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Kinases have been intensively investigated as drug targets 
for the past 30 years, with 38 kinase inhibitors approved 
to date1. These drugs are predominantly multitargeted 
receptor tyrosine kinase (RTK) inhibitors approved for 
the treatment of cancer2, such as imatinib. There are 518 
kinases encoded in the human genome, and these enzymes 
phosphorylate up to one-third of the proteome3,4. Virtually 
every signal transduction process occurs via a phospho-
transfer cascade, indicating that kinases provide multiple 
nodes for therapeutic intervention in many aberrantly reg-
ulated biological processes5. Indeed, in addition to cancer, 
deregulation of kinase function has been demonstrated to 
play an important role in immunological, inflammatory, 
degenerative, metabolic, cardiovascular and infectious 
diseases6,7. The established druggability and the clinical 
safety profile of approved kinase inhibitors make kinases 
attractive targets. However, the majority of kinases have 
been historically understudied, indicating that the field of 
kinase inhibitor discovery is still immature8–10.
In 2013, Cohen and Alessi2 outlined some of the most 
important challenges that remained in kinase inhibitor 
drug discovery, which were limiting the full potential of 
kinases as drug targets in oncology and beyond. This list 
included validating novel kinase targets, utilizing kinase 
inhibitors in non-oncology therapeutic areas, overcom-
ing drug resistance, obtaining target selectivity to reduce 
off-target-mediated toxicity and developing efficient 
compound screening and profiling technologies. Over 
the course of the past 5 years, immense progress has been 
made towards these goals, and the field of kinase inhibitor 
discovery has expanded rapidly in oncology in addition 
to forging into different disease areas, including auto-
immune and inflammatory disease as well as degenerative 
disorders (FIG. 1).
Technologies for assessing the selectivity of kinase 
inhibitors have also become increasingly sophisticated. In 
particular, the development of techniques that measure 
inhibitor profiles in a physiological environment is an 
important milestone. Such techniques include the use 
of a multitargeted kinase probe for use in cell com-
petition labelling or fluorescence experiments11 and 
thermal proteome profiling (TPP)12. Cheminformatics 
programs have also been developed to harness the vast 
amount of profiling data in the public domain in order 
to inform kinase inhibitor medicinal chemistry projects. 
In computer- aided drug design, the use of free-energy 
perturbation (FEP) calculations for compound ranking 
has yielded highly promising results13.
This Review aims to provide insight into the ever- 
diversifying therapeutic space occupied by kinase targets 
and highlight the opportunities and challenges posed by 
each disease area. Additionally, we explore the novel 
experimental and computational methods that have ena-
bled rapid expansion in the field, discussing examples of 
successful application and insights into the strengths and 
limitations of each technique, thus providing guidance to 
researchers entering the field.
New kinase targets in oncology
The therapeutic potential of kinase inhibition in oncology 
has been rapidly expanding beyond its origins in RTK 
oncogenes14. The emergence of resistance mechanisms to 
existing kinase-targeting drugs has motivated a search for 
alternative targets15. Promising results have been obtained 
by shifting the focus from oncogene inhibition to the 
inhibition of basal cellular processes that cancers exploit 
and become disproportionately reliant on, compared with 
healthy cells16. These processes are not typically identified 
via analysis of overexpressed or mutated genes but rather 
from focused mechanistic studies of normal and malignant 
states17. Two areas where this approach has been successful 
are targeting kinases that regulate transcription and target-
ing kinases that regulate the immune response. Promising 
recent examples from these two fields are discussed below.
1Department of Cancer 
Biology, Dana-Farber Cancer 
Institute, Boston, MA, 
United States.
2Department of Biological 
Chemistry and Molecular 
Pharmacology, Harvard 
Medical School, Boston, 
MA, United States
*e-mail: nathanael_gray@
dfci.harvard.edu
doi:10.1038/nrd.2018.21
Published online 16 Mar 2018
Free-energy perturbation
(FEP). A method for computing 
free-energy differences from 
molecular dynamics 
simulations on the basis of 
statistical mechanics.
Kinase inhibitors: the road ahead
Fleur M. Ferguson1,2 and Nathanael S. Gray1,2*
Abstract | Receptor tyrosine kinase signalling pathways have been successfully targeted to inhibit 
proliferation and angiogenesis for cancer therapy. However, kinase deregulation has been firmly 
demonstrated to play an essential role in virtually all major disease areas. Kinase inhibitor drug 
discovery programmes have recently broadened their focus to include an expanded range of 
kinase targets and therapeutic areas. In this Review, we provide an overview of the novel targets, 
biological processes and disease areas that kinase-targeting small molecules are being 
developed against, highlight the associated challenges and assess the strategies and 
technologies that are enabling efficient generation of highly optimized kinase inhibitors.
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Targeting transcriptional kinases
Mutations affecting transcription are prevalent malig-
nant drivers. Transcription factors such as p53, a tumour 
suppressor, and the MYC oncoproteins, broadly acting 
transcriptional activators, are among the most frequently 
dysregulated genes in cancer18. High levels of transcription 
facilitate the maintenance of oncogenic gene expression 
programmes driven by these transcriptional regula-
tors17,19–21. Many tumours display a marked ‘transcriptional 
addiction’, with extraordinary levels of transcription 
required to sustain their rapid proliferation rates22.
Super-enhancers (SEs) are large clusters of transcrip-
tional enhancers that normally drive the expression of 
genes that define cell identity23. Tumour cells acquire SEs 
at key oncogenes and at genes associated with the acqui-
sition of the hallmarks of cancer24,25. Thus, deregulated 
transcription is a central mediator of oncogenic transfor-
mation. Although SEs drive high-level gene expression, 
they can be especially sensitive to perturbation, giving rise 
to a therapeutic window26. Many key oncogenic drivers, 
such as MYC, also have very short half-lives at both the 
protein27 and the mRNA level28. These short-lived species 
are particularly sensitive to transcriptional disruption29.
This understanding of how neoplastic cells affect 
transcriptional reprogramming in order to drive cancer 
provides a rationale for targeting the basal transcriptional 
machinery. It has been proposed that these targets may 
also be less prone to bypass mechanisms of therapeutic 
resistance30.
Historically, the transcription apparatus has been 
viewed as an intractable target for small-molecule drug 
discovery as many of its functions are exerted through 
protein–protein and protein–DNA interactions. The 
transcription- associated kinases however, are essential 
components of the basal transcriptional machinery that 
are also druggable targets. Recently, selective chemical 
probes have been developed for the majority of known 
transcriptional cyclin-dependent kinases (CDKs), dis-
cussed below (FIG. 2). These probes have aided the study 
of the functions of these CDKs in both normal and 
malignant transcriptional programmes. Promising CDK 
targets,such as CDK7, have been identified by these 
studies, presenting opportunities for the development 
of therapeutics targeting transcription-addicted cancers 
(TABLE 1). There are many more (putative) transcription-
ally associated kinases implicated in cancer (for exam-
ple, dual-specificity tyrosine-phosphorylation-regulated 
kinase 1A (DYRK1A)31,32 and CDK11 (REF. 33)) that have 
not yet been validated with selective kinase inhibitors, 
and this is an area for potential future growth in the 
field (FIG. 2).
CDK7. CDK7 has roles in both cell cycle control and 
transcriptional control, bridging the two CDK families. 
CDK7 forms a trimeric complex with cyclin H and CDK-
activating kinase assembly factor MAT1 (also known as 
MNAT1), where it functions as a CDK-activating kinase 
for the cell cycle-associated CDK1 and CDK2 (REF. 34). 
CDK7 functions within the general transcription factor 
TFIIH to phosphorylate the RNA polymerase II (Pol II) 
carboxy-terminal domain, enabling promoter clearance35. 
Figure 1 | Kinase inhibitors in diverse biological processes and new therapeutic 
areas. Cancer: proto-oncogenes such as breakpoint cluster region protein (BCR)–
Abelson tyrosine kinase (ABL), phosphoinositide 3-kinase catalytic subunit-α 
(PIK3CA) and mitogen-activated protein kinase (MAPK) kinases drive aberrant 
proliferation in cancer. Approved anticancer drugs, such as imatinib, target this 
family. Receptor tyrosine kinases, such as epidermal growth factor receptor (EGFR) 
and vascular endothelial growth factor receptor (VEGFR), can also drive cancer 
proliferation and angiogenesis. Approved anticancer drugs such as erlotinib target 
this class of kinases282. Transcription-associated kinases, such as cyclin-dependent 
kinase 7 (CDK7) and CDK9, play key roles in regulating transcription. Recently, 
these kinases have emerged as potential cancer drug targets; the most advanced 
kinase inhibitors targeting transcriptional kinases are in phase I/II clinical trials17. 
