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News Article | October 25, 2016
Site: www.nature.com

Strains of P. falciparum (Dd2, 3D7, D6, K1, NF54, V1/3, HB3, 7G8, FCB and TM90C2B) were obtained from the Malaria Research and Reference Reagent Resource Center (MR4). PfscDHODH, the transgenic P. falciparum line expressing S. cerevisiae DHODH19, was a gift from A. B. Vaidya. P. falciparum isolates were maintained with O-positive human blood in an atmosphere of 93% N , 4% CO , 3% O at 37 °C in complete culturing medium (10.4 g l−1 RPMI 1640, 5.94 g l−1 HEPES, 5 g l−1 albumax II, 50 mg l−1 hypoxanthine, 2.1 g l−1 sodium bicarbonate, 10% human serum and 43 mg l−1 gentamicin). Parasites were cultured in medium until parasitaemia reached 3–8%. Parasitaemia was determined by checking at least 500 red blood cells from a Giemsa-stained blood smear. For the compound screening, a parasite dilution at 2.0% parasitaemia and 2.0% haematocrit was created with medium. 25 μl of medium was dispensed into 384-well black, clear-bottom plates and 100 nl of each compound in DMSO was transferred into assay plates along with the control compound (mefloquine). Next, 25 μl of the parasite suspension in medium was dispensed into the assay plates giving a final parasitaemia of 1% and a final haematocrit of 1%. The assay plates were incubated for 72 h at 37 °C. 10 μl of detection reagent consisting of 10× SYBR Green I (Invitrogen; supplied in 10,000× concentration) in lysis buffer (20 mM Tris-HCl, 5 mM EDTA, 0.16% (w/v) Saponin, 1.6% (v/v) Triton X-100) was dispensed into the assay plates. For optimal staining, the assay plates were left at room temperature for 24 h in the dark. The assay plates were read with 505 dichroic mirrors with 485 nm excitation and 530 nm emission settings in an Envision (PerkinElmer). High-throughput screening hits were hierarchically clustered by structural similarity using average linkage on pairwise Jaccard distances43 between ECFP4 fingerprints44. Pipeline Pilot45 was used for fingerprint and distance calculation; clustering and heat-map generation was done in R (ref. 46). HepG2 cells (ATCC) were maintained in DMEM, 10% (v/v) FBS (Sigma), and 1% (v/v) antibiotic–antimycotic in a standard tissue culture incubator (37 °C, 5% CO ). P. berghei (ANKA GFP–luc) infected A. stephensi mosquitoes were obtained from the New York University Langone Medical Center Insectary. For assays, ∼17,500 HepG2 cells per well were added to a 384-well microtitre plate in duplicate. After 18–24 h at 37 °C the media was exchanged and compounds were added. After 1 h, parasites obtained from freshly dissected mosquitoes were added to the plates (4,000 parasites per well), the plates were spun for 10 min at 1,000 r.p.m. and then incubated at 37 °C. The final assay volume was 30 μl. After a 48-h incubation at 37 °C, Bright-Glo (Promega) was added to the parasite plate to measure relative luminescence. The relative signal intensity of each plate was evaluated with an EnVision (PerkinElmer) system. Micropatterned co-culture (MPCC) is an in vitro co-culture system of primary human hepatocytes organized into colonies and surrounded by supportive stromal cells. Hepatocytes in this format maintain a functional phenotype for up to 4–6 weeks without proliferation, as assessed by major liver-specific functions and gene expression47, 48, 49. In brief, 96-well plates were coated homogenously with rat-tail type I collagen (50 μg ml−1) and subjected to soft-lithographic techniques to pattern the collagen into 500-μm-island microdomains that mediate selective hepatocyte adhesion. To create MPCCs, cryopreserved primary human hepatocytes (BioreclamationIVT) were pelleted by centrifugation at 100g for 6 min at 4 °C, assessed for viability using Trypan blue exclusion (typically 70–90%), and seeded on micropatterned collagen plates (each well contained ~10,000 hepatocytes organized into colonies of 500 μM) in serum-free DMEM with 1% penicillin–streptomycin. The cells were washed with serum-free DMEM with 1% penicillin–streptomycin 2–3 h later and replaced with human hepatocyte culture medium48. 3T3-J2 mouse embryonic fibroblasts were seeded (7,000 cells per well) 24 h after hepatocyte seeding. 3T3-J2 fibroblasts were courtesy of H. Green50. MPCCs were infected with 75,000 sporozoites (NF54) (Johns Hopkins University) 1 day after hepatocytes were seeded48, 49. After incubation at 37 °C and 5% CO for 3 h, wells were washed once with PBS, and the respective compounds were added. Cultures were dosed daily. Samples were fixed on day 3.5 after infection. For immunofluorescence staining, MPCCs were fixed with −20 °C methanol for 10 min at 4 °C, washed twice with PBS, blocked with 2% BSA in PBS, and incubated with mouse anti-P. falciparum Hsp70 antibodies (clone 4C9, 2 μg ml−1) for 1 h at room temperature. Samples were washed with PBS then incubated with Alexa 488-conjugated secondary goat anti-mouse for 1 h at room temperature. Samples were washed with PBS, counterstained with the DNA dye Hoechst 33258 (Invitrogen; 1:1,000), and mounted on glass slides with fluoromount G (Southern Biotech). Images were captured on a Nikon Eclipse Ti fluorescence microscope. Diameters of developing liver stage parasites were measured and used to calculate the corresponding area. All rhesus macaques (Macaca