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A promising new compound class for treating human malaria is the imidazolopiperazines (IZP) class. IZP compounds KAF156 (Ganaplacide) and GNF179 are effective against Plasmodium symptomatic asexual blood-stage infections, and are able to prevent transmission and block infection in animal models. But despite the identification of resistance mechanisms in P. falciparum, the mode of action of IZPs remains unknown. To investigate, we here combine in vitro evolution and genome analysis in Saccharomyces cerevisiae with molecular, metabolomic, and chemogenomic methods in P. falciparum. Our findings reveal that IZP-resistant S. cerevisiae clones carry mutations in genes involved in Endoplasmic Reticulum (ER)-based lipid homeostasis and autophagy. In Plasmodium, IZPs inhibit protein trafficking, block the establishment of new permeation pathways, and cause ER expansion. Our data highlight a mechanism for blocking parasite development that is distinct from those of standard compounds used to treat malaria, and demonstrate the potential of IZPs for studying ER-dependent protein processing., Imidazolopiperazines (IZPs) are a class of compounds under clinical development for malaria, but their mechanism of action is unclear. Here, the authors show that IZPs inhibit the parasite’s secretory pathway, affecting protein trafficking and export.

SummaryIn vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in the model microbe, Saccharomyces cerevisiae. Analysis of 355 curated, laboratory-evolved clones, resistant to 80 different compounds, demonstrates differences in the types of mutations that are identified in selected versus neutral evolution and reveals numerous new, compound-target interactions. Through enrichment analysis we further identify a set of 137 genes strongly associated with or conferring drug resistance as indicated by CRISPR-Cas9 engineering. The set of 25 most frequently mutated genes was enriched for transcription factors and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function, single nucleotide variants found in 170-amino-acid domains in two Zn2C6 transcription factors, YRR1 and YRM1 (p < 1x 10 −100). This remarkable enrichment for transcription factors as drug resistance genes may explain why it is challenging to develop effective antifungal killing agents and highlights their important role in evolution.

The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare’s most potent antibiotics are becoming obsolete. Approximately two-thirds of the world’s antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, in order to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 101 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.

Permanent pacemaker (PPM) insertion is widely used to treat cardiac rhythm disorders; approximately 600,000 pacemakers are implanted annually in the US (Wood and Ellenbogen, 2002). Almost 9% of patients who receive a permanent pacemaker, however, experience a variety of medical complications such as infections, battery problems, programming issues, lead migration, or lead fracture (Greenspon et al., 2012). Moreover 1-2% of these patients will encounter severe lead-related problems within 30 days of their pacemaker insertion (Kirkfeldt et al., 2014; Kiviniemi et al., 1999). In this report, we focus on an uncommon but serious complication of PPM insertion: right ventricular lead perforation leading to a pericardial effusion. Although lead perforation is a relatively rare occurrence, this event can be life-threatening, and should be considered in the differential diagnosis when patients present to the emergency department (ED) with relevant symptoms and recent PPM insertion. Specifically, patients who experience complications from pacemaker insertion may present to the ED with a variety of symptoms such as chest pain, syncope, dyspnea, or even dizziness (Squire and Niemann, 2006). Pacemaker complications include pneumothorax, pleural and/or pericardial effusions, and infection, placing the patient at serious risk for significant harm (Squire and Niemann, 2006; Shingaki et al., 2015). The evaluation of a lead-related issue typically involves chest radiography to visualize abnormal lead placement and check for a pneumothorax or pleural effusion, and a 12‑lead electrocardiogram (ECG) to detect pacing errors. We present the case of a patient who presented to the ED three days after his pacemaker insertion with chest pain and dyspnea; he was subsequently diagnosed with a lead perforation into the pericardial space resulting in a pericardial effusion.

Recent advances in cell-based, high-throughput phenotypic screening have identified new chemical compounds that are active against eukaryotic pathogens. A challenge to their future development lies in identifying these compounds' molecular targets and binding modes. In particular, subsequent structure-based chemical optimization and target-based screening require a detailed understanding of the binding event. Here, we use directed evolution and whole-genome sequencing of a drug-sensitive S. cerevisiae strain to identify the yeast ortholog of TcCyp51, lanosterol-14-alpha-demethylase (TcCyp51), as the target of MMV001239, a benzamide compound with activity against Trypanosoma cruzi, the etiological agent of Chagas disease. We show that parasites treated with MMV0001239 phenocopy parasites treated with another TcCyp51 inhibitor, posaconazole, accumulating both lanosterol and eburicol. Direct drug-protein binding of MMV0001239 was confirmed through spectrophotometric binding assays and X-ray crystallography, revealing a binding site shared with other antitrypanosomal compounds that target Cyp51. These studies provide a new probe chemotype for TcCyp51 inhibition.

Pediatric patients with hematologic malignancies undergoing allogeneic hematopoietic stem cell transplantation (aHSCT) comprise a patient cohort at highest risk of developing disseminated fungal infections. Invasive aspergillosis post-HSCT is associated with unacceptably high mortality in pediatric patients with overall survival of only 15-34%. Hospital construction and excavation further potentiate the risk of fungal related morbidity and mortality in the post-HSCT setting. The current standard of care for anti-fungal prophylaxis for children undergoing aHSCT is the use of triazoles. However, 40% of healthcare associated mold infections in pediatric leukemia patients exposed to hospital construction are historically resistant to voriconazole. Methods to optimize prevention of fungal infections in this high-risk population are critical to improving pediatric aHSCT survival outcomes. We hypothesized that pre-emptive ambisome prophylaxis would be tolerated in the post-HSCT setting and would decrease the incidence of voriconazole resistant healthcare-associated fungal infections and resultant morbidity. We explored the use of intermediate dose daily ambisome (3mg/kg/day) as fungal prophylaxis in 5 patients with hematologic malignancies (2=ALL, 2=AML, 1=Lymphoblastic lymphoma) undergoing allogeneic stem cell transplantation in proximity to construction and excavation. Patient demographics, disease, donor source, conditioning regimen, methotrexate course and transplant related morbidity are shown in table 1. We found that 5 of 5 patients experienced delayed clearance of low dose methotrexate (MTX). This delayed clearance resulted in delayed methotrexate dosing in 3 of 5 patients and a missed methotrexate dose in 1 patient who subsequently developed GVHD and complications from high dose steroids. 4 of 5 patients experienced acute kidney injury (AKI), demonstrated by doubling of the pre-HSCT creatinine value following MTX administration. This identified creatinine elevation is increased as compared to historical controls receiving standard anti-fungal prophylaxis with azole agents. It has been described that AKI delays the clearance of high dose methotrexate. Here, we demonstrate that intermediate doses of daily ambisome following allogeneic HSCT is associated with AKI and delayed clearance of low doses of methotrexate used for GVHD prophylaxis in pediatric patients. Delayed methotrexate clearance was associated with development of morbidity including inadequate GVHD prophylaxis and possible resultant development of GVHD. Combined ambisome and low dose MTX is associated with AKI and delayed MTX clearance and thus is a constrained strategy for prevention of invasive fungal disease in the post-HSCT pediatric setting. The implication of these finding can be extrapolated beyond the construction setting implying cautious use of intermediate dose ambisome prophylaxis in combination with low dose MTX GVHD prophylaxis in pediatric patients post aHSCT. Table 1 Table 1. Disclosures Porteus: CRISPR Therapeutics: Consultancy, Equity Ownership.