Immune system-associated kinases, such as the TAM kinases (TYRO3, AXL and MER), 
play a key role in regulating the immune system; therefore, inhibiting these kinases 
may be beneficial both in cancer and in alleviating immunosuppression (for 
example, in the latter stages of septic shock) or as vaccine adjuvants. Immune 
system: T cell checkpoint inhibitors achieve a complete and durable response in a 
small number of cancer patients. As oncogenic kinases, such as EGFR and CDK4 
and/or CDK6, aid immune system evasion in cancer, identifying kinase inhibitors that 
synergize with T cell checkpoint inhibitor therapy and sensitize resistant cancers to 
its effects has been the focus of extensive investigation101. Kinase inhibitors are also 
relevant for the treatment of autoimmune and inflammatory disorders, such as 
rheumatoid arthritis, where Janus kinase (JAK) inhibitors were recently approved103. 
Degenerative disease: excessive endoplasmic reticulum stress drives degenerative 
diseases such as retinitis pigmentosa and diabetes mellitus. Inhibition of kinases in 
the unfolded protein response pathway, such as IRE1α, are promising targets for 
these orphan diseases131. Kinases that drive angiogenesis are also highly relevant 
targets in ocular degenerative diseases, such as wet age-related macular 
degeneration151. Finally, there are a number of promising but relatively 
underexplored kinase targets in neurodegenerative diseases, such as leucine-rich 
repeat serine/threonine-protein kinase 2 (LRRK2) and CDK5 (REFS 156,283). BTK, 
Bruton tyrosine kinase; CSF1R, macrophage colony-stimulating factor 1 receptor; 
DLK, dual leucine zipper kinase; FAK, focal adhesion kinase; HER2, human 
epidermal growth factor receptor 2; IGF1R, insulin-like growth factor 1 receptor; 
PDGFR, platelet-derived growth factor receptor; PERK, PRKR-like ER kinase; PI3Kδ, 
phosphoinositide 3-kinase-δ; SE, super-enhancer; SRPK1, SFRS protein kinase 1; 
SYK, spleen tyrosine kinase.
Nature Reviews | Drug Discovery
Transcription, 
SE-targeting therapies
(e.g. CDK7, CDK8,
CDK9, CDK12 and CDK13)
T cell checkpoint inhibitor
synergy (e.g. FAK, EGFR,
MEK and CDK4 and/or CDK6)
Proto-oncogenes
(e.g. BCR–ABL, mutant
PIK3CA and MAPK kinases)
Inȯammatory and
autoimmune disease
(e.g. JAK kinases,
PI3Kδ and/or PI3Kγ, 
BTK–SYK)
Immunosuppression
and vaccine adjuvants
(e.g. TAM kinases)
Neurodegenerative
disease (e.g. LRRK2
and CDK5)
ER stress (e.g.
IRE1α, PERK 
and DLK)
Angiogenesis
(e.g. VEGFR,
PDGFR and SRPK1)
Receptor tyrosine
kinase signalling
(e.g. EGFR, KIT,
PDGFR, MET and HER2)
Kinase
target
Immune system activation (e.g.
TAM kinases, CSF1R and IGF1R)
Cancer Immune system
Degenerative disease
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Super-enhancers
(SEs). Large clusters of 
transcriptional enhancers, 
which normally drive 
expression of genes that define 
cell identity. Tumour cells 
acquire SEs at oncogenes and 
at genes associated with the 
acquisition of the hallmarks of 
cancer.
The covalent dual CDK7 and CDK12 inhibitor THZ1 dis-
proportionately reduces transcription at SE-associated 
genes in cancer, such as RUNX1 in T cell acute lympho-
blastic leukaemia (T-ALL)19 and MYCN in neuro- 
blastoma21. Following THZ1 treatment, the oncogenic 
gene expression programme in T-ALL cells is lost and 
subsequent cell death occurs19. Non-transformed reti-
nal pigmented epithelial (RPE-1) cells undergo cell cycle 
arrest, rather than apoptosis, under the same THZ1 dos-
ing regimen, providing the first indication that CDK7 
inhibition may have an acceptable therapeutic window 
for cancer treatment19. Phase I clinical trials of a CDK7 
inhibitor (SY-1365) are ongoing36.
CDK8. As part of the mediator complex, CDK8 is highly 
enriched at SE elements in tumours37. Interestingly, 
although the mediator complex is a transcriptional co- 
activator, inhibition of CDK8 can result in either positive 
or negative regulation of SE-associated gene transcription 
depending on the context. Selective inhibition of CDK8 
by the natural product cortistatin A results in upregu-
lation of SE-associated genes and subsequent cell death 
in acute myeloid leukaemia (AML)38. Remarkably, these 
cell lines are sensitive to downregulation of the same 
gene set by the bromodomain and extra-terminal (BET) 
protein inhibitor JQ1, highlighting the acute sensitivity 
of AML cell lines to the dosage of SE-associated genes38. 
Conversely, Dale et al.14 showed that CDK8 kinase inhi-
bition by the small molecule CCT251545 can downreg-
ulate the expression of WNT pathway-regulated genes 
and shows efficacy in WNT-driven breast and colorectal 
cancer models. An optimized derivative of this molecule 
is currently in preclinical trials39.
CDK9. CDK9 comprises the enzymatic subunit of pos-
itive transcription elongation factor b (P-TEFb), which 
triggers the transition of promoter-proximal paused Pol II 
to productive elongation by phosphorylation of DRB 
sensitivity-inducing factor (DSIF) and negative elon-
gation factor (NELF). CDK9 inhibition by the multi-
targeted CDK inhibitor flavopiridol (Alvocidib; Tolero 
Pharmaceuticals) is synergistic with BET bromodo-
main inhibition and abrogates SE complex function in 
MV4-11 AML cell lines and in murine xenograft mod-
els40. CDK9-targeted inhibitors described to date have 
typically exhibited high levels of polypharmacology 
and suffered from adverse effects, such as dose- limiting 
toxicity in the bone marrow and the gastrointestinal 
tract in clinical trials41–43. Novartisrecently described 
highly selective CDK9 and CDK10 inhibitors, iCDK9 
and NVP-2, which cause genome-wide Pol II pausing 
in cells44,45. The only selective CDK9-branded inhibitor 
in clinical trials is BAY1251152, which is currently in 
phase I (TABLE 1).
CDK12 and CDK13. The mechanisms of CDK12 and 
CDK13 in transcriptional regulation are less well stud-
ied, but both have been implicated in transcriptional 
elongation and regulation of RNA processing genes46. 
CDK12 knockdown also reduces transcription of DNA 
damage response (DDR) genes, and CDK13 knockdown 
decreases the expression of genes involved in the regu-
lation of protein translation46. The covalent CDK12 and 
CDK13 inhibitor THZ531 downregulates DDR genes at 
low doses and SE-associated driver genes RUNX1, MYB, 
T cell acute lymphocytic leukaemia protein 1 (TAL1) and 
trans-acting T cell-specific transcription factor GATA3 
at higher doses in T-ALL cells47. Consequently, in high-
grade serous ovarian cancer and triple-negative breast 
cancer (TNBC), THZ531 effectively synergizes with 
inhibition of poly(ADP-ribose) polymerase (PARP), a 
protein in the DDR pathway that detects single-strand 
DNA breaks (SSBs) and recruits SSB repair machin-
ery48. Inhibition of CDK12 by the pan-CDK inhibitor 
Figure 2 | Opportunities for modulating transcription via inhibition 
of kinases in the basal transcriptional machinery. Blue boxes indicate 
kinases with published selective chemical tools available. Green boxes 
indicate kinases that have not been therapeutically validated with selective 
inhibitors. Inhibition of kinases such as cyclin-dependent kinase 8 (CDK8), 
which act within transcription factors, can alter the recruitment of RNA 
polymerase II (Pol II) to the transcription start site, modulating transcriptional 
activity at the transcription factors’ (TFs) target genes. Inhibition of kinases 
that phosphorylate the Pol II carboxy-terminal domain (CTD) in the 
pre-initiation complex, such as CDK7, can hinder initiation and promoter 
clearance and downregulate transcription. Inhibition of CTD kinases that 
enable productive elongation, such as CDK12 and/or CDK13 and CDK9, can 
also be targeted to downregulate transcription. DLK, dual leucine zipper 
kinase; DSIF, DRB sensitivity-inducing factor; DYRK1A, dual-specificity 
tyrosine- phosphorylation-regulated kinase 1A; m7G, 7-methyl guanosine; 
NELF, negative elongation factor; P-TEFb, positive transcription elongation 
factor b; S2, Pol II CTD serine 2; pS2, phospho-Pol II CTD serine 2; TF, 
transcription factor.
