# Patent

## Title
Ethoxyphenyl thienyl compounds and methods for the treatment of bacterial infections

## Abstract

This invention relates generally to the discovery of a method of inhibiting, preventing or treating bacterial infections. The invention also relates to a method of inhibiting bacterial capsule biogenesis.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. application Ser. No. 14/305,649 filed Jun. 16, 2014 entitled “COMPOSITIONS AND METHODS FOR THE TREATMENT OF BACTERIAL INFECTIONS” and U.S. Provisional Appn. 61/890,930, filed Oct. 15, 2013, entitled “COMPOSITIONS AND METHODS FOR THE TREATMENT OF BACTERIAL INFECTIONS” which are hereby incorporated by reference in their entireties.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under Grant No. MH090791 and HG005031 awarded by the National Institutes of Health. The United States Government has certain rights in the invention.


1. FIELD OF THE INVENTION
This invention relates generally to the discovery of a method of inhibiting, preventing or treating bacterial infections. The invention also relates to a method of inhibiting bacterial capsule biogenesis.
2. BACKGROUND OF THE INVENTION
2.1. Introduction
Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infections (UTIs). Over 100 million UTIs occur annually throughout the world, including more than 7 million cases in U.S. adolescents and adults (14). UTIs in younger children are associated with greater risk of morbidity and mortality than in older children and adults. Antimicrobial resistance among UPEC is on the rise (10, 15-18), driving efforts to discover vulnerable targets in the molecular pathogenesis of infection.
During UTI, UPEC lives in intracellular and extracellular locales. UPEC adheres to the apical bladder epithelium and invades into it (19-21). Within the bladder epithelium, UPEC typically reproduces in a biofilm-like state called intracellular bacterial communities (IBC; (5)). After maturation of IBCs, UPEC disperses away from the IBC and exits the infected cells. Extracellular UPEC must then re-adhere, initiating the invasion and intracellular reproduction phases again. Past studies have revealed bacteria encased in the IBC within a complex matrix of fibrous protein assemblies and polysaccharides (5). Our prior studies have also shown that disruption of the IBC pathway aborts experimental UTI, highlighting the importance of this intracellular lifecycle (22-25). A detailed study of urine samples from women with acute UTI demonstrated IBC in shed bladder epithelial cell, showing that the pathway is conserved in humans (26).
Investigators have found that bacterial encapsulation is an important UPEC virulence factor (4-6), and experiments show that the K capsule contributes to multiple aspects of pathogenesis, including IBC formation. K capsules, also called K antigens, are enveloping structures composed of high-molecular-weight polysaccharides. Among UPEC, the K antigens K1, K2, K5, K30, and K92 are thought to be most prevalent (27). Capsules are well-established virulence factors for a variety of pathogens that are thought to protect the cell from opsonophagocytosis and complement-mediated killing (reviewed in (28, 29)). While they did not study the effects of K antigen from UPEC, Llobet et al. recently demonstrated that the highly acidic polysaccharide capsules of diverse organisms including Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae interact strongly with APs, acting as “sponges” to sequester and neutralize the APs (30).
Of the different K types, the Group 2 and Group 3 capsules are most prevalent among UPEC isolates, with K1 and K5 being leading types. Although the capsules have different compositions, they are regulated, synthesized, assembled, and exported by functionally homologous factors, leading us to hypothesize that we can develop small molecular inhibitors of K-type encapsulation that target the most medically important K capsule types. Furthermore, the medically important infectious agents Campylobacter jejuni, Haemophilus influenzae, Neisseria meningitides, and Salmonella typhimurium among others, use homologous components in the biogenesis of their capsules. The K1 capsule type is closely associated with pathogenic isolates; not only is it the leading type in UTI, but it also accounts for much of the extra-urinary tract complications. Animals studies of E. coli K1 sepsis demonstrated that injection of a K1 capsule degrading enzyme abrogates infection (7). However, the enzyme treatment is immunogenic; accordingly, chemical inhibition may prove to be a superior approach.
There are currently no therapeutics that specifically inhibit the formation of any bacterial capsule, and this is a novel strategy for preventing or decreasing the prevalence of chronic or re-occurring urinary tract infections. New insights into the roles of K1 capsules in UPEC virulence during UTI make capsules an attractive target for therapeutic intervention. Antimicrobial resistance among UPEC is on the rise (11, 12, 15, 31, 32), and the discovery of novel small molecules that can act as probes or lead compounds for the investigation and treatment of UTI will add to the arsenal of compounds available for single or combination therapies.
3. SUMMARY OF THE INVENTION
The invention provides compounds having the structure below:




each R1, R2, and R3 may independently be aryl, C1-8 alkyl, C1-8 alkyl(aryl), C1-8 alkoxy, C1-8 alkoxy aryl, C1-8 haloalkoxy, C2-8 alkenyl, C3-8 alkynyl, C3-8 cycloalkyl, —CF3, —(CH3-8)xNR4R5, —CN, —CONR4R5, —COR4, —CO2(CH2)xNR4R5, —CO2R4, haloaryl, halogen, heteroaryl, hydroxyl, —N3, —NHCOR4, —NHSO2C1-8 alkyl, —NHCO2C1-8 alkyl, —NO2, —NR4R5, —O(CH2)xNR4R5, —O(CH2)xCO2R4, —OCOC1-8 alkyl, —OCO(CH2)xNR4R5, —SO(1-3)R4, or —SR4; each R4 and R4 are independently aryl, C1-8 alkyl, C1-8 alkyl alcohol, C1-8 alkyl amino, C1-8 alkyl amido, C1-8 alkyl(aryl), C1-8 alkyl (C3-8 cycloalkyl), C1-8 alkyl guanidinyl, C1-8 alkyl heteroaryl, C1-8 alkyl imidazolyl, C1-8 alkyl indolyl, C1-8 alkyl thioether, C1-8 alkyl thiol, C2-8 alkenyl, C3-8 alkynyl, C3-8 cycloalkyl, or H; or R4 and R5 together make a 4-8 member ring which may be substituted with one or more heteroatoms; n is 0, 1, 2, 3, 4 or 5; and each x is independently 0-8. The invention also includes salts thereof.
The invention also provides compounds and uses having the structure:




wherein each R1, R6, R7 and R8 may independently be C1-8 alkyl, C1-8 alkyl(aryl), C1-8 alkoxy, C1-8 haloalkoxy, C1-8 alkoxy aryl, C2-8 alkenyl, C3-8 alkynyl, C3-8 cycloalkyl, —CF3, —CN, halogen, or hydrogen.




where R1 is C1-8 alkyl or C1-8 haloalkoxy. Compound 3 where R1 is ethoxy is also referred to as DU011 or ML317 in this disclosure. Compound 3 where R1 is n-butoxy is CID 56643007 and R′ is n-trifluoropropyloxy is CID 56643020.




where each of R1 and R9 is C1-8 alkyl, C1-8 haloalkoxy or halogen. Compound 4 where R1 is n-trifluoropropyloxy and R9 is 5-bromo is CID 56643022. Compound 4 where R1 is n-butoxy and R9 is 5-bromo is CID 56643021 and n-trifluoropropyloxy is CID 56643020.
In particular non-limiting embodiments, the present invention provides a method of inhibiting capsule biogenesis in a bacterium which comprises administering to the bacterium an effective amount of a composition comprising Compound 1, 2, 3, or 4 or salt thereof.
The invention also provides a method of treating a subject suffering from a bacterial infection comprising administering a therapeutically effective amount of a composition comprising Compound 1, 2, 3, or 4 and/or salts thereof. The bacterial infection may be a urinary tract infection (UTI), a bladder infection, a kidney infection, or a disseminated staphylococcus infection.
The bacterium may be a gram-negative bacteria such as a Campylobacter jejuni, Enterobacter cloacae, Haemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Methicillin-resistant Staphylococcus aureus (MRSA), Neisseria meningitides, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella typhimurium, Serratia marcescens, Staphylococcus aureus, or a combination thereof. In the methods above, they may further comprise administering an agent that targets a bacterial cell wall such as a penicillin or a cephalosporin.
The subject may be a mammal such as a human.



4. BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Capsule biogenesis inhibitors. Panel A: E. coli capsule biogenesis components and conservation between sequenced pathogenic isolates. Panel B: The bacteriophage-dependent screen for chemical inhibitors. In the first step, E. coli is grown in the presence of chemicals to be tested, permitting the elimination of chemicals producing simple growth defects. In the next step, the bacteriophage K1F is added to growing cultures with putative chemical inhibitors. The K1F phage requires the K1 polysaccharide capsule for binding and cellular entry, which when successful results in lysis of the target bacterium. In the presence of a chemical inhibitor of capsule biogenesis or a genetic capsule mutant, K1F fails to lyse the target cells. Thus inhibitors of capsule biogenesis produce growth of E. coli in the presence of the K1F phage. The chemical 3-(2,6-difluorobenzamido)-5-(4-ethoxyphenyl)thiophene-2-carboxylic acid as disclosed in this document was identified using this assay.
FIG. 2. Dose-dependent capsule inhibition by N-pyridin-4-yl-1,3-benzothiazole-6-carboxamide and 3-(2,6-difluorobenzamido)-5-(4-ethoxyphenyl)thiophene-2-carboxylic acid leading to T7 phage lysis of target bacteria. Bacteria were grown with or without T7 bacteriophage and with DMSO or chemical inhibitor at increasing micromolar concentrations. A high % phage inhibition indicates loss of polysaccharide capsule that normal precludes T7 phage attachment, entry, and lysis of target bacteria.
FIG. 3. The orcinol reaction and capsule antigen dot blots to demonstrate reduction in capsule after treatment with N-pyridin-4-yl-1,3-benzothiazole-6-carboxamide (DU003) and 3-(2,6-difluorobenzamido)-5-(4-ethoxyphenyl)thiophene-2-carboxylic acid (DU011). Panel A: Orcinol biochemical tests for extracted K1 capsule polysaccharide from wild type (UT189), genetic capsule mutants (UTI DRegion1 and UTI DRegion11), and chemical treatment (UTI+DU003 at 50 μM). Results are shown as a percentage of wild type. Note that orcinol reacts with other non-capsule sugars in the extract preparations providing some background reactivity even in a capsule synthesis mutant (UTI DRegion11). Panel B: Whole cell immunodot blot using anti-K1 capsule antibody. UTI indicates the wild type E. coli strain treated with vehicle control. ΔRI and ΔRII are genetic capsule mutants treated with vehicle control DU003 indicates cells treated with the chemical N-pyridin-4-yl-1,3-benzothiazole-6-carboxamide at 50 μM. LB indicates a negative control in which bacterial growth medium alone was applied to the membrane. Duplicate independent experiments are shown side by side.
FIG. 4. Graph depicting the stability for ML317 after 48 hours in two separate solvent systems
FIG. 5. Graph depicting stability of the probe to thiol.
FIG. 6. Synthetic route for probe and analogue generation.
FIG. 7. Five analogues chosen to support probe ML317.
FIG. 8. HTS to compound hit flowchart.
FIGS. 9 and 10. Efficacy and cytotoxicity analysis of ML317.
FIG. 11. Regions of the compound hit identified for initial SAR exploration.
FIG. 12. Concentration-response inhibition of K1 and T7 phage-mediated cell lysis. K1 (A, C) and T7 (B, D) phage activity in E. coli strain UTI89 or EV36 (K1:K-12 hybrid strain), respectively, following treatment with various concentrations of DU003 (A, B) or DU011 (C, D).
FIG. 13. Biochemical and immunologic verification of E. coli Group 2 capsule inhibition through small molecules. A) Orcinol reactivity of capsular material released by mild acid treatment of cultures grown with 1% DMSO vehicle (UTI89 and genetic capsule mutants) or 100 μM C7, DU001, DU003, DU005, DU007, DU008, or DU011. Data represent independent experiments performed in duplicate. Treatment of K1 strain UTI89 with compounds reduces amount of orcinol-reactive polysaccharides on surface of bacteria by  ̃80%. B) Whole-cell anti-K1 dot blots of cultures of UTI89 or indicated genetic capsule mutants treated with 1% DMSO or 100 μM DU001, DU003, DU005, DU007, DU008, or DU011 indicate that treatment of cultures with compounds reduces K1 reactive material to levels comparable to those of genetic capsule mutants. ΔRI and ΔRII indicate a complete deletion of Region I of the capsule kps and Region II capsule neu loci, respectively.
FIG. 14. Inhibitor treatment decreases capsule production in different pathogenic E. coli serotypes. A) K5 E. coli was grown in vehicle or with different inhibitors (50 and 100 μM) and then challenged with K5 lytic phage, which results in cell death in the presence of capsule. Growth was measured by absorbance at OD600. B) Capsular material was isolated from multiple strains grown with and without inhibitor DU011 (200 μM). Capsule preparations were performed in at least 3 independent trials. A single representative image is shown.
FIG. 15. Capsule inhibitors sensitize UPEC K1 strain to serum-mediated killing. E. coli UTI89 and genetic capsule mutants were grown in the presence and absence of DU003 or DU011 at 50 μM and exposed to human serum. Bacterial metabolism and viability was measured using MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). UTI89 grown in the presence of 50 μM DU003 or DU011 were significantly more sensitive to pooled human serum compared to control UTI89 (** p=0.0067). This was similar to the serum sensitivity of the capsule mutant UTI89 ΔRII. ΔRI and ΔRII indicate a complete deletion of Region I of the capsule kps and Region II capsule neu loci, respectively.
FIG. 16. ML317 (DU011) protects mice against a lethal dose of K1 E. coli. A) C57BL/6 mice were administered subcutaneous 1% DMSO (control) or DU011 (100 μL, of 1 mg/ml in 1% DMSO) 12 hours prior to lethal intraperitoneal injection with 108 CFU of UTI89 prepared in media containing 1% DMSO or DU011 (200 μM in 1% DMSO). Surviving animals continued to receive DMSO or DU011 each 12 hours through the course of the experiment, according to their groups (B) Weight was monitored during DMSO and DU011 administration and after infection.
FIG. 17. Inhibition of Methicillin Resistant Staphylococcus aureus (MRSA) Strain USA300 by ML317 (DU011). USA300 was grown shaking in TSB medium buffered at different pH as indicated in the figure with the addition of different concentrations of the chemical probe ML317. Growth was measured by absorbance readings as indicated. Concentrations of 25 to 50 μM of ML317 were sufficient to produce inhibition of MRSA at pH 5 and 5.5. ML317 inhibited growth of MRSA at pH 7 when introduced at concentrations of 100 and 200 μM. Culture of bacteria from the experiments indicated that ML317 was bactericidal under the experimental conditions.



5. DETAILED DESCRIPTION OF THE INVENTION
Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infections (UTIs). Over 100 million UTIs occur annually throughout the world, including more than 7 million cases in U.S. adolescents and adults. UTIs in younger children are associated with greater risk of morbidity and mortality than in older children and adults. During UTI, UPEC exists in both intracellular and extracellular spaces. Infection is initiated by adherence to the apical bladder epithelium and then invading this layer of cells. Within the bladder epithelium, UPEC typically reproduces in a biofilm-like state composed of intracellular bacterial communities (IBC). After maturation of IBCs, UPEC disperses away from the IBC and exits the infected cells. Extracellular UPEC must then re-adhere, initiating the invasion and intracellular propagation phases again. Bacterial-epithelial interactions incite a strong inflammatory response through which the UPEC must persist. One persistence factor is the K type polysaccharide capsule. Capsule protects against phagocytosis, complement action, and antimicrobial peptide killing. Recent studies have also revealed that capsule along with fibrous protein assemblies is a key part of the IBC formation. Antimicrobial resistance among UPEC is increasing, driving efforts to identify therapeutic targets in the molecular pathogenesis of infection. Capsules are an attractive target because of new insights into the roles of bacterial K capsules in UPEC virulence during UTI. Specific investigations have shown that K capsule contributes to multiple aspects of pathogenesis, including IBC formation. In this program we used a cell-based assay to screen 335,740 compounds from the MLSMR library and identified 1,767 hits that inhibited K1 bacterial capsule formation. Of those hits, 59 were confirmed as active in a dose-responsive manner, and eight compounds were shown in secondary assays to specifically inhibit capsule formation. Of those eight compounds, three of those were further characterized for structure-activity relationships, mechanism of action, and therapeutic index. The probe compound, 3-[(2,6-difluorobenzoyl)amino]-5-(4-ethoxyphenyl)thiophene-2-carboxylic acid, was identified as a small molecule inhibitor of K1 capsule formation with an IC50 value of 4.5±2.4 μM and a >10-fold selectivity index (SI) in BC5637 bladder cells. The probe has been broadly profiled for off-target liabilities and assessed for aqueous solubility, parallel artificial membrane permeability, and hepatocyte microsome and plasma stability. It is suitable for use as a lead compound for inhibition of K1 capsule formation.
Probe Structure & Characteristics:












ML317









 



















Secondary Assay(s)



Target
IC50 (μM)
Anti-target
CC50 (μM)
Fold
Name: IC50 (μM)


SID/CID/ML#
Name
[AID]
Name(s)
[SID, AID]
Selectivea
[AID]





103147605/
K1
4.5 ± 2.4;
Mammalian
CC50 =
10.5
T7 phage assay


23602075/
Capsule
[488970]
cell
47.2 ± 7.2;

<0.39 μM;


ML317


toxicity
[10314760],

AID 488970


(commercial



AIDs

Orcinol assay 24% of


sample)



488970,

control value; AID






493020,

488970, 624060






504769,








504831,








588399




126497311/
K1
1.89 ± 1.56;
Mammalian
CC50 =
27.3
T7 phage assay


23602075/
Capsule
[488970]
cell
51.6 ± 13.69;

<0.625 μM;


ML317


toxicity
[126497311,

AID 488970


(synthesized



AIDs

Orcinol assay 21%


sample)



488970,

of control value; AID






493020,

488970, 624060






504769,








504831,








588399





aCalculated as CC50/IC50






This team previously reported a probe ML317. In short, the probe ML317 was found to have an IC50 of 1.89 μM in a bacterial viability assay in the presence of K1 phage, a TC50 (toxicity) of 51.6 μM, a selectivity of 27, a T7 phage bacterial viability assay IC50 of <0.39 μM, and to reduce the bacterial capsule-dependent orcinol stain to 21% of the control sample. Additional biological characterization for probe ML317 is provided in Section 4.1 of this report.




