Antibacterial Diamines Targeting Bacterial Membranes

Article abstract of DOI:10.1021/acs.jmedchem.5b01912

Antibiotic resistance is a growing threat to human health exacerbated by a lack of new antibiotics. We now describe a series of substituted diamines that produce rapid bactericidal activity against both Gram-positive and Gram-negative bacteria, including

Full text of DOI:10.1021/acs.jmedchem.5b01912

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Article
Antibacterial Diamines Targeting Bacterial Membranes
Bo Wang, Boobalan Pachaiyappan, Jordan D. Gruber,
Michael G. Schmidt, YongMei Zhang, and Patrick M. Woster
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.5b01912 • Publication Date (Web): 10 Mar 2016
Downloaded from http://pubs.acs.org on March 14, 2016
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Antibacterial Diamines Targeting Bacterial
Membranes
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‡
, †, 1, ,
‡, ¶, 2
1
3
Bo Wang,
Boobalan Pachaiyappan,
Jordon D. Gruber, Michael G. Schmidt, Yong-
1
2*
Mei Zhang and Patrick M Woster
1
Department of Biochemistry and Molecular Biology, Medical University of South Carolina,
Charleston, South Carolina, USA
2
Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina,
Charleston, South Carolina, USA
3
Department of Microbiology & Immunology, Medical University of South Carolina, Charleston,
South Carolina, USA
4
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing, PR China
KEYWORDS: diamine, antibacterial, bacterial membrane, depolarization, biofilm,
Pseudomonas aeruginosa, Staphylococcus aureas.
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ABSTRACT
Antibiotic resistance is a growing threat to human health exacerbated by a lack of new
antibiotics. We now describe a series of substituted diamines that produce rapid bactericidal
activity against both Gram-positive and Gram-negative bacteria, including methicillin-resistant
Staphylococcus aureus and stationary-phase bacteria. These compounds reduce biofilm
formation and promote biofilm dispersal in Pseudomonas aeruginosa. The most potent analogue,
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(1,13-bis{[(2,2-diphenyl)-1-ethyl]thioureido}-4,10-diazatridecane), primarily acts by
depolarization and permeabilization of the bacterial outer membrane. Transmission electron
microscopy confirmed that 3 disrupts membrane integrity rapidly. Compound 3 is also
synergistic with kanamycin, demonstrated by the checkerboard method and by time-kill kinetic
experiments. In human cell toxicity assays, 3 showed limited adverse effects against the
HEK293T human kidney embryonic cells and A549 human adenocarcinoma cells. In addition, 3
produced no adverse effects on Caenorhabditis elegans development, survival and reproduction.
Collectively, diamines related to 3 represent a new class of broad-spectrum antibacterials against
drug-resistant pathogens.
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Introduction
Infections caused by drug-resistant bacteria have become an increasing threat to human health.
Despite the rapidly increasing incidence of antibacterial resistance, few new antibiotics are
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currently being developed. Thus, there is an urgent need to identify new antibiotics from distinct
chemical classes and with novel mechanisms of action. Unlike conventional antibiotics, cationic
antimicrobial peptides (AMPs) are known to act primarily by disrupting the bacterial cell
membrane. Moreover, this charge-charge interaction between AMPs and bacterial cell membrane
does not target intracellular bacterial organelles. Thus, bacteria find it difficult to develop
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resistance against AMPs. However, AMPs are mainly limited by their potential for toxicity,
high susceptibility to proteolytic degradation, and the high cost of manufacture. In the recent
past, several classes of cationic small molecules that mimic the AMPs have shown some promise
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as potential antibiotics, and some of them are undergoing clinical trials.
By virtue of the cationic groups in their structure, natural polyamines exhibit a broad range of
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biological functions that promote bacterial fitness and pathogenesis. Recent studies have shown
that natural polyamines and their analogues can impair membrane integrity and biofilm
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formation
without affecting planktonic bacterial growth, and also increase antibiotic
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susceptibility.
Synthetic polyamine-containing sterol analogues related to squalamine also
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5-17
exhibit antimicrobial activities.
These data suggest that there is considerable potential for the
use of synthetic diamines as potential antibacterial drug candidates.
Herein we report the design and development of synthetic diamines 1-16 (Figure 1);
compounds 1-12 are bactericidal against Staphylococcus aureus, Pseudomonas aeruginosa,
Escherichia coli, and methicillin-resistant Staphylococcus aureus (MRSA), while 13-16 were
designed to evaluate the requirement for the central charged nitrogens. Importantly, these
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compounds also strongly inhibit biofilm formation and promote biofilm dispersal in the gram-
negative pathogen P. aeruginosa. The most effective of these analogues, compound 3, was
selected for use as a chemical tool to elucidate the exact mechanism of the bactericidal activity
for these agents, which until now was unclear. We hypothesize that positively charged diamines
such as 1-12 can interact with the negatively charged bacterial cell membrane. Therefore, we
employed multiple methods to elucidate the effects of synthetic diamines on membrane
homeostasis. We also determined the effect of 3 in combination with selected commercial
antibiotics to determine whether they act synergistically. Finally, we determined the effect of 3
against non-dividing bacterial cells and evaluated its protease tolerance and toxicity in human
cells and Caenorhabditis elegans. Findings from this study provide evidence that diamines are
membrane-targeting inhibitors that are active against drug-resistant pathogens.
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Chemistry
The (bis)ureido- and (bis)thioureido diamines 1-12 described in this manuscript were
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synthesized according to our recently published pathway, as shown in Scheme 1. The synthesis
of compound 3 is described below, and all other compounds were synthesized in exactly the
same manner. 1,5-Diaminopentane 17 was (bis)cyanoethylated (acrylonitrile, ethanol, reflux)
and the central nitrogens were protected [(Boc)
previously described (bis)-N-Boc protected intermediate 18.
the presence of Raney nickel (H , 50 psi, NH OH) to form the (bis)-N-Boc protected diamine 19.
