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.     

Receptor-assisted combinatorial chemistry: thermodynamics and kinetics in drug discovery

Current drug discovery using combinatorial chemistry involves synthesis followed by screening, but emerging methods involve receptor-assistance to combine these steps. Adding stoichiometric amounts of receptor during library synthesis alters the kinetics or thermodynamics of the synthesis in a way that identifies the best-binding library members. Three main methods have emerged thus far in receptor-assisted combinatorial chemistry: dynamic combinatorial libraries, receptor-accelerated synthesis, and a new method, pseudo-dynamic libraries. Pseudo-dynamic libraries apply both thermodynamics and kinetics to amplify library members to easily observable levels, and attain selectivity heretofore unseen in receptor-assisted systems.     

Generation of a dynamic combinatorial library using sialic acid aldolase and in situ screening against wheat germ agglutinin

This paper describes the generation of a dynamic combinatorial library of sialic acid analogues using sialic acid aldolase. Addition of wheat germ agglutinin to the equilibrating libraries results in selective amplification of one or more members.     

Dissipative Assembly of Macrocycles Comprising Multiple Transient Bonds

Dissipative assembly has great potential for the creation of new adaptive chemical systems. However, while molecular assembly at equilibrium is routinely used to prepare complex architectures from polyfunctional monomers, species formed out of equilibrium have, to this point, been structurally very simple. In most examples the fuel simply effects the formation of a single short‐lived covalent bond. Herein, we show that chemical fuels can assemble bifunctional components into macrocycles containing multiple transient bonds. Specifically, dicarboxylic acids give aqueous dianhydride macrocycles on treatment with a carbodiimide. The macrocycles are assembled efficiently as a consequence of both fuel‐dependent and fuel‐independent mechanisms; they undergo slower decomposition, building up as the fuel recycles the components, and are a favored product of the dynamic exchange of the anhydride bonds. These results create new possibilities for generating structurally sophisticated out‐of‐equilibrium species.     

The dark side of disulfide-based dynamic combinatorial chemistry

During the last two decades, disulfide-based dynamic combinatorial chemistry has been extensively used in the field of molecular recognition to deliver artificial receptors for molecules of biological interest. Commonly, the nature of library members and their relative amounts are provided from HPLC-MS analysis of the libraries, allowing the identification of potential binders for a target (bio)molecule. By re-investigating dynamic combinatorial libraries generated from a simple 2,5-dicarboxy-1,4-dithiophenol building block in water, we herein demonstrated that multiple analytical tools were actually necessary in order to comprehensively describe the libraries in terms of size, stereochemistry, affinity, selectivity, and finally to get a true grasp on the different phenomena at work within dynamic combinatorial systems.

We show that multiple analytical tools are necessary in order to describe the different phenomena within disulfide-based dynamic combinatorial libraries in terms of size, stereochemistry, affinity and selectivity.     

Integrating replication-based selection strategies in dynamic covalent systems

In the past 15 years, the chemistry of reversible covalent bond formation (dynamic covalent chemistry (DCC)) has been exploited to engineer networks of interconverting compounds known as dynamic combinatorial libraries (DCLs). Classically, the distribution of library components is governed by their relative free energies, and so, processes that manipulate the free energy landscape of the DCL can influence the distribution of library members. Within the same time frame, the design and implementation of molecules capable of copying themselves--so-called replicators--has emerged from the field of template-directed synthesis. Harnessing the nonlinear kinetics inherent in replicator behavior offers an attractive strategy for amplification of a target structure within a DCL and, hence, engendering high levels of selectivity within that library. The instructional nature of replicating templates also renders the combination of replication and DCC a potential vehicle for developing complex reaction networks; a prerequisite for the development of the emerging field of systems chemistry. This Concept article explores the role of kinetically and thermodynamically controlled processes within different DCC frameworks. The effects of embedding a replicating system within these DCC frameworks is explored and the consequences of the different topologies of the reaction network for amplification and selectivity within DCLs is highlighted.     

An Allosteric Receptor by Simultaneous “Casting” and “Molding” in a Dynamic Combinatorial Library

Allosteric synthetic receptors are difficult to access by design. Herein we report a dynamic combinatorial strategy towards such systems based on the simultaneous use of two different templates. Through a process of simultaneous casting (the assembly of a library member around a template) and molding (the assembly of a library member inside the binding pocket of a template), a Russian‐doll‐like termolecular complex was obtained with remarkable selectivity. Analysis of the stepwise formation of the complex indicates that binding of the two partners by the central macrocycle exhibits significant positive cooperativity. Such allosteric systems represent hubs that may have considerable potential in systems chemistry.     

