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de Almeida OGG, von Zeska Kress MR. Harnessing Machine Learning to Uncover Hidden Patterns in Azole-Resistant CYP51/ERG11 Proteins. Microorganisms 2024; 12:1525. [PMID: 39203367 PMCID: PMC11356363 DOI: 10.3390/microorganisms12081525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Fungal resistance is a public health concern due to the limited availability of antifungal resources and the complexities associated with treating persistent fungal infections. Azoles are thus far the primary line of defense against fungi. Specifically, azoles inhibit the conversion of lanosterol to ergosterol, producing defective sterols and impairing fluidity in fungal plasmatic membranes. Studies on azole resistance have emphasized specific point mutations in CYP51/ERG11 proteins linked to resistance. Although very insightful, the traditional approach to studying azole resistance is time-consuming and prone to errors during meticulous alignment evaluation. It relies on a reference-based method using a specific protein sequence obtained from a wild-type (WT) phenotype. Therefore, this study introduces a machine learning (ML)-based approach utilizing molecular descriptors representing the physiochemical attributes of CYP51/ERG11 protein isoforms. This approach aims to unravel hidden patterns associated with azole resistance. The results highlight that descriptors related to amino acid composition and their combination of hydrophobicity and hydrophilicity effectively explain the slight differences between the resistant non-wild-type (NWT) and WT (nonresistant) protein sequences. This study underscores the potential of ML to unravel nuanced patterns in CYP51/ERG11 sequences, providing valuable molecular signatures that could inform future endeavors in drug development and computational screening of resistant and nonresistant fungal lineages.
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Affiliation(s)
| | - Marcia Regina von Zeska Kress
- Faculdade de Ciências Farmacêuticas de Ribeirao Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, SP, Brazil;
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2
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Ribeiro dos Santos A, Gade L, Misas E, Litvintseva AP, Nunnally NS, Parnell LA, Rajeev M, de Souza Carvalho Melhem M, Takahashi JPF, Oliboni GM, Bonfieti LX, Araujo LS, Cappellano P, Venturini J, Lockhart SR, Sexton DJ. Bimodal distribution of azole susceptibility in Sporothrix brasiliensis isolates in Brazil. Antimicrob Agents Chemother 2024; 68:e0162023. [PMID: 38385701 PMCID: PMC10989022 DOI: 10.1128/aac.01620-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Sporothrix brasiliensis is an emerging zoonotic fungal pathogen that can be difficult to treat. Antifungal susceptibility testing was performed on the mold phase of a convenience sample of 61 Sporothrix spp. isolates from human and cat sporotrichosis cases in Brazil using the Clinical and Laboratory Standards Institute standard M38. A bimodal distribution of azole susceptibility was observed with 50% (28/56) of S. brasiliensis isolates showing elevated itraconazole minimum inhibitory concentrations ≥16 µg/mL. Phylogenetic analysis found the in vitro resistant isolates were not clonal and were distributed across three different S. brasiliensis clades. Single nucleotide polymorphism (SNP) analysis was performed to identify potential mechanisms of in vitro resistance. Two of the 28 resistant isolates (MIC ≥16 mg/L) had a polymorphism in the cytochrome P450 gene, cyp51, corresponding to the well-known G448S substitution inducing azole resistance in Aspergillus fumigatus. SNPs corresponding to other known mechanisms of azole resistance were not identified in the remaining 26 in vitro resistant isolates.
