Structural and molecular glycobiology

Les lectines sont desLectins are protein receptors capable of specifically recognizing carbohydrates, especially glycoconjugates, without modifying them. The lectin-glycoconjugate interactions are essential in many cellular processes such as tissue cohesion, immunity, fertilization but also in pathological processes such as infection. Lectins are thus able to decipher the glycocode which is one of the main objectives of glycomics, a rapidly expanding discipline that still requires many tools and technological advances. Lectins have great potential for biotechnological and biomedical applications. They can be purified from natural sources, taking advantage of almost infinite biodiversity as a result of the variety of living organisms. When their gene is identified, we try to produce them in recombinant form and characterize them by biochemistry, biophysics and structural biology approaches. We are interested in the identification of new lectins both in their folding or their specificity, in obtaining the atomic bases governing carbohydrate-protein interactions and in lectin engineering to modify their specificity or their multivalency. We have set up a new classification of lectins according to their structure and prediction tools in collaboration with the Swiss Institute of Bioinformatics and the University of Geneva (Bonnardel et al, NAR, 2019, 47: D1236). The PropLec server allowed us to predict the formation of a six-bladed beta-propellant by dimerization of 3 tandem repeats for the bacterial lectin KhozL. This has been confirmed experimentally and structurally (Bonnardel et al, Structure, 2019, 27 (5): 764, cf figure).

Lectins play a critical role in host-pathogen interactions, either as a first-line defense molecule against foreign organisms or by promoting microbial adhesion, a crucial step in the initiation of infections. We have characterized several lectins that play a role in the adhesion of opportunistic bacteria and fungi responsible for severe pulmonary infections in immunocompromised or cystic fibrosis patients. These lectins are now targeted for the development of glycocompounds for a non-adhesive therapy that could be used as new anti-infectives (see figure). A patent has recently been filed for multivalent fucosylated compounds with antifungal properties in collaboration with the group of Sébastien Gouin, Nantes (Lehot et al, Chemistry, 2018, 24 (72): 19243). Many collaborations are in progress with several glycochemists in which we evaluate the potential of the synthetizes glucodrugs such as the groups of Sébastien Vidal, Orsay, France; Alexander Titz, Saarbrücken, Germany; Prof. Roland Pieters, University of Utrecht, Netherlands; Prof. Anna Bernardi, University of Milan, Italy, Prof Olivier Renaudet, DCM, Grenoble, France or Nicolas Winssinger, University of Geneva.

Cancers are associated with glycosylation changes that can be specifically recognized by lectins. Lectins are therefore tools sought to help in the diagnosis and prognosis of cancers because they can differentiate healthy cells from cancer cells but also for the control of glycosylation, a complex process or glycoprofiling. We possess a series of lectins in recombinant form highly characterized with very fine or strict recognition of specific carbohydrate patterns whose presence is looked at in glycomics and research against cancer. For example, the PhoSL fungal lectin strictly recognizes the core fucosylation, a tumor associated carbohydrate antigen (TACA) unlike the lectins currently used label it (Cabanettes et al., Angew Chem Int Ed Engl, 2018, 57 (32): 10178). Its structure revealed a new protein fold we called b-prism III and a signature for the recognition of core fucose (cf figure below).

The GBMS team is developing docking methods for modeling protein / carbohydrate complexes that are validated using experiment thermodynamic data. The flexibility of oligosaccharide ligands and, therefore, their dynamics are key factors underlying their interaction with proteins. It happens that during the interaction, unusual conformations can be selected or induced. This must be taken into account for the design of glycomimetics of therapeutic interest. Special efforts have been made to parameterize the force field to account for the presence of calcium ions in protein binding sites or to treat non-canonical amino acids (Tobola et al, ACS Chem Biol, 2018, 13 (8): 2211, Leipsik et al, Eur J Med Chem, 2019. 177: 212).

A: Rare N-acetyl conformation in Lewis x oligosaccharide was observed crystallographically in complex with bacterial Ca2+-dependent lectin. The explanation was based on molecular dynamics simulations which in turn needed a development of force-field parametrisations of calcium ions. B: Impact of tryptophan fluorination on the binding of Lewis x by the lectin RSL from Ralstonia solanacearum.