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Laureano de Souza M, Lapierre TJWJD, Vitor de Lima Marques G, Ferraz WR, Penteado AB, Henrique Goulart Trossini G, Murta SMF, de Oliveira RB, de Oliveira Rezende C, Ferreira RS. Molecular targets for Chagas disease: validation, challenges and lead compounds for widely exploited targets. Expert Opin Ther Targets 2023; 27:911-925. [PMID: 37772733 DOI: 10.1080/14728222.2023.2264512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/24/2023] [Indexed: 09/30/2023]
Abstract
INTRODUCTION Chagas disease (CD) imposes social and economic burdens, yet the available treatments have limited efficacy in the disease's chronic phase and cause serious adverse effects. To address this challenge, target-based approaches are a possible strategy to develop new, safe, and active treatments for both phases of the disease. AREAS COVERED This review delves into target-based approaches applied to CD drug discovery, emphasizing the studies from the last five years. We highlight the proteins cruzain (CZ), trypanothione reductase (TR), sterol 14 α-demethylase (CPY51), iron superoxide dismutase (Fe-SOD), proteasome, cytochrome b (Cytb), and cleavage and polyadenylation specificity factor 3 (CPSF3), chosen based on their biological and chemical validation as drug targets. For each, we discuss its biological relevance and validation as a target, currently related challenges, and the status of the most promising inhibitors. EXPERT OPINION Target-based approaches toward developing potential CD therapeutics have yielded promising leads in recent years. We expect a significant advance in this field in the next decade, fueled by the new options for Trypanosoma cruzi genetic manipulation that arose in the past decade, combined with recent advances in computational chemistry and chemical biology.
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Affiliation(s)
- Mariana Laureano de Souza
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Gabriel Vitor de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Witor Ribeiro Ferraz
- Departamento de Farmacia, Faculdade de Ciencias Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - André Berndt Penteado
- Departamento de Farmacia, Faculdade de Ciencias Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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2
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Martín-Montes Á, Martínez-Camarena Á, Lopera A, Bonastre-Sabater I, Clares MP, Verdejo B, García-España E, Marín C. The Bioactivity of Xylene, Pyridine, and Pyrazole Aza Macrocycles against Three Representative Leishmania Species. Pharmaceutics 2023; 15:pharmaceutics15030992. [PMID: 36986853 PMCID: PMC10059905 DOI: 10.3390/pharmaceutics15030992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/22/2023] Open
Abstract
Due to the urgent need for finding effective and free of secondary effect treatments for every clinical form of Leishmaniasis, a series of synthetic xylene, pyridine and, pyrazole azamacrocycles were tested against three Leishmania species. A total of 14 compounds were tested against J774.2 macrophage cells which were models for host cells, and against promastigote and amastigote forms of each studied Leishmania parasite. Amongst these polyamines, one proved effective against L. donovani, another one for L. braziliensis and L. infantum, and another one was selective solely for L. infantum. These compounds showed leishmanicidal activity and reduced parasite infectivity and dividing ability. Action mechanism studies gave a hint that compounds were active against Leishmania due to their ability to alter parasite metabolic pathways and reduce (except Py33333) parasitic Fe-SOD activity.
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Affiliation(s)
- Álvaro Martín-Montes
- Departamento de Parasitología, Instituto de Investigación Biosanitaria (IBS. Granada), Hospitales Universitarios de Granada, Universidad de Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | - Álvaro Martínez-Camarena
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Alberto Lopera
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Irene Bonastre-Sabater
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - M. Paz Clares
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Begoña Verdejo
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
- Correspondence: (E.G.-E.); (C.M.)
| | - Clotilde Marín
- Departamento de Parasitología, Instituto de Investigación Biosanitaria (IBS. Granada), Hospitales Universitarios de Granada, Universidad de Granada, Severo Ochoa s/n, 18071 Granada, Spain
- Correspondence: (E.G.-E.); (C.M.)
