Modelación por homología y caracterización estructural in silico de la enzima lanosterol 14α-demetilasa de Cryptococcus neoformans var. Grubii
Keywords:
homology modelling, Cryptococcus neoformans, CYP51, heme groupAbstract
Cryptococcal meningitis mostly affect immunocompromised patients, whose pathogens have developed drug resistance mechanisms. Modern biotechnology has laid hands on theoretical-computational methods, since fight against these pathogens involves structural characterization of pharmacological targets. A refined homology model was built for enzyme CYP51 from Cryptococcus neoformans. Quality assessment confirmed model reliability: stereochemical analysis yielded 97,46 % of residues located in allowed regions of Ramachandran Plots; ProSA analysis placed the model within expected interval in Z-score scatter plot (Z-score = -8,34); distribution of 3D-1D correlation left 84,83 % of residues with average score ≥ 0,2. Two access tunnels towards active site were described, as well as heme cofactor inside catalytic pocket, whose interactions with surrounding residues points to a pronounced hydrophobicity of that region. Evolutionary analysis showed high conservation in residues forming the catalytic site. Computational site-directed generation of three reported point mutations allowed to gain an insight into azole-resistance mechanisms in the species.
References
BADIEE, P.; HASHEMIZADEH, Z. “Opportunistic invasive fungal infections: diagnosis & clinical management”. The Indian journal of medical research. 2014, 139 (2), 195-204. ISSN: 0971-5916.
DENNING, D.; BROMLEY, M. “How to bolster the antifungal pipeline”. Science. 2015, 347 (165), 1414-1416. ISSN: 0036-8075.
BERMAS, A.; GEDDES MCALISTER, J. “Combatting the evolution of antifungal resistance in Cryptococcus neoformans”. Molecular Microbiology. 2020, 114 (5), 721-734. ISSN: 0950-382X.
WILLIAMSON, P.R., et al. “Cryptococcal meningitis: epidemiology, immunology, diagnosis and therapy”. Nature reviews. Neurology.2017, 13 (1), 13-24. ISSN: 1759-4758.
HENDRICKSON, J.A., et al. “Antifungal resistance: a concerning trend for the present and future”. Current infectious disease reports. 2019, 21 (12), 47. ISSN: 1523-3847.
ZHU, X., et al. “Co-infection with respiratory pathogens among COVID-2019 cases”. Virus Research, 2020. 285, 198005. ISSN: 0168-1702.
MONK, B.C., et al. “Fungal Lanosterol 14α-demethylase: A target for next-generation antifungal design”. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics. 2020, 1868 (3), 140206. ISSN: 1570-9639.
ROSE, P.W., et al. “The RCSB Protein Data Bank: views of structural biology for basic and applied research and education”. Nucleic acids research. 2014, 43 (D1), D345-D356. ISSN: 1362-4962.
BOECKMANN, B., et al. “The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003”. Nucleic acids research. 2003, 31 (1), 365-370. ISSN: 1362-4962.
SHENG, C., et al. “Three-dimensional model of lanosterol 14α-demethylase from Cryptococcus neoformans: Active-site characterization and insights into azole binding”. Antimicrobial agents and chemotherapy. 2009, 53 (8), 3487-3495. ISSN: 0066-4804.
GASTEIGER, E., et al. “Protein identification and analysis tools on the ExPASy server”. In: Walker, J.M. (Ed.). The proteomics protocols handbook, 1st ed. New Jersey: Humana Press (Springer), 2005, pp. 571-607. ISBN: 978-1-59259-890-8.
BUCHAN, D.W.; JONES, D.T. “The PSI-PRED protein analysis workbench: 20 years on”. Nucleic acids research. 2019, 47 (W1), W402-W407. ISSN: 0305-1048.
FISER, A.; ŠALI, A. “Modeller: generation and refinement of homology-based protein structure models”. Methods in enzymology. 2003, 374, 461-491. ISSN: 0076-6879.
AN, J.-Y., et al. “Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix”. Oncotarget. 2016, 7 (50), 82440. ISSN: 1949-2553
PAPADOPOULOS, J.S.; AGARWALA, R. “COBALT: constraint-based alignment tool for multiple protein sequences”. Bioinformatics. 2007, 23 (9), 1073-1079. ISSN: 1460-2059.
PETTERSEN, E.F., et al. “UCSF Chimera: a visualization system for exploratory research and analysis”. Journal of computational chemistry. 2004, 25 (13), 1605-1612. ISSN: 1096-987X.
BHATTACHARYA, D.; CHENG, J. “3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization”. Proteins: Structure, Function, and Bioinformatics. 2013, 81 (1), 119-131. ISSN: 1097-0134.
BHATTACHARYA, D., et al. “3Drefine: an interactive web server for efficient protein structure refinement”. Nucleic acids research. 2016, 44 (W1), W406-W409. ISSN: 0305-1048.
