Decarboxylative C–C and C–N Bond Formation by Ligand-Accelerated Iron Photocatalysis

Article abstract of DOI:10.1002/ejoc.201901381

The photoexcited state lifetimes of iron complexes are typically much shorter than those of iridium and ruthenium complexes. For that reason, iron complexes find less application in photochemical organic synthesis. Through iron photocatalysis, a mild and

Full text of DOI:10.1002/ejoc.201901381

Letter
pubs.acs.org/acsmedchemlett
Cite This: ACS Med. Chem. Lett. 2019, 10, 1260−1265
Structure Based Design of Potent Selective Inhibitors of Protein
Kinase D1 (PKD1)
Jianwen A. Feng,*,†,⊥ Patrick Lee,† Moulay Hicham Alaoui,† Kathy Barrett,† Georgette Castanedo,†
Robert Godemann,§ Paul McEwan,∥ Xiaolu Wang,§ Ping Wu,† Yamin Zhang,‡ Seth F. Harris,†
and Steven T. Staben*,†
†Genentech, 1 DNA way, South San Francisco, California 94080, United States
‡Pharmaron Beijing Co., Ltd. 6 Taihe Road, BDA, Beijing, P.R. China, 100176
§Evotec AG, Manfred Eigen Campus, Essener Bogen, Hamburg, Germany 22419
∥Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4Rz, U.K.
S
* Supporting Information
ABSTRACT: We previously disclosed a series of type I 1/2 inhibitors of NF-κB inducing kinase (NIK). Inhibition of NIK by
these compounds was found to be strongly dependent on the inclusion and absolute stereochemistry of a propargyl tertiary
alcohol as it forms critical hydrogen bonds (H-bonds) with NIK. We report that inhibition of protein kinase D1 (PKD1) by this
class of compounds is not dependent on H-bond interactions of this tertiary alcohol. This feature was leveraged in the design of
highly selective inhibitors of PKD1 that no longer inhibit NIK. A structure-based hypothesis based on the position and flexibility
of the α-C-helix of PKD1 vs NIK is presented.
KEYWORDS: Structure-based drug design, kinase inhibitor, PKD1 (protein kinase D1), NIK (NF-κB inducing kinase)
electivity remains a paramount challenge in the discovery
and development of novel kinase inhibitors. In over 20
II pharmacophores provide an opportunity to reach regions
with differential plasticity and lower sequence conservation
among kinases potentiating improved selectivity. The identi-
fication of inhibitors that fit the type I 1/2 pharmacophore is,
however, dependent on the steric size of the gatekeeper
residue.
S
years of kinase-directed drug discovery, researchers have used
numerous strategies to achieve sufficient selectivity for singular,
or families of, kinases.1,2 Among these strategies, differences in
the so-called gatekeeper residue3 are often exploited to achieve
improved selectivity for active site inhibitors. Selectivity against
off-target kinases with Phe or Tyr gatekeepers can be achieved
by designing ligands that sterically clash with those larger
residues. Polar or van der Waals contact withand/or
extension pastthe gatekeeper residue by a ligand can provide
enhanced selectivity in many cases.4,5 The importance of the
gatekeeper residue to kinase inhibitor binding is underscored
in drug-induced resistance mutations (i.e., EGFR T90M post
erlotinib treatment6 or Abl T315I post imatinib treatment7).
Kinase inhibitors that bind to the DFG-in form, extend from
the hinge past the gatekeeper residue, and interact with the
DFG backbone and acidic α-C-helix residue are colloquially
referred to as type I 1/2 kinase inhibitors (Figure 1a).3,4
Zuccotto and Angiolini3 postulate these hybrids of type I and
We4,5,8 and others,9 have published type I 1/2 inhibitors of
methionine gatekeeper kinases that include propargyl alcohol
substitution. Exemplified by a ligand bound crystal structure of
NIK (Figure 1b), an alkyne extends past the methionine
gatekeeper and presents a tertiary alcohol to donate an H-bond
to the conserved α-C-helix Glu and accept an H-bond from a
backbone N−H from the DFG-motif Phe. Potent and selective
inhibitors of several kinases including NIK,4,8 AKT10 (protein
kinase B), and PAK4/5/65 have been achieved through
Received: December 31, 2018
Accepted: July 24, 2019
Published: July 24, 2019
© 2019 American Chemical Society
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ability of these compounds to inhibit NIK was highly
dependent on the stereochemistry of the propargylic alcohol.
