1
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Roy PK, Paul A, Lalchhuanawmi S, Babu NK, Singh S. Pyridoxal kinase gene deletion leads to impaired growth, deranged redox metabolism and cell cycle arrest in Leishmania donovani. Biochimie 2024; 222:72-86. [PMID: 38403043 DOI: 10.1016/j.biochi.2024.02.009] [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: 09/14/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Pyridoxal kinase (PdxK) is a vitamin B6 salvage pathway enzyme which produces pyridoxal phosphate. We have investigated the impact of PdxK deletion in Leishmania donovani on parasite survivability, infectivity and cellular metabolism. LdPdxK mutants were generated by gene replacement strategy. All mutants showed significant reduction in growth in comparison to wild type. For PdxK mediated biochemical perturbations, only heterozygous mutants and complementation mutants were used as the growth of null mutants were compromised. Heterozygous mutant showed reduction invitro infectivity and higher cytosolic and mitochondrial ROS levels. Glutathione levels decreased significantly in heterozygous mutant indicating its involvement in cellular oxidative metabolism. Pyridoxal kinase gene deletion resulted in reduced ATP levels in parasites and arrest at G0/G1 phase of cell cycle. All these perturbations were rescued by PdxK gene complementation. This is the first report to confirm that LdPdxK plays an indispensable role in cell survival, pathogenicity, redox metabolism and cell cycle progression of L. donovani parasites. These results provide substantial evidence supporting PdxK as a therapeutic target for the development of specific antileishmanial drug candidates.
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Affiliation(s)
- Pradyot Kumar Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Anindita Paul
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Sandra Lalchhuanawmi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Neerupudi Kishore Babu
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India.
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2
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Pilesi E, Tesoriere G, Ferriero A, Mascolo E, Liguori F, Argirò L, Angioli C, Tramonti A, Contestabile R, Volontè C, Vernì F. Vitamin B6 deficiency cooperates with oncogenic Ras to induce malignant tumors in Drosophila. Cell Death Dis 2024; 15:388. [PMID: 38830901 PMCID: PMC11148137 DOI: 10.1038/s41419-024-06787-3] [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: 12/20/2023] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Vitamin B6 is a water-soluble vitamin which possesses antioxidant properties. Its catalytically active form, pyridoxal 5'-phosphate (PLP), is a crucial cofactor for DNA and amino acid metabolism. The inverse correlation between vitamin B6 and cancer risk has been observed in several studies, although dietary vitamin B6 intake sometimes failed to confirm this association. However, the molecular link between vitamin B6 and cancer remains elusive. Previous work has shown that vitamin B6 deficiency causes chromosome aberrations (CABs) in Drosophila and human cells, suggesting that genome instability may correlate the lack of this vitamin to cancer. Here we provide evidence in support of this hypothesis. Firstly, we show that PLP deficiency, induced by the PLP antagonists 4-deoxypyridoxine (4DP) or ginkgotoxin (GT), promoted tumorigenesis in eye larval discs transforming benign RasV12 tumors into aggressive forms. In contrast, PLP supplementation reduced the development of tumors. We also show that low PLP levels, induced by 4DP or by silencing the sgllPNPO gene involved in PLP biosynthesis, worsened the tumor phenotype in another Drosophila cancer model generated by concomitantly activating RasV12 and downregulating Discs-large (Dlg) gene. Moreover, we found that RasV12 eye discs from larvae reared on 4DP displayed CABs, reactive oxygen species (ROS) and low catalytic activity of serine hydroxymethyltransferase (SHMT), a PLP-dependent enzyme involved in thymidylate (dTMP) biosynthesis, in turn required for DNA replication and repair. Feeding RasV12 4DP-fed larvae with PLP or ascorbic acid (AA) plus dTMP, rescued both CABs and tumors. The same effect was produced by overexpressing catalase in RasV12 DlgRNAi 4DP-fed larvae, thus allowing to establish a relationship between PLP deficiency, CABs, and cancer. Overall, our data provide the first in vivo demonstration that PLP deficiency can impact on cancer by increasing genome instability, which is in turn mediated by ROS and reduced dTMP levels.
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Affiliation(s)
- Eleonora Pilesi
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Giulia Tesoriere
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Angelo Ferriero
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Elisa Mascolo
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Francesco Liguori
- Experimental Neuroscience and Neurological Disease Models, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
- CNR, Institute for Systems Analysis and Computer Science, 00185, Rome, Italy
| | - Luca Argirò
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Chiara Angioli
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, 00185, Rome, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, 00185, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, 00185, Rome, Italy
| | - Cinzia Volontè
- Experimental Neuroscience and Neurological Disease Models, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
- CNR, Institute for Systems Analysis and Computer Science, 00185, Rome, Italy
| | - Fiammetta Vernì
- Dept. of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy.
