# Patent

## Title
Antibiotic and anti-parasitic agents that modulate class II fructose 1,6-bisphosphate aldolase

## Abstract

This invention provides a family of compounds that inhibit Class II fructose 1,6-bisphosphate aldolase (FBA), which is implicated in the pathogenic activity of a broad range of bacterial and parasitic agents. The compounds were identified by empirical testing, and provide a basis for further derivatization and optimization of 8-hydroxyquinoline-2-carboxylic acid and related compounds. Crystal structure shows that the compounds don't bind directly to the catalytic site of the enzyme, and so are not defined simply as substrate analogs. Instead, they create a pocket by induced fit, resulting a powerful and specific inhibitory effect on FBA activity.

## Background
RELATED APPLICATION
This application claims the priority benefit of U.S. provisional patent application 61/821,184, filed May 8, 2013. The priority application is hereby incorporated herein by reference for all purposes.


REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE
The Sequence Listing written in file 92154-907655—ST25.TXT, created Jun. 6, 2014, 17,149 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference.
FIELD OF THE INVENTION
This application relates to the field of treatment and prevention of bacterial and parasitic conditions. The compounds of the invention inhibit enzyme activity of Class II fructose 1,6-bisphosphatase aldolase of the microorganism targeted for therapy.
BACKGROUND
Mycobacterium tuberculosis, the causative agent for Tuberculosis (TB), currently infects one third of the world's population in its latent form. In 2011 alone, 8.7 million new cases of TB were detected and 1.4 million deaths were attributed to infection by this pathogenic bacteria. World Health Organization, Global tuberculosis Report 2012. For the U.S. in particular, the danger of TB has been significantly risen recently with the by the rapid increasing prevalence of TB cases amongst HIV infected patients. World Health Organization, UNAIDS, and UNICEF, Global HIV/AIDS response: epidemic update and health sector progress towards universal access: Progress Report 2011.
Current treatment for TB, Directly Observed Therapy, Short Course (DOTS), involves the administration of a four-drug cocktail over a two month time span with continuous two-drug treatments for an additional 2-4 months. Implementing the Stop TB Strategy: a handbook for national tuberculosis, 2008, World Health Organization: Geneva, Switzerland. p. 1-198. Despite increasing global efforts to eradicate TB, the estimated rate of curing TB cases has actually declined in last couple of years. Part of this decline has been an upsurge of cases involving multidrug resistant TB strains, MDR-TB and XDR-TB, as well as the increased difficulty of patients complying the lengthy DOTS regiment.
Unfortunately, M. tuberculosis is not the only pathogenic bacterium that has become resistant to current antibiotics. Increasing incidents of other drug resistant bacterium such as Methicillin-resistant Staphylococcus aureus (MRSA) and Carbapenem-resistant Enterobacteriaceae (CRE) are also on the rise. Perez F. et al., Cleve. Clin J Med, 2013. 80(4):225-33; Scheffler, R. J, et al., Appl Microbiol Biotechnol, 2013. 97(3):969-78. Additionally, the threat of drug-resistant weaponized bacterium such as Bacillus anthracia and Yersinia pestis still persists. Froude, J. W, et al., Antibodies for biodefense. MAbs, 2011. 3(6):517-27.
With the global decreasing effectiveness of current therapeutics against TB, increasing prevalence the multi-drug resistant strains MDR-TB and XDR-TB as well as other pathogenic bacterium, there is a strong need for development of antibiotics targeting novel pharmacological targets within pathogenic bacterium such as M. tuberculosis. 
SUMMARY OF THE INVENTION
This invention provides antibiotics and anti-parasitic agents that inhibits Class II fructose 1,6-bisphosphate aldolase (FBA). Typically, they inhibit Class II FBA of the microorganism targeted for treatment, or a homolog thereof, but not Class I FBAs such as may be expressed in human or mammalian subjects.
Model compounds have the structure shown in Formula (I).




In some embodiments of the invention, R7=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH; R6=H, alkyl, alkenyl, alkynyl, F, Cl, Br, or CF3; R5=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH; AH4=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH; AH3=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH; and Z2=CO2H, CO2R, CONH2, CONHR, aryl, or heteroaryl.

