Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

Abstract

Mammalian C-type lectin receptors (CTLRS) are involved in many aspects of immune cell regulation such as pathogen recognition, clearance of apoptotic bodies, and lymphocyte homing. Despite a great interest in modulating CTLR recognition of carbohydrates, the number of specific molecular probes is limited. To this end, we predicted the druggability of a panel of 22 CTLRs using DoGSiteScorer. The computed druggability scores of most structures were low, characterizing this family as either challenging or even undruggable. To further explore these findings, we employed a fluorine-based nuclear magnetic resonance screening of fragment mixtures against DC-SIGN, a receptor of pharmacological interest. To our surprise, we found many fragment hits associated with the carbohydrate recognition site (hit rate = 13.5%). A surface plasmon resonance-based follow-up assay confirmed 18 of these fragments (47%) and equilibrium dissociation constants were determined. Encouraged by these findings we expanded our experimental druggability prediction to Langerin and MCL and found medium to high hit rates as well, being 15.7 and 10.0%, respectively. Our results highlight limitations of current in silico approaches to druggability assessment, in particular, with regard to carbohydrate-binding proteins. In sum, our data indicate that small molecule ligands for a larger panel of CTLRs can be developed.

Identification of Multiple Druggable Secondary Sites by Fragment Screening against DC‐SIGN

“…This increases the avidity of the low-affinity monovalent carbohydrate recognition (K d (mannose) = 3.5 mm [5] )i nto the nanomolar range for multivalent interactions (K d (gp120) = 1-2 nm [6] ). [10] However, such approaches capitalize on the presence of extended binding sites that allow for affinity maturation of the core scaffold by the attachment of hydrophobic substituents.S uch secondary sites are often neither well-described nor directly accessible from the analysis of crystallographic structures as they might stem from minor alterations of the protein geometry.P revious reports indicated the presence of binding sites for drug-like molecules to DC-SIGN, [9,11] and as these inhibitors lack functional groups to directly interact with the primary Ca 2+ ion, an allosteric mechanism was proposed. [8] In contrast, such noncarbohydrate,d rug-like DC-SIGN inhibitors are limited to quinoxalinones.…”

Report from the Third Annual Symposium of the RIKEN–Max Planck Joint Research Center for Systems Chemical Biology

“…33 Shinobu Kitazume (RIKEN Disease Glycomics Team) presented evidence that the antiapoptotic function of platelet endothelial cell adhesion molecule (PECAM) is associated with its function as a lectin that binds to epithelial sialic acid containing glycans. 34 A talk given by Christoph Rademacher (MPI of Colloids and Interfaces) posed the question whether lectins are druggable proteins. Results from fragment-based screens against C-type lectins suggested indeed the occurrence of sites suitable for small molecule binding.…”

Fragmentbasierte Wirkstoffentwicklung

“…c) Beispiele für Affinitätsbestimmungen mit Oberflächenplamonenresonanz-Spektroskopie (SPR). 10,13) Übertragung von Ergebnissen aus der Grundlagenforschung in neue Therapien in Zukunft beschleunigen, da Hochschulen und Industrie methodisch näher zusammenrücken. 14) growing 15) und merging 16) .…”