Metal-ion induced amplification of three receptors from dynamic combinatorial libraries of peptide-hydrazones

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.

Well-Defined pH-Responsive Self-Assembled Block Copolymers for the Effective Codelivery of Doxorubicin and Antisense Oligonucleotide to Breast Cancer Cells

The worldwide steady increase in the number of cancer patients motivates the development of innovative drug delivery systems for combination therapy as an effective clinical modality for cancer treatment. Here, we explored a design concept based on poly(ethylene glycol)-b-poly(2-(dimethylamino)ethyl methacrylate)-b-poly(2-hydroxyethyl methacrylate-formylbenzoic acid) [PEG-b-PDMAEMA-b-P(HEMA-FBA)] for the dual delivery of doxorubicin (DOX) and GTI2040 (an antisense oligonucleotide for ribonucleotide reductase inhibition) to MCF-7 breast cancer cells. PEG-b-PDMAEMA-b-PHEMA, the precursor copolymer, was prepared through chain extensions from a PEG-based macroinitiator via two consecutive atom transfer radical polymerization (ATRP) steps. Then, it was modified at the PHEMA block with 4-formylbenzoic acid (FBA) to install reactive aldehyde moieties. A pH-responsive polymer-drug conjugate (PDC) was obtained by conjugating DOX to the polymer structure via acid-labile imine linkages, and subsequently self-assembled in an aqueous solution to form DOX-loaded self-assembled nanoparticles (DOX-SAN) with a positively charged shell. DOX-SAN condensed readily with negatively charged GTI2040 to form GTI2040/DOX-SAN nanocomplexes. Gel-retardation assay confirmed the affinity between GTI2040 and DOX-SAN. The GTI2040/DOX-SAN nanocomplex at N/P ratio of 30 exhibited a volume-average hydrodynamic size of 136.4 nm and a zeta potential of 21.0 mV. The pH-sensitivity of DOX-SAN was confirmed by the DOX release study based on the significant cumulative DOX release at pH 5.5 relative to pH 7.4. Cellular uptake study demonstrated favorable accumulation of GTI2040/DOX-SAN inside MCF-7 cells compared with free GTI2040/DOX. In vitro cytotoxicity study indicated higher therapeutic efficacy of GTI2040/DOX-SAN relative to DOX-SAN alone because of the downregulation of the R2 protein of ribonucleotide reductase. These outcomes suggest that the self-assembled pH-responsive triblock copolymer is a promising platform for combination therapy, which may be more effective in combating cancer than individual therapies.

Hydrazone exchange: a viable route for the solid-tethered synthesis of [2]rotaxanes

Using a hydrazone exchange methodology, resin beads were functionalised with [2]rotaxanes at up to 80% efficiency—higher than using other dynamic or irreversible synthetic approaches to form self-assembled structures on solid supports.

Evidence for Ion-Templation During Macrocyclooligomerization of Depsipeptides

The ion-mediated Mitsunobu macrocyclooligomerization (M-MCO) reaction of hydroxy acid depsipeptides provides small collections of cyclic depsipeptides with good mass recovery. The approach can produce good yields of a single macrocycle or provide rapid access to multiple oligomeric macrocycles in good overall yield. While Lewis acidic alkali metal salts are known to play a role in the outcome of MCO reactions, it is unclear whether their effect is due to an organizational (e.g., templating) mechanism. Isothermal titration calorimetry (ITC) was used to study macrocycle-metal ion binding interactions, and this report correlates these thermodynamic measurements to the (kinetically determined) size distributions of depsipeptides formed during a Mitsunobu-based macrocyclooligomerization (MCO). Key trends have been identified in quantitative metal ion-cyclic depsipeptide binding affinity ( Ka), enthalpy of binding (Δ H), and stoichiometry of complexation across discrete series of macrocycles, and they provide the first analytical platform to rationally select a metal-ion template for a targeted size regime of cyclic oligomeric depsipeptides.

Cyclic acetals as cleavable linkers for affinity capture

Labeling proteins with biotin is a widely used method to identify target proteins due to biotin's strong binding affinity for streptavidin. Combined with alkyne-azide cycloaddition, which enables the coupling of probes to targeted proteins, biotin tags linked to an alkyne or azide have become a powerful tool for purification and analysis of proteins in proteomics. However, biotin requires harsh elution conditions to release the captured protein from the bead matrix. Use of these conditions reduces signal to noise and complicates the analysis. To improve affinity capture, cleavable linkers have been introduced. Here, we demonstrate the use of a cyclic acetal biotin probe that is prepared easily from commercially available starting materials, is stable to cell lysates, yet is cleaved under mildly acidic conditions, and which provides an aldehyde for further elaboration of the protein, if desired.

