Core Replacements in a Potent Series of VEGFR-2 Inhibitors and Their Impact on Potency, Solubility, and hERG

Article abstract of DOI:10.1021/acsmedchemlett.6b00018

Anti-VEGF therapy has been a clinically validated treatment of age-related macular degeneration (AMD). We have recently reported the discovery of indole based oral VEGFR-2 inhibitors that provide sustained ocular retention and efficacy in models of wet-AMD. We disclose herein the synthesis and the biological evaluation of a series of novel core replacements as an expansion of the reported indole based VEGFR-2 inhibitor series. Addition of heteroatoms to the existing core and/or rearranging the heteroatoms around the 6-5 bicyclic ring structure produced a series of compounds that generally retained good on-target potency and an improved solubility profile. The hERG affinity was proven not be dependent on the change in lipophilicity through alteration of the core structure. A serendipitous discovery led to the identification of a new indole-pyrimidine connectivity: from 5-hydroxy to 6-hydroxyindole with potentially vast implication on the in vitro/in vivo properties of this class of compounds.

Full text of DOI:10.1021/acsmedchemlett.6b00018

Subscriber access provided by Purdue University Libraries
Letter
Core Replacements in a Potent Series of VEGFR-2
Inhibitors and Their Impact on Potency, Solubility and hERG
Nello Mainolfi, James Powers, Erik L Meredith, Jason Elliott, Karl
G Gunderson, Stephen Poor, Fang Liu, and Karen Anderson
ACS Med. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/acsmedchemlett.6b00018 • Publication Date (Web): 16 Mar 2016
Downloaded from http://pubs.acs.org on March 18, 2016
Just Accepted
“Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted
online prior to technical editing, formatting for publication and author proofing. The American Chemical
Society provides “Just Accepted” as a free service to the research community to expedite the
dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts
appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been
fully peer reviewed, but should not be considered the official version of record. They are accessible to all
readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered
to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published
in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just
Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor
changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers
and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors
or consequences arising from the use of information contained in these “Just Accepted” manuscripts.
ACS Medicinal Chemistry Letters is published by the American Chemical Society. 1155
Sixteenth Street N.W., Washington, DC 20036
Published by American Chemical Society. Copyright © American Chemical Society.
However, no copyright claim is made to original U.S. Government works, or works
produced by employees of any Commonwealth realm Crown government in the course
of their duties.

Page 1 of 7
ACS Medicinal Chemistry Letters
1
2
3
4
5
6
7
8
9
Core Replacements in a Potent Series of VEGFR-2 Inhibitors and
Their Impact on Potency, Solubility and hERG
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Nello Mainolfi,*,a,† James Powers,*,a Erik Meredith,a Jason Elliott,a Karl G. Gunderson,a Stephen Poor,b Fang Liu,b Karen Anderꢀ
sonb
a Novartis Institutes for Biomedical Research, Global Discovery Chemistry, 100 Technology Square, Cambridge, MA, 02139
USA; b Novartis Institutes for Biomedical Research, Ophthalmology, 500 Technology Square, Cambridge, MA, 02139 USA.
KEYWORDS: Vascular Endothelial Growth Factor Receptor 2, VEGF, KDR, bicyclic core, scaffold morphing, AMD.
ABSTRACT: Anti VEGF therapy has been a clinically validated treatment of age related macular degeneration (AMD). We have
recently reported the discovery of indole based oral VEGFRꢀ2 inhibitors that provide sustained ocular retention and efficacy in
models of wetꢀAMD. We disclose herein the synthesis and the biological evaluation of a series of novel core replacements as an
expansion of the reported indole based VEGFRꢀ2 inhibitor series. Addition of heteroatoms to the existing core and/or rearranging
the heteroatoms around the 6ꢀ5 bicyclic ring structure produced a series of compounds that generally retained good onꢀtarget potenꢀ
cy and an improved solubility profile. The hERG affinity was proven not be dependent on the change in lipophilicity through alteraꢀ
tion of the core structure. A serendipitous discovery led to the identification of a new indoleꢀpyrimidine connectivity: from 5ꢀ
hydroxy to 6ꢀhydroxyindole with potentially vast implication on the in vitro/in vivo properties of this class of compounds.
