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Research Article

Antifungal drug discovery for targeting Candida albicans morphogenesis through structural dynamics study

, , , , , , , , , , & show all
Received 24 Jan 2024, Accepted 13 Mar 2024, Published online: 18 Apr 2024

References

  • Arné, P., & Lee, M. D. (2020). Fungal infections. Diseases of Poultry, 1109–1133. https://doi.org/10.1002/9781119371199.ch25
  • Bajrai, L. H., Almalki, A. A., Sahoo, A. K., Dwivedi, V. D., & Azhar, E. I. (2024). Exploring plant-derived small molecules as inhibitors of marburg virus RNA binding protein activity. Journal of Biomolecular Structure & Dynamics, 1–11. https://doi.org/10.1080/07391102.2024.2306500
  • Bauer, P., Hess, B., & Lindahl, E. (2022). GROMACS 2022.2 Manual.
  • Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, IN., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Bhattacharya, S., Sae-Tia, S., & Fries, B. C. (2020). Candidiasis and mechanisms of antifungal resistance. Antibiotics, 9(6), 312. https://doi.org/10.3390/antibiotics9060312
  • Bohner, F., Papp, C., & Gácser, A. (2022). The effect of antifungal resistance development on the virulence of candida species. FEMS Yeast Research, 22(1), foac019. https://doi.org/10.1093/femsyr/foac019
  • Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., & Sacerdoti, F. D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. pp. 84-es.
  • Caplan, T., Lorente-Macías, Á., Stogios, P. J., Evdokimova, E., Hyde, S., Wellington, M. A., Liston, S., Iyer, K. R., Puumala, E., Shekhar-Guturja, T., Robbins, N., Savchenko, A., Krysan, D. J., Whitesell, L., Zuercher, W. J., & Cowen, L. E. (2020). Overcoming fungal echinocandin resistance through inhibition of the non-essential stress kinase Yck2. Cell Chemical Biology, 27(3), 269–282.e5. https://doi.org/10.1016/j.chembiol.2019.12.008
  • Ciurea, C. N., Kosovski, I.-B., Mare, A. D., Toma, F., Pintea-Simon, I. A., & Man, A. (2020). Candida and candidiasis—Opportunism versus pathogenicity: A review of the virulence traits. Microorganisms, 8(6), 857. https://doi.org/10.3390/microorganisms8060857
  • da Silva Rocha, S. F. L., Olanda, C. G., Fokoue, H. H., & Sant’Anna, C. M. R. (2019). Virtual screening techniques in drug discovery: Review and recent applications. Current Topics in Medicinal Chemistry, 19(19), 1751–1767. https://doi.org/10.2174/1568026619666190816101948
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
  • Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
  • Essential Dynamics Sampling – GROMACS. (2023). 3 Documentation. https://manual.gromacs.org/current/reference-manual/algorithms/essential-dynamics.html
  • Hanks, S. K., & Hunter, T. (1995). The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification 1. FASEB Journal, 9(8), 576–596. https://doi.org/10.1096/fasebj.9.8.7768349
  • Houšť, J., Spížek, J., & Havlíček, V. (2020). Antifungal drugs. Metabolites, 10(3), 106. https://doi.org/10.3390/metabo10030106
  • Huang, J., & MacKerell, A. D. Jr. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
  • Ibe, C., & Munro, C. A. (2021). Fungal cell wall: An underexploited target for antifungal therapies. PLoS Pathogens, 17(4), e1009470. https://doi.org/10.1371/journal.ppat.1009470
  • Jung, S.-I., Rodriguez, N., Irrizary, J., Liboro, K., Bogarin, T., Macias, M., Eivers, E., Porter, E., Filler, S. G., & Park, H. (2017). Yeast casein kinase 2 governs morphology, biofilm formation, cell wall integrity, and host cell damage of Candida albicans. PLoS One, 12(11), e0187721. https://doi.org/10.1371/journal.pone.0187721
  • Kagami, L. P., das Neves, G. M., Timmers, L. F. S. M., Caceres, R. A., & Eifler-Lima, V. L. (2020). Geo-measures: A PyMOL plugin for protein structure ensembles analysis. Computational Biology and Chemistry, 87, 107322. https://doi.org/10.1016/j.compbiolchem.2020.107322
  • Labbé, C. M., Rey, J., Lagorce, D., Vavruša, M., Becot, J., Sperandio, O., Villoutreix, B. O., Tufféry, P., & Miteva, M. A. (2015). MTiOpenScreen: A web server for structure-based virtual screening. Nucleic Acids Research, 43(W1), W448–W454. https://doi.org/10.1093/nar/gkv306
  • Lagorce, D., Maupetit, J., Baell, J., Sperandio, O., Tufféry, P., Miteva, M. A., Galons, H., & Villoutreix, B. O. (2011). The FAF-Drugs2 server: A multistep engine to prepare electronic chemical compound collections. Bioinformatics (Oxford, England), 27(14), 2018–2020. https://doi.org/10.1093/bioinformatics/btr333
  • Lass-Flörl, C., & Steixner, S. (2023). The changing epidemiology of fungal infections. Molecular Aspects of Medicine, 95, 101240. https://doi.org/10.1016/j.mam.2023.101240
