Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum

Plasmodium falciparum is a protozoan parasite and the causative agent of malaria, which kills upwards of 1 million people annually. With the increasing prevalence of drug-resistant parasites, considerable interest now exists in the identification of new biological targets for the development of new malaria chemotherapeutics. However, given the genetic intractability inherent in studying P. falciparum, it is imperative that novel approaches be developed if we are to understand the role of essential enzymes. My work presented here focuses on the development and use of chemical tools to study malarial proteases, a class of enzymes that have been shown to play essential roles throughout the parasite lifecycle, but the majority of which though are still uncharacterized. In Chapter 2 I develop a novel set of activity-based probes (ABPs) based on the natural product metallo-aminopeptidase (MAP) inhibitor bestatin. I show the bestatin-based ABP allows the functional characterization of MAP activity within a complex proteome. In Chapter 3, I utilize an extended library of bestatin-based ABPs to define the function of two essential malarial MAPs, PfA-M1 and Pf-LAP. I find that PfA-M1 is necessary in the proteolysis of hemoglobin and that lethal inhibition starves parasites of amino acids. I also show that Pf-LAP has a role other than hemoglobin digestion, as parasites are susceptible to its inhibition prior to the onset of this process. In Chapter 4, I use a suite of specific small molecules to validate the P. falciparum signal peptide peptidase (PfSPP) as a drug target. This work shows that PfSPP is a druggable enzyme and that parasites are extremely vulnerable to its inhibition. Evidence is also presented that suggests this enzyme may play an important role in the parasite\u27s endoplasmic reticulum stress-response

PhD

dissertationAfter young adult male rate were injected intraperitoneally with NH4C1, the content of K (hereafter, CP [K]) within the epithelial cells of the choroid plexus increased greatly while that of Na (CP [K]) decreased. This dissertation has focused on elucidating the primary stimulus and mechanism of the NH4C1-induced increase in CP [K], with some investigative focus on the induced decrease in CP [Na]. The primary stimuli under consideration are the NH4C1-induced increases in plasma [NH4], [K]. and [H], and decreases in [HCO3] and [Na]. An acidosis-induced augmentation in the concentration of catecholamines available to CP beta-adrenoceptors has also been considered. Since sympathectomy, adrenalectomy or pretreatment with beta-adrenoceptor blockers did not reduce the effects of NH4C1, it was possible to rule out an involvement of catecholamines as the stimulus. A comparison of the time-courses of plasma [ammonia] with CP [K] and [Na} indicated that the primary stimulus was not plasma [NH4]. A comparison of the effects of nine individual salt treatments on plasma [K] with CP [K] and [Na}, revealed that plasma [K] was not the primary stimulus. Significant statistical correlations were drawn between plasma [H] and the induce increase in CP [K] and decrease in CP [Na]. Since an elevation of plasma [H] was most consistently associated with and increase in CP [K], the mechanism through which [H] operates was investigated. The increase in CP [K] and decrease in CP [Na] must result from wither an increase in Na-k exchange (Na-K Atpase), or from a decrease in K efflux and Na influx; or perhaps a combination of both. With a physiological analog of K (i.e., Rb), it was demonstrated that acidosis does not increase the slope of the initial ‘linear uptake of 86Rb in vitro; thus no effect of acidosis to increase Na-Rb exchange (i.e., Na-K exchange) was found. Since acidosis augments the steady-state volume of distribution of 86Rb in vitro, without an increase in Na-Rb exchange, it would appear that acidosis augments CP Rb by effecting a reduction in Rb efflux and, by analogy, would also reduce the efflux of CP K. In conclusion, NH4C1 induces an increase in CP [K] by increasing plasma [H] which in turn acts to reduce the efflux of K across the apical and/or basolateral membranes of the CP. An in vivo indication that acidosis reduces the efflux of K across the apical membrane was suggested by a decrease in CSF [K]

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OBJECTIVE: It has previously been shown that a combination of inhaled nitric oxide (iNO) and intravenous (IV) steroid attenuates endotoxin-induced organ damage in a 6-hour porcine endotoxemia model. We aimed to further explore these effects in a 30-hour model with attention to clinically important variables. DESIGN: Randomized controlled trial. SETTING: University animal laboratory. SUBJECTS: Domestic piglets (n = 30). INTERVENTIONS: Animals were randomized into 5 groups (n = 6 each): 1) Controls, 2) LPS-only (endotoxin/lipopolysaccharide (LPS) infusion), 3) LPS + iNO, 4) LPS + IV steroid, 5) LPS + iNO + IV steroid. MEASUREMENTS AND MAIN RESULTS: Exposure to LPS temporarily increased pulmonary artery mean pressure and impeded renal function with elevated serum creatinine and acidosis compared to a control group over the 30-hour study period. Double treatment with both iNO and IV steroid tended to blunt the deterioration in renal function, although the only significant effect was on Base Excess (p = 0.045). None of the LPS + iNO + IV steroid treated animals died during the study period, whereas one animal died in each of the other LPS-infused groups. CONCLUSIONS: This study suggests that combined early therapy with iNO and IV steroid is associated with partial protection of kidney function after 30 hours of experimental LPS infusion

Clinical application of high frequency jet ventilation in stereotactic liver ablations – a methodological study [version 1; referees: 2 approved]

