Sampling and storage
Table 2: Date, depth and location of the sampling of G. Barretti and G. Macandrewii
Species Sampling
date
Location Depth
(meter)
Labelling
G. barretti 11.05.13 Saltfjorden, Nordland 127 1
G. barretti 11.05.13 Bliksvær, Nordland 125 2
G. barretti 13.05.13 Lekshammeren, Trondheimsfjorden
193 3
G. barretti 14.05.13 Borgenfjorden, Trondheimsfjorden
246 4
G. macandrewii 11.05.13 Bliksvær, Nordland 127 5
G. macandrewii 09.05.13 Saltfjorden, Nordland 129 6
All the biomass samples were stored at -22ºC in the dark.
Extractions of G. baretti and G. macandrewii Materials used
DCM (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA) MeOH (≥99.9 %, Sigma-Aldrich, St. Louis, MO, USA) MilliQ water (Millipore, Billerica, MA, USA)
Equipment used
A11 Basic grinder (IKA Works, Staufen, Germany) Centrifuge: Heraus Multifuge 3 S-R (Hanau, Germany)
Freeze-drier: Heto PowerDry PL9000 and Heto PowerDry PL6000 (Thermo Fisher Scientific, Waltman, MA, USA)
Mortar and pestle: MTC Haldenwanger (W.Haldenwanger Technische Keramik, Berlin, Germany)
Rotary evaporator: Heidolph Laborata 4002 (Nürnberg, Germany) Scale: Mettler Toledo PB3002-S Fact ( Greifensee, Switzerland) Whatman filter paper 125 Ø (no.3) (Springfield Mill, England)
22 Sample preparation
The sponges were cut into approximately 1 cm3 pieces while still frozen before transferring the material to Pyrex dishes. The dishes were covered with perforated aluminium foil and freeze-dried for 2 days.
Aqueous extraction
The freeze-dried sponges were pulverized and transferred to tared 1 L Duran bottles and weighed. The material was then transferred to 0.6 L centrifuge bottles and MilliQ water was added, approximately ten times the weight of the dry weight of the material, and shaken until the suspension got a slurry consistency. The extraction was performed at 5ºC to minimize the risk of bacterial decomposition of the compounds and to maintain sample stability. The suspension was centrifuged at 3400 g, at 5ºC for 30 minutes. The water supernatant was transferred to Pyrex dishes and the pellet re-extracted with MilliQ water, approximately half of the amount used in the first round but enough to give the suspension the slurry consistency.
The suspension was shaken and put in the refrigerator for a minimum of approximately 40 minutes before it was centrifuged again at 3400 g, at 5ºC for 30 minutes. After the
centrifugation the supernatant was first transferred to Pyrex dishes, and then the pellet was transferred to separate Pyrex dishes. All the dishes were covered with perforated aluminium foil and stored at -22ºC until freeze-drying. The water extracts were frozen at -80ºC for 30-45 minutes before freeze-drying for 3 days. The material was grinded with mortar and pestle, transferred to 50 ml centrifuge tubes and stored at -22ºC.
Organic extract
The freeze-dried pellet left over from the aqueous extraction was grinded and transferred to tara 1 L Duran bottles before extraction with the solvent mixture DCM-MeOH (1:1, v/v), approximately ten times the weight of the material, until the suspension got a slurry consistency. The suspension was stored in the refrigerator until the next day when it was vacuum filtrated with Whatman filters. Afterwards the solid material was transferred back into the Duran bottle and re-extracted with the solvent mixture DCM/MeOH (1:1, v/v),
approximately half of the amount used in the first round but enough to give the suspension the slurry consistency. The suspension was shaken and stored in the refrigerator for
approximately 40 minutes before repeating the filtration process. The filtrate was then concentrated to 10-20 mL using a rotavapor before transferred to a 50 ml round flask and evaporated under reduced pressure in the rotavapor until dry and stored at -22ºC.
23
Preparation of the samples for MS analysis Materials used
MeOH (≥99.9 %, Sigma-Aldrich, St. Louis, MO, USA)
Approximately 150 mg of the organic extract from each of the samples was dissolved in sufficient amount of MeOH to achieve 100 mg/ml of sample.
