Inhibitors designed for the active site of dihydroorotase

Article abstract of DOI:10.1016/j.bioorg.2005.08.001

Four new compounds have been synthesized as potential inhibitors of dihydroorotase from Escherichia coli. NMR spectroscopy was used to show that 4,6-dioxo-piperidine-2(S)-carboxylic acid (3), exists in solution as a mixture of the hydrate (7), enol (8), a

Full text of DOI:10.1016/j.bioorg.2005.08.001

Bioorganic Chemistry 33 (2005) 470–483
www.elsevier.com/locate/bioorg
Inhibitors designed for the active site
q
of dihydroorotase
Yingchun Li, Frank M. Raushel *
Department of Chemistry, PO Box 30012, Texas A&M University, College Station, TX 77842-3012, USA
Received 3 August 2005
Available online 6 October 2005
Abstract
Four new compounds have been synthesized as potential inhibitors of dihydroorotase from Esch-
erichia coli. NMR spectroscopy was used to show that 4,6-dioxo-piperidine-2(S)-carboxylic acid (3),
exists in solution as a mixture of the hydrate (7), enol (8), and enolate (9) tautomeric forms. This
compound was found to be a competitive inhibitor versus dihydroorotate and thio-dihydroorotate
at pH values of 7–9. The Ki of 76 lM was lowest at pH 7.0 where the ketone and hydrate forms
of the inhibitor 3 predominate in solution. Compound 3 was reduced to the two diastereomeric 4-
hydroxy derivatives (4 and 5) and then dehydrated to yield the alkene derivative, 1,2,3,6-tetrahy-
dro-6-oxopyridine-2(S)-carboxylic acid (6). Compounds 4–6 were competitive inhibitors versus
thio-dihydroorotate at pH 8.0 with Ki values of 3.0, 1.6, and 2.3 mM. Dihydroorotase was unable
to dehydrate the 4-hydroxy derivative 4 or 5 to the alkene 6 or catalyze the reverse reaction.
ꢀ 2005 Elsevier Inc. All rights reserved.
Keywords: Dihydroorotase inhibitors; Substrate analogue inhibitor
1. Introduction
Dihydroorotase (DHO1) is a zinc metalloenzyme that catalyzes the reversible intercon-
version between N-carbamoyl-L-aspartate (1) and L-dihydroorotate (2) during the
q
This work was supported in part by the NIH (GM33894).
Corresponding author. Fax: +1 979 845 9452.
*
E-mail address: raushel@tamu.edu (F.M. Raushel).
Abbreviations used: DHO, dihydroorotase; TFA, trifluoroacetic acid; THF, tetrahydrofuran; TLC, thin-layer
1
chromatography; Boc, t-butoxycarbonyl; Bn, benzyl; PMBn; p-methoxybenzyl.
0045-2068/$ - see front matter ꢀ 2005 Elsevier Inc. All rights reserved.
doi:10.1016/j.bioorg.2005.08.001

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
471
biosynthesis of pyrimidine nucleotides as shown in Scheme 1. This enzyme has been
subdivided into two structural classes based upon differences in amino acid sequences
[1]. The class I proteins are found in higher organisms and are bigger (ꢀ45 kDa) than their
class II counterparts found in many bacteria and fungi. Members of the same class of
DHO share more than 40% identity in their amino sequences, while less than 20% se-
quence identity is found for members between the two classes. The DHO from hamster,
a member of class I, has been extensively characterized and studied by Christopherson
[2–6]. A number of potential inhibitors, designed as transition-state or substrate ana-
logues, have been synthesized and assayed against the hamster DHO because of the poten-
tial of these compounds as anticancer or antimalarial drugs [7–11].
The crystal structure of the DHO from Escherichia coli was determined in the presence
of an equilibrium mixture of substrate and product [12]. The crystal structure revealed that
the active site contains two zinc ions which are bridged by hydroxide. The structural study
confirmed the prediction that DHO is a member of the amidohydrolase superfamily with a
(ba)8-barrel protein fold. The binuclear metal center at the active site is identical to those
observed previously for phosphotriesterase and urease [12,13]. Based on these structural
features, a mechanism that involves both zinc ions in the catalytic process has been pro-
posed and subsequently support by mutagenesis, metal replacement, and kinetic measure-
ments [14]. The proposed mechanism is presented in Scheme 2.
The class II dihydroorotases are generally found in bacteria and fungi and inhibitors of
this enzyme are potential antimicrobial agents. Based on the proposed mechanism of ac-
tion, 4,6-dioxo-piperidine-2-carboxylic acid (3) and the derivatives 4–6 are potential inhib-
itors of the reaction catalyzed by the bacterial dihydroorotase (Scheme 3). All four
compounds can be considered as substrate analogues of dihydroorotate. In addition to
acting as a substrate analogue of dihydroorotate, compound 3 may bind to the active site
after the addition of water to form an analogue of the proposed tetrahedral intermediate
HO
HN
O
O
O
NH2
O
O
HN
O
OH-
O
O
N
H
C
O
O
N
C
O
O
N
H
C
O
H
(1)
(2)
Scheme 1.
β
α
O
O
O
C
O
H
O
C
C
α
β
α
β
O
O
O
O
O
O
O
HN
H
O
NH2
C
H
N
O
O
N
H
C
O
O
N
H
N
C
O
O
C
O
H
O
Scheme 2.