LASKOWSKI, R.A., et al. “PROCHECK: a program to check the stereochemical quality of protein structures”. Journal of applied crystallography. 1993, 26 (2), 283-291. ISSN: 0021-8898.
WIEDERSTEIN, M.; SIPPL, M.J. “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins”. Nucleic acids research. 2007, 35 (suppl_2), W407-W410. ISSN: 1362-4962.
EISENBERG, D.; LÜTHY, R.; BOWIE, J.U. “[20]VERIFY3D: assessment of protein models with three-dimensional profiles”. In Carter, Ch.W.Jr.; Sweet, R.M. (Eds.). Methods in enzymology, 1st ed. Boston: Academic Press (Elsevier), 1997, Vol. 277, pp. 396-404. ISBN: 978-0-12-182178-4.
ASHKENAZY, H., et al. “ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules”. Nucleic acids research. 2016, 44 (W1), W344-W350. ISSN: 0305-1048.
LASKOWSKI, R.A.; SWINDELLS, M.B. “LigPlot+: multiple ligand–protein interaction diagrams for drug discovery”. Journal of chemical information and modeling. 2011, 51, 2778-2786. ISSN: 1549-9596.
CHOVANCOVA, E., et al. “CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures”. PLoS Comput Biol. 2012, 8 (10), e1002708. ISSN: 1553-7358.
GUCKEISEN, T.; HOSSEINPOUR, S.; PEUKERT, W. “Isoelectric points of proteins at the air/liquid interface and in solution”. Langmuir. 2019, 35 (14), 5004-5012. ISSN: 0743-7463.
GUO, X., et al. “Characterization of a highly thermostable and organic solvent-tolerant copper-containing polyphenol oxidase with dye-decolorizing ability from Kurthia huakuii LAM0618T”. PloS one. 2016, 11 (10), e0164810. ISSN: 1932-6203.
BOGDANOV, M.; DOWHAN, W.; VITRAC, H. “Lipids and topological rules governing membrane protein assembly”. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research. 2014, 1843 (8), 1475-1488. ISSN: 0167-4889.
ŠALI, A., et al. “Evaluation of comparative protein modeling by MODELLER”. Proteins: Structure, Function, and Bioinformatics. 1995, 23 (3), 318-326. ISSN: 1097-0134.
SCIOR, T.; QUIROGA-MONTES, I.; KAMMERER, B. “Inquiry of Literature Evidence for Induced Fit of Cytochrome P450 2C9 for Warfarin, Phenprocoumon, Flurbiprofen and Clopidogrel: A Critical Review”. SCIOL Biotechnol. 2018, 1, 30-48. ISSN: 2631-4061.
HONG, C.M., et al. “Conformational selection as the mechanism of guest binding in a flexible supramolecular host”. Journal of the American Chemical Society. 2017, 139 (23), 8013-8021. ISSN: 0002-7863.
BABAZADEH-QAZIJAHANI, M., et al. “Imidazolylchromanones containing non-benzylic oxime ethers: Synthesis and molecular modeling study of new azole antifungals selective against Cryptococcus gattii”. European Journal of Medicinal Chemistry. 2014, 76, 264-273. ISSN: 0223-5234.
SINGH, A.; KAUSHIK, R.; JAYARAM, B. “Quality Assessment of Protein Tertiary Structures: Past, Present, and Future”. In Shanker, A. (Ed.). Bioinformatics: Sequences, Structures. Phylogeny. Singapore: Springer Science & Business Media, 2018, pp. 271-288. ISBN: 978-981-13-1562-6.
BREZOVSKY, J.; KOZLIKOVA, B.; DAMBORSKY, J. “Computational analysis of protein tunnels and channels”. In Bornscheuer, U.T.; Höhne, M. (Eds.). Protein Engineering, 1st ed. New York: Humana Press (Springer), 2018, pp. 25-42. ISBN: 978-1-4939-7366-8
DE OLIVEIRA-CEITA, G., et al. “Analysis of the ergosterol biosynthesis pathway cloning, molecular characterization and phylogeny of lanosterol 14α-demethylase (ERG11) gene of Moniliophthora perniciosa”. Genetics and molecular biology. 2014, 37 (4), 683-693. ISSN: 1415-4757.
SELB, R., et al. “Molecular typing and in vitro resistance of Cryptococcus neoformans clinical isolates obtained in Germany between 2011 and 2017”. International Journal of Medical Microbiology. 2019, 309 (6), 151336. ISSN: 1438-4221.
SAGATOVA, A.A., et al. “Structural insights into binding of the antifungal drug fluconazole to Saccharomyces cerevisiae lanosterol 14α-demethylase”. Antimicrobial agents and chemotherapy. 2015, 59 (8), 4982-4989. ISSN: 0066-4804.
Downloads
Published
How to Cite
Issue
Section
License
This journal provides immediate open access to its content, based on the principle that offering the public free access to research helps a greater global exchange of knowledge. Each author is responsible for the content of each of their articles.