From simplicity to complex systems with bioinspired pseudopeptides

This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).

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

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Mimicking nature with synthetic macromolecules capable of recognition

Nature has, through billions of years of evolution, assembled a multitude of polymeric macromolecules capable of exquisite molecular recognition. This functionality arises from the precise control exerted over their biosynthesis that results in key residues being anchored in the appropriate positions to interact with target substrates. Developing 'wholly synthetic' macromolecular analogues that can mimic this behaviour presents a considerable challenge to chemists, who lack the 'biological machinery' used in nature to assemble polymers with such precision. In addressing this challenge, familiar chemical concepts, such as combinatorial methods and supramolecular interactions, have been adapted for application in the macromolecular arena. Working from a limited set of residues, synthetic macromolecules have been produced that display surprisingly high binding affinities towards target proteins, even possessing useful in vivo activities. These observations are all the more surprising when one considers the heterogeneity inherent within these synthetic macromolecular receptors, and provoke intriguing questions regarding our assumptions about the design of receptors.

Fast alpha nucleophiles: structures that undergo rapid hydrazone/oxime formation at neutral pH

Hydrazones and oximes are widely useful structures for conjugate formation in chemistry and biology, but their formation can be slow at neutral pH. Kinetics studies were performed for a range of structurally varied hydrazines, and a surprisingly large variation in reaction rate was observed. Structures that undergo especially rapid reactions were identified, enabling reaction rates that rival orthogonal cycloaddition-based conjugation chemistries.

Dynamic combinatorial libraries for the recognition of heavy metal ions

We present the use of hydrazone dynamic combinatorial libraries (DCLs) to identify macrocyclic receptors that are selective for alkaline earth metal ions over alkali metal ions. In particular, the toxic heavy metal ions Sr(2+) and Ba(2+) induce characteristic changes in the DCLs. Four macrocycles were isolated and characterised by LCMS, HRMS, NMR and X-ray crystallography; binding studies by UV-Vis spectroscopy confirm the selectivity observed in the DCLs.

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

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

Reversible covalent chemistries compatible with the principles of constitutional dynamic chemistry: new reactions to create more diversity

An approach to make chemical diversity space more manageable is to search for smaller molecules, or fragments, and then combine or elaborate these fragments. Dynamic Combinatorial Chemistry (DCC) is a powerful approach whereby a number of molecular elements each with binding potential can be reversibly combined via covalent or noncovalent linkages to generate a dynamic library of products under thermodynamic equilibrium. Once a target molecule has been added, the distribution of products can be shifted to favor products that bind to the target. Thus the approach can be employed to identify products that selectively recognize the target. Although the size of the repertoire of reversible covalent reactions suitable for DCC has increased significantly over the past 5-10 years, the discovery of new reactions that satisfy all the criteria of reversibility and biocompatibility remains an exciting challenge for chemists. Increasing the number of chemical reactions will enable the engineering of larger and more diverse DCLs, which remains a key step toward a broader use of DCC. In this review, we aim to provide a nonexhaustive list of reversible covalent reactions that are compatible with the concept of DCC, focusing mainly on the most recent examples that were reported in the literature in the past 5 years.

Dynamic combinatorial chemistry with hydrazones: libraries incorporating heterocyclic and steroidal motifs

We expand the possibilities in hydrazone based dynamic combinatorial chemistry with a series of new building blocks incorporating heterocyclic motifs. The synthetic procedure allows efficient access to building blocks with the general structure (MeO)(2)CH-Heterocycle-C(O)NHNH(2), originating from heterocycles with an amine and an ester functionality. The equilibrium distribution of macrocyclic N-acyl hydrazones formed upon deprotection of the building blocks with TFA in organic solvents is reported. The mixing behaviour of these heterocycle-based building blocks with our cholate-based building blocks is described, particularly the observation of kinetic intermediates that disappear following 'proof-reading'.

