WO2019016781A1 - Compounds and use thereof for the treatment of microbial infections - Google Patents

Compounds and use thereof for the treatment of microbial infections Download PDF

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Publication number
WO2019016781A1
WO2019016781A1 PCT/IB2018/055458 IB2018055458W WO2019016781A1 WO 2019016781 A1 WO2019016781 A1 WO 2019016781A1 IB 2018055458 W IB2018055458 W IB 2018055458W WO 2019016781 A1 WO2019016781 A1 WO 2019016781A1
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butyl
alkenyl
compounds
alkyl
compound
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PCT/IB2018/055458
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French (fr)
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Yi Tsun Richard Kao
Peng Gao
Xuechen Li
Ming Liu
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University of Hong Kong HKU
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University of Hong Kong HKU
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Priority to CN201880048665.6A priority Critical patent/CN111094280B/en
Priority to AU2018304613A priority patent/AU2018304613A1/en
Priority to KR1020207003291A priority patent/KR102655541B1/en
Priority to JP2020501516A priority patent/JP7232238B2/en
Priority to BR112020001277-7A priority patent/BR112020001277B1/en
Priority to CA3070205A priority patent/CA3070205A1/en
Application filed by University of Hong Kong HKU filed Critical University of Hong Kong HKU
Priority to EP18835480.7A priority patent/EP3655404A4/en
Publication of WO2019016781A1 publication Critical patent/WO2019016781A1/en
Priority to IL271863A priority patent/IL271863B/en
Anticipated expiration legal-status Critical
Priority to AU2022279489A priority patent/AU2022279489A1/en
Ceased legal-status Critical Current

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    • C07D209/04—Indoles; Hydrogenated indoles
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    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
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    • A61K31/167—Amides, e.g. hydroxamic acids having aromatic rings, e.g. colchicine, atenolol, progabide having the nitrogen of a carboxamide group directly attached to the aromatic ring, e.g. lidocaine, paracetamol
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    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
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    • A61K31/454—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
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Definitions

  • the present invention relates to compounds and derivatives thereof, composition comprising said compounds and/or derivatives, and use thereof for treating microbial infections and/or related diseases or conditions. More specifically, the present compounds, derivatives, composition comprising thereof, and use are for bacterial infections.
  • Staphylococcus aureus is a major human pathogen in communities and hospitals, causing a variety of infections that ranges from harmless infections to life threatening conditions [18]. With the wide-spread dissemination of methicillin-resistant S. aureus (MRS A) in hospitals and in communities, treating S. aureus associated infections has become increasingly difficult [19]. Staphyloxanthin has been proven to be an important factor in promoting bacterial invasion [1]. Five genes, crtOPQMN, located in an operon are responsible for the biosynthesis of the pigment. The transcription of the operon is driven by a o B -dependent promoter upstream of crtO, and ends with a terminator downstream of crtN [2]. The pigments that endow S. aureus with a golden color also make it resistant to attack from reactive oxygen species (ROS) and neutrophils [3]. Pigmented bacteria have increased resistance to the host's immune defenses [4].
  • ROS reactive oxygen species
  • Dehydrosqualene synthase catalyses the first step of the biosynthetic pathway, was shown to be a target for anti-infective therapy based on virulence factor neutralization.
  • Diphenylamine was found to be an inhibitor of 4,4-diapophytoene desaturase (CrtN) at high micromolar level [5].
  • CrtN 4,4-diapophytoene desaturase
  • Another potential inhibitor of CrtN, naftifine, a FDA approved antifungal compound was shown to reduce bacterial load in different mice infection models [6].
  • CrtM Dehydrosqualene synthase
  • R 1 , R 2 , and R 3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; al
  • R 1 and R 2 can be bonded together to form a four-, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl;
  • R 4 and R 5 can be independently or jointly selected from the group consisting of: a (Ci- 4 )alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C 2- 4 )alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl.
  • a (Ci- 4 )alkyl such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl
  • (C 2- 4 )alkenyl such as ethenyl, propenyl, butenyl, where the double bond can be located
  • the present compounds and/or the derivatives thereof can be an anti- virulent agent for bacteria.
  • the present compounds and/or the derivatives thereof are effective in reducing virulence of bacteria.
  • the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise Staphylococci sp.
  • the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise Staphylococcus aureus (S. aureus).
  • the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise methicillin-resistant S. aureus (MRSA).
  • MRSA methicillin-resistant S. aureus
  • said reducing the virulence of bacteria by the compounds and/or derivatives thereof comprises inhibiting biosynthesis of staphyloxanthin in said bacteria and/or inhibiting or reducing production of pigments that are resistant to the bacterial host's immune defenses.
  • a composition for preventing and/or treating the microbial infections and/or related diseases or conditions comprising an effective amount of the compounds and/or the derivatives thereof in the first aspect is also provided herein.
  • said microbial infections are bacterial infections.
  • said microbial infections comprise staphylococcal infections.
  • the composition further comprises a pharmaceutically acceptable carrier, salt, ester, expicient, vehicle, prodrug, solvent, and diluent, or any combination thereof.
  • the present invention provides use of the present compounds and/or the derivatives thereof for preventing and/or treating the microbial infections and/or related diseases or conditions including using said compounds and/or derivatives thereof in preparation of a composition for preventing and/or treating microbial infections and/or related diseases or conditions in a subject in need thereof, wherein said composition comprises an effective amount of one or more compounds of Formula (I):
  • R 1 , R 2 , and R 3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; al
  • R 1 and R 2 can be bonded together to form a four-, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl; and where R 4 and R 5 can be independently or jointly selected from the group consisting of: a (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec -butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl.
  • R 1 and R 2 are independently or jointly selected from ⁇ ⁇ ⁇ " ⁇ ° " * and ; R 3 is H or methyl.
  • the microbial infections are bacterial infection.
  • the microbial infections comprise Staphylococcal infections.
  • the microbial infections and/or related diseases or conditions are caused by Staphylococci sp.
  • the Staphylococci sp. comprise Staphylococcus aureus (S. aureus).
  • S. aureus comprise methicillin-resistant S. aureus (MRSA).
  • the microbial infections and/or related diseases or conditions comprise infections of the skin and soft tissue, bone and joint, surgical wound, indwelling devices, lung and heart valves.
  • the present use further comprises reducing virulence of bacteria causing the microbial infections and/or related disease or conditions in said subject being administered with said composition.
  • the present use further comprises inhibiting biosynthesis of staphyloxanthin in said bacteria and/or inhibiting or reducing production of pigments that are resistant to the bacterial host's immune defenses in said subject being administered with said composition.
  • said subject or bacterial host is a mammal.
  • said subject or bacterial host is human.
  • FIGs. 1 A-1D show the in vitro pigment inhibition by compound NP16:
  • FIG. 1A shows the inhibition of wild-type (WT) S. aureus pigmentation using increasing concentrations of NP16;
  • FIG. IB shows the pigment inhibition by NP16;
  • the IC50 for pigment formation is -300 nM;
  • FIG. 1C depicts the chemical structure of compound NP16;
  • FIG. ID shows the growth curve of S. aureus COL in the presence of different concentrations of NP16. All data represent mean values ⁇ SD.
  • FIGs. 2A-2D show that NP16 treatment leads to increased sensitivity to oxidation and neutrophil killing:
  • FIG. 2A depicts the cytotoxic activity of compound NP16 on MDCK cells;
  • FIG. 2B shows the increased susceptibility of the NP16-treated S. aureus COL strain to killing by hydrogen peroxide;
  • FIG. 2C shows the increased susceptibility of the NP16-treated S. aureus COL to killing by neutrophils;
  • FIG. 2D is the UV spectrum of carotenoids extracted from different strains, with or without NP16 treatment. All data represent mean values ⁇ SD (***P ⁇ 0.001; ****P ⁇ 0.0001). P values were determined using GraphPad Prism using an unpaired parametric t test with Welch's correction.
  • FIGs. 3A-3F show the in vivo effect of CrtN and its inhibition by NP16.
  • FIGs. 3 A and 3B show the bacteria recovered from the livers and spleens, respectively, of mice infected with the wild-type COL or COL-AcrtN strains;
  • FIGs. 3C and 3D show the bacteria recovered from the livers and spleens, respectively, of mice infected with the COL strain, with or without compound NP16 treatment;
  • FIG. 3E shows the bacteria recovered from the kidneys of mice infected with clinical isolate strain AE052 or AE052-AcrtN;
  • FIG. 3F shows the bacteria recovered from the kidneys of mice infected with strain AE052, with or without compound NP16 treatment.
  • NP16 and its derivatives have block pigment production in S. aureus by targeting the 4,4- diapophytoene desaturase (CrtN).
  • CrtN 4,4- diapophytoene desaturase
  • S. aureus staphyloxanthin contributes substantially to pathogenesis by interfering with host immune clearance mechanisms, but has little impact on ex vivo survival of the bacteria. Without wanting to be bound by theory, it is provided that agents blocking staphyloxanthin production may discourage the establishment and maintenance of bacterial infection without exerting selective pressure for antimicrobial resistance.
  • NP16 and its derivatives can be represented by Formula (I):
  • R 1 , R 2 , and R 3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; al
  • R 1 and R 2 can be bonded together to form a fo -, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl, such as and ;
  • R 3 is H or methyl;
  • R 4 and R 5 can be independently or jointly selected from the group: a (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl.
  • a (Ci-4)alkyl such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec
  • the compounds of Formula (I) can include, but are not limited to, those compounds listed in Table 1.
  • One or more compounds of Formula (I) can be combined and/or mixed with one or more of a pharmaceutically acceptable carrier, salt, ester, expicient, vehicle, prodrug, solvent, and diluent to make a composition.
  • the phrase "pharmaceutically acceptable” can mean approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals and/or in humans.
  • carrier can refer to a diluent, adjuvant, excipient, and/or vehicle with which the compound and/or antibiotic are administered.
  • Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • phrases “pharmaceutically acceptable salt” can refer to derivatives of the compounds defined herein, wherein the parent compound is modified by making acid or base salts thereof.
  • the method of treating and/or preventing a microbial infection in a subject can include, but is not limited to, administering to a subject an effective amount of one or more compounds of Formula (I).
  • compositions for preventing and/or treating a microbial infection and/or related diseases or conditions can include, but not limited to, using said compound and/or derivatives in preparation of said composition wherein said composition comprises an effective amount of said compound and/or the derivatives thereof, a pharmaceutical carrier, a salt, an ester, an excipient, a vehicle, a prodrug, a solvent, a diluent, or any combination thereof.
