Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Orally Bioavailable and Brain Penetrant Mutant IDH1 Inhibitors

Article abstract of DOI:10.1021/acsmedchemlett.8b00182

Mutant isocitrate dehydrogenase 1 (IDH1) is an attractive therapeutic target for the treatment of various cancers such as AML, glioma, and glioblastoma. We have evaluated 3-pyrimidin-4-yl-oxazolidin-2-ones as mutant IDH1 inhibitors that bind to an allosteric, induced pocket of IDH1^R132H. This Letter describes SAR exploration focused on improving both the in vitro and in vivo metabolic stability of the compounds, leading to the identification of 19 as a potent and selective mutant IDH1 inhibitor that has demonstrated brain penetration and excellent oral bioavailability in rodents. In a preclinical patient-derived IDH1 mutant xenograft tumor model study, 19 efficiently inhibited the production of the biomarker 2-HG.

Full text of DOI:10.1021/acsmedchemlett.8b00182

Subscriber access provided by EDINBURGH UNIVERSITY LIBRARY | @ http://www.lib.ed.ac.uk
Letter
Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Orally
Bioavailable and Brain Penetrant Mutant IDH1 Inhibitors
Qian Zhao, James R Manning, James Sutton, Abran Costales, Martin Sendzik, Cynthia M. Shafer,
Julian R. Levell, Gang Liu, Thomas Caferro, Young Shin Cho, Mark Palermo, Gregg Chenail, Julia
Dooley, Brian Villalba, Ali Farsidjani, Jinyun Chen, Stephanie Dodd, Ty Gould, Guiqing Liang, Kelly
Slocum, Minying Pu, Brant Firestone, Joseph D. Growney, Tycho Heimbach, and Raymond Pagliarini
ACS Med. Chem. Lett., Just Accepted Manuscript • Publication Date (Web): 11 Jun 2018
Downloaded from http://pubs.acs.org on June 11, 2018
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 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 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.
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
Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Orally Bioa-
vailable and Brain Penetrant Mutant IDH1 Inhibitors
Qian Zhao,*,† James R. Manning,*,† James Sutton,†,‡ Abran Costales,†,§ Martin Sendzik,†,⊥ Cynthia M.
Shafer,† Julian R. Levell,⊥,║ Gang Liu,⊥ Thomas Caferro,⊥ Young Shin Cho,⊥ Mark Palermo,⊥ Gregg
Chenail,⊥ Julia Dooley,⊥ Brian Villalba,⊥ Ali Farsidjani,⊥ Jinyun Chen,⊥ Stephanie Dodd,⊥ Ty Gould,⊥
Guiqing Liang,⊥ Kelly Slocum,⊥ Minying Pu,⊥ Brant Firestone,⊥ Joseph Growney,⊥ Tycho Heimbach,⊥
and Raymond Pagliarini⊥
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
†Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
⊥Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
KEYWORDS mutant IDH1, inhibition of 2-HG production, in vivo anticancer activity, brain penetration, clinical candidate
ABSTRACT: Mutant isocitrate dehydrogenase 1 (IDH1) is an attractive therapeutic target for the treatment of various cancers such
as AML, glioma and glioblastoma. We have evaluated 3ꢀpyrimidinꢀ4ꢀylꢀoxazolidinꢀ2ꢀones as mutant IDH1 inhibitors that bind to
an allosteric, induced pocket of IDH1R132H. This letter describes SAR exploration focused on improving both the in vitro and in
vivo metabolic stability of the compounds, leading to the identification of 19 as a potent and selective mutant IDH1 inhibitor that
has demonstrated brain penetration and excellent oral bioavailability in rodents. In a preclinical patientꢀderived IDH1 mutant xenꢀ
ograft tumor model study, 19 efficiently inhibited the production of the biomarker, 2ꢀHG.
As an isocitrate dehydrogenase, NADP+ꢀdependent IDH1 cataꢀ
lyzes the oxidative decarboxylation of isocitrate to produce αꢀ
ketoglutarate (αꢀKG) as part of the citric acid cycle in aerobic
metabolism,1ꢀ5 while NADP+ is reduced to NADPH.2ꢀ4 Heterꢀ
ozygous mutations in human IDH1 at Arg132 (R132*) have
been identified in multiple cancer types, including acute myeꢀ
loid leukemia (AML), glioblastoma, glioma, chondrosarcoma
and cholangiocarcinoma. The gainꢀofꢀfunction mutant loses
normal enzymatic function and reduces αꢀKG to 2ꢀ
hydroxyglutarate (2ꢀHG), resulting in elevated intracellular
levels of this metabolite.6 2ꢀHG has been found to inhibit
enzymatic function of many αꢀKGꢀdependent dioxygenases,
including histone and DNA demethylases, causing widespread
alterations in histone and DNA methylation which may potenꢀ
tially contribute to tumorigenesis.7 Recently, a firstꢀinꢀclass
inhibitor of mutant IDH1 has shown efficacy against IDH1ꢀ
mutant glioma and cholangiocarcinoma in clinical studies.8,9
A number of preclinical studies also provided evidence to
support targeting mutant IDH1 tumors with small molecule
inhibitors.10ꢀ15
O
O
N
N
N
O
HN
N
N
HN
N
N
O
O
HN
N
N
O
N
N
A
A
N
N
F
B
B
N
1 (IDH125)
2 (IDH889)
3 (IDH305)
F
CF3
Figure 1. SAR progression from hitꢀtoꢀlead to clinical candiꢀ
date
As reported previously, our hitꢀtoꢀlead optimization efforts
from 1 produced a potent and selective lead compound,
IDH889 (2).17 Oral dosing of 2 in a murine IDH1 mutant tuꢀ
mor xenograft model resulted in robust reduction of tumorꢀ
derived 2ꢀHG, a PD biomarker of mutant IDH1R132* activity.
