Dynamic Combinatorial Chemistry: Lysozyme Selects an Aromatic Motif That Mimics a Carbohydrate Residue

Potential Dental Biofilm Inhibitors: Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that Target Bacterial Glucosyltransferase

We applied dynamic combinatorial chemistry (DCC) to find novel ligands of the bacterial virulence factor glucosyltransferase (GTF) 180. GTFs are the major producers of extracellular polysaccharides, which are important factors in the initiation and development of cariogenic dental biofilms. Following a structure‐based strategy, we designed a series of 36 glucose‐ and maltose‐based acylhydrazones as substrate mimics. Synthesis of the required mono‐ and disaccharide‐based aldehydes set the stage for DCC experiments. Analysis of the dynamic combinatorial libraries (DCLs) by UPLC‐MS revealed major amplification of four compounds in the presence of GTF180. Moreover, we found that derivatives of the glucose‐acceptor maltose at the C1‐hydroxy group act as glucose‐donors and are cleaved by GTF180. The synthesized hits display medium to low binding affinity (K_D values of 0.4–10.0 mm) according to surface plasmon resonance. In addition, they were investigated for inhibitory activity in GTF‐activity assays. The early‐stage DCC study reveals that careful design of DCLs opens up easy access to a broad class of novel compounds that can be developed further as potential inhibitors.

Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination

Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.

Bivalent enzyme inhibitors discovered using dynamic covalent chemistry

A bivalent dynamic covalent chemistry (DCC) system has been designed to selectively target members of the homodimeric glutathione-S-transferase (GST) enzyme family. The dynamic covalent libraries (DCLs) use aniline-catalysed acylhydrazone exchange between bivalent hydrazides and glutathione-conjugated aldehydes and the bis-hydrazides act as linkers to bridge between each glutathione binding site. The resultant DCLs were found to be compatible and highly responsive to templating with different GST isozymes, with the best results coming from the M and Schistosoma japonicum (Sj) class of GSTs, targets in cancer and tropical disease, respectively. The approach yielded compounds with selective, nanomolar affinity (K(i) =61 nM for mGSTM1-1) and demonstrates that DCC can be used to simultaneously interrogate binding sites on different subunits of a dimeric protein.

Driven Evolution of a Constitutional Dynamic Library of Molecular Helices Toward the Selective Generation of [2 × 2] Gridlike Arrays under the Pressure of Metal Ion Coordination

Constitutional dynamics, self-assembly, and helical-folding control are brought together in the efficient Sc(OTf)3/microwave-catalyzed transimination of helical oligohydrazone strands, yielding highly diverse dynamic libraries of interconverting constituents through assembly, dissociation, and exchange of components. The transimination-type mechanism of the ScIII-promoted exchange, as well as its regioselectivity, occurring only at the extremities of the helical strands, allow one to perform directional terminal polymerization/depolymerization processes when starting with dissymmetric strands. A particular library is subsequently brought to express quantitatively [2 x 2] gridlike metallosupramolecular arrays in the presence of ZnII ions by component recombination generating the correct ligand from the dynamic set of interconverting strands. This behavior represents a process of driven evolution of a constitutional dynamic chemical system under the pressure (coordination interaction) of an external effector (metal ions).

DyNAs: Constitutional Dynamic Nucleic Acid Analogues

Dynamic cationic polymers were generated in aqueous media from functionally complementary monomers bearing nucleobase groups. (1)H NMR spectroscopy was used to follow the polycondensation reaction of the nucleobase-appended dihydrazides 1 and 2 with the dialdehydes B and C. The reversibility of these polymers was established by proton NMR spectroscopy through exchange of the dihydrazide 2 with polymer 1 B. The polymers 1 B, 2 B, 1 C, and 2 C represent dynamic biopolymers of nucleic acid type, DyNAs. Electrostatic interaction of these polymers with polyanionic entities, such as polyphosphates, polynucleotides, and polyaspartic acid, was shown to take place. It induces a change in size of the dynamic polymer, as it responds by an increase in degree of polymerization to an increase of the overall anionic charge introduced, that is, to the total electrostatic interaction.

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.

Protonic and Temperature Modulation of Constituent Expression by Component Selection in a Dynamic Combinatorial Library of Imines

The constitutional recomposition of a dynamic library of imines displays a complex behavior under the effect of two parameters, acidity and temperature. A qualitative analysis of the quantitative data is presented. The results illustrate the response of such a dynamic system to a physical stimulus (temperature) and a chemical effector (H+), thus demonstrating its adaptive behavior under the pressure of external factors. They also point to the possibility of modulating a given functional property (optical, electronic, ionic) by constitutional recomposition induced by a specific trigger. Such features are of great interest for the development of stimuli-responsive, functional dynamic materials.

Utilization of Self-Sorting Processes To Generate Dynamic Combinatorial Libraries with New Network Topologies

The synthesis of water-soluble, organometallic macrocycles is described. They were obtained by self-assembly in reactions of the half-sandwich complexes [[Ru(C6H5Me)Cl2]2], [[Ru(p-cymene)Cl2]2], [[Rh(Cp)Cl2]2], and [[Ir(Cp*)Cl2]2] with the ligand 5-dimethylaminomethyl-3-hydroxy-2-methyl-4-(1H)-pyridone in buffered aqueous solution at pH 8. The structure of the Ru-(p-cymene) complex was determined by single-crystal X-ray crystallography. Upon mixing, these complexes undergo scrambling reactions to give dynamic combinatorial libraries. In combination with structurally related complexes based on amino-methylated 3-hydroxy-2-(1H)-pyridone ligands, an exchange of metal fragments but no mixing of ligands was observed. This self-sorting behavior was used to construct dynamic combinatorial libraries of macrocycles, in which two four-component sub-libraries are connected by two common building blocks. This type of network topology influences the adaptive behavior of the library as demonstrated in selection experiments with lithium ions as the target.