The compounds of the invention can be selected to have antibiotic and/or anti-parasitic activity for a broad range of pathogenic agents or for certain pathogenic agents in particular. The compounds in inhibits growth or replication of organisms such as M. tuberculosis, or any of the other organisms referred to in this disclosure. Model compounds may be selected as having any one or more of the properties explained in this disclosure in any combination. For example, a model compound may bind to a Class II fructose 1,6 bisphosphate aldolase (FBA) such as those having an amino acid sequence according to any one or more of SEQ. ID NOs:1 to 5. FBA binding of the compound may have a dissociation constant (Kd) of less than about 100 μM, 10 μM, 1 μM, or 0.1 μM. The compound may substantially inhibit enzymatic activity of a Class II fructose 1,6 bisphosphate aldolase (FBA) such as SEQ. ID NOs:1 to 5, with minimal inhibition of a Class II or mammalian FBA such as SEQ. ID NO:6. Some model compounds of this invention induce their own binding site in the flexible Z loop structure of Class II FBA.
Reference to any drug or active agent in this disclosure includes any and all isomers, stereoisomers, pharmaceutically compatible salts, solvates, and pharmaceutical compositions thereof that retain at least some of the physiological or chemotherapeutic effects of the drug itself, unless such isomers, salts, solvates, and/or compositions are explicitly excluded. Any such compound may be used as an alternative to the drug itself to improve efficacy, tolerability, delivery, or pharmacokinetics, or simply by choice within the good judgment of the manufacturer, distributor, pharmacist, clinician, or end user.
Other aspects of the invention are pharmaceutical compositions, disinfectants, and soaps that comprise one or more compounds of this invention. They may be used in the treatment of infection, in the disinfecting of surfaces and equipment, and in the manufacture of medicaments. Another aspect of the invention is a method of killing or modulating growth of a bacterium or parasite, comprising contacting the bacterium or parasite with a compound or composition as described herein. Another aspect of the invention is a method for treatment of an infection by any bacterial or parasitic agent, such as an agent which expresses Class II fructose 1,6-bisphosphate aldolase (FBA), and which rely on FBA activity for viability, growth, or metabolism.
Another aspect of the invention is a screening method for identifying compounds suitable for use as antibiotics or anti-parasitic agents. The method comprises measuring enzymatic activity of a Class II fructose 1,6-bisphosphate aldolase (FBA) in the presence and absence of the compound, and determining whether the compound inhibits the enzymatic activity of the FBA. The method may further comprise measuring enzymatic activity of a Class I FBA, determining whether the compound inhibits growth or metabolism of a bacterium or a parasite, and/or determining the crystal structure of an FBA to which the compound has bound.
This invention provides additional compounds and derivatives of 8-hydroxyquinoline-2-carboxylic acid (HCA) that are identified as having antibiotic and/or anti-parasitic activity and/or FBA inhibitory capacity according to the methods of this invention.
Other aspects of the invention will be apparent from the description that follows.



DRAWINGS
FIG. 1 is a schematic depiction of the role of Fructose-bisphosphate aldolase (FBA) in the gluconeogenesis and glycolysis pathways in Mycobacterium tuberculosis (MtFBA).
FIG. 2 shows how compounds and derivatives of 8-hydroxyquinoline-2-carboxylic acid (HCA) having antibiotic and/or anti-parasitic activity according to this invention bind in the X-ray crystallographic structure of MtFBA. In FIG. 2A HCA (the bicyclic compound) is shown bound to neighboring amino acid residues in MtFBA. FIG. 2B is another view with MtFBA-PGH structure overlaid. Zn(II) and residues in frame belonging to the MtFBA-PGH structure are rendered in grey. FIG. 2C shows HCA binding cavity on MtFBA.
FIG. 3 shows similarity of key residues of FBA from different pathogens around about the HCA binding pocket. Due to the conserved nature of Class II 1,6-bisphosphate aldolases, HCA can be used to treat and manage a wide range of other pathogenic bacteria and parasitic eukaryotes. Sequence legend: TDHC (SEQ ID NO:1, residues 94-97); IEIGVV (SEQ ID NO:1, residues 160-165); TDHC (SEQ ID NO:2, residues 109-112); IELGCT (SEQ ID NO:2, residues 174-179); LDHG (SEQ ID NO:3, residues 84-87); AELGTV (SEQ ID NO:3, residues 136-141); LDHG (SEQ ID NO:4, residue 84-87); AELGTV (SEQ ID NO:4, residues 136-141); LDHG (SEQ ID NO:5, residues 83-86); AELGTI (SEQ ID NO:5, residues 135-140).
FIGS. 4A and 4B illustrate chemical synthesis of the HCA compounds and derivatives of this invention.
FIG. 5 provides data from the calorimetric titration of HCA. Left-side panels show 5 mM of the compound designated as Regis 5 titrated into 700 μM of MtFBA demonstrating a dissociation constant Kd=6.94±0.97 μM. Right-side panels show the same compound titrated into MtFBA buffer in the presence of 200 μM ZnCl2, showing no appreciable binding. Top graphs represent raw heat data and bottom graphs are integrated heat peaks gained at 25° C.
FIG. 6 illustrate MtFBA inhibitor properties of HCA. FIG. 6A is a Lineweaver-Burk plot of the kinetics of inhibition of MtFBA by 8-hydroxyquinoline-2-carboxylic acid against MtFBA for varying concentrations of FBP. The inset is a Michaelis-Menten plot of inhibition of MtFBA. FIG. 6B is isothermal Titration calorimetry (ITC) of HCA binding to MtFBA.
FIG. 7A is the amino acid sequence alignment of Class II FBAs from pathogenic bacteria. FBAs are from the H37RV strain of M. tuberculosis (SEQ. ID NO:1), Yersinia pesti (SEQ. ID NO:2), Staphylococcus aureus (SEQ. ID NO:3), Bacillus anthracia (SEQ. ID NO:4), and Klebsiella pneumonia (SEQ. ID NO:5). Asterisks denote residues involved in hydrophobic interactions as well as hydrogen bonds formed between MtFBA and HCA. FIG. 7B is the amino acid sequence of human Class I FBA (SEQ. ID NO:6).
FIG. 8A shows the general chemical structure of 8-hydroxyquinoline-2-carboxylic acid and its chemical scaffold. FIG. 8B is the X-ray crystal structure of 8-hydroxyquinoline-2-carboxylic acid bound to MtFBA. FIG. 8C is a surface rendering that shows 8-hydroxyquinoline-2-carboxylic acid bound to MtFBA binding cavity.
FIG. 9 illustrates HCA's potential as a class II FBA broad-spectrum inhibitor. A single concentration of HCA at 25 μM inhibits class IIa FBA isolated from E. coli and class IIb FBA originating from methicillin-resistant S. aureus (MRSA).
FIG. 10 shows the active site for S. aureus FBA (SaFBA) in the crystal structure with citrate bound in the HCA-like pocket. Z-loop flexibility is characteristic of both MtFBA and SaFBA, a likely common mode of inhibition by HCA.
FIG. 11 shows the binding of 6F substituted HCA bound to MtFBA. This increases potency towards the enzyme by 50%, and further validates that the HCA scaffold is acting through displacement of the Z-loop.