However, in addition to low aqueous solubility (39 µM at pH
6.8), 2 also displayed poor rodent PK due to its high in vivo
clearance (Table 1). This correlated with high in vitro intrinꢀ
sic
clearance
(CLint)
across
different
species
(rat/mouse/dog/human 588/143/548/205 µL/min/mg). Thus,
improving the CLint was identified as a top priority for the
series.
We recently reported the identification of clinical candidate
IDH305 (3) as a brain penetrant, potent and selective mutant
IDH1 inhibitor (Figure 1).16 A major part of the lead optimiꢀ
zation efforts focused on improving intrinsic clearance without
compromising physicochemical properties (e.g. solubility). In
this letter, we describe the rational design of fluoromethyl and
fluoroethyl (as in 3) substituted oxazolidinones to enhance
metabolic stability.
In silico and in vivo metabolic studies had identified debenꢀ
zylation resulting from benzylic oxidation as a major metabolꢀ
ic pathway for 1 (Scheme 1). Common strategies to improve
metabolic stability focus on: reducing the lipophilicity of the
molecule to affect binding to cytochrome P450 proteins
(CYPs), and blocking metabolically labile sites.19
Scheme 1. Major Metabolite of 1 in Rat Liver Microsomes
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Our early optimization efforts focused on the exploration of 5ꢀ
Page 2 of 7
In parallel to the work on the heteroaromatic analogs, comꢀ
pounds that displayed acceptable CLint (although were insuffiꢀ
ciently potent) were evaluated to understand what structural
characteristics were important for metabolic stability. For inꢀ
stance, unsubstituted oxazolidinone 7 (Figure 3) had low
clearance, while the corresponding isopropyl analog 8 disꢀ
played high clearance. It seemed counterintuitive that analogs
containing sterically encumbered oxazolidinone rings would
undergo ring metabolism more readily than their unsubstituted
congeners. We hypothesized that the substituents on the oxaꢀ
zolidinone might play a role in CYP recognition and binding
that could be important for the metabolic stability of the moleꢀ
cules.
1
2
3
4
5
6
7
8
membered heterocyclic aromatic rings on the amine side
chain, which were expected to reduce benzylic oxidation20
through the inductive effect of the electronegative heteroatoms
and reduction of the overall lipophilicity of the molecule. We
elected to maintain the isopropyl group on the oxazolidinone
ring throughout our initial studies because it enhanced potency
relative to compounds lacking this moiety. This is likely due
both to its interaction with the hydrophobic protein pocket,
and, more importantly, its van der Waals contact with the aryl
group of the amine side chain. Indeed, both the bound and
small molecule Xꢀray structures of 1 overlay closely, suggestꢀ
ing a prearrangement of the molecule into the active binding
conformation that is driven by hydrophobic collapse.17,18 We
believe this ligand preorganization is critical for maintaining
mutant IDH1 potency. Additionally, a coꢀcrystal structure of
217 with the homodimer of IDH1R132H showed a hydrogen bond
between Ser278 and one of the ortho nitrogen atoms in the pyꢀ
rimidine ring. Therefore, in our optimization efforts, at least
one hydrogen bond acceptor, either a nitrogen or oxygen atom,
was maintained in ring A (Figure 1).
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
Scheme 2. Major Metabolites of 4 in Rat Liver Microsomes
Figure 3. Biochemical Potency and Rat Liver Microsomal
CLint for 7 and 8.
The coꢀcrystal structures of both IDH125 and IDH88917
showed van der Waals interactions between the isopropyl
group and ring A. Thus, the decreased potency of 7 relative to
isopropyl analog 8 was not surprising because of the ligand
preorganization resulting from the aforementioned hydrophoꢀ
bic collapse.17 However, the relative importance of the isoproꢀ
pyl group to inducing the hydrophobic collapse was unclear.
