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Identification of small molecules that selectively inhibit streptokinase expression without suppression of viability in Group A streptococci - Probe 3

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Author Information

,1 ,1 ,1 ,1 ,1 ,1 ,1 ,2 ,1 ,1 and 1,3.*

1 The Broad Institute Probe Development Center, Cambridge, MA
2 University of Missouri, Columbia, MO
3 Howard Hughes Medical Institute, Chemistry & Chemical Biology, Harvard University, Cambridge, MA
*Corresponding author email: gro.etutitsnidaorb@naf

Received: ; Last Update: March 11, 2011.

Streptokinase is a major group A streptococcus (GAS) virulence factor and plays critical roles in GAS pathogenicity. We set out to identify and develop novel small molecule probes that inhibit streptokinase (SK) expression in GAS without suppressing cell growth to minimize potential drug resistance. We screened the Molecular Libraries Probe Centers Network (MLPCN) library of over 300,000 compounds and identified a third small molecular probe. The probe (CID-2769229/ML135), 2-chloro-N-(3-cyano-4-((4-methoxyphenyl)thio)phenyl)benzamide, selectively inhibits SK expression with an IC50 of 1.9 μM in a GAS strain and has no effect on bacterial growth. A series of analogs were synthesized to explore the structure activity relationships. These analogs showed over 10-fold range in potency of inhibition of SK expression, and revealed key structural requirements for optimal potency and selectivity. The probe (CID-576989/ML135) and its analogs are another set of excellent molecular tools to investigate regulation of SK expression and mechanisms of GAS infection.

Assigned Assay Grant No.: 1R03DA026214-01

Screening Center Name & PI: Broad Institute Probe Development Center, Stuart Schreiber, PhD

Chemistry Center Name & PI: Broad Institute Probe Development Center, Stuart Schreiber, PhD

Assay Submitter & Institution: Hongmin Sun, PhD. University of Missouri, Columbia

PubChem Summary Bioassay Identifier (AID): 1677

Probe Structure & Characteristics

Compound Summary in PubChem

IUPAC Chemical Name2-chloro-N-(3-cyano-4-((4- methoxyphenyl)thio)phenyl)benzamide
PubChem CID2769229
Molecular Weight394.874
Molecular FormulaC21H15ClN2O2S
XLogP3-AA5.26
H-Bond Donor1
H-Bond Acceptor3
Rotatable Bond Count5
Exact Mass394.054276
Topological Polar Surface Area87.420
Heavy Atom Count27
CID/ML No.Target NameIC50/EC50 (nM) [SID, AID]Anti-target Name(s)IC50/EC50 (nM) [SID, AID]SelectivitySecondary Assay(s) Name: Viability IC50/EC50 (nM) [SID, AID]
2769229Streptokinase expression1900 [99430880, 504351]Bacterial cell viabilityinactive [99430880, 504396]1900 nM vs inactiveinactive [99430880, 504396]

Recommendations for scientific use of the probe

The goal of the project is to identify and develop novel small molecule probes that inhibit streptokinase (SK) expression in group A streptococcus (GAS). Streptokinase is a major GAS virulence factor that activates human plasminogen (1,2,3). Novel antimicrobial agents that suppress pathogen virulence without selecting for drug-resistant mutants provide a promising alternative approach for treatment of infectious diseases (4,5,6,7). Based on the critical role of SK in GAS pathogenicity, we are attempting to identify chemical compounds that specifically reduce the expression of bacterial SK, without affecting bacterial viability.

The probe (CID-2769229/ML135) described in this report selectively inhibits the expression of bacterial SK in GAS without affecting bacterial cell viability. The probe (CID-2769229/ML135) inhibits SK expression with an IC50 of 1.9 μM and was inactive in suppressing bacterial cell viability in the non-engineered UMAA2616 strain at concentrations at high as 50 μM.

The probe (CID-2769229/ML135) will be used to explore the contribution of SK to GAS infection. This probe may also serve as a starting point for trying to identify small molecules suitable for new mouse models. The Assay Provider, Dr. Hongmin Sun, has established that transgenic mice expressing human plasminogen (Tg+) are highly susceptible to GAS infection and are a useful model to test the impact of hit compounds in attenuating GAS virulence (8,9). In vivo efficacy of compounds is assessed in Tg+ mice that are first infected with SK(+)GAS and then injected with doses of test compound intraperitoneally daily for 5 days, starting 1 day after infection.

1. Introduction

Scientific Rationale

Group A streptococcus (GAS) is among the most common human pathogens affecting millions of people globally each year. Even though treatment with antibiotics has greatly reduced mortality in the developed world, complications of GAS infection are sometimes still lethal. Further, emergence of epidemic invasive GAS diseases poses another critical medical challenge, but little is known about the mechanism of invasiveness (3). Knowledge of the underlying molecular mechanisms required for infection by this important pathogen will be crucial for the development of novel therapies for GAS infection.

