Structure of a Glycomimetic/DC-SIGN complex highlights potency and selectivity improvements designed by fragment-based virtual screening

S10.2 Cell surface glycans
Location (hall): 
Start/end time: 
Thursday, July 4, 2019 - 17:15 to 17:30

Silvia Achilli1, Laura Medve2, Michel Thépaut1, Joao Guzman Caldentey3, Corinne Vivès1, Sonsoles Martin Santamaria3, Anna Bernardi2Franck Fieschi1

1Univ. Grenoble Alpes, CEA,CNRS, Institut de Biologie Structurale, Grenoble, France, 2Dip. di Chimica, Università degli Studi di Milano, Via Golgi 19, Milano, Italy, 3Center for Biological Research, Superior Council for Scientific Research, Madrid, Spain

C-type Lectin Receptors (CLRs) are carbohydrate-binding proteins expressed on the surface of Dendritic Cells (DCs). They recognize pathogens or damaged cells by interacting with glycan features. The encounter between the CLR and its ligand is the necessary step for the activation of the adaptive immune system and, therefore, CLRs are attractive targets to tailor immunity response. Molecules selective to each individual CLR have to be developed and one approach is based on the synthesis of glycomimetics that mimic the natural sugar. 

Recently, our group has addressed the question of the overlapping affinity between DC-SIGN and langerin, in the context of HIV recognition. A rational design approach was exploited and used to selectively target DC-SIGN in disfavour to langerin [1].

A deeper affinity towards DC-SIGN was sought. We used fragment-based virtual screening approach to identify interesting moieties that could positively interact with the protein in the vicinity of the primary binding site. The best fragment candidate combines the presence of an ammonium ion and an aromatic ring. On the basis of these fragments, new glycomimetics, incorporating these feature into previously first generation compounds, were produced and tested toward DC-SIGN and Langerin CLRs. Thanks to SPR competition assay and/or ITC measurements, one compound in particular, called Man69, have been identified as really promising. SPR analysis revealed an IC50 of 80 μM, with a selective inhibition of DC-SIGN and ITC experiments confirmed the μM range of the interaction (Kd of 57 μM). Finally, the crystal structure of DC-SIGN co-crystallized with Man069 was obtained, highlighting an unexpected and unprecedented binding mode that will be presented and analysed in detail. Analysis, by Analytical ultracentrifugation,  of the interaction between Man69 and DC-SIGN in solution allowed to fully understand the binding properties and to state on the properties observed within the crystal structure.

  1. Porkolab, V.; Chabrol, E.; Varga, N.; Ordanini, S.; Sutkevičiutė, I.; Thépaut, M.; García-Jiménez, M. J.; Girard, E.; Nieto, P. M.; Bernardi, A.; Fieschi, F. ACS Chem Biol 2018, 13 (3), 600.