Therefore, the unsubstituted oxazolidinone was viewed as
providing a starting point for building in potency while mainꢀ
taining good metabolic stability. In addition to high clearance,
isopropyl analogs also generally displayed low aqueous soluꢀ
bility and high plasma protein binding across species. Substitꢀ
uents that would reduce lipophilicity as compared to isopropyl
would likely improve the overall physicochemical profile of
the series and lead to better drugꢀlike properties.
Most of the heterocyclic analogs thus prepared did indeed
attenuate the aforementioned benzylic oxidation observed in
Met ID studies; however, the rat in vitro microsomal CLint
remained high. For example, benzylic oxidation of oxadiazole
4 was reduced during incubation with rat liver microsomes
(Scheme 2), but the major observed metabolites now resulted
from oxazolidinone ring opening and oxidation. The change in
the site of metabolism observed with 4 was not predicted by in
silico modeling, but we were nonetheless encouraged by the
reduced benzylic oxidation observed with 4 and paraꢀchloro
analog 5, which is more potent and has improved CLint. The
tetraꢀmethyl substituted analog of 5 (6) (Figure 2) was deꢀ
signed and synthesized to block oxazolidinone ring oxidation.
Unfortunately, this resulted in a 20ꢀfold loss in potency, and
only a slight improvement in CLint was observed.
Toward this goal, an effort was initiated to evaluate various
substituents on both the oxazolidinone and the biaryl amine
side chain to identify a suitable combination of metabolic staꢀ
bility and potency. A number of 5,6ꢀ and 6,6ꢀmembered biaryl
analogs were synthesized, and the imidazole analog 9 was
identified as a promising lead, with a cellular IC50 of 0.5 µM
and much improved in vitro CLint across species
(mouse/rat/human 73/34/59 µL/min/mg). The addition of a
methyl group onto the oxazolidinone ring (10) increased celluꢀ
lar potency 10ꢀfold, while only moderately increasing the rat
CLint (103 µL/min/mg) as compared to 2 and other isopropyl
analogs (Table 1). Compound 10 also displayed significantly
lower in vivo clearance vs 2 (17 vs 41 mL/min/kg) during
pharmacokinetic profiling in rat (IV/PO 1/10 mg/kg). This
translated to a 35ꢀfold increase in oral AUC and a 17ꢀfold
improvement in bioavailability vs 2 at the same oral dosage.
Figure 2. Biochemical Potency and Rat Liver Microsomal
CLint for 5 and 6.
2
ACS Paragon Plus Environment

Page 3 of 7
ACS Medicinal Chemistry Letters
Table 1. Cellular Potency, in vitro CLint and Rat PK Data
of 9, 10 and 2
ify the phenyl substitutions of the biaryl amine side chain and
identified a number of potent compounds with low to medium
CLint, exemplified by 18 and 19.
1
2
3
4
5
Table 2. Cellular Potency and CLint in Rat liver Micro-
somes
6
7
8
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
9
10
2
cellular HCT116ꢀIDH1R132H/+
0.56
0.047
0.014
(IC50/µM)
Cmpd
X
Y
R
Cellular
Rat liver
HCT116ꢀ microsomal
IDH1R132H
CLint
in vitro liver microsomal CLint
(µL/min/mg)
34
101
17
588
41
/+
(µL/min/m
(IC50/µM)
in vivo plasma clearance
n.d.a
g)
(mL/min/kg)
Cl
Cl
Cl
F
F
F
Me
Et
0.047
0.013
0.24
103
448
237
10
11
12
n.d.
n.d.
14
67
0.4
4
oral AUC (µM·h)
oral bioavailability (%)
a. Not determined
(R)ꢀ1ꢀ
FꢀEt
Cl
F
(S)ꢀ1ꢀ
FꢀEt
0.022
272
13
Given these encouraging results, we continued to explore the
oxazolidinone substitutions to further improve the stability and
potency of the imidazole series. We anticipated that the oxaꢀ
zolidinone SAR would translate beyond the imidazole series
described here and that the findings could prove useful for the
optimization of the other biaryl series as well. The data sumꢀ
marized in Table 2 highlights both steric and electronic effects
of the substituents on cellular IC50 and microsomal CLint.
Ethyl analog 11 was about 3ꢀfold more potent than methyl
analog 10; however, the CLint of 11 was significantly higher.
Introduction of a fluorine atom generated a pair of fluoroethyl
diastereomers, 12 and 13. While both isomers demonstrated a
trend towards improved stability over ethyl analog 11, Sꢀ
isomer 13 was shown to be the more potent diastereomer by
10ꢀfold over 12. A significant improvement in stability was
obtained with fluoromethyl analog 14 with maintenance of
cellular potency.
