Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

Biodynamers: applications of dynamic covalent chemistry in single-chain polymer nanoparticles

Dynamic Covalent Chemistry (DCC) enables the development of responsive molecular systems through the integration of reversible bonds at the molecular level. These systems are thermodynamically stable and capable of undergoing various molecular assemblies and transformations, allowing them to adapt to changes in environmental conditions like temperature and pH. Introducing DCC into the field of polymer science has led to the design of Single-Chain Nanoparticles (SCNPs), which are formed by self-folding via intramolecular crosslinking mechanisms. Defined by their adaptability, SCNPs mimic biopolymers in size and functionality. Biodynamers, a subclass of SCNPs, are specifically designed for their stimuli-responsive and tunable, dynamic properties. Mimicking complex biological structures, their scope of application includes target-specific and pH-responsive drug delivery, enhanced cellular uptake and endosomal escape. In this manuscript, we discuss the integration of DCC for the design of SCNPs, focusing particularly on the characteristics of biodynamers and their biomedical and pharmaceutical applications. By underlining their potential, we highlight the factors driving the growing interest in SCNPs, providing an overview of recent developments and future perspectives in this research field.

Target-Directed Dynamic Combinatorial Chemistry Affords Binders of Mycobacterium tuberculosis IspE

In the search for new antitubercular compounds, we leveraged target-directed dynamic combinatorial chemistry (tdDCC) as an efficient hit-identification method. In tdDCC, the target selects its own binders from a dynamic library generated in situ, reducing the number of compounds that require synthesis and evaluation. We combined a total of 12 hydrazides and six aldehydes to generate 72 structurally diverse N-acylhydrazones. To amplify the best binders, we employed anti-infective target 4-diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE) from Mycobacterium tuberculosis (Mtb). We successfully validated the use of tdDCC as hit-identification method for IspE and optimized the analysis of tdDCC hit determination. From the 72 possible N-acylhydrazones, we synthesized 12 of them, revealing several new starting points for the development of IspE inhibitors as antibacterial agents.

Recent Progress of pH-Responsive Peptides, Polypeptides, and Their Supramolecular Assemblies for Biomedical Applications

Peptides and polypeptides feature a variety of active functional groups on their side chains (including carboxylic acid, hydroxyl, amino, and thiol groups), enabling diverse chemical modifications. This versatility makes them highly valuable in stimuli-responsive systems. Notably, pH-responsive peptides and polypeptides, due to their ability to respond to pH changes, hold significant promise for applications in cellular pathology and tumor targeting. Extensive researches have highlighted the potentials of low pH insertion peptides (pHLIPs), peptide-drug conjugates (PDCs), and antibody-drug conjugates (ADCs) in biomedicine. Peptide self-assemblies, with their structural stability, ease of regulation, excellent biocompatibility, and biodegradability, offer immense potentials in the development of novel materials and biomedical applications. We also explore specific examples of their applications in drug delivery, tumor targeting, and tissue engineering, while discussing future challenges and potential advancements in the field of pH-responsive self-assembling peptide-based biomaterials.

Sulfinamide Crossover Reaction

This study unveils a new catalytic crossover reaction of sulfinamides. Leveraging mild acid catalysis, the reaction demonstrates a high tolerance to structural variations, yielding equimolar products across diverse sulfinamide substrates. Notably, small sulfinamide libraries can be selectively oxidized to sulfonamides, providing a new platform for ligand optimization and discovery in medicinal chemistry. This crossover chemotype provides a new tool for high-throughput experimentation in discovery chemistry.

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.

Activation of Anthraquinone's Electrophilicity by Light for a Dynamic C-O Bond

Coupling of photoswitching with dynamic covalent chemistry enables control of the formation and cleavage of covalent bonds by light irradiation. peri-Aryloxyanthraquinones feature an exclusive ability to switch electrophilicity by interconversion between para- and ana-quinone isomers, which was used for the first time for the implementation of a dynamic C-O bond. Photogenerated ana-isomers undergo a concerted oxa-Michael addition of phenols to give hitherto unknown 4-hydroxy-10,10-diaryloxyanthracen-9-ones. These species were found to be in equilibrium with the corresponding ana-quinones, thus forming a dynamic covalent system of a new type. Withdrawal of the colored ana-quinones from the equilibria by visible light irradiation resulted in two para-quinones with "locked" aryloxy groups.