P
Nature Reviews | Drug Discovery
TF binding Pre-initiation complex
TFIIF
TFIIE
TFIIH
Pol II Pol II
TFIID TFIIB
S5
S2
CTD kinases
General TF
kinase, CDK7
P-TEFb
ETS2
complex
Mediator
complex
Gene-speciȮc
TF kinases 
Transcription
start site
Gene-speciȮc CTD
kinases (e.g. DYRK1A)
m7G
Broadly acting
CTD kinases
(e.g. CDK12)
Positive transcriptional
elongation factor
kinase, CDK9
General transcriptional
co-activator kinase, CDK8
Mediator activating
kinases (e.g. CDK11)
Promoter Gene
Initiation, promoter proximal pausing
pS5
S2
NELF
DSIF
Productive elongation
P
DSIF
Pol II
pS5
pS2
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Table 1 | Clinical status of selected kinase inhibitors in cancer
Kinase 
target(s)
Compound name Company Indication Current development 
phasea
Refs
Selected kinase inhibitors targeting transcription-associated kinases
CDK7 SY-1365 Syros 
Pharmaceuticals
Advanced solid tumours Phase I (NCT03134638) 36
CDK8 Cortistatin A Merck AML Preclinical 38,63
CCT251545 Merck Colorectal cancer Preclinical 14,39
BCD-115 Biocad ER+ and HER2– local 
advanced and metastatic 
breast cancer
Phase I (NCT03065010) 36
CDK9 Flavopiridol (Alvocidib), in 
combination with cytarabine and 
mitoxantrone
Tolero 
Pharmaceuticals
Relapsed and/or refractory 
AML
Phase II (NCT02520011) 152
NVP-2 Novartis Transcriptionally addicted 
cancers
Preclinical 44,45
BAY1251152 Bayer Advanced blood cancers Phase I (NCT02745743) 284
Advanced cancers Phase I (NCT02635672) 152
Selected kinase inhibitors targeting immune-system-associated kinases
AXL BGB324 BerGenBio ASA AML and MDS Phase Ib/II (NCT02488408) 152
BGB324, in combination with 
erlotinib
BerGenBio ASA NSCLC Phase Ib/II (NCT02424617) 152
BGB324, in combination with 
docetaxel
BerGenBio ASA Previously treated NSCLC Phase I (NCT02922777) 284
BGB324, in combination with 
pembrolizumab or dabrafenib 
and/or trametinib
BerGenBio ASA Metastatic melanoma Phase Ib/II (NCT02872259) 284
TP-0903 Tolero 
Pharmaceuticals
Advanced solid tumours Phase I (NCT02729298) 284
MET and AXL BPI-9016 M Betta 
Pharmaceutical
Advanced solid tumours Phase I (NCT02478866) 152
AXL, MER and 
TYRO3
ONO-7475 Ono Pharmaceutical Newly diagnosed AML Phase I (NCT03176277) 36
CSF1R BLZ945 Novartis 
Pharmaceuticals
Advanced solid tumours Phase I/II (NCT02829723) 284
PI3Kδ Idelalisib Gilead CLL, FL and SLL FDA approved 67
PI3Kδ and 
PI3Kγ
IPI-145 Verastem Relapsed or refractory CLL 
and/or SLL
Phase III (NCT02004522) 285
Refractory indolent 
non-Hodgkin lymphoma
Phase II (NCT01882803) 285
IPI-145 in combination with 
romidepsin or bortezomib
Verastem Relapsed and/or refractory 
T cell lymphomas
Phase I (NCT02783625) 284
PI3Kγ IPI-549 Infinity 
Pharmaceuticals
NSCLC, melanoma and 
squamous cell cancer of the 
head and neck
Phase I (NCT02637531) 152
Selected kinase inhibitors in combination with T cell checkpoint immunotherapy
AXL BGB324, in combination with 
pembrolizumab
BerGenBio ASA Advanced NSCLC Phase II (NCT03184571) 36
TNBC Phase II (NCT03184558) 36
CSF1R PLX3397, in combination with 
pembrolizumab
Plexxikon/Daiichi 
Sankyo
Advanced melanoma and 
other solid tumours
Phase I/II (NCT02452424) 152
Metastatic and/or advanced 
pancreatic or colorectal 
cancers
Phase I (NCT02777710) 284
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Tumour microenvironment
The cellular environment in 
which the tumour exists, which 
is composed of surrounding 
blood vessels, immune cells, 
fibroblasts, inflammatory cells, 
lymphocytes, signalling 
molecules and the 
extracellular matrix. 
The tumour microenvironment 
and the tumour are constantly 
interacting; thus, the tumour 
microenvironment affects 
tumour development 
and progression.
T cell checkpoint inhibitors
Antibody-based therapies that 
block inhibitory pathways that 
regulate the adaptive immune 
response. Currently approved 
T cell checkpoint inhibitors 
target programmed cell death 
protein 1 (PD1), PDL1 (PD1 
ligand 1) and cytotoxic T lym-
phocyte-associated protein 4 
(CTLA4).
dinaciclib also disrupts transcription of homologous 
recombination (HR) genes and reverses both de novo 
and acquired PARP inhibitor resistance in models of 
TNBC49. Single-agent PARP inhibitor efficacy is currently 
restricted to HR-deficient cancers50; however, combined 
inhibition of CDK12 could expand the efficacy of PARP 
inhibitors to an HR-proficient setting.
Targeting immuno-regulatory kinases
Immune system evasion isa hallmark of cancer24,25. 
The tumour microenvironment often contains increased 
numbers of regulatory, immunosuppressive T cells51, 
which enable disease progression and metastasis52. T cell 
checkpoint inhibitors that reactivate the immune system 
to facilitate tumour clearance have emerged as effec-
tive methods for targeting cancer and are US Food and 
Drug Administration (FDA)-approved for metastatic 
melanoma, non-small-cell lung cancer (NSCLC), head 
and neck squamous cell carcinoma (SCC) and bladder 
cancer, with trials ongoing for a number of other indi-
cations53.The success of these drugs has proved that the 
immune system can be stimulated to recognize malig-
nant cells, prompting a search for other strategies that 
can induce anticancer immunity.
Kinases have been pursued for target validation stud-
ies in this area as they constitute key nodes in immune 
signalling, and there has been a surge in the under-
standing of the pathways via which kinases regulate the 
immune system2. Importantly, kinases are also amenable 
to inhibition by small molecules. Small-molecule ther-
apies could offer a number of advantages over currently 
available biologics, including increased compliance due 
to oral dosing, reduced costs and the ability to access 
intracellular targets. In addition, tumour-associated 
immune cells may be less prone to the development of 
resistance mutations against kinase inhibitors than can-
cer cells are, owing to their genetic stability52. Below, 
we discuss recent key examples of how inhibition of 
immune-related kinases can induce anticancer immunity 
as single agents.
TAM kinases. The TAM family of RTKs — tyrosine-
 protein kinase receptors AXL, TYRO3 and MER (also 
known as MERTK) — function as part of the regula-
tory arm of the inflammation cycle through multiple 
mechanisms, including inhibition of the Janus kinase 
(JAK)–signal transducer and activator of transcription 
(STAT) pathway54. This family of kinases is also cru-
cial for apoptotic cell recognition and phagocytosis55, 
and TAM signalling in the bone marrow is required for 
the end-stage differentiation of natural killer (NK) cells56. 
Overexpression of AXL is a mechanism of acquired 
clinical resistance to targeted tyrosine kinase inhibitors 
(TKIs), such as erlotinib in human NSCLC57. In in vitro 
and in vivo models of erlotinib-resistant NSCLC, genetic 
or pharmacological inhibition of AXL resensitized the 
Table 1 (cont.) | Clinical status of selected kinase inhibitors in cancer
Kinase 
target(s)
Compound name Company Indication Current development 
phasea
Refs
Selected kinase inhibitors in combination with T cell checkpoint immunotherapy (cont.)
PI3Kδ TGR 1202, in combination with 
brentuximab vedotin
TG Therapeutics Hodgkin lymphoma Phase II (NCT02164006) 286
TGR 1202, in combination with 
obinutuzumab
TG Therapeutics CLL Phase I (NCT02100852) 286
TGR 1202, in combination with 
ublituximab
TG Therapeutics CLL Phase II (NCT02656303) 284
TGR 1202, in combination 
with ublituximab ± Ibrutinib or 
bendamustine
TG Therapeutics B cell malignancies Phase I (NCT02006485) 285
TGR 1202, in combination with 
ublituximab ± bendamustine
TG Therapeutics Previously treated 
non-Hodgkin lymphoma
Phase IIb (NCT02793583) 284
TGR 1202, in combination with 
ublituximab and pembrolizumab
TG Therapeutics Relapsed–refractory CLL or 
Richter’s transformation
Phase I/II (NCT02535286) 152
TGR 1202, in combination with 
ublituximab, compared with 
obinutuzumab + chlorambucil
TG Therapeutics Previously untreated CLL Phase III (NCT02612311) 152
Obinutuzumab ± TGR-1202, 
lenalidomide or combination 
chemotherapy
National Cancer 
Institute
Relapsed or refractory-grade 
I–IIIa follicular lymphoma
Phase II (NCT03269669) 36
PI3Kγ IPI-549 in combination with 
nivolumab
Infinity 
Pharmaceuticals
Advanced solid tumours Phase I (NCT02637531) 152
AML, acute myeloid leukaemia; CDK, cyclin-dependent kinase; CLL, chronic lymphocytic leukaemia; CSF1R, macrophage colony-stimulating factor 1 receptor; ER, 
oestrogen receptor; FDA, US Food and Drug Administration; FL, follicular B cell non-Hodgkin lymphoma; HER2, human epidermal growth factor receptor 2; MDS, 
myelodysplastic syndrome; NSCLC, non-small-cell lung cancer; PI3K, phosphoinositide 3-kinase; SLL, small lymphocytic lymphoma; TNBC, triple-negative breast 
cancer. aClinical trial number given in parentheses where applicable.
