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Quan W, Wang A, Li C, Xie L. Allelopathic potential and allelochemical composition in different soil layers of Rhododendron delavayi forest, southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.963116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forests habituated by Rhododendron delavayi often lack understory vegetation, which could possibly be a consequence of allelopathy. It is a phenomenon by virtue of which certain plant species produce allelochemicals that affect the growth and behavior of surrounding plants. To elucidate the allelopathic potential and allelochemicals present in the different layers of a R. delavayi forest, extracts obtained from three layers of the forest were used for seed germination bioassays and gas chromatography-mass spectrometry (GC–MS) analysis. Aqueous extracts of the litter and humus layers significantly inhibited the seed germination of R. delavayi, Festuca arundinacea, and Lolium perenne, with the litter layer causing the strongest inhibitory effect. A total of 26 allelochemicals were identified in the litter, humus, and soil layers by GC–MS analysis. The primary allelochemicals in the soil and humus layer were organic acids, while the main allelochemicals in the litter layer were phenolic acids. The redundancy analysis revealed the significance of total nitrogen (TN) and relative water content (RWC) in explaining the distribution of the allelochemicals. The results indicated that the litter layer exerted the maximum allelopathic effect due to presence of maximum amount of allelochemical especially the phenolic acids.
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Czeczot ADM, Roth CD, Ducati RG, Pissinate K, Rambo RS, Timmers LFSM, Abbadi BL, Macchi FS, Pestana VZ, Basso LA, Machado P, Bizarro CV. 8-Mercaptoguanine-based inhibitors of Mycobacterium tuberculosis dihydroneopterin aldolase: synthesis, in vitro inhibition and docking studies. J Enzyme Inhib Med Chem 2021; 36:847-855. [PMID: 33752554 PMCID: PMC7993393 DOI: 10.1080/14756366.2021.1900157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The dihydroneopterin aldolase (DHNA, EC 4.1.2.25) activity of FolB protein is required for the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and glycolaldehyde (GA) in the folate pathway. FolB protein from Mycobacterium tuberculosis (MtFolB) is essential for bacilli survival and represents an important molecular target for drug development. S8-functionalized 8-mercaptoguanine derivatives were synthesised and evaluated for inhibitory activity against MtFolB. The compounds showed IC50 values in the submicromolar range. The inhibition mode and inhibition constants were determined for compounds that exhibited the strongest inhibition. Additionally, molecular docking analyses were performed to suggest enzyme-inhibitor interactions and ligand conformations. To the best of our knowledge, this study describes the first class of MtFolB inhibitors.
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Affiliation(s)
- Alexia de Matos Czeczot
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida Deves Roth
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rodrigo Gay Ducati
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari, Lajeado, Brazil
| | - Kenia Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Raoní Scheibler Rambo
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Bruno Lopes Abbadi
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Souza Macchi
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Víctor Zajaczkowski Pestana
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano Valim Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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Falcão VCA, Villela AD, Rodrigues-Junior VS, Pissinate K, Eichler P, Pinto AFM, Basso LA, Santos DS, Bizarro CV. Validation of Mycobacterium tuberculosis dihydroneopterin aldolase as a molecular target for anti-tuberculosis drug development. Biochem Biophys Res Commun 2017; 485:814-819. [PMID: 28257847 DOI: 10.1016/j.bbrc.2017.02.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022]
Abstract
An early step of target validation in antimicrobial drug discovery is to prove that a gene coding for a putative target is essential for pathogen's viability. However, little attention has been paid to demonstrate the causal links between gene essentiality and a particular protein function that will be the focus of a drug discovery effort. This should be considered an important step in target validation since a growing number of proteins are found to exhibit multiple and unrelated tasks. Here, we show that the Mycobacterium tuberculosis (Mtb) folB gene is essential and that this essentiality depends on the dihydroneopterin aldolase/epimerase activities of its protein product, the FolB protein from the folate biosynthesis pathway. The wild-type (WT) MtFolB and point mutants K99A and Y54F were cloned, expressed, purified and monitored for the aldolase, epimerase and oxygenase activities using HPLC. In contrast to the WT MtFolB, both mutants have neither aldolase nor epimerase activities in the conditions assayed. We then performed gene knockout experiments and showed that folB gene is essential for Mtb survival under the conditions tested. Moreover, only the WT folB sequence could be used as a rescue copy in gene complementation studies. When the sequences of mutants K99A or Y54F were used for complementation, no viable colonies were obtained, indicating that aldolase and/or epimerase activities are crucial for Mtb survival. These results provide a solid basis for further work aiming to develop new anti-TB agents acting as inhibitors of the aldolase/epimerase activities of MtFolB.