For example, the (R)-enantiomers of 1 and 2 maintained
strong inhibition of NIK while the (S)-enantiomers lost >80-
fold inhibitory potency. This stereodependent activity is readily
rationalized through analysis of ligand soaked X-ray structures:
key H-bond interactions of the tertiary alcohol and positioning
of the heterocycle in the back pocket can only be
accommodated by the (R)-enantiomer (vide infra). Of interest
to the current study however, inhibitory activity against specific
counter target PKD1 was not as strongly dependent on
stereochemistry. For example, only an ∼3-fold loss in PKD1
potency was observed between (R)- and (S)-2.
This observation persisted with different propargyl alcohol
substitution and was not specific to these subseries (select
examples are shown in Table 2). Inhibitors bearing 2-methyl-5-
Table 2. NIK and PKD1 Inhibition by Small Molecules with
Common 5-Methyloxazol-2-yl Propargyl Alcohol
Substitution
Figure 1. 2D and 3D representations of murine NIK with an inhibitor
bound (PDB ID: 5T8O). (a) Schematic representation of an
exemplar type I 1/2 kinase inhibitor. Gray dashed lines represent
the ligand binding site. Green and blue arrows indicate ligand-protein
hydrogen bonds. The inhibitor occupies the AP front subpocket,
extends past the gatekeeper residue occupying the BP−I-B subpocket,
and interacts with the acidic residue of the α-C-helix and a DFG-
backbone N−H in the BP-II_in subpocket. Pocket nomenclature
follows that of the KLIFS database.2 (b) X-ray structure of murine
NIK and a propargyl alcohol containing type I 1/2 inhibitor.4
utilization of this propargyl alcohol-driven pharmacophore.
Herein we report that inhibition of PKD1 by this class of small
molecules, in sharp contrast to other Met-gatekeeper kinases,
does not require the tertiary alcohol. This somewhat unique
characteristic was utilized in a structure-based design effort to
discover highly selective inhibitors of PKD1.
a
We previously disclosed4 several subseries of NIK inhibitors
exemplified by compounds 1 and 2 (Table 1). We found the
See Supporting Information for assay experimental details.
oxazolyl substituted propargyl alcohols were found to be
stronger inhibitors of PKD1 compared to NIK; the (S)-
enantiomers demonstrating highest selectivity for PKD1
derived from steep loss of potency for NIK. Compound (S)-
3 was determined to have a NIK Ki > 1250 nM and a PKD1 Ki
= 4.2 nM, a selectivity ratio of >298. Structurally distinct
benzimidazole 4 displayed similar enantioselective behavior;
(R)-4 was very selective for NIK while (S)-4 was moderately
selective for PKD1. Comparing (S)-3 with (S)-4, bridged
bicycle series possessed a clear advantage over benzimidazoles
in terms of selectivity for PKD1.
Introduction of a cyclopropyl group in the 3 position of the
imidazole ring within this series further improves PKD1
inhibitory activity (Table 3). Compounds (R)-5 and (R)-6
were determined to have PKD1 Ki values of 5.9 nM and <0.2
nM, respectively. We hypothesize the >30-fold decrease in
PKD1 Ki is a result of favorable van der Waals interactions with
a leucine residue in the P-loop of PKD1 as the lipophilic ligand
Table 1. NIK and PKD1 Inhibition by Enantiomeric Pairs of
Small Molecules
NIK ADP FP
PKD1 ADP FP NIK ADP FP Ki/PKD1
a
a
Compound
Ki(nM)
Ki(nM)
ADP FP Ki
(R)-1
(S)-1
(R)-2
(S)-2
0.8
582
3.1
0.9
65
4.9
14
0.9
9
0.6
>18
>250
a
See Supporting Information for assay experimental details
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Table 3. A Cyclopropyl Group Improves PKD1 Activity but
Is Potency Neutral for NIK
NIK ADP
Compound FP Ki(nM)
PKD1 ADP
PKD1 NIK Ki/
a
a
FP Ki(nM)
LogDpH7.4
LLE
PKD1 Ki
(R)-5
(R)-6
1.0
1.7
5.9
<0.2
3.3
3.7
4.9
>6.1
0.17
>8.5
a
See Supporting Information for assay experimental details
efficiency (LLE)11 for (R)-6 improved from 4.9 to >6.1(Figure
2). We believe that potency improvements were not observed
Figure 2. Model of (R)-6 bound to a homology model of PKD1
where a cyclopropyl group interacts with a leucine on the P-loop of
PKD1. Corresponding leucine residue in NIK is flexible.