Through the efforts of the Seed lab toward developing assay and screening techniques for inhibitors of bacterial capsule biogenesis, a sample of 2,195 compounds obtained from the Developmental Therapeutics Program at the National Cancer Institute were tested. In the K1F phage lysis 96-well plate format assay, 35 (1.59%) of the compounds were found to have inhibitory activity, of which only nine compounds gave reproducible phage lysis inhibition activity in shaken tube format. These nine compounds were taken onto a secondary screening process from which two capsule biogenesis inhibitors emerged. Malachite green oxalate (NCS5550), a compound not known to inhibit capsule biogenesis, was found to produce metabolites with previously reported toxicities to mammalian systems and was thus discarded. The second inhibitor, 2-(4-phenylphenyl)-benzo[g]quinoline-4-carboxylic acid (NSC136469), or C7, was employed as a prototype small molecule inhibitor of capsule biogenesis since it inhibited K1F phage lysis of UPEC K1 strain UTI80 reproducibly in the tests following HTS. Furthermore, this inhibition was found to behave in a dose-dependent manner with the inhibitory effect reaching saturation at approximately 25 μM C7, producing approximately 50% inhibition of K1F phage lysis of UPEC at 12.5-25 μM (33).
The present disclosure provides compositions and methods for the treatment of bacterial infections.
5.1. Definitions
The term “administration” or “administering,” as used herein, refers to providing, contacting, and/or delivery of a composition by any appropriate route to achieve the desired effect. These composition may be administered to a subject in numerous ways including, but not limited to, orally, ocularly, nasally, intravenously, topically, as aerosols, suppository, etc. and may be used in combination.
“Alkenyl” refers to an unsaturated branched, straight-chain or cyclic alkyl group having at least one carbon-carbon double bond derived by the removal of one hydrogen atom from a single carbon atom of a parent alkene. The group may be in either the Z- and E-forms (or cis or trans conformation) about the double bond(s). Typical alkenyl groups include, but are not limited to, ethenyl; propenyls such as prop-1-en-1-yl, prop-1-en-2-yl, prop-2-en-1-yl (allyl), prop-2-en-2-yl, cycloprop-1-en-1-yl; cycloprop-2-en-1-yl; butenyls such as but-1-en-1-yl, but-1-en-2-yl, 2-methyl-prop-1-en-1-yl, but-2-en-1-yl, but-2-en-1-yl, but-2-en-2-yl, buta-1,3-dien-1-yl, buta-1,3-dien-2-yl, cyclobut-1-en-1-yl, cyclobut-1-en-3-yl, cyclobuta-1,3-dien-1-yl; and the like. The alkenyl group may be substituted or unsubstituted. In certain embodiments, an alkenyl group has from 2 to 20 carbon atoms and in other embodiments from 2 to 8 carbon atoms.
“Alkoxy” refers to a radical —OR where R represents an alkyl, alkyl, cycloalkyl, aryl, or heteroaryl group as defined herein. Representative examples include, but are not limited to, methoxy, ethoxy, propoxy, butoxy, cyclohexyloxy, and the like.
“Alkyl” refers to a saturated, branched or straight-chain monovalent hydrocarbon group derived by the removal of one hydrogen atom from a single carbon atom of a parent alkane. Typical alkyl groups include, but are not limited to, methyl, ethyl, propyls such as propan-1-yl, propan-2-yl, and cyclopropan-1-yl, butyls such as butan-1-yl, butan-2-yl, 2-methyl-propan-1-yl, 2-methyl-propan-2-yl, cyclobutan-1-yl, tert-butyl, and the like. The alkyl group may be substituted or unsubstituted. In certain embodiments, an alkyl group comprises from 1 to 20 carbon atoms. Alternatively, an alkyl group may comprise from 1 to 8 carbon atoms.
“Alkyl(aryl)” refers to an acyclic alkyl group in which one of the hydrogen atoms bonded to a carbon atom, typically a terminal or sp3 carbon atom, is replaced with an aryl group. Typical alkyl(aryl) groups include, but are not limited to, benzyl, 2-phenylethan-1-yl, 2-phenylethen-1-yl, naphthylmethyl, 2-naphthylethan-1-yl, 2-naphthylethen-1-yl, naphthobenzyl, 2-naphthophenylethan-1-yl and the like. In certain embodiments, an alkyl(aryl) group can be (C6-20) alkyl(aryl) e.g., the alkyl group may be (C1-10) and the aryl moiety may be (C5-10).
“Alkynyl” refers to an unsaturated branched or straight-chain having at least one carbon-carbon triple bond derived by the removal of one hydrogen atom from a single carbon atom of a parent alkyne. Typical alkynyl groups include, but are not limited to, ethynyl, propynyl, butenyl, 2-pentynyl, 3-pentynyl, 2-hexynyl, 3-hexynyl and the like. The alkynyl group may be substituted or unsubstituted. In certain embodiments, an alkynyl group has from 3 to 20 carbon atoms and in other embodiments from 3 to 8 carbon atoms.
“Aryl” refers to a monovalent aromatic hydrocarbon group derived by the removal of one hydrogen atom from a single carbon atom of a parent aromatic ring system. Aryl encompasses 5- and 6-membered carbocyclic aromatic rings, for example, benzene or cyclopentadiene; bicyclic ring systems wherein at least one ring is carbocyclic and aromatic, for example, naphthalene, indane; or two aromatic ring systems, for example benzyl phenyl, biphenyl, diphenylethane, diphenylmethane. The aryl group may be substituted or unsubstituted.
As used herein, the term “bacteria” and “bacterium” are used interchangeable any to any bacteria that has a polysaccharide capsule. IN some embodiments, the bacteria comprises a gram-negative bacteria. In certain embodiments, the bacteria is selected from the group consisting of E. coli, C. jejuni, N. meningitides, K. kingea, Proteus mirabilis, Enterobacter cloacae, Serratia marcescens, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa and/or combinations thereof.
“Cycloalkyl” refers to a saturated or unsaturated cyclic alkyl group. Where a specific level of saturation is intended, the nomenclature “cycloalkanyl” or “cycloalkenyl” is used. Typical cycloalkyl groups include, but are not limited to, groups derived from cyclopropane, cyclobutane, cyclopentane, cyclohexane, and the like. The cycloalkyl group may be substituted or unsubstituted. In certain embodiments, the cycloalkyl group can be C3-10 cycloalkyl, such as, for example, C6 cycloalkyl.
“Disease” refers to any disease, disorder, condition, symptom, or indication.
“Halogen” refers to a fluoro, chloro, bromo, or iodo group.
“Heteroaryl” refers to a monovalent heteroaromatic group derived by the removal of one hydrogen atom from a single atom of a parent heteroaromatic ring system. Heteroaryl encompasses: 5- to 7-membered aromatic, monocyclic rings containing one or more, for example, from 1 to 4, or in certain embodiments, from 1 to 3, heteroatoms chosen from N, O, and S, with the remaining ring atoms being carbon; and polycyclic heterocycloalkyl rings containing one or more, for example, from 1 to 4, or in certain embodiments, from 1 to 3, heteroatoms chosen from N, O, and S, with the remaining ring atoms being carbon and wherein at least one heteroatom is present in an aromatic ring. The heteroaryl group may be substituted or unsubstituted. The substituted heteroaryl group may be a halo substituted thiophene, e.g., bromo thiophene.
For example, heteroaryl includes a 5- to 7-membered heteroaromatic ring fused to a 5- to 7-membered cycloalkyl ring and a 5- to 7-membered heteroaromatic ring fused to a 5- to 7-membered heterocycloalkyl ring. For such fused, bicyclic heteroaryl ring systems wherein only one of the rings contains one or more heteroatoms, the point of attachment may be at the heteroaromatic ring or the cycloalkyl ring. When the total number of S and O atoms in the heteroaryl group exceeds 1, those heteroatoms are not adjacent to one another. In certain embodiments, the total number of S and O atoms in the heteroaryl group is not more than 2. In certain embodiments, the total number of S and O atoms in the aromatic heterocycle is not more than 1. Typical heteroaryl groups include, but are not limited to, groups derived from acridine, arsindole, carbazole, β-carboline, chromane, chromene, cinnoline, furan, imidazole, indazole, indole, indoline, indolizine, isobenzofuran, isochromene, isoindole, isoindoline, isoquinoline, isothiazole, isoxazole, naphthyridine, oxadiazole, oxazole, perimidine, phenanthridine, phenanthroline, phenazine, phthalazine, pteridine, purine, pyran, pyrazine, pyrazole, pyridazine, pyridine, pyrimidine, pyrrole, pyrrolizine, quinazoline, quinoline, quinolizine, quinoxaline, tetrazole, thiadiazole, thiazole, thiophene, triazole, xanthene, and the like. In certain embodiments, the heteroaryl group can be between 5 to 20 membered heteroaryl, such as, for example, a 5 to 10 membered heteroaryl. In certain embodiments, heteroaryl groups can be those derived from thiophene, pyrrole, benzothiophene, benzofuran, indole, pyridine, quinoline, imidazole, oxazole, and pyrazine.
“Stereoisomer” refers to an isomer that differs in the arrangement of the constituent atoms in space. Stereoisomers that are mirror images of each other and optically active are termed “enantiomers,” and stereoisomers that are not mirror images of one another and are optically active are termed “diastereoisomers.”
“Subject” includes mammals and humans. The terms “human” and “subject” are used interchangeably herein.
“Substituted” refers to a group in which one or more hydrogen atoms are each independently replaced with the same or different substituent(s). Typical substituents include, but are not limited to, CO2H, halogen, hydroxyl, —N3, —NH2, —SO(1-3)H, or —SH.
As used herein, the term “subject” is intended to include human and non-human animals. Exemplary human subjects include a human patient having a bacterial infection. The term “non-human animals” includes all vertebrates, e.g., non-mammals (such as chickens, amphibians, reptiles) and mammals, such as non-human primates, domesticated and/or agriculturally useful animals (such as sheep, dogs, cats, cows, pigs, etc.), and rodents (such as mice, rats, hamsters, guinea pigs, etc.).
As used herein, the term “therapeutically effective” refers to a dosage of a composition (e.g., N-pyridin-4-yl-1,3-benzothiazole-6-carboxamide, analogues thereof, derivatives thereof, and/or salts thereof) that is effective for eliciting a desired effect. This term as used herein may also refer to an amount effective at bringing about a desired in vivo effect in an animal, mammal, or human, such as reducing inflammation, fever and the like that is commonly associated with a bacterial infection. A therapeutically effective amount may be administered in one or more administrations (e.g., the composition may be given as a preventative treatment or therapeutically at any stage of disease progression, before or after infection, before or after the onset of symptoms, and the like), applications or dosages and is not intended to be limited to a particular formulation, combination or administration route. It is within the scope of the present disclosure that the composition may be administered at various times during the course of infection of the subject. The times of administration and dosages used will depend on several factors, such as the goal of treatment (e.g., treating v. preventing), condition of the subject, etc. and can be readily determined by one skilled in the art. For example, in one embodiment the composition is administered at the onset of infection. In other embodiments, the composition is administered after infection, but prior to symptoms. In yet other embodiments, the composition is administered after symptoms have manifested. In yet other embodiments, the composition is administered prior to the onset of infection.
In certain embodiments, the composition may be in the form of a pharmaceutical compositions. As used herein, the term “pharmaceutical composition” refers to the combination of compound (i.e., N-pyridin-4-yl-1,3-benzothiazole-6-carboxamide, analogues thereof, derivatives thereof, and/or salts thereof) with a pharmaceutically acceptable carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo, in vivo or ex vivo. A “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents. The compositions also can include stabilizers and preservatives. For examples of carriers, stabilizers and adjuvants. (See e.g., Martin, Remington's Pharmaceutical Sciences, 15th Ed., Mack Publ. Co., Easton, Pa. (1975)).
As used herein, the term “pharmaceutically acceptable salt” refers to any pharmaceutically acceptable salt (e.g., acid or base) of a composition of the present invention which, upon administration to a subject, is capable of providing a composition of this invention or an active metabolite or residue thereof. “Salts” of the compounds of the present invention may be derived from inorganic or organic acids and bases. Examples of acids include, but are not limited to, hydrochloric, hydrobromic, sulfuric, nitric, perchloric, fumaric, maleic, phosphoric, glycolic, lactic, salicylic, succinic, toluene-p-sulfonic, tartaric, acetic, citric, methanesulfonic, ethanesulfonic, formic, benzoic, malonic, naphthalene-2-sulfonic, benzenesulfonic acid, and the like. Other acids, such as oxalic, while not in themselves pharmaceutically acceptable, may be employed in the preparation of salts useful as intermediates in obtaining the compounds of the invention and their pharmaceutically acceptable acid addition salts.
Examples of bases include, but are not limited to, alkali metals (e.g., sodium) hydroxides, alkaline earth metals (e.g., magnesium), hydroxides, ammonia, and compounds of formula NW4+, wherein W is C1-4 alkyl, and the like.
Examples of salts include, but are not limited to: acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, flucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, palmoate, pectinate, persulfate, phenylpropionate, picrate, pivalate, propionate, succinate, tartrate, thiocyanate, tosylate, undecanoate, and the like. Other examples of salts include anions of the compounds of the present invention compounded with a suitable cation such as Na+, NH4+, and NW4+ (wherein W is a C1-4 alkyl group), and the like. For therapeutic use, salts of the compounds of the present invention are contemplated as being pharmaceutically acceptable. However, salts of acids and bases that are non-pharmaceutically acceptable may also find use, for example, in the preparation or purification of a pharmaceutically acceptable compound.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object(s) of the article. By way of example, “an element” means one or more elements.
Throughout the specification the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps. The present invention may suitably “comprise”, “consist of”, or “consist essentially of”, the steps, elements, and/or reagents described in the claims.
It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely”, “only” and the like in connection with the recitation of claim elements, or the use of a “negative” limitation.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
The following Examples further illustrate the invention and are not intended to limit the scope of the invention. In particular, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
6. EXAMPLES
Examples Section 1
Introduction: Urinary tract infections are the second most common infection in humans, and the bacterium Escherichia coli accounts for >80% of the infections in the community and >50% of the nosocomial infections. Polysaccharide capsules are ubiquitous among these pathogenic strains and the mechanism of capsule biogenesis is different than that for the related commensal strains. Pathogenic E. coli causing urinary tract infections have surged in antibiotic resistance in the past decade, particularly for the most commonly used oral agents, thus necessitating the development of new targets and chemical probes against these targets to disable the organism during infection. This disclosure describes our novel development of a screening process to identify inhibitors of E. coli capsule biogenesis.
Materials and Methods
Overall Assay Strategy:
The ability of the T1 bacteriophage to bind to bacterial capsule, infect, and lyse E. coli UT189 was used as the primary assay to identify the effects of screened compounds on bacterial capsule formation. The phenotypic end-point assay measured the fluorescence generated by cellular processing of Alamar Blue as a direct indicator of cell viability. A total of 335,740 compounds were screened using the primary assay. Following this, a concentration-dependent confirmatory assay (in a compound concentration range of 50-0.19 μM) was used in parallel with a eukaryotic cytotoxicity counterscreen (same concentration range) to determine hit IC50s and CC50s (and selective indices). Hits were further evaluated using three secondary assays for alternative measurement of compound-induced reduction in bacterial capsule formation (secondary assays 1 and 2) and specificity (secondary assays 3 and 4). Confirmed actives with an SI>5 were further investigated and subjected to chemical optimization, followed by secondary assay evaluation. Secondary assays more closely characterized the ability of the compounds to reduce bacterial capsule formation and can be used to examine the mechanism of action of the compounds. The combination of primary assay (to measure capsule reduction), counter assay (for general eukaryotic cell toxicity) and secondary assay (to measure reduction in capsule formation and specificity) were combined to allow a determination of probe efficacy, selectivity, and specificity.
A chemical probe for this project was defined as a small molecule that:
Has an IC50 of <10 μM in the primary and confirmatory Alamar Blue Screen of E. coli strain UT189 lysis (primary assay)
Has a therapeutic index of >5 relative to the cytotoxicity in the bladder cell line Hu5637 (counterscreen)
Has an IC50 of <10 μM in the confirmatory Bacterial Growth Screen of E. coli strain UT189 lysis (secondary assay 1)
Has an IC50 of <10 μM in the T7 lysis inhibition assay, indicating the desired target specificity (secondary assay 2)
Will yield low orcinol levels that are 50% of the levels for capsule export control strain (secondary assay 3)
Will yield K5 phage sensitivity in E. coli strain DS17 (secondary assay 4).
2.1 Assays
A. Primary Assay: Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: The primary inhibition assay using E. coli UT189 and bacteriophage K1F was conducted to screen the MLSMR 300K compound library, to confirm 1,767 hits from the primary screen, and to verify the activity for purchased/synthesized compounds.
Summary AID: 488970
Assigned AID: 488966
B. Counterscreen: Cytotoxicity Screening for Potential Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This cell-based assay measures the cytotoxicity of compounds in bladder carcinoma 5637 cells using luminescent cell viability assay readout.
Summary AID: 488970
Assigned AID: 493020, 504769, 504831, 588399
C. Secondary Assay 1: Screening for Inhibitors of Bacterial Capsule Biogenesis—E. coli Strain UT189 with C7 Control
Purpose: This confirmatory cell-based assay provides an alternative measurement of inhibitory activity on phage-induced lysis. It measures reduction in bacterial capsule formation using an absorbance readout at A600 instead of the alamar blue reagent.
Summary AID: 488970
Assigned AID: 504358, 504543, 504675, 504768, 588321, 588386, 588395
D. Secondary Assay 2: Screening for Inhibitors of Bacterial Capsule Biogenesis—T7 Lysis Inhibition
Purpose: This secondary assay measures the compound mechanistic specificity for inhibition of bacterial capsule formation and excludes inhibitors of phage replication using a different bacteriophage (T7). In this assay, an increase in phage-induced lysis correlates to a decrease in capsule formation.
Summary AID: 488970
Assigned AID: 504349, 504538, 504676, 504767, 588322
E. Secondary Assay 3: Orcinol Secondary Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This assay was performed only on the probe candidate. This is an end-point assay to measure the amount of K1 bacterial cell capsule formation in the presence of a test compound. The ability of the test compounds to inhibit the K1 capsule formation was measured by a reduction in absorbance due to the complex formed by orcinol and the capsule polysaccharide. The biochemical determination of cell-surface associated capsule was performed using UTI89 or the Delta Region I and Delta Region II capsule mutant bacterial strains.
Summary AID: 488970
Assigned AID: 504733, 624060
F. Secondary Assay 4: K5 Secondary Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This assay was performed only on the probe candidate, and determined if compounds considered active in the T7 and orcinol secondary assays were able to also inhibit K5 capsule biogenesis. This assay was performed using a method identical to the T7 assay test with modification of only the test strain and bacteriophage used. In this validation test, we used E. coli strain DS17, a pyelonephritis clinical isolate expressing a K5 capsule. DS17 is highly susceptible to K5 phage mediated lysis. Thus, compounds that were active in the K1F phage assay and promoted lysis in the T7 phage assay were analyzed using this assay. The positive control drug C7 was used in this assay.
Summary AID: 488970
Assigned AID: 624061
2.2 Probe Chemical Characterization
2.2.1. Probe Chemical Structure and Properties




