Antibacterial barbituric acid analogues inspired from natural 3-acyltetramic acids; Synthesis, tautomerism and structure and physicochemical property-antibacterial activity relationships

Article abstract of DOI:10.3390/molecules20033582

The synthesis, tautomerism and antibacterial activity of novel barbiturates is reported. In particular, 3-acyl and 3-carboxamidobarbiturates exhibited antibacterial activity, against susceptible and some resistant Gram-positive strains of particular inter

Full text of DOI:10.3390/molecules20033582

Molecules 2015, 20, 3582-3627; doi:10.3390/molecules20033582
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Antibacterial Barbituric Acid Analogues Inspired from
Natural 3-Acyltetramic Acids; Synthesis, Tautomerism and
Structure and Physicochemical Property-Antibacterial
Activity Relationships
Yong-Chul Jeong and Mark G. Moloney *
Chemistry Research Laboratory, Mansfield Rd, University of Oxford, OX1 3TA, UK;
E-Mail: ycjchem@gmail.com
* Author to whom correspondence should be addressed; E-Mail: mark.moloney@chem.ox.ac.uk;
Tel: +44-186-527-5656.
Academic Editor: Peter J. Rutledge
Received: 7 January 2015 / Accepted: 12 February 2015 / Published: 20 February 2015
Abstract: The synthesis, tautomerism and antibacterial activity of novel barbiturates is
reported. In particular, 3-acyl and 3-carboxamidobarbiturates exhibited antibacterial
activity, against susceptible and some resistant Gram-positive strains of particular interest
is that these systems possess amenable molecular weight, rotatable bonds and number of
proton-donors/acceptors for drug design as well as less lipophilic character, with
physicochemical properties and ionic states that are similar to current antibiotic agents for
oral and injectable use. Unfortunately, the reduction of plasma protein affinity by the
barbituric core is not sufficient to achieve activity in vivo. Further optimization to reduce
plasma protein affinity and/or elevate antibiotic potency is therefore required, but we
believe that these systems offer unusual opportunities for antibiotic drug discovery.
Keywords: barbiturates; antibacterial; synthesis; tautomerism
1. Introduction
The use of natural products as leads for antibacterial drug discovery is enjoying a resurgence of
interest, forced by the failure of existing drug discovery strategies, the particular requirements of
antibacterial therapies, the emergence of virulent bacterial strains and the paucity of new development

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candidates working their way through the drug development pipeline [1,2]. In this regard, the tetramic
acid scaffold (especially with a 3-acyl side chain moiety) [3–8] is of particular interest, since naturally
occurring 3-acyltetramic acids such as reutericyclin (bacterial membrane disruption) [5], streptolydigin
(bacterial RNA polymerase (RNAP) inhibitor) [6], kibdelomycin (bacterial type II topoisomerase
inhibitor) [7] and signermycin B (the dimerization domain of histidine kinase WalK inhibitor) [8] all
exhibit antibacterial activity with novel modes of action. Aiming to develop both the biological activity
and bioavailability of these systems, methodology for the modification of ring substituents in natural
3-acyltetramic acids (R1-R4 in 1a) [9–14] as well as the replacement of the 3-acyl side chain group by
3-carboxamide (1b) [13,15–18] and 3-enamine functionalities (1c, Figure 1) [13,19] has been reported.
These investigations revealed that 3-acyl 1a and 3-carboxamide 1b substitutions can impart good
antibacterial activity, resulting from novel modes of action including bacterial membrane disruption,
inhibition of bacterial RNAP or undecaprenyl pyrophosphate synthase (UPPS), while 3-enamine 1c
exhibits much weaker antibacterial activity and without a clear mode of action. Furthermore, it has been
found that the 5-membered tetramic acid core scaffold may also be replaced by the 6-membered
piperidine-2,4-dione unit with 3-acyl (1d) [14] and 3-carboxamide (1e) [16,18] pendant functionality,
and that these systems show similar antibacterial activity and mode of action compared to tetramates 1a,b.
Figure 1. Optimization of core scaffold.
Although 3-acyl and 3-carboxamide tetramate analogues reported in our previous papers [13–15]
showed good antibacterial activity, novel modes of action and acceptable toxicity, their high plasma
protein binding (PPB) affinity interfered with further biological study in vivo for antibiotic drug
discovery. In order to overcome this PPB affinity, we decided to conduct further structural optimization
of the core scaffold, by moving from the tetramic acid to the 6-membered barbituric acid system. This
scaffold possesses similar chemical structure compared to tetramic acids and piperidine-2,4-diones
(especially around the C(3) position), but importantly has additional polar functional groups at the 5-
and 6-positions, and we expected that these groups might help to reduce PPB affinity. Further validation
of this proposal comes from the fact that arylidene barbituric acids 1f are reported to have mild
antibacterial activity [20–23]. In this paper, with the inspiration from related analogues 1a–f, novel
barbituric acids 2–28 (with 3-acyl), 29–32 (with 3-carboxamide) and 33–37 (with 3-enamine) have been
prepared and their tautomeric behavior, antibacterial activity and structure-activity relationships (SARs)
have been studied. Furthermore, in order to understand trends of biological activity for further drug
optimization, their physicochemical property-activity relationships have been investigated and compared
with the tetramic acids reported in our previous papers [13–15,19] as well as clinical antibiotics. To the

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best of our knowledge, the antibacterial activity of 3-acylbarbituric acids with only limited functionality
has been reported in the literature [20,21], and the 3-carboxamide and the 3-enamine analogues are as
yet completely unreported.
2. Result and Discussion
2.1. Synthesis
The starting barbituric templates 40a–c were prepared by known methods, while templates 40d,e
were commercially available (Scheme 1). Thus, urea 39a–c was condensed with malonic acid in the
presence of acetic acid and acetic anhydride to provide barbituric acids 40a–c, respectively [24].
N-Disubstituted 40b,c, along with 3-acetyl 2b,c [20,25] as minor products, respectively, could be
purified by flash column chromatography, while N-monosubstituted 40a was best obtained by
precipitation in ethyl acetate solution. For this reaction, urea 39c was efficiently obtained from amine 38
and ethyl isocyanate [20,26], while ureas 39a,b were commercially available.
Scheme 1. Synthesis of barbituric acid analogues. Reaction conditions; (a) ethyl isocyanate
(1.0 eq), CH2Cl2, 0 °C ; (b) malonic acid (1.0 eq), acetic acid, acetic anhydride, 60–90 °C ;
(c) 3,5,5-trimethylhexanoyl chloride (1.1 eq), triethylamine (1.2 eq), CH2Cl2, r.t.; (d) DMAP
(1.2 eq), CH2Cl2, r.t.; (e) R3CO2H (1.1 eq), DCC (1.1 eq), DMAP (1.2 eq), CH2Cl2, r.t.;
(f) RNH2 (1.0 eq), toluene, reflux; (g) RNH2 (1.1 eq), CH3OH, reflux; (h) butyl
chloroformate (1.2 eq), DMAP (2.2 eq), CH2Cl2, r.t.; Abbreviation; DCC; N,N′-
dicyclohexylcarbodiimide, DMAP; 4-(dimethylamino)pyridine.

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With templates 40a–e in hand, the synthesis of 3-acyl, 3-carboxamide and 3-enamine tetramic acids
using recently reported approaches were successfully applied to the synthesis of the corresponding
barbituric acid analogues [13–15,19,27]. 3-Acyl analogues 3–28 (with the exception of 5a) were
prepared via direct 3-acylation of templates 40a–e with the required carboxylic acid promoted by 1.1
equivalent of DCC and 1.2 equivalent of DMAP, while stepwise 3-acylation via O-acylation using the
acid chloride in the presence of triethylamine followed by acyl migration promoted by DMAP
(1.2 equivalent) gave analogue 5a. Although other synthetic methods for 3-acylbarbituric acids have
been reported [20–21,28–30], this direct acylation approach provides efficient access to systems with a
wide variety of substituents at the acyl group. Furthermore, it is also applicable to N-unsubstituted,
-mono and di-substituted barbituric acids. 3-Enamines 33–37 were prepared by reaction of the
corresponding 3-acyl analogue with an amine in refluxing toluene [25,31–33]. In the case of compound
36, methanol instead of toluene was required as solvent. Alternatively, 3-alkoxycarbonyl barbiturates
42a–d needed as starting materials for 3-carboxamides 29–32 were conveniently prepared from the
corresponding barbituric acids by treatment with butyl chloroformate in the presence of 1.2 equivalents
of DMAP. Conventional direct amine exchange of the 3-alkoxycarbonlys in toluene allowed preparation
of 3-carboxamides 29–32. To the best of our knowledge, this is the first example of the preparation of
3-carboxamidobarbituric acids.
2.2. Tautomerism
Similar to tetramic acid derivatives [14,15,19,27], 3-acyl, 3-carboxamide, 3-alkoxycarbonyl and
3-enamine barbituric acids can exist as endo- and exo-enol and keto tautomers in solution (Figure 2). In
the case of barbiturates derived from symmetrical barbituric acids 40b,d,e, one set of peaks in their NMR
spectra was observed, while in the case of asymmetric barbituric acids 40a,c, split signals (rather than
two sets from two tautomeric isomers) were observed. The enol tautomer was assigned from the
chemical shift of the C(3)-carbon (80–90 ppm for sp2 carbon) as well as the absence of the H(3)-proton
signal. The observation of one set of signals for endo- and exo-enol tautomers supports the fact that
equilibration between endo- and exo-enol tautomers is fast on the NMR time scale, resulting in
coalescence of the peaks of the two enol tautomers.
In order to identify the favored enol-form, the ground state energies of simplified analogues, 3-acyl
2a, 3-carboxamide 43a, 3-alkoxycarbonyl 43b and 3-enamine 43c in endo- and exo-enol tautomers were
calculated (Figure 2). The exo-enol form of 3-acyl 2a and endo-enol form of 3-alkoxycarbonyl 43b were
found to be more stable than the alternative enol form, and these results are similar to the favoured
tautomer of tetramic acids [15,27]. In contrast, 3-carboxamidobarbiturate 43a favours the exo-enol
tautomer, while the corresponding 3-carboxamidotetramate favours the endo-enol tautomer [15]. In the
case of 3-enamine 43c, the ground state energy of the endo-enol tautomer is much less stable than the
exo-enol tautomer (compare the geometry of 3-enamine 43c between endo- and exo-enol tautomers in
Supplementary Figure 1g,h in the Supporting Information). From this computational result, 3-acyl,
3-carboxamide and 3-enamine barbituric acids all preferentially exist as exo-enol tautomers, and
3-alkoxycarbonyl as endo-enol tautomers. In addition, HMBC NMR spectra of representative analogues
were acquired and the correlations for the main ring were established (Supplementary Figure 2 in