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.

Behavior of a Dynamic Covalent Library Driven by Combined Pd(II) and Biphasic Effectors for Metal Transport between Phases

This work reports the effect of Pd(II) as chemical effector on an acylhydrazone-based dynamic covalent library (DCL) in biphasic systems (water/chloroform). The constituents of the DCL are self-built and distributed in the two phases, two of them are lipophilic enough to play the role of a carrier agent that may transfer Pd(II) from the aqueous phase to the organic phase. Upon addition of Pd(II), the DCL of components exhibits a strong amplification of the constituent that is the most adapted to stabilize Pd(II) in chloroform as well as its agonist in water. This evolution is driven by the combination of the interaction of the DCL with Pd(II) and the presence of the two phases. This study paves the way to a novel approach for liquid/liquid extraction and metal recovery by means of adaptive extractant species generated in situ by a DCL.

Isomerization of bioactive acylhydrazones triggered by light or thiols

The acylhydrazone unit is well represented in screening databases used to find ligands for biological targets, and numerous bioactive acylhydrazones have been reported. However, potential E/Z isomerization of the C=N bond in these compounds is rarely examined when bioactivity is assayed. Here we analysed two ortho-hydroxylated acylhydrazones discovered in a virtual drug screen for modulators of N-methyl-D-aspartate receptors and other bioactive hydroxylated acylhydrazones with structurally defined targets reported in the Protein Data Bank. We found that ionized forms of these compounds, which are populated under laboratory conditions, photoisomerize readily and the isomeric forms have markedly different bioactivity. Furthermore, we show that glutathione, a tripeptide involved with cellular redox balance, catalyses dynamic E⇄Z isomerization of acylhydrazones. The ratio of E to Z isomers in cells is determined by the relative stabilities of the isomers regardless of which isomer was applied. We conclude that E/Z isomerization may be a common feature of the bioactivity observed with acylhydrazones and should be routinely analysed.

Mutual leveraging of proximity effects and click chemistry in chemical biology

Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.

Dynamic covalent chemistry with azines

Dynamic covalent chemistry is used in many applications that require both the stability of covalent bonds and the possibility to exchange building blocks. Here we present azines as a dynamic covalent functional group that combines the best characteristics of imines and acylhydrazones. We show that azines are stable in the presence of water and that dynamic combinatorial libraries of azines and aldehydes equilibrate in less than an hour.

Identification of RAD51–BRCA2 Inhibitors Using N-Acylhydrazone-Based Dynamic Combinatorial Chemistry

RAD51 is an ATP-dependent recombinase, recruited by BRCA2 to mediate DNA double-strand breaks repair through homologous recombination and represents an attractive cancer drug target. Herein, we applied for the first-time protein-templated dynamic combinatorial chemistry on RAD51 as a hit identification strategy. Upon design of N-acylhydrazone-based dynamic combinatorial libraries, RAD51 showed a clear templating effect, amplifying 19 N-acylhydrazones. Screening against the RAD51–BRCA2 protein–protein interaction via ELISA assay afforded 10 inhibitors in the micromolar range. Further ¹⁹F NMR experiments revealed that 7 could bind RAD51 and be displaced by BRC4, suggesting an interaction in the same binding pocket of BRCA2. These results proved not only that ptDCC could be successfully applied on full-length oligomeric RAD51, but also that it could address the need of alternative strategies toward the identification of small-molecule PPI inhibitors.

Recent advances in DNA-encoded dynamic libraries

The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.

Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches

Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.

Identification of potent α-amylase inhibitors via dynamic combinatorial chemistry

In this study, we report for the first time the discovery of potent α-amylase inhibitors using principle of dynamic combinatorial chemistry. The best compound identified exhibited not only high inhibitory efficiency but also low cytotoxicity. The binding mode and possible mechanism are determined in the subsequent kinetic and molecular docking studies.

