Computational Approach to study the effect of point mutations in the development of antifungal resistance to Azoles and Flucytosine Drugs in Candida auris
Background: Candida auris is associated with invasive and severe candidemia, multi-drug resistance and high mortalities. Azoles and Flucytosine are commonly used antifungal drugs. Lanosterol alpha-demethylase (ERG11), Uracil phosphoribosyl transferase (FUR1) are two principal proteins involved in ergosterol biosynthesis and pyrimidine metabolism. However, crystal structures of these proteins from C. auris have not yet been established. We constructed structural model of ERG11 and FUR1 proteins for South-African Clade using homology modelling, molecular docking and molecular dynamics simulations. To investigate how point mutations affect drug interaction, we used the same methods on ERG11 mutants (Y132F, K143R) and FUR1 mutants (F211I). Methodology: Homology modelling was used to construct 3D structure of proteins. Reliability of models was analysed by using validation tools. The drug interaction in wild and mutant variants was studied using molecular docking, and binding energy was calculated. Finally, we investigated structural significance of point-mutation between two variants of FUR1 through MD Simulation. Result: Structural models of ERG11 and FUR1 were compared based on binding energy and hydrogen bonding. Few azole compounds showed no effect of mutation on interaction. Further, it was found that binding affinity for 5-fluorocytosine decreases in the mutant variant of FUR1. MD Simulation of wild variant FUR1-5FC complex showed stabilisation till 7ns while mutated complex was stable for 4.5ns. Conclusion: C. auris resistance to antifungal drugs poses a significant risk to public health. The study sheds light on how drug interactions are influenced by mutations and aids in the development of antifungal drugs.
- Candida auris,
- Antifungal Resistance,
- Point Mutations,
- Molecular Docking,
- Molecular Dynamic Simulation
- F. Prestinaci, P. Pezzotti, A. Pantosti, Antimicrobial resistance: A global multifaceted phenomenon, Pathogens and global health, 109 (2015) 309-318.
- P. Nordmann, L. Poirel, The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide, Clinical Microbiology and Infection, 20 (2014) 821-830.
- K. Satoh, K. Makimura, Y. Hasumi, Y. Nishiyama, K. Uchida, H. Yamaguchi, Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital, Microbiology and immunology, 53 (2009) 41-44.
- E. Cendejas-Bueno, A. Kolecka, A. Alastruey-Izquierdo, B. Theelen, M. Groenewald, M. Kostrzewa, M. Cuenca-Estrella, A. Gómez-López, T. Boekhout, Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: Three multiresistant human pathogenic yeasts, Journal of clinical microbiology, 50 (2012) 3641-3651.
- A.J. Lepak, M. Zhao, E.L. Berkow, S.R. Lockhart, D.R. Andes, Pharmacodynamic optimization for treatment of invasive Candida auris infection, Antimicrob Agents Chemother, 61 (2017) e00791-17.
- E.L. Berkow, S.R. Lockhart, Fluconazole resistance in Candida species: A current perspective, Infection and drug resistance, 11 (2017) 237-245.
- R. Ben-Ami, J. Berman, A. Novikov, E. Bash, Y. Shachor-Meyouhas, S. Zakin, Y. Maor, J. Tarabia, V. Schechner, A. Adler, T. Finn, Multidrug-Resistant Candida haemulonii and C. auris , Tel Aviv, Israel, Emerging infectious diseases, 23 (2017) 195-203.
- European Centre for Disease Prevention and Control, (2016) Rapid Risk Assessment. Candida auris in healthcare settings-Europe.
- S.M. Rudramurthy, A. Chakrabarti, R.A. Paul, P. Sood, H. Kaur, M.R. Capoor, A.J. Kindo, R.S.K. Marak, A. Arora, R. Sardana, S. Das, D. Chhina, A. Patel, I. Xess, B. Tarai, P. Singh, A. Ghosh, Candida auris candidaemia in Indian ICUs: Analysis of risk factors, Journal of Antimicrobial Chemotherapy, 72 (2017) 1794-1801.
