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Pierdominici‐Sottile G, Palma J, Ferrelli ML, Sobrado P. The dynamics of the flavin, NADPH, and active site loops determine the mechanism of activation of class B flavin-dependent monooxygenases. Protein Sci 2024; 33:e4935. [PMID: 38501462 PMCID: PMC10962481 DOI: 10.1002/pro.4935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Flavin-dependent monooxygenases (FMOs) constitute a diverse enzyme family that catalyzes crucial hydroxylation, epoxidation, and Baeyer-Villiger reactions across various metabolic pathways in all domains of life. Due to the intricate nature of this enzyme family's mechanisms, some aspects of their functioning remain unknown. Here, we present the results of molecular dynamics computations, supplemented by a bioinformatics analysis, that clarify the early stages of their catalytic cycle. We have elucidated the intricate binding mechanism of NADPH and L-Orn to a class B monooxygenase, the ornithine hydroxylase fromAspergillus $$ Aspergillus $$ fumigatus $$ fumigatus $$ known as SidA. Our investigation involved a comprehensive characterization of the conformational changes associated with the FAD (Flavin Adenine Dinucleotide) cofactor, transitioning from the out to the in position. Furthermore, we explored the rotational dynamics of the nicotinamide ring of NADPH, shedding light on its role in facilitating FAD reduction, supported by experimental evidence. Finally, we also analyzed the extent of conservation of two Tyr-loops that play critical roles in the process.
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Affiliation(s)
- Gustavo Pierdominici‐Sottile
- Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
| | - Juliana Palma
- Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
| | - María Leticia Ferrelli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP‐CONICET), Facultad de Ciencias ExactasUniversidad Nacional de La PlataLa PlataBuenos AiresArgentina
| | - Pablo Sobrado
- Department of BiochemistryVirginia TechBlacksburgVirginiaUSA
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Happacher I, Aguiar M, Yap A, Decristoforo C, Haas H. Fungal siderophore metabolism with a focus on Aspergillus fumigatus: impact on biotic interactions and potential translational applications. Essays Biochem 2023; 67:829-842. [PMID: 37313590 PMCID: PMC10500206 DOI: 10.1042/ebc20220252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Iron is an essential trace element that is limiting in most habitats including hosts for fungal pathogens. Siderophores are iron-chelators synthesized by most fungal species for high-affinity uptake and intracellular handling of iron. Moreover, virtually all fungal species including those lacking siderophore biosynthesis appear to be able to utilize siderophores produced by other species. Siderophore biosynthesis has been shown to be crucial for virulence of several fungal pathogens infecting animals and plants revealing induction of this iron acquisition system during virulence, which offers translational potential of this fungal-specific system. The present article summarizes the current knowledge on the fungal siderophore system with a focus on Aspergillus fumigatus and its potential translational application including noninvasive diagnosis of fungal infections via urine samples, imaging of fungal infections via labeling of siderophores with radionuclides such as Gallium-68 for detection with positron emission tomography, conjugation of siderophores with fluorescent probes, and development of novel antifungal strategies.
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Affiliation(s)
- Isidor Happacher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Mario Aguiar
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Annie Yap
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Clemens Decristoforo
- Department of Nuclear Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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Ng JPL, Han Y, Yang LJ, Birkholtz LM, Coertzen D, Wong HN, Haynes RK, Coghi P, Wong VKW. Antimalarial and antitumour activities of the steroidal quinone-methide celastrol and its combinations with artemiside, artemisone and methylene blue. Front Pharmacol 2022; 13:988748. [PMID: 36120293 PMCID: PMC9479156 DOI: 10.3389/fphar.2022.988748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Artemisinin, isolated from the traditional Chinese medicinal plant qīng hāo 青蒿 (Artemisia annua) and its derivatives are used for treatment of malaria. With treatment failures now being recorded for the derivatives and companion drugs used in artemisinin combination therapies new drug combinations are urgently required. The amino-artemisinins artemiside and artemisone display optimal efficacies in vitro against asexual and sexual blood stages of the malaria parasite Plasmodium falciparum and are active against tumour cell lines. In continuing the evolution of combinations of the amino-artemisinins with new drugs, we examine the triterpenoid quinone methide celastrol isolated from the traditional Chinese medicinal plant léi gōng téng 雷公藤 (Tripterygium wilfordii). This compound is redox active, and has attracted considerable attention because of potent biological activities against manifold targets. We report that celastrol displays good IC50 activities ranging from 0.50–0.82 µM against drug-sensitive and resistant asexual blood stage Pf, and 1.16 and 0.28 µM respectively against immature and late stage Pf NF54 gametocytes. The combinations of celastrol with each of artemisone and methylene blue against asexual blood stage Pf are additive. Given that celastrol displays promising antitumour properties, we examined its activities alone and in combinations with amino-artemisinins against human liver HepG2 and other cell lines. IC50 values of the amino-artemisinins and celastrol against HepG2 cancer cells ranged from 0.55–0.94 µM. Whereas the amino-artemisinins displayed notable selectivities (SI > 171) with respect to normal human hepatocytes, in contrast, celastrol displayed no selectivity (SI < 1). The combinations of celastrol with artemiside or artemisone against HepG2 cells are synergistic. Given the promise of celastrol, judiciously designed formulations or structural modifications are recommended for mitigating its toxicity.