Molecules 2015, 20
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Supporting Information). In this assignment, the free carbonyl (around 160 ppm) and hydrogen-bonded
carbonyl (165–170 ppm) on C(2) and (C4) were readily identified.
Figure 2. Tautomeric behavior of barbituric acid analogues; the energy difference between
endo- and exo-enol tautomers (∆E = Eendo − Eexo) was calculated by using DFT B3LYP
(6-31G*) in Spartan 02.
2.3. Antibacterial Activity
Minimum inhibition concentration (MIC) values for the in vitro in vitro antibacterial activity of 73
barbiturates was determined (shown in Table 1) against Gram-positive bacteria such as Staphylococcus
aureus (methicillin sensitive S1, vancomycin susceptible S26, non-resistant S4 and methicillin-resistant
in vivo, MRSA, S2), Enterococcus faecalis (vancomycin susceptible, VSE, E1), E. faecium (vancomycin
resistant, VRE, E2) and S. pneumonia (erythromycin susceptible P1 and multi drug resistant, MDRSP,
P9) as well as Gram-negative bacteria such as Pseudomonas aeruginosa, Escherichia coli (efflux-positive
Ec50 and -negative Ec49) and Haemophilus influenzae (efflux-positive H3 and -negative H4). In general,
the activity trend for barbiturates is similar to that for tetramates [13–15,19,34]; firstly, none of the analogues
was active against both P. aeruginosa and efflux-positive and -negative E. coli, (MIC ≥ 32 µg/mL) while
the activity against the other strains depended on their ring substituents. Secondly, templates 40a–e,
3-alkoxycarbonyls 42a–d, and O-acyl derivative 41 did not exhibit antibacterial activity against any
strains, while the activity of 3-acyls 2–28 (Figure 3), 3-carboxamides 29–32 and 3-enamines 33–37
(Figure 4) depended both upon the identity of the bacterial strains as well as their chemical substituents,
with 3-acyls and 3-carboxamides tending to be more effective than 3-enamines. Third, N-disubstituted
barbituric acids (especially 3-acyls) exhibited excellent activity whereas N-monosubstituted and
N-unsubstituted analogues were inactive (see below in detail). These two results reveal that the
functional group located on the C(3) position, as seen for tetramates (e.g., 3-acyl and 3-carboxamide),
as well as the N-substitution in the barbituric acid templates, are critical factors for the observation of

Molecules 2015, 20
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antibacterial activity. Lastly, of particular importance is that, depending on the substituents, the
analogues exhibited excellent antibacterial selectivity against resistant and susceptible strains (S1, S26,
S2, E1, E2, P1 and P9). By comparison, the activity of ciprofloxacin against MRSA S2 and VRE E2 and
amoxicillin against MDRSP P9 dropped more than 50-fold compared to that of the non-resistant
strain [15]. In conclusion, 3-acyls 7a,b and 3-carboxamides 32 possessing adamantyl groups exhibited
excellent antibacterial activity against Gram-positive strains and Gram-negative H. influenzae (MIC; up
to 0.25 µg/mL).
Figure 3. 3-Acylbarbituric acids (50 analogues).

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Figure 4. 3-Carboxamides (7 analogues) and 3-enamine (6 analogues) barbituric acids.
Despite replacement of the tetramic acid with the more hydrophilic barbituric acid core, PPB affinity
of barbiturates was only slightly reduced when compared with that of tetramates [13–15,19]; overall,
MICs of barbiturates against S. pneumonia P9 in the presence of 2.5% horse blood were only slightly
shifted from the values without blood (Table 1). For example, (±)-5a,b, 6a,b, 7a,b, 8a,b and 18b,g
against S. aureus S26 in the presence of 10% human serum exhibited weak activity (MIC = 64 µg/mL)
which were approximately 4-fold worse compared to those without serum. Moreover, it appears that the
3-acyl group might be better than the 3-carboxamide group for PPB binding in this family ((±)-5b; 8 to
64 µg/mL versus 31a; 8 to >64 µg/mL, and 6a; 16 to 64 µg/mL and 7a; 1 to 64 µg/mL versus 32; 1 to
>64 µg/mL by 10% human serum).
Table 1. In vitro antibacterial activity (MIC, µg/mL) of barbituric acid analogues a−f
.
S1
16
4
S26
16
8
S26S
64
S4
16
4
S2
16
8
E1
16
4
E2
16
8
P1
8
P9
8
P9B
8
H3
8
H4
4
(±)-5a
(±)-5b
(±)-5c
6a
64
4
4
4
32
64
8
8
8
32
16
8
>64
64
32
8
16
16
8
16
8
16
8
16
8
16
8
16
8
32
2
8
6b
4
64
4
4
8
4
4
4
16
64
8
4
6c
8
8
>64
64
4
4
4
4
4
4
4
16
1
c
7a
-
1
2
2
1
2
0.5
2
0.5
2
2
7b
0.5
16
4
2
64
2
1
0.5
8
1
4
16
8
8
8a
16
4
64
16
2
16
4
16
2
8
8
8
2
8b
64
0.5
32
>64
1
1
1
8
2
9
32
>64
32
>64
>64
>64
16
>64
32
>64
16
>64
16
64
16
64
16
8
>64
>64
16
64
14

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Table 1. Cont.
S1
>64
32
>64
64
8
S26
S26S
S4
>64
32
>64
64
8
S2
E1
>64
32
64
64
8
E2
P1
32
32
32
32
4
P9
32
16
32
32
4
P9B
>64
16
32
32
4
H3
>64
>64
>64
16
16
32
16
>64
16
16
8
H4
64
8
c
c
15a
15b
16
-
-
>64
32
>64
64
8
>64
32
64
64
4
64
>64
>64
8
>64
>64
>64
>64
>64
64
8
17a
17c
18a
18b
18c
18e
18f
8
2
32
4
64
4
64
4
64
4
32
2
32
4
32
2
32
2
32
4
4
2
64
8
64
8
>64
>64
>64
64
64
8
64
8
64
4
16
4
32
4
32
4
64
8
32
2
4
4
4
4
4
4
2
2
2
2
18g
19a
19b
20
8
8
4
4
4
4
2
2
4
2
1
2
>64
>64
>64
>64
>64
>64
>64
>64
>64
>64
>64
>64
2
2
2
1
2
0.5
8
0.5
8
4
16
32
16
8
8
16
4
16
8
16
8
16
8
8
16
2
8
8
4
2
2
4
2
22
64
64
>64
64
32
32
8
64
64
>64
64
>64
64
8
32
64
>64
64
64
16
8
64
32
>64
32
32
32
4
32
32
>64
64
>64
64
8
32
64
64
64
64
64
8
32
64
>64
64
64
64
8
32
64
>64
>64
64
>64
8
32
>64
>64
>64
64
>64
8
4
23a
26c
26d
29a
30
32
32
32
32
32
64
64
2
16
64
16
16
16
8
31a
31b
32
Lined
Cipd
Amod
2
4
4
4
4
8
4
4
4
4
1
1
0.5
2
1
0.25
2
0.5
2
0.25
1
0.25
0.5
1
0.5
0.5
1
0.25
4
2
2
2
16
0.5
0.12
0.5
0.5
0.12
16
1
32
1
≤0.06
c
c
c
c
c
c
c
c
c
c
-
-
-
-
-
-
-
>0.03
8
-
-
-
Notes: a; Abbreviation; S1; S. aureus 1, ATCC13709 in vivo (methicillin sensitive), S26; S. aureus 26,
ATCC25923 (vancomycin susceptible), S26S; S. aureus 26 in presence of 10% human serum, S4; S. aureus 4,
Oxford, S2; S. aureus 2, MRSA in vivo (methicillin resistant), E1; E. faecalis 1, ATCC29212 VanS
(vancomycin susceptible), E2; E. faecium 1, VanA (vancomycin resistant), P1; S. pneumonia 1, ATCC49619
(erythromycin susceptible), P9; S. pneumonia 9, PenR (penicillin and erythromycin resistant), P9B;
S. pneumonia 9 in presence of 2.5% horse blood, H3; H. influenzae 3, ATCC31517 MMSA, H4; H. influenzae
4, LS2 Efflux knock-out, Line; linezolid, Cip; ciprofloxacin, Amo; amoxicillin, b; All analogues are inactive
against E. coli 1, ATCC25922 (non Pathogenic strain), E. coli 50, Ec49 No Efflux and P. aeruginosa 1,
ATCC27853 (MIC > 32 μg/mL), c; Not determined, d; reported in our previous papers [13–15,19], e; 3-Acyls
2a–c, 3, cis-11–13, 17b, 25a, (±)-25b and 26a,b, 3-carboxamides 29b,c, 3-enamines 33a,b, 35 and 36,
3-alkoxycarbonyls 42a-d, O-acyl 41 and barbituric acid templates 40a-e were inactive against all strains (MIC >
32 μg/mL), f; 3-Acyls 4, (±)-10, 18d, 21, 23b and 24 and 3-enamines 34 and (±)-37 were only mild active
against H4 (8 ≤ MIC ≤ 32 μg/mL) while they were inactive against the other strains (MIC > 32 μg/mL).

Molecules 2015, 20
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2.4. Structure-Activity Relationships
Among the 3-acylbarbiturates, 3-acetyl derivatives 2a–c did not exhibit antibacterial activity, whereas
branched alkyls (±)-5a–c possessing a bulky lipophilic group exhibited good antibacterial activity.
In addition, the adamantylacetyl substituent, possessing a similar steric effect to the branched alkyl
group, retained activity ((±)-5a versus 6a) while methyl substitutions at R1 and R2 in the adamantyl
group did not affect the activity (6a–c). In contrast, replacements of the branched alkyl to smaller
tert-butyl ((±)-5b versus 4) but also of adamantyl to the smaller cyclohexyl (7a versus 8a) decreased
activity. Although the steric effect of 3, 9, (±)-10 and cis-11 is similar to active compounds (±)-5a, 7a,
8b and 6c, respectively, their activities were abolished, probably by the polar heteroatom in the 3-acyl
group. However, the longer bridge between the 3-acyl and cyclic functionality provided better activity
(6a versus 7a; 8a versus 8b). In addition, longer and polar N-substituents on the barbituric core gave
similar activity (7a versus 7b; (±)-5a,b versus (±)-5c) while the longer and lipophilic N-diethyl group
provided improved activity compared with N-dimethyl groups ((±)-5a versus (±)-5b; 18g versus 19a).
On the other hand, compounds (±)-10-16, all possessing bigger and more polar substituents which had
been expected to give reduction of PPB affinity, had no or only slight activity.
From the previous finding that 3-acyltetramic acids possessing substituted phenyl groups with a C3-
C4 chain length bridge exhibited good antibacterial activity [14], the SAR of 17–19 were studied in
detail. It was found that lipophilicity is a crucial factor for cell permeability in the whole-cell antibacterial
assay (see below for details). The more lipophilic analogues 17c (compared with 17a,b), 18b (compared
with 17a and 18a) and 19a (compared with 18g and 19b) all exhibited better activity. Of particular
interest is that di-substituted phenyl 18e (R1 and R4) and 18f,g (R1 and R2) exhibited better activity than
di-substituted phenyl 18c (R2 and R3) and 18d (R3 and R4), even though they all possess similar steric
effects and lipophilicity. This result indicates that the activity is sensitive to the nature of phenyl
substitution (especially at R1 position). In addition, compounds 21–24 possessing polar atoms on the
3-acyl group and/or shorter bridge than 17–19 exhibited poor activity, with the exception of compound 20.
As mentioned above, N-unsubstituted or -monosubstituted 25–28 dropped in activity, even though
the 3-acyl functionality of (±)-25b and 26b,d is identical to that of active barbiturates (±)-5a-c and 18g,
respectively. On the other hand, alkyl carboxamides 31 and 32 (possessing similar functionality with
active 3-acyl barbiturates as well as 3-acyl and 3-carboxamide tetramic acids [13–15]) tended to exhibit
better activity than aryl carboxamides 29 and 30 (possessing similar functionality with active 3-carboxamide
tetramic acids), while 3-enamines 33–37 had no or only weak antibacterial activity, similarly to
3-enamine tetramic acids [19].
2.5. Physicochemical Property-Antibacterial Activity Relationships
Examination of physicochemical property-activity relationships [35], especially in order to understand
any trends for bacterial cell permeability, including transportation by efflux pump and PPB affinity, for
antibiotic discovery was made. Figure 5 presents a plot of ClogD7.4 against molecular surface area
(MSA) of 3-acyl (50 analogues), 3-carboxamide (7 analogues) and 3-enamine (6 analogues)
barbituric acids 2–37 along with the corresponding tetramic acids (326 analogues) from our previous
reports [13–15,19], classified into active (MIC ≤ 4 µg/mL), mild (4 < MIC ≤ 32 µg/mL) and inactive