DETAILED DESCRIPTION
This invention provides a family of compounds that inhibit Class II fructose 1,6-bisphosphate aldolase (FBA), which is implicated in the pathogenic activity of a broad range of bacterial and parasitic agents. The compounds were identified by empirical testing, and provide a basis for further derivatization and optimization of 8-hydroxyquinoline-2-carboxylic acid (HCA) and related compounds. Crystal structure shows that the compounds don't bind directly to the catalytic site of the enzyme, and so are not defined simply as substrate analogs. Instead, they create a pocket by induced fit, resulting a powerful and specific inhibitory effect.
Fructose 1,6-Bisphosphate Aldolase (FBA) Activity in Pathogenic Bacteria
A molecular target for treating tuberculosis (TB) and other pathogenic bacteria is Class II fructose 1,6-bisphosphate aldolase (FBA). Class II FBAs are critical for bacterial, fungal and protozoan glycolytic/gluconeogenesis pathways due to their ability to catalyze the reversible enol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P) to fructose 1,6-bisphosphate (FBP). Importantly, humans lack this type of aldolase, which make Class II FBA a promising therapeutic target. Small drug-like molecules that inhibit Class II FBA represent a new class of compounds structurally divergent from existing antibiotics, for which bacterial resistance has evolved.
Fructose-bisphosphate aldolase (FBA) (EC 4.1.2.13) is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP). There are two families of aldolases. Class II FBA differ from Class I FBA in that instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, Class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming DHAP and GAP. Class II FBA play an essential role in pathogenic bacteria, and accordingly are potential antibacterial targets. Although structural studies of Class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for Class II FBAs was not previously identified.
We have used the potent Class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. We observed well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. The structure of MtFBA in its holoenzyme form is described by S. Pegan et al., Biochemistry. 2013 Feb. 5; 52(5):912-25.
FIG. 1 shows MtFBA's essential role in the gluconeogenesis and glycolysis pathways. Fructose 1,6-bisphosphate (FBP) is depicted in the linear MtFBA substrate form.
Antibiotic Activity of Compounds Derived from 8-Hydroxyquinoline-2-Carboxylic Acid (HCA)
To identify new antibiotics targeting MtFBA, chemical fragments were screened for their ability to simulate the enolate transition state's hydroxamic acid of DHAP with MtFBA's active site Zn(II), but be devoid of groups that would be interfere with pharmaceutical development. 8-hydroxyquinoline-2-carboxylic acid (HCA) and derivatives thereof, as described in more detail below, were identified as having superior activity.
There is no logical basis that would suggest a priori that HCA and related structures would act as selective inhibitors of MtFBA. In fact, the data show that HCA interacts with MtFBA through an induced fit mechanism. In other words, HCA creates its own binding pocket. 8-hydroxyquinoline like derivatives that have been studied previously were viewed as acting on tuberculosis and other bacteria by chelating free metals in solution. Thus, no rational attempt to improve them, or give rise to the 8-hydroxyquinoline like derivatives proposed here to bind selectively with MtFBA would have logically occurred.
FIG. 2 shows X-ray structure of HCA bound to MtFBA. In FIG. 2A HCA (the bicyclic compound) is shown bound to neighboring amino acid residues in MtFBA. The density shell shown around the HCA reflects fo-fc density at 3σ. The density around the amino acid residues reflects 2fo-fc at 1σ for MtFBA residues forming non-hydrophobic interactions with HCA. Dashed lines illustrate specific interactions with water rendered as a cyan sphere. FIG. 2B is another view with MtFBA-PGH structure overlaid. Zn(II) and residues in frame belonging to the MtFBA-PGH structure are rendered in grey. FIG. 2C shows HCA binding cavity on MtFBA. Waters are represented as in panel (A) with two prominent pockets denoted.
Advantages Over Currently Available Antibiotics:
The antibiotic compounds of this invention represents a new class that are structurally divergent from existing antibiotics, for which bacterial resistance has evolved. As Class II FBA is central to M. tuberculosis as well as other bacterial and parasitic protozoan organisms, alterations to this enzyme in an effort to build drug-resistance would be deleterious to the bacteria and protozoan. As a result, pathogenic bacteria and protozoan are less likely to be able to build a resistance to 8-hydroxyquinoline-2-carboxylic acid based inhibitors of Class II fructose 1,6-bisphosphate aldolase than previously available antibiotics.
Previously known Class II FBA inhibitors have been substrate mimics. In other words, variations on the Class II FBA substrates dihydroxyacetone or fructose 1,6-bisphosphate. As a result, they have phosphate groups that are required for specificity and potency but also impede their ability to cross the cellular membranes of mammalian cells and tuberculosis. 8-hydroxyquinoline-2-carboxylic acid has no such groups or requirements for them to achieve equal or better inhibition.
HCA analogues according to this invention are drug-like according to Lipinski's rule of 5 and other pharmaceutical guidelines. Using the widely viewed parameters of drug-likeness, MW≦500, clogP≦5, H-bond donors≦5, H-bond acceptors≦10, tPSA≦100, and rotatable bonds≦8, 8-hydroxyquinoline-2-carboxylic acid has a MW of 189.2, clogP of 1.3, two H-bond donors, four H-bond acceptors, and a tPSA of 70.4. Lipinski, C. A, et al., Adv. Drug Delivery Rev. 2001. 46(1-3):3-26; Rees, D. C, et al., Nat Rev Drug Discov, 2004. 3(8):660-72.; Veber, D. F, et al., J Med Chem, 2002. 45(12):2615-23.
All previous Class II FBA inhibitors have focused on the narrow and highly charged Class II FBAs active sites. This impedes any further addition of chemical groups to enhance in vitro, or in vivo, efficacy. However, HCA and associated analogues alter the MtFBA's active site. By doing so, they generate openings for additional chemical groups that can facilitate further pharmacological improvement.
Human analogues for Class II FBAs do not exist. By all previous Class II FBA inhibitors maintaining similarity to FBA substrates there is an inherent possibility of toxicity via either class I FBAs, or other human enzymes that utilize DHAP, G3P, or FBP. As 8-hydroxyquinoline-2-carboxylic acid and other listed derivatives create a unique binding pocket in Class II FBA and don't mimic FBA substrates, the risk of toxicity by them serving as a substrate for other human enzymes is predictably lower.
Model Compounds
This invention provides antibiotics for tuberculosis and other pathogenic bacteria through the noncompetitive inhibition of M. tuberculosis Class II 1,6-bisphosphate aldolase.
FIG. 3 shows similarity of key residues of FBA from different pathogens around about the HCA binding pocket. Due to the conserved nature of Class II 1,6-bisphosphate aldolases, HCA can be used to treat and manage a wide range of other pathogenic bacteria and parasitic eukaryotes.
Model compounds are based on or derivatized from 8-hyroxyquinoline-2-carboxylic acid (HCA). Exemplary are compounds having the structure shown in Formula (I).