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Affiliation(s)
- Amanda Ribeiro dos Santos
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elizabeth Misas
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Natalie S. Nunnally
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lindsay A. Parnell
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Malavika Rajeev
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marcia de Souza Carvalho Melhem
- School of Medicine, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
- Graduate Program in Tropical Diseases, Universidade Estadual Paulista, Botucatu, SP, Brazil
- Parasitology and Mycology Center, Instituto Adolfo Lutz, São Paulo, SP, Brazil
| | - Juliana Possato Fernandes Takahashi
- School of Medicine, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
- Parasitology and Mycology Center, Instituto Adolfo Lutz, São Paulo, SP, Brazil
| | - Gabriel Manzi Oliboni
- Graduate Program in Sciences, Coordenadoria de Controle de Doenças, Secretary of Health, São Paulo, Brazil
| | | | - Lisandra Siufi Araujo
- Central Public Health Laboratory of Mato Grosso do Sul, Secretary of Health, Campo Grande, MS, Brazil
| | | | - James Venturini
- School of Medicine, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Shawn R. Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - D. Joseph Sexton
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Gómez-Gaviria M, Martínez-Álvarez JA, Mora-Montes HM. Current Progress in Sporothrix brasiliensis Basic Aspects. J Fungi (Basel) 2023; 9:jof9050533. [PMID: 37233242 DOI: 10.3390/jof9050533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
Sporotrichosis is known as a subacute or chronic infection, which is caused by thermodimorphic fungi of the genus Sporothrix. It is a cosmopolitan infection, which is more prevalent in tropical and subtropical regions and can affect both humans and other mammals. The main etiological agents causing this disease are Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa, which have been recognized as members of the Sporothrix pathogenic clade. Within this clade, S. brasiliensis is considered the most virulent species and represents an important pathogen due to its distribution and prevalence in different regions of South America, such as Brazil, Argentina, Chile, and Paraguay, and Central American countries, such as Panama. In Brazil, S. brasiliensis has been of great concern due to the number of zoonotic cases that have been reported over the years. In this paper, a detailed review of the current literature on this pathogen and its different aspects will be carried out, including its genome, pathogen-host interaction, resistance mechanisms to antifungal drugs, and the caused zoonosis. Furthermore, we provide the prediction of some putative virulence factors encoded by the genome of this fungal species.
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Affiliation(s)
- Manuela Gómez-Gaviria
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, Guanajuato 36050, Mexico
| | - José A Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, Guanajuato 36050, Mexico
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, Guanajuato 36050, Mexico
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4
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Bombassaro A, Spruijtenburg B, Medeiros F, Jacomel Favoreto de Souza Lima B, Ballardin LB, Farias MRD, Vicente VA, de Queiroz‐Telles F, Meis JF, de Groot T. Genotyping and antifungal susceptibility testing of
Sporothrix brasiliensis
isolates from Southern Brazil. Mycoses 2023. [DOI: 10.1111/myc.13584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
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5
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De Carolis E, Posteraro B, Sanguinetti M. Old and New Insights into Sporothrix schenckii Complex Biology and Identification. Pathogens 2022; 11:pathogens11030297. [PMID: 35335621 PMCID: PMC8948913 DOI: 10.3390/pathogens11030297] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Sporothrix schenckii is a worldwide-distributed thermally dimorphic fungus, which usually causes a subacute to chronic infection through traumatic implantation or inoculation of its infectious propagules. The fungus encompasses a group of phylogenetically closely related species, thus named the S. schenckii complex, of which S. schenckii sensu stricto and S. brasiliensis are main causative species of sporotrichosis. Owing to a multifaceted molecular dynamic, the S. schenckii complex can switch between the mycelium and the yeast form. This characteristic along with a varying cell wall composition account for significant species-specific differences in the host range, virulence, and susceptibility to antifungal drugs. While culture remains the gold standard to diagnose sporotrichosis, polymerase chain reaction (PCR) or matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry-based methods have become an essential for accurate species identification in many clinical laboratories. If directly applied on tissue samples, molecular methods are helpful to improve both sensitivity of and time to the etiological diagnosis of sporotrichosis. This mini-review aims to put together the old and new knowledge on the S. schenckii complex biology and identification, with particular emphasis on the laboratory diagnosis-related aspects of disease.