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Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
O
OH
OH
O
O
O
O
O
N
H
C
O
O
N
H
C
O
O
N
H
C
O
O
N
H
C
O
(3)
(4)
(5)
(6)
Scheme 3.
O
O
OH
HO
OH
O
O
O
O
N
O
C
O
O
N
H
C
O
N
H
C
O
O
N
H
C
O
H
O
(8)
(7)
(9)
(3)
Scheme 4.
(7). Alternatively, ketone 3 may enolize to 8 or 9 (Scheme 4). In addition, compounds 4
and 5 may be dehydrated by DHO to 6 or compound 6 may be enzymatically hydrated
to 4 or 5. Here, we report the chemical synthesis and characterization of these compounds
as potential inhibitors and substrates for the reaction catalyzed by dihydroorotase from
E. coli.
2. Materials and methods
2.1. Inhibition assays
To evaluate the inhibitory properties of compounds 3–6, the kinetic parameters for the
DHO-catalyzed hydrolysis of dihydroorotate and 4-thio-dihydroorotate in the presence of
these compounds were measured. For compound 3, the equilibrium between the ketone
and enol tautomeric forms are affected by pH in aqueous solution. Therefore, the kinetic
parameters were measured at pH 7–9 for the inhibition by ketone 3. The DHO used in
these assays was a quadruple mutant (C221S/C263S/C265S/C268S) from E. coli and
was purified as previously described [6]. This mutant is relatively stable to oxidation
and has kinetic parameters consistent with the previously reported values for wild type
DHO [15,16].
The assay methods for monitoring the enzymatic hydrolysis of dihydroorotate and
thio-dihydroorotate were established previously [14,17,18]. The DHO-catalyzed hydroly-
sis of dihydroorotate or thio-dihydroorotate was monitored spectrophotometrically at
230 and 280 nm, respectively, using a SPECTRAmax (Molecular Device) plate reader.
The assays were conducted in a 96-well quartz plate in a volume of 250 lL. The buffer
used in all the assays was 100 mM potassium phosphate. The concentration of dihydro-
orotate and thio-dihydroorotate was varied in the range of 50–200 and 10–100 lM,
respectively.

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
473
For data analysis, the initial rate for substrate hydrolysis in the presence of the inhibitor
at different concentrations of the substrate was fitted to each of the following equations for
competitive, uncompetitive, and noncompetitive inhibition [19]. In these equations v is
the initial rate, A is the substrate concentration, I is the inhibitor concentration, kcat
is the turnover number, Ka is the Michaelis constant for the substrate, and Kis and Kii
are the slope and intercept inhibition constants.
v=Et ¼ ðkcatAÞ=ðKað1 þ I=KisÞ þ AÞ
ð1Þ
ð2Þ
ð3Þ
v=Et ¼ ðkcatAÞ=ðKa þ Að1 þ I=KiiÞÞ
v=Et ¼ ðkcatA=ðKað1 þ I=KisÞ þ Að1 þ I=KiiÞÞÞ.
2.2. 2-(S)-tert-Butoxycarbonylamino-3-oxo-pentanedioic acid 1-benzyl ester 5-ethyl
ester (11)
Carbonyldiimidazole (9.2 g, 57 mmol) was added to a solution of N-Boc-O-Bn protected
L-aspartic acid (10) (16.7 g, 52 mmol) in THF (250 ml). After the reaction mixture was stir-
red at room temperature for 8 h, into it was added potassium malonate mono ester (16.3 g,
57 mmol). The reaction mixture was stirred for another 24 h. The solvent was removed un-
der reduced pressure and the residue partitioned between ethyl ether (250 ml) and an aque-
ous solution of hydrogen chloride (2 M, 250 ml). After separation, the aqueous phase was
extracted with ethyl ether (2 · 100 ml). The ether solutions were combined and dried with
1
sodium sulfate. Removal of solvent gave product 11 (19.9 g, 98%) as a colorless solid. H
NMR (ppm, CDCl3): 7.38–7.30 (5H, m, aromatic); 5.5 (1H, NH, br); 5.16 (2H, s); 4.58 (1H,
m); 4.18 (2H, q, J = 7.1 Hz); 3.42 (2H, s); 3.28 (1H, dd, J1 = 18.3 Hz, J2 = 3.7 Hz); 3.11
(1H, dd, J1 = 18.3 Hz; J2 = 4.3 Hz); 1.43 (9H, s); 1.26 (3H, t, J = 7.1 Hz). 13C NMR
(ppm, CDCl3); 201.2; 171.2; 166.7; 155.7; 135.5; 128.8; 128.6; 128.4; 80.4; 67.7; 61.8;
49.8; 49.4; 45.0; 28.5; 14.3. MS: M+H+, 394.2 (calcd), 394.2 (found).
2.3. 4-Oxo-2(S)-(pent-4-enoyl)-amino-hexanedioic acid 1-benzyl ester 6-ethyl ester (12)
To a solution of 11 (7.0 g, 17 mmol) in dichloromethane (10 ml) was added TFA
(10 ml). The reaction mixture was stirred at room temperature for 1 h and then condensed
to dryness under reduced pressure. The residue was dissolved in dichloromethane (40 ml)
and into it was added 4-pentenoic anhydride (3.7 g, 1.2 equiv) and triethylamine (3.5 g,
2.0 equiv). The reaction mixture was stirred at room temperature for 8 h and then poured
into 200 ml of ethyl ether. The solution was washed with water (3 · 20 ml), dried with
anhydrous sodium sulfate, and condensed to about 50 ml and a colorless crystalline solid
precipitated from the solution. After filtration and washing with cold ethyl ether, the solid
was isolated after drying (3.6 g). The residue was chromatographed on silica gel to yield
1
another portion of the product 12 (1.6 g) with a total yield of 86%. H NMR (ppm,
CDCl3): 7.40–7.30 (5H, m, aromatic); 6.52 (1H, NH, d, br, J = 7.82 Hz); 5.84–5.74 (1H,
m); 5.17 (2H, s); 5.08–4.95 (2H, m); 4.89–4.82 (2H, m); 4.18 (2H, q, J = 7.1 Hz); 3.41
(2H, s); 3.31 (1H, dd, J1 = 18.5 Hz; J2 = 4.4 Hz); 3.15 (1H, dd, J1 = 18.5 Hz,
J2 = 4.2 Hz); 2.40–2.29 (4H, m); 1.27 (3H, J = 7.1 Hz). 13C NMR (ppm, CDCl3): 201.4,
172.4; 170.8; 166.7; 137.0; 135.4; 128.8; 128.7; 128.5; 115.9; 67.8; 61.8; 49.3; 48.3; 44.6;
35.7; 29.6; 14.3. MS: M+H+, 376.2 (calcd), 376.2 (found).

