Piperazinobenzodiazepinones: New Encephalitic Alphavirus Inhibitors via Ring Expansion of 2-Dichloromethylquinazolinones.

Venezuelan and eastern equine encephalitis viruses are disease-causing, neuropathic pathogens with no approved treatment options in humans. While expanding the pharmacophoric model of antialphaviral amidines prepared via a quinazolinone rearrangement, we discovered that diamine-treated, 2-dihalomethylquinolinones unexpectedly afforded ring-expanded piperazine-fused benzodiazepinones. Notably, this new chemotype (19 examples) showed potent, submicromolar inhibition of virus-induced cell death, >7-log reduction of viral yield, and tractable structure-activity relationships across both viruses. Antiviral activity was confirmed in primary human neuronal cells. A mechanistic rationale for product formation is proposed, and key structural elements were comparatively modeled between a similarly substituted antiviral amidine and piperazinobenzodiazepinone prototypes to guide future antiviral development.

Feasibility and Clinical Utility of Ultra-Widefield-Navigated Swept-Source Optical Coherence Tomography Imaging.

Purpose: This work aims to evaluate the clinical utility and feasibility of a novel scanning laser ophthalmoscope-based navigated ultra-widefield swept-source optical coherence tomography (UWF SS-OCT) imaging system. Methods: A retrospective, single-center, consecutive case series evaluated patients between September 2019 and October 2020 with UWF SS-OCT (modified Optos P200TxE, Optos PLC) as part of routine retinal care. The logistics of image acquisition, interpretability of images captured, nature of the peripheral abnormality, and clinical utility in management decisions were recorded. Results: Eighty-two eyes from 72 patients were included. Patients were aged 59.4 ± 17.1 years (range, 8-87 years). During imaging, 4.4 series of images were obtained in 4.1 minutes, with 86.4% of the image series deemed to be diagnostic of the peripheral pathology on blinded image review. The most common pathologic findings were chorioretinal scars (18 eyes). In 31 (38%) eyes, these images were meaningful in supporting clinical decision-making with definitive findings. Diagnoses imaged included retinal detachment combined with retinoschisis, retinal hole with overlying vitreous traction and subretinal fluid, vitreous inflammation overlying a peripheral scar, Coats disease, and peripheral retinal traction in sickle cell retinopathy. Conclusions: Navigated UWF SS-OCT imaging was clinically practical and provided high-quality characterization of peripheral retinal lesions for all eyes. Images directly contributed to management plans, including laser, injection or surgical treatment, for a clinically meaningful set of patients (38%). Future studies are needed to further assess the value of this imaging modality and its role in diagnosing, monitoring, and treating peripheral lesions.

Ruthenium-Catalyzed Asymmetric Allylic Alkylation of Isatins.

A new ruthenium-based catalytic system for branched-selective asymmetric allylic alkylation is disclosed and applied to the synthesis of chiral isatin derivatives. The catalyst, which is generated in situ from commercially available CpRu(MeCN)3PF6 and a BINOL-derived phosphoramidite, is both highly active (TON up to 180) and insensitive to air and moisture. Additionally, the N-alkylated isatins accessible using this methodology are versatile building blocks that are readily transformed into chiral analogs of achiral drug molecules.

Copper/TEMPO Redox Redux: Analysis of PCET Oxidation of TEMPOH by Copper(II) and the Reaction of TEMPO with Copper(I).

Copper salts and organic aminoxyls, such as TEMPO (2,2,6,6-tetramethylpiperidine-N-oxyl), are versatile catalysts for aerobic alcohol oxidation. Previous reports in the literature contain conflicting proposals concerning the redox interactions that take place between copper(I) and copper(II) salts with the aminoxyl and hydroxylamine species, TEMPO and TEMPOH, respectively. Here, we reinvestigate these reactions in an effort to resolve the conflicting claims in the literature. Under anaerobic conditions, CuIIX2 salts [X = acetate (OAc), trifluoroacetate (TFA), and triflate (OTf)] are shown to promote the rapid proton-coupled oxidation of TEMPOH to TEMPO: CuIIX2 + TEMPOH → CuIX + TEMPO + HX. In the reaction with acetate, however, slow reoxidation of CuIOAc occurs. This process requires both TEMPO and HOAc and coincides with the reduction of TEMPO to 2,2,6,6-tetramethylpiperidine. Analogous reactivity is not observed with trifluoroacetate and triflate species. Overall, the facility of the proton-coupled oxidation of TEMPOH by CuII salts suggests that this process could contribute to catalyst regeneration under aerobic oxidation conditions.

Mechanistic insights into copper-catalyzed aerobic oxidative coupling of N-N bonds.