2.2.2. Structure Verification and Purity: 1H NMR, 13C NMR, RP HPLC/UV/HRMS Data
Proton and carbon NMR data for ML317/MLS004256629/SID 126497311/CID 23602075: Detailed analytical methods and associated instrumentation are described in section 2.3, entitled “Probe Preparation”, under general experimental and analytical details. The numerical experimental proton and carbon NMR data are presented below.
Proton NMR Data for ML317/SID 126497311/CID 23602075: 1H NMR (400 MHz, DMSO) δ 13.62 (s, 1H), 8.24 (s, 1H), 7.68 (d, J=6.8 Hz, 2H), 7.64 (m, 1H), 7.31 (t, J=6.8 Hz, 2H), 7.03 (d, J=7.2 Hz, 2H), 4.09 (q, J=5.6 Hz, 2H), 1.36 (t, J=5.6 Hz, 3H) ppm.
Carbon NMR Data for ML317/SID 126497311/CID 23602075: 13C NMR (100 MHz, DMSO) δ 164.6, 160.2, 159.6, 158.2, 158.1, 157.0, 148.4, 142.6, 133.5, 133.3, 127.4, 124.7, 116.7, 115.2, 113.5, 112.7, 112.5, 111.1, 63.3, 14.5 ppm.
RP HPLC/UV/HRMS Data for ML317/SID 126497311/CID 23602075: Detailed analytical methods and associated instrumentation are described in section 2.3, entitled “Probe Preparation”, under general experimental and analytical details. Purity assessment by RP HPLC/UV/HRMS at 214 nm for SID 126497311 (CID 23602075) revealed purity of 97.6% (retention time=2.423 minutes). The experimental RP HPLC/UV/HRMS spectra were measured (data not shown). HRMS (m/z) calcd for C20H15F2NO4S [M+H+] 404.0763. found 404.0770.
2.2.3. Aqueous Solubility:
Solubility was measured in phosphate buffered saline (PBS) at room temperature (23° C.). PBS by definition is 137 mM NaCl, 2.7 mM KCl, 10 mM sodium phosphate dibasic, 2 mM potassium phosphate monobasic and a pH of 7.4 (34). Probe ML317 (SID 103147597/CID18109210) was found to have a solubility measurement of 92.6 μg/mL, or 230 μM, under these conditions. Solubility was also assessed in primary assay media (Luria-Bertani Broth). Probe ML317 was determined to have an assay media solubility of 68 μg/mL or 169 μM. The solubility in PBS buffer is good, and only slightly less than in assay media, and, in any case, the solubility for the probe is well above its activity in the K1 and T7 assays.
2.2.4. Aqueous Stability:
Aqueous stability for the probe was assessed using two solvent systems (100% aqueous PBS, and 50:50 aqueous PBS: acetonitrile). The probe stability was measured in aqueous PBS (no antioxidants or other protectants, DMSO concentration below 0.1%, room temperature) and the results are reported as circles in the graph in FIG. 4. The probe stability was also measured in 50:50 aqueous PBS and acetonitrile and the results are reported as squares in the graph in FIG. 4. Stability data in each case is depicted as the loss of compound with time over 48 hours with a minimum of six time points and providing the percent compound remaining after 48 hours. ML317 was found to be stable in both solvent systems under these experimental conditions over the entire 48 hour study (FIG. 4).
Thiol Stability:
Compounds were dissolved at 10 μM in PBS at pH 7.4 (1% DMSO) and incubated at room temperature with either no thiol source as a negative control, 50 μM glutathione (GSH), or 50 μM dithiothreitol (DTT). The mixtures were sampled every hour for eight hours and analyzed by RP HPLC/UV/HRMS. The analytical RP HPLCUV/HRMS system utilized for the analysis was a Waters Acquity system with UV-detection and mass-detection (Waters LCT Premier). The analytical method conditions included a Waters Acquity HSS T3 C18 column (2.1×50 mm, 1.8 um) and elution with a linear gradient of 1% water to 100% CH3CN at 0.6 mL/min flow rate. Peaks on the 214 nm chromatographs were integrated using the Waters OpenLynx software. Absolute areas under the curve were compared at each time point to determine relative percent compound remaining. The masses of potential adducts were searched for in the final samples to determine if any detectable adduct formed. All samples were prepared in duplicate (FIG. 5). Ethacrynic acid, a known Michael acceptor, was used as a positive control. If solubility of the compound was an issue at 10 μM, PBS was substituted with PBS with 50% acetonitrile (35).
ML317 was found to be completely stable to the presence of five times its concentration of both glutathione and DTT thiol sources across all time points in our analysis (FIG. 5). Statistically, there is no drop in the % remaining concentration of ML317 in the course of these experiments. This data is easily contrasted to the data for the ethacrynic acid control compound, which is shown to react rapidly with five times its concentration of glutathione and even more rapidly with DTT.
2.2.6. Synthesis Route:
The probe compound ML317 and numerous analogues were synthesized using the reaction sequence shown in FIG. 6. Briefly, a series of aryl ketones was converted to (Z)-3-chloro-3-arylacrylonitriles through treatment with POCl3, DMF and hydroxylamine. These nitriles were then converted via Fisselman reaction to tert-butyl 3-amino-5-(aryl)thiophene-2-carboxylates through a reaction with sodium methoxide and tert-butyl 2-mercaptoacetate. Lastly, these amines were coupled with various acid chlorides in the presence of triethylamine in dichloromethane followed by a removal of the tert-butyl group with trifluoroacetic acid in dichloromethane.
2.2.7. Submission of Probe and Five Analogues to the MLSMR
Samples of the probe and five analogues were prepared, analytically characterized, and shipped to the MLSMR. The structures for the five supporting analogues are shown in FIG. 7.







TABLE. 2.2.7.1







Five probe analogues with screening data














K1 phage
Cytotoxicity
Selec-
T7 phage


Entry
PubChemID
IC50 (μM)
IC50 (μM)
tivity 
IC50 (μM)















A
SID 126722926
13.02 ± 4.6 
51.01 ± 2.62
3.91
1.355



CID 53495055







MLS004256633






B
SID 126497314
11.11 ± 3.33
50.48 ± 0.52
4.55
1.235



CID 53470446







MLS004256631






C
SID 134419009
0.84
41.67
49.61
<0.625



CID 56643022







MLS004256634






D1
SID 126497335
>100
72.06
ND
14.12



CID 53470417







MLS004256632






E
SID 126497312
17.03 ± 4.49
49.72 ± 6.49
2.92
3.335



CID53470415







MLS004256630





1Compound selected as negative control






2.3 Probe Preparation
General Experimental and Analytical Details:
All reagents were used as received from commercial suppliers. The 1H and 13C spectra were recorded on a Bruker Avance 400 MHz or 500 MHz spectrometer. Chemical shifts are reported in parts per million and were referenced to residual proton solvent signals. Flash column chromatography separations were performed using the Teledyne Isco CombiFlash RF using RediSep RF silica gel columns TLC was performed on Analtech UNIPLATE silica gel GHLF plates (gypsum inorganic hard layer with fluorescence). TLC plates were developed using iodine vapor. RP HPLC/UV/HRMS analysis was carried out with gradient elution (5% CH3CN to 100% CH3CN) on an Agilent 1200 RRLC with a photodiode array UV detector and an Agilent 6224 TOF mass spectrometer (also used to produce high resolution mass spectra). Purification was carried out by mass directed fractionation with gradient elution (a narrow CH3CN gradient was chosen based on the retention time of the target from LCMS analysis of the crude sample) on an Agilent 1200 instrument with photodiode array detector, an Agilent 6120 quadrupole mass spectrometer, and a HTPAL LEAP autosampler. Fractions were triggered using a MS and UV threshold determined by RP HPLC/UVHRMS analysis of the crude sample. The conditions for RP HPLC analysis included the following: Waters BEH C-18, 1.7 μm, 2.1×50 mm column; 0.6 ml/min flow rate; and pH 9.8 NH4OH aqueous mobile phase. The conditions for purification included: Waters XBridge C18 5 μm, 19×150 mm column; 20 ml/min flowrate pH 9.8 NH4OH aqueous mobile phase.
The probe was prepared using the following protocols:




(Z)-3-Chloro-3-(4-ethoxyphenyl)acrylonitrile: Prepared according to an experimental outlined by Romagnoli et al. (36). To an ice cold solution of dry dimethyl formamide (8.90 g, 122 mmol) was added phosphorus oxychloride (5.57 ml, 60.9 mmol) dropwise while stirring for 15 minutes. To this cold mixture, 1-(4-ethoxyphenyl)ethanone (5.00 g, 30.5 mmol) was added dropwise while maintaining the temperature between 45-55° C. via external heat source for ten minutes. The reaction mixture was then cooled to room temperature and allowed to stir for 30 minutes. Then, a solution of hydroxylamine hydrochloride (8.46 g, 122 mmol) in dry DMF was added slowly (7 mL of 33 mL for 10 g reaction). This mixture was allowed to stir at 80° C. (an ice bath was briefly employed to control a rapid exotherm) for five minutes. Then, the remaining hydroxylamine solution was added so that the reaction mixture heated exothermically to no greater than 150° C. After the completion of addition, the reaction mixture was allowed to cool to RT and stir for an additional 30 minutes. The reaction mixture was cooled to 0° C. Cold water was then added and the reaction mixture was extracted with chloroform. The crude product was purified via normal phase, silica gel chromatography (98:2 ethylacetate/hexane) (59.1%, 6.32 g). 1H NMR (400 MHz, DMSO) δ 7.62 (d, J=9.2, 2H), 6.93 (d, J=9.2 Hz, 2H), 5.89 (s, 1H), 4.09 (q, J=7.2 Hz, 2H), 1.46 (t, J=6.8 Hz, 3H); ppm; 13C NMR (100 MHz, DMSO) δ 162.1, 152.9, 128.7, 126.3, 115.9, 114.7, 93.4, 63.9, 14.7 ppm; IR (ATR) 2983, 2217, 1593, 1506, 1238, 1039 cm−1.




tert-Butyl 3-amino-5-(4-ethoxyphenyl)thiophene-2-carboxylate: Following the protocol outlined by Gokaraju et al. (37), to a solution of tert-butyl 2-mercaptoacetate (1.1 g, 7.42 mmol) in methanol (5 mL) was added a solution of sodium methoxide (0.401 g, 7.42 mmol) in methanol (5 mL). The reaction mixture was then stirred for 30 minutes. A solution of (Z)-3-chloro-3-(4-ethoxyphenyl)acrylonitrile (1.23 g, 5.94 mmol) in DMF was added dropwise for 10 minutes to the reaction mixture and then stirred at 60° C. for an additional two hours. Then, a solution of sodium methoxide (0.802 g, 14.84 mmol) in methanol (10 mL) was added dropwise to the reaction mixture which was then stirred for another two hours at 60° C. Cold water was added to the reaction mixture and the mixture was allowed to stir for 15 minutes. The aqueous solution was extracted three times with chloroform. The combined organic phases were washed with water, brine, dried over sodium sulfate and then concentrated in vacuo. The crude residue was purified with a DCM/MeOH eluent on a normal phase, silica gel column, giving the product (60.5%, 1.67 g). 1H NMR (400 MHz, DMSO) δ 7.51 (d, J=8.8 Hz, 2H), 6.89 (d, J=8.8 Hz, 2H), 6.64 (s, 1H), 5.37 (s, 2H), 4.06 (q, J=6.8 Hz, 2H), 1.57 (s, 9H), 1.41 (t, J=6.8 Hz, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 164.3, 159.6, 148.4, 127.2, 126.2, 114.8, 114.5, 80.6, 63.6, 28.6, 14.8 ppm; IR (ATR) 3459, 3352, 2978, 1664, 1602, 1548, 1460 cm−1; HRMS calcd for C17H21NO3S [M+H+] 320.1242. found 320.1320.




