Live‐Cell‐Templated Dynamic Combinatorial Chemistry

Dynamic covalent chemistry combines in a single step the screening and synthesis of ligands for biomolecular recognition. In order to do that, a chemical entity is used as template within a dynamic combinatorial library of interconverting species, so that the stronger binders are amplified due to the efficient interaction with the target. Here we employed whole A549 living cells as template in a dynamic mixture of imines, for which amplification reflects the efficient and selective interaction with the corresponding extracellular matrix. The amplified polyamine showed strong interaction with the A549 extracellular matrix in on‐cell NMR experiments, while combination of NMR, SPR, and molecular dynamics simulations in model systems provided insights on the molecular recognition event. Notably, our work pioneers the use of whole living cells in dynamic combinatorial chemistry, which paves the way towards the discovery of new bioactive molecules in a more biorelevant environment.     

A remarkably flexible and selective receptor for Ba2+ amplified from a hydrazone dynamic combinatorial library

A new [2+2] tetra-hydrazone macrocyclic receptor was significantly amplified in a dynamic combinatorial library upon templation with alkaline earth metal ions. After optimisation the product could be isolated in 95% yield and its interaction with ions was investigated by NMR and UV-Vis spectroscopy.     

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.     

An in situ Dynamic Continuum of Supramolecular Phosphoglycopeptides Enables Formation of 3D Cell Spheroids

Higher‐order assemblies of proteins, with a structural and dynamic continuum, is an important concept in biology, but these insights have yet to be applied in designing biomaterials. Dynamic assemblies of supramolecular phosphoglycopeptides (sPGPs) transform a 2D cell sheet into 3D cell spheroids. A ligand–receptor interaction between a glycopeptide and a phosphopeptide produces sPGPs that form nanoparticles, which transform into nanofibrils upon partial enzymatic dephosphorylation. The assemblies form dynamically and hierarchically in situ on the cell surface, and interact with the extracellular matrix molecules and effectively abolish contact inhibition of locomotion (CIL) of the cells. Integrating molecular recognition, catalysis, and assembly, these active assemblies act as a dynamic continuum to disrupt CIL, thus illustrating a new kind of biomaterial for regulating cell behavior.     

The development of a semiautomated procedure for the synthesis and screening of a large group of molecularly imprinted polymers

A method for synthesis and evaluation of molecularly imprinted polymers (MIPs) on a semiautomated miniature scale is reported. This technique combines molecular imprinting with the combinatorial chemistry approach, allowing rapid screening and optimizations of libraries of MIPs. The polymers were prepared and evaluated in situ by rebinding utilizing powder dispensing and liquid handling systems. MIPs were prepared by a combinatorial approach using methacrylic acid (MAA), 4-vinylpyridine (4-VP), acrylamide, and styrene as functional monomers, and acetonitrile and toluene as porogenic solvents. A drug substance having aromatic, hydroxyl, -O-CONH2 functional groups was selected as the template molecule for this study. The MIP library results demonstrated that the polymer prepared with MAA as functional monomer shows the strongest binding affinity, and therefore, is preferred for the preparation of this particular template molecule. Due to the low consumption of reagents, and more importantly, the demonstrated ability of this method to effectively identify optimal imprinting conditions, this small-scale combinatorial protocol is well suited for fast and efficient screening and optimizations of MIPs.     

Evaluation of the Polymerization and Recognition Mechanism for Phenol Imprinting SPE

In order to develop more efficient preparation technologies for imprinted polymers (MIPs), the nature of pre-polymerization and molecular recognition in MIP was investigated by molecular dynamics modeling (MD), ¹H NMR, FTIR and some indirect techniques. Phenol was used as the template for the study of mechanism through the analysis of hydrogen bonding, hydrophobic and π–π bonding interaction. The 4-vinylpyridine-based MIP had the highest selectivity to its phenol template. Hydrogen bonding was proved to be present by characterizing the pre-polymerization complex and evaluating the recognition process and the effects of rebinding solvents were also studied. It was found that a good rebinding solvent should have less affinity with both template and polymer, but good solubility. MD modeling and some indirect techniques demonstrated that 4-vinylpyridine-based MIP recognized phenol mainly through hydrophobic interactions when the rebinding medium was water, while hydrogen bonding was present in the recognition process when the rebinding solvent was n-hexane.     

