Kinase inhibition in autoimmunity and inflammation

Abstract

Despite recent advances in the treatment of autoimmune and inflammatory diseases, unmet medical needs in some areas still exist. One of the main therapeutic approaches to alleviate dysregulated inflammation has been to target the activity of kinases that regulate production of inflammatory mediators. Small-molecule kinase inhibitors have the potential for broad efficacy, convenience and tissue penetrance, and thus often offer important advantages over biologics. However, designing kinase inhibitors with target selectivity and minimal off-target effects can be challenging. Nevertheless, immense progress has been made in advancing kinase inhibitors with desirable drug-like properties into the clinic, including inhibitors of JAKs, IRAK4, RIPKs, BTK, SYK and TPL2. This Review will address the latest discoveries around kinase inhibitors with an emphasis on clinically validated autoimmunity and inflammatory pathways.

Conflict of interest statement

A.A.Z. is an employee of TRexBio and holds stock in TRexBio and the Roche Group. K.B. is an employee of Genentech. P.L. is an employee of Synthekine and holds stock in Synthekine and the Roche Group. D.V. is an employee of Genentech and holds stock and options in the Roche Group.

Figures

Fig. 1. Current landscape of major druggable inflammatory receptors and corresponding kinases implicated in human disease.

Major inflammatory pathways and downstream kinases are depicted to show surface versus intracellular drug targets, highlighting drugs that are currently being clinically evaluated or already approved. All biologics that are included have mostly been evaluated in phase II trials and beyond. All small-molecule kinase inhibitors have been evaluated in phase I and beyond. BAFFR, B cell activating-factor receptor; BCMA, B cell maturation antigen; BCR, B cell receptor; BTK, Bruton’s tyrosine kinase; CD40L, CD40 ligand; CSF1R, colony-stimulating factor 1 receptor; CTLA4, cytotoxic T lymphocyte-associated protein 4; FcεR, Fcε receptor; IKKε, inhibitor of NF-κB subunit-ε; IL-1R, IL-1 receptor; IRAK, IL-1R-associated kinase; ITK, IL-2-inducible T cell kinase; JAK, Janus-associated kinase; MD2, myeloid differentiation factor 2; NF-κB, nuclear factor-κ-light-chain-enhancer of activated B cells; NIK, NF-κB-inducing kinase; RANKL, receptor activator of NF-κB ligand; RIP1, receptor-interacting protein 1; RLK, resting lymphocyte kinase; ST2, IL-1R-like 1; SYK, spleen tyrosine kinase; TACI, transmembrane activator and CAML interactor; TBK1, TANK-binding kinase 1; TCR, T cell receptor; TEC, Tec protein tyrosine kinase; TLR, Toll-like receptor; TNF, tumour necrosis factor; TNFR, TNF receptor; TPL2, tumour progression locus 2; TSLP, thymic stromal lymphopoietin; TYK2, tyrosine kinase 2.

Fig. 2. JAK1, JAK2, JAK3 and TYK2 integrate the signalling cascades of a diverse set of cytokine and growth receptors.

The binding of extracellular ligands leads to pathway activation via changes to the receptors that permit trans-phosphorylation of associated Janus-associated kinases (JAKs). Activated JAKs then phosphorylate both the receptor and cognate signal transducer and activator of transcription (STAT) proteins. Activated and dimerized STATs then enter the nucleus to bind to transcriptional regulatory sites of target genes. Receptors that use JAK2 and JAK3, JAK3 alone, tyrosine kinase 2 (TYK2) alone or JAK3 and TYK2 have not been described. EPO, erythropoietin; GH, growth hormone; GM-CSF, granulocyte–macrophage colony-stimulating factor; LIF, leukaemia inhibitory factor; OSM, oncostatin M; P, phosphorus; TPO, thrombopoietin; TSLP, thymic stromal lymphopoietin.

Fig. 3. IRAK4 is the upstream kinase that transduces TLRs and IL-1R signals.

IL-1 receptor (IL-1R)-associated kinase 1 (IRAK1) and IRAK4 function is regulated by protein–protein interactions and by post-translational modifications that may be uniquely regulated in different cell types to fine-tune an immune response. IL-1R or Toll-like receptor (TLR; except for TLR3) engagement causes the recruitment of adaptor protein myeloid differentiation primary response 88 (MyD88) to the intracellular Toll/IL-1R receptor (TIR) domains to initiate the Myddosome assembly. MyD88 recruits IRAK4 via death domain interactions. IRAK4 is activated via autophosphorylation and is also K63-ubiquitylated (grey circles). Phosphorylated IRAK4 can activate IRAK1, which facilitates IRAK1–tumour necrosis factor receptor-associated factor 6 (TRAF6) complex formation. K48 ubiquitylation (blue circles) of IRAK1 is required for the activation of TGFβ-activated kinase 1-binding protein 1 (TAK1), and its binding to TAB1 and TAB2 to drive the formation of the inhibitor of NF-κB (IKK) complex and subsequent NF-κB inhibitor-α (IκBα) activation, which then leads to NF-κB, mitogen-activated protein kinase (MAPK) and interferon-regulatory factor (IRF) activation to induce the transcription of pro-inflammatory cytokines and cellular processes, such as proliferation and activation,. The mechanism of IRF activation by MyD88 is less understood. Downstream of IRAK4 activation, TAK1 and IKKβ complex can mediate IRF5 phosphorylation, nuclear translocation and transcription in monocytes, but IRAK1 can also directly bind and phosphorylate IRF7 in plasmacytoid dendritic cells. The mechanism of IRAK4 kinase activity-independent action is less understood but may involve K63-ubiquitylated signalling hubs and other novel molecular scaffolds. AP-1, activator protein 1; CREB, cAMP response element-binding protein; P, phosphorus; TAB, TGFβ-activated kinase 1 binding protein; Ub, ubiquitin.