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Affiliation(s)
- Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
- Correspondence:
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
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6
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Zhang Q, Qu Z, Zhou Y, Zhou J, Yang J, Li S, Xu Q, Zhou X. In vitro study on the effect of cornin on the activity of cytochrome P450 enzymes. BMC Complement Med Ther 2021; 21:138. [PMID: 33966625 PMCID: PMC8108370 DOI: 10.1186/s12906-021-03309-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Cornin is a commonly used herb in cardiology for its cardioprotective effect. The effect of herbs on the activity of cytochrome P450 enzymes (CYP450s) can induce adverse drug-drug interaction even treatment failure. Therefore, it is necessary to investigate the effect of cornin on the activity of CYP450s, which can provide more guidance for the clinical application of cornin. Methods Cornin (100 μM) was incubated with eight isoforms of CYP450s, including CYP1A2, 2A6, 3A4, 2C8, 2C9, 2C19, 2D6, and 2E1, in pooled human liver microsomes. The inhibition model and corresponding parameters were also investigated. Results Cornin exerted significant inhibitory effect on the activity of CYP3A4, 2C9, and 2E1 in a dose-dependent manner with the IC50 values of 9.20, 22.91, and 14.28 μM, respectively (p < 0.05). Cornin inhibited the activity of CYP3A4 non-competitively with the Ki value of 4.69 μM, while the inhibition of CYP2C9 and 2E1 by cornin was competitive with the Ki value of 11.31 and 6.54 μM, respectively. Additionally, the inhibition of CYP3A4 by cornin was found to be time-dependent with the KI/Kinact value of 6.40/0.055 min− 1·μM− 1. Conclusions The inhibitory effect of cornin on the activity of CYP3A4, 2C9, and 2E1 indicated the potential drug-drug interaction between cornin and drugs metabolized by these CYP450s, which needs further investigation and validation.
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Affiliation(s)
- Qun Zhang
- Shanghai Baoshan Aged-nursing hospital, Shanghai, 201900, China
| | - Zengqiang Qu
- Department of Invasive Technology, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, China
| | - Yanqing Zhou
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.,Clinical research center, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Jin Zhou
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.,Clinical research center, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Junwei Yang
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.,Clinical research center, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Shengjian Li
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.,Clinical research center, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Qiuping Xu
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
| | - Xuedong Zhou
- Clinical research center, Shanghai Baoshan Luodian Hospital, No.121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
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7
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Shang J, Ma S, Zang C, Bao X, Wang Y, Zhang D. Gut microbiota mediates the absorption of FLZ, a new drug for Parkinson's disease treatment. Acta Pharm Sin B 2021; 11:1213-1226. [PMID: 34094829 PMCID: PMC8148066 DOI: 10.1016/j.apsb.2021.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/04/2020] [Accepted: 11/03/2020] [Indexed: 01/07/2023] Open
Abstract
The gut microbiota plays an important role in regulating the pharmacokinetics and pharmacodynamics of many drugs. FLZ, a novel squamosamide derivative, has been shown to have neuroprotective effects on experimental Parkinson's disease (PD) models. FLZ is under phase Ⅰ clinical trial now, while the underlying mechanisms contributing to the absorption of FLZ are still not fully elucidated. Due to the main metabolite of FLZ was abundant in feces but rare in urine and bile of mice, we focused on the gut microbiota to address how FLZ was metabolized and absorbed. In vitro studies revealed that FLZ could be exclusively metabolized to its major metabolite M1 by the lanosterol 14 alpha-demethylase (CYP51) in the gut microbiota, but was almost not metabolized by any other metabolism-related organs, such as liver, kidney, and small intestine. M1 was quickly absorbed into the blood and then remethylated to FLZ by catechol O-methyltransferase (COMT). Notably, dysbacteriosis reduced the therapeutic efficacy of FLZ on the PD mouse model by inhibiting its absorption. The results show that the gut microbiota mediate the absorption of FLZ through a FLZ-M1-FLZ circulation. Our research elucidates the vital role of the gut microbiota in the absorption of FLZ and provides a theoretical basis for clinical pharmacokinetic studies and clinical application of FLZ in the treatment of PD.
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Affiliation(s)
| | | | | | - Xiuqi Bao
- Corresponding authors. Tel./fax: +86 10 63165203.
| | - Yan Wang
- Corresponding authors. Tel./fax: +86 10 63165203.
| | - Dan Zhang
- Corresponding authors. Tel./fax: +86 10 63165203.