The current approved therapies for the treatment of wet or
Previously
Discussed
"allosteric pocket"
binding region
neovascular AMD are the antiꢀVEGFꢀA antibody ranibiꢀ
zumab, the antiꢀVEGFꢀA aptamer pegaptanib, and the antiꢀ
VEGFꢀA trap fusion protein aflibercept. Each of these wetꢀ
AMD treatments must be delivered by intravitreal injections
and sixty percent of patients do not experience a clinically
significant gain of visual acuity (≥15 letters).1 Based on this
we have envisioned an opportunity for orally available inhibiꢀ
tor of the receptor tyrosine kinase (RTK) VEGFRꢀ2 (KDR,
Fltꢀ1) to provide an alternative wetꢀAMD treatment paradigm.
The role of VEGFꢀA in the regulation of angiogenesis is well
established and although new vessel growth and maturation
are highly complex processes, requiring the sequential activaꢀ
tion of a series of receptors by numerous ligands, VEGFꢀA
signaling often represents a critical rateꢀlimiting step.2 VEGFꢀ
A promotes growth of vascular endothelial cells and is also
known to induce vascular leakage. Ocular VEGFꢀA levels are
increased in neovascular diseases of the retina such as neovasꢀ
cular AMD.3,4
O
N
O
HN
HN
N
N
"hinge" binding region
1
O
N
core replacements
Baf3-KDR IC50 = 0.003 uM
HT-Sol (pH 6.8) = 18 uM
hERG IC50 = 28 uM
1
Discussed
Herein
Figure 1. Representative example (1) of previously reported inꢀ
dole pyrimidine scaffold.5
We decided to investigate how, the introduction of heteroaꢀ
toms (especially nitrogens) in the 6ꢀ5 bicyclic aromatic system
would impact its potency against VEGFRꢀ2, aqueous solubiliꢀ
ty at pH 6.8, and hERG channel activity. In order to facilitate
interpretation of the data the pyrimidine and the urea moieties
were mostly kept constant in the selection of compounds preꢀ
sented herein (Figure 1).
We have recently disclosed the medicinal chemistry efforts
around the indoleꢀpyrimidine series of VERGRꢀ2 inhibitors5
where several approaches were taken towards modulation of
onꢀtarget potency, solubility, pk, and in vivo efficacy. This
was accomplished by focusing on the optimization of the two
extremities of the molecules: the urea and the pyrimidine.5
Herein, we focus on the modification/replacement of the inꢀ
dole core and discuss how those changes modulate in vitro
potency, solubility, and hERG activity (Figure 1).
Introducing heteroatoms in flat aromatic rings is often used
to reduce lipophilicity hence improve aqueous solubility, reꢀ
duce hERG activity,6ꢀ16 and generally enhance the overall deꢀ
velopability profile of drug candidates.17,18
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Page 2 of 7
a
CHEMISTRY
Reagents and conditions: (a) 7 (3 eq.), EtOH, 72 °C, 3h;
1
2
3
4
5
6
7
8
(b) 9 (1.5 eq.), PyBOP (1.3 eq.), DBU (4 eq.), CH3CN, 60 °C,
3h; (c) LiOH (40 eq.), THF/H2O (1:1), rt; (d) oxalyl chloride
(1.5 eq.), DMF (cat.), DCM, 0 °C then 12 (8 eq.), pyridine (20
eq.), rt, overnight; (e) DCM/TFA (1:1), 1h.
The synthetic strategy to access most of the compounds in
this class of VEGFRꢀ2 inhibitors entails a condensation beꢀ
tween hydroxy indole core 4 and chloropyrimidine 5 (Scheme
1) in addition to a urea formation reaction between the indole
NH and an activated carbamate like 2. A conceptually similar
overall synthetic plan was used for the synthesis of the new
core structures presented below.