Towards Identification of Protein-Protein Interaction Stabilizers via Inhibitory Peptide-Fragment Hybrids Using Templated Fragment Ligation

Using the hDMX/14-3-3 interaction, acylhydrazone-based ligand-directed fragment ligation was used to identify protein-protein interaction (PPI) inhibitory peptide-fragment hybrids. Separation of the peptide-fragment hybrids into the components yielded fragments that stabilized...

Assembly of pH-Responsive Antibody-Drug-Inspired Conjugates

With the advent of chemical strategies that allow the design of smart bioconjugates, peptide- and protein-drug conjugates are emerging as highly efficient therapeutics to overcome limitations of conventional treatment, as exemplified by antibody-drug conjugates (ADCs). While targeting peptides serve similar roles as antibodies to recognize overexpressed receptors on diseased cell surfaces, peptide-drug conjugates suffer from poor stability and bioavailability due to their low molecular weights. Through a combination of a supramolecular protein-based assembly platform and a pH-responsive linker, the authors devise herein the convenient assembly of a trivalent protein-drug conjugate. The conjugate should ideally possess distinct features of ADCs such as 1) recognition sites that recognize cell receptor and are arranged on 2) distinct locations on a high molecular weight protein scaffold, 3) a stimuli-responsive linker, as well as 4) an attached payload such as a drug molecule. These AD-like conjugates target cancer cells that overexpress somatostatin receptors, can enable controlled release in the microenvironment of cancer cells through a new pH-responsive biotin linker, and exhibit stability in biological media.

Nucleophilic catalysis of p-substituted aniline derivatives in acylhydrazone formation and exchange

Hydrazone bond formation is a versatile reaction employed in several research fields. It is one of the most popular reversible reactions in dynamic combinatorial chemistry. Under physiological conditions, hydrazone exchange benefits from the addition of a nucleophilic catalyst. We report a mechanistic study and superior performance of electron-rich p-substituted aniline derivatives as catalysts for efficient hydrazone formation and exchange in both protic and aprotic solvents. Rigorous kinetic analyses demonstrate that imine formation with 3-hydroxy-4-nitrobenzaldehyde and aniline derivatives proceeds with unprecedented third-order kinetics in which the aldehyde consistently shows a partial order of two. Computational investigations provide insights into the mechanisms of these transformations.

Tuning the exchange dynamics of boronic acid hydrazones and oximes with pH and redox control

Dynamic bonds continually form and dissociate at equilibrium. Carbonyl compounds with proximal boronic acids, including 2-formylphenylboronic acid (2-FPBA), have been reported to form highly dynamic covalent hydrazone and oxime bonds in physiological conditions, but strategies to tune the dynamics have not yet been reported. Here, we characterize the dynamics of 2-FPBA-derived hydrazones and oximes and account for both the rapid rate of formation (∼102-103 M-1 s-1) and the relatively fast rate of hydrolysis (∼10-4 s-1) at physiological pH. We further show that these substrates undergo exchange with α-nucleophiles, which can be reversibly paused and restarted with pH control. Finally, we show that oxidation of the arylboronic acid effectively abolishes the rapid dynamics, which slows the forward reaction by more than 30 000 times and increases the hydrolytic half-life from 50 minutes to 6 months at physiological pH. These results set the stage to explore these linkages in dynamic combinatorial libraries, reversible bioconjugation, and self-healing materials.

