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Huai Z, Yang H, Sun Z. Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations. J Comput Aided Mol Des 2021; 35:643-656. [PMID: 33759016 DOI: 10.1007/s10822-021-00382-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
Human purine nucleoside phosphorylase (hPNP) plays a significant role in the catabolism of deoxyguanosine. The trimeric protein is an important target in the treatment of T-cell cancers and autoimmune disorders. Experimental studies on the inhibition of the hPNP observe that the first ligand bound to one of three subunits effectively inhibits the protein, while the binding of more ligands to the subsequent sites shows negative cooperativities. In this work, we performed extensive end-point and alchemical free energy calculations to determine the binding thermodynamics of the trimeric protein-ligand system. 13 Immucillin inhibitors with experimental results are under calculation. Two widely accepted charge schemes for small molecules including AM1-BCC and RESP are adopted for ligands. The results of RESP are in better agreement with the experimental reference. Further investigations of the interaction networks in the protein-ligand complexes reveal that several residues play significant roles in stabilizing the complex structure. The most commonly observed ones include PHE200, GLU201, MET219, and ASN243. The conformations of the protein in different protein-ligand complexes are observed to be similar. We expect these insights to aid the development of potent drugs targeting hPNP.
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Affiliation(s)
- Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, 200062, China
| | - Huaiyu Yang
- College of Engineering, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, 200062, China.
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2
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Calcagno DM, Zhang C, Toomu A, Huang K, Ninh VK, Miyamoto S, Aguirre AD, Fu Z, Heller Brown J, King KR. SiglecF(HI) Marks Late-Stage Neutrophils of the Infarcted Heart: A Single-Cell Transcriptomic Analysis of Neutrophil Diversification. J Am Heart Assoc 2021; 10:e019019. [PMID: 33525909 PMCID: PMC7955351 DOI: 10.1161/jaha.120.019019] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background Neutrophils are thought to be short‐lived first responders to tissue injuries such as myocardial infarction (MI), but little is known about their diversification or dynamics. Methods and Results We permanently ligated the left anterior descending coronary arteries of mice and performed single‐cell RNA sequencing and analysis of >28 000 neutrophil transcriptomes isolated from the heart, peripheral blood, and bone marrow of mice on days 1 to 4 after MI or at steady‐state. Unsupervised clustering of cardiac neutrophils revealed 5 major subsets, 3 of which originated in the bone marrow, including a late‐emerging granulocyte expressing SiglecF, a marker classically used to define eosinophils. SiglecFHI neutrophils represented ≈25% of neutrophils on day 1 and grew to account for >50% of neutrophils by day 4 post‐MI. Validation studies using quantitative polymerase chain reaction of fluorescent‐activated cell sorter sorted Ly6G+SiglecFHI and Ly6G+SiglecFLO neutrophils confirmed the distinct nature of these populations. To confirm that the cells were neutrophils rather than eosinophils, we infarcted GATA‐deficient mice (∆dblGATA) and observed similar quantities of infiltrating Ly6G+SiglecFHI cells despite marked reductions of conventional eosinophils. In contrast to other neutrophil subsets, Ly6G+SiglecFHI neutrophils expressed high levels of Myc‐regulated genes, which are associated with longevity and are consistent with the persistence of this population on day 4 after MI. Conclusions Overall, our data provide a spatial and temporal atlas of neutrophil specialization in response to MI and reveal a dynamic proinflammatory cardiac Ly6G+SigF+(Myc+NFϰB+) neutrophil that has been overlooked because of negative selection.