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3
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Hickson J, Athayde LFA, Miranda TG, Junior PAS, Dos Santos AC, da Cunha Galvão LM, da Câmara ACJ, Bartholomeu DC, de Souza RDCM, Murta SMF, Nahum LA. Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment. Parasit Vectors 2022; 15:194. [PMID: 35668508 PMCID: PMC9169349 DOI: 10.1186/s13071-022-05319-2] [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: 12/22/2021] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Components of the antioxidant defense system in Trypanosoma cruzi are potential targets for new drug development. Superoxide dismutases (SODs) constitute key components of antioxidant defense systems, removing excess superoxide anions by converting them into oxygen and hydrogen peroxide. The main goal of the present study was to investigate the genes coding for iron superoxide dismutase (FeSOD) in T. cruzi strains from an evolutionary perspective. Methods In this study, molecular biology methods and phylogenetic studies were combined with drug assays. The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl–TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. Evolutionary trees were reconstructed based on Bayesian inference and maximum likelihood methods. Drugs that potentially interacted with T. cruzi FeSODs were identified and tested against the parasites. Results Our results suggest that T. cruzi FeSOD types are members of distinct families. Gene copies of FeSOD-A (n = 2), FeSOD-B (n = 4) and FeSOD-C (n = 4) were identified in the genome of the T. cruzi reference clone CL Brener. Phylogenetic inference supported the presence of two functional variants of each FeSOD type across the T. cruzi strains. Phylogenetic trees revealed a monophyletic group of FeSOD genes of T. cruzi TcIV strains in both distinct genes. Altogether, our results support the hypothesis that gene duplication followed by divergence shaped the evolution of T. cruzi FeSODs. Two drugs, mangafodipir and polaprezinc, that potentially interact with T. cruzi FeSODs were identified and tested in vitro against amastigotes and trypomastigotes: mangafodipir had a low trypanocidal effect and polaprezinc was inactive. Conclusions Our study contributes to a better understanding of the molecular biodiversity of T. cruzi FeSODs. Herein we provide a successful approach to the study of gene/protein families as potential drug targets. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05319-2.
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Affiliation(s)
- Jéssica Hickson
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Felipe Almeida Athayde
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Thainá Godinho Miranda
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Policarpo Ademar Sales Junior
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Coqueiro Dos Santos
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Lúcia Maria da Cunha Galvão
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte State, Natal, Rio Grande do Norte, Brazil
| | - Antônia Cláudia Jácome da Câmara
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte State, Natal, Rio Grande do Norte, Brazil
| | - Daniella Castanheira Bartholomeu
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rita de Cássia Moreira de Souza
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Silvane Maria Fonseca Murta
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.
| | - Laila Alves Nahum
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil. .,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil. .,Promove College of Technology, Belo Horizonte, Minas Gerais, Brazil.
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4
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Martín-Montes Á, Clares MP, Martín-Escolano R, Delgado-Pinar E, Marín C, Verdejo B, Martínez-Camarena Á, Molina-Carreño D, García-España E, Sánchez-Moreno M. Heterocyclic Diamines with Leishmanicidal Activity. ACS Infect Dis 2021; 7:3168-3181. [PMID: 34734686 DOI: 10.1021/acsinfecdis.1c00215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leishmaniasis is one of the world's most neglected diseases with a worldwide prevalence of 12 million people. There are no effective human vaccines for its prevention, and outdated drugs hamper treatment. Therefore, research aimed at developing new therapeutic tools to fight leishmaniasis remains a crucial goal today. With this purpose in mind, here, we present 10 new compounds made up by linking alkylated ethylenediamine units to pyridine or quinoline heterocycles with promising in vitro and in vivo efficacy against promastigote and amastigote forms of Leishmania infantum, Leishmania donovani, and Leishmania braziliensis species. Three compounds (2, 4, and 5) showed a selectivity index much higher in the amastigote form than the reference drug glucantime. These three derivatives affected the parasite infectivity rates; the result was lower parasite infectivity rates than glucantime tested at an IC25 dose. In addition, these derivatives were substantially more active against the three Leishmania species tested than glucantime. The mechanism of action of these compounds has been studied, showing alterations in glucose catabolism and leading to greater levels of iron superoxide dismutase inhibition. These molecules could be potential candidates for leishmaniasis chemotherapy due to their effectiveness and their ready synthesis.
