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Anchau Wegermann C, Santana Bezerra E, Gomes de Macedo Sant'Anna I, Ortega De Oliveira PC, da Costa Silva R, Rocco Machado T, Wanderley Tinoco L, Vieira de Souza MCB, Pascutti P, Santos Boechat FDC, de Moraes MC. Insights into nucleoside hydrolase from Leishmania donovani inhibition: A new bioaffinity chromatography-based screening assay and docking studies. Bioorg Chem 2024; 146:107302. [PMID: 38521010 DOI: 10.1016/j.bioorg.2024.107302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
Leishmaniasis, a group of neglected infectious diseases, encompasses a serious health concern, particularly with visceral leishmaniasis exhibiting potentially fatal outcomes. Nucleoside hydrolase (NH) has a fundamental role in the purine salvage pathway, crucial for Leishmania donovani survival, and presents a promising target for developing new drugs for visceral leishmaniasis treatment. In this study, LdNH was immobilized into fused silica capillaries, resulting in immobilized enzyme reactors (IMERs). The LdNH-IMER activity was monitored on-flow in a multidimensional liquid chromatography system, with the IMER in the first dimension. A C18 analytical column in the second dimension furnished the rapid separation of the substrate (inosine) and product (hypoxanthine), enabling direct enzyme activity monitoring through product quantification. LdNH-IMER exhibited high stability and was characterized by determining the Michaelis-Menten constant. A known inhibitor (1-(β-d-Ribofuranosyl)-4-quinolone derivative) was used as a model to validate the established method in inhibitor recognition. Screening of three additional derivatives of 1-(β-d-Ribofuranosyl)-4-quinolone led to the discovery of novel inhibitors, with compound 2a exhibiting superior inhibitory activity (Ki = 23.37 ± 3.64 µmol/L) compared to the employed model inhibitor. Docking and Molecular Dynamics studies provided crucial insights into inhibitor interactions at the enzyme active site, offering valuable information for developing new LdNH inhibitors. Therefore, this study presents a novel screening assay and contributes to the development of potent LdNH inhibitors.
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Affiliation(s)
- Camila Anchau Wegermann
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil; Laboratório GQCBio, Grupo de Química de Coordenação Biológica, Departamento de Química Geral e Inorgânica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Evelyn Santana Bezerra
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Isabella Gomes de Macedo Sant'Anna
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Pamella Christina Ortega De Oliveira
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Rodrigo da Costa Silva
- Laboratório LNHC, Instituto de Química, Departamento de Química Orgânica, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Thamires Rocco Machado
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luzineide Wanderley Tinoco
- Núcleo de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, 21941-902 Rio de Janeiro, RJ, Brazil
| | | | - Pedro Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda da Costa Santos Boechat
- Laboratório LNHC, Instituto de Química, Departamento de Química Orgânica, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Marcela Cristina de Moraes
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil.
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2
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Patrone M, Galasyn GS, Kerin F, Nyitray MM, Parkin DW, Stockman BJ, Degano M. A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis. J Biol Chem 2023; 299:105077. [PMID: 37482279 PMCID: PMC10474468 DOI: 10.1016/j.jbc.2023.105077] [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: 04/11/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023] Open
Abstract
Pathogenic parasites of the Trichomonas genus are causative agents of sexually transmitted diseases affecting millions of individuals worldwide and whose outcome may include stillbirths and enhanced cancer risks and susceptibility to HIV infection. Trichomonas vaginalis relies on imported purine and pyrimidine nucleosides and nucleobases for survival, since it lacks the enzymatic activities necessary for de novo biosynthesis. Here we show that T. vaginalis additionally lacks homologues of the bacterial or mammalian enzymes required for the synthesis of the nicotinamide ring, a crucial component in the redox cofactors NAD+ and NADP. Moreover, we show that a yet fully uncharacterized T. vaginalis protein homologous to bacterial and protozoan nucleoside hydrolases is active as a pyrimidine nucleosidase but shows the highest specificity toward the NAD+ metabolite nicotinamide riboside. Crystal structures of the trichomonal riboside hydrolase in different states reveals novel intermediates along the nucleoside hydrolase-catalyzed hydrolytic reaction, including an unexpected asymmetry in the homotetrameric assembly. The active site structure explains the broad specificity toward different ribosides and offers precise insights for the engineering of specific inhibitors that may simultaneously target different essential pathways in the parasite.
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Affiliation(s)
- Marco Patrone
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy; Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
| | - Gregory S Galasyn
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Fiona Kerin
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Mattias M Nyitray
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - David W Parkin
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Brian J Stockman
- Department of Chemistry, Adelphi University, Garden City, New York, USA.
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy; Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy.
