ACS Medicinal Chemistry Letters
Letter
Author Contributions
compounds such as 10 that fit poorly in α-C helix in
conformations. Map4K4 and PKD1 meanwhile have longer
β3−αC loops (15 and 18 residues, respectively). We
hypothesize the longer loop imparts less energetic barrier to
helix C out conformations and is reflected in better binding
affinity for compound 10.
Compounds 10−12 are exquisitely selective and highly
potent PKD1 inhibitors, making them potentially valuable tool
compounds to interrogate PKD1 biology in immunology,
oncology, and cardiology.15−17 They also have reasonable in
vitro ADME properties (Table 6). For example, compound
(S)-12 is predicted to have moderate in vivo clearance given its
low measured logD and moderate liver microsomal clearance
in human and rat.
The manuscript was written through contributions of all
authors. All authors have given approval to the final version of
the manuscript.
Notes
The authors declare the following competing financial
interest(s): JAF is an employee and stockholder for Denali.
MHA, KB, NB, GC, PW, SFH, and STS are employees and
stockholders for Roche.
ACKNOWLEDGMENTS
■
We thank the Genentech purification and analytical groups for
support. We acknowledge the use of synchrotron X-ray source
SSRL supported by the Department of Energy’s (DOE) Office
of Science, Office of Biological and Environmental Research,
and the National Institutes of Health (NIH). The authors
thank the staff at Diamond Light Source beamline I04-1 and
Stanford Synchrotron Radiation Light Source beamline 12-2.
Table 6. In Vitro ADME Properties of PKD1 Inhibitors
Kinetic
Solubility
LM stability
(mL/min/kg) H/R/M
Permeability A to
B/B to A
LogD
pH7.4
10
11
(S)-
12
3.7
4.4
2.0
13 μM
35 μM
124 μM
18/26/74
19/45/84
9.5/35/78
19.3/14.9
13.8/14.1
7.1/16.0
ABBREVIATIONS
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PKD1,protein kinase D1; AKT,protein kinase B; PAK,p21-
activated kinase; NIK,NF-κB inducing kinase; LLE,ligand
lipophilic efficiency (pIC50 − LogD).
In conclusion, we discovered a series of highly selective
PKD1 inhibitors that exhibit subnanomolar biochemical
potency. These pseudo type I1/2 inhibitors derive their
selectivity by extending past the methionine gatekeeper and
favoring kinases that can adopt α-C-helix “out” conformations.
Type I1/2 kinase inhibitors interact with a conserved α-C-helix
glutamate residue, therefore requiring the helix C “in”
conformation. The crystal structure of compound 10 bound
to surrogate kinase Map4K4 shows it adopting a helix C “out”
conformation. The novel combination of extending past the
gatekeeper residue and requiring helix C “out” conformation
provides structural rationale for the observed exquisite
selectivity of compounds 10−12. Given successful generation
of selective inhibitors of several methionine gatekeeper kinases
(PKD1, NIK, AKT, PAKs) utilizing an alkyne-driven binding
mode, we believe this could be a generalizable strategy for
generating tool compounds of methionine gatekeeper kinases.
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ASSOCIATED CONTENT
* Supporting Information
The Supporting Information is available free of charge on the
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AUTHOR INFORMATION
Corresponding Authors
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ORCID
Present Address
⊥Denali Therapeutics Inc., 161 Oyster Point Blvd, South San
Francisco, CA 94080.
1264
ACS Med. Chem. Lett. 2019, 10, 1260−1265