In situ generation and screening of a dynamic combinatorial carbohydrate library against concanavalin A

Dominant behaviours in the expression of human carbonic anhydrase hCA I activity

Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.

Dynamic combinatorial chemistry with diselenides and disulfides in water

Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water at physiological pH.

Multivalency in heterogeneous glycoenvironments: hetero-glycoclusters, -glycopolymers and -glycoassemblies

Despite efficiently imitating functional ligand presentations in terms of valency and density, most of the reported multivalent carbohydrate prototypes barely reflect the inherent heterogeneity of biological systems, therefore underestimating the potential contribution of synergistic or antagonistic effects to molecular recognition events. To address this question, the design of novel molecular and supramolecular entities displaying different saccharide motifs in a controlled manner is of critical importance. In this review we highlight the current efforts made to synthesize heteromultivalent glycosystems on different platforms (peptides, dendrimers, polymers, oligonucleotides, calixarenes, cyclodextrins, microarrays, vesicles) and to evaluate the influence of heterogeneity in carbohydrate-protein (lectin, antibody) recognition phenomena. Although the number of publications on this topic is limited as compared to the huge volume of reports on homomultivalent sugar displays, the current body of results has already unravelled the existence of new binding mechanisms that operate in heterogeneous environments whose exact biological significance remains to be unveiled.

In situ click chemistry: a powerful means for lead discovery

Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.

Synthesis of heteroglycoclusters by using orthogonal chemoselective ligations

Synthetic heteroglycoclusters are being subjected to increasing interest due to their potential to serve as selective ligands for carbohydrate-binding proteins. In this paper, we describe an expedient strategy to prepare cyclopeptides displaying well-defined distributions and combinations of carbohydrates. By using both oxime ligation and copper(I)-catalyzed alkyne–azide cycloaddition, two series of compounds bearing binary combinations of αMan, αFuc or βLac in an overall tetravalent presentation, and either 2:2 or 3:1 relative proportions, have been prepared.

Multicomponent assembly of cavitand-based polyacylhydrazone nanocapsules

The thermodynamically controlled syntheses of different di-, tetra-, and hexacavitand polyacylhydrazone nanocapsules are reported. [2+4]-, [4+8]-, and [6+12]-nanocapsules assemble upon reacting a tetraformyl cavitand with two equivalents of isophthalic dihydrazide, or terephthalic dihydrazide in the presence of trifluoroacetic acid, whereby the building blocks are linked together through 8, 16, or 24 newly formed acylhydrazone bonds. Futhermore, the reaction of the tetraformylcavitands with different trigonal planar trihydrazides, simultaneously leads to the formation of [2+4]- and [6+8]-nanocapsules in varying ratios that depend on the cavitand to trihydrazide ratio and the nature of the cavitand and trihydrazide building blocks. The product ratios are rationalized with the different conformational strain of the acylhydrazone linkages in these nanocapsules. Diffusion NMR experiments with the hexacavitand polyacylhydrazone nanocapsules yield solvodynamic radii that range from 1.6 to 2.5 nm, consistent with estimates from force field calculations, and support, that these capsules have solvent filled, spherical interiors, the sizes of which approaches those of smaller proteins.

Symmetric dithiodigalactoside: strategic combination of binding studies and detection of selectivity between a plant toxin and human lectins

Thioglycosides offer the advantage over O-glycosides to be resistant to hydrolysis. Based on initial evidence of this recognition ability for glycosyldisulfides by screening dynamic combinatorial libraries, we have now systematically studied dithiodigalactoside on a plant toxin (Viscum album agglutinin) and five human lectins (adhesion/growth-regulatory galectins with medical relevance e.g. in tumor progression and spread). Inhibition assays with surface-presented neoglycoprotein and in solution monitored by saturation transfer difference NMR spectroscopy, flanked by epitope mapping, as well as isothermal titration calorimetry revealed binding properties to VAA (K(a): 1560 ± 20 M(-1)). They were reflected by the structural model and the affinity on the level of toxin-exposed cells. In comparison, galectins were considerably less reactive, with intrafamily grading down to very minor reactivity for tandem-repeat-type galectins, as quantitated by radioassays for both domains of galectin-4. Model building indicated contact formation to be restricted to only one galactose moiety, in contrast to thiodigalactoside. The tested glycosyldisulfide exhibits selectivity between the plant toxin and the tested human lectins, and also between these proteins. Therefore, glycosyldisulfides have potential as chemical platform for inhibitor design.

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.