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Affiliation(s)
- Álvaro Martín-Montes
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - María Paz Clares
- Instituto de Ciencia Molecular Universidad De Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Rubén Martín-Escolano
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, United Kingdom
| | - Estefanía Delgado-Pinar
- Instituto de Ciencia Molecular Universidad De Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
- University of Coimbra, Department of Chemistry, CQC, 3004-535 Coimbra, Portugal
| | - Clotilde Marín
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Begoña Verdejo
- Instituto de Ciencia Molecular Universidad De Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Álvaro Martínez-Camarena
- Instituto de Ciencia Molecular Universidad De Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Daniel Molina-Carreño
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular Universidad De Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Manuel Sánchez-Moreno
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
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5
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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6
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Synthesis of new N,S-acetal analogs derived from juglone with cytotoxic activity against Trypanossoma cruzi. J Bioenerg Biomembr 2020; 52:199-213. [PMID: 32418003 DOI: 10.1007/s10863-020-09834-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
A series of 11 new N,S-acetal juglone derivatives were synthesized and evaluated against T. cruzi epimastigote forms. These compounds were obtained in good to moderate yields using a microwave irradiation protocol. Among all compounds, two N,S-acetal analogs, showed significant trypanocidal activity. Notably, one compound 11g exhibited selectivity index 10-fold higher than the reference drug benznidazole for epimastigote. The compound 11h was more effective for amastigote forms. Both prototypes exhibited S.I. higher than the benznidazole description. Thus, both compounds proving to be useful candidate molecules to further studies in infected animals.
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7
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Romero AH, Rodríguez N, Oviedo H, Lopez SE. Antileismanial activity, mechanism of action study and molecular docking of 1,4‐bis(substituted benzalhydrazino)phthalazines. Arch Pharm (Weinheim) 2019; 352:e1800299. [DOI: 10.1002/ardp.201800299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/04/2019] [Accepted: 02/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Angel H. Romero
- Cátedra de Química General, Facultad de FarmaciaUniversidad Central de VenezuelaCaracas Venezuela
- Laboratorio de Ingeniería GenéticaInstituto de Biomedicina, Hospital VargasCaracas Venezuela
- Laboratorio de Química Medicinal y Heterociclos, Departamento de QuímicaUniversidad Simón BolívarSartenejas, Baruta Venezuela
| | - Noris Rodríguez
- Laboratorio de Ingeniería GenéticaInstituto de Biomedicina, Hospital VargasCaracas Venezuela
| | - Henry Oviedo
- Laboratorio de Ingeniería GenéticaInstituto de Biomedicina, Hospital VargasCaracas Venezuela
| | - Simón E. Lopez
- Department of ChemistryUniversity of FloridaGainesville Florida
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8
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Piacenza L, Trujillo M, Radi R. Reactive species and pathogen antioxidant networks during phagocytosis. J Exp Med 2019; 216:501-516. [PMID: 30792185 PMCID: PMC6400530 DOI: 10.1084/jem.20181886] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/04/2019] [Accepted: 02/04/2019] [Indexed: 11/23/2022] Open
Abstract
This review discusses the generation of phagosomal cytotoxic reactive species by activated macrophages and neutrophils for the control of intracellular pathogens, and the mechanisms by which microbes combat host-derived oxidants via antioxidant networks that mitigate the redox-dependent control of infection. The generation of phagosomal cytotoxic reactive species (i.e., free radicals and oxidants) by activated macrophages and neutrophils is a crucial process for the control of intracellular pathogens. The chemical nature of these species, the reactions they are involved in, and the subsequent effects are multifaceted and depend on several host- and pathogen-derived factors that influence their production rates and catabolism inside the phagosome. Pathogens rely on an intricate and synergistic antioxidant armamentarium that ensures their own survival by detoxifying reactive species. In this review, we discuss the generation, kinetics, and toxicity of reactive species generated in phagocytes, with a focus on the response of macrophages to internalized pathogens and concentrating on Mycobacterium tuberculosis and Trypanosoma cruzi as examples of bacterial and parasitic infection, respectively. The ability of pathogens to deal with host-derived reactive species largely depends on the competence of their antioxidant networks at the onset of invasion, which in turn can tilt the balance toward pathogen survival, proliferation, and virulence over redox-dependent control of infection.
