Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Different-Length Hydrazone Activated Polymers for Plasmid DNA Condensation and Cellular Transfection

The recent advances in genetic engineering demand the development of conceptually new methods to prepare and identify efficient vectors for the intracellular delivery of different nucleotide payloads ranging from short single-stranded oligonucleotides to larger plasmid double-stranded circular DNAs. Although many challenges still have to be overcome, polymers hold great potential for intracellular nucleotide delivery and gene therapy. We here develop and apply the postpolymerization modification of polyhydrazide scaffolds, with different degree of polymerization, for the preparation of amphiphilic polymeric vehicles for the intracellular delivery of a circular plasmid DNA. The hydrazone formation reactions with a mixture of cationic and hydrophobic aldehydes proceed in physiologically compatible aqueous conditions, and the resulting amphiphilic polyhydrazones are directly combined with the biological cargo without any purification step. This methodology allowed the preparation of stable polyplexes with a suitable size and zeta potential to achieve an efficient encapsulation and intracellular delivery of the DNA cargo. Simple formulations that performed with efficiencies and cell viabilities comparable to the current gold standard were identified. Furthermore, the internalization mechanism was studied via internalization experiments in the presence of endocytic inhibitors and fluorescence microscopy. The results reported here confirmed that the polyhydrazone functionalization is a suitable strategy for the screening and identification of customized polymeric vehicles for the delivery of different nucleotide cargos.

Self-assembled orthoester cryptands: orthoester scope, post-functionalization, kinetic locking and tunable degradation kinetics

Dynamic adaptability and biodegradability are key features of functional, 21st century host-guest systems. We have recently discovered a class of tripodal supramolecular hosts, in which two orthoesters act as constitutionally dynamic bridgeheads. Having previously demonstrated the adaptive nature of these hosts, we now report the synthesis and characterization - including eight solid state structures - of a diverse set of orthoester cages, which provides evidence for the broad scope of this new host class. With the same set of compounds, we demonstrated that the rates of orthoester exchange and hydrolysis can be tuned over a remarkably wide range, from rapid hydrolysis at pH 8 to nearly inert at pH 1, and that the Taft parameter of the orthoester substituent allows an adequate prediction of the reaction kinetics. Moreover, the synthesis of an alkyne-capped cryptand enabled the post-functionalization of orthoester cryptands by Sonogashira and CuAAC "click" reactions. The methylation of the resulting triazole furnished a cryptate that was kinetically inert towards orthoester exchange and hydrolysis at pH > 1, which is equivalent to the "turnoff" of constitutionally dynamic imines by means of reduction. These findings indicate that orthoester cages may be more broadly useful than anticipated, e.g. as drug delivery agents with precisely tunable biodegradability or, thanks to the kinetic locking strategy, as ion sensors.

Guiding principles for peptide nanotechnology through directed discovery

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

Coacervation of dynamic covalent surfactants with polyacrylamides: properties and applications

Dynamic covalent surfactants have been prepared from a mixture of 4-formyl-N,N,N-trimethylbenzenaminium iodide (FBA) with heptylamine (C7A) or octylamine (C8A) in alkaline aqueous solutions. The reversible pH-dependent nature of the imine bond is characterized by 1H NMR and fluorescence analysis. The dynamic covalent surfactants self-assemble into micelles under alkaline conditions and exhibit coacervation with 10% hydrolyzed polyacrylamide (PAM) over a wide concentration range. The coacervate phase with a network structure was found to effectively extract the anionic dye Conge Red (CR). When the solution is adjusted to acidity, the imine bond is hydrolyzed, leading to the transition of the coacervates into a homogeneous and clear solution, and the precipitation of CR into purple-black solids due to the protonation of sulfonic groups. Thus, the extraction and release of CR molecules are realized with this dynamic covalent surfactant/PAM system. Moreover the initial components, FBA, amine, and PAM, can be easily regenerated with hydrochloric acid. This method shows potential applications in wastewater treatment.