Tailored polymer-supported templates in dynamic combinatorial libraries: simultaneous selection, amplification and isolation of synthetic receptors

The thermodynamically controlled synthesis and isolation of macrocyclic receptors from dynamic combinatorial libraries has been achieved in a single step using a polymer-supported template. The templates were cinchona alkaloids which show interesting enantio- and diastereoselective molecular recognition events in libraries based on pseudo-dipeptide building blocks. The synthetic routes used to derivatise the alkaloids and attach them to polymer supports minimised any influence of the tethering linkage on the templating activity. Systematic studies have been carried out to probe how the polymer morphology and the template loading affect the selectivity and isolation yield of the macrocyclic receptors. Molecular recognition between solid-phase bound templates and selected receptors also enabled their affinity-type chromatographic separation.     

Discovery of linear receptors for multiple dihydrogen phosphate ions using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry to discover a new series of linear hydrazone-based receptors that bind multiple dihydrogen phosphate ions. Through the use of a template-driven, selection-based approach to receptor synthesis, dynamic combinatorial chemistry allows for the identification of unexpected host structures and binding motifs. Notably, we observed the unprecedented selection of these linear receptors in preference to competing macrocyclic hosts. Furthermore, linear receptors containing up to nine building blocks and three different building blocks were amplified in the dynamic combinatorial library. The receptors were formed using a dihydrazide building block based on an amino acid-disubstituted ferrocene scaffold. A detailed study of the linear pentamer revealed that it forms a helical ditopic receptor that employs four acylhydrazone hydrogen-bond donor motifs to cooperatively bind two dihydrogen phosphate ions.     

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.     

Library Design Strategies To Accelerate Fragment-Based Drug Discovery

Fragment-based drug discovery (FBDD) has become an established approach for the generation of early lead candidates. However, despite its success and inherent advantages, hit-to-candidate progression for FBDD is not necessarily faster than that of traditional high-throughput screening. Thus, new technology-driven library design strategies have emerged as a means to facilitate more efficient fragment screening and/or subsequent fragment-to-hit chemistry. This minireview discusses such strategies, which cover the use of labeled fragments for NMR spectroscopy, X-ray crystallographic screening of specialized fragments, covalent linkage for mass spectrometry, dynamic combinatorial chemistry, and fragments optimized for easy elaboration.     

Diffusion NMR spectroscopy in supramolecular and combinatorial chemistry: an old parameter--new insights

Intermolecular interactions in solution play an important role in molecular recognition, which lies at the heart of supramolecular and combinatorial chemistry. Diffusion NMR spectroscopy gives information over such interactions and has become the method of choice for simultaneously measuring diffusion coefficients of multicomponent systems. The diffusion coefficient reflects the effective size and shape of a molecular species. Applications of this technique include the estimation of association constants and mapping the intermolecular interactions in multicomponent systems as well as investigating aggregation, ion pairing, encapsulation, and the size and structure of labile systems. Diffusion NMR spectroscopy can also be used to virtually separate mixtures and screen for specific ligands of different receptors, and may assist in finding lead compounds.     

Combinatorial chemistry approach to chiral catalyst engineering and screening: rational design and serendipity

An efficient asymmetric catalyst relies on the successful combination of a large number of interrelated variables, including rational design, intuition, persistence, and good fortune-not all of which are necessarily well-understood; this renders such practice largely empirical. As a result, the possibility of using combinatorial chemistry methods in asymmetric catalysis research has been widely recognized to be highly desirable. In this account, we attempt to show the principle and application of combinatorial approach in the discovery of chiral catalysts for enantioselective reactions. The concept focuses on the strategy for the creation of a modular chiral catalyst library by two-component ligand modification of metal ions on the basis of molecular recognition and assembly. The self-assembled chiral catalyst with two different ligands indeed exhibited synergistic effects in terms of both enantioselectivity and activity in comparison with its corresponding homocombinations in many reactions. The examples described in this paper demonstrated the powerfulness of combinatorial approach for the discovery of novel chiral catalyst systems, particularly for the development of highly efficient, enantioselective, and practical catalysts for enantioselective reactions. We hope this concept will stimulate further work on the discovery of more highly efficient and enantioselective catalysts, as well as unexpected classes of catalysts or catalytic enantioselective reactions in the future with the help of a combinatorial chemistry approach.     