Intermediate 19 was then reacted with the appropriate isocyanate or isothiocyanate (in this case
,2-diphenylethyl isothiocyanate 20) to yield the protected precursor 21. Removal of the N-Boc
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O, NaHCO
3
, CHCl
3
/H
2
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Compound 18 was reduced in
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protecting groups with mild acid (HCl in EtOAc) then afforded the desired target compound 3.
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Compounds 13-16, which lack the two internal secondary nitrogens found in 1-12, were
synthesized as described in Scheme 2. Briefly, 1,11-diaminoundecane 22 was allowed to react
with 2 equivalents of 3,3-diphenylpropyl isocyanate 23 to afford the corresponding target
compound 13. Likewise, 1,12-diaminododecane 24 was coupled to the appropriate isocyanate or
isothiocyanate 25-27 to afford the corresponding analogues 14-16.
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Results
Antibacterial screen. In order to determine whether synthetic diamines 1-16 possessed an
acceptable minimum inhibitory concentration (MIC) in multiple organisms, the MIC99 of
ꢀ
compounds 1-16 was determined against a Gram-positive organism (Staphylococcus aureus
strain RN4220) and 2 Gram-negative organisms (Pseudomonas aeruginosa strain PA01 and
Escherichia coli strain ANS1). The MIC99 assay for the antibacterial activity of
compound was performed by the micro-broth dilution method of the Clinical and Laboratory
Standards Institute of America. MIC was defined as the lowest compound concentration at
a 96-well plate
The results of these studies are summarized in Table 1.
ꢀe ach test
ꢀ
ꢀ
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which bacterial growth was completely inhibited after overnight incubation in
(Nunc) at 37°C without shaking.
ꢀ
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Commercially available antibiotics from 4 different classes were used as positive controls: the
penicillin derivative ampicillin (AMC), the aminoglycoside kanamycin (KAN), the
fluoroquinoline norfloxacin (NOR) and the polymixin antibiotic colistin. The natural polyamines
spermidine and spermine were also assayed as negative control compounds. Synthetic diamines
1-4 and 7-12 produced significant antibacterial activity, with MIC99 values between 2 and 32
µg/mL (with one exception: compound 1 had an MIC99 value of 256 µg/mL against P.
aeruginosa). The most effective of these analogues, 3, exhibited MIC99 values of 2.0, 8.1 and 2.2
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µg/mL against S. aureus RN4220, P. aeruginosa PA01 and E. coli ANS1, respectively.
Compounds 13-16 were synthesized to determine whether the presence of the two central
nitrogens was required for activity. Importantly, compounds 13-16 produced no detectable
inhibitory effect against any of the 3 tested strains. A direct comparison could be made between
active compounds 10-12 and inactive (control) analogues 14-16, since each of these compounds
possessed a chain length of 12 atoms between the terminal substituted ureas or thioureas.
Substitution of carbon for the internal nitrogens in 10-12 produced a complete abolition of
antibacterial activity. Based on the fact that simple polyamine analogues such as spermidine and
spermine do not produce antibacterial effects, it would appear that the presence of both the
central charged nitrogens and the terminal diaryl moieties are required for activity. It may be that
the aromatic ring structures produce additional affinity for the bacterial membrane due to a
hydrophobic effect. However, this effect in itself in not sufficient to produce the observed
antibacterial activity, since 13-16 are inactive. Interestingly, it has been shown that the natural
polyamines spermidine and spermine, as well as simple diamines like putrescine and cadaverine,
have no antibacterial effects, no effect on outer membrane permeability, and did not cause
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membrane rupture. These amine derivatives have no inherent antibacterial activity in
pseudomonas, and are in fact biosynthesized and imported by numerous bacteria, including
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Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Although diamines
such as those mentioned above have no inherent antibacterial activity, addition of exogenous
spermidine (1.0 mM) or other polyamines to the pseudomonas growth medium increased the
MIC values of multiple antibiotics, including polycationic antibiotics, aminoglycosides,
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quinolones, and fluorescent dyes. In a subsequent study by the same group, spermine was
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shown to decrease the MIC values for chloramphenicol and b-lactam antibiotics. Taken
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together, these data support the contention that both the central charged nitrogens and the
terminal diaryl moieties in 1-12 are required for the observed antibacterial activity.
A clear structure/activity trend was also observed by comparing the MIC99 values of
compounds 1-12. Compounds with (bis)aryl substitutions on the terminal alkyl group were
significantly more potent than those with monoaryl substituents, as reflected in MIC99 values.
Also, the (bis)arylthioureido analogues were slightly more effective than the corresponding
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(bis)arylureido analogues, although this difference may not be indicative of a trend. Also, as
outlined above, the central charged nitrogen species in 1-12 are required for activity. Because
compound 3 was very effective in all three organisms, it was chosen for the experiments
described below.
Antibacterial activity of compound 3 against methacillin-resistent Staphylococcus aureus. To
further probe the activity of antimicrobial diamines 1-12, compound 3 was evaluated for the
ability to kill methacillin-resistant Staphylococcus aureus (MRSA) in vitro. Five MRSA isolates
from the Medical University of South Carolina collection were selected for antibacterial activity
testing. These isolates represented the most commonly found SPA types in the MUSC collection.
Strain 10082 B is SPA type 1, 10076 B is SPA type 2, 30253 CA is SPA type 7, 20225 B is SPA
type 15, and 20467 BA is SPA type 59. Compound 3 exhibited potent anti-MRSA activity,
exhibiting MIC99 values of 1-2 µg/mL against each isolate (Table 2). These MIC values are
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comparable to the MIC value of 3 against S. aureus RN4220 (2 µg/mL, see Table 1).