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Affiliation(s)
- Jerome P. L. Ng
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yu Han
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Li Jun Yang
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria Institute Malaria for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Dina Coertzen
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria Institute Malaria for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Ho Ning Wong
- Centre of Excellence for Pharmaceutical Sciences, School of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Richard K. Haynes
- Centre of Excellence for Pharmaceutical Sciences, School of Health Sciences, North-West University, Potchefstroom, South Africa
- *Correspondence: Richard K. Haynes, Paolo Coghi, Vincent Kam Wai Wong,
| | - Paolo Coghi
- School of Pharmacy, Macau University of Science and Technology, Macau, China
- *Correspondence: Richard K. Haynes, Paolo Coghi, Vincent Kam Wai Wong,
| | - Vincent Kam Wai Wong
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- *Correspondence: Richard K. Haynes, Paolo Coghi, Vincent Kam Wai Wong,
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Shyam Mohan AH, Rao SN, D S, Rajeswari N. In silico structural, phylogenetic and drug target analysis of putrescine monooxygenase from Shewanella putrefaciens-95. J Genet Eng Biotechnol 2022; 20:57. [PMID: 35412199 PMCID: PMC9005580 DOI: 10.1186/s43141-022-00338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The enormous and irresponsible use of antibiotics has led to the emergence of resistant strains of bacteria globally. A new approach to combat this crisis has been nutritional immunity limiting the availability of nutrients to pathogens. Targeting the siderophore biosynthetic pathway that helps in iron acquisition, an essential microelement in the bacterial system has been the topic of interest in recent days that backs the concept of nutritional immunity. Supporting this view, we have chosen to study a key enzyme in the biosynthetic pathway of putrebactin called putrescine monooxygenase (SpPMO) from Shewanella putrefaciens. In our previous study, we co-expressed putrescine monooxygenase recombinantly in Escherichia coli BL21 Star (DE3). The bioinformatic analysis and screening of inhibitors will broaden the scope of SpPMO as a drug target. RESULTS In the present study, we have analysed the physicochemical properties of the target enzyme and other N-hydroxylating monooxygenases (NMOs) using ExPASy server. The target enzyme SpPMO and most of the selected NMOs have a slightly acidic isoelectric point and are medially thermostable and generally insoluble. The multiple sequence alignment identified the GXGXX(N/A), DXXXFATGYXXXXP motives and conserved amino acids involved in FAD binding, NADP binding, secondary structure formation and substrate binding. The phylogenetic analysis indicated the distribution of the monooxygenases into different clades according to their substrate specificity. Further, a 3D model of SpPMO was predicted using I-TASSER online tool with DfoA from Erwinia amylovora as a template. The model was validated using the SAVES server and deposited to the Protein Model Database with the accession number PM0082222. The molecular docking analysis with different substrates revealed the presence of a putrescine binding pocket made of conserved amino acids and another binding pocket present on the surface of the protein wherein all other ligands interact with high binding affinity. The molecular docking of naturally occurring inhibitor molecules with SpPMO 3D model identified curcumin and niazirin with 1.83 and 2.81 μM inhibition constants as two promising inhibitors. Further studies on kinetic parameters of curcumin and niazirin inhibitors in vitro determined the Ki to be 2.6±0.0036 μM and 18.38±0.008 μM respectively. CONCLUSION This analysis will help us understand the structural, phylogenetic and drug target aspects of putrescine monooxygenase from Shewanella putrefaciens-95 in detail. It sheds light on the precautionary measures that can be developed to inhibit the enzyme and thereby the secondary infections caused by them.
