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Antimicrobial Agents and Chemotherapy, October 2002, p. 3168-3174, Vol. 46, No. 10
0066-4804/02/$04.00+0 DOI: 10.1128/AAC.46.10.3168-3174.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
In Vitro Antimicrobial Activity of GSQ1530, a New Heteroaromatic Polycyclic Compound
Yigong Ge,1* Stacey Difuntorum,1 Sofia Touami,1 Ian Critchley,2 Roland Bürli,1 Vernon Jiang,1 Ken Drazan,1 and Heinz Moser1
Genesoft Inc., South San Francisco, California,1
Focus Technologies, Herndon, Virginia2
Received 19 March 2002/
Returned for modification 10 May 2002/
Accepted 24 June 2002

ABSTRACT
GSQ1530 is a compound derived from a newly identified class
of antibiotics referred to as heteroaromatic polycyclic (HARP)
antibiotics. The aim of this study was to assess the in vitro
antimicrobial activity of GSQ1530. By using an NCCLS broth microdilution
assay, the activities of GSQ1530 and other antibiotics were
coevaluated against 215 clinical isolates. The MICs at which
90% of isolates are inhibited (MIC
90s) of GSQ1530 for methicillin-susceptible
Staphylococcus aureus and methicillin-resistant
S. aureus (MRSA)
were 2 and 4 µg/ml, respectively. The MIC
90s of GSQ1530
for the streptococci tested were 2 µg/ml or less, regardless
of their susceptibilities to other antibiotics. The MIC
90 of
GSQ1530 for the enterococci tested (including vancomycin-resistant
enterococci) was 4 µg/ml. No cross-resistance was found
between GSQ1530 and other known antibiotics. In a separate assay,
GSQ1530 demonstrated excellent activity against vancomycin-intermediate-susceptible
staphylococci (MIC
90, 1 µg/ml). The minimal bactericidal
concentration test was conducted with 73 clinical isolates;
GSQ1530 was cidal against streptococci and staphylococci but
static against enterococci. An in vitro killing kinetic study
revealed a time-dependent profile, with at least a 3-log reduction
of bacterial growth within 6 h after exposure to four times
the MICs of GSQ1530 for both
S. aureus and
Streptococcus pneumoniae.
The checkerboard study showed that GSQ1530 had a synergistic
interaction with rifampin against MRSA. The test medium was
found to have little effect on in vitro antimicrobial potency.
The MICs of GSQ1530 for gram-positive cocci were 4- to 32-fold
higher in the presence of serum proteins. GSQ1530 has high levels
of plasma protein binding (91 and 89% for rat and human plasma,
respectively). These preliminary results demonstrate that GSQ1530,
a representative compound of our novel HARP antibiotics, has
broad-spectrum activity against gram-positive bacteria. This
novel class of antibacterial compounds is profiled in vivo to
assess the therapeutic potential in humans. Ongoing in vivo
studies will assess whether this class of molecules has promising
in vivo efficacy and safety profiles.

INTRODUCTION
The rates of resistance of pathogenic microorganisms to commercialized
antimicrobial agents are increasing with an alarming frequency.
A significant percentage of clinical isolates, including species
of streptococci, staphylococci, enterococci, enterobacteria,
and
Pseudomonas spp., are resistant to commonly used antibiotics,
e.g., new ß-lactams, glycopeptides, fluoroquinolones,
and macrolides (
3,
5,
10,
11,
12,
14). Therefore, there is an
urgent medical need for antibiotics with novel antimicrobial
mechanisms.
Heteroaromatic polycyclic (HARP) antibiotics, a class of small DNA-binding molecules, were discovered by screening a diverse library of DNA-binding molecules that preferentially target A/T-rich sites commonly found in bacterial promoters and replication origins (R. Bürli, M. Taylor, Y. Ge, E. Baird, S. Touami, and H. Moser, Abstr. 41st Intersci. Conf. Antimicrob. Agents Chemother., abstr. F-1685, p. 241, 2001). This class of molecules exerts its antibacterial activity by binding to the minor groove of DNA, resulting in inhibition of DNA function and DNA-dependent RNA transcription (Y. Ge, J. Wu, and S. White, Abstr. 41st Intersci. Conf. Antimicrob. Agents Chemother., abstr. F-1686, p. 241, 2001). Optimization of early hits has produced antimicrobial lead compounds with greatly improved potencies. GSQ1530 is a small DNA-binding molecule that was synthesized as part of the lead compound optimization program (Fig. 1). The objective of this study was to investigate the in vitro activity profiles of this class of molecules in detail by using GSQ1530 as a representative compound.
