Synthetic analogues of marine bisindole alkaloids as potent selective inhibitors of MRSA pyruvate kinase
- Veale, Clinton Gareth Lancaster
- Authors: Veale, Clinton Gareth Lancaster
- Date: 2014 , 2014-04-02
- Subjects: Alkaloids , Pyruvate kinase , Staphylococcus aureus , Antibiotics , Sponges -- South Africa , Imidazoles , Biological assay , Antibacterial agents
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4563 , http://hdl.handle.net/10962/d1020893
- Description: Globally, methicillin resistant Staphylococcus aureus (MRSA) has become increasingly difficult to manage in the clinic and new antibiotics are required. The structure activity relationship (SAR) study presented in this thesis forms part of an international collaborative effort to identify potent and selective inhibitors of an MRSA pyruvate kinase (PK) enzyme target. In earlier work the known marine natural product bromodeoxytopsentin (1.6), isolated from a South African marine sponge Topsentia pachastrelloides, exhibited selective and significant inhibition of MRSA PK (IC₅₀ 60 nM). Accordingly bromodeoxytopsentin provided the initial chemical scaffold around which our SAR study was developed. Following a comprehensive introduction, providing the necessary background to the research described in subsequent Chapters, this thesis has been divided into three major parts. Part one (Chapter 2) documents the synthesis of two natural imidazole containing topsentin analogues 1.40, 1.46, five new synthetic analogues 1.58—1.61, 2.104. In the process we developed a new method for the synthesis of topsentin derivatives via selenium dioxide mediated oxidation of N-Boc protected 3-acetylindoles to yield glyoxal intermediates which were subsequently cyclized and deprotected to yield the desired products. Interestingly we were able to demonstrate a delicate relationship between the relative equivalents of selenium dioxide and water used during the oxidation step, careful manipulation of which was required to prevent the uncontrolled formation of side products. Synthetic compounds 1.40, 1.46, 1.58—1.61 were found to be potent inhibitors of MRSA PK (IC₅₀ 238, 2.1, 23, 1.4, 6.3 and 3.2 nM respectively) with 1000-10000 fold selectivity for MRSA PK over four human orthologs. In the second part of this thesis (Chapter 3) we report the successful synthesis of a cohort of previously unknown thiazole containing bisindole topsentin analogues 1.62—1.68 via a Hantzsch thiazole synthesis. Bioassay results revealed that these compounds were only moderate inhibitors of MRSA PK (IC₅₀ 5.1—20 μM) which suggested that inhibitory activity was significantly reduced upon substitution of the central imidazole ring of topsentin type analogues with a thiazole type ring. In addition in Chapter 3 we describe unsuccessful attempts to regiospecifically synthesize oxazole and imidazole topsentin analogues through a similar Hantzsch method. As a consequence of our efforts in this regard we investigated three key reactions in depth, namely the synthesis of 2.2, 3.38, 3.40, 3.41 via α-bromination of 3-acetylindole and the synthesis of indolyl-3-carbonylnitriles 2.13, 3.45—3.47 and α-oxo-1H-indole-3-thioacetamides 3.48—3.51. The investigation of the latter led to the isolation and elucidation of two anomalous N,N-dimethyl-1H-indole-3-carboxamides 3.52 and 3.53. Finally the third part of this thesis (Chapter 4) deals with in silico assessment of the binding of both the imidazole and thiazole containing bisindole alkaloids to the MRSA PK protein which initially guided our SAR studies. In this chapter we reveal that there appears to be no correlation between in silico binding predictions and in vitro MRSA PK inhibitory bioassay data. Superficially it seems that binding energy as determined by the docking program used for these studies correlated with the size of the indole substituents and did not reflect IC₅₀ MRSA PK inhibitory data. Although this led us to computationally explore possible alternative binding sites no clear alternative has been identified.