Streptokinase (SK) is a key virulence factor for GAS infection through interacting with host plasminogen (2,8,9). This project aims to take advantage of this observation and discover novel antimicrobial agents for the treatment of GAS infection. One key design of the project is to target specifically the bacterial virulence without impact on bacterial growth. Such agents provide a promising alternative approach for treatment of infectious diseases by reducing the risks of antibiotic resistance. Antibiotic resistance represents an increasing concern as a major global public health threat contributed by widespread use of antibiotics that cause death or growth arrest in the target bacteria. This screening campaign has identified a probe (CID-2769229/ML135), 2-chloro-N-(3-cyano-4-((4-methoxyphenyl)thio)phenyl)benzamide, with an IC50 of 1.9 μM, which is inactive in a bacterial viability test within a range of testing concentrations up to 50 μM.

2. Materials and Methods

Materials and Reagents

All reagents and solvents were purchased from commercial vendors and used as received. Phosphate-buffered saline (PBS) was acquired from the Broad Institute Supply and Quality Management (SQM; Cambridge, MA). SK assay solution was acquired from Innov Research (Novi, Michigan), and S2403 was acquired from Diapharma (West Chester, OH). BacTiter-Glo was purchased from Promega (catalog no. G8233; Madison, WI). White assay plates were purchased from Corning (catalog no. 3570; Corning, NY), and clear plates were purchased from Nunc (catalog no. 242757; Rochester, NY).

Growth Medium

  • THY/S (30 g/L THB; Catalog no. 249240, Becton Dickinson, Sparks, MD/0.2% yeast extract; Catalog no. Y2010, US Biological, Swampscott, MA) with 100 μg/mL streptomycin (Catalog no. S9137; Sigma, St. Louis, MO)
  • THY/S/S medium (30 g/L THB/0.2% yeast extract with 100 μg/mL streptomycin/100 μg/ml spectinomycin (Catalog no. S1317; Sigma, St. Louis, MO)
  • THY/K medium (THY plus 40 μg/ml kanamycin) (Catalog no. S1637; Sigma, St. Louis, MO)

Cell Lines

The SKKanGAS strain and UMAA 2616 were provided by the Assay Provider, Dr. Hongmin Sun (University of Missouri). Human plasma was obtained from Innovative Research (Novi, Michigan).

2.1. Assays

A summary listing of completed assays and corresponding PubChem AID numbers is provided in Appendix A. Refer to Appendix B for the detailed assay protocols.

2.1.1. Primary Screen in SKKanGAS Strain (AID-1662)

On Day 1, the SKKanGAS strain was streaked out on THY/S/S medium plate (30 g/L THB/0.2% yeast extract with streptomycin 100 μg/mL, spectinomycin 100 μg/ml) agar, (1.5%; Catalog no. 281230; Becton Dickinson, Sparks, MD), and incubated at 37ºC overnight. On Day 2, a single colony was picked and grown overnight in THY/S/S medium at 37ºC. On Day 3, the overnight culture was diluted 20-fold into fresh THY/S/S medium in a flask and grown until it reached OD600 of 0.6–0.8. The culture was again diluted into cold THY/K (THY plus 40 μg/ml kanamycin) medium to result in OD600 value of 0.038, and the diluted culture was kept at 4°C overnight. On Day 4, the diluted culture was warmed to room temperature and 20 μl per well was dispensed with a Combi multidrop (Thermo Fisher Scientific Inc., Waltham, MA ) into assay plates that contained 30 μl per well of THY/K. Next, 100 nL per well of compound was pinned with Cybi-Well (CyBio; Woburn, MA). Next, the plates were incubated at 37ºC for 6 hours then cooled to room temperature for 30 minutes. Then, 30 μl per well of diluted BacTiter-Glo (25 μl per well BacTiter-Glo and 5 μl per well PBS) was added to the culture with a Combi multidrop. The plates were incubated at room temperature for 10 minutes, and luminescence was detected on an EnVision (Perkin Elmer, Waltham, MA) multimode reader.

2.1.2. Primary Retest in SKKanGAS Strain

Repeat of primary screen at dose in SKKanGAS cells using BacTiter-Glo.