  • LeBlanc, E. V., Polvi, E. J., Veri, A. O., Privé, G. G., & Cowen, L. E. (2020). Structure-guided approaches to targeting stress responses in human fungal pathogens. Journal of Biological Chemistry, 295(42), 14458–14472. https://doi.org/10.1074/jbc.REV120.013731
  • Ledoux, M.-P., Herbrecht, R., Nett, J., Andes, D., Andes, D., Safdar, N., Baddley, J., Tissot, F., Agrawal, S., & Pagano, L. (2020). Antifungal therapy: New and evolving therapies. Thieme Medical Publishers, 41, 158–174.
  • Lee, Y., Puumala, E., Robbins, N., & Cowen, L. E. (2020). Antifungal drug resistance: Molecular mechanisms in Candida albicans and beyond. Chemical Reviews, 121(6), 3390–3411. https://doi.org/10.1021/acs.chemrev.0c00199
  • Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
  • Mateev, E., Valkova, I., Angelov, B., Georgieva, M., & Zlatkov, A. (2022). Validation through re-docking, cross-docking and ligand enrichment in various well-resoluted MAO-B receptors. International Journal of Pharmaceutical Sciences and Research, 13, 1099–1107.
  • MTiOpenScreen. (2024). https://bioserv.rpbs.univ-paris-diderot.fr/services/MTiOpenScreen/
  • Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2015). GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Computer Physics Communications, 186, 105–107. https://doi.org/10.1016/j.cpc.2014.09.010
  • Pathak, R. K., Kim, W.-I., & Kim, J.-M. (2023). Targeting the PEDV 3CL protease for identification of small molecule inhibitors: An insight from virtual screening, ADMET prediction, molecular dynamics, free energy landscape, and binding energy calculations. Journal of Biological Engineering, 17(1), 29. https://doi.org/10.1186/s13036-023-00342-y
  • Pathakumari, B., Liang, G., & Liu, W. (2020). Immune defence to invasive fungal infections: A comprehensive review. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 130, 110550. https://doi.org/10.1016/j.biopha.2020.110550
  • Perfect, J. R., & Ghannoum, M. (2020). Emerging issues in antifungal resistance. Infectious Disease Clinics of North America, 34(4), 921–943. https://doi.org/10.1016/j.idc.2020.05.003
  • Perlin, D. S., Rautemaa-Richardson, R., & Alastruey-Izquierdo, A. (2017). The global problem of antifungal resistance: Prevalence, mechanisms, and management. Lancet. Infectious Diseases, 17(12), e383–e392. https://doi.org/10.1016/S1473-3099(17)30316-X
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Rutherford, J. C., Bahn, Y.-S., Van Den Berg, B., Heitman, J., & Xue, C. (2019). Nutrient and stress sensing in pathogenic yeasts. Frontiers in Microbiology, 10, 442. https://doi.org/10.3389/fmicb.2019.00442
  • Saito, H., Nagao, H., Nishikawa, K., & Kinugawa, K. (2003). Molecular collective dynamics in solid para-hydrogen and ortho-deuterium: The Parrinello–Rahman-type path integral centroid molecular dynamics approach. Journal of Chemical Physics, 119(2), 953–963. https://doi.org/10.1063/1.1578474
  • Shapiro, R. S., Robbins, N., & Cowen, L. E. (2011). Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiology and Molecular Biology Reviews: MMBR, 75(2), 213–267. https://doi.org/10.1128/MMBR.00045-10
  • Shaw, D. E. (2020). Schrödinger Release 2020-4: Desmond Molecular Dynamics System.
  • Shukla, D., Alanazi, A. M., Panda, S. P., Dwivedi, V. D., & Kamal, M. A. (2023). Unveiling the antiviral potential of plant compounds from the Meliaceae family against the Zika virus through QSAR Modeling and MD simulation analysis. Journal of Biomolecular Structure & Dynamics, 1–16. https://doi.org/10.1080/07391102.2023.2259498
  • Talapko, J., Juzbašić, M., Matijević, T., Pustijanac, E., Bekić, S., Kotris, I., & Škrlec, I. (2021). Candida albicans—The virulence factors and clinical manifestations of infection. Journal of Fungi, 7(2), 79. https://doi.org/10.3390/jof7020079
  • Vanommeslaeghe, K., & MacKerell, A. D. Jr. (2012). Automation of the CHARMM general force field (CGenFF) I: Bond perception and atom typing. Journal of Chemical Information and Modeling, 52(12), 3144–3154. https://doi.org/10.1021/ci300363c
  • Venerando, A., Bustos, V. H., Pinna, L. A., & Cozza, G. (2022). Editorial: Casein kinases in human diseases. Frontiers in Molecular Biosciences, 9, 1094922. https://doi.org/10.3389/fmolb.2022.1094922
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
  • Wang, Y., Suzek, T., Zhang, J., Wang, J., He, S., Cheng, T., Shoemaker, B. A., Gindulyte, A., & Bryant, S. H. (2014). PubChem BioAssay: 2014 update. Nucleic Acids Research, 42(Database issue), D1075–D1082. https://doi.org/10.1093/nar/gkt978

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