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3
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Tramonti A, Donkor AK, Parroni A, Musayev FN, Barile A, Ghatge MS, Graziani C, Alkhairi M, AlAwadh M, di Salvo ML, Safo MK, Contestabile R. Functional and structural properties of pyridoxal reductase (PdxI) from Escherichia coli: a pivotal enzyme in the vitamin B6 salvage pathway. FEBS J 2023; 290:5628-5651. [PMID: 37734924 PMCID: PMC10872706 DOI: 10.1111/febs.16962] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023]
Abstract
Pyridoxine 4-dehydrogenase (PdxI), a NADPH-dependent pyridoxal reductase, is one of the key players in the Escherichia coli pyridoxal 5'-phosphate (PLP) salvage pathway. This enzyme, which catalyses the reduction of pyridoxal into pyridoxine, causes pyridoxal to be converted into PLP via the formation of pyridoxine and pyridoxine phosphate. The structural and functional properties of PdxI were hitherto unknown, preventing a rational explanation of how and why this longer, detoured pathway occurs, given that, in E. coli, two pyridoxal kinases (PdxK and PdxY) exist that could convert pyridoxal directly into PLP. Here, we report a detailed characterisation of E. coli PdxI that explains this behaviour. The enzyme efficiently catalyses the reversible transformation of pyridoxal into pyridoxine, although the reduction direction is thermodynamically strongly favoured, following a compulsory-order ternary-complex mechanism. In vitro, the enzyme is also able to catalyse PLP reduction and use NADH as an electron donor, although with lower efficiency. As with all members of the aldo-keto reductase (AKR) superfamily, the enzyme has a TIM barrel fold; however, it shows some specific features, the most important of which is the presence of an Arg residue that replaces the catalytic tetrad His residue that is present in all AKRs and appears to be involved in substrate specificity. The above results, in conjunction with kinetic and static measurements of vitamins B6 in cell extracts of E. coli wild-type and knockout strains, shed light on the role of PdxI and both kinases in determining the pathway followed by pyridoxal in its conversion to PLP, which has a precise regulatory function.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Akua K. Donkor
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Alessia Parroni
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Faik N. Musayev
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Anna Barile
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Mohini. S. Ghatge
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Claudio Graziani
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Mona Alkhairi
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed AlAwadh
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Martin K. Safo
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
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4
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Moorthy H, Yadav M, Tamang N, Mavileti SK, Singla L, Choudhury AR, Sahal D, Golakoti NR. Antiplasmodial and Antimalarial Activity of 3,5-Diarylidenetetrahydro-2H-pyran-4(3H)-ones via Inhibition of Plasmodium falciparum Pyridoxal Synthase. ChemMedChem 2023; 18:e202200411. [PMID: 36251345 DOI: 10.1002/cmdc.202200411] [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: 07/26/2022] [Revised: 10/13/2022] [Indexed: 01/24/2023]
Abstract
A series of 22 different 3,5-diarylidenetetrahydro-2H-pyran-4(3H)-ones (DATPs) were synthesized, characterized, and screened for their in vitro antiplasmodial activities against chloroquine (CQ)-sensitive Pf3D7, CQ-resistant PfINDO, and artemisinin-resistant PfMRA-1240 strains of Plasmodium falciparum. DATP 19 (3,5-bis(4-hydroxy-3,5-dimethoxybenzylidene)tetrahydro-2H-pyran-4(3H)-one) was found to be the most potent (IC50 1.07 μM) against PfMRA-1240, whereas 21 (3,5-bis(3,4,5-trimethoxybenzylidene)tetrahydro-2H-pyran-4(3H)-one) showed IC50 values of 1.72 and 1.44 μM against Pf3D7 and PfINDO, respectively. Resistance indices (RI) as low as 0.2 to 0.5 for 10 (3,5-bis(4-nitrobenzylidene)tetrahydro-2H-pyran-4(3H)-one) and 20 (3,5-bis(3-nitrobenzylidene)tetrahydro-2H-pyran-4(3H)-one), and <1 for most other DATPs reveals their greater potency against resistant strains than the sensitive one. The single-crystal XRD data for DATP 21 are reported. In silico support was obtained through docking studies. Killing all three strains within 4-8 h, these DATPs showed rapid kill kinetics toward the trophozoite stage. Furthermore, DATP 18 (3,5-bis(quinolin-4-ylmethylene)tetrahydro-2H-pyran-4(3H)-one) inhibited PfPdx1 enzyme activity with IC50 20.34 μM, which is about twofold lower than that (IC50 43 μM) for an already known inhibitor 4PEHz. At an oral dose of 300 mg/kg body weight, DATPs 19 and 21 were found to be nontoxic to mice, and at 100 mg/kg body weight, DATP 19 was found to suppress parasitaemia, which led to an increase in median survival time by three days relative to untreated control mice in a malaria curative study.