  • treatment can refer to arresting or inhibiting, or attempting to arrest or inhibit, the development or progression of an infection and/or causing, or attempting to cause, the reduction, suppression, regression, or remission of an infection and/or a symptom thereof.
  • various clinical and scientific methodologies and assays may be used to assess the development or progression of an infection, and similarly, various clinical and scientific methodologies and assays may be used to assess the reduction, regression, or remission of an infection or its symptoms.
  • Treatment refers to both therapeutic treatment and prophylactic or preventative measures.
  • the infection being treated can include, but is not limited to, Staphylococcus aureus infection. In other forms, the infection being treated is a microbial infection.
  • the administration can include, but is not limited to: administration though oral pathways, which administration includes administration in capsule, tablet, granule, spray, syrup, or other such forms; administration through non-oral pathways, which administration includes administration as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like; administration via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, intradermally, or the like; as well as administration topically; and administration via controlled released formulations, depot formulations, and infusion pump delivery.
  • the compounds can be packaged in solutions of sterile isotonic aqueous buffer to make the composition.
  • the composition can also include a solubilizing agent.
  • the composition of the compounds can be supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or concentrated solution in a hermetically sealed container such as an ampoule or sachette indicating the amount of active agent.
  • the compound If the compound is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
  • an ampoule of sterile water or saline can be provided so that the ingredients may be mixed prior to injection.
  • the term “subject” can refer to an animal.
  • the terms “subject” and “patient” may be used interchangeably herein in reference to a subject.
  • a “subject” can include a human that is being treated for a microbial infection as a patient.
  • animal can refer to a mouse, rat, dog, cat, rabbit, pig, monkey, chimpanzee, and human.
  • an effective amount can be used interchangeably, as applied to the compounds, antibiotics, and pharmaceutical compositions described can mean the quantity necessary to render the desired therapeutic result.
  • an effective amount is a level effective to treat, cure, or alleviate the symptoms of an infection for which the composition and/or antibiotic, or pharmaceutical composition, is/are being administered.
  • Amounts effective for the particular therapeutic goal sought will depend upon a variety of factors including the infection being treated and its severity and/or stage of development/progression; the bioavailability and activity of the specific compound and/or antibiotic, or pharmaceutical composition, used; the route or method of administration and introduction site on the subject; the rate of clearance of the specific composition and other pharmacokinetic properties; the duration of treatment; inoculation regimen; drugs used in combination or coincident with the specific composition; the age, body weight, sex, diet, physiology and general health of the subject being treated; and like factors well known to one of skill in the relevant scientific art. Some variation in dosage will necessarily occur depending upon the condition of the subject being treated, and the physician or other individual administering treatment will, in any event, determine the appropriate dosage for an individual patient. Furthermore, the therapeutic methods described would not only apply to treatment in a subject, but could be applied to cell cultures, organs, tissues, or individual cells in vivo, ex vivo or in vitro.
  • hydrocarbyl as used herein includes reference to a moiety consisting exclusively of hydrogen and carbon atoms; such a moiety may comprise an aliphatic and/or an aromatic moiety. The moiety may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 carbon atoms.
  • hydrocarbyl groups include Ci- 6 alkyl (e.g. Ci, C 2 , C 3 or C 4 alkyl, for example methyl, ethyl, propyl, isopropyl, n-butyl, sec -butyl or tert-butyl); Ci-6 alkyl substituted by aryl (e.g.
  • benzyl or by cycloalkyl (e.g. cyclopropylmethyl); cycloalkyl (e.g. cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl); aryl (e.g. phenyl, naphthyl or fluorenyl) and the like.
  • cycloalkyl e.g. cyclopropylmethyl
  • cycloalkyl e.g. cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl
  • aryl e.g. phenyl, naphthyl or fluorenyl
  • alkyl as used herein includes reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 carbon atoms.
  • alkyl groups include "Ci- 6 alkyl” and "C2-10 alkyl”.
  • the term "Ci- 6 alkyl” as used herein include reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5 or 6 carbon atoms.
  • C2-10 alkyl as used herein include reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 carbon atoms.
  • This term includes reference to groups such as methyl, ethyl, propyl (n-propyl or isopropyl), butyl (n-butyl, sec- butyl or tert-butyl), pentyl, hexyl and the like.
  • the alkyl moiety may have 1, 2, 3, 4, 5 or 6 carbon atoms.
  • alkenyl and C2-6 alkenyl as used herein include reference to a straight or branched chain alkyl moiety having 2, 3, 4, 5 or 6 carbon atoms and having, in addition, at least one double bond, of either E or Z stereochemistry where applicable. This term includes reference to groups such as ethenyl, 2-propenyl, 1-butenyl, 2-butenyl, 3- butenyl, 1-pentenyl, 2-pentenyl, 3-pentenyl, 1-hexenyl, 2-hexenyl and 3-hexenyl and the like.
  • alkynyl and C2-6 alkynyl as used herein include reference to a straight or branched chain alkyl moiety having 2, 3, 4, 5 or 6 carbon atoms and having, in addition, at least one triple bond. This term includes reference to groups such as ethynyl, 1- propynyl, 2- propynyl, 1-butynyl, 2-butynyl, 3-butynyl, 1-pentynyl, 2-pentynyl, 3-pentynyl, 1-hexynyl, 2- hexynyl and 3-hexynyl and the like.
  • alkoxy and Ci-6 alkoxy as used herein include reference to -O-alkyl, wherein alkyl is straight or branched chain and comprises 1, 2, 3, 4, 5 or 6 carbon atoms. In one class of embodiments, alkoxy has 1, 2, 3 or 4 carbon atoms. This term includes reference to groups such as methoxy, ethoxy, propoxy, isopropoxy, butoxy, tert- butoxy, pentoxy, hexoxy and the like.
  • cycloalkyl as used herein includes reference to an alicyclic moiety having 3, 4, 5, 6, 7 or 8 carbon atoms. The group may be a bridged or polycyclic ring system.
  • cycloalkyl groups are monocyclic. This term includes reference to groups such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, norbomyl, bicyclo[2.2.2]octyl and the like.
  • aryl as used herein includes reference to an aromatic ring system comprising 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 ring carbon atoms.
  • Aryl is often phenyl but may be a polycyclic ring system, having two or more rings, at least one of which is aromatic. This term includes reference to groups such as phenyl, naphthyl, fluorenyl, azulenyl, indenyl, anthryl and the like.
  • Cyclic group means a ring or ring system, which may be unsaturated or partially unsaturated but is usually saturated, typically containing 5 to 13 ring-forming atoms, for example a 5- or 6-membered ring.
  • the ring or ring system may be substituted with one or more hydrocarbyl groups. Cyclic group includes carbocyclyl and heterocyclyl moeities.
  • carbocyclyl as used herein includes reference to a saturated (e.g. cycloalkyl) or unsaturated (e.g. aryl) ring moiety having 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 or 16 carbon ring atoms.
  • carbocyclyl includes a 3- to 10-membered ring or ring system and, in particular, 5- or 6-membered rings, which may be saturated or unsaturated.
  • the ring or ring system may be substituted with one or more hydrocarbyl groups.
  • a carbocyclic moiety is, for example, selected from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, norbornyl, bicyclo[2.2.2]octyl, phenyl, naphthyl, fluorenyl, azulenyl, indenyl, anthryl and the like.
  • heterocyclyl as used herein includes reference to a saturated (e.g. heterocycloalkyl) or unsaturated (e.g. heteroaryl) heterocyclic ring moiety having from 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15 or 16 ring atoms, at least one of which is selected from nitrogen, oxygen, phosphorus, silicon and sulphur.
  • heterocyclyl includes a 3- to 10- membered ring or ring system and more particularly a 5- or 6- membered ring, which may be saturated or unsaturated.
  • the ring or ring system may be substituted with one or more hydrocarbyl groups.
  • a heterocyclic moiety is, for example, selected from oxiranyl, azirinyl, 1, 2- oxathiolanyl, imidazolyl, thienyl, furyl, tetrahydrofuryl, pyranyl, thiopyranyl, thianthrenyl, isobenzofuranyl, benzofuranyl, chromenyl, 2H-pyrrolyl, pyrrolyl, pyrrolinyl, pyrrolidinyl, pyrrolizidinyl, imidazolyl, imidazolidinyl, benzimidazolyl, pyrazolyl, pyrazinyl, pyrazolidinyl, thiazolyl, isothiazolyl, dithiazolyl, oxazolyl, isoxazolyl, pyridyl, pyrazinyl, pyrimidinyl, piperidyl, piperazinyl, pyridaziny
  • heterocycloalkyl as used herein includes reference to a saturated heterocyclic moiety having 3, 4, 5, 6 or 7 ring carbon atoms and 1 , 2, 3, 4 or 5 ring heteroatoms selected from nitrogen, oxygen, phosphorus and sulphur.
  • the group may be a polycyclic ring system but more often is monocyclic.
  • This term includes reference to groups such as azetidinyl, pyrrolidinyl, tetrahydrofuranyl, piperidinyl, oxiranyl, pyrazolidinyl, imidazolyl, indolizidinyl, piperazinyl, thiazolidinyl, morpholinyl, thiomorpholinyl, quinohzidinyl and the like.
  • the ring or ring system may be substituted with one or more hydrocarbyl groups.
  • heteroaryl as used herein includes reference to an aromatic heterocyclic ring system having 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 ring atoms, at least one of which is selected from nitrogen, oxygen and sulphur.
  • the group may be a polycyclic ring system, having two or more rings, at least one of which is aromatic, but is more often monocyclic.
  • the ring or ring system may be substituted with one or more hydrocarbyl groups.
  • This term includes reference to groups such as pyrimidinyl, furanyl, benzo[b]thiophenyl, thiophenyl, pyrrolyl, imidazolyl, pyrrolidinyl, pyridinyl, benzo[b] furanyl, pyrazinyl, purinyl, indolyl, benzimidazolyl, quinolinyl, phenothiazinyl, triazinyl, phthalazinyl, 2H-chromenyl, oxazolyl, isoxazolyl, thiazolyl, isoindolyl, indazolyl, purinyl, isoquinohnyl, quinazohnyl, pteridinyl and the like.
  • halogen as used herein includes reference to F, CI, Br or I.
  • halogen containing moiety includes reference to a moiety comprising 1 to 30 plural valence atoms selected from carbon, nitrogen, oxygen and sulphur which moiety includes at least one halogen.
  • the moiety may be hydrocarbyl for example C 1-6 alkyl or C 1-6 alkoxy, or carbocyclyl for example aryl.
