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.     

Ligand amplification in a dynamic combinatorial glycopeptide library

N-acetyl glucosamine binding protein amplifies the concentration of one member in a dynamic combinatorial glycopeptide library based on exchanging disulfides.     

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.     

Discovery of a novel synthetic phosphatase from a bead-bound combinatorial library

Using split/pool encoded synthesis and a colorimetric catalysis assay, a number of synthetic phosphatase catalysts were developed.     

Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation

The predictable relationship between beta-amino acid sequence and folding has inspired several biological applications of beta-peptides. For many such applications, it would be desirable to prepare and screen beta-peptide libraries. However, standard peptide synthesis protocols are not efficient enough to support a library approach for many types of beta-peptides. We recently optimized the solid-phase synthesis of beta-peptides using microwave irradiation, and we have now adapted this approach to synthesis on polystyrene macrobeads. We rapidly prepared a high-quality beta-peptide combinatorial library via a split-and-mix strategy. This library was screened in search of beta-peptide antagonists of the p53-MDM2 protein-protein interaction.     

Chemoinformatic analysis of a supertargeted combinatorial library of styryl molecules

Styryl dyes are fluorescent, lipophilic cations that have been used as specific labeling probes of mitochondria in living cells. For specific applications such as epifluorescence microscopy or flow cytometry, it is often desirable to synthesize fluorescent derivatives with optimized excitation, emission, and localization properties. Here, we present a chemoinformatic strategy suitable for multiparameter analysis of a combinatorial library of styryl molecules supertargeted to mitochondria. The strategy is based on a simple additive model relating the spectral and subcellular localization characteristics of styryl compounds to the two chemical building blocks that are used to synthesize the molecules. Using a cross-validation approach, the additive model predicts with a high degree of confidence the subcellular localization and spectral properties of the styryl product, from numerical scores that are independently associated with the individual building blocks of the molecule. The fit of the data indicates that more complex, nonadditive interactions between the two building blocks play a minor role in determining the molecule's optical or biological properties. Moreover, the observed additive relationship allows mechanistic inferences to be made regarding the structure-property relationship observed for this particular class of molecules. It points to testable, mechanistic hypotheses about how chemical structure, fluorescence, and localization properties are related.     

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.     

Prediction of enantiomeric excess in a combinatorial library of catalytic enantioselective reactions

A quantitative structure-enantioselectivity relationship was established for a combinatorial library of enantioselective reactions performed by addition of diethyl zinc to benzaldehyde. Chiral catalysts and additives were encoded by their chirality codes and presented as input to neural networks. The networks were trained to predict the enantiomeric excess. With independent test sets, predictions of enantiomeric excess could be made with an average error as low as 6% ee. Multilinear regression, perceptrons, and support vector machines were also evaluated as modeling tools. The method is of interest for the computer-aided design of combinatorial libraries involving chiral compounds or enantioselective reactions. This is the first example of a quantitative structure-property relationship based on chirality codes.     

A novel approach to combinatorial library design

We address the problem of designing a general-purpose combinatorial library to screen for pharmaceutical leads. Conventional approaches focus on diversity as the primary factor in designing such libraries. We suggest making screening libraries out of a set of pharmaceutically relevant scaffolds, with multiple analogs per scaffold. The rationale for this rests on the fact that even though the hit-rate in active series is much higher than in the database as a whole, often a large fraction of the compounds in active series are inactive. This is especially true when the series has not been optimized for the target under study. We introduce the concept of hit-rate within a series and use historic screening data to arrive at a crude estimate for it. We then use simple probability arguments to show that 50-100 compounds are required in each series in order to be nearly certain of finding at least one active compound in each true active series for any given target.     

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.     

Quantitative determination of single-bead metal content from a peptide combinatorial library

An electrothermal vaporizer inductively coupled plasma mass spectrometer (ETV-ICPMS) was used to quantitatively screen metals bound to single polystyrene (TentaGel) beads with immobilized oligopeptides. Tests were performed using ETV-ICPMS to screen a series of identical beads as well as a series of combinatorial library beads exposed to a multimetal solution composed of Mg2+, Mn2+, Ni2+, Cu2+, Cd2+, Eu2+, and Pb2+. The residual metal content remaining bound to the beads after acid extractions was also analyzed by solid sampling of the entire bead using oxygen ashing in the ETV. Nine beads (80 mesh, 0.25 mmol g(-1) nominal capacity) containing covalently attached polyaspartic acid (PLAsp; n = 20) showed metal extract concentrations in the range of 4-130 ng mL(-1). After normalizing by bead volume, the precision of capacity measurements in a single bead (7-14%) was primarily dictated by analysis error and contributions from bead diameter measurement with negligible contributions, surprisingly, from variations in site density from bead to bead. A sample combinatorial library of the sequence GXXGXXGXXGXX (X = cysteine, aspartic acid, or glutamic acid and G = glycine) (60 mesh, 0.25 mmol g(-1) nominal capacity) was also used to demonstrate the utility of this method. Metal extract concentrations ranged from 1 to 1300 ng mL(-1) with significant concentration variation between beads, indicating the individual selectivity on each bead. For these larger beads, analysis precision (i.e., capacity precision) was further improved to 3-10% due to the overall increase in bead metal content. Through metal extract determinations, ETV-ICPMS was shown to be a viable nondestructive tool for full metal characterization of "hit" sequences belonging to a combinatorial library.     

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.     

Inhibitor fingerprinting of matrix metalloproteases using a combinatorial peptide hydroxamate library

We report the inhibitor fingerprints of seven matrix metalloproteases, representing all five established families of this important class of enzymes, against a highly diversified small-molecule library. A total of 1400 peptide hydroxamates were individually prepared by systematically permuting both natural and unnatural amino acids across the P1', P2', and P3' positions, thereby generating an inhibitor library with three-pronged structural diversity. High-throughput screenings were efficiently conducted in microtiter plate format, providing a rapid and quantitative determination of inhibitor potency across the panel of enzymes. Despite similarities in substrate preferences and structural homologies within this class of enzymes, our findings revealed distinct patterns of inhibition for each MMP against varied chemical scaffolds. The resulting inhibitor fingerprints readily facilitated the identification of inhibitors with good potency as well as desirable selectivity, potentially minimizing adverse effects when developing such leads into candidate drugs. The strategy also offers a novel method for the functional classification of matrix metalloproteases, on the basis of the characteristic profiles obtained using the diverse set of inhibitors. This approach thus paves the way forward in lead identification by providing a rapid and quantitative method for selectivity screening at the outset of the drug discovery process.     

A consecutive Diels-Alder approach toward a Tet repressor directed combinatorial library

A combinatorial library of 180 tetracycline analogs was generated by solution phase parallel synthesis applying a consecutive Diels-Alder strategy. Chemical methodology suitable for three-dimensional solution phase parallel synthesis was developed that enabled us to generate a collection of potential TetR inducers. The synthesis was built on cross-conjugated trienes as central building blocks facilitating two consecutive cycloaddition processes with different dienophiles. Upon sequential exposure to naphthoquinone and maleimide derivatives, the generation of a carbocyclic skeleton of type 2 incorporating the diversity elements R¹-R⁵ was envisaged.