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Affiliation(s)
- David M Calcagno
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Claire Zhang
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Avinash Toomu
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Kenneth Huang
- Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
| | - Van K Ninh
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Shigeki Miyamoto
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Aaron D Aguirre
- Cardiology Division Center for Systems Biology Wellman Center for Photomedicine Massachusetts General Hospital Boston MA.,Harvard Medical School Boston MA
| | - Zhenxing Fu
- Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
| | - Joan Heller Brown
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Kevin R King
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA.,Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
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3
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Timofeev VI, Zhukhlistova NE, Abramchik YA, Muravieva TI, Esipov RS, Kuranova IP. Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir. Acta Crystallogr F Struct Biol Commun 2018; 74:402-409. [PMID: 29969103 PMCID: PMC6038453 DOI: 10.1107/s2053230x18008087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/31/2018] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive targets for drug design against some pathogens. Acyclovir (ACV) is an acyclic derivative of the PNP substrate guanosine and is used as an antiviral drug for the treatment of some human viral infections. The crystalline complex of E. coli PNP with acyclovir was prepared by co-crystallization in microgravity using counter-diffusion through a gel layer in a capillary. The structure of the E. coli PNP-ACV complex was solved at 2.32 Å resolution using the molecular-replacement method. The ACV molecule is observed in two conformations and sulfate ions were located in both the nucleoside-binding and phosphate-binding pockets of the enzyme. A comparison with the complexes of other hexameric and trimeric PNPs with ACV shows the similarity in acyclovir binding by these enzymes.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Nadezhda E. Zhukhlistova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
| | - Yuliya A. Abramchik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
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Hydroxyl-related differences for three dietary flavonoids as inhibitors of human purine nucleoside phosphorylase. Int J Biol Macromol 2018; 118:588-598. [PMID: 29894785 DOI: 10.1016/j.ijbiomac.2018.06.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 01/19/2023]
Abstract
In this work, the hydroxyl-related differences of binding properties and inhibitory activities of dietary flavonoids, namely chrysin, baicalein and apigenin against purine nucleoside phosphorylase (PNP) were investigated. It was found that the hydroxylation on position C4' of chrysin (→apigenin) mildly decreased the binding affinities for PNP, whereas on the position C6 of chrysin (→baicalein) significantly increased binding affinities. Comparatively, the hydroxylation on position C4' and C6 greatly improved their PNP inhibitory effects. The IC50 values of apigenin and baicalein were 6.09 × 10-5 M and 8.94 × 10-5 M, respectively, which is significantly lower than that of chrysin (2.13 × 10-4 M). Results from molecular modeling revealed that there are two binding sites, i.e. active site (major) and tryptophan site (minor) on PNP, and the binding of these flavonoids might induce a serious conformational destabilization of PNP as a result of altering the micro-environment and morphology by flavonoids.
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Dalberto PF, Rodrigues-Junior V, Almeida Falcão VC, Pinto AFM, Abbadi BL, Bizarro CV, Basso LA, Villela AD, Santos DS. Assessing the role of deoD gene in Mycobacterium tuberculosis in vitro growth and macrophage infection. Microb Pathog 2018; 119:60-64. [PMID: 29608932 DOI: 10.1016/j.micpath.2018.03.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/12/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022]
Abstract
Purine nucleoside phosphorylase from Mycobacterium tuberculosis (MtPNP), encoded by deoD gene (Rv3307), is an enzyme from the purine salvage pathway, which has been widely studied as a molecular target for the development of inhibitors with potential antimycobacterial activity. However, the role of MtPNP in tuberculosis pathogenesis and dormancy is still unknown. The present work aims to construct a deoD knockout strain from M. tuberculosis, to evaluate the role of MtPNP in the growth of M. tuberculosis under oxygenated condition and in a dormancy model, and to assess whether deoD gene is important for M. tuberculosis invasion and growth in macrophages. The construction of a knockout strain for deoD gene was confirmed at DNA level by PCR and protein level by Western blot and LC-MS/MS. The deoD gene is not required for M. tuberculosis growth and survival under oxygenated and hypoxic conditions. The disruption of deoD gene did not affect mycobacterial ability to invade and grow in RAW 264.7 cells under the experimental conditions employed here.
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Affiliation(s)
- Pedro Ferrari Dalberto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Valnês Rodrigues-Junior
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Virginia Carla Almeida Falcão
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Antônio Frederico Michel Pinto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Bruno Lopes Abbadi
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, Brazil
| | - Anne Drumond Villela
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
| | - Diógenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
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Cattaneo G, Ubiali D, Calleri E, Rabuffetti M, Höfner GC, Wanner KT, De Moraes MC, Martinelli LK, Santos DS, Speranza G, Massolini G. Development, validation and application of a 96-well enzymatic assay based on LC-ESI-MS/MS quantification for the screening of selective inhibitors against Mycobacterium tuberculosis purine nucleoside phosphorylase. Anal Chim Acta 2016; 943:89-97. [DOI: 10.1016/j.aca.2016.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
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7
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Structural and Theoretical Evidence of the Depleted Proton Affinity of the N3-Atom in Acyclovir. CRYSTALS 2016. [DOI: 10.3390/cryst6110139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Purine and pyrimidine nucleoside and nucleotide analogs have been extensively studied as anticancer and antiviral agents. In addition to this, they have recently shown great potential against Mycobacterium Tuberculosis, the causative agent of TB. TB ranks as the tenth most common cause of death in the world. The current treatment for TB infection is limited by side effects and cost of the drugs and most importantly by the development of resistance to the therapy. Therefore the development of novel drugs, capable of overcoming the drawbacks of the existing treatments, has become the focus of many research programs. In parallel to that, a tremendous effort has been made to elucidate the unique metabolism of this pathogen with the aim to identify new possible targets. This review presents the state of the art in nucleoside and nucleotide analogs in the treatment of TB. In particular, we report on the inhibitory activity of this class of compounds, both in enzymatic and whole-cell assays, providing a brief insight to which reported target these novel compounds are hitting.