2.1.3. Secondary Screen for SK Expression in UMAA 2616 Strain (AID nos. 1914, 2137, 504351)

On Day 1, UMAA 2616 was streaked out on THY/S medium (30g/L THB/0.2% yeast extract with streptomycin 100 μg/mL), and incubated at 37°C overnight. On Day 2, a single colony was picked and grown overnight in THY/S medium at 37°C. On Day 3, the overnight culture was diluted 20-fold into fresh THY/S medium in a flask and grown until it reached OD600 of 0.6–0.8. The culture was again diluted into cold THY/S medium to result in OD600 value of 0.038, and the diluted culture was kept at 4°C overnight. On Day 4, the diluted culture was warmed to room temperature, and 20 μl per well of culture was dispensed with a Combi (Thermo Fisher Scientific Inc., Waltham, MA) into assay plates that contained 30 μl per well of THY/S medium. Next, 100 nL per well of compound was pinned with Cybi-Well (CyBio; Woburn, MA), and the plates were incubated at 37°C for 6 hours in a Liconic incubator. The cells were pelleted at 3000 rpm in a Sorvall centrifuge. Next, 10 μl per well of the supernatant was transferred twice but into separate clear plates with Cybi-Well Vario and stored at −20°C. The culture plates were warmed to room temperature for 30 minutes. Then, 50 μl per well of half strength BacTiter-Glo was added with a Combi multidrop. The plates were incubated at room temperature for 10 minutes, and luminescence was detected on an EnVision (Perkin Elmer; Waltham, MA) multimode reader for indications of bacterial cell viability.

SK expression was measured by adding 50 μl/well of SK assay solution (5 μl per well of human plasma, 1.2 μl to 2.4 μl per well of 4.2 mg/ml S2403, and 43.8 μl per well of PBS) to the 10 μl per well supernatant that had been thawed and warmed up to room temperature in clear SK assay plates. Compound CID-657963 was used as a positive control in the SK expression assay (see Figure 1). OD405 was taken at 0 h and after 1.5 h to 2.5 h of incubation at 37°C depending on the lot of the S2403.

Figure 1. Prior Art Compound CID-657963 for SK Expression.

Figure 1

Prior Art Compound CID-657963 for SK Expression. Compound CID-657963 (positive control) in the SK expression assay. This compound did not significantly inhibit bacterial cell viability up to approximately 100 μM.

2.1.4. Secondary Screen for Bacterial Cell Viability in UMAA 2616 Strain (AID nos. 1915, 2138, 504396)

As described in the secondary screen for SK expression.

2.2. Probe Chemical Characterization

After preparation as described in Section 2.3, the probe (CID-2769229/ML135, SID 104170243) was analyzed by UPLC, 1H NMR, 13C NMR, and LC-MS. The data obtained from NMR spectroscopy were consistent with the structure of the probe (CID-2769229/ML135), and UPLC indicated an isolated purity of 100%. The relevant data are provided in Appendix C.

The observed solubility of the probe (CID-2769229/ML135) was calculated to be less than 1 μM in PBS solution. The stability of the probe (CID-2769229/ML135) in PBS (0.1% DMSO) was measured over 48 hours, and the data is shown in Figure 2 (blue line). We suspected that poor solubility as the reason behind the shift in the amount of sample over time. To test this, we added acetonitrile to each well (final concentration 50%) and measured the amount of the probe. Amounts detected after addition of acetonitrile are shown in Figure 2 (red line). Although we still observed shift in the amount of sample over time, it can be safely concluded from these results that the probe is stable in PBS and 100% of the probe is still present after 48 hours of incubation in PBS.

Figure 2. PBS Stability Data for the Probe (CID-2769229/ML135).

Figure 2

PBS Stability Data for the Probe (CID-2769229/ML135).

Plasma protein binding (PPB) was determined to be 99% bound in human plasma. The probe (CID-2769229/ML135) demonstrates excellent stability in both human and murine plasma with approximately 99.2% and 89.3% remaining, respectively, after a 5-hour incubation period. The solubility, PPB, and plasma stability results are summarized in Section 3.4 (entry 1, Table 1).

Table 1. SAR Analysis and Properties of Substituted Phenyl Analogs.

Table 1

SAR Analysis and Properties of Substituted Phenyl Analogs.

The probe (CID-2769229/ML135) and three additional analogs were submitted to the SMR collection MLS002699833 (probe), MLS002699831 (CID-1471787), MLS002699832 (CID-2769158), and MLS002699834 (CID-2769230).

2.3. Probe Preparation

Chemistry Experimental Methods

The probe compound (CID-2769229/ML135; SID-104170243) was prepared in one step outlined in Scheme 1.

Scheme 1. Synthesis of the Probe (CID-2769229/ML135).

Scheme 1

Synthesis of the Probe (CID-2769229/ML135).