Sweet Switch: Sugar-Responsive Bioactive Surfaces Based on Dynamic Covalent Bonding

Smart bioactive surfaces that can modulate interactions with biological systems are of great interest. In this work, a surface with switchable bioactivity in response to sugars has been developed. It is based on dynamic covalent bonding between phenylboronic acid (PBA) and secondary hydroxyls on the "wide" rim of β-cyclodextrin (β-CD). The system reported consists of gold surface modified with PBA-containing polymer brushes and a series of functional β-CD derivatives conjugated to diverse bioactive ligands (CD-X). CD-X molecules are attached to the surface to give specified bioactivity such as capture of a specific protein or killing of attached bacteria. Subsequent treatment with cis-diol containing biomolecules having high affinity for PBA (e.g. fructose) leads to the release of CD-X together with the captured proteins, killed bacteria, and so forth from the surface. The surface bioactivity is thereby "turned off". Effectively, this constitutes an on-off bioactivity switch in a mild and noninvasive way, which has the potential in the design of dynamic bioactive surfaces for biomedical applications.

Target-guided screening of fragments (TGSOF) in the discovery of inhibitors against EV-A71 3C protease

Target-guided screening of fragments (TGSOF) was developed and employed in the identification of EV-A71 3C protease (3Cpro) inhibitors. We identified 4-acetylpyridine and 3-acetylpyridine as effective P3 fragments of an inhibitor and obtained the corresponding irreversible inhibitors 12c and 12fvia this method. Furthermore, based on 12c and 12f, we have obtained reversible inhibitors 17c and 17f. These results demonstrated that TGSOF is a useful strategy for identifying suitable fragments in developing leads in drug discovery.

Exploring the emergence of complexity using synthetic replicators

A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.

Dynamic Covalent Chemistry within Biphenyl Scaffolds: Reversible Covalent Bonding, Control of Selectivity, and Chirality Sensing with a Single System

Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a versatile platform for the binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between an open aldehyde and its cyclic hemiaminal within biphenyl derivatives enabled the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. Selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli. Through induced helicity as a result of central-to-axial chirality transfer, the handedness and ee values of chiral monoalcohol and monoamine analytes were reported by circular dichroism. The strategies introduced herein should find application in many contexts, including assembly, sensing, and labeling.

Resolving a Reactive Organometallic Intermediate from Dynamic Directing Group Systems by Selective C-H Activation

Catalyst discovery from systems of potential precursors is a challenging endeavor. Herein, a new strategy applying dynamic chemistry to the identification of catalyst precursors from C-H activation of imines is proposed and evaluated. Using hydroacylation of imines as a model reaction, the selection of an organometallic reactive intermediate from a dynamic imine system, involving many potential directing group/metal entities, is demonstrated. The identity of the amplified reaction intermediate with the best directing group could be resolved in situ by ESI-MS, and coupling of the procedure to an iterative deconvolution protocol generated a system with high screening efficiency.

Dynamic diselenide-containing polyesters from alcoholysis/oxidation of γ-butyroselenolactone

A versatile protocol for the synthesis of a variety of multiresponsive diselenide-containing polyesters was investigated.

Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library

Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.

A user's guide to the thiol-thioester exchange in organic media: scope, limitations, and applications in material science

The dynamic exchange of thiols and thioesters in organic media was explored, leading to room temperature plasticity in crosslinked polymers.

Synthesis of 2,2-bis(pyridin-2-yl amino)cyclobutanols and their conversion into 5-(pyridin-2-ylamino)dihydrofuran-2(3H)-ones

A two-step protocol is presented for the preparation of 5-(pyridin-2-ylamino)dihydrofuran-2(3H)-ones from 2-hydroxycyclobutanone and some 2-aminopyridines via a catalyst-free synthesis of 2,2-bis(pyridin-2-ylamino)cyclobutanols followed by Dess-Martin periodinane mediated ring expansion.

Saccharide-Containing Dynamic Proteoids

Dynamic proteoids are dynamic covalent analogues of proteins, which can be used as new adaptive biomaterials. We designed and synthesized a range of sugar-containing dynamic proteoid biodynamers based on the polycondensation of different types of amino acid and dipeptide hydrazides with a biological aliphatic dialdehyde and a nonbiological aromatic dialdehyde. By using the saccharide-based dialdehyde, the biocompatibility of biodynamers should be enhanced compared to previously reported biodynamers.