Molecules 2015, 20
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(MIC > 32 µg/mL) analogues. In addition, Supplementary Figures 3–5 in the Supporting Information
presents the plots of ClogP, polar surface area (PSA) and relative-PSA (rel-PSA = PSA/MSA),
respectively (see also Supplementary Table 1 in Supporting Information for physicochemical properties
in detail). As shown in Figure 5A and Supplementary Figures 3A–5A, analogues with a wide range of
physicochemical properties permeate Gram-positive bacteria whereas the cell permeabilityof Gram-negative
bacteria is limited to a much narrower range of physicochemical properties (with an especially higher
threshhold for lipophilicity). This is clearly indicated by the limited activity against efflux-positive
H. influenzae H3 shown in Figure 5B and the inactivity against P. aeruginosa and Escherichia coli.
Since analogues with a wider range of physicochemical properties exhibit better antibacterial activity
against efflux-negative H. influenzae H3 than the efflux-positive strain (Figure 5B,C), and the fact that
tetramic acids exhibited antibacterial activity against TolC negative E. coli and Klebsiella pneumonia in
our previous study [13], the main obstacle to Gram-negative bacteria cell permeability appears to
transportation by efflux-pumps.
6
4
(B) HI3
(A) MRSA
2
0
-2
6
4
300
600
MSA
900
(C) HI4
Tetramic acid analogues
Active Mild
Barbituric acid analogues
Active Mild
Inactive
Inactive
2
0
-2
300
600
900
MSA
Figure 5. Plot of ClogD7.4 against MSA of barbituric acids 2–37 along with tetramic
acids in our previous reports [13–15,19] against (A) MRSA; (B) H. influenzae 3 and
(C) efflux-negative H. influenzae 4. Active, mild and inactive mean that the values are
MIC ≤ 4 µg/mL, 4 µg/mL < MIC ≤ 32 µg/mL and MIC > 32 µg/mL, respectively.
In this analysis, barbiturates active against MRSA (red-filled circles) and efflux-negative H4 are
positioned in the same range of ClogD7.4, ClogP, PSA and MSA for active tetramates (blue-filled circles)
and tend to be less lipophilic, have higher PSA and smaller MSA character than active 3-acyltetramic
acids [14,19] (Figure 5A,C and Supplementary Figures 3A,C and 4A,C); however, active barbiturates
possess slightly higher rel-PSA than active tetramates (Supplementary Figure 5A,C). Of particular

Molecules 2015, 20
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interest is that the active barbiturates possess similar physicochemical properties to clinical antibiotics
for oral or injectable use (−3.0 < ClogD7.4 < 2.0; 0 < ClogP < 3.0; 60 < PSA < 120 Å2; 10 < rel-PSA < 30%
and 270 < MSA < 650 Å3, see below) as well as acceptable molecular weight (<400 Da), rotatable bonds
(usually less than 6) and the number of proton-donor (1–2) and -acceptor (4–6) for oral availability in
the rule of five (Supplementary Table 1) [36].
In our previous analysis with tetramates [13,14,19] presented as blue-filled circles in Figure 5B and
C and Supplementary Figure 3B,C, tetramates possessing less lipophilic (ClogD7.4 < 3.0 and ClogP <
4.0) and smaller (MSA < 620 Å3) characteristics tended to be less easily transported by efflux pumps in
H. influenzae. Although the active barbiturates are in this zone of lipophilicity and MSA, they were
slightly more easily transported than tetramates. This may be due to the fact that barbiturates possess
higher PSA (78 < PSA < 100 Å2) than tetramates (65< PSA < 90 Å2), arein the same range of MSA (420
< MSA < 650 Å3) and this results in higher rel-PSA (15 < rel-PSA < 20% versus 10 < rel-PSA < 15%).
This phenomena agrees with the observation that compounds possessing higher topological PSA are
more easily transported by multidrug resistance-associated protein 1 (MRP1/ABBC1) [37].
2.6. Physicochemical Property-Plasma Protein Binding Affinity Relationships
In order to investigate physicochemical property-PPB affinity relationships, plots of MIC difference
against MSA, PSA, rel-PSA, ClogP and ClogD7.4 of barbiturates (32 analogues) used in this study along
with tetramates (208 analogues) from our previous studies [13–15,17] were made (Figure 6). In this
analysis, the MIC difference is defined as the value from MIC against S. pneumonia P9 in the presence
of 2.5% blood divided by MIC without blood (inactive analogues against any one of these panels were
not considered). Since PPB affinity is affected by multiple interactions in many proteins such as human
serum albumin, lipoprotein, glycoprotein and globulins in blood, there is no linear correlation between
the MIC difference and the physicochemical properties in Figure 6. However, this analysis, which uses
a larger number of analogues than in our previous analysis [13,14], shows clearer trends (especially
against MSA and PSA). As with the ClogP-PPB affinity relationship in the literature [38,39], PPB
affinity is more closely related to lipophilicity as represented by rel-PSA, ClogP and ClogD7.4 (Figure
6C–E) than MSA and PSA (Figure 6A,B). It appears that less lipophilic analogues (rel-PSA > 16%,
ClogP < 1.5 and ClogD7.4 < −0.69) exhibit higher probability of having lower PPB affinity (MIC
difference ≤ 2) while those analogues with high PPB affinity (MIC difference > 30) are positioned in the
area of highly lipophilic regions (rel-PSA < 13%, ClogP > 2.9 and ClogD7.4 > 2.9, Figure 6C–E).
Although the trends of PPB affinity with steric effect (MSA) and PSA are weaker than lipophilicity, the
analogues in the range of MSA between 600 and 900 Å3 and PSA being less than 100 Å2 exhibit a higher
probability of possessing high PPB affinity (Figure 6A,B). However, the barbiturate library (red-filled
circles) tended to exhibit lower PPB affinity compared to the tetramate library because of their less
lipophilic (rel-PSA > 14%, ClogP < 2.0 and ClogD7.4 < 1.0) and smaller MSA (MSA < 650 Å3) character
on average.

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50
(B)
(A)
30
20
10
0
600
900
60
90
120
MSA
PSA
50
(C)
(D)
30
20
10
0
10
15
rel-PSA
20 24 25
0
2
4
6
ClogP
50
(E)
Tetramic acid analogues
Barbituric acid analogues
30
20
10
0
-2
0
2
4
ClogD7.4
Figure 6. Plot of MIC difference against (A) MSA; (B) PSA; (C) rel-PSA; (D) ClogP (E)
ClogD7.4 of barbituric acids along with tetramic acids in our previous reports [13–15,17].
The MIC difference is defined as MIC with 2.5% blood/ MIC without blood against
S. pneumonia 9.
In fact, potency enhancements of 3-acyltetramic acids [13,14] arising from improvement of
lipophilicity and molecular size (ClogD7.4 >2.0 and MSA >600 Å3) are unlikely to provide both lower
PPB affinity as well as efflux pump transport. In contrast, we believe that active barbiturates and
3-carboxamide tetramic acids [13,15] exhibit amenable PPB affinity for in vivo activity because of their
similar physicochemical properties with clinical antibiotics used for oral or injectable administration as
well as being an anionic microspecies under weakly basic conditions (see below). Indeed, the ability to
control PPB affinity by adjustment of physicochemical properties proved to be limited; therefore,
although appropriate physicochemical properties might be necessary for overcoming PPB affinity, there
appear to be other factors involved. One possible hypothesis is that the main core (tetramic and barbituric
acids) with its inherent acidic character might be responsible for binding to serum albumin, the major
protein in blood, at the sites for aromatic carboxylic acids such as salicylates and ibuprofen. In order to
understand whether this is the case, computational and NMR study of serum albumin affinity with our
analogues is under investigation.

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2.7. Physicochemical Property-Activity Relationships of Small Molecule Antibacterial Agents
Although physicochemical properties of antibacterial agents have been discussed in detail in the
previous literature [1,40], an examination of the desirable properties for small molecule antibacterial
agents, especially to understand cell permeability and PPB affinity, was made using cheminformatic
analysis. In order to achieve a more reliable comparison with our library (Mw < 650 Da), antibiotic
families with a large molecular weight (Mw > 600 Da), such as glycopeptides which act at the
peptidoglycan layer and do not therefore require the penetration of a lipid membrane, and macrolides,
have been excluded. In this study, 8 bins for each antibiotic family along with a separate bin for topical
antibiotic agents but without consideration of their family, were created. The plots of lipophilicity
descriptors (ClogD7.4, and ClogP) and polar surface descriptors (PSA and rel-PSA) against steric effect
descriptor (MSA) were made (Figure 7, see also Supplementary Table 2–10 in Supporting Information
for the physicochemical properties in detail). In this analysis, most antibiotics, with the exception of
topical agents, tended to have a higher limit for lipophilicity (ClogD7.4 < 2.0 and ClogP < 3.0) and a
lower limit for polar surface area (PSA > 60 Å2 and rel-PSA > 13%). Furthermore, it is noteworthy that
the bigger antibiotics (MSA > 650 Å3) tend to have a stricter limit for lipophilicity (ClogD7.4 < −4.0 and
ClogP < 0) and polar surface area (PSA > 120 Å2 and rel-PSA > 20%). That these margins might result
from PPB affinity is supported by the fact that topical agents, for which PPB affinity is less important,
are free from these boundaries, although of course other factors such as intrinsic antibacterial activity
and ADMET are clearly important (for example, antibiotics with higher antibacterial activity
compensate for higher PPB affinity for oral or injectable use). However, the lipophilicity (ClogD7.4 and
ClogP) and the PSA are in inverse proportion to the MSA while the rel-PSA is not affected by the MSA,
generally displaying values between 12%–38%. The analogues as shown in Figure 5 and Supplementary
Figures 3–5 are opposite to this tendency. Since bigger tetramic acids (MSA > 600 Å3) usually possess
more lipophilic character, it would be worth investigating antibacterial activity and PPB affinity of
libraries with bigger and less lipophilic character (MSA > 700 Å3, ClogD7.4 < −4.0) in the future.
From a consideration of their physicochemical properties, on the other hand, the 8 bins for oral or
injectable antibiotics can be classified into 3 sub-types. The first one is aminoglycosides populating the
most hydrophilic (lowest ClogP and ClogD7.4 and highest PSA and rel-PSA) and the biggest (MSA >
600 Å3) regions. Due to this hydrophilicity (ClogD7.4 < −12), their oral administration has been generally
limited as a result of problems with absorption. The second class includes Gram-negative active
β-lactams and tetracyclines, and this class of antibiotics possesses lipophilicity and MSA between
aminoglycosides and the third class of antibiotics. The third class includes antibiotics of natural origin
such as Gram-positive only active penicillins and amphenicols as well as synthetic origin antibiotics
such as fluoroquinolones, sulfa drugs and oxazolidinones, possessing higher lipophilic character and
smaller MSA than both of the other classes. Of particular interest is that the third class displays a narrow
zone of physicochemical properties (−3.0 < ClogD7.4 < 2.0; 0 < ClogP < 3.0; 60 < PSA < 120 Å2, 270 <
MSA < 650 Å3) with the exception of rel-PSA, while the two other classes populate a wider range of the
physicochemical space, with the preference for lower lipophilicity and bigger MSA than the third class.
The physicochemical space populated by the third class is amenable to general drug design, and appears
to be the most suitable for antibiotic development. As shown in Figure 5 and Supplementary Figures 3–5,
our active barbiturates in this study and 3-carboxamide tetramic acids from the previous study [13,15]

