Discovery of novel leukotriene A4 hydrolase inhibitors based on piperidine and piperazine scaffolds

Article abstract of DOI:10.1016/j.bmcl.2010.03.047

Novel piperidine and piperazine derivatives have been designed and tested as inhibitors of LTA₄ hydrolase (LTA₄H). Most potent compounds showed good potency in both enzymatic and functional human whole blood assay. Crystallography studies further confirmed observed structure-activity relationship and LTA₄H binding mode for analogs from the piperidine series.

Full text of DOI:10.1016/j.bmcl.2010.03.047

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2851–2854
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery of novel leukotriene A4 hydrolase inhibitors based on piperidine
and piperazine scaffolds
Vincent Sandanayaka a, Bjorn Mamat b, Nikhil Bhagat a, Louis Bedell a, Gudrun Halldorsdottir b,
Heida Sigthorsdottir b, Þorkell Andrésson b, Alex Kiselyov a, Mark Gurney a,b, Jasbir Singh a,
*
a Medicinal Chemistry Department, deCODE Chemistry, Inc. 2501 Davey Road, Woodridge, IL 60517, United States
b deCODE Genetics, Inc., Sturlugata 8, IS-101, ReykjaVik, Iceland
a r t i c l e i n f o
a b s t r a c t
Article history:
Novel piperidine and piperazine derivatives have been designed and tested as inhibitors of LTA4 hydro-
lase (LTA4H). Most potent compounds showed good potency in both enzymatic and functional human
whole blood assay. Crystallography studies further confirmed observed structure–activity relationship
and LTA4H binding mode for analogs from the piperidine series.
Received 27 December 2009
Revised 7 March 2010
Accepted 9 March 2010
Available online 12 March 2010
Ó 2010 Published by Elsevier Ltd.
Keywords:
Human LTA4H Inhibitors
LTA4 hydrolase inhibitors
Structure-based design
Piperidine and piperazine derivatives
Leukotriene A4 hydrolase (LTA4H) is a key enzyme in the leuko-
triene pathway, which hydrolyzes leukotriene A4 (LTA4) to leuko-
Based on our internal structural data,15 the active site of LTA4H
is buried deep in the protein, and a small opening is exposed to the
solvent (Fig. 1A). Several key residues, namely Gln-134, Gln-136,
and Tyr-267 in the hydrophobic and linker regions could be accom-
modated in the ligand design process, as shown in Figure 1. Thus,
our design exploited several unique features of the active site,
namely: (a) large hydrophobic pocket, (b) three tightly bound,
structurally conserved water molecules residing in the hydropho-
bic site, (c) hydrophilic pocket containing catalytic Zn2+ ion, and
(d) L-shaped junction featuring ca. 90° angle that separates the
hydrophobic and hydrophilic sites (Fig. 1B). These structural data
combined with the structure–activity relationship (SAR) reported
by our group earlier led to the identification of a lead series based
on prolinol template15,16 and a Phase II clinical candidate DG-051
(5). This agent displayed IC50 values of 87 nM in the LTA4H enzyme
and 449 nM in a physiologically relevant secondary functional as-
say, where human whole blood (hWB) was used to assess inhibi-
triene B4 (LTB4),
a
proinflammatory mediator.1 There is
substantial evidence that LTB4 plays a significant role in many dis-
eases such as inflammatory bowel disease (IBD),2 rheumatoid
arthritis,3 psoriasis,4 gout,5 and inflammatory lung diseases includ-
ing asthma.6 In addition, LTB4 also stimulates the production of
cytokines and may play a role in immunoregulation.7
We became interested in this target as a result of our human
population genetic studies, which indicated LTA4H as a potential
therapeutic target for cardiovascular (CV) disease including acute
myocardial infarction (AMI) and stroke.8 A number of LTA4H inhib-
itors have been reported over the past two decades.9 Design of the
earlier agents was based on the substrate, LTA4 while later mole-
cules were directed towards Zn-chelation as exemplified by 1,10
3,11 and 4.12 A non-peptidic molecule 2 was introduced as a non-
Zn chelating LTA4H inhibitor.13
Crystal structure of LTA4H has been reported;14 however, there
were no systematic studies elaborating on the potential of LTA4H
active site in the drug design context. Considering the significance
of our genetic findings and potential broader applications of LTA4H
inhibitors in multiple disease areas, we used both X-ray crystallog-
raphy and ligand data from the literature to identify novel chemo-
types active in both enzymatic and functional assays.
tion (IC50)
of LTB4 production after stimulation with Ca2+
ionophore. In our subsequent efforts to identify additional potent
chemical series based on the fragment-based approach,15,17 we
turned our attention to the six-membered alicyclic templates
including piperidine and piperazine exemplified by 6 (Scheme 1).
In designing a feasible synthetic route to the targeted mole-
cules, we used cyclic sulfamidate analog 11a (Y = CH2, Scheme 2)
available either directly from 8a or from the corresponding sulfox-
ide 9a (Scheme 1). Compound 11a was reacted with a series of
phenols 10 followed by N-alkylation of piperidine moiety with
R2X to furnish derivatives 13–34. In order to further expand the
* Corresponding author. Tel.: +1 630 904 2218.
E-mail addresses: jsingh@decode.com, Jasbir@Jasinds.com (J. Singh).
0960-894X/$ - see front matter Ó 2010 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2010.03.047