Combinatorial Synthesis and Multidimensional NMR Spectroscopy: An Approach to Understanding Protein–Ligand Interactions

Combinatorial chemistry is a laboratory emulation of natural recombination and selection processes. Strategies in this developing discipline involve the generation of diverse, molecular libraries through combinatorial synthesis and the selection of compounds that possess a desired property. Such approaches can facilitate the identification of ligands that bind to biological receptors, promoting our chemical understanding of cellular processes. This article illustrates that the coupling of combinatorial synthesis, multidimensional NMR spectroscopy, and biochemical methods has enhanced our understanding of a protein receptor used commonly in signal transduction, the Src Homology 3 (SH3) domain. This novel approach to studying molecular recognition has revealed a set of rules that govern SH3–ligand interactions, allowing models of receptor–ligand complexes to be constructed with only a knowledge of the polypeptide sequences. Combining combinatorial synthesis with structural methods provides a powerful new approach to understanding how proteins bind their ligands in general.     

Dynamic combinatorial libraries: new opportunities in systems chemistry

Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of these molecular networks at systems level is essential for their use as a selection tool and creates exciting new opportunities in systems chemistry. In this feature article we discuss selected examples and considerations related to the advanced exploitation of dynamic combinatorial libraries for their originally conceived purpose of identifying strong binding interactions. Also reviewed are examples illustrating a trend towards increasing complexity in terms of network behaviour and reversible chemistry. Finally, new applications of dynamic combinatorial chemistry in self-assembly, transport and self-replication are discussed.     

Salt‐Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media

Dynamic combinatorial libraries are powerful systems for studying adaptive behaviors and relationships, as models of more complex molecular networks. With this aim, we set up a chemically diverse dynamic library of pseudopeptidic macrocycles containing amino‐acid side chains with differently charged residues (negative, positive, and neutral). The responsive ability of this complex library upon the increase of the ionic strength has been thoroughly studied. The families of the macrocyclic members concentrating charges of the same sign showed a large increase in its proportion as the ionic strength increases, whereas those with residues of opposite charges showed the reverse behavior. This observation suggested an electrostatic shielding effect of the salt within the library of macrocycles. The top‐down deconvolution of the library allowed us to obtain the fundamental thermodynamic information connecting the library members (exchange equilibrium constants), as well as to parameterize the adaptation to the external stimulus. We also visualized the physicochemical driving forces for the process by structural analysis using NMR spectroscopy and molecular modeling. This knowledge permitted the full understanding of the whole dynamic library and also the de novo design of dynamic chemical systems with tailored co‐adaptive relationships, containing competing or cooperating species. This study highlights the utility of dynamic combinatorial libraries in the emerging field of systems chemistry.     

Characterisation of glycoprotein ligands synthesised using solid-phase combinatorial chemistry

A combination of rational design based on mimicking natural protein-carbohydrate interactions and solid-phase combinatorial chemistry has led to the identification of an affinity ligand which displays selectivity for the mannose moiety of glycoproteins. The ligand was initially identified as 32/18, a triazine scaffold substituted with 2-acetylpyrrole (32) and 5-aminoindan (18). However, characterisation of the immobilised ligand by release from the matrix via a cleavable linker, (4s,5s)-4,5-di(aminomethyl)-2,2-dimethyldioxolane, and using a non-destructive on-resin method, 13C NMR spectroscopy, confirmed that the putative ligand 32/18 was, in fact, 18/18, the disubstituted 5-aminoindan. 1H NMR studies on the interaction of alpha-D-methylmannoside with the ligand 18/18 in solution confirm the involvement of the hydroxyl group in the C-2 position.     

p‐Azidophenylarsenoxide: An Arsenical “Bait” for the In Situ Capture and Identification of Cellular Arsenic‐Binding Proteins