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Affiliation(s)
- Anil H Shyam Mohan
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru-78, Karnataka, India
| | - Saroja Narsing Rao
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, Karnataka, 584104, India.
| | - Srividya D
- Department of Biotechnology, Davangere University, Shivagangothri, Davangere, Karnataka, 577007, India
| | - N Rajeswari
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru-78, Karnataka, India
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Next-generation microbial drugs developed from microbiome's natural products. ADVANCES IN GENETICS 2021; 108:341-382. [PMID: 34844715 DOI: 10.1016/bs.adgen.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel "magic bullets" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some "hit molecules" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.
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Luo Z, Luo S, Ju Y, Ding P, Xu J, Gu Q, Zhou H. Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis. FASEB J 2021; 35:e21575. [PMID: 33826776 DOI: 10.1096/fj.202002287rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 11/11/2022]
Abstract
Staphylopine (StP) and other nicotianamine-like metallophores are crucial for many pathogens to acquire the transition metals from hosts during invasion. CntL from Staphylococcus aureus (SaCntL) catalyzes the condensation of the 2-aminobutyrate (Ab) moiety of S-adenosylmethionine (SAM) with D-histidine in the biosynthesis of StP. Here, we report the crystal structures of SaCntL in complex with either SAM or two products. The structure of SaCntL consists of an N-terminal four-helix bundle (holding catalytic residue E84) and a C-terminal Rossmann fold (binding the substrates). The sequence connecting the N- and C-terminal domains (N-C linker) in SaCntL was found to undergo conformational alternation between open and closed states. Our structural and biochemical analyses suggested that this intrinsically dynamic interdomain linker forms an additional structural module that plays essential roles in ligand diffusion, recognition, and catalysis. We confirmed that SaCntL stereoselectively carries out the catalysis of D-His but not its enantiomer, L-His, and we found that the N-C linker and active site of SaCntL could accommodate both enantiomers. SaCntL is likely able to bind L-His without catalysis, and as a result, L-His could show inhibitory effects toward SaCntL. These findings provide critical structural and mechanistic insights into CntL, which facilitates a better understanding of the biosynthesis of nicotianamine-like metallophores and the discovery of inhibitors of this process.
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Affiliation(s)
- Zhiteng Luo
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Siting Luo
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingchen Ju
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Ding
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Xu
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiong Gu
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huihao Zhou
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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Reis RAG, Li H, Johnson M, Sobrado P. New frontiers in flavin-dependent monooxygenases. Arch Biochem Biophys 2021; 699:108765. [PMID: 33460580 DOI: 10.1016/j.abb.2021.108765] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of redox reactions in important biological processes and are responsible for the synthesis of highly complex natural products. Although much has been learned about FMO chemistry in the last ~80 years of research, several aspects of the reactions catalyzed by these enzymes remain unknown. In this review, we summarize recent advancements in the flavin-dependent monooxygenase field including aspects of flavin dynamics, formation and stabilization of reactive species, and the hydroxylation mechanism. Novel catalysis of flavin-dependent N-oxidases involving consecutive oxidations of amines to generate oximes or nitrones is presented and the biological relevance of the products is discussed. In addition, the activity of some FMOs have been shown to be essential for the virulence of several human pathogens. We also discuss the biomedical relevance of FMOs in antibiotic resistance and the efforts to identify inhibitors against some members of this important and growing family enzymes.