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Affiliation(s)
- Lucía Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay .,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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9
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Yu M, Ma X, Cao H, Chong B, Lai L, Liu Z. Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle. Proteins 2018; 86:1075-1087. [PMID: 30019778 DOI: 10.1002/prot.25586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/22/2018] [Accepted: 07/04/2018] [Indexed: 01/21/2023]
Abstract
Many proteins exhibit a critical property called allostery, which enables intra-molecular transmission of information between distal sites. Microscopically, allosteric response is closely related to correlated atomic fluctuations. Conventional correlation analysis correlates the atomic fluctuations at two sites by taking the dot product (DP) between the fluctuations, which accounts only for the parallel and antiparallel components. Here, we present a singular value decomposition (SVD) method that analyzes the correlation coefficient of fluctuation dynamics with an arbitrary angle between the correlated directions. In a model allosteric system, the second PDZ domain (PDZ2) in the human PTP1E protein, approximately one third of the strong correlations have near-perpendicular directions, which are underestimated in the conventional method. The discrimination becomes more prominent for residue pairs with larger separation. The results of the proposed SVD method are more consistent with the experimentally determined PDZ2 dynamics than those of conventional method. In addition, the SVD method improved the prediction accuracy of the allosteric sites in a dataset of 23 known allosteric monomer proteins. The proposed method may inspire extended investigation not only into allostery, but also into protein dynamics and drug design.
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Affiliation(s)
- Miao Yu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaomin Ma
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Huaiqing Cao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bin Chong
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, and BNLMS, Peking University, Beijing, China.,State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, and BNLMS, Peking University, Beijing, China.,State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing, China
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10
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Schatzman SS, Culotta VC. Chemical Warfare at the Microorganismal Level: A Closer Look at the Superoxide Dismutase Enzymes of Pathogens. ACS Infect Dis 2018. [PMID: 29517910 DOI: 10.1021/acsinfecdis.8b00026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Superoxide anion radical is generated as a natural byproduct of aerobic metabolism but is also produced as part of the oxidative burst of the innate immune response design to kill pathogens. In living systems, superoxide is largely managed through superoxide dismutases (SODs), families of metalloenzymes that use Fe, Mn, Ni, or Cu cofactors to catalyze the disproportionation of superoxide to oxygen and hydrogen peroxide. Given the bursts of superoxide faced by microbial pathogens, it comes as no surprise that SOD enzymes play important roles in microbial survival and virulence. Interestingly, microbial SOD enzymes not only detoxify host superoxide but also may participate in signaling pathways that involve reactive oxygen species derived from the microbe itself, particularly in the case of eukaryotic pathogens. In this Review, we will discuss the chemistry of superoxide radicals and the role of diverse SOD metalloenzymes in bacterial, fungal, and protozoan pathogens. We will highlight the unique features of microbial SOD enzymes that have evolved to accommodate the harsh lifestyle at the host-pathogen interface. Lastly, we will discuss key non-SOD superoxide scavengers that specific pathogens employ for defense against host superoxide.