Fig. 4. RIP kinases regulate cell death and inflammatory pathways.

Tumour necrosis factor (TNF) signalling can lead to receptor-interacting protein 1 (RIP1)-dependent apoptosis (mediated by caspase 8) or necroptosis (mediated by RIP3 and mixed-lineage kinase domain-like protein (MLKL)) to cause tissue damage and an inflammatory milieu. RIP1 inhibition can block RIP1-mediated apoptosis and necroptosis, and reduce inflammation by inhibiting inflammatory cell death. The kinase domain of RIP2 allows the binding of E3 ligase X-linked inhibitor of apoptosis protein (XIAP) and subsequent RIP2 ubiquitylation, which is a critical mediator of nucleotide-binding oligomerization domain-containing protein 2 (NOD2) inflammatory signalling. Consequently, RIP2 kinase inhibitors prevent XIAP binding and RIP2 ubiquitylation to inhibit NOD2 pathway-activated NF-κB and mitogen-activated protein kinase (MAPK) signalling, and consequent production and release of pro-inflammatory cytokines, thus blocking inflammation. FADD, FAS-associated death domain; IAP1/2, inhibitor of apoptosis 1 and 2; LUBAC, linear ubiquitin chain assembly complex; MDP, muramyl dipeptide; P, phosphorus; TNFR1, TNF receptor 1; TRADD, TNFR-associated death domain; TRAF2, TNFR-associated factor 2; Ub, ubiquitin.

Fig. 5. ITK and BTK in antigen receptor, TLR and FcR signalling.

a | In T cells, IL-2 inducible T cell kinase (ITK) phosphorylates secondary messengers to activate nuclear factor of activated T cells, cytoplasmic 1 (NFATc) and calcium signalling to positively regulate cytokines (such as IL-2) or negatively regulate certain genes such as FASLG. Following T cell receptor (TCR) engagement, active lymphocyte-specific protein tyrosine kinase (LCK) phosphorylates the immunoreceptor tyrosine-based activation motifs (ITAMs), Zap70 and IL-2-inducible T cell kinase (ITK). Zap70 phosphorylates SLP76 and linker for activation of T cells (LAT); ITK phosphorylates phospholipase Cγ1 (PLCγ1). Activated PLCγ1 then hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to produce diacylglcycerol (DAG) and inositol 1,4,5-trisphosphate (IP3), leading to increased calcium flux. b | Bruton’s tyrosine kinase (BTK) regulates multiple receptors including B cell receptor (BCR) or Toll-like receptors (TLRs) in B cells, Fcγ receptor (FCγR) or TLRs in macrophages or plasmacytoid dendritic cells (pDCs) and FCγR or TLRs in basophils and mast cells. Upon BCR engagement, BTK is activated by Src kinases and phosphorylates PLCγ2. PLCγ2 activates NFAT and enhances Ca2+ flux, and activates mitogen-activated protein kinase (MAPK) and NF-κB. BTK has also been implicated in TLR, IC and FCγR or FCεR signalling in multiple cell types via Ca2+ or as yet unknown pathways. AICD, activation-induced cell death; AP-1, activator protein 1; FasL, Fas ligand; IC, immune complex; IRAK4, IL-1 receptor-associated kinase 4; LYN, Lck/Yes-related novel tyrosine kinase; MHC, major histocompatibility complex; MyD88, myeloid differentiation primary response 88; P, phosphorus; PIP3, phosphatidylinositol 3,4,5-trisphosphate; PKC, protein kinase C; SYK, spleen tyrosine kinase.

Fig. 6. TPL2 regulatory inflammatory response downstream of TLRs, TNFR and IL-1R.