(This work was presented in part at the 41st Interscience Conference
on Antimicrobial Agents and Chemotherapy, 16 to 19 December
2001, Chicago, Ill. [Y. Ge, S. Touami, I. Critchley, M. Taylor,
E. Baird, R. Bürli, A. Pennell, and H. Moser, Abstr. 41st
Intersci. Conf. Antimicrob. Agents Chemother., abstr. F-1687,
p. 241, 2001].)

MATERIALS AND METHODS
Bacteria and agents.
The clinical isolates tested were recently collected (over the
last 4 years) from hospitals throughout the United States. Recent
clinical isolates of vancomycin-intermediate-susceptible staphylococci
(VIS) were acquired from the Network on Antimicrobial Resistance
in
Staphylococcus aureus Repository. GSQ1530 was synthesized
and purified as an acetate salt (Bürli et al., 41st ICAAC),
dissolved in 100% dimethyl sulfoxide (10 mg/ml), and stored
at -80°C. Antibacterial agents used as controls were purchased
from qualified vendors or directly from the manufacturers. These
antibiotics were prepared for testing according to the instructions
of the manufacturers.
MIC and MBC tests.
The in vitro susceptibility tests (MIC and minimal bactericidal concentration [MBC] tests) were conducted by the NCCLS broth microplate assay (7, 8). For fastidious species, appropriate supplements and media were used according to standard protocols. For testing of clinical isolates other than VIS, premanufactured drug panel plates (Trek Diagnostic Systems Inc., Westlake, Ohio) that contained a total of six antimicrobial agents (see Table 1) were used. To determine the effects of protein and serum on in vitro antimicrobial properties, MIC tests were performed in the presence of 25% mouse serum (Equitech-Bio Inc., Ingram, Tex.) (either heat inactivated at 56°C for 30 min or non-heat inactivated) or 4% human plasma albumin (HPA; from a 30% HPA stock; Calbiochem-Novabiochem Corp., Pasadena, Calif.).
In vitro killing-curve assay.
In vitro killing kinetic studies were performed by a previously
described method (
6). In brief, 10
6 CFU of fresh log-phase cells
per ml were treated with appropriate concentrations of agents,
and at the designated time point, bacterial cultures were harvested
and plated in duplicate for viability counting. For groups treated
with a high dose of drug (10 times the MIC), the bacteria were
further diluted up to 10-fold before they were plated to reduce
the concentration of drug carried over, and then 0.5 ml of the
cultures was plated on 150-mm-diameter plates for colony counting.
PAE.
The log-phase bacteria were collected and adjusted to a concentration of 4 x 108 CFU/ml. After the treatment of the bacterial cultures in the presence of GSQ1530 at one or two times the MIC for 1 h, the cells were diluted 1:200 in fresh medium and then incubated and plated out at the appropriate time points for viability determination. The postantibiotic effect (PAE) was calculated by the standard equation, T - C, where T is the time required for the CFU count in the test culture to increase 10-fold above the count observed immediately after drug removal, and C is the time required for the count for the untreated control to increase 10-fold under the same conditions (6).
Synergistic study.
A standard checkerboard assay was performed by a well-established method (6). The fractional inhibitory concentration (FIC) index was calculated by a previously described method (6). An FIC index between two compounds less than or equal to 0.5 is considered synergism, an FIC index between 0.5 and 2 is considered indifference, and an FIC index equal to or more than 2 is considered antagonism.
Measurement of in vitro protein-binding affinity.
