Dynamic Combinatorial Chemistry Research Articles

Development of Receptor for Advanced Glycation End Products (RAGE) ligands through target directed dynamic combinatorial chemistry: a novel class of possible antagonists.

RAGE is a transmembrane receptor of immunoglobulin family that can bind various endogenous and exogenous ligands, initiating the inflammatory downstream signaling pathways, including inflammaging. Therefore, RAGE represents an attractive drug target for age-related diseases. For the development of small-molecule RAGE antagonists, we employed protein-templated dynamic combinatorial chemistry (ptDCC) using RAGE's VC1 domain as a template, the first application of this approach in the context of RAGE. The affinities of DCC hits were validated using microscale thermophoresis. Subsequent screening against AGE2 (glyceraldehyde-modified AGE)-sRAGE (solubleRAGE) (AGE2-BSA/sRAGE) interaction using ELISA tests led to the identification of antagonists with micromolar potency. Our findings not only demonstrate the successful application of ptDCC on RAGE but also highlight its potential to address the pressing need for alternative strategies for the development of small-molecule RAGE antagonists, an area of research that has experienced a slowdown in recent years.

Generalist versus Specialist Self-Replicators.

Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.

Hit optimization by dynamic combinatorial chemistry on Streptococcus pneumoniae energy-coupling factor transporter ECF-PanT.

Herein, we present the first application of target-directed dynamic combinatorial chemistry (tdDCC) to the whole complex of the highly dynamic transmembrane, energy-coupling factor (ECF) transporter ECF-PanT in Streptococcus pneumoniae. In addition, we successfully employed the tdDCC technique as a hit-identification and -optimization strategy that led to the identification of optimized ECF inhibitors with improved activity. We characterized the best compounds regarding cytotoxicity and performed computational modeling studies on the crystal structure of ECF-PanT to rationalize their binding mode. Notably, docking studies showed that the acylhydrazone linker is able to maintain the crucial interactions.

Discovery of selective monosaccharide receptors via Dynamic Combinatorial Chemistry

The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly...

Photoswitchable imines: aryliminopyrazoles quantitatively convert to long-lived Z-isomers with visible light

Simple structural modifications significantly boost the photochromic performance of imine-based photoswitches. This work lays a foundation for exploring new motifs in light-addressable dynamic combinatorial chemistry.

Hydrogen Sulfate-Templated Synthesis of a Bis-Ferrocene Macrocycle

AbstractA bis-ferrocene macrocycle was synthesized by reversible acylhydrazone formation under thermodynamic control, starting from a ferrocene functionalized with hydrazide and protected aldehyde moieties. A hydrogen sulfate anion acts as a template to direct the synthesis specifically toward the macrocyclic dimer, due to a weak but selective binding interaction. This work highlights the utility of dynamic combinatorial chemistry as an approach to macrocycle synthesis.

Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides.

Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.

Identification of HuR–RNA Interfering Compounds by Dynamic Combinatorial Chemistry and Fluorescence Polarization

Identification of HuR–RNA Interfering Compounds by Dynamic Combinatorial Chemistry and Fluorescence Polarization

Pushing the Boundaries of Diversity: Innovative Design and Synthesis of Hydrazone-Based Dynamic Combinatorial Libraries of Macrocycles

Pushing the Boundaries of Diversity: Innovative Design and Synthesis of Hydrazone-Based Dynamic Combinatorial Libraries of Macrocycles

Combinatorial Synthesis of Covalent Organic Framework Particles with Hierarchical Pores and Their Catalytic Application.

Precise tailoring of the aggregation state of covalent organic frameworks (COFs) to form a hierarchical porous structure is critical to their performance and applications. Here, we report a one-pot and one-step strategy of using dynamic combinatorial chemistry to construct imine-based hollow COFs containing meso- and macropores. It relies on a direct copolymerization of three or more monomers in the presence of two monofunctional competitors. The resulting particle products possess high crystallinity and hierarchical pores, including micropores around 0.93 nm, mesopores widely distributed in the range of 3.1-32 nm, and macropores at about 500 nm, while the specific surface area could be up to 748 m2·g-1, with non-micropores accounting for 60% of the specific surface area. The particles demonstrate unique advantages in the application as nanocarriers for in situ loading of Pd catalysts at 93.8% loading efficiency in the copolymerization of ethylene and carbon monoxide. The growth and assembly of the copolymer could thus be regulated to form flower-shaped particles, efficiently suppressing the fouling of the reactor. The copolymer's weight-average molecular weight and the melting temperature are also highly improved. Our method provides a facile way of fabricating COFs with hierarchical pores for advanced applications in catalysis.

