Targeting undruggable carbohydrate recognition sites through focused fragment library design

Abstract

Carbohydrate-protein interactions are key for cell-cell and host-pathogen recognition and thus, emerged as viable therapeutic targets. However, their hydrophilic nature poses major limitations to the conventional development of drug-like inhibitors. To address this shortcoming, four fragment libraries were screened to identify metal-binding pharmacophores (MBPs) as novel scaffolds for inhibition of Ca2+-dependent carbohydrate-protein interactions. Here, we show the effect of MBPs on the clinically relevant lectins DC-SIGN, Langerin, LecA and LecB. Detailed structural and biochemical investigations revealed the specificity of MBPs for different Ca2+-dependent lectins. Exploring the structure-activity relationships of several fragments uncovered the functional groups in the MBPs suitable for modification to further improve lectin binding and selectivity. Selected inhibitors bound efficiently to DC-SIGN-expressing cells. Altogether, the discovery of MBPs as a promising class of Ca2+-dependent lectin inhibitors creates a foundation for fragment-based ligand design for future drug discovery campaigns.

Multivalent glycocyclopeptides: conjugation methods and biological applications

“…The utilization of advanced computational modelling methods 155 is undoubtedly a key tool to achieve this purpose by driving the design of glycomimetics or non-carbohydrate druglike lectin inhibitors capable to target secondary binding pockets of these proteins. 156,157 Besides this, the heterogenous expression of glycans at the surface of both normal and cancer cells is a crucial aspect to consider, making the design of multivalent systems much more complex than the simple multimerization of glycans on a scaffold. Due to the development of multi-click conjugation methods and glycodendrimer arrays, heterovalent structures combining diverse glycans in a variety of tridimensional geometry are now accessible to be screened as cell surface glycocalyx mimics.…”

Discovery of N-β-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB

“…20,26−28 Novel concepts were also reported such as the development of covalent lectin inhibitors, 29 addressing a subpocket between the two adjacent carbohydrate binding sites, 30 or the development of noncarbohydrate glycomimetics. 31,32 LecB also forms homotetramers and possesses two calcium ions per carbohydrate binding site mediating binding to its fucoside or mannoside ligands. 33 The affinity of fucosides is increased compared to mannosides due to an additional lipophilic interaction of the fucose C6 methyl group with the protein at Thr45, resulting in submicromolar binding (Figure1A, K d of Me-α-L-Fuc = 0.43 μM, 34 K d of Me-α-D-Man = 71 μM 34 ).…”

“…LecA forms homotetramers and binds to d -galactosides via a calcium ion in its carbohydrate binding site . Several monovalent galactosides were synthesized as LecA inhibitors reaching moderate binding in the micromolar range. − In contrast, divalent galactoside inhibitors with simultaneous binding to two adjacent carbohydrate binding sites of the LecA tetramer gave low nanomolar inhibitors. ,− Novel concepts were also reported such as the development of covalent lectin inhibitors, addressing a subpocket between the two adjacent carbohydrate binding sites, or the development of noncarbohydrate glycomimetics. , …”

“… 20 , 26 − 28 Novel concepts were also reported such as the development of covalent lectin inhibitors, 29 addressing a subpocket between the two adjacent carbohydrate binding sites, 30 or the development of noncarbohydrate glycomimetics. 31 , 32 …”

Mannobioside biomimetics that trigger DC-SIGN binding selectivity

“…6 Although the monovalent affinities are low (in the mM range), biologically useful values are achieved in Nature through several mechanisms linked to the multivalent presentation of the intervening epitopes. 7 Other mono and oligosaccharides, 1,8 and even non-carbohydrate molecules, 9 can also bind the lectins, but they may lead to disparate immune response outcomes.…”