The more unique core structure present in the VEGFRꢀ2 inꢀ
hibitor 20 (Scheme 3), was prepared starting from the hydroxy
pyridine 14. Transient protection of the phenolic OH was used
to facilitate the deprotonation and subsequent functionalization
of the pyridyl 2ꢀmethyl group to afford ester 16. After PyBOP
mediated coupling20 with pyrimidine 9, intermediate 17 was
condensed with 2ꢀchloroacetaldehyde in presence of a weak
base (NaHCO3) to give pyrrolopyridine 18.21 Trimethylalumiꢀ
num mediated transꢀamidation with pyrazole 19 followed by
deprotection afforded the wanted final compound 20. Unfortuꢀ
nately, amide formation did not proceed well when aminoꢀ
isoxazole 12 was used in place of aminoꢀpyrazole 19.
Scheme 1. Retrosynthetic scheme to access compounds 1.5
Replacements of hydroxy indole 4 will be discussed herein.
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
O
N
O
N
O
BocN
O
HN
O
HN
H
O
N
HN
N
N
N
+
O
N
Scheme 3. Synthesis of pyrrolopyridine 18 and its use in the
synthesis of VEGFRꢀ2 inhibitor 20.a
N
3
1
2
O
O
BocN
b
a
N
+
N
N
N
60%
quant.
O
O
N
H
9
OH
OH
BocN
Cl
Si
16
H
14
N
N
+
15
OH
N
O
O
O
4
BocN
O
BocN
O
O
5
c
d
N
N
55%
50%
N
N
N
N
The imidazopyridine core, present in 13 (Scheme 2), was
formed by simple condensation of aminopyridine 6 and chloꢀ
roaldehyde 7 to give the desired core 8.19 Hydroxyꢀimidazo
pyridine 8 was coupled with pyrimidinone 9 using modified
peptide coupling conditions (PyBOP, DBU)20 to give intermeꢀ
diate 10. After basic hydrolysis of the ethyl ester, the isoxazole
amide was formed using standard conditions. The desired
novel compound 13 was obtained after final Boc removal usꢀ
ing a mixture of DCM and TFA.
18
17
H
N
HN
N
N
O
HN
O
HN
H2N
e,
19
then f, 50%
N
N
N
20
a Reagents and conditions: (a) tBuMe2SiCl (1 eq.), imidazole
(2 eq.), DCM, 0 °C to rt, 2 h; (b) LDA (4 eq.), dimethyl carꢀ
bonate (4.1 eq.), ꢀ 78 °C, 1h, then 1N HCl in ether (1 eq.),
MeOH, rt; (c) same as (b) in Scheme 2; (d) 2ꢀ
chloroacetaldehyde (10 eq.), NaHCO3 (6 eq.), acetone, 70 °C,
overnight; (e) 19 (20 eq.), Me3Al (20 eq.), toluene, 100 °C, 8
h; (f) DCM/TFA (1:1), 0 °C, 2 h.
Scheme 2. Synthesis of imidazopyridine 8 and its use in the
synthesis of VEGFRꢀ2 inhibitor 13.a
O
BocN
OH
O
O
O
a
N
N
+
+
O
H
60%
O
N
H
N
H2N
N
OH
Cl
8
9
7
6
Azaindole core 23 (Scheme 4) was accessed using the wellꢀ
established nucleophilic addition to pyridine Nꢀoxides.22ꢀ27
Interestingly, it was found that if pyridine Nꢀoxide 22 was
heated to reflux in acetic anhydride, a meta addition of the
acetate group was observed leading, after deprotection, to the
initially undesired azaindole 24. In order to access the desired
azaindole 23, treatment with TFAA at rt was found to be the
optimal reaction condition. Transformation of 23 and 24 to
their respective final compounds 25 and 26 was achieved folꢀ
lowing the same protocols as reported in reference 5 for comꢀ
pound 1.
O
O
BocN
O
O
BocN
O
HO
c
b
55%
N
N
N
N
quant.