Exemplary substituents include the following:

    
    
        R7=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH
        R6=H, alkyl, alkenyl, alkynyl, F, Cl, Br, or CF3 
        R5=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH
        AH4=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH
        AH3=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH
        Z2=CO2H, CO2R, CONH2, or CONHR, where R is alkyl, alkenyl, alkynyl, aryl, or heteroaryl.
    
    


The term “alkyl” as used in this disclosure refers to a branched or unbranched, saturated or unsaturated or cyclic hydrocarbon radical of between 1 and 50 carbon atoms or between 1 and 20 carbon atoms. Unless specified otherwise, an alkyl group may be an unsubstituted hydrocarbyl, or it may be a heteroalkyl in which one or more hydrogen atoms and/or any carbon of the alkyl is replaced by a heteroatom such as N, O, P, or S. Similarly, an alkenyl or alkynyl group may be branched, unbranched, or cyclical; it may be a hydrocarbyl or comprise a heteroatom such as N, O, P, or S.
The term “aryl” refers to an aromatic substituent, which may be a single aromatic ring or multiple aromatic rings that are fused together, linked covalently, or linked to a common group such as a methylene or ethylene biradical. Aryl groups may have between 1 and 50 carbon atoms or between 1 and 20 carbon atoms. Unless specified otherwise, aryl groups may be hydrocarbyl groups, or heteroaryl groups wherein one or more carbon atoms of the aromatic ring(s), substituents or bridges are replaced by a heteroatom(s) such as N, O, P, or S. In some embodiments of the invention, the —OH group depicted in Formula I may be substituted with a sulfhydryl or alkoxyl group. In general terms, Z2 may be a carboxylic acid, ester, alkoxyl group, alcoxylamine, a sulfhydryl derivative, or an aryl or heteroaryl group.
Particular illustrations are as follows:










wherein:

    
    
        1 8-hydroxy-6-methylquinoline-2-carboxylic acid
        2 8-hydroxy-5-methylquinoline-2-carboxylic acid
        3 8-hydroxy-7-methylquinoline-2-carboxylic acid
        4 methyl 8-hydroxy-6-methylquinoline-2-carboxylate
        5 methyl 8-hydroxy-5-methylquinoline-2-carboxylate
        6 methyl 8-hydroxy-7-methylquinoline-2-carboxylate
        7 8-hydroxy-6-methylquinoline-2-carboxamide
        8 8-hydroxy-5-methylquinoline-2-carboxamide
        9 8-hydroxy-7-methylquinoline-2-carboxamide
        10 6-fluoro-8-hydroxyquinoline-2-carboxylic acid
        11 5-fluoro-8-hydroxyquinoline-2-carboxylic acid
        12 7-fluoro-8-hydroxyquinoline-2-carboxylic acid
        13 5,6,7-trifluoro-8-hydroxyquinoline-2-carboxylic acid
        14 5-fluoro-8-hydroxy-6-methylquinoline-2-carboxylic acid
        15 7-fluoro-8-hydroxy-6-methylquinoline-2-carboxylic acid
        16 2-(1H-imidazol-5-yl)-6-methylquinolin-8-ol
        17 2-(1H-imidazol-5-yl)-5-methylquinolin-8-ol
        18 2-(1H-imidazol-5-yl)-7-methylquinolin-8-ol
        19 6-fluoro-2-(1H-imidazol-5-yl)quinolin-8-ol
        20 5-fluoro-2-(1H-imidazol-5-yl)quinolin-8-ol
        21 7-fluoro-2-(1H-imidazol-5-yl)quinolin-8-ol
        22: 2-(benzo[d]oxazol-2-yl)-6-fluoroquinolin-8-ol
        23: 2-(benzo[d]thiazol-2-yl)-6-fluoroquinolin-8-ol
        24: 2-(1H-benzo[d]imidazol-2-yl)-6-fluoroquinolin-8-ol
    
    