3-(2,6-Difluorobenz amido)-5-(4-ethoxyphenyl)thiophene-2-carboxylic acid (ML317, SID 126497311, CID 23602075): To a solution of tert-butyl 3-amino-5-(4-ethoxyphenyl)thiophene-2-carboxylate (0.1866 g, 0.584 mmol) and triethylamine (0.163 mL, 1.168 mmol) in dichloromethane was added 2,6-difluorobenzoyl chloride (0.103 g, 0.584 mmol) dropwise. The reaction mixture was allowed to stir overnight. Then, 1N HCl was added to the reaction mixture. The organic phase was then washed with brine, concentrated en vacuo. A 1:3 solution of trifluoroacetic acid:dichloromethane was added slowly to the residue. The reaction was allowed to stir for two hours. The reaction was then concentrated and the residue was triturated with diethyl ether, resulting in a white solid (94%, 0.221 g). 1H NMR (400 MHz, DMSO) δ 13.62 (s, 1H), 8.24 (s, 1H), 7.68 (d, T=6.8 Hz, 2H), 7.64 (m, 1H), 7.31 (t, J=6.8 Hz, 2H), 7.03 (d, J=7.2 Hz, 2H), 4.09 (q, J=5.6 Hz, 2H), 1.36 (t, J=5.6 Hz, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 164.6, 160.2, 159.6, 158.2, 158.1, 157.0, 148.4, 142.6, 133.5, 133.3, 127.4, 124.7, 116.7, 115.2, 113.5, 112.7, 112.5, 111.1, 63.3, 14.5 ppm; IR (ATR) 3319, 2942, 2531, 1693, 1651, 1607, 1565, 1449, 1254, 1024 cm−1; HRMS calcd for C20H15F2NO4S [M+H+] 404.0763. found 404.0770.
3 Results
3.1 Summary of Screening Results
Primary assay: An end-point assay to measure the amount of K1 phage-induced bacterial cell lysis was employed to determine the compound effect on capsule biogenesis. K1 bacteriophage specifically binds the bacterial capsule during the initial stages of infection. Bacteria without capsule cannot be infected and lysed by the bacteriophage. The ability of the test compounds to inhibit the K1 capsule formation was measured by an increase in the fluorescence of Alamar Blue, which correlated with the amount of intact bacterial cells compared to control reaction wells Inhibition of phage-induced lysis indicated an active compound in the primary screen. A total of 338,740 compounds were screened at 100 μM in the primary screen Inhibition of phage lysis was calculated relative to the mean of the bacterial (positive) control on each microtiter plate. Primary screen average Z values=0.75; average signal to background (S/B)=11; and average coefficient of variance=4.6%. For calculation of S/B/Z value, and CV, the following formulae (in which SD stands for standard deviation) were used: S/B=mean signal/mean background; Z=1-3SD of sample+3SD of control mean of sample−mean of control; % CV=(SD mean signal/mean signal)×100.
Confirmatory efficacy: The background cutoff (15% inhibition) for the primary screen was calculated using the mean of all compound results plus 3×SD. Compounds that inhibited more than 30% (1,767) were considered for evaluation by confirmatory dose response and cytotoxicity counter screening assays. Only 1,219 compounds were available for confirmatory assays. The confirmatory efficacy assay was performed as described for the primary screen except that each compound was tested at 10 concentration points starting from 300 μM and continuing to lower concentrations by serial 2-fold dilutions to 0.69 μM. Twenty-six compounds were confirmed as effective at inhibiting the formation of capsule at compound concentrations below 50 μM. Confirmatory screen average Z values=0.79; average signal to background (S/B)=32; and average coefficient of variance=6.4%. IC50 values were calculated using a 4 parameter Levenburg-Marquardt algorithm, with the maximum and minimum locked at 0 and 100 respectively.
Cytotoxicity assay: The cytotoxicity assay was performed as described in Section 6: Appendix. Hit cytotoxicity and the 50% toxic concentration (CC50) was determined and compared to the IC50 to calculate the selectivity index. Twenty-nine compounds were tested, and 11 were inactive (CC50>50 μM).
Outcome
3.2 Dose Response Curves for Probe
The primary assay (Summary AID: 488970) and counterscreen methods (AID: 493020); were used to measure both probe efficacy and cytotoxicity. The probe ML317 potency in the primary phase lysis inhibition assay was determined: IC50=4.5±2.4 μM, and the CC50 47.2±7.2 μM. The calculated selectivity was determined as (CC50/IC50)=10.5. The ML317 dose response profiles for efficacy and cytotoxicity curves are graphed below (FIG. 3.2.1).
FIG. 9 and FIG. 10. Efficacy and cytotoxicity analysis of ML317. The graph on the left shows the efficacy of the probe in the primary bacterial phage lysis inhibition assay (n=3). The small gray inset magnifies the corresponding region in the larger graph. The graph on the right shows the probe cytotoxicity after a 72 hr incubation with bladder carcinoma 5637 cells (n=2).
3.3 Scaffold/Moiety Chemical Liabilities
The probe compound and analogues appears to be stable based on our observations from day-to-day handling related to their synthesis, analysis, dissolution-transfer, lyophilization, and storage. The probe compound and analogues do not contain moieties that are known or expected to be reactive. The probe was found to be stable in aqueous solution and in the presence of thiol (please see sections 2.2.4 and 2.2.5).
3.4 SAR Tables
The HTS of 338,740 compounds at 100 μM in the primary screen (AID 488966) resulted in a cluster of 20 thiophene analogues, in which one hit (CID 23602075) was discovered. Structures of six of the 19 inactive analogues as well as the active hit are shown in Table 3.4.1. In the best case, one might discern useful SAR information from the HTS data, however we found these initial data to be of limited value.







TABLE 3.4.1







HTS data for compounds in the thiophene chemotype




























CID



% Inhibition


#
SID
R1
R2
R3
at 100 μM





1
23602075
EtO
2,6-dimethoxyphenyl
CO2H
9.12



49649781






2
 6710528
H
Phenyl
CO2Me
4.18



17514982






3
 3669658
H
p-F-phenyl
CO2Me
2.58



17514946






4
 3268361
H
2,6-dimethoxy
CO2Me
2.52



17514798






5
16012569
H
m-F-phenyl
CO2Me
0.19



49668096






6
 4114774
H
Me
CO2Me
0.68



24816444






7
 2814791
Cl
o-CO2H
CO2Me
−0.17 



26728894









To gain insight on where to focus our SAR optimization efforts, a set of 14 compounds was purchased, which included the hit itself, as well as 13 structurally related analogues. Each compound was screened thoroughly to determine IC50 values in K1 phage, cytotoxicity, and T7 phage assays (Table 3.4.2). The sample for the original compound hit (CID 23602075, SID 103147605) gave IC50 values in the K1 phage, cytotoxicity and T7 phage assays of 4.5±2.4 μM, 47.2±7.2 μM and <0.39 μM, respectively, with a selectivity of 10.49; all values consistent with the probe criteria. Other SAR information was discovered from this set of compounds, in that, converting the carboxylic acid to a methyl ester at the two-position of the thiophene core resulted in a loss of desired activity. This is seen in comparing entry 1 to entry 11, in which our K1 phage IC50 went from 4.5±2.4 μM to >100 μM. Also, para-phenyl substitution was determined to be important since when R1 was substituted with hydrogen instead of an ethoxy group, as in the case of comparing entry 1 to entry 10, K1 phage activity was lost with an accompanied fourfold increase in cytotoxicity. When examining R2, substitutions involving halogenation gave better overall activity. The SAR observation is supported when comparing entries 4 and 5, where K1 phage, cytotoxicity, selectivity and T7 phage activity are all improved by switching a methyl group for a bromine substituent at the five position of the thiophene 2-carboxamide.







TABLE 3.4.2







Purchased Analogue series



















K1 phage  (μM) (n = # replicated)
Cytotoxicity  (μM) (n = # repli pcated)

T7 phage (μM)






















CID





IC50


IC50
Selectivity


IC50


#
SID
R1
R2
R3
n
IC50
STDEV
n
IC50
STDEV
(Cyt./K1)
n
IC50
STDEV
























 1
 23602075
EtO
2,6-difluorophenyl
CO2H
3
4.5
2.4
2
47.2 
7.2
10.49
2
<0.39
ND*



103147605















 2
16393058
H
cyclopentyl
CO2H
3
>100

2
169  

ND
2
56.6 
ND*



121360790















 3
 16393057
H
cyclohexyl
CO2H
3
>100

2
114.6 

ND
2
65.2 
ND*



121360791















 4
 17546665
H
2-(5-Me-thiophene)
CO2H
3
>100

2
63.6 

ND
2
29.7 
ND*



121360792















 5
 17546666
H
2-(5-Br-thiophene)
CO2H
3
50.28
11.49
2
78.91
36.1 
1.57
2
8.9
ND*



121360795















 6
 17546661
H
2-(3-Me-benzofuran)
CO2H
3
>100

2
48.7 

ND
2
33.3 
ND*



121360796















 7
 17547200
H
2-(5-Cl-thiophene)
CO2H
3
>100

2
71.5 

ND
2
15.1 
ND*



121360798















 8
 9945365
H
2-thiophene
CO2H
3
75.39
10.34
2
62.01
38.59
0.82
2
6.9
ND*



121360799















 9
 17548073
H
2-benzofuran
CO2H
3
>100

2
167.1 

ND
2
6.7
ND*



121360800















10
121360801
H
2,6-difluorophenyl
CO2H
3
>100

2
10.4 

ND
2
ND
ND*



 23602069















11
 16012549
EtO
2,6-difluorophenyl
CO2Me
3
>100

2
>300  

ND
2
ND
ND*



121360802















12
 23602077
H
3-Cl-phenyl
CO2H
3
84.5
1.43
2
43.81
12.43
0.52
2
34.4 
ND*



121360803















13
 16012569
H
3-F-phenyl
CO2H
3
>100

2
76.9 

ND
2
26.9 
ND*



121360805















14
 23602082
EtO
3,4-dimethoxyphenyl
CO2H
3
57.94
2.74
2
72.31
14.84
1.25
2
8.0
ND*



121360806





*ND = not determined






Having exhausted the commercial supply of interesting analogues for the chemotype, the team turned to synthesis of analogues in order to expand the SAR. Given that the set of purchased compounds showed that the carboxylic acid moiety was important, we decided not to attempt to tune it further, but chose to focus on varying the 3-carboxamide and 5-aryl substituents of the thiophene core highlighted in red and blue, respectively, in FIG. 11.
Initially, 32 analogues were synthesized in parallel to assess the effects of methoxy, ethoxy, methyl, isopropyl, tert-butyl, trifluoromethyl and trifluoromethoxy aryl substitution, as well as 2,6-difluorophenyl, m-fluorophenyl, 5-bromofuran-2-yl, benzofuran-2-yl and the 5-bromothiophen-2-yl carboxamide substitution, on anti-capsule activity (Table 3.4.3). Upon screening these compounds through the same four assays as used for the purchased analogues, it was immediately noticeable that every analogue displayed statistically significant activity in the T7 phage assay. In fact, only three analogues (entries 13, 24 and 27) did not exhibit T7 phage IC50 values within the probe criteria of <10 μM. Interestingly, these three analogues contained the benzofuran-2-yl, m-fluorophenyl and 5-bromothiophe-2-yl carboxamide moieties; features shared by many of the analogues that performed poorly in the K1 phage assay (entries 2, 8, 11, 13, 14, 18, 19, 22, 24, 26, 27, 29, 31, 32). However, quite notable activity was observed for analogues with the 2,6-difluorophenyl and 5-bromofuran-2-yl carboxamide substituents. Furthermore, the compounds shown in entries 5 (resynthesized hit), 7, 15, 17 and 30 met probe criteria (IC50<10 μM) for both K1 phage and T7 phage anti-capsule activity, while three of these analogues (entries 5, 7 and 17) also met probe criteria for selectivity based on cytotoxicity (selectivity index >10). Lastly, when examining the aryl substitution, there was an activity trend, in which ethoxy>methoxy>methyl≈tert-butyl, which is evident when examining entries 3, 7, 12 and 17. In Table 3.4.3, confirmatory assay efficacy and standard deviations are provided for all compounds with determined IC50 values.







TABLE 3.4.3







First Round of Synthetic Analogues



















K1 phage  (μM) (n = # replicated)
Cytotoxicity (μM) (n = # replicated)

T7 phage (μM)





















CID




IC50


IC50
Selectivity


IC50


#
SID
R1
R2
n
IC50
STDEV
n
IC50
STDEV
(Cyt./K1)
n
IC50
STDEV























 1
 53470430
MeO
2,6-difluorophenyl
3
>100

3
238.8

ND
2
2.645
ND*



126497317














 2
 53470445
MeO
m-F-phenyl
3
>100

3
44.77

ND
2
8.36
ND*



126497316














 3
 53470446
MeO
5-Br-furan-2-yl
3
11.11
3.33
3
50.48
0.52
 4.55
2
1.235
ND*



126497314














 4
 53470443
MeO
Benzofuran-2-yl
3
>100

3
44.77

ND
2
8.36
ND*



126497315














 5
 23602075
EtO
2,6-difluorophenyl
3
1.89
1.56
3
51.6
13.69
27.3 
2
<0.625
ND*



126497311














 6
 23602076
EtO
m-F-phenyl
3
14.68
2.31
3
61.34
5.86
 4.18
2
2.61
ND*



126497308














 7
 23602086
EtO
5-Br-furan-2-yl
3
3.42
1.55
3
68.71
7.42
20.09
2
<0.625
ND*



126497309














 8
 53470427
EtO
Benzofuran-2-yl
3
>100

3
193.17

ND
2
2.75
ND*



126497310














 9
 53470415
EtO
5-Br-thiophen-2-yl
3
17.03
4.49
3
49.72
6.49
 2.92
2
3.335
ND*



126497312














10
 53470422
Me
2,6-difluorophenyl
3
40.26
26.84
3
57.29
2.76
 1.42
2
2.425
ND*



126497338














11
 53470441
Me
m-F-phenyl
3
53.73
13.07
3
43.94
6.41
 0.82
2
7.205
ND*



126497320














12
 53470423
Me
5-Br-furan-2-yl
3
15.7
6.14
3
50.72
4.04
 3.23
2
1.0125
ND*



126497319














13
 53470436
Me
Benzofuran-2-yl
3
>100

3
94.58

ND
2
19.955
ND*



126497337














14
 53470429
Me
5-Br-thiophen-2-yl
3
>50

3
64.04

ND
2
10.73
ND*



126497321














15
 53470439
i-Pr
2,6-difluorophenyl
3
7.09
2.7
3
32.36
2.83
 4.56
2
1.27
ND*



126797324














16
 53470444
i-Pr
m-F-phenyl
3
24.82
9.14
3
37.55
2.31
 1.51
2
2.81
ND*



126497323














17
 53470420
i-Pr
5-Br-furan-2-yl
3
3.075
0.37
3
50.35
8.46
16.37
2
1.245
ND*



126497336














18
 53470434
i-Pr
Benzofuran-2-yl
3
42.88
27.32
3
47.18
6.4
 1.10
2
2.705
ND*



126497322














19
 53470432
i-Pr
5-Br-thiophen-2-yl
3
>100

3
33.06

ND
2
2.745
ND*



126497325














20
 53470433
t-Bu
2,6-difluorophenyl
3
11.53
6.42
3
35.07
7.5
 3.04
2
1.635
ND*



126497329














21
 53470435
t-Bu
m-F-phenyl
3
19.88
14.36
3
21.12
0.76
 1.06
2
2.7
ND*



126497328














22
 53470424
t-Bu
Benzofuran-2-yl
3
>100

3
34.47

ND
2
2.825
ND*



126497327














23
 53470440
F3C
2,6-difluorophenyl
3
23.67
3.84
3
44.77
0.73
 1.89
2
3.8
ND*



126497333














24
 53470418
F3C
m-F-phenyl
3
>100

3
35.13

ND
2
12.79
ND*



126497332














25
 53470416
F3C
5-Br-furan-2-yl
3
12.29
3.61
3
47.52
14.03
 3.87
2
2.59
ND*



126497331














26
 53470417
F3C
Benzofuran-2-yl
3
>100

3
72.06

ND
2
7.175
ND*



126497335














27
 53470428
F3C
5-Br-thiophen-2-yl
3
>50

3
38.52

ND
2
14.12
ND*



126497334














28
 53495055
F3CO
2,6-difluorophenyl
3
13.02
4.6
3
51.01
2.62
 3.92
2
1.355
ND*



126722926














29
 53495056
F3CO
m-F-phenyl
3
>100

3
52.14

ND
2
>5
ND*



126722925














30
 53495057
F3CO
5-Br-furan-2-yl
3
6.39
1.73
3
33.62
2.88
 5.26
2
1.165
ND*



126722927














31
 53495058
F3CO
Benzofuran-2-yl
3
>100

3
40.63

ND
2
3.83
ND*



126722924














32
 53495054
F3CO
5-Br-thiophen-2-yl
3
>100

3
20.45

ND
2
2.695
ND*



126722928









Since, overall, ethoxy aryl substitution gave better activity than methoxy aryl substitution, the team chose to homologate this group further to see if the trend would continue. Trifluoroalkylation at the aryl position was also studied in order to anticipate PK issues that might be associated with hydrocarbon chain elongation. Thirdly, because halogenation of carboxamide substituents provided useful anti-capsule activity, we further halogenated at these sites (Table 3.4.3). In every case, except in comparing entries 15 to 16, adding additional halogen groups resulted in a drastic loss in activity in the K1 phage assay. We also found that hydrocarbon chain elongation resulted in more potent analogues as exemplified by comparing the K1 phage activity of CID 53470446, CID 23602086 and 56643021 (entry 9) that gave IC50 values of 11.11 μM, 3.42 μM and 0.85 μM, respectively, as well as comparing the K1 phage activity of CID 53470430, CID 23602075 and CID 56643007 (entry 7) that gave IC50 values of >100 μM, 1.89 μM and <0.78 μM, respectively. This trend was somewhat mirrored with the trifluoro analogues in that, while examining the 2,6-difluorophenylcarboxamide series, in comparing trifluoromethoxy (CID 53495055), trifluoroethoxy (CID 56643002, entry 4), and trifluoropropoxy (CID 56643020, entry 1), the activity increased in the K1 phage assay as chain length increased with IC50 values of 13.02 μM, 2.86 μM and 0.84 μM, respectively. However, when increasing the chain length one more carbon unit as seen in the trifluorobutoxy analogue, the K1 phage IC50 value increased to 10.32 μM.
This final round of SAR has resulted in the most potent analogue to date, entry 1, Table 3.4.3, exhibiting a K1 phage IC50 of 0.84 μM, a cytotoxicity IC50 of 68.41 μM, a selectivity index of 81.44 and a T7 phage IC50 of <0.156 μM.







