Methods for direct synthesis of compounds having complementary structure to a desired molecular entity and use thereof

Abstract

Compounds which possess a complementary structure to a desired molecule, such as a biomolecule, in particular polymeric or oligomeric compounds, which are useful as in vivo or in vitro diagnostic and therapeutic agents are provided. Also, various methods for producing such compounds are provided. These polymeric or oligomeric compounds are useful in particular as antimicrobial agents, receptor, hormone or enzyme agonists and antagonists.

1 . A method for producing a compound suitable for in vitro or in vivo usage as a diagnostic, therapeutic or prophylactic agent that possesses a complementary structure to a desired molecule or portion thereof comprising the following steps: 
 (i) selecting a particular molecule to which a compound having a complementary structure is to be produced;    (ii) contacting such molecule with one or more complementary monomers under conditions wherein such monomers associate around one or more residues of such molecule;    (iii) effecting polymerization of such associated monomers optionally in the presence of at least one crosslinking agent to produce a polymeric coating that is comprised on the surface of said molecule and which possesses a complementary structure to said molecule or a portion thereof;    (iv) removing said molecule under conditions that result in a polymeric compound that possesses a complementary structure to said molecule or portion thereof; and    (v) optionally effecting one or more cleavage and/or dissociation steps to produce compounds that are suitable for in vivo usage as a diagnostic, therapeutic and/or prophylactic agent.    
     
     
         2 . The method of  claim 1 , wherein said molecule is immobilized to a support.  
     
     
         3 . The method of  claim 1 , wherein said molecule is a biomolecule and is selected from the group consisting of a protein, a nucleic acid sequence, a carbohydrate, a peptide, a glycoprotein, a cell, a virus, a pathogen, and a tissue.  
     
     
         4 . The method of  claim 3 , wherein said protein is selected from the group consisting of an enzyme, antigen, antibody, hormone, receptor, and a fragment thereof.  
     
     
         5 . The method of  claim 1 , wherein the crosslinking agent comprises at least one cleavable crosslinker.  
     
     
         6 . The method of  claim 5 , wherein said crosslinker is selected from the group consisting of bis-acrylcystamine, N,N-diallyltartardiamide, N,N-(1,2-dihydroxyethylen) bisacrylamide, or N,N′-bis-(acryloyl)cystomine, N1-(CE)-1-(4-vinylphenyl)methylidene)-4-vinyl aniline, allyl disulfide, bis(2-(methacyl, 1-oxyethyl)) disulfide.  
     
     
         7 . A method of using the compound in vivo produced according to  claim 1  as a therapeutic or diagnostic agent comprising administering to a subject in need of such treatment a therapeutically or diagnostically effective amount of said compound.  
     
     
         8 . The method according to  claim 1 , wherein the molecule to which a compound having a complementary structure is to be produced is insoluble.  
     
     
         9 . The method of  claim 8 , wherein said molecule is an enzyme crystal or a crosslinked enzyme.  
     
     
         10 . An improved method of affinity purification which purifies a compound using a compound that specifically binds thereto, wherein the improvement comprising using a compound produced according to  claim 1  to effect purification.  
     
     
         11 . An improved assay method which includes the use of a competitive affinity ligand wherein the improvement comprises using as the competitive affinity ligand a compound produced according to  claim 1 .  
     
     
         12 . The method of  claim 1 , wherein the compound produced by said method is suitable for use as an active agent selected from the group consisting of a hormone, enzyme, or receptor antagonist or agonist; gene expression modulator, antimicrobial agent, and an anti-tumor agent.  
     
     
         13 . The method of  claim 1 , wherein the compound which results from said method is subsequently attached to a therapeutic or diagnostic agent.  
     
     
         13 . A method for producing a polymeric compound that exhibits complementary structure to a microbial or mammalian cell comprising the following steps: 
 (i) immobilizing a microbial or mammalian cell to a support;    (ii) coating said support and immobilized microbial or mammalian cell with a polymer that is crosslinkable under specific conditions;    (iii) selectively crosslinking the portion of the molecular coating that is proximate to the immobilized mammalian or microbial cell; and    (iv) removing the resultant molecular coating from the microbial or mammalian cell.    
     
     
         15 . The method of claim  14 , wherein the polymer is a photocrosslinkable polymer.  
     
     
         16 . The method of  claim 15 , wherein the polymers areas not proximate to the immobilized microbial or mammalian cell are covered with a photomask during photocrosslinking.  
     
     
         17 . The method of claim  14 , wherein the support is a thin layer support.  
     
     
         18 . The method of claim  14 , wherein the polymer coating in step (ii) is introduced by a method selected from the group consisting of spray-coating, dip-coating, and spin-coating.  
     
     
         19 . The method of claim  14 , wherein the resultant polymeric coating is suitable for use as a cell separating material.  
     
     
         20 . The method of claim  14 ,wherein the molecular coating is subsequently cleaved into oligomers which function as anti-microbial agents.  
     
     
         21 . A method for producing a compound that has a complementary structure to the active site of a desired molecule comprising the following steps: 
 (i) providing a support which is coated with a first monomer layer coating;    (ii) applying to said first monolayer a second layer which comprises at least one crosslinkable monomer which is able to move freely in said second layer;    (iii) exposing said second layer to a molecule containing at least one active site and allowing for said crosslinkable monomer to associate around said at least one active site;    (iv) providing a crosslinking agent and effecting crosslinking to produce a crosslinked compound that possesses a complementary structure to said at least one active site; and    (v) recovering said crosslinked compound that possesses a complementary structure to said at least one active site or sites.    
     
     
         22 . The method of  claim 21 , wherein said molecule is an enzyme or a receptor.  
     
     
         23 . The method of  claim 22 , wherein the resultant polymeric compound functions as an antagonist or agonist.  
     
     
         24 . A method for producing a polymeric or oligomeric compounds that has a complementary structure to a desired molecule comprises the following steps: 
 (i) providing a preformed functionalized polymer that is linear or lightly crosslinked and contacting same with a desired molecular entity such that specific functional groups on the polymer interact covalently or non-covalently with specific residues on the molecular entity;    (ii) allowing for such non-covalent or covalent interactions between the functional groups on the polymer and the molecular entity to equilibrate;    (iii) subjecting the resultant equilibrated covalent or complex non-covalent between the polymer and the molecular entity be at least one of the following steps: 
 (1) chemically treating the functional groups on the polymer that interact least strongly with the molecular entity by site-selective chemical modification;  
 (2) chemically treating the functional groups on the polymer that interact most strongly with the molecular entity by site-selective chemical modification; and  
 (3) crosslinking the polymer;  
   (iv) separating the molecular entity from the resultant polymer.    
     
     
         25 . The method of  claim 24 , wherein the molecular entity is in solution or immobilized to a support.  
     
     
         26 . The method of  claim 24 , wherein crosslinking is effected using a reversible cleavable crosslinking agent.  
     
     
         27 . A compound produced according to  claim 1 .  
     
     
         28 . A compound produced according to claim  14 .  
     
     
         29 . A compound produced according to  claim 21 .  
     
     
         30 . A compound produced according to  claim 25 .  
     
     
         31 . The method of  claim 1 , wherein the resultant polymer or oligomer ranges in molecular weight from about 1000 to about 200,00.  
     
     
         32 . The method of  claim 31 , wherein the molecular weight more preferably ranges from about 5,000 to 50,000.  
     
     
         33 . The method of  claim 1 , wherein the chain length of the resultant polymer or oligomer ranges from about 25 to 2500 angstroms.  
     
     
         34 . The method of  claim 33 , wherein the chain length more preferably ranges from 250 to 1000 angstroms.