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8
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Msomi NN, Padayachee T, Nzuza N, Syed PR, Kryś JD, Chen W, Gront D, Nelson DR, Syed K. In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria. Molecules 2021; 26:1538. [PMID: 33799696 PMCID: PMC7998510 DOI: 10.3390/molecules26061538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.
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Affiliation(s)
- Ntombizethu Nokuphiwa Msomi
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Puleng Rosinah Syed
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Justyna Dorota Kryś
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
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9
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Waller SB, Dalla Lana DF, Quatrin PM, Ferreira MRA, Fuentefria AM, Mezzari A. Antifungal resistance on Sporothrix species: an overview. Braz J Microbiol 2021; 52:73-80. [PMID: 32476087 PMCID: PMC7966672 DOI: 10.1007/s42770-020-00307-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION The treatment of human and animal sporotrichosis is often performed with antifungal agents; however, the emergence of antifungal-resistant strains of Sporothrix species has been reported. We aimed to discuss the ability of Sporothrix species in developing resistance to the conventional antifungals and mechanisms for this. METHODOLOGY Published data on databases (PubMed, Science Direct, Google Scholar) were investigated using a combination of keywords from 2008 to 2019 by the StArt tool. RESULTS The minimal inhibitory concentrations values based on the Clinical and Laboratory Standards Institute (CLSI) from eight references were classified according to the epidemiological cutoff values in wild-type or non-wild-type strains. In this way, non-wild-type S. schenckii and, mainly, S. brasiliensis isolates were recognized on itraconazole, amphotericin B, terbinafine, and voriconazole, which are strains that deserve more attention toward antifungal control, with a probable risk of mutation to antifungal resistance. Among the few reviewed studied on antifungal resistance, the melanin production capacity (DHN-melanin, L-DOPA melanin, and pyomelanin), the low genetic diversity due to the abnormal number of chromosomes, and the mutation in cytochrome P450 are some of the factors for developing resistance mechanism. CONCLUSIONS The emergence of Sporothrix species with in vitro antifungal resistance was evidenced and the possible mechanisms for resistance development may be due to the melanin production capacity, genetic diversity and mutations in cytochrome P450. Further studies should be carried out targeting gene expression for the development of antifungal resistance on Sporothrix species in order to prospect new therapeutic targets for human and veterinary use.
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Affiliation(s)
- Stefanie Bressan Waller
- Department of Preventive Veterinary, Faculty of Veterinary, Federal University of Pelotas, Pelotas, RS, 96010-900, Brazil.
| | - Daiane Flores Dalla Lana
- Postgraduate Program in Pathology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, RS, Brazil
| | - Priscilla Maciel Quatrin
- Postgraduate Program in Agricultural and Environmental Microbiology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | - Adelina Mezzari
- Department of Analysis, Faculty of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Ji X, Ding B, Wu X, Liu F, Yang F. In vitro study on the effect of ophiopogonin D on the activity of cytochrome P450 enzymes. Xenobiotica 2020; 51:262-267. [PMID: 33115303 DOI: 10.1080/00498254.2020.1842941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ophiopogonin D is a commonly used herb in cardiology and pediatrics for its variuos pharmacological effects. It is necessary to investigate the effect of ophiopogonin D on the activity of cytochrome P450 enzymes (CYP450s) to provide more guidance for the clinical application of ophiopogonin D. Eight isoforms of CYP450s, including CYP1A2, 2A6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4 were incubated with 100 μM ophiopogonin D in pooled human liver microsomes. The inhibition model and corresponding parameters were also investigated. Ophiopogonin D exerted a significant inhibitory effect on the activity of CYP3A4, 2C9, and 2E1 in a dose-dependent manner with the IC50 values of 8.08, 12.92, and 22.72 μM, respectively (p < 0.05). The inhibition of CYP3A4 by ophiopogonin D was performed non-competitively and time-dependently with the Ki value of 4.08 μM and the KI/Kinact value of 5.02/0.050 min-1·μM-1. Whereas, ophiopogonin D acts as a competitive inhibitor of CYP2E1 and 2C9 with the Ki value of 6.69 and 11.07 μM, respectively. The inhibitory effect of ophiopogonin D on the activity of CYP3A4, 2C9, and 2E1 indicated the potential drug-drug interaction between ophiopogonin D and drugs metabolized by these CYP450s, which needs further in vivo investigation and validation.