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3
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Palatnik-de-Sousa CB. Nucleoside Hydrolase NH 36: A Vital Enzyme for the Leishmania Genus in the Development of T-Cell Epitope Cross-Protective Vaccines. Front Immunol 2019; 10:813. [PMID: 31040850 PMCID: PMC6477039 DOI: 10.3389/fimmu.2019.00813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/27/2019] [Indexed: 01/27/2023] Open
Abstract
NH36 is a vital enzyme of the DNA metabolism and a specific target for anti-Leishmania chemotherapy. We developed second-generation vaccines composed of the FML complex or its main native antigen, the NH36 nucleoside hydrolase of Leishmania (L.) donovani and saponin, and a DNA vaccine containing the NH36 gene. All these vaccines were effective in prophylaxis and treatment of mice and dog visceral leishmaniasis (VL). The FML-saponin vaccine became the first licensed veterinary vaccine against leishmaniasis (Leishmune®) which reduced the incidence of human and canine VL in endemic areas. The NH36, DNA or recombinant protein vaccines induced a Th1 CD4+IFN-γ+ mediated protection in mice. Efficacy against VL was mediated by a CD4+TNF-α T lymphocyte response against the NH36-F3 domain, while against tegumentary leishmaniasis (TL) a CD8+ T lymphocyte response to F1 was also required. These domains were 36-41 % more protective than NH36, and a recombinant F1F3 chimera was 21% stronger than the domains, promoting a 99.8% reduction of the parasite load. We also identified the most immunogenic NH36 domains and epitopes for PBMC of active human VL, cured or asymptomatic and DTH+ patients. Currently, the NH36 subunit recombinant vaccine is turning into a multi-epitope T cell synthetic vaccine against VL and TL.
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Affiliation(s)
- Clarisa Beatriz Palatnik-de-Sousa
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Faculty of Medicine, Institute for Research in Immunology, University of São Paulo, São Paulo, Brazil
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4
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Kores K, Lešnik S, Bren U, Janežič D, Konc J. Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. J Chem Inf Model 2019; 59:2467-2478. [PMID: 30883115 DOI: 10.1021/acs.jcim.8b00981] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Resveratrol is a polyphenol known for its antioxidant and anti-inflammatory properties, which support its use as a treatment for variety of diseases. There are already known connections of resveratrol to chemoprevention of cancer because of its ability to prevent tumor initiation and inhibit tumor promotion and progression. Resveratrol is also believed to be important in cardiovascular diseases and neurological disorders, such as Alzheimer's disease. Using an inverse molecular docking approach, we sought to find new potential targets of resveratrol. Docking of resveratrol into each ProBiS predicted binding site of >38 000 protein structures from the Protein Data Bank was examined, and a number of novel potential targets into which resveratrol was docked successfully were found. These explain known actions or predict new effects of resveratrol. The results included three human proteins that are already known to bind resveratrol. A majority of proteins discovered however have no already described connections with resveratrol. We report new potential target human proteins and proteins connected with different organisms into which resveratrol can dock. Our results reveal previously unknown potential target human proteins, whose connection with cardiovascular and neurological disorders could lead to new potential treatments for variety of diseases. We believe that our research could help in future experimental studies on revestratol bioactivity in humans.
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Affiliation(s)
- Katarina Kores
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Urban Bren
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia.,National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Dušanka Janežič
- University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
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5
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Lenz SAP, Wetmore SD. Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations. J Comput Aided Mol Des 2018; 32:1375-1388. [PMID: 30478756 DOI: 10.1007/s10822-018-0178-y] [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: 07/20/2018] [Accepted: 11/21/2018] [Indexed: 11/25/2022]
Abstract
Parasitic protozoa rely on nucleoside hydrolases that play key roles in the purine salvage pathway by catalyzing the hydrolytic cleavage of the N-glycosidic bond that connects nucleobases to ribose sugars. Cytidine-uridine nucleoside hydrolase (CU-NH) is generally specific toward pyrimidine nucleosides; however, previous work has shown that replacing two active site residues with Tyr, specifically the Thr223Tyr and Gln227Tyr mutations, allows CU-NH to process inosine. The current study uses molecular dynamics (MD) simulations to gain atomic-level insight into the activity of wild-type and mutant E. coli CU-NH toward inosine. By examining systems that differ in the identity and protonation states of active site catalytic residues, key enzyme-substrate interactions that dictate the substrate specificity of CU-NH are identified. Regardless of the wild-type or mutant CU-NH considered, our calculations suggest that inosine binding is facilitated by interactions of the ribose moiety with active site residues and Ca2+, and π-interactions between two His residues (His82 and His239) and the nucleobase. However, the lack of observed activity toward inosine for wild-type CU-NH is explained by no residue being correctly aligned to stabilize the departing nucleobase. In contrast, a hydrogen-bonding network between hypoxanthine and a newly identified general acid (Asp15) is present when the two Tyr mutations are engineered into the active site. Investigation of the single CU-NH mutants reveals that this hydrogen-bonding network is only maintained when both Tyr mutations are present due to a π-interaction between the residues. These results rationalize previous experiments that show the single Tyr mutants are unable to efficiently hydrolyze inosine and explain how the Tyr residues work synergistically in the double mutant to stabilize the nucleobase leaving group during hydrolysis. Overall, our simulations provide a structural explanation for the substrate specificity of nucleoside hydrolases, which may be used to rationally develop new treatments for kinetoplastid diseases.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada.
