Publications by authors named "Case W McNamara"

47 Publications

Prioritization of Molecular Targets for Antimalarial Drug Discovery.

ACS Infect Dis 2021 Sep 15. Epub 2021 Sep 15.

Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom.

There is a shift in antimalarial drug discovery from phenotypic screening toward target-based approaches, as more potential drug targets are being validated in species. Given the high attrition rate and high cost of drug discovery, it is important to select the targets most likely to deliver progressible drug candidates. In this paper, we describe the criteria that we consider important for selecting targets for antimalarial drug discovery. We describe the analysis of a number of drug targets in the Malaria Drug Accelerator (MalDA) pipeline, which has allowed us to prioritize targets that are ready to enter the drug discovery process. This selection process has also highlighted where additional data are required to inform target progression or deprioritization of other targets. Finally, we comment on how additional drug targets may be identified.
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http://dx.doi.org/10.1021/acsinfecdis.1c00322DOI Listing
September 2021

Drug repurposing screens identify chemical entities for the development of COVID-19 interventions.

Nat Commun 2021 06 3;12(1):3309. Epub 2021 Jun 3.

Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA.

The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here, we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. We screen a best-in-class drug repurposing library, ReFRAME, against two high-throughput, high-content imaging infection assays: one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells. From nearly 12,000 compounds, we identify 49 (in HeLa-ACE2) and 41 (in Calu-3) compounds capable of selectively inhibiting SARS-CoV-2 replication. Notably, most screen hits are cell-line specific, likely due to different virus entry mechanisms or host cell-specific sensitivities to modulators. Among these promising hits, the antivirals nelfinavir and the parent of prodrug MK-4482 possess desirable in vitro activity, pharmacokinetic and human safety profiles, and both reduce SARS-CoV-2 replication in an orthogonal human differentiated primary cell model. Furthermore, MK-4482 effectively blocks SARS-CoV-2 infection in a hamster model. Overall, we identify direct-acting antivirals as the most promising compounds for drug repurposing, additional compounds that may have value in combination therapies, and tool compounds for identification of viral host cell targets.
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http://dx.doi.org/10.1038/s41467-021-23328-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175350PMC
June 2021

Repurposing Infectious Disease Hits as Anti- Leads.

ACS Infect Dis 2021 05 19;7(5):1275-1282. Epub 2021 Mar 19.

Department of Medicine Division of Allergy Infectious Disease Center for Emerging Reemerging Infectious Diseases, University of Washington, Seattle, Washington 98109, United States.

New drugs are critically needed to treat infections, particularly for malnourished children under 2 years old in the developing world and persons with immunodeficiencies. Bioactive compounds from the Tres-Cantos GSK library that have activity against other pathogens were screened for possible repurposing against growth. Nineteen compounds grouped into nine structural clusters were identified using an iterative process to remove excessively toxic compounds and screen related compounds from the Tres-Cantos GSK library. Representatives of four different clusters were advanced to a mouse model of infection, but only one compound, an imidazole-pyrimidine, led to significant clearance of infection. This imidazole-pyrimidine compound had a number of favorable safety and pharmacokinetic properties and was maximally active in the mouse model down to 30 mg/kg given daily. Though the mechanism of action against was not definitively established, this imidazole-pyrimidine compound inhibits the known drug target, calcium-dependent protein kinase 1, with a 50% inhibitory concentration of 2 nM. This compound, and related imidazole-pyrimidine molecules, should be further examined as potential leads for therapeutics.
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http://dx.doi.org/10.1021/acsinfecdis.1c00076DOI Listing
May 2021

MalDA, Accelerating Malaria Drug Discovery.

Trends Parasitol 2021 06 26;37(6):493-507. Epub 2021 Feb 26.

Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA. Electronic address:

The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of new chemically and biologically validated targets, as well as future scientific directions.
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http://dx.doi.org/10.1016/j.pt.2021.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261838PMC
June 2021

An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease.

Pathogens 2021 Jan 14;10(1). Epub 2021 Jan 14.

Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO 63110, USA.