Surface immobilized azomethine for multiple component exchange

Diazonium chemistry concomitant with in situ electrochemical reduction was used to graft an aryl aldehyde to indium-tin oxide (ITO) coated glass substrates. This served as an anchor for preparing electroactive azomethines that were covalently bonded to the transparent electrode. The immobilized azomethines could undergo multiple step-wise component exchanges with different arylamines. The write-erase-write sequences were electrochemically confirmed. The azomethines could also be reversibly hydrolyzed. This was exploited for multiple azomethine-hydrolysis cycles resulting in discrete electroactive immobilized azomethines. The erase-rewrite sequences were also electrochemically confirmed.

Dynamic Covalent Chemistry of Aldehyde Enamines: BiIII - and ScIII -Catalysis of Amine-Enamine Exchange

The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry.

Mechanistic applications of click chemistry for pharmaceutical drug discovery and drug delivery

The concept of click chemistry (CC), first introduced by K.B. Sharpless, has been widely adopted for use in drug discovery, novel drug delivery systems (DDS), polymer chemistry, and material sciences. In this review, we outline novel aspects of CC related to drug discovery and drug delivery, with a brief overview of molecular mechanisms underlying each click reaction commonly used by researchers, and the main patents that paved the way for further diverse medicinal applications. We also describe recent progress in drug discovery and polymeric and carbon material-based drug delivery for potential pharmaceutical applications and advancements based on the CC approach, and discuss some intrinsic limitations of this popular conjugation reaction. The use of CC is likely to significantly advance drug discovery and bioconjugation development.

Aqueous dispersions of nanostructures formed through the self-assembly of iminolipids with exchangeable hydrophobic termini

The addition of amines to an aldehyde surfactant, which was designed to be analogous to didodecyldimethylammonium bromide, gave exchangeable "iminolipids" that self-assembled to give stable aqueous dispersions of nano-sized vesicles. For example, sonication of suspensions of the n-hexylamine-derived iminolipid gave vesicles 50 to 200 nm in diameter that could encapsulate a water-soluble dye. The iminolipids could undergo dynamic exchange with added amines, and the resulting equilibrium constants (K_rel) were quantified by ¹H NMR spectroscopy. In the absence of lipid self-assembly, in CDCl₃, the assayed primary amines gave very similar K_rel values. However in D₂O the value of K_rel generally increased with increasing amine hydrophobicity, consistent with partitioning into a self-assembled bilayer. Amines with aromatic groups showed significantly higher values of K_rel in D₂O compared to similarly hydrophobic alkylamines, suggesting that π-π interactions favor lipid self-assembly. Given this synergistic relationship, π-rich pyrenyliminolipids were created and used to exfoliate graphite, leading to aqueous dispersions of graphene flakes that were stable over several months.

Oligocarboxylates as useful templates in dynamic combinatorial chemistry

Dynamic combinatorial chemistry deals with systems (libraries) of multiple compounds formed by reversible reactions. Interactions of all library components with introduced template molecule are reflected in modification of library composition and are analysed simultaneously. In our studies we investigated a single-substrate dynamic combinatorial library of macrocycles, based on dipicolinic acid diamide, with disulphide bond exchange as the reversible reaction. The library components equipped with hydrogen bond donors interact with anionic guests – carboxylates which act as templates inducing amplification of selected library members. We proved that quantitative analysis of interactions with templates is possible, which led us to a novel method of analysis of association constants of static receptors introduced to the system. With a large set of carboxylates differing in number of anionic groups, size, shape, and flexibility of the linker, we proved that the library is very sensitive to structural parameters of the template. We also showed that with mediation of a photoswitchable azobenzene-based template it is possible to change the library composition by light stimulus. Similarly, with mediation of EDTA the library is sensitive to introduction of metal cations.

Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung

Proteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.

Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery

Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.

Antiparallel Dynamic Covalent Chemistries

The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.

Formation of Imidazo[1,5-a]pyridine Derivatives Due to the Action of Fe2+ on Dynamic Libraries of Imines

An imidazo[1,5-a]pyridine derivative was unexpectedly obtained through the action of Fe²⁺ on a dynamic library of imines generated in situ via condensation of benzaldehyde and 2-picolylamine. The reaction product was easily isolated as the only nitrogen-containing product eluted from the chromatographic column. A reaction mechanism is proposed, in which combined kinetic and thermodynamic effects exerted by Fe²⁺ on the various steps of the complex reaction sequence are discussed. The Fe²⁺ nature of the added metal cation was found to be pivotal for the achievement of the imidazo[1,5-a]pyridine derivative as well as its amount in the reaction mixture. When the electronic effects were evaluated, gratifying yields were obtained only in the presence of moderately electron-releasing or moderately electron-withdrawing groups on the aldehyde reactant. No traces of imidazo[1,5-a]pyridine derivatives were obtained for p-OCH₃ and p-NO₂ benzaldehyde.