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Wielgus-Kutrowska B, Grycuk T, Bzowska A. Part-of-the-sites binding and reactivity in the homooligomeric enzymes - facts and artifacts. Arch Biochem Biophys 2018; 642:31-45. [PMID: 29408402 DOI: 10.1016/j.abb.2018.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/13/2018] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
For a number of enzymes composed of several subunits with the same amino acid sequence, it was documented, or suggested, that binding of a ligand, or catalysis, is carried out by a single subunit. This phenomenon may be the result of a pre-existent asymmetry of subunits or a limiting case of the negative cooperativity, and is sometimes called "half-of-the-sites binding (or reactivity)" for dimers and could be called "part-of-the-sites binding (or reactivity)" for higher oligomers. In this article, we discuss molecular mechanisms that may result in "part-of-the-sites binding (and reactivity)", offer possible explanations why it may have a beneficial role in enzyme function, and point to experimental problems in documenting this behaviour. We describe some cases, for which such a mechanism was first reported and later disproved. We also give several examples of enzymes, for which this mechanism seems to be well documented, and profitable. A majority of enzymes identified in this study as half-of-the-sites binding (or reactive) use it in the flip-flop version, in which "half-of-the-sites" refers to a particular moment in time. In general, the various variants of the mechanism seems to be employed often by oligomeric enzymes for allosteric regulation to enhance the efficiency of enzymatic reactions in many key metabolic pathways.
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Affiliation(s)
- Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
| | - Tomasz Grycuk
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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7
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Barbosa Santos ML, Nico D, de Oliveira FA, Barreto AS, Palatnik-de-Sousa I, Carrillo E, Moreno J, de Luca PM, Morrot A, Rosa DS, Palatnik M, Bani-Corrêa C, de Almeida RP, Palatnik-de-Sousa CB. Leishmania donovani Nucleoside Hydrolase (NH36) Domains Induce T-Cell Cytokine Responses in Human Visceral Leishmaniasis. Front Immunol 2017; 8:227. [PMID: 28321221 PMCID: PMC5338038 DOI: 10.3389/fimmu.2017.00227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/16/2017] [Indexed: 11/15/2022] Open
Abstract
Development of immunoprotection against visceral leishmaniasis (VL) focused on the identification of antigens capable of inducing a Th1 immune response. Alternatively, antigens targeting the CD8 and T-regulatory responses are also relevant in VL pathogenesis and worthy of being included in a preventive human vaccine. We assessed in active and cured patients and VL asymptomatic subjects the clinical signs and cytokine responses to the Leishmania donovani nucleoside hydrolase NH36 antigen and its N-(F1), central (F2) and C-terminal (F3) domains. As markers of VL resistance, the F2 induced the highest levels of IFN-γ, IL-1β, and TNF-α and, together with F1, the strongest secretion of IL-17, IL-6, and IL-10 in DTH+ and cured subjects. F2 also promoted the highest frequencies of CD3+CD4+IL-2+TNF-α-IFN-γ-, CD3+CD4+IL-2+TNF-α+IFN-γ-, CD3+CD4+IL-2+TNF-α-IFN-γ+, and CD3+CD4+IL-2+TNF-α+IFN-γ+ T cells in cured and asymptomatic subjects. Consistent with this, the IFN-γ increase was correlated with decreased spleen (R = -0.428, P = 0.05) and liver sizes (R = -0.428, P = 0.05) and with increased hematocrit counts (R = 0.532, P = 0.015) in response to F1 domain, and with increased hematocrit (R = 0.512, P 0.02) and hemoglobin counts (R = 0.434, P = 0.05) in response to F2. Additionally, IL-17 increases were associated with decreased spleen and liver sizes in response to F1 (R = -0.595, P = 0.005) and F2 (R = -0.462, P = 0.04). Conversely, F1 and F3 increased the CD3+CD8+IL-2+TNF-α-IFN-γ-, CD3+CD8+IL-2+TNF-α+IFN-γ-, and CD3+CD8+IL-2+TNF-α+IFN-γ+ T cell frequencies of VL patients correlated with increased spleen and liver sizes and decreased hemoglobin and hematocrit values. Therefore, cure and acquired resistance to VL correlate with the CD4+-Th1 and Th-17 T-cell responses to F2 and F1 domains. Clinical VL outcomes, by contrast, correlate with CD8+ T-cell responses against F3 and F1, potentially involved in control of the early infection. The in silico-predicted NH36 epitopes are conserved and bind to many HL-DR and HLA and B allotypes. No human vaccine against Leishmania is available thus far. In this investigation, we identified the NH36 domains and epitopes that induce CD4+ and CD8+ T cell responses, which could be used to potentiate a human universal T-epitope vaccine against leishmaniasis.
