Inhibiting Mitochondrial Phosphate Transport As an Unexploited Antifungal Strategy

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Inhibiting Mitochondrial Phosphate Transport As an Unexploited Antifungal Strategy ARTICLE PUBLISHED ONLINE: 11 DECEMBER 2017 | DOI: 10.1038/NCHEMBIO.2534 Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy Catherine A McLellan1,2,10, Benjamin M Vincent1,3,8,10, Norma V Solis4, Alex K Lancaster1,8 , Lucas B Sullivan5 , Cathy L Hartland6,8, Willmen Youngsaye6,8, Scott G Filler4,7 , Luke Whitesell1,8* & Susan Lindquist1,2,9 The development of effective antifungal therapeutics remains a formidable challenge because of the close evolutionary rela- tionship between humans and fungi. Mitochondrial function may present an exploitable vulnerability because of its differential utilization in fungi and its pivotal roles in fungal morphogenesis, virulence, and drug resistance already demonstrated by others. We now report mechanistic characterization of ML316, a thiohydantoin that kills drug-resistant Candida species at nanomolar concentrations through fungal-selective inhibition of the mitochondrial phosphate carrier Mir1. Using genetic, biochemical, and metabolomic approaches, we established ML316 as the first Mir1 inhibitor. Inhibition of Mir1 by ML316 in respiring yeast diminished mitochondrial oxygen consumption, resulting in an unusual metabolic catastrophe marked by citrate accumulation and death. In a mouse model of azole-resistant oropharyngeal candidiasis, ML316 reduced fungal burden and enhanced azole activity. Targeting Mir1 could provide a new, much-needed therapeutic strategy to address the rapidly rising burden of drug- resistant fungal infection. health crisis from fungal diseases is looming, as there is a mitochondria, where it is used by ATP synthase to generate ATP. marked increase in at-risk populations and a rising preva- Guided by this insight, we used the compound as a probe to inves- A lence of drug resistance. The limited number of antifungal tigate the surprising biological consequences of disrupting fungal classes available and the unacceptably high mortality rate from respiration at its terminal step and to explore the translational ther- invasive infections make the need for new antifungals dire. Fungi apeutic potential of inhibiting Mir1 in culture and in mice. are eukaryotes, and as such share many conserved proteins and pro- cesses with humans, which presents a daunting challenge for the RESULTS development of new, mechanistically distinct antifungals1,2. With ML316 is fungicidal under respiratory conditions this challenge in mind, we executed a high-throughput phenotypic As previously reported5, ML316 (1) exhibited more potent antifungal screen for compounds that could reverse resistance to the widely activity against azole-resistant C. albicans than our original screen used antifungal fluconazole in a clinical isolate of Candida albi- hit (2), whereas substitution of oxygen for sulfur in the thiohy- cans (National Center for Biotechnology Information. PubChem dantoin core (3) greatly diminished activity (Fig. 1a). Although Bioassay Database; AID 2007, https://pubchem.ncbi.nlm.nih. ML316 was equally effective at inhibiting the growth of wild-type gov/bioassay/2007). A particularly intriguing hit to emerge from C. albicans in media with either glucose or nonfermentable glyc- this screen was a thiohydantoin (PubChem CID 3889161), which erol as the sole carbon source, it only inhibited growth of the model exerted potent antifungal activity as a single agent with no apparent fungal organism, Saccharomyces cerevisiae, when it was grown in toxicity to mammalian cells. Substructure searches did not reveal glycerol to enforce respiration (Fig. 1b). C. albicans is a facultative any assay interference alerts3. Its thiohydantoin core is present in aerobe and respires when oxygen is present, regardless of the carbon enzalutamide, an androgen-receptor antagonist used in the treat- source. S. cerevisiae, on the other hand, solely ferments glucose even ment of prostate cancer4. Follow-up synthesis and testing of 51 ana- in the presence of abundant oxygen6. A distantly related Candida logs in a limited SAR study yielded the designated probe compound species, Candida glabrata, also shuts off respiration in the presence ML316, a para-fluoro phenyl derivative with improved potency of glucose. As demonstrated in the probe report, toxicity in this fun- and selectivity5. gal species was similarly dependent on growth in glycerol, confirm- The promising attributes of ML316 encouraged further inves- ing a requirement for respiration in ML316 toxicity and suggesting a tigation, and we now report discovery of its molecular mecha- mode of action targeting some aspect of mitochondrial function. © 2018 Nature America, Inc., part of Springer Nature. All rights reserved. All rights part Nature. of Springer Inc., America, Nature © 2018 nism of action through a combination of genetic and biochemical In addition to effectively inhibiting wild-type Candida growth, approaches. This drug-like compound, distinct from all previously ML316 exhibited potent antifungal activity against the moderately- characterized mitochondrial poisons, selectively inhibits Mir1, azole-resistant C. albicans strain CaCi-2 (ref. 7) as a single agent the major mitochondrial phosphate carrier protein (PiC). Mir1 (MIC 0.05 μg/ml; Fig. 1c). Despite its clinically acquired azole transports inorganic phosphate into the inner matrix of fungal resistance, when CaCi-2 was simultaneously exposed to ML316 1Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA. 2Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. 3Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. 4Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA. 5Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. 6Chemical Biology Platform and Probe Development Center, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. 7David Geffen School of Medicine at UCLA, Los Angeles, California, USA. 8Present addresses: Benjamin M. Vincent, Yumanity Therapeutics Cambridge, Massachusetts, USA (B.M.V.); Ronin Institute, Montclair, N.J., USA (A.K.L.); Center for Developmental Therapeutics, Broad Institute, Cambridge, Massachusetts, USA (C.L.H.); Ra Pharmaceuticals, Cambridge, Massachusetts, USA (W.Y.) Department of Molecular Genetics,University of Toronto, Toronto, Ontario, Canada (L.W.). 9Deceased. 10These authors contributed equally to this work. *e-mail: [email protected] NATURE CHEMICAL BIOLOGY | VOL 14 | FEBRUARY 2018 | www.nature.com/naturechemicalbiology 135 ARTICLE NAture CHemiCAl BiOlOGY Doi: 10.1038/NchEmbio.2534 a b S. cerevisiae, Glu C. albicans, Glu strains (Fig. 1d). For these experiments, a series of clinical isolates (1) (2) S. cerevisiae, Gly C. albicans, Gly EtO O EtO cultured from a single HIV-infected patient over a 2-year period O O 7,9 O 1.00 μ N was assessed . ML316 remained very active (MIC 0.5 g/ml) as a N N O N O single agent against all the isolates tested, including the most flu- S S 0.75 F ML316 Screen hit Me conazole-resistant strain in the series, CaCi-17 (fluconazole MIC MIC = 0.06 µg/ml MIC = 0.3 µg/ml 0.50 >128 μg/ml). ML316 retained activity against this strain despite the (3) EtO Relative growth fact that a major contributor to the high-level azole-resistance of O 0.25 O N CaCi-17 is upregulation of both the ATP-binding cassette (ABC) N O 0.00 and multidrug resistance (MDR) efflux pump systems7, which con- O 0.001 0.01 0.1 1 Me Inactive ML316 (µg/ml) fer pleiotropic resistance to many small molecules by limiting their MIC > 7 µg/ml d Fluconazole (mg/ml) intracellular accumulation. To confirm that activity was not limited 10 c 1.00 0 0.1250.25 0.5 1 2 4 8 16 32 64 128 to one patient series, we tested other azole-resistant strains and ML 316 CaCi2 ML 316 + Flu CaCi8 found that they also remained sensitive to ML316 (Supplementary 0.75 CaCi12 CaCi15 Table 1). Four strains of the emerging pathogen Candida auris, a CaCi17 1.0 0.50 0.8 cause of increasing alarm because of its frequent resistance to known ML316 (µg/ml) 0.6 0.4 antifungals and potential for epidemic spread in hospital settings, 11 Relative growth 0.25 0.2 0 0.0160.0310.0620.1250.25 0.5 1 2 4 8 16 0 were also tested , and were all found to be sensitive to ML316 as CaCi2 Relative growth well (Supplementary Table 1). 0.00 CaCi8 0.001 0.01 0.11CaCi12 Because respiration was required for toxicity in fungi, we evalu- ML316 (µg/ml) CaCi15 CaCi17 e 1.00 ated the selectivity of ML316 using human cells grown under con- f ML316 (µg/ml) ditions enforcing respiration. As expected, a classical inhibitor of 0.75 respiration, antimycin A, was highly toxic to both 293T (kidney- 3.5 1.75 0.86 0.44 0.22 0.11 0.05 0 12 0.50 293T ML316 derived) and HepG2 (liver-derived) cells . Under these same con- HepG2 ML316 30 °C Relative growth ditions, however, ML316 had no effect on the growth and survival 0.25 293T antimycin 10 mm HepG2 antimycin of these cells (Fig. 1e). To rule out potential effects of serum on 0.00 0.01 0.1137 °C the bioavailability or stability of ML316, experiments were repeated Concentration (µg/mL) under serum-free growth conditions in which ML316 remained nontoxic to respiring human cells (Supplementary Fig. 2). Figure 1 | ML316 is a potent, highly selective fungicide. (a) Structures of Many widely used antifungals are cytostatic, stopping the ML316, the original screen hit and the inactive analog. Minimal inhibitory growth of yeast but not killing them. To characterize the nature of concentrations (MICs) are indicated for the C. albicans strain CaCi-2. ML316’s antifungal effects, we performed clonogenic survival assays Conversion factor for ML316, 1 μM = 0.35 μg/ml. (b) Glucose-grown using the CaCi-2 strain and a broad range of ML316 concentra- S. cerevisiae are not sensitive to ML316. Standard antifungal susceptibility tions (Fig. 1f). Fungicidal amphotericin and fungistatic fluconazole testing was performed in YNB-CSM media with either glucose (Glu, 2% served as controls (Supplementary Fig.
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