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Affiliation(s)
- Sabrina S. Schatzman
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Pubic Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Valeria C. Culotta
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Pubic Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland 21205, United States
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11
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Fonseca-Júnior NJ, Afonso MQ, Oliveira LC, Bleicher L. PFstats: A Network-Based Open Tool for Protein Family Analysis. J Comput Biol 2018; 25:480-486. [DOI: 10.1089/cmb.2017.0181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Néli J. Fonseca-Júnior
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Marcelo Q.L. Afonso
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Lucas C. Oliveira
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Lucas Bleicher
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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12
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Romero AH, López SE. In silico molecular docking studies of new potential 4-phthalazinyl-hydrazones on selected Trypanosoma cruzi and Leishmania enzyme targets. J Mol Graph Model 2017; 76:313-329. [DOI: 10.1016/j.jmgm.2017.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/19/2023]
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13
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Romero AH, Medina R, Alcala A, García-Marchan Y, Núñez-Duran J, Leañez J, Mijoba A, Ciangherotti C, Serrano-Martín X, López SE. Design, synthesis, structure-activity relationship and mechanism of action studies of a series of 4-chloro-1-phthalazinyl hydrazones as a potent agent against Leishmania braziliensis. Eur J Med Chem 2017; 127:606-620. [DOI: 10.1016/j.ejmech.2017.01.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/29/2022]
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14
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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15
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O'Rourke KF, Gorman SD, Boehr DD. Biophysical and computational methods to analyze amino acid interaction networks in proteins. Comput Struct Biotechnol J 2016; 14:245-51. [PMID: 27441044 PMCID: PMC4939391 DOI: 10.1016/j.csbj.2016.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/04/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Globular proteins are held together by interacting networks of amino acid residues. A number of different structural and computational methods have been developed to interrogate these amino acid networks. In this review, we describe some of these methods, including analyses of X-ray crystallographic data and structures, computer simulations, NMR data, and covariation among protein sequences, and indicate the critical insights that such methods provide into protein function. This information can be leveraged towards the design of new allosteric drugs, and the engineering of new protein function and protein regulation strategies.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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16
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Phan IQH, Davies DR, Moretti NS, Shanmugam D, Cestari I, Anupama A, Fairman JW, Edwards TE, Stuart K, Schenkman S, Myler PJ. Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures. Acta Crystallogr F Struct Biol Commun 2015; 71:615-21. [PMID: 25961325 PMCID: PMC4427173 DOI: 10.1107/s2053230x15004185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022] Open
Abstract
Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.
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Affiliation(s)
- Isabelle Q. H. Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Douglas R. Davies
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Nilmar Silvio Moretti
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Igor Cestari
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Atashi Anupama
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - James W. Fairman
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Kenneth Stuart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
| | - Sergio Schenkman
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
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17
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Russo Krauss I, Merlino A, Pica A, Rullo R, Bertoni A, Capasso A, Amato M, Riccitiello F, De Vendittis E, Sica F. Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases. RSC Adv 2015. [DOI: 10.1039/c5ra13559a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metal-dependent activity and X-ray structures of superoxide dismutase (SOD) fromStreptococcus mutansandStreptococcus thermophilussuggest that they are members of the Mn-like group of cambialistic SODs.
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Affiliation(s)
- Irene Russo Krauss
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Antonello Merlino
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Andrea Pica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Rosario Rullo
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo
- CNR
- 80147 Napoli
- Italy
| | - Alessandra Bertoni
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Alessandra Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Massimo Amato
- Dipartimento di Medicina e Chirurgia
- Università di Salerno
- SA
- Italy
| | - Francesco Riccitiello
- Dipartimento di Neuroscienze