General details. All reagents and solvents were purchased from commercial vendors and used as received. Unless otherwise mentioned, all of the reactions were run in over-dried, round- bottom flasks or in regular vials under nitrogen. 1H and 13C NMR spectra were recorded on a Bruker 300 MHz spectrometer. Proton and carbon chemical shifts are reported in ppm (δ) relative to tetramethylsilane (1H δ 0.00) or residual chloroform in CDCl3 solvent (1H δ 7.24, 13C δ 77.0). NMR data are reported as follows: chemical shifts, multiplicity (s = singlet, m = multiplet); coupling constant(s) in Hz; integration. Unless otherwise indicated NMR data were collected at 25°C. Flash chromatography was performed using 40 μm to 60 μm Silica Gel (60 Å mesh) on a Teledyne Isco Combiflash Rf system. Tandem Liquid Chromatography/Mass Spectrometry (LC/MS) was performed on a Waters 2795 separations module and 3100 mass detector. Analytical thin layer chromatography (TLC) was performed on EM Reagent 0.25 mm silica gel 60-F plates. Visualization was accomplished with UV light and aqueous potassium permanganate (KMnO4) stain followed by heating.

Synthesis of 2-chloro-N-(3-cyano-4-((4-methoxyphenyl)thio)phenyl)benzamide. To a solution of 2-chlorobenzoyl chloride (396 mg, 2.26 mmol, 1.45 equivalents) in anhydrous dichloromethane (16 mL) was treated with triethylamine (316 mg, 0.435 mL, 3.12 mmol, 2.0 equivalents) under nitrogen. The reaction mixture was stirred at room temperature for 5 minutes and then 5-amino-2-(4-methoxyphenyl thio)benzonitrile (400 mg, 1.56 mmol, 1.0 equivalents) was added in one portion. The reaction mixture was stirred overnight and was then quenched with saturated aqueous sodium bicarbonate (NaHCO3) solution, and extracted with ethyl acetate (EtOAc). The combined organic extracts were dried (sodium sulfate; Na2SO4), filtered, and concentrated. The desired monoacylated product was purified from the diacylated compound by column chromatography over silica gel (hexanes/ethyl acetate: 100/0 to 50/50) to give rise to the probe compound (CID-2769229/ML135) as a white solid (339 mg, 55%).

1H NMR (300 MHz, CDCl3): δ 8.01-7.97 (m, 2H), 7.77-7.75 (m, 1H), 7.64-7.61 (m, 1H), 7.48-7.37 (m, 5H), 7.05-7.02 (m, 1H), 6.96-6.93 (m, 2H), 3.84 (s, 3H); 13C NMR (75 MHz, CDCl3): δ 163.4, 159.5, 138.3, 135.0, 134.6, 133.1, 131.0, 129.4, 129.32, 129.27, 128.8, 126.3, 123.5, 123.3, 120.7, 115.4, 114.2, 111.3, 54.3; ESI-MS (M): m/z 394.

The 1H NMR spectra, 13C NMR spectra, and UPLC chromatograms of the probe (CID-1612038/ML134) and analogs are provided in Appendix C.

2.4. Additional Analytical Analysis

Plasma Protein Binding. Plasma protein binding was determined by equilibrium dialysis using the Rapid Equilibrium Dialysis (RED) device (Pierce Biotechnology, Rockford, IL) for both human and mouse plasma. Each compound was prepared in duplicate at 5 μM in plasma (0.95% acetonitrile, 0.05% DMSO) and added to one side of the membrane (200 μL) with PBS (350 μL; pH 7.4) added to the other side. The compounds were incubated at 37°C for 5 hours in an orbital shake at 250 rpm. Following the incubation, the samples were analyzed by UPLC-MS (Waters, Milford, MA) with compounds detected by SIR detection on a single quadrupole mass spectrometer.

Plasma Stability. Plasma stability was determined at 37°C for 5 hours in both human and mouse plasma. Each compound was prepared in duplicate at 5 μM in plasma diluted 50/50 (v/v) with PBS pH 7.4 (0.95% acetonitrile, 0.05% DMSO). The compounds were incubated at 37°C for 5 hours in an orbital shake at 250 rpm with time points taken at 0 hours and 5 hours. The samples were analyzed by UPLC-MS (Waters, Milford, MA) with compounds detected by SIR detection on a single quadrupole mass spectrometer.

3. Results

Probe Attributes

  • IC50 ≤ 10 μM
  • 30- to 100-fold selectivity as defined by: IC50 ratios of the inhibition of SK expression and the inhibition of cell growth where both IC50 ratios are measurable.
  • Compounds that are active in SK expression with IC50 ≤ 10 μM but don’t result in cell growth inhibition at test concentrations no less than 50 μM.

The project included a primary high-throughput screen of the entire MLSMR collection (greater than 300,000 substances). Approximately 1% of the compounds tested were selected for dose retest and selectivity. Of these, approximately 60 compounds were identified as having the desired potency and selectivity. Resupply of these compounds was ordered from commercial sources for subsequent verification. In addition to these commercially available compounds, multiple rounds of chemistry were performed to generate new compounds for determination of the SAR of on the scaffolds. Compounds with the best combination of potency and selectivity and chemical properties were designated as the probes. This report concerns one structural series, Probe 3 (CID-2769229/ML135).

3.1. Summary of Screening Results

Figure 3 displays the critical path for probe development.