in NIK because the corresponding Leu406 residue is flexible
and adopts multiple conformations as observed in human NIK
crystal structures (4DN5, 4G3D, 4IDT, 4IDV).12,8
Figure 3. (a) X-ray structure of compound (R)-7 in mNIK (PDB ID:
6MYN). (b) Expanded image of (a) showing the interaction of the
propargyl alcohol with Glu442 and Phe537. In the apo structure
(PDB ID: 4G3C), Glu442 and Phe537 interact with a water molecule
(labeled displaced water) that would be presumably displaced by
compound (R)-7 and similar analogs. Model of the (S)-enantiomer
swaps positions of methyl and hydroxyl groups resulting in the
inability to maintain these hydrogen bonds.
Compound (R)-7, a 14 nM NIK inhibitor, was soaked into
murine NIK, and the X-ray structure was solved at 2.74 Å
resolution (PDB ID: 6MYN). Modest ligand density was
sufficient to describe the binding mode but did indicate partial
ligand occupancy, refined to ∼0.6 and 0.7 in the two copies
present in the crystallographic asymmetric unit. The binding
mode was as expected based on observations for similar
compounds:4 the primary amide interacting with the hinge
residues Leu474 and Glu472, the alkyne projecting past the
Met471 gatekeeper, the isoxazole occupying a hydrophobic
pocket between the α-C-helix and gatekeeper, and the tertiary
alcohol making the key donor/acceptor interactions consistent
with type I1/2 description (Figure 3a). Of note is the position
of the tertiary alcohol that is hypothesized to replace a key
water observed in a 2.15 Å apo-structure (Figure 3b, apo
structure in gray, PDB ID: 4G3C).4,8,9 A model of the (S)-
enantiomer indicates swapping of methyl and hydroxyl groups
results in the inability of the ligand to form key hydrogen
bonding interactions with NIK. We believe these results to be
consistent with observed enantioselective NIK inhibition.
Based on the above models and enantiomer-dependent SAR
for PKD1, we hypothesized ligands absent of the tertiary
alcohol would inhibit PKD1 but not NIK. While 1-alkynyl-1-
cyclopentanol 8 was similarly active against PKD1 and NIK,
deletion of the hydroxyl as in 1-alkynylcyclopentane 9 resulted
in a large loss in affinity for NIK (>125-fold) but not PKD1
(<2-fold) (Table 4). The drastic loss of potency against NIK
Table 4. Influence of Hydroxyl Removal on Inhibition of
NIK and PKD1
NIK ADP FP
PKD1 ADP FP NIK ADP FP Ki/ PKD1
a
a
Compound
Ki(nM)
Ki(nM)
25
ADP FP Ki
0.4
8 (R =
OH)
10
9 (R = H)
>1250
44
>28
a
See Supporting Information for assay experimental details.
for 9 is striking compared to 8 especially given the increased
lipophilicity (cLogD7.4 4.0, 2.8, respectively): the LLE drops
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ACS Medicinal Chemistry Letters
Letter
from 5.2 to <1.9, pointing to the importance of mimicking a
key water molecule with a hydroxyl function group for NIK.8
Molecular modeling and SAR suggested that the hydroxyl
could be directly replaced by a methyl group.
Analogs 10 and 11 combined 2-methyl-5-oxazolyl sub-
stitution and replaced the tertiary hydroxyl with a methyl
group (Table 5). Introduction of a secondary amide group in
analogs 10 and 11 were among the most potent for PKD1 and
highly selective over NIK (PKD1 Ki < 0.2 nM; NIK Ki > 1250
nM; > 6250-fold selective, Table 5). Replacing the tertiary
hydroxyl group is critical for selectivity over NIK.
Compound (S)-12 was tested in a panel of kinases at
Invitrogen at 0.1 μM, a concentration >500-fold its measured
PKD1 Ki, and was found to be highly selective for PKD1.
Among the 220 kinases tested, only PKD1 was inhibited at
>30% (see Supporting Information for details). Included in
this panel were a number of kinases bearing a methionine
gatekeeper, none of which were strongly inhibited (i.e., AKT1,
4% inhibition; JAK1, 1%; Map4K4, 21%; Mink1, 20%; PAK4,
7%). Selectivity over NIK can be attributed to S stereo-
chemistry of the tertiary alcohol as it is geometrically prevented
from forming hydrogen bonds with Glu442 and Phe537.