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Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
2.4. 4-Hydroxy-2-(pent-4-enoyl)-amino-hexanedioic acid 1-benzyl ester 6-ethyl ester (13a
and b)
A solution of ketone 12 (2.42 g) in a mixed solvent of methanol and THF (5 ml, 3:1 v/v)
was cooled to 0 ꢁC with an ice-water bath. To this solution was added sodium borohydride
(0.12 g, 3.1 mmol) in three portions at intervals of 10 min. When the starting material was
almost depleted (as monitored by TLC) the reaction mixture was poured onto ice and
extracted with ethyl ether (3 · 100 ml). The solution of ethyl ether was dried with sodium
sulfate and then condensed to dryness. The resulting residue was applied to a column of
silica gel and eluted with a mixture of ethyl acetate and hexanes (1:4). Fractions containing
each of the desired products were collected and condensed to dryness to yield the 13a
(4S, 2S, Rf = 0.32) and 13b (4R, 2S, Rf = 0.25) diastereomers (0.85 g and 0.84 g, respec-
tively) with a total yield of 70% in a ratio ꢀ1:1. Compound 13a: 1H NMR (ppm, CDCl3):
7.32–7.44 (5H, m, aromatic); 6.60 (1H, NH, d, br); 5.77–5.90 (1H, m); 5.20 (2H, s)
5.13–5.01 (2H, m); 4.89–4.83 (1H, m) 4.20 (1H, s, br); 4.16 (2H, q, J = 7.1 Hz); 4.03–
3.96 (1H, m); 2.53 (1H, dd, J1 = 15.9 Hz, J2 = 8.3 Hz); 2.46–2.35 (5H, m);
1.99–1.91 (1H, m); 1.79–1.71 (1H, m); 1.27 (3H, t, J = 7.1 Hz). MS: M+H+, 378.2 (calcd),
378.2 (found). Compound 13b: 1H NMR (ppm, CDCl3): 7.42–7.32 (5H, m, aromatic); 6.54
(1H, NH, dd, J = 6.1 Hz, br); 5.89–5.78 (1H, m); 5.32 (1H, s); 5.25 (1H, d, J = 12.0 Hz);
5.19 (2H, d, J = 12.0 Hz); 5.13–4.49 (2H, m); 4.67 (1H, q, J = 5.62 Hz); 4.21–4.10 (3H, m);
2.50 (6H, m); 2.13–1.96 (2H, m); 1.28 (3H, CH3, J = 7.1 Hz). MS: M+H+, 378.2 (calcd),
378.2 (found).
2.5. 4(S)-(4-Methoxy-phenoxy)-2(S)-(pent-4-enoyl)amino-hexanedioic acid 6-ethyl ester
1-(2-vinyl-but-2-enyl) ester (14a)
Lanthanum triflate (154 mg) was added to a solution of alcohol 13a (1.8 g, 5.3 mmol)
and p-methoxybenzyl trichloroacetimidate (3.0 g, 11 mmol) in toluene (20 ml). The reac-
tion mixture was stirred at room temperature until the starting alcohol was depleted in
about 4 h. After removal of the solvent at reduced pressure, the residue was applied to
a silica gel column and eluted with a mixture of ethyl acetate and hexanes (1:3) to yield
1
the product as a colorless oil (2.0 g, 80%). Compound 14a: H NMR (ppm, CDCl3):
7.42–7.32 (5H, m, aromatic); 7.27 (2H, d, J = 8.2 Hz); 6.87 (2H, d, J = 8.2 Hz); 6.66
(1H, d, J = 8.1 Hz); 5.80–5.70 (1H, m); 5.22–5.16 (2H, m); 5.02–4.59 (2H, m); 4.83–4.77
(1H, m); 4.88 (1H, d, J = 10 Hz); 4.25 (1H, d, J = 10 Hz); 4.15 (2H, q, J = 7.1 Hz);
3.94–3.86 (1H, m); 3.80 (3H, CH3, s); 2.67 (1H, dd, J1 = 15.4 Hz, J2 = 12.6 Hz); 2.46
(1H, dd, J1 = 15.4 Hz; J2 = 7.3 Hz); 2.29–2.18 (2H, m); 2.14–1.98 (4H, m); 1.27 (3H,
CH3, t, J = 7.1 Hz). 13C NMR (ppm, CDCl3): 172.4; 172.0; 171.1; 159.7; 137.2; 135.7;
115.5; 114.2; 74.3; 72.0; 67.4; 61.0; 55.5; 50.7; 39.5; 36.6; 35.7; 29.5; 14.2. MS: M+H+,
498.2 (calcd), 498.2 (found).
2.6. 4(R)-(4-Methoxy-benzyloxy)-2(S)-(pent-4-enoyl)-amino-hexanedioic acid 6-ethyl
ester 1-(2-vinyl-but-2-enyl) ester (14b)
This compound was obtained in the same manner as described above for 14a. 1H NMR
(ppm, CDCl3): 7.40–7.26 (5H, m, aromatic); 7.25 (2H, d, J = 8.9 Hz); 6.87 (2H, d,
J = 8.9 Hz); 6.21 (1H, NH, d, J = 7.1 Hz, br); 5.86–5.70 (1H, m); 5.10–4.90 (3H, m);