Peptide and Peptidomimetic Assemblies in Dynamic Combinatorial Chemistry

AbstractA strong revival of interest has been dedicated to peptides over the last few years, in different fields including drug discovery, biosensing and material sciences. The use of dynamic covalent chemistry has allowed the development of self‐adaptative peptides or peptidomimetics, responsive to their environment. The development of methods allowing the building, screening or deconvolution of libraries of peptides is a highly active research area and dynamic combinatorial chemistry represents an innovative and underexploited method in this field. This Review gives an overview of the use of dynamic covalent chemistry as a tool to produce peptides or peptidomimetics, with particular attention to applications in dynamic combinatorial chemistry.

De Novo Design of pre-miR-21 Maturation Inhibitors: Synthesis and Activity Assessment.

Targeting RNA with small molecules is a major challenge of current medicinal chemistry, and the identification and design of original scaffolds able to selectively interact with an RNA target remains difficult. Various approaches have been developed based on classical medicinal chemistry strategies (fragment-based drug design, dynamic combinatorial chemistry, HTS or DNA-encoded libraries) as well as on advanced structural biology and biochemistry methodologies (such as X-ray, cryo-EM, NMR, or SHAPE). Here, we report the de novo design, synthesis, and biological evaluation of RNA ligands using a straightforward and sustainable chemistry combined with molecular docking and biochemical and biophysical studies that allowed us to identify a novel pharmacophore for RNA binding. Specifically, we focused on the targeting of biogenesis of microRNA-21, the re-known oncogene. This led us not only to promising inhibitors but also to a better understanding of the interactions formed between the small molecule compounds and the RNA target paving the way for the rational design of efficient inhibitors with potential anticancer activity.

Deciphering dynamic combinatorial libraries of glycoclusters with miniaturized weak affinity chromatography coupled with mass spectrometry (nano-FAC-MS)

We report an original methodology based on affinity chromatography coupled with mass spectrometry to decipher the complexity of dynamic combinatorial libraries (DCLs) of glycoclusters. Such libraries are intended to boost the design of potential therapeutic anti-infectious agents targeting Pseudomonas aeruginosa, which is responsible for numerous diseases, mostly found in hospitals as major a cause of nosocomial infections. Dynamic combinatorial chemistry provides a rapid access to an equilibrating mixture of glycocluster candidates through the formation of reversible covalent bonds under thermodynamic control. Identifying each molecule in the complex mixture overcomes challenges due to the dynamic process. Selection of glycoclusters candidates was first realized on a model lectin (Concanavalin A, ConA). Home-made affinity nanocolumns, containing covalently immobilized ConA and have volumes in the microliter range, were used to separate DCLs of glycoclusters with respect to their specific lectin binding properties under buffered aqueous conditions. Miniaturization facilitates the inline coupling with MS detection in such purely aqueous and buffered conditions and reduces target protein consumption. Monolithic lectin-affinity columns prepared by immobilization of ConA were first characterized using a known ligand. The amount of active binding immobilized lectin is 61 ± 5 pmol on 8.5-cm length column. We demonstrated the ability of our approach to evaluate individual dissociation constants of species directly in the complex mixture. The concept was then successfully applied to the screening of DCLs of more complex glycoclusters to identify (by mass spectrometry) and rank the ligands (by relative breakthrough curve delay) according to their affinity for the immobilized lectin in a single experiment.

Templated Enzymatic Synthesis of δ-Cyclodextrin.

While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.

Sequence-selective duplex formation and template effect in recognition-encoded oligoanilines.

A new family of duplex-forming recognition encoded oligomers, capable of sequence selective duplex formation and template directed synthesis, was developed. Monomers equipped with both amine and aldehyde groups were functionalized with 2-trifluoromethylphenol or phosphine oxide as H-bond recognition units. Duplex formation and assembly properties of homo- and hetero-oligomers were studied by 19F and 1H NMR experiments in chloroform. The designed backbone prevents the undesired 1,2-folding allowing sequence-selective duplex formation, and the stability of the antiparallel duplex is 3-fold higher than the parallel arrangement. Dynamic combinatorial chemistry was exploited for the templated synthesis of complementary oligomers, showing that an aniline dimer can template the formation of the complementary imine. The key role of the H-bond recognition confers to the system the ability to discriminate a mutated donor monomer incapable of H-bonding. Sequence selective duplex formation combined with the template effect makes this system an attractive target for further studies.

Nucleic acids as templates and catalysts in chemical reactions: target-guided dynamic combinatorial chemistry and in situ click chemistry and DNA/RNA induced enantioselective reactions.

