Molecular amplification in a dynamic system by ammonium cations

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.

Introducing a static receptor to compete with a dynamic combinatorial library in template binding

Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.

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.

"Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates

A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.

Probing the mechanism and dynamic reversibility of trianglimine formation using real-time electrospray ionization time-of-flight mass spectrometry

RATIONALE

The [3+3]-cyclocondensation reactions of chiral (1R,2R)-1,2-diaminocyclohexane with aromatic or aliphatic bis-aldehydes to form trianglimine macrocycles were reported a decade ago and were believed to proceed through a stepwise mechanistic pathway; however, no intermediates were ever isolated or detected and characterized.

METHODS

We investigated the mechanism of the [3+3]-cyclocondensation reaction using a selection of dialdehyde starting materials using real-time electrospray ionization time-of-flight mass spectrometry.

RESULTS

We observed up to a maximum of 16 reaction intermediates along the reaction pathway, more than for any other multistep reaction reported. We also probed the dynamic reversibility of trianglimines using selected small dynamic combinatorial libraries and showed that trianglimine formation is indeed fully reversible.

CONCLUSIONS

This study represents a significant contribution towards understanding the mechanism of trianglimine formation and its potential applicability can be extended to include other cascade reactions.

Thermoresponsive dynamers: thermally induced, reversible chain elongation of amphiphilic poly(acylhydrazones)

A nanostructured poly(acylhydrazone), which is reversibly formed in acidic aqueous solution from di(aldehyde) and di(acylhydrazine) monomers with appended hexaglyme groups, was found to display lower critical solution (LCS) behavior. Remarkably, under acidic conditions in which polymerization is reversible, large and reversible molecular weight (M(w)) increases were observed in response to elevated temperatures, both below and above the LCS temperature. No variation in M(w) was evident under neutral and alkaline conditions, in which the acylhydrazone condensation is essentially irreversible. Results of turbidometry studies, size-exclusion chromatography-multiangle laser light scattering (SEC-MALLS), and transmission electron microscopy (TEM) suggest that heating the polymer below the LCS temperature leads to polymer growth with preservation of the characteristic nanostructured morphology, whereas the onset of the microphase separated state causes a fundamental change in morphology, in which the polymer chains aggregate into larger bundles and fibers. van't Hoff analysis of a small molecule model system indicates that the acylhydrazone condensation is enthalpy driven (ΔH(eq) = -8.2 ± 0.2 kcal·mol(-1) and ΔS(eq) = -11.1 ± 0.4 = cal·mol(-1)·K(-1)), which suggests that the observed polymer growth with temperature is not a consequence of the intrinsic thermodynamics of the intermonomer linkage but is likely the result of the thermoresponsive characteristics conferred by the multiple hexaglyme groups. The system described displays double control of the dynamer state by two orthogonal agents, heat and protons (pH). It also represents a prototype for dynamic materials displaying multiple control adaptive behavior.

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'.

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.

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.

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.

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.

Self-assembly using dynamic combinatorial chemistry

The principles of an evolution-selection approach to the synthesis of systems capable of molecular recognition are described. Using this dynamic combinatorial self-assembly concept in bulk solution, a variety of successful synthetic receptors have been prepared. The reversible chemistries employed include metalloporphyrin-ligand coordination, hydrazone exchange and disulfide exchange. The prospects for extension of the approach to surfaces are briefly considered.

Complexation of diphenyl(phenylacetenyl)phosphine to rhodium(III) tetraphenyl porphyrins: synthesis and structural, spectroscopic, and thermodynamic studies

The coordination of diphenyl(phenylacetenyl)phosphine (DPAP, 1) to (X)Rh(III)TPP (X = I (2) or Me (3); TPP = tetraphenyl porphyrin) was studied in solution and in the solid state. The iodide is readily displaced by the phosphine, leading to the bis-phosphine complex [(DPAP)(2)Rh(TPP)](I) (4). The methylide on rhodium in 3 is not displaced, leading selectively to the mono-phosphine complex (DPAP)(Me)Rh(TPP) (5). The first and second association constants, as determined by isothermal titration calorimetry and UV-vis titrations, are in the range 10(4)-10(7) M(-1) (in CH(2)Cl(2)). Using LDI-TOF mass spectrometry, the mono-phosphine complexes can be detected but not the bis-phosphine complexes. The electronic spectrum of 4 is similar to those previously reported with other tertiary phosphine ligands, whereas (DPAP)(I)Rh(TPP) (6) displays a low energy B-band absorption and a high energy Q-band absorption. In contrast to earlier reports, displacement of the methylide on rhodium in 5 could not be observed at any concentration, and the electronic spectra of 4 and 5 are almost identical. Isothermal titration calorimetry experiments showed that all binding events are exothermic, and all are enthalpy driven. The largest values of DeltaG degrees are found for 6. The thermodynamic and UV-vis data reveal that the methylide and the phosphine ligand have an almost identical electronic trans-influence on the sixth ligand.

Selection and amplification of hosts from dynamic combinatorial libraries of macrocyclic disulfides

We have discovered two receptors for two different guests from a single dynamic combinatorial library. Each of the two guests amplifies the formation of a tightly binding host at the expense of unfit library members. Small differences in host-guest binding translate into useful differences in amplification. The selected hosts could be readily synthesized using biased dynamic libraries that contain only the right ratio of those building blocks that were selected by the guests. These results establish dynamic combinatorial chemistry as a practical method not only for the discovery but also for the synthesis of new receptors.

Recent developments in dynamic combinatorial chemistry

Generating combinatorial libraries under equilibrium conditions has the important advantage that the libraries are adaptive (i.e. they can respond to exterior influences in the form of molecular recognition events). Thus, a ligand will direct and amplify the formation of its ideal receptor and vice versa. Proof of principle of this approach has been established using small libraries showing highly efficient amplification of selected receptors. The approach has recently been extended to address folding of macromolecules, including peptides.

Dynamic covalent chemistry

Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.

Dynamic combinatorial chemistry

A combinatorial library that responds to its target by increasing the concentration of strong binders at the expense of weak binders sounds ideal. Dynamic combinatorial chemistry has the potential to achieve exactly this. In this review, we will highlight the unique features that distinguish dynamic combinatorial chemistry from traditional combinatorial chemistry, and that could make a useful addition to the set of combinatorial techniques used in drug discovery.