- Full Text:
- Date Issued: 2014
- Authors: Veale, Clinton Gareth Lancaster
- Date: 2014 , 2014-04-02
- Subjects: Alkaloids , Pyruvate kinase , Staphylococcus aureus , Antibiotics , Sponges -- South Africa , Imidazoles , Biological assay , Antibacterial agents
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4563 , http://hdl.handle.net/10962/d1020893
- Description: Globally, methicillin resistant Staphylococcus aureus (MRSA) has become increasingly difficult to manage in the clinic and new antibiotics are required. The structure activity relationship (SAR) study presented in this thesis forms part of an international collaborative effort to identify potent and selective inhibitors of an MRSA pyruvate kinase (PK) enzyme target. In earlier work the known marine natural product bromodeoxytopsentin (1.6), isolated from a South African marine sponge Topsentia pachastrelloides, exhibited selective and significant inhibition of MRSA PK (IC₅₀ 60 nM). Accordingly bromodeoxytopsentin provided the initial chemical scaffold around which our SAR study was developed. Following a comprehensive introduction, providing the necessary background to the research described in subsequent Chapters, this thesis has been divided into three major parts. Part one (Chapter 2) documents the synthesis of two natural imidazole containing topsentin analogues 1.40, 1.46, five new synthetic analogues 1.58—1.61, 2.104. In the process we developed a new method for the synthesis of topsentin derivatives via selenium dioxide mediated oxidation of N-Boc protected 3-acetylindoles to yield glyoxal intermediates which were subsequently cyclized and deprotected to yield the desired products. Interestingly we were able to demonstrate a delicate relationship between the relative equivalents of selenium dioxide and water used during the oxidation step, careful manipulation of which was required to prevent the uncontrolled formation of side products. Synthetic compounds 1.40, 1.46, 1.58—1.61 were found to be potent inhibitors of MRSA PK (IC₅₀ 238, 2.1, 23, 1.4, 6.3 and 3.2 nM respectively) with 1000-10000 fold selectivity for MRSA PK over four human orthologs. In the second part of this thesis (Chapter 3) we report the successful synthesis of a cohort of previously unknown thiazole containing bisindole topsentin analogues 1.62—1.68 via a Hantzsch thiazole synthesis. Bioassay results revealed that these compounds were only moderate inhibitors of MRSA PK (IC₅₀ 5.1—20 μM) which suggested that inhibitory activity was significantly reduced upon substitution of the central imidazole ring of topsentin type analogues with a thiazole type ring. In addition in Chapter 3 we describe unsuccessful attempts to regiospecifically synthesize oxazole and imidazole topsentin analogues through a similar Hantzsch method. As a consequence of our efforts in this regard we investigated three key reactions in depth, namely the synthesis of 2.2, 3.38, 3.40, 3.41 via α-bromination of 3-acetylindole and the synthesis of indolyl-3-carbonylnitriles 2.13, 3.45—3.47 and α-oxo-1H-indole-3-thioacetamides 3.48—3.51. The investigation of the latter led to the isolation and elucidation of two anomalous N,N-dimethyl-1H-indole-3-carboxamides 3.52 and 3.53. Finally the third part of this thesis (Chapter 4) deals with in silico assessment of the binding of both the imidazole and thiazole containing bisindole alkaloids to the MRSA PK protein which initially guided our SAR studies. In this chapter we reveal that there appears to be no correlation between in silico binding predictions and in vitro MRSA PK inhibitory bioassay data. Superficially it seems that binding energy as determined by the docking program used for these studies correlated with the size of the indole substituents and did not reflect IC₅₀ MRSA PK inhibitory data. Although this led us to computationally explore possible alternative binding sites no clear alternative has been identified.