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
475
4.63 (1H, q, J = 6.0 Hz); 4.47 (1H, d, J = 10.1 Hz); 4.28 (1H, d, J = 10.1 Hz); 4.14 (2H, q,
J = 7.1 Hz); 3.96–3.90 (1H, m); 3.80 (3H, s, CH3); 2.67 (1H, dd, J1 = 15.1 Hz,
J2 = 5.3 Hz); 2.51 (1H, dd, J1 = 15.1 Hz, J2 = 6.7 Hz); 2.37–2.30 (2H, m); 2.22–2.13
(4H, m); 1.26 (3H, t, J = 7.1 Hz). MS: M+H+, 498.2 (calcd), 498.2 (found).
2.7. 4(S)-(4-Methoxy-benzyloxy)-6-oxo-piperidine-2(S)-carboxylic acid benzyl ester
(15a)
Compound 14a (0.68 g) was dissolved in THF (10 ml). To this solution was added
water (10 ml) immediately followed by addition of iodine (1.05 g). The reaction mixture
was stirred vigorously for 30 min. Portions of sodium thiosulfate were added until the
reaction mixture was colorless. The reaction mixture was concentrated to dryness and then
resuspended in THF (10 ml). The solid was filtered and washed with THF (3 · 5 ml). The
THF solutions were combined, dried with sodium sulfate, and condensed to dryness. The
residue was applied to a silica gel column and eluted with a mixture of hexanes and ethyl
acetate (2:1). The ninhydrin positive fractions were collected and condensed to dryness to
yield the free amine. The amine was then dissolved in benzene (5 ml) and refluxed for 4 h.
The reaction mixture was condensed to dryness and the residue applied to a column of sil-
ica gel and eluted with ethyl acetate. Fractions that were UV positive were collected and
1
condensed to dryness to yield the cyclized product 15a (0.15 g, 29%) as an oil. H NMR
(ppm, CDCl3): 7.40–7.26 (5H, m, aromatic); 7.22 (2H, d, J = 7.8 Hz, aromatic); 6.87
(2H, d, J = 8.7 Hz, aromatic); 6.23 (1H, NH, s, br); 5.13 (1H, d, J = 12.1 Hz); 5.05
(1H, d, J = 12.1); 4.43 (1H, s); 4.13–4.08 (1H, m); 3.19–3.85 (1H, m); 3.80 (3H, CH3, s);
2.66 (1H, dd, J1 = 17.3 Hz, J2 = 5.0 Hz); 2.25 (1H, dd, J1 = 17.3, J2 = 6.4 Hz);
2.40–2.33 (1H, m); 2.33–2.25 (1H, m). 13C NMR (ppm, CDCl3): 171.2; 170.2; 159.5;
135.4; 130.1; 129.4; 128.8; 128.7; 128.6; 114.0; 70.3; 70.2; 67.7; 55.5; 52.1; 37.8; 30.0.
MS: M+H+, 370.2 (calcd), 370.2 (found).
2.8. 4(R)-(4-Methoxy-benzyloxy)-6-oxo-piperidine-2(S)-carboxylic acid benzyl ester
(15b)
Compound 15b was synthesized in the same manner as described for 15a from 14b with
a yield of 35%. 1H NMR (ppm, CDCl3): 7.43–7.34 (5H, m, aromatic); 7.24 (2H, d,
J = 8.6 Hz); 6.88 (2H, d, J = 8.6 Hz); 6.47 (1H, NH, s, br); 5.24 (1H, d, J = 12.4 Hz);
5.18 (1H, d, J = 12.4 Hz); 4.48 (1H, d, J = 11.5 Hz); 4.46 (1H, d, J = 11.5 Hz); 4.41
(1H, dd, J1 = 10.3 Hz, J2 = 4.6 Hz); 3.96 (1H, m); 3.81 (3H, s, CH3); 2.64–2.57 (1H, m);
2.49 (1H, dd, J1 = 17.8 Hz, J2 = 4.4 Hz); 2.46–2.39 (1H, m); 1.94–1.85 (1H, m). 13C
NMR (ppm, CDCl3): 171.4; 169.9; 159.9; 135.2; 130.0; 129.4; 129.0; 128.9; 128.7; 114.1;
70.4; 69.5; 67.8; 55.5; 51.2; 36.9; 30.1. MS: M+H+, 370.2 (calcd), 370.2 (found).
2.9. 4(S)-Hydroxy-6-oxo-piperidine-2(S)-carboxylic acid benzyl ester (16a)
Compound 15a (0.38 g) was added to 5 ml of TFA and the resulting dark red colored
solution was stirred at room temperature for 20 min and then condensed to dryness. The res-
idue was applied to a column of silica gel and chromatographed. The second series of UV
positive fractions were collected and condensed to dryness to yield product 16a as a colorless
solid (0.26 g, 99%). The product was recrystallized from chloroform and the single crystal