Cl
Cl
Cl
F
H
H
FꢀMe
0.024
0.015
0.004
28
14
15
16
iꢀPr
489
148
(S)ꢀ1ꢀ
FꢀEt
Cl
H
H
FꢀMe
0.030
0.015
75
72
17
18
CF2H
(S)ꢀ1ꢀ
FꢀEt
CF3
H
FꢀMe
0.039
7
19
Throughout our medicinal chemistry campaign, both the 5ꢀ
fluoro and 5ꢀhydrogen pyrimidine cores had been explored,
and the 5ꢀsubstituent was identified as a handle for the fineꢀ
tuning of potency, lipophilicity and physicochemical properꢀ
ties. As observed in the other biaryl series, isopropyl analog
15 displayed good potency and high CLint. The (S)ꢀfluoroethyl
analog of 15 (16) demonstrated an improvement in potency (4ꢀ
fold) and stability vs 15. Once again, lower CLint was observed
with fluoromethyl analog 17 relative to 16. However, unlike
with the 5ꢀfluoro pyrimidines (13ꢀ14), the cellular potency
dropped over 7ꢀfold from 16 to 17.
Both 18 and 19 demonstrated a good balance of cellular poꢀ
tency, in vitro clearance, permeability and aqueous solubility
(Table 3). Although 19 was about 2ꢀfold less potent than 18,
its superior microsomal CLint correlated with significantly
improved in vivo clearance, AUC and oral bioavailability in
rat vs 18. When rat plasma protein binding data were used to
approximate unbound plasma AUC, 10 mg/kg oral dosing of
18 and 19 provided cellular IC50 coverage for roughly the
same amount of time (Figure SIꢀ1). The AUC brain to plasma
ratio of 19 in rat at 10 mg/kg was 0.17, suggesting 19 is brain
penetrant. The limited exposure of 18 in rat brain is presumaꢀ
bly due to the pꢀglycoprotein driven efflux mechanism
(MDR1ꢀMDCK efflux ratio >9).
Encouraged by the improvement in CLint with the fluoromeꢀ
thyl and (S)ꢀ1ꢀfluoroethyl oxazolidinones, we decided to modꢀ
3
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Page 4 of 7
Table 3. Physicochemical Properties and Rodent PK Data
for 18 and 19 (IV/PO 1/10 mg/kg for rat and mouse)
1
2
3
18
19
4
5
6
cellular HCT116ꢀIDH1R132H/+ IC50
0.015
0.039
(µM)
7
8
9
422
124
solubility at pH 6.8 (µM)
Cacoꢀ2 Papp (AB/BA)
21/31
6/57
20/24
11/39
98/98
7.7/11
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
MDR1ꢀMDCK (AB/BA)
plasma protein binding (rat/mouse)
95/92
72/63
in vitro liver microsomal CLint
(µL/min/mg) (rat/mouse)
in vivo plasma clearance (mL/min/kg)
20/n.d.a
2.6/5
(rat/mouse)
15/n.d. 180/172
oral AUC (µM·h) (rat/mouse)
oral bioavailability(%) (rat/mouse)
82/n.d.
< 0.1
127/
149
Figure 4. Percent 2ꢀHG inhibition in HCT116ꢀIDH1R132H/+
xenograft tumor tissue in correlation with total and calculated
unbound plasma concentration following (a) 150 mg/kg dose
of 19 and (b) 200 mg/kg dose of 3.
brain to plasma (total) AUC ratio (rat)
a. Not determined
0.17
Compound 19 was evaluated for specificity against mutant
IDH1 relative to wildꢀtype (WT) IDH1 in a biochemical assay
measuring consumption (mutant) or production (WT) of
NADPH.21 Compound 19 exhibited over 50 to 100ꢀfold selecꢀ
tivity for mutant IDH1 isoforms vs WT (IDH1R132H IC50 0.021
µM; IDH1R132C IC50 0.045 µM; IDH1WT IC50 2.52 µM). Comꢀ
pound 19 was also profiled in a patientꢀderived IDH1 mutant
HCT116ꢀIDH1R132H/+ mechanistic xenograft tumor model in
mice to evaluate in vivo inhibition of 2ꢀHG production. Comꢀ
pound 19, dosed orally at 150 mg/kg, inhibited new 2ꢀHG
production. Given the high baseline tissue concentration of 2ꢀ
HG, it takes several hours for it to be cleared from tissues, as
observed previously in the pharmacodynamic (PD) study with
2.17 Unbound plasma concentration of 19, approximated from
mouse plasma protein binding of 98%, stayed above the
HCT116ꢀIDH1R132H/+ cellular IC50 for 24 hours. This resulted
in reduction of tumor 2ꢀHG concentration (Figure 4), with
maximal 2ꢀHG inhibition of over 90% relative to the vehicleꢀ
treated tumors at 16ꢀ24 hours postꢀtreatment. As a compariꢀ
son, when 3 was dosed orally at 200 mg/kg in the same PK/PD
study,16 2ꢀHG levels began to rebound after 16 hours postꢀ
treatment as the free concentration of 3 dropped below the in
vitro cellular IC50.