Table 3: Amount of organic extract dissolved in amount of MeOH and the concentration of the solution.
Organic extract (mg) MeOH (mL) Sample concentration (mg/mL)
150,1 1,501 100
ACN (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA) Formic Acid (98.0%, Sigma-Aldrich, St. Louis, MO, USA) MeOH (≥99.9 %, Sigma-Aldrich, St. Louis, MO, USA) MilliQ water (Millipore, Billerica, MA, USA)
Equipment used
Acquity UPLC ® BEH, 2.1×100 mm, 1.7 µm column (Waters, Milford, MA, USA) Waters Acquity UPLC
Waters LCT Premier detector
Mobile phases:
A: 0.1 % formic acid in Milli-Q water B: 0.1 % formic acid in acetonitrile
24 Table 4: Gradient used for UPLC-HR-MS analysis
Time Flow (mL/min) % A % B
Each sample was injected 6 times.
Instrument parameters
Retention time window: 0.2 minutes Mass window: 0.1 Da
The program was set to de-isotope, meaning it would remove signals from common isotopes such as 13C.
The MarkerLynx analysis detected a potential novel compound that was labelled MBC-169 in sample 5 and 6. Therefore, MBC-169 had to be isolated and sample 5 was the chosen sample.
25
Preparation of sample 5 for HPLC isolation of MBC-169 Materials used
ACN (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA) Formic Acid (98.0%, Sigma-Aldrich, St. Louis, MO, USA) Hexane (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA) MilliQ water (Millipore, Billerica, MA, USA)
Rotary evaporator: Heidolph Laborata 4002 (Nürnberg, Germany)
4.0031 g of the organic extract was dissolved in 200 ml hexane, and subsequently liquid-liquid extracted twice with 100 ml 90% ACN. Under the first liquid-liquid-liquid-liquid extraction there was a slight problem separating the two phases when the ACN phase also showed a cluster of particles due to saturation. This was removed and added 50 ml ACN and shaken until the particles was dissolved and the ACN phases was then combined before the second liquid-liquid extraction. Both phases were collected and concentrated using a rotavapor, the hexane phase until dryness and the ACN phase to approximately 10 ml. The hexane phase was then stored in the freezer and the ACN phase was used in the continued process. 1 ml of sample from the ACN phase was then added 2 ml MeOH and used in HPLC isolation.
26
1st HPLC isolation of MBC-169 Materials used
ACN (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA) Formic Acid (98.0%, Sigma-Aldrich, St. Louis, MO, USA) MeOH (≥99.9 %, Sigma-Aldrich, St. Louis, MO, USA) MilliQ water (Millipore, Billerica, MA, USA)
Equipment used
Atlantis ® Prep C18, 10 µm, 10×250 mm column
Freeze-drier: Heto PowerDry PL9000 (Thermo Fisher Scientific, Waltman, MA, USA) Rotary evaporator: Heidolph Laborata 4002 (Nürnberg, Germany)
Software: MassLynx 4.1
Waters 600 Controller (Milford, MA, USA) Waters 2996 photodiode array detector Waters 3100 mass detector B: 0.1 % formic acid in acetonitrile
Make-up pump solution: 80 % aqueous MeOH w/ 0.2 % formic acid
The make-up pump maintains the flow from the splitter necessary to provide a stable signal.
Wash solution 1: 5 % MeOH in Milli-Q water Wash solution 1: Acetonitrile
Injection volume: 250 µL
27 Conditions:
Polarity: ES+
Source Temp (C): 120 Desolvation Temp (C): 300 Desolvation Gas Flow (L/hr): 650
After 7 injections attempting to adjust a linear gradient which could isolate the compound in best way possible without succeeding, an isocratic gradient was chosen consisting of 65 % mobile phase B and 35 % mobile phase A to the continued isolation.
All the collected fractions were transferred to a round-bottomed flask and concentrated in the rotary evaporator before being transferred to a glass tube and freeze-dried for 48 hours.
2nd HPLC isolation of MBC-169 Materials used
ACN (≥99.8 %, Sigma-Aldrich, St. Louis, MO, USA)
Ammonium bicarbonate (Sigma-Aldrich, St. Louis, MO, USA) Formic Acid (98.0 %, Sigma-Aldrich, St. Louis, MO, USA) MilliQ water (Millipore, Billerica, MA, USA)
The same set-up from the first isolation was used for the second isolation but with a different method where the mobile phase and the gradient were changed.