In reference to FIG. 8A, some embodiments of the invention optionally contain a pharmacophore that comprises a two ring conjugated system that provide stability for a hydrogen donor at position R8 (depicted in Formula (I) as a hydroxyl group), as well as a chemical moiety containing a hydrogen donor/accepter at position Z2, such as a carboxylic acid. The addition of foliage in the terms of a hydrophobic entity at position R6 and other hydrogen donor/acceptors at R7, R5, AH4, and/or AH3 to facilitate ligand-protein H-bonds may be used to increase potency. Alteration of the zinc interacting pharmacophore could occur by alternating the nitrogen with another nucleophile such as sulfur or oxygen. Also, the carboxylic acid could be substituted with other nucleophile containing groups such as an imidazole ring system.
Preparation
The synthesis of HCA derivatives according to this invention can be achieved by applying the Skraup reaction to commercially available anilines. The reader is generally referred to Manske, R. H, The chemistry of quinolines. Chemical Reviews, 1942. 30(1):113-144.
Referring to FIG. 4A, an analine according to Formula (2) is converted to a bicyclic compound as described in Manske, supra. This process is tolerant of unprotected phenols and results in the formation of differentially substituted quinoline ring systems of Formula (3) in high yields. The quinolines can then be subjected to an established four-step sequence to append the 2-carboxylic acid moiety giving a set of HCA derivatives according to Formula (4). Shrader, W. D. et al., Tetrahedron Letters, 1988. 29(12):1351-1354. These compounds are then tested in binding assays to provide initial SAR data.
Replacement of the 2-carboxylic acid moiety, designated “Z2” in Formula (1), can serve as an additional point of diversity and optimization. Various ester and amide analogs could be prepared using standard organic synthesis. A pyridine ring at the 2-position can also be incorporated into the 8-hydroxyquinoline scaffolds by employing the Friedländer condensation of readily available materials. El Ojaimi et al., Inorganic Chemistry, 2011. 50(21):10966-10973.
The Doebner-Miller reaction (Irving, H. et al., J. Chem. Soc. 1954, 3782-3785) can also be applied for synthesis of HCA derivatives, as depicted in FIG. 4B. This process allows for methyl group incorporation at C2 directly from the cyclization event to give products of Formula (5). A benzylic oxidation to the carboxylic acid is then readily achieved using selenium dioxide (SeO2). Nycz, J. E. et al., J. Mol. Struct. 2013, 1032, 159-168. This method complements the Skraup reaction protocol in preparation of HCA analogs with various R groups on the aniline of Formula (2).
Depending on initial SAR data obtained from binding assays, replacement of the 2-carboxylic acid moiety can then serve as an additional point of diversity. Various ester and amide analogs can be prepared using standard organic synthesis. A pyridine ring at the 2-position can also be incorporated into the 8-hydroxyquinoline scaffolds by employing the Friedländer condensation of readily available materials. Ojaimi, M. E. et al., Inorg. Chem. 2011, 50, 10966-10973.
Testing
Enzymatic activity of candidate antibiotic and antiparasitic compounds of this invention can be assessed using isolated or recombinant Class II FBA of bacterial or parasite origin, preferably derived from or related to the intended target microorganism. Enzymatic activity is measured by contacting the enzyme with a suitable substrate, such as fructose 1,6-bisphosphate, and measuring formation of a product such as dihydroxyacetone phosphate (DHAP) or glyceraldehyde 3-phosphate (GAP). If the activity is measurably lower in the presence of the candidate compound than in its absence, then the compound has FBA inhibitory activity and is a candidate antibiotic and antiparasitic compound. The compound may also be screened with recombinant or isolated Class I FBA (for example, of human or mammalian origin) to determine cross-inhibition. Compounds that specifically inhibit Class II FBA but not Class I FBA are generally preferred.
Alternatively or in addition, compounds can be screened for antibiotic and/or antiparasitic activity by contacting them with the target microorganism, for example, in tissue culture. Efficacy and safety can be confirmed in preclinical animal models and human clinical trials.
Use in Therapy
The essential role of Class II FBAs in bacteria can be illustrated through knockout studies of gram positive and negative bacteria including M. tuberculosis, E. coli, Streptomyces galbus, Bacillus subtilis, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Candida albicans. Even when bacteria such as E. coli and other autotrophic prokaryotes possess both class I and Class II FBAs, class I FBAs are only conditionally expressed with Class II FBAs being essential.
FIG. 3 shows the high similarity amongst Class II FBAs from different bacteria around HCA induced pocket. Structural alignments of MtFBA a Class IIa FBA with E. coli 's Class IIa FBA and that of B. anthracis's Class IIb FBA further reinforces the conserved nature of the HCA induced pocket. Accordingly, the antibiotic compounds of this invention can be employed for treatment of a wide range of bacteria.
With respect to parasites, Class II FBAs in G. lamblia (Giardia), cryptosporidium parvum (Crypto), Trypanosoma brucei (Trypanosomiasis), and Plasmodium falciparum (malaria) are predicted to be essential. As with bacteria, Class II FBAs from these protozoan also have high similarity within the hydroxyquinoline-2-carboxylic acid induced Class II FBA pocket. As a result, 8-hydroxyquinoline-2-carboxylic acid based inhibitors could practically be employed to treat or protect against infection by any of these agents, and (by analogy) a broad range of similar parasitic organisms.
One or more HCA compounds and derivatives according to this invention may be formulated in a suitable excipient or carrier for administration orally, by injection, or topically. For oral administration, a dose of 1 to 25 mg/kg/day (or 5 to 10 mg/kg/day) may constitute a therapeutically effective amount. When the compound is used as part of a soap or disinfectant, a concentration of 0.05 to 1%, or about 0.3% (wt/wt) may be suitable. A “therapeutically effective amount” of a drug refers to an amount of a drug that, when administered to a patient to treat a condition such as cancer, will have a beneficial effect, such as alleviation, amelioration, palliation or elimination infection, a reduction in symptoms or signs of the disease, or cosmetic improvement.
Suitable dosage forms formulated as a medicament can be produced and distributed as a the combination or kit which may also contain or be marketed in combination with written instructions that direct the clinician on the use of the elements of the kit for chemotherapy in accordance with the invention.
EXAMPLES
FIG. 5 provides data from the calorimetric titration of 8-hydroxyquinoline-2-carboxylic acid (HCA). Left-side panels show 5 mM Regis 5 titrated into 700 μM of MtFBA demonstrating a Kd=6.94±0.97 μM, ΔH=−28.73±0.58 kJ mol−1, ΔS=2.44±3.12 J mol−1 K−1, and n=0.94±0.14. Right-side panels show 1 mM Regis 5 titrated into MtFBA buffer with 200 μM ZnCl2, exhibiting no appreciable binding. Top graphs represent raw heat data and bottom graphs are integrated heat peaks gained at 25° C. from 25 injections of Regis 5 into 170 μL of 20 mM Tricine pH 8.0, 100 mM NaCl, and either (a) 700 μM MtFBA with 100 μM ZnCl2 or (b) 200 μM ZnCl2. Data sets were collected in duplicate, analyzed with NanoAnalyzeTM software, and fit to an independent model concurrently with a bank constant model to adjust for a heat of dilution. The line shows the best fit to an independent model.
FIG. 6 provide MtFBA inhibitor properties of HCA. FIG. 6A is a Lineweaver-Burk plot of the kinetics of inhibition of MtFBA by 8-hydroxyquinoline-2-carboxylic acid against MtFBA for varying concentrations of FBP (●) 9.375 μM, (◯) 18.75 μM, (▾) 37.5 μM, and (▪) 150 μM. The inset is a Michaelis-Menten plot of inhibition of MtFBA by serial dilutions of 8-hydroxyquinoline-2-carboxylic acid against MtFBA demonstrating an IC50=17±2.1 μM. FIG. 6B is Isothermal Titration calorimetry (ITC) of HCA binding to MtFBA (solid curved line), or blank Zn(II) buffer (top dotted line).
FIG. 7A is the amino acid sequence alignment of Class II FBAs from pathogenic bacteria. FBAs are from the H37RV strain of M. tuberculosis (protein accession code NP_334786) (SEQ. ID NO:1), Yersinia pestis (protein accession code ZP_04518851) (SEQ. ID NO:2), Staphylococcus aureus (protein accession code QHE75) (SEQ. ID NO:3), Bacillus anthracia (PDB code 3Q94) (SEQ. ID NO:4), and Klebsiella pneumonia (protein accession code ZP_14594173) (SEQ. ID NO:5). Asterisks denote residues involved in hydrophobic interactions as well as hydrogen bonds formed between MtFBA and HCA. FIG. 7B is the amino acid sequence of human Class I FBA (SEQ. ID NO:6).
FIG. 8 is another depiction of the binding of 8-hydroxyquinoline-2-carboxylic acid (HCA) to tuberculosis MtFBA. FIG. 8A shows the general chemical structure of 8-hydroxyquinoline-2-carboxylic acid and its chemical scaffold. FIG. 8B is the X-ray crystal structure of 8-hydroxyquinoline-2-carboxylic acid bound to MtFBA. FIG. 8C is a surface rendering to reveal 8-hydroxyquinoline-2-carboxylic acid bound to MtFBA binding cavity.
The following table shows the limited structure activity relationship of a portion of the chemical space surrounding the active site zinc interacting pharmacophore of 8-hydroxyquinoline-2-carboxylic acid. Numbering of the substituents is in accordance with FIG. 8A.



