The protein assay was conducted by a previously described protocol (2). An aliquot of the stock solution of GSQ1530 or linezolid (control), each dissolved in methanol at 2 mg/ml, was added to 2 ml of rat plasma (Pel-Freez Biologicals, Rogers, Ark.) or human plasma (Plasma Care, Cincinnati, Ohio) to give a final concentration of 2.0 µg/ml. The spiked plasma samples were then incubated at 37°C for 20 min. An aliquot of 0.2 ml was taken out and saved at 4°C as the precentrifugation plasma control to measure the total drug concentration in the following test. The remaining 1.8 ml of the plasma sample was subjected to one round of high-speed centrifugation (300,000 x g for 3 h at 4°C) with an ultracentrifuge (model Optima TLX; Beckman, Fullerton, Calif.) with a Beckman 110K rotor. An aliquot of 0.2 ml of the supernatant was taken to determine the free drug concentration. Both the precentrifugation plasma sample and the supernatant were precipitated with acetonitrile that contained an internal standard and were then subjected to a round of centrifugation at 1,462 x g (with a model 6R centrifuge with a GH 3.8 rotor; Beckman) for 5 min. Finally, an aliquot of the supernatants from each of the samples was analyzed by liquid chromatography-mass spectrometry. The relative concentration was defined as the ratio of the peak area of the compound to that of the internal standard. The relative concentration was used to calculate the free drug percentage of percent binding to the protein. The limit of quantitation of the liquid chromatography-mass spectrometry method was 2 ng/ml. The relative standard deviation in the intraday variation was less than 10%, which was acceptable for this assay.

RESULTS
In vitro antibacterial potencies and spectra of activity.
The MICs of GSQ1530 and six other antibiotic agents for 215
gram-positive isolates were determined (Table
1). GSQ1530 displayed
excellent activities against staphylococci, such as methicillin-susceptible
S. aureus (MSSA), methicillin-resistant
S. aureus (MRSA), methicillin-susceptible
Staphylococcus epidermidis (MSSE), and methicillin-resistant
S. epidermidis (MRSE), with MICs at which 90% of isolates are
inhibited (MIC
90s) ranging from 2 to 4 µg/ml. In a separate
study (Table
2), GSQ1530 displayed excellent activity (MIC
90,
1 µg/ml) against VIS (a total of 45 isolates), including
the species
S. aureus,
Staphylococcus haemolyticus, and
S. epidermidis.
The strains of VIS showed significant resistance to the other
comparative antibiotics tested (with the exception of linezolid),
as indicated by the wide range of MICs for those isolates and
the significant differences between the MIC
50s and MIC
90s. The
MIC
90s of GSQ1530 for
Streptococcus pneumoniae, group A
Streptococcus,
group B
Streptococcus, and viridans group streptococci were
approximately 1 to 2 µg/ml, irrespective of their susceptibilities
to the other antibiotics tested (Table
1). Enterococcus spp.,
including vancomycin-resistant enterococci (VRE), was also inhibited
by GSQ1530 (MIC range, 1 to 4 µg/ml). In addition to the
species delineated in Table
1, we also conducted limited tests
with other gram-positive aerobic and anaerobic bacteria, including
Bacillus spp.,
Listeria monocytogenes,
Micrococcus spp.,
Corynebacterium spp.,
Clostridium spp.,
Peptostreptococcus spp., and
Propionibaterium acnes. GSQ1530 displayed superior activities against those species,
with the MICs ranging from 0.008 to 1 µg/ml (data not
shown). Despite the superior activity of GSQ1530 against gram-positive
bacteria, GSQ1530 was inactive against gram-negative bacteria,
such as
Escherichia coli,
Haemophilus influenzae,
Acinetobacter spp., and
Pseudomonas aeruginosa (MICs, >64 µg/ml),
but had weak activity against
Moraxella catarrhalis (MICs, 16
to 64 µg/ml) (data not shown).
Bactericidal activities of GSQ1530.
To assess the killing potency of GSQ1530, we conducted both
MBC and killing-curve studies. MBCs were measured for a total
of 67 clinical isolates, including isolates of MSSA (8 isolates),
MRSA (10 isolates), MSSE (10 isolates), MRSE (10 isolates),
S. pneumoniae (7 isolates), group A
Streptococcus (10 isolates),
and
Enterococcus faecium (12 isolates). With the exception of
Enterococcus spp., the differences between the MICs and the
MBCs were less than 4 twofold dilutions for most of the streptococci
and staphylococci tested, suggesting that GSQ1530 has cidal
activity against these species. By contrast, the MBCs for
Enterococcus faecalis were at least 3 twofold dilutions higher than the MICs.