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also satisfy these properties, in contrast to active 3-acyltetramic acids which generally possess higher
ClogP and ClogD7.4 values [13,14]. From a consideration of MSA of the third class of antibacterial
agents (MSA < 650) as well as from the fact that smaller molecules (MSA < 620 Å3) tend to be less
easily transported by the efflux pump in H. influenzae as described above (Figure 5B,C), and that
analogues with 600 < MSA < 900 Å3 exhibit a higher probability of higher PPB affinity (Figure 6A),
both lipophilicity and molecular size might be crucial factors for antibiotic discovery in which smaller
analogues (MSA < 600 Å3) are likely to have a benefit for both PPB affinity and cell permeability.
Aminoglycosides,
Tetracyclines,
Sulfa drugs,
Beta lactam antibiotics
Fluoroquinolones
Amphenicols
G+ only active penicillins,
Topical antibiotics
G+ only active antibiotics
(B)
8.1
8.0
(A)
4
2
0
3
0
-4
-3
-6
-9
-8
-12
-16
(D)
(C)
40
30
20
10
0
300
240
180
120
60
300
600
900 300
600
MSA
900
MSA
Figure 7. Plot of (A) ClogD7.4, (B) ClogP, (C) PSA and (D) rel-PSA against MSA of small
molecule antibacterial agents.
2.8. Ionic State of Small Molecule Antibacterial Agents
Since for bacterial cell permeability (including the transportation by efflux pump), ionic state (related
to pKa) might be expected to be a major factor, the major microspecies at pH 7.4 were calculated (data
not shown, see Supplementary Figures 6–14 for the structures of antibacterial agents). Of particular
interest is that Gram-negative active agents favoured anionic(s) and zwitterionic(s) microspecies, while
aminoglycosides exist as cationic forms, generally as a result of the presence of the amine functionality.
Fluoroquinolones, tetracyclines and Gram-negative active β-lactams exist as various forms of
zwitterionic and anionic microspecies. This might result from the fact that their key skeletons include an
acidic carboxylic acid (fluoroquinolones and β-lactams) or two acidic enols and a basic amine group
(tetracyclines), which make them easily able to form anionic or zwitterionic species under weakly basic
conditions (pH = 7.4). In addition, sulfa drugs mainly exist as an anionic form on the nitrogen in the
sulfone amide group, in some cases with a minor amount of the uncharged form. In this family,

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sulfaguanidine (used in the treatment of gastrointestinal infections) exceptionally exists as a neutral
microspecies under weakly basic conditions but is cationic in acidic conditions (pH = 1.0). In addition,
amphenicols also exist as a mixture of a neutral and an anionic (on the nitrogen of amide functionality)
microspecies. On the other hand, Gram-positive only active antibiotics generally exist as an anionic
(rather than a zwitterionic, Gram-positive only β-lactams), neutral (oxazolidinones) or a mixture of a
neutral and cationic (lincosamides and 2,4-diaminopyrimidines) microspecies, and tend to be less
charged state than Gram-negative active agents. In general, Gram-negative antibacterial agents tend to
be more charged than the Gram-positive only agents to penetrate outer membrane via porins as well as
prevent efflux.
3. Experimental Section
3.1. General
All starting materials and 3-acyl 2a were commercially available. Melting points were checked by
STUART SCIENTIFIC SMP1. The 1H-, 13C- and HMBC-NMR spectra were obtained using a Bruker
1
13
1
AVB500 (500 MHz for H-NMR and 126 MHz for C-NMR) or DPX400 (400 MHz H-NMR and
13
101 MHz for C-NMR). Mass spectra (MS) and high resolution MS were obtained with Micro Mass
LCT and GCT spectrometers under the conditions of electrospray ionization (ESI) and chemical
ionization (CI) respectively, and values were reported as a ratio of mass to charge in Daltons. The
energies at ground state were computed with Density Functional B3LYP (6-31G*) in Spartan 02 in each
enol form and the physicochemical properties were calculated with MarvinSketch version 5.3.8. in which
VG method for ClogP and ClogD7.4, van der Waals method for MSA were selected and sulfur atoms
were excluded in the calculation of PSA. In vitro antibacterial activity was performed using standard
methodology as described in our previous paper [13].
3.2. Synthesis of Barbituric Acid Templates 40a–c
3.2.1. Synthesis of Compounds 40c and 2c
Synthesis of Urea 39c
To the solution of 2-methoxy ethylamine 38 (3.2 g, 42.2 mmol) in dichloromethane (50 mL) was
slowly added ethyl isocyanate (3.0 g, 42.2 mmol) at 0 °C under nitrogen atmosphere and the mixture
was stirred for 30 min. Concentration in vacuo followed by precipitation in ethyl acetate and petrol
solution gave urea 30c (5.9 g, 40.2 mmol, 95% yield) as a solid (M.P.; 40.0 °C).
1H-NMR (400 MHz, CDCl3); 5.56 (brs, 1H, NH), 5.46 (brs, 1H, NH), 3.40 (t, 2H, J = 5.2 Hz, C5),
3.32–3.28 (m, 5H, C4 and C6), 3.17–1.10 (m, 2H, C2), 1.06 (t, 3H, J = 7.2 Hz, C1). 13C-NMR

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(100 MHz, CDCl3); 159.0 (C3), 72.2 (C5), 58.5 (C6), 39.9 (C4), 34.8 (C2), 15.3 (C1). MS (ES+); 169.08
(M+Na); HRMS (M+Na); calcd for C6H14N2Na1O2; 169.0947; found; 169.0950.
Synthesis of Barbituric Acid 40c and 3-acetylbarbituric Acid 2c
To the solution of urea 39c (5.9 g, 40.15 mmol) in acetic acid (80 mL) was added malonic acid
(3.9 g, 40.15 mmol) at room temperature. The mixture was slowly added acetic anhydride (60 mL) at
60 °C for 30 min and the mixture was stirred at 90 °C for 5 h. Concentration in vacuo followed by flash
column chromatography gave barbituric acid 40c (6.1 g, 28.5 mmol, 71%) as oil and 3-acetylbarbituric
acid 2c (1.0 g, 3.90 mmol, 10%) as oil.
Compound 40c; 1H-NMR (400 MHz, CDCl3); 4.01 (t, 2H, J = 5.6 Hz, C9), 3.84 (q, 2H, J = 6.8 Hz, C7),
3.59 (s, 2H, C3), 4.01 (t, 2H, J = 5.6 Hz, C10), 3.24 (s, 3H, C11), 1.11 (t, 3H, J = 6.8 Hz, C8).
13C NMR (100 MHz, CDCl3); 164.6 (C=O), 164.3 (C=O), 151.1 (C6), 68.9 (C10), 58.4 (C11), 40.3 (C9),
39.4 (C3), 37.0 (C7), 12.9 (C8). MS (ES−); 213.08 (M−H); MS (ES+); 237.09 (M+Na); HRMS (M+Na);
calcd for C9H14N2Na1O4; 237.0846; found; 237.0848.
Compound 2c; 1H-NMR (400 MHz, CDCl3); 4.17–4.12 (m, 2H, C9), 4.01–3.93 (m, 2H, C7), 3.62–3.56
(m, 2H, C10), 3.33 and 3.32 (2 of s, 3H, C11), 2.69 and 2.68 (2 of s, 3H, C13), 1.24–1.17 (m, 3H, C8).
13C-NMR (100 MHz, CDCl3); 196.3 and 196.1 (C12), 169.4 and 169.2 (C2), 160.9 and 160.7 (C4), 149.8
and 149.7 (C6), 96.0 and 95.9 (C3), 69.3 and 69.2 (C10), 58.7 and 58.6 (C11), 40.1 and 40.0 (C9), 36.7
and 36.6 (C7), 24.7 and 24.6 (C13), 13.1 (C8). MS (ES−); 255.11 (M−H); MS (ES+); 279.10 (M+Na);
HRMS (M+Na); calcd for C11H16N2Na1O5; 279.0951; found; 279.0946.
3.2.2. Synthesis of Barbituric Acid 40b and 3-acetylbarbituric Acid 2b
Barbituric acid 40b (3.9 g, 21.2 mmol, 82%) as oil and 3-acetylbarbituric acid 2b (660 mg, 2.93 mmol,
11%) as a solid (M.P.; 68 °C) were obtained from 1,3-diethyl urea 39b (3.0 g, 25.8 mmol) and malonic
acid (2.7 g, 25.8 mmol) as the same method with synthesis of compounds 40c and 2c.