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Natural killer cells
Lymphocytes able to bind to 
certain tumour cells and 
virus-infected cells and kill 
them by the injection of 
granzymes. Unlike T cells, 
natural killer cells can 
recognize stressed cells in the 
absence of antibodies or 
major histocompatibility 
complex (MHC) expression, 
and elicit rapid immune 
responses.
tumours to erlotinib57,58. Reversal of tumour immuno-
suppression via TAM kinase blockade is being tested in 
the clinic with the first AXL-branded inhibitor, BGB324, 
which is currently in phase II clinical trials for NSCLC 
in combination with erlotinib59. Many approved cancer 
drugs, such as cabozantinib and sunitinib, have potent 
AXL off-target activity, indicating that inhibition of this 
target may be tolerated, or even beneficial, in the clinic60. 
Pan-TAM kinase inhibitors and MER kinase inhibitors 
are also currently being explored in phase I clinical 
trials61 (TABLE 1).
CDK8. CDK8 also acts as a regulator of NK cell activa-
tion via phosphorylation of STAT1 at S727. CDK8 knock-
down or STAT1-S727A mutation results in elevated 
levels of perforin, a pore-forming cytolytic protein, and 
elevated levels of granzyme B, a serine protease. Together, 
these proteins are secreted by NK cells to induce apop-
tosis in target cells; thus, STAT1-S727A mice display 
enhanced NK cell cytotoxicity and tumour surveillance, 
consequently reducing their susceptibility to tumour for-
mation and metastasis in murine models of melanoma, 
leukaemia and metastasizing breast cancer62. These find-
ings highlight CDK8 as a promising target for increasing 
NK cell-mediated tumour control62. Small molecule- 
mediated CDK8 inhibition also enhances secretion of 
the anti-inflammatory cytokine interleukin-10 (IL-10) 
from activated dendritic cells, which may be a use-
ful method of reducing inflammation in the tumour 
micro environment63. The CDK8 inhibitor BCD-115 is 
currently in phase I clinical trials (TABLE 1).
CSF1R. Macrophages depend on macrophage colony- 
stimulating factor 1 (CSF1) for differentiation and 
survival. CSF1 promotes macrophage polarization 
from pro-inflammatory M1 to anti-inflammatory M2 
(REF. 64). Blockade of the CSF1 receptor (CSF1R) with the 
kinase inhibitor BLZ945 impairs the tumour- promoting 
functions of tumour-associated macrophages, without 
depletion, and leads to improved symptom-free sur-
vival in murine models of glioblastoma64. However, 
after long-term treatment, changes in the tumour micro-
environment promote recurrence. In glioma, the stim-
ulation of phosphoinositide 3-kinase (PI3K) signalling 
by insulin-like growth factor 1 (IGF1) drives resistance65. 
Combination of either IGF1 receptor (IGF1R) inhibi-
tion or PI3K inhibition plus CSF1R inhibition prolonged 
survival in murine models of glioblastoma65. BLZ945 is 
currently in phase I/II clinical trials for advanced solid 
tumours (TABLE 1).
PI3Kδ and PI3Kγ. PI3Kδ signalling drives malignant B 
cell proliferation66. Selective inhibition of PI3Kδ using theFDA-approved small-molecule inhibitor idelalisib is an 
effective treatment for chronic lymphocytic leukaemia 
(CLL), follicular B cell non-Hodgkin lymphoma (FL) and 
small lymphocytic lymphoma (SLL)67. PI3Kδ inhibition 
may also have broader immuno-oncology applications 
as it preferentially suppresses regulatory T (Treg) cell 
function, leading to effector T cell activation in mouse 
models of breast cancer and solid tumours68.
As PI3Kδ and PI3Kγ play distinct and complemen-
tary roles in immune function, dual inhibition is also an 
attractive strategy for broadly targeting haematological 
malignancies69. Inhibition of PI3Kδ and PI3Kγ is well 
tolerated, with mild, reversible side effects reported in 
the clinic70. The dual inhibitor duvelisib is currently 
in phase III clinical trials for CLL and SLL, phase II 
clinical trials for indolent non-Hodgkin lymphoma and 
phase I clinical trials for T cell lymphomas71 (TABLE 1).
Combining kinase inhibitors with immunotherapy
Antibodies targeting cancer immune evasion via T 
cell checkpoint blockade effect complete and long- 
lasting remission in a fairly small subset of patients72. 
De novo immunotherapy resistance may be due to the 
potent immunosuppressive effects of well-established 
tumours73. Conversely, targeted kinase inhibitors, such 
as erlotinib, elicit responses in the majority of patients 
harbouring the relevant oncogene (for example, mutant 
epidermal growth factor receptor (EGFR) in NSCLC)74. 
However, the resultant tumour regression is often short 
lived, and acquired resistance inevitably occurs75.
Kinase inhibitors able to rapidly abate established 
tumours may sensitize the remaining cancer to immuno-
therapy, which in turn could confer durability to the 
kinase inhibitor-mediated remission. Furthermore, 
by interfering with oncogene addiction and trigger-
ing senescence, kinase inhibitors may also facilitate 
tumour clearance by reactivated T cells76. New evidence 
is emerging that kinase oncogenes can play a role in 
immune escape and T cell checkpoint inhibitor resist-
ance77. Therefore, much effort has been invested into 
discovering existing kinase inhibitors that can synergize 
effectively with T cell checkpoint blockade. This effort 
has already begun to yield exciting preclinical results78–80. 
Selected examples are discussed below.
PI3Kγ. The properties of tumour-associated macro-
phages are modulated by PI3Kγ, which acts as a 
molecular switch that turns on immunosuppression 
while shutting down immune-stimulatory activities81. 
Inhibition of PI3Kγ with the dual PI3Kδ and PI3Kγ 
inhibitor TG100-115 re-educates macrophages, stimu-
lates T cell activity against tumours and shows enhanced 
benefits when combined with anti-programmed cell 
death protein 1 (PD1) immunotherapy81. Derivative 
TGR 1202 (umbralisib) is currently undergoing eight 
different clinical trials in combination with various 
immunotherapy biologics (TABLE 1).
PI3Kγ activation is also crucial for inflamma-
tory cell recruitment to tumours (in particular mye-
loid cells), which can also be attenuated by knockdown 
or pharmaco logical inhibition82. High infiltration of 
immune- suppressive myeloid cells correlates with poor 
prognosis and resistance to T cell checkpoint block-
ade83,84. Treatment with the highly selective PI3Kγ inhib-
itor IPI-549 restored sensitivity to immunotherapy and 
remodelled the tumour microenvironment in preclinical 
mouse models85,86. IPI-549 is currently in phase I clin-
ical trials in combination with the anti-PD1 antibody 
nivolumab for advanced solid tumours (TABLE 1).
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MEK. MEK inhibition has pleiotropic effects in T cells; 
it blocks naive CD8+ T cell priming in lymph nodes 
but also increases the number of effector-phenotype 
antigen-specific CD8+ T cells87. In mouse models of 
KRAS-G12D-driven colon carcinoma, MEK inhibition 
protected tumour-infiltrating CD8+ T cells from chronic 
T cell receptor stimulation-induced death while sparing 
their cytotoxic activity. Although MEK inhibition or 
anti-PD1 ligand 1 (PDL1) single-agent treatment pro-
duced only modest anticancer effects, their combination 
resulted in long-term tumour regression87.
FAK. In SCC, oncogenic nuclear focal adhesion kinase 
(FAK) upregulates transcription of chemokine ligands 
and receptors, such as CC-chemokine ligand 5 (CCL5), 
to promote Treg recruitment and CD8+ T cell exhaus-
tion88. FAK kinase inhibition reduces intratumoural Treg 
levels, leading to CD8+ T cell-mediated tumour immu-
nity88. These anti-immunosuppressive effects provide 
a rationale for combining FAK inhibitors with CD8+ 
T cell-stimulating therapies to increase tumour sen-
sitivity in SCC. FAK kinase activity also modulates the 
migration of cancer- associated fibroblasts, monocytes 
and macrophages in pancreatic cancer, enabling their 
recruitment to tumours89. Accordingly, FAK inhibitors 
sensitize immunotherapy- resistant tumours to checkpoint 
blockade in the KPC mouse model of pancreatic cancer90.
EGFR. In 2013, a correlation between oncogenic EGFR-
driven tumours and the presence of T cell exhaustion 
markers in lung cancer was discovered91–93. Mutant EGFR 
was shown to remodel the tumour microenvironment to 
trigger immune escape and induce PDL1 expression, 
indicating that combining EGFR kinase inhibition and 
PD1 blockade may be an attractive therapeutic strategy 
in lung cancer92,93.
Studies have suggested that other oncogenes have 
additional functions contributing to immune evasion, 
opening up many new avenues of investigation76. For 
example, dual CDK4 and CDK6 inhibition has recently 
been shown to augment antitumour immunity94,95. 
