From carbohydrate leads to glycomimetic drugs

Abstract

Carbohydrates are the most abundant natural products. Besides their role in metabolism and as structural building blocks, they are fundamental constituents of every cell surface, where they are involved in vital cellular recognition processes. Carbohydrates are a relatively untapped source of new drugs and therefore offer exciting new therapeutic opportunities. Advances in the functional understanding of carbohydrate-protein interactions have enabled the development of a new class of small-molecule drugs, known as glycomimetics. These compounds mimic the bioactive function of carbohydrates and address the drawbacks of carbohydrate leads, namely their low activity and insufficient drug-like properties. Here, we examine examples of approved carbohydrate-derived drugs, discuss the potential of carbohydrate-binding proteins as new drug targets (focusing on the lectin families) and consider ways to overcome the challenges of developing this unique class of novel therapeutics.

Figure 1. Carbohydrate and carbohydrate-derived drugs.

Structures of currently approved drugs (trade name in brackets). These include glycosidase inhibitors that prevent the digestion of carbohydrates for the treatment of diabetes (voglibose, miglitol and acarbose) and the prevention of influenza virus infections (zanamivir and oseltamivir); and sulphated glycosaminoglycans, which function as anticoagulants by binding to antithrombin III for the treatment of thrombosis (fondaparinux, dalteparin, ardeparin, nardoparin and enoxaparin). In addition, carbohydrate-derived drugs are used to treat Gaucher's disease (miglustat), epilepsy (topiramate) and osteoarthritis (sodium hyaluronate).

Figure 2. Ligands of dendritic cell-specific ICAM3-grabbing non-integrin 1 (DC-SIGN).

DC-SIGN co-crystallized with the natural epitopes Galβ(1-4)[Fucα(1-3)]GlcNAcβ(1-3)Gal (Protein Data Bank code 1SL5) (a) and Manα(1-6)[Manα(1-3)]Manα(1-6)Man (PDB code 1SL4) (b). The protein backbone is depicted in ribbon style, carbohydrates are shown in ball and stick style and the grey sphere is Ca²⁺. Part c shows the structures of DC-SIGN antagonists. The glycomimetics compound 1 (Ref. 69) and compound 2 (Ref. 72) have only a slightly improved affinity compared with the natural ligands Manα(1-2)Man and Lewis^x (Ref. 72), whereas the non-carbohydrate antagonists compound 3 and compound 4 have half-maximal inhibitory concentration (IC₅₀) values in the low micromolar range.

Figure 3. Myelin-associated glycoprotein (MAG) antagonists.

a | MAG, nogo 66 and myelin oligodendrocyte glycoprotein (MOG) bind to the reticulon 4 receptor (RTN4R; also known as the nogo receptor). The inhibitory signal is transduced into the cytosol of the neuron through the co-receptor NGFR (nerve growth factor receptor; also known as p75NTR). MAG bound to the brain gangliosides GD1a, GT1b and GQ1bα also transduces the inhibitory signal, with the help of NGFR as a co-receptor, into the cytosol. b | GQ1bα is the brain ganglioside with the highest affinity for MAG; replacement of its inner sialic acids by sulphates (to produce compound 5) led to a fourfold increase in affinity. The tetrasaccharide compound 6 (Ref. 87) is the minimal carbohydrate epitope of GQ1bα for MAG binding and has served as a lead structure for the development of antagonists; with compound 7, an excellent correlation between the degree of neurite outgrowth and the binding affinities was established. Further modifications involved the replacement of the Galβ(1-3)GalNAc core (to produce compound 8 (Ref. 166)) or the α(2-6)-linked Neu5Ac (to produce compound 9 (Ref. 135)). Following studies on compound 10 (Ref. 167), numerous Neu5Ac derivatives^,, for example, compound 11, with up to nanomolar affinities have been synthesized. Affinity data of the different compounds should be compared with caution as they were obtained from different assays. IC₅₀, half-maximal inhibitory concentration; K_d, dissociation constant; RIP, relative inhibitory potency.

Figure 4. PA-IL and PA-IIL inhibitors.

a | Binding sites of PA-I galactophilic lectin (PA-IL) complexed with D-galactose (Protein Data Bank code: 1OKO (Ref. 170)). b | Binding sites of fucose-binding lectin PA-IIL complexed with L-fucose (PDB code: 1GZT). In parts a and b, the protein backbones are depicted in ribbon style, carbohydrates are shown in ball and stick style and the grey spheres are Ca²⁺. c | The monovalent ligands compound 12 (Ref. 101) and compound 13 (Ref. 99) exhibit affinity for PA-IL and PA-IIL that is similar to that of Lewis^a (Ref. 100); the most potent oligovalent ligand is compound 14 (Ref. 102), but it has only a modest effect on a per saccharide basis; the heterobifunctional glycodendrimer compound 15 (Ref. 104) and the low-molecular-mass glycomimetic compound 16 (Ref. 105) bind to both PA-IL and PA-IIL from Pseudomonas aeruginosa.

Figure 5. FimH antagonists.

The crystal structure representation shows the mannose derivative compound 21 docked to the mannose-binding pocket of FimH (Protein Data Bank code: 1KFL). The relative inhibitory potencies (RIPs) of the FimH antagonists compounds 18 to 28are based on methyl α-D-mannoside (compound 17; RIP = 1). As the RIPs were obtained from different assays (yeast agglutination, adherence to cell lines derived from human urinary bladder epithelium or guinea pig epithelial cells as well as surface plasmon resonance experiments with immobilized FimH), they should be compared with caution.

Figure 6. Enhancing the affinity of carbohydrate-derived drugs.

a | The affinity of carbohydrate-derived drugs can be improved by pre-organization in the bioactive conformation. In solution, the core conformation (shown in red) of sialyl Lewis^x is in the range of +10° to −60° and the acid orientation (shown in blue) is in the range of +80° to +150°. In the bioactive conformation (complex 29), the core conformation is approximately −40° and an acid orientation is approximately 110° (Refs –178). The degree of pre-organization of a mimetic in the bioactive conformation, as shown in complex 30, can be correlated with its affinity^,. b | Affinity can be improved by establishing new enthalpic interactions; comparisons of the binding mode of Neu5Ac2en (compound 31), zanamivir (Relenza) and oseltamivir (Tamiflu) to neuraminidase are depicted. bb, backbone; sc, side chains.