mulatta) used in this study were bred in captivity for research purposes, and were housed at the Biomedical Primate Research Centre (BPRC; AAALAC-certified institute) facilities under compliance with the Dutch law on animal experiments, European directive 86/609/EEC and with the ‘Standard for Humane Care and Use of Laboratory Animals by Foreign Institutions’ identification number A5539-01, provided by the Department of Health and Human Services of the US National Institutes of Health. The local independent ethical committee first approved all protocols. Non-randomized rhesus macaques (male or female; 5−14 years old; one animal per month) were infected with 1 × 106 P. cynomolgi (M strain) blood-stage parasites, and bled at peak parasitaemia. Approximately 300 female A. stephensi mosquitoes (Sind-Kasur strain, Nijmegen University Medical Centre St Radboud) were fed with this blood as described previously51. Rhesus monkey hepatocytes were isolated from liver lobes as described by previously52. Sporozoite infections were performed within 3 days of hepatocyte isolation. Sporozoite inoculation of primary rhesus monkey hepatocytes was performed as described previously53, 54. On day 6, intracellular P. cynomolgi malaria parasites were fixed, stained with purified rabbit antiserum reactive against P. cynomolgi Hsp70.1 (ref. 53), and visualized with FITC-labelled goat anti-rabbit IgG antibodies. Quantification of small ‘hypnozoite’ exoerythrocytic forms (1 nucleus, a small round shape, a maximal diameter of 7 μm) or large ‘developing parasite’ exoerythrocytic forms (more than 1 nucleus, larger than 7 μm and round or irregular shape) was determined for each well using a high-content imaging system (Operetta, PerkinElmer). P. falciparum 3D7 stage IV–V gametocytes were isolated by discontinuous Percoll gradient centrifugation of parasite cultures treated with 50 mM N-acetyl-d-glucosamine for 3 days to kill asexual parasites. Gametocytes (1.0 × 105) were seeded in 96-well plates and incubated with compounds for 72 h. In vitro anti-gametocyte activity was measured using CellTiter-Glo (Promega). A detailed description of the method is published elsewhere55. In brief, NF54pfs16-LUC-GFP highly synchronous gametocytes were induced from a single intra-erythrocytic asexual replication cycle. On day 0 of gametocyte development, spontaneously generated gametocytes were removed by VarioMACS magnetic column (MAC) technology. Early stage I gametocytes were collected on day 2 of development and late-stage gametocytes (stage IV) on day 8 using MAC columns. Percentage parasitaemia and haematocrit was adjusted to 10 and 0.1, respectively. 45 μl of parasite sample were added to PerkinElmer Cell carrier poly-d-lysine imaging plates containing 5 μl of test compound at 16 doses, including control wells containing 4% DMSO and 50 μM puromycin (0.4% and 5 μM final concentrations, respectively), the plates sealed with a membrane (Breatheasy or 4ti-05 15/ST) and incubated for 72 h in standard incubation conditions of 5% CO , 5% O , 90% N and 60% humidity at 37 °C. After incubation, 5 μl of 0.07 μg ml−1 MitoTracker Red CM-H2XRos (MTR) (Invitrogen) in PBS was added to each well, and plates were resealed with membranes and incubated overnight under standard conditions. The following day, the plates were brought to room temperature for at least one hour before being measured on the Opera QEHS Instrument. Image analysis was performed using an Acapella (PerkinElmer)-based algorithm that identifies gametocytes of the expected morphological shape with respect to degree of elongation and specifically those parasites that are determined as viable by the MitoTracker Red CM-H2XRos fluorescence size and intensity. IC values were determined using GraphPad Prism 4, using a 4-parameter log dose, nonlinear regression analysis, with sigmoidal dose–response (variable slope) curve fit. P. falciparum transmission-blocking activity of BRD7929 was assessed in a standard membrane feeding assay as previously described56. In brief, P. falciparumNF54 hsp70-GFP-luc reporter parasites were cultured up to stage V gametocytes (day 14). Test compounds were serially diluted in DMSO and subsequently in RPMI medium to reach a final DMSO concentration of 0.1%. Diluted compound was either pre-incubated with stage V gametocytes for 24 h (indirect mode) or directly added to the blood meal (direct mode). Gametocytes were adjusted to 50% haematocrit, 50% human serum and fed to A. stephensi mosquitoes. All compound dilutions were tested in duplicate in independent feeders. After 8 days, mosquitoes were collected and the relative decrease in oocysts density in the midgut was determined by measurement of luminescence signals in 24 individual mosquitoes from each cage. For each vehicle (control) cage, an additional 10 mosquitoes were dissected and examined by microscopy to determine the baseline oocyst intensity. In vitro resistance selections were performed as previously described15. In brief, approximately 1 × 109 P. falciparum Dd2 parasites were treated with 60 nM (EC ) or 150 nM (10 × EC ) of BRD1095 in each of four independent flasks for 3–4 days. After the compounds were removed, the cultures were maintained in compound-free complete RPMI growth medium with regular media exchange until healthy parasites reappeared. Once