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Affiliation(s)
- Micheli Luize Barbosa Santos
- Laboratório de Biologia Molecular, Hospital Universitário, Departamento de Medicina, Universidade Federal de Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Dirlei Nico
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabrícia Alvisi de Oliveira
- Laboratório de Biologia Molecular, Hospital Universitário, Departamento de Medicina, Universidade Federal de Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Aline Silva Barreto
- Laboratório de Biologia Molecular, Hospital Universitário, Departamento de Medicina, Universidade Federal de Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Iam Palatnik-de-Sousa
- Laboratório de Biometrologia, Programa de Pós-Graduação em Metrologia, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eugenia Carrillo
- WHO Collaborating Centre for Leishmaniasis, Instituto de Salud Carlos III, Centro Nacional de Microbiologia, Madrid, Comunidad de Madrid, Spain
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, Instituto de Salud Carlos III, Centro Nacional de Microbiologia, Madrid, Comunidad de Madrid, Spain
| | - Paula Mello de Luca
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz (IOC), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Morrot
- Laboratório de Imunologia Integrada, Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela Santoro Rosa
- Faculdade de Medicina, Instituto de Investigação em Imunologia, Universidade de São Paulo (USP), São Paulo, Brazil
- Laboratório de Vacinas experimentais, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Marcos Palatnik
- Laboratório de Imunohematologia, Faculdade de Medicina, Hospital Universitário Clementino Fraga-Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Bani-Corrêa
- Departamento de Morfologia, Universidade Federal de Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Roque Pacheco de Almeida
- Laboratório de Biologia Molecular, Hospital Universitário, Departamento de Medicina, Universidade Federal de Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
- Faculdade de Medicina, Instituto de Investigação em Imunologia, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Clarisa Beatriz Palatnik-de-Sousa
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
- Faculdade de Medicina, Instituto de Investigação em Imunologia, Universidade de São Paulo (USP), São Paulo, Brazil
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8
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Singh RK, Steyaert J, Versées W. Structural and biochemical characterization of the nucleoside hydrolase from C. elegans reveals the role of two active site cysteine residues in catalysis. Protein Sci 2017; 26:985-996. [PMID: 28218438 DOI: 10.1002/pro.3141] [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: 12/06/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/28/2022]
Abstract
Nucleoside hydrolases (NHs) catalyze the hydrolysis of the N-glycoside bond in ribonucleosides and are found in all three domains of life. Although in parasitic protozoa a role in purine salvage has been well established, their precise function in bacteria and higher eukaryotes is still largely unknown. NHs have been classified into three homology groups based on the conservation of active site residues. While many structures are available of representatives of group I and II, structural information for group III NHs is lacking. Here, we report the first crystal structure of a purine-specific nucleoside hydrolase belonging to homology group III from the nematode Caenorhabditis elegans (CeNH) to 1.65Å resolution. In contrast to dimeric purine-specific NHs from group II, CeNH is a homotetramer. A cysteine residue that characterizes group III NHs (Cys253) structurally aligns with the catalytic histidine and tryptophan residues of group I and group II enzymes, respectively. Moreover, a second cysteine (Cys42) points into the active site of CeNH. Substrate docking shows that both cysteine residues are appropriately positioned to interact with the purine ring. Site-directed mutagenesis and kinetic analysis proposes a catalytic role for both cysteines residues, with Cys253 playing the most prominent role in leaving group activation.