Filarial worms cause multiple debilitating diseases in millions of people worldwide, including river blindness. Currently available drugs reduce transmission by killing larvae (microfilariae), but there are no effective cures targeting the adult parasites (macrofilaricides) which survive and reproduce in the host for very long periods. To identify effective macrofilaricides, we carried out phenotypic screening of a library of 2121 approved drugs for clinical use against adult and prioritized the hits for further studies by integrating those results with a computational prioritization of drugs and associated targets. This resulted in the identification of 18 hits with anti-macrofilaricidal activity, of which two classes, azoles and aspartic protease inhibitors, were further expanded upon. Follow up screening against spp. (adult and pre-adult ) confirmed activity for 13 drugs (the majority having IC < 10 μM), and a counter screen of a subset against microfilariae showed the potential to identify selective drugs that prevent adverse events when co-infected individuals are treated. Stage specific activity was also observed. Many of these drugs are amenable to structural optimization, and also have known canonical targets, making them promising candidates for further optimization that can lead to identifying and characterizing novel anti-macrofilarial drugs.
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http://dx.doi.org/10.3390/pathogens10010071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7830784PMC
January 2021

Bicyclic azetidines kill the diarrheal pathogen in mice by inhibiting parasite phenylalanyl-tRNA synthetase.

Sci Transl Med 2020 09;12(563)

Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA.

is a protozoan parasite and a leading cause of diarrheal disease and mortality in young children. Currently, there are no fully effective treatments available to cure infection with this diarrheal pathogen. In this study, we report a broad drug repositioning effort that led to the identification of bicyclic azetidines as a new anticryptosporidial series. Members of this series blocked growth in in vitro culture of three isolates with EC s in 1% serum of <0.4 to 96 nM, had comparable potencies against and , and was effective in three of four highly susceptible immunosuppressed mice with once-daily dosing administered for 4 days beginning 2 weeks after infection. Comprehensive genetic, biochemical, and chemical studies demonstrated inhibition of phenylalanyl-tRNA synthetase (PheRS) as the mode of action of this new lead series. Introduction of mutations directly into the gene by CRISPR-Cas9 genome editing resulted in parasites showing high degrees of compound resistance. In vitro, bicyclic azetidines potently inhibited the aminoacylation activity of recombinant PheRS. Medicinal chemistry optimization led to the identification of an optimal pharmacokinetic/pharmacodynamic profile for this series. Collectively, these data demonstrate that bicyclic azetidines are a promising series for anticryptosporidial drug development and establish a broad framework to enable target-based drug discovery for this infectious disease.
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http://dx.doi.org/10.1126/scitranslmed.aba8412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8381743PMC
September 2020

Phenotypic screening techniques for drug discovery.

Expert Opin Drug Discov 2021 01 7;16(1):59-74. Epub 2020 Sep 7.

Calibr, a division of The Scripps Research Institute , La Jolla, CA, USA.

: Two landmark epidemiological studies identified spp. as a significant cause of diarrheal disease in pediatric populations in resource-limited countries. Notably, nitazoxanide is the only approved drug for treatment of cryptosporidiosis but shows limited efficacy. As a result, many drug discovery efforts have commenced to find improved treatments. The unique biology of presents challenges for traditional drug discovery methods, which has inspired new assay platforms to study parasite biology and drug screening. : The authors review historical advancements in phenotypic-based assays and techniques for drug discovery, as well as recent advances that will define future drug discovery. The reliance on phenotypic-based screens and repositioning of phenotypic hits from other pathogens has quickly created a robust pipeline of potential cryptosporidiosis therapeutics. The latest advances involve new culture methods for oocyst generation, continuous culturing capabilities, and more physiologically relevant assays for testing compounds. : Previous phenotypic screening techniques have laid the groundwork for recent cryptosporidiosis drug discovery efforts. The resulting improved methodologies characterize compound activity, identify, and validate drug targets, and prioritize new compounds for drug development. The most recent improvements in phenotypic assays are poised to help advance compounds into clinical development.
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http://dx.doi.org/10.1080/17460441.2020.1812577DOI Listing
January 2021

High-Throughput Screening of the ReFRAME Library Identifies Potential Drug Repurposing Candidates for .

Microorganisms 2020 Mar 26;8(4). Epub 2020 Mar 26.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.

Chagas disease, caused by the kinetoplastid parasite , affects between 6 and 7 million people worldwide, with an estimated 300,000 to 1 million of these cases in the United States. In the chronic phase of infection, can cause severe gastrointestinal and cardiac disease, which can be fatal. Currently, only benznidazole is clinically approved by the FDA for pediatric use to treat this infection in the USA. Toxicity associated with this compound has driven the search for new anti-Chagas agents. Drug repurposing is a particularly attractive strategy for neglected diseases, as pharmacological parameters and toxicity are already known for these compounds, reducing costs and saving time in the drug development pipeline. Here, we screened 7680 compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library, a collection of drugs or compounds with confirmed clinical safety, against . We identified seven compounds of interest with potent in vitro activity against the parasite with a therapeutic index of 10 or greater, including the previously unreported activity of the antiherpetic compound 348U87. These results provide the framework for further development of new leads that can potentially move quickly to the clinic.
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http://dx.doi.org/10.3390/microorganisms8040472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232187PMC
March 2020

Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium .

Mar Drugs 2020 03 18;18(3). Epub 2020 Mar 18.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

A new cyclic peptide, kakeromamide B (), and previously described cytotoxic cyanobacterial natural products ulongamide A (), lyngbyabellin A (), 18-lyngbyaloside C (), and lyngbyaloside () were identified from an antimalarial extract of the Fijian marine cyanobacterium . Compounds and exhibited moderate activity against blood-stages with EC values of 0.89 and 0.99 µM, respectively, whereas was more potent with an EC value of 0.15 nM, respectively. Compounds , , and displayed moderate liver-stage antimalarial activity against liver schizonts with EC values of 1.1, 0.71, and 0.45 µM, respectively. The threading-based computational method FINDSITE predicted the binding of and to potentially druggable proteins of , prompting formulation of hypotheses about possible mechanisms of action. Kakeromamide B () was predicted to bind to several actin-like proteins and a sortilin protein suggesting possible interference with parasite invasion of host cells. When 1 was tested in a mammalian actin polymerization assay, it stimulated actin polymerization in a dose-dependent manner, suggesting that 1 does, in fact, interact with actin.
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http://dx.doi.org/10.3390/md18030167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142784PMC
March 2020

Probing the Open Global Health Chemical Diversity Library for Multistage-Active Starting Points for Next-Generation Antimalarials.

ACS Infect Dis 2020 04 4;6(4):613-628. Epub 2020 Mar 4.

School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.

Most phenotypic screens aiming to discover new antimalarial chemotypes begin with low cost, high-throughput tests against the asexual blood stage (ABS) of the malaria parasite life cycle. Compounds active against the ABS are then sequentially tested in more difficult assays that predict whether a compound has other beneficial attributes. Although applying this strategy to new chemical libraries may yield new leads, repeated iterations may lead to diminishing returns and the rediscovery of chemotypes hitting well-known targets. Here, we adopted a different strategy to find starting points, testing ∼70,000 open source small molecules from the Global Health Chemical Diversity Library for activity against the liver stage, mature sexual stage, and asexual blood stage malaria parasites in parallel. In addition, instead of using an asexual assay that measures accumulated parasite DNA in the presence of compound (SYBR green), a real time luciferase-dependent parasite viability assay was used that distinguishes slow-acting (delayed death) from fast-acting compounds. Among 382 scaffolds with the activity confirmed by dose response (<10 μM), we discovered 68 novel delayed-death, 84 liver stage, and 68 stage V gametocyte inhibitors as well. Although 89% of the evaluated compounds had activity in only a single life cycle stage, we discovered six potent (half-maximal inhibitory concentration of <1 μM) multistage scaffolds, including a novel cytochrome bc1 chemotype. Our data further show the luciferase-based assays have higher sensitivity. Chemoinformatic analysis of positive and negative compounds identified scaffold families with a strong enrichment for activity against specific or multiple stages.
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http://dx.doi.org/10.1021/acsinfecdis.9b00482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155171PMC
April 2020

Short-course quinazoline drug treatments are effective in the Litomosoides sigmodontis and Brugia pahangi jird models.

Int J Parasitol Drugs Drug Resist 2020 04 10;12:18-27. Epub 2019 Dec 10.

Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.

The quinazolines CBR417 and CBR490 were previously shown to be potent anti-wolbachials that deplete Wolbachia endosymbionts of filarial nematodes and present promising pre-clinical candidates for human filarial diseases such as onchocerciasis. In the present study we tested both candidates in two models of chronic filarial infection, namely the Litomosoides sigmodontis and Brugia pahangi jird model and assessed their long-term effect on Wolbachia depletion, microfilariae counts and filarial embryogenesis 16-18 weeks after treatment initiation (wpt). Once per day (QD) oral treatment with CBR417 (50 mg/kg) for 4 days or twice per day (BID) with CBR490 (25 mg/kg) for 7 days during patent L. sigmodontis infection reduced the Wolbachia load by >99% and completely cleared peripheral microfilaremia from 10-14 wpt. Similarly, 7 days of QD treatments (40 mg/kg) with CBR417 or CBR490 cleared >99% of Wolbachia from B. pahangi and reduced peritoneal microfilariae counts by 93% in the case of CBR417 treatment. Transmission electron microscopy analysis indicated intensive damage to the B. pahangi ovaries following CBR417 treatment and in accordance filarial embryogenesis was inhibited in both models after CBR417 or CBR490 treatment. Suboptimal treatment regimens of CBR417 or CBR490 did not lead to a maintained reduction of the microfilariae and Wolbachia load. In conclusion, CBR417 or CBR490 are pre-clinical candidates for filarial diseases, which achieve long-term clearance of Wolbachia endosymbionts of filarial nematodes, inhibit filarial embryogenesis and clear microfilaremia with treatments as short as 7 days.
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http://dx.doi.org/10.1016/j.ijpddr.2019.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6931063PMC
April 2020

High-Content Screening for Cryptosporidium Drug Discovery.