parasitaemia reached 2–4%, compound pressure was repeated and these steps were executed for about 2 months until the initial EC shift was observed. Three out of four independent selections pressured at 60 nM developed a phenotypic EC shift. None of the selections pressured at 150 nM resulted in resistant parasites. After an initial shift in the dose–response phenotype was observed, selection at an increased concentration was repeated in the same manner until at least a threefold shift in EC was observed. Selected parasites were then cloned by limiting dilution. BRD73842-resistant selections were conducted in a similar manner except that parasites were initially treated at 0.5 μM (10× EC ) for 4 days or 150 nM (EC ) for 2 days in each of two independent flasks. The Y1356N mutant was derived from a flask pressured at 0.5 μM and the L1418F mutant was developed from one of the flasks exposed to the 150 nM. DNA libraries were prepared for sequencing using the Illumina Nextera XT kit (Illumina), and quality-checked before sequencing on a Tapestation. Libraries were clustered and run as 100-bp paired-end reads on an Illumina HiSeq 2000 in RapidRun mode, according to the manufacturer’s instructions. Samples were analysed by aligning to the P. falciparum 3D7 reference genome (PlasmoDB v. 11.1). To identify SNVs and CNVs, a sequencing pipeline developed for P. falciparum (Plasmodium Type Uncovering Software, Platypus) was used as previously described, with the exception of an increase in the base quality filter from 196.5 to 1,000 (ref. 57). Substrate-dependent inhibition of recombinant P. falciparum DHODH protein was assessed in an in vitro assay in 384-well clear plates (Corning 3640) as described previously58. A 20-point dilution series of inhibitor concentrations were assayed against 2–10 nM protein with 500 μM l-dihydroorotate substrate (excess), 18 μM dodecylubiquinone electron acceptor (~K ), and 100 μM 2,6-dichloroindophenol indicator dye in assay buffer (100 mM HEPES pH 8.0, 150 mM NaCl, 5% glycerol, 0.5% Triton X-100). Assays were incubated at 25 °C for 20 min and then assessed via OD . Data were normalized to 1% DMSO and excess inhibitor (25 μM DSM265; ref. 7). Substrate-dependent inhibition of recombinant human DHODH protein was assessed in an in vitro assay in 384-well clear plates (Corning 3640) as described previously59. A 20-point dilution series of inhibitor concentrations was assayed against 13 nM protein with 1 mM l-dihydroorotate substrate (excess), 100 μM dodecylubiquinone electron acceptor, and 60 μM 2,6-dichloroindophenol indicator dye in assay buffer (50 mM Tris HCl pH 8.0, 150 mM KCl, 0.1% Triton X-100). Assays were incubated at 25 °C for 20 min and then assessed via OD . Data were normalized to 1% DMSO and no enzyme. The synthetic gene for full-length P. vivax PI4K (PVX_098050) was synthesized from GeneArt (ThermoScientific), and was expressed and purified as previously described20. Aliquots of P. vivax PI4Kβ were flash-frozen in liquid nitrogen and stored at −80°C. Full-length human PI4KB (uniprot gene Q9UBF8-2) was expressed and purified as previously described60. 100 nM extruded lipid vesicles were made to mimic Golgi organelle vesicles (20% phosphatidylinositol, 10% phosphatidylserine, 45% phosphatidylcholine and 25% phosphatidylethanolamine) in lipid buffer (20 mM HEPES pH 7.5 (room temperature), 100 mM KCl, 0.5 mM EDTA). Lipid kinase assays were carried out using the Transcreener ADP2 FI Assay (BellBrook Labs) following the published protocol as previously described61. 4-μl reactions ran at 21 °C for 30 min in a buffer containing 30 mM HEPES pH 7.5, 100 mM NaCl, 50 mM KCl, 5 mM MgCl , 0.25 mM EDTA, 0.4% (v/v) Triton X-100, 1 mM TCEP, 0.5 mg ml−1 Golgi-mimic vesicles and 10 μM ATP. P. vivax PI4Kβ was used at 7.5 nM and human PI4KB was used at 200 nM. Fluorescence intensity was measured using a Spectramax M5 plate reader with excitation at 590 nm and emission at 620 nm (20-nm bandwidth). IC values were calculated from triplicate inhibitor curves using GraphPad Prism software. The model was built using the SWISS-MODEL online resource62, 63, 64 and Prime65 (Schrödinger Release 2015-2: Prime, version 4.0, Schrödinger), with human PheRS (PDB accession 3L4G) as a template for P. falciparum PheRS (PlasmoDB Gene ID: PF3D7_0109800). The template was chosen based on highest sequence identity and similarity identified via PSI-BLAST. Target-template alignment was made using ProMod-II and validated with Prime STA. Coordinates from residues that were conserved between the target and the template were copied from the template to the model, and remaining sites were remodelled using segments from known structures. The side chains were then rebuilt, and the model was finally refined using a force field. Protein sequences of both α- (PF3D7_0109800) and β- (PF3D7_1104000) subunits of cytoplasmic P. falciparum PheRS were obtained from PlasmoDB ( http://plasmodb.org/plasmo/). Full length α- and β-subunit gene sequences optimized for expression in E. coli were cloned into pETM11 (Kanamycin resistance) and pETM20 (ampicillin resistance) expression vectors using Nco1 and Kpn1 sites and co-transformed into E. coli B834 cells. Protein expression was induced by addition of 0.5 mM isopropyl β-d-1-thiogalactopyranoside (IPTG) and cells were grown until an