These new findings also raise questions about the rele-
vance of current cellular assays and xenograft models in 
immunodeficient mice, which are frequently used to judge 
the anticancer activity of kinase inhibitors in preclinical 
studies. Indeed, Vladimer et al.96 reported that 10% of the 
1,402 FDA-approved drugs screened in a cell–cell interac-
tion assay showed previously unreported immunomod-
ulatory activity, including four kinase inhibitors. This 
finding highlights an opportunity to develop new meth-
ods that encapsulate effects deriving from the tumour 
microenvironment, possibly leading to improved preclin-
ical prediction of outcomes in the clinic97. To this end, 
immuno-oncology screening panels are emerging in the 
commercial assay service market and have the potential 
to become part of the standard characterization of can-
cer therapeutics. Numerous challenges remain, including 
substantial differences between the murine and human 
immune systems and potentially divergent pharmacology 
arising from kinase inhibitor treatment in tumour versus 
immune cells.
Kinase inhibitors outside of oncology
Kinase inhibitors have been explored in inflammatory 
disease for decades and are now beginning to reach their 
potential in the clinic (FIG. 3). The pan-JAK inhibitor tofac-
itinib was recently approved by the FDA for the treatment 
of rheumatoid arthritis (RA), providing a proof of concept 
that kinase inhibitors can be developed into safe and effi-
cacious drugs for non-terminal inflammatory diseases98,99. 
This approval has prompted a surge in research efforts in 
inflammatory disease that mirrors the surge in research 
efforts in oncology following the approval of imatinib, and 
indicates that this is an area of increasing importance. 
In this section, we cover key examples from the grow-
ing field of inflammatorydisease and also highlight two 
therapeutic areas where the application of kinase inhibi-
tors is in its infancy: degenerative disease and infectious 
disease. Exemplary successful projects and strategies for 
expanding the development and application of kinase 
inhibitors into these areas are outlined.
Autoimmune and inflammatory diseases
Three intracellular kinase signalling pathways have 
historically been the focus of major efforts in this field 
— JAK–STAT, Bruton tyrosine kinase (BTK)–spleen 
tyrosine kinase (SYK) and mitogen-activated pro-
tein kinase (MAPK)–p38 — all of which feed into the 
myeloid differentiation primary response protein 88 
(MYD88) pathway100. These efforts have been extensively 
reviewed101,102.
The greatest clinical success has resulted from target-
ing the JAK kinases, which are downstream effectors of 
type I and/or II cytokine receptor signalling. The pan-
JAK inhibitor tofacitinib98,99 was recently approved by the 
FDA for the treatment of RA. Approximately 20 other 
JAK inhibitors, with varying selectivity profiles, are cur-
rently being tested in clinical trials for a plethora of auto-
immune diseases, including psoriasis, alopecia areata, 
ankylosing spondylitis and lupus103. Determining the 
optimal JAK selectivity profile may prove key for refining 
second-generation JAK inhibitors104.
Nature Reviews | Drug Discovery
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Figure 3 | US Food and Drug Administration-approved kinase inhibitors for 
oncology and non-oncology indications (autoimmune and inflammatory disease) 
over time. NCE, new chemical entity.
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Targeting of p38α MAPK kinase has been less suc-
cessful in the clinic, with most trials failing owing to 
toxicity or a lack of efficacy105. This is now understood 
to be due to the pleiotropic effects on the immune sys-
tem stemming from p38α MAPK inhibition but was not 
predicted by preclinical murine inflammation studies106, 
demonstrating the challenge of generating models with 
sufficient predictive value. The convergence of early 
efforts in inflammatory disease around drugging p38α 
MAPK kinase meant that progress in developing inhib-
itors against other kinase targets for the treatment of 
inflammatory and autoimmune disease stalled. In recent 
years, the field has benefited from a greater understand-
ing of relevant signalling cascades, including and beyond 
the MYD88 pathway2, and from the increased availability 
of suitable kinase inhibitors.
Targeting the BTK–SYK pathway has yielded mixed 
results. The SYK inhibitor fostamatinib showed promise 
in murine models of RA but later failed in preliminary 
phase III studies106. However, phase II trials are still on go-
ing in immunoglobulin A (IgA) nephropathy, an inflam-
matory kidney disease107–109. Several BTK inhibitors have 
been approved for the treatment of multiple myeloma, 
lymphoma and B cell leukaemia110. Repurposing these 
inhibitors for the treatment of RA and systemic lupus 
erythematosus has yielded positive preclinical results in 
murine disease models, with clinical studies ongoing111–115 
(TABLE 2). High-quality chemical probes exist for other tar-
gets in this pathway, including IL-1 receptor- associated 
kinase 1 (IRAK1), IRAK4 and MAPK-activated protein 
kinase 2 (MK2), and their benefits in treating inflamma-
tory disease are still under evaluation116–119.
In autoimmune and inflammatory diseases, many 
of the molecular targets or misregulated biological pro-
cesses are shared with cancer, which has facilitated val-
idation of a number of targets in this area. For example, 
the multi targeted CSF1R inhibitor PLX3397 is currently 
in phase III trials for the joint disorders pigmented villo-
nodular synovitis and giant cell tumour of the tendon 
sheath (TABLE 2).
Similarly, the oncotargets PI3Kδ and PI3Kγ, play 
distinct and complementary roles in immune function; 
therefore, dual PI3Kδ and PI3Kγ inhibition is an attractive 
strategy for targeting inflammatory disorders120. The dual 
inhibitor IPI-145 (duvelisib) has potent joint- protective 
effects in murine models of RA121. Furthermore, a 
phase IIa exploratory clinical trial in mild allergic asthma 
met several secondary end points, indicating promise 
for next-generation dual PI3Kδ and PI3Kγ inhibitors in 
this area122.
Activated PI3Kδ syndrome (APDS) is an immuno-
deficiency disorder characterized by the presence 
of pathogenic gain-of-function variants of PI3Kδ123. 
Overactivation of this pathway results in an accumu-
lation of transitional B cells, senescent T cells and lym-
phadenopathy123. Leniolisib (CDZ173), a highly selective 
PI3Kδ inhibitor124, is currently undergoing phase II/III 
trials for APDS. In the first cohort of 12 patients, 
leniolisib was able to normalize the levels of transi-
tional B cells, reduce the number of senescent T cells 
and inflammatory markers and reduce lymph node 
and spleen volumes125. Leniolisib is also currently under-
going phase II clinical trials for the autoimmune disease 
primary Sjögren syndrome (TABLE 2).
Table 2 | Clinical status of selected kinase inhibitors outside of oncology
Kinase 
target(s)
Compound 
name
Company Indication Current development 
phase
Refs
Pan-JAK Tofacitinib Pfizer Rheumatoid arthritis Approved 98,99
BTK HM71224 Hanmi Pharmaceutical Rheumatoid arthritis Phase I (NCT01765478) 285
CC-292 Celgene Rheumatoid arthritis Phase II (NCT01975610) 285
M2951 Merck/EMD Serono Research 
& Development Institute
Rheumatoid arthritis Phase II (NCT02784106) 284
Evobrutinib Merck/EMD Serono Research 
& Development Institute
Rheumatoid arthritis Phase IIb (NCT03233230) 152
MSC2364447C Merck/EMD Serono Research 
& Development Institute
Systemic lupus erythematosus Phase I (NCT02537028) 152
PI3Kδ Leniolisib 
(CDZ173)
Novartis Activated PI3Kδ syndrome Phase II/III (NCT02435173) 152
Primary Sjögren syndrome Phase II (NCT02775916) 284
PI3Kδ and/or 
PI3Kγ
Duvelisib Verastem Mild asthma Phase II (NCT01653756) 287
CSF1R PLX3397 Plexxikon/Daiichi Sankyo Pigmented villonodular synovitis or 
giant cell tumour of the tendon sheath
Phase III (NCT02371369) 152
VEGFR and/or 
PDGFR
X-82 Tyrogenex Wet AMD Phase II (NCT02348359) 287
VEGFR Novartis Novartis Wet AMD Preclinical 132,153
SRPK1 SPHINX31 Exonate Wet AMD Preclinical 155
AMD, age-related macular degeneration; BTK, Bruton tyrosine kinase; CSF1R, macrophage colony-stimulating factor 1 receptor; JAK, Janus kinase; PDGFR, 
platelet-derived growth factor receptor; PI3K, phosphoinositide 3-kinase; SRPK1, SFRS protein kinase 1; VEGFR, vascular endothelial growth factor receptor.
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In addition, the TAM kinase agonist growth arrest- 
specific protein 6 (GAS6) is overexpressed in the latter 
stages of septic shock, hindering the patient’s ability to 
clear their infection54. Therefore, inhibition of the TAM 
kinases is relevant in thecontext of treating immuno-
suppression in the latter stages of septic shock and for use 
in vaccine adjuvants for immunization54,126,127.
In conclusion, the intensified efforts in the inflam-
matory disease area have begun to come to fruition 
through both novel targets and through repurposing of 
cancer drugs.