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

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

Facile acetal dynamic combinatorial library

We herein report our first results on the use of simple acetalation chemistry in the service of dynamic combinatorial libraries (DCLs); the reaction between triethylene glycol and 4-nitrobenzaldehyde afforded a DCL of more than 15 cyclic and acyclic species; all of which were separated and characterized; the smaller macrocyclic compounds were successfully amplified by the use of ammonium ions.

Supramolecular self-assembly of β-cyclodextrin: an effective carrier of the antimicrobial agent chlorhexidine

The supramolecular assembly between chlorhexidine and cyclomaltoheptaose (beta-cyclodextrin, betaCD) was characterized using NMR spectroscopy ((1)H, T(1), and ROESY), ESIMS and ITC. NMR data suggest the formation of high ordered complexes. ESIMS and ITC allowed the confirmation of the average stoichiometry as 1:4 and the thermodynamic data, also obtained by ITC, showed that the assembly is strongly stabilized by short distance interactions, but suffers a strong, opposite effect of entropy reduction. The antimicrobial activity of 1:1, 1:2, 1:3, and 1:4 Clx/betaCD molar ratio mixtures was investigated in aqueous solution and after incorporation into mucoadhesive gels. These were used to determine the initial and the long-term antimicrobial activity, respectively, toward Actinobacillus actinomycetemcomitans (A.a.) (Y4-FDC) and Enterococcus faecalis (E.f.) (ATCC 14508) strains. The results showed that A.a. and E.f. were more susceptible to the 1:4 molar ratio mixture in either solution or gel (p<0.05).

Dynamic Combinatorial Libraries Based on Hydrogen-Bonded Molecular Boxes

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the amplification and selection of the best binder. Receptors (1a-d)3.(DEB)6 are formed by the self-assembly of six diethyl barbiturate (DEB) and calix[4]arene dimelamine derivatives 1a-d by using hydrogen bonds. The largest amplification factor (2.8) for a host assembly (1a3.(DEB)6) was observed after the addition of 2a to four-component library 1a(n).1b(3-n).(DEB)6 (n=0-3). Addition of 2a to twenty-component library 1a(n).1b(m).1c(o).1d(3-(n+m+o)).(DEB)6 (n, m, o=0-3; (n+m+o)<or=3) also showed amplification of receptor 1a3.(DEB)6. The second part of this article describes the complexation of libraries of different alizarin-like guest molecules (2a-d) and the self-assembled receptor 1a3.(DEB)6. This receptor is able to template the formation of the best-fitting guest trimer.

Dynamic combinatorial libraries of hydrazone-linked pseudo-peptides: dependence of diversity on building block structure and chirality

Expanding on our earlier building block architecture [(MeO)(2)CH-Linker-Pro-X-NHNH(2) where X = Phe, Cha], we have produced a series of new pseudo-dipeptides [(MeO)(2)CH-Linker-Pro-X-NHNH(2) where X = Val, Leu, Ile, Ala] for use in hydrazone-based dynamic combinatorial libraries (DCLs); reverse order analogues [Phe-Pro and Val-Pro] and two enantio-analogues [Pro-Phe and Pro-Val] were also prepared. The behaviours of these building blocks in DCLs, as single components and in mixtures, were studied systematically using HPLC and mass spectrometry in order to gain insight into the relationship between building block structure and good library diversity. Subtle changes in building block structure lead to significant changes in library distribution and in the ability to produce diverse libraries in mixtures.

Molecular amplification of two different receptors using diastereomeric templates

Two different macrocyclic members of a pseudo-peptide hydrazone dynamic combinatorial library were amplified using the diastereomeric templates quinine and quinidine.

Cyclic esters and cyclodepsipeptides derived from lactide and 2,5-morpholinediones

The reaction between Bu(n)Li in benzene and the solid polystyrene support PS-C6H4CH2NH2 leads to a lithiated species that can be represented as PS-C6H4CH2NHLi(LiBu)x, where x approximately 4, which is active in the ring-opening of the cyclic esters L-lactide, rac-lactide, and 2,5-morpholinediones. With approximately 10 eq of these monomeric six-membered rings and with heating, cyclic esters (MeCHC(O)O)n and [MeCHC(O)OCHRC(NH)O]n are reversibly released to the solution. These have been characterized by electrospray ionization MS, and some small rings have been separated by gel-permeation chromatography. Addition of NaBPh4 to a heated benzene solution containing these rings preferentially removes the 18-membered rings from solution. For lactide this is shown to form the basis for chemical amplification from a dynamic combinatorial library and lactide can be converted to (MeCHC(O)O)6 in >80% yield. Metallated supports derived from Me2Mg and Et2Zn are less reactive but do show some ability for lactide ring-enlarging. The 18-membered ring (R,R,R,S,S,S)- and meso-(R,S,R,S,R,S)-(MeCHC(O)O)6 and the 24-membered ring (MeCHC(O)OCHPr(i)C(NH)O)4 have been characterized by single-crystal x-ray diffraction studies, together with the complex Na[eta3-S,S,S,S,S,S-(MeCHC(O)O)6]2BPh4.