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Affiliation(s)
- Xiaofei Ji
- Department of Pediatrics, Weifang Yidu Central Hospital, Weifang, China
| | - Baodong Ding
- Department of Pediatrics, Weifang Yidu Central Hospital, Weifang, China
| | - Xiaoyou Wu
- Department of Pediatrics, Weifang Yidu Central Hospital, Weifang, China
| | - Fengyi Liu
- Qingzhou Dongxia Central Health Center, Weifang, China
| | - Fengqi Yang
- Department of Pediatrics, Qujing First People's Hospital at Kunming Medical University, Qujing, China
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11
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Padayachee T, Nzuza N, Chen W, Nelson DR, Syed K. Impact of lifestyle on cytochrome P450 monooxygenase repertoire is clearly evident in the bacterial phylum Firmicutes. Sci Rep 2020; 10:13982. [PMID: 32814804 PMCID: PMC7438502 DOI: 10.1038/s41598-020-70686-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms' primary and secondary metabolism. Research on eukaryotes such as animals, plants, oomycetes and fungi has shown that P450s profiles in these organisms are affected by their lifestyle. However, the impact of lifestyle on P450 profiling in bacteria is scarcely reported. This study is such an example where the impact of lifestyle seems to profoundly affect the P450 profiles in the bacterial species belonging to the phylum Firmicutes. Genome-wide analysis of P450s in 972 Firmicutes species belonging to 158 genera revealed that only 229 species belonging to 37 genera have P450s; 38% of Bacilli species, followed by 14% of Clostridia and 2.7% of other Firmicutes species, have P450s. The pathogenic or commensal lifestyle influences P450 content to such an extent that species belonging to the genera Streptococcus, Listeria, Staphylococcus, Lactobacillus, Lactococcus and Leuconostoc do not have P450s, with the exception of a handful of Staphylococcus species that have a single P450. Only 18% of P450s are found to be involved in secondary metabolism and 89 P450s that function in the synthesis of specific secondary metabolites are predicted. This study is the first report on comprehensive analysis of P450s in Firmicutes.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa.
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Ngcobo NS, Chiliza ZE, Chen W, Yu JH, Nelson DR, Tuszynski JA, Preto J, Syed K. Comparative Analysis, Structural Insights, and Substrate/Drug Interaction of CYP128A1 in Mycobacterium tuberculosis. Int J Mol Sci 2020; 21:E4816. [PMID: 32650369 PMCID: PMC7404182 DOI: 10.3390/ijms21144816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are well known for their role in organisms' primary and secondary metabolism. Among 20 P450s of the tuberculosis-causing Mycobacterium tuberculosis H37Rv, CYP128A1 is particularly important owing to its involvement in synthesizing electron transport molecules such as menaquinone-9 (MK9). This study employs different in silico approaches to understand CYP128 P450 family's distribution and structural aspects. Genome data-mining of 4250 mycobacterial species has revealed the presence of 2674 CYP128 P450s in 2646 mycobacterial species belonging to six different categories. Contrast features were observed in the CYP128 gene distribution, subfamily patterns, and characteristics of the secondary metabolite biosynthetic gene cluster (BGCs) between M. tuberculosis complex (MTBC) and other mycobacterial category species. In all MTBC species (except one) CYP128 P450s belong to subfamily A, whereas subfamily B is predominant in another four mycobacterial category species. Of CYP128 P450s, 78% was a part of BGCs with CYP124A1, or together with CYP124A1 and CYP121A1. The CYP128 family ranked fifth in the conservation ranking. Unique amino acid patterns are present at the EXXR and CXG motifs. Molecular dynamic simulation studies indicate that the CYP128A1 bind to MK9 with the highest affinity compared to the azole drugs analyzed. This study provides comprehensive comparative analysis and structural insights of CYP128A1 in M. tuberculosis.
