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

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.

Glucose Binding Drives Reconfiguration of a Dynamic Library of Urea-Containing Metal-Organic Assemblies

A bis-urea-functionalized ditopic subcomponent assembled with 2-formylpyridine and Fe^II , resulting in a dynamic library of metal-organic assemblies: an irregular Fe^II ₄ L₆ structure and three Fe^II ₂ L₃ stereoisomers: left- and right-handed helicates and a meso-structure. This library reconfigured in response to the addition of monosaccharide derivatives, which served as guests for specific library members, and the rate of saccharide mutarotation was also enhanced by the library. The (P) enantiomer of the Fe^II ₂ L₃ helical structure bound β-D-glucose selectively over α-D-glucose. As a consequence, the library collapsed into the (P)-Fe^II ₂ L₃ helicate following glucose addition. The α-D-glucose was likewise transformed into the β-D-anomer during equilibration and binding. Thus, β-D-glucose and (P)-3 amplified each other in the product mixture, as metal-organic and saccharide libraries geared together into a single equilibrating system.

Tetrameric psuedo-peptide receptors with allosteric properties

This paper reports the binding properties of tetrameric pseudo-peptide receptors for protonated cytidines. The receptors, which were isolated from a dynamic combinatorial chemistry (DCC) experiment, bind the analytes with affinities that depend on the presence or absence of excess acid, and with a stoichiometry that is both concentration and temperature dependent.

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).

A recognition-mediated reaction drives amplification within a dynamic library

A single, appropriately designed, recognition event targets and transforms one of two reactive members of an exchanging pool of compounds through a recognition-mediated irreversible cycloaddition reaction, altering dramatically the final composition and kinetic behaviour of the dynamic library.

Design, preparation, and selection of DNA-encoded dynamic libraries

We report a method for the preparation and selection of DNA-encoded dynamic libraries (DEDLs). The library is composed of two sets of DNA-linked small molecules that are under dynamic exchange through DNA hybridization. Addition of the protein target shifted the equilibrium, favouring the assembly of high affinity bivalent binders. Notably, we introduced a novel locking mechanism to stop the dynamic exchange and "freeze" the equilibrium, thereby enabling downstream hit isolation and decoding by PCR amplification and DNA sequencing. Our DEDL approach has circumvented the limitation of library size and realized the analysis and selection of large dynamic libraries. In addition, this method also eliminates the requirement for modified and immobilized target proteins.

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.

"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.

DCC in the development of nucleic acid targeted and nucleic acid inspired structures

Nucleic acids were one of the first biological targets explored with DCC, and research into the application has continued to yield novel and useful structures for sequence- and structure-selective recognition of oligonucleotides. This chapter reviews major developments in DNA- and RNA-targeted DCC, including methods under development for the conversion of DCC-derived lead compounds into probe molecules suitable for studies in vitro and in vivo. Innovative applications of DCC for the discovery of new materials based on nucleic acids and new methods for the modification of nucleic acid structure and function are also discussed.

Controlling the transmission of stereochemical information through space in terphenyl-edged Fe4L6 cages

A series of terphenyl-edged Fe(4)L(6) cages were synthesized from substituted 4,4''-diamino-p-terphenyls, 2-formylpyridine, and iron(II). For the parent diaminoterphenyl, all three possible diastereomers, with T, S(4), and C(3) point symmetries, were formed in nearly equal amounts, as determined by (1)H and (13)C NMR. When 2,2″-dimethylterphenylenediamine was used, the T-symmetry diastereomer was observed to predominate. The use of 2',3',5',6'-tetramethylterphenylenediamine generated predominantly the S(4) cage diastereomer, whereas 2',5'-dimethylterphenylenediamine produced the C(3)-symmetric cage to a greater degree than the other two diastereomers. The factors contributing to the transfer of chiral information between metal vertices were analyzed, and the general principles underlying the delicately balanced thermodynamics were determined.

From static to dynamic: escaping kinetic traps in hydrazone-based dynamic combinatorial libraries

Thermodynamic control over kinetically-trapped mixtures of hydrazone-based macrocycles is achieved by addition of an aromatic monohydrazide to generate dynamic combinatorial libraries (DCLs) of linear and macrocyclic oligomers.

