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.

Description

[0001] This application is a continuation-in-part of U.S. Ser. No. 08 / 626,342 filed Apr. 12, 1996 which is incorporated by reference in its entirety herein. This application claims priority to PCT / SE95 / 00135, in turn, Application No. 9400450-4, filed Feb. 10, 1994.[0002] 1. Field of the Invention[0003] The present invention pertains to methods for the direct synthesis of compounds, e.g., polymeric or oligomeric compounds, that possess a complementary structure to a desired template molecule, e.g., a compound having biological activity. The present invention further pertains to compounds, e.g., polymers or oligomers produced by such methods, and the use thereof, e.g., as therapeutics or diagnostics based on their complementary structure to a molecule having a known activity. The direct synthesis methods provided herein, which are an extension of the technique generally known as "molecular imprinting," provide a powerful means of producing a compound having a desired activity. While t...

AI Technical Summary

Benefits of technology

[0043] (ii) allowing for the interactions between the functional groups on the preformed polymer and the biomolecule to equilibrate;

[0073] Thus, if it were possible to directly produce a compound comprising specific residues that specifically interact with such surface residues of a desired compound, e.g., a biomolecule, such compounds would be highly useful since they will likely affect the biological activity of the desired compound. Moreover, direct production would be further advantageous in that it would eliminate, or at least substantially reduce the need for highly complex and often fruitless drug screening methods. Moreover, such direct production would potentially give rise to compounds having enhanced properties in relation to compounds produced by conventional methods, e.g., enhanced solubility, stability, activity, affinity and / or avidity relative to ligands isolated from conventional sources.

[0077] The covalent approach requires a polymerizable derivative of the imprint species that is subsequently incorporated into the polymeric matrix during polymerization. These covalent bonds must be cleavable. The most common types of linkages are either esters of carboxylic / boronic acids, ketals or imines (Schiff bases). The necessary synthetic routes to accomplish such derivatives constrain the versatility of the approach and reduces the number of species that can be imprinted. After the polymer is formed, the imprint species is extracted by cleavage of these covalent bonds, usually by acid hydrolysis. Rebinding of the imprint species to the matrix is then achieved by re-establishing the covalent bonds between the print molecule and the matrix.

[0078] The other, non-covalent approach exclusively uses non-covalent interactions in the recognition of the imprint species. The greater the variety of interactions that are available between the imprint species and the functional monomers, the better the artificial binding site becomes. Typical interaction types that have been exploited are ionic interactions, hydrogen bonds, .pi.-90 -interactions, and hydrophobic interactions. Since they are strongly dependent on the polarity of the solvent, the best imprints are made in organic solvents such as chloroform or toluene. When these normally weak interactions have been established in solution, polymerization is initiated and a porous polymeric matrix is formed around the imprint species. The formed macromolecular architecture is thus complementary to the shape and function of the imprint species. After polymer formation the imprint molecule can be almost quantitatively recovered by mild extraction from the matrix. Association and dissociation of the original print molecule to the artificial binder takes place without requiring any covalent bond formation or cleavage. The target molecule simply diffuses in and out of the complementary sites.

[0079] Because the limited number of synthetic alternatives for reversible covalent interactions reduces the flexibility of this technique, the non-covalent protocol may be more versatile. The use of non-covalent interactions allows for the selection of several different monomers for simultaneous interaction with the imprint molecule. This in turn leads to a higher degree of selectivity of the imprinting site. A judiciously chosen "cocktail" of monomers may be the best way of making tailor-made artificial binding sites.

Problems solved by technology

These methods generally entail complex purification and characterization procedures, and the eventual identification of a natural product having biological activity, e.g., an antimicrobial agent.

While these methods have resulted in useful drugs, both natural and synthetic variants, they are generally very inefficient.

This is problematic as many assays, in particular animal testing, require large quantities of compound.

This is disadvantageous as it limits the number of compounds which can be feasibly tested.

Also, such methods are inherently complex and unpredictable.

Often it is difficult to predict and establish the structure / activity relationship among different compounds tested for activity.

This is difficult to assess, especially if the tested compounds vary significantly in structure.

This makes it difficult to determine the particular portion of the molecule that is significant for activity.

Also, such methods are prone to error.

Conversely, compounds which score negative in vitro may actually be active but score negative because of solubility problems which enable an otherwise active compound to cross the cell membrane in vivo.

However, these methods also suffer significant disadvantages.

In particular, peptides are often costly to synthesize, may be unstable (e.g., in the presence of proteases), and often are unable to cross cellular membranes.

However, such screening processes still are often ineffective.

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