Catalytic N-N coupling is a valuable transformation for chemical synthesis and energy conversion. Here, mechanistic studies are presented for two related copper-catalyzed oxidative aerobic N-N coupling reactions, one involving the synthesis of a pharmaceutically relevant triazole and the other relevant to the oxidative conversion of ammonia to hydrazine. Analysis of catalytic and stoichiometric N-N coupling reactions support an "oxidase"-type catalytic mechanism with two redox half-reactions: (1) aerobic oxidation of a CuI catalyst and (2) CuII-promoted N-N coupling. Both reactions feature turnover-limiting oxidation of CuI by O2, and this step is inhibited by the N-H substrate(s). The results highlight the unexpected facility of the N-N coupling step and establish a foundation for development of improved catalysts for these transformations.

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps.

Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology.  Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map.  Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps.  Preparation of the data and construction of a heat map is rarely a simple linear process.  Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches.  Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.

Efficacy of Care for Blind Painful Eyes.

PURPOSE: Pain relief for a blind painful eye often follows an escalating paradigm of interventions. This study compares the efficacy of common interventions. METHODS: A retrospective chart review of blind painful eye cases was conducted at a single tertiary institution from April 2012 to December 2016. Demographics, etiology, treatment, and pain level were assessed. RESULTS: Among 99 blind painful eyes, 96 eyes initially received medical therapy (topical steroids, cycloplegics, and/or hypotensives), with pain relief in 39% of eyes. Minimally invasive interventions (laser cyclophotocoagulation, retrobulbar injection, or corneal electrocautery) were performed 41 times in 36 eyes, 34 of which had failed medical therapy, and led to pain relief in 75% of eyes. Evisceration or enucleation was performed in 28 eyes, and long-term pain relief was achieved in 100% of eyes. Surgery allowed discontinuation of oral analgesics in 100% of cases versus 20% for minimally invasive therapy (p = 0.005) and 14% for medical therapy (p = 0.0001). Compared with medical therapy, minimally invasive therapy was 2.5 times more likely to achieve lasting pain relief (p = 0.003) and surgical therapy 35.6 times more likely to achieve lasting pain relief (p = 0.011). High initial pain score was associated with nonsurgical treatment failure. CONCLUSIONS: Medical therapy provides pain relief in a moderate number of patients with a blind painful eye. When medical therapy fails, minimally invasive therapy and surgical interventions are successively more effective in relieving ocular pain. High initial pain score is a risk factor for nonsurgical therapy failure and may merit an earlier discussion of surgical intervention.

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

The Chromosome-centric Human Proteome Project (C-HPP) seeks to comprehensively characterize all protein products coded by the genome, including those expressed sequence variants confirmed via proteogenomics methods. The closely related Biology/Disease-driven Human Proteome Project (B/D-HPP) seeks to understand the biological and pathological associations of expressed protein products, especially those carrying sequence variants that may be drivers of disease. To achieve these objectives, informatics tools are required that interpret potential functional or disease implications of variant protein sequence detected via proteogenomics. Toward this end, we have developed an automated workflow within the Galaxy for Proteomics (Galaxy-P) platform, which leverages the Cancer-Related Analysis of Variants Toolkit (CRAVAT) and makes it interoperable with proteogenomic results. Protein sequence variants confirmed by proteogenomics are assessed for potential structure-function effects as well as associations with cancer using CRAVAT's rich suite of functionalities, including visualization of results directly within the Galaxy user interface. We demonstrate the effectiveness of this workflow on proteogenomic results generated from an MCF7 breast cancer cell line. Our free and open software should enable improved interpretation of the functional and pathological effects of protein sequence variants detected via proteogenomics, acting as a bridge between the C-HPP and B/D-HPP.

Cu-Catalyzed Aerobic Oxidative N-N Coupling of Carbazoles and Diarylamines Including Selective Cross-Coupling.

A Cu-catalyzed method has been identified for aerobic oxidative dimerization of carbazoles and diarylamines to the corresponding N-N coupled bicarbazoles and tetraarylhydrazines. The reactions proceed under mild conditions (1 atm O2, 60-80 °C) with a catalyst composed of CuBr·dimethylsulfide and N, N-dimethylaminopyridine. Reactions between carbazole and diarylamines show unusually selective cross-coupling, even with a 1:1 ratio of the two substrates. This behavior was found to arise from reversible formation of the tetraarylhydrazine. Formation of this species is kinetically favored, but cleavage of the N-N bond under the reaction conditions leads to selective formation of the thermodynamically favored cross-coupling product.

Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA.