Figure 3. Critical Path for Probe Development.

Figure 3

Critical Path for Probe Development.

A high-throughput screen of 303,546 compounds (AID-1662) was performed in duplicate in the engineered strain SKKanGAS, in which the kanamycin resistance gene was placed under control of the SK promoter to identify compounds that can inhibit kanamycin resistance. Using a cutoff of 50% inhibition at a screening concentration of 7.5 μM average, 3962 hits were identified as SK expression inhibitors; among these, 3268 were available as cherry picks. The picked compounds were retested in dose in the SKKanGAs strain to confirm their inhibitory activity as well as in SK(-)GAS strain where the kanamycin gene is driven by an SK-independent promoter to investigate promoter dependence.

The next set of secondary tests provided a more physiologically relevant analysis of the compounds specificity and potency. Interference with SK expression was measured in the non-engineered UMAA 2616 strain by measuring SK activity in culture supernatant via activation of plasminogen enzymatic activity (AID nos. 1914, 2137, 504351). Bacterial viability was also measured via ATP content from the assay sample (AID nos. 915, 2138, 504396). From this secondary panel, 95 compounds were prioritized, and 61 dry powders were obtained and tested multiple times in the secondary assays.

From this set of dry powder compounds, a benzamide series was prioritized, and additional analogs were synthesized and tested in the secondary assays. This benzamide series became probe series 3 with a group of 33 compounds (AID nos. 2137, 2138; 504351, 504396) (see Table 1, Section 3.4).

3.2. Dose Response Curves for Probe

The probe (CID-2769229/ML135) met the defined probe criteria and was not active in the bacterial cell viability assay. Approximately 100% inhibition of endogenous streptokinase in the non-engineered strain UMAA2616 is obtained. Figure 4 displays dose response curves for the probe (CID-2769229/ML135).

Figure 4. Concentration-dependent Activities (%) of Probe (CID-2769229/ML135) in the Target Assay and Counterscreen Assays.

Figure 4

Concentration-dependent Activities (%) of Probe (CID-2769229/ML135) in the Target Assay and Counterscreen Assays. Probe CID-2769229/ML135 concentration-dependent activities: SK expression (IC50=1.9 μM; AID-504351) (A); Bacterial viability (inactive; (more...)

3.3. Scaffold/Moiety Chemical Liabilities

The scaffold does not have obvious chemical liabilities. The probe (CID-2769229/ML135, SID-104170243) is stable over 48 hours in PBS buffer and shows good stability in human and murine plasma. A PubChem activity survey performed on February 24, 2011 revealed no other confirmatory non-streptokinase assay (out of 414 reported in PubChem) in which the probe (CID-2769229/ML135) was active. A structure-based search in SciFinder and Reaxys did not identify any publications or patents in which the probe compound appeared. Therefore, the probe is considered not to be a promiscuous binder.

3.4. SAR Tables

The initial hit from the HTS campaign was 2-chloro-N-(3-cyano-4-((4-methoxyphenyl)thio)phenyl)benzamide (entry 1, Table 1; CID-2769229). A collection of 18 structurally related analogs were synthesized and evaluated for their ability to inhibit SK expression in the primary assay and an array of secondary assays. Three diversification points selected for chemical modification are depicted in Figure 5. The biological assay data and physical properties of the HTS hit and the analogs are presented in Table 1, Table 2, and Table 3.

Figure 5. Summary of SAR Performed on the Benzamide Scaffold.

Figure 5

Summary of SAR Performed on the Benzamide Scaffold. Three diversity points (highlighted in red, green and blue) were explored and the number of analogs screened for each site is specified.

Table 2. SAR Analysis and Properties of Analogs with Other Functionality.

Table 2

SAR Analysis and Properties of Analogs with Other Functionality.

Table 3. SAR Analysis and Properties of Various Sulfone and Thiophenol Analogs.

Table 3

SAR Analysis and Properties of Various Sulfone and Thiophenol Analogs.

Table 1 presents the initial hit and several derivatives of it wherein the phenyl ring of the benzoyl side chain of the benzamide scaffold was substituted with various electron-withdrawing and electron-donating groups on the ortho-, meta- and para- positions to probe the SAR of this region. It is interesting to see from Table 1 how potency is affected by moving the substituent around the phenyl ring. Presence of substituents at the ortho- position generally retains the potency (except for ortho-nitrile substituent) suggesting that twisting the phenyl ring out of the plane of the amide bond is the preferred inhibitor conformation (entries 1–7, Table 1). In contrast, the meta-chloro derivative (entry 8, Table 1) would be planar, and is much less active, although the meta- position could also be a site on the ring that does not tolerate a large substituent. The effect of electron-donating substituents at the para- position is not beneficial as the para-methoxy and para-methyl analogs lose the potency (entries 10–11, Table 1). It is also important to note that the diacylated analog of the HTS hit (entry 13, Table 1) is significantly less active.

