Bioorganic & Medicinal Chemistry Letters
Development of 2-(4-pyridyl)-benzimidazoles as PKN2 chemical tools to
probe cancer
Fiona Scotta, , Angela M. Falab,c, Lewis E. Pennicotta, Tristan D. Reuillona, Katlin B. Massirerb,c
,
Jonathan M. Elkinsd, Simon E. Warda,e
a Sussex Drug Discovery Centre, University of Sussex, Sussex House, Falmer, Brighton BN1 9RH, United Kingdom
b Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP
13083-875, Brazil
c Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
d Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
e Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
A R T I C L E I N F O
A B S T R A C T
Keywords:
Kinases are signalling proteins which have proven to be successful targets for the treatment of a variety of
diseases, predominantly in cancers. However, only a small proportion of kinases (< 20%) have been investigated
for their therapeutic viability, likely due to the lack of available chemical tools across the kinome. In this work
we describe initial efforts in the development of a selective chemical tool for protein kinase N2 (PKN2), a
relatively unexplored kinase of interest in several types of cancer. The most successful compound, 5, has a
measured IC50 of 0.064 μM against PKN2, with ca. 17-fold selectivity over close homologue, PKN1.
Kinases
Cancer
Heart failure
Inflammation
AGC kinase
PKN2
PRK2
Protein kinase N2
Benzimidazole
Chemical probe
Chemical tool
Chemical tools/probes are drug-like compounds used to answer
biological questions. They need not possess all the properties of a drug
candidate, which can be dialled in at a later point in the drug devel-
opment process. These compounds only need to be sufficiently stable,
kinome has been well-studied,5 and selective inhibitors are only
available for an even smaller fraction of those kinases.
Protein kinase N2 (PKN2) (Fig. 1) is one of these understudied ki-
more than 60 AGC protein kinases in the human genome with 14 fur-
ther classifications. PKN2 falls into the PKN sub-family, closely related
to the PKC sub-family, and is one of three homologues (PKN1/2/3). It
has a number of pseudonyms which include protein kinase C-related
kinase 2 (PRK2), PKNγ, PAK2, PRO2, and STK7.6
Historically, the approval of imatinib3 as an effective Abl kinase
inhibitor for treating chronic myeloid leukaemia stimulated efforts to
better understand the 518 human protein kinases and their role in
disease. Trends in research4 suggest that less than 20% of the human
Abbreviations: PKN, protein kinase N; Abl, Abelson murine leukemia viral oncogene; IC50, half maximal inhibitory concentration; AGC, protein kinase A/G/C
families; PKC, protein kinase C; PRK, protein kinase C-related kinase; PAK2, p21 activated kinase 2; PRO2, glutamate 5-kinase Pro2; STK, serine/threonine kinase;
PDB, protein databank; PARP, poly(ADP-ribose) polymerase; ChEMBL, European Molecular Biology Laboratory Chemical database; CLK, CDC2-like kinase; SAR,
structure activity relationship; CDI, 1,1′-carbonyldiimidazole; TR-FRET, time resolved fluorescence resonance energy transfer; THF, tetrahydrofuran; EtOH, ethanol;
HATU, hexafluorophosphate azabenzotriazole tetramethyl uronium; DIPEA, N,N-diisopropylethylamine; DCM, dichloromethane; AcOH, acetic acid; DMF, N,N-
dimethyl-formamide; KD, dissociation constant; Ki, inhibitor constant; NMR, nuclear magnetic resonance; DMSO, dimethyl sulfoxide; MeOH, methanol; GST, glu-
tathione S-transferase; DNA, deoxyribonucleic acid; SFM, scanning force microscopy; HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; TCEP, tris(2-
carboxyethyl)phosphine; EDTA, ethylenediaminetetraacetic acid; SDS, sodium dodecyl sulfate; PAGE, polyacrylamide gel electrophoresis; ATP, adenosine tripho-
sphate; EGTA, egtazic acid; CV, column volumes
⁎ Corresponding author.
Pleasecitethisarticleas:FionaScott,etal.,Bioorganic&MedicinalChemistryLetters,https://doi.org/10.1016/j.bmcl.2020.127040