N
N
N
N
10
11
O
N
O
N
O
HN
HN
d, H2N
12
then e, 60%
N
N
Indazole 27 and azaindole 28 (in Table 1) were accessed
starting respectively from commercially available 1Hꢀ
pyrrolo[2,3ꢀb]pyridinꢀ5ꢀol (CAS: 98549ꢀ88ꢀ3) and 1Hꢀ
indazolꢀ5ꢀol (CAS: 15579ꢀ15ꢀ4) following the same protocols
N
O
N
13
ACS Paragon Plus Environment

Page 3 of 7
ACS Medicinal Chemistry Letters
as reported in reference 5 for compound 1. Indoles 29 and 30 (9.2 ꢁM). The novel pyrrolopyridine core containing comꢀ
1
2
3
4
5
6
7
8
(in Table 2) were accessed starting from commercially availaꢀ
ble 1HꢀIndolꢀ6ꢀol (CAS: 2380ꢀ86ꢀ1) following the same proꢀ
tocols as reported in reference 5 for their 5ꢀhydroxyindole
analogs.
pound, 20, (Entry 5, Table 1) was also found to be a potent
VEGFRꢀ2 inhibitor (55 nM and 51 nM respectively in the
biochemical and cell assay). Although direct comparison of
the changes in solubility and hERG in this compound are conꢀ
founded by the different heterocycle in the amide region, 20
shows good solubility and minimal hERG affinity. It has been
shown previously that amino pyrazoles are in general more
efficient in improving both solubility and hERG profile of
compounds of this type.5 4ꢀAzaindole 25 (Entry 6, Table 1)
was pleasantly still potent against the target (160 nM and 33
nM respectively in the biochemical and cell assay) and also
provided increased aqueous solubility (260 vs 18 ꢁM in 1).
The 6ꢀhydroxyꢀ4ꢀazaindole 26 (Entry 6, Table 1), serendipiꢀ
tously synthesized as a result of an unexpected reversed selecꢀ
tivity in the formation of its core structure (Scheme 4) was
surprisingly still a potent VEGFRꢀ2 inhibitor (450 nM and 55
nM respectively in the biochemical and cell assay). This findꢀ
ing highlighted the conformational flexibility of the connectivꢀ
ity between the core and hinge binding region. Solubility and
hERG activity were similar to its 5ꢀhydroxy analog 25.
Scheme 4. Synthesis of azaindoles 23 and 24 and their use
in the synthesis of VEGFRꢀ2 inhibitors 25 and 26 respectiveꢀ
ly.a
9
O
O
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
a
N
70%
N+
O-
N
21
22
O
N
H
N
O
OH
NH
HN
b
85%
O
N
N
24
ref. 5
N
N
N
Further investigation in this new series of 1ꢀ6 connected inꢀ
doleꢀpyrimidines showed that the nitrogen in the 4 position of
the indole core in 26 was actually not needed for potency, and
in fact a simple and commercially available 6ꢀhydroxyindole
core as in 29 (Entry 1, Table 2) was able to give rise to an
exquisitely potent compound with comparable potency to the
well optimized 5ꢀhydroxyindole analog. Further investigation
into the potential binding mode showed that whilst in the 5ꢀ
hydroxyindole series, the pyrimidine substitution allows for a
very diverse SAR,5 this is not the case for the 6ꢀhydroxyindole
series. Initial exploration seems to point to the importance of
the 6,5ꢀbyclic pyrimidine present in 29. In fact when a 6,6ꢀ
substitued pyrimidine was coupled onto the 6ꢀhydroxyindole
core, compound 30 (Entry 3, Table 2), a >100 fold loss in poꢀ
tency against VEFGRꢀ2 was observed compared to its 5ꢀ
hydroxyindole analog (Entry 4, Table 2).
26
22
O
N
H
N
O
HN
O
HN
c
70%
N
N
ref. 5
OH
N
23
N
N
25
a
Reagents and conditions: (a) mꢀCPBA (2 eq.), DCM, rt,
overnight; (b) Ac2O (32 eq.), reflux, overnight, then K2CO3
(1.4 eq.), MeOH, 1h; (c) TFAA (5 eq.), DCM, 0 °C to rt,
overnight, then NH4OH.