Selective recognition of a cyclic peptide hormone in human plasma by hydrazone bond-oriented surface imprinted nanoparticles

As a kind of artificial recognition material, molecularly imprinted polymers (MIPs) offer a promising perspective to be developed as synthetic chemical binders capable of selectively recognize biomacromolecules. However, owing to the large size and conformational flexibility of proteins and peptides, imprinting of these biomacromolecules remains a challenge. Novel imprinting strategies still need exploration for the improvement of recognition performance of MIPs. Herein, we developed a hydrazone bond-oriented surface imprinting strategy for an endogenous peptide hormone, human atrial natriuretic peptide (ANP). Surface-oriented imprinting of peptide via reversible covalent bond anchoring approach increased the orientation homogeneity of imprinted cavities as well as the utility of templates. The prepared nanoparticles exhibited high selectivity and fast recognition kinetics for ANP epitope. The dissociation constant between ANP epitope and MIP was measured as 5.3 μM. The applicability of the material in real samples was verified by the selective magnetic extraction of ANP from human plasma samples. This hydrazone bond-oriented surface imprinting strategy provides an alternative approach for the separation of peptides or proteins in complex bio-samples.

Quadruplex DNA-guided ligand selection from dynamic combinatorial libraries of acylhydrazones

Dynamic combinatorial libraries of acylhydrazones were prepared from diacylhydrazides and several cationic or neutral aldehydes in the presence of 5-methoxyanthranilic acid catalyst. Pull-down experiments with magnetic beads functionalized with a G-quadruplex (G4)-forming oligonucleotide led to the identification of putative ligands, which were resynthesized or emulated by close structural analogues. G4-binding properties of novel derivatives were assessed by fluorimetric titrations, mass spectrometry and thermal denaturation experiments, giving evidence of strong binding (Kd < 10 nM) for two compounds.

Biomimetic selenocystine based dynamic combinatorial chemistry for thiol-disulfide exchange

Dynamic combinatorial chemistry applied to biological environments requires the exchange chemistry of choice to take place under physiological conditions. Thiol-disulfide exchange, one of the most popular dynamic combinatorial chemistries, usually needs long equilibration times to reach the required equilibrium composition. Here we report selenocystine as a catalyst mimicking Nature's strategy to accelerate thiol-disulfide exchange at physiological pH and low temperatures. Selenocystine is able to accelerate slow thiol-disulfide systems and to promote the correct folding of an scrambled RNase A enzyme, thus broadening the practical range of pH conditions for oxidative folding. Additionally, dynamic combinatorial chemistry target-driven self-assembly processes are tested using spermine, spermidine and NADPH (casting) and glucose oxidase (molding). A non-competitive inhibitor is identified in the glucose oxidase directed dynamic combinatorial library.

Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation

β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

Design, synthesis and applications of responsive macrocycles

Inspired by the lock and key principle, the development of supramolecular macrocyclic chemistry has promoted the prosperous growth of host-guest chemistry. The updated induced-fit and conformation selection model spurred the emerging research on responsive macrocycles (RMs). This review introduces RMs, covering their design, synthesis and applications. It gives readers insight into the dynamic control of macrocyclic molecules and the exploration of materials with desired functions.

Hydrogen-Bond Catalysis of Imine Exchange in Dynamic Covalent Systems

The reversibility of imine bonds has been exploited to great effect in the field of dynamic covalent chemistry, with applications such as preparation of functional systems, dynamic materials, molecular machines, and covalent organic frameworks. However, acid catalysis is commonly needed for efficient equilibration of imine mixtures. Herein, it is demonstrated that hydrogen bond donors such as thioureas and squaramides can catalyze the equilibration of dynamic imine systems under unprecedentedly mild conditions. Catalysis occurs in a range of solvents and in the presence of many sensitive additives, showing moderate to good rate accelerations for both imine metathesis and transimination with amines, hydrazines, and hydroxylamines. Furthermore, the catalyst proved simple to immobilize, introducing both reusability and extended control of the equilibration process.

Protein-Directed Dynamic Combinatorial Chemistry: An Efficient Strategy in Drug Design

Protein-directed dynamic combinatorial chemistry (P-D DCC) is considered a powerful strategy to identify ligands to pharmacologically relevant protein targets. The protein selects its affinity ligands in situ through a thermodynamic templated effect in which the library composition shifts to the formation of specific library members at the expense of other (nonbinding) species. The increase in concentration of the selected species is known as amplification and leads to the discovery of new hit compounds for protein targets. This Mini-Review contains an updated overview of the protein-directed DCC applications and the fundamental aspects to take into account when designing a P-D DCC experiment such as the most biocompatible reversible reactions and the methodology used to analyze the experiments.

