63 research outputs found

    Identification, Design and Biological Evaluation of Bisaryl Quinolones Targeting Plasmodium falciparum Type II NADH:Quinone Oxidoreductase (PfNDH2)

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    A program was undertaken to identify hit compounds against NADH:ubiquinone oxidoreductase (PfNDH2), a dehydrogenase of the mitochondrial electron transport chain of the malaria parasite Plasmodium falciparum. PfNDH2 has only one known inhibitor, hydroxy-2-dodecyl-4-(1H)-quinolone (HDQ), and this was used along with a range of chemoinformatics methods in the rational selection of 17 000 compounds for high-throughput screening. Twelve distinct chemotypes were identified and briefly examined leading to the selection of the quinolone core as the key target for structure-activity relationship (SAR) development. Extensive structural exploration led to the selection of 2-bisaryl 3-methyl quinolones as a series for further biological evaluation. The lead compound within this series 7-chloro-3-methyl-2-(4-(4-(trifluoromethoxy)benzyl)phenyl)quinolin-4(1H)-one (CK-2-68) has antimalarial activity against the 3D7 strain of P. falciparum of 36 nM, is selective for PfNDH2 over other respiratory enzymes (inhibitory IC(50) against PfNDH2 of 16 nM), and demonstrates low cytotoxicity and high metabolic stability in the presence of human liver microsomes. This lead compound and its phosphate pro-drug have potent in vivo antimalarial activity after oral administration, consistent with the target product profile of a drug for the treatment of uncomplicated malaria. Other quinolones presented (e.g., 6d, 6f, 14e) have the capacity to inhibit both PfNDH2 and P. falciparum cytochrome bc(1), and studies to determine the potential advantage of this dual-targeting effect are in progress

    Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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    Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

    Sheep as a Large-Animal Model for Otology Research: Temporal Bone Extraction and Transmastoid Facial Recess Surgical Approach

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    Purpose Sheep are used as a large-animal model for otology research and can be used to study implantable hearing devices. However, a method for temporal bone extraction in sheep, which enables various experiments, has not been described, and literature on middle ear access is limited. We describe a method for temporal bone extraction and an extended facial recess surgical approach to the middle ear in sheep. Methods Ten temporal bones from five Hampshire sheep head cadavers were extracted using an oscillating saw. After craniotomy and removal of the brain, a coronal cut was made at the posterior aspect of the orbit followed by a midsagittal cut of the occipital bone and disarticulation of the atlanto-occipital joint. Temporal bones were surgically prepared with an extended facial recess approach. Micro-CT scans of each temporal bone were obtained, and anatomic dimensions were measured. Results Temporal bone extraction was successful in 10/10 temporal bones. Extended facial recess approach exposed the malleus, incus, stapes, and round window while preserving the facial nerve, with the following surgical considerations: minimally pneumatized mastoid; tegmen (superior limit of mastoid cavity) is low-lying and sits below temporal artery; chorda tympani sacrificed to optimize middle ear exposure; incus buttress does not obscure view of middle ear. Distance between the superior aspect of external auditory canal and tegmen was 2.7 (SD 0.9) mm. Conclusion We identified anatomic landmarks for temporal bone extraction and describe an extended facial recess approach in sheep that exposes the ossicles and round window. This approach is feasible for studying implantable hearing devices
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