The importance of the o-chlorobenzoyl core of the molecule was further evident from the fact that free amine lost significant activity (entry 1, Table 2). Replacement of the amide moiety with urea functionality (entry 3, Table 2) or amine (entry 2, Table 2) led to 5-fold drop in activity suggesting amide functionality is optimal for potency.

Table 3 presents synthetic analogs that suggest m-nitrile is not crucial for the potency (entries 1 and 2; Table 3). Although the analog lacking p-methoxy group at the thiophenol moiety retains the activity (entry 2, Table 3), it dramatically loses selectivity and affects bacterial viability. On the other hand, p-methylsulfone analog (entry 3, Table 3) was completely inactive.

In conclusion, several analogs of the original hit were synthesized and assayed to better understand the structure-activity relationships. The previously reported probe for the benzamide series 2-chloro-N-(3-cyano-4-((4-methoxyphenyl)thio)phenyl)benzamide (entry 1, Table 1; CID-2769229) remains as one of the most active analogs and will retain its’ status as the declared probe.

3.5. Cellular Activity

The SK expression assay and the bacterial cell viability assay are bacterial cell-based phenotypic assays. Therefore, active compounds possess reasonable permeability across the bacterial membrane. No mammalian cell permeability was measured.

3.6. Profiling Assays

A PubChem activity survey performed on February 24, 2011 using Broad’s internal algorithm revealed no other confirmatory non-streptokinase assay in which the probe (CID-2769229/ML135) was active (out of 414 reported in PubChem). Other profiling screens (e.g., CEREP) have not been performed with this compound to date.

4. Discussion

4.1. Comparison to Existing Art and How the New Probe is an Improvement

The benzamide probe (CID-2769229/ML135) has demonstrated selective inhibition of SK expression in a GAS strain without any effect on bacterial growth. The probe (CID-2769229/ML135) fulfilled all the probe criteria (Table 4) and will serve quite well in further cell-based investigations concerning SK expression. It is interesting to see from Table 1, Table 2, and Table 3 how potency is affected by the various alkoxy groups and modification of phenyl ring substituents. The range of potencies provides some confidence that the carbazole analogs are binding to one target specifically (i.e., a target that must control SK gene expression). The probe (CID-2769229/ML135) and the structural analogs shown are fairly hydrophobic molecules, possibly reflecting the hydrophobic character of the site to which they bind.

Table 4. Probe Criteria.

Table 4

Probe Criteria.

To support the novelty of the probe (CID-2769229/ML135) and its’ phenotypic effects, an investigation into the relevant prior art was performed by searching the following databases: SciFinder, Reaxys, PubChem, PubMed, US Patent and Trademark Office (USPTO), PatFT, AppFT, and World Intellectual Property Organization (WIPO). Specifically, we were looking for reports of chemical matters that demonstrated inhibition of streptokinase expression. The search terms applied and hit statistics are provided in Table 5. Abstracts were obtained for all references returned including journal articles, patents, and other form of public disclosures and were analyzed for relevance to the current project. The searches were performed on, and are current as of, January 28, 2011.

Table 5. Search Strings and Databases Employed in the Prior Art Search.

Table 5

Search Strings and Databases Employed in the Prior Art Search.

The literature and patent searches in Table 5 uncovered no known small molecule that is capable of inhibiting SK expression. The only compound (CID-657963) that is known to inhibit SK inhibition is shown in Figure 6. This compound was identified by the Assay Provider, Dr. Hongmin Sun, for this probe development project (Note: Initial results associated with the discovery of CID-657963 are not yet published). The moderate potency (≥ 10.0 μM) and the presence of a reactive alkylthioacetonitrile moiety in CID-657963 have motivated us to discover a superior scaffold with higher inhibitory potency from the MLPCN compound collection. The improved potency and no obvious chemical liabilities will make the benzamide probe (CID-2769229/ML135) a very useful tool molecule to better understand the biology of streptokinase expression in group A streptococci.

Figure 6. Compound (CID-657963) Inhibitor of SK Inhibition.

Figure 6

Compound (CID-657963) Inhibitor of SK Inhibition.

4.2. Mechanism of Action Studies

The experimental scope of this project did not include target identification due to the complexity of and considerably much more resource commitment to such tasks. Researchers can carry out mechanism of action (MOA) studies through the following approaches. First, determine if the decreased level of SK expression is due to transcriptional control. Second, if transcription is a control mechanism, quantitative gene expression measurement can be used to test the activities of known pathways and/or expression level of known pathway components that control SK expression. Third, based on the knowledge gained from the above experiments, one can generate specific hypotheses of possible protein targets and test activity of these targets biochemically. Alternatively, researchers can employ several affinity-based techniques using the probe (CID-2769229/ML135) (or its’ active but modified version) as “bait’ to fish out proteins that specifically interact with the probe (CID-2769229/ML135). Inactive structurally similar analogs provided in this report are excellent control compounds for this purpose. The biological insight gained from the initial MOA studies should help narrow down the likelihood of the real targets if multiple specific binding proteins are identified.