Methods Mol Biol 2020 ;2052:303-317

Calibr at Scripps Research, La Jolla, CA, USA.

High-content screening (HCS) is a cell-based type of phenotypic screening that combines multiple simultaneous readouts with a high level of throughput. A particular benefit of this form of screening for drug discovery is the ability to perform the interrogation in a biologically relevant system. This approach has greatly advanced the field of drug discovery for cryptosporidiosis, a diarrheal disease caused by protozoan parasites of Cryptosporidium spp. These parasites are obligate intracellular parasites and cannot be cultured in vitro without the support of a host cell, limiting the options for potential assay readout. Here we describe an established 384- or 1536-well format high-content imaging (HCI) assay of Cryptosporidium-infected HCT-8 human ileocecal adenocarcinoma cells. This HCS assay is a powerful tool to assess large numbers of compounds to power drug discovery, as well as to phenotypically characterize known Cryptosporidium-active compounds.
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http://dx.doi.org/10.1007/978-1-4939-9748-0_17DOI Listing
November 2020

Advances in Antiwolbachial Drug Discovery for Treatment of Parasitic Filarial Worm Infections.

Trop Med Infect Dis 2019 Jul 18;4(3). Epub 2019 Jul 18.

Calibr at Scripps Research, La Jolla, CA 92037, USA.

The intracellular bacteria now known as were first described in filarial worms in the 1970s, but the idea of being used as a macrofilaricidal target did not gain wide attention until the early 2000s, with research in filariae suggesting the requirement of worms for the endosymbiont. This new-found interest prompted the eventual organization of the Anti- Consortium (A-WOL) at the Liverpool School of Tropical Medicine, who, among others have been active in the field of antiwolbachial drug discovery to treat filarial infections. Clinical proof of concept studies using doxycycline demonstrated the utility of the antiwolbachial therapy, but efficacious treatments were of long duration and not safe for all infected. With the advance of robotics, automation, and high-speed computing, the search for superior antiwolbachials shifted away from smaller studies with a select number of antibiotics to high-throughput screening approaches, centered largely around cell-based phenotypic screens due to the rather limited knowledge about, and tools available to manipulate, this bacterium. A concomitant effort was put towards developing validation approaches and in vivo models supporting drug discovery efforts. In this review, we summarize the strategies behind and outcomes of recent large phenotypic screens published within the last 5 years, hit compound validation approaches and promising candidates with profiles superior to doxycycline, including ones positioned to advance into clinical trials for treatment of filarial worm infections.
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http://dx.doi.org/10.3390/tropicalmed4030108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789823PMC
July 2019

Identification of a potent benzoxaborole drug candidate for treating cryptosporidiosis.

Nat Commun 2019 06 27;10(1):2816. Epub 2019 Jun 27.

Department of Medicine, University of Vermont Robert R. Larner College of Medicine, Burlington, VT, 05405, USA.

Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children and causes chronic diarrhea in AIDS patients, but the only approved treatment is ineffective in malnourished children and immunocompromised people. We here use a drug repositioning strategy and identify a promising anticryptosporidial drug candidate. Screening a library of benzoxaboroles comprised of analogs to four antiprotozoal chemical scaffolds under pre-clinical development for neglected tropical diseases for Cryptosporidium growth inhibitors identifies the 6-carboxamide benzoxaborole AN7973. AN7973 blocks intracellular parasite development, appears to be parasiticidal, and potently inhibits the two Cryptosporidium species most relevant to human health, C. parvum and C. hominis. It is efficacious in murine models of both acute and established infection, and in a neonatal dairy calf model of cryptosporidiosis. AN7973 also possesses favorable safety, stability, and PK parameters, and therefore, is an exciting drug candidate for treating cryptosporidiosis.
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http://dx.doi.org/10.1038/s41467-019-10687-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597546PMC
June 2019

Peyssonnosides A-B, Unusual Diterpene Glycosides with a Sterically Encumbered Cyclopropane Motif: Structure Elucidation Using an Integrated Spectroscopic and Computational Workflow.