OD of 0.6–0.8 was reached at 37 °C. They were then allowed to grow at 18 °C for 20 h after induction. Cells were separated by centrifugation at 5,000g for 20 min and the bacterial pellets were suspended in a buffer consisting of 50 mM Tris–HCl (pH 7.5), 200 mM NaCl, 4 mM β-mercaptoethanol, 15% (v/v) glycerol, 0.1 mg ml−1 lysozyme and 1 mM phenylmethylsulfonyl fluoride (PMSF). Cells were lysed by sonication and cleared by centrifugation at 20,000g for 1 h. The supernatant was applied on to prepacked NiNTA column (GE Healthcare), and bound proteins were eluted by gradient-mixing with elution buffer (50 mM Tris–HCl (pH 7.5), 80 mM NaCl, 4 mM β-mercaptoethanol, 15% (v/v) glycerol, 1 M imidazole). Pure fractions were pooled and loaded on to heparin column for further purification. Again, bound proteins were eluted using gradient of heparin elution buffer 50 mM Tris–HCl (pH 7.5), 1 M NaCl, 4 mM β-mercaptoethanol, 15% (v/v) glycerol). Pure fractions were again pooled and dialysed overnight into a buffer containing 50 mM Tris–HCl (pH 7.5), 200 mM NaCl, 4 mM β-mercaptoethanol, 1 mM DTT and 0.5 mM EDTA. TEV protease (1:50 ratio of protease:protein) was added to the protein sample and incubated at 20 °C for 24 h to remove the polyhistidine tag. Protein was further purified via gel-filtration chromatography on a GE HiLoad 60/600 Superdex column in 50 mM Tris–HCl (pH 7.5), 200 mM NaCl, 4 mM β-mercaptoethanol, 1 mM MgCl . The eluted protein (a heterodimer of P. falciparum cPheRS) were collected, assessed for purity via SDS–PAGE and stored at −80 °C. Nuclear encoded tRNAPhe from P. falciparum was synthesized using an in vitro transcription method as described earlier22, 66. Aminoacylation and enzyme inhibition assays for P. falciparum cytosolic PheRS were performed as described earlier22, 67. Enzymatic assays were performed in buffer containing 30 mM HEPES (pH 7.5), 150 mM NaCl, 30 mM KCl, 50 mM MgCl , 1 mM DTT, 100 μM ATP, 100 μM l-phenylalanine, 15 μM P. falciparum tRNAPhe, 2 U ml−1 E. coli inorganic pyrophosphatase (NEB) and 500 nM recombinant P. falciparum PheRS at 3 °C. Reactions at different time points were stopped by the addition of 40 mM EDTA and subsequent transfer to ice. Recombinant maltose binding protein was used as negative control. The cPheRS inhibition assays were performed using inhibitor concentrations of 0.01 nM, 0.1 nM, 1 nM, 10 nM, 100 nM, 1 μM, 5 μM and 10 μM for strong binders and 1 nM, 10 nM, 100 nM, 1 μM, 10 μM, 100 μM and 500 μM for weaker binders in the assay buffer. Enzymatic and inhibition experiments were performed twice in triplicate. Mammalian cells (HepG2, A549, and HEK293) were obtained from the ATCC and cultured routinely in DMEM with 10% FBS and 1% (v/v) antibiotic–antimycotic. For cytotoxicity assays, 1 × 106 cells were seeded into 384-well plates 1 day before compound treatment. Cells were treated with ascending doses of compound for 72 h, and viability was measured using Cell-Titer Glo (Promega). All cell lines were tested for Mycoplasma contamination using Universal mycoplasma Detection Kit (ATCC). In vitro characterization assays (protein binding, microsomal stability, hepatocyte stability, cytochrome P450 (CYP) inhibition, and aqueous solubility) were performed according to industry-standard techniques. Ion channel inhibition studies were performed using the Q-Patch system using standard techniques. All animal experiments were conducted in compliance with institutional policies and appropriate regulations and were approved by the institutional animal care and use committees for each of the study sites (the Broad Institute, 0016-09-14; Harvard School of Public Health, 03228; Eisai, 13-05, 13-07, 14-C-0027). No method of randomization or blinding was used in this study. CD-1 mice (n = 4 per experimental group; female; 6–7-week-old; 20–24 g, Charles River) were intravenously inoculated with approximately 1 × 105 P. berghei (ANKA GFP-luc) blood-stage parasites 24 h before treatment and compounds were administered orally (at 0 h). Parasitaemia was monitored by the in vivo imaging system (IVIS SpectrumCT, Perkinelmer) to acquire the bioluminescence signal (150 mg kg-1 of luciferin was intraperitoneally injected approximately 10 min before imaging). In addition, blood smear samples were obtained from each mouse periodically, stained with Giemsa, and viewed under a microscope for visual detection of blood parasitaemia. Animals with parasitaemia exceeding 25% were humanely euthanized. CD-1 mice (n = 4 per experimental group; female; 6–7-week-old; 20–24 g, Charles River) were inoculated intravenously with approximately 1 × 105 P. berghei (ANKA GFP-luc) sporozoites freshly dissected from A. stephensi mosquitoes. Immediately after infection, the mice were treated with single oral doses of BRD7929; infection was monitored as described for the P. berghei erythrocytic-stage assay. For time-course experiments, the time of compound treatment (single oral dose of 10 mg kg−1) was varied from 5 days before infection to 2 days after infection. CD-1 (n = 3 per experimental group; female; 6–7-week-old; 21–24 g, Charles River) mice were infected with P. berghei (ANKA GFP-luc) for 96 h before treatment with vehicle or BRD7929 (day 0). On day 2, female A. stephensi mosquitoes were allowed to feed on the mice for 20 min. After 1 week (day 9), the