The synthesis of 19 is described in Scheme 3. Condensation of
(S)ꢀ2ꢀmethylpropaneꢀ2ꢀsulfinamide22 and tertꢀbutyl 4ꢀformylꢀ
1Hꢀimidazoleꢀ1ꢀcarboxylate provided 20 in 74% yield. The
addition
of
methylmagnesium
bromide
to
tertꢀ
butanesulfinimine 20,23 followed by Boc deprotection gave 21
in 86% yield over two steps. Palladiumꢀcatalyzed crossꢀ
coupling24 of 21 with 1ꢀbromoꢀ4ꢀ(trifluoromethyl)benzene
followed by removal of the tertꢀbutanesulfinyl group, provided
amine 22 efficiently in 81% yield over two steps. Silyl protecꢀ
tion of (S)ꢀ4ꢀ(hydroxymethyl)oxazolidinꢀ2ꢀone (23) produced
24 in 86% yield, and the subsequent SNAr reaction of 24 with
2,4ꢀdifluoropyrimidine afforded compound 25 in 81% yield.
The removal of the silyl protecting group and subsequent conꢀ
version to fluoromethyl compound 26 was achieved efficiently
in oneꢀpot using perfluorobutanesulfonyl fluoride (PFBSF)
and triethylamine trihydrofluoride.24 Coupling of 22 and 26 in
DMSO then provided 19 in 74% yield.
Scheme 3. Synthesis of 19
4
ACS Paragon Plus Environment

Page 5 of 7
ACS Medicinal Chemistry Letters
SAR was also applied to other biaryl series and a number of
1
2
3
compounds with good potency and desirable in vivo properꢀ
ties, including the clinical candidate IDH305, were subseꢀ
quently identified.
4
5
6
ASSOCIATED CONTENT
Supporting Information
7
8
9
Synthetic procedures, analytical data, assay protocols, PK, PK/PD
and efficacy study protocols and data (PDF). This material is
available free of charge on the ACS Publications website.
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
AUTHOR INFORMATION
Corresponding Authors
* Email: qianz53705@gmail.com.
* Tel: (510) 879ꢀ9429. Email: james.manning@novartis.com.
Present Addresses
‡ (J.S.) Ideaya Biosciences, 280 Utah Avenue, Suite 250, South
San Francisco, CA 94080
§(A.C.) Chevron Oronite LLC, 100 Chevron Way, Richmond, CA
94802
║(J.R.L.) Constellation Pharmaceuticals, 215 First Street, Suite
200, Cambridge, MA 02142
Notes
The authors declare the following competing financial interest(s):
The authors are all current or former employees of Novartis and
some own shares in Novartis.
Examples can be found in the literature demonstrating that
metabolism can be reduced for some molecules when a metaꢀ
ACKNOWLEDGMENT
bolically labile C–H is replaced by C–F. These include the
cholesterolꢀabsorption inhibitor Ezetimibe26 and the cathepsin
K inhibitor Odanacatib27 for the treatment of osteoporosis.
Multiple factors may contribute to the improvement of CLint of
the fluoroalkylꢀsubstituted analogs (12ꢀ14, 16ꢀ19), including a
reduction in potential for oxazolidinone ring oxidation by an
inductive effect of the electronegative fluorine atom. Another
factor could be the effect of fluorine on molecular lipophiliciꢀ
ty. Examples of a hydrogenꢀtoꢀfluorine substitution decreasing
lipophilicity have been reported by Roche scientists.28 Those
compounds contained a common motif whereby an oxygen
atom was located either two or three carbons away from a
fluorine. The decreased lipophilicity was attributed to the poꢀ
larization of the oxygen atom by the neighboring fluorine.
Interestingly, this structural pattern is also observed in our
fluoroalkyl analogs. It is noted that some modifications to the
biaryl amine side chain modestly improved CLint of the isoꢀ
propylꢀsubstituted analogs, but not as substantially as the reꢀ
placement of the isopropyl group with methyl, fluoromethyl or
fluoroethyl groups. This suggests that the compounds may be
recognized differently within the CYP enzyme active site, and
that the substituents on the oxazolidinone ring can affect the
binding of the compounds in the active site.
The authors would like to thank Dazhi Tang and Weiping Jia for
analytical support; and Bill Sellers, Karin Briner, Tim Ramsey,
Michael Dillon, Juliet Williams, and Travis Stams for project
support.
REFERENCES
1. Dimitrov, L.; Hong, C. S.; Yang, C.; Zhuang, Z.; Heiss J. D.
New developments in the pathogenesis and therapeutic targetꢀ
ing of the IDH1 mutation in glioma. International Journal of
Medical Sciences 2015, 12 (3), 201–213.
2. Molenaar, R. J.; Radivoyevitch, T.; Maciejewski, J. P.; van
Noorden, C. J. F.; Bleeker, F. E. The driver and passenger efꢀ
fects of isocitrate dehydrogenase 1 and 2 mutations in oncoꢀ
genesis and survival prolongation. Biochimica et Biophysica
Acta 2014, 1846 (2), 326–341.