Effect of compound 3 on biofilm formation in Pseudomonas aeruginosa. As shown in Figure 2,
compound 3 inhibited P. aeruginosa biofilm formation at 64 µg/mL, which was comparable to
the commercial antibiotics tetracycline (TET) and NOR, whereas KAN displayed no inhibitory
effect below 1024 µg/mL (Figure 2A). Interestingly, 3 had a significantly stronger effect on the
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dispersal of formed biofilm (Figure 2B) when compared to TET, NOR and KAN. The term drug
tolerance refers to the non-inherited drug resistance that develops against antibiotics in non-
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dividing cells such as bacteria in the stationary phase. Because we suspected that diamines
target the bacterial membrane (see below), we hypothesized that they would be bactericidal
against non-dividing cells. Thus the effect of compound 3 on drug tolerant cells was evaluated
using bacteria in stationary phase. Actively dividing cells in exponential phase were used for the
purpose of comparison. An in vitro time-kill assay for 3 against stationary phase S. aureus and
P. aeruginosa revealed the remarkable and rapid bactericidal activity against both
multiplying bacteria and non-dividing stationary cells (Figure 3). By contrast, the traditional
antibiotics AMC, KAN and NOR displayed strong bactericidal activity against dividing bacteria,
but did not kill stationary phase bacteria efficiently. When tested at bactericidal concentrations
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(4X MIC99), AMC, KAN, NOR and compound 3 showed similar bactericidal activity against
log phase S. aureus cells (Figure 3A). However, stationary-phase S. aureus were resistant to
AMC, KAN and NOR, while remaining susceptible to 3 (Figure 3B). Following 4-hour
treatment, NOR reduced the viable cell numbers only by 2 logs while 3 eliminated all viable
cells. Log phase P. aeruginosa responded weakly to AMC and KAN, while NOR and 3 both
produced a 4 log reduction in viable bacteria (Figure 3C). P. aeruginosa in stationary phase was
completely resistant to AMC and KAN, and displayed increased resistance to NOR compared to
log phase cells. However, compound 3 elicited potent bactericidal activity against stationary
phase P. aeruginosa (Figure 3D), and eliminated all bacteria after 4 hours. These data
demonstrate that the membrane-targeting diamine 3 can circumvent drug tolerance in non-
dividing cells, since both dividing log phase and non-dividing stationary phase bacteria require
intact membranes to survive.
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Antibacterial activity in plasma. One of the major disadvantages of AMPs is their potential for
proteolytic inactivation. This is reflected in the subsequent loss of antibacterial activity of AMPs
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in the presence
ꢀo f plasma. To determine whether antibacterial diamines are resistant to
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hydrolysis by proteases, the MIC value of 3 in the presence of plasma was measured. A stock
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solution was prepared containing 10% fetal bovine serum (FBS), and the MIC99 assay was
performed by the micro-broth dilution method as described above. Following 12 hour pre-
incubation in the presence of plasma, 3 displayed no loss of activity when cultured in the
presence of 10% FBS (data not shown).
Hemolytic activity and cytotoxicity. The toxicity of compound 3 in mammalian cells was
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measured by its ability to lyse human red blood cells using the method of Kustanovich, and the
results were represented as the HC50 value (the concentration at which 50% of the red blood cells
are lysed). The HC50 of compound 3 was 64 µg/mL, indicating that the compound produced
selective toxicity towards bacterial cells. The cytotoxicity of compound 3 was also monitored in
two additional mammalian cell lines, the HEK293T human kidney embryonic cell line and the
A549 human alveolar basal epithelial adenocarcinoma cell line. The results of these studies are
shown in Table 3. The selectivity index (SI) in each cell line was the ratio of the CC50 value of
cytotoxicity against a given human cell line divided by the MIC99 value for a given bacterial
strain. Compound 3 possessed a favorable SI (defined as an SI > 10) between 16 and 64 against
S. aureus, E. coli and MRSA clinical isolates. The SI against P. aeruginosa was lower (either 4
or 8), suggesting that additional structure optimization is required to identify a compound that
kills P. aeruginosa with an acceptable SI.
Toxicity against Caenorhabditis elegans. C. elegans has been successfully used to study acute
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bacterial infections,
and has also been employed to assess toxicity. For our purposes, we
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incubated C. elegans with high concentrations of 3, gentamicin and 5-fluorodideoxyuridine
(5FU). Gentamicin and 5FU are both toxic towards eukaryotic cells at high concentrations and
3
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were used as controls throughout the assay.
Prior to this study, we evaluated the effect of
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lysed E. coli as a food source for nematodes because 3 has demonstrated the ability to lyse
bacterial membranes. C. elegans incubated with mechanically-lysed E. coli displayed no
alterations in development and procreation (data not shown). C. elegans eggs, L1 and L4
development stages were incubated with 64 µg/mL of 3 for 96 h, which provided enough time to
assess the complete life cycle. We observed no changes in C. elegans egg development, and
larvae that hatched produced viable eggs and displayed no deleterious genotypic effects. Juvenile
and adult nematodes were also not affected as evidenced by 100% survival, no changes in
locomotion, and maintenance of egg production. High concentrations of gentamicin or 5FU were
toxic towards C. elegans, specifically affecting the viability of eggs produced and killing
juvenile nematodes. Collectively, the assessment of the toxicity of 3 in C. elegans suggests that
the compound does not produce overt toxicity in vivo and should be further evaluated in a higher
organism. These data also indicate that the toxicity of 3 is low, an observation that is in
agreement with our results from toxicity testing in human cells.
Mechanism of action. The mechanism of action of compound 3 was investigated using various
spectroscopic methods that revealed that the diamines primarily acted by targeting the bacterial
cell membrane. As described below, our results show that the diamines exhibit rapid and potent
bactericidal activity. This fast killing activity was indicative of membrane targeting activities,
which could be mediated by an electrostatic interaction between the positively charged central
nitrogens in 3 and its analogues, and the negatively charged bacterial membrane. This hypothesis
is consistent with the fact that positively charged AMPs can disrupt bacterial membrane integrity
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and depolarize bacterial membranes. To test this hypothesis, we first measured the effect of 3
on bacterial membrane potential using a membrane-potential sensitive fluorescent probe (DiSC -
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5
). In buffer-treated control cells, the fluorescent signal of the probe was quenched by cell
membranes with intact membrane potential (Figure 4A and B). The addition of compound 3 at
X MIC99 (8 µg/mL) and 1X MIC99 (2 µg/mL) concentrations against S. aureus caused a rapid
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increase in the probe fluorescence intensity (Figure 4A), indicating the membrane potential was
dissipated by the diamine. Treatment of P. aeruginosa by compound 3 led to a similar abrupt
increase in DiSC -5 fluorescence (Figure 4B), demonstrating the cell membrane of both Gram-
3
positive and Gram-negative bacteria can be depolarized. There is now increasing evidence that
cationic antimicrobial agents can depolarize the cytoplasmic membrane. However, it is unclear if
depolarization is a consequence of the dying bacteria or is truly tied to the mechanism. To this
end, we performed simultaneous testing of bactericidal kinetics and depolarization (Figure 5).