- Scienze Riproduttive e Odontostomatologiche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Emmanuele De Vendittis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Filomena Sica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
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18
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Prakash K, Goyal M, Soni A, Siddiqui AJ, Bhardwaj J, Puri SK. Molecular cloning and biochemical characterization of iron superoxide dismutase from the rodent malaria parasite Plasmodium vinckei. Parasitol Int 2014; 63:817-25. [DOI: 10.1016/j.parint.2014.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/11/2014] [Accepted: 07/16/2014] [Indexed: 10/24/2022]
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19
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Pelé J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M. Comparative analysis of sequence covariation methods to mine evolutionary hubs: Examples from selected GPCR families. Proteins 2014; 82:2141-56. [DOI: 10.1002/prot.24570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 03/11/2014] [Accepted: 03/19/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Julien Pelé
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
| | - Matthieu Moreau
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
| | - Hervé Abdi
- The University of Texas at Dallas; School of Behavioral and Brain Sciences; Richardson, TX 75080-3021 USA
| | - Patrice Rodien
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
- Department of Endocrinology, Reference Centre for the pathologies of hormonal receptivity; Centre Hospitalier Universitaire of Angers; 4 rue Larrey 49933 Angers France
| | - Hélène Castel
- INSERM U982, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, DC2N; University of Rouen; 76821 Mont-Saint-Aignan France
| | - Marie Chabbert
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
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20
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Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS. Superoxide dismutases and superoxide reductases. Chem Rev 2014; 114:3854-918. [PMID: 24684599 PMCID: PMC4317059 DOI: 10.1021/cr4005296] [Citation(s) in RCA: 569] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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21
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Martinez A, Peluffo G, Petruk AA, Hugo M, Piñeyro D, Demicheli V, Moreno DM, Lima A, Batthyány C, Durán R, Robello C, Martí MA, Larrieux N, Buschiazzo A, Trujillo M, Radi R, Piacenza L. Structural and molecular basis of the peroxynitrite-mediated nitration and inactivation of Trypanosoma cruzi iron-superoxide dismutases (Fe-SODs) A and B: disparate susceptibilities due to the repair of Tyr35 radical by Cys83 in Fe-SODB through intramolecular electron transfer. J Biol Chem 2014; 289:12760-78. [PMID: 24616096 DOI: 10.1074/jbc.m113.545590] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, contains exclusively iron-dependent superoxide dismutases (Fe-SODs) located in different subcellular compartments. Peroxynitrite, a key cytotoxic and oxidizing effector biomolecule, reacted with T. cruzi mitochondrial (Fe-SODA) and cytosolic (Fe-SODB) SODs with second order rate constants of 4.6 ± 0.2 × 10(4) M(-1) s(-1) and 4.3 ± 0.4 × 10(4) M(-1) s(-1) at pH 7.4 and 37 °C, respectively. Both isoforms are dose-dependently nitrated and inactivated by peroxynitrite. Susceptibility of T. cruzi Fe-SODA toward peroxynitrite was similar to that reported previously for Escherichia coli Mn- and Fe-SODs and mammalian Mn-SOD, whereas Fe-SODB was exceptionally resistant to oxidant-mediated inactivation. We report mass spectrometry analysis indicating that peroxynitrite-mediated inactivation of T. cruzi Fe-SODs is due to the site-specific nitration of the critical and universally conserved Tyr(35). Searching for structural differences, the crystal structure of Fe-SODA was solved at 2.2 Å resolution. Structural analysis comparing both Fe-SOD isoforms reveals differences in key cysteines and tryptophan residues. Thiol alkylation of Fe-SODB cysteines made the enzyme more susceptible to peroxynitrite. In particular, Cys(83) mutation (C83S, absent in Fe-SODA) increased the Fe-SODB sensitivity toward peroxynitrite. Molecular dynamics, electron paramagnetic resonance, and immunospin trapping analysis revealed that Cys(83) present in Fe-SODB acts as an electron donor that repairs Tyr(35) radical via intramolecular electron transfer, preventing peroxynitrite-dependent nitration and consequent inactivation of Fe-SODB. Parasites exposed to exogenous or endogenous sources of peroxynitrite resulted in nitration and inactivation of Fe-SODA but not Fe-SODB, suggesting that these enzymes play distinctive biological roles during parasite infection of mammalian cells.
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Affiliation(s)
- Alejandra Martinez
- From the Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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22
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Olmo F, Clares MP, Marín C, González J, Inclán M, Soriano C, Urbanová K, Tejero R, Rosales MJ, Krauth-Siegel RL, Sánchez-Moreno M, García-España E. Synthetic single and double aza-scorpiand macrocycles acting as inhibitors of the antioxidant enzymes iron superoxide dismutase and trypanothione reductase in Trypanosoma cruzi with promising results in a murine model. RSC Adv 2014. [DOI: 10.1039/c4ra09866h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthetic scorpiand-like azamacrocycles selectively inhibit SOD and TR enzymes of Trypanosoma cruzi in mice causing death of the parasites and increasing the mouse survival rate after infection and treatment.