Alternative splicing is a critical event in the posttranscriptional regulation of gene expression. To investigate whether this process influences radiation-induced gene expression we defined the effects of ionizing radiation on the generation of alternative transcripts in total cellular mRNA (the transcriptome) and polysome-bound mRNA (the translatome) of the human glioblastoma stem-like cell line NSC11. For these studies, RNA-Seq profiles from control and irradiated cells were compared using the program SpliceSeq to identify transcripts and splice variations induced by radiation. As compared to the transcriptome (total RNA) of untreated cells, the radiation-induced transcriptome contained 92 splice events suggesting that radiation induced alternative splicing. As compared to the translatome (polysome-bound RNA) of untreated cells, the radiation-induced translatome contained 280 splice events of which only 24 were overlapping with the radiation-induced transcriptome. These results suggest that radiation not only modifies alternative splicing of precursor mRNA, but also results in the selective association of existing mRNA isoforms with polysomes. Comparison of radiation-induced alternative transcripts to radiation-induced gene expression in total RNA revealed little overlap (about 3%). In contrast, in the radiation-induced translatome, about 38% of the induced alternative transcripts corresponded to genes whose expression level was affected in the translatome. This study suggests that whereas radiation induces alternate splicing, the alternative transcripts present at the time of irradiation may play a role in the radiation-induced translational control of gene expression and thus cellular radioresponse.

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data.

Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bioinformatics platform. We illustrate the algorithm and available computational tool using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project. Cancer Res; 77(21); e23-26. ©2017 AACR.

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.

Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and interpret. Diligent analysis and quality control can require multiple computational tools of distinct utility and producing disparate output, creating additional challenges for the investigator. The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation mapping and quality control, impact prediction and extensive annotation, gene- and mutation-level interpretation, including joint prioritization of all nonsilent mutation consequence types, and structural and mechanistic visualization. Results from CRAVAT submissions are explored in an interactive, user-friendly web environment with dynamic filtering and sorting designed to highlight the most informative mutations, even in the context of very large studies. CRAVAT can be run on a public web portal, in the cloud, or downloaded for local use, and is easily integrated with other methods for cancer omics analysis. Cancer Res; 77(21); e35-38. ©2017 AACR.

Assessment of a Tele-education System to Enhance Retinopathy of Prematurity Training by International Ophthalmologists-in-Training in Mexico.

PURPOSE: To evaluate a tele-education system developed to improve diagnostic competency in retinopathy of prematurity (ROP) by ophthalmologists-in-training in Mexico. DESIGN: Prospective, randomized cohort study. PARTICIPANTS: Fifty-eight ophthalmology residents and fellows from a training program in Mexico consented to participate. Twenty-nine of 58 trainees (50%) were randomized to the educational intervention (pretest, ROP tutorial, ROP educational chapters, and posttest), and 29 of 58 trainees (50%) were randomized to a control group (pretest and posttest only). METHODS: A secure web-based educational system was created using clinical cases (20 pretest, 20 posttest, and 25 training chapter-based) developed from a repository of over 2500 unique image sets of ROP. For each image set used, a reference standard ROP diagnosis was established by combining the clinical diagnosis by indirect ophthalmoscope examination and image-based diagnosis by multiple experts. Trainees were presented with image-based clinical cases of ROP during a pretest, posttest, and training chapters. MAIN OUTCOME MEASURES: The accuracy of ROP diagnosis (e.g., plus disease, zone, stage, category) was determined using sensitivity and specificity calculations from the pretest and posttest results of the educational intervention group versus control group. The unweighted kappa statistic was used to analyze the intragrader agreement for ROP diagnosis by the ophthalmologists-in-training during the pretest and posttest for both groups. RESULTS: Trainees completing the tele-education system had statistically significant improvements (P < 0.01) in the accuracy of ROP diagnosis for plus disease, zone, stage, category, and aggressive posterior ROP (AP-ROP). Compared with the control group, trainees who completed the ROP tele-education system performed better on the posttest for accurately diagnosing plus disease (67% vs. 48%; P = 0.04) and the presence of ROP (96% vs. 91%; P < 0.01). The specificity for diagnosing AP-ROP (94% vs. 78%; P < 0.01), type 2 ROP or worse (92% vs. 84%; P = 0.04), and ROP requiring treatment (89% vs. 79%; P < 0.01) was better for the trainees completing the tele-education system compared with the control group. Intragrader agreement improved for identification of plus disease, zone, stage, and category of ROP after completion of the educational intervention. CONCLUSIONS: A tele-education system for ROP education was effective in improving the diagnostic accuracy of ROP by ophthalmologists-in-training in Mexico. This system has the potential to increase competency in ROP diagnosis and management for ophthalmologists-in-training from middle-income nations.

Indenylmetal Catalysis in Organic Synthesis.

Synthetic organic chemists have a long-standing appreciation for transition metal cyclopentadienyl complexes, of which many have been used as catalysts for organic transformations. Much less well known are the contributions of the benzo-fused relative of the cyclopentadienyl ligand, the indenyl ligand, whose unique properties have in many cases imparted differential reactivity in catalytic processes toward the synthesis of small molecules. In this Review, we present examples of indenylmetal complexes in catalysis and compare their reactivity to their cyclopentadienyl analogues, wherever possible.