Following a 5-minute treatment with 3 at 4X MIC99 (8 µg/mL), colony-forming unit (CFU) titers
of S. aureus and P. aeruginosa decreased more than 2 log10 units, an effect that was equal to the
positive control compound dinitrophenol (DNP). Colistin, a cationic antimicrobial peptide that
targets the membrane of Gram-negative bacteria, produced a similar effect in P. aeruginosa. The
time-kill kinetics produced by 3 paralleled the observed membrane depolarization, suggesting a
causal relationship between the rapid bactericidal effect of 3 and membrane depolarization.
Bacterial outer membrane permeabilization of P. aeruginosa was evaluated using another
fluorescent probe, 1-N-phenylnaphthylamine (NPN). Intact outer membranes exclude the
hydrophobic NPN while membranes with increased fluidity and permeability allow entry of the
3
4
probe, resulting in a higher fluorescent signal. The aminoglycoside antibiotic gentamicin
3
5
increases the outer membrane permeability of Gram-negative bacteria, and was thus included
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as a positive control. As shown in Figure 4C, the NPN fluorescence signal was increased rapidly
in P. aeruginosa treated with 3 at 4X MIC99 (32 µg/mL) and 1x MIC99 (8 µg/mL) in a manner
similar to that of gentamicin. These results suggest that 3 increases the permeability of the outer
bacterial membrane. Transmission electron microscopy (TEM) was subsequently used to
visualize bacterial cell morphology at high resolution and provide direct evidence of the
membrane effects caused by 3. Untreated S. aureus (Figure 6A) and P. aeruginosa (Figure 6D)
possessed an intact cell envelope with both a well-defined peptidoglycan cell wall and a lipid
bilayer membrane. Following treatment with 3 at 2x MIC99 for 30-60 minutes, S. aureus formed
numerous spherical, double layered mesosome-like structures (Figure 6B). Cellular debris of
completely lysed cells was also observed after the treatment with 3 (Figure 6C). Similarly, P.
aeruginosa treated with 3 at 2x MIC99 (15 minutes) exhibited extensive membrane damage, as
illustrated by the appearance of lysed cells and the release of cell contents (Figure 6E and 6F).
Interaction between compound 3 and antibiotics. The interactions between the membrane-
targeting diamines and antibiotics with different cellular targets were investigated using
checkerboard assays. The checkerboard fractional inhibitory concentration (FIC) for S. aureus
and P. aeruginosa treated with 3 was determined in combination with AMC, NOR, or KAN.
Based on the resulting FIC values and MIC99 isobolograms (Figure 7), compound 3 at 0.5X
MIC99 was synergistic with KAN, causing an 8-fold reduction in the MIC99 for KAN against S.
aureus (from 16 to 2 µg/ml) and P. aeruginosa (from 64 to 8 µg/ml). By contrast, 3 was not
synergistic with AMC or NOR. The synergistic interaction between 3 and KAN is consistent
with previous reports that aminoglycosides interact with the bacterial cell envelope and cause
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membrane damage.
Because the checkerboard method has been reported to be error prone,
the synergy between 3 and KAN was verified using a time-kill kinetic assay. Eliopoulos and
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Eliopoulos have suggested that an interpretation of “synergistic” requires a ≥ 2 log10 decrease in
CFU/mL by the combination compared with the most active constituent after 24 hr, and a ≥ 2
3
8
log10 decrease in CFU/mL below the starting inoculum. Our results show that the interaction
between 3 and KAN meet these criteria (Figure 8) and confirm the synergistic relationship. S.
aureus treated with 0.5X the MIC99 of compound 3 combined with 0.5X the MIC99 of KAN
reached more than 2 log10 decrease in viable cell count compared with treatment with 1X the
MIC99 of KAN alone, and to treatment at 1X the MIC99 of 3 alone (Figure 8A). Similarly,
treatment of P. aeruginosa with 0.5X the MIC99 of 3 plus 0.5X the MIC99 of KAN produced the
same effect (Figure 8B).
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Discussion
In order to discover antibacterial agents with novel mechanisms of action, many recent studies
have focused on identifying new bacterial targets or metabolic pathways. A relatively smaller
number of studies have described compounds targeted to the bacterial membrane and the
formation and disruption of biofilm. The cationic antimicrobial AMPs have shown promise as
2
antibiotics that are potentially able to overcome bacterial resistance. The antimicrobial action of
AMPs is mediated through interaction of their positively charged structures and hydrophobic
moieties with the bacterial cell membrane. In this study, we investigated the antibacterial
properties of functionalized diamines containing positive moieties that can mimic the AMPs and
confirmed that these compounds have potent bactericidal activity by depolarizing membrane
potential and disrupting bacterial membrane integrity. The importance of the positive charges in
mediating this activity is underscored by the fact that compounds 13-16, which lack the central
nitrogen moieties and thus are uncharged at physiological pH, have no detectable activity as
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compared to diamines with the same internal chain length. Both Gram-positive S. aureus and
Gram-negative P. aeruginosa and E. coli bacteria were susceptible to the bactericidal effect of
the synthetic diamine 3, which was chosen for further investigation. Importantly, compound 3
showed impressive activity against drug-resistant MRSA, dispersed biofilm in log phase and
stationary-phase bacteria, and produced a synergistic interaction with the aminoglycoside
antibiotic KAN. These effects were accompanied by a desirable selectivity index between the
human cells evaluated in this study and bacteria.