midguts of the mosquitoes were dissected out and oocysts were enumerated microscopically (12.5× magnification). In vivo adapted P. falciparum (3D7HLH/BRD) were selected as described previously68. In brief, NSG mice (n = 2 per experimental group; female; 4–5-week-old; 19–21 g; The Jackson Laboratory) were intraperitoneally injected with 1 ml of human erythrocytes (O-positive, 50% haematocrit, 50% RPMI 1640 with 5% albumax) daily to generate mice with humanized circulating erythrocytes (huRBC NSG). Approximately 2 × 107 blood-stage P. falciparum 3D7HLH/BRD (ref. 69) were intravenously infected to huRBC NSG mice and >1% parasitaemia was achieved 5 weeks after infection. After three in vivo passages, the parasites were frozen and used experimentally. Approximately 48 h after infection with 1 × 107 blood-stage of P. falciparum 3D7HLH/BRD, the mean parasitaemia was approximately 0.4%. huRBC NSG mice were orally treated with a single dose of compound and parasitaemia was monitored for 30 days by IVIS to acquire the bioluminescence signal (150 mg kg-1 of luciferin was intraperitoneally injected approximately 10 min before imaging). huRBC NSG mice (n = 2 per experimental group; female; 4–5-week-old; 18–20 g; Jackson Laboratory) were infected with blood-stage P. falciparum 3D7HLH/BRD for 2 weeks to allow the development of mature gametocytes. Subsequently, the mice were treated with a single oral dose of BRD7929. Blood samples were collected for 11 days. For molecular detection of parasite stages, 40 μl of blood was obtained from control and treated mice. In brief, total RNA was isolated from blood samples using RNeasy Plus Kit with genomic DNA eliminator columns (Qiagen). First-strand cDNA synthesis was performed from extracted RNA using SuperScript III First-Strand Synthesis System (Life Technologies). Parasite stages were quantified using a stage-specific qRT–PCR assay as described previously33, 69. Primers were designed to measure transcript levels of PF3D7_0501300 (ring stage parasites), PF3D7_1477700 (immature gametocytes) and PF3D7_1031000 (mature gametocytes). Primers for PF3D7_1120200 (P. falciparum UCE) transcript were used as a constitutively expressed parasite marker. The assay was performed using cDNA in a total reaction volume of 20 μl, containing primers for each gene at a final concentration of 250 nM. Amplification was performed on a Viia7 qRT–PCR machine (Life Technologies) using SYBR Green Master Mix (Applied Biosystems) with the following reaction conditions: 1 cycle × 10 min at 95 °C and 40 cycles × 1 s at 95 °C and 20 s at 60 °C. Each cDNA sample was run in triplicate and the mean C value was used for the analysis. C values obtained above the cut-off (negative control) for each marker were considered negative for the presence of specific transcripts. Blood samples from each mouse before parasite inoculation were also tested for ‘background noise’ using the same primer sets. No amplification was detected from any samples. FRG knockout on C57BL/6 (human repopulated, >70%) mice (huHep FRG knockout; n = 2 per experimental group; female; 5.5–6-month-old; 19–21 g; Yecuris) were inoculated intravenously with approximately 1 × 105 P. falciparum (NF54HT-GFP-luc) sporozoites and BRD7929 was administered as a single 10 mg kg−1 oral dose one day after inoculation31. Infection was monitored daily by IVIS. Daily engraftment of human erythrocytes (0.4 ml, O-positive, 50% haematocrit, 50% RPMI 1640 with 5% albumax) was initiated 5 days after inoculation. For qPCR analysis, blood samples (40 μl) were collected 7 days after inoculation. For molecular detection of the blood-stage parasite, 40 μl of blood was obtained from control and treated mice. In brief, total RNA was isolated from blood samples using RNeasy Plus Kit with genomic DNA eliminator columns (Qiagen). First-strand cDNA synthesis was performed from extracted RNA using SuperScript III First-Strand Synthesis System (Life Technologies). The presence of the blood-stage parasites was quantified using a highly stage-specific qRT–PCR assay as described previously33, 70. Primers were designed to measure transcript levels of PF3D7_1120200 (P. falciparum UCE). The assay was performed using cDNA in a 20 μl total reaction volume containing primers for each gene at a final concentration of 250 nM. Amplification was performed on a Viia7 qRT–PCR machine (Life Technologies) using SYBR Green Master Mix (Applied Biosystems) and the reaction conditions are as follows: 1 cycle × 10 min at 95 °C and 40 cycles × 1 s at 95 °C and 20 s at 60 °C. Each cDNA sample was run in triplicate and the mean C value was used for the analysis. C values obtained above the cut-off (negative control) for each marker were considered negative for presence of specific transcripts. Blood samples from each mouse were also tested for background noise using the same primer sets before parasite inoculation. No amplification was detected from any samples. In vitro cultures of P. falciparum Dd2, with the initial inocula ranging from 105 to 109 parasites, were maintained in complete medium supplemented with 20 nM of BRD7929 (EC against Dd2). Media was replaced with fresh compound added daily and cultures monitored for 60 days to identify propensity for recrudescent parasitaemia as described34. Atovaquone was used as a control (EC  = 2 