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Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
was used to determine the stereochemical configuration at the C4 position by X-ray
crystallography. The crystal structure analysis showed that C4 has the S-configuration.
1H NMR (ppm, CDCl3): 7.4–7.3 (5H, m, aromatic); 6.91 (1H, NH, br); 5.21 (1H, d,
J = 12.1 Hz); 5.17 (1H, d, J = 12.1 Hz); 4.24–4.17 (1H, m); 4.14–4.09 (1H, m); 3.24 (1H,
OH, s, br); 2.62 (1H, dd, J1 = 17.7 Hz, J2 = 4.7 Hz); 2.32–2.25 (1H, m); 2.25–2.15 (1H,
m). 13C NMR (ppm, D2O): 171.8; 171.1; 135.3; 128.9; 128.6; 67.8; 63.9; 52.0; 40.0; 32.5.
MS: M+H+, 250.1 (calcd), 250.1 (found).
2.10. 4(R)-Hydroxy-6-oxo-piperidine-2(S)-carboxylic acid benzyl ester (16b)
Compound 16b was synthesized following the procedure used above for 16a starting
1
from compound 15b and isolated as a colorless solid with a yield of 95%. H NMR
(ppm, CDCl3): 7.41–7.31 (5H, m, aromatic); 6.88 (1H, NH, s, br); 5.21 (1H, d,
J = 12.4 Hz); 5.17 (1H, d, 12.4 Hz); 4.48 (1H, dd, J1 = 10.27 Hz, J2 = 5.0 Hz); 4.31 (1H,
m); 3.62 (1H, OH, s, br); 2.56–2.43 (2H, m); 2.39–2.13 (1H, m); 1.88–1.80 (1H, m). 13C
NMR (ppm, CDCl3): 171.6; 171.2; 135.2; 128.95; 128.9; 128.6; 67.8; 62.9; 51.0; 39.5;
32.1. MS: M+H+, 250.1 (calcd), 250.1 (found).
2.11. 4(S)-Hydroxy-6-oxo-piperidine-2(S)-carboxylic acid (4)
Compound 16a (0.12 g) was dissolved in THF (5 ml) and to this solution was added the
catalyst Pd/C (20 mg). The suspension was then stirred under hydrogen for 8 h. The cat-
alyst was removed from the reaction mixture by filtration through a Celite pad (3 cm
thick) and washed with THF. The filtrate and washing solution were combined and con-
densed to dryness under reduced pressure to yield product 4 as a colorless crystalline solid
1
(64 mg) with a yield of 87%. H NMR (ppm, D2O): 4.16–4.08 (2H, m); 2.62 (1 H, ddd,
J1 = 17.5Hz, J2 = 5.22 Hz, J3 = 1.62 Hz); 2.33–2.4 (1H, m); 2.27 (1H, dd, J1 = 17.5 Hz,
J2 = 7.5 Hz), 1.99–1.90 (1H, m). 13C NMR (ppm, D2O): 173.8, 172.2, 63.8, 51.8, 39.4,
33.1. MS: M+H+, 160.0 (calcd), 160.0 (found).
2.12. 4(R)-Hydroxy-6-oxo-piperidine-2(S)-carboxylic acid (5)
Compound 5 (0.058 g), a colorless crystalline solid was synthesized from compound 16b
1
(0.098 g) following the procedure described above for compound 4 with a yield 93%. H
NMR (ppm, D2O): 4.21 (1H, dd, J1 = 8.3 Hz, J2 = 5.21 Hz), 4.12–4.07 (1H, m), 2.48
(1H, dd, J1 = 17.6 Hz, J2 = 4.6 Hz), 2.21 (1H, ddd, J1 = 17.6 Hz, J2 = 4.8 Hz,
J3 = 1.5 Hz), 2.13–2.06 (1 H, m), 1.95–1.88 (1 H, m). 13C NMR (ppm, D2O): 175.1,
173.3, 63.5, 52.1, 40.2, 33.4. MS: M+H+, 160.0 (calcd), 160.0 (found).
2.13. 4,6-Dioxo-piperidine-2-(S)-carboxylic acid (3)
Di-tert-butyl-(2S)-4,6-dioxo-1,2-piperidine dicarboxylate (1.54 g) was added to TFA
(10 ml). The resulting solution was stirred at room temperature for 1 h and then condensed
to dryness. After the residue was washed with ethyl ether (3 · 10 ml), the solid was dried
under reduced pressure to yield the ketone 3 as a colorless solid. The ketone form domi-
nates (67%) in aqueous solution at pH 2. The other component of the solution is the hy-
drate 7 (33%), which is characterized below. Compound 3: 1H NMR (ppm, D2O): 4.4 (1H,