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Affiliation(s)
| | - Hao Li
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Maxim Johnson
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Blacksburg, VA, 24061, USA; Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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9
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Campbell AC, Robinson R, Mena-Aguilar D, Sobrado P, Tanner JJ. Structural Determinants of Flavin Dynamics in a Class B Monooxygenase. Biochemistry 2020; 59:4609-4616. [PMID: 33226785 DOI: 10.1021/acs.biochem.0c00783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ornithine hydroxylase known as SidA is a class B flavin monooxygenase that catalyzes the first step in the biosynthesis of hydroxamate-containing siderophores in Aspergillus fumigatus. Crystallographic studies of SidA revealed that the FAD undergoes dramatic conformational changes between out and in states during the catalytic cycle. We sought insight into the origins and purpose of flavin motion in class B monooxygenases by probing the function of Met101, a residue that contacts the pyrimidine ring of the in FAD. Steady-state kinetic measurements showed that the mutant variant M101A has a 25-fold lower turnover number. Pre-steady-state kinetic measurements, pH profiles, and solvent kinetic isotope effect measurements were used to isolate the microscopic step that is responsible for the reduced steady-state activity. The data are consistent with a bottleneck in the final step of the mechanism, which involves flavin dehydration and the release of hydroxy-l-ornithine and NADP+. Crystal structures were determined for M101A in the resting state and complexed with NADP+. The resting enzyme structure is similar to that of wild-type SidA, consistent with M101A exhibiting normal kinetics for flavin reduction by NADPH and wild-type affinity for NADPH. In contrast, the structure of the M101A-NADP+ complex unexpectedly shows the FAD adopting the out conformation and may represent a stalled conformation that is responsible for the slow kinetics. Altogether, our data support a previous proposal that one purpose of the FAD conformational change from in to out in class B flavin monooxygenases is to eject spent NADP+ in preparation for a new catalytic cycle.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Reeder Robinson
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Didier Mena-Aguilar
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States.,Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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Misslinger M, Hortschansky P, Brakhage AA, Haas H. Fungal iron homeostasis with a focus on Aspergillus fumigatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118885. [PMID: 33045305 DOI: 10.1016/j.bbamcr.2020.118885] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023]
Abstract
To maintain iron homeostasis, fungi have to balance iron acquisition, storage, and utilization to ensure sufficient supply and to avoid toxic excess of this essential trace element. As pathogens usually encounter iron limitation in the host niche, this metal plays a particular role during virulence. Siderophores are iron-chelators synthesized by most, but not all fungal species to sequester iron extra- and intracellularly. In recent years, the facultative human pathogen Aspergillus fumigatus has become a model for fungal iron homeostasis of siderophore-producing fungal species. This article summarizes the knowledge on fungal iron homeostasis and its links to virulence with a focus on A. fumigatus. It covers mechanisms for iron acquisition, storage, and detoxification, as well as the modes of transcriptional iron regulation and iron sensing in A. fumigatus in comparison to other fungal species. Moreover, potential translational applications of the peculiarities of fungal iron metabolism for treatment and diagnosis of fungal infections is addressed.
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Affiliation(s)
- Matthias Misslinger
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany; Department Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hubertus Haas
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
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11
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Campbell AC, Stiers KM, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. J Biol Chem 2020; 295:13239-13249. [PMID: 32723870 DOI: 10.1074/jbc.ra120.014750] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022] Open
Abstract
The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N-monooxygenase that catalyzes the NADPH-dependent hydroxylation of l-ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l-ornithine bound (resting state). The resting state structure reveals a new out active site conformation characterized by large rotations of the FAD isoalloxazine around the C1-'C2' and N10-C1' bonds, coupled to a 10-Å movement of the Tyr-loop. Additional structures show that either flavin reduction or the binding of NADP(H) is sufficient to drive the FAD to the in conformation. The structures also reveal protein conformational changes associated with the binding of NADP(H) and l-ornithine. Some of these residues were probed using site-directed mutagenesis. Docking was used to explore the active site of the out conformation. These calculations identified two potential ligand-binding sites. Altogether, our results provide new information about conformational dynamics in flavin-dependent monooxygenases. Understanding the different active site conformations that appear during the catalytic cycle may allow fine-tuning of inhibitor discovery efforts.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Kyle M Stiers
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | | | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA; Department of Chemistry, University of Missouri, Columbia, Missouri, USA.
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12
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Houšť J, Spížek J, Havlíček V. Antifungal Drugs. Metabolites 2020; 10:metabo10030106. [PMID: 32178468 PMCID: PMC7143493 DOI: 10.3390/metabo10030106] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
We reviewed the licensed antifungal drugs and summarized their mechanisms of action, pharmacological profiles, and susceptibility to specific fungi. Approved antimycotics inhibit 1,3-β-d-glucan synthase, lanosterol 14-α-demethylase, protein, and deoxyribonucleic acid biosynthesis, or sequestrate ergosterol. Their most severe side effects are hepatotoxicity, nephrotoxicity, and myelotoxicity. Whereas triazoles exhibit the most significant drug–drug interactions, echinocandins exhibit almost none. The antifungal resistance may be developed across most pathogens and includes drug target overexpression, efflux pump activation, and amino acid substitution. The experimental antifungal drugs in clinical trials are also reviewed. Siderophores in the Trojan horse approach or the application of siderophore biosynthesis enzyme inhibitors represent the most promising emerging antifungal therapies.