Compound 11 had equally exquisite kinase selectivity where
Aurora B was the only off-target inhibited at greater than 40%.
Compound 10 was also very selective when tested in the same
panel at 0.1 μM concentration, most notably inhibiting
Map4K4 (57%), Mink1 (51%), and Aurora B (45%) in
addition to PKD1.
Table 5. Influence of Hydroxyl to Methyl Substitution and
Imidazole Substitution on Inhibition of NIK and PKD1
NIK ADP FP
PKD1 ADP FP NIK ADP FP Ki/ PKD1
a
a
Compound
Ki(nM)
Ki(nM)
ADP FP Ki
10
11
(S)-12
>1250
>1250
>1250
<0.2
<0.2
<0.2
>6250
>6250
>6250
a
See Supporting Information for assay experimental details
We sought to understand the molecular basis of the PKD1
versus NIK selectivity for ligands such as 10−12. An X-ray
structure of PKD1 has not been published. However,
compound 10 possesses some affinity for Map4K4 (57%
inhibition at 0.1 μM) and, having similarity in a longer β3-αC
helix loop length (vide infra), we believed a Map4K4 structure
might provide improved understanding of potential binding
modes of these compounds in PKD1.13 An X-ray structure of
10 (2.3 Å resolution, PDB ID: 5W5Q) is displayed in Figure
4a. As expected, the amide group forms two H-bond
interactions with Map4K4’s kinase hinge residues. The alkynyl
linker projects an oxazole group that occupies a hydrophobic
pocket partly formed by the gatekeeper methionine. Unlike
propargyl alcohol-containing NIK inhibitors, compound 10
lacks a hydroxyl group that can form hydrogen bonds with the
conserved Phe backbone NH or α-C helix Glu.4 In fact, the
MAP4K4 α-C helix is in the kinase inactive “out” position,
further supporting our hypothesis that PKD1 inhibitors do not
need a H-bonding hydroxyl group to achieve high affinity.
Figure 4b shows an overlay of compound 7 bound to NIK
(green) and compound 10 bound to Map4K4 (brown). Near
perfect overlay of compounds 7 and 10 in the respective NIK
and Map4K4 structures indicates consistent binding modes
relative to the kinase hinge and general ATP pocket. A striking
difference is observed, however, in the outward shift of
Map4K4’s α-C helix that explains compound 10’s selectivity
profile. The length of the β3-αC loop that precedes the α-C
helix has been observed to affect α-C helix position and
mobility, and hence kinase activity and sensitivity to certain
classes of inhibitors.14 Longer loops, as measured by the
number of residues between the conserved catalytic lysine and
the acidic Glu on helix C (e.g., 16, 17, or 14 as observed in
EGFR, RAF, or SrcA/B family kinases, respectively), allow
outward helix C positions and accommodate larger type II
kinase inhibitors, while deletions of ∼5 residues in these loops
favor α-C helix “in” conformations making the mutant kinases
more active and resistant to the larger inhibitors. The NIK α-C
helix is constrained by both a short β3−αC loop (11 residues)
and the presence of an unusual additional amino terminal helix
that packs against and stabilizes the α-C helix-“in” feature.
Consistent with shorter loop examples,14 NIK is a
constitutively active kinase and has reduced affinity for
compound 10 improved both NIK and PKD1 potency by
forming an internal H-bond with the hinge binding amide (2.7
Å), potentially reducing electrostatic repulsion between
primary amide carbonyl and protein backbone carbonyl
(Figure 4a). Compounds 11 and 12 contain cyclopropyl
imidazole substitutions to improve PKD1 activity. Achiral
Figure 4. (a) X-ray structure of 10 bound to Map4K4 (PDB ID:
5W5Q). The primary amide in 10 forms expected H-bonding
interactions with the Map4K4 kinase hinge. Gem-dimethyl groups
cannot form H-bonds with the conserved Phe in DFG or Glu in α-C
helix. (b) X-ray structure of compound 7 in mNIK (PDB ID: 6MYN)
overlaid with compound 10 in Map4K4. Map4k4 adopts an α-C helix
out conformation while NIK maintains an α-C helix in conformation.
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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
■
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.
REFERENCES
■
(1) Davis, M. I.; Hunt, J. P.; Herrgard, S.; Ciceri, P.; Wodicka, L. M.;
Pallares, G.; Hocker, M.; Treiber, D. K.; Zarrinkar, P. P.
Comprehensive Analysis of Kinase Inhibitor Selectivity. Nat.