- S. Schelenz, F. Hagen, J.L. Rhodes, A. Abdolrasouli, A. Chowdhary, A. Hall, L. Ryan, J. Shackleton, R. Trimlett, J.F. Meis, D. Armstrong-James, M.C. Fisher, First hospital outbreak of the globally emerging Candida auris in a European hospital, Antimicrobial Resistance & Infection Control, 5 (2016) 1-7.
- S. Tsay, R.M. Welsh, E.H. Adams, N.A. Chow, L. Gade, E.L. Berkow, E. Poirot, E. Lutterloh, M. Quinn, S. Chaturvedi, J. Kerins, S.R. Black, S.K. Kemble, P.M. Barrett, K. Barton, D.J. Shannon, K. Bradley, S.R. Lockhart, A.P. Litvintseva, H. Moulton-Meissner, A. Shugart, A. Kallen, S. Vallabhaneni, T.M. Chiller, B.R. Jackson, Notes from the Field: Ongoing Transmission of Candida auris in Health Care Facilities — United States, June 2016–May 2017, MMWR. Morbidity and mortality weekly report, 66 (2017) 514.
- S. Vallabhaneni, A. Kallen, S. Tsay, N. Chow, R. Welsh, J. Kerins, S.K. Kemble, M. Pacilli, S.R. Black, E. Landon, J. Ridgway, T.N. Palmore, A. Zelzany, E.H. Adams, M. Quinn, S. Chaturvedi, J. Greenko, R. Fernandez, K. Southwick, E.Y. Furuya, D.P. Calfee, C. Hamula, G. Patel, P. Barrett, P. Lafaro, E.L. Berkow, H. M. Meissner, J. N. Wang, R. P. Fagan, B. R. Jackson, S.R. Lockhart, A. P. Litvintseva, T. M. Chiller, Investigation of the first seven reported cases of Candida auris, a globally emerging invasive, multidrug-resistant fungus-United States, May 2013–August 2016, Morbidity and Mortality Weekly Report, 65 (2016) 1234-1237.
- A.M. Borman, A. Szekely, E.M. Johnson, Comparative Pathogenicity of United Kingdom Isolates of the Emerging Pathogen Candida auris and Other Key Pathogenic Candida Species, MSphere, 1 (2016).
- E. Larkin, C. Hager, J. Chandra, P.K. Mukherjee, M. Retuerto, I. Salem, L. Long, N. Isham, L. Kovanda, K. Borroto-Esoda, S. Wring, D. Angulo, M. Ghannoum, The emerging pathogen Candida auris: Growth phenotype, virulence factors, activity of antifungals, and effect of SCY-078, a novel glucan synthesis inhibitor, on growth morphology and biofilm formation, Antimicrob. Agents Chemother, 61 (2017) e02396-16.
- L. Sherry, G. Ramage, R. Kean, A. Borman, E.M. Johnson, M.D. Richardson, R. Rautemaa-Richardson, Biofilm-forming capability of highly virulent, multidrug-resistant Candida auris, Emerging infectious diseases, 23 (2017) 328-331.
- Centers for Disease Control and Prevention, (2019) Tracking Candida auris: Candida auris Fungal Diseases CDC, Centers Dis. Control Prev.
- A. Chowdhary, C. Sharma, J.F. Meis, Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally, PLOS pathogens, 13 (2017) e1006290.
- A. Chowdhary, V.A. Kumar, C. Sharma, A. Prakash, K. Agarwal, R. Babu, K.R. Dinesh, S. Karim, S.K. Singh, F. Hagen, J. F. Meis, Multidrug-resistant endemic clonal strain of Candida auris in India, European journal of clinical microbiology & infectious diseases, 33 (2014) 919-926.
- B. Todd, Clinical alert: Candida auris, American Journal of Nursing, 117 (2017) 53-55.
- M. Kordalewska, Y. Zhao, S.R. Lockhart, A. Chowdhary, I. Berrio, D.S. Perlina, Rapid and accurate molecular identification of the emerging multidrug-resistant pathogen Candida auris, Journal of clinical microbiology, 55 (2017) 2445-2452.