Mobile phases:
A: Aqueous phase with buffer B: 0.1 % formic acid in acetonitrile
Mobil phase A: 1.58 g of ammonium bicarbonate was dissolved in 2 L Milli-Q water and the pH adjusted with formic acid to 7.8.
Make-up pump solution: 80 % aqueous MeOH w/ 0.2 % formic acid Wash solution 1: 5 % MeOH in Milli-Q water
Wash solution 1: Acetonitrile
28 Table 5: Gradient used for isolation of MBC-169
Time Flow (mL/min) % A % B
Initial 6 55 45
10 6 45 55
11 6 0 100
15 6 0 100
16 6 55 45
Injection volume: 100 µL
Afterwards all of the tubes containing the isolated compound were transferred to a round-bottomed flask and concentrated in the rotary evaporator before being transferred to a glass tube and freeze-dried for 24 hours.
H1-NMR-analysis
Johan Isaksson at Smallstruct, the Department of Chemistry at the University of Tromsø performed this procedure and interpretation of data.
The NMR data was acquired on a Varian (now Agilent) Inova spectrometer operating at 599.934 MHz for 1H, equipped with a cryogenically enhanced inverse triple resonance probe (HCN).
Data & software: All data was acquired using VnmrJ 3.2A and chempack 6, using standard pulse sequences, where applicable, gradient- and adiabatic pulse- versions with homospoils between scans were utilized. For heteronuclear experiments, BIP versions with gradient selection and sensitivity enhancement were used. All spectra processing and spectra simulations were made in Mnova 8.1.2.
29
Cellular Antioxidant Activity Assays Materials and equipment used
2, 7 dichlorofluorescin diacetat (DCFH-DA, Sigma-Aldrich, St.Louis, MO, USA) AAPH (Cayman)
Bodipy ® 581/591 C11 (Lipid peroxidation Sensor, Invitrogen) Bürkes Countingchamber
CumOOH (Sigma-Aldrich, St.Louis, MO, USA) DMSO (99.5 %, Sigma-Aldrich, St.Louis, MO, USA) Ethanol (EtOH, 96 % Sigma-Aldrich, St.Louis, MO, USA) Fetal Bovine Serum (Biochrom)
Growth medium (GM): E-mem (Biochrom) with 10 % FBS, 500 mL:
- Gentamycin 500 µL - NEA 5 mL
- Sodium Pyruvate 5 mL - L-Alanyl-glutamin 5 mL - FBS 50 ml
Hank`s saline solution (Biochrom)
Heidolph Incubator 1000 (VWR International) Luteolin (Cayman)
Milli-Q water (Millipore, Billerica, MA, USA) Microscope
Microtiter plates; black 96-well plates with optical bottom (Costar, Cornings) Multichannel pipette
Phosphate buffered saline solution (PBS)
Shaking apparatus: Edmund Bühler GmbH SM 30 Treatment medium without FBS
- Same as growth medium, only without FBS Trypan blue (VWR International)
Trypsin (Gibco, NY, USA)
Victor 3 Multilabel Counter (Perkin Elmer, Waltham MA, USA)
30 Cell splitting and seeding
HepG2- cells are humane hepatocellular cells from a 15 year old boys liver tissue. The cells are epithelial, chromosome no.55.
Phosphate buffered saline solution (PBS) and treatment medium (TM) were preheated to 37ºC in the incubator, and trypsin to room temperature. The cells were inspected in a microscope to ensure a healthy cell population before the cell medium was decanted and 10 mL PBS was added to the cell layer. The container with cells and PBS was gently tilted from side to side to make sure all the cells were washed before the PBS was pipetted out. 4 mL trypsin was added, the container tilted from side to side to cover the cells with trypsin and then the surplus of trypsin was poured out carefully to avoid loss of cells. The container was incubated at 37ºC for 5 minutes and inspected in the microscope to ensure that the cells had unlatched from the surface of the container. Then 20 mL growth medium (GM) were added and the suspension was resuspended several times to avoid the cells to clump together. In order for the cells to be counted 200 µL of the cell suspension was added to 200 µL of Trypan blue and mixed
together. 10 µL was put in a Bürkes counting chamber and counted under the microscope.