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V. Sandanayaka et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2851–2854
Selected compounds from these series were evaluated in the re-
combinant human LTA4H enzyme assay and functional human
whole blood (hWB) LTB4 production assay (Table 1). Early racemic
compounds 13–14 displayed comparable potency in both enzyme
and hWB assays. Enantiomers containing either methylene or
ether bridge (15–17) featured very good activity in these assays.
Biphenyl ether analogs 16 and 17 were two-fold more active than
the respective biphenyl methylene compond 15. When a phenyl
group was introduced at the para-position of the terminal phenyl
ring (e.g., 18, 19), enzymatic activity dropped, whereas hWB po-
tency improved. A variety of other para-substituents were well tol-
erated yielding molecules (22–24) active in both enzymatic and
functional settings. Similar to unsubstituted phenyl analogs, 4-
chlorophenyl derivatives afforded better activity in biphenyl series
featuring ether versus methylene linker (compare 13 vs. 14 and 23
vs. 24).
In order to optimize the position of CO2H group complexing to
Zn2+, we varied acyclic alkyl chain between piperidine nitrogen
and carboxylic acid (25–28) using 24 as a template. Oxadizole 29
was about a log order less active compared with the carboxylic acid
analog 24. Ethylene linker yielded four-fold more potent com-
pound (26) than the corresponding methylene derivative (25). Bu-
tyric acid derivatives (27, 28) displayed further enhancement in
potency. The R-enantiomer 28 exhibited an IC50 of 56 nM in the
enzymatic and 6 nM in the hWB assays. We believe, this profile
is due to the optimized interactions of the piperidine template
with both Gln-134 and Gln-136 residues. Encouraged by this result,
we further investigated the left hand side of the molecule by incor-
porating substituents at the terminal phenyl ring. Our rationale for
this synthetic step was to displace structurally conserved water
molecules and thereby increase the potency of the resulting mole-
cules. Specifically, we prepared several compounds containing
five-membered heterocycles at the para-position of the phenyl ring
(30–33). Notably, these analogs showed good potency against the
enzyme, with compounds 32 and 33 featuring IC50 values of 1
and 6 nM, respectively, in the hWB assay. A co-crystal structure
of 33 with LTA4H unequivocally showed displacement of the cen-
tral water molecule with the 3-thienyl substituent, thus confirm-
ing our design hypothesis.16
Figure 1. (A) Surface representation of LTA4H showing large solvent-accessible
cavity and narrow hydrophobic pocket; area associated with peptidase activity
(green) and hydrophobic region related to hydrolase activity (red) are highlighted.
(B) Active site with surface targeted in our drug discovery effort; dot surface shown
is for compound 5 (DG-051), the crystallographic waters and zinc ion are shown as
CPK (Corey, Pauling and Koltun) rendering in red and white, respectively; key
residues are highlighted.
diversity within our structure–activity relationship (SAR) studies,
we also prepared several relevant piperazine analogs 35 and 36
from 8b following similar synthetic route.
We also prepared racemic piperazine derivatives 34 and 35 as
described above (Scheme 2). These compounds were generally less
potent compared to piperidine analogs with the enzymatic poten-
O
O
H
N
O
HO
O
OH
N
H
O
N
OH
O
2
1
H
NH2
O
O
OH
N
SH
N
S
OH
OH
O
HO
O
N
O
3
4
X
R2
N
O
R1
O
N
Cl
O
*
Y
5 (DG-051)
Scheme 1. Previously reported LTA4H inhibitors and new series (6).

