Recent Progress in the Molecular Recognition and Therapeutic Importance of Interleukin-1 Receptor-Associated Kinase 4

Abstract

Toll-like receptors (TLRs) are the most upstream pattern recognition receptors in the cell, which detect pathogen associated molecular patterns and initiate signal transduction, culminating in the transcription of pro-inflammatory cytokines and antiviral interferon. Interleukin-1 receptor-associated kinase 4 (IRAK4) is a key mediator in TLR (except for TLR3) and interleukin-1 receptor signaling pathways. The loss of kinase function of IRAK4 is associated with increased susceptibility to various pathogens, while its over-activation causes autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and cancer. The therapeutic importance of this master kinase has been advocated by a number of recent preclinical studies, where potent inhibitors have been administered to improve various TLR-mediated pathologies. Increasing studies of X-ray crystallographic structures with bound inhibitors have improved our knowledge on the molecular recognition of ligands by IRAK4, which will be crucial for the development of new inhibitors with improved potencies. In this review, we briefly discuss the structural aspect of ligand recognition by IRAK4 and highlight its therapeutic importance in the context of TLR-associated unmet medical needs.

Keywords: IRAK4; TLR; X-ray crystallography; autoimmunity; inhibitor.

Figure 1

Domain architecture of interleukin-1 receptor-associated kinase (IRAK) family members. IRAK family members commonly contain an N-terminal death domain (DD) that interacts with myeloid differentiation primary response gene 88 (MyD88), a central kinase domain (KD) that phosphorylates IRAK1, and a C-terminal domain (CD), which is essential for TNF receptor associated factor 6 (TRAF6) recruitment. A proline, serine, threonine-rich (ProST) linker of unknown structure connects the DD and KD. ProST region is rich in proline, serine, and threonine residues that are heavily autophosphorylated, causing release of IRAK1-TRAF6 complex from the receptor complex. IRAK4 lacks a CD; thus, it is shorter than other IRAK members. IRAK2 and IRAK3 contain a pseudokinase domain that is kinase inactive.

Figure 2

Toll-like receptor (TLR) signaling pathways. IRAK4) is the central kinase that mediates signal transduction from all TLRs, except TLR3 and TIR-domain-containing adapter-inducing interferon-β (TRIF)-dependent TLR4. MyD88 recruits IRAK4, which autophosphorylates and then phosphorylates IRAK1. The phosphorylated IRAK1 recruits TRAF6 and propagates signal transduction, resulting in the nuclear translocation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB).

Figure 3

Overall structure of IRAK4 kinase domain. IRAK4 kinase domain consists of an N-terminal and a C-terminal lobe with the ATP-binding pocket lying between the two lobes. The binding site of IRAK4 inhibitors overlaps with that of ATP. The region highlighted in blue color mediates substrate (IRAK1) binding and phosphorylation.

Figure 4

Interaction of compound 1 (2NRU) with the catalytic site of IRAK4 kinase domain. Compound 1 (N-acyl 2-aminobenzimidazole) displays three kinase-specific interactions: a π-π interaction with the gatekeeper Tyr262, an H-bond with the backbone of hinge Met265, and an H-bond with the catalytic Lys213. Compound 1 perfectly occupies the ATP binding site with the amide linker positioned at the ATP-adenine pocket and the N-propanol substitution positioned at the ATP-ribose binding area.

Figure 5

Interactions of co-crystallized inhibitors with IRAK4 residues. The figure describes the typical interactions that the co-crystallized ligands (A) diaminopyrimidine 1, (B) pyrazole 1, (C) pyrimidine 1, (D) compound 18, and (E) compound 37 make with the catalytic site of IRAK4. The most unusual interaction was observed between the lead compound pyrazole 1 and IRAK4. Pyrazole 1 forms three H-bonds with the hinge backbone region, in contrast with other inhibitors, which form one. All inhibitors bind IRAK4 in a nearly planar orientation, which is a crucial feature required for π-stacking with the gatekeeper Tyr262. IC₅₀ = inhibitory concentration.

Figure 6

Illustration of Type-I, Type-II, and Type-III binding pockets of IRAK4 kinase domain. Type-I and type-II binding pockets are determined by the positions of Phe and Asp residues from the Asp-Phe-Gly (DFG) motif. Type-I binding site is formed in DFG-in condition, where the side chain of Phe faces towards the catalytic center, while the side chain of Asp faces in the opposite direction. Type-II binding site is formed when Phe and Asp side chains rotate 180°. Type-III binding site is the allosteric site, where IRAK1 is phosphorylated by IRAK4.