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Nazik H, Sass G, Ansari SR, Ertekin R, Haas H, Déziel E, Stevens DA. Novel intermicrobial molecular interaction: Pseudomonas aeruginosa Quinolone Signal (PQS) modulates Aspergillus fumigatus response to iron. MICROBIOLOGY-SGM 2019; 166:44-55. [PMID: 31778108 DOI: 10.1099/mic.0.000858] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pseudomonas aeruginosa (Pa) and Aspergillus fumigatus (Af), the commonest bacterium and fungus in compromised host airways, compete for iron (Fe). The Pseudomonas quinolone signal (PQS), a Pa quorum sensing molecule, also chelates Fe, and delivers Fe to the Pa cell membrane using Pa siderophores. In models of Af biofilm formation or preformed biofilms, PQS inhibited Af in a low Fe environment. AfΔsidA (mutant unable to produce siderophores) biofilm was more sensitive to PQS inhibition than wild-type (WT), as was planktonic AfΔsidA growth. PQS decreased WT Af growth on agar. All these inhibitory actions were reversed by Fe. The Pa siderophore pyoverdin, or Af siderophore inhibitor celastrol, act cooperatively with PQS in Af inhibition. These findings all indicate PQS inhibition is owing to Fe chelation. Remarkably, in high Fe environments, PQS enhanced Af biofilm at 1/100 to 1/2000 Fe concentration required for Fe alone to enhance. Planktonic Af growth, and on agar, Af conidiation, were also enhanced by PQS+Fe compared to Fe alone. In contrast, neither AfΔsidA biofilm, nor planktonic AfΔsidA, were enhanced by PQS-Fe compared to Fe. When Af siderophore ferricrocin (FC),+PQS, were added to AfΔsidA, Af was then boosted more than by FC alone. Moreover, FC+PQS+Fe boosted AfΔsidA more than Fe, FC, FC+Fe, PQS+FC or PQS+Fe. Thus PQS-Fe maximal stimulation requires Af siderophores. PQS inhibits Af via chelation under low Fe conditions. In a high Fe environment, PQS paradoxically stimulates Af efficiently, and this involves Af siderophores. PQS production by Pa could stimulate Af in cystic fibrosis airways, where Fe homeostasis is altered and Fe levels increase, supporting fungal growth.
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Affiliation(s)
- Hasan Nazik
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA.,California Institute for Medical Research, San Jose, CA, USA
| | - Gabriele Sass
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA.,California Institute for Medical Research, San Jose, CA, USA
| | - Shajia R Ansari
- California Institute for Medical Research, San Jose, CA, USA
| | - Reyhan Ertekin
- California Institute for Medical Research, San Jose, CA, USA
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Eric Déziel
- INRS-Institut Armand-Frappier, Laval, Quebec, Canada
| | - David A Stevens
- California Institute for Medical Research, San Jose, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Iron: an essential nutrient for Aspergillus fumigatus and a fulcrum for pathogenesis. Curr Opin Infect Dis 2019; 31:506-511. [PMID: 30379731 DOI: 10.1097/qco.0000000000000487] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Aspergillus fumigatus is a ubiquitous saprophytic fungus that can cause life-threatening invasive aspergillosis in immunocompromised patients. Apart from the immune status of the host only a few characterized virulence factors have been identified. In this review, we describe the role of iron in the manifestation of A. fumigatus virulence. RECENT FINDINGS We gathered recent clinical evidence suggesting that tissue iron overload increases the risk of invasive aspergillosis occurrence. Furthermore, we summarize the mechanisms that A. fumigatus employs to achieve iron homeostasis and their importance in A. fumigatus proliferation in vitro. We describe two recent in-vivo models that clearly demonstrate the importance of iron in A. fumigatus growth and invasion. SUMMARY Based on these recent findings, therapy aimed at managing A. fumigatus iron homeostasis locally could make conditions more favorable to the host.