4.3. Planned Future Studies

In addition to the MOA studies proposed above, researchers can further evaluate the probe (CID-2769229/ML135) or activity of its’ active analogs in animal models if the pharmacokinetic parameters are favorable. An animal model successfully used in the Assay Provider’s laboratory to evaluate compound activity is provided in Sun et al. (2).

5. References

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2.
Christner R, Li Z, Raeder R, Podbielski A, Boyle MD. Identification of key gene products required for acquisition of plasmin-like enzymatic activity by group A streptococci. J Infect Dis. 1997 May;175(5:):1115–1120. [PubMed: 9129074]
3.
Sun H, Wang X, Degen JL, Ginsburg D. Reduced thrombin generation increases host susceptibility to group A streptococcal infection. Blood. 2009 Feb 5;113(6:):1358–1364. Epub 2008 Dec 3. [PMC free article: PMC2637198] [PubMed: 19056689]
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Escaich S. Antivirulence as a new antibacterial approach for chemotherapy. Curr Opin Chem Biol. 2008 Aug;12(4:):400–408. Epub 2008 Jul 17. Review. [PubMed: 18639647]
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Oxoby M, Moreau F, Durant L, Denis A, Genevard JM, Vongsouthi V, Escaich S, Gerusz V. Towards gram-positive antivirulence drugs: new inhibitors of Streptococcus agalactiae Stk1. Bioorg Med Chem Lett. 2010 Jun 15;20(12:):3486–3490. [PMC free article: PMC2923816] [PubMed: 20529681]
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Appendix A. Assay Summary Table

Table A1Summary of Completed Assays and AIDs

PubChem AIDTypeTargetConcentration Range (μM)Samples Tested
1662PrimaryGrowth inhibition, Ska promoterAverage 7.5303,546
1900CounterscreenNon-Ska promoter15-0.063,268
1902DR in PrimarySka promoter15-0.063,268
1914SecondarySK expression15-0.063,268
1915SecondaryBacterial Viability15-0.063,268
2137SecondarySK expression50-0.0261
2138SecondaryBacterial Viability50-0.0261
504351SecondarySK expression50-0.0157
504396SecondaryBacterial Viability50-0.0157
1677SummaryNANANA

Appendix B. Detailed Assay Protocols

Primary Screen Protocol in SKKanGAS Strain (AID no. 1662)

  1. Day 1: Streak out SKKanGAS for colonies on THY/S/S medium (30 g/L THB/0.2% yeast extract with streptomycin 100 μg/ml, spectinomycin 100 μg/ml) plate. Incubate at 37ºC overnight.
  2. Day 2: Grow an overnight culture in THY/S/S medium from a single colony. Incubate at 37ºC overnight.
  3. Day 3: Measure OD600 of the overnight culture, and then dilute the culture into fresh THY/S/S medium (1:20) in a flask. Monitor OD600 until it reaches 0.6-0.8 (between 3–5 hours).
  4. Dispense assay plates at 30 μl/well of THY/kanamycin (THY plus 40 μg/ml kanamycin) with Combi. Load plates into incubators.
  5. Dilute the 0.8 OD culture down to OD 0.038 in cold THY/kanamycin; keep the diluted culture at 4ºC overnight.
  6. Day 4: Warm the diluted culture to room temperature. Dispense 20 μl/well of diluted culture with a Combi onto the pinned assay plates containing 30 μl/well of THY/S medium.
  7. Pin approximately 100 nL/well of compounds with Cybi-Well, and incubate the plates at 37ºC for 6 hours.
  8. Cool plates to room temperature for 30 minutes.
  9. Add 30 μl/well solution (25 μl/well BacTiter-Glo and 5 μl/well PBS) to the culture, and incubate at room temperature for 10 minutes.
  10. Read on an EnVision plate reader.

Secondary Assay Protocol (SK Expression and Bacterial Cell Viability)(AID nos. 1914,1915, 2137, 2138)

