Dynamic Combinatorial Chemistry Research Articles

Amplification of a metallacyclic receptor out of a dynamic combinatorial library.

We present herein the Pt(ii)-directed self-assembly in water of a new conformationally flexible N-monoalkyl-4,4-bipyridinium-based ditopic ligand into a library of six different metallacyclic structures. This constitutionally dynamic library can be pushed to increase the production of one of the supramolecules in aqueous media, either by controlling the concentration of the building blocks or upon addition of an appropriate aromatic substrate.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media.

A straightforward four-step synthesis leads to the preparation of C2-symmetric dithiols containing a central aromatic core and amino acid side chains. These building blocks allow the preparation of dynamic covalent libraries of pseudopeptidic macrocycles in aqueous media that cover a broad range of polarities, functional groups and bulkiness mirroring the diversity found in natural peptides. The versatility of the generated dynamic libraries has been illustrated by the amplification of two different members from the same library upon the action of two biologically relevant templates.

From Dynamic Combinatorial Chemistry to in Vivo Evaluation of Reversible and Irreversible Myeloperoxidase Inhibitors.

The implementation of dynamic combinatorial libraries allowed the determination of highly active reversible and irreversible inhibitors of myeloperoxidase (MPO) at the nanomolar level. Docking experiments highlighted the interaction between the most active ligands and MPO, and further kinetic studies defined the mode of inhibition of these compounds. Finally, in vivo evaluation showed that one dose of irreversible inhibitors is able to suppress the activity of MPO after inducing inflammation.

Thermodynamic Selection of Supramolecular Nanomaterials from Dynamic Peptide Libraries

Short peptide sequences are powerful building blocks for designing new nanomaterials, but their self-assembled structures are difficult to predict. In the latest issue of Nature Nanotechnology , Ulijn and colleagues present a methodology to select peptide sequences from dynamic combinatorial libraries that produce the most stable supramolecular nanostructures.

DNA functionalization by dynamic chemistry.

Dynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

Dynamic peptide libraries for the discovery of supramolecular nanomaterials.

Sequence-specific polymers, such as oligonucleotides and peptides, can be used as building blocks for functional supramolecular nanomaterials. The design and selection of suitable self-assembling sequences is, however, challenging because of the vast combinatorial space available. Here we report a methodology that allows the peptide sequence space to be searched for self-assembling structures. In this approach, unprotected homo- and heterodipeptides (including aromatic, aliphatic, polar and charged amino acids) are subjected to continuous enzymatic condensation, hydrolysis and sequence exchange to create a dynamic combinatorial peptide library. The free-energy change associated with the assembly process itself gives rise to selective amplification of self-assembling candidates. By changing the environmental conditions during the selection process, different sequences and consequent nanoscale morphologies are selected.

Click and chemically triggered declick reactions through reversible amine and thiol coupling via a conjugate acceptor

It has now been shown that amines and thiols can be tethered together through a Meldrum's acid-derived conjugate acceptor for applications ranging from dynamic combinatorial chemistry to biochemistry to polymer chemistry. Furthering the utility of this chemistry, the ability to then chemically ‘declick' back to the unaltered amine and thiol components is also demonstrated.

ChemInform Abstract: The Dynamic Covalent Chemistry of Esters, Acetals and Orthoesters

AbstractReview: [fundamental aspects of three related reversible covalent reactions and their uses in dynamic combinatorial libraries and the self‐assembly of stimuli‐responsive molecules and materials; 63 refs.

Acylhydrazone-based dynamic combinatorial libraries: study of the thermodynamic/kinetic evolution, configurational and coordination dynamics

Se describe la selectividad cinética y termodinámica de la formación de acil-hidrazona en librerías combinatorias dinámicas (DCL). Se generaron reacciones competitivas a partir de hidrazidas: isoniazida, 4-nitro-benzohidrazida, 4-dimetilamino-benzohidrazida y hidrazida nicotínica; así como a partir de los derivados de aldehído: benzaldehído y 2-piridin-carboxaldehido. Las especies obtenidas y la distribución de los DCLs fueron monitoreados mediante espectroscopia 1H-NMR, encontrándose que las acil-hidrazonas que contenían la 4-dimetilamino-benzohidrazida son tanto el producto cinético, como el termodinámico de sus respectivas librerías. También se investigaron las dinámicas de configuración y de coordinación para algunas de estas librerías. Los resultados obtenidos permitieron estudiar la redistribución de los componentes y la amplificación de uno o más productos usando luz e iones metálicos como plantillas físicas y químicas, respectivamente.

Four Simultaneously Dynamic Covalent Reactions. Experimental Proof of Orthogonality.