J Org Chem 2019 07 18;84(13):8531-8541. Epub 2019 Jun 18.

Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

Two sulfated diterpene glycosides featuring a highly substituted and sterically encumbered cyclopropane ring have been isolated from the marine red alga Peyssonnelia sp. Combination of a wide array of 2D NMR spectroscopic experiments, in a systematic structure elucidation workflow, revealed that peyssonnosides A-B (1-2) represent a new class of diterpene glycosides with a tetracyclo [7.5.0.0.0] tetradecane architecture. A salient feature of this workflow is the unique application of quantitative interproton distances obtained from the rotating frame Overhauser effect spectroscopy (ROESY) NMR experiment, wherein the β-d-glucose moiety of 1 was used as an internal probe to unequivocally determine the absolute configuration, which was also supported by optical rotatory dispersion (ORD). Peyssonnoside A (1) exhibited promising activity against liver stage Plasmodium berghei and moderate antimethicillin-resistant Staphylococcus aureus (MRSA) activity, with no cytotoxicity against human keratinocytes. Additionally, 1 showed strong growth inhibition of the marine fungus Dendryphiella salina indicating an antifungal ecological role in its natural environment. The high natural abundance and novel carbon skeleton of 1 suggests a rare terpene cyclase machinery, exemplifying the chemical diversity in this phylogenetically distinct marine red alga.
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http://dx.doi.org/10.1021/acs.joc.9b00884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614789PMC
July 2019

Novel chemical starting points for drug discovery in leishmaniasis and Chagas disease.

Int J Parasitol Drugs Drug Resist 2019 08 22;10:58-68. Epub 2019 May 22.

Calibr at Scripps Research, La Jolla, CA, USA. Electronic address:

Visceral leishmaniasis (VL) and Chagas disease (CD) are caused by kinetoplastid parasites that affect millions of people worldwide and impart a heavy burden against human health. Due to the partial efficacy and toxicity-related limitations of the existing treatments, there is an urgent need to develop novel therapies with superior efficacy and safety profiles to successfully treat these diseases. Herein we report the application of whole-cell phenotypic assays to screen a set of 150,000 compounds against Leishmania donovani, a causative agent of VL, and Trypanosoma cruzi, the causative agent of CD, with the objective of finding new starting points to develop novel drugs to effectively treat and control these diseases. The screening campaign, conducted with the purpose of global open access, identified twelve novel chemotypes with low to sub-micromolar activity against T. cruzi and/or L. donovani. We disclose these hit structures and associated activity with the goal to contribute to the drug discovery community by providing unique chemical tools to probe kinetoplastid biology and as hit-to-lead candidates for drug discovery.
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http://dx.doi.org/10.1016/j.ijpddr.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545338PMC
August 2019

Discovery of Kirromycins with Anti- Wolbachia Activity from Streptomyces sp. CB00686.

ACS Chem Biol 2019 06 10;14(6):1174-1182. Epub 2019 May 10.

Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States.

Lymphatic filariasis and onchocerciasis diseases caused by filarial parasite infections can lead to profound disability and affect millions of people worldwide. Standard mass drug administration campaigns require repetitive delivery of anthelmintics for years to temporarily block parasite transmission but do not cure infection because long-lived adult worms survive the treatment. Depletion of the endosymbiont Wolbachia, present in most filarial nematode species, results in death of adult worms and therefore represents a promising target for the treatment of filariasis. Here, we used a high-content imaging assay to screen the pure compounds collection of the natural products library at The Scripps Research Institute for anti- Wolbachia activity, leading to the identification of kirromycin B (1) as a lead candidate. Two additional congeners, kirromycin (2) and kirromycin C (3), were isolated and characterized from the same producing strain Streptomyces sp. CB00686. All three kirromycin congeners depleted Wolbachia in LDW1 Drosophila cells in vitro with half-maximal inhibitory concentrations (IC) in nanomolar range, while doxycycline, a registered drug with anti- Wolbachia activity, showed lower activity with an IC of 152 ± 55 nM. Furthermore, 1-3 eliminated the Wolbachia endosymbiont in Brugia pahangi ovaries ex vivo with higher efficiency (65%-90%) at 1 μM than that of doxycycline (50%). No cytotoxicity against HEK293T and HepG2 mammalian cells was observed with 1-3 at the highest concentration (40 μM) used in the assay. These results suggest kirromycin is an effective lead scaffold, further exploration of which could potentially lead to the development of novel treatments for filarial nematode infections.
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http://dx.doi.org/10.1021/acschembio.9b00086DOI Listing
June 2019

Discovery of short-course antiwolbachial quinazolines for elimination of filarial worm infections.