TABLE 3.4.3







Second Round of Synthetic Analogues



















K1 phage (μM) (n = # replicated)
Cytotoxicity (μM) (n = # replicated)





















CID




IC50


IC50
Selectivity
T7 phage (μM)




















#
SID
R1
R2
n
IC50
STDEV
n
IC50
STDEV
(Cyt./K1)
n
IC50
STDEV























 1
 56643020
n-trifluoropropoxy
2,6-difluorophenyl
3
 0.84
0.51
3
68.41
 5.49
81.44
2
  <.0156
ND*



134419017














 2
 56643010
n-trifluoropropoxy
2,4,6-trifluorophenyl
3
 3.11
0.86
3
63.63
 4.22
20.46
2
 <0.625
ND*



134419022














 3
 56643022
n-trifluoropropoxy
5-Br-furan-2-yl
3
 0.84
0.66
3
41.67
 1.26
49.61
2
 <0.625
ND*



134419009














 4
 56643002
trifluoroethoxy
2,6-difluorophenyl
3
 2.86
1.25
3
75.18
 9.85
26.29
2
 <0.625
ND*



134419021














 5
 56643012
trifluoroethoxy
2,4,6-trifluorophenyl
3
94.94
7.58
3
161.1 
11.58
1.7
2
2.5-5  
ND*



134419020














 6
 56643003
trifluoroethoxy
5-Br-furan-2-yl
3
 4.90
1.20
3
50.0 
 3.65
10.2 
2
 0.625
ND*



134419010














 7
 56643007
n-butoxy
2,6-difluorophenyl
3
<0.78

3
42.63

>54.65 
2
 <0.625
ND*



134419008














 8
 56643023
n-propoxy
2,4,6-trifluorophenyl
3
 8.06
2.75
3
85.57
 8.12
10.62
2
 <0.625
ND*



134419018














 9
 56643021
n-butoxy
5-Br-furan-2-yl
3
 0.85
1.07
3
43.43
 2.58
51.09
2
 <0.625
ND*



134419012














10
 56643019
n-butoxy
4,5-dibromo-furan-
3
23.26
2.65
3
31.66
 4.97
 1.36
2
1.25-2.5 
ND*



134419014

2-yl












11
 56643016
n-propyl
2,6-difluorophenyl
3
 2.63
1.40
3
54.87
 6.88
20.86
2
 <0.625
ND*



134419019














12
 56643011
n-propyl
2,4,6-trifluorophenyl
3
15.88
2.39
3
69.9 
12.41
4.4
2
2.5-5  
ND*



134419023














13
 56643013
n-propyl
5-Br-furan-2-yl
3
 1.43
0.88
3
46.39
 3.77
32.44
2
 <0.625
ND*



134419007














14
 56643005
n-propyl
4,5-dibromo-furan-
3
 6.78
0.95
3
40.99
 2.53
 6.05
2
<5.0 
ND*



134419011

2-yl












15
 56643024
n-trifluorobutoxy
2,6-difluorophenyl
3
10.32
2.21
3
241.21 
12.68
23.37
2
<2.5 
ND*



134419031














16
 56643015
n-trifluorobutoxy
2,4,6-trifluorophenyl
3
 5.53
5.84
3
54.72
 7.81
9.9
2
<1.25
ND*



134419016














17
 56643008
n-trifluorobutoxy
5-Br-furan-2-yl
3
 1.78
0.50
3
38.69
 1.69
21.74
2
<2.5 
ND*



134419013














18
 56643009
n-trifluorobutoxy
4,5-dibromo-furan-
3
>100  

3
250.98 

ND
2
<2.5 
ND*



134419030

2-yl












19
 56643025
n-Azidoethoxy
2,6-difluorophenyl
3
17.52
3.68
3
273.32 
26.84
15.6 
2
 <0.625
ND*



134419029














20
 56643017
Ethoxy
2-trifluoromethyl-6-
3
52.59
5.75
3
62.03
 7.91
 1.18
2
<5 
ND*



134419004

fluorophenyl












21
 56643006
Ethoxy
2,4,6-trifluorophenyl
3
19.99
2.48
3
76.62
 6.82
 3.83
2
<5 
ND*



134419025





*ND = not determined






Probe Selection:
Several compounds generated during these studies met the criteria established at the outset of the project for a useful probe compound. Early in the project, however, ML317 was found to have good activity across the suite of assays used to define the probe criteria and in a suite of in vitro PK assays. In addition, in PubChem, the probe ML317 is reported to have shown activity in only 16 of 341 bioassays in which it was tested (4.7% hit rate), which suggests that ML317 is not a promiscuous hitter. In as much, this compound was used for advanced, preliminary studies such as those described in sections 3.5, 4.2, and 4.3. In any case, as was mentioned previously, quite a number of useful compounds were identified across the ML317 chemotype, and, depending on the specific intended use for these compounds, many of them could have been chosen as probes (for example, CID56643007, entry 7, Table 3.4.3; CID56643020, entry 1, Table 3.4.3; CID56643021, entry 9, Table 3.4.3 and CID56643022, entry 3, Table 3.4.3).
3.5 Cellular Activity
ML317 was identified using a phenotypic bacterial cell-based assay that determined the amount of bacterial capsule formation in the presence of the probe compound. No biochemical assays were used for determination of compound biological activity. Additional cell-based assays were performed to determine probe specificity. Also, a counterassay was performed to determine eukaryotic cytoxicity using human bladder cell carcinoma 5637 cells, which are considered the physiologically-relevant target cell type. The compound was shown to have no effect on bacterial cell viability in the highest tested concentration (100 μM), and the cytotoxic concentration was 47.2±7.2 μM, which determined a calculated selective index of 10.5. Although the primary and secondary assays were performed using bacterial cultures, it is recognized that probe will be used in in vitro eukaryotic and in vivo assay systems. Because of this, each synthesized probe and analogs were routinely tested using the cytotoxicity counterassay.
3.6 Profiling Assays
In Vitro Pharmacokinetics Profiling:
The in vitro pharmacokinetic (PK) properties of the probe (ML317) were profiled using a standard panel of assays (Table 3.6.2) across which the probe displayed encouraging results.







TABLE 3.6.2







Summary of in vitro ADME properties of ML317
















Plasma Protein
Plasma
Hepatic





PAMPA
Binding
Stabilityd
Microsome
Hepatic


Aqueous
Assay Media
Pec
(% Bound)
Human
Stabilitye
Toxicityf














Solubilitya
Solubilityb
(×10−6 cm/s
Human
Mouse
Mouse/1:1
Human/
LC50


(μg/mL, μM)
(μg/mL, μM)
@ Donor pH)
1 μM/10 μM
1 μM/10 μM
Plasma:PBS
Mouse
(μM)





93/229
68/169
14 @ 5.0
99.68/99.85
98.97/99.31
95.3/78.4
89.6/74.3
26




209 @ 6.2 









52 @ 7.4





ain 1x PBS, pH 7.4


bin Luria-Bertani broth (10 g tryptone, 5 g yeast extract, 10 g NaCl)


cin aqueous buffer (pION),; Donor compartment pH 5.0/6.2/7.4; Acceptor compartment pH 7.4 @ RT


d% remaining at 3 hr @ 37° C.


e% remaining at 1 hr @ 37° C.


ftowards Fa2N-4 immortalized human hepatocytes






Broad-spectrum Target Profiling:
The probe compound ML317 was submitted to Ricerca for LeadProfiling to assess off-target pharmacology. The probe was tested in duplicate at 10 μM concentration and no significant activity was noted across the panel of 67 targets (i.e., <50% inhibition, see Appendix 2 for the complete list of results). In addition, in PubChem, the probe ML317 is reported to have shown activity in only 16 of 341 (4.7%) bioassays in which it was tested. These results suggest that ML317 is not a promiscuous compound with respect to off-target effects.
4 Discussion
4.1 Comparison to Existing Art and how the New Probe is an Improvement
Traditional anti-infectives for the treatment of UTI are almost exclusively directed toward inhibiting central metabolic and structural targets such as folate metabolism, protein synthesis, DNA replication machinery, and cell wall assembly. Traditional targets of inhibition are attractive because of the potential broad spectrum of inhibition of a variety of organisms. However, the lack of specificity then also means that microbes not involved in an infectious process and not intended as targets of the therapeutic are indiscriminately targeted. The major consequences are two-fold: 1) Normal flora are eliminated, resulting in side effects such as antibiotic-associated diarrhea and the emergence of pathogens such as Clostridium difficile, and 2) stress within microbial reservoirs such as the enteric tract drives the acquisition and emergence of antibiotic resistance. Furthermore, more traditional anti-infectives are not disease specific, and thus the multiplicity of their use for a variety of infection prevention and treatment increases the amount of human and agricultural exposure to these agents, further driving antibiotic resistance.
Targeting factors required by microbial pathogens almost exclusively during infection, so called anti-virulence therapeutics, is predicted to dramatically reduce chemical stress on commensal microbes and thus lessen the emergence of resistance. Furthermore, many infections may be cleared by inhibiting microbial factors that subvert the host immune response, thus allowing natural clearance of the infection and possibly enhancing immune memory of the infectious agent to allow the immune system to better recognize and clear subsequent infections. Since the vast majority of UTI occur in the community in other healthy individuals with competent immune systems, this strategy for novel anti-virulence agents is rationale and practical.
The probe described herein is entirely novel with the only precedent being the structurally dissimilar molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid that we previously described in proof-of-concept studies (33). The probe described herein is uniquely poised for development as an infection-specific prevention and treatment therapeutic that enhances natural immune clearance of an infection, namely UTI. The highly soluble probe abrogates capsule development in several K type UPEC as demonstrated through capsule-specific phage assays and orcinol biochemical tests. However, the probe has no effect on in vitro growth and viability of UPEC in the absence of immune factors. Unlike with many traditional antibiotics, exposure of UPEC to a range of concentrations of the probe has not resulted in the emergence of spontaneous resistance in the laboratory, consistent with the concept that this probe does not induce stress and adaptive changes that confer resistance. Furthermore, this probe would be expected to act upon traditional antibiotic resistant strains of E. coli. 
As previously outlined, 2-(4-phenylphenyl)-benzo[g]quinoline-4-carboxylic acid C7, was used as the prototype small-molecule inhibitor of capsule biogenesis and serves as the only prior art for this probe development project. The probe discovered during this MLPCN project demonstrates improved potency in the K1 phage assay, a better selectivity index, similar performance in the orcinol screen, and greater than an order-of-magnitude lower IC50 value in the T7 phage assay (FIG. 12). Furthermore, we have demonstrated the synthetic tractability for the ML317 chemotype, and prepared an array of highly active analogues, whereas C7 does not share either of positive these attributes. We feel these factors to be of utmost importance, since these compounds are believed to have a unified mode of action. To further demonstrate the usefulness of ML317 as a probe, we have shown ML317 to have good in vitro pharmacokinetic properties. Aqueous stability in 1×PBS at pH 7.4, aqueous stability in LB, both human and mouse hepatic microsomal stability, PAMPA permeability and both human and mouse stability were all found to be good. In contrast, while C7 has not been screened in such in vitro PK assays, one might predict poor results. For example, one would not imagine a compound such as C7 to have good solubility characteristics. Lastly, the many aryl rings of the C7 structure pose liabilities to oxidative metabolism that might render this compound less attractive compared to ML317.
Mechanism of Action Studies
Studies to date indicate that UPEC treatment with the probe results in significantly reduced transcript for the capsule genes from each of the two major promoters. These data suggest that the ultimate mechanism through which capsule expression is inhibited is by reduction of transcription. Genetic studies of the currently known regulators of both capsule promoters have not indicated their role in this process, suggesting an alternative regulatory system is responsible.
Moving forward, genetic and biochemical approaches are being employed to identify the mechanism of action. Currently, overexpression of a whole genome open reading frame library of E. coli is being used to identify gene products that enhance or reduce susceptibility to the probe. The screen is expected to select transporters of the probe and a regulatory target that interacts with the probe. The target of the probe may be within a signal transduction pathway to capsule regulation but distinct from the actual transcription factor affecting capsule expression. Cellular localization of probe-interacting factors and biochemical studies of probe-target interactions will be explored.