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Although the precise mechanism of action of antibacterial diamines such as 3 has not been
fully elucidated, our findings strongly suggest that the Gram positive and Gram negative
bacterial membrane is the primary target for these diamines. The interaction between diamines
related to 3 and the bacterial membrane is likely mediated by an electrostatic interaction between
the negatively charged bacterial membrane and the positively charged compounds. Binding of 3
to the membrane dissipated cell membrane potential, increased membrane permeability, and led
to cell content release and lysis. Transmission electron microcopy provided the most direct
evidence of the membrane disrupting action of 3; cells treated with 3 formed abnormal
membranous structures and exhibited extensive cell membrane damage. Preliminary structure
activity relationship experiments demonstrate that analogues of 3 lacking charged central
nitrogens were not effective against S. aureus and P. aeruginosa. While the positive charge of
the compound is required for activity, it is also likely that this charge contributes to the
20, 39
cytotoxicity observed with these analogues at higher concentrations.
However, this toxicity
can be effectively managed when compounds related to 3 are used at lower doses as
4
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antimicrobial agents.
Hit-to-lead optimization of antimicrobial diamines such as 3 is an
ongoing concern in our laboratories.
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Classical antibiotics are effective in killing actively dividing cells, but they are ineffective
against bacteria that are not dividing, a phenomenon known as non-inherited antibiotic
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resistance. Membrane-active compounds can overcome this problem and are promising
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antibacterial drug candidates, since both actively dividing cells and drug-resistant dormant cells
4
2
require an intact membrane to stay viable. Consistent with its membrane-targeting activity,
compound 3 exhibited bactericidal activity against both exponential phase and stationary phase
bacteria. Interestingly, the stationary phase cells were more susceptible to 3 than the exponential
phase cells (Figure 3). The increased sensitivity of stationary phase cells may be due to changes
in bacterial surface charges between the two growth phases. For example, the increased negative
4
3
charge in the stationary-phase S. aureus membrane may enhance the attraction of 3, causing
increased sensitivity. However, the precise mechanism of this increased sensitivity remains to be
fully elucidated. The Gram-negative outer membrane is also highly negatively charged.
Stationary-phase P. aeruginosa secretes membrane vesicles with more negative surface charges
4
4
than log phase cells, suggesting increased negative charges on the outer membrane. Finally, E.
coli MG1655 also shows increased negative charge on the outer membrane as cells enter
4
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stationary phase.
As outlined above, results from checkerboard assays demonstrated a synergistic interaction
between 3 and KAN (Table 4 and Figures 7 and 8). The molecular basis for synergistic
interactions is complex, however, synergy often occurs between compounds targeting
46
overlapping pathways. In addition to inhibiting protein synthesis, cationic aminoglycosides
interact with the outer membrane of Gram-negative bacteria by displacing essential metal
3
7
cations. Aminoglycosides bind to outer membrane lipopolysaccharides, form transient small
35-37
holes, and increase outer membrane permeability.
The cationic diamine 3 also increased
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outer membrane permeability (Figure 4), suggesting that it may have a similar effect on the outer
membrane permeability as the aminoglycosides.
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Conclusion. In conclusion, this report illustrates the synthetic diamines, which contain
positively charged structures, not only hold promise as potent broad-spectrum bactericidal
antibiotics, but also can be used in combination to increase the efficacy of other antibiotics by
increasing outer membrane permeability.
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Experimental
Synthesis. All reagents and dry solvents were purchased from Aldrich Chemical Co.
Milwaukee, WI), Sigma Chemical Co. (St. Louis, MO), VWR (Radnor, PA) or Fisher Scientific
Chicago, IL) and were used without further purification except as noted below. Pyridine was
(
(
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dried by passing it through an aluminum oxide column and then stored over KOH. Triethylamine
was distilled from potassium hydroxide and stored in a nitrogen atmosphere. Dry methanol, ethyl
acetate, tetrahydrofuran, dimethyl formamide and hexane were prepared using a Glass Contour
Solvent Purification System (Pure Process Technology, LLC, Nashua, NH). Routine
chromatographic purification on silica gel was performed on a Teledyne Isco CombiFlash Rf200.
Preparative scale chromatographic procedures were carried out using a CombiFlash Rf200
chromatography system (Teledyne-Isco, Lincoln, NE)fitted with silica gel 60 cartridges (230-440
mesh). Thin layer chromatography was conducted on Merck precoated silica gel 60 F-254. Ion
exchange chromatography was conducted on Dowex1X8-200 anion exchange resin.
1
13
All H- and C-NMR spectra were recorded on a Varian Mercury 400 mHz spectrometer, and
all chemical shifts are reported as δ values referenced to TMS or DSS. Splitting patterns are
1
indicated as follows: s, singlet; d, doublet; t, triplet; m, multiplet; br, broad peak. In all cases, H-
13
NMR, C-NMR and MS spectra were consistent with assigned structures. Mass spectra were
recorded by LC/MS on a Waters autopurification liquid chromatography with a model 3100
mass spectrometer detector. Prior to biological testing procedures, all compounds were
determined to be >95% pure by UPLC chromatography (95% H O/5% acetonitrile to 20%
2
H O/80% acetonitrile over 10 minutes) using a Waters Acquity H-series ultrahigh-performance
2
liquid chromatography fitted with a C18 reversed-phase column (Acquity UPLC BEH C18 1.7
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M, 2.1 X 50 mm). Experimental details and analytical data for compounds 1-12 appear in
1
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previous publications.
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,11-bis-[(3,3-diphenylpropyl)ureido]undecane (13). A 0.255 g (1.07 mmol) portion of 3,3-
diphenylpropyl-1-isocyanate 23 in 10 mL of dichloromethane was slowly added to 0.100 g
o
(
0.537 mmol) of 1,11-diaminoundecane 22 in 10 mL of dichloromethane with stirring at 0 C.
o
The reaction mixture was stirred for 15 min at 0 C, warmed to room temperature and allowed to
stir overnight. Completion of the reaction was verified by TLC, the solvent was evaporated and
the crude product was chromatographed on silica gel 5% ethyl acetate in hexane to afford 0.634
1
g of pure 13 (89.6%) as a white, crystalline solid. H NMR (CDCl ): δ 7.23 (m, 20H), 4.71 (s,
3
4
H), 3.92 (t, 2H, J=19 Hz), 3.12 (t, 4H, J=17 Hz), 3.04 (t, 4H, J=19 Hz), 2.24 (q, 4H, J=19 Hz),
1
3
1.40 (m, 4H, J=15 Hz), 1.24 (m, 14H, J=12 Hz); C-NMR (CDCl
3
): δ 162.1, 147.3, 131.7,
+
128.6, 125.3, 42.8, 36.6, 29.7, 28.2, 26.4; MS calculated 660.44, found 661.89 ([M+1] ).