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Affiliation(s)
- F. Olmo
- Departamento de Parasitología
- Instituto de Investigación Biosanitaria ibs. Granada
- Universidad de Granada
- Granada, Spain
| | - M. P. Clares
- Instituto de Ciencia Molecular
- Departamento de Química Inorgánica
- Universidad de Valencia
- Valencia, Spain
| | - C. Marín
- Departamento de Parasitología
- Instituto de Investigación Biosanitaria ibs. Granada
- Universidad de Granada
- Granada, Spain
| | - J. González
- Instituto de Ciencia Molecular
- Departamento de Química Inorgánica
- Universidad de Valencia
- Valencia, Spain
| | - M. Inclán
- Instituto de Ciencia Molecular
- Departamento de Química Inorgánica
- Universidad de Valencia
- Valencia, Spain
| | - C. Soriano
- Departamento de Química Orgánica
- Universidad de Valencia
- Valencia, Spain
| | - K. Urbanová
- Departamento de Parasitología
- Instituto de Investigación Biosanitaria ibs. Granada
- Universidad de Granada
- Granada, Spain
| | - R. Tejero
- Departamento de Química Física
- Universidad de Valencia
- Valencia, Spain
| | - M. J. Rosales
- Departamento de Parasitología
- Instituto de Investigación Biosanitaria ibs. Granada
- Universidad de Granada
- Granada, Spain
| | | | - M. Sánchez-Moreno
- Departamento de Parasitología
- Instituto de Investigación Biosanitaria ibs. Granada
- Universidad de Granada
- Granada, Spain
| | - E. García-España
- Instituto de Ciencia Molecular
- Departamento de Química Inorgánica
- Universidad de Valencia
- Valencia, Spain
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23
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Melnikov V, Espinoza-Gomez F, Newton-Sanchez O, Delgado-Ensiso I, Montesinos-Lopez OA, Dalin MV, Espinoza B, Martinez I, Sheklakova LA, Dobrovinskaya O, Karpenko LP. Integral Approach to Evaluation of the Pathogenic Activity of Trypanosoma Cruzi Clones as Exemplified by the Mexican Strain. Bull Exp Biol Med 2013; 156:70-2. [DOI: 10.1007/s10517-013-2280-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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24
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Ferreira-Júnior JR, Bleicher L, Barros MH. Her2p molecular modeling, mutant analysis and intramitochondrial localization. Fungal Genet Biol 2013; 60:133-9. [DOI: 10.1016/j.fgb.2013.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/07/2013] [Accepted: 06/22/2013] [Indexed: 02/05/2023]
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25
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Afonso MQL, de Lima LHF, Bleicher L. Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box. BMC Genomics 2013; 14 Suppl 6:S1. [PMID: 24564869 PMCID: PMC3908500 DOI: 10.1186/1471-2164-14-s6-s1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Nuclear receptors (NRs) are transcription factors which bind small hormones, whose evolutionary history and the presence of different functional surfaces makes them an interesting target for a correlation based analysis. Results Correlation analysis of ligand binding domains shows that correlated residue subsets arise from the differences between functional sites in different nuclear receptor subfamilies. For the DNA binding domain, particularly, the analysis shows that the main source of correlation comes from residues that regulate hormone response element specificity, and one of the conserved residue sub-sets arises due to the presence of an unusual sequence for the DNA binding motif known as P-box in nematodes, suggesting the existence of different DBD-DNA specificities in nuclear receptors. Conclusions We conclude that DNA specificity and functional surface specialization has independently driven nuclear receptor evolution, and suggest possible binding modes for the class of divergent nuclear receptors in nematodes.