Indoline Catalyzed Acylhydrazone/Oxime Condensation under Neutral Aqueous Conditions

Acylhydrazones formation has been widely applied in materials science and biolabeling. However, their sluggish condensation rate under neutral conditions limits its application. Herein, indolines with electron-donating groups are reported as a new catalyst scaffold, which can catalyze acylhydrazone, hydrazone, and oxime formation via an iminium ion intermediate. This new type of catalyst showed up to 15-fold rate enhancement over the traditional aniline-catalyzed reaction at neutral conditions. The identified indoline catalyst was successfully applied in hydrogel formation.

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.

Size-selective Catalytic Polymer Acylation with a Molecular Tetrahedron

Selective catalysis at the molecular level represents a cornerstone of chemical synthesis. However, it still remains an open question how to elevate tunable catalysis to larger length scales to functionalize whole polymer chains in a selective manner. We now report a hydrazone-linked tetrahedron with wide openings, which acts as a catalyst to size-selectively functionalize polydisperse polymer mixtures. Our experimental and computational evidence supports a dual role of the hydrazone-linked tetrahedron. To accelerate functionalization of the polymer substrates, the tetrahedron (i) unfolds the polymer substrates and/or breaks the polymer aggregates as well as (ii) enables target sites (amino groups) on the polymers to coordinate with catalytic units (triglyme) attached to the tetrahedron. With the tetrahedron as the catalyst, we find that the reactivity of the shorter polymers increases selectively. Our findings enable the possibility to engineer hydrolytically stable molecular polyhedra as organocatalysts for size-selective polymer modification.

Nanogel receptors for high isoelectric point protein detection: influence of electrostatic and covalent polymer-protein interactions

An aldehyde acrylate-based functional monomer was incorporated into poly(N-isopropylacrylamide-co-methacrylic acid) nanogels for use as protein receptors. The aldehyde component forms dynamic imines with surface exposed lysine residues, while carboxylic acid/carboxylate moieties form electrostatic interactions with high isoelectric point proteins. Together, these interactions effect protein adsorption and recognition.

Discovery of Small-Molecule Stabilizers of 14-3-3 Protein-Protein Interactions via Dynamic Combinatorial Chemistry

Protein-protein interactions (PPIs) play an important role in numerous biological processes such as cell-cycle regulation and multiple diseases. The family of 14-3-3 proteins is an attractive target as they serve as binding partner to various proteins and are therefore capable of regulating their biological activities. Discovering small-molecule modulators, in particular stabilizers, of such complexes via traditional screening approaches is a challenging task. Herein, we pioneered the first application of dynamic combinatorial chemistry (DCC) to a PPI target, to find modulators of 14-3-3 proteins. Evaluation of the amplified hits from the DCC experiments for their binding affinity via surface plasmon resonance (SPR), revealed that the low-micromolar (K _D 15-16 μM) acylhydrazones are 14-3-3/synaptopodin PPI stabilizers. Thus, DCC appears to be ideally suited for the discovery of not only modulators but even the more elusive stabilizers of notoriously challenging PPIs.

Photodynamic Control of the Chain Length in Supramolecular Polymers: Switching an Intercalator into a Chain Capper