Nucleic acids play crucial roles in transferring cellular information and gene regulations. DNA and RNA molecules have been associated with multiple human diseases and thus offer opportunities for exploring small molecule-based therapeutics. However, developing target-selective molecules possessing well-defined biological activity, has always been challenging. In the current scenario, where the world is continuously experiencing outbreaks of new infectious diseases, it is always important to expand the scope of chemical toolsets to override conventional drug discovery strategies for developing therapeutically relevant drug candidates. The template-directed synthetic approach has emerged as a promising tool for rapid drug discovery. It allows a biological target to template the selection or synthesis of its ligands from a pool of reactive fragments. There are two main template-directed synthetic strategies: thermodynamically controlled dynamic combinatorial chemistry (DCC) and kinetically controlled target-guided in situ click chemistry. Though discovered only two decades ago, these techniques have proven their usefulness for nucleic acid targets, as exemplified by the increasing number of applications with therapeutically important DNA and RNA targets. However, nucleic acid templated synthetic techniques are relatively unexplored in drug discovery compared to protein targets. In this review article, we have presented a detailed discussion of all the reported nucleic acid templated synthetic studies to portray the great potential of this strategy for efficient hit discovery and lead optimisation. This article would assist in expanding the scope and utility of this strategy through a summary of the advancements and emerging applications. Additionally, a brief overview of the catalytic potential of nucleic acids in asymmetric synthesis has been provided to give a valuable vision of the use of nucleic acids to induce enantioselectivity in chiral drug-like candidates.

Detection and differentiation of per- and polyfluoroalkyl substances (PFAS) in water using a fluorescent imprint-and-report sensor array.

Widespread industrial use of per- and polyfluoroalkyl substances (PFAS) as surfactants has led to global contamination of water sources with these persistent, highly stable chemicals. As a result, humans and wildlife are regularly exposed to PFAS, which have been shown to bioaccumulate and cause adverse health effects. Methods for detecting PFAS in water are currently limited and primarily utilize mass spectrometry (MS), which is time-consuming and requires expensive instrumentation. Thus, new methods are needed to rapidly and reliably assess the pollution level of water sources. While some fluorescent PFAS sensors exist, they typically function in high nanomolar or micromolar concentration ranges and focus on sensing only 1-2 individual PFAS. Our work aims to address this problem by developing a fluorescent sensor for both individual PFAS, as well as complex PFAS mixtures, and demonstrate its functionality in tap water samples. Here we show that dynamic combinatorial libraries (DCLs) with simple building blocks can be templated with a fluorophore and subsequently used as sensors to form an array that differentially detects each PFAS species and various mixtures thereof. Our method is a high-throughput analysis technique that allows many samples to be analyzed simultaneously with a plate reader. This is one of the first examples of a fluorescent PFAS sensor array that functions at low nanomolar concentrations, and herein we report its use for the rapid detection of PFAS contamination in water.

Light-controlled enzymatic synthesis of γ-CD using a recyclable azobenzene template.

Cyclodextrins (CDs) are important molecular hosts for hydrophobic guests in water and extensively employed in the pharmaceutical, food and cosmetic industries to encapsulate drugs, flavours and aromas. Compared with α- and β-CD, the wide-scale use of γ-CD is currently limited due to costly production processes. We show how the yield of γ-CD in the enzymatic synthesis of CDs can be increased 5-fold by adding a tetra-ortho-isopropoxy-substituted azobenzene template irradiated at 625 nm (to obtain the cis-(Z)-isomer) to direct the synthesis. Following the enzymatic reaction, the template can then be readily recovered from the product mixture for use in subsequent reaction cycles. Heating induces thermal cis-(Z) to trans-(E) relaxation and consequent dissociation from γ-CD whereupon the template can then be precipitated by acidification. For this study we designed and synthesised a set of three water-soluble azobenzene templates with different ortho-substituents and characterised their photoswitching behaviour using UV/vis and NMR spectroscopy. The templates were tested in cyclodextrin glucanotransferase-mediated dynamic combinatorial libraries (DCLs) of cyclodextrins while irradiating at different wavelengths to control the cis/trans ratios. To rationalise the behaviour of the DCLs, NMR titrations were carried out to investigate the binding interactions between α-, β- and γ-CD and the cis and trans isomers of each template.

Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles.

Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.

Fragment-Based Dynamic Combinatorial Chemistry for Identification of Selective α-Glucosidase Inhibitors.

Efforts to combine advantages of fragment-based drug design (FBDD) and dynamic combinatorial chemistry (DCC) for the development of selective α-glucosidase inhibitors were described. Starting from 5 rationally designed fragments, two iterative dynamic combinatorial libraries (DCLs) comprising 29 acylhydrazone products were generated and screened using α-glucosidase and α-amylase as the templates. The optimal ligand identified showed substantial α-glucosidase inhibition with high selectivity over α-amylase as well as low cytotoxicity. Furthermore, inhibition type and detailed ligand/enzyme binding interactions were elucidated by the binding kinetic study and docking simulation, respectively.