De Novo Modular Development of a Foldameric Protein-Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach

Protein-protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface-mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work, a modular bottom-up approach is implemented by identifying short foldameric recognition segments that interact with the independent hot spots, and connecting them through dynamic covalent library (DCL) optimization. The independent hot spots of a model target (calmodulin) are mapped with hexameric β-peptide helices using a pull-down assay. Recognition segment hits are subjected to a target-templated DCL ligation through thiol-disulfide exchange. The most potent derivative displays low nanomolar affinity towards calmodulin and effectively inhibits the calmodulin-TRPV1 interaction. The DCL assembly of the folded segments offers an efficient approach towards the de novo development of a high-affinity inhibitor of protein-protein interactions.

Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular biodynamers are commonly produced in aqueous media under mild or even physiological conditions to suit their biorelated applications. In contrast to static biopolymers emphasizing structural stability and unity by using irreversible covalent bonds, molecular biodynamers are seeking relative structural adaptability and diversity through the formation of reversible covalent bonds. Based on these considerations, molecular biodynamers are capable of reorganizing their monomers, generating, identifying, and amplifying the fittest structures in response to environmental factors. Hence, molecular biodynamers have received considerable research attention over the past decades. Accordingly, the construction of molecular biodynamers through equilibrium polymerization of nucleobase-, carbohydrate- or amino-acid-based monomers can lead to the fabrication of dynamic analogues of nucleic acids (DyNAs), polysaccharides (glycodynamers), or proteins (dynamic proteoids), respectively. In this Account, we summarize recent advances in developing different types of molecular biodynamers as structural or functional biomimetics of biopolymers, including DyNAs, glycodynamers, and dynamic proteoids. We introduce how chemists utilize various reversible reactions to generate molecular biodynamers with specific sequences and well-ordered structures in aqueous medium. We also discuss and list their potential applications in various research fields, such as drug delivery, drug discovery, gene sensing, cancer diagnosis, and treatment.

3D-QSAR predictions for α-cyclodextrin binding constants using quantum mechanically based descriptors

Binding of organic chemicals to α-cyclodextrin (αCD) is a typical example for host-guest complexation that is influenced by the 3D-structure of both the binding site (host) and the solute (guest). Prediction of the binding constant is challenging and requires a successful representation of the binding site-solute interactions in the 3D-space. In this study, we tested if a 3D quantitative structure activity relationship (3D-QSAR) model with quantum mechanically based local sigma profiles (LSPs) derived from the COSMOsar3D method is capable of predicting αCD binding constants from the most recent literature and how the model performs in comparison to a standard comparative molecular field analysis and to a reference 2D-QSAR. The results showed that the new 3D-QSAR model was more predictive than both reference models (RMSE 0.45 vs 0.53/0.52, R² 0.70 vs 0.53/0.68). Furthermore, only the new model captured the differences in the binding constants between structural isomers of aliphatic alcohols and allowed an extrapolation of the prediction to another literature data set. The high performance of the 3D-QSAR model with LSPs tested in this study and its theoretical robustness suggest that this modeling approach should be applicable to other binding processes including protein binding.

Long, self-assembled molecular ladders by cooperative dynamic covalent reactions

The dynamic covalent self-assembly of peptoid-based oligomers bearing n complementary functional groups yields molecular ladders with n covalent rungs.

An α-helical peptidomimetic scaffold for dynamic combinatorial library formation

A novel oligobenzamide-based α-helix mimetic was designed and synthesised with either imine or hydrazone functionalities that serve both to pre-organise the side-chain vectors to mimic the i, i + 4 and i + 7 residues of an α-helix, and to allow for the facile creation of dynamic libraries.

Identification of inhibitors targeting Mycobacterium tuberculosis cell wall biosynthesis via dynamic combinatorial chemistry

In this study, we report a dynamic combinatorial approach along with highly efficient in situ screening to identify inhibitors of UDP-galactopyranose mutase (UGM), an essential enzyme involved in mycobacterial cell wall biosynthesis.