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Affiliation(s)
- Nokwanda Samantha Ngcobo
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
| | - Zinhle Edith Chiliza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Jack A. Tuszynski
- Department of Physics and Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino TO, Italy
| | - Jordane Preto
- Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69622 Lyon, France
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
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Feline sporotrichosis: a case series of itraconazole-resistant Sporothrix brasiliensis infection. Braz J Microbiol 2020; 52:163-171. [PMID: 32388779 DOI: 10.1007/s42770-020-00290-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
The treatment of feline sporotrichosis is a challenge for veterinary clinicians since refractory cases may occur, due either to patient and/or to pharmacological management errors or due to the development of antifungal resistance. Thus, we aimed to describe the therapeutic history of feline cases infected by itraconazole-resistant Sporothrix brasiliensis in an endemic region of Southern Brazil. Medical records of cats attended at the Veterinary Clinic Hospital (Pelotas/RS, Brazil) between 2016 and 2017 were reviewed. Twelve cases of infection by S. brasiliensis with that showed high minimum inhibitory concentration (MIC) values (≥ 4 μg/mL) to itraconazole by M38-A2 of CLSI were selected. At the hospital consultation, disseminated (cats 1-l0, 12) and localized (cat 11) skin lesions remained in the cats, even after treatment with fluconazole, ketoconazole (02/12), and itraconazole (ITZ, 09/12) performed before this study. High doses (25-100 mg/kg/day) of ITZ for up to 4 months (03/12, cats 2, 6, 12) or over 12 months (05/12, cats 1, 5, 7, 8, 11) did not provide a clinical cure, except for the association of ITZ plus potassium iodide (01/12, cat 12) for 3 months, which proved useful in infections with itraconazole-resistant S. brasiliensis. However, the combined issues of abandonment of therapy by owners for financial reasons, difficulties surrounding therapy administration (03/12, cats 6, 11, 12), and the inappropriate choice of medication (01/12, cat 6), together reflect the reality of this endemic region, which greatly compromises clinical healing. This study highlighted the occurrence of refractory cases by itraconazole-resistant S. brasiliensis in cats from Southern Brazil, as well as the abandonment of treatment and therapeutic errors. We warn of the need for antifungal susceptibility tests to adapt therapeutic protocols in feline sporotrichosis.
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Hussain R, Ahmed M, Khan TA, Akhter Y. Fungal P 450 monooxygenases - the diversity in catalysis and their promising roles in biocontrol activity. Appl Microbiol Biotechnol 2019; 104:989-999. [PMID: 31858195 DOI: 10.1007/s00253-019-10305-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/28/2019] [Accepted: 12/08/2019] [Indexed: 02/08/2023]
Abstract
The fungal P450s catalyze vital monooxygenation reactions in primary and secondary metabolism, which may lead to the production of diverse secondary metabolites. Many of these, such as from the family of trichothecenes, involve in biocontrol activities. The diversified nature of fungal P450 monooxygenases makes their host organisms adoptable to various ecological niches. The available genome data analysis provided an insight into the activity and mechanisms of the fungal P450s. However, still more structural and functional studies are needed to elucidate the details of its catalytic mechanism, and the advance studies are also required to decipher further about their dynamic role in various aspects of trichothecene oxygenations. This mini review will provide updated information on different fungal P450 monooxygenases, their genetic diversity, and their role in catalyzing various biochemical reactions leading to the production of plant growth promoting secondary metabolites.
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Affiliation(s)
- Razak Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Mushtaq Ahmed
- Department of Environmental Science, School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh, 176206, India
| | - Tabreiz Ahmad Khan
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India.