3. Kim, H.–J.; Fei, X.; Cho, S.–C.; Choi, B. Y.; Ahn, H.–C.;
Lee, K; Seo, S.–Y.; Keum, Y.–S. Discovery of αꢀmangostin
as a novel competitive inhibitor against mutant isocitrate deꢀ
hydrogenaseꢀ1. Bioorg. Med. Chem. Lett. 2015, 25, 5625–
5631.
4. Guo, C.; Pirozzi, C. J.; Lopez, G. Y.; Yan, H. Isocitrate dehyꢀ
drogenase mutations in gliomas: mechanisms, biomarkers and
therapeutic target. Curr. Opin. Neurol. 2011, 24 (6): 648–652.
5. Xu, X.; Zhao, J.; Xu, Z.; Peng, B.; Huang, Q.; Arnold, E.;
Ding, J. Structures of human cytosolic NADPꢀdependent isoꢀ
citrate dehydrogenase reveal a novel selfꢀregulatory mechaꢀ
nism of activity. J. Biol. Chem. 2004, 279, 33946–33957.
6. Turkalp, Z.; Karamchandani, J.; Das, S. IDH mutation in gliꢀ
oma: new insights and promises for the future. JAMA Neurol-
ogy 2014, 71, 1319–1325.
In conclusion, our optimization of lead compound 2 with a
focus on improving in vitro CLint led to the discoveries of both
the imidazole subseries and fluoroalkylꢀsubstituted oxazoliꢀ
dinones that demonstrated improved metabolic stability. Poꢀ
tent, orally bioavailable and brainꢀpenetrant mutant IDH1 inꢀ
hibitor 19 effectively inhibited 2ꢀHG production in a precliniꢀ
cal xenograft tumor model. The fluoroalkyl oxazolidinone
7. Liu, X.; Ling, Z. Q. Role of isocitrate dehydrogenase 1/2
(IDH 1/2) gene mutations in human tumors. Histology and
Histopathology 2015, 30, 1155–1160.
5
ACS Paragon Plus Environment

ACS Medicinal Chemistry Letters
Page 6 of 7
8. Hansen, E.; Quivoron, C.; Straley, K.; Lemieux, R.
D.; Kulathila, R.; Lin, F.; McKay, D.; Rodrigues, L.; Sage,
D.; Touré, B. B.; van der Plas, S.; Wright, K.; Xu, M.; Yin,
H.; Levell, J.; Pagliarini, R. A. Allosteric mutant IDH1 inhibiꢀ
tors reveal mechanisms for IDH1 mutant and isoform selecꢀ
tivity. Structure 2017, 25, 506–513.
M.; PopoviciꢀMuller, J.; Sadrzadeh, H.; Fathi, A. T.; Gliser,
C.; David, M.; Saada, V.; Micol, J.–B.; Bernard,O.; Dorsch,
M.; Yang, H.; Su, M.; Agresta, S.; de Botton, S.; Penardꢀ
Lacronique, V.; Yen, K. AGꢀ120, an oral, selective, firstꢀinꢀ
class, potent inhibitor of mutant IDH1, reduces intracellular
2HG and induces cellular differentiation in TFꢀ1 R132H cells
and primary human IDH1 mutant AML patient samples treatꢀ
ed ex vivo. Blood 2014, 124, 3734.
1
2
3
4
5
6
19. Nassar, A.–E. F.; Kamel, A. M.; Clarimont, C. Improving the
decisionꢀmaking process in the structural modification of drug
candidates: enhancing metabolic stability. Drug Discovery
Today, 2004, 9, 1020–1028.
7
8
9
9. Mondesir, J.; Willekens, C.; de Botton, S. IDH1 and IDH2
mutations as novel therapeutic targets: current perspectives. J.
Blood Med. 2016; 7, 171–180.
20. Ioannidis, S.; Lamb, M. L.; Wang, T.; Almeida, L.; Block, M.
H.; Davies, A. M.; Peng, B.; Mei, S.; Zhang, H.–J.; Hoffꢀ
mann, E.; Rivard, C.; Green, I.; Howard, T.; Pollard, H.;
Read, J.; Alimzhanov, M.; Bebernitz, G.; Bell, K.; Ye, M.;
Huszar, D.; Zinda, M. Discovery of 5ꢀChloroꢀN2ꢀ[(1S)ꢀ1ꢀ(5ꢀ
fluoropyrimidinꢀ2ꢀyl)ethyl]ꢀN4ꢀ(5ꢀmethylꢀ1Hꢀpyrazolꢀ3ꢀ
yl)pyrimidineꢀ2,4ꢀdiamine (AZD1480) as a Novel Inhibitor of
the Jak/Stat Pathway. J. Med. Chem. 2011, 54, 262–276.