nM). Solubility was determined in PBS pH 7.4 with 1% DMSO. Each compound was prepared in triplicate at 100 μM in both 100% DMSO and PBS with 1% DMSO. Compounds were allowed to equilibrate at room temperature with a 750 r.p.m. vortex shake for 18 h. After equilibration, samples were analysed by UPLC–MS (Waters) with compounds detected by single-ion reaction detection on a single quadrupole mass spectrometer. The DMSO samples were used to create a two-point calibration curve to which the response in PBS was fit. Plasma protein binding was determined by equilibrium dialysis using the Rapid Equilibrium Dialysis (RED) device (Pierce Biotechnology) for both human and mouse plasma. Each compound was prepared in duplicate at 5 μM in plasma (0.95% acetonitrile, 0.05% DMSO) and added to one side of the membrane (200 μl) with PBS pH 7.4 added to the other side (350 μl). Compounds were incubated at 37 °C for 5 h with 350 r.p.m. orbital shaking. After incubation, samples were analysed by UPLC–MS (Waters) with compounds detected by SIR detection on a single quadrupole mass spectrometer. The required potency to inhibit the hERG channel in expressed cell lines were evaluated using an automated patch-clamp system (QPatch-HTX). Pharmacokinetics of BRD3444 and BRD1095 were performed by Shanghai ChemPartner Co. Ltd., following single intravenous and oral administrations to female CD-1 mice. BRD3444 and BRD1095 were formulated in 70% PEG400 and 30% aqueous glucose (5% in H O) for intravenous and oral dosing. Test compounds were dosed as a bolus solution intravenously at 0.6 mg kg−1 (dosing solution; 70% PEG400 and 30% aqueous glucose, 5% in H O) or dosed orally by gavage as a solution at 1 mg kg−1 (dosing solution; 70% PEG400 and 30% aqueous glucose, 5% in H O) to female CD-1 mice (n = 9 per dose route). Pharmacokinetic parameters of BRD7929 and BRD3316 were determined in CD-1 mice. BRD7929 and BRD3316 were formulated in 10% ethanol, 4% Tween, 86% saline for both intravenous and oral dosing. Pharmacokinetic parameters were estimated by non-compartmental model using WinNonlin 6.2. Pharmacokinetic parameters for BRD7929 and BRD3316 were estimated by a non-compartmental model using proprietary Eisai software. Pharmacokinetic parameters of BRD7539 and BRD9185 were determined in CD-1 mice. Compounds were formulated in 70% PEG300 and 30% (5% glucose in H O) at 0.5 mg ml−1 for oral dosing, and 5% DMSO, 10% cremophor, and 85% H O at 0.25 mg ml−1 for intravenous formulation. Pharmacokinetic parameters were estimated by non-compartmental model using WinNonlin 6.2. Pharmacokinetics of BRD7539 and BRD9185 were performed by WuXi AppTec. The protocol was approved by Eisai IACUC, 13-07, 13, 05, and 14-c-0027. Compounds were evaluated in vitro to determine their metabolic stability in incubations containing liver microsomes or hepatocytes of mouse and human. In the presence of NADPH, liver microsomes (0.2 mg ml−1) from mouse (CD-1) and human were incubated with compounds (0.5 and 5 μM) for 0, 10 and 90 min. The depletion of compounds in the incubation mixtures, determined using liquid chromatography tandem mass spectromety LC–MS/MS, was used to estimate K and V values and determine half-lives for both mouse and human microsomes. Compounds were evaluated in vitro for the potential inhibition of human cytochrome P450 (CYP) isoforms using human liver microsomes. Two concentrations (1 and 10 μM) of compound were incubated with pooled liver microsomes (0.2 mg ml−1) and a cocktail mixture of probe substrates for selective CYP isoform. The selective activities tested were CYP1A2-mediated phenacetin O-demethylation, CYP2C8-mediated rosiglitazone para-hydroxylation, CYP2C9-mediated tolbutamide 4′-hydroxylation, CYP2C19-mediated (S)-mephenytoin 4′-hydroxylation, CYP2D6-mediated (±)-bufuralol 1′-hydroxylation and, CYP3A4/5-mediated midazolam 1′-hydroxylation. The positive controls tested were α-naphthoflavone for CYP1A2, montelukast for CYP2C8, sulfaphenazole for CYP2C9, tranylcypromine for CYP2C19, quinidine for CYP2D6, and ketoconazole for CYP3A4/5. The samples were analysed by LC–MS/MS. IC values were estimated using nonlinear regression. The time-dependent inactivation potential of compounds were assessed in human liver microsomes for CYP2C9, CYP2D6, and CYP3A4/5 by determining K and k values when appropriate. Two concentrations (6 and 30 μM) of compound were incubated in primary reaction mixtures containing phosphate buffer and 0.2 mg ml−1 human liver microsomes for 0, 5, and 30 min in a 37 °C water bath. The reactions were initiated by the addition of NADPH. Phosphate buffer was substituted for NADPH solution for control. At the respective times, 25 μl of primary incubation was diluted tenfold into pre-incubated secondary incubation mixture containing each CYP-selective probe substrate in order to assess residual activity. The second incubation time was 10 min. The probe substrates used for CYP1A, 2C9, CYP2C19, CYP2D6, and CYP3A4 were phenacetin (50 μM), tolbutamide (500 μM), (S)-mephenytoin (20 μM), bufuralol (50 μM), and midazolam (30 μM), respectively. The CYP time- dependent inhibitors used were furafyllin, tienilic acid, ticlopidine, paroxetin and troleandomycin for CYP2C8, CYP2C9, CYP2C19, CYP2D6 and CYP3A, respectively, at two concentrations. The samples were analysed by LC–MS/MS.