Through the SAR around DU011, SID134419029 (shown), an azide derivative of ML317, has been synthesized that is amenable to copper-free click chemistry to permit straightforward additions of R groups including biotin and fluorophore labels. Preliminary studies indicate that this DU011 analogue retains substantial capsule inhibitor activity with an approximate IC50 of 17 μM. Using a fluorophore labeled derivative, the localization of the compound (outer membrane, periplasm, inner membrane, or cytoplasm) will be determined by microscopy. A biotinylated derivative will be employed for affinity isolation of the target using bacterial fractions to which the probe localizes. Mass spectrometry will be used to identify the target. Biochemical and genetic studies will be used to elucidate the interaction between the probe and putative target.
Recent studies have also employed chemical mutagenesis to derive strains resistant to the action of the probe. Whole genome sequencing using Illumina Hiseq technology has been completed on five independent isolates. An analysis of polymorphisms shared among independent resistant bacterial clones will be used to localize putative factors that interact with the probes. These may be transporters or the actual target of the probe. The genes from the mutant and wild type strains will be cloned and expressed in the isogenic bacterial backgrounds to ascertain their roles in sensitivity to the probe. The biochemical affinity tools described earlier in this section may then be used to examine direct interactions of the probe with these resistance-associated factors.
4.3 Planned Future Studies
The probe will be advanced through medicinal chemistry to improve in vitro pharmacokinetics and biological activity. Subsequently, in vivo pharmacokinetic measurements will be collected in a murine preclinical murine model with additional optimization of the probe for bioavailability and renal excretion. After completion of these studies and refinements to the probe, the refined probe will be employed in prophylaxis and treatment trials using preclinical murine infection models of E. coli urinary tract infection and bloodstream infection.
References Section 1
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Appendix Section 1
Appendix
6.1 Detailed Assay Descriptions
6.1.a Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: The primary screening was conducted to screen the MLSMR 300K compound library for selection of 1,767 hit compounds.
Summary AID: 488966
Assigned AID: 488970
Assay Description: Screening for Inhibitors of Bacterial Capsule Biogenesis.
Primary assay: The primary assay was conducted in the 1,536 well plate format. Bacterial cultures of E. coli K1 strain UTI89 (cystitis isolate) and isogenic capsule mutant strains (as controls for phage infection) were grown and prepared at the screening center immediately prior to use. Overnight starting cultures of UTI89 were grown at 37° C., and inoculated into 1 liter of LB (starting OD600 ̃0.03), which was sufficient for screening 40 plates (including  ̃10% waste) and  ̃40,000 compounds as single points.
Control wells contained UTI89 (wt K1) with 0.5% DMSO as a simulated positive control; UTI89 with 0.5% DMSO and tetracycline for a negative growth control; and media plus vehicle control. 50 mL of LB Broth was inoculated with stock 150 μL E. coli UT189 and grown overnight at 37° C. The next day, cultures were diluted 1:75 in 1 L of LB Broth containing 0.5% DMSO. 3 μL of this culture was added to each plate well, and plates were incubated, inverted, at 37° C. for 2 hr. The K1F bacteriophage stock was diluted 1:8 in LB Broth containing 0.5% DMSO, and 1.5 μL of diluted phage (or media only) was added to the pre-plated test compound wells and appropriate control wells. The plates were centrifuged briefly, and then were incubated, inverted, at 37° C. for an additional 2 hr. Afterward, Alamar Blue reagent (Invitrogen, #DAL1100) was diluted 1:2 with LB broth and 1 μL was added to each plate well. The plates were again centrifuged briefly, and then were further incubated, inverted, at 37° C. for 30 min.
Single Dose Compound Preparation: For single dose screening, compounds or carrier control (DMSO) were diluted to a final well concentration of 1:200 in assay media. Compounds (45 nL in 100% DMSO) were dispensed to assay plates using an Echo non-contact dispenser. Compounds from the libraries were added to the plates at a final concentration of 100 μM, before the addition of bacteria or phage. Each compound was tested as a single point, and  ̃1200 compounds were tested per plate. The entire primary screening campaign was divided into eight batches, each screened in this manner.
Control Drug: The positive control drug C7 in 1% DMSO (2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid) that was previously identified in a pilot screen was not used in the primary screen due to aqueous insolubility. Tetracycline (50 μM) was used as a negative growth control drug.
Endpoint Read: The plates were read at ambient temperature from the top for fluorescence intensity in an Envision plate reader (Perkin Elmer) by excitation at 560 nm and emission at 590 nm, and the degree of phage-mediated lysis was determined based on the metabolic processing of Alamar Blue by live bacterial cells. A positive hit was defined by the compound producing greater than a 50% inhibition of phage-induced lysis.
Dose Response Compound Preparation:
Concentration dependent confirmatory and cytotoxicity assays. Dose response testing (dose range=300-0.58 μM) was used to confirm and characterize the primary screen hits, which was necessary to determine the number of compounds advanced to secondary screens.
Efficacy: Compounds were plated in 1536-well microplates, and the dose response efficacy assay was performed as described for the primary screen, with the exception that each compound was tested in duplicate at 10 concentration points starting from 300 μM and continuing to lower concentrations by 2-fold serial dilutions. The strain UTI89 delta-kpsM, a K1 capsule export mutant, was evaluated with the wt strain as a phage insensitive control (mimicking 100% capsule inhibition).
6.1.b Counterscreen: Cytotoxicity screening for potential Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This cell-based assay measures the cytotoxicity of compounds in bladder carcinoma 5637 cells using luminescent cell viability assay readout.
Summary AID: 488970
Assigned AID: 493020, 504769, 504831, 588399
Assay Description: Cytotoxicity: Dose response testing (dose range=300-0.58 μM) established the hit cytotoxicity data. Compounds were plated in 384-well microplates in a stacked dose response format using the same doses used in the efficacy dose response. Bladder carcinoma 5637 cells were added to the compounds, and 72 hr later cell viability was measured using CellTiter Glo (38). Hit cytotoxicity and the 50% toxic concentration (TC50) was determined and compared to the IC50 to calculate the therapeutic index. Test compounds are serially diluted in a plate to plate matrix or stacked plate matrix. All 320 compounds in a source plate are diluted together resulting in a 10 point dose response dilution series. It is visualized as a serial dilution series proceeding vertically through a stack of plates with the high dose plate on top and the low dose plate on the bottom.
Control Drug: Hyamine was used as a positive cytotoxic control. All wells contained 0.5% DMSO.
Preparation of Bladder carcinoma 5637 cells: Cells are harvested and resuspended to 80,000 cells per ml in Complete DMEM/F12®.
Endpoint Read: Following the three day incubation period, the assay plates were equilibrated to room temperature for 30 min and an equal volume (30 μL) of Cell Titer-Glo® reagent (Promega Inc.) is added to each well using a WellMateTM (Matrix, Hudson, N.H.) and plates are incubated for an additional 10 min at room temperature. At the end of the incubation, luminescence is measured using a Perkin Elmer EnvisionTM multi-label reader (PerkinElmer, Wellesley, Mass.) with an integration time of 0.1 s.
6.1.c Secondary Assay: Screening for Inhibitors of Bacterial Capsule Biogenesis E. coli Strain UT189
Purpose: This confirmatory cell-based assay provides an alternative measurement of inhibitory activity on phage-induced lysis. It measures reduction in bacterial capsule formation using an absorbance readout at A600 instead of the alamar blue reagent.
Summary AID: 488970
Assigned AID: 504358, 504543, 504675, 504768, 588321, 588386, 588395
Assay Set-up: This secondary assay was conducted in the 96 well plate format. Bacterial cultures of E. coli K1 strain UTI89 (cystitis isolate) and isogenic capsule mutant strains (as controls for phage infection) were grown and prepared at the screening center immediately prior to use. Overnight starting cultures of UTI89 were grown at 37° C., and diluted 1:100 into LB. Compounds were added to plates in a concentration dependent manner in the range of 100-0.39 μM, followed by addition of 100 μL of bacterial culture. Each concentration was tested in quadruplicate. 1% DMSO (final well concentration) was included. The plates were tape sealed and shaken vigorously for 1.5 hr. An initial OD600 reading at the time of infection was measured to identify compounds that cause growth retardation or bacterial killing in the absence of phage. Next, K1F phage (5 μL) was added to all of the test wells. The plates were resealed and shaken vigorously at 37° C., and measurements of OD600 for phage-mediated lysis were taken after 3 hr.
Endpoint Read: The plates were read at ambient temperature from the bottom for absorbance at A600 in an Envision plate reader (Perkin Elmer) and the degree of phage-mediated lysis was determined based on the absorbance.
6.1.d Secondary Assay: Screening for Inhibitors of Bacterial Capsule Biogenesis—T7 Lysis Inhibition
Purpose: This secondary assay measures the compound mechanistic specificity for inhibition of bacterial capsule formation using a different bacterial phage (T7). In this assay, an increase in phage-induced lysis correlates to a decrease in capsule formation.
Summary AID: 488970 Assigned AID: 504349, 504538, 504676, 504767, 588322
Assay Description: T7 phage-mediated lysis assay: This assay determined if the mechanism of action of the compound is inhibition of phage infectivity or replication. The T7 phage has a nearly identical genome to K1F, without encoding an endosialidase. Its cycle of replication is similar to that of K1F as well. However, T7 entry into E. coli is inhibited by K capsules. This secondary assay was conducted in the 96 well plate format. Bacterial cultures of E. coli K1 strain UTI89 (cystitis isolate) and isogenic capsule mutant strains (as controls for phage infection) were grown and prepared immediately prior to use. Overnight starting cultures of UTI89 were grown at 37° C., and diluted 1:100 into LB. Compounds were added in quadruplicate to plates in a concentration dependent manner in the range of 100-0.39 μM, followed by addition of 100 μL of bacterial culture. 1% DMSO (final well concentration) was included. The plates were tape sealed and shaken vigorously for 1.5 hr. An initial OD600 reading was measured to identify compounds that cause growth retardation or bacterial killing in the absence of phage. Next, T7 phage (5 μL) was added to all of the test wells. The plates were resealed and shaken vigorously at 37° C., and measurements of OD600 for phage-mediated lysis were taken after 3 hr. True inhibitors of capsule yielded bacteria that were susceptible to T7 phage and lysed within 2 hr of the addition of phage. However, compounds inhibiting phage replication did not promote bacterial lysis. The positive control drug C7 (100 μM final well concentration) was used in this screen.
Endpoint Read: The plates were read at ambient temperature from the bottom for absorbance at A600 in a BioTek Quantplate reader and the degree of phage-mediated lysis was determined based on the absorbance.
6.1.e Secondary Assay: Orcinol Secondary Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This assay was performed only on the probe candidate. This is an end-point assay to measure the amount of K1 bacterial cell capsule formation in the presence of a test compound concentration range. The ability of the test compounds to inhibit the K1 capsule formation was measured by a reduction of absorbance from the complex formed by orcinol and the capsule polysaccharide. The biochemical determination of cell-surface associated capsule was performed using UTI89 or the delta Region I and Region II capsule mutant bacterial strains.
Summary AID: 488970
Assigned AID: 504733, 624060
Assay Description: The biochemical measurement of cell-surface associated capsule was performed. UTI89 or capsule mutants were grown in culture tubes with and without the test compound (50 μM). The cultures were centrifuged, and the cell pellets were washed in PBS and resuspended in Tris buffer, pH5. We have found that low pH releases surface polysaccharide without lysing the bacteria. Released polysaccharide was harvested by separation from whole bacteria by centrifugation followed by deproteination with phenol/chloroform and precipitation with ethanol. The precipitated material was subjected to acid hydrolysis (pH 2 at 80° C. for 1 hr) and incubated with orcinol, which reacts with periodic intermediates to produce a violet color quantified at OD 570 (3) Inhibitors reducing or abrogating surface encapsulation yielded low orcinol levels similar to the capsule export and synthesis mutants (Region I and II). The positive control drug C7 (100 μM final well concentration) was used in this screen.
Endpoint Read: The samples were read at ambient temperature from the bottom for absorbance at A570 in a BioTek Quantplate reader and the degree of orcinol-reactive material was determined based on the absorbance compared to a wild-type encapsulated strain (UTI89) and a standard curve using purified sialic acid.
6.1.f Secondary Assay: K5 Secondary Screening for Inhibitors of Bacterial Capsule Biogenesis.
Purpose: This assay was performed only on the probe, and determined if compounds considered active in the T7 and orcinol secondary assays were able to inhibit also inhibit K5 capsule biogenesis.
Summary AID: 488970
Assigned AID: 624061
Assay Description: This assay was performed only on the probe candidate, and determined if compounds considered active in the T7 and orcinol secondary assays were able to also inhibit K5 capsule biogenesis. This assay was performed in a method identical to the T7 assay test, but a different bacterial test strain and bacteriophage are used. In this validation test, we used E. coli strain DS17, a pyelonephritis clinical isolate expressing a K5 capsule. DS17 is highly susceptible to K5 phage-mediated lysis. Thus, compounds that were active in the K1F phage assay but did not inhibit phage in the T7 phage assay were analyzed using this assay. This secondary assay was conducted in the 96 well plate format. Bacterial cultures of E. coli strain DS 17 were grown and prepared immediately prior to use. Overnight starting cultures of DS17 were grown at 37° C. and diluted 1:100 in LB. Compounds were added to plates in quadruplicate at 50 and 100 μM, followed by addition of 100 μL of bacterial culture. 1% DMSO (final well concentration) was included. The plates were tape sealed and shaken vigorously for 1.5 hr. An initial OD600 reading was measured to identify compounds that cause growth retardation or bacterial killing in the absence of phage. Next, K5 bacteriophage (5 μL) was added to all of the test wells. The plates were resealed and shaken vigorously at 37° C., and measurements of OD600 for phage-mediated lysis were taken after 3 hr. True inhibitors of capsule yielded bacteria that were not susceptible to K5 bacteriophage and did not show lysis within 2 hr of the addition of phage. The positive control drug C7 (100 μM final well concentration) was used in this screen.
Endpoint Read: The plates were read at ambient temperature from the bottom for absorbance at A600 in a BioTek Quantplate reader and the degree of inhibition of phage-mediated lysis was determined based on the absorbance.
Analytical Characterization Data for the Five Supporting Analogues




(Z)-3-Chloro-3-(4-ethoxyphenyl)acrylonitrile: 1H NMR (400 MHz, DMSO) δ 7.62 (d, J=9.2, 2H), 6.93 (d, J=9.2 Hz, 2H), 5.89 (s, 1H), 4.09 (q, J=7.2 Hz, 2H), 1.46 (t, J=6.8 Hz, 3H); ppm; 13C NMR (100 MHz, DMSO) δ 162.1, 152.9, 128.7, 126.3, 115.9, 114.7, 93.4, 63.9, 14.7 ppm; IR (ATR) 2983, 2217, 1593, 1506, 1238, 1039 cm−1.




(Z)-3-Chloro-3-(4-(trifluoromethoxy)phenyl)acrylonitrile: 1H NMR (400 MHz, DMSO) δ 7.72 (d, J=9.2 Hz, 2H), 7.28 (dd, J=0.8, 8.0 Hz, 2H), 6.03 (s, 1H) ppm; 13C NMR (100 MHz, DMSO) δ ppm; IR (ATR) 2979, 2223, 1603, 1506, 1414, 1250, 1160 cm−1.




(Z)-3-Chloro-3-(4-methoxyphenyl)acrylonitrile: 1H NMR (400 MHz, DMSO) δ 7.67 (d, J=9.2 Hz, 2H), 6.97 (d, J=8.8 Hz, 2H), 5.93 (s, 1H), 3.89 (s, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 164.1, 153.3, 145.9, 136.9, 130.6, 125.9, 125.9, 116.8, 81.2, 28.5 ppm; IR (ATR) 3051, 2562, 2211, 1594, 1504 cm−1.




(Z)-3-Chloro-3-(4-(trifluoromethyl)phenyl)acrylonitrile: 1H NMR (400 MHz, DMSO) δ 7.8 (d, J=8.0 Hz, 2H), 7.71 (d, J=8.4 Hz, 2H), 6.12 (s, 1H) ppm; 13C NMR (100 MHz, DMSO) δ 151.6, 137.5, 128.8, 127.4, 126.1, 125.3, 124.7, 114.8, 98.53 ppm; IR (ATR) 2978, 2224, 1604, 1410, 1322, 1169, 1118, 1068 cm−1.




tert-Butyl 3-amino-5-(4-(trifluoromethyl)phenyl)thiophene-2-carboxylate: 1H NMR (400 MHz, DMSO) δ 7.69 (d, J=8.4 Hz, 2H), 7.64 (d, J=8.4 Hz, 2H), 6.82 (s, 1H), 5.41 (s, 2H), 1.58 (s, 9H) ppm; 13C NMR (100 MHz, DMSO) δ 164.1, 153.3, 145.9, 136.9, 130.6, 130.3, 126.0, 125.9, 116.8, 81.2, 28.5 ppm; IR (ATR) 3350, 2981, 1659, 1604, 1320, 1169, 1107 cm−1; HRMS calcd for C16H16F3NO2S [M+H+] 342.0853. found 342.0755.




tert-Butyl 3-amino-5-(4-(trifluoromethoxy) phenyl)thiophene-2-carboxylate: 1H NMR (400 MHz, DMSO) δ 7.61 (d, J=8.8 Hz, 2H), 7.23 (d, J=8.8 Hz, 2H), 6.73 (s, 1H), 5.39 (s, 2H), 1.58 (s, 9H) ppm; 13C NMR (100 MHz, DMSO) δ 164.1, 153.4, 149.4, 146.3, 132.4, 127.3, 121.7, 119.1, 116.2, 81.0, 28.5, 27.9 ppm; IR (ATR) 3489, 3351, 2981, 1658, 1603, 1549, 1281, 1124 cm−1; HRMS calcd for C16H6F3NO3S [M+H+] 359.0803. found 360.0884.




tert-Butyl 3-amino-5-(4-(trifluoromethoxy) phenyl)thiophene-2-carboxylate: 1H NMR (400 MHz, DMSO) δ 7.25 (d, J=8.8 Hz, 2H), 6.90 (d, J=8.8 Hz, 2H), 6.65 (s, 1H), 5.30 (s, 1H), 4.23 (t, J=8.0 Hz, 2H), 2.64 (m, 2H), 1.65 (s, 9H) ppm; 13C NMR (100 MHz, DMSO) δ 164.3, 158.6, 153.6, 147.9, 127.3, 127.2, 127.1, 124.5, 114.9, 114.8, 80.7, 61.1, 34.2, 28.5 ppm; IR (ATR) 3394, 2986, 1671, 1598, 1241, 1129, 1067, 827 cm−1; HRMS calcd for C18H20F3NO3S [M+H+] 387.1116. found 387.1132.




3-(2,6-Difluoro benzamido)-5-(4-(trifluoro methoxy) phenyl)thiophene-2-carboxylic acid (CID-53495055, SID-126722926): 1H NMR (400 MHz, DMSO) δ 13.72 (s, 1H), 10.85 (s, 1H), 8.37 (s, 1H), 7.89 (d, J=7.2 Hz, 2H), 7.67 (m, 1H), 7.47 (d, J=6.4 Hz, 2H), 7.30 (t, J=6.8 Hz, 2H) ppm; 13C NMR (100 MHz, DMSO) δ 164.4, 160.2, 158.2, 157.1, 148.8, 146.1, 142.3, 133.5, 133.3, 131.5, 1127.9, 121.8, 118.9, 113.4, 112.6, 112.4 ppm; IR (ATR) 2908, 1668, 1572, 1259, 1212, 1168, 1004 cm−1; HRMS calcd for C19H10F5NO4S [M+H+] 444.0323. found 444.0312.




3-(Benzofuran-2-carboxamido)-5-(4-(trifluoro methyl) phenyl)thiophene-2-carboxylic acid (CID-53470417, SID-126497335): 1H NMR (400 MHz, DMSO) δ 13.91 (s, 1H), 11.41 (s, 1H), 8.54 (s, 1H), 7.98 (d, J=6.4 Hz, 1H), 7.84-7.80 (m, 4H), 7.73 (d, J=6.8 Hz, 1H), 7.57 (t, J=6.4 Hz, 1H), 7.38 (t, J=6.0 Hz, 1H) ppm; 13C NMR (100 MHz, DMSO) δ 164.8, 155.0, 154.5, 147.5, 145.7, 142.9, 136.1, 129.3, 127.9, 127.2, 126.6, 124.2, 123.2, 119.1, 112.8, 111.9 ppm; IR (ATR) 1678, 1589, 1452, 1246, 1114 cm−1; HRMS calcd for C16H16F3NO3S [M+H+] 430.0366. found 430.0375.