Biotechnol. 2011, 29 (11), 1046−1051.
(2) van Linden, O. P. J.; Kooistra, A. J.; Leurs, R.; de Esch, I. J. P.; de
Graaf, C. KLIFS: a Knowledge-Based Structural Database to Navigate
Kinase−Ligand Interaction Space. J. Med. Chem. 2014, 57 (2), 249−
277.
(3) Zuccotto, F.; Ardini, E.; Casale, E.; Angiolini, M. Through the
“Gatekeeper Door”: Exploiting the Active Kinase Conformation. J.
Med. Chem. 2010, 53 (7), 2681−2694.
(4) Castanedo, G. M.; Blaquiere, N.; Beresini, M.; Bravo, B.;
Brightbill, H.; Chen, J.; Cui, H.-F.; Eigenbrot, C.; Everett, C.; Feng, J.;
Godemann, R.; Gogol, E.; Hymowitz, S.; Johnson, A.; Kayagaki, N.;
Kohli, P. B.; Knuppel, K.; Kraemer, J.; Kruger, S.; Loke, P.; McEwan,
̈ ̈
P.; Montalbetti, C.; Roberts, D. A.; Smith, M.; Steinbacher, S.;
Sujatha-Bhaskar, S.; Takahashi, R.; Wang, X.; Wu, L. C.; Zhang, Y.;
Staben, S. T. Structure-Based Design of Tricyclic NF-κB Inducing
Kinase (NIK) Inhibitors That Have High Selectivity Over
Phosphoinositide-3-Kinase (PI3K). J. Med. Chem. 2017, 60 (2),
627−640.
ASSOCIATED CONTENT
* Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acsmedchem-
lett.8b00658.
■
S
(5) Staben, S. T.; Feng, J. A.; Lyle, K.; Belvin, M.; Boggs, J.; Burch, J.
D.; Chua, C.-C.; Cui, H.; DiPasquale, A. G.; Friedman, L. S.; Heise,
C.; Koeppen, H.; Kotey, A.; Mintzer, R.; Oh, A.; Roberts, D. A.;
Rouge, L.; Rudolph, J.; Tam, C.; Wang, W.; Xiao, Y.; Young, A.;
Zhang, Y.; Hoeflich, K. P. Back Pocket Flexibility Provides Group II
P21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase
Inhibitors. J. Med. Chem. 2014, 57 (3), 1033−1045.
Details of PKD1 enzyme inhibition assay, crystallog-
raphy, kinase selectivity for compounds 10, 11, and (S)-
12, synthetic procedures, and analytical data (PDF)
(6) Bell, D. W.; Gore, I.; Okimoto, R. A.; Godin-Heymann, N.;
Sordella, R.; Mulloy, R.; Sharma, S. V.; Brannigan, B. W.; Mohapatra,
G.; Settleman, J.; Haber, D. A. Inherited Susceptibility to Lung
Cancer May Be Associated with the T790M Drug Resistance
Mutation in EGFR. Nat. Genet. 2005, 37 (12), 1315−1316.
(7) Shah, N. P.; Tran, C.; Lee, F. Y.; Chen, P.; Norris, D.; Sawyers,
C. L. Overriding Imatinib Resistance with a Novel ABL Kinase
Inhibitor. Science 2004, 305 (5682), 399−401.
(8) de Leon-Boenig, G.; Bowman, K. K.; Feng, J. A.; Crawford, T.;
Everett, C.; Franke, Y.; Oh, A.; Stanley, M.; Staben, S. T.; Starovasnik,
M. A.; Wallweber, H. J. A.; Wu, J.; Wu, L. C.; Johnson, A. R.;
Hymowitz, S. G. The Crystal Structure of the Catalytic Domain of the
AUTHOR INFORMATION
Corresponding Authors
*Jianwen A. Feng, jw.a.feng@gmail.com.
*Steven T. Staben, stevents@gene.com.
■
ORCID
Jianwen A. Feng: 0000-0003-1221-7605
Steven T. Staben: 0000-0002-6137-6517
Present Address
⊥Denali Therapeutics Inc., 161 Oyster Point Blvd, South San
Francisco, CA 94080.
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Letter
NF-ΚB Inducing Kinase Reveals a Narrow but Flexible Active Site.
Structure 2012, 20 (10), 1704−1714.