  • substituted as used herein in reference to a moiety means that one or more, especially up to 5, more especially 1, 2 or 3, of the hydrogen atoms in said moiety are replaced independently of each other by the corresponding number of the described substituents.
  • optionally substituted as used herein means substituted or un- substituted. It will, of course, be understood that substituents are only at positions where they are chemically possible, the person skilled in the art being able to decide (either experimentally or theoretically) without inappropriate effort whether a particular substitution is possible.
  • enantiomer as used herein means one of two stereoisomers that have mirror images of one another.
  • racemate as used herein means a mixture of equal amounts of enantiomers of a chiral molecule.
  • diastereomer as used herein means one of a class of stereoisomers that are not enantiomers, but that have different configurations at one or more of the equivalent chiral centers.
  • Example of diasteromers are epimers that differ in configuration of only one chiral center.
  • stereoisomer as used herein means one of a class of isomeric molecules that have the same molecular formula and sequence of bonded atoms, but different three- dimensional orientations of their atoms in space.
  • prodrug refers to a medication that is administered as an inactive (or less than fully active) chemical derivative that is subsequently converted to an active pharmacological agent in the body, often through normal metabolic processes.
  • mice were purchased from Charles River Laboratories. S. aureus was propagated in Terrific broth (TB) or on TB agar (Life Technologies). Unless otherwise indicated, all experiments were performed with bacteria derived from light-protected S. aureus 36-48 h stationary phase cultures, the point at which pigmentation phenotypes were readily apparent.
  • MIC was determined by inoculating 5 x 10 4 S. aureus cells in 100 ⁇ BHI medium in 96-well plates with a serial dilution of antibiotics. The MIC was defined as the minimum concentration resulting in a cell density less than 0.05 OD at 620 nm, which corresponded to no visible growth, after incubating for 18 h at 37 °C.
  • S. aureus was propagated in Brain Heart Infusion broth (BHI) or on BHI agar (Oxoid).
  • BHI Brain Heart Infusion broth
  • Oxoid BHI agar
  • the in vitro pigment inhibition studies were performed by S. aureus USA300 cultured in BHI with or without the presence of inhibitor compounds at 37°C and 250 rpm for 36-48 hours.
  • the bacteria were washed twice with PBS prior to the staphyloxanthin purification with methanol.
  • the OD of the extracts were monitor at 450nm using DTX880 multi-plate reader spectrophotometer (Beckman).
  • the concentration range tested for the compounds were between 300nM to 700nM, and control groups were added with equal volume of DMSO.
  • NP16 The cytotoxicity of NP16 in MDCK cells was evaluated by MTT (3-[4,5- dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay according to manufacturer's instructions. A toxic control (1%) SDS was included to ensure the MTT assay was effective. The highest concentration of NP16 that could be used was 500 ⁇ due to solubility limitations. SigmaPlot 11.0 (SPSS, IL) was used for graph plotting. Experiments were repeated twice in triplicate.
  • IC50 values were obtained by fitting the inhibition data to a normal dose-response curve in SigmaPlot (CA).
  • cytotoxicity of NP-16 and some of it analogues in Raw 264.7 cells was also evaluated by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay according to manufacturer's instructions. A toxic control (1%) SDS was included to ensure the MTT assay was working properly. The highest concentration of NP-16 analogues used was 500 ⁇ due to solubility limitations. SigmaPlot 11.0 (SPSS, IL) was used for graph plotting. Experiments were carried out in triplicate and repeated twice. [0081] The cytotoxicity of NP- 16 and some of it analogues was tested against Raw 264.7 cells, and the cell tolerance of each compounds were documented in Table 3.
  • the compounds can exert staphyloxanthin production inhibition.
  • the staphyloxanthin from the overnight- cultured bacteria were extracted with methanol and quantified in via spectrophotometry. The results were presented in relative ratio to NP-16 in both the inhibition ratio as well as the TC50 in Table 3 (compound / analogue numbers correspond to those listed in Table 1).
  • CrtN with a histidine-maltose binding protein (MBP) tag was overexpressed in E. coli Rosetta (DE3) cells.
  • a 10 ml overnight culture was transferred into 1 L of LB medium supplemented with 100 ⁇ g/ml ampicillin.
  • Induction was carried out with 1 mM IPTG for 12 hours at 16°C at an OD of 0.6 at 600 nm.
  • the cell lysate was loaded onto a Ni-NTA column, and CrtN was eluted using a 75-ml linear gradient of 0-0.4 M imidazole in 50 mM sodium phosphate buffer, with 400 mM sodium chloride, pH 6.6.
  • the collected fractions were analysed by SDS-PAGE to confirm the peak for MBP-CrtN.
  • the target peak fractions were concentrated and the buffer was exchanged to loading buffer without imidazole using a PD-10 column (GE Healthcare).
  • the collected solution was treated with TEV protease at 4°C overnight.
  • the protein sample was applied to a maltose column, and the flow-through was collected as native CrtN protein.
  • the substrate (4,4'-diapophytoene) and product (4,4'-diaponeurosporene) were extracted from strains COL-AcrtN and COL-AcrtOP.
  • Carotenoids were extracted from cell pellets using 300 ml of methanol per liter of cultured bacteria pellet until all visible pigments were removed. After centrifugation (4°C and 8,000 g), colored supernatants were pooled and concentrated to 50 ml using an EZ-2 Plus centrifugal evaporator (Genevac Inc., Gardiner, NY, USA). A sample was mixed with 100 ml of EtOAc and 200 ml of NaCl (2.5 M).
  • the extract sample in the upper organic phase was collected, washed with same volume of distilled water, and dried using the EZ-2 Plus evaporator. Dried samples were ready for silica gel isolation or stored at -70 °C prior to analysis.
  • carotenoids were identified using a combination of HPLC retention times, UV-visible absorption spectra, and mass fragmentation spectra. Mass fragmentation spectra were monitored using both negative and positive ion modes in a mass range of mlz 200-1000 on the Varian 1200L LC/MS system equipped with an atmospheric pressure chemical ionization interface.
  • S. aureus was grown in BHI with or without NP16 (40 ⁇ ). After 2 days, bacteria were washed twice in PBS, diluted to a concentration of lxlO 7 CFUs per 100 ⁇ reaction mixture in a 96-well plate. Hydrogen peroxide (H2O2) in PBS was added to a 440 mM final concentration, and the plate was incubated for 1 hr at 37°C with shaking. The reaction was stopped by the addition of l,000U/ml of exogenous catalase (Sigma- Aldrich, St. Louis, MO), and bacterial viability was assessed by plating dilutions on BHI agar plates.
  • H2O2 Hydrogen peroxide
  • PMNs human polymorphonuclear leukocytes
  • mice Eight- to ten-week-old female BALB/c mice were injected intraperitoneally (i.p) with 4xl0 8 CFUs of early stationary phase S. aureus COL. After 3 d, animals were euthanized, the liver and spleen were isolated, homogenized in PBS, and plated on to obtain viable counts. For the treatment study, mice were randomized into two groups at the start of the experiment and administered, i.p., either 0.35 mg of NP16 or PBS with 5% Tween-80 as a control, twice per day, starting on d -1 to d 2 (a total of eight doses for each). Intraperitoneal challenge with 4xl0 8 CFUs of early stationary phases S. aureus COL was performed on d 0. The mice were sacrificed on d 3 for enumeration of bacterial CFUs in liver and spleen homogenates.
  • Compound NP16 (structure shown in FIG. 1C) had potent activity against S. aureus pigment formation in vitro, as shown in FIG. 1A, with IC50 values ranging from 100 to 300 nM (FIG. IB).
  • IC50 values ranging from 100 to 300 nM (FIG. IB).
  • the product of CrtN, 4,4'- diaponeurosporene is a yellowish compound while products prior to CrtM catalysis are colorless.
  • NP16 treatment is proposed to target CrtM or CrtN or other regulators that affect the expression of the crtOPQMN cluster, such as sigB or ispA [10].
  • the MIC of NP16 for USA300 was greater than 500 ⁇ (FIG. ID).
  • oxidation of the terminal methyl group of 4,4'- diaponeurosporene is catalyzed by a mixed function oxidase CrtP, to form 4,4'- diaponeurosporenic acid.
  • glycosyl 4,4'-diaponeurosporenoate is formed by esterification of glucose at the CI" position of 4,4'-diaponeurosporenic acid with CrtQ, a glycosyltransferase involved.
  • glucose at the C6" position is esterified with the carboxyl group of 12- methyltetradecanoic acid by the acyltransferase CrtO to yield staphyloxanthin.
  • Staphyloxanthin was identified as ⁇ -D-glucopyranosyl l-0-(4,4'-diaponeurosporen-4-oate) - 6-0- (12-methyltetradecanoate).
  • mice 14
  • NP16 0.35 mg
  • NP16 0.35 mg
  • a second group 12
  • S. aureus COL bacterial counts in the livers and spleens of mice treated with compound NP16 were significantly lower than those of the control group (P ⁇ 0.01) (FIGs. 3c and 3d).
  • NP-16 is an inhibitor for CrtN and can exhibit anti-virulence effect on S. aureus.
  • CrtM and CrtN are key enzymes in staphyloxanthin biosynthesis [11]. While staphyloxanthin plays a major role in S. aureus tolerance to host defence, it provides a basis for potential target for rational drug design for the use against S. aureus. It is proposed that a novel anti-infective drug without direct bactericidal properties, only targeting mechanisms that renders the pathogens susceptible to normal host innate immune clearance, is provided. As there is 30% sequence identity between the human SQS and the bacterial CrtM, and they share significant structural features.
  • CrtM has no homologous enzyme in the human cholesterol biosynthesis pathway, making it an attractive drug target.
  • a recently proposed CrtN inhibitor, nafitifine is a topically administered antifungal compound [13], which has been shown to suppress chemotaxis, chemokinesis, chemiluminescence, and superoxide anion production of polymorphonuclear leukocytes at high concentrations [14].
  • ROS are employed by phagocytic cells to eliminate bacteria. They are generated by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase [15].
  • NADPH nicotinamide adenine dinucleotide phosphate
  • the bacterial carotenoids expressed by S. aureus may have a protective function against these defensive molecules [4, 16].
  • Using intra-bacterial inhibition assay system showed that the isogenic crtN mutant, which exhibited interrupted carotenoid synthesis, was more sensitive to purified human neutrophils. This confirmed the importance of CrtN in the intracellular survival of S. aureus.
  • CrtN inhibitors without direct bactericidal properties should possess theoretical advantages of not exerting a direct selective pressure on the pathogen or normal flora to develop drug resistance.