Identification of arsenic‐binding proteins is important for understanding arsenic health effects and for developing arsenic‐based therapeutics. We report here a strategy for the capture and identification of arsenic‐binding proteins in living cells. We designed an azide‐labeled arsenical, p‐azidophenylarsenoxide (PAzPAO), to serve bio‐orthogonal functions: the trivalent arsenical group binds to cellular proteins in situ, and the azide group facilitates click chemistry with dibenzylcyclooctyne. The selective and efficient capture of arsenic‐binding proteins enables subsequent enrichment and identification by shotgun proteomics. Applications of the technique are demonstrated using the A549 human lung carcinoma cells and two in vitro model systems. The technique enables the capture and identification of 48 arsenic‐binding proteins in A549 cells incubated with PAzPAO. Among the identified proteins are a series of antioxidant proteins (e.g., thioredoxin, peroxiredoxin, peroxide reductase, glutathione reductase, and protein disulfide isomerase) and glyceraldehyde‐3‐phosphate dehydrogenase. Identification of these functional proteins, along with studies of arsenic binding and enzymatic inhibition, points to these proteins as potential molecular targets that play important roles in arsenic‐induced health effects and in cancer treatment.     

The dark side of disulfide-based dynamic combinatorial chemistry

During the last two decades, disulfide-based dynamic combinatorial chemistry has been extensively used in the field of molecular recognition to deliver artificial receptors for molecules of biological interest. Commonly, the nature of library members and their relative amounts are provided from HPLC-MS analysis of the libraries, allowing the identification of potential binders for a target (bio)molecule. By re-investigating dynamic combinatorial libraries generated from a simple 2,5-dicarboxy-1,4-dithiophenol building block in water, we herein demonstrated that multiple analytical tools were actually necessary in order to comprehensively describe the libraries in terms of size, stereochemistry, affinity, selectivity, and finally to get a true grasp on the different phenomena at work within dynamic combinatorial systems.

We show that multiple analytical tools are necessary in order to describe the different phenomena within disulfide-based dynamic combinatorial libraries in terms of size, stereochemistry, affinity and selectivity.     

Dynamic combinatorial chemistry: on the road to fulfilling the promise

Dynamic combinatorial chemistry makes use of reversible reactions between functionalised monomeric building blocks to generate a mixture of products (dimers or oligomers) under thermodynamic equilibrium. This system reorganises upon addition of a target so that species that bind to, and are therefore stabilised by the target, are favourably formed and are thus amplified. Since the mid-1990's, dynamic combinatorial chemistry has been successfully applied to the identification/selection of ion receptors, enzyme inhibitors, catalysts, materials and nucleic acid ligands. Although it is now established as a powerful tool with broad applications some intrinsic limitations appeared when working on systems of increasing complexity. We present here the most recent advances in the field of dynamic combinatorial chemistry that have been developed to overcome these limitations and explore new areas of application.     

Determination and Characterization of the Uptake of Voriconazole in Human Lung Epithelial Cells by High-Performance Liquid Chromatography–Tandem Mass Spectrometry

Voriconazole is used to prevent invasive pulmonary aspergillosis. However, little is known about the concentrations of voriconazole in human lung epithelial cells (A549), which is the target for preventing invasive pulmonary aspergillosis. The goal of this study was to develop a high-performance liquid chromatography–tandem mass spectrometry method to quantify voriconazole in A549 cells. A triple-quadrupole mass spectrometer in selected reaction monitoring mode was used with positive electrospray ionization. The total duration of each run was 5?min. The calibration curves fit a least squares model for the voriconazole concentration ranging from 0.625 to 160?ng/mL. Intraday and interday coefficients of variation were less than 10%. Recoveries at the concentrations of the quality control samples where greater than 85%, and the matrix effects showed that the ratios of the peak response exhibited a 15% suppression of the signal in the matrix compared to water. Voriconazole may penetrate A549 cells. However, the voriconazole uptake was slow in A549 cells, reaching a plateau at 2?h, where the dose-dependent intracellular voriconazole concentrations were 1.98?±?0.38, 4.43?±?0.54, and 8.14?±?0.52?ng/mg protein for extracellular voriconazole concentrations of 5, 10, and 20?µg/mL, respectively. The uptake of voriconazole by A549 cells was linear at extracellular concentrations from 0 to 20?µg/mL. This study established a rapid and sensitive method suitable for determining voriconazole in A549 cells and described the kinetic properties of the absorption of voriconazole by A549 cells.