3-(5-Bromofuran-2-carboxamido)-5-(4-methoxy phenyl)thiophene-2-carboxylic acid (CID-53470446, SID-126497314): 1H NMR (400 MHz, DMSO) δ 13.63 (s, 1H), 11.13 (s, 1H), 8.21 (s, 1H), 7.66 (d, J=7.2 Hz, 2H), 7.35 (d, J=2.8 Hz, 1H), 7.03 (d, J=6.8 Hz, 2H), 6.91 (d, J=2.8 Hz, 1H), 3.80 (s, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 16531, 160.3, 153.2, 148.4, 148.3, 143.3, 127.3, 126.1, 124.9, 118.5, 116.2, 115.2, 114.7, 109.7, 55.3 ppm; IR (ATR) 2941, 2834, 2562, 1674, 1648, 1591, 1017 cm−1; HRMS calcd for C17H12BrNO5S [M+H+] 421.9527. found 421.9534.




3-(5-Bromothiophene-2-carboxamido)-5-(4-ethoxy phenyl)thiophene-2-carboxylic acid (CID-53470415, SID-126497312): 1H NMR (400 MHz, DMSO) δ 13.64 (s, 1H), 11.07 (s, 1H), 8.13 (s, 1H), 7.65 (d, J=7.2 Hz, 2H), 7.56 (d, J=3.2 Hz, 1H), 7.42 (d, J=3.2 Hz, 1H), 7.01 (d, J=6.8 Hz, 2H), 4.09 (q, J=5.6 Hz, 2H), 1.35 (d, J=5.6 Hz, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 165.2, 159.6, 157.1, 148.3, 143.4, 139.9, 132.2, 129.9, 127.2, 124.7, 118.9, 116.4, 115.1, 110.1, 63.3, 14.5 ppm; IR (ATR) 3351, 1648, 1590, 1415, 1259, 1184 cm−1; HRMS calcd for C18H14BrNO4S2 [M+H+] 451.9455. found 451.9472.




3-(5-Bromofuran-2-carboxamido)-5-(4-ethoxy phenyl)thiophene-2-carboxylic acid: 1H NMR (400 MHz, DMSO) δ 13.71 (s, 1H), 11.15 (s, 1H), 8.22 (s, 1H), 7.67 (d, J=6.8 Hz, 2H), 7.37 (d, J=2.8 Hz, 1H), 7.03 (s, J=7.2 Hz, 2H), 6.93 (d, J=2.8 Hz, 1H), 4.11 (q, J=5.6 Hz, 2H), 1.36 (t, J=5.6 Hz, 3H) ppm; 13C NMR (100 MHz, DMSO) δ 165.1, 159.6, 153.3, 148.4, 143.3, 127.3, 126.11, 124.8, 118.6, 116.2, 115.2, 109.7, 63.3, 14.5 ppm; IR (ATR) 3736, 2979, 2300, 1974, 1677, 1636, 1591, 1523, 1178 cm−1; HRMS calcd for C18H14BrNO5S [M+H+] 435.9684. found 435.9685.
Appendix 2: Ricerca LeadProfiling Report for ML317
Study Objective:
To evaluate, in radioligand binding assays, the activity of probe compound ML317 across a panel of 68 receptors.
Methods:
Methods employed in this study have been adapted from the scientific literature to maximize reliability and reproducibility. Reference standards were run as an integral part of each assay to ensure the validity of the results obtained.
Where presented, IC50 values were determined by a non-linear, least squares regression analysis using MathIQTM (ID Business Solutions Ltd., UK). Where inhibition constant (Ki) are presented, the Ki values were calculated using the equation of Cheng and Prusoff (Cheng. Y., Prusoff, W. H., Biochem. Pharmacol. 22:3099-3108, 1973) using the observed IC50 of the tested compound, the concentration of radioligand employed in the assay, and the historical values of the KD of the ligand (obtained experimentally at Ricerca Biosciences, LC). Where presented, the Hill coefficient (nH), defining the slope of the competitive binding curve, was calculated using MathIQTM. Hill coefficients significantly different than 1.0, may suggest that the binding displacement does not follow the laws of mass action with a single binding site. Where IC50, and/or nH data are presented without Standard Error of the Mean (SEM), data are insufficient to be quantitative, and the values presented (Ki, IC50, nH) should be interpreted with caution.
Detailed methods for any of the listed assays can be found by searching by catalog number for the assay (listed) at:
https ://pharmacology.ricerca.com/Catalog/AssayCatalog/AssayCatalog.aspx



















Cat #
Assay Name
Batch*
Spec.
Rep.
Conc.
% Inh.
IC5







Compound: KUC107784N-02, PT #: 1160398

















200510
Adenosine A1
314096
hum
2
10 μM
28



200610
Adenosine A2A
314151
hum
2
10 μM
19



200720
Adenosine A3
314213
hum
2
10 μM
29



203100
Adrenergic α1A
314153
rat
2
10 μM
16



203200
Adrenergic α1B
314154
rat
2
10 μM
0



203400
Adrenergic α1D
314156
hum
2
10 μM
2



203620
Adrenergic α2A
314100
hum
2
10 μM
−1



204010
Adrenergic β1
314161
hum
2
10 μM
2



204110
Adrenergic β2
314163
hum
2
10 μM
3



285010
Androgen (Testosterone) AR
314097
rat
2
10 μM
−5



212510
Bradykinin B1
314221
hum
2
10 μM
3



212620
Bradykinin B2
314223
hum
2
10 μM
6



214510
Calcium Channel L-Type, Benzothiazepine
314226
rat
2
10 μM
2



214600
Calcium Channel L-Type, Dihydropyridine
314169
rat
2
10 μM
32



216000
Calcium Channel N-Type
314227
rat
2
10 μM
−16



217030
Cannabinoid CB1
314171
hum
2
10 μM
13



219500
Dopamine D1
314173
hum
2
10 μM
5



219700
Dopamine D2S
314174
hum
2
10 μM
4



219800
Dopamine D3
314297
hum
2
10 μM
4



219900
Dopamine D42
314238
hum
2
10 μM
7



224010
Endothelin ETA
314240
hum
2
10 μM
8



224110
Endothelin ETB
314241
hum
2
10 μM
3



225510
Epidermal Growth Factor (EGF)
314243
hum
2
10 μM
6



226010
Estrogen ERα
314245
hum
2
10 μM
9



226600
GABAA, Flunitrazepam, Central
314115
rat
2
10 μM
16



226500
GABAA, Muscimol, Central
314175
rat
2
10 μM
9



228610
GABAB1A
314248
hum
2
10 μM
5



232030
Glucocorticoid
314321
hum
2
10 μM
−2



232700
Glutamate, Kainate
314298
rat
2
10 μM
11



232810
Glutamate, NMDA, Agonism
314250
rat
2
10 μM
9



232910
Glutamate, NMDA, Glycine
314253
rat
2
10 μM
−1



233000
Glutamate, NMDA, Phencyclidine
314178
rat
2
10 μM
6



239610
Histamine H1
314180
hum
2
10 μM
2
















Cat #
Assay Name
Batch*
Spec.
Rep.
Conc.
% Inh.





239710
Histamine H2
314258
hum
2
10 μM
2


239820
Histamine H3
314302
hum
2
10 μM
14


241000
Imidazoline I2, Central
314181
rat
2
10 μM
−1


243520
Interleukin IL-1
314186
mouse
2
10 μM
3


250460
Leukotriene, Cysteinyl CysLT1
314262
hum
2
10 μM
0


251600
Melatonin MT1
314266
hum
2
10 μM
3


252610
Muscarinic M1
314320
hum
2
10 μM
1


252710
Muscarinic M2
314183
hum
2
10 μM
−8


252810
Muscarinic M3
314185
hum
2
10 μM
14


257010
Neuropeptide Y Y1
314271
hum
2
10 μM
5


257110
Neuropeptide Y Y2
314303
hum
2
10 μM
−3


258590
Nicotinic Acetylcholine
314188
hum
2
10 μM
13


258700
Nicotinic Acetylcholine α1, Bungarotoxin
314189
hum
2
10 μM
8


260130
Opiate δ1, (OP1, DOP)
314191
hum
2
10 μM
0


260210
Opiate κ(OP2, KOP)
314304
hum
2
10 μM
14


260410
Opiate μ(OP3, MOP)
314194
hum
2
10 μM
3


264500
Phorbol Ester
314195
mouse
2
10 μM
−1


265010
Platelet Activating Factor (PAF)
314197
hum
2
10 μM
4


265600
Potassium Channel [KATP]
314201
ham
2
10 μM
9


265900
Potassium Channel hERG
314202
hum
2
10 μM
−11


268420
Prostanoid EP4
314208
hum
2
10 μM
−4


268700
Purinergic P2X
314300
rabbit
2
10 μM
−2


268810
Purinergic P2Y
314301
rat
2
10 μM
8


270000
Rolipram
314203
rat
2
10 μM
9


271110
Serotonin (5-Hydroxytryptamine) 5-HT1A
314275
hum
2
10 μM
4


271700
Serotonin (5-Hydroxytryptamine) 5-HT2B
314205
hum
2
10 μM
11


271910
Serotonin (5-Hydroxytryptamine) 5-HT3
314281
hum
2
10 μM
−11


278110
Sigma σ1
314095
hum
2
10 μM
5


255520
Tachykinin NK1
314269
hum
2
10 μM
7


285900
Thyroid Hormone
314309
rat
2
10 μM
−3


220320
Transporter, Dopamine (DAT)
314094
hum
2
10 μM
8


226400
Transporter, GABA
314450
rat
2
10 μM
10


204410
Transporter, Norepinephrine (NET)
314086
hum
2
10 μM
13


274030
Transporter, Serotonin (5-Hydroxytryptamine)
314284
hum
2
10 μM
8



(SERT)





Note:


Items meeting criteria for significance (≧50% stimulation or inhibition) are highlighted.


*Batch: Represents compounds tested concurrently in the same assay(s).


R = See Remarks (if any) at end of this section.


