Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library

A high-affinity, induced-fit receptor for NMe4I was discovered using dynamic combinatorial chemistry. The addition of the guest to a dynamic combinatorial library made using a racemic mixture of chiral building blocks caused the strong and highly diastereoselective amplification of the receptor at the expense of other library components. The receptor and its mode of binding were characterized by NMR, ITC, and re-equilibration experiments, from which it was deduced that the receptor probably forms a folded four-stave barrel shape on binding of the guest.     

Highly diastereoselective amplification from a dynamic combinatorial library of macrocyclic oligoimines

Cadmium promoted diastereoselective amplification of a single member from a dynamic combinatorial library of stereoisomeric oligoimines of different sizes allows the efficient preparation of a new macrocyclic polyamine.     

Templating a polymer-scaffolded dynamic combinatorial library

A water soluble polymer-scaffolded dynamic combinatorial library whose members can interconvert through acylhydrazone exchange was prepared and shown to re-equilibrate in the presence of macromolecular templates.     

Facile acetal dynamic combinatorial library

We herein report our first results on the use of simple acetalation chemistry in the service of dynamic combinatorial libraries (DCLs); the reaction between triethylene glycol and 4-nitrobenzaldehyde afforded a DCL of more than 15 cyclic and acyclic species; all of which were separated and characterized; the smaller macrocyclic compounds were successfully amplified by the use of ammonium ions.     

A topologically segregated one-bead-one-compound combinatorial glycopeptide library for identification of lectin ligands

A glycopeptide library containing more than 500,000 compounds has been constructed from a combination of Asn-linked carbohydrates using one-bead-one-compound combinatorial methodologies. The library was encoded with peptide markers that were topologically segregated on the interior of the solid support to negate interference with carbohydrate/protein recognition during lectin screening. Both the peptide backbone and carbohydrate components were randomized, but the glycosamine was limited to position 3 at the center of the pentapeptide to evaluate the influence of the peptide backbone in lectin recognition. Of the four lectins that were evaluated, remarkable selectivity was observed with wheat germ agglutinin (WGA), which recognizes N-acetyl glucosamine (GlcNAc). From more than 80,000 possible combinations, only six ligands were identified, all possessing GlcNAc. These compounds were independently synthesized, characterized, and evaluated in solution. All six of the glycopeptides showed higher affinity for WGA than GlcNAc, with one having a 4-fold increase. Modeling studies indicate that the peptide backbone is capable of interacting with amino acids in the active site of WGA, but these interactions are not strongly correlated with activity, suggesting that the primary role of the peptide is to properly orient the sugar in the recognition process.     

Tubulin-guided dynamic combinatorial library of thiocolchicine-podophyllotoxin conjugates

The use of tubulin as a target to influence the composition of the mixture from a dynamic combinatorial library, based on the disulfide bond exchange reaction, is described. ESI-FT-ICR-MS was used to determine the composition of the library. The heterodimeric compound amplified by this approach was used to design the homologous derivative with a two-carbon spacer in place of the disulfide function. The ability of the compounds to inhibit tubulin polymerization is reported and compared to thiocolchicine.     

Direct screening of a dynamic combinatorial library using mass spectrometry

A dynamic combinatorial library (DCL) screening approach is described that permits direct identification of the effective (from ineffective) combination of building blocks in the equilibrating DCL. The approach uses Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) together with sustained off-resonance irradiation collision activated dissociation (SORI-CAD) to detect noncovalent protein-DCL ligand complexes under native conditions. It was shown that in a single, rapid experiment one could concurrently identify all the ligands of interest from the DCL against a background of inactive DCL ligands while still in the presence of the target protein. This result has demonstrated that mass spectrometry may provide a fast preliminary screening approach to identify DCL candidates for later verification with more traditional but time-consuming analysis. The MS/MS enables DCL mixtures to be effectively deconvoluted without the need for either chromatography, synthesis of DCL sub-libraries, conversion of the DCL to a static library, or disruption of the protein-ligand complexes before analysis--all typically necessary for the current screening method for DCLs.     

Amplification of bifunctional ligands for calmodulin from a dynamic combinatorial library

A well known strategy to prepare high affinity ligands for a biological receptor is to link together low affinity ligands. DCC (dynamic combinatorial chemistry) was used to select bifunctional protein ligands with high affinity relative to the corresponding monofunctional ligands. Thiol to disulfide linkage generated a small dynamic library of bifunctional ligands in the presence of calmodulin, a protein with two independently mobile domains. The binding constant of the bifunctional ligand (disulfide) most amplified by the presence of calmodulin is nearly two orders of magnitude higher than that of the corresponding monofunctional ligand (thiol).     

Correlation between host-guest binding and host amplification in simulated dynamic combinatorial libraries

We present a versatile computer model of diverse dynamic combinatorial libraries, and examine how molecular recognition between library members and a template can be used to amplify the best binders. The correlation between host-guest binding and amplification was examined for a set of 50 libraries with >300 components each over a wide range of template and building block concentrations. Depending on these concentrations correlations vary from poor (when using a large excess of template) to good (for very dilute libraries and/or substoichiometric template concentrations), highlighting the need to choose the experimental conditions for dynamic combinatorial libraries thoughtfully.     

Amplification of a cyclic mixed-metalloporphyrin tetramer from a dynamic combinatorial library through orthogonal metal coordination

A cyclic porphyrin tetramer, consisting of two bis-phosphine substituted zinc(II) porphyrin units and two Rh(III)TPP units, is selected and amplified virtually quantitatively from a dynamic combinatorial library using 4,4'-bipy as a scaffold and using orthogonal binding modes.     

Target-induced selection of ligands from a dynamic combinatorial library of mono- and bi-conjugated oligonucleotides

A dynamic library of 15 mono- and bi-conjugated oligonucleotides was generated from a pool of three aldehydes and an oligonucleotide bearing two reactive amino groups. Addition of complementary target to the equilibrating mixture of imines resulted in selective amplification of one conjugate. UV-melting experiments confirmed that it was the best ligand among those that were tested. This study emphasizes that dynamic combinatorial chemistry can be used to simultaneously identify the type and the location of appended residues for stabilizing oligonucleotide complexes.