Prediction of novel and potent inhibitors of lanosterol 14-α demethylase

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Bhattacharya, S., Sae-Tia, S., & Fries, B. C. (2020). Candidiasis and mechanisms of antifungal resistance. Antibiotics, 9(6), 312.
   Google Scholar
• Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466.
   PubMed Web of Science ®Google Scholar
• CDC. (2021). Invasive candidiasis statistics. Centers for disease control and preventions. https://www.cdc.gov/fungal/diseases/candidiasis/invasive/statistics.html
   Google Scholar
• Cleveland, A. A., Harrison, L. H., Farley, M. M., Hollick, R., Stein, B., Chiller, T. M., Lockhart, S. R., & Park, B. J. (2015). Declining incidence of candidemia and the shifting epidemiology of Candida resistance in two US metropolitan areas, 2008–2013:R from population-based surveillance. PLoS One. 10(3), e0120452. https://doi.org/10.1371/journal.pone.0120452
   PubMed Web of Science ®Google Scholar
• da Silva, A. W. S., & Vranken, W. F. (2012). ACPYPE-antechamber python parser interface. BMC Research Notes, 5(1), 367.
   PubMedGoogle Scholar
• El-Garhy, O. H. (2015). An overview of the azoles of interest. Int J Curr Pharm Res, 7(1), 1–6.
   Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749.
   PubMed Web of Science ®Google Scholar
• Fuentefria, A. M., Pippi, B., Dalla Lana, D. F., Donato, K. K., & de Andrade, S. F. (2018). Antifungals discovery: An insight into new strategies to combat antifungal resistance. Letters in Applied Microbiology, 66(1), 2–13.
   PubMed Web of Science ®Google Scholar
• GAFFI. (2015). Improving outcomes for patients with fungal infections across the world: A roadmap for the next decade. http://gaffi.org/wp-content/uploads/GAFFI_Road_Map_interactive-final0415.%0Apdf
   Google Scholar
• Hafidi, Z., El Achouri, M., O., Sousa, F. F., & Pérez, L. (2021). Antifungal activity of amino-alcohols based cationic surfactants and in silico, homology modeling, docking and molecular dynamics studies against lanosterol 14-α-demethylase enzyme. Journal of Biomolecular Structure and Dynamics, 1–17. https://doi.org/10.1080/07391102.2021.1902396
   Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759.
   PubMed Web of Science ®Google Scholar
• Hassan, Y., Chew, S. Y., & Than, L. T. L. (2021). Candida glabrata: Pathogenicity and resistance mechanisms for adaptation and survival. Journal of Fungi, 7(8), 667.
   Web of Science ®Google Scholar
• Huang, X., Pearce, R., Omenn, G. S., & Zhang, Y. (2021). Identification of 13 guanidinobenzoyl-or aminidinobenzoyl-containing drugs to potentially inhibit TMPRSS2 for COVID-19 treatment. International Journal of Molecular Sciences, 22(13), 7060.
   PubMed Web of Science ®Google Scholar
• Jacob, K., S., Ganguly, S., Kumar, P., Poddar, R., & Kumar, A. (2017). Homology model, molecular dynamics simulation and novel pyrazole analogs design of Candida albicans CYP450 lanosterol 14 $α$-demethylase, a target enzyme for antifungal therapy. Journal of Biomolecular Structure & Dynamics, 35(7), 1446–1463.
   PubMed Web of Science ®Google Scholar
• Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748.
   PubMed Web of Science ®Google Scholar
• Kaluzhskiy, L. A., Ershov, P. V., Yablokov, E. O., Mezentsev, Y. V., Gnedenko, O. V., Shkel, T. V., Gilep, A. A., Usanov, S. A., & Ivanov, A. S. (2021). Screening of potential non-azole inhibitors of lanosterol 14-alpha demethylase (CYP51) of the Сandida fungi. Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry, 15(3), 215–223.
   Google Scholar
• Keniya, M. V., Sabherwal, M., Wilson, R. K., Woods, M. A., Sagatova, A. A., Tyndall, J. D. A., & Monk, B. C. (2018). Crystal structures of full-length lanosterol 14$α$-demethylases of prominent fungal pathogens Candida albicans and Candida glabrata provide tools for antifungal discovery. Antimicrobial Agents and Chemotherapy, 62(11), e01134–18.
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Consortium, O. S. D. D., Lynn, A, & Open Source Drug Discovery Consortium. (2014). g_mmpbsa— A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. ACS Publications.