Chiral cyclopentadienylruthenium sulfoxide catalysts for asymmetric redox bicycloisomerization.

A full account of our efforts toward an asymmetric redox bicycloisomerization reaction is presented in this article. Cyclopentadienylruthenium (CpRu) complexes containing tethered chiral sulfoxides were synthesized via an oxidative [3 + 2] cycloaddition reaction between an alkyne and an allylruthenium complex. Sulfoxide complex 1 containing a p-anisole moiety on its sulfoxide proved to be the most efficient and selective catalyst for the asymmetric redox bicycloisomerization of 1,6- and 1,7-enynes. This complex was used to synthesize a broad array of [3.1.0] and [4.1.0] bicycles. Sulfonamide- and phosphoramidate-containing products could be deprotected under reducing conditions. Catalysis performed with enantiomerically enriched propargyl alcohols revealed a matched/mismatched effect that was strongly dependent on the nature of the solvent.

Development of a Coordinatively Unsaturated Chiral Indenylruthenium Catalyst.

An unprecedented coordinatively unsaturated chiral indenylruthenium complex 12 was designed and synthesized to provide additional coordination sites for Ru-catalyzed asymmetric transformations. In an attempt to catalyze an asymmetric enyne cycloisomerization reaction of 1,6-enyne, significant amounts of hydroxycyclization were observed. Up to 84:16 er of the hydroxycyclization product was obtained in 2-MeTHF. This chiral indenylruthenium catalyst could also perform an asymmetric redox isomerization/C-H insertion reaction in up to 90:10 er.

Distinct epigenetic features of differentiation-regulated replication origins.

BACKGROUND: Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence features, but their activity also responds to changes in transcription and cellular differentiation status. RESULTS: To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role of chromatin structure in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNase hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 40,000 regions that actively initiated replication in all cell types and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group included origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type-specific origins preferentially replicated during late S-phase. CONCLUSIONS: These observations are in line with the hypothesis that differentiation-associated changes in chromatin and gene expression affect the activation of specific replication origins.

Diagnostic Discrepancies in Retinopathy of Prematurity Classification.

PURPOSE: To identify the most common areas for discrepancy in retinopathy of prematurity (ROP) classification between experts. DESIGN: Prospective cohort study. PARTICIPANTS: A total of 281 infants were identified as part of a multicenter, prospective, ROP cohort study from 7 participating centers. Each site had participating ophthalmologists who provided the clinical classification after routine examination using binocular indirect ophthalmoscopy (BIO) and obtained wide-angle retinal images, which were independently classified by 2 study experts. METHODS: Wide-angle retinal images (RetCam; Clarity Medical Systems, Pleasanton, CA) were obtained from study subjects, and 2 experts evaluated each image using a secure web-based module. Image-based classifications for zone, stage, plus disease, and overall disease category (no ROP, mild ROP, type II or pre-plus, and type I) were compared between the 2 experts and with the clinical classification obtained by BIO. MAIN OUTCOME MEASURES: Inter-expert image-based agreement and image-based versus ophthalmoscopic diagnostic agreement using absolute agreement and weighted kappa statistic. RESULTS: A total of 1553 study eye examinations from 281 infants were included in the study. Experts disagreed on the stage classification in 620 of 1553 comparisons (40%), plus disease classification (including pre-plus) in 287 of 1553 comparisons (18%), zone in 117 of 1553 comparisons (8%), and overall ROP category in 618 of 1553 comparisons (40%). However, agreement for presence versus absence of type 1 disease was >95%. There were no differences between image-based and clinical classification except for zone III disease. CONCLUSIONS: The most common area of discrepancy in ROP classification is stage, although inter-expert agreement for clinically significant disease, such as presence versus absence of type 1 and type 2 disease, is high. There were no differences between image-based grading and clinical examination in the ability to detect clinically significant disease. This study provides additional evidence that image-based classification of ROP reliably detects clinically significant levels of ROP with high accuracy compared with the clinical examination.

A Ruthenium/Phosphoramidite-Catalyzed Asymmetric Interrupted Metallo-ene Reaction.

Allylic chlorides prepared from commercially available trans-1,4-dichloro-2-butene were converted to trans-disubstituted 5- and 6-membered ring systems with perfect diastereoselectivity and high enantioselectivity under chiral ruthenium catalysis. These products contain stereodefined secondary and tertiary alcohols that originate from the trapping of an alkylruthenium intermediate with adventitious water. Key to the success of this transformation was the development of a new BINOL-based phosphoramidite ligand containing bulky substitution at its 3- and 3'-positions. As a demonstration of product utility, diastereoselective Friedel-Crafts reactions were performed on the chiral benzylic alcohols in high yield and stereoselectivity.