V. Sandanayaka et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2851–2854
2853
O
O
BOC
N
O S
H
N
N
(i)
(ii)
HO
HO
Y
Y
Y
9a, Y = CH2
8a, Y = CH2
8b, Y = N-Bn
7
9b, Y = N-Bn
(iv)
(iii)
O
O S O
N
X
R2
N
X
(v, vi, vii)
+
OH
R1
R1
O
Y
10
Y
13-34, Y = CH2
11a, Y = CH2
12b, Y = N-Bn
35, Y = N-Bn
36, Y = NH
Scheme 2. Reagents and conditions: (i) (a) BH3ÁTHF; (b) 4 M HCl, p-dioxane, 0–5 °C to rt, 2 h (89–99%); (ii) SOCl2, Et3N, CH2Cl2, 0–5 °C, 45 min (36–95%); (iii) SO2Cl2, Et3N,
CH2Cl2, À78 °C,18 h then at rt, 2 h (39%); (iv) NaIO4, RuCl3, 0–5 °C (10 min), then rt for 20 min (50–76%); (v) K2CO3, DMF, 50 °C, 18 h, 65 °C, 7 h (20–54%); (vi) R2X, Et3N, rt to
30 °C, 6–18 h (35–60%); (vii) for ester hydrolysis step: 12 N HCl p-dioxane, 55 °C, 5 h (90–99%).
Table 1
In vitro assay results for piperidine and piperazine analogs
X
R2
N
R1
O
*
Y
a
a
Compound
R1
X
Y
*
R2
IC50
(l
M) (hLTA4H)
IC50 (lM) (hWB)
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
H
H
H
H
H
Ph
Ph
CF3
F
Cl
Cl
Cl
Cl
Cl
Cl
Cl
CH2
O
CH2
O
O
O
O
O
O
CH2
CH2
O
O
O
O
O
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
NBn
NH
R/S
R/S
R
R
S
R
S
R
S
R
S
S
S
S
S
R
S
H
H
H
H
H
H
H
H
H
H
H
H
0.134
0.070
0.094
0.048
0.044
0.096
0.114
0.093
0.174
0.315
0.438
0.110
0.880
0.212
0.106
0.053
6.900
0.056
0.060
0.093
0.049
0.660
0.342
0.105
0.207
0.060
0.126
0.286
0.029
0.043
0.173
0.090
ND
ND
0.040
ND
CH2CO2H
(CH2)2CO2H
(CH2)3CO2H
(CH2)3CO2H
CH2(1,2,4-oxadiazole)
H
H
H
ND
0.023
0.006
ND
ND
ND
0.001
0.006
ND
Cl
Thiophene-2-yl
Thiophene-3-yl
Thiophene-3-yl
Thiophene-3-yl
H
CH2
CH2
O
CH2
CH2
CH2
S
S
S
R
R/S
R/S
(CH2)3CO2H
H
H
H
ND
a
Assay was performed as reported previously, see Ref. 16 for details.
cies of 660 nM and 350 nM for 34 and 35, respectively. This chem-
otype was not pursued further.
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fragments 4, 14 and 16 from Ref. 15 were used for this piperidine series.