The killing kinetic assays were done with three species:
S. aureus (MRSA),
S. pneumoniae, and
E. faecalis (Fig.
2). In the
presence of 2.5 and 10 times the MICs of GSQ1530, more than
3-log reductions in the counts of
S. aureus and
S. pneumoniae were observed within the first 6 h. In the presence of GSQ1530
at 10 times the MIC, more than 10
6 CFU of pneumococcal cells
per ml were rapidly eliminated to levels beyond the threshold
of detection. No regrowth was noted over 24 h (data not shown).
By contrast, the killing curve for
E. faecalis showed neither
growth nor a decline, indicating that GSQ1530 was static against
this species.
Medium and growth condition effects.
To investigate the influences of the growth medium and growth
conditions on antimicrobial potency, we measured the changes
in the MICs of GSQ1530 and the other (control) agents as a function
of inoculum size, medium pH, medium ion concentration, and growth
phase (Table
3). The growth phase, the ion concentration in
the growth medium, and the inoculum size (1
x 10
5 to 5
x 10
7)
did not significantly affect the in vitro activities of GSQ1530
against
S. aureus and
E. faecalis. With an extremely large inoculum
(>10
8 CFU/ml), however, both GSQ1530 and the control antibiotics
lost their activities (MICs, > 32 µg/ml). The pH of
the medium appeared to directly influence the in vitro activity
of GSQ1530 against
S. aureus; the MICs decreased gradually from
2 to 0.031 µg/ml between pH 5.0 and pH 9.0 (Table
3).
This trend was not observed for either of the control drugs
(vancomycin and ofloxacin). In contrast, the effect of the medium
pH on the activity of GSQ1530 against
E. faecalis was not as
dramatic as it was in the case of
S. aureus. As demonstrated
in Table
4, mouse serum and HPA were observed to have inhibitory
effects on the in vitro antimicrobial activity of GSQ1530: the
presence of 25% mouse serum or 4% HPA increased the MICs of
GSQ1530 for MRSA,
S. pneumoniae, and
E. faecalis. A similar
effect was also observed for fusidic acid, while mouse serum
or 4% HPA had only a minimal effect on the in vitro antimicrobial
activities of the other antibiotics tested. There was no difference
in MICs between heat-inactivated and normal serum.
Protein binding. We assessed the level of protein binding in
rat and human plasma by a centrifugation assay. GSQ1530 appeared
to have a strong affinity for binding to both rat and human
plasma proteins (92 and 89% binding, respectively) compared
with that (22%) for linezolid (to rat plasma), which was used
as a control. Those values are consistent with a higher level
of protein binding, as suggested above from the MICs determined
in the presence of proteins.
In vitro PAE.
The in vitro PAEs of GSQ1530 against S. aureus and S. pneumoniae were examined. Only relatively short PAEs were observed: 0.1 and 0.4 h for MRSA and S. pneumoniae, respectively.
Synergism study.
A standard checkerboard study was conducted by a broth microplate method to determine the in vitro drug interaction between GSQ1530 and antibiotics of other classes, including vancomycin, ofloxacin, amoxicillin, linezolid, rifampin, and kanamycin, against MRSA and S. pneumoniae. GSQ1530 showed a synergistic interaction with rifampin against MRSA, with an FIC index of less than 0.4. No drug interactions were observed between GSQ1530 and representatives of the other classes of antibiotics tested, with FIC indices ranging from 1 to 2.

DISCUSSION
HARP antibiotics are among the most active DNA-binding antimicrobial
molecules that have been reported to date. GSQ1530 is more active
than other polypyrrole carboxamides that target the minor groove,
such as distamycin and netropsin, against gram-positive bacteria
(Y. Ge, and J. Wu, unpublished data). GSQ1530 demonstrated excellent
potencies against gram-positive bacteria, including MRSA, vancomycin-intermediate
S. aureus, MRSE, VRE, and penicillin-resistant
S. pneumoniae (PRSP). The in vitro potencies and spectra of activity of GSQ1530
are comparable to those of drugs with activities against gram-positive
organisms, such as vancomycin and linezolid: MIC
90s are 2 to
4 µg/ml for all gram-positive pathogens (
4,
9). In addition
to its general effect, GSQ1530 also works effectively in vitro
against VIS. As shown in this study, strains of VIS had reduced
susceptibilities to vancomycin and also demonstrated multiple-drug-resistant
profiles, with resistance to ofloxacin, ampicillin, fusidic
acid, erythromycin, and rifampin. In contrast, only GSQ1530
and linezolid are consistently active against these isolates.