21. Gao, H.; Korn, J. M.; Ferretti, S.; Monahan, J. E.; Wang, Y.;
Singh, M.; Zhang, C.; Schnell, C.; Yang, G.; Zhang, Y.; Balꢀ
bin, O. A.; Barbe, S.; Cai, H.; Casey, F.; Chatterjee, S.;
Chiang, D. Y.; Chuai, S.; Cogan, S. M.; Collins, S. D.;
Dammassa, E.; Ebel, N.; Embry, M.; Green, J.; Kauffmann,
A.; Kowal, C.; Leary, R. J.; Lehar, J.; Liang, Y.; Loo, A.; Loꢀ
renzana, E.; McDonald III, E. R.; McLaughlin, M. E.; Merkin,
J.; Meyer, R.; Naylor, T. L.; Patawaran, M.; Reddy, A.;
Röelli, C.; Ruddy, D. A.; Salangsang, F.; Santacroce, F.;
Singh, A. P.; Tang, Y.; Tinetto, W.; Tobler, S.; Velazquez, R.;
Venkatesan, K.; Von Arx, F.; Wang, H. Q.; Wang, Z.; Wiesꢀ
mann, M.; Wyss, D.; Xu, F. Bitter, H.; Atadja, P.; Lees, E.;
Hofmann, F.; Li, E.; Keen, N.; Cozens, R.; Jensen, M. R.;
Pryer, N. K.; Williams, J. A.; Sellers, W. R. Highꢀthroughput
screening using patientꢀderived tumor xenografts to predict
clinical trial drug response. Nat. Med. 2015, 21, 1318–1325.
22. Collados, J. F.; Toledano, E.; Guijarro, D.; Yus, M. Microꢀ
waveꢀassisted solventꢀfree synthesis of enantiomerically pure
Nꢀ(tertꢀbutylsulfinyl)imines. J. Org. Chem. 2012, 77, 5744–
5750.
10. PopoviciꢀMuller, J.; Saunders, J. O.; Salituro, F. G.; Travins,
J. M.; Yan, S.; Zhao, F.; Gross, S.; Dang, L.; Yen, K. E.;
Yang, H.; Straley, K. S.; Jin, S.; Kunii, K.; Fantin, V. R.;
Zhang, S.; Pan, Q.; Shi, D.; Biller, S. A.; Su, S. M. Discovery
of the first potent inhibitors of mutant IDH1 that lower tumor
2ꢀHG in vivo. ACS Med. Chem. Lett. 2012, 3, 850–855.
11. Liu, Z.; Yao, Y.; Kogiso, M.; Zheng, B.; Deng, L.; Qiu, J. J.;
Dong, S.; Lv, H.; Gallo, J. M.; Li, X.–N.; Song, Y. Inhibition
of cancerꢀassociated mutant isocitrate dehydrogenases: synꢀ
thesis, structure–activity relationship, and selective antitumor
activity. J. Med. Chem. 2014, 57, 8307−8318.
12. Brooks, E.; Wu, X.; Hanel, A.; Nguyen, S.; Wang, J.; Zhang,
J. H.; Harrison, A.; Zhang, W. Identification and characterizaꢀ
tion of smallꢀmolecule inhibitors of the R132H/R132H mutant
isocitrate dehydrogenase 1 homodimer and R132H/wildꢀtype
heterodimer. J. Biomol. Screen. 2014, 19, 1193–1200.
13. Deng, G; Shen, J.; Yin, M.; McManus, J.; Mathieu, M.; Gee,
P.; He, T.; Shi, C.; Bedel, O.; McLean, L. R.; LeꢀStrat, F.;
Zhang, Y.; Marquette, J.–P.; Gao, Q.; Zhang, B.; Rak, A.;
Hoffmann, D.; Rooney, E.; Vassort, A.; Englaro, W.; Li, Y.;
Patel, V.; Adrian, F.; Gross, S.; Wiederschain, D.; Cheng, H.;
Licht, S. Selective inhibition of mutant isocitrate dehydrogenꢀ
ase 1 (IDH1) via disruption of a metal binding network by an
allosteric small molecule. J. Biol. Chem. 2015, 290, 762–774.
14. Rohle, D.; PopoviciꢀMuller, J.; Palaskas, N.; Turcan, S.;
Grommes, C.; Campos, C.; Tsoi, J.; Clark, O.; Oldrini, B.;
Komisopoulou, E.; Kunii, K.; Pedraza, A.; Schalm, S.; Silꢀ
verman, L.; Miller, A.; Wang, F.; Yang, H.; Chen, Y.; Kernyꢀ
tsky, A.; Rosenblum, M. K.; Liu, W.; Biller, S. A.; Su, S. M.;
Brennan, C. W.; Chan, T. A.; Graeber, T. G.; Yen, K. E.;
Mellinghoff, I. K. An inhibitor of mutant IDH1 delays growth
and promotes differentiation of glioma cells. Science 2013,
340, 626–630.