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Sass G, Ansari SR, Dietl AM, Déziel E, Haas H, Stevens DA. Intermicrobial interaction: Aspergillus fumigatus siderophores protect against competition by Pseudomonas aeruginosa. PLoS One 2019; 14:e0216085. [PMID: 31067259 PMCID: PMC6505954 DOI: 10.1371/journal.pone.0216085] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/12/2019] [Indexed: 12/27/2022] Open
Abstract
Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens frequently co-inhabiting immunocompromised patient airways, particularly in people with cystic fibrosis. Both microbes depend on the availability of iron, and compete for iron in their microenvironment. We showed previously that the P. aeruginosa siderophore pyoverdine is the main instrument in battling A. fumigatus biofilms, by iron chelation and denial of iron to the fungus. Here we show that A. fumigatus siderophores defend against anti-fungal P. aeruginosa effects. P. aeruginosa supernatants produced in the presence of wildtype A. fumigatus planktonic supernatants (Afsup) showed less activity against A. fumigatus biofilms than P. aeruginosa supernatants without Afsup, despite higher production of pyoverdine by P. aeruginosa. Supernatants of A. fumigatus cultures lacking the sidA gene (AfΔsidA), unable to produce hydroxamate siderophores, were less capable of protecting A. fumigatus biofilms from P. aeruginosa supernatants and pyoverdine. AfΔsidA biofilm was more sensitive towards inhibitory effects of pyoverdine, the iron chelator deferiprone (DFP), or amphothericin B than wildtype A. fumigatus biofilm. Supplementation of sidA-deficient A. fumigatus biofilm with A. fumigatus siderophores restored resistance to pyoverdine. The A. fumigatus siderophore production inhibitor celastrol sensitized wildtype A. fumigatus biofilms towards the anti-fungal activity of DFP. In conclusion, A. fumigatus hydroxamate siderophores play a pivotal role in A. fumigatus competition for iron against P. aeruginosa.
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Affiliation(s)
- Gabriele Sass
- California Institute for Medical Research, San Jose, California, United States of America
- * E-mail:
| | - Shajia R. Ansari
- California Institute for Medical Research, San Jose, California, United States of America
| | - Anna-Maria Dietl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Eric Déziel
- INRS-Institut Armand-Frappier, Laval, Quebec, Canada
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - David A. Stevens
- California Institute for Medical Research, San Jose, California, United States of America
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
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Song J, Shang N, Baig N, Yao J, Shin C, Kim BK, Li Q, Malwal SR, Oldfield E, Feng X, Guo RT. Aspergillus flavus squalene synthase as an antifungal target: Expression, activity, and inhibition. Biochem Biophys Res Commun 2019; 512:517-523. [DOI: 10.1016/j.bbrc.2019.03.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022]
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17
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Sun Q, Li C, Lin J, Peng X, Wang Q, Jiang N, Xu Q, Zhao G. Celastrol ameliorates Aspergillus fumigatus keratitis via inhibiting LOX-1. Int Immunopharmacol 2019; 70:101-109. [PMID: 30798158 DOI: 10.1016/j.intimp.2019.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE To investigate the effect of Celastrol (CLT) on Aspergillus fumigatus (A. fumigatus) keratitis. METHODS Primary peritoneal macrophages of C57BL/6 mice were pretreated with CLT before A. fumigatus hyphae stimulation. C57BL/6 mice were infected with A. fumigatus. Mice corneas were treated with CLT from 1 day post infection. Clinical score, PCR, ELISA and Western blot were used to test expression of anti-inflammatory mediators, proinflammatory mediators and Lectin-like oxidized low-density lipoprotein receptor 1(LOX-1). The protein levels of p38MAPK after pretreated with CLT in macrophages of C57BL/6 mice challenged with A. fumigatus were tested by Western blot. RESULTS C57BL/6 mice treated with CLT from 1 day post infection showed decreased disease, IL-1β, TNF-α, IL-10, TGF-β, MIP-2 and LOX-1 levels. CLT treatment markedly inhibiting mRNA and proteins levels of anti-inflammatory mediators, proinflammatory mediators and LOX-1 in macrophages of C57BL/6 mice compared with control group. CLT pretreatment before A. fumigatus stimulation obviously inhibiting protein levels of p38MAPK versus DMSO pretreated group in macrophages of C57BL/6 mice challenged with A. fumigatus. CONCLUSION These data provide evidences that CLT ameliorates A. fumigatus keratitis of C57BL/6 mice via inhibiting LOX-1. CLT pretreatment before A. fumigatus stimulation decreased levels of inflammation in macrophages of C57BL/6 mice, which may be regulated by p-p38MAPK.