Degenerative disease
Degenerative diseases constitute a large unmet medical 
need, with the number of patients expected to increase as 
the average lifespan becomes progressively longer.
This field is exceptionally challenging owing to the 
current poor understanding of the disease mechanism in 
the majority of cases128. Consequently, few predictive ani-
mal models exist129,130. In addition, as the site of degenera-
tive disease is frequently the brain or the eye, compounds 
must be optimized to traverse the blood–brain barrier or 
the blood–ocular barrier and accumulate in these areas 
in order to be efficacious and avoid systemic effects, 
presenting an additional developmental hurdle.
Despite these challenges, encouraging preclinical 
results with kinase inhibitors have recently been obtained 
in diseases where dysregulated processes can be identi-
fied, such as the unfolded protein response (UPR) in ret-
initis pigmentosa131 and angiogenesis in wet age-related 
macular degeneration (AMD)132.
Unfolded protein response. When cells undergo endo-
plasmic reticulum (ER) stress, inositol-requiring enzyme 
1α (IRE1α; also known as ERN1) promotes either adap-
tation or apoptosis133. Homo-oligomerization of IRE1α 
stimulates trans-autophosphorylation via the kinase 
domain, which promotes further oligomerization and 
activates the IRE1α RNase domain134. This activation 
promotes specific cleavage of the transcription factor 
X-box-binding protein 1 (XBP1), a key step in initiating 
the UPR135,136.
Chronic or excessive ER stress results in the forma-
tion of high-molecular-mass IRE1α oligomers. Beyond a 
critical size, these oligomers acquire an increased mRNA 
substrate repertoire, which triggers apoptosis137. This 
response is deregulated in the degenerative diseases reti-
nitis pigmentosa and diabetes mellitus138. Small-molecule 
inhibition of the IRE1α kinase by APY29 can dissociate 
oligomers and inhibit RNase activity, promoting cell sur-
vival under ER stress in murine models of diabetes and in 
rat models of retinal degeneration131.
A second exciting kinase target for mitigating 
ER-stress-related disorders is PRKR-like ER kinase 
(PERK; also known as EIF2AK3). The PERK– 
eukaryotic translation initiation factor 2 subunit 1 (eIF2α; 
also known as EIF2S1) branch of the UPR mediates the 
transient shutdown of translation in response to ris-
ing levels of misfolded proteins139. However, prolonged 
repression of translation results in loss of critical pro-
teins and eventual neuronal death. Therefore, PERK 
has been investigated as a target in prion disease140 and 
tau- mediated neurodegeneration141. In mouse models 
of the latter, treatment with the PERK kinase inhibi-
tor GSK2606414 resulted in restoration of translation, 
reduction in tau phosphorylation and neuroprotection142. 
However, systemic effects indicative of PERK inhibition in 
the pancreas (namely, weight loss and insulin deficiency) 
were also observed. If PERK inhibitors able to accumu-
late in the brain can be developed, this approach may be 
translatable to the clinic.
The dual leucine zipper kinase (DLK) functions as an 
activator of PERK and is implicated in chronic neurode-
generative disease and acute neuronal injury143. Recently, 
reported central nervous system-penetrant, selective DLK 
inhibitors have shown activity in an in vivo nerve injury 
model144 and protective effects in two separate murine 
models of neurodegeneration, providing important 
proof-of concept studies for targeting this pathway145.
Angiogenesis. Inhibition of angiogenesis via the vascular 
endothelial growth factor (VEGF) pathway has proved 
beneficial in the macular degenerative disease wet AMD. 
Wet AMD occurs as a result of abnormal growth of 
blood vessels, which penetrate the retina and leak fluid 
and blood that damages photoreceptor cells and causes 
visual degeneration143,146. Currently, the only approved 
treatment options are anti-VEGF biologics that require 
dosing via intravitreal injection every 4–8 weeks147.
The VEGF and platelet-derived growth factor (PDGF) 
pathways play complementary roles in vascularization, 
with VEGF supporting new vessel growth and PDGF 
stabilizing maturing vessels148. Dual inhibition of VEGF 
receptor (VEGFR) and PDGF receptor (PDGFR) kinases 
has proved beneficial in cancer148. These oncology drugs 
are now being repurposed for the treatment of wet AMD. 
The pan-RTK inhibitors sorafenib149 and pazopanib150, 
along with X-82 (REF. 151), a novel orally available dual 
inhibitor of VEGFR and PDGFR, have shown benefit in 
wet AMD in preclinical studies, and X-82 is now being 
assessed in phase I/II clinical trials152. Novartis recently 
reported a series of orally available VEGFR inhibitors 
that selectively accumulate in ocular tissues, reducing the 
likelihood of undesired systemic effects occurring dur-
ing treatment132,153. Kinase inhibitors that can be admin-
istered via oral dosing have the potential to dramatically 
improve patient comfort, compliance and ocular safety 
in this field and may be able to prevent the development 
of disease in the second eye in some cases.
SFRS protein kinase 1 (SRPK1) is an upstream target 
of the VEGF pathway that regulates VEGF pre-mRNA 
splicing to alter the balance between the proangio-
genic VEGF-A165a and antiangiogenic VEGF-A165b154. 
Inhibition of SRPK1 is an attractive therapeutic strat-
egy as it allows splice isoform-selective targeting of 
proangiogenic VEGF.
Batson et al.155 recently developed the first reported 
potent and selective SRPK1 kinase inhibitor, SPHINX31, 
by taking advantage of an SRPK1-specific insert close to 
the hinge region of the kinase. SPHINX31 is capable of 
ocular penetration after topical application as well as rapid 
clearance, which is advantageous in this dosing model 
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to avoid off-target effects. In a murine wet AMD model, 
SPHINX31 application via eye drops inhibited blood 
vessel growth and macrophage infiltration at levels com-
parable to intravitreal injection of established anti-VEGF 
therapies, such as aflibercept155.
In the exceptionally challenging field of neurodegen-
erative diseases, two well-studied kinases have emerged 
as potential targets: mammalian target of rapamycin 
(mTOR) has been implicated in a wide variety of neuro-
logical diseases, and leucine-rich repeat serine/threonine- 
protein kinase 2 (LRRK2) has been identified as a putative 
target for Parkinson disease (PD). Potent, selective and 
brain-penetrant clinical development candidates for these 
kinases have been identified156,157, but the challenge of 
understanding the neuronal functions of these kinases, 
and whether, or how, this contributes to disease pathol-
ogy remain158–160. Results from future studies are eagerly 
anticipated.
Overall, improved understanding of the drivers and 
dependencies of degenerative diseases is required. Once 
these mechanisms can be identified, kinases represent 
tractable targets for intervention, as demonstrated by 
the preclinical examples given above.
Infectious diseases
The increased prevalence of malaria resistance to cur-
rently available medication is a rising concern andthe 
identification of new therapeutic strategies is vital.
A small number of kinases have been validated as 
novel antimalarial targets161. An elegant study used a 
cell-based screen against Plasmodium falciparum asexual 
blood-stage parasites to optimize a series of imidazopyra-
zines162. Forward genetics identified the target as plasmo-
dium phosphatidylinositol-4- hydroxykinase (PfPI(4)K) 
type IIIβ. The tool PfPI(4)K inhibitor KDU691 showed 
efficacy against a number of plasmodium strains, includ-
ing drug-resistant strains, both in vitro and in vivo, and 
was able to target multiple stages of the plasmodium life 
cycle162. This exciting study provides proof of concept; 
targeting parasite kinases can be an effective strategy to 
prevent malarial transmission. Additionally, it outlines a 
preclinical pipeline for small-molecule antimalarial drug 
development and target identification that may serve as 
a blueprint for future kinase inhibitor target discovery.
In a separate study, a biochemical screen against 
five P. falciparum kinases identified inhibitors of plas-
modium calcium-dependent protein kinase 4 (CDPK4; 
also known as CPK4) with minimal off-target activity 
on human kinases163. Dual PfCDPK1 and PfCDPK4 
inhibitors with low cytotoxicity against human HepG2 
cells were also identified. These results indicate that it 
may be possible to develop plasmodial-kinase selective 
inhibitors with a high therapeutic index163.
Chemical genomics screens have identified many 
additional putative antimalarial kinase targets, includ-
ing plasmodial cell division control protein 2 homologue 
(PK5; also known as CRK2) and Plasmodium berghei 
glycogen synthase kinase 3 (GSK3)164.
These studies suggest that plasmodium kinase- focused 
medicinal chemistry can produce the next generation 
of antimalarial drugs. The development of accessible 
resources for these endeavours, such as plasmodium- 
kinase biochemical assays, crystal structures and screening 
panels, is needed to enable rapid progress in this field.
Looking further afield, kinase targets are beginning 
to be explored in other infectious disease areas, such as 
viral diseases165, including Ebola (RHO kinase)166 and 
dengue virus (ABL kinase)167, and bacterial pathogens168, 
including drug-resistant Mycobacterium tuberculosis (for 
example, shikimate kinase and serine/threonine-protein 
kinases PknA and PknB)169–171.