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1
Compound 40b; H-NMR (400 MHz, CDCl3); 3.87 (q, 4H, J = 7.2 Hz, C7 and C9), 3.60 (s, 2H, C3),
1.15 (t, 6H, J = 7.2 Hz, C8 and C10). 13C-NMR (100 MHz, CDCl3); 164.4 (C2 and C4), 150.9 (C6), 39.5
(C3), 37.0 (C7 and C9), 13.0 (C8 and C10). MS (ES−); 183.06 (M−H); HRMS (M−H); calcd for
C8H11N2O3; 183.0775; found; 183.0771.
1
Compound 2b; H-NMR (400 MHz, CDCl3); 4.00–3.92 (m, 4H, C7 and C9), 2.67 (s, 3H, C12),
13
1.23–1.16 (m, 6H, C8 and C10). C-NMR (100 MHz, CDCl3); 196.1 (C11), 169.2 (C2), 160.7 (C4),
149.5 (C6), 95.9 (C3), 36.5 (N-CH2), 36.4 (N-CH2), 24.7 (C12), 13.1 (C8 and C10). MS (ES−); 225.08
(M−H); HRMS (M−H); calcd for C10H13N2O4; 225.0881; found; 225.0882.
3.2.3. Synthesis of Barbituric Acid 40a
To the solution of N-allylurea 39a (2.0 g, 20.0 mmol) in acetic acid (60 mL) was added malonic acid
(2.1 g, 20.0 mmol) at room temperature. The mixture was slowly added acetic anhydride (40 mL) at
60 °C for 30 min and the mixture was stirred at 90 °C for 5 h. Concentration in vacuo followed by
precipitation in ethyl acetate gave barbituric acid 40a (960 mg, 5.71 mmol, 30%) as a solid (M.P.; 158 °C).
1H-NMR (400 MHz, DMSO, keto form); 11.35 (brs, 1H, NH), 5.82–5.72 (m, 1H, C8), 5.17 (dd, 1H,
J1 = 17.6 Hz, J2 = 1.6 Hz, C9), 5.08 (dd, 1H, J1 = 10.4 Hz, J2 = 1.6 Hz, C9), 4.27 (d, 2H, J = 4.8 Hz,
C7), 3.64 (s, 2H, C3). 13C-NMR (100 MHz, DMSO, keto form); 166.5 (C2 and C4), 151.4 (C6), 132.5
1
(C8), 116.2 (C9), 41.9 (C7), 39.9 (C3). H-NMR (400 MHz, CD3OD, enol form); 5.89–5.79 (m, 1H,
C8), 5.23 (dd, 1H, J1 = 17.2 Hz, J2 = 1.2 Hz, C9), 5.14 (dd, 1H, J1 = 10.0 Hz, J2 = 1.2 Hz, C9), 4.84 (brs,
13
2H, NH, OH and C3), 4.40 (d, 2H, J = 5.6 Hz, C7). C-NMR (100 MHz, CD3OD, enol form, due to
deuterium exchange, C3 signal is not appeared); 168.2 (C2 and C4), 152.9 (C6), 133.4 (C8), 118.0 (C9),
43.9 (C7). MS (ES−); 167.04 (M−H), HRMS (M−H); calcd for C7H7N2O3; 167.0462; found; 167.0454.

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3.3. Synthesis of 3-alkoxycarbonyl Barbituric Acid Templates 41a–d
General procedure; To the solution of barbituric acid (1 eq) and DMAP (2.2 eq) in dichloromethane
was slowly added butyl chloroformate (1.2 eq) at 0 °C under nitrogen atmosphere, and the mixture was
stirred overnight at room temperature under nitrogen atmosphere. Then the mixture was washed with
2 M HCl. The organic layer was dried over MgSO4 and evaporated in vacuo to give 3-alkoxycarbonyl
barbituric acid templates 41a–d contained about 10%–20% impurity. The impure 3-alkoxycarbonyl
barbituric acid template was used for next step without further purification.
3.3.1. Synthesis of Compound 41a
Yield; 85%; M.P. 33 °C; 1H-NMR (400 MHz, CDCl3); 4.33 (t, 2H, J = 6.8 Hz, C12), 4.03–3.92 (m,
4H, C7 and C9), 1.78–1.71 (m, 2H, C13), 1.48–1.39 (m, 2H, C14), 1.25 (t, 3H, J = 6.8 Hz, CH3), 1.17
(t, 3H, J = 6.8 Hz, CH3), 0.92 (t, 3H, J = 7.2 Hz, C15). 13C-NMR (100 MHz, CDCl3); 173.5 (C11), 168.7
(C2), 158.2 (C4), 148.9 (C6), 82.9 (C3), 66.5 (C12), 37.7 (N-CH2), 36.4 (N-CH2), 30.4 (C13), 18.9
(C14), 13.6 (C15), 13.3 (CH3), 12.9 (CH3). MS (ES−); 283.14 (M−H); MS (ES+); 307.13 (M+Na);
HRMS (M+Na); calcd for C13H20N2Na1O5; 307.1264; found; 307.1256.
3.3.2. Synthesis of Compound 41b
Yield; 65% (oil); 1H-NMR (400 MHz, CDCl3); 4.34 (t, 2H, J = 6.8 Hz, C13), 4.17–3.90 (m, 4H, C7
and C9), 3.61–3.54 (m, 2H, C10), 3.30 (s, 3H, C11), 1.78–1.70 (m, 2H, C14), 1.45–1.40 (m, 2H, C15),
13
1.25–1.14 (m, 3H, C8), 0.92 (t, 3H, J = 7.2 Hz, C16). C-NMR (100 MHz, CDCl3); 173.5 and 173.4
(C12), 169.0 and 168.8 (C2), 158.3 and 158.0 (C4), 149.3 and 149.1 (C6), 82.8 (C3), 69.1 (C10), 66.5
(C13), 58.5 (C11), 41.2 and 40.0 (C9), 37.8 and 36.5 (C7), 30.4 (C14), 18.9 (C15), 13.5 (C16), 13.2
(C8). MS (ES−); 313.15 (M−H); MS (ES+); 315.16 (M+H), 337.14 (M+Na); HRMS (M+Na); calcd for
C14H22N2Na1O6; 337.1370; found; 337.1369.

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3.3.3. Synthesis of Compound 41c
Yield; 90%; M.P.; 59 °C ; 1H-NMR (500 MHz, CDCl3); 4.29 (t, 2H, J = 5.5 Hz, C10), 3.28 (brs, 6H,
C7 and C8), 1.73–1.67 (m, 2H, C11), 1.44–1.37 (m, 2H, C12), 0.88 (t, 3H, J = 7.5 Hz, C13). 13C-NMR
(125 MHz, CDCl3); 173.2 (C9), 168.7 (C2), 158.3 (C4), 149.6 (C6), 82.6 (C3), 66.4 (C10), 30.2 (C11),
28.4 (N-CH3), 27.8 (N-CH3), 18.8 (C12), 13.4 (C13). MS (ES−); 255.09 (M−H); HRMS (M−H); calcd
for C11H15N2O5; 255.0986; found; 255.0987.
3.3.4. Synthesis of Compound 41d
Yield; 56 %; M.P.; 259 °C ; 1H-NMR (400 MHz, DMSO); 11.58 (brs, 2H, NH), 4.23 (t, 2H, J = 6.4 Hz,
C8), 1.65–1.58 (m, 2H, C9), 1.40–1.35 (m, 2H, C10), 0.89 (t, 3H, J = 7.2 Hz, C11). 13C-NMR (125 MHz,
DMSO); 171.9 (C7), 167.9 (C2), 165.0 (C4), 148.8 (C6), 82.2 (C3), 65.2 (C8), 30.2 (C9), 18.6 (C10),
13.6 (C11). MS (ES−); 227.07 (M−H); MS (ES+); 251.07 (M+Na); HRMS (M+Na); calcd for
C9H12N2Na1O5; 251.0638; found; 251.0640.
3.4. Direct acylation of Barbituric Acid Templates
General procedure: To a solution of carboxilic acid (1.0 eq) in dichloromethane were added DCC (1.1
eq), barbituric acid (1.0 eq) and DMAP (1.2 eq) at room temperature. The mixture was stirred overnight
at room temperature. The crude reaction mixture was filtered with dichloromethane. Concentration in
vacuo followed by flash column chromatography gave metal-chelated barbituric acid. The crude product
was dissolved in dichloromethane and washed with 1M HCl. The organic layer was dried with MgSO4
and concentrated in vacuo to give 3-acylbarbituric acid.
3.4.1. Synthesis of Compound 3
1
Yield; 51%; M.P.; 92 °C ; H-NMR (400 MHz, CDCl3); 3.73 (t, 2H, J = 6.4 Hz, C11), 3.36 (t, 2H,
13
J = 6.4 Hz, C10), 3.35 (s, 3H, C7), 3.31 (s, 3H, C8), 1.16 (s, 9H, C13–C15). C-NMR (100 MHz,
CDCl3); 197.5 (C9), 169.7 (C2), 160.8 (C4), 150.3 (C6), 95.7 (C3), 73.2 (C12), 57.5 (C11), 38.3 (C10),

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28.0 (N-CH3), 27.8 (N-CH3), 27.4 (C13–C15). MS (ES−); 283.14 (M−H), MS (ES+); 307.14 (M+Na),
HRMS (M+Na); calcd for C13H20N2Na1O5; 307.1264; found; 307.1269.
3.4.2. Synthesis of Compound 4
1
Yield; 57% (oil); H-NMR (400 MHz, CDCl3); 3.98–3.89 (m, 4H, C7 and C9), 3.14 (s, 2H, C12),
13
1.22–1.13 (m, 6H, C8 and C10), 1.02 (s, 9H, C14–C16). C-NMR (100 MHz, CDCl3); 198.5 (C11),
169.5 (C2), 160.6 (C4), 149.3 (C6), 96.8 (C3), 46.8 (C12), 36.5 (C7 and C9), 33.4 (C13), 29.9
(C14–C16), 13.1 (C8 and C10). MS (ES−); 281.15 (M−H); HRMS (M−H); calcd for C14H21N2O4;
281.1507; found; 281.1505.
3.4.3. Synthesis of Compound (±)-5b
Yield; 71% (oil); 1H-NMR (400 MHz, CDCl3); 4.03–3.94 (m, 4H, C7 and C9), 3.08 (d, 2H, J = 7.2 Hz,
C12), 2.22–2.12 (m, 1H, C13), 1.35 (dd, 1H, J1 = 14.0 Hz, J2 = 3.2 Hz, C14), 1.26–1.15 (m, 7H, C8,
13
C10 and C14), 1.01 (d, 3H, J = 6.8 Hz, C19), 0.90 (s, 9H, C16-C18). C-NMR (100 MHz, CDCl3);
199.3 (C11), 169.6 (C2), 160.5 (C4), 149.7 (C6), 96.0 (C3), 50.7 (C14), 45.5 (C12), 36.6 (NCH2), 36.5
(NCH2), 31.1 (C15), 29.9 (C16–C18), 27.7 (C13), 22.7 (C19), 13.2 (C8 and C10). MS (ES−); 323.20
(M−H); HRMS (M−H); calcd for C17H27N2O4; 323.1976; found; 323.1980.
3.4.4. Synthesis of Compound (±)-5c
1
Yield; 42% (oil); H-NMR (400 MHz, CDCl3); 4.17–4.12 (m, 2H, C9), 4.00–3.92 (m, 2H, C7),
3.62–3.55 (m, 2H, C10), 3.33 and 3.32 (2 of s, 3H, C11), 3.06 (d, 2H, J = 7.2 Hz, C13), 2.19–2.12 (m,
1H, C14), 1.35–1.30 (m, 1H, C15), 1.24–1.12 (m, 4H, C8 and C15), 0.99 and 0.98 (2 of d, 3H, J = 6.8 Hz,
13
C20), 0.87 (s, 9H, C17–C19). C-NMR (100 MHz, CDCl3); 199.3 and 199.2 (C12), 169.7 and 169.5
(C2), 160.6 and 160.3 (C4), 149.7 and 149.6 (C6), 95.9 and 95.8 (C3), 69.3 and 69.2 (C10), 58.7 and