From the grid, the cell numbers in 5 squares were counted and the average from those 5 was used to calculate cells/mL:
2 (adjusting for trypan blues contribution) x no. cells counted x 104
The formula used to calculate cell concentration:
C1 x V1 = C2 x V2
C1 = concentration of cells in the suspension till this point V1 = the unknown volume
C2 = desired concentration of cells (CAA = 80 000 cell/well, CLPAA = 90 000 cell/well) V2 = desired volume of cell suspension
The suspension was then again suspended several times before transferred to the plates, 100 µL to each well. The plates were then incubated over 24 hours in 37ºC and 5 % CO2.
31 Cellular Antioxidant Activity (CAA) Assay 1st screening:
PBS and TM were heated up (10 mL for each plate). The cells were inspected in a microscope. A healthy cell population will form peninsula shapes and cover most of the bottom of the wells with little space between each cell. If the cells are circular and far apart, the cells are damaged and cannot be used in this assay. Cell medium from the day before was removed from the cells using a vacuum pipette. The pipetting was done carefully to avoid damage or loss of cells. TM with DCFH-DA was made immediately prior to use. 15.6 µL of DCFH-DA was added to 10 mL TM (for each plate). The wells were then washed with 100 µL PBS. 20 µL of the compound being tested were added to four wells, 80 µL TM was added to the same wells and to the control wells. The rest of the wells not containing the compound being tested for this thesis are being used to test other compounds by Mabcent with slightly different concentrations (5 µL of a given test compound and 95 µL TM). 20 µL of the known antioxidant Luteolin (250 µL/mL) were added to four wells, also 20 µL MQ-H2O to the (+) and (-) controls. The plates were then incubated for 1 hour at 37ºC and 5 % CO2. See table # for a schematic set up.
Reading:
The instrument was set to 37ºC. A 600 µM AAPH in Hank`s solution was prepared (30 µL AAPH was added to 10 mL Hank`s for each plate). The cell medium added an hour earlier was then removed with a vacuum pipette and the plate washed with 100 µL PBS. 100 µL of Hank`s was added the negative control wells (-). Then 100 µL of the prepared Hank`s with AAPH was added to all the remaining wells. Fluorescence was measured at 485/520 nm in Victor plate reader with 12 readings every 240th second. The plates were then incubated for 1 hour at 37ºC and 5 % CO2 and the absorbance was measured again.
Cellular Lipid Peroxidation Antioxidant Activity (CLPAA) Assay
C11-BODIPY were dissolved in DMSO to 6.25 mM and stored in -80ºC prior to the experiment. Immediately prior to use 15.9 µL BODIPY (6.25 Mm) was added 11 mL TM, which resulted in 10 µM concentration on the plate. The CumOOH was also prepared
immediately prior to use as following; 10 µL 6M CumOOH was added to 590 µL 70% EtOH.
Then diluted to 50 µM by adding 5 µL 0.1 M CumOOH to 9995 µL Hanks.
32 1st screening:
PBS and TM were heated up (11 mL for each plate). The cells were inspected in a microscope. (A healthy cell population will form peninsula shapes and cover most of the bottom of the wells with little space between each cell. If the cells are circular and far apart, the cells are damaged and cannot be used in this assay). Cell medium from the day before was removed from the cells using a vacuum pipette. The pipetting was done carefully to avoid damage or loss of cells. Then the wells were washed with 100 µL PBS. TM with 10 µM C11 -Bodipy was made immediately prior to use. 100 µL TM with -Bodipy was added to the control wells and then the plates were incubated 37ºC and 5 % CO2 for 30 minutes to enable the cells to absorb the fatty compound Bodipy. Afterwards the TM was removed from the wells with a manual pipette. 80 µL of TM without Bodipy was added to all the sample wells, and 80 µL of TM without Bodipy was added to the control wells. 20 µL of the compound being tested were added to four wells. (The rest of the wells not containing the compound being tested for this thesis are being used to test other compounds by Mabcent). 20 µL Luteolin (250 µL/mL) were added to four wells, also 20 µL MQ-H2O to the (+) and (-) controls. The plates were then incubated for 1 hour at 37ºC and 5 % CO2. See table # for a schematic set up.