Challenges in kinase inhibitor development
Despite the expanding applications of kinase inhibitors 
in oncology and inflammatory disease, and their poten-
tial to transform neglected therapeutic areas, challenges 
remain in kinase-directed medicinal chemistry.
The emergence of resistance is a major barrier to 
achieving long-term remission in cancer. Development of 
resistance-mutant specific inhibitors can prolong patient 
survival, but sequential resistance inevitably occurs74. For 
example, the recently approved third- generation EGFR 
T790M inhibitor osimertinib is rendered ineffective by an 
EGFR C797S mutation172. Other resistance mechanisms, 
such as kinase upregulation (for example, the upregula-
tion of breakpoint cluster region (BCR)–Abelson tyrosine 
kinase (ABL), which has been shown to confer imatinib 
resistance to chronic myeloid leukaemia173) or compensa-
tion and/or bypass (such as the upregulation of EGFR and 
mast/stem cell growth factor receptor KIT (also known as 
SCFR) that occurs to facilitate crizotinib resistance in lung 
cancers harbouring an anaplastic lymphoma kinase (ALK) 
translocation174), are harder to overcome, prompting 
a search for treatments that are less prone to resistance.
Attaining the selectivity required for pharmacologi-
cal target validation remains one of the largest hurdles in 
an early-stage kinase inhibitor project. However, this is 
essential for both understanding the target biology and 
mitigating off-target toxicity175,176. For more advanced 
compounds, achieving the desired pharmacodynamic 
properties, in particular drug residence time, is essential 
for efficacy. Historically, limited strategies have existed for 
rational optimization of this property, and covalent tar-
geting of kinases has been limited to those containing 
cysteine adjacent to the ATP site177.
Below, we discuss recent breakthroughs in kinase- 
directed medicinal chemistry and the discovery of new 
approaches to therapeutic kinase inhibition aimed at 
addressing these challenges. Notable strategies include 
small molecule-mediated promotion of kinase degrada-
tion via hijacking of the ubiquitin ligase system and devel-
opment of new covalent and reversible covalent warheads, 
which allow rational tuning of inhibitor residence times, 
or targeting of noncysteine residues.
Innovation in selectivity profiling has established 
robust kinome-wide and proteome-wide screening 
methodologies that can be performed in a native context, 
allowing unprecedented insight into the cellular targets of 
kinase inhibitors. In computer-aided drug design, incor-
poration of water molecules and use of FEP calculations 
have improved the compound ranking ability of molecular 
docking approaches to support discovery chemistry.
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PROTACs
Proteolysis-targeting chimaeras 
(PROTACs) are two-headed 
molecules capable of removing 
unwanted proteins by inducing 
selective intracellular 
proteolysis through induction 
of their ubiquitylation.
Advances in medicinal chemistry
An extensive knowledge base in kinase structural biol-
ogy and medicinal chemistry has been accumulated and 
reviewed extensively6,178. However, continued innova-
tion and discovery is required to overcome the remain-
ing challenges outlined above. Medicinal chemistry 
researchers have risen to this task by developing small 
molecules with novel mechanisms of action — from 
induced degradation to reversible covalent inhibition 
and targeting of remote cysteines. A wide array of tac-
tics has been effectively utilized to develop novel kinase 
inhibitors with unparalleled kinome-wide selectivity. 
Below, selected applications of these new techniques, 
and examples of how they are being used to overcome 
drug resistance and to tune target profiles and optimize 
pharmacodynamic properties, are discussed.
Promotion of kinase degradation
Many kinase domain-containing proteins undergo a 
plethora of additional interactions, including protein–
protein interactions, the formation of multimeric com-
plexes and the enzymatic activities carried out by other 
functional domains. Therefore, results from genetic target 
validation techniques that knock down full-length protein 
levels, such as RNA interference or CRISPR, are often not 
fully reproduced by kinase inhibition alone. Drugging of 
these additional interactions is challenging. In order to 
mimic loss of the entire protein, rather than just loss of 
kinase function, there have been intensive efforts towards 
developing methods of small- molecule-induced protein 
knockdown (FIG. 4).
Drug-induced degradation of oncogenic kinases 
to overcome multiple mechanisms of resistance was 
first achieved in crizotinib-resistant (nucleophosmin 
(NPM))–ALK expressing BaF3 cells via heat shock pro-
tein 90 (HSP90) inhibition179,180. HSP90 is a molecular 
chaperone that assists in late-stage protein folding and 
is overexpressed in a wide range of cancers. A subset of 
mutated or translocated oncogenes, such as echinoderm 
microtubule-associated protein-like 4 (EMAP4)–ALK, 
are highly sensitive clients of HSP90, leadingto their 
preferential degradation upon HSP90 inhibition181–183. In 
the clinic, HSP90 inhibitors displayed unacceptable lev-
els of toxicity, limiting their therapeutic index. Recently, 
exciting new methods detailing more selective ways to 
degrade oncogenic kinase targets have been reported184.
Small-molecule CRBN ligands. Krönke et al.185 discov-
ered that the small-molecule drug lenalidomide, but not 
its closely related analogues thalidomide, pomalidomide 
and CC-122, can repurpose the CRL4CRBN ubiquitin ligase 
to degrade casein kinase Iα (CKIα), while all four ana-
logues can induce degradation of the transcription factors 
Ikaros family zinc-finger protein  1 (IKZF1) and IKZF3. 
This anti-CKI-α activity contributes to the efficacy of 
lenalidomide in myelodysplastic syndrome with deletion 
of chromosome 5q. Structural studies revealed the bind-
ing mode of lenalidomide and its analogues to cereblon 
(CRBN), the substrate receptor of CRL4, as well as the 
structural basis of the small-molecule-induced dimer-
ization of CRBN and CKI-α186. The differences in the 
induced dimerization profiles of these four closely related 
compounds suggest that new lenalidomide analogues can 
be developed to direct CRL4CRBN to other targets. Broad 
application of this technique will require development of 
innovative assays and docking protocols to enable rational 
design of induced protein–protein interactions.
Small-molecule kinase ligands. Small-molecule kinase 
ligands can induce proteasome-dependent degradation of 
kinases; one example of this is observed for inhibitors 
of maternal embryonic leucine zipper kinase (MELK)187. 
Although the mechanism of this degradation is unre-
solved, it is postulated to occur either via allosteric effects 
on protein conformation leading to recognition by the 
proteasome system or via destabilization due to loss of 
autophosphorylation marks. To date, inhibitor- induced 
degradation events have been discovered serendipitously 
rather than designed de novo.
A more rational approach to catalysing kinase deg-
radation via conformational change is to stabilize inter-
mediates in the protein-folding process, preventing 
the kinase from reaching its mature, active state. This 
finding has been demonstrated for DYRK1A, where 
molecules that inhibit S97 autophosphorylation, part of 
the DYRK1A folding process, induce degradation of the 
kinase in cells. These molecules do not inhibit phospho-
rylation of the DYRK1A substrate tau by the mature, 
folded kinase, indicating that they are selective for a 
DYRK1A folding intermediate188.
Proteolysis-targeting chimaeras. Linking an E3-ligase 
binding molecule, such as thalidomide, to a drug that 
recruits a second protein target, generates a hetero- 
bifunctional molecule capable of catalysing selective 
target ubiquitylation and degradation189. These com-
pounds, known as PROTACs (proteolysis-targeting chi-
maeras), enable targeting of both the enzymatic and the 
scaffolding functions of a protein with a small molecule. 
Although these compounds often have a higher molec-
ular mass than a typical drug, their pharmacodynamic 
effect endures beyond what their pharmacokinetic profile 
would predict, as the compounds act at substoichiometric 
concentrations, and targeted proteins must be resynthe-
sized. Additionally, by targeting tissue-specific ligases, 
regional control of target degradation may be achieved, 
potentially opening up new therapeutic avenues190. This 
rapidly expanding field has recently been reviewed191–193.
PROTACs have been developed for an ever- expanding 
number of kinases, including AKT194, BCR–ABL195, 
PI3K196, receptor-interacting serine/threonine-protein 
kinase 2 (RIPK2)189, TBK1197 and CDK9 (REFS 198,199), 
demonstrating that this target class is highly amenable 
to small molecule-induced degradation. The technique 
may be especially relevant to pseudokinases, which have 
no catalytic function but are crucial for activation of 
other kinases. Hydrophobic tagging (HyT) approaches 
have resulted in effective lysosomal degradation of 
human epidermal growth factor receptor 3 (HER3; also 
known as ERBB3)200, indicating that degradation may be 
an effective way of targeting this previously intractable 
family of oncogenes.
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Through extensive empirical studies that involve 
varying the linker, E3 ligase ligand and kinase ligand, it 
has been shown that all three components contribute to 
the degradation profile of a molecule195,197,201. The fac-
tors governing which kinases can be degraded by which 
E3 ligases, and how to design the most efficient and 
selective PROTAC for any given target, are active areas of 
research. Progress in determining the X-ray crystal struc-
tures of E3 ligase–PROTAC–target ternary complexes 
has enabled structure-based rational design of linkers 
joining the two PROTAC warheads in a small number 
of cases186,202–204. Multitargeted kinase inhibitor PROTACs 
have been used to survey the landscape of kinases that are 
highly amenable to CRBN-mediated degradation205,206.