ham = Hamster; hum = Human






7. EXAMPLES SECTION 3
Methods
Bacterial strains, phage, and growth conditions. All E. coli strains and phage used in the present study are listed in Table 1. Unless otherwise indicated, bacteria were routinely grown at 37° C. in Luria-Bertani medium (LB) with shaking at 250 rpm. LB was supplemented with 1% dimethyl sulfoxide (DMSO; Acros) with or without compound. Phage lysates were prepared from 50 mL cultures of E. coli strains UTI89 (for K1F phage), MG1655 (for T7 phage) or DS17 (for K5 phage) and stored at 4° C. over several drops of chloroform as described [37].
Screen for Inhibitors of Bacterial Capsule Biogenesis.
Primary assay. The primary assay consisted of detection of the presence and absence of the K1 capsule on the E. coli urinary tract isolate UTI89 under growth conditions with compounds from a large chemical library. The assay was conducted as previously described [36] with the following modifications. The primary assay was conducted in 1,536-well plate format. UTI89 ΔkpsM, an isogenic K1 capsule export mutant, was included as an unencapsulated control. Tetracycline, 50 μM, was used as a negative growth control. A 1:75 dilution of overnight cultures were made in LB broth containing 0.5% DMSO, and 3 μL of this culture was added to each plate well, and plates were incubated, inverted, at 37° C. for 2 hr. K1F phage stock was diluted 1:8 in LB Broth containing 0.5% DMSO, and 1.5 μL of diluted phage (or media only) was added to the pre-plated test compound wells and appropriate control wells. The plates were centrifuged briefly, and then were incubated, inverted, at 37° C. for an additional 2 hr. To increase sensitivity of detection of viable bacteria, 1 μL of a 1:2 dilution of AlamarBlue reagent (Invitrogen, #DAL1100) in LB broth was added to each plate well. Alamar Blue, resazurin, is converted in living cells to the fluorescent molecule, resorufin. The plates were again centrifuged briefly, and then were further incubated, inverted, at 37° C. for 30 min Resorufin fluorescence was measured using excitation of 560 nm and emission of 590 nm, as per the manufacturer's recommendations.
Compounds from the NIH Molecular Libraries Small Molecule Repository (MLSMR) were utilized in the primary assay. The MLSMR collection of over 300,000 compounds generically grouped into one of the following five categories: (a) specialty sets, comprising bioactive compounds such as known drugs and toxins, (b) non-commercial compounds, mainly from academic labs, (c) targeted libraries, (d) natural products, and (e) diversity compounds [38]. The MLSMR library covers a diverse sample of the chemical space occupied by drugs and natural products, but only narrowly represents combinatorial chemical space [39]. Compounds or vehicle control (DMSO) were diluted to a final well concentration of 1:200 in assay media. Compounds (22.5 nL in 100% DMSO) were dispensed to assay plates using an Echo non-contact dispenser (Labcyte). Compounds from the libraries were added to the plates at a final concentration of 50 μM, before the addition of bacteria or phage. Each compound was tested as a single point, and  ̃1,200 compounds were tested per plate. A positive hit was defined by the compound producing greater than a 50% inhibition of K1F phage-induced lysis. Compound hits were further confirmed using an optical density-based detection method in a 96-well format as previously described [36].
Concentration-response to chemical inhibition. Concentration-response testing (concentration range=0.58-300 μM) was used to confirm and characterize the primary screen hits, which was necessary to determine the number of compounds advanced to secondary screens. Compounds were plated in 1536-well microplates, and the concentration-response efficacy assay was performed as described for the primary screen, with the exception that each compound was tested in duplicate at 10 concentration points starting from 300 μM and continuing to lower concentrations by 2-fold serial dilutions. The strain UTI89 ΔkpsM, a K1 capsule export mutant, was evaluated with the wild-type strain as a phage-insensitive control (mimicking 100% capsule inhibition).
T7 phage counter assay. This secondary assay was performed as previously described [36] and was used to distinguish compounds with phage inhibitory effects from true polysaccharide capsule inhibitors. T7 phage has a nearly identical genome to K1F phage and thus a similar life cycle [40]; however, T7 phage does not encode for an endosialidase, and its entry into E. coli is inhibited by K capsules. Thus, the presence of a capsule inhibits T7-mediated lysis [41]. In this assay, an increase in phage-induced lysis correlates to a decrease in capsule formation. True inhibitors of capsule yielded bacteria that were susceptible to T7 phage and lysed within 2 hr of the addition of phage. However, compounds inhibiting phage replication did not promote bacterial lysis. The positive control molecule C7 (100 μM final well concentration) was used in this screen.
Pan Assay Interference Compound (PAINS) analysis. Groups of compound substructural features are associated with compound biological promiscuity, and compounds containing these features arise as frequent hits in biochemical high throughput screens. These molecules have been described as PAINS [42]. To determine if molecules of interest were within chemical groups with known non-specific interference with the bioassays, the structures for compounds DU001, DU003, DU005, DU007, DU008, and DU011 were retrieved from PubChem and saved in the Structure Data Format (SDF). The structures were then compared to the SYBYL PAINS compounds library, to see which, if any, of the compounds contain PAINS functional groups [43].
Cytotoxicity. Testing was performed essentially as previously described [36,44]. Concentration-response testing was performed over a range 0.58-300 μM in a 386 well plate format. Bladder carcinoma 5637 cells (ATCC HTB-9) were added to the compounds, and 72 hrs later cell viability was measured using CellTiter Glo (Promega). The 50% toxic concentration (TC50) was determined and compared to the IC50 to calculate the therapeutic index. Hyamine was used as a positive cytotoxic control. All wells contained 0.5% DMSO.
Evaluation of off-target effects. Off target effects of lead molecules of interest were evaluated using the LeadProfilingScreen commercial assay at Eurofins Panlabs (Bothell, Wash.). Reference standards were run as an integral part of each assay to ensure the validity of the results obtained. Assay results are presented as the percent inhibition of specific binding or activity (for n=2 replicates) for the probe compound tested at a concentration of 10 μM. Details regarding the individual assays and methods are provided in Supplementary Information File 51.
Orcinol assay for released capsule material. Orcinol reactivity was used as a biochemical confirmation of altered extracellular capsule after compound treatment. UTI89 or an isogenic capsule mutant was grown in 100 μM of test compound or 1% DMSO. The assay was performed as previously described [36]. The molecule C7 (100 μM final concentration) was used as a positive control. The assay was performed 3 times with replicate samples.
K1 antigen dot blot. K1 antigen was detected by dot blot assays of culture extracts probed with anti-K1 H46 serum. The assay was performed as previously described [36]. The experiment was repeated twice with similar results, and a representative dot blot is shown.
Visualization of capsule using Alcian blue staining. Overnight cultures of clinical E. coli strains were diluted 1:100 in the presence of 1% DMSO or 100 μM DU011. Cultures were grown for  ̃6 hrs (OD600=1.2) at 37° C. Samples were centrifuged at 13,200 RPM for 5 min. The medium was removed and the cells were resuspended in 500 μL of Tris-Acetate (pH 5) and shaken for 1 hr at 37° C. Samples were re-centrifuged, and the supernatant was concentrated  ̃100 fold in Amicon 3K microconcentrators. The preparations were separated on a 7.5% SDS-PAGE gel and stained with 0.125% Alcian blue as previously described [45].
K5 phage assay. This assay determined if compounds found to be active in the K1F, T7, orcinol, and K1 antigen dot blot secondary assays were able to also inhibit K5 capsule biogenesis. The assay was performed in a method identical to the T7 assay test [36]. E. coli strain DS17, a pyelonephritis clinical isolate expressing a K5 capsule and susceptible to K5 phage (K5), was used as a K5 prototypic test strain. The degree of inhibition of phage-mediated lysis was determined based on the absorbance (OD600).
Human serum sensitization by capsule inhibitor treatment. Overnight cultures of UTI89 were diluted 1:100 and grown with or without 50 μM compound for approximately 1.5 hrs on a shaker at 37° C. Then 25 μL of anonymous, non-identified, sterile filtered pooled human serum (purchased from Equitech Bio) was added per 100 μL of growth media. This was returned to the shaker for another 3 hrs, after which 20 μL of 5 mg/mL MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) was added. MTT is reduced to purple formazan by bacterial reductase enzymes, thus measuring viable bacteria. This was shaken for another 15 min at 37° C. The sample was spun to remove the growth media, followed by two washes with PBS. The formazan crystals were dissolved in 100 μL of DMSO and measured at OD570.
Murine UPEC sepsis model and treatment with DU011. Groups of five 6-7 week old C57BL/6NCr female mice (purchased from Frederick National Laboratory for Cancer Research) were injected subcutaneously twice daily with 100 μL of 1% DMSO (vehicle control) or DU011 (1 mg/ml) starting 12 hrs prior to the intra peritoneal infection. Weights were recorded twice daily to monitor health of the animals and tolerance to the compound. Mice were challenged by intraperitoneal injection with 108 CFU of the indicated E. coli UTI89 in 100 μL of PBS. Briefly, cultures were prepared by diluting overnight cultures (18 hrs) 1:100 into 3 mL of LB supplemented with 1% DMSO final or 100 μM DU011 (1% DMSO final). Shaken cultures were grown at 37° C. for 6 hours to an OD600 of 1.2, and then cells were pelleted and resuspended in 1 mL of PBS. Absorbance was adjusted to OD600 of 0.8 in PBS, and the cultures were then diluted 1:10 in sterile PBS Animals were also given an intraperitoneal dose of 1% DMSO or DU011, in a site different than the administration of bacteria, to ensure sufficient systemic delivery of drug. Animal survival was assessed after 12 hours. Surviving mice were re-dosed according to the treatment groups and continued to be monitored. The experiment was concluded 48 hours post infection. The entire experiment was repeated with similar results.
Throughout each experiment, animals were monitored each 6 hours from the time of infection until conclusion for serious morbidity, including ruffled fur, decreased activity, slowed respirations, and ill appearance. Animals were provided gel packs for easily accessible additional hydration throughout the experiments. When a moribund state was suspected or anticipated by these criteria, animals were immediately euthanized to minimize potential pain and/or suffering. Of the total animals with an outcome categorized as death, the following numbers were euthanized for terminal morbidity prior to septic death (euthanized/total deaths): 3/10, no prior treatment; 3/5 prior chemical treatment of bacteria alone; 0/2 prior chemical treatment of mice alone. Euthanasia for all animals was through complete respiratory cessation using the inhaled anesthetic isoflurane followed by secondary assurance of death using bilateral thoracotomy. All animal experiments were conducted with prior approval from the Institutional Animal Care and Use Committee of Duke University.
Statistical analyses. Results were calculated as averages and standard deviations of the means using the Graph Pad Prism 5 software package (San Diego, Calif.). Nonparametric t-tests were used for statistical analysis of data and calculation of p-values using Graph Pad Prism 5 or Graph Pad online calculators. Significant differences are highlighted with a single asterisk when the p value is less than 0.05, with two asterisks when the p value is less than 0.01, and three asterisks when the p value is less than 0.001.
Results
Primary screen for novel capsule inhibitors. Our initial screen of 2,195 compounds from the Developmental Therapeutics Program at the National Cancer Institute successfully identified a small-molecule inhibitor of uropathogenic E. coli Group 2 capsule biogenesis. We described this compound, termed C7, in a previous report as proof-of-principle that small-molecule inhibition of capsule biogenesis is possible and that these novel anti-infectives can block encapsulation and attenuate a pathogen through exposure to host innate immune factors [36]. Based on this proof-of-concept, the primary assay was adapted to a 1,536-well format with the modifications for high-throughput screening necessary to search for additional active molecules in significantly larger chemical repositories. The K1 encapsulated strain of uropathogenic E. coli UTI89 was grown in a 1,536-well plate format in the presence of 50 μM compounds. After an initial growth step, K1F phage specific for K1 capsule was added. Compounds with no effect on capsule biogenesis allowed the growth of organisms with an intact capsule that were subsequently lysed by the addition of the K1F phage. However, those compounds that presumably inhibited capsule biogenesis and allowed growth of the unencapsulated organism did not lyse with the addition of the K1F phage. These compounds were then selected for a secondary assay.
In total, 338,740 compounds were screened in the primary assay (using K1F phage), and 1,767 compounds associated with resistance to phage lysis (0.52% of total) were tested in concentration-response format. Of these, 29 compounds passed concentration-response validation (1.6% of compounds passing the primary screen), and 6 were selected after demonstrating high activity in the T7 phage secondary assay, the reciprocal phage assay in which chemical unencapsulation sensitizes a K1:K12 hybrid strain, EV36, to lysis by the T7 phage. Concentration response curves for 2 of these compounds are shown in FIG. 12. Compounds with promising chemical structures and low cytotoxicity to cultured bladder epithelial cells were selected for further characterization. As seen in Table 2, the activity of these compound hits in primary and secondary assays is consistent with molecules with capsule inhibitory action. Cytotoxicity data further indicate that these molecules are non-toxic to cultured bladder epithelial cells. Furthermore, these new compounds, designated DU001, DU003, DU005, DU007, DU008, and DU011, are more active in the phage assays than the original proof-of-concept agent C7, with IC50 values in the micromolar range.
Identification of potential Pan Assay Interference Compounds (PAINS) among capsule inhibitor hits. A number of compound substructural features have been identified that are associated with compound biological promiscuity, and, in particular, compounds with certain structural features appear as frequent hits in biochemical high throughput screens. These molecules have been described as PAINS. Although PAINS may remain useful hits, we sought to prioritize the compound hits DU001, DU003, DU005, DU007, DU008, and DU011 by identifying and removing PAINS-like molecules from our prioritization. Three of the six most active and selective compound hits, DU005, DU007, and DU008, are considered PAINS [40], and thus were not submitted for additional biological characterization.
Confirmation of primary hits and spectrum of activity. Compounds were further characterized by determining biochemically the level of surface capsule upon compound treatment of a wild-type K1 encapsulated UPEC strain. We used mild-acid to release capsule from cultures of UTI89 grown in the presence of 100 μM compound. We then used the orcinol reagent to quantify the amount of released material. As shown in FIG. 12 panel A, orcinol reactivity as % of wild-type for compound treatment indicates that cultures treated with capsule inhibitors had decreased surface reactive material, similar to levels observed for capsule synthesis and assembly mutants.
As another independent measure of capsule inhibition by the DU compounds, K1 antigen was evaluated using whole-cell dot blots with anti-K1 serum. In all cases, treatment with these molecules reduced reactivity to levels resembling those of genetic capsule mutants (FIG. 12 panel B). The combined results from the phage, orcinol, and immune-dot blots demonstrate that these molecules inhibit normal capsule production and assembly, significantly reducing the amount of surface assembled capsule.
A major consideration was whether the inhibitors of K1 encapsulation were also able to inhibit the production of other important E. coli Group 2 capsule types. To confirm the range of activity, we first demonstrated that treatment with each of confirmed inhibitory molecules also inhibited K5 phage infection of a K5 capsule-expressing strain, DS 17 (FIG. 13 panel A). We next determined if leading capsule inhibitors would also inhibit the production of capsule in non-K1 serotypes. Capsular material was isolated from strains 536 (K15 serotype), CFT073 (K2 serotype) and DS17 (K5 serotype), and UTI89 (K1 serotype) in the presence and absence of capsule inhibitors. Capsule was isolated from the same amount of bacteria after growth in vehicle or with inhibitor DU011 (200 μM). Isolated material was separated on a polyacrylamide gel and stained with the cationic dye alcian blue. As shown in FIG. 13 panel B, capsule was reduced in each strain following growth with DU011, regardless of serotype. Although visibly reduced in capsule after growth in DU011, the reduction in capsular material from treated CFT073 appeared slightly less than the other serotypes tested. A similar reduction in extracted capsule was also seen with DU003 (data not shown).
Chemical inhibition sensitized UPEC to serum-mediated killing. Capsule offers protection against serum-mediated killing. In order to test whether compound treatment of UPEC increased serum-mediated killing, an in vitro serum resistance assay was used. As shown in FIG. 14, pooled human serum decreased the amount of viable UPEC as measured by an MTT metabolic activity assay. Treatment of UPEC with either 50 μM DU003 or DU011 further increased serum-mediated killing, thus significantly reducing the measurable bacteria as compared to DMSO treated cells (p=0.0067). This decrease was similar to the serum sensitivity observed for a genetic capsule mutant (Δneu).
DU003 & DU011 are biologically selective. DU003 and DU011 were submitted to the Eurofins Panlabs LeadProfilingScreen to assess off-target pharmacology 1421. Both compounds were tested in duplicate at 10 μM concentration and showed no significant activity across the panel of 68 targets (i.e., <32% inhibition for DU011 and <30% inhibition for DU003, except for one target, the norepinephrine transporter, for which 58% inhibition was observed; full data and assays are provided in Supplementary Information File S1). In review of PubChem data, DU011 (CID23602075) is reported to have shown activity in only 21 of 467 (4.5%, as of Sep. 5, 2013) bioassays in which it was tested (assays unrelated to the current project). Per PubChem, DU003 (CID18109210) is reported to have shown activity in only 5 of 427 (1.2%, as of Sep. 5, 2013) bioassays in which it was tested (assays unrelated to the current project). Together, these results suggest that DU011 and DU003 are not biologically promiscuous compounds.
Attenuation of E. coli disseminated infection by DU011. In order to test the ability of these compounds to prevent lethal systemic E. coli infection in mice, we selected DU011 for animal testing based on its favorable solubility, permeability, and plasma and microsome stability profiles (Table 3). As shown in FIG. 15 panel A, C57BL/6 mice were administered DU011 or 1% DMSO 12 hours prior to lethal challenge with 108 CFU of UPEC UTI89 by intraperitoneal injection. All previously untreated mice receiving non-pretreated bacteria were moribund or died within 24 hr post-infection. In contrast, pretreatment of the bacteria and mice with DU011 conferred complete protection with 100% survival for the duration of the experiments (48 hrs) and recovery of pre-infection weights (FIG. 15 panel B), similar to the 100% survival of animals administered UTI89 ΔRII, an unencapsulated isogenic mutant (data not shown). Administration of subcutaneous DU011 and untreated UTI89 provided 80% survival with stabilization of weights at the end of the experiment. Pre-treatment of bacteria without pretreatment of the mice produced 50% survival with ongoing weight loss among surviving animals. Mice tolerated DU011 without evident side effects. These data indicate that pretreatment of mice with DU011 was able to significantly reduce mortality due to disseminated E. coli infection, demonstrating the potency of polysaccharide inhibition in vivo.
Discussion
E. coli infections play a significant role in community-acquired UTI with substantial morbidity and associated costs. With a diminishing arsenal of antibiotics available for the treatment of UTI, new therapeutics are in great demand. Anti-virulence agents capable of specifically attenuating a pathogenic organism during its infectious cycle hold great potential as they may spare the microbiota in commensal niches.
Previous work in our lab and in others has highlighted the importance of capsular polysaccharides in the pathogenesis of uropathogenic E. coli [27-29]. Group 2 and 3 capsules are highly conserved and represent the predominant circulating capsule types [46]. We have previously described the identification and characterization of a novel agent designated C7 that is active (IC50 between 12.5-25 μM), blocks the production of K1 and K5 capsule biogenesis, and lacks obvious toxicity to cultured bladder epithelial cells [36]. We have since conducted a high-throughput screen for additional broad-spectrum capsule inhibitors, finding several structurally distinct and highly active new molecules with promising therapeutic characteristics.
Herein, we described the initial identification and characterization of these new small molecules. This group of capsule inhibitors features lower IC50 values and improved solubility, permeability, and plasma and microsome stability profiles. We have demonstrated their activity in assays with human serum (FIG. 14). Most importantly, dosing of mice with DU011 had no detectable adverse effects on the animals and protected against a lethal E. coli systemic challenge (FIG. 15). In vivo results are shown in Figure This new approach may provide the basis for the next pre-clinical steps to test these inhibitors as UTI-specific therapeutics that render microbes vulnerable to host clearance mechanisms such as innate immunity, enhancing the adaptive immune responses in the process by allowing greater engagement of the immune system. While dosing and delivery will need to be evaluated in future pre-clinical pharmacokinetic and pharmacodynamics studies, we believe these data highlight the potential use of capsule inhibitors as specific anti-virulence therapeutics. The compounds listed in Tables 2 and 3 are synthetically amenable lead compounds and work is currently underway to improve upon their properties. Synthesis of large lots of DU011 and other compound hits has made animal testing possible as well as facilitated work on the mechanism of action of these compounds. This will aid in the identification of their biological target and will advance our understanding of capsule biogenesis and regulation in E. coli and other organisms with similarly conserved capsule loci. This could lead to the attenuation of diverse encapsulated organisms sharing similar capsule assembly and regulatory mechanisms. The generation of novel highly active small-molecule inhibitors of capsule biogenesis will also aid in our understanding of the role of the innate and adaptive immune systems in control of encapsulated bacterial pathogens during systemic infections. A better understanding of how DU003, DU011 and others affect the interaction of the bacterium with host immune responses will significantly aid in the development better anti-infectives that not only attenuate the organism, but also actively engage the host immune system to promote clearance.
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It is to be understood that, while the invention has been described in conjunction with the detailed description, thereof, the foregoing description is intended to illustrate and not limit the scope of the invention. Other aspects, advantages, and modifications of the invention are within the scope of the claims set forth below. All publications, patents, and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

## Claims

1. A method of inhibiting capsule biogenesis in a bacterium which comprises administering to the bacterium an effective amount of a composition comprising



wherein R1 is C1-8 alkyl, C1-8 alkoxy, C1-8 haloalkoxy;
R2 is hydrogen; and
R3 is substituted aryl or substituted furan group.

2. The method of claim 1, wherein the capsule biogenesis is K1 or K5 capsule biogenesis.

3. The method of claim 1, wherein the bacterium is a gram-negative bacteria.

4. The method of claim 3, wherein the gram-negative bacteria is Campylobacter jejuni, Enterobacter cloacae, Escherichia Coli, Haemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Methicillin-resistant Staphylococcus aureus (MRSA), Neisseria meningitides, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella typhimurium, Serratia marcescens, Staphylococcus aureus or a combination thereof.

5. A method of treating a subject suffering from a bacterial infection comprising administering a therapeutically effective amount of a composition comprising



wherein R1 is C1-8 alkyl, C1-8 alkoxy, C1-8 haloalkoxy;
R2 is hydrogen; and
R3 is substituted furan group.

6. The method of claim 5, wherein the bacterium is a gram-negative bacteria.

7. The method of claim 6, wherein the gram-negative bacteria is Campylobacter jejuni, Enterobacter cloacae, Escherichia Coli, Haemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Methicillin-resistant Staphylococcus aureus (MRSA), Neisseria meningitides, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella typhimurium, Serratia marcescens, Staphylococcus aureus or a combination thereof.

8. The method of claim 5, further comprising administering an agent that targets a bacterial cell wall.

9. The method of claim 8, wherein the agent is a penicillin or a cephalosporin.

10. The method of claim 5, wherein the bacterial infection is a urinary tract infection (UTI), or a disseminated staphylococcus infection.

11. The method of claim 10, wherein the bacterial infection is a urinary tract infection (UTI).

12. The method of claim 11 wherein the urinary tract infection (UTI) is a bladder infection.

13. The method of claim 11 wherein the urinary tract infection (UTI) is a kidney infection.

14. The method of claim 5, wherein the subject is a mammal.

15. The method of claim 14, wherein the mammal is a human.

16. The method of claim 1, wherein R1 is a fluoro alkoxy group.

17. The method of claim 1, wherein R1 is a methoxy, ethoxy, propoxy, or butoxy group.

18. The method of claim 1, wherein R3 is a substituted aryl group with one or more fluoro substituents.

19. The method of claim 1, wherein R3 is a bromo substituted furan group.