Discovery of a Potent Small Molecule IL-2 Inhibitor through Fragment Assembly

Abstract

Using a site-directed fragment discovery method called tethering, we have identified a 60 nM small molecule antagonist of a cytokine/receptor interaction (IL-2/IL2Ralpha) with cell-based activity. Starting with a low micromolar hit, we employed a combination of tethering, structural biology, and computational analysis to design a focused set of 20 compounds. Eight of these compounds were at least 5-fold more active than the original hit. One of these compounds showed a 50-fold enhancement and represents the highest affinity inhibitor reported against this protein-protein target class. This method of coupling selected fragments with a low micromolar hit shows great potential for generating high-affinity lead compounds.

Hot-spot mimicry of a cytokine receptor by a small molecule

“…However, mutational studies suggest that protein-protein interactions are driven by a small set of the contact residues, termed ''hot spots,'' whose footprints are not significantly larger than those covered by small molecules (4)(5)(6). Moreover, there have been several reports of small molecules that disrupt discontinuous protein-protein interactions with reasonable potencies (K i values Ͻ1 M), and their binding sites have been confirmed by highresolution structural analysis (7)(8)(9)(10)(11)(12).…”

“…Recently, SP4206, a small molecule (Structure 1) was discovered that binds with high affinity (K d Ϸ 70 nM) to IL-2 ( Fig. 1A) and blocks binding to its natural receptor, IL-2R␣ (8,9). SP4206 was assembled from smaller fragments by using a structureguided approach with a binding and functional assay (8,9).…”

“…1A) and blocks binding to its natural receptor, IL-2R␣ (8,9). SP4206 was assembled from smaller fragments by using a structureguided approach with a binding and functional assay (8,9). Subsequently, the structure of IL-2 bound to the IL-2R␣ (K d Ϸ 10 nM) was described (Fig.…”

A review of recent progress (2002-2012) on the biological activities of pyrazoles

“…Based on lead compound 179 and following this methodology, a potent small inhibitor 180 (IC50 = 60nM) of the IL-2 I IL-2Ra was found. 173 Cat S, found predominantly on antigen presenting cells, has been considered a therapeutic target for asthma. Progress towards Cat S selective inhibitors has been reported such as pyrazolebased inhibitor JNJ-10329670 (181) with a Cat S potency (IC50 = 100 nM) and selectivity over other cathepsins including Cats K and L (IC50 >50 M).…”

17 The protein epitope mimetic approach to protein-protein interaction inhibitors

“…From this starting point, new molecules that bind to IL-2 were optimized, with dissociation constant in the mid-nanomolar range. These molecules were assembled in a fragment-based approach, guided by X-ray structures and medicinal chemistry (Arkin et al 2003;Braisted et al 2003;Raimundo et al 2004). Although the small molecules were assembled before the structure of the IL-2-IL-2Rα complex had been reported (Rickert et al 2005), they bind close to the center of the receptor contact region on IL-2.…”