- Full Text:
- Date Issued: 2014
A study of electrospun nanofibers and diatomaceous earth materials for the extraction of alkaloids, flavonoids and aromatic amines in various matrices
- Mothibedi, Kediemetse (Kedimetse)
- Authors: Mothibedi, Kediemetse (Kedimetse)
- Date: 2013 , 2013-04-07
- Subjects: Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4288 , http://hdl.handle.net/10962/d1003052 , Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Description: The thesis explored the use of different sorbent materials in solid phase extraction method development. The methods included the use of the polymeric Agilent Bond Elut Plexa solid phase extraction and electrospun polymer-silica composite sorbents for clean-up and preconcentration. Sample clean-up for alkaloids (hydrastine and berberine) in goldenseal, Hydrastis canadensis and flavonoids (quercetin, kaempferol and isorhamnetin) in Ginkgo biloba was achieved using Bond Elut Plexa SPE sorbent. Clean-up of flavonoids in Ginkgo biloba was also achieved using electrospun polymer-silica composite (polystyrene-silica, polyacrylonitrile-silica and nylon 6-silica) sorbents. All analysis of flavonoids and alkaloids was carried out using an Agilent 1200 Series HPLC coupled with a diode array detector. Good peak separation was achieved in less than 6 min employing an Agilent ZORBAX Eclipse Plus C18 column (4.6 x 75 mm, 3.5 μm) at 35⁰C. The mobile phases employed were 0.1% phosphoric acid/methanol gradient and 0.5% phosphoric acid/methanol (40:60) for alkaloids and flavonoids respectively. The calibration curves exhibited linearity up to 120 μg mL⁻¹ with correlation coefficients of more than 0.9980. The recoveries ranged from 73-109% with relative standard deviation of less than 5% for all analytes. Agilent Chem Elut supported liquid extraction was employed for the development of a sample preparation method for the determination of 24 banned aromatic amines from azo dyes in textile following the EU standard method EN 14362-1:2003 (E) and the Chinese standard method GB/T 17592-2006. The supported liquid extraction was effective in the extraction of the aromatic amines from textile (cotton, wool and polyester/cotton [80%:20%]). Most of the recoveries obtained were conforming to the minimum requirements set in the EN 14362-1:2003 (E) standard method and the relative standard deviations were less than 15%. Good peak separation was obtained within 70 min run time using the Agilent Zorbax SB-Phenyl column (4.6 mm x 250 mm, 5-micron) or the Agilent DB-35 MS (J & W) (30 m x 0.25 mm, 0.25 μm film thickness. It was demonstrated that the polymeric Agilent Bond Elut Plexa, electrospun nanofibers and diatomaceous earth were effective in extraction of alkaloids, flavonoids and aromatic amines in different matrices. The developed methods were simple, rapid and reproducible.
- Full Text:
- Date Issued: 2013
- Authors: Mothibedi, Kediemetse (Kedimetse)
- Date: 2013 , 2013-04-07
- Subjects: Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4288 , http://hdl.handle.net/10962/d1003052 , Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Description: The thesis explored the use of different sorbent materials in solid phase extraction method development. The methods included the use of the polymeric Agilent Bond Elut Plexa solid phase extraction and electrospun polymer-silica composite sorbents for clean-up and preconcentration. Sample clean-up for alkaloids (hydrastine and berberine) in goldenseal, Hydrastis canadensis and flavonoids (quercetin, kaempferol and isorhamnetin) in Ginkgo biloba was achieved using Bond Elut Plexa SPE sorbent. Clean-up of flavonoids in Ginkgo biloba was also achieved using electrospun polymer-silica composite (polystyrene-silica, polyacrylonitrile-silica and nylon 6-silica) sorbents. All analysis of flavonoids and alkaloids was carried out using an Agilent 1200 Series HPLC coupled with a diode array detector. Good peak separation was achieved in less than 6 min employing an Agilent ZORBAX Eclipse Plus C18 column (4.6 x 75 mm, 3.5 μm) at 35⁰C. The mobile phases employed were 0.1% phosphoric acid/methanol gradient and 0.5% phosphoric acid/methanol (40:60) for alkaloids and flavonoids respectively. The calibration curves exhibited linearity up to 120 μg mL⁻¹ with correlation coefficients of more than 0.9980. The recoveries ranged from 73-109% with relative standard deviation of less than 5% for all analytes. Agilent Chem Elut supported liquid extraction was employed for the development of a sample preparation method for the determination of 24 banned aromatic amines from azo dyes in textile following the EU standard method EN 14362-1:2003 (E) and the Chinese standard method GB/T 17592-2006. The supported liquid extraction was effective in the extraction of the aromatic amines from textile (cotton, wool and polyester/cotton [80%:20%]). Most of the recoveries obtained were conforming to the minimum requirements set in the EN 14362-1:2003 (E) standard method and the relative standard deviations were less than 15%. Good peak separation was obtained within 70 min run time using the Agilent Zorbax SB-Phenyl column (4.6 mm x 250 mm, 5-micron) or the Agilent DB-35 MS (J & W) (30 m x 0.25 mm, 0.25 μm film thickness. It was demonstrated that the polymeric Agilent Bond Elut Plexa, electrospun nanofibers and diatomaceous earth were effective in extraction of alkaloids, flavonoids and aromatic amines in different matrices. The developed methods were simple, rapid and reproducible.
- Full Text:
- Date Issued: 2013
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