Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency

Abstract

Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.

Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis

“…These results favor our hypothesis that a limited set of uveitogenic peptides drive T cell mediated pathology in Birdshot [18]. However, ERAP2 has different peptide preferences compared to ERAP1 [27,29] and MHC-I peptidome studies support separate contributions of Hap10 and ERAP2 in manipulating the peptide composition presented on the cell surface [35]. This reflects the lack of LD between the protein-coding Figure 9).…”

“…This finding suggests that a change in expression, and not merely the presence of ERAP2, confers risk for Birdshot and other ERAP2-linked conditions [40]. Thus, future treatment strategies to dampen ERAP2 expression may complement current research efforts focused on the pharmacological inhibition of its aminopeptidase activity [41,42].…”

“…In the absence of ERAP2 protein, cells with distinct ERAP1 haplotypes show substantial differences in HLA-A29 peptidome composition, which demonstrates that ERAP1 is able to directly influence HLA-A29 [45]. Also, ERAP2 has different peptide preferences compared to ERAP1 [36,41] and MHC-I peptidome studies support separate contributions of Hap10 and ERAP2 in manipulating the peptide composition presented on the cell surface [46]. This reflects the lack of LD between the protein-coding ERAP2 haplotype and MHC-I-opathy linked Hap10 and Hap2/Hap1 in ~3000 controls.…”

Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis

“…This finding suggests that a change in expression, and not merely the presence of ERAP2, confers risk for Birdshot and other ERAP2-linked conditions ( 28 ). Thus, future treatment strategies to dampen ERAP2 expression may complement current research efforts focused on the pharmacological inhibition of its aminopeptidase activity ( 29 ).…”

The genetics, structure and function of the M1 aminopeptidase oxytocinase subfamily and their therapeutic potential in immune-mediated disease

“…For example, significant rearrangements of the GAMEN motif in IRAP were observed upon ligand binding, which coupled to the transition between the original partially open and a new, fully closed conformation of the protein [23]. Similarly, co-crystal structures of ERAP2 with various inhibitors showed a mixture of single conformation complexes and those with two or more alternate binding configurations [24] due to rearrangement of the active site residues. The structures also shed light on the differential substrate specificity of the enzymes, in particular the 'molecular ruler' aspect peculiar to ERAP1 activity where the enzyme is highly active on model substrates of more than 9 residues but effectively inactive on shorter peptides.…”