  1. Day 1: Streak out UMAA 2616 for colonies on THY/S medium (30 g/L THB/0.2% yeast extract with streptomycin 100 μg/mL) plate. Incubate at 37°C overnight.
  2. Day 2: Grow an overnight culture in THY/S medium from a single colony. Incubate at 37ºC overnight.
  3. Day 3: Dilute the overnight culture into fresh THY/S medium (1:20) in a flask. Monitor OD600 until it reaches 0.6–0.8 (between 3–5 hours).
  4. Dilute the 0.8 OD culture down to OD 0.038 in cold THY/S medium; keep the diluted culture at 4 °C overnight.
  5. Day 4: Warm the diluted culture to room temperature. Dispense 20 μl/well of diluted culture with a Combi onto the pinned assay plates containing 30 μl/well of THY/S medium.
  6. Pin 100 nL/well of compounds with Cybi-Well, and incubate the plates at 37ºC for 6 hours in a Liconic incubator.
  7. Pellet the cells at 3000 rpm in a Sorvall centrifuge. Transfer 10 μl/well of supernatant twice into separate, clear plates for assay with Cybi-Well Vario. Store at -20ºC.
  8. Warm the culture plates to room temperature for 30 minutes, then add 50 μl/well of BacTiter-Glo (1/2x).
  9. Incubate at room temperature for 10 minutes. Read on an EnVision plate reader.
  10. Add 50 μl/well of SK assay solution (5 μl/well of human plasma, 1.2 μl/well of 4.2 mg/ml S2403, 43.8 μl/well of PBS) to the 10 μl/well supernatant (thawed and warmed to room temperature) in clear SK assay plates with a Combi.
  11. Read OD405 at 0 hours and after incubation at 37ºC for 1.5–2.5 hours depending on the specific lot of substrate.
  12. Read OD405.

Appendix C. NMR and UPLC Data of Probe and Analogs

1H NMR (300 MHz, CDCl3) Spectrum of Probe CID 2769229/ML135.

1H NMR (300 MHz, CDCl3) Spectrum of Probe CID 2769229/ML135

13 C NMR (75 MHz, CDCl3 ) Spectrum of Probe CID 2769229/ML135.

13 C NMR (75 MHz, CDCl3 ) Spectrum of Probe CID 2769229/ML135

UPLC Chromatogram of Probe CID-2769229/ML135.

UPLC Chromatogram of Probe CID-2769229/ML135

Spectroscopic Data for SAR Analogs

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925845.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925845

UPLC Chromatogram of Analog CID-46925845.

UPLC Chromatogram of Analog CID-46925845

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925847.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925847

UPLC Chromatogram of Analog CID-46925847.

UPLC Chromatogram of Analog CID-46925847

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925837.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925837

UPLC Chromatogram of Analog CID-46925837.

UPLC Chromatogram of Analog CID-46925837

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925842.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925842

UPLC Chromatogram of Analog CID-46925842.

UPLC Chromatogram of Analog CID-46925842

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925851.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925851

UPLC Chromatogram of Analog CID-46925851.

UPLC Chromatogram of Analog CID-46925851

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925830.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925830

UPLC Chromatogram of Analog CID-46925830.

UPLC Chromatogram of Analog CID-46925830

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769230.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769230

UPLC Chromatogram of Analog CID-2769230.

UPLC Chromatogram of Analog CID-2769230

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-1471787.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-1471787

UPLC Chromatogram Spectrum of Analog CID-1471787.

UPLC Chromatogram Spectrum of Analog CID-1471787

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925852.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925852

UPLC Chromatogram of Analog CID-46925852.

UPLC Chromatogram of Analog CID-46925852

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925829.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46925829

UPLC Chromatogram of Analog CID-46925829.

UPLC Chromatogram of Analog CID-46925829

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769158.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769158

UPLC Chromatogram of Analog CID-2769158.

UPLC Chromatogram of Analog CID-2769158

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843050.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843050

UPLC Chromatogram of Analog CID-49843050.

UPLC Chromatogram of Analog CID-49843050

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769212.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-2769212

UPLC Chromatogram of Analog CID-2769212.

UPLC Chromatogram of Analog CID-2769212

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46926572.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46926572

UPLC Chromatogram of Analog CID-46926572.

UPLC Chromatogram of Analog CID-46926572

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46926577.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-46926577

UPLC Chromatogram of Analog CID-46926577.

UPLC Chromatogram of Analog CID-46926577

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843412.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843412

UPLC Chromatogram of Analog CID-49843412.

UPLC Chromatogram of Analog CID-49843412

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843053.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-49843053

UPLC Chromatogram of Analog CID-49843053.

UPLC Chromatogram of Analog CID-49843053

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-36037231.

1H NMR (300 MHz, CDCl3) Spectrum of Analog CID-36037231

UPLC Chromatogram of Analog CID-36037231.

UPLC Chromatogram of Analog CID-36037231

Appendix D. Compounds Submitted to BioFocus

Table 2Probe and Analog Information

BROAD IDPUBCHEM SIDPUBCHEM CIDP/AMLS No.ML No.
BRD-K40087974-001-05-5873340302769229PMLS002699833ML135
BRD-K70771662-001-01-3873340321471787AMLS002699831NA
BRD-K43069600-001-01-1873340292769158AMLS002699832NA
BRD-K36087356-001-01-8873340202769230AMLS002699834NA

A = analog; P = probe

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