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Affiliation(s)
- Qiaoqiao Sun
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Cui Li
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Jing Lin
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Xudong Peng
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Qian Wang
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Nan Jiang
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Qiang Xu
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Guiqiu Zhao
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China.
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Liu N, Tu J, Dong G, Wang Y, Sheng C. Emerging New Targets for the Treatment of Resistant Fungal Infections. J Med Chem 2018; 61:5484-5511. [DOI: 10.1021/acs.jmedchem.7b01413] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Na Liu
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Jie Tu
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Yan Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
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Abstract
The devastating infections that fungal pathogens cause in humans are underappreciated relative to viral, bacterial and parasitic diseases. In recent years, the contributions to virulence of reductive iron uptake, siderophore-mediated uptake and heme acquisition have been identified in the best studied and most life-threatening fungal pathogens: Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus. In particular, exciting new work illustrates the importance of iron acquisition from heme and hemoglobin in the virulence of pathogenic yeasts. However, the challenge of establishing how these fungi gain access to hemoglobin in blood and to other sources of heme remains to be fully addressed. Recent studies are also expanding our knowledge of iron uptake in less-well studied fungal pathogens, including dimorphic fungi where new information reveals an integration of iron acquisition with morphogenesis and cell-surface properties for adhesion to host cells. Overall, the accumulating information provides opportunities to exploit iron acquisition for antifungal therapy, and new work highlights the development of specific inhibitors of siderophore biosynthesis and metal chelators for therapeutic use alone or in conjunction with existing antifungal drugs. It is clear that iron-related therapies will need to be customized for specific diseases because the emerging view is that fungal pathogens use different combinations of strategies for iron acquisition in the varied niches of vertebrate hosts.
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Affiliation(s)
- Gaurav Bairwa
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 456-756, Republic of Korea
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Martin Del Campo JS, Eckshtain-Levi M, Vogelaar NJ, Sobrado P. Identification of Aspergillus fumigatus UDP-Galactopyranose Mutase Inhibitors. Sci Rep 2017; 7:10836. [PMID: 28883473 PMCID: PMC5589893 DOI: 10.1038/s41598-017-11022-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/17/2017] [Indexed: 01/08/2023] Open
Abstract
Aspergillus fumigatus is an opportunistic human pathogen responsible for deadly, invasive infections in immunocompromised patients. The A. fumigatus cell wall is a complex network of polysaccharides among them galactofuran, which is absent in humans. UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactofuranose (UDP-Galf) to UDP-galactopyranose (UDP-Galp) and is an important virulence factor. UGM is a flavin-dependent enzyme that requires the reduced flavin for activity; flavin reduction is achieved by reaction with NADPH. The aim of this work was to discover inhibitors of UGM by targeting the NADPH binding site using an ADP-TAMRA probe in a high-throughput screening assay. The flavonoids (2S)-hesperetin and (2S)-naringenin were validated as competitive inhibitors of UGM against NADPH with Ki values of 6 µM and 74 µM, respectively. To gain insight into the active chemical substituents involved in the inhibition of UGM, several derivatives of these inhibitors were studied. The results show that the hydroxyl groups of (2S)-hesperetin are important for inhibition, in particular the phenyl-chroman moiety. Congo red susceptibility assay and growth temperature effects showed that these compounds affected cell wall biosynthesis in A. fumigatus. This work is the first report of inhibition studies on UGM from eukaryotic human pathogens.
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Affiliation(s)
| | | | - Nancy J Vogelaar
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA. .,Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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Abstract
Human-associated microorganisms have the potential to biosynthesize numerous secondary metabolites that may mediate important host-microbe and microbe-microbe interactions. However, there is currently a limited understanding of microbiome-derived natural products. A variety of complementary discovery approaches have begun to illuminate this microbial "dark matter," which will in turn allow detailed mechanistic studies of the effects of these molecules on microbiome and host. Herein, we review recent efforts to uncover microbiome-derived natural products, describe the key approaches that were used to identify and characterize these metabolites, discuss potential functional roles of these molecules, and highlight challenges related to this emerging research area.
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Affiliation(s)
- Matthew R Wilson
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Li Zha
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emily P Balskus
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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