To date no cross-resistance between GSQ1530 and other classes
of antibiotics has been found. Unlike linezolid, the bactericidal
spectrum of GSQ1530 is comparable to that of vancomycin: it
is cidal against staphylococci (MRSA) and streptococci but static
against enterococci. The time-dependent killing kinetics of
GSQ1530 against MRSA and PRSP are similar to those of vancomycin,
with the notable exception of the killing kinetics against
S. pneumoniae, which shows a greater sensitivity to killing by
GSQ1530. This rapid and complete bactericidal property against
PRSP may give HARP antibiotics an advantage over other classes
of antibiotics. In addition, preliminary data show that bacterial
killing activity is replication dependent: GSQ1530 exerts its
killing activity only against replicating cells (data not shown),
suggesting that the antimicrobial mechanisms of this compound
are not directed against the cell membrane and essential cellular
respiratory systems. Although the proposed mode of action of
this class of molecules (inhibition of DNA function and RNA
transcription) cannot be used to directly explain its rapid
cidal activity, it is assumed that molecules of this class are
also able to trigger other modes of killing action, including
the induction of autolysis or programmed death, at a relatively
high dose.
GSQ1530 is not active against wild-type gram-negative species. However, it shows an inhibitory effect on an E. coli outer membrane-deficient mutant (MIC, 0.5 µg/ml) (data not shown), suggesting that GSQ1530 acts by inhibiting similar intracellular targets in both gram-positive and gram-negative species. The outer membrane barrier of gram-negative bacteria appears to limit the uptake of this molecule and inactivate it against those species.
In general, the medium used and the growth conditions seemed to have minimal effects on the in vitro antimicrobial activity of GSQ1530. Interestingly, basic conditions seem to enhance the antibacterial activity of GSQ1530. Conceivably, the molecule is deprotonated at high pH and is thus more readily taken up into cells. The in vitro activity of GSQ1530 was reduced in the presence of 25% mouse serum or a physiological concentration of HPA. It appears that some heat-insensitive components in serum interfered with the antimicrobial activity of this compound. This finding was confirmed by the observation that GSQ1530 had a higher percentage of plasma protein binding (over 89%) than the control antibiotic, linezolid (22%). Among several control antibiotics tested, only fusidic acid shared a similar behavior that has been well documented (1). No loss of activity of linezolid is noted in the presence of HPA. It is conceivable that the plasma protein binding of GSQ1530 reduces the concentration of free drug in the medium, resulting in higher MICs. Whether the higher level of protein binding of GSQ1530 has any adverse impact in an in vivo setting remains to be demonstrated.
A preliminary mechanistic study has demonstrated that the HARP antibiotic class of molecules kills bacteria by blocking DNA functions and other DNA-dependent enzymatic activities (Ge et al., 41st ICAAC, abstr. F-1686). Theoretically, GSQ1530 should have a good synergistic interaction with rifampin since the two drugs work on different targets of the bacterial transcriptional apparatus; GSQ1530 works by binding to bacterial promoters or other adjacent sequences to block bacterial transcription initiation and/or the elongation process, while rifampin exerts its antibacterial effect by directly binding to the ß subunit of RNA polymerase to inactivate its enzymatic activity (13). Interestingly, such a synergistic effect was only observed against MRSA and was not observed against VRE or PRSP. The species dependence for this observed effect is not fully understood.
In conclusion, GSQ1530 is a representative compound of a new class of antimicrobials named HARP antibiotics. Members of this novel family of compounds exhibit broad-spectrum activity against common drug-resistant gram-positive pathogens. Focused lead compound optimization of GSQ1530 analogs is in progress to identify potential clinical candidates with improved profiles for the treatment of infections caused by gram-positive bacteria.

ACKNOWLEDGMENTS
This study was funded in part by a DARPA grant (grant N65236-99-1-5427).

FOOTNOTES
* Corresponding author. Mailing address: Genesoft Inc., 7300 Shoreline Ct., South San Francisco, CA 94080. Phone (650) 837-1826. Fax (650) 827-0475. E-mail:
jge{at}genesoft.com.


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Antimicrobial Agents and Chemotherapy, October 2002, p. 3168-3174, Vol. 46, No. 10
0066-4804/02/$04.00+0 DOI: 10.1128/AAC.46.10.3168-3174.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
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