1
,12-bis-[(1,1-diphenylmethyl)ureido]dodecane (14).Compound 14 was prepared exactly as
described for compound 13 above from 1,12-diaminododecane 24 and 1,1-(diphenyl)methyl-1-
1
isocyanate 25 (0.978 g, 73.2%) as a white amorphous solid. H NMR (CDCl ): δ 7.73 (m, 20H),
3
6
1
.41 (s, 2H), 5.85 (s, 2H), 5.80 (s, 2H), 3.83 (t, 4H, J=17 Hz), 1.90 (m, 4H, J=14 Hz), 1.75 (m,
1
3
6H, J=19 Hz); C-NMR (CDCl
3
): δ 163.4, 143.3, 130.1, 127.9, 124.3, 62.2, 39.7, 30.5, 29.6,
+
2
9.1, 26.6; MS calculated 618.39, found 619.77 ([M+1] )
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,12-bis-[(1,1-diphenylmethyl)thioureido]dodecane (15). Compound 15 was prepared exactly
as described for compound 13 above from 1,12-diaminododecane 24 and 1,1-(diphenyl)methyl-
1
1
2
-isothiocyanate 26 (0.980 g, 68.4%) as a white amorphous solid. H NMR (CDCl ): δ 7.31 (m,
3
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0H), 6.40 (s, 2H), 5.61 (s, 2H), 5.30 (s, 2H), 3.44 (t, 4H, J=19 Hz), 3.41 (m, 4H, J=13 Hz), 1.52
1
3
(
m, 4H), 1.40 (m, 4H), 0.85 – 1.28 (m, 8H); C-NMR (CDCl
3
): δ 183.2, 142.6, 129.7, 128.8,
+
1
25.0, 63.7, 46.6, 31.2, 28.4, 28.5; MS calculated 650.35, found 651.78 ([M+1] )
1,12-bis-[(2,2-diphenylethyl)ureido]dodecane (16). Compound 16 was prepared exactly as
described for compound 13 above from 1,12-diaminododecane 24 and 2,2-(diphenyl)ethyl-1-
1
isocyanate 27 (1.1 g, 81.2%) as a white amorphous solid. H NMR (CDCl ): δ 7.28 (m, 20H),
3
5
.36 (s, 4H), 4.21 (m, 2H, J=14 Hz), 3.75 (d, 4H, J=17 Hz), 3.59 (m, 4H, J=12 Hz), 1.41 (m, 4H,
1
3
J=19 Hz), 1.24 (m, 16H); C-NMR (CDCl
3
): δ 159.9, 140.8, 128.7, 128.4, 125.5, 44.2, 40.7,
+
39.3, 28.5, 27.9, 26.4; MS calculated 646.42, found 647.85 ([M+1] )
Strains and growth medium. Staphylococcus aureus strain RN4220 (ATCC No. 35556),
4
7
Pseudomonas aeruginosa strain PA01 (ATCC No. 47085), and Escherichia coli strain ANS1
were grown in Luria-Bertani (LB) medium. Methicillin-resistant Staphylococcus aureus
(MRSA) clinic isolates were grown in Mueller-Hinton (MH) medium. Human kidney cells
HEK293T/17 (ATCC CRL11268) and lung cells A549 (ATCC CCL-185) were grown in
Dulbecco's minimum essential medium (DMEM) with 10% heat inactivated fetal bovine serum
(FBS). Nematode Caenorhabditis elegans strain N2 were obtained from the Caenorhabditis
Genetics Center at University of Minnesota and worms were grown in nematode growth
medium (NGM) for toxicity experiments.
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MIC assay for S. aureus strain RN4220, P. aeruginosa strain PA01 and E. coli strain ANS1.
99
The MIC assay for the antibacterial activity of
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micro-broth dilution method of the Clinical and
MIC99 was defined as the lowest compound
ꢀ
ꢀ
ꢀ
ꢀ
99
standard deviation (SD).
ꢀ
MIC assay for methacillin-resistant S. aureus (MRSA). Strains were isolated from Medical
University of South Carolina ICU rooms with high touch objects fabricated using US-EPA
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registered antimicrobial copper alloys in concert with the studies described.
Briefly, surfaces
2
of 100 cm were sampled once a week with wipes using uniform pressure and motion, 5 strokes
horizontally and 5 strokes vertically, for a total of 10 strokes. MRSA isolates were recovered
5
0
from MRSA-Chromagar and were then subjected to PFGE with subsequent SPA typing. The
isolates were stored at -80°C until they were re-animated via cultivation on Mueller-Hinton
(
MH) broth for antimicrobial susceptibility testing. MIC99 values of test compounds against
MRSA strains were determined using the micro-broth dilution method described above.
Overnight cultures of five MRSA strains in MH broth were diluted in fresh medium. Ten
microliters of diluted cell suspension were used to inoculate 96-well plates containing 100 µl of
5
serially diluted compounds to yield ~10 CFU/ml. The plates were incubated at 37°C for 24
hours before cell density was measured by absorbance at 620 nm using a Thermo MultiSkan FC
plate reader.
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Time-kill assay against exponential phase and stationary phase cells. 10 ml overnight
ꢀ
of strain RN4220 or PA01 were harvested, then washed and re-suspended in PBS to
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ꢀ
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(
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shaking at 200 rpm. At 0, 2, 4, and 6 hr time points, viable bacterial densities were
diluting, plating, and counting the colony-forming unit (CFU) on LB agar plates.