The Discovery of an Enantioselective Receptor for (−)-Adenosine from a Racemic Dynamic Combinatorial Library

The use of laser polarimetry detection coupled with HPLC is demonstrated to enable the discovery of enantioselective receptors from racemic dynamic combinatorial libraries. Templating with an enantiopure analyte, such as (-)-adenosine, leads to amplification of one enantiomer of the cyclic dimer. A result confirmed with a pseudo-racemic library wherein one of the enantiomers was d-labeled for mass spec analysis. The resulting dimer is thus an enantioselective receptor for (-)-adenosine.

Utilization of Self-Sorting Processes To Generate Dynamic Combinatorial Libraries with New Network Topologies

The synthesis of water-soluble, organometallic macrocycles is described. They were obtained by self-assembly in reactions of the half-sandwich complexes [[Ru(C6H5Me)Cl2]2], [[Ru(p-cymene)Cl2]2], [[Rh(Cp)Cl2]2], and [[Ir(Cp*)Cl2]2] with the ligand 5-dimethylaminomethyl-3-hydroxy-2-methyl-4-(1H)-pyridone in buffered aqueous solution at pH 8. The structure of the Ru-(p-cymene) complex was determined by single-crystal X-ray crystallography. Upon mixing, these complexes undergo scrambling reactions to give dynamic combinatorial libraries. In combination with structurally related complexes based on amino-methylated 3-hydroxy-2-(1H)-pyridone ligands, an exchange of metal fragments but no mixing of ligands was observed. This self-sorting behavior was used to construct dynamic combinatorial libraries of macrocycles, in which two four-component sub-libraries are connected by two common building blocks. This type of network topology influences the adaptive behavior of the library as demonstrated in selection experiments with lithium ions as the target.

Highly diastereoselective amplification from a dynamic combinatorial library of macrocyclic oligoimines

Cadmium promoted diastereoselective amplification of a single member from a dynamic combinatorial library of stereoisomeric oligoimines of different sizes allows the efficient preparation of a new macrocyclic polyamine.

Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library

A high-affinity, induced-fit receptor for NMe4I was discovered using dynamic combinatorial chemistry. The addition of the guest to a dynamic combinatorial library made using a racemic mixture of chiral building blocks caused the strong and highly diastereoselective amplification of the receptor at the expense of other library components. The receptor and its mode of binding were characterized by NMR, ITC, and re-equilibration experiments, from which it was deduced that the receptor probably forms a folded four-stave barrel shape on binding of the guest.

Amplification of Acetylcholine-Binding Catenanes from Dynamic Combinatorial Libraries

Directed chemical synthesis can produce a vast range of molecular structures, but the intended product must be known at the outset. In contrast, evolution in nature can lead to efficient receptors and catalysts whose structures defy prediction. To access such unpredictable structures, we prepared dynamic combinatorial libraries in which reversibly binding building blocks assemble around a receptor target. We selected for an acetylcholine receptor by adding the neurotransmitter to solutions of dipeptide hydrazones [proline-phenylalanine or proline-(cyclohexyl)alanine], which reversibly combine through hydrazone linkages. At thermodynamic equilibrium, the dominant receptor structure was an elaborate [2]-catenane consisting of two interlocked macrocyclic trimers. This complex receptor with a 100 nM affinity for acetylcholine could be isolated on a preparative scale in 67% yield.

Expanding diversity in dynamic combinatorial libraries: simultaneous exchange of disulfide and thioester linkages

Dynamic combinatorial libraries have been prepared which feature two simultaneous covalent exchange reactions in aqueous solution at neutral pH. This allows for diversity, not only of the subunits that are linked, but also of the linkage itself.