Ham C.,UK National Institute for Biological Standards and Control | Srinivasan P.,Centers for Disease Control and Prevention | Thorstensson R.,SIIDC | Verschoor E.,BPRC | And 6 more authors.
Journal of Clinical Microbiology | Year: 2010

An international multicenter study was conducted to assess the performance of a panel of simian immuno-deficiency virus (SIV) RNA reference materials for plasma viral load determinations. Reliable quantification was demonstrated across an ∼6 log10 dynamic range. Availability of external reference materials will enable independent calibration of SIV plasma viral load assays. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Osier F.H.A.,Center for Geographic Medicine Research | Osier F.H.A.,London School of Hygiene and Tropical Medicine | Weedall G.D.,London School of Hygiene and Tropical Medicine | Weedall G.D.,University of Liverpool | And 10 more authors.
Infection and Immunity | Year: 2010

Although Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate, extensive allelic diversity may compromise its vaccine potential. We have previously shown that naturally acquired antibodies to AMA1 were associated with protection from clinical malaria in this Kenyan population. To assess the impact of allelic diversity on naturally acquired immunity, we first sequenced the ectodomainencoding region of P. falciparum ama1 from subjects with asymptomatic, mild, and severe malaria and measured allele frequency distributions. We then measured antibodies to three allelic AMA1 proteins (AMA1-3D7, AMA1-FVO, and AMA1-HB3) and used competition enzyme-linked immunosorbent assays (ELISAs) to analyze allele-specific antibodies. Seventy-eight unique haplotypes were identified from 129 alleles sampled. No clustering of allelic haplotypes with disease severity or year of sampling was observed. Differences in nucleotide frequencies in clinical (severe plus mild malaria) versus asymptomatic infections were observed at 16 polymorphic positions. Allele frequency distributions were indicative of balancing selection, with the strongest signature being identified in domain III (Tajima's D = 2.51; P < 0.05). Antibody reactivities to each of the three allelic AMA1 proteins were highly correlated (P < 0.001 for all pairwise comparisons). Although antibodies to conserved epitopes were abundant, 48% of selected children with anti-AMA1 IgG (n = 106) had detectable reactivity to allele-specific epitopes as determined by a competition ELISA. Antibodies to both conserved and allele-specific epitopes in AMA1 may contribute to clinical protection. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Kifer I.,Agilent Technologies | Ben-Dor A.,Agilent Technologies | Yakhini Z.,Agilent Technologies | Yakhini Z.,Technion - Israel Institute of Technology | And 3 more authors.
Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 | Year: 2014

IEF LC-MS/MS (Iso-Electric-Focusing Liquid-Chromatography Tandem-Mass-Spectrometry) is an analytical method that incorporates a two-step sample separation prior to MS identification of proteins. When analyzing complex samples this preparatory separation allows for higher analytical depth and improved quantification accuracy of proteins and PTMs. IEF fractionation builds upon isoelectric point (pI) differences between peptides or proteins. In standard IEF LC-MS/MS, each fraction is separately profiled using LC-MS/MS. The cost of the complete assay, therefore, is strongly dependent on the number of pI fractions being analyzed. Commonly, studies are focused on a specific group of proteins. We propose an approach that selects a subset of fractions for LC-MS/MS analysis that is highly informative in the context of the proteins of interest. Specifically, our method allows a significant reduction in cost and instrument time as compared to the standard protocol of running all fractions, with little compromise to coverage. We develop algorithmics to optimize the selection of the IEF fractions on which to run LC-MS/MS. We translate the fraction optimization task to Minimum Set Cover (MSC), a well-studied NP-hard problem. We develop heuristic solutions and compare them in terms of effectiveness and of practical running times. We provide examples to demonstrate advantages and limitations of each algorithmic approach. Finally, we test our methodology by applying it to experimental data obtained from IEF LC-MS/MS analysis of yeast and human samples. We demonstrate the benefit of this approach for analyzing complex samples with a focus on different protein sets of interest. © 2014 IEEE.