Sci Transl Med 2019 05;11(491)

Research Foundation in Tropical Diseases and the Environment, Buea, Cameroon.

Parasitic filarial nematodes cause debilitating infections in people in resource-limited countries. A clinically validated approach to eliminating worms uses a 4- to 6-week course of doxycycline that targets , a bacterial endosymbiont required for worm viability and reproduction. However, the prolonged length of therapy and contraindication in children and pregnant women have slowed adoption of this treatment. Here, we describe discovery and optimization of quinazolines CBR417 and CBR490 that, with a single dose, achieve >99% elimination of in the in vivo filarial infection model. The efficacious quinazoline series was identified by pairing a primary cell-based high-content imaging screen with an orthogonal ex vivo validation assay to rapidly quantify elimination in filarial ovaries. We screened 300,368 small molecules in the primary assay and identified 288 potent and selective hits. Of 134 primary hits tested, only 23.9% were active in the worm-based validation assay, 8 of which contained a quinazoline heterocycle core. Medicinal chemistry optimization generated quinazolines with excellent pharmacokinetic profiles in mice. Potent antiwolbachial activity was confirmed in , , and in vivo preclinical models of filarial disease and in vitro selectivity against (a safety concern in endemic areas). The favorable efficacy and in vitro safety profiles of CBR490 and CBR417 further support these as clinical candidates for treatment of filarial infections.
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http://dx.doi.org/10.1126/scitranslmed.aav3523DOI Listing
May 2019

A suite of phenotypic assays to ensure pipeline diversity when prioritizing drug-like Cryptosporidium growth inhibitors.

Nat Commun 2019 04 23;10(1):1862. Epub 2019 Apr 23.

Department of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA.

Cryptosporidiosis is a leading cause of life-threatening diarrhea in children, and the only currently approved drug is ineffective in malnourished children and immunocompromised people. Large-scale phenotypic screens are ongoing to identify anticryptosporidial compounds, but optimal approaches to prioritize inhibitors and establish a mechanistically diverse drug development pipeline are unknown. Here, we present a panel of medium-throughput mode of action assays that enable testing of compounds in several stages of the Cryptosporidium life cycle. Phenotypic profiles are given for thirty-nine anticryptosporidials. Using a clustering algorithm, the compounds sort by phenotypic profile into distinct groups of inhibitors that are either chemical analogs (i.e. same molecular mechanism of action (MMOA)) or known to have similar MMOA. Furthermore, compounds belonging to multiple phenotypic clusters are efficacious in a chronic mouse model of cryptosporidiosis. This suite of phenotypic assays should ensure a drug development pipeline with diverse MMOA without the need to identify underlying mechanisms.
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http://dx.doi.org/10.1038/s41467-019-09880-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478823PMC
April 2019

Modular, stereocontrolled C-H/C-C activation of alkyl carboxylic acids.

Proc Natl Acad Sci U S A 2019 04 17;116(18):8721-8727. Epub 2019 Apr 17.

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;

The union of two powerful transformations, directed C-H activation and decarboxylative cross-coupling, for the enantioselective synthesis of vicinally functionalized alkyl, carbocyclic, and heterocyclic compounds is described. Starting from simple carboxylic acid building blocks, this modular sequence exploits the residual directing group to access more than 50 scaffolds that would be otherwise extremely difficult to prepare. The tactical use of these two transformations accomplishes a formal vicinal difunctionalization of carbon centers in a way that is modular and thus, amenable to rapid diversity incorporation. A simplification of routes to known preclinical drug candidates is presented along with the rapid diversification of an antimalarial compound series.
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http://dx.doi.org/10.1073/pnas.1903048116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500144PMC
April 2019

Antibacterial Oligomeric Polyphenols from the Green Alga Cladophora socialis.

J Org Chem 2019 05 3;84(9):5035-5045. Epub 2019 Apr 3.

Aquatic Chemical Ecology Center , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

A series of oligomeric phenols including the known natural product 3,4,3',4'-tetrahydroxy-1,1'-biphenyl (3), the previously synthesized 2,3,8,9-tetrahydroxybenzo[ c]chromen-6-one (4), and eight new related natural products, cladophorols B-I (5-12), were isolated from the Fijian green alga Cladophora socialis and identified by a combination of NMR spectroscopy, mass spectrometric analysis, and computational modeling using DFT calculations. J-resolved spectroscopy and line width reduction by picric acid addition aided in resolving the heavily overlapped aromatic signals. A panel of Gram-positive and Gram-negative pathogens used to evaluate pharmacological potential led to the determination that cladophorol C (6) exhibits potent antibiotic activity selective toward methicillin-resistant Staphylococcus aureus (MRSA) with an MIC of 1.4 μg/mL. Cladophorols B (5) and D-H (7-11) had more modest but also selective antibiotic potency. Activities of cladophorols A-I (4-12) were also assessed against the asexual blood stages of Plasmodium falciparum and revealed cladophorols A (4) and B (5) to have modest activity with EC values of 0.7 and 1.9 μg/mL, respectively.
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http://dx.doi.org/10.1021/acs.joc.8b03218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503470PMC
May 2019

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.