E2
E3
E2
Nature Reviews | Drug Discovery
a
b
Allosteric eȭects or
autophosphorylation
inhibition
E3
Ub
Ub
Ub
Ub
E3E3E3
E3 binder
PROTAC
molecule
E3 binder
recycled
26S
proteosome
Degraded
target
Target
Target
E2
E2
Ub
26S
proteosome
PROTAC
molecule
recycled
Degraded
target
E3
Ub
HyT
molecule
d
Kinase
inhibitor
Chaperone
Target
Destabilized
target
20S
proteosome
Kinase
inhibitor
recycled
Degraded
target
c
Chaperone
Chaperone
Target
Destabilized
target 20S
proteosome
Degraded
target
HyT
molecule
recycled
Model 1
Model 2
Ub
Ub
Ub
Ub
Figure 4 | Chemical methods of inducing kinase degradation. a | Induced protein–protein interaction by E3 binder. 
A small molecule binds at the interface of the E3 ligase and a target to induce a protein–protein interaction and 
subsequent target ubiquitinylation. b | PROTAC (proteolysis-targeting chimaeras) approach. A heterobifunctional 
molecule containing an E3 ligase binder linked to a target bait brings the two proteins together and induces target 
ubiquitinylation and degradation. c | Hydrophobic tagging (HyT) approach. A heterobifunctional molecule containing 
a hydrophobic group, such as adamantane, linked to a target bait induces target degradation as the hydrophobic 
portion of the molecule is recognized by the ubiquitin (Ub)–proteasome system and tags the target for ubiquitinylation. 
d | Destabilization of kinase fold via kinase inhibitor. Certain kinase inhibitors may stabilize an alternate protein fold. 
This misfolded structure is then recognized by the Ub–proteasome system, and the target is degraded.
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Covalent kinase inhibitors
Kinase inhibitors that contain 
a weakly reactive electrophile. 
Upon a reversible binding 
interaction, the electrophilic 
warhead is brought into close 
proximity with a nucleophilic 
residue in the kinase, often 
cysteine, which subsequently 
reacts to form a covalently 
bonded complex.
The development of kinase inhibitors withclin-
ical efficacy still faces considerable challenges from 
acquired resistance. For example, resistance to the 
recently approved CDK4 and CDK6 inhibitors abemac-
iclib, ribociclib and palbociclib has been shown to occur 
via acquired upregulation of CDK6 (REF. 207) and cyc-
lin D1 in oestrogen receptor-positive breast cancer208. 
Induced kinase protein knockdown has been purported 
to overcome some of these challenges, particularly tar-
get upregulation. This result has already been realized 
in metastatic castration-resistant prostate cancer in the 
form of a PROTAC molecule able to efficiently degrade 
the androgen receptor (AR)209. This compound is able 
to overcome resistance to the standard-of-care anti- 
androgen treatments, enzalutamide and abiraterone, 
which occurs owing to increased levels of androgen 
production, increased AR expression or specific AR 
mutations209. Application of this technology to upreg-
ulated kinase targets, such as CDK6, holds promise for 
overcoming acquired inhibitor resistance in cancer.
Finally, inhibitors of kinases in the p38 MAPK 
pathway have been reported to stimulate the 26S pro-
teasome’s activity and increase PROTAC-mediated 
degradation210. These inhibitors may prove useful for 
enhancing the efficacy of a wide range of PROTACs, 
and specifically for serving as PROTAC co-catalysts in 
neurodegenerative diseases, in which proteasome activ-
ity is typically decreased, expanding the potential utility 
of PROTACs210.
Advances in covalent targeting of kinases
Irreversible kinase inhibitors offer a number of potential 
advantages over their reversible counterparts, including 
prolonged pharmacodynamics, suitability for rational 
design, high potency and the ability to validate phar-
macological specificity through mutation of the reac-
tive cysteine residue211. However, they also pose a set of 
unique challenges, including the potential for hapteni-
zation, irreversible labelling of off-target proteins, and, 
for obligate–covalent inhibitors, acquired drug resist-
ance via cysteine mutation212. Their application is also 
typically limited to kinases that contain an accessible, 
reactive cysteine close to the ATP binding site. To date, 
three irreversible inhibitors have received FDA approval: 
afatinib and osimertinib targeting mutant EGFR and 
ibrutinib targeting BTK213. Renewed interest in devel-
oping covalent kinase inhibitors has sparked innovative 
research to overcome some of these potential issues212.
Alternative cysteine targeting electrophiles. Although 
many covalent drugs preferentially react with the desired 
target, the number of labelled off-targets builds over 
time owing to the irreversible nature of the reaction. 
The kinetic selectivity of a compound is dependent on 
the relative rates of on-target and off-target labelling at 
a given concentration.
Covalent inhibition occurs as a two-step mechanism 
as shown below. The protein target (P) reacts reversibly 
with inhibitor (I) to form the reversibly bound com-
plex P∙I. The KI is the potency of the reversible bind-
ing, defined as the concentration of I required for the 
covalent bond formation step to occur at half the maxi-
mal rate. Subsequently, inhibitor I reacts covalently with 
target P to form the covalent adduct P-I. The Kinact is the 
first- order rate constant defining the maximal poten-
tial rate of covalent bond formation. Kinact/KI is the sec-
ond-order rate constant that defines the rate of overall 
conversion of free target (P) to covalent adduct (P-I)214.
Kinact/KI is determined experimentally by measuring 
compound binding or activity over time, at multiple con-
centrations215,216. From this, an observed rate of inactiva-
tion can be calculated at each concentration. The initial 
slope of the inactivation rate versus concentration plot 
is the Kinact/KI (REF. 214).
It is recommended that covalent compounds are 
ranked and optimized on the basis of their rate of on- 
target inactivation (Kinact/KI values) rather than solely on 
the basis of their half-maximal inhibitory concentra-
tion (IC50) values (equation 1)214,217. However, methods 
for tuning the rate of on-target inactivation for a given 
compound bearing an acrylamide warhead are limited, 
and efforts to generate the structure–activity relation-
ship (SAR) of a covalent series on the basis of Kinact/KI 
are often hindered by the time-consuming nature of the 
assays used to measure this parameter.
A novel approach to facilitate rapid development 
of kinetically selective covalent inhibitors was recently 
reported. In this approach, the acrylamide in the cova-
lent kinase inhibitor of interest is replaced with a fuma-
rate ester warhead218. The electrophilic fumarate ester 
reacts rapidly to form a covalent bond with the desired 
target (BTK); any remaining unreacted drug is metab-
olized by cellular carboxylesterases into an unreactive 
fumaric acid derivative, eliminating the potential for 
build-up of off-target cysteine labelling218. When applied 
to ibrutinib, this acrylamide replacement increased the 
initial on-target reactivity of the modified drug and 
maintained the kinetic BTK selectivity in cells over a 
24-hour time period218. By contrast, ibrutinib was shown 
to label significant amounts of the proteome under the 
same experimental conditions.
Another recently developed strategy to overcome 
irreversible off-target labelling is the development of 
warheads capable of undergoing a reversible cova-
lent interaction with the target protein213. Substituted 
cyano-acrylamides not only allow for improved covalent 
selectivity compared with their unsubstituted acryla-
mide counterparts, but also theoretically reduce the risk 
of haptenization as the ligand dissociates after unfold-
ing or proteolysis of the target219. The β-elimination rate 
of the Michael addition product can be tuned by chang-
ing the properties of the other cyano-acrylamide sub-
stituents220. These substituents can be designed to make 
additional noncovalent interactions with the target 
kinase, contributing to the molecule’s overall potency 
Nature Reviews | Drug Discovery
P + I PuI
KI Kinact
P-I (1)
(2)P + I
Kinact/KI
P-I
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and selectivity. Importantly, the t1/2 of the E1cB elimina-
tion of the inhibitor–β-mercaptoethanol (BME) adducts 
can be reliably predicted using density functional theory 
calculations of the proton affinity (ΔGaq) of the conjugate 
base (the α-carbanion), enabling rational design of drug 
residence times. Longer residence times promote kinetic 
selectivity and require lower exposures in vivo and are 
therefore often desirable in kinase inhibitors. Using a 
reversible covalent approach, Bradshaw et al.221 were able 
to generate BTK and fibroblast growth factor receptor 
(FGFR) inhibitors with prolonged and tunable in vivo 
residence times. Separately, Forster et al.222 used this 
technique to develop an exquisitely selective reversible 
covalent inhibitor of JAK3 with picomolar biochemical 
affinity and extended residence time.
Covalent docking campaigns (DOCKovalent)223 and 
reversible covalent fragment screens224 have also been 
successfully employed to find chemical leads and new 
kinase targets amenable to reversible covalent inhibi-
tion. In this manner, London et al.223 generated the first 
reported reversible covalent inhibitors of JAK3.
Identifying and expanding targetable residues. 
Bioinformatic studies estimate that up to one-third 
of human protein kinases