(9) Li, K.; McGee, L. R.; Fisher, B.; Sudom, A.; Liu, J.; Rubenstein,
S. M.; Anwer, M. K.; Cushing, T. D.; Shin, Y.; Ayres, M.; Lee, F.;
Eksterowicz, J.; Faulder, P.; Waszkowycz, B.; Plotnikova, O.; Farrelly,
E.; Xiao, S.-H.; Chen, G.; Wang, Z. Inhibiting NF-κB-Inducing Kinase
(NIK): Discovery, Structure-Based Design, Synthesis, Structure−
Activity Relationship, and Co-Crystal Structures. Bioorg. Med. Chem.
Lett. 2013, 23 (5), 1238−1244.
(10) Rouse, M. B.; Seefeld, M. A.; Leber, J. D.; McNulty, K. C.; Sun,
L.; Miller, W. H.; Zhang, S.; Minthorn, E. A.; Concha, N. O.;
Choudhry, A. E.; Schaber, M. D.; Heerding, D. A. Aminofurazans as
Potent Inhibitors of AKT Kinase. Bioorg. Med. Chem. Lett. 2009, 19
(5), 1508−1511.
(11) Leeson, P. D.; Springthorpe, B. The Influence of Drug-Like
Concepts on Decision-Making in Medicinal Chemistry. Nat. Rev.
Drug Discovery 2007, 6 (11), 881−890.
(12) Liu, J.; Sudom, A.; Min, X.; Cao, Z.; Gao, X.; Ayres, M.; Lee, F.;
Cao, P.; Johnstone, S.; Plotnikova, O.; Walker, N.; Chen, G.; Wang,
Z. Structure of the Nuclear Factor B-Inducing Kinase (NIK) Kinase
Domain Reveals a Constitutively Active Conformation. J. Biol. Chem.
2012, 287 (33), 27326−27334.
(13) Crawford, T. D.; Ndubaku, C. O.; Chen, H.; Boggs, J. W.;
Bravo, B. J.; DeLaTorre, K.; Giannetti, A. M.; Gould, S. E.; Harris, S.
F.; Magnuson, S. R.; McNamara, E.; Murray, L. J.; Nonomiya, J.;
Sambrone, A.; Schmidt, S.; Smyczek, T.; Stanley, M.; Vitorino, P.;
Wang, L.; West, K.; Wu, P.; Ye, W. Discovery of Selective 4-Amino-
Pyridopyrimidine Inhibitors of MAP4K4 Using Fragment-Based Lead
Identification and Optimization. J. Med. Chem. 2014, 57 (8), 3484−
3493.
̈
(14) Foster, S. A.; Whalen, D. M.; Ozen, A.; Wongchenko, M. J.;
Yin, J.; Yen, I.; Schaefer, G.; Mayfield, J. D.; Chmielecki, J.; Stephens,
P. J.; Albacker, L. A.; Yan, Y.; Song, K.; Hatzivassiliou, G.; Eigenbrot,
C.; Yu, C.; Shaw, A. S.; Manning, G.; Skelton, N. J.; Hymowitz, S. G.;
Malek, S. Activation Mechanism of Oncogenic Deletion Mutations in
BRAF, EGFR, and HER2. Cancer Cell 2016, 29 (4), 477−493.
(15) Sundram, V.; Chauhan, S. C.; Jaggi, M. Emerging Roles of
Protein Kinase D1 in Cancer. Mol. Cancer Res. 2011, 9 (8), 985−996.
(16) Meredith, E. L.; Beattie, K.; Burgis, R.; Capparelli, M.; Chapo,
J.; DiPietro, L.; Gamber, G.; Enyedy, I.; Hood, D. B.; Hosagrahara, V.;
Jewell, C.; Koch, K. A.; Lee, W.; Lemon, D. D.; McKinsey, T. A.;
Miranda, K.; Pagratis, N.; Phan, D.; Plato, C.; Rao, C.; Rozhitskaya,
O.; Soldermann, N.; Springer, C.; van Eis, M.; Vega, R. B.; Yan, W.;
Zhu, Q.; Monovich, L. G. Identification of Potent and Selective
Amidobipyridyl Inhibitors of Protein Kinase D. J. Med. Chem. 2010,
53 (15), 5422−5438.
(17) Hao, Q.; Wang, L.; Tang, H. Vascular Endothelial Growth
Factor Induces Protein Kinase D-Dependent Production of
Proinflammatory Cytokines in Endothelial Cells. AJP: Cell Physiology
2009, 296 (4), C821−C827.
1265
DOI: 10.1021/acsmedchemlett.8b00658
ACS Med. Chem. Lett. 2019, 10, 1260−1265