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Affiliation(s)
- Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
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9
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Alves-Silva MV, Nico D, Morrot A, Palatnik M, Palatnik-de-Sousa CB. A Chimera Containing CD4+ and CD8+ T-Cell Epitopes of the Leishmania donovani Nucleoside Hydrolase (NH36) Optimizes Cross-Protection against Leishmania amazonesis Infection. Front Immunol 2017; 8:100. [PMID: 28280494 PMCID: PMC5322207 DOI: 10.3389/fimmu.2017.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/20/2017] [Indexed: 12/23/2022] Open
Abstract
The Leishmania donovani nucleoside hydrolase (NH36) and NH A34480 of Leishmania amazonensis share 93% of sequence identity. In mice, the NH36 induced protection against visceral leishmaniasis is mediated by a CD4+ T cell response against its C-terminal domain (F3). Besides this CD4+ Th1 response, prevention and cure of L. amazonensis infection require also additional CD8+ and regulatory T-cell responses to the NH36 N-terminal (F1 domain). We investigated if mice vaccination with F1 and F3 domains cloned in tandem, in a recombinant chimera, with saponin, optimizes the vaccine efficacy against L. amazonensis infection above the levels promoted by the two admixed domains or by each domain independently. The chimera induced the highest IgA, IgG, and IgG2a anti-NH36 antibody, IDR, IFN-γ, and IL-10 responses, while TNF-α was more secreted by mice vaccinated with F3 or all F3-contaning vaccines. Additionally, the chimera and the F1 vaccine also induced the highest proportions of CD4+ and CD8+ T cells secreting IL-2, TNF-α, or IFN-γ alone, TNF-α in combination with IL-2 or IFN-γ, and of CD4+ multifunctional cells secreting IL-2, TNF-α, and IFN-γ. Correlating with the immunological results, the strongest reductions of skin lesions sizes were determined by the admixed domains (80%) and by the chimera (84%), which also promoted the most pronounced and significant reduction of the parasite load (99.8%). Thus, the epitope presentation in a recombinant chimera optimizes immunogenicity and efficacy above the levels induced by the independent or admixed F1 and F3 domains. The multiparameter analysis disclosed that the Th1-CD4+ T helper response induced by the chimera is mainly directed against its FRYPRPKHCHTQVA epitope. Additionally, the YPPEFKTKL epitope of F1 induced the second most important CD4+ T cell response, and, followed by the DVAGIVGVPVAAGCT, FMLQILDFYTKVYE, and ELLAITTVVGNQ sequences, also the most potent CD8+ T cell responses and IL-10 secretion. Remarkably, the YPPEFKTKL epitope shows high amino acid identity with a multipotent PADRE sequence and stimulates simultaneously the CD4+, CD8+ T cell, and a probable T regulatory response. With this approach, we advanced in the design of a NH36 polytope vaccine capable of inducing cross-protection to cutaneous leishmaniasis.
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Affiliation(s)
- Marcus Vinícius Alves-Silva
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dirlei Nico
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Morrot
- Laboratório de Imunologia Integrada, Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Palatnik
- Programa de Pós-Graduação em Clínica Médica, Faculdade de Medicina-Hospital Universitario Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarisa B. Palatnik-de-Sousa
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Faculdade de Medicina, Instituto de Investigação em Imunologia, Universidade de São Paulo (USP), São Paulo, São Paulo, Brazil
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10
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Lenz SAP, Kohout JD, Wetmore SD. Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis. J Phys Chem B 2016; 120:12795-12806. [PMID: 27933981 DOI: 10.1021/acs.jpcb.6b09620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO-···H2O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol-1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO- as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H2O nucleophile) by ∼15-20 kJ mol-1, the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH- nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol-1. Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol-1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Johnathan D Kohout
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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11
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Chen N, Zhao Y, Lu J, Wu R, Cao Z. Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase. J Chem Theory Comput 2015; 11:3180-8. [DOI: 10.1021/acs.jctc.5b00045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People’s Republic of China
| | - Yuan Zhao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
| | - Jianing Lu
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People’s Republic of China
| | - Zexing Cao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
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12
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Immucillins Impair Leishmania (L.) infantum chagasi and Leishmania (L.) amazonensis Multiplication In Vitro. PLoS One 2015; 10:e0124183. [PMID: 25909893 PMCID: PMC4409337 DOI: 10.1371/journal.pone.0124183] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 02/26/2015] [Indexed: 11/25/2022] Open
Abstract
Chemotherapy against visceral leishmaniasis is associated with high toxicity and drug resistance. Leishmania parasites are purine auxotrophs that obtain their purines from exogenous sources. Nucleoside hydrolases release purines from nucleosides and are drug targets for anti-leishmanial drugs, absent in mammal cells. We investigated the substrate specificity of the Leishmania (L.) donovani recombinant nucleoside hydrolase NH36 and the inhibitory effect of the immucillins IA (ImmA), DIA (DADMe-ImmA), DIH (DADMe-ImmH), SMIH (SerMe-ImmH), IH (ImmH), DIG (DADMe-ImmG), SMIG (SerMe-ImmG) and SMIA (SerME-ImmA) on its enzymatic activity. The inhibitory effects of immucillins on the in vitro multiplication of L. (L.) infantum chagasi and L. (L.) amazonensis promastigotes were determined using 0.05–500 μM and, when needed, 0.01–50 nM of each drug. The inhibition on multiplication of L. (L.) infantum chagasi intracellular amastigotes in vitro was assayed using 0.5, 1, 5 and 10 μM of IA, IH and SMIH. The NH36 shows specificity for inosine, guanosine, adenosine, uridine and cytidine with preference for adenosine and inosine. IA, IH, DIH, DIG, SMIH and SMIG immucillins inhibited L. (L.) infantum chagasi and L. (L.) amazonensis promastigote growth in vitro at nanomolar to micromolar concentrations. Promastigote replication was also inhibited in a chemically defined medium without a nucleoside source. Addition of adenosine decreases the immucillin toxicity. IA and IH inhibited the NH36 enzymatic activity (Ki = 0.080 μM for IA and 0.019 μM for IH). IA, IH and SMIH at 10 μM concentration, reduced the in vitro amastigote replication inside mice macrophages by 95% with no apparent effect on macrophage viability. Transmission electron microscopy revealed global alterations and swelling of L. (L.) infantum chagasi promastigotes after treatment with IA and IH while SMIH treatment determined intense cytoplasm vacuolization, enlarged vesicles and altered kinetoplasts. Our results suggest that IA, IH and SMIH may provide new chemotherapy agents for leishmaniasis.