News Article | November 10, 2016
Site: www.prweb.com

Abel Communications today announced that it will host ‘Becoming an Expert: A Night of Thought Leadership, Cocktails & Conversation’ on November 15 from 6pm – 8.30pm. The event will feature a local menu of Baltimore food and drink from the likes of Five and Dime, Union Brewery, Waverly Brewery and DuClaw. Additionally, attendees can reserve a spot to have a complimentary professional headshot taken by award-winning photographer, Chelsea Clough. Held in collaboration with Baltimore Public Relations Council (BPRC) and the voice of the Baltimore Ravens, Gerry Sandusky, the event aims to help attendees understand what it takes to become a well-known, often quoted, in-demand industry expert. Greg Abel, president and founder of Abel Communications, and Gerry Sandusky, best-selling author and sports director at Baltimore’s WBAL TV, will team up to tackle the issue. Greg will share his experiences as a PR leader and journalist to provide insight into the qualities and attributes of thought leaders who succeed with the media, while providing tips to develop effective messaging and positioning. Gerry, who is a long-time media training and executive presentation consultant, will highlight what executives and professionals should do to impress in front of any audience. “Being a recognized thought leader opens the door to many conversations and opportunities,” said Greg Abel. “By thinking strategically and planning ahead, many executives and companies can become the expert that others turn to for guidance and clarity. We look forward to sharing case studies and tips for our colleagues and friends at the event.” Sandusky added, "Becoming a thought leader often means developing new habits and behaviors to command an audience. Those who are successful deliver information in a way that is engaging and useful. It’s a skill that requires discipline and practice and I’m looking forward to sharing best practices.” The event will be held at Abel Communications, 3355 Keswick Road, Suite 300, Baltimore, MD 21211. The event is $20 for BPRC members; $30 for non-members; $10 for students; and guests of members are free. Attendees who register before November 8th will receive a $5 discount and walk-ins will be charged an additional $10. For more information about the event or to register, visit: https://baltimoreprcouncil.org/pr-events/becoming-an-expert-a-night-of-thought-leadership-cocktails-conversation-november-15/ About Abel Communications Abel Communications is a results-driven public relations firm specializing in campaigns to support clients in professional services, health and wellness, and non-profits. We offer a range of services including comprehensive communications planning, media relations, photo and video, social media and strategic content development. Abel Communications’ clients include UnitedHealthcare, Medifast, STX, MRIS, 1st Mariner, Force 3, and CohnReznick. For more information, visit http://www.abelcommunications.com


Rane L.,Karolinska University Hospital | Rahman S.,Karolinska University Hospital | Magalhaes I.,Karolinska University Hospital | Magalhaes I.,Karolinska Hospital | And 8 more authors.
Genes and Immunity | Year: 2011

Interleukin-7 (IL-7) and the IL-7 receptor (IL-7R) have been shown to be alternatively spliced in infectious diseases. We tested IL-7 and IL-7R splicing in a tuberculosis (TB)-vaccine/Mycobacterium tuberculosis (Mtb)-challenge model in non-human primates (NHPs). Differential IL-7 splicing was detected in peripheral blood mononuclear cells (PBMCs) from 15/15 NHPs showing 6 different IL-7 spliced isoforms. This pattern did not change after infection with virulent Mtb. We demonstrated increased IL-7 (6 exon) and IL-17 protein production in lung tissue along with concomitant decreased transforming growth factor-Β (TGF-Β) from NHPs (vaccinated with a recombinant BCG (rBCG)) who showed increased survival after Mtb challenge. IL-7 increased IL-17 and interferon-γ (IFN-γ) gene and protein expression in PBMCs. Mtb-infected NHPs showed differential IL-7R splicing associated with the anatomical location and tissue origin, that is, in lung tissue, hilus, axillary lymph nodes (LNs) and spleen. Differential splicing of the IL-7R was typical for healthy (non-Mtb infected) and for Mtb-infected lung tissue with a dominant expression of soluble IL-7R (sIL-7R) receptor lacking exon 6 (9:1 ratio of sIL-7R/cell-bound IL-7R). Differential ratios of cell-bound vs sIL-7R could be observed in hilus and axillary LNs from Mtb-infected NHPs with an inversed ratio of 1:9 (sIL-7R/cell-bound IL-7R) in spleen and PBMCs. Soluble IL-7R is exclusively present in lung tissue. © 2011 Macmillan Publishers Limited All rights reserved.


de Groot N.G.,BPRC | Blokhuis J.H.,BPRC | Blokhuis J.H.,Stanford University | Otting N.,BPRC | And 3 more authors.
Immunological Reviews | Year: 2015

Summary: Researchers dealing with the human leukocyte antigen (HLA) class I and killer immunoglobulin receptor (KIR) multi-gene families in humans are often wary of the complex and seemingly different situation that is encountered regarding these gene families in Old World monkeys. For the sake of comparison, the well-defined and thoroughly studied situation in humans has been taken as a reference. In macaques, both the major histocompatibility complex class I and KIR gene families are plastic entities that have experienced various rounds of expansion, contraction, and subsequent recombination processes. As a consequence, haplotypes in macaques display substantial diversity with regard to gene copy number variation. Additionally, for both multi-gene families, differential levels of polymorphism (allelic variation), and expression are observed as well. A comparative genetic approach has allowed us to answer questions related to ancestry, to shed light on unique adaptations of the species' immune system, and to provide insights into the genetic events and selective pressures that have shaped the range of these gene families. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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