  • Our approach, as well as other virulence factor-based concepts [3, 17] for highly specific anti-staphylococcal therapy relies mainly on the host normal innate immune response for pathogen clearance.
  • Such strategies are much more ideal for clinical treatment and prophylactic applications with limited risk of developing drug resistant pathogen unlike the case observed with antibiotics.

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Abstract

Provided herein are compounds, derivatives thereof, composition comprising one or more of said compounds and derivatives, and use thereof for prevention and/or treatment of microbial infections and/or related diseases or conditions. The present compounds and/or derivatives thereof can be represented by Formula (I): (I). The present use includes preparing a composition comprising an effective amount of one or more compounds of Formula (I) for preventing and/or treating microbial infections and/or related diseases or conditions. In one embodiment, said microbial infections are bacterial infections. More specifically, said bacterial infections are staphylococcal infections.

Description

COMPOUNDS AND USE THEREOF FOR THE TREATMENT OF MICROBIAL
INFECTIONS
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] The present application claims priority from a U.S. provisional patent application serial number 62/535,540 filed July 21st, 2017 and a U.S. non-provisional patent application serial number 16/041,836 filed July 22nd, 2018, and the disclosures of which are incorporated herein by reference in their entirety.
TECHNICAL FIELD
[0002] The present invention relates to compounds and derivatives thereof, composition comprising said compounds and/or derivatives, and use thereof for treating microbial infections and/or related diseases or conditions. More specifically, the present compounds, derivatives, composition comprising thereof, and use are for bacterial infections.
BACKGROUND OF THE INVENTION
[0003] Staphylococcus aureus is a major human pathogen in communities and hospitals, causing a variety of infections that ranges from harmless infections to life threatening conditions [18]. With the wide-spread dissemination of methicillin-resistant S. aureus (MRS A) in hospitals and in communities, treating S. aureus associated infections has become increasingly difficult [19]. Staphyloxanthin has been proven to be an important factor in promoting bacterial invasion [1]. Five genes, crtOPQMN, located in an operon are responsible for the biosynthesis of the pigment. The transcription of the operon is driven by a oB-dependent promoter upstream of crtO, and ends with a terminator downstream of crtN [2]. The pigments that endow S. aureus with a golden color also make it resistant to attack from reactive oxygen species (ROS) and neutrophils [3]. Pigmented bacteria have increased resistance to the host's immune defenses [4].
[0004] In a mouse subcutaneous model of infection, animals infected with a wild-type strain of S. aureus had higher bacterial loads and larger visible lesions than those infected with non- pigmented bacteria [4]. The reduced virulence of bacterial strains with defective carotenoid synthesis was also shown in a mouse systemic S. aureus infection model [3]. In vitro and in vivo data suggest that blocking pigment synthesis may reduce pathogenicity.
[0005] Dehydrosqualene synthase (CrtM) catalyses the first step of the biosynthetic pathway, was shown to be a target for anti-infective therapy based on virulence factor neutralization. Diphenylamine was found to be an inhibitor of 4,4-diapophytoene desaturase (CrtN) at high micromolar level [5]. Another potential inhibitor of CrtN, naftifine, a FDA approved antifungal compound was shown to reduce bacterial load in different mice infection models [6]. However, there remains a need for new compounds, methods of treatment, and use of the compounds in preparing a composition for treating and/or preventing staphylococcal infections.
SUMMARY OF THE INVENTION
[0006] Provided herein are compounds and use thereof for prevention and/or treatment of microbial infections and/or related disease or conditions. In a first aspect, the present invention provides compounds and/o ted by Formula (I):
Figure imgf000003_0001
where R1, R2, and R3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; acylamino; hydroxyl; thiol; thioalkyl; alkoxy; alkylthio; alkoxyalkyl; aryloxy; arylalkoxy; acyloxy; nitro; carbamoyl; trifluoromethyl; phenoxy; benzyloxy; phosphonic acid; phosphate ester; sulfonic acid (- SO3H); sulfonate ester; sulfonamide; alkaryl; arylalkyl; carbamate; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; alkylthio; heteroalkyl; alkyltriphenylphosphonium; heterocyclyl; ketone (=0); ether (-OR4); and ester (-COOR5 and -OC(=0)R5);
where R1 and R2 can be bonded together to form a four-, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl; and
where R4 and R5 can be independently or jointly selected from the group consisting of: a (Ci- 4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2- 4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl.
[0007] In one embodiment, the present compounds and/or the derivatives thereof can be an anti- virulent agent for bacteria.
[0008] In another embodiment, the present compounds and/or the derivatives thereof are effective in reducing virulence of bacteria.
[0009] In other embodiment, the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise Staphylococci sp.
[0010] In yet another embodiment, the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise Staphylococcus aureus (S. aureus).
[0011] In still another embodiment, the bacteria that the present compounds and/or the derivatives thereof are effective in reducing their virulence comprise methicillin-resistant S. aureus (MRSA).
[0012] In other embodiment, said reducing the virulence of bacteria by the compounds and/or derivatives thereof comprises inhibiting biosynthesis of staphyloxanthin in said bacteria and/or inhibiting or reducing production of pigments that are resistant to the bacterial host's immune defenses.
[0013] A composition for preventing and/or treating the microbial infections and/or related diseases or conditions comprising an effective amount of the compounds and/or the derivatives thereof in the first aspect is also provided herein.
[0014] In one embodiment, said microbial infections are bacterial infections.
[0015] In another embodiment, said microbial infections comprise staphylococcal infections. [0016] In other embodiment, the composition further comprises a pharmaceutically acceptable carrier, salt, ester, expicient, vehicle, prodrug, solvent, and diluent, or any combination thereof.
[0017] In a second aspect, the present invention provides use of the present compounds and/or the derivatives thereof for preventing and/or treating the microbial infections and/or related diseases or conditions including using said compounds and/or derivatives thereof in preparation of a composition for preventing and/or treating microbial infections and/or related diseases or conditions in a subject in need thereof, wherein said composition comprises an effective amount of one or more compounds of Formula (I):
Figure imgf000005_0001
(I),
where R1, R2, and R3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; acylamino; hydroxyl; thiol; thioalkyl; alkoxy; alkylthio; alkoxyalkyl; aryloxy; arylalkoxy; acyloxy; nitro; carbamoyl; trifluoromethyl; phenoxy; benzyloxy; phosphonic acid; phosphate ester; sulfonic acid (- SO3H); sulfonate ester; sulfonamide; alkaryl; arylalkyl; carbamate; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; alkylthio; heteroalkyl; alkyltnphenylphosphonium; heterocyclyl; ketone (=0); ether (-OR4); and ester (-COOR5 and
-OC(=0)R5);
where R1 and R2 can be bonded together to form a four-, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl; and where R4 and R5 can be independently or jointly selected from the group consisting of: a (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec -butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl. Optionally, R1 and R2 are independently or jointly selected from ο ^Γ"^°"* and ; R3 is H or methyl.
[0018] In one embodiment, the microbial infections are bacterial infection.
[0019] In another embodiment, the microbial infections comprise Staphylococcal infections.
[0020] In other embodiment, the microbial infections and/or related diseases or conditions are caused by Staphylococci sp.
[0021] In yet another embodiment, the Staphylococci sp. comprise Staphylococcus aureus (S. aureus).
[0022] In still another embodiment, S. aureus comprise methicillin-resistant S. aureus (MRSA).
[0023] In other embodiment, the microbial infections and/or related diseases or conditions comprise infections of the skin and soft tissue, bone and joint, surgical wound, indwelling devices, lung and heart valves.
[0024] In certain embodiments, the present use further comprises reducing virulence of bacteria causing the microbial infections and/or related disease or conditions in said subject being administered with said composition.
[0025] In some other embodiments, the present use further comprises inhibiting biosynthesis of staphyloxanthin in said bacteria and/or inhibiting or reducing production of pigments that are resistant to the bacterial host's immune defenses in said subject being administered with said composition.
[0026] In another embodiment, said subject or bacterial host is a mammal.
[0027] In other embodiment, said subject or bacterial host is human.
BRIEF DESCRIPTION OF THE DRAWINGS
[0028] In the following detailed description, reference is made to the accompanying figures, depicting exemplary, non-limiting and non-exhaustive embodiments of the invention. So that the manner in which the above recited features of the present invention can be understood in detail, a more particular description of the invention, briefly summarized above, can be had by reference to the embodiments, some of which are illustrated in the appended figures. It should be noted, however, that the figures illustrate only typical embodiments of this invention and are therefore not to be considered limiting of its scope, for the invention can admit to other equally effective embodiments.
[1] FIGs. 1 A-1D show the in vitro pigment inhibition by compound NP16: FIG. 1A shows the inhibition of wild-type (WT) S. aureus pigmentation using increasing concentrations of NP16; FIG. IB shows the pigment inhibition by NP16; the IC50 for pigment formation is -300 nM; FIG. 1C depicts the chemical structure of compound NP16; FIG. ID shows the growth curve of S. aureus COL in the presence of different concentrations of NP16. All data represent mean values ± SD.
[0029] FIGs. 2A-2D show that NP16 treatment leads to increased sensitivity to oxidation and neutrophil killing: FIG. 2A depicts the cytotoxic activity of compound NP16 on MDCK cells; FIG. 2B shows the increased susceptibility of the NP16-treated S. aureus COL strain to killing by hydrogen peroxide; FIG. 2C shows the increased susceptibility of the NP16-treated S. aureus COL to killing by neutrophils; FIG. 2D is the UV spectrum of carotenoids extracted from different strains, with or without NP16 treatment. All data represent mean values ± SD (***P < 0.001; ****P < 0.0001). P values were determined using GraphPad Prism using an unpaired parametric t test with Welch's correction.
[0030] FIGs. 3A-3F show the in vivo effect of CrtN and its inhibition by NP16. FIGs. 3 A and 3B show the bacteria recovered from the livers and spleens, respectively, of mice infected with the wild-type COL or COL-AcrtN strains; FIGs. 3C and 3D show the bacteria recovered from the livers and spleens, respectively, of mice infected with the COL strain, with or without compound NP16 treatment; FIG. 3E shows the bacteria recovered from the kidneys of mice infected with clinical isolate strain AE052 or AE052-AcrtN; FIG. 3F shows the bacteria recovered from the kidneys of mice infected with strain AE052, with or without compound NP16 treatment. All data represent mean values ± SEM (*P < 0.05; **P < 0.01; ***P < 0.001). P values were determined using GraphPad Prism using an unpaired parametric t test with Welch's correction. DETAILED DESCRIPTION OF THE INVENTION
[0031] Following an established screening method for finding agents that reduce Staphyloccous aureus pigmentation [7], it is identified that the present compounds, termed NP16 and its derivatives, have block pigment production in S. aureus by targeting the 4,4- diapophytoene desaturase (CrtN). CrtN is proposed as a novel target for anti-virulence treatments in S. aureus. S. aureus staphyloxanthin contributes substantially to pathogenesis by interfering with host immune clearance mechanisms, but has little impact on ex vivo survival of the bacteria. Without wanting to be bound by theory, it is provided that agents blocking staphyloxanthin production may discourage the establishment and maintenance of bacterial infection without exerting selective pressure for antimicrobial resistance.