在肽库中进行小肽筛选的初步研究

以合成六肽ＤＧＧＳＡＡ为模型对在噬菌体肽库中进行小肽筛选做了初步研究。结果表明，含有可形成氢键和离子键残基的小肽能够在噬菌体肽库中进行筛选。并用明显提高了筛选的专一性。     

Correlation between host-guest binding and host amplification in simulated dynamic combinatorial libraries

We present a versatile computer model of diverse dynamic combinatorial libraries, and examine how molecular recognition between library members and a template can be used to amplify the best binders. The correlation between host-guest binding and amplification was examined for a set of 50 libraries with >300 components each over a wide range of template and building block concentrations. Depending on these concentrations correlations vary from poor (when using a large excess of template) to good (for very dilute libraries and/or substoichiometric template concentrations), highlighting the need to choose the experimental conditions for dynamic combinatorial libraries thoughtfully.     

Live‐Cell‐Templated Dynamic Combinatorial Chemistry

Dynamic covalent chemistry combines in a single step the screening and synthesis of ligands for biomolecular recognition. In order to do that, a chemical entity is used as template within a dynamic combinatorial library of interconverting species, so that the stronger binders are amplified due to the efficient interaction with the target. Here we employed whole A549 living cells as template in a dynamic mixture of imines, for which amplification reflects the efficient and selective interaction with the corresponding extracellular matrix. The amplified polyamine showed strong interaction with the A549 extracellular matrix in on‐cell NMR experiments, while combination of NMR, SPR, and molecular dynamics simulations in model systems provided insights on the molecular recognition event. Notably, our work pioneers the use of whole living cells in dynamic combinatorial chemistry, which paves the way towards the discovery of new bioactive molecules in a more biorelevant environment.     

Evolution of a Constitutional Dynamic Library Driven by Self‐Organisation of a Helically Folded Molecular Strand

Conversion of macrocyclic imine entities into helical strands was achieved through three‐ and four‐component exchange reactions within constitutionally dynamic libraries. The generation of sequences of the intrinsic helicity codon, based on the hydrazone–pyrimidine fragment obtained by condensation of pyrimidine dialdehyde A with pyrimidine bis‐hydrazine B , shifted the equilibrium between all the possible macrocycles and strands towards the full expression (>98%) of helical product [ A / B ]. Furthermore, it was shown that chain folding accelerated the dynamic exchange reactions among the library members. Lastly, in four‐component experiments (involving A , B , E and either C or D ), even though the macrocyclic entities ([ A / C ], [ B / E ]; [ A / D ], [ B / E ]) were the kinetically preferred products, over time dialdehyde A relinquished its initial diamine partners C or D to opt for bis‐hydrazine B , which allowed the preferential formation of the helically folded strand. The present results indicate that self‐organisation pressure was able to drive the dynamic system towards the selective generation of the strand undergoing helical folding.     

Partial alloc-deprotection approach for ladder synthesis of "one-bead one-compound" combinatorial libraries

The topologically segregated bilayer-bead concept has been applied to encoded "one-bead one-compound"(OBOC) combinatorial libraries to avoid the interference of coding tags with biological screening. In this paper, we report on the development of a novel partial Alloc-deprotection (PAD) approach and the use of this approach to establish a new ladder-synthesis method for OBOC combinatorial libraries to further exploit the concept. In the PAD approach, Alloc-protected beads are partially deprotected, sequentially layer by layer, starting from the outer layer toward the bead interior. The degree of deprotection (or thickness of each layer) is controlled by the time of exposure to the deprotecting agent, palladium. By repetitive use of the PAD approach, a small portion of Alloc-protected N termini in the bead interior is liberated in each synthetic cycle for generation of an additional ladder member such that each library bead will carry a full-length library compound on the bead surface and a series of truncated ladder members in the bead interior. For the libraries containing isobaric residues, a simple encoding strategy is introduced in the ladder-synthesis method so that the isobaric residues can be differentiated by the coding tags. One advantage of this encoding strategy is that the coding tags are confined together with the truncated ladder members in the bead interior, thus maintaining the arrangement that only the library compounds are displayed on the bead surface. The PAD approach of forming multiple concentric functional layers inside a bead is simple, reliable, and may have other applications in addition to OBOC combinatorial library bead encoding, such as the development of novel optically encoded beads for multiplex immunodiagnostics or even information recording.     