ꢀ
Biofilm inhibition assay. Biofilm inhibition experiment was performed with slight modification
5
1
as mentioned before. P. aeruginosa PA01 was grown in LB for 2 h with shaking at 37°C, and
5
then diluted 1:1000 in 10% LB-PBS to reach a concentration of 3×10 CFU/ml. The first step of
the assay is to fill each well of the clear-bottomed 96-well plate (Nunc) with 25 µl of medium
containing the culture inoculums. 50 µl of serial diluted compounds were added into each well
and 10% LB-PBS was tested as the control. Then the 96-well plate was covered with the
transferable solid-phase (TSP) pegged-lids (Nunc) and the plate was incubated at 37°C for 24 h
without shaking. After 24 h incubation, biofilms formed on the pegged lid were washed twice by
submerging the lid into a basin of sterilized water and then stained with 0.1% crystal violet (CV)
in a new 96-well plate for 15 min with gently shaking. After this, the excess CV was washed off
with sterilized water. The CV maintained in the biofilms was eluted into 150 µl 95 % ethanol
and the solublized CV was quantitated spectrophotometrically at 600 nm using a Biotek Synergy
HT plate reader.
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To investigate the dispersal effect of the diamines, we grew the biofilms on the pegged lid
without test compounds for 24 h as described above. And then, biofilms formed on the pegged
lid were washed twice by submerging the lid into a basin of sterilized water. 100 µl of serial
diluted compounds or 10% LB-PBS were added into a new 96-well plate. Then the pegged lid
with biofilms was transferred into the 96-well plate, and then incubated at 37°C for other 24 h.
The biofilms maintained in the pegged lid were measured as described above. 300 µM EDTA
was used as the positive control for biofilm dispersal.
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Cytoplasmic membrane depolarization assay. The membrane depolarization activity of
compound 3 was determined using a fluorescent probe 3, 3’-dipropylthiacarbocyanine DiSC -
3
52
5
(Sigma), which is sensitive to membrane potential. Briefly, cells from log phase culture
(OD
~ 0.7) were harvested, washed, and re-suspended in 5mM HEPES buffer pH=7.2
600
containing 5 mM glucose and 100 mM KCl to an OD
of 0.05. The cell suspension was
6
00
incubated with 0.4 µM DiSC -5 in darkness, until a stable and approximately 90% reduction in
3
fluorescence signal was reached. The reduction of the probe signal was due to the quenching in
the cell with an intact membrane potential. After compound 3 was added (at 4x or 1x MIC99
concentration), changes in fluorescence due to the collapse of the cytoplasmic membrane
potential were continuously recorded at 25°C using a fluorophotometer (Photon Technology),
with an excitation wavelength of 622 nm and an emission wavelength of 670 nm. Compound 3
exhibited no fluorescence disturbance of the probe signal. 2,4-dinitrophenol (DNP) (Acros),
which was a known inhibitor that depolarized the membrane potential and was used as a positive
5
3
control.
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Outer membrane permeabilization assay. The effect of compound 3 on the permeability of the
outer membrane of P. aeruginosa strain PA01 was determined by the 1-N-phenylnapthyl-amine
3
5, 54
(NPN) (Acros) assay described previously.
Cells from strain PA01 culture at OD
~0.5
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were harvested, washed, and re-suspended in 5 mM HEPES buffer pH=7.2, NPN was added to
the cell suspension to reach 10 µM final concentration, and sodium azide was added to reach 10
mM final concentration. After gently mixing, the cell suspension was incubated at room
temperature for 30 minutes in darkness. Compound 3 at 4x or 1x MIC99 concentration was
added, and changes of NPN fluorescence were continuously recorded at the excitation
wavelength of 350 nm and emission wavelength of 420 nm. Gentamicin is a known inhibitor
3
5
that increases outer membrane permeability and was used as a positive control at 4x MIC99
concentration.
Transmission electron microscopy. Membrane damage caused by compound 3 was visualized
with transmission electron microscopy. Bacteria were grown to the early exponential phase in
LB (OD
~ 0.4) and treated with compound 3 at 2x MIC99 concentration for 15-60 min. Cells
600
were harvested, washed twice with phosphate buffer, and then fixed with 2.5% glutaraldehyde.
Samples were prepared and analyzed by transmission electron microscopy as described (24).
Drug interaction by the checkerboard MIC99 assay. The interactions between compound 3 and
three different classes of antibiotics: ampicillin (AMP), kanamycin (KAN) and norfloxacin
(NOR) were determined by the checkerboard MIC99 method as previously described (25, 26).
Briefly, compound 3 was serially diluted along the ordinate of a 96-well plate while the
antibiotic was serially diluted along the abscissa in 100 µl of LB. Each well was inoculated with
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× 10 CFU in 100µl LB, and the plates were incubated at 37°C for 24 hours. The combined
fractional inhibitory concentration (ΣFIC) was calculated as follows: ΣFIC = FIC A + FIC B,
where FIC A is the MIC99 of drug A in the combination/MIC99 of drug A alone, and FIC B is the
MIC99 of drug B in the combination/MIC99 of drug B alone. The drug combination is considered
synergistic when the ΣFIC is less than 0.5, indifferent when the ΣFIC is between 0.5 to 4, and
antagonistic when the ΣFIC is greater than 4 (26).
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Drug interaction by the time-kill assay. The synergistic interaction between compound 3 and
kanamycin was further confirmed by the time-kill assay. The test groups were: compound 3 or
kanamycin alone at 1x and 0.5x the MIC99 and in combination at 0.5x the MIC99. Strain RN4220
6
or PA01 was used to inoculate the culture at 1x10 CFU/ml, and all cultures were incubated at
3
7°C with shaking at 300 rpm. At 0, 3, 6, and 24 hr time points, viable bacterial densities were
estimated by diluting, plating, and colony counting on LB agar.
55
Hemolysis assay. Hemolytic experiments were performed as previously described. Human
red blood cells were purchased from Fisher and kept in 4 °C before use. Briefly, in a 96-well
plate, 150 µl of red blood cell suspension was added into 50 µl of serially diluted compound 3.
The plate was incubated for 1h at 37°C without shaking. And then the plate was centrifuged at
3500 rpm for 5 min. 100 µl of the supernatant was transferred to a new 96-well plate, and A540
was measured. Triton X-100 was the positive control.