Proc Natl Acad Sci U S A 2019 04 20;116(14):7015-7020. Epub 2019 Mar 20.

Department of Life Sciences, Imperial College, South Kensington, SW7 2AZ London, United Kingdom.

Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage and in cell-culture studies. Target deconvolution in has shown that cladosporin inhibits lysyl-tRNA synthetase (KRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both KRS1 and KRS (KRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between KRS1 and KRS. This series of compounds inhibit KRS and and in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for KRS1 and KRS vs. (human) KRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.
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http://dx.doi.org/10.1073/pnas.1814685116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452685PMC
April 2019

Boron-Pleuromutilins as Anti- Wolbachia Agents with Potential for Treatment of Onchocerciasis and Lymphatic Filariasis.

J Med Chem 2019 03 26;62(5):2521-2540. Epub 2019 Feb 26.

Calibr , 11119 North Torrey Pines Road , Suite 100, La Jolla , California 92037 , United States.

A series of pleuromutilins modified by introduction of a boron-containing heterocycle on C(14) of the polycyclic core are described. These analogs were found to be potent anti- Wolbachia antibiotics and, as such, may be useful in the treatment of filarial infections caused by Onchocerca volvulus, resulting in Onchocerciasis or river blindness, or Wuchereria bancrofti and Brugia malayi and related parasitic nematodes resulting in lymphatic filariasis. These two important neglected tropical diseases disproportionately impact patients in the developing world. The lead preclinical candidate compound containing 7-fluoro-6-oxybenzoxaborole (15, AN11251) was shown to have good in vitro anti- Wolbachia activity and physicochemical and pharmacokinetic properties providing high exposure in plasma. The lead was effective in reducing the Wolbachia load in filarial worms following oral administration to mice.
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http://dx.doi.org/10.1021/acs.jmedchem.8b01854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421521PMC
March 2019

Open-source discovery of chemical leads for next-generation chemoprotective antimalarials.

Science 2018 12;362(6419)

Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D. W. Brooks Drive, Athens, GA 30602, USA.

To discover leads for next-generation chemoprotective antimalarial drugs, we tested more than 500,000 compounds for their ability to inhibit liver-stage development of luciferase-expressing spp. parasites (681 compounds showed a half-maximal inhibitory concentration of less than 1 micromolar). Cluster analysis identified potent and previously unreported scaffold families as well as other series previously associated with chemoprophylaxis. Further testing through multiple phenotypic assays that predict stage-specific and multispecies antimalarial activity distinguished compound classes that are likely to provide symptomatic relief by reducing asexual blood-stage parasitemia from those which are likely to only prevent malaria. Target identification by using functional assays, in vitro evolution, or metabolic profiling revealed 58 mitochondrial inhibitors but also many chemotypes possibly with previously unidentified mechanisms of action.
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http://dx.doi.org/10.1126/science.aat9446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516198PMC
December 2018

The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis.

Proc Natl Acad Sci U S A 2018 10 3;115(42):10750-10755. Epub 2018 Oct 3.

California Institute for Biomedical Research, La Jolla, CA 92037;

The chemical diversity and known safety profiles of drugs previously tested in humans make them a valuable set of compounds to explore potential therapeutic utility in indications outside those originally targeted, especially neglected tropical diseases. This practice of "drug repurposing" has become commonplace in academic and other nonprofit drug-discovery efforts, with the appeal that significantly less time and resources are required to advance a candidate into the clinic. Here, we report a comprehensive open-access, drug repositioning screening set of 12,000 compounds (termed ReFRAME; Repurposing, Focused Rescue, and Accelerated Medchem) that was assembled by combining three widely used commercial drug competitive intelligence databases (Clarivate Integrity, GVK Excelra GoStar, and Citeline Pharmaprojects), together with extensive patent mining of small molecules that have been dosed in humans. To date, 12,000 compounds (∼80% of compounds identified from data mining) have been purchased or synthesized and subsequently plated for screening. To exemplify its utility, this collection was screened against spp., a major cause of childhood diarrhea in the developing world, and two active compounds previously tested in humans for other therapeutic indications were identified. Both compounds, VB-201 and a structurally related analog of ASP-7962, were subsequently shown to be efficacious in animal models of infection at clinically relevant doses, based on available human doses. In addition, an open-access data portal (https://reframedb.org) has been developed to share ReFRAME screen hits to encourage additional follow-up and maximize the impact of the ReFRAME screening collection.
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http://dx.doi.org/10.1073/pnas.1810137115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196526PMC
October 2018

The Deconstructed Granuloma: A Complex High-Throughput Drug Screening Platform for the Discovery of Host-Directed Therapeutics Against Tuberculosis.