[0032] NP16 and its derivatives can be represented by Formula (I):
Figure imgf000008_0001
where R1, R2, and R3 can independently or jointly be selected from the group: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; acylamino; hydroxyl; thiol; thioalkyl; alkoxy; alkylthio; alkoxyalkyl; aryloxy; arylalkoxy; acyloxy; nitro; carbamoyl; trifluoromethyl; phenoxy; benzyloxy; phosphonic acid; phosphate ester; sulfonic acid (- SO3H); sulfonate ester; sulfonamide; alkaryl; arylalkyl; carbamate; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; alkylthio; heteroalkyl; alkyltriphenylphosphonium; heterocyclyl; ketone (=0); ether (-OR4); and ester (-COOR5 and
-OC(=0)R5); where R1 and R2 can be bonded together to form a fo -, five-, or six-membered heterocyclyl, cycloalkenyl, or cycloalkyl, such as
Figure imgf000009_0001
and ; R3 is H or methyl; and where R4 and R5 can be independently or jointly selected from the group: a (Ci-4)alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl; (C2-4)alkenyl, such as ethenyl, propenyl, butenyl, where the double bond can be located at any position in the alkenyl carbon chain, and including any alkenyl conformational isomers; and alkynyl.
[0033] The compounds of Formula (I) can include, but are not limited to, those compounds listed in Table 1.
Figure imgf000009_0002
Figure imgf000010_0001
Figure imgf000011_0001
3-(4-acetoxylphenyl)-N-[4-( 1 -
19 pyrrolidinylsulfonyl)phenyl]acryl f ί T ¾ amide 1 J H
3-(5-phenylpheny])-N-[4-(l- ? f Ύ ¾
20 pyrrolidinylsulfonyl)phenyl]acryl ! j H
amide
[0034] One or more compounds of Formula (I) can be combined and/or mixed with one or more of a pharmaceutically acceptable carrier, salt, ester, expicient, vehicle, prodrug, solvent, and diluent to make a composition.
[0035] As used herein, the phrase "pharmaceutically acceptable" can mean approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals and/or in humans.
[0036] As used herein, the term "carrier" can refer to a diluent, adjuvant, excipient, and/or vehicle with which the compound and/or antibiotic are administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
[0037] As used herein, the phrase "pharmaceutically acceptable salt" can refer to derivatives of the compounds defined herein, wherein the parent compound is modified by making acid or base salts thereof.
[0038] The method of treating and/or preventing a microbial infection in a subject can include, but is not limited to, administering to a subject an effective amount of one or more compounds of Formula (I).
[0039] The use of the present compound or the derivatives thereof in the preparation of a composition for preventing and/or treating a microbial infection and/or related diseases or conditions can include, but not limited to, using said compound and/or derivatives in preparation of said composition wherein said composition comprises an effective amount of said compound and/or the derivatives thereof, a pharmaceutical carrier, a salt, an ester, an excipient, a vehicle, a prodrug, a solvent, a diluent, or any combination thereof.
[0040] As used herein, the terms "treatment" or "treating" can refer to arresting or inhibiting, or attempting to arrest or inhibit, the development or progression of an infection and/or causing, or attempting to cause, the reduction, suppression, regression, or remission of an infection and/or a symptom thereof. As would be understood by those skilled in the art, various clinical and scientific methodologies and assays may be used to assess the development or progression of an infection, and similarly, various clinical and scientific methodologies and assays may be used to assess the reduction, regression, or remission of an infection or its symptoms. "Treatment" refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those already with the infection as well as those prone to have the infection or those in whom the infection is to be prevented. In at least some forms, the infection being treated can include, but is not limited to, Staphylococcus aureus infection. In other forms, the infection being treated is a microbial infection.
[0041] The administration can include, but is not limited to: administration though oral pathways, which administration includes administration in capsule, tablet, granule, spray, syrup, or other such forms; administration through non-oral pathways, which administration includes administration as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like; administration via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, intradermally, or the like; as well as administration topically; and administration via controlled released formulations, depot formulations, and infusion pump delivery.
[0042] For intravenous administration, the compounds can be packaged in solutions of sterile isotonic aqueous buffer to make the composition. When necessary, the composition can also include a solubilizing agent. The composition of the compounds can be supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or concentrated solution in a hermetically sealed container such as an ampoule or sachette indicating the amount of active agent. If the compound is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. When the compound is administered by injection, an ampoule of sterile water or saline can be provided so that the ingredients may be mixed prior to injection.
[0043] As used herein, the term "subject" can refer to an animal. Typically, the terms "subject" and "patient" may be used interchangeably herein in reference to a subject. As such, a "subject" can include a human that is being treated for a microbial infection as a patient.
[0044] As used herein, the term "animal" can refer to a mouse, rat, dog, cat, rabbit, pig, monkey, chimpanzee, and human.
[0045] As used herein, the terms "effective amount" and "therapeutically effective amount," can be used interchangeably, as applied to the compounds, antibiotics, and pharmaceutical compositions described can mean the quantity necessary to render the desired therapeutic result. For example, an effective amount is a level effective to treat, cure, or alleviate the symptoms of an infection for which the composition and/or antibiotic, or pharmaceutical composition, is/are being administered. Amounts effective for the particular therapeutic goal sought will depend upon a variety of factors including the infection being treated and its severity and/or stage of development/progression; the bioavailability and activity of the specific compound and/or antibiotic, or pharmaceutical composition, used; the route or method of administration and introduction site on the subject; the rate of clearance of the specific composition and other pharmacokinetic properties; the duration of treatment; inoculation regimen; drugs used in combination or coincident with the specific composition; the age, body weight, sex, diet, physiology and general health of the subject being treated; and like factors well known to one of skill in the relevant scientific art. Some variation in dosage will necessarily occur depending upon the condition of the subject being treated, and the physician or other individual administering treatment will, in any event, determine the appropriate dosage for an individual patient. Furthermore, the therapeutic methods described would not only apply to treatment in a subject, but could be applied to cell cultures, organs, tissues, or individual cells in vivo, ex vivo or in vitro.
[0046] The term "hydrocarbyl" as used herein includes reference to a moiety consisting exclusively of hydrogen and carbon atoms; such a moiety may comprise an aliphatic and/or an aromatic moiety. The moiety may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 carbon atoms. Examples of hydrocarbyl groups include Ci-6 alkyl (e.g. Ci, C2, C3 or C4 alkyl, for example methyl, ethyl, propyl, isopropyl, n-butyl, sec -butyl or tert-butyl); Ci-6 alkyl substituted by aryl (e.g. benzyl) or by cycloalkyl (e.g. cyclopropylmethyl); cycloalkyl (e.g. cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl); aryl (e.g. phenyl, naphthyl or fluorenyl) and the like.
[0047] The term "alkyl" as used herein includes reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 carbon atoms. Examples of alkyl groups include "Ci-6 alkyl" and "C2-10 alkyl". The term "Ci-6 alkyl" as used herein include reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5 or 6 carbon atoms. The term "C2-10 alkyl" as used herein include reference to a straight or branched chain alkyl moiety having 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 carbon atoms. This term includes reference to groups such as methyl, ethyl, propyl (n-propyl or isopropyl), butyl (n-butyl, sec- butyl or tert-butyl), pentyl, hexyl and the like. In particular, the alkyl moiety may have 1, 2, 3, 4, 5 or 6 carbon atoms.
[0048] The terms "alkenyl" and "C2-6 alkenyl" as used herein include reference to a straight or branched chain alkyl moiety having 2, 3, 4, 5 or 6 carbon atoms and having, in addition, at least one double bond, of either E or Z stereochemistry where applicable. This term includes reference to groups such as ethenyl, 2-propenyl, 1-butenyl, 2-butenyl, 3- butenyl, 1-pentenyl, 2-pentenyl, 3-pentenyl, 1-hexenyl, 2-hexenyl and 3-hexenyl and the like.
[0049] The terms "alkynyl" and "C2-6 alkynyl" as used herein include reference to a straight or branched chain alkyl moiety having 2, 3, 4, 5 or 6 carbon atoms and having, in addition, at least one triple bond. This term includes reference to groups such as ethynyl, 1- propynyl, 2- propynyl, 1-butynyl, 2-butynyl, 3-butynyl, 1-pentynyl, 2-pentynyl, 3-pentynyl, 1-hexynyl, 2- hexynyl and 3-hexynyl and the like.
[0050] The terms "alkoxy" and "Ci-6 alkoxy" as used herein include reference to -O-alkyl, wherein alkyl is straight or branched chain and comprises 1, 2, 3, 4, 5 or 6 carbon atoms. In one class of embodiments, alkoxy has 1, 2, 3 or 4 carbon atoms. This term includes reference to groups such as methoxy, ethoxy, propoxy, isopropoxy, butoxy, tert- butoxy, pentoxy, hexoxy and the like. [0051] The term "cycloalkyl" as used herein includes reference to an alicyclic moiety having 3, 4, 5, 6, 7 or 8 carbon atoms. The group may be a bridged or polycyclic ring system. More often cycloalkyl groups are monocyclic. This term includes reference to groups such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, norbomyl, bicyclo[2.2.2]octyl and the like.
[0052] The term "aryl" as used herein includes reference to an aromatic ring system comprising 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 ring carbon atoms. Aryl is often phenyl but may be a polycyclic ring system, having two or more rings, at least one of which is aromatic. This term includes reference to groups such as phenyl, naphthyl, fluorenyl, azulenyl, indenyl, anthryl and the like.
[0053] "Cyclic group" means a ring or ring system, which may be unsaturated or partially unsaturated but is usually saturated, typically containing 5 to 13 ring-forming atoms, for example a 5- or 6-membered ring. The ring or ring system may be substituted with one or more hydrocarbyl groups. Cyclic group includes carbocyclyl and heterocyclyl moeities.