Molecules 2015, 20
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58.6 (C11), 50.6 (C15), 45.4 and 45.3 (C13), 40.1 and 40.0 (C9), 36.7 and 36.6 (C7), 31.0 (C16), 29.8
(C17–C19), 27.7 (C14), 22.7 (C20), 13.1 (C8). MS (ES−); 353.22 (M−H); MS (ES+); 355.23 (M+H),
377.20 (M+Na); HRMS (M+Na); calcd for C18H30N2Na1O5; 377.2047; found; 377.2040.
3.4.5. Synthesis of Compound 6a
Yield; 90%; M.P.; 133 °C ; 1H-NMR (500 MHz, CDCl3); 3.35 (s, 3H, C7), 3.31 (s, 3H, C8), 3.06 (s,
2H, C10), 1.99 (brs, 3H, C18–C20), 1.65–1.34 (m, 12H, C12–C17). 13C-NMR (125 MHz, CDCl3); 197.8
(C9), 169.7 (C2), 161.1 (C4), 150.2 (C6), 97.1 (C3), 47.9 (C10), 42.6 (CH2), 36.6 (CH2), 36.3 (C11),
28.8 (N-CH3), 28.1 (CH), 27.8 (CH). MS (ES−); 331.18 (M−H), HRMS (M−H); calcd for C18H23N2O4;
331.1663; found; 331.1657.
3.4.6. Synthesis of Compound 6b
Yield; 54% (oil); 1H-NMR (400 MHz, CDCl3); 3.36 (s, 3H, C7), 3.31 (s, 3H, C8), 3.08 (s, 2H, C10),
13
1.99 (brs, 2H, C18 and C19), 1.65–1.34 (m, 12H, C12-C17), 0.78 (s, 3H, C21). C-NMR (100 MHz,
CDCl3); 197.8 (C9), 169.7 (C2), 161.1 (C4), 150.2 (C6), 97.1 (C3), 49.6 (CH2), 47.6 (C10), 43.6 (CH2),
41.8 (CH2), 37.0 (C11), 35.8 (CH2), 30.9 (C21), 30.8 (C20), 29.3 (C18 and C19), 28.1 (N-CH3), 27.8
(N-CH3). MS (ES−); 345.20 (M−H), HRMS (M−H); calcd for C19H25N2O4; 345.1820; found; 345.1811.
3.4.7. Synthesis of Compound 6c
1
Yield; 39%; M.P.; 77 °C ; H-NMR (400 MHz, CDCl3); 3.37 (s, 3H, C7), 3.32 (s, 3H, C8), 3.10
(s, 2H, C10), 2.05–2.02 (m, 1H, C20), 1.52–1.07 (m, 12H, C12–C17), 0.79 (s, 6H, C21 and C22).
13C-NMR (100 MHz, CDCl3); 197.8 (C9), 169.7 (C2), 161.1 (C4), 150.2 (C6), 97.1 (C3), 50.8 (CH2),
48.9 (CH2), 47.3 (C10), 42.9 (CH2), 41.0 (CH2), 37.7 (C18 and C19), 31.5 (C11), 30.5 (C21 and C22),

Molecules 2015, 20
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29.8 (C20), 28.2 (N-CH3), 27.8 (N-CH3). MS (ES−); 359.18 (M−H), HRMS (M-H); calcd for
C20H27N2O4; 359.1976; found; 359.1965.
3.4.8. Synthesis of Compound 7a
Yield; 50%; M.P.; 130 °C ; 1H-NMR (400 MHz, CDCl3); 3.36 (s, 3H, C7), 3.33 (s, 3H, C8), 3.11–3.07
(m, 2H, C10), 1.98 (brs, 3H, C19–C21), 1.73–1.54 (m, 12H, C13–C18), 1.45–1.41 (m, 2H, C11).
13C-NMR (100 MHz, CDCl3); 201.2 (C9), 169.7 (C2), 160.8 (C4), 150.4 (C6), 95.2 (C3), 42.0 (C10),
40.0 (CH2), 37.0 (CH2), 32.4 (C12), 30.8 (CH2), 28.6 (N-CH3), 28.0 (CH), 27.8 (CH). MS (ES−); 345.19
(M−H), HRMS (M−H); calcd for C19H25N2O4; 345.1820; found; 345.1815.
3.4.9. Synthesis of Compound 7b
1
Yield; 44% (oil); H-NMR (400 MHz, CDCl3); 4.18–4.14 (m, 2H, C9), 4.02–3.95 (m, 2H, C7),
3.63–3.57 (m, 2H, C10), 3.34 and 3.33 (2 of s, 3H, C11), 3.11–3.07 (m, 2H, C13), 1.96 (brs, 3H,
C22–C24), 1.71–1.61 (m, 6H, C16, C17 and C20), 1.52 (brs, 6H, C18, C19 and C21), 1.44–1.40 (m, 2H,
13
C14), 1.26–1.18 (m, 3H, C8). C-NMR (100 MHz, CDCl3); 201.3 and 201.2 (C12), 169.7 and 169.5
(C2), 160.5 and 160.3 (C4), 149.8 and 149.7 (C6), 95.3 and 95.2 (C3), 69.4 and 69.2 (C10), 58.7 and
58.6 (C11), 42.0 (C16, C17 and C20), 40.1 and 40.0 (C9), 39.8 and 39.7 (C13), 37.0 (C18, C19 and
C21), 36.7 and 36.6 (C7), 32.3 (C15), 30.8 and 30.7 (C14), 28.6 (C22–C24), 13.2 and 13.1 (C8). MS
(ES−); 403.23 (M-H); MS (ES+); 427.21 (M+Na); HRMS (M+Na); calcd for C22H32N2Na1O5; 427.2203;
found; 427.2191.
3.4.10. Synthesis of Compound 8a
Yield; 25%; M.P.; 55 °C ; 1H-NMR (400 MHz, CDCl3); 3.34 (s, 3H, C7), 3.31 (s, 3H, C8), 3.14–3.10
(m, 2H, C10), 1.76–1.62 (m, 5H, CH2), 1.58–1.52 (m, 2H, C11), 1.37–1.27 (m, 1H, C12), 1.23–1.11 (m,

Molecules 2015, 20
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3H, CH2), 0.98–0.89 (m, 2H, CH2). 13C-NMR (100 MHz, CDCl3); 200.3 (C9), 169.7 (C2), 160.7 (C4),
150.3 (C6), 95.1 (C3), 37.6 (C12), 34.4 (C10), 33.1 (C11), 32.9 (CH2), 28.0 (N-CH3), 27.7 (N-CH3),
26.5 (CH2), 26.2 (CH2). MS (ES−); 293.16 (M−H), HRMS (M−H); calcd for C15H21N2O4; 293.1507;
found; 293.1510.
3.4.11. Synthesis of Compound 8b
Yield; 53% (oil); 1H-NMR (400 MHz, CDCl3); 3.34 (s, 3H, C7), 3.30 (s, 3H, C8), 3.09 (t, 2H, J = 7.6 Hz,
13
C10), 1.71–1.60 (m, 7H, C13 and CH2), 1.30–1.09 (m, 6H, CH2), 0.91–0.81 (m, 2H, CH2). C-NMR
(100 MHz, CDCl3); 199.9 (C9), 169.7 (C2), 160.7 (C4), 150.3 (C6), 95.1 (C3), 37.3 (C13), 37.1 (CH2),
36.9 (CH2), 33.1 (CH2), 27.9 (N-CH3), 27.7 (N-CH3), 26.6 (CH2), 26.2 (CH2), 23.1 (CH2). MS (ES−);
307.16 (M−H); HRMS (M−H); calcd for C16H23N2O4; 307.1663; found; 307.1661.
3.4.12. Synthesis of Compound 9
Yield; 84%; M.P.; 67 °C ; 1H-NMR (400 MHz, CDCl3); 5.00 (d, 1H, J = 20.4 Hz, C10), 4.87 (d, 1H,
J = 20.4 Hz, C10), 3.33 (s, 3H, C7), 3.27 (s, 3H, C8), 3.21–3.15 (m, 1H, C11), 2.29–2.21 (m, 1H, C15),
2.09–2.05 (m, 1H, C16), 1.62–1.57 (m, 2H, CH2), 1.35–1.27 (m, 2H, C12 and C18), 1.00–0.80 (m, 11H,
C13, C14, C16, C19 and C20), 0.74 (d, 3H, J = 6.8 Hz, C17). 13C-NMR (100 MHz, CDCl3); 197.1 (C9),
169.4 (C2), 160.5 (C4), 150.1 (C6), 93.5 (C3), 80.5 (C11), 69.3 (C10), 47.9 (C12), 39.9 (C16), 34.3
(C14), 31.4 (N-CH3), 27.7 (N-CH3), 25.5 (C15), 23.2 (C13), 22.1 (C18), 20.8 (C19 and C20), 16.2 (C17).
MS (ES−); 351.19 (M-H); MS (ES+); 375.22 (M+H); HRMS (M−H); calcd for C18H27N2O5; 351.1925;
found; 351.1922.
3.4.13. Synthesis of Compound (±)-10
Yield; 51% (oil); 1H-NMR (500 MHz, CDCl3); 3.32 (s, 3H, C7), 3.28 (s, 3H, C8), 3.15–3.05 (m, 2H,
C10), 2.25–2.21 (m, 1H, C13), 2.18 (d, 1H, J = 12.5 Hz, C16), 2.07 (d, 1H, J = 12.5 Hz, C16),

Molecules 2015, 20
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2.02–1.97 (m, 1H, C17), 1.88–1.81 (m, 1H, C12), 1.69–1.63 (m, 2H, C11), 1.62–1.43 (m, 3H, C15 and
C17), 1.30–1.21 (m, 1H, C12), 1.01 (s, 3H, CH3), 0.83 (s, 3H, CH3). 13C-NMR (125 MHz, CDCl3); 212.4
(C14), 199.3 (C9), 169.6 (C2), 160.7 (C4), 150.3 (C6), 95.1 (C3), 54.8 (C16), 49.1 (C13), 37.9 (C10),
36.9 (C17), 36.6 (C18), 31.3 (CH3), 29.4 (C12 or C15), 28.8 (C12 or C15), 27.9 (N-CH3), 27.7 (N-CH3),
25.5 (CH3), 23.3 (C11). MS (ES−); 349.19 (M−H); MS (ES+); 351.21 (M+H), 373.19 (M+Na); HRMS
(M+Na); calcd for C18H26N2Na1O5; 373.1734; found; 373.1723.
3.4.14. Synthesis of Compound cis-11
1
Yield; 46 % (oil); H-NMR (400 MHz, CDCl3); 3.99–3.91 (m, 4H, C7 and C9), 3.20 (dd, 1H,
J1 = 15.2 Hz, J2 = 6.4 Hz, C12), 3.05 (dd, 1H, J1 = 15.2 Hz, J2 = 8.0 Hz, C12), 2.84 (dd, 1H, J1 = 10.0 Hz,
J2 = 7.6 Hz, C15), 2.43–2.34 (m, 1H, C13), 2.11–2.03 (m, 1H, C14), 2.01 (s, 3H, C20), 1.92–1.85 (m,
1H, C14), 1.31 (s, 3H, C17), 1.23–1.16 (m, 6H, C8 and C10), 0.90 (s, 3H, C17). 13C NMR (100 MHz,
CDCl3); 207.3 (C20), 198.8 (C11), 169.5 (C2), 160.4 (C4), 149.4 (C6), 95.2 (C3), 54.2 (C15), 43.7
(C16), 38.5 (C13), 37.3 (C12), 36.6 (NCH2), 36.5 (NCH2), 30.0 (C18 and C20), 23.2 (C14), 17.5 (C17),
13.1 (C8 and C10). MS (ES−); 349.18 (M−H); MS (ES+); 373.18 (M+Na); HRMS (M+Na); calcd for
C18H26Na1N2O5; 373.1734; found; 373.1728.
3.4.15. Synthesis of Compound (±)-12
Yield; 35% (oil); 1H-NMR (400 MHz, CDCl3); 4.73 (brs, 1H, C18), 4.21 (d, 1H, J = 15.6 Hz, C17),
4.12 (d, 1H, J = 15.6 Hz, C17), 3.79–3.74 (m, 1H, C22), 3.47–3.43 (m, 1H, C22), 3.30 (s, 3H, C7), 3.25
(s, 3H, C8), 3.07 (t, 2H, J = 7.2 Hz, C10), 2.28–2.16 (m, 2H, C14), 1.78–1.45 (m, 10H, CH2). 13C-NMR
(100 MHz, CDCl3); 199.3 (C9), 169.6 (C2), 160.6 (C4), 150.1 (C6), 96.3 (C18), 95.0 (C3), 86.0 (C15),
75.9 (C16), 61.7 (C22), 54.4 (C17), 36.4 (C10), 30.1 (CH2), 28.4 (CH2), 28.0 (CH2), 27.8 (N-CH3), 27.6
(N-CH3), 25.2 (CH2), 25.1 (CH2), 18.9 (CH2), 18.5 (CH2). MS (ES−); 391.19 (M−H); HRMS (M+Na);
calcd for C20H28N2Na1O6; 415.1840; found; 415.1821.