% Inhibition 



Compound
R8
R7
R6
R5
AH4
AH3
Z2
at 1 mM
IC50 (μM)
























5
OH
H
H
H
H
H
COOH
95 ± 4.1
  14 ± 2.0


6
OH
H
H
H
H
H
H
54 ± 18 
300 ± 67


7
OH
H
H
H
H
H
NH2
56 ± 2.6
NA


8
OH
H
H
H
H
H
OH
65 ± 4.1
NA


18
NH2
H
H
H
H
H
H
68 ± 2.2
 79 ± 10


19
H
H
H
H
H
H
COOH
 11 ± 0.05
NA


23
NH(SO2)CH3
H
H
H
H
H
H
32 ± 1.1
NA


28
H
H
H
H
H
H
OH
12 ± 9.5
NA


31
COOH
H
H
H
H
H
H
9.9 ± 1.6 
NA


32
H
H
H
H
H
H
NH2
12 ± 9.5
NA


34
OH
H
H
H
H
H
NH(SO2)CH3
12 ± 5.4
570 ± 87


35
NO2
H
H
H
H
H
COOH
31 ± 8.0
NA


36
NH2
H
H
H
H
H
COOH
22 ± 6.2
NA


43
OH
H
H
H
OH
H
COOH
12 ± 4.4
NA









FIG. 9 illustrates HCA's potential as a class II FBA broad-spectrum inhibitor. Class II FBAs can be broken down into two families (a/b) whose distribution among bacterium is independent of Gram staining determined phylogenetic groups. In this illustration, a single concentration of HCA at 25 μM was tested for the inhibition of class IIa FBA isolated from E. coli and class IIb FBA originating from methicillin-resistant S. aureus (MRSA).
As shown in FIG. 9, HCA demonstrated a 42.2±2.8% inhibition against E. coli and 64.3±0.6% inhibition against MRSA. Error bars represent standard deviations from the average. To demonstrate that HCA is selective for class II FBAs over their class I counterparts, class I FBAs isolated from both rabbit and human muscle were tested against HCA. Unlike class II FBAs, HCA showed no inhibitory affects against either class I FBA even at concentrations as high as 1 mM, which forecasts a low probability of toxicity through class I FBA inhibition in humans.
FIG. 10 shows the active site for SaFBA in the crystal structure with citrate bound in the HCA-like pocket. The X-ray structure was determined to 2.1 Å resolution of the class IIb FBA from MRSA (SaFBA). A citrate molecule was visualized within the SaFBA's active sites occupying a pocket similarly to that formed by HCA in the class II FBA originating from Mycobacterium tuberculosis (MtFBA). The binding of citrate by SaFBA, as was the case with HCA and MtFBA, displaced the structural motif, known as the Z-loop, in SaFBA. As a result, the SaFBA-citrate complex demonstrates that Z-loop flexibility is not limited to just MtFBA. With HCA also inhibiting SaFBA with comparable potency, the SaFBA-citrate complex points to a likely common mode of inhibition of HCA for SaFBA.
FIG. 11 shows the 6F derivative of HCA bound to MtFBA. Using the X-ray structure of class II FBA originating from Mycobacterium tuberculosis (MtFBA) bound to HCA, the HCA scaffold's potency toward the enzyme was improved by the addition of fluorine at position 6 (6F-HCA). Adding fluorine at position 6 was sourced from the fact that a void in the MtFBA-HCA structure was present by valine residue 165. A 2.1 Å X-ray structure of 6F-HCA bound to MtFBA found not only to occupy this space, but also increase potency toward the enzyme by 50%. This further validates that the HCA scaffold is acting through displace the Z-loop. Activity of compounds based on the HCA scaffold can be rationally improved by addition of functional groups, as illustrated earlier in this disclosure.
Additional Information


    1. Global tuberculosis control—surveillance, planning, financing, 2008, World Health Organization: Geneva, Switzerland. p. 1-5.
    2. World Health Organization, Global tuberculosis report 2012 (in IRIS). 2012, Geneva: World Health Organization. viii, 272 p.
    3. World Health Organization, UNAIDS, and UNICEF, Global HIV/AIDS response: epidemic update and health sector progress towards universal access: progress report 2011. 2011, Geneva: World Health Organization. viii, 224 p.
    4. Implementing the Stop TB Strategy: a handbook for national tuberculosis, 2008, World Health Organization: Geneva, Switzerland. p. 1-198.
    5. Perez, F. and D. Van Duin, Carbapenem-resistant Enterobacteriaceae: A menace to our most vulnerable patients. Cleve Clin J Med, 2013. 80(4):225-33.
    6. Scheffler, R. J, et al., Antimicrobials, drug discovery, and genome mining. Appl Microbiol Biotechnol, 2013. 97(3):969-78.
    7. Froude, J. W, et al., Antibodies for biodefense. MAbs, 2011. 3(6):517-27.
    8. de la Paz Santangelo, M, et al., Glycolytic and non-glycolytic functions of Mycobacterium tuberculosis fructose-1,6-bisphosphate aldolase, an essential enzyme produced by replicating and non-replicating bacilli. J Biol Chem, 2011. 286(46):40219-31.
    9. Fonvielle, M, et al., Synthesis and biochemical evaluation of selective inhibitors of Class II fructose bisphosphate aldolases: towards new synthetic antibiotics. Chemistry, 2008. 14(28):8521-9.