[0054] The term "carbocyclyl" as used herein includes reference to a saturated (e.g. cycloalkyl) or unsaturated (e.g. aryl) ring moiety having 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 or 16 carbon ring atoms. In particular, carbocyclyl includes a 3- to 10-membered ring or ring system and, in particular, 5- or 6-membered rings, which may be saturated or unsaturated. The ring or ring system may be substituted with one or more hydrocarbyl groups. A carbocyclic moiety is, for example, selected from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, norbornyl, bicyclo[2.2.2]octyl, phenyl, naphthyl, fluorenyl, azulenyl, indenyl, anthryl and the like.
[0055] The term "heterocyclyl" as used herein includes reference to a saturated (e.g. heterocycloalkyl) or unsaturated (e.g. heteroaryl) heterocyclic ring moiety having from 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15 or 16 ring atoms, at least one of which is selected from nitrogen, oxygen, phosphorus, silicon and sulphur. In particular, heterocyclyl includes a 3- to 10- membered ring or ring system and more particularly a 5- or 6- membered ring, which may be saturated or unsaturated. The ring or ring system may be substituted with one or more hydrocarbyl groups.
[0056] A heterocyclic moiety is, for example, selected from oxiranyl, azirinyl, 1, 2- oxathiolanyl, imidazolyl, thienyl, furyl, tetrahydrofuryl, pyranyl, thiopyranyl, thianthrenyl, isobenzofuranyl, benzofuranyl, chromenyl, 2H-pyrrolyl, pyrrolyl, pyrrolinyl, pyrrolidinyl, pyrrolizidinyl, imidazolyl, imidazolidinyl, benzimidazolyl, pyrazolyl, pyrazinyl, pyrazolidinyl, thiazolyl, isothiazolyl, dithiazolyl, oxazolyl, isoxazolyl, pyridyl, pyrazinyl, pyrimidinyl, piperidyl, piperazinyl, pyridazinyl, morpholinyl, thiomorpholinyl, especially thiomorpholino, indolizinyl, isoindolyl, 3H-indolyl, indolyl, benzimidazolyl, cumaryl, indazolyl, triazolyl, tetrazolyl, purinyl, 4/V-quinolizinyl, isoquinolyl, quinolyl, tetrahydroquinolyl, tetrahydroisoquinolyl, decahydroquinolyl, octahydroisoquinolyl, benzofuranyl, dibenzofuranyl, benzothiophenyl, dibenzothiophenyl, phthalazinyl, naphthyridinyl, quinoxalyl, quinazohnyl, quinazohnyl, cinnolinyl, pteridinyl, carbazoiyl, β- carbolinyl, phenanthridinyl, acridinyl, perimidinyl, phenanthrolinyl, furazanyl, phenazinyl, phenothiazinyl, phenoxazinyl, chromenyl, isochromanyl, chromanyl and the like.
[0057] The term "heterocycloalkyl" as used herein includes reference to a saturated heterocyclic moiety having 3, 4, 5, 6 or 7 ring carbon atoms and 1 , 2, 3, 4 or 5 ring heteroatoms selected from nitrogen, oxygen, phosphorus and sulphur. The group may be a polycyclic ring system but more often is monocyclic. This term includes reference to groups such as azetidinyl, pyrrolidinyl, tetrahydrofuranyl, piperidinyl, oxiranyl, pyrazolidinyl, imidazolyl, indolizidinyl, piperazinyl, thiazolidinyl, morpholinyl, thiomorpholinyl, quinohzidinyl and the like. The ring or ring system may be substituted with one or more hydrocarbyl groups.
[0058] The term "heteroaryl" as used herein includes reference to an aromatic heterocyclic ring system having 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 ring atoms, at least one of which is selected from nitrogen, oxygen and sulphur. The group may be a polycyclic ring system, having two or more rings, at least one of which is aromatic, but is more often monocyclic. The ring or ring system may be substituted with one or more hydrocarbyl groups. This term includes reference to groups such as pyrimidinyl, furanyl, benzo[b]thiophenyl, thiophenyl, pyrrolyl, imidazolyl, pyrrolidinyl, pyridinyl, benzo[b] furanyl, pyrazinyl, purinyl, indolyl, benzimidazolyl, quinolinyl, phenothiazinyl, triazinyl, phthalazinyl, 2H-chromenyl, oxazolyl, isoxazolyl, thiazolyl, isoindolyl, indazolyl, purinyl, isoquinohnyl, quinazohnyl, pteridinyl and the like.
[0059] The term "halogen" as used herein includes reference to F, CI, Br or I.
[0060] The expression "halogen containing moiety" as used herein includes reference to a moiety comprising 1 to 30 plural valence atoms selected from carbon, nitrogen, oxygen and sulphur which moiety includes at least one halogen. The moiety may be hydrocarbyl for example C1-6 alkyl or C1-6 alkoxy, or carbocyclyl for example aryl.
[0061] The term "substituted" as used herein in reference to a moiety means that one or more, especially up to 5, more especially 1, 2 or 3, of the hydrogen atoms in said moiety are replaced independently of each other by the corresponding number of the described substituents. The term "optionally substituted" as used herein means substituted or un- substituted. It will, of course, be understood that substituents are only at positions where they are chemically possible, the person skilled in the art being able to decide (either experimentally or theoretically) without inappropriate effort whether a particular substitution is possible.
[0062] The term "enantiomer" as used herein means one of two stereoisomers that have mirror images of one another.
[0063] The term "racemate" as used herein means a mixture of equal amounts of enantiomers of a chiral molecule.
[0064] The term "diastereomer" as used herein means one of a class of stereoisomers that are not enantiomers, but that have different configurations at one or more of the equivalent chiral centers. Example of diasteromers are epimers that differ in configuration of only one chiral center.
[0065] The term "stereoisomer" as used herein means one of a class of isomeric molecules that have the same molecular formula and sequence of bonded atoms, but different three- dimensional orientations of their atoms in space.
[0066] The term "prodrug" as used herein refers to a medication that is administered as an inactive (or less than fully active) chemical derivative that is subsequently converted to an active pharmacological agent in the body, often through normal metabolic processes.
[0067] The term "independently" used herein refers to two or more moieties each selected from a list of atoms or groups, which means that the moieties may be the same or different. The identity of each moiety is therefore independent of the identities of the one or more other moieties.
[0068] The term "jointly" used herein refers to two or more moieties are identical selected from a list of atoms or groups. In other words, the identity of each moiety is therefore dependent of the identities of the one or more other moieties being referred to be "jointly" selected from the list of atoms or groups. EXAMPLES
[0069] The examples and embodiments described herein are for illustrative purposes only and various modifications or changes in light thereof will be suggested to persons skilled in the art and are included within the spirit and purview of this application. In addition, any elements or limitations of any invention or embodiment thereof disclosed herein can be combined with any and/or all other elements or limitations (individually or in any combination) or any other invention or embodiment thereof disclosed herein, and all such combinations are contemplated with the scope of the invention without limitation thereto.
[0070] Bacteria, Mice, and Chemical Reagents
[0071] The strains of S. aureus and E. coli are listed in Table 2. BALB/c mice were purchased from Charles River Laboratories. S. aureus was propagated in Terrific broth (TB) or on TB agar (Life Technologies). Unless otherwise indicated, all experiments were performed with bacteria derived from light-protected S. aureus 36-48 h stationary phase cultures, the point at which pigmentation phenotypes were readily apparent.
Figure imgf000019_0001
[0072] Minimum Inhibitory Concentration (MIC) Tests
[0073] MIC was determined by inoculating 5 x 104 S. aureus cells in 100 μΐ BHI medium in 96-well plates with a serial dilution of antibiotics. The MIC was defined as the minimum concentration resulting in a cell density less than 0.05 OD at 620 nm, which corresponded to no visible growth, after incubating for 18 h at 37 °C.
[0074] Evaluation ofNP-16 analogues in Staphyloxanthin production
[0075] S. aureus was propagated in Brain Heart Infusion broth (BHI) or on BHI agar (Oxoid). The in vitro pigment inhibition studies were performed by S. aureus USA300 cultured in BHI with or without the presence of inhibitor compounds at 37°C and 250 rpm for 36-48 hours. The bacteria were washed twice with PBS prior to the staphyloxanthin purification with methanol. The OD of the extracts were monitor at 450nm using DTX880 multi-plate reader spectrophotometer (Beckman). The concentration range tested for the compounds were between 300nM to 700nM, and control groups were added with equal volume of DMSO.
[0076] Cytotoxicity Evaluation ofNP16 in MOCK Cells
[0077] The cytotoxicity of NP16 in MDCK cells was evaluated by MTT (3-[4,5- dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay according to manufacturer's instructions. A toxic control (1%) SDS was included to ensure the MTT assay was effective. The highest concentration of NP16 that could be used was 500 μΜ due to solubility limitations. SigmaPlot 11.0 (SPSS, IL) was used for graph plotting. Experiments were repeated twice in triplicate.
[0078] The IC50 values were obtained by fitting the inhibition data to a normal dose-response curve in SigmaPlot (CA).
[0079] Cytotoxicity evaluation of other NP-16 analogues in Raw 264.7 cells
[0080] The cytotoxicity of NP-16 and some of it analogues in Raw 264.7 cells was also evaluated by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay according to manufacturer's instructions. A toxic control (1%) SDS was included to ensure the MTT assay was working properly. The highest concentration of NP-16 analogues used was 500 μΜ due to solubility limitations. SigmaPlot 11.0 (SPSS, IL) was used for graph plotting. Experiments were carried out in triplicate and repeated twice. [0081] The cytotoxicity of NP- 16 and some of it analogues was tested against Raw 264.7 cells, and the cell tolerance of each compounds were documented in Table 3. Along with the in vitro staphyloxanthin production of the NP-16 analogues were being tested, the compounds can exert staphyloxanthin production inhibition. The staphyloxanthin from the overnight- cultured bacteria were extracted with methanol and quantified in via spectrophotometry. The results were presented in relative ratio to NP-16 in both the inhibition ratio as well as the TC50 in Table 3 (compound / analogue numbers correspond to those listed in Table 1).