RESULTS and DISCUSSION
CONCLUSIONS
In vitro activity against the target VEGFRꢀ2 receptor tyrosine
kinase was assessed with two primary assays: a KDR receptor
tyrosine kinase biochemical assay and a cellular assay with
BaF3ꢀTelꢀKDR cells (an immortalized murine bone marrowꢀ
derived proꢀBꢀcell line) that are engineered to constitutively
require VEGFRꢀ2 kinase domain activity for survival and proꢀ
liferation. The addition of an extra nitrogen to the 2 position of
the indole core of 1, to give indazole 27 (Entry 2, Table 1),
resulted in a marked loss of potency (>1000 fold). Whilst
aqueous solubility was similar for compound 1 and 27, counter
intuitively (usually addition of polarity reduces affinity for
hERG channel) the hERG affinity was enhanced. 7ꢀAzaindole
28 (Entry 3, Table 1) exhibited a slight drop in potency (~ 10
fold). The solubility profile was not altered, however in this
case the affinity for the hERG channel was reduced (5.7 vs 28
ꢁM in 1). To our delight, the imidazopyridine (13, Entry 4,
Table 1), which was a major departure from the usual indoleꢀ
type core (note that the urea was now replaced with an amide),
was found to be a potent VEGFRꢀ2 inhibitor (90 nM and 78
nM respectively in the biochemical and cell assay). Additionꢀ
ally, 13 provided a large improvement in solubility (456 vs 18
ꢁM in 1). Again, it was disappointing to find that the polarity
increase did not affect its ability to block the hERG channel
The synthesis of a series of indoleꢀcore replacement within
an optimized series of VEGFRꢀ2 inhibitors and their impact
on onꢀtarget potency, solubility and hERG affinity was reportꢀ
ed herein. Generally, introducing additional nitrogens in the
core structure was reasonably well tolerated, including cases
where the connectivity of the core with the aminoheterocycle
was changed from urea to amide. The most noticeable positive
effect of such changes was observed on aqueous solubility,
whilst the hERG affinity did not seem to be broadly reduced.
The serendipitous synthesis of a 6ꢀhydroxyindole analog led to
the uncovering of a novel connectivity for such series of comꢀ
pounds with potential vast implication on offꢀtarget profile, in
vivo activity and pk.
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Page 4 of 7
1
2
3
4
Table 1. “Core replacementꢀ” SAR: VERGRꢀ2 potency, solubility and hERG.
KDR IC50 (µM)a Baf3-KDR IC50 (µM)a
hERG IC50 (µM)a,b
pH 6.8 Sol (µM)
Entry
Inhibitor/Structure
5
6
7
O
N
O
HN
HN
8
9
0.008
0.003
18
28
1
N
N
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
O
N
1
O
N
O
HN
O
HN
HN
HN
HN
2.3
4.4
9
7.7
2
3
4
5
N
N
N
N
27
O
N
O
HN
O
0.077
0.036
0.078
0.051
25
5.7
N
N
N
N
28
O
N
O
HN
O
0.09
456
9.2
N
N
N
N
13
HN
N
O
HN
O
0.055
280
> 30
N
N
N
20
O
N
O
HN
O
HN
0.160
0.033
0.055
260
240
26
6
7
N
N
N
N
25
O
N
O
NH
HN
0.45
> 30
O
N
N
N
N
26
a Values are means of at least two experiments. b Radioligand binding assay.
ACS Paragon Plus Environment

Page 5 of 7
ACS Medicinal Chemistry Letters
1
2
Table 2. 6ꢀhydroxyindole SAR and comparison with 5ꢀhydroxyindole analogs.
3
4
KDR IC50 (µM)a
Baf3-KDR IC50 (µM)a
hERG IC50 (µM)a,b
pH 6.8 Sol (µM)
Entry
Inhibitor/Structure
5
6
7
O
N
O
8
9
NH
HN
0.048
0.003
0.003
81
18
21
28
1
2
O
N
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
N
29
0.008
5-hydroxyindole analog of 29 (1)
CF3
O
N
O
NH
HN
0.16
0.134
0.001
3
8.6
7.4
3
4
O
N
N
N
30
5-hydroxyindole analog of 30 (ref 5b)
0.040
34
a Values are means of at least two experiments. b Radioligand binding assay.
verteporfin for neovascular ageꢀrelated macular degeneration. N.
Engl. J. Med. 2006, 355, 1432ꢀ1444.
2 Ferrara N., DavisꢀSmyth T. The biology of vascular endothelial
growth factor. Endocr. Rev. 1997, 18(1), 4ꢀ25.