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
477
dd, J1 = 6.5 Hz, J2 = 5.3 Hz); 2.91 (1H, dd, J1 = 17.1 Hz, J2 = 6.5 Hz); 2.73 (1H, dd,
J1 = 17.1 Hz, J2 = 5.1 Hz). 13C NMR (ppm, D2O): 206.6; 174.3; 172.1; 51.2; 46.6; 40.1.
MS: MꢁH+, 156.0 (calcd), 156.0 (found).
2.14. 4,4-Dihydroxy-6-oxo-piperidine-2(S)-carboxylic acid (7)
1H NMR (ppm, D2O): 4.16 (1H, dd, J1 = 6.8 Hz, J2 = 6.3 Hz); 2.25 (1H, dd,
J1 = 13.7 Hz, J2 = 6.3 Hz); 2.17 (1H, dd, J1 = 13.8 Hz, J2 = 6.8 Hz). 13C NMR (ppm,
D2O): 175.4; 172.9; 91.8; 52.2; 43.8; 35.9. MS: M+H+, 176.0 (calcd), 176.0 (found).
2.15. Dianion of 1,2,3,6-tetrahydro-4-hydroxy-6-oxo-piperidine-2(S)-carboxylic acid (9)
Ketone 3 exits solely as the dianion after titration to pH 10 with potassium hydroxide
(10 M in H2O). 1H NMR (ppm, D2O–H2O = 1:4): 6.01 (1H, br), 4.41 (1H, br), 3.9 (1H, t,
J = 7.5 Hz), 2.44 (1H, dd, J1 = 16.5 Hz, J2 = 6.8 Hz), 2.35 (1H, dd, J1 = 16.5,
J2 = 8.8 Hz). 13C NMR (ppm, D2O–H2O = 1:4): 185.1; 179.6; 175.6; 88.4; 54.9; 36.2.
2.16. (S)-1,2,3,6-Tetrahydro-6-oxopyridine-2-carboxylic acid (6)
Neat trifluoroacetic acid (2 ml) was added to a solution of 20 (238 mg) in dichlorometh-
ane (2 ml). The resulting solution was stirred at room temperature for 2 h and then con-
densed to dryness under reduced pressure. The residue was washed with ethyl ether
(3 · 10 ml) and dried under reduced pressure to yield the crystalline product 6 (106 mg,
94%). 1H NMR (ppm, D2O): 6.72–6.66 (1H, m), 5.8 (1H, dt, J1 = 10.7 Hz,
J2 = 1.77 Hz), 4.24 (1H, t, J = 6.6 Hz), 2.81–2.67 (2H, m). 13C NMR (ppm, D2O):
173.2, 166.9, 140.7, 123.8, 52.0, 26.5. MS: M+H+, 142.0 (calcd), 142.0 (found).
3. Results and discussion
3.1. Synthesis of inhibitors
The syntheses of alcohols 4 and 5 were carried out following the pathway shown in
Scheme 5. Commercially available N-tert-butoxycarbonyl-a-O-benzyl-S-aspartic acid
(10) was activated by reaction with carbonyl diimidazole (CDI) in THF and then reacted
with the magnesium salt of ethyl hydrogen malonate to yield the b-ketone 11 [20,21]. The
Boc group in 11 was changed to pent-4-enyl, which can be selectively cleaved under oxi-
dation by I2 [22]. This transformation gave 12 in 85% yield upon cleavage of the Boc pro-
tecting group with TFA and subsequent acylation with pent-4-enoic anhydride. Reduction
of 12 with NaBH4 in methanol provided the diasteromeric mixture of alcohols 13a and b in
a ratio of about 1:1, and subsequently resolved from one another by silica gel chromatog-
raphy. After the alcohols were protected to yield 14a and b with a p-methoxybenzyl group
[23,24], the pent-4-enyl group was selectively cleaved to yield the corresponding amines
which partially cyclized during purification on silica gel. After the crude amine was re-
fluxed in benzene for 8 h, the cyclization was complete to give the products 15a and b.
Treatment of 15a and b in dichloromethane with TFA yielded the corresponding alcohols,
16a or b, quantitatively. Reduction of 16a or b by Pt-catalyzed hydrogenation yielded the
desired product 4 or 5 in quantitative yield. A single crystal of 16a was recrystallized from

478
Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
O
O
Bn
O
O
OH
Bn
O
O
Bn
O
O
Bn
O
O
O
O
O
O
EtO
EtO
NH
NH
O
HO
EtO
HN Boc
HN Boc
O
10
11
13a, 13b
12
PMBn
OH
OH
O
PMBn
O
O
Bn
O
O
EtO
O
N
H
COOH
NH
O
N
H
COOBn
O
N
H
COOBn
O
4, 5
16a, 16b
15a, 15b
14a, 14b
Scheme 5.
chloroform and the structure solved by X-ray crystallography. The structure of 16a is pre-
sented in Fig. 1. The structural analysis showed that C4 in 16a has the S-configuration and
thus C4 in 16b is of the R-configuration.
A more convenient pathway to compounds 3, 4, and 6 starting from compound 17 was
described by Marin et al. as shown in Scheme 6 [25]. Deprotection of 18–20 by neat TFA
gave 3, 4, and 6 in quantitative yield. The NMR spectra of 4 made from 16a are consistent
with those of 4 made from 19, and thus the stereochemistry at C4 is of the S-configuration.
No racemization of the carbon at C2 was observed in any of the reactions described above.
1
The H NMR spectrum of 3 in DMSO-d6 shows that 3 exists as two tautomeric forms
(Fig. 2A). The two doublets at 3.22 and 3.08 ppm are characteristic of the resonances for
the two protons attached to C5 of ketone 3. The other proton signals are assigned based
on the integral ratio, chemical shifts, and splitting patterns. The signals at 4.79 and
10.48 ppm, which show coupling with none of the other protons, are assigned to the
hydrogen at C5 and the hydroxyl of enol 8, respectively. The ratio of ketone 3 to enol 8
Figure 1. Crystal structure of compound 16a with H atoms omitted except for those at C4 and C6. This structure
confirms the S-stereochemistry at C4. The carbon, oxygen, nitrogen, and hydrogen atoms are presented as gray,
red, blue, and white spheres, respectively. (For interpretation of the references to colors in this figure legend, the
reader is referred to the web version of this paper.)