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Distribution and Diversity of Cytochrome P450 Monooxygenases in the Fungal Class Tremellomycetes. Int J Mol Sci 2019; 20:ijms20122889. [PMID: 31200551 PMCID: PMC6627453 DOI: 10.3390/ijms20122889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/25/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
Tremellomycetes, a fungal class in the subphylum Agaricomycotina, contain well-known opportunistic and emerging human pathogens. The azole drug fluconazole, used in the treatment of diseases caused by some species of Tremellomycetes, inhibits cytochrome P450 monooxygenase CYP51, an enzyme that converts lanosterol into an essential component of the fungal cell membrane ergosterol. Studies indicate that mutations and over-expression of CYP51 in species of Tremellomycetes are one of the reasons for fluconazole resistance. Moreover, the novel drug, VT-1129, that is in the pipeline is reported to exert its effect by binding and inhibiting CYP51. Despite the importance of CYPs, the CYP repertoire in species of Tremellomycetes has not been reported to date. This study intends to address this research gap. Comprehensive genome-wide CYP analysis revealed the presence of 203 CYPs (excluding 16 pseudo-CYPs) in 23 species of Tremellomycetes that can be grouped into 38 CYP families and 72 CYP subfamilies. Twenty-three CYP families are new and three CYP families (CYP5139, CYP51 and CYP61) were conserved across 23 species of Tremellomycetes. Pathogenic cryptococcal species have 50% fewer CYP genes than non-pathogenic species. The results of this study will serve as reference for future annotation and characterization of CYPs in species of Tremellomycetes.
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Similarities, variations, and evolution of cytochrome P450s in Streptomyces versus Mycobacterium. Sci Rep 2019; 9:3962. [PMID: 30850694 PMCID: PMC6408508 DOI: 10.1038/s41598-019-40646-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 02/21/2019] [Indexed: 11/18/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) found in all domains of life are known for their catalytic versatility and stereo- and regio-specific activity. While the impact of lifestyle on P450 evolution was reported in many eukaryotes, this remains to be addressed in bacteria. In this report, Streptomyces and Mycobacterium, belonging to the phylum Actinobacteria, were studied owing to their contrasting lifestyles and impacts on human. Analyses of all P450s and those predicted to be associated with secondary metabolism have revealed that different lifestyles have affected the evolution of P450s in these bacterial genera. We have found that while species in both genera have essentially the same number of P450s in the genome, Streptomyces P450s are much more diverse than those of Mycobacterium. Moreover, despite both belonging to Actinobacteria, only 21 P450 families were common, and 123 and 56 families were found to be unique to Streptomyces and Mycobacterium, respectively. The presence of a large and diverse number of P450s in Streptomyces secondary metabolism contributes to antibiotic diversity, helping to secure the niche. Conversely, based on the currently available functional data, types of secondary metabolic pathways and associated P450s, mycobacterial P450s seem to play a role in utilization or synthesis of lipids.
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Ngwenya ML, Chen W, Basson AK, Shandu JS, Yu JH, Nelson DR, Syed K. Blooming of Unusual Cytochrome P450s by Tandem Duplication in the Pathogenic Fungus Conidiobolus coronatus. Int J Mol Sci 2018; 19:ijms19061711. [PMID: 29890717 PMCID: PMC6032100 DOI: 10.3390/ijms19061711] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 11/16/2022] Open
Abstract
While the Zygomycete fungus Conidiobolus coronatus primarily infects insects, it can be pathogenic to mammals as well, including humans. High variability in the treatment of this fungal infection with currently available drugs, including azole drugs is a very common phenomenon. Azoles bind to the cytochrome P450 monooxygenases (P450s/CYP) including CYP51, a sterol 14-α-demethylase, inhibiting the synthesis of cell membrane ergosterol and thus leading to the elimination of infecting fungi. Despite P450’s role as a drug target, to date, no information on C. coronatus P450s has been reported. Genome-wide data mining has revealed the presence of 142 P450s grouped into 12 families and 21 subfamilies in C. coronatus. Except for CYP51, the remaining 11 P450 families are new (CYP5854-CYP5864). Despite having a large number of P450s among entomopathogenic fungi, C. coronatus has the lowest number of P450 families, which suggests blooming P450s. Further analysis has revealed that 79% of the same family P450s is tandemly positioned, suggesting that P450 tandem duplication led to the blooming of P450s. The results of this study; i.e., unravelling the C. coronatus P450 content, will certainly help in designing experiments to understand P450s’ role in C. coronatus physiology, including a highly variable response to azole drugs with respect to P450s.
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Affiliation(s)
- Mathula Lancelot Ngwenya
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Albert Kotze Basson
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Jabulani Siyabonga Shandu
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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