Reading:
The instrument was set to 37ºC. A 50 µM CumOOH in Hank`s solution was prepared.
The cellmedium added earlier was removed with a pipette and the plate was washed with 100 µL PBS. 100 µL of the prepared Hank`s with CumOOH was added to all the wells except the four control wells, where 100 µL of Hank`s without CumOOH was added. Fluorescence was measured at 590/632 nm in a Victor plate reader (CW-lamp at 10 000) for red fluorescence with a reading every 3rd minute for an hour, 21 readings total. Followed by a new measuring at 485/520 nm (CW-lamp at 20 000) for green fluorescence also every 3rd minute for an hour.
33
Table 6: Assay set up for CAA and CLPAA. The outer wells were not used for the samples due to edge effect.
Negative controls are marked with (-), positive controls with (+). The known antioxidant Luteolin were marked (L). Compounds tested for this thesis: (C) and the rest marked (X) were compounds tested by MabCent.
C X X X X X X X - -
Kinase RR-analysis: PKA and ABL inhibition testing Materials and equipment used
ABL (ProQinase,Boston, MA, USA) Centrifuge: Heraeus multifuge 1 S
Dithriotreitol (DTT, Sigma-Aldrich, St.Louis, MO, USA) DMSO (99.5 %, Sigma-Aldrich, St.Louis, MO, USA) Glasscontainer
Kinase RR-kit (Biothema)
Milli-Q water (Millipore, Billerica, MA, USA) Peptidsubstrate (KEMP-TID, ABL-TID) Pipettes (10 µL, 100 µL, 1000 µL) PKA (ProQinase,Boston, MA, USA)
Plates: 384- well plates with flat, white bottoms (Perkin Elmer Optiplate -384) Shaking apparatus: Edmund Bühler GmbH SM 30
Staurosporin (10 µM, Sigma-Aldrich, St.Louis, MO, USA) EnVision (Perkin Elmer, Waltham MA, USA)
Controls:
- Blank: No peptidsubstrate (KEMP-TID or ABL-TID) = Inactive mix + Milli-Q water - Control: Active mix + Milli-Q water
- Positive control: Active mix + 1µM staurosporin
34
MBC-169 was already dissolved in 100% DMSO to 10mg/mL. It was diluted to 500 µg/mL, 250µg/mL and 5µg/mL, making the concentration in the wells 100µg/mL, 50 µg/mL and 1 µg/mL. 5 µL of each concentration was added to individual wells on the plates (one plate for PKA and one plate for ABL). The master mix was prepared according to the Kinase RR- kit.
The content is presented in table 7.
Table 7: PKA- and ABL- master mix
PKA- master mix ABL-master mix
7500 µL Kinase RR-buffer 7500 µL Kinase RR-buffer
1200 µL ATP-reagent-SL 1200 µL ATP-reagent-SL
37.5 µL 0.4 M DTT 37.5 µL 0.4 M DTT
74161 µL Millie-Q water 161 µL Milli-Q water
7.8 µL PKA-enzyme (dilute to 1:10 from stock)
Take out 117.5 µL for blank control Ad 2.5 µL Milli-Q water for this
19 µL ABL-enzyme
Take out 117.5 µL for blank control Ad 2.5 µL Milli-Q water for this 184 µL KEMP-TID (KEMP2)-substrate (2 mM) 92 µL ABL-TID-substrate (4 mM)
15 µL of the master mix was pipetted to each well except for the blank controls. The controls were added as following:
Blank (b): 5 µL Milli-Q water + 15 µL inactive mix were added to well B7, B8 and B9.
Control (c): 5 µL Milli-Q water + 15 µL active mix were added to well D7, D8 and D9.
Positive control (pc): 5 µL staurosporin + 15 µL active mix were added to well F7, F8 and F9.
35
Table 8: Set-up for PKA and ABL inhibition testing, where (x) is MBC-169 and (b), (c), (pc) are the controls.