ASSOCIATED CONTENT
Supporting Information
Experimental details and 1H NMR of compounds in Table 1 and
Table 2. This material is available free of charge via Internet at
http://pubs.acs.org.
3 Bates D. O., Curry F. E. Vascular endothelial growth factor inꢀ
creases microvascular permeability via a Ca2+ꢀdependent pathway.
Am. J. Physiol. 1997, 273(2 Pt 2), H687ꢀ694.
4
Lopez P. F., Sippy B. D., Lambert H. M., Thach A. B., Hinton
D. R. Transdifferentiated retinal pigment epithelial cells are immuꢀ
noreactive for vascular endothelial growth factor in surgically exꢀ
cised ageꢀrelated macular degenerationꢀrelated choroidal neovascuꢀ
lar membranes. Invest. Ophthalmol. Vis. Sci. 1996, 37(5), 855ꢀ868.
AUTHOR INFORMATION
Corresponding Author
5
Meredith, E.L; Mainolfi, N.; Poor, S.; Qiu, Y.; Miranda, K;
Powers, J.; Liu, D.; Ma, Fupeng; Solovay, C.; Rao, C.; Johnson, L.;
Ji, N.; Artman, G.; Hardegger, L.; Hanks, S.; Shen, S.; Woolfenden,
A.; Fassbender, E.; Sivak, J.; Zhang, Y.; Long, D.; Cepeda, R.; Liu,
F.; Hosagrahara, V.; Lee, W.; Tarsa, P.; Anderson, K.; Elliott, J.;
Jaffee, B. Discovery of Oral VEGFRꢀ2 Inhibitors with Prolonged
Ocular Retention that are Efficacious in Models of Wet Ageꢀ
Related Macular Degeneration, J. Med. Chem., 2015, 58 (23),
9273–9286.
* For N.M.: phone, 1ꢀ857ꢀ201ꢀ2763; Eꢀmail, nello@razetx.com.
For J.P.: phone, 1ꢀ617ꢀ871ꢀ7876; Eꢀmail,
james.powers@novartis.com.
Present Addresses
†For N.M.: Raze Therapeutics, 400 Technology Square, Camꢀ
bridge, MA 02139.
6
Shultz, M. D.; Cao, X.; Chen, C. H.; Cho, Y. S.; Davis, N.R.;
ACKNOWLEDGMENT
Eckman, J.; Fan, J.; Fekete, A.; Firestone, B.; Flynn, J.; Green, J.;
Growney, J. D.; Holmqvist, M.; Hsu, M.; Jansson, D.; Jiang, L.;
Kwon, P.; Liu, G.; Lombardo, F; Lu, Q.; Majumdar, D.; Meta, C.;
Perez, L.; Pu, M.; Ramsey, T.; Remiszewski, S.; Skolnik, S.; Traeꢀ
bert, M.; Urban, L.; Uttamsingh, L.; Wang, P.; Whitebread, S.;
Whitehead, L.; YanꢀNeale, Y.; Yao, YꢀM; Zhou, L.; Atadja, P.
Optimization of the in Vitro Cardiac Safety of HydroxamateꢀBased
Histone Deacetylase Inhibitors. J. Med. Chem. 2011, 54, 4752–
4772.
The authors acknowledge the contribution of the Analytical
Sciences group at the Novartis Institutes for Biomedical Reꢀ
search for support in generating the analytical details for the
compounds described herein.
ABBREVIATIONS
VEGFRꢀ2, Vascular Endothelial Growth Factor Receptor 2;
hERG, human EtherꢀàꢀgoꢀgoꢀRelated Gene; PyBOP, benzotriaꢀ
zolꢀ1ꢀylꢀoxytripyrrolidinophosphonium hexafluorophosphate;
DBU, 1,8ꢀDiazabicyclo[5.4.0]undecꢀ7ꢀene; SAR, Structure
Activity Relationship; FCC, Flash Column Chromatography;
LCMS, Liquid Chromatography Mass Spectrometry.
7
Bell, I. M.; Gallicchio, S. N.; Abrams, M.; Beshore, D. C.;
Buser, C. A.;Culberson, J. C.; Davide, J.; EllisꢀHutchings, M.; Ferꢀ
nandes, C.; Gibbs, J. B.; Graham, S. L.; Hartman, G. D.; Heimꢀ
brook, D. C.; Homnick, C. F.; Huff, J. R.; Kassahun, K.; Koblan, K.