Figure imgf000021_0001
[0083] CrtN with a histidine-maltose binding protein (MBP) tag was overexpressed in E. coli Rosetta (DE3) cells. A 10 ml overnight culture was transferred into 1 L of LB medium supplemented with 100 μg/ml ampicillin. Induction was carried out with 1 mM IPTG for 12 hours at 16°C at an OD of 0.6 at 600 nm. The cell lysate was loaded onto a Ni-NTA column, and CrtN was eluted using a 75-ml linear gradient of 0-0.4 M imidazole in 50 mM sodium phosphate buffer, with 400 mM sodium chloride, pH 6.6. The collected fractions were analysed by SDS-PAGE to confirm the peak for MBP-CrtN. The target peak fractions were concentrated and the buffer was exchanged to loading buffer without imidazole using a PD-10 column (GE Healthcare). The collected solution was treated with TEV protease at 4°C overnight. The protein sample was applied to a maltose column, and the flow-through was collected as native CrtN protein. For enzyme assay, 10 μg of purified CrtN was incubated with 100 μΐ of 4,4'-diapophytoene liposomes (containing 5 nmol of 4,4'-diapophytoene), 150 μΜ FAD and buffer II (20 mM phosphate buffer pH 8.0, 100 mM NaCl) in a total volume of 660 μΐ at 37°C for 2 h (standard assay). The reaction was stopped by adding 1 volume of CHCb: MeOH (2: 1, v/v). Followed by mixing, the sample was centrifuged at 16,000 g for 10 min. The organic phase was dried for LC/MS analysis.
[0084] Isolation of Carotenoids
[0085] The substrate (4,4'-diapophytoene) and product (4,4'-diaponeurosporene) were extracted from strains COL-AcrtN and COL-AcrtOP. Carotenoids were extracted from cell pellets using 300 ml of methanol per liter of cultured bacteria pellet until all visible pigments were removed. After centrifugation (4°C and 8,000 g), colored supernatants were pooled and concentrated to 50 ml using an EZ-2 Plus centrifugal evaporator (Genevac Inc., Gardiner, NY, USA). A sample was mixed with 100 ml of EtOAc and 200 ml of NaCl (2.5 M). The extract sample in the upper organic phase was collected, washed with same volume of distilled water, and dried using the EZ-2 Plus evaporator. Dried samples were ready for silica gel isolation or stored at -70 °C prior to analysis. For structural elucidation, carotenoids were identified using a combination of HPLC retention times, UV-visible absorption spectra, and mass fragmentation spectra. Mass fragmentation spectra were monitored using both negative and positive ion modes in a mass range of mlz 200-1000 on the Varian 1200L LC/MS system equipped with an atmospheric pressure chemical ionization interface.
[0086] Hydrogen Peroxide Susceptibility Assay
[0087] S. aureus was grown in BHI with or without NP16 (40 μΜ). After 2 days, bacteria were washed twice in PBS, diluted to a concentration of lxlO7 CFUs per 100 μΐ reaction mixture in a 96-well plate. Hydrogen peroxide (H2O2) in PBS was added to a 440 mM final concentration, and the plate was incubated for 1 hr at 37°C with shaking. The reaction was stopped by the addition of l,000U/ml of exogenous catalase (Sigma- Aldrich, St. Louis, MO), and bacterial viability was assessed by plating dilutions on BHI agar plates.
[0088] Bactericidal Activity of Polymorphonuclear Leukocytes
[0089] The killing of S. aureus by human polymorphonuclear leukocytes (PMNs) was determined as previously described [9], with some modifications. Briefly, PMNs (106) were mixed with ~10 opsonized S. aureus bacteria MOI=10 in 24-well tissue culture plates. After centrifuged at 380 g for 8 min, plates were incubated at 37°C for up to 1.5 h. PMNs were lysed with saponin (20 min on ice) and plated on BHIA plates. The percent survival was calculated by normalized with time zero. Statistics were performed with the Student's t-test (GraphPad Prism).
[0090] Murine Model of Intraperitoneal Infection
[0091] Eight- to ten-week-old female BALB/c mice were injected intraperitoneally (i.p) with 4xl08 CFUs of early stationary phase S. aureus COL. After 3 d, animals were euthanized, the liver and spleen were isolated, homogenized in PBS, and plated on to obtain viable counts. For the treatment study, mice were randomized into two groups at the start of the experiment and administered, i.p., either 0.35 mg of NP16 or PBS with 5% Tween-80 as a control, twice per day, starting on d -1 to d 2 (a total of eight doses for each). Intraperitoneal challenge with 4xl08 CFUs of early stationary phases S. aureus COL was performed on d 0. The mice were sacrificed on d 3 for enumeration of bacterial CFUs in liver and spleen homogenates.
[0092] For the clinical isolate S. aureus strain AE052, all operations were similar to those used for the COL strain, except 108 CFUs of early stationary phase bacteria were used in the infection model, and kidneys were collected for monitoring bacterial loads. Statistics were performed using the Student's t-test (GraphPad Prism).
[0093] Compound NP16 Reduces Pigment Production
[0094] Compound NP16 (structure shown in FIG. 1C) had potent activity against S. aureus pigment formation in vitro, as shown in FIG. 1A, with IC50 values ranging from 100 to 300 nM (FIG. IB). In the biosynthesis of staphyloxanthin, the product of CrtN, 4,4'- diaponeurosporene, is a yellowish compound while products prior to CrtM catalysis are colorless. Thus, NP16 treatment is proposed to target CrtM or CrtN or other regulators that affect the expression of the crtOPQMN cluster, such as sigB or ispA [10]. The MIC of NP16 for USA300 was greater than 500 μΜ (FIG. ID).
[0095] The functions of the five encoded enzymes were characterized by product analysis of gene deletion mutants. Firstly, in staphyloxanthin biosynthesis, two molecules of farnesyl diphosphate are condensed head-to-head to form dehydrosqualene (4,4'-diapophytoene), catalyzed by the dehydrosqualene synthase CrtM. Secondly, dehydrosqualene is dehydrogenated by the dehydrosqualene desaturase CrtN to form the yellow intermediate 4,4'-diaponeurosporene. Thirdly, oxidation of the terminal methyl group of 4,4'- diaponeurosporene is catalyzed by a mixed function oxidase CrtP, to form 4,4'- diaponeurosporenic acid. Then, glycosyl 4,4'-diaponeurosporenoate is formed by esterification of glucose at the CI" position of 4,4'-diaponeurosporenic acid with CrtQ, a glycosyltransferase involved. Finally, glucose at the C6" position is esterified with the carboxyl group of 12- methyltetradecanoic acid by the acyltransferase CrtO to yield staphyloxanthin. Staphyloxanthin was identified as β-D-glucopyranosyl l-0-(4,4'-diaponeurosporen-4-oate) - 6-0- (12-methyltetradecanoate).
[0096] Inhibition of CrtN by NP16 results in H2O2 and Neutrophil Killing
[0097] To probe the biological activities of CrtN, an isogenic crtN mutant in the COL strain via allelic replacement was generated. The mutation resulted in loss of yellow pigment. Compound NP16 had no effect on the growth of MDCK cells (FIG. 2A). A decrease in pigment production was found in S. aureus grown in the presence of this NP16 (FIG. 1A). Blocking S. aureus pigment formation has led to an increase in the susceptibility of the pathogen to hydrogen peroxide killing. For the non-pigmented strain RN6390, the susceptibility was similar irrespective of NP16 treatment (FIG. 2B). Additionally, as a carotenoid producing strain (FIG. 2D), COL survived significantly better than RN6390 and NP16-treated COL in human neutrophils (FIG. 2C).
[0098] Animal Studies
[0099] Using a systemic S. aureus infection model, the enzyme CrtM from S. aureus was identified to be a target for anti-infective therapy, based on virulence factor neutralization [3]. A similar model was applied to determine if crtN is also essential for infections in mice. The loss of staphyloxanthin reduced invasive disease potential, as mice inoculated with the isogenic S. aureus mutant COL- AcrtN showed lower bacterial population from the liver and spleen, compared with the 4X108 CFUs of wild-type S. aureus (by intraperitoneal injection), which led to a sustained infection (FIGs. 3a and 3b). Because the COL strain is a low virulence strain, no bacteria were detected in the kidneys from day 1 to day 3. [00100] Another highly virulent clinical isolate, AE052, and its isogenic S. aureus mutant lacking the CrtN enzyme were also examined by these tests. Compared to wildtype strain, mutant strain in kidney was cleared by host after 72 hours post infection (FIG. 3E).
[00101] With the same intraperitoneal challenge used in FIGs. 3a, 3b and 3e, one group of mice (n = 14) was treated with 0.35 mg of NP16 twice per day (days -1, 0, 1 and 2), and a second group (n = 12) with a vehicle control. Upon sacrificing the mice at 72 hours, S. aureus COL bacterial counts in the livers and spleens of mice treated with compound NP16 were significantly lower than those of the control group (P<0.01) (FIGs. 3c and 3d). In the case of AE052 infections, bacterial counts in the kidneys of the mice (n=10 for both groups) treated with NP16 were significantly lower than those of the control group (P < 0.001), with 6 of 10 below the detection threshold, versus only 2 of 10 in the control group (FIG. 3F). This result indicates a 98% decrease in surviving bacteria in the treatment groups infected with COL or AE052.
[00102] Discussion
[00103] It is identified that NP-16 is an inhibitor for CrtN and can exhibit anti-virulence effect on S. aureus. CrtM and CrtN are key enzymes in staphyloxanthin biosynthesis [11]. While staphyloxanthin plays a major role in S. aureus tolerance to host defence, it provides a basis for potential target for rational drug design for the use against S. aureus. It is proposed that a novel anti-infective drug without direct bactericidal properties, only targeting mechanisms that renders the pathogens susceptible to normal host innate immune clearance, is provided. As there is 30% sequence identity between the human SQS and the bacterial CrtM, and they share significant structural features. The presence of such homologue discouraged the employment of CrtM as druggable target this is further supported by a study focusing on the improvement of the specificity of BPH652 against CrtM was published recently [12]. Compared with CrtM, CrtN has no homologous enzyme in the human cholesterol biosynthesis pathway, making it an attractive drug target. A recently proposed CrtN inhibitor, nafitifine, is a topically administered antifungal compound [13], which has been shown to suppress chemotaxis, chemokinesis, chemiluminescence, and superoxide anion production of polymorphonuclear leukocytes at high concentrations [14]. The effects of naftifine are not stable in different organ (from no effect to reduced bacterial load for nearly 4 log) and inconsistency with CrtN mutant (always reduced bacterial load from 0.2 to 2 log at most). It is believed that this indicates that CrtN should not be the primary target of naftifine [6]·
[00104] ROS are employed by phagocytic cells to eliminate bacteria. They are generated by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase [15]. The bacterial carotenoids expressed by S. aureus may have a protective function against these defensive molecules [4, 16]. Evidence supported that a pigment-deficient S. aureus strain was more sensitive to oxidants, hydrogen peroxide and singlet oxygen, in vitro, as compared to a wild- type S. aureus strain [1]. Using intra-bacterial inhibition assay system, showed that the isogenic crtN mutant, which exhibited interrupted carotenoid synthesis, was more sensitive to purified human neutrophils. This confirmed the importance of CrtN in the intracellular survival of S. aureus.