Molecules 2015, 20
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3.4.16. Synthesis of Compound 13
Yield; 87%; M.P.; 245 °C (decomposed); 1H-NMR (400 MHz, CDCl3); 3.35 (s, 3H, C7), 3.32 (s, 3H,
C8), 3.20–3.05 (m, 2H), 2.94–2.81 (m, 3H), 2.37–1.81 (m, 15H), 1.70–1.57 (m, 2H), 1.39 (s, 3H, C32),
1.33–1.24 (m, 2H), 1.07 (s, 3H, C31), 0.92 (d, 3H, J = 6.4 Hz, C13). 13C-NMR (100 MHz, CDCl3); 211.8
(C=O), 209.0 (C=O), 208.7 (C=O), 200.1 (C=O), 169.7 (C2), 160.7 (C4), 150.3 (C6), 95.2 (C3), 56.9
(C18), 51.7 (CH), 48.9 (CH), 46.8 (CH), 45.7 (CH), 45.5 (CH), 44.9 (CH2), 42.7 (CH2), 38.6 (CH2), 36.4
(CH2), 36.3 (C12), 35.9 (C26), 35.2 (CH2), 34.3 (CH2), 33.9 (CH2), 31.5 (CH2), 28.0 (N-CH3), 27.8
(N-CH3), 27.6 (CH2), 25.6 (CH2), 25.1 (CH2), 24.9 (CH2), 21.8 (C13), 18.7 (C32), 11.8 (C31). MS (ES−);
539.30 (M−H), HRMS (M-H); calcd for C30H39N2O7; 539.2763; found; 539.2763.
3.4.17. Synthesis of Compound 14
Yield; 66%; M.P. 96 °C; 1H-NMR (500 MHz, CDCl3); 5.79 (d, 1H, J = 10.0 Hz, C13), 5.42 (s, 1H,
C17), 3.62–3.56 (m, 1H, C11), 3.50–3.44 (m, 1H, C11), 3.36 (s, 3H, C7), 3.32 (s, 3H, C8), 2.81 (t, 2H,
J = 6.5 Hz, C10), 2.59–2.52 (m, 1H, C14), 2.36 (td, 1H, J1 = 13.5 Hz, J2 = 3.5 Hz, CH2), 2.05–2.00 (m,
1H, CH2), 1.91–1.85 (m, 1H, CH2), 1.79–1.69 (m, 2H, C24 and CH2), 1.63–1.59 (m, 1H, C15), 1.51–1.40
(m, 1H, CH2), 1.43 (s, 3H, C26), 1.38–1.24 (m, 3H, C21, C22 and C24), 1.04–0.99 (m, 1H, CH2), 0.95
(d, 3H, J = 6.0 Hz, C27), 0.85 (d, 3H, J = 7.0 Hz, C25). 13C-NMR (125 MHz, CDCl3); 197.4 (C9), 171.0
(C12), 169.7 (C2), 160.7 (C4), 150.2 (C6), 104.4 (C18), 95.2 (C3), 92.2 (C13), 91.4 (C17), 80.0 (C16),
51.5 (C21), 45.2 (C15), 37.2 (C22), 36.1 (CH2), 34.0 (CH2), 31.9 (C11), 31.8 (C14), 28.6 (C10), 27.9
(N-CH3), 27.8 (N-CH3), 25.9 (C26), 24.5 (CH2), 21.9 (C24), 20.2 (C27), 12.0 (C25). MS (ES−); 521.22
(M−H); HRMS (M−H); calcd for C25H33N2O10; 521.2141; found; 521.2148.

Molecules 2015, 20
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3.4.18. Synthesis of Compound 15a
Yield; 27%; M.P.; 118 °C ; 1H-NMR (400 MHz, CDCl3); 6.83 (brs, 1H, NH), 4.98 (s, 2H, CH2), 4.07
(s, 2H, CH2), 3.38 (s, 3H, C7), 3.34–3.28 (m, 5H, C8 and C13), 2.38–2.32 (m, 1H, C18), 2.16–2.18 (m,
1H, C14), 1.98–1.81 (m, 5H, C15, C16, C19 and C20), 1.54–1.44 (m, 1H, C19), 1.18 (s, 3H, C21), 1.03
13
(s, 3H, C22), 0.89 (d, 1H, J = 9.6 Hz, C18). C-NMR (100 MHz, CDCl3); 195.2 (C9), 169.5 (C12),
168.6 (C2), 160.4 (C4), 150.0 (C6), 93.9 (C3), 72.1 (CH2), 71.3 (CH2), 44.4 (C13), 43.7 (CH), 41.2
(CH), 41.2 (CH), 38.6 (C17), 33.1 (CH2), 28.0 (CH3), 27.9 (CH3), 27.8 (CH3), 25.9 (CH2), 23.1 (CH3),
19.7 (CH2). MS (ES−); 406.20 (M−H); HRMS (M−H); calcd for C20H28N3O6; 406.1984; found;
406.1986.
3.4.19. Synthesis of Compound 15b
Yield; 43% (oil); 1H-NMR (500 MHz, CDCl3); 5.95 (brs, 1H, NH), 3.34–3.16 (m, 10H, C7, C8, C10
and C14), 2.30–2.27 (m, 1H, C21), 2.25 (s, 2H, C12), 2.17–2.10 (m, 1H, C17), 1.92–1.77 (m, 5H, C18,
C20, C22 and C23), 1.47–1.41 (m, 1H, C22), 1.12 (s, 9H, CH3), 0.98 (s, 3H, CH3), 0.84 (d, 1H, J = 9.5 Hz,
C21). 13C-NMR (125 MHz, CDCl3); 198.4 (C9), 170.7 (C13), 169.9 (C2), 160.8 (C4), 149.9 (C6), 96.8
(C3), 48.3 (CH2), 45.0 (CH2), 44.5 (CH2), 43.8 (CH), 41.3 (CH), 41.2 (CH), 38.5 (C19), 35.4 (C11),
33.0 (CH2), 28.1 (CH3), 28.1 (CH3), 27.8 (CH3), 25.8 (CH2), 23.1 (CH3), 19.8 (CH2). MS (ES−); 432.24
(M−H); MS (ES+); 434.29 (M+H), 456.27 (M+Na); HRMS (M+H); calcd for C23H36N3O5; 434.2649;
found; 434.2634.
3.4.20. Synthesis of Compound 16
Yield; 49%; M.P.; 102 °C ; 1H-NMR (500 MHz, CDCl3); 8.39 (brs, 1H, ArH), 7.39 (brs, 1H, ArH),
7.14 (d, 1H, J = 7.5 Hz, C20), 3.98 (brs, 4H, C24 and C25), 3.43 (s, 2H, C10), 3.37 (s, 3H, C7), 3.31 (s,
13
3H, C8), 3.21 (brs, 4H, C22 and C23), 2.43 (s, 2H, C12), 1.22 (s, 6H, C14 and C15). C-NMR (125

Molecules 2015, 20
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MHz, CDCl3); 198.2 (C9), 170.0 (C2), 162.7 (C13), 162.0 (C4), 155.5 (d, JC-F = 245 Hz, C19), 149.9
(C6), 135.6 (C21), 120.3 (C16), 115.5 (Ar-tert C), 115.5 (Ar-tert C), 109.0 (d, JC-F = 25.5 Hz, C17), 97.0
(C3), 66.0 (C24 and C25), 51.8 (C22 and C23), 48.2 (CH2), 44.4 (CH2), 36.0 (C11), 28.3 (C14 and C15),
28.2 (N-CH3), 28.0 (N-CH3). MS (ES−); 475.20 (M−H), MS (ES+); 499.23 (M+Na), HRMS (M+Na);
calcd for C23H29F1N4Na1O6; 499.1963; found; 499.1964.
3.4.21. Synthesis of Compound 17a
1
Yield; 84%; M.P.; 95 °C ; H-NMR (500 MHz, CDCl3); 7.27–7.23 (m, 2H, C16 and C17), 6.91
(t, 1H, J = 7.0 Hz, C18), 6.85 (d, 2H, J = 8.0 Hz, C14 and C15), 4.05 (t, 2H, J = 6.0 Hz, C12), 3.37–3.34
(m, 5H, C10 and C7), 3.29 (s, 3H, C8), 2.23–2.17 (m, 2H, C11). 13C-NMR (125 MHz, CDCl3); 198.8
(C9), 169.6 (C2), 160.7 (C4), 158.6 (C13), 150.1 (C6), 129.2 (C16 and C17), 120.6 (C18), 114.3 (C14
and C15), 95.3 (C3), 66.7 (C12), 33.6 (C10), 27.8 (N-CH3), 27.7 (N-CH3), 25.1 (C11). MS (ES−); 317.13
(M−H), HRMS (M−H); calcd for C16H17N2O5; 317.1143; found; 317.1141.
3.4.22. Synthesis of Compound 17b
1
Yield; 63%; M.P.; 84 °C ; H-NMR (400 MHz, CDCl3); 7.34–7.23 (m, 5H, C15-C19), 4.49 (s, 2H,
C13), 3.58 (t, 2H, J = 6.0 Hz, C12), 3.33 (s, 3H, C7), 3.31 (s, 3H, C8), 3.27 (t, 2H, J = 6.0 Hz, C10),
2.07–2.00 (m, 2H, C11). 13C-NMR (100 MHz, CDCl3); 199.4 (C9), 169.6 (C2), 160.8 (C4), 150.2 (C6),
138.3 (C14), 128.2 (C17 and C18), 127.5 (C15 and C16), 127.4 (C19), 95.2 (C3), 72.8 (C13), 69.4 (C12),
33.8 (C10), 27.9 (N-CH3), 27.7 (N-CH3), 25.7 (C11). MS (ES−); 331.13 (M−H); MS (ES+); 355.14
(M+Na); HRMS (M+Na); calcd for C17H20N2Na1O5; 355.1264; found; 355.1262.
3.4.23. Synthesis of Compound 17c