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Satoh M, Saburi H, Tanaka T, Matsuura Y, Naitow H, Shimozono R, Yamamoto N, Inoue H, Nakamura N, Yoshizawa Y, Aoki T, Tanimura R, Kunishima N. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation. FEBS Open Bio 2015. [PMID: 26199865 PMCID: PMC4506958 DOI: 10.1016/j.fob.2015.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Keap1 is useful target for the design of drugs that regulate the response to oxidative stresses. We determined two complex crystal structures of Keap1 with a small molecule ligand. The ligand binds to Keap1 so as to mimic the physiological substrate Nrf2. From molecular dynamics simulation results, the binding modes observed may be atypical in solution. Key residues for ligand binding are common between crystal and MD structures.
Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development.
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Affiliation(s)
- Mikiya Satoh
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Hajime Saburi
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Tomoyuki Tanaka
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rieko Shimozono
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Naoyoshi Yamamoto
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Hideki Inoue
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Noriko Nakamura
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Yoshitaka Yoshizawa
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Takumi Aoki
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Ryuji Tanimura
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Naoki Kunishima
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Corresponding author. Tel.: +81 791 58 2937; fax: +81 791 58 2917.
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Pérez-Toro I, Domínguez-Martín A, Choquesillo-Lazarte D, Vílchez-Rodríguez E, González-Pérez JM, Castiñeiras A, Niclós-Gutiérrez J. Lights and shadows in the challenge of binding acyclovir, a synthetic purine-like nucleoside with antiviral activity, at an apical-distal coordination site in copper(II)-polyamine chelates. J Inorg Biochem 2015; 148:84-92. [PMID: 25863571 DOI: 10.1016/j.jinorgbio.2015.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/08/2015] [Accepted: 03/09/2015] [Indexed: 11/25/2022]
Abstract
Several nucleic acid components and their metal complexes are known to be involved in crucial metabolic steps. Therefore the study of metal-nucleic acid interactions becomes essential to understand these biological processes. In this work, the synthetic purine-like nucleoside acyclovir (acv) has been used as a model of guanosine recognition with copper(II)-polyamine chelates. The chemical stability of the N9-acyclic arm in acv offers the possibility to use this antiviral drug to deepen the knowledge of metal-nucleoside interactions. Cu(II) chelates with cyclam, cyclen and trien were used as suitable receptors. All these copper(II) tetraamine chelates have in common the potential ability to yield a Cu-N7(apical) bond assisted by an appropriate (amine)N-H⋯O6(acv) intra-molecular interligand interaction. A series of synthesis afforded the following compounds: [Cu(cyclam)(ClO4)2] (1), {[Cu(cyclam)(μ2-NO3)](NO3)}n (2), {[Cu(cyclam)(μ2-SO4)]·MeOH}n (3), {[Cu(cyclam)(μ2-SO4)]·5H2O}n (4), [Cu(cyclen)(H2O)]SO4·2H2O (5), [Cu(cyclen)(H2O)]SO4·3H2O (6), [Cu(trien)(acv)](NO3)2·acv (7) and [Cu(trien)(acv)]SO4·0.71H2O (8). All these compounds have been characterized by X-ray crystallography and FT-IR spectroscopy. Our results reveal that the macrochelates Cu(cyclen)(2+) and Cu(cyclam)(2+) are unable to bind acv at an apical site. In contrast, the Cu(trien)(2+) complex has proved to be an efficient receptor for acv in compounds (7) and (8). In the ternary complex [Cu(trien)(acv)](2+), the metal binding pattern of acv consists of an apical Cu-N7 bond assisted by an intra-molecular (primary amino)N-H⋯O6(acv) interligand interaction. Structural comparisons reveal that this unprecedented apical role of acv is due to the acyclic nature of trien together with the ability of the Cu(trien)(2+) chelate to generate five-coordinated (type 4+1) copper(II) complexes.