Anions as templates in coordination and supramolecular chemistry

This review aims to highlight the most important recent advances in the area of anion-templated syntheses in supramolecular and coordination chemistry. We published a comprehensive review on this area in 2003 and hence examples prior to this date will only be discussed when essential for clarity of presentation. The current review has been divided into three main sections: (a) anion-templated synthesis of systems with well-defined molecular weights; this includes macrocycles and cages, interlocked species (such as catenanes and rotaxanes), helical assemblies and other selected examples. (b) Anions as templates in polymeric systems; this includes metal-organic frameworks, molecularly imprinted polymers and other selected examples, such as liquid crystalline materials. (c) Anion templates in dynamic combinatorial libraries.     

Perspectives in Chemistry—Steps towards Complex Matter

Chemistry is progressively unraveling the processes that underlie the evolution of matter towards states of higher complexity and the generation of novel features along the way by self‐organization under the pressure of information. Chemistry has evolved from molecular to supramolecular to become adaptive chemistry by way of constitutional dynamics, which allow for adaptation, through component selection in an equilibrating set. Dynamic systems can be represented by weighted dynamic networks that define the agonistic and antagonistic relationships between the different constituents linked through component exchange. Such networks can be switched through amplification/up‐regulation of the best adapted/fittest constituent(s) in a dynamic set. Accessing higher level functions such as training, learning, and decision making represent future lines of development for adaptive chemical systems.     

Induced Circular‐Dichroism Chirality Probes for Selective Amino Acid Detection through Screening of a Dynamic Combinatorial Library of Lanthanide Complexes

A dynamic combinatorial library of lanthanide complexes was prepared to develop induced‐circular‐dichroism (CD) chirality probes. It totaled 168 combinations of coordinative N‐aromatic chromophores, trivalent lanthanide centers, and guest amino acids. Eu³⁺ and Tb³⁺ complexes prepared with quinolinecarboxylic acid were particularly effective as induced‐CD chirality probes for selective alanine detection, whereas a Yb³⁺ complex with terpyridine exhibited glutamine selectivity. The former two complexes highly preferred alanine to the corresponding amine, ester, amino alcohol, and carboxylic acid derivatives. As such, the present combinatorial screening of a dynamic lanthanide complex library has led to a new series of induced‐CD chirality probes for specific amino acids.     

Dissipative Assembly of Macrocycles Comprising Multiple Transient Bonds

Dissipative assembly has great potential for the creation of new adaptive chemical systems. However, while molecular assembly at equilibrium is routinely used to prepare complex architectures from polyfunctional monomers, species formed out of equilibrium have, to this point, been structurally very simple. In most examples the fuel simply effects the formation of a single short-lived covalent bond. Herein, we show that chemical fuels can assemble bifunctional components into macrocycles containing multiple transient bonds. Specifically, dicarboxylic acids give aqueous dianhydride macrocycles on treatment with a carbodiimide. The macrocycles are assembled efficiently as a consequence of both fuel-dependent and fuel-independent mechanisms; they undergo slower decomposition, building up as the fuel recycles the components, and are a favored product of the dynamic exchange of the anhydride bonds. These results create new possibilities for generating structurally sophisticated out-of-equilibrium species.     

Synthesizing Macrocycles under Thermodynamic Control – Dynamic Combinatorial Libraries and Templates

An effective way to synthesize macrocycles using a dynamic combinatorial library is demonstrated for the reaction of pyridine-2,6-dicarbaldehydes with several long diamines. According to the template ions present, a given library can be shifted towards several macrocycles as desired.     

Selective Host Molecules Obtained by Dynamic Adaptive Chemistry

Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis–optimization process. The second was the use of a “brutal force” approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, “rational design” often resulted in time‐consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. “Combinatorial chemistry” suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry.     

The measurement of molecular diversity: A three-dimensional approach

Summary This paper describes a method for selecting a small, highly diverse subset from a large pool of molecules. The method has been employed in the design of combinatorial synthetic libraries for use in high-throughput screening for pharmaceutical lead generation. It computes diversity in terms of the main factors relevant to ligand-protein binding, namely the three-dimensional arrangement of steric bulk and of polar functionalities and molecular entropy. The method was used to select a set of 20 carboxylates suitable for use as side-chain precursors in a polyamine-based library. The method depends on estimates of various physical-chemical parameters involved in ligand-protein binding; experiments examined the sensitivity of the method to these parameters. This paper compares the diversity of randomly and rationally selected side-chain sets; the results suggest that careful design of synthetic combinatorial libraries may increase their effectiveness several-fold.