The shaded wells are used by MabCent to test other compounds.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 A
B b b b
C
D c c c
E
F pc pc pc
G
H x x x
I
J x x x
K
L x x x
M N O P
5 µL of ATP was added to each well before the plates were centrifuged for 1 minute at 190 G, then shaken for 2 minutes in the minishaker. The plates were read in the platereader.
36 Minimum Inhibiting Concentration (MIC) Assay Materials and equipment used
Brain Heart Infusion (BHI broth, Merck) Erlenmeyerflask (sterile)
Falcontubes LB-plates Microtiterplates
Milli-Q water (sterile, Millipore, Billerica, MA, USA) Mueller-Hinton (MH broth, Oxoid Ltd)
Multichannelpipette
NaCl, 0.9% (sterile, Sigma-Aldrich, St.Louis, MO, USA) Loops
Shaking incubator: Heidolph Unimax 1010, Heidolph Inkubator 1000) Victor 3 Multilabel Counter (Perkin Elmer, Waltham MA, USA)
The sample was diluted until the final concentration on the plate was 50µg/mL.
On the first day bacterial strains were sown from the blood plates to 8 mL growth medium and incubated in suitable atmosphere overnight. The growth medium was chosen by two criteria. The first is that it had to be a good growth environment for the bacteria. The second is that it could not have any influence on the sample being tested.
On the second day 2 mL of the bacterial suspension from day one were transferred to 25 mL fresh medium for exponential growth. The bacterial suspension was incubated in the shaking incubator according to table 9. The differences in incubation time in the table are due to differences in the bacterial strains; some take longer time to go into log-phase and the incubation time was adapted accordingly. Bacterial growth was sufficient when the turbidity reached 0.5 McFarland standards (1.0×108 bacteria/ mL).
37
Table 9: Demonstrating incubation time and growth medium for each of the different bacterial strains and the appropriate bacterial density.
Bacterial strain Growth medium Incubation time Bacterial density
S.aureus MH- broth 2.5 hours 0.5-3×105 CFU/mL (2500-15000 CFU/ well) E.coli MH- broth 1.5 hours 0.5-3×105 CFU/mL (2500-15000 CFU/ well) E.faecalis BHI- broth 1.5 hours 0.5-3×105 CFU/mL (2500-15000 CFU/ well) P.aeruginosa MH- broth 2.5 hours 3-7×104 CFU/mL (2500-15000 CFU/ well) S.agalactiae BHI- broth 1.5 hours 0.5-3×105 CFU/mL (2500-15000 CFU/ well)
50 µL of sample were added in 4 parallels on the microtiterplates for each strain (the rest of the places were used for testing of other compounds by MabCent). The different bacterial strains were placed on different mikrotiterplates, so that each plate only tested one bacterial strain. The bacterial suspension was diluted, first 1:100 and then 1:10 in the growth medium before adding 50 µL of the diluted suspension to the plates. To uphold viable cell density, the bacterial suspension was added within 30 minutes after the standardization. The plates were incubated for approximately 20 hours at 37ºC.
Table 10: Assay set up for MIC. Positive controls are marked with (P), negative controls with (N). The compound tested in this thesis is marked (C), and the rest are fractions tested by Mabcent marked (X).
1 2 3 4 5 6 7 8 9 10 11 12
Negative controls: 50 µL growth medium + 50 µL sterile Milli-Q water.
Positive controls: 50 µL sterile Milli-Q water + 50 µL bacterial suspension.
38
Gentamycin was used as control for the set up and for precision between each experiment.
To achieve measurable values of the bacteria the solution was diluted to approximately 1×102- 1×103 bacteria/mL. The dilution was done in 0.9% NaCl as following: 1) 1:100, 2) 1:100, 3) 1:10, 4) 1:10. Then 100 µL were plated out from the final dilution in two parallels on LB-plates and incubated overnight
The plates were read visually, where visual turbidity indicates inactive compound (I). Wells without visual turbidity indicates inhibition of bacteria and active compound (A). When in doubt, the compound is set as questionable (Q). A photometric reading using the Victor platereader was performed, where absorbance units (AU) was used to classify the compound.
AU: < 0.05 = A, AU: 0.05-0.09 = Q, AU: > 0.09 = I.
39