    10. Fonvielle, M, et al., New highly selective inhibitors of Class II fructose-1,6-bisphosphate aldolases. Bioorg Med Chem Lett, 2004. 14(11):2923-6.
    11. Gallein, A, et al., Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase. Biochemistry, 2009. 48(14):3186-96.
    12. Gerdes, S. Y, et al., Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol, 2003. 185(19):5673-84.
    13. Labbe, G, et al., Evaluation of four microbial Class II fructose 1,6-bisphosphate aldolase enzymes for use as biocatalysts. Protein Expr Purif, 2011. 80(2):224-33.
    14. Labbe, G, et al., Development of metal-chelating inhibitors for the Class II fructose 1,6-bisphosphate (FBP) aldolase. J Inorg Biochem, 2012. 112:49-58.
    15. Pegan, S. D, et al., Active site loop dynamics of a Class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. Biochemistry, 2013. 52(5):912-25.
    16. Pegan, S. D, et al., Structural basis for catalysis of a tetrameric Class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. J Mol Biol, 2009. 386(4):1038-53.
    17. Ramsaywak, P. C, et al., Molecular cloning, expression, purification, and characterization of fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis—a novel Class II A tetramer. Protein Expr Purif, 2004. 37(1):220-8.
    18. Gavalda, S, et al., N-Sulfonyl hydroxamate derivatives as inhibitors of Class II fructose-1,6-diphosphate aldolase. Bioorg Med Chem Lett, 2005. 15(24):5375-7.
    19. Li, Z, et al., Rational design, synthesis and evaluation of first generation inhibitors of the Giardia lamblia fructose-1,6-biphosphate aldolase. J Inorg Biochem, 2011. 105(4):509-17.
    20. Manske, R. H, The chemistry of quinolines. Chemical Reviews, 1942. 30(1):113-144.
    21. Shrader, W. D, et al., Synthesis of a Novel Hexadentate Chelating Agent Based on 8-Hydroxyquinoline. Tetrahedron Letters, 1988. 29(12):1351-1354.
    22. El Ojaimi, M. and R. P. Thummel, Polydentate Analogues of 8-Hydroxyquinoline and Their Complexes with Ruthenium. Inorganic Chemistry, 2011. 50(21):10966-10973.
    23. Baba, T, et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol, 2006. 2:2006 0008.
    24. Giaever, G, et al., Functional profiling of the Saccharomyces cerevisiae genome. Nature, 2002. 418(6896):387-91.
    25. Jacobs, M. A, et al., Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci USA, 2003. 100(24):14339-44.
    26. Kobayashi, K, et al., Essential Bacillus subtilis genes. Proc Natl Acad Sci USA, 2003. 100(8):4678-83.
    27. Liberati, N. T, et al., An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci USA, 2006. 103(8):2833-8.
    28. Rodaki, A, T. Young, and A. J. Brown, Effects of depleting the essential central metabolic enzyme fructose-1,6-bisphosphate aldolase on the growth and viability of Candida albicans: implications for antifungal drug target discovery. Eukaryot Cell, 2006. 5(8):1371-7.
    29. Sassetti, C. M, D. H. Boyd, and E. J. Rubin, Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol, 2003. 48(1):77-84.
    30. Song, J. H, et al., Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. Mol Cells, 2005. 19(3):365-74.
    31. Wehmeier, U. F, Molecular cloning, nucleotide sequence and structural analysis of the Streptomyces galbus DSM40480 fda gene: the S. galbus fructose-1,6-bisphosphate aldolase is a member of the Class II aldolases. FEMS Microbiol Lett, 2001. 197(1):53-8.
    32. Stribling, D. and R. N. Perham, Purification and characterization of two fructose diphosphate aldolases from Escherichia coli (Crookes' strain). Biochem J, 1973. 131(4):833-41.
    33. Scamuffa, M. D. and R. M. Caprioli, Comparison of the mechanisms of two distinct aldolases from Escherichia coli grown on gluconeogenic substrates. Biochim Biophys Acta, 1980. 614(2):583-90.
    34. Henze, K, et al., Sequence and phylogenetic position of a Class H aldolase gene in the amitochondriate protist, Giardia lamblia. Gene, 1998. 222(2):163-8.
    35. Clayton, C. E, Structure and regulated expression of genes encoding fructose biphosphate aldolase in Trypanosoma brucei. EMBO J, 1985. 4(11):2997-3003.
    36. Knapp, B, E. Hundt, and H. A. Kupper, Plasmodium falciparum aldolase: gene structure and localization. Mol Biochem Parasitol, 1990. 40(1):1-12.
    37. Lipinski, C. A, et al., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 2001. 46(1-3):3-26.
    38. Rees, D. C, et al., Fragment-based lead discovery. Nat Rev Drug Discov, 2004. 3(8):660-72.
    39. Veber, D. F, et al., Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem, 2002. 45(12):2615-23.