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Piacenza L, Peluffo G, Alvarez MN, Martínez A, Radi R. Trypanosoma cruzi antioxidant enzymes as virulence factors in Chagas disease. Antioxid Redox Signal 2013; 19:723-34. [PMID: 22458250 PMCID: PMC3739954 DOI: 10.1089/ars.2012.4618] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Chagas disease (CD) affects several million people in Latin America and is spreading beyond its classical boundaries due to the migration of infected host and insect vectors, HIV co-infection, and blood transfusion. The current therapy is not adequate for treatment of the chronic phase of CD, and new drugs are warranted. RECENT ADVANCES Trypanosoma cruzi is equipped with a specialized and complex network of antioxidant enzymes that are located at different subcellular compartments which defend the parasite against host oxidative assaults. Recently, strong evidence has emerged which indicates that enzyme components of the T. cruzi antioxidant network (cytosolic and mitochondrial peroxiredoxins and trypanothione synthetase) in naturally occurring strains act as a virulence factor for CD. This precept is recapitulated with the observed increased resistance of T. cruzi peroxirredoxins overexpressers to in vivo or in vitro nitroxidative stress conditions. In addition, the modulation of mitochondrial superoxide radical levels by iron superoxide dismutase (FeSODA) influences parasite programmed cell death, underscoring the role of this enzyme in parasite survival. CRITICAL ISSUES The unraveling of the biological significance of FeSODs in T. cruzi programmed cell death in the context of chronic infection in CD is still under examination. FUTURE DIRECTIONS The role of the antioxidant enzymes in the pathogenesis of CD, including parasite virulence and persistence, and their feasibility as pharmacological targets justifies further investigation.
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Affiliation(s)
- Lucía Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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27
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Bleicher L, Lemke N, Garratt RC. Using amino acid correlation and community detection algorithms to identify functional determinants in protein families. PLoS One 2011; 6:e27786. [PMID: 22205928 PMCID: PMC3243672 DOI: 10.1371/journal.pone.0027786] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 10/25/2011] [Indexed: 11/21/2022] Open
Abstract
Correlated mutation analysis has a long history of interesting applications, mostly in the detection of contact pairs in protein structures. Based on previous observations that, if properly assessed, amino acid correlation data can also provide insights about functional sub-classes in a protein family, we provide a complete framework devoted to this purpose. An amino acid specific correlation measure is proposed, which can be used to build networks summarizing all correlation and anti-correlation patterns in a protein family. These networks can be submitted to community structure detection algorithms, resulting in subsets of correlated amino acids which can be further assessed by specific parameters and procedures that provide insight into the relationship between different communities, the individual importance of community members and the adherence of a given amino acid sequence to a given community. By applying this framework to three protein families with contrasting characteristics (the Fe/Mn-superoxide dismutases, the peroxidase-catalase family and the C-type lysozyme/α-lactalbumin family), we show how our method and the proposed parameters and procedures are related to biological characteristics observed in these protein families, highlighting their potential use in protein characterization and gene annotation.
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Affiliation(s)
- Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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28
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Trypanosoma cruzi: Correlation of muscle lesions with contractile properties in the acute phase of experimental infection in mice (Mus musculus). Exp Parasitol 2011; 128:301-8. [DOI: 10.1016/j.exppara.2011.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 02/10/2011] [Accepted: 02/14/2011] [Indexed: 11/23/2022]
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29
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de C. Palmieri L, Lima LMTR, Freire JBB, Bleicher L, Polikarpov I, Almeida FCL, Foguel D. Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition. J Biol Chem 2010; 285:31731-41. [PMID: 20659897 PMCID: PMC2951245 DOI: 10.1074/jbc.m110.157206] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Indexed: 11/06/2022] Open
Abstract
Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. Zn(2+) binding perturbs loop E-α-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases ∼5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the α-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.
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Affiliation(s)
| | | | | | - Lucas Bleicher
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Igor Polikarpov
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Fabio C. L. Almeida
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil and
| | - Debora Foguel
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
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Busso C, Bleicher L, Ferreira-Júnior JR, Barros MH. Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding. FEBS Lett 2010; 584:1609-14. [DOI: 10.1016/j.febslet.2010.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/08/2010] [Accepted: 03/15/2010] [Indexed: 11/30/2022]
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