Background: Computer-assisted navigation during thermal ablation of liver tumours, may help to correct needle placement and improve ablation efficacy in percutaneous, laparoscopic and open interventions. The potential advantage of using high frequency jet-ventilation technique (HFJV) during the procedure is by minimising the amplitude of respiration-related upper-abdominal organs movements. The aim of this clinical methodological trial was to establish whether HFJV would give less ventilatory induced liver movements than conventional ventilation, during stereotactic navigated ablation of liver metastases under open surgery. Methods: Five consecutive patients scheduled for elective, open liver ablation under general propofol and remifentanil anaesthesia were included in the study protocol. During the stereotactic targeting of the tumours, HFJV was chosen for intraoperative lung ventilation. For tracking of liver movement, a rigid marker shield was placed on the liver surface and tracked with an optical position measurement system. A 4D position of the marker shield was measured for HFJV and conventional tidal volume lung ventilation (TV). At each time point the magnitude of liver displacement was calculated as an Euclidean distance between translational component of the marker shield's 3D position and previously estimated centroid of the translational motion. Results: The mean Euclidean liver displacement was 0.80 (0.10) mm for HFJV and 2,90 (1.03) mm for TV with maximum displacement going as far as 12 mm on standard ventilation (p=0.0001). Conclusion: HFJV is a valuable lung ventilation method for patients undergoing stereotactic surgical procedures in general anaesthesia when reduction of organ displacement is crucial

Apicomplexan Parasites Co-Opt Host Calpains to Facilitate Their Escape from Infected Cells

Apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii (the causative agents of malaria and toxoplasmosis, respectively), are responsible for considerable morbidity and mortality worldwide. These pathogenic protozoa replicate within an intracellular vacuole inside of infected host cells, from which they must escape to initiate a new lytic cycle. By integrating cell biological, pharmacological, and genetic approaches, we provide evidence that both Plasmodium and Toxoplasma hijack host cell calpain proteases to facilitate parasite egress. Immunodepletion or inhibition of calpain-1 in hypotonically lysed and resealed erythrocytes prevented the escape of P. falciparum parasites, which was restored by adding purified calpain-1. Similarly, efficient egress of T. gondii from mammalian fibroblasts was blocked by either small interfering RNA– mediated suppression or genetic deletion of calpain activity and could be restored by genetic complementation

The NASA Exoplanet Archive: Data and Tools for Exoplanet Research

We describe the contents and functionality of the NASA Exoplanet Archive, a database and tool set funded by NASA to support astronomers in the exoplanet community. The current content of the database includes interactive tables containing properties of all published exoplanets, Kepler planet candidates, threshold-crossing events, data validation reports and target stellar parameters, light curves from the Kepler and CoRoT missions and from several ground-based surveys, and spectra and radial velocity measurements from the literature. Tools provided to work with these data include a transit ephemeris predictor, both for single planets and for observing locations, light curve viewing and normalization utilities, and a periodogram and phased light curve service. The archive can be accessed at http://exoplanetarchive.ipac.caltech.edu.Comment: Accepted for publication in the Publications of the Astronomical Society of the Pacific, 4 figure

Screening the medicines for Malaria Venture "Malaria Box" against the Plasmodium falciparum aminopeptidases, M1, M17 and M18

Malaria is a parasitic disease that remains a global health burden. The ability of the parasite to rapidly develop resistance to therapeutics drives an urgent need for the delivery of new drugs. The Medicines for Malaria Venture have compounds known for their antimalarial ac- tivity, but not necessarily the molecular targets. In this study, we assess the ability of the “MMV 400” compounds to inhibit the activity of three metalloaminopeptidases from Plasmo- dium falciparum, PfA-M1, PfA-M17 and PfM18 AAP. We have developed a multiplex assay system to allow rapid primary screening of compounds against all three metalloaminopepti- dases, followed by detailed analysis of promising compounds. Our results show that there were no PfM18AAP inhibitors, whereas two moderate inhibitors of the neutral aminopepti- dases PfA-M1 and PfA-M17 were identified. Further investigation through structure-activity relationship studies and molecular docking suggest that these compounds are competitive inhibitors with novel binding mechanisms, acting through either non-classical zinc coordina- tion or independently of zinc binding altogether. Although it is unlikely that inhibition of PfA- M1 and/or PfA-M17 is the primary mechanism responsible for the antiplasmodial activity re- ported for these compounds, their detailed characterization, as presented in this work, pave the way for their further optimization as a novel class of dual PfA-M1/PfA-M17 inhibitors uti- lising non-classical zinc binding groups

Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation in Trypanosoma brucei

Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested. We report here the X-ray structures of three kinetoplastid acidic LAPs (LAP-As from Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major) which were solved in the metal-free and unliganded forms, as well as in a number of ligand complexes, providing insight into ligand binding, metal ion requirements, and oligomeric state. In addition, we analyzed mutant cells defective in LAP-A in Trypanosoma brucei, strongly suggesting that the enzyme is not required for the growth of this parasite either in vitro or in vivo. In procyclic cells, LAP-A was equally distributed throughout the cytoplasm, yet upon starvation, it relocalizes in particles that concentrate in the perinuclear region. Overexpression of the enzyme conferred a growth advantage when parasites were grown in leucine-deficient medium. Overall, the results suggest that in T. brucei, LAP-A may participate in protein degradation associated with nutrient depletion. IMPORTANCE Leucine aminopeptidases (LAPs) catalyze the hydrolysis of the N-terminal amino acid of peptides and are considered potential drug targets. They are involved in multiple functions ranging from host cell invasion and provision of essential amino acids to site-specific homologous recombination and transcription regulation. In kinetoplastid parasites, there are at least three distinct LAPs. The availability of the crystal structures provides important information for drug design. Here we report the structure of the acidic LAPs from three kinetoplastids in complex with different inhibitors and explore their role in Trypanosoma brucei survival under various nutrient conditions. Importantly, the acidic LAP is dispensable for growth both in vitro and in vivo, an observation that questions its use as a specific drug target. While LAP-A is not essential, leucine depletion and subcellular localization studies performed under starvation conditions suggest a possible function of LAP-A in the response to nutrient restriction