Synthesis of phototrappable shape-shifting molecules for adaptive guest binding

We have designed and synthesized oligosubstituted bullvalenes 1 and 2 as adaptive molecules that can change their shapes in order to bind tightly to a suitable guest. By incorporation of a photolabile o-nitroveratryloxycarbonate (NVOC) group into bullvalenes 1 and 2, tightly binding species can be selectively isolated from a population of hundreds of interconverting structural isomers. Spontaneous strain-assisted Cope rearrangements allow these shape-shifting molecules to exist in a dynamic equilibrium of configurationally distinct valence isomers, as revealed by dynamic NMR and HPLC studies. When NVOC bullvalenes 1 and 2 were exposed to UV light, the cleavage of the NVOC group resulted in a mixture of static isomers of the corresponding bullvalone. Binding studies of NVOC bisporphyrin bullvalene 1 demonstrated that the dynamic isomeric equilibrium shifted in the presence of C(60), favoring configurations with more favorable binding affinities. Irradiation of a mixture of 1 and C(60) with UV light and isolation of the major static isomer yielded an isomer of bisporphyrin bullvalone with a binding affinity for C(60) that was ∼2 times larger than that of the nonadapted isomer bisporphyrin bullvalone 41.

Discovery of linear receptors for multiple dihydrogen phosphate ions using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry to discover a new series of linear hydrazone-based receptors that bind multiple dihydrogen phosphate ions. Through the use of a template-driven, selection-based approach to receptor synthesis, dynamic combinatorial chemistry allows for the identification of unexpected host structures and binding motifs. Notably, we observed the unprecedented selection of these linear receptors in preference to competing macrocyclic hosts. Furthermore, linear receptors containing up to nine building blocks and three different building blocks were amplified in the dynamic combinatorial library. The receptors were formed using a dihydrazide building block based on an amino acid-disubstituted ferrocene scaffold. A detailed study of the linear pentamer revealed that it forms a helical ditopic receptor that employs four acylhydrazone hydrogen-bond donor motifs to cooperatively bind two dihydrogen phosphate ions.

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'.

Rapid enantiomeric excess and concentration determination using simple racemic metal complexes

Racemic-metal complexes were used to determine identity, enantiomeric excess, and concentration of chiral diamines using metal-to-ligand charge transfer bands in circular dichroism spectroscopy. It takes under just 2 min per sample to determine [G]t and %R with tolerable errors (19% and 4%, respectively). The simplicity of the achiral receptors employed confers to this technique great potential for high-throughput screening.

Target-driven selection in a dynamic nitrone library

Nitrones undergo dynamic exchange in chloroform at room temperature through two mechanisms-hydrolysis and recombination or hydroxylamine addition/elimination; this dynamic exchange is harnessed to select a nitrone-based bis(amidopyridine) receptor for diacids from a group of four nitrones through its binding to a glutaric acid-based target.

Disulfides, Imines, and Metal Coordination within a Single System: Interplay between Three Dynamic Equilibria

We report a system in which three distinct dynamic linkages, disulfide (S-S), imine (C=N), and coordinative (N-->metal) bonds were shown to be capable of simultaneous reversible exchange. The "disulfide layer" of the system under study consists of two homo-disulfides, bis(4-aminophenyl) disulfide 1 and bis(4-methoxyphenyl) disulfide 2 that equilibrate in the presence of catalytic amount of triethylamine to favor the formation of a hetero-disulfide product, 4-aminophenyl-4'-methoxyphenyl disulfide 3. The addition of 2-formylpyridine and a metal salt strongly perturbed this 1+2<-->3 equilibrium through the formation of metal complexes incorporating disulfide 1 as a subcomponent. CuI perturbed the equilibrium by a factor of 3.3, and FeII by a factor of 179, in both cases in favor of the homo-disulfides. The disulfide equilibrium could be further modified, following metal-complex formation, by coordinative (transmetallation: substitution of FeII for CuI) or covalent (imine exchange: the substitution of one amine residue for another) exchange. Thus, although the three kinds of dynamic linkages were demonstrated to be mutually compatible, changes at one kind of linkage could be used to predictably perturb an equilibrium involving another.

Dynamic combinatorial chemistry: on the road to fulfilling the promise

Dynamic combinatorial chemistry makes use of reversible reactions between functionalised monomeric building blocks to generate a mixture of products (dimers or oligomers) under thermodynamic equilibrium. This system reorganises upon addition of a target so that species that bind to, and are therefore stabilised by the target, are favourably formed and are thus amplified. Since the mid-1990's, dynamic combinatorial chemistry has been successfully applied to the identification/selection of ion receptors, enzyme inhibitors, catalysts, materials and nucleic acid ligands. Although it is now established as a powerful tool with broad applications some intrinsic limitations appeared when working on systems of increasing complexity. We present here the most recent advances in the field of dynamic combinatorial chemistry that have been developed to overcome these limitations and explore new areas of application.

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.