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
479
O
OH
O
O
tBu
O
HO
O
N
COOtBu
HN Boc
O
N
COOtBu
O
N
COOtBu
Boc
Boc
19
Boc
18
17
20
O
OH
O
N
H
COOH
O
N
H
COOH
O
N
H
COOH
6
4
3
Scheme 6.
A
3H5
3H3
3H2
8H3
8H2
B
3H3
3H2
21H3
21H2
8H3
8H2
C
3H3
3H2
7H3
7H2
8H2
8H3
4.6
4.2
3.8
3.4
3.0
2.6
2.2
ppm
Figure 2. 1H NMR of ketone 3 at 300 MHz. The solvent used in these spectra are (A) DMSO-d6; (B) CD3COD;
and (C) D2O.
is about 2:1. The 1H spectrum of 3 in deuterated methanol shows no signal for the C5 pro-
tons due to exchange between these protons and the deuterium of the solvent (Fig. 2B).
However, the characteristic signals for the protons at C2 and C3 of the ketone 3 and enol
8 are clearly present. In addition to these signals, two more sets of resonances appear at
4.14, 4.08, 2.38, and 2.06 ppm and are assigned to the protons at C3 and C2 of the two
diastereomers of hemiacetal 21. The 1H NMR spectrum of ketone 3 in D2O at pH 1.8 indi-
cates that ketone 3 and its hydrate 7 are the dominant species but some enol 8 is observed
(Fig. 2C). The resonances at 4.15 ppm and those at 2.25 and 2.17 ppm are assigned to the
C2 and C3 protons of the hydrate 7.

480
Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
A
3C4
7C4
B
C
3C4
7C4
9C5
200
180
160
140
120
100
80
60
40 ppm
Figure 3. 13C NMR spectra of ketone 3 in aqueous solution at different pH values. (A) 1.9; (B) 7.0; and (C) 10.
The identification of ketone 3 and hydrate 7 and enolate 9 is also confirmed by mea-
surement of the 1H and 13C NMR spectra of ketone 3 in aqueous solutions at various val-
ues of pH (Fig. 3). The 13C NMR spectra of ketone 3 show two sets of signals at pH 1.8
and 7.0 (Figs. 3A and B). The dominant species is ketone 3 and is indicated by the reso-
nance at 207.8 ppm corresponding to the signal for the carbonyl carbon at C4 of ketone 3.
The other characteristic resonance at 92.4 ppm is assigned to C4 of hydrate 7. This later
assignment is also supported by the absence of this resonance in a proton-attached DEPT
spectra obtained with ketone 3 in a mixture D2O and H2O. As the pH increases around 8,
the relative amount of hydrate and ketone decrease and that of the enol or enolate in-
1
crease. Both the H NMR and 13C NMR resonances of the ketone, enol, and enolate
(which can be observe when the pH is higher than 7) are broadened at pH ꢀ 8. The broad-
ening of the NMR signals indicate an intermediate exchange rate between ketone 3 and
enol 8 or enolate 9. When the pH is greater than 8, the enolate dominates the distribution
of species. When the pH is 10 only the enolate 9 can be observed in the 1H and 13C NMR
spectra (Fig. 3C). The characteristic signal of C5 of enolate 9 appears at 88.4 ppm. This
signal also appears in the DEPT spectra as one of the CH carbon atoms that confirms
the identification of the enolate 9. The UV spectrum of ketone 3 in aqueous solution varies
with changes in pH. A new species appears with a maximum absorption at 277 nm when
the pH is greater than 7 (Fig. 4). This species should be the enol or enolate as indicated by
1
the H and 13C NMR spectra. The pKa for the absorbance change is 8.2.
3.2. Inhibition of dihydroorotase
Compounds 3–6 were tested as inhibitors of the reaction catalyzed by the dihydrooro-
tase from E. coli. A summary of the kinetic constants are presented in Table 1. All of the
compounds were found to be competitive inhibitors versus dihydroorotate and thio-dihy-
droorotate. Compounds 4–6 are relatively weak competitive inhibitors versus thio-dihy-
droorotate at pH 8. The Ki values varied from 1.6 to 3.0 mM. The variations in the