Dynamic covalent reactions are widely used in dynamic combinatorial chemistry. Most of these reactions are run under differing reaction conditions and exhibit cross-reactivity when components of multiple reactions are present in one reaction vessel. Herein, we report the study of four dynamic covalent reactions that react reversibly under identical reaction conditions and do not exhibit any cross-reactivity. Dynamic behavior was shown via (1)H NMR based exchange experiments. Computational deconvolution of (1)H NMR spectra containing the components for more than one of the orthogonal reactions allowed for a semiquantitative analysis of the complex mixtures formed, showing that the reactions proceed independently of each other. Therefore, it is possible to use all four reactions in one pot in a simultaneous, yet orthogonal fashion. This opens up possibilities for the preprogrammed formation of complex thermodynamic assemblies.

Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery.

Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry.

Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X‐ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis‐acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240‐fold improvement in potency compared to the parent hits. Subsequent X‐ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit‐identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit‐to‐lead optimization.

Hexavalent glycoclusters having tris-bipyridine ferrous complex cores as minimum combinatorial libraries for probing carbohydrate–carbohydrate interactions

2,2′-Bipyridines having two lactoside- or maltoside-appendages were prepared and then, complexed with ferrous ion to afford the corresponding tris-bipyridine ferrous complexes presenting hexavalent lactoside/maltoside clusters. Each of these complexes provided a simple dynamic combinatorial library composed of two diastereomeric stereoisomers (Δ and Λ) whose ratios depend on their relative stabilities. These tris-bipyridine ferrous complexes showed different responses from each other towards alkaline/alkaline-earth metal salts. For example, the lactoside cluster showed unique two-step binding profiles, whereas the maltoside cluster did simple Langmuir-type ones. Our referential experiments revealed that intermolecular lactoside–lactoside interactions mediated by the alkaline/alkaline-earth metal cations play essential roles in the two-step binding profiles.

ChemInform Abstract: Experimental Binding Energies in Supramolecular Complexes

AbstractReview: 764 refs.

Experimental Binding Energies in Supramolecular Complexes.

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.

Supramolecular detection of geometrical differences of azobenzene carboxylates

In dynamic combinatorial chemistry, the geometry of a template can be translated into the composition of a library of interchanging components. In this study, such a dynamic combinatorial library was used for the first time to detect and evaluate differences in the geometry of isomers of photoswitchable azobenzene based templates.

Probing the geometric constraints of RNA binding via dynamic covalent chemistry

Dynamic Combinatorial Chemistry (DCC) has proven to be a reliable method for identifying hit compounds for target nucleic acid (DNA and RNA) sequences. Typically, these hit compounds are subjected to a lengthy process of optimization via traditional medicinal chemistry. Here, we examine the potential of DCC to also generate and test variations on a hit compound as a method for probing the binding site of an RNA-targeted compound. Specifically, we demonstrate that addition of linker dithiols to a disulfide library containing a known binder to the HIV-1 frameshift-stimulatory RNA (a critical regulator of the HIV life cycle) can yield a mixture of new bridged structures incorporating the dithiol, depending on dithiol structure. Equilibration of this library with the HIV FSS RNA resulted in selection of the original disulfide in preference to bridged structures, suggesting incorporation of the bridge is not compatible with this particular binding site. Application of this strategy to other RNA targets should allow for rapidly profiling the affinity of modified compounds.

Identification of inhibitors for vascular endothelial growth factor receptor by using dynamic combinatorial chemistry

The novel analysis method consisting of size-exclusion chromatography (SEC) and HRMS analysis was firstly applied in the discovery of potential inhibitors towards cancer drug targets. With vascular endothelial growth factor receptor (VEGFR-2) as a target, dynamic combinatorial libraries (DCLs) were prepared by reacting aldehydes with amines. Four sensitive binders targeted VEGFR-2 were directly isolated from the library. Antitumor activity test in vitro and inhibition experiments toward angiogenesis were also carried out.

Spectroscopic and Computational Investigations of The Thermodynamics of Boronate Ester and Diazaborole Self-Assembly.

The solution phase self-assembly of boronate esters, diazaboroles, oxathiaboroles, and dithiaboroles from the condensation of arylboronic acids with aromatic diol, diamine, hydroxythiol, and dithiol compounds in chloroform has been investigated by (1)H NMR spectroscopy and computational methods. Six arylboronic acids were included in the investigations with each boronic acid varying in the substituent at its 4-position. Both computational and experimental results show that the para-substituent of the arylboronic acid does not significantly influence the favorability of forming a condensation product with a given organic donor. The type of donor, however, greatly influences the favorability of self-assembly. (1)H NMR spectroscopy indicates that condensation reactions between arylboronic acids and catechol to give boronate esters are the most favored thermodynamically, followed by diazaborole formation. Computational investigations support this conclusion. Neither oxathiaboroles nor dithiaboroles form spontaneously at equilibrium in chloroform at room temperature. Computational results suggest that the effect of borylation on the frontier orbitals of each donor helps to explain differences in the favorability of their condensation reactions with arylboronic acids. The results can inform the use of boronic acids as they are increasingly utilized in the dynamic self-assembly of organic materials and as components in dynamic combinatorial libraries.