   Google Scholar
• Lockhart, S. R., Iqbal, N., Cleveland, A. A., Farley, M. M., Harrison, L. H., Bolden, C. B., Baughman, W., Stein, B., Hollick, R., Park, B. J., & Chiller, T. (2012). Species identification and antifungal susceptibility testing of Candida bloodstream isolates from population-based surveillance studies in two US cities from 2008 to 2011. Journal of Clinical Microbiology, 50(11), 3435–3442. https://doi.org/10.1128/JCM.01283-12
   PubMed Web of Science ®Google Scholar
• Ma, C.-M., Kully, M., Khan, J. K., Hattori, M., & Daneshtalab, M. (2007). Synthesis of chlorogenic acid derivatives with promising antifungal activity. Bioorganic & Medicinal Chemistry, 15(21), 6830–6833. https://doi.org/10.1016/j.bmc.2007.07.038
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234.
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., Sherman, W., Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234.
   PubMed Web of Science ®Google Scholar
• Mahindra, A., Sharma, K. K., Rathore, D., Khan, S. I., Jacob, M. R., & Jain, R. (2014). Synthesis and antimicrobial activities of His (2-aryl)-Arg and Trp-His (2-aryl) classes of dipeptidomimetics. MedChemComm, 5(5), 671–676.
   PubMed Web of Science ®Google Scholar
• Mota, S., Alves, R., Carneiro, C., Silva, S., Brown, A. J., Istel, F., Kuchler, K., Sampaio, P., Casal, M., Henriques, M., & Paiva, S. (2015). Candida glabrata susceptibility to antifungals and phagocytosis is modulated by acetate. Frontiers in Microbiology, 6, 919.
   PubMed Web of Science ®Google Scholar
• Newman, D. J., & Cragg, G. M. (2016). Natural products as sources of new drugs from 1981 to 2014. Journal of Natural Products, 79(3), 629–661. https://doi.org/10.1021/acs.jnatprod.5b01055
   PubMed Web of Science ®Google Scholar
• Release, S. (2019). Schrödinger release 2019-4: LigPrep. Schrödinger, LLC.
   Google Scholar
• Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. Journal of Molecular Biology, 178(1), 63–89. https://doi.org/10.1016/0022-2836(84)90231-6
   PubMed Web of Science ®Google Scholar
• Rana, R., Sharma, R., & Kumar, A. (2019). Repurposing of fluvastatin against Candida albicans CYP450 lanosterol 14 α-demethylase, a target enzyme for antifungal therapy: An in silico and in vitro study. Current Molecular Medicine, 19(7), 506–524.
   PubMed Web of Science ®Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Sayre, P. H., Finer-Moore, J. S., Fritz, T. A., Biermann, D., Gates, S. B., MacKellar, W. C., Patel, V. F., & Stroud, R. M. (2001). Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases. Journal of Molecular Biology, 313(4), 813–829.
   PubMed Web of Science ®Google Scholar
• Tahiri, O., Atmani-Kilani, D., Sanchez-Fidalgo, S., Aparicio-Soto, M., Alarcón-de-la-Lastra, C., Barrajón-Catalán, E., Micol, V., & Atmani, D. (2017). The flavonol-enriched Cistus albidus chloroform extract possesses in vivo anti-inflammatory and anti-nociceptive activity. Journal of Ethnopharmacology, 209, 210–218.
   PubMed Web of Science ®Google Scholar
• Timmermans, B., De Las Peñas, A., Castaño, I., & Van Dijck, P. (2018). Adhesins in Candida glabrata. Journal of Fungi, 4(2), 60.
   Web of Science ®Google Scholar
• Tudela, J. L. R., & Denning, D. W. (2017). Recovery from serious fungal infections should be realisable for everyone. The Lancet Infectious Diseases, 17(11), 1111–1113.
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174.
   PubMed Web of Science ®Google Scholar
• Wang, R., Lai, L., & Wang, S. (2002). Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-Aided Molecular Design, 16(1), 11–26.
   PubMed Web of Science ®Google Scholar
• Wang, S., Li, X., Chen, B., Li, S., Wang, J., Wang, J., Yang, M., Xu, X., Wang, H., & Yang, W. (2022). Dimension-enhanced ultra-high performance liquid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry combined with intelligent peak annotation for the rapid characterization of the multiple components from seeds of Descurainia sophia. Phyton, 91(3), 541. https://doi.org/10.32604/phyton.2022.018571
   Web of Science ®Google Scholar
• Warrilow, A. G., Parker, J. E., Kelly, D. E., & Kelly, S. L. (2013). Azole affinity of sterol 14α-demethylase (CYP51) enzymes from Candida albicans and Homo sapiens. Antimicrobial Agents and Chemotherapy, 57(3), 1352–1360.
   PubMed Web of Science ®Google Scholar