- S. Kathuria, P.K. Singh, C. Sharma, A. Prakash, A. Masih, A. Kumar, J.F. Meis, A. Chowdhary, Multidrug-resistant Candida auris misidentified as Candida haemulonii: Characterization by matrix-assisted laser desorption ionization-time of flight mass spectrometry and DNA sequencing and its antifungal susceptibility profile variability by vitek 2, CLSI broth microdilution, and Etest method, Journal of clinical microbiology, 53 (2015) 1823-1830.
- A. Prakash, C. Sharma, A. Singh, P. Kumar Singh, A. Kumar, F. Hagen, N.P. Govender, A.L. Colombo, J.F. Meis, A. Chowdhary, Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphism, Clinical Microbiology and Infection, 22 (2016) 1-9.
- M.C. Arendrup, A. Prakash, J. Meletiadis, C. Sharma, A. Chowdhary, Comparison of EUCAST and CLSI Reference Microdilution MICs of Eight Antifungal Compounds for Candida auris and Associated Tentative Epidemiological Cutoff Values, Antimicrobial agents and chemotherapy, 61 (2017) e00485-17.
- A.J. Lepak, M. Zhao, E. Berkow, S. Lockhart, D.R. Andes, Pharmacodynamic Optimization for the Treatment of Invasive Candida auris Infection, In Open Forum Infectious Diseases, 4 (2017) 73.
- S.R. Lockhart, K.A. Etienne, S. Vallabhaneni, J. Farooqi, A. Chowdhary, N.P. Govender, A.L. Colombo, B. Calvo, C.A. Cuomo, C. A. Desjardins, E.L. Berkow, M. Castanheira, R.E. Magobo, K. Jabeen, R.J. Asghar, J.F. Meis, B. Jackson, T. Chiller, A.P. Litvintseva, Simultaneous emergence of multidrug resistant Candida auris on three continents confirmed by whole genome sequencing and epidemiological analyses, Clinical Infectious Diseases, 64 (2017) 134-140.
- J. Yang, R. Yan, A. Roy, D. Xu, J. Poisson, Y. Zhang, The I-TASSER suite: Protein structure and function prediction, Nature methods, 12 (2014) 7-8.
- Y. Zhang, I-TASSER server for protein 3D structure prediction, BMC Bioinformatics. 9 (2008) 1-8.
- A. Roy, A. Kucukural, Y. Zhang, I-TASSER: A unified platform for automated protein structure and function prediction, Nature protocols, 5 (2010) 725-738.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, UCSF Chimera - A visualization system for exploratory research and analysis, Journal of computational chemistry, 25 (2004) 1605-1612.
- J.U. Bowie, R. Lüthy, D. Eisenberg, A method to identify protein sequences that fold into a known three-dimensional structure, Science. 253 (1991) 164-70.
- R. Lüthy, J.U. Bowie, D. Eisenberg, Assessment of protein models with three-dimensional profiles, Nature, 356 (1992) 83-85.
- C. Colovos, T.O. Yeates, Verification of protein structures: Patterns of nonbonded atomic interactions, Protein science, 2 (1993) 1511-1519.
- R.A. Laskowski, M.W. MacArthur, D.S. Moss, J.M. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, Journal of applied crystallography, 26 (1993) 283-291.
- N. Guex, M.C. Peitsch, SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling, Electrophoresis, 18 (1997) 2714-2723.
- T. Oleg, O.J. Arthur, AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading, Journal of computational chemistry, 31 (2010) 455-461.
- B. Huang, Metapocket: A meta-approach to improve protein ligand binding site prediction, OMICS A Journal of Integrative Biology, 13 (2009) 325-330.
- R.A. Laskowski, M.B. Swindells, LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery, Journal of Chemical Information and Modeling, 51 (2011) 2778-2786.
- D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, H.J.C. Berendsen, GROMACS: Fast, flexible, and free, Journal of computational chemistry, 26 (2005) 1701-1718.
- J. Rhodes, A. Abdolrasouli, R.A. Farrer, C.A. Cuomo, D.M. Aanensen, D. Armstrong-James, M.C. Fisher, S. Schelenz, Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris article, Emerging microbes & infections, 7 (2018) 1-12.