S.; Kohl, N. E.; Lobell, R. B.; Lynch, J. J., Jr.; Miller, P. A.; Omer,
C. A.; Rodrigues, A. D.; Walsh, E. S.; Williams, T. M. Design and
Biological
Activity
of
(S)ꢀ4ꢀ(5ꢀ{[1ꢀ(3ꢀChlorobenzyl)ꢀ2ꢀ
oxopyrrolidinꢀ3ꢀylamino]methyl}imidazolꢀ1ꢀylmethyl)benzonitrile,
a 3ꢀAminopyrrolidinone Farnesyltransferase Inhibitor with Excelꢀ
lent Cell Potency. J. Med. Chem. 2001, 44, 2933ꢀ2949.
REFERENCES
1 Brown, D. M., Kaiser, P. K., Michels, M., Soubrane, G., Heier,
J. S., Kim, R. Y., Sy, J. P., and Schneider, S. Ranibizumab versus
8
Siu, T.; Li, Y.; Nagasawa, J.; Liang, J.; Tehrani, L; Chua, P.;
Jones, R. E.; DefeoꢀJones, D.; Barnett, S. F.; Robinson, R. G. The
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Page 6 of 7
design and synthesis of potent and cellꢀactive allosteric dual Akt 1
18 Meanwell, N. A. Improving drug candidates by design: a focus
and 2 inhibitors devoid of hERG activity. Bioorg. Med. Chem. Lett.
2008, 18, 4191–4194.
on physicochemical properties as a means of improving compound
1
2
3
4
5
6
7
8
disposition and safety. Chem. Res. Toxicol., 2011, 24, 1420ꢀ1456.
9
19
For an excellent review of hERG Optimization in Medicinal
Ikemoto, T.; Kawamoto, T.; Wada, H.; Ishida, T.; Ito, T.;
Chemistry, see: (e) Jamieson, C.; Moir, E. M.; Rankovic, Z.;
Wishart, G. Medicinal chemistry of hERG optimizations: Highlights
and hangꢀups. J. Med. Chem. 2006, 49, 5029ꢀ5046.
Isogami, Y.; Miyano, Y.; Mizuno, Y.; Tomimatsu, K.; Hamamura,
K.; Takatani, M.; Wakimasu, M. Largeꢀscale Synthesis of new
Cyclazines, 5ꢀthiaꢀ1,8bꢀdiazaacenaphthleneꢀ3ꢀcarboxylic acid deꢀ
rivatives having the peripheral 12ꢀπ electron ring system. Tetrahe-
dron, 2002, 58, 489ꢀ493.
10 Tamargo, J. Drugꢀinduced torsade de pointes: from molecularꢀ
biology to bedside. Jpn. J. Pharmacol. 2000, 83, 1–19.
11 Witchel, H. J.; Hancox, J. C. Familial and acquired longqt synꢀ
drome and the cardiac rapid delayed rectifier potassium current.
Clin. Exp. Pharmacol. Physiol. 2000, 27, 753–766.
Wan Z.ꢀK.; Wacharasindhu, S.; Levins, C. G.; Lin, M.; Tabei,
20
K.; Mansour, T. S. The Scope and Mechanism of Phosphoniumꢀ
Mediated SNAr Reactions in Heterocyclic Amides and Ureas. J.
Org. Chem. 2007, 72, 10194ꢀ10210.
9
12 Recanatini, M.; Poluzzi, E.; Masetti, M.; Cavalli, A.; De, P. F.
QT prolongation through hERG K(+) channel blockade: current
knowledge and strategies for the early prediction during drug develꢀ
opment. Med. Res. Rev. 2005, 25, 133–166.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
21
Modified from: Bragg D. R.; Wibberley, D. G. Preparation of
Indolixines from Ethyl 2 –Pyridylacetate. J. Chem. Soc., 1962,
2627ꢀ2629.
13 Lagrutta, A. A.; Trepakova, E. S.; Salata, J. J. The hERG chanꢀ
nel and risk of drugꢀacquired cardiac arrhythmia: an overview.
