Targeting fungal BET bromodomains as a pan-Candida antifungal strategy

Small molecules that target one or both bromodomains (BDs) of human BET proteins are intensely studied as potential new therapeutics against cancer, diabetes and other diseases. The BDs of the fungal BET protein Bdf1 are essential for the human fungal pathogen Candida albicans, suggesting BET inhibition as a potential antifungal strategy. However, while the inactivation of both Bdf1 BDs is lethal, that of a single BD only modestly affects viability, implying the need to develop antifungal compounds that selectively target both Bdf1 BDs without inhibiting human BDs. Here, we investigate Bdf1 as a potential antifungal target in Candida glabrata, an invasive Candida species phylogenetically distant from C. albicans and of increasing medical concern. We show that Bdf1 BD functionality is essential in C. glabrata and identify a phenyltriazine derivative that targets both Bdf1 BDs with selectivity over human BET BDs. We show that human BET BDs can functionally replace Bdf1 BDs in C. glabrata and we use the humanized strains to demonstrate on-target antifungal activity of the phenyltriazine compound. Moreover, by exploiting the humanized and parental fungal strains we identified BET inhibitor I-BET726 to have potent antifungal activity against a broad spectrum of Candida species, including azole- and echinocandin-resistant clinical C. albicans and C. glabrata isolates. Crystal structures suggest how to improve the potency and selectivity of these compounds. Taken together, our findings provide compelling support for the development of BET inhibitors as potential pan-Candida antifungal therapeutics.

[1]  A. Mai,et al.  Modulation of Virulence-Associated Traits in Aspergillus fumigatus by BET Inhibitor JQ1 , 2022, Microorganisms.

[2]  C. Petosa,et al.  Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding , 2022, J. Comput. Chem..

[3]  J. Rubio-Arias,et al.  Effects of medium- and long-distance running on cardiac damage markers in amateur runners: a systematic review, meta-analysis, and metaregression , 2019, Journal of sport and health science.

[4]  Guanghua Huang,et al.  Candida auris: Epidemiology, biology, antifungal resistance, and virulence , 2020, PLoS pathogens.

[5]  I. Martín-Loeches,et al.  Invasive candidiasis in critical care: challenges and future directions , 2020, Intensive Care Medicine.

[6]  J. Berman,et al.  Drug resistance and tolerance in fungi , 2020, Nature Reviews Microbiology.

[7]  M. Bassetti,et al.  Changes in the relative prevalence of candidaemia due to non‐albicans Candida species in adult in‐patients: A systematic review, meta‐analysis and meta‐regression , 2020, Mycoses.

[8]  T. Khan,et al.  The Economic Burden of Candidemia and Invasive Candidiasis: A Systematic Review. , 2020, Value in health regional issues.

[9]  G. Rabut,et al.  Sensitive detection of protein ubiquitylation using a protein fragment complementation assay , 2019, Journal of Cell Science.

[10]  G. Furtado,et al.  Epidrugs: targeting epigenetic marks in cancer treatment , 2019, Epigenetics.

[11]  R. Sims,et al.  Bromodomains: a new target class for drug development , 2019, Nature Reviews Drug Discovery.

[12]  M. Antonelli,et al.  Incidence and outcome of invasive candidiasis in intensive care units (ICUs) in Europe: results of the EUCANDICU project , 2019, Critical Care.

[13]  E. Levy,et al.  Genome-wide C-SWAT library for high-throughput yeast genome tagging , 2018, Nature Methods.

[14]  Lucia Altucci,et al.  Cancer epigenetics: Moving forward , 2018, PLoS genetics.

[15]  Felix Bongomin,et al.  Global and Multi-National Prevalence of Fungal Diseases—Estimate Precision , 2017, Journal of fungi.

[16]  S. Bailly,et al.  ICU-acquired candidaemia in France: Epidemiology and temporal trends, 2004-2013 - A study from the REA-RAISIN network. , 2017, The Journal of infection.

[17]  C. Petosa,et al.  Selective BET bromodomain inhibition as an antifungal therapeutic strategy , 2017, Nature Communications.

[18]  Alicia P. Higueruelo,et al.  Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures , 2017, Journal of molecular biology.

[19]  A. Boland,et al.  Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes , 2017, PLoS genetics.

[20]  J. Govin,et al.  Histone Deacetylases and Their Inhibition in Candida Species , 2016, Front. Microbiol..

[21]  C. Petosa,et al.  Bromodomains: Structure, function and pharmacology of inhibition. , 2016, Biochemical pharmacology.

[22]  Matthias Meurer,et al.  One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy , 2016, Nature Methods.

[23]  Brock F. Binkowski,et al.  NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells. , 2016, ACS chemical biology.

[24]  M. Oppikofer,et al.  A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. , 2015, Structure.

[25]  J. Guinea,et al.  Next-generation sequencing offers new insights into the resistance of Candida spp. to echinocandins and azoles. , 2015, The Journal of antimicrobial chemotherapy.

[26]  B. Kullberg,et al.  Invasive Candidiasis. , 2015, The New England journal of medicine.

[27]  Yu Shen,et al.  The Yeast BDF1 Regulates Endocytosis via LSP1 Under Salt Stress , 2015, Current Microbiology.

[28]  S. Knapp,et al.  Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit , 2012, Journal of medicinal chemistry.

[29]  David M. Wilson,et al.  Identification of a novel series of BET family bromodomain inhibitors: binding mode and profile of I-BET151 (GSK1210151A). , 2012, Bioorganic & medicinal chemistry letters.

[30]  A. Gingras,et al.  Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family , 2012, Cell.

[31]  E. Mohammadi,et al.  Barriers and facilitators related to the implementation of a physiological track and trigger system: A systematic review of the qualitative evidence , 2017, International journal for quality in health care : journal of the International Society for Quality in Health Care.

[32]  S. Robson,et al.  Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia , 2011, Nature.

[33]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[34]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[35]  S. Berger,et al.  Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis. , 2010, Genes & development.

[36]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[37]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[38]  Jeroen Krijgsveld,et al.  Cooperative binding of two acetylation marks on a histone tail by a single bromodomain , 2009, Nature.

[39]  Hua Xiao,et al.  N Terminus of Swr1 Binds to Histone H2AZ and Provides a Platform for Subunit Assembly in the Chromatin Remodeling Complex* , 2009, Journal of Biological Chemistry.

[40]  James B Metcalfe,et al.  Moving forward. , 2008, Canadian Urological Association journal = Journal de l'Association des urologues du Canada.

[41]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.

[42]  J. Šubík,et al.  Biology of the pathogenic yeast Candida glabrata. , 2006, Folia microbiologica.

[43]  Koji Nomura,et al.  Challenges and Future Directions , 2005 .

[44]  Wei-Hua Wu,et al.  ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex , 2004, Science.

[45]  Huiming Ding,et al.  A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. , 2003, Molecular cell.

[46]  J. Wendland,et al.  New modules for PCR‐based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region , 2003, Yeast.

[47]  R. Tjian,et al.  Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. , 2003, Molecular cell.

[48]  S. Buratowski,et al.  Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. , 2003, Molecular cell.

[49]  J. Wendland,et al.  An improved transformation protocol for the human fungal pathogen Candida albicans , 2003, Current Genetics.

[50]  S. Buratowski,et al.  Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. , 2000, Genes & development.

[51]  B. Séraphin,et al.  The yeast BDF1 gene encodes a transcription factor involved in the expression of a broad class of genes including snRNAs. , 1994, Nucleic acids research.