Molecules 2015, 20
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Yield; 70%; M.P.; 142 °C ; 1H-NMR (400 MHz, CDCl3); 7.77–7.70 (m, 3H, C16, C19 and C20), 7.44
(dd, 1H, J1=J2 = 6.8 Hz, C21), 7.33 (dd, 1H, J1=J2 = 6.8 Hz, C22), 7.12–7.11 (m, 2H, C14 and C15),
4.20 (t, 2H, J = 5.6 Hz, C12), 3.41 (t, 2H, J = 5.6 Hz, C10), 3.36 (s, 3H, C7), 3.29 (s, 3H, C8), 2.31–2.25
13
(m, 2H, C11). C-NMR (100 MHz, CDCl3); 198.9 (C9), 169.7 (C2), 160.8 (C4), 156.6 (C13), 150.2
(C6), 134.5 (quart C), 129.3 (tert C), 128.9 (quart C), 127.6 (tert C), 126.6 (tert C), 126.3 (tert C), 123.6
(tert C), 118.8 (tert C), 95.4 (C3), 66.9 (C12), 33.7 (C10), 27.9 (N-CH3), 27.8 (N-CH3), 25.2 (C11). MS
(ES−); 367.14 (M−H); MS (ES+); 369.19 (M+H), 391.14 (M+Na); HRMS (M+Na); calcd for
C20H20N2Na1O5; 391.1264; found; 391.1261.
3.4.24. Synthesis of Compound 18a
Yield; 75%; M.P.; 87 °C ; 1H-NMR (400 MHz, CDCl3); 7.09 (d, 2H, J = 8.0 Hz, C16 and C17), 6.80
(d, 2H, J = 8.0 Hz, C14 and C15), 4.05 (t, 2H, J = 6.0 Hz, C12), 3.38–3.34 (m, 5H, C7 and C10), 3.31
(s, 3H, C8), 2.58 (q, 2H, J = 7.6 Hz, C19), 2.23–2.17 (m, 2H, C11), 1.21 (t, 3H, J = 7.6 Hz, C20).
13C-NMR (100 MHz, CDCl3); 199.0 (C9), 169.7 (C2), 160.8 (C4), 156.7 (C13), 150.3 (C6), 130.5 (C18),
128.6 (C16 and C17), 114.3 (C14 and C15), 95.4 (C3), 66.9 (C12), 33.7 (C10), 28.0 (N-CH3), 27.9
(C19), 27.8 (N-CH3), 25.3 (C11), 15.8 (C20). MS (ES−); 345.15 (M−H); MS (ES+); 369.16 (M+Na);
HRMS (M+Na); calcd for C18H22N2Na1O5; 369.1421; found; 369.1412.
3.4.25. Synthesis of Compound 18b
Yield; 58%; M.P.; 92 °C ; 1H-NMR (400 MHz, CDCl3); 7.29 (d, 2H, J = 8.8 Hz, C16 and C17), 6.81
(d, 2H, J = 8.8 Hz, C14 and C15), 4.06 (t, 2H, J = 6.4 Hz, C12), 3.39–3.35 (m, 5H, C7 and C10), 3.31
(s, 3H, C8), 2.24–2.17 (m, 2H, C11), 1.30 (s, 9H, C20–C22). 13C-NMR (100 MHz, CDCl3); 199.0 (C9),
169.7 (C2), 160.8 (C4), 156.4 (C13), 150.2 (C6), 143.4 (C18), 126.1 (C16 and C17), 113.4 (C14 and
C15), 95.4 (C3), 66.9 (C12), 34.0 (C19), 33.7 (C10), 31.5 (C20–C22), 27.9 (N-CH3), 27.8 (N-CH3), 25.3
(C11). MS (ES−); 373.19 (M−H); MS (ES+); 397.20 (M+Na); HRMS (M+Na); calcd for C20H26N2Na1O5;
397.1734; found; 397.1740.

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3.4.26. Synthesis of Compound 18c
Yield; 67%; M.P.; 150 °C ; 1H-NMR (400 MHz, CDCl3); 7.00 (d, 2H, J = 7.6 Hz, C16 and C17), 6.91
(dd, 1H, J1 = 7.6 Hz, J2= 7.6 Hz, C18), 3.87 (t, 2H, J = 6.4 Hz, C12), 3.44 (t, 2H, J = 6.4 Hz, C10), 3.39
(s, 3H, C7), 3.35 (s, 3H, C8), 2.29 (s, 6H, C19 and C20), 2.25–2.18 (m, 2H, C11). 13C-NMR (100 MHz,
CDCl3); 199.1 (C9), 169.7 (C2), 160.8 (C4), 155.7 (C13), 150.3 (C6), 130.8 (C14 or C15), 128.8 (C16
and C17), 123.7 (C18), 95.3 (C3), 70.9 (C12), 33.7 (C10), 28.0 (N-CH3), 27.8 (N-CH3), 26.1 (C11), 16.3
(C19 and C20). MS (ES−); 345.16 (M−H); MS (ES+); 347.20 (M+H), 369.17 (M+Na); HRMS (M+Na);
calcd for C18H22N2Na1O5; 369.1421; found; 369.1415.
3.4.27. Synthesis of Compound 18d
Yield; 72%; M.P.; 139 °C ; 1H-NMR (400 MHz, CDCl3); 7.00 (d, 1H, J = 7.2 Hz, C16), 6.67 (d, 1H,
J = 7.2 Hz, C18), 6.63 (s, 1H, C15), 4.07 (t, 2H, J = 6.0 Hz, C12), 3.42–3.38 (m, 5H, C7 and C10), 3.33
(s, 3H, C8), 2.32 (s, 6H, C20), 2.27–2.20 (m, 2H, C11), 2.17 (s, 6H, C19). 13C-NMR (100 MHz, CDCl3);
199.0 (C9), 169.7 (C2), 160.8 (C4), 156.6 (C13), 150.3 (C6), 136.4 (C17), 130.3 (C16), 123.5 (C14),
120.8 (C18), 111.8 (C15), 95.3 (C3), 66.7 (C12), 33.7 (C10), 27.9 (N-CH3), 27.8 (N-CH3), 25.3 (C11),
21.3 (C20), 15.7 (C19). MS (ES−); 345.15 (M−H); MS (ES+); 347.18 (M+H), 369.16 (M+Na); HRMS
(M+Na); calcd for C18H22N2Na1O5; 369.1421; found; 369.1407.
3.4.28. Synthesis of Compound 18e
Yield; 43%; M.P.; 127 °C ; 1H-NMR (400 MHz, CDCl3); 7.17 (d, 1H, J = 8.8 Hz, C16), 6.72 (d, 1H,
J = 2.8 Hz, C15), 6.62 (dd, 1H, J1 = 8.8 Hz, J2= 2.8 Hz, C14), 4.01 (t, 2H, J = 6.0 Hz, C12), 3.36–3.29
13
(m, 8H, C7, C8 and C10), 2.30 (s, 3H, C19), 2.21–2.14 (m, 2H, C11). C-NMR (100 MHz, CDCl3);
198.7 (C9), 169.7 (C2), 160.7 (C4), 157.2 (C13), 150.2 (C6), 136.8 (C17 or C18), 129.4 (C16), 125.7
(C17 or C18), 116.9 (C14 or C15), 112.9 (C14 or C15), 95.3 (C3), 67.1 (C12), 35.6 (C10), 27.9
(N-CH3), 27.8 (N-CH3), 25.1 (C11), 20.2 (C19). MS (ES−); 365.11 (M−H), HRMS (M+Na); calcd for
C17H19Cl1N2Na1O5; 389.0875; found; 389.0863.

Molecules 2015, 20
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3.4.29. Synthesis of Compound 18f
Yield; 70%; M.P.; 123 °C ; 1H-NMR (400 MHz, CDCl3); 7.31 (s, 1H, C17), 7.14 (d, 1H, J = 8.8 Hz,
C16), 6.81 (d, 1H, J = 8.8 Hz, C14), 4.09 (t, 2H, J = 6.0 Hz, C12), 3.39–3.35 (m, 5H, C10 and C7), 3.29
(s, 3H, C8), 2.28–2.21 (m, 2H, C11). 13C-NMR (100 MHz, CDCl3); 198.5 (C9), 169.7 (C2), 160.8 (C4),
153.0 (C13), 150.2 (C6), 129.8 (C17), 127.4 (C16), 125.6 (C18), 123.6 (C15), 113.8 (C14), 95.4 (C3),
68.4 (C12), 33.5 (C10), 27.9 (N-CH3), 27.8 (N-CH3), 24.9 (C11). MS (ES−); 385.06 (M−H), HRMS
(M−H); calcd for C16H15Cl2N2O5; 385.0364; found; 385.0368.
3.4.30. Synthesis of Compound 18g
Yield; 56%; M.P.; 148 °C ; 1H-NMR (400 MHz, CDCl3); 7.09–7.07 (m, 2H, C16 and C17), 6.70 (d,
1H, J = 8.0 Hz, C14), 4.04 (t, 2H, J = 6.0 Hz, C12), 3.40–3.36 (m, 5H, C10 and C7), 3.33 (s, 3H, C8),
2.26–2.20 (m, 2H, C11), 2.18 (s, 3H, C19). 13C-NMR (100 MHz, CDCl3); 198.8 (C9), 169.8 (C2), 160.8
(C4), 155.4 (C13), 150.3 (C6), 130.3 (C17), 128.7 (C15), 126.2 (C16), 125.0 (C18), 111.8 (C14), 95.4
(C3), 67.2 (C12), 33.7 (C10), 28.0 (N-CH3), 27.8 (N-CH3), 25.2 (C11), 16.0 (C19). MS (ES−); 365.10
(M−H), HRMS (M−H); calcd for C17H18Cl1N2O5; 365.0910; found; 365.0901.
3.4.31. Synthesis of Compound 19a
Yield; 37%; M.P. 77 °C; 1H-NMR (400 MHz, CDCl3); 7.07–7.05 (m, 2H, C18 and C19), 6.69 (d, 1H,
J = 8.4 Hz, C17), 4.04–3.94 (m, 6H, C7, C9 and C14), 3.37 (t, 2H, J = 7.2 Hz, C12), 2.25–2.18 (m, 2H,
C13), 2.17 (s, 3H, C21), 1.25 (t, 3H, J = 7.6 Hz, CH3), 1.20 (t, 3H, J = 7.6 Hz, CH3). 13C-NMR
(100 MHz, CDCl3); 198.9 (C11), 169.5 (C2), 160.4 (C4), 155.4 (C15), 149.3 (C6), 130.3 (C18), 128.6
(quart C), 126.2 (C19), 124.9 (quart C), 111.7 (C17), 95.4 (C3), 67.1 (C14), 36.7 (N-CH2), 36.5
(N-CH2), 33.7 (C12), 25.0 (C13), 16.0 (C21), 13.2 (CH3), 13.1 (CH3). MS (ES−); 393.12 (M−H); HRMS
(M−H); calcd for C19H22Cl1N2O5; 393.1223; found; 393.1215.