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Affiliation(s)
- V C A Falcão
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - A D Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - V S Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - K Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - P Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - A F M Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - L A Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - D S Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - C V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil.
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Biochemical characterization of a dihydroneopterin aldolase used for methanopterin biosynthesis in methanogens. J Bacteriol 2014; 196:3191-8. [PMID: 24982305 DOI: 10.1128/jb.01812-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding 7,8-dihydroneopterin aldolase (DHNA) was recently identified in archaea through comparative genomics as being involved in methanopterin biosynthesis (V. Crécy-Lagard, G. Phillips, L. L. Grochowski, B. El Yacoubi, F. Jenney, M. W. Adams, A. G. Murzin, and R. H. White, ACS Chem. Biol. 7:1807-1816, 2012, doi:10.1021/cb300342u). Archaeal DHNA shows a unique secondary and quaternary structure compared with bacterial and plant DHNAs. Here, we report a detailed biochemical examination of DHNA from the methanogen Methanocaldococcus jannaschii. Kinetic studies show that M. jannaschii DHNA possesses a catalytic capability with a kcat/Km above 10(5) M(-1) s(-1) at 70°C, and at room temperature it exhibits a turnover number (0.07 s(-1)) comparable to bacterial DHNAs. We also found that this enzyme follows an acid-base catalytic mechanism similar to the bacterial DHNAs, except when using alternative catalytic residues. We propose that in the absence of lysine, which is considered to be the general base in bacterial DHNAs, an invariant water molecule likely functions as the catalytic base, and the strictly conserved His35 and Gln61 residues serve as the hydrogen bond partners to adjust the basicity of the water molecule. Indeed, substitution of either His35 or Gln61 causes a 20-fold decrease in kcat. An invariant Tyr78 is also shown to be important for catalysis, likely functioning as a general acid. Glu25 plays an important role in substrate binding, since replacing Glu25 by Gln caused a ≥25-fold increase in Km. These results provide important insights into the catalytic mechanism of archaeal DHNAs.
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Contreras H, Joens MS, McMath LM, Le VP, Tullius MV, Kimmey JM, Bionghi N, Horwitz MA, Fitzpatrick JAJ, Goulding CW. Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins. J Biol Chem 2014; 289:18279-89. [PMID: 24855650 PMCID: PMC4140288 DOI: 10.1074/jbc.m114.570119] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/19/2014] [Indexed: 01/24/2023] Open
Abstract
Mycobacterium tuberculosis has evolved various mechanisms by which the bacterium can maintain homeostasis under numerous environmental assaults generated by the host immune response. M. tuberculosis harbors enzymes involved in the oxidative stress response that aid in survival during the production of reactive oxygen species in activated macrophages. Previous studies have shown that a dye-decolorizing peroxidase (DyP) is encapsulated by a bacterial nanocompartment, encapsulin (Enc), whereby packaged DyP interacts with Enc via a unique C-terminal extension. M. tuberculosis also harbors an encapsulin homolog (CFP-29, Mt-Enc), within an operon with M. tuberculosis DyP (Mt-DyP), which contains a C-terminal extension. Together these observations suggest that Mt-DyP interacts with Mt-Enc. Furthermore, it has been suggested that DyPs may function as either a heme-dependent peroxidase or a deferrochelatase. Like Mt-DyP, M. tuberculosis iron storage ferritin protein, Mt-BfrB, and an M. tuberculosis protein involved in folate biosynthesis, 7,8-dihydroneopterin aldolase (Mt-FolB), have C-terminal tails that could also interact with Mt-Enc. For the first time, we show by co-purification and electron microscopy that mycobacteria via Mt-Enc can encapsulate Mt-DyP, Mt-BfrB, and Mt-FolB. Functional studies of free or encapsulated proteins demonstrate that they retain their enzymatic activity within the Mt-Enc nanocompartment. Mt-DyP, Mt-FolB, and Mt-BfrB all have antioxidant properties, suggesting that if these proteins are encapsulated by Mt-Enc, then this nanocage may play a role in the M. tuberculosis oxidative stress response. This report provides initial structural and biochemical clues regarding the molecular mechanisms that utilize compartmentalization by which the mycobacterial cell may aid in detoxification of the local environment to ensure long term survival.
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Affiliation(s)
- Heidi Contreras
- From the Departments of Molecular Biology and Biochemistry and
| | - Matthew S Joens
- the Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, and
| | - Lisa M McMath
- From the Departments of Molecular Biology and Biochemistry and
| | - Vincent P Le
- From the Departments of Molecular Biology and Biochemistry and
| | - Michael V Tullius
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Jaqueline M Kimmey
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Neda Bionghi
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Marcus A Horwitz
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - James A J Fitzpatrick
- the Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, and
| | - Celia W Goulding
- From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California, Irvine, California 92697,
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