (h) further analyzing products found to have a characteristic of interest in step (g) by an analytical method that generates a like type of patterns as that type generated for the recognition patterns in step (b);    (i) comparing the analytical patterns generated in step (h) to said recognition patterns;    (j) evaluating said analytical patterns to arrive at a qualitative and quantitative assessment of the output of a reaction sequence of interest, thereby identifying all products, quantities and yields of each of incomplete reactions, side reactions and previously unknown reactions in said sequence of interest.    
     
     
         72 . A mass-based, non-chemical method for recording the reaction history of a reaction series in solution, said method comprising: 
 (a) preparing, a plurality of agents each having a unique defined mass within each of a group of solution reaction wells, such that each of said group of reaction wells contains an agent having a defined mass that is different from any other agent within any other of said reaction wells;    (b) reacting each different defined mass agent with a different first chemical reagent in each well;    (c) mixing said groups together in to a resulting batch and then dividing said batch into a plurality of wells for a second intermediate or final stage;    (d) repeating said reacting with a chemical reagent at least once to provide a plurality of final products, having different products within said wells;    said unique defined mass agents being capable of being analyzed and wherein said analysis defines the choice of said first chemical reagent.    
     
     
         73 . A programmed computer system for executing a mass-based method for recording the reaction history of at least a portion of a reaction series of interest on each of a plurality of solid supports or in each or a plurality of reaction vessels, wherein one or more chemical reagents or chemical conditions are discretely identifiable by one or more recognition patterns and wherein said reaction series chemical products are subjected to analytical means that generate analytical patterns for each of said products; comprising: 
 first input means for introducing unique recognition patterns into the computer system, each pattern representing one of a plurality of agents each having a unique defined mass;    memory means for storing said recognition pattern;    second input means for introducing said resultant analytical patterns; and    means for comparing said resulting analytical patterns to said recognition patterns in order to generate an output which is the identity of one or more of said chemical reagents or chemical conditions.    
     
     
         74 . The programmed computer system as claimed in  claim 73 , additionally comprising means for controlling a robot means for performing one or more steps of said reaction series of interest.  
     
     
         75 . The programmed computer system as claimed in  claim 73 , additionally comprising means for generating said unique recognition patterns.  
     
     
         76 . The programmed computer system as claimed in  claim 73 , additionally comprising means for subjecting said reaction products to analytical means and generating analytical patterns.  
     
     
         77 . A mass-based, non-chemical method for identifying different chemical compounds in a mixture of said chemical compounds, said method comprising: 
 (a) preparing a plurality of chemical agents each having a unique defined mass;    (b) preparing a group of chemical compounds to be identified;    each of said unique defined mass agents being chemically linked or reacted with each of said chemical compounds to be identified to form a plurality of unique covalently bound one-to-one pairs of unique defined mass agents with compounds to be identified;    said unique defined mass agents being capable of being analyzed on the basis of its mass, and wherein said analysis thus identifies the chemical compound reacted with said analyzed mass agent.    
     
     
         78 . A mass-based, non-chemical method for identifying a chemical compound, said method comprising: 
 (a) preparing a chemical agent having a unique defined mass;    (b) preparing a chemical compound to be identified;    said unique defined mass agent being chemically linked or reacted with said chemical compound to be identified to form a unique covalently bound one-to-one pairing of unique defined mass agent with compound to be identified;    said unique defined mass agent being capable of being analyzed on the basis of its mass, and wherein said analysis thus identifies the chemical compound reacted with said analyzed mass agent.