In-crystal chemical ligation for lead compound generation

A new fragment-based growth strategy for lead compound generation is proposed, which is based onin situchemical ligation and is operable in X-ray-based fragment screening format. The method involves two classes of bifunctional molecules, referred to as anchor molecules and tuning molecules. The anchor molecules are designed to form stable complexes with target proteins and to connect with the tuning molecules. The procedure begins with the introduction of the anchor molecule into the target protein, to which the tuning molecule is linked in the crystal. Proof-of-concept experiments using trypsin crystals charged withpara-aldehyde benzamidine showed that the crystals acted as a platform to select self-assembled ligation products. Furthermore, time-resolved crystallography allowed identification of the reaction field and direct visualization of the reaction pathway. The ability to rapidly gain an understanding of the relations between a set of chemical modifications and their interactions with target proteins would accelerate the hit-to-lead process. A potential crystallographic growth strategyviathe self-assembly technique and its biological implications are discussed.

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

Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site.

Affinity chromatography in dynamic combinatorial libraries: one-pot amplification and isolation of a strongly binding receptor

We report the one-pot amplification and isolation of a nanomolar receptor in a multibuilding block aqueous dynamic combinatorial library using a polymer-bound template. By appropriate choice of a poly(N,N-dimethylacrylamide)-based support, nonselective ion-exchange type behaviour between the oppositely charged cationic guest and polyanionic hosts was overcome, such that the selective molecular recognition arising in aqueous solution reactions is manifest also in the analogous templated solid phase DCL syntheses. The ability of a polymer bound template to identify and isolate a synthetic receptor via dynamic combinatorial chemistry was not compromised by the large size of the library, consisting of well over 140 theoretical members, demonstrating the practical advantages of a polymer-supported DCL methodology.

Supramolecular interactions between library members modulate the behavior of dynamic combinatorial libraries

The presence of a supramolecular network of interactions between library members can lead to very different responses when libraries with identical molecular composition are exposed to the same template. Numerical simulations demonstrate that supramolecular interactions between library members of covalent dynamic combinatorial libraries (DCLs) can affect both degree and selectivity of the response of the library when a template molecule is added.

In situ click chemistry: probing the binding landscapes of biological molecules

Combinatorial approaches to the discovery of new functional molecules are well established among chemists and biologists, inspired in large measure by the modular composition of many systems and molecules in Nature. Many approaches rely on the synthesis and testing of individual members of a candidate combinatorial library, but attention has also been paid to techniques that allow the target to self-assemble its own binding agents. These fragment-based methods, grouped under the general heading of target-guided synthesis (TGS), show great promise in lead discovery applications. In this tutorial review, we review the use of the 1,3-dipolar cycloaddition reaction of organic azides and alkynes in a kinetically-controlled TGS approach, termed in situ click chemistry. The azide-alkyne reaction has several distinct advantages, most notably high chemoselectivity, very low background ligation rates, facile synthetic accessibility, and the stability and properties of the 1,2,3-triazole products. Examples of the discovery of potent inhibitors of acetylcholinesterases, carbonic anhydrase, HIV-protease, and chitinase are described, as are methods for the templated assembly of agents that bind DNA and proteins.

A small molecule receptor that selectively recognizes trimethyl lysine in a histonepeptide with native protein-like affinity

Synthetic yet selective: Small molecule receptors have been identified from a dynamic combinatorial library that mimic the HP1 chromodomain’s affinity and selectivity for trimethyl lysine in a histone tail relative to lower methylation states of lysine.

Dynamic template-assisted strategies in fragment-based drug discovery

Fragment-based methods for drug discovery are increasingly popular because they provide drug leads with greater ligand efficiency than conventional high-throughput screening. However, established methods for fragment detection do not address the central question in fragment-based ligand discovery: how can a primary ligand be optimally extended by a secondary fragment? Dynamic screening methods solve this issue by using a protein target as a template for ligand assembly, thus yielding high-affinity binders from low-affinity fragments. This review summarizes recent work on dynamic screening methodology, which resulted in the development of several high-affinity binders for various targets. Strengths and limitations of the published approaches are discussed and possible contributions of dynamic screening methodology to the drug discovery process are highlighted.

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.

From nature to the laboratory and into the clinic

Natural products possess a broad diversity of structure and function, and they provide inspiration for chemistry, biology, and medicine. In this review article, we highlight and place in context our laboratory's total syntheses of, and related studies on, complex secondary metabolites that were clinically important drugs, or have since been developed into useful medicines, namely amphotericin B (1), calicheamicin gamma(1)(I) (2), rapamycin (3), Taxol (4), the epothilones [e.g., epothilones A (5) and B (6)], and vancomycin (7). We also briefly highlight our research with other selected inspirational natural products possessing interesting biological activities [i.e., dynemicin A (8), uncialamycin (9), eleutherobin (10), sarcodictyin A (11), azaspiracid-1 (12), thiostrepton (13), abyssomicin C (14), platensimycin (15), platencin (16), and palmerolide A (17)].

Polymer-supported cationic templates for molecular recognition of anionic hosts in water

Translocating solution-phase molecular recognition of oppositely charged hosts and guests to the solid phase represents a major challenge; we report a successful immobilisation strategy which allows selective host-guest interactions in water unencumbered by unwanted ion exchange-type interactions.