Curr. Top. Med. Chem. 2008, 8, 1102–1112.
22 Keith, J. M. Oneꢀstep Conversion of Azine Nꢀoxides to Alphaꢀ
1,2,4ꢀtriazoloꢀ, 1,2,3ꢀtriazolo, imidazoloꢀ, and Pyrazoloheteꢀ
roarenes. J. Org. Chem. 2010, 75, 2722–2725.
14
Redfern, W. S.; Carlsson, L.; Davis, A. S.; Lynch, W. G.;
23 Storz, T.; Bartberger, M. D.; Sukits, S.; Wilde, C.; Soukup, T.
The First Practical and Efficient OneꢀPot Synthesis of 6ꢀSubstituted
7ꢀAzaindoles via a Reissert—Henze Reaction. Synthesis 2008, 2,
201–214.
MacKenzie, I.; Palethorpe, S.; Siegl, P. K.; Strang, I.; Sullivan, A.
T.; Wallis, R.; Camm, A. J.; Hammond, T. G. Relationships beꢀ
tween preclinical cardiac electrophysiology, clinical QT interval
prolongation and torsade de pointes for a broad range of drugs:
evidence for a provisional safety margin in drug development. Car-
diovasc. Res. 2003, 58, 32–45.
24 Yin, J.; Xiang, B.; Huffman, M. A.; Raab, C. E.; Davies, I. W.
A General and Efficient 2ꢀAmination of Pyridines and Quinolines.
J. Org. Chem. 2007, 72, 4554–4557.
15 Kerr, J. S.; Galloway, S.; Lagrutta, A.; Armstrong, M.; Miller,
T.; Richon, V. M.; Andrews, P. A. Nonclinical safety assessment of
the histone deacetylase inhibitor vorinostat. Int. J. Toxicol. 2010,
29, 3–19. Munster, P. N.; Rubin, E. H.; Van, B. S.; Friedman, E.;
Patterson, J. K.; Van, D. K.; Li, X.; Comisar, W.; Chodakewitz, J.
A.; Wagner, J. A.; Iwamoto, M. A single supratherapeutic dose of
vorinostat does not prolong the QTc interval in patients with adꢀ
vanced cancer. Clin. Cancer Res. 2009, 15, 7077–7084.
Solekhova, M. A.; Kurbatov, Y. V. Reductive Amination of
25
Quinoline NꢀOxide with Aminopyridines and Their NꢀTozyl Derivꢀ
atives. Zh. Org. Khim. 2002, 38, 1192–1194.
26
Hayashida, M.; Honda, H.; Hamana, M. Deoxygenative 2ꢀ
Alkoxylation of Quinoline 1ꢀOxide Heterocycles 1990, 31, 1325–
31.
27 LaMontagne, M. P.; Blumbergs, P.; Smith, D. C. Synthesis of
2ꢀsubstituted analogues of 8ꢀ[(4ꢀaminoꢀ1ꢀmethylbutyl)amino]ꢀ6ꢀ
methoxyꢀ4ꢀmethylꢀ5ꢀ[3ꢀ (trifluoromethyl)phenoxy]quinoline as
candidate antimalarials J. Med. Chem. 1989, 32, 1728–32.
16
Borchard, U.; Hafner, D. Ion channels and arrhythmias. Z.
Kardiol. 2000, 89 (Suppl 3), 6–12.
17 Ritchie, T. J.; Macdonald, S. J. F.; Peace S.; Pickett S. D.; Lusꢀ
combe C. N. The developability of heteroaromatic and heteroaliꢀ
phatic rings – do some have a better pedigree as potential drug molꢀ
ecules than others? Med Chem Commun, 2012, 3(9), 1062ꢀ1069.
ACS Paragon Plus Environment

Page 7 of 7
ACS Medicinal Chemistry Letters
Insert Table of Contents artwork here
1
2
3
4
5
6
7
"allosteric pocket"
binding region
O
8
9
N
O
HN
HN
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
N
"hinge" binding region
O
N
core replacements
Potency
Solubility
hERG
more polar 6,5
bicyclic systems
7
ACS Paragon Plus Environment