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13
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Nico D, Gomes DC, Palatnik-de-Sousa I, Morrot A, Palatnik M, Palatnik-de-Sousa CB. Leishmania donovani Nucleoside Hydrolase Terminal Domains in Cross-Protective Immunotherapy Against Leishmania amazonensis Murine Infection. Front Immunol 2014; 5:273. [PMID: 24966857 PMCID: PMC4052736 DOI: 10.3389/fimmu.2014.00273] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/27/2014] [Indexed: 11/13/2022] Open
Abstract
Nucleoside hydrolases of the Leishmania genus are vital enzymes for the replication of the DNA and conserved phylogenetic markers of the parasites. Leishmania donovani nucleoside hydrolase (NH36) induced a main CD4(+) T cell driven protective response against L. chagasi infection in mice which is directed against its C-terminal domain. In this study, we used the three recombinant domains of NH36: N-terminal domain (F1, amino acids 1-103), central domain (F2 aminoacids 104-198), and C-terminal domain (F3 amino acids 199-314) in combination with saponin and assayed their immunotherapeutic effect on Balb/c mice previously infected with L. amazonensis. We identified that the F1 and F3 peptides determined strong cross-immunotherapeutic effects, reducing the size of footpad lesions to 48 and 64%, and the parasite load in footpads to 82.6 and 81%, respectively. The F3 peptide induced the strongest anti-NH36 antibody response and intradermal response (IDR) against L. amazonenis and a high secretion of IFN-γ and TNF-α with reduced levels of IL-10. The F1 vaccine, induced similar increases of IgG2b antibodies and IFN-γ and TNF-α levels, but no IDR and no reduction of IL-10. The multiparameter flow cytometry analysis was used to assess the immune response after immunotherapy and disclosed that the degree of the immunotherapeutic effect is predicted by the frequencies of the CD4(+) and CD8(+) T cells producing IL-2 or TNF-α or both. Total frequencies and frequencies of double-cytokine CD4 T cell producers were enhanced by F1 and F3 vaccines. Collectively, our multifunctional analysis disclosed that immunotherapeutic protection improved as the CD4 responses progressed from 1+ to 2+, in the case of the F1 and F3 vaccines, and as the CD8 responses changed qualitatively from 1+ to 3+, mainly in the case of the F1 vaccine, providing new correlates of immunotherapeutic protection against cutaneous leishmaniasis in mice based on T-helper TH1 and CD8(+) mediated immune responses.
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Affiliation(s)
- Dirlei Nico
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniele Crespo Gomes
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Iam Palatnik-de-Sousa
- Programa de Pós Graduação em Metrologia, Laboratório de Biometrologia, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Morrot
- Laboratório de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Palatnik
- Programa de Pós Graduação em Clínica Médica, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarisa Beatriz Palatnik-de-Sousa
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Nico D, Gomes DC, Alves-Silva MV, Freitas EO, Morrot A, Bahia D, Palatnik M, Rodrigues MM, Palatnik-de-Sousa CB. Cross-Protective Immunity to Leishmania amazonensis is Mediated by CD4+ and CD8+ Epitopes of Leishmania donovani Nucleoside Hydrolase Terminal Domains. Front Immunol 2014; 5:189. [PMID: 24822054 PMCID: PMC4013483 DOI: 10.3389/fimmu.2014.00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 04/10/2014] [Indexed: 12/11/2022] Open
Abstract
The nucleoside hydrolase (NH) of Leishmania donovani (NH36) is a phylogenetic marker of high homology among Leishmania parasites. In mice and dog vaccination, NH36 induces a CD4+ T cell-driven protective response against Leishmania chagasi infection directed against its C-terminal domain (F3). The C-terminal and N-terminal domain vaccines also decreased the footpad lesion caused by Leishmania amazonensis. We studied the basis of the crossed immune response using recombinant generated peptides covering the whole NH36 sequence and saponin for mice prophylaxis against L. amazonensis. The F1 (amino acids 1-103) and F3 peptide (amino acids 199-314) vaccines enhanced the IgG and IgG2a anti-NH36 antibodies to similar levels. The F3 vaccine induced the strongest DTH response, the highest proportions of NH36-specific CD4+ and CD8+ T cells after challenge and the highest expression of IFN-γ and TNF-α. The F1 vaccine, on the other hand, induced a weaker but significant DTH response and a mild enhancement of IFN-γ and TNF-α levels. The in vivo depletion with anti-CD4 or CD8 monoclonal antibodies disclosed that cross-protection against L. amazonensis infection was mediated by a CD4+ T cell response directed against the C-terminal domain (75% of reduction of the size of footpad lesion) followed by a CD8+ T cell response against the N-terminal domain of NH36 (57% of reduction of footpad lesions). Both vaccines were capable of inducing long-term cross-immunity. The amino acid sequence of NH36 showed 93% identity to the sequence of the NH A34480 of L. amazonensis, which also showed the presence of completely conserved predicted epitopes for CD4+ and CD8+ T cells in F1 domain, and of CD4+ epitopes differing by a single amino acid, in F1 and F3 domains. The identification of the C-terminal and N-terminal domains as the targets of the immune response to NH36 in the model of L. amazonensis infection represents a basis for the rationale development of a bivalent vaccine against leishmaniasis.