The action of both mitogen-activated protein kinase (MAPK) and NF-κB orchestrates the transcription of target genes. In the resting state, p105 prevents and masks tumour progression locus 2 (TPL2) kinase effector function. Agonist stimulation activates the inhibitor of NF-κB (IKK)/NF-κB essential modulator (NEMO) complex. Subsequently, IKKβ phosphorylates IKKα, targeting IKKα for proteasomal degradation. Then, released RelA/p50 dimers are translocated to the nucleus and modulate target gene expression. IKKβ also phosphorylates the target residues S927 and S932 in p105, leading to its proteasomal degradation that results in TPL2 liberation. IKKβ phosphorylates TPL2 at residue S400 to enhance its kinase activity. Free TPL2 then activates MEK1 and MEK2 as well as MEK3 and MEK6 to positively regulate ERK1/2 or p38α/δ to regulate gene transcription via cAMP response element-binding protein (CREB)/activator protein 1 (AP-1) as well as mRNA stability and protein production. The function of A20-binding inhibitor of NF-κB (ABIN2) is not completely understood and involves regulation of protaglandin E2 (PGE2) and cyclooxygenase 2 (COX2) in fibroblasts. TPL2 binds to a small fraction of p105 but the p50 domain of processed p105 can directly impact gene transcription. Post-transcriptional regulation of cytokines and chemokines by MAPKs involves AU-rich elements (AREs) on messenger RNAs to dictate their stability (in the case of tumour necrosis factor (TNF) or IL-6, for instance) or cellular localization (TNF). In addition, other regulatory processes such as CAP-dependent RNA translation and protein export via TNFα-converting enzyme (TACE) (in the case of TNF) are regulated by the TPL2/MAPK axis. Therefore, the net effect of TPL2 inhibition has a profound effect on inflammatory outputs without compromising the NF-κB pathway. IL-1R, IL-1 receptor; P, phosphorus; TLR, Toll-like receptor; TNFR, TNF receptor; Ub, ubiquitin.

Fig. 7. IKKε and TBK1 kinases integrate signalling from nucleic acid sensors.

Nucleic acid sensors include the endosomal Toll-like receptors (TLRs) TLR3, TLR7, TLR8 and TLR9; the cytosolic DNA sensor cyclic GMP–AMP synthase (cGAS); and retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). RLRs are RNA sensors that include RIG-I and melanoma differentiation-associated protein 5 (MDA5). Unusual RNAs (double-strand RNA (dsRNA), 5′-phosphorylated (5′P) mRNA) can activate RIG-I or MDA5. Multimerized RIG-I and MDA5 can then bind to create a mitochondrial antiviral-signalling protein (MAVS), mitochondrial-associated membranes and peroxisomes, which in turn activate TANK-binding kinase 1 (TBK1) and inhibitor of NF-κB subunit-ε (IKKε) to activate interferon-regulatory factor 3 (IRF3) and IRF7. Double-stranded DNA (dsDNA; such as self-DNA) can induce an allosteric structural change in cGAS that, in turn, activates second messengers to promote stimulator of interferon genes (STING) to undergo dimerization to form a complex with TBK1 and IKKε that phosphorylates IRF3 to activate gene transcription. DNA-dependent activator of interferon-regulatory factors (DAI; also known as Z-DNA-binding protein 1 (ZBP1)) can also act as a sensor of Z-dsDNA (left-handed double-helical structure), often acquired during viral infection in a cell type-specific manner. DAI recruits TBK1 and IRF3 upon DNA binding and may get further phosphorylated to amplify the DAI/TBK1/IRF3 circuit. Numb-associated kinases (adaptor protein 2 (AP2)-associated protein kinase 1 (AAK1) and cyclin G-associated kinase (GAK)) regulate intracellular viral trafficking during entry, assembly and release of unrelated viruses. Disruption of endocytosis by inhibiting AAK1/GAK can prevent the virus passage into cells. Endosomal TLRs (TLR7/8/9) recruit myeloid differentiation primary response 88 (MyD88) and signal through IL-1 receptor-associated kinase 4 (IRAK4) to activate IRFs similar to cell surface TLRs (see Fig. 3). TIR-domain-containing adapter-inducing IFNβ (TRIF)-dependent and MyD88-independent signalling could also activate TBK1/IKKε to activate IRF-mediated gene transcription. P, phosphorus; ssDNA, single-strand DNA.

Fig. 8. Multiple immune receptors trigger NF-κB canonical and non-canonical pathways.

NF-κB-inducing kinase (NIK) itself is regulated at the basal level by a destruction complex, and signal-induced non-canonical NF-κB signalling involves NIK stabilization. The canonical NF-κB pathway involves activation of inhibitor of NF-κB (IKK) complex by TGFβ-activated kinase 1-binding protein 1 (TAK1), IKK-mediated NF-κB inhibitor-α (IκBα) phosphorylation and subsequent degradation, resulting in rapid and transient nuclear translocation of the NF-κB heterodimer RelA/p50. NIK protein levels remain low via active degradation using ubiquitin ligase complex, comprising tumour necrosis factor receptor-associated factor 3 (TRAF3), TRAF2 and inhibitor of apoptosis 1 and 2 (IAP1/2). Receptor activation by agonists recruits this complex to the receptor where activated IAP mediates K48 ubiquitylation and proteasomal degradation of TRAF3, resulting in stabilization and accumulation of NIK. Subsequently, NIK activates IKKα to trigger p100 phosphorylation and processing to enforce persistent activation of RelB/p52 complex to activate gene transcription. BAFF, B cell-activating factor; BCR, B cell receptor; LTβ, lymphotoxin-β; P, phosphorus; TCR, T cell receptor; TLR, Toll-like receptor; TWEAK, tumour necrosis factor-related weak inducer of apoptosis; Ub, ubiquitin.