For all purposes in the United States of America, each and every publication and patent document cited herein is incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference.
While the invention has been described with reference to the specific embodiments, changes can be made and equivalents can be substituted to adapt to a particular context or intended use, thereby achieving benefits of the invention without departing from the scope of what is claimed.

## Claims

1. A compound according to Formula (I)



wherein
R7=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH
R6=F
R5=H, alkyl, alkenyl, alkynyl, F, Cl, Br, CF3, or OH
AH4=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH
AH3=H, alkyl, alkenyl, alkynyl, aryl, F, Cl, Br, CF3, or OH
Z2=CO2H, CO2R, CONH2, CONHR, aryl, or heteroaryl,

wherein the compound is one of the following compounds:
6-fluoro-8-hydroxyquinoline-2-carboxylic acid,
5,6,7-trifluoro-8-hydroxyquinoline-2-carboxylic acid,
6-fluoro-2-(1H-imidazol-5-yl)quinolin-8-ol,
2-(benzo[d]oxazol-2-yl)-6-fluoroquinolin-8-ol,
2-(benzo[d]thiazol-2-yl)-6-fluoroquinolin-8-ol, and
2-(1H-benzo[d]limidazol-2-yl)-6-fluoroquinolin-8-ol.

2. The compound of claim 1, which inhibits Class II fructose 1,6-bisphosphate aldolase (FBA) of M. tuberculosis (SEQ. ID NO:1), but not Class I FBA of homo sapiens (SEQ. ID NO:6).

3. A pharmaceutical product comprising a compound according to claim 1 in a pharmaceutical excipient formulated for oral administration.

4. A compound according to claim 1, formulated as a soap or disinfectant.

5. The compound 6-fluoro-8-hydroxyquinoline-2-carboxylic acid

6. A compound according to claim 1, which is 5,6,7-trifluoro-8-hydroxyquinoline-2-carboxylic acid

7. The compound 6-fluoro-2-(1H-imidazol-5-yl)quinolin-8-ol

8. A compound according to claim 1, which is 2-(benzo[d]oxazol-2-yl)- 6-fluoroquinolin-8-ol

9. A compound according to claim 1, which is 2-(benzo[d]thiazol-2-yl)- 6-fluoroquinolin-8-ol

10. A compound according to claim 1, which is 2-(1H-benzo[d]imidazol-2-yl)- 6-fluoroquinolin-8-ol

11. A pharmaceutical product comprising a composition according to claim 3 packaged with instructions for treatment or prevention of a bacterial or parasitic infection.