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Affiliation(s)
- Inmaculada Pérez-Toro
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Alicia Domínguez-Martín
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain.
| | - Duane Choquesillo-Lazarte
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Av. de las Palmeras 4, E-18100 Armilla, Granada, Spain
| | - Esther Vílchez-Rodríguez
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | | | - Alfonso Castiñeiras
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan Niclós-Gutiérrez
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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Synthesis and biological evaluation of cationic fullerene quinazolinone conjugates and their binding mode with modeled Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase enzyme. J Mol Model 2013; 19:3201-17. [PMID: 23625031 DOI: 10.1007/s00894-013-1820-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 03/07/2013] [Indexed: 10/26/2022]
Abstract
The present work reports a series of novel cationic fullerene derivatives bearing a substituted-quinazolinone moiety as a side arm. Fullerene-quinazolinone conjugates synthesized using the 1,3-dipolar cycloaddition reaction of C60 with azomethine ylides generated from the corresponding Schiff bases of substituted quinazolinone were characterized by elemental analysis, FT-IR, (1)H NMR, (13)C NMR and ESI-MS and screened for their antibacterial activity against Mycobacterium tuberculosis (H 37 Rv strain). All the compounds exhibited significant activity with the most effective having MIC in the range of 1.562-3.125 μg/mL. Compound 9f exhibited good biological activity compared to standard drugs. We developed a computational strategy based on the modeled M. tuberculosis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) using homology modeling techniques and studied its binding pattern with synthesized fullerene derivatives. We then explored the surface geometry of the protein to place the cage adjacent to the active site while optimizing its quinazolinone side arm to establish H bonding with active site residues.
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12
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Munack S, Leroux V, Roderer K, Ökvist M, van Eerde A, Gundersen LL, Krengel U, Kast P. When Inhibitors Do Not Inhibit: Critical Evaluation of Rational Drug Design Targeting Chorismate Mutase fromMycobacterium tuberculosis. Chem Biodivers 2012; 9:2507-27. [DOI: 10.1002/cbdv.201200322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Indexed: 12/16/2022]
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13
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de Giuseppe PO, Martins NH, Meza AN, dos Santos CR, Pereira HD, Murakami MT. Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases. PLoS One 2012; 7:e44282. [PMID: 22957058 PMCID: PMC3434127 DOI: 10.1371/journal.pone.0044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 07/31/2012] [Indexed: 01/07/2023] Open
Abstract
The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.
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Affiliation(s)
- Priscila O. de Giuseppe
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Nadia H. Martins
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Andreia N. Meza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila R. dos Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Humberto D’Muniz Pereira
- Instituto de Física de São Carlos, Grupo de Cristalografia, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Mario T. Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- * E-mail:
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14
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Konrad A, Piškur J, Liberles DA. The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1. Gene 2012; 510:154-61. [PMID: 22967797 DOI: 10.1016/j.gene.2012.08.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/15/2022]
Abstract
Nucleoside phosphorylases are essential for the salvage and catabolism of nucleotides in bacteria and other organisms, and members of this enzyme superfamily have been of interest for the development of antimicrobial and cancer therapies. The nucleotide phosphorylase superfamily 1 encompasses a number of different enzymes which share a general superfold and catalytic mechanism, while they differ in the nature of the nucleophiles used and in the nature of characteristic active site residues. Recently, one subfamily, the uridine phosphorylases, has been subdivided into two types which differ with respect to the mechanism of transition state stabilization, as dictated by differences in critical amino acid residues. Little is known about the phylogenetic distribution and relationship of the two different types, as well as the relationship to other NP-1 superfamily members. Here comparative genomic analysis illustrates that UP-1s and UP-2s fall into monophyletic groups and are biased with respect to species representation. UP-1 evolved in Gram negative bacteria, while Gram positive species tend to predominantly contain UP-2. PNP (a sister clade to all UPs) contains both Gram positive and Gram negative species. The findings imply that the nucleoside phosphorylase superfamily 1 evolved through a series of three important duplications, leading to the separate, monophyletic enzyme families, coupled to individual lateral transfer events. Extensive horizontal transfer explains the occurrence of unexpected uridine phosphorylases in some genomes. This study provides a basis for understanding the evolution of uridine and purine nucleoside phosphorylases with respect to DNA/RNA metabolism and with potential utility in the design of antimicrobial and anti-tumor drugs.
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Affiliation(s)
- Anke Konrad
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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