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
481
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
5
6
7
8
9
10
11
pH
Figure 4. Change in absorbance at 277 nm of ketone 3 (27 lM) as a function of pH.
Table 1
Inhibition of dihydroorotase by compounds 3–6a
Compound
pH
3
3
3
4
5
6
7.0
8.0
9.0
8.0
8.0
8.0
Ki
Dihydroorotate
Thio-dihydroorotate
76
96
4
7
210 10
120
440 65
320 32
NA
3000 300
NA
1600 340
NA
2300 160
5
a
The data were fit to Eq. (2).
functional group attached to C4 do not contribute significantly to binding to the active
site. It was anticipated that the attachment of a hydroxyl group at C4 would mimic
and/or replace the hydroxide that bridges the two divalent cations within the active site
of DHO. In the crystal structure of DHO complexed with dihydroorotate in the active site
˚
the bridging hydroxide is 2.8 A away from the re-face of the amide group of the substrate
[12]. This observation would predict that compound 5 should be a better inhibitor than the
diastereomer 4. In fact the Ki for 5 is approximately two-fold smaller than the Ki for 4. If
the hydroxyl group in 4 or 5 binds predominantly to the b-metal ion then one would also
predict that 5 would be bound more tightly than 4. The introduction of a double bond be-
tween carbons 4 and 5 in compound 6 did not significantly enhance or diminish the ability
of this compound to bind to the active site of DHO. The relatively small competitive inhib-
itory activities exhibited by compounds 4–6 can largely be attributed to anchoring inter-
action of the free carboxylate group that has been determined to electrostatically
interact with Asn-44, Arg-20, and His-254 in the enzyme [12].
The ketone 3 is the most active inhibitor among the four compounds prepared for this
investigation. The ketone group at C4 can be hydrated in aqueous solution and the acidic
protons at C5 can promote the formation of the enolic form of 3. The composition of pos-
sible structures in solution is variable with pH. At low pH the NMR spectrum of ketone 3
indicates that it is a mixture of the ketone 3 and the hydrate 7. The ratio of 3 to 7 at low

482
Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
pH is 2:1. As the pH is raised to 7, ketone 3, enol 8, and hydrate 7 are the dominant species
in the ratio of 1.0:1.0:0.6. At pH 8 the enol 8, enolate 9, and hydrate 7 are found in a ratio
of 1.0:1.0:0.2. At pH 9, only enolate 9 is found in solution. In the inhibition experiments,
ketone 3 showed the strongest inhibition at pH 7 and the apparent Ki is comparable to the
Km of the substrate dihydroorotate. As the pH of the medium increases the composite Ki
for compound 3 also increases. These results indicate that ketone 3 and/or hydrate 7 are
more inhibitory than the enol 8 and/or enolate 9.
The best inhibitor of DHO reported to date is cis-4-carboxy-6-(mercaptomethyl)-
3,4,5,6-tetrahydropyridin-2(1H)-one, 22, with a Ki of 0.14 lM [8]. The strong binding to
the active center has been attributed to the strength of the interaction of Zn(II) to the thiol
substituent in 22 relative to the same interaction with an oxygen in either a hydroxyl or
carbonyl functional group. The carboxylate analogue, 23, was found to bind to DHO
about 30 times stronger than dihydroorotate [9]. The strong binding can be attributed
to the chelation of the C4 carboxylate to either of the two zinc ions within the active site.
Analogues designed to mimic potential transition-state structures such as 24 were found to
have no significant inhibitory activity against DHO [9]. The three phosphinate mimics, 25,
26, and 27, of the transition-state showed surprisingly weak inhibition against DHO from
hamster with Ki values of 4.0, 2.9, and 3.1 mM, respectively [10,11]. A promising transi-
tion-state analogue inhibitor 28 has been suggested by Levenson and Meyer but this com-
pound has thus far eluded synthesis [7]. The structures of 22–28 are presented in Scheme 7.
3.3. Substrate activity of 4–6
DHO has the demonstrated catalytic activity for the addition and release of water from
dihydroorotase and carbamoyl aspartate. Therefore we felt that it may be possible for
DHO to catalyze the hydration of alkene 6 to form either alcohol 4 or 5. Alternatively,
alcohols 4 and/or 5 could be dehydrated to 6, depending on the thermodynamic equilib-
rium constant between the alkene and alcohol. To determine if DHO is able to catalyze the
interconversion between alcohols 4 or 5 and the alkene 6, each of these compounds was
incubated with DHO for 40 h in aqueous solution at pH 8 buffered with phosphate. In
these assays, the final concentration of the enzyme, substrate analogue (4, 5, or 6) and
the buffer were 1.8 · 10ꢁ3 mM, 1.0 and 100 mM, respectively. The changes in the absor-
bance were monitored from 200–300 nm at various times up to 40 h. The alkene 6 shows
a broad absorbance that occurs at 248 nm due to conjugation with the carbonyl group at
C6. After 40 h we could obtain no evidence for enzymatic equilibration between 6 and
either 4 or 5. The estimated upper limit to the hydration/dehydration reaction is 0.1 sꢁ1
.
In summary, compounds 3–6 have been synthesized and assayed for their inhibitory
activity against dihydroorotase from E. coli. The inhibitory activity of ketone 3, the hy-
drate 7 and the two tautomers, enol 8 and enolate 9, were measured as a function of
HS
HN
HO
HN
O
O
O
O
O
O
O
OH
SH
SH
OH
S
P
P
P
P
HN
HN
O
N
H
COOH
O
N
H
COOH
O
N
H
COOH
O
N
H
COOH
O
N
H
COOH
O
N
COOH
O
N
COOH
H
H
22
23
24
25
Scheme 7.
26
27
28

Y. Li, F.M. Raushel / Bioorganic Chemistry 33 (2005) 470–483
483
pH. The inhibitory activities of these compounds and the tautomeric forms of 3 increases
in the following order 4 < 6 < 5 < 8, 9 < 3, 7. Compounds 3 and 7 may form transition-
state like structures in the active site of DHO and provide the strongest inhibition among
the compounds synthesized for this investigation. DHO does not catalyze the elimination
of water from alcohols 4 or 5 or the hydration of ketone 6.
Acknowledgment
We thank Dr. Tamiko Porter for the preparation of the dihydroorotase used in this
investigation.
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