Supramolecular systems are intrinsically dynamic and sensitive to changes in molecular structure and external conditions. Because of these unique properties, strategies to control polymer length, composition, comonomer sequence, and morphology have to be developed for sufficient control over supramolecular copolymerizations. We designed photoresponsive, mono acyl hydrazone functionalized benzene-1,3,5-tricarboxamide (m-BTA) monomers that play a dual role in the coassembly with achiral alkyl BTAs (a-BTA). In the E isomer form, the chiral m-BTA monomers intercalate into stacks of a-BTA and dictate the chirality of the helices. Photoisomerization to the Z isomer transforms the intercalator into a chain capper, allowing dynamic shortening of chain length in the supramolecular aggregates. We combine optical spectroscopy and light-scattering experiments with theoretical modeling to show the reversible decrease in length when switching from the E to Z isomer of m-BTA in the copolymer with inert a-BTA. With a mass-balance thermodynamic model, we gain additional insights into the composition of copolymers and length distributions of the species over a broad range of concentrations and mixing ratios of a-BTA/m-BTA. Moreover, the model was used to predict the impact of an additive (chain capper and intercalator) on the chain length over a range of concentrations, showing a remarkable amplification of efficiency at high concentrations. By employing a stimuli-responsive comonomer in a mostly inert polymer, we can cooperatively amplify the effect of the switching and obtain photocontrol of polymer length. Moreover, this dynamic decrease in chain length causes a macroscopic gel-to-sol phase transformation of the copolymer gel, although 99.4% of the organogel is inert to the light stimulus.

Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase

β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition. X-ray crystallography validated the dimeric mechanism of inhibition, and compounds demonstrated high selectivity against related proteases, good target engagement, and tryptase inhibition in HMC1 xenograft models. Screening 3872 possible combinations from 44 boronic acid and 88 diol derivatives revealed several combinations that produced nanomolar inhibition, and seven unique pairs produced greater than 100-fold improvement in potency over monomeric inhibition. These heterodimeric tryptase inhibitors demonstrate the power of target-driven combinatorial chemistry to deliver bivalent drugs in a small molecule form.

Straightforward synthesis of gold nanoparticles by adding water to an engineered small dendrimer

A small water-soluble phosphorus-containing dendrimer was engineered for the complexation of gold(I) and for its reduction under mild conditions. Gold nanoparticles were obtained as colloidal suspensions simply and only when the powdered form of this dendrimer was dissolved in water, as shown by transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDX) analyses. The dendrimers acted simultaneously as mild reducers and as nanoreactors, favoring the self-assembly of gold atoms and promoting the growth and stabilization of isolated gold nanoparticles. Thus, an unprecedented method for the synthesis of colloidal suspensions of water-soluble gold nanoparticles was proposed in this work.

Development of a multivalent acetylcholinesterase inhibitor via dynamic combinatorial chemistry

In this study, we report the generation of a polymer based dynamic combinatorial library (DCL) using aldehyde-functionalized linear poly(glycidol) and hydrazide derivatives as initial building blocks. In combination with tetrameric acetylcholinesterase (AChE), a certain type of amplified acylhydrazone side chain is identified and further used for the synthesis of a multivalent AChE inhibitor. The cytotoxicity and inhibition properties of the multivalent inhibitor are evaluated, and the results indicate superior bioactivity compared to the commercial reference Edrophonium chloride.

Insights into real-time chemical processes in a calcium sensor protein-directed dynamic library

Dynamic combinatorial chemistry (DCC) has proven its potential in drug discovery speeding the identification of modulators of biological targets. However, the exchange chemistries typically take place under specific reaction conditions, with limited tools capable of operating under physiological parameters. Here we report a catalyzed protein-directed DCC working at low temperatures that allows the calcium sensor NCS-1 to find the best ligands in situ. Ultrafast NMR identifies the reaction intermediates of the acylhydrazone exchange, tracing the molecular assemblies and getting a real-time insight into the essence of DCC processes at physiological pH. Additionally, NMR, X-ray crystallography and computational methods are employed to elucidate structural and mechanistic aspects of the molecular recognition event. The DCC approach leads us to the identification of a compound stabilizing the NCS-1/Ric8a complex and whose therapeutic potential is proven in a Drosophila model of disease with synaptic alterations.

Dynamic combinatorial chemistry (DCC) is instrumental in the discovery of ligands for pharmaceutical targets. Here, the authors adapted DCC to work at 4 degrees Celsius and used it to identify a ligand for Neuronal Calcium Sensor-1 that promotes NCS-1/Ric8a protein-protein interaction.