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Affiliation(s)
- Dirlei Nico
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniele Crespo Gomes
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcus Vinícius Alves-Silva
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisangela Oliveira Freitas
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Morrot
- Laboratório de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diana Bahia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcos Palatnik
- Programa de Pós Graduação em Clínica Médica Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauricio M. Rodrigues
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Terapia Celular e Molecular, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Clarisa B. Palatnik-de-Sousa
- Laboratório de Biologia e Bioquímica de Leishmania, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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15
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Giannese F, Berg M, Van der Veken P, Castagna V, Tornaghi P, Augustyns K, Degano M. Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1553-66. [PMID: 23897478 DOI: 10.1107/s0907444913010792] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 04/20/2013] [Indexed: 11/11/2022]
Abstract
Sleeping sickness is a deadly disease that primarily affects sub-Saharan Africa and is caused by protozoan parasites of the Trypanosoma genus. Trypanosomes are purine auxotrophs and their uptake pathway has long been appreciated as an attractive target for drug design. Recently, one tight-binding competitive inhibitor of the trypanosomal purine-specific nucleoside hydrolase (IAGNH) showed remarkable trypanocidal activity in a murine model of infection. Here, the enzymatic characterization of T. brucei brucei IAGNH is presented, together with its high-resolution structures in the unliganded form and in complexes with different inhibitors, including the trypanocidal compound UAMC-00363. A description of the crucial contacts that account for the high-affinity inhibition of IAGNH by iminoribitol-based compounds is provided and the molecular mechanism underlying the conformational change necessary for enzymatic catalysis is identified. It is demonstrated for the first time that metalorganic complexes can compete for binding at the active site of nucleoside hydrolase enzymes, mimicking the positively charged transition state of the enzymatic reaction. Moreover, we show that divalent metal ions can act as noncompetitive IAGNH inhibitors, stabilizing a nonproductive conformation of the catalytic loop. These results open a path for rational improvement of the potency and the selectivity of existing compounds and suggest new scaffolds that may be used as blueprints for the design of novel antitrypanosomal compounds.
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Affiliation(s)
- Francesca Giannese
- Biocrystallography Unit, Department of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, via Olgettina 58, 20132 Milano, Italy
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16
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Chen N, Ge H, Xu J, Cao Z, Wu R. Loop motion and base release in purine-specific nucleoside hydrolase: A molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1117-24. [DOI: 10.1016/j.bbapap.2013.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/25/2022]
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17
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Nico D, Feijó DF, Maran N, Morrot A, Scharfstein J, Palatnik M, Palatnik-de-Sousa CB. Resistance to visceral leishmaniasis is severely compromised in mice deficient of bradykinin B2-receptors. Parasit Vectors 2012; 5:261. [PMID: 23151408 PMCID: PMC3514163 DOI: 10.1186/1756-3305-5-261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/03/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Kinins liberated from plasma-borne kininogens, are potent innate stimulatory signals. We evaluated whether resistance to infection by Leishmania (L.) chagasi depends on activation of G-protein coupled bradykinin B2 receptors (B2R). FINDINGS B2R⁻/⁻ C57BL/6 knock-out (KOB2) and B2R⁺/⁺ C57BL/6-wild type control mice (C57) were infected with amastigotes of Leishmania (L.) chagasi. Thirty days after infection, the KOB2 mice showed 14% and 32% relative increases of liver (p< 0.017) and spleen weights (p<0.050), respectively, whereas liver parasite load increased 65% (p< 0.011) in relation to wild type mice. The relative weight increases of liver and spleen and the parasite load were positively correlated (R = 0.6911; p< 0.007 to R = 0.7629; p< 0.001, respectively). Conversely, we found a negative correlation between the increased liver relative weight and the weakened DTH response (a strong correlate to protection or natural resistance to VL) or the decreased levels of IgG2b antibodies to leishmanial antigen. Finally, we also found that IFN-γ secretion by splenocytes, an adaptive response that was significantly decreased in KOB2 mice (p< 0.002), was (i) negatively correlated to the increase in liver LDU (R = -0.6684; p = 0.035) and liver/body relative weight (R = -0.6946; p = 0.026) and (ii) positively correlated to serum IgG2b levels (R = 0.8817; p = 0.001). CONCLUSIONS We found that mice lacking B2R display increased susceptibility to the infection by Leishmania (L.) chagasi. Our findings suggest that activation of the bradykinin/B2R pathway contributes to development of host resistance to visceral leishmaniasis.