Front Cell Infect Microbiol 2018 14;8:275. Epub 2018 Aug 14.

Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States.

(Mtb) continues to be a threat to Global Public Health, and its control will require an array of therapeutic strategies. It has been appreciated that high-throughput screens using cell-based assays to identify compounds targeting Mtb within macrophages represent a valuable tool for drug discovery. However, the host immune environment, in the form of lymphocytes and cytokines, is completely absent in a chemical screening platform based on infected macrophages alone. The absence of these players unnecessarily limits the breadth of novel host target pathways to be interrogated. In this study, we detail a new drug screening platform based on dissociated murine TB granulomas, named the Deconstructed Granuloma (DGr), that utilizes fluorescent Mtb reporter strains screened in the host immune environment of the infection site. The platform has been used to screen a collection of known drug candidates. Data from a representative 384-well plate containing known anti-bacterial compounds are shown, illustrating the robustness of the screening platform. The novel deconstructed granuloma platform represents an accessible, sensitive and robust high-throughput screen suitable for the inclusive interrogation of immune targets for Host-Directed Therapeutics.
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http://dx.doi.org/10.3389/fcimb.2018.00275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102409PMC
August 2019

Author Correction: A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum.

Nat Commun 2018 06 8;9(1):2317. Epub 2018 Jun 8.

Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, 33612, Tampa, FL, USA.

The original version of this Article contained an error in the spelling of Richard Thomson-Luque, which was incorrectly given as Richard Thomson Luque. This error has now been corrected in both the PDF and HTML versions of the Article.
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http://dx.doi.org/10.1038/s41467-018-04817-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993793PMC
June 2018

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum.

Nat Commun 2018 05 9;9(1):1837. Epub 2018 May 9.

Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA.

Malaria liver stages represent an ideal therapeutic target with a bottleneck in parasite load and reduced clinical symptoms; however, current in vitro pre-erythrocytic (PE) models for Plasmodium vivax and P. falciparum lack the efficiency necessary for rapid identification and effective evaluation of new vaccines and drugs, especially targeting late liver-stage development and hypnozoites. Herein we report the development of a 384-well plate culture system using commercially available materials, including cryopreserved primary human hepatocytes. Hepatocyte physiology is maintained for at least 30 days and supports development of P. vivax hypnozoites and complete maturation of P. vivax and P. falciparum schizonts. Our multimodal analysis in antimalarial therapeutic research identifies important PE inhibition mechanisms: immune antibodies against sporozoite surface proteins functionally inhibit liver stage development and ion homeostasis is essential for schizont and hypnozoite viability. This model can be implemented in laboratories in disease-endemic areas to accelerate vaccine and drug discovery research.
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http://dx.doi.org/10.1038/s41467-018-04221-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943321PMC
May 2018

Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors.

Proc Natl Acad Sci U S A 2018 06 7;115(26):6834-6839. Epub 2018 May 7.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;

New drugs are needed to treat gram-negative bacterial infections. These bacteria are protected by an outer membrane which prevents many antibiotics from reaching their cellular targets. The outer leaflet of the outer membrane contains LPS, which is responsible for creating this permeability barrier. Interfering with LPS biogenesis affects bacterial viability. We developed a cell-based screen that identifies inhibitors of LPS biosynthesis and transport by exploiting the nonessentiality of this pathway in We used this screen to find an inhibitor of MsbA, an ATP-dependent flippase that translocates LPS across the inner membrane. Treatment with the inhibitor caused mislocalization of LPS to the cell interior. The discovery of an MsbA inhibitor, which is universally conserved in all gram-negative bacteria, validates MsbA as an antibacterial target. Because our cell-based screen reports on the function of the entire LPS biogenesis pathway, it could be used to identify compounds that inhibit other targets in the pathway, which can provide insights into vulnerabilities of the gram-negative cell envelope.
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http://dx.doi.org/10.1073/pnas.1804670115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042065PMC
June 2018
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