Protein-Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol

Dynamic combinatorial chemistry (DCC) is a powerful tool to identify bioactive compounds. This efficient technique allows the target to select its own binders and circumvents the need for synthesis and biochemical evaluation of all individual derivatives. An ever-increasing number of publications report the use of DCC on biologically relevant target proteins. This minireview complements previous reviews by focusing on the experimental protocol and giving detailed examples of essential steps and factors that need to be considered, such as protein stability, buffer composition and cosolvents.

Traceless synthesis of protein thioesters using enzyme-mediated hydrazinolysis and subsequent self-editing of the cysteinyl prolyl sequence

A traceless thioester-producing protocol featuring carboxypeptidase Y-mediated hydrazinolysis of cysteinyl prolyl leucine-tagged peptides has been developed. The hydrazinolysis followed by thioesterification affords cysteinyl prolyl thioesters. Self-editing of the tag and subsequent trans-thioesterification yields peptide thioesters. The developed protocol was successfully applied to the conversion of recombinant proteins to thioesters.

Multiple adaptation of constitutional dynamic networks and information storage in constitutional distributions of acylhydrazones

We report a study of the behavior of four dynamic covalent libraries (DCLs) based on acylhydrazones aAbB and of the corresponding square constitutional dynamic networks (CDNs) NA-ND under the effect of three agents, namely, metal cations, base + metal cations and light irradiation; in particular, the successful switching of the CDN NB between two orthogonal distributions results, respectively, from metallo-selection and photo-selection. The four DCLs undergo triple adaptation when subjected to the three agents with the generation of specific CDN distributions characteristic of each of the four DCLs. The ternary outputs displayed by the DCLs present three states (-1, 0 and 1) related to three different constitutional distributions expressed in response to the triple inputs applied. This latter process amounts to the storage of molecular information in dynamic distributions rather than in selective interactions between complementary entities undergoing molecular recognition.

A pillar[5]arene with an amino-terminated arm stabilizes the formation of aliphatic hemiaminals and imines

A self-included mono-amino substituted pillar[5]arene efficiently stabilizes the hemiaminal and imine formation from the reaction of aliphatic amines and aldehydes.

Discovery of a Biologically Active Bromodomain Inhibitor by Target-Directed Dynamic Combinatorial Chemistry

Target-directed dynamic combinatorial chemistry (DCC) has emerged as a strategy for the identification of inhibitors of relevant therapeutic targets. In this contribution, we use this strategy for the identification of a high-affinity binder of a parasite target, the Trypanosoma cruzi bromodomain-containing protein TcBDF3. This protein is essential for viability of T. cruzi, the protozoan parasite that causes Chagas disease. A small dynamic library of acylhydrazones was prepared from aldehydes and acylhydrazides at neutral pH in the presence of aniline. The most amplified library member shows (a) high affinity for the template, (b) interesting antiparasitic activity against different parasite forms, and (c) low toxicity against Vero cells. In addition, parasites are rescued from the compound toxicity by TcBDF3 overexpression, suggesting that the toxicity of this compound is due to the TcBDF3 inhibition, i.e., the binding event that initially drives the molecular amplification is reproduced in the parasite, leading to selective toxicity.

Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3

Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC₅₀ =2.6 μm) and ALKBH3 (8; IC₅₀ =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.

Target-Directed Self-Assembly of Homodimeric Drugs Against β-Tryptase

Tryptase, a serine protease released from mast cells, is implicated in many allergic and inflammatory disorders. Human tryptase is a donut-shaped tetramer with the active sites facing inward forming a central pore. Bivalent ligands spanning two active sites potently inhibit this configuration, but these large compounds have poor drug-like properties. To overcome some of these challenges, we developed self-assembling molecules, called coferons, which deliver a larger compound in two parts. Using a pharmacophoric core and reversibly binding linkers to span two active sites, we have successfully produced three novel homodimeric tryptase inhibitors. Upon binding to tryptase, compounds reassembled into flexible homodimers, with significant improvements in IC₅₀ (0.19 ± 0.08 μM) over controls (5.50 ± 0.09 μM), and demonstrate good activity in mast cell lines. These studies provide validation for this innovative technology that is especially well-suited for the delivery of dimeric drugs to modulate intracellular macromolecular targets.