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Affiliation(s)
- Dirlei Nico
- Instituto de Microbiologia Paulo de Góes, CCS, Universidade Federal do Rio de Janeiro-UFRJ, Avda Carlos Chagas 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro 21941-902, Caixa Postal 68040, Brazil
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18
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Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B 2012; 116:1984-91. [DOI: 10.1021/jp211403j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruibo Wu
- School of
Pharmaceutical Sciences,
East Campus, Sun Yat-sen University, Guangzhou
510006, China
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Wengjin Gong
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Ting, Liu
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Zexing Cao
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
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19
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Vandemeulebroucke A, Minici C, Bruno I, Muzzolini L, Tornaghi P, Parkin DW, Versées W, Steyaert J, Degano M. Structure and Mechanism of the 6-Oxopurine Nucleosidase from Trypanosoma brucei brucei,. Biochemistry 2010; 49:8999-9010. [DOI: 10.1021/bi100697d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- An Vandemeulebroucke
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Claudia Minici
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Ilaria Bruno
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Laura Muzzolini
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Paola Tornaghi
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - David W. Parkin
- Department of Chemistry, Adelphi University, Garden City, New York 11530-0701
| | - Wim Versées
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Jan Steyaert
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Massimo Degano
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
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20
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Evaluation of nucleoside hydrolase inhibitors for treatment of African trypanosomiasis. Antimicrob Agents Chemother 2010; 54:1900-8. [PMID: 20194690 DOI: 10.1128/aac.01787-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this paper, we present the biochemical and biological evaluation of N-arylmethyl-substituted iminoribitol derivatives as potential chemotherapeutic agents against trypanosomiasis. Previously, a library of 52 compounds was designed and synthesized as potent and selective inhibitors of Trypanosoma vivax inosine-adenosine-guanosine nucleoside hydrolase (IAG-NH). However, when the compounds were tested against bloodstream-form Trypanosoma brucei brucei, only one inhibitor, N-(9-deaza-adenin-9-yl)methyl-1,4-dideoxy-1,4-imino-d-ribitol (UAMC-00363), displayed significant activity (mean 50% inhibitory concentration [IC(50)] +/- standard error, 0.49 +/- 0.31 microM). Validation in an in vivo model of African trypanosomiasis showed promising results for this compound. Several experiments were performed to investigate why only UAMC-00363 showed antiparasitic activity. First, the compound library was screened against T. b. brucei IAG-NH and inosine-guanosine nucleoside hydrolase (IG-NH) to confirm the previously demonstrated inhibitory effects of the compounds on T. vivax IAG-NH. Second, to verify the uptake of these compounds by T. b. brucei, their affinities for the nucleoside P1 and nucleoside/nucleobase P2 transporters of T. b. brucei were tested. Only UAMC-00363 displayed significant affinity for the P2 transporter. It was also shown that UAMC-00363 is concentrated in the cell via at least one additional transporter, since P2 knockout mutants of T. b. brucei displayed no resistance to the compound. Consequently, no cross-resistance to the diamidine or the melaminophenyl arsenical classes of trypanocides is expected. Third, three enzymes of the purine salvage pathway of procyclic T. b. brucei (IAG-NH, IG-NH, and methylthioadenosine phosphorylase [MTAP]) were investigated using RNA interference. The findings from all these studies showed that it is probably not sufficient to target only the nucleoside hydrolase activity to block the purine salvage pathway of T. b. brucei and that, therefore, it is possible that UAMC-00363 acts on an additional target.
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21
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Onega M, Domarkas J, Deng H, Schweiger LF, Smith TAD, Welch AE, Plisson C, Gee AD, O’Hagan D. An enzymatic route to 5-deoxy-5-[18F]fluoro-d-ribose, a [18F]-fluorinated sugar for PET imaging. Chem Commun (Camb) 2010; 46:139-41. [DOI: 10.1039/b919364b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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