15. Zheng, B.; Yao, Y.; Liu, Z.; Deng, L.; Anglin, J. L.; Jiang, H.;
Prasad, B. V. V.; Song Y. Crystallographic investigation and
selective inhibition of mutant isocitrate dehydrogenase. ACS
Med. Chem. Lett. 2013, 4, 542–546.
16. Cho,Y. S.; Levell, J. R.; Liu, G.; Caferro, T.; Sutton, J.; Shafꢀ
er, C. M.; Costales, A.; Manning, J. R.; Zhao, Q,; Sendzik,
M.; Shultz, M.; Chenail, G.; Dooley, J.; Villalba, B.; Farsidjaꢀ
ni, A.; Chen, J.; Kulathila, R.; Xie, X.; Dodd, S.; Gould, T.;
Liang, G.; Heimbach, T.; Slocum, K.; Firestone, B.; Pu, M.;
Pagliarini, R. Growney, J. D. Discovery and evaluation of
clinical candidate IDH305, a brain penetrant mutant IDH1 inꢀ
hibitor. ACS Med. Chem. Lett. 2017, 10, 1116–1121.
17. Levell, J. R.; Caferro, T.; Chenail, G.; Dix, I.; Dooley, J.;
Firestone, B.; Fortin, P. D.; Giraldes, J.; Gould, T.; Growney,
J. D.; Jones, M. D.; Kulathila, R.; Lin, F.; Liu, G.; Mueller,
A.; van der Plas, S.; Slocum, K.; Smith, T.; Terranova, R.;
Touré, B. B.; Tyagi, V.; Wagner, T.; Xie, X.; Xu, M.; Yang,
F. S.; Zhou, L. X.; Pagliarini, R.; Cho, Y. S. Optimization of
3ꢀpyrimidinꢀ4ꢀylꢀoxazolidinꢀ2ꢀones as allosteric and mutant
specific inhibitors of IDH1. ACS Med. Chem. Lett. 2017, 8,
151–156.
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
23. Liu, G.; Cogan, D. A.; Ellman, J. A. Catalytic asymmetric
synthesis of tertꢀbutanesulfinamide. Application to the asymꢀ
metric synthesis of amines. J. Am. Chem. Soc. 1997, 119,
9913–9914.
24. Ueda, S.; Ali, S.; Fors, B. P.; Buchwald, S. L.
Me3(OMe)tBuXPhos: A surrogate ligand for Me4tBuXPhos in
palladiumꢀcatalyzed C–N and C–O bondꢀforming reactions.
J. Org. Chem. 2012, 77, 2543–2547.
25. Yin, J.; Zarkowsky, D. S.; Thomas, D. W.; Zhao, M. M.;
Huffman, M. A. Direct and convenient conversion of alcohols
to fluorides. Org. Lett. 2004, 6, 1465–1468.
26. Van Heek, M..; France, C. F.; Compton, D. S.; Mcleod, R.
L.; Yumibe, N. P.; Alton, K. B.; Sybertz, E. J.; Davis Jr, H.
R. In vivo metabolismꢀbased discovery of a potent cholesterol
absorption inhibitor, SCH58235, in the rat and rhesus monkey
through the identification of the active metabolites of
SCH48461. J. Pharmacol. Exp. Ther. 1997, 283, 157–163.
27. Gauthier, J. Y.; Chauret, N.; Cromlish, W.; Desmarais, S.;
Duong, L. T.; Falgueyret, J.–P.; Kimmel, D. B.; Lamontagne,
S.; Léger, S.; LeRiche, T.; Li, C. S.; Massé, F.; McKay, D. J.;
NicollꢀGriffith, D. A.; Oballa, R. M.; Palmer, J. T.; Percival,
M. D.; Riendeau, D.; Robichaud, J.; Rodan, G. A.; Rodan, S.
B.; Seto, C.; Thérien, M.; Truong, V.–L.; Venuti, M. C.; Weꢀ
solowski, G.; Young, R. N.; Zamboni, R.; Black, W. C. The
discovery of odanacatib (MKꢀ0822), a selective inhibitor of
cathepsin K. Bioorg. Med. Chem. Lett. 2008, 18, 923–928.
28. Böhm, H.–J.; Banner, D.; Bendels, S.; Kansy, M.; Kuhn, B.;
Müller, K.; ObstꢀSander, U.; Stahl, M. Fluorine in medicinal
chemistry. ChemBioChem. 2004, 5, 637–643.
18. Xie, X.; Baird, D.; Bowen, K.; Capka, V.; Chen, J.; Chenail,
G.; Cho, Y. S.; Dooley, J.; Farsidjani, A.; Fortin, P.; Kohls,
6
ACS Paragon Plus Environment

Page 7 of 7
ACS Medicinal Chemistry Letters
For Table of Contents Only
1
2
3
4
5
6
7
8
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
7
ACS Paragon Plus Environment