[00105] CrtN inhibitors without direct bactericidal properties should possess theoretical advantages of not exerting a direct selective pressure on the pathogen or normal flora to develop drug resistance. Our approach, as well as other virulence factor-based concepts [3, 17] for highly specific anti-staphylococcal therapy relies mainly on the host normal innate immune response for pathogen clearance. Such strategies are much more ideal for clinical treatment and prophylactic applications with limited risk of developing drug resistant pathogen unlike the case observed with antibiotics.
[00106] It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application.
[00107] All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.
[00108] It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of the invention. One having ordinary skill in the relevant art, however, will readily recognize that the invention can be practiced without one or more of the specific details or practiced with other methods, protocols, reagents, cell lines and animals. The present invention is not limited by the illustrated ordering of acts or events, as some acts may occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts, steps or events are required to implement a methodology in accordance with the present invention. Many of the techniques and procedures described, or referenced herein, are well understood and commonly employed using conventional methodology by those skilled in the art.
[00109] Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and/or as otherwise defined herein.
REFERENCE
[00110] The following references are incorporated herein by reference in their entirety:
1. Clauditz, A., et al., Staphyloxanthin plays a role in the fitness of Staphylococcus aureus and its ability to cope with oxidative stress. Infect Immun, 2006. 74(8): p. 4950-3.
2. Pelz, A., et al., Structure and biosynthesis of staphyloxanthin from Staphylococcus aureus. J Biol Chem, 2005. 280(37): p. 32493-8.
3. Liu, C.I., et al., A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Science, 2008. 319(5868): p. 1391-4.
4. Liu, G.Y., et al., Staphylococcus aureus golden pigment impairs neutrophil killing and promotes virulence through its antioxidant activity. J Exp Med, 2005. 202(2): p. 209-15.
5. Raisig, A. and G. Sandmann, 4,4'-diapophytoene desaturase: catalytic properties of an enzyme from the C(30) carotenoid pathway of Staphylococcus aureus. J Bacteriol, 1999. 181(19): p. 6184-7. 6. Chen, F., et al., Small-molecule targeting of a diapophytoene desaturase inhibits S. aureus virulence. Nat Chem Biol, 2016.
7. Sakai, K., et al., Search method for inhibitors of Staphyloxanthin production by methicillin-resistant Staphylococcus aureus. Biol Pharm Bull, 2012. 35(1): p. 48-53.
8. Ho, P.L., et al., Community-associated methicillin-resistant Staphylococcus aureus skin and soft tissue infections in Hong Kong. Hong Kong Med J, 2009. 15 Suppl 9: p. 9-11.
9. Kobayashi, S.D., et al., Bacterial pathogens modulate an apoptosis differentiation program in human neutrophils. Proc Natl Acad Sci U S A, 2003. 100(19): p. 10948-53.
10. Lan, L., et al., Golden pigment production and virulence gene expression are affected by metabolisms in Staphylococcus aureus. J Bacteriol, 2010. 192(12): p. 3068-77.
11. Ku, B., et al., Preparation, characterization, and optimization of an in vitro C30 carotenoid pathway. Appl Environ Microbiol, 2005. 71(11): p. 6578-83.
12. Song, Y., et al., Phosphonosulfonates are potent, selective inhibitors of dehydrosqualene synthase and staphyloxanthin biosynthesis in Staphylococcus aureus. J Med Chem, 2009. 52(4): p. 976-88.
13. Favre, B. and N.S. Ryder, Characterization of squalene epoxidase activity from the dermatophyte Trichophyton rubrum and its inhibition by terbinafine and other antimycotic agents. Antimicrob Agents Chemother, 1996. 40(2): p. 443-7.
14. Vago, T., et al., Effects of naftifine and terbinafine, two allylamine antifungal drugs, on selected functions of human polymorphonuclear leukocytes. Antimicrob Agents Chemother, 1994. 38(11): p. 2605-11.
15. Fang, F.C., Antimicrobial reactive oxygen and nitrogen species: concepts and controversies. Nat Rev Microbiol, 2004. 2(10): p. 820-32.
16. Liu, G.Y., et al., Sword and shield: linked group B streptococcal beta- hemolysin/cytolysin and carotenoid pigment function to subvert host phagocyte defense. Proc Natl Acad Sci U S A, 2004. 101(40): p. 14491-6.
17. Sully, E.K., et al., Selective chemical inhibition of agr quorum sensing in Staphylococcus aureus promotes host defense with minimal impact on resistance. PLoS Pathog, 2014. 10(6): p. el004174. 18. Crossley, K.B., Staphylococci in human disease. 2nd ed. 2010, Chichester, West Sussex ; Hoboken, NJ: Wiley-Blackwell. xii, 623 p., 10 p. of plates.
19. Blot, S.I., et al., Outcome and attributable mortality in critically 111 patients with bacteremia involving methicillin-susceptible and methicillin-resistant Staphylococcus aureus. Arch Intern Med, 2002. 162(19): p. 2229-35.
20. Peng Gao, Julian Davies and Richard Yi Tsun Kao, "Dehydrosqualene desaturase as a novel target for antimicrobial therapeutics in Staphylococcus aureus", mBio, 8:e01224-17, (2017)

Claims

1. A compound having formula (I):
Figure imgf000030_0001
(I), and derivatives thereof, wherein R1, R2, and R3 are independently or jointly selected from the group consisting of: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl comprising methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, and tert-butyl; (C2-4)alkenyl comprising ethenyl, propenyl, butenyl, wherein a double bond is optionally located at any position in the alkenyl carbon chain, and any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; acylamino; hydroxyl; thiol; thioalkyl; alkoxy; alkylthio; alkoxyalkyl; aryloxy; arylalkoxy; acyloxy; nitro; carbamoyl; trifluoromethyl; phenoxy; benzyloxy; phosphonic acid; phosphate ester; sulfonic acid (-SO3H); sulfonate ester; sulfonamide; alkaryl; arylalkyl; carbamate; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; alkylthio; heteroalkyl; alkyltriphenylphosphonium; heterocyclyl; ketone (=0); ether (-OR4); and ester (- COOR5 and -OC(=0)R5),
wherein R1 and R2 are optionally bonded together to form a four-, five-, or six- membered heterocyclyl, cycloalkenyl, or cycloalkyl; and
wherein R4 and R5 are independently or jointly selected from the group consisting of: a (Ci-4)alkyl comprising methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, and tert- butyl; (C2-4)alkenyl comprising ethenyl, propenyl, butenyl, wherein a double bond is optionally located at any position in the alkenyl carbon chain, and any alkenyl conformational isomers thereof; and alkynyl.
2. The comp claim 1, wherein R1 and R2 are independently or jointly selected from ^"^" and
Figure imgf000031_0001
The compound of claim 1, wherein R3 is H or methyl.
The compound of claim 1, wherein the derivatives comprise:
Figure imgf000031_0002
The compound of claim 1, wherein the derivatives comprise:
Figure imgf000032_0001
The compound of claim 1, wherein the derivatives comprise:
Figure imgf000033_0001
Ϊ o I Tb
Figure imgf000034_0001
Figure imgf000034_0002
Figure imgf000034_0003
Figure imgf000034_0004
Figure imgf000035_0001
7. A composition comprising the compound according to any one of claims 1 to 6, the derivatives thereof, a pharmaceutical carrier, a salt, an ester, an excipient, a vehicle, a prodrug, a solvent, a diluent, or any combination thereof.
8. Use of one or more compounds in preparation of a composition for treating and/or preventing microbial infections and/or related diseases or conditions in a subject,
said composition comprising an effective amount of the one or more compounds of formula (I),
Figure imgf000035_0002
wherein R1, R2, and R3 are independently or jointly selected from the group consisting of: H; F; CI; Br; I; OH; CN; (Ci-4)alkyl comprising methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, and tert-butyl; (C2-4)alkenyl comprising ethenyl, propenyl, butenyl, wherein a double bond is optionally located at any position in the alkenyl carbon chain, and any alkenyl conformational isomers thereof; alkynyl; aralkyl; alkaryl; halogenated alkyl; heteroalkyl; aryl; heterocyclyl; cycloalkyl; cycloalkenyl; cycloalkynyl; hydroxyalkyl; aminoalkyl; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; acylamino; hydroxyl; thiol; thioalkyl; alkoxy; alkylthio; alkoxyalkyl; aryloxy; arylalkoxy; acyloxy; nitro; carbamoyl; trifluoromethyl; phenoxy; benzyloxy; phosphonic acid; phosphate ester; sulfonic acid (-SO3H); sulfonate ester; sulfonamide; alkaryl; arylalkyl; carbamate; amino; alkylamino; arylamino; dialkylamino; alkylarylamino; diarylamino; alkylthio; heteroalkyl; alkyltriphenylphosphonium; heterocyclyl; ketone (=0); ether (-OR4); and ester (-COOR5 and -OC(=0)R5),
wherein R1 and R2 are optionally bonded together to form a four-, five-, or six- membered heterocyclyl, cycloalkenyl, or cycloalkyl; and
wherein R4 and R5 are independently or jointly selected from the group consisting of: a (Ci-4)alkyl comprising methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, and tert- butyl; (C2-4)alkenyl comprising ethenyl, propenyl, butenyl, wherein a double bond is optionally located at any position in the alkenyl carbon chain, and any alkenyl conformational isomers thereof; and alkynyl. claim 8, wherein R1 and R2 are independently or jointly selected from
Figure imgf000036_0001
The use of claim 8, wherein R3 is H or methyl.
11. The use of claim 8, wherein the one or more compounds comprise:
Figure imgf000036_0002
Figure imgf000037_0001
12. The use of claim 8, wherein the one or more compounds comprise:
Figure imgf000037_0002
Figure imgf000038_0001
The use of claim 8, wherein the one or more compounds comprise:
Figure imgf000038_0002
Figure imgf000038_0003
Figure imgf000039_0001
Figure imgf000039_0002
Figure imgf000039_0003
Figure imgf000039_0004
Figure imgf000040_0001
Figure imgf000040_0002
14. The use of any one of claims 8 to 13, wherein the microbial infections comprise staphylococcal infection.
15. The use of any one of claims 8 to 13, wherein the method reduces the production of pigment in Staphylococcus aureus.
16. The use of any one of claims 8 to 13, wherein the microbial infections and/or related diseases or conditions comprise infections of the skin and soft tissue, bone and joint, surgical wound, indwelling devices, lung and heart valves.
17. The use of any one of claims 8 to 13, wherein said subject is a mammal.
The use of any one of claims 8 to 13, wherein said subject is human.
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