Cytotoxicity in human cells. Human embryonic kidney cells HEK293T/17 and human
o
epithelial lung cells A549 were cultured in DMEM supplemented with 10% FBS at 37 C with
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% CO
2
. The cells were seeded into tissue-culture treated 96-well plate and at a density of
4
1
0 cells per well. Twenty four hours post seeding, the cells were washed with sterile PBS once
to remove the unattached cells, and then 100 µl serially-diluted compound 3 was added into the
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adherent cells and incubated for 48 hours. Cytotoxicity was determined using the MTS
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conversion assay (Promega) mentioned previously. The concentration of the test compound
that reduced the cell viability by 50% (CC50) was determined by nonlinear regression analysis
using GraphPad Prism4 software.
C. elegans toxicity assay. The nematode C. elegans has emerged as a good model for
5
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toxicology testing, and was used to further determine the toxicity of diamines. Strain N2 worms
were maintained on NGM agar at 22 C between passages and synchronization. The effects of the
test compound on adult worm survival and reproduction, juvenile worm development, and egg
̊
3
0
hatching were determined. NGM agar containing compound 3 was prepared by mixing the
compound with warm molten agar. Adult L4 and juvenile L2 worms were selected and
transferred onto the test plate using a platinum wire. Eggs were gathered from maintenance
plates using the synchronization protocol and transferred onto the test plate. Worms were
incubated at 22°C and monitored every 12 hours for death, development, and egg production.
Statistical analysis. Values are presented as means ± standard deviations (SD) and analyzed by
one-way ANOVA analysis of variance (Graphpad Prism). For all analyses, the criterion for
significance was a P value of <0.05.
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FIGURE LEGENDS
Figure 1. Structures of (bis)ureido or (bis)thioureido(N,N’-alkyl)diamines 1-12 and (bis)ureido
or (bis)thioureidoalkanes 13-16.
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Figure 2. Effect of 3 on biofilm formation (A) and dispersal (B). The pegged-lid method was
used
norfloxacin (NOR) and kanamycin (KAN). EDTA was used as a positive control for biofilm
dispersal. Each data point is the average of 3 determinations + S.E.M.
ꢀt o grow P. aeruginosa biofilm and the effect of 3 was compared with tetracycline (TET),
ꢀ
ꢀ
ꢀ
Figure 3. Viability of exponential-phase and stationary-phase bacteria in the presence of 3 or
indicated antibiotics. (A) exponential-phase S. aureus and (B) stationary-phase S. aureus were
treated with antibiotics at the following concentrations: 0.5 μg/ml ampicillin sodium (1.35 µM),
2 μg/ml kanamycin sulfate (54.9 µM), 2 μg/ml norfloxacin (6.26 µM), and 8 μg/ml 3 (10.4
µM). (C) exponential-phase P. aeruginosa and (D) stationary-phase P. aeruginosa were treated
with 512 μg/ml ampicillin sodium (1.38 mM), 128 μg/ml kanamycin sulfate (219.6 µM), 2 μg/ml
norfloxacin (6.26 µM), and 32 μg/ml 3 (41.6 µM).
ꢀt he
ꢀ
3
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
Figure 4. (A) S. aureus cytoplasmic membrane depolarization promoted by 3. (B) P. aeruginosa
cytoplasmic membrane depolarization promoted by 3. (C) P. aeruginosa outer membrane
permeabilization promoted by 3. The arrow indicates the time point when the inhibitor was
added. Experiments were performed three times
experiment are shown.
ꢀ
ꢀ
ꢀ
ꢀ
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Figure 5. (A) Bactericidal kinetics resulting from cytoplasmic membrane depolarization of S.
aureus by 3. (B) Bactericidal kinetics resulting from cytoplasmic membrane depolarization of P.
aeruginosa by 3. ꢀE ach data point is the average of 3 determinations + S.E.M.
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Figure 6. Transmission electron micrographs of (A) untreated S. aureus; (B, C) S. aureus treated
with 3 at 2x its MIC ; (D) untreated P. aeruginosa; (E, F) P. aeruginosa treated with 3 at 2x its
99
MIC . The arrows mark areas of membrane damage and cell content release.
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Figure 7. Isobolograms showing the synergistic effects of 3 with kanamycin against S. aureus
and P. aeruginosa.
Figure 8. Interaction of 3 and kanamycin (KAN) against (A) S. aureus and (B) P.
aeruginosa, ꢀd etermined by a time-kill experiment. were performed three times independently. ꢀ
Each data point is the average of 3 determinations + S.E.M.
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X
X
R
R
N
N
N
H
N
N
N
H
H
H
H
H
1 R = benzyl, X = S
2 R = diphenylmethyl, X = S
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R = diphenylethyl, X = S
R = diphenylpropyl, X = S
R = phenyl, X = O
R = benzyl, X = O
R = diphenylmethyl, X = O
R = diphenylethyl, X = O
R = diphenylpropyl, X = O
X
H
N
H
N
H
N
R
N
H
N
H
N
H
R
X
10 R = diphenylmethyl, X = S
1 R = diphenylethyl, X = O
2 R = diphenylpropyl, X = S
1
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X
X
R
R
N
H
N
H
N
H
N
H
n
1
1
1
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3 R = diphenylpropyl, X = O, n = 1
4 R = diphenylmethyl, X = O, n = 2
5 R = diphenylmethyl, X = S, n = 2
6 R = diphenylethyl, X = O, n = 2
Figure 1. Structures of (bis)ureido or (bis)thioureido(N,N’-alkyl)diamines 1-10 and (bis)ureido
or (bis)thioureidoalkanes 10-16.
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Figure 2. Effect of 3 on biofilm formation (A) and dispersal (B). The pegged-lid method was
used
norfloxacin (NOR) and kanamycin (KAN). EDTA was used as a positive control for biofilm
dispersal. Each data point is the average of 3 determinations + S.E.M.
ꢀt o grow P. aeruginosa biofilm and the effect of 3 was compared with tetracycline (TET),
ꢀ
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