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Affiliation(s)
- Hariharan Moorthy
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Mamta Yadav
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Nitesh Tamang
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Kiran Mavileti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Labhini Singla
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, S. A. S. Nagar, Manauli P.O., Mohali, Punjab, 140306, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, S. A. S. Nagar, Manauli P.O., Mohali, Punjab, 140306, India
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Nageswara Rao Golakoti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
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5
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Barra ALC, Ullah N, Morão LG, Wrenger C, Betzel C, Nascimento AS. Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions. Front Cell Infect Microbiol 2021; 11:688380. [PMID: 34327152 PMCID: PMC8313854 DOI: 10.3389/fcimb.2021.688380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is still today one of the most concerning diseases, with 219 million infections in 2019, most of them in Sub-Saharan Africa and Latin America, causing approx. 409,000 deaths per year. Despite the tremendous advances in malaria treatment and prevention, there is still no vaccine for this disease yet available and the increasing parasite resistance to already existing drugs is becoming an alarming issue globally. In this context, several potential targets for the development of new drug candidates have been proposed and, among those, the de novo biosynthesis pathway for the B6 vitamin was identified to be a promising candidate. The reason behind its significance is the absence of the pathway in humans and its essential presence in the metabolism of major pathogenic organisms. The pathway consists of two enzymes i.e. Pdx1 (PLP synthase domain) and Pdx2 (glutaminase domain), the last constituting a transient and dynamic complex with Pdx1 as the prime player and harboring the catalytic center. In this review, we discuss the structural biology of Pdx1 and Pdx2, together with and the understanding of the PLP biosynthesis provided by the crystallographic data. We also highlight the existing evidence of the effect of PLP synthesis inhibition on parasite proliferation. The existing data provide a flourishing environment for the structure-based design and optimization of new substrate analogs that could serve as inhibitors or even suicide inhibitors.
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Affiliation(s)
- Angélica Luana C Barra
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil.,Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Luana G Morão
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
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Rokkam SK, Yadav M, Joshi M, Choudhury AR, Sahal D, Golakoti NR. Synthesis, in vitro anti-plasmodial potency, in-silico-cum-SPR binding with inhibition of PfPyridoxal synthase and rapid parasiticidal action by 3,5-bis{( E) arylidene}- N-methyl-4-piperidones. NEW J CHEM 2021. [DOI: 10.1039/d1nj04604g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DANMPs have been identified as new pharmacophores that have the ability to target PfPyridoxal synthase and cause rapid killing of the malaria parasite.
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Affiliation(s)
- Siva Kumar Rokkam
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Mamta Yadav
- Malaria Drug Discovery Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Mayank Joshi
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Sector 81, S. A. S. Nagar, Manauli PO, Mohali, Punjab, 140306, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Sector 81, S. A. S. Nagar, Manauli PO, Mohali, Punjab, 140306, India
| | - Dinkar Sahal
- Malaria Drug Discovery Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Nageswara Rao Golakoti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
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7
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Contestabile R, di Salvo ML, Bunik V, Tramonti A, Vernì F. The multifaceted role of vitamin B 6 in cancer: Drosophila as a model system to investigate DNA damage. Open Biol 2020; 10:200034. [PMID: 32208818 PMCID: PMC7125957 DOI: 10.1098/rsob.200034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A perturbed uptake of micronutrients, such as minerals and vitamins, impacts on different human diseases, including cancer and neurological disorders. Several data converge towards a crucial role played by many micronutrients in genome integrity maintenance and in the establishment of a correct DNA methylation pattern. Failure in the proper accomplishment of these processes accelerates senescence and increases the risk of developing cancer, by promoting the formation of chromosome aberrations and deregulating the expression of oncogenes. Here, the main recent evidence regarding the impact of some B vitamins on DNA damage and cancer is summarized, providing an integrated and updated analysis, mainly centred on vitamin B6. In many cases, it is difficult to finely predict the optimal vitamin rate that is able to protect against DNA damage, as this can be influenced by a given individual's genotype. For this purpose, a precious resort is represented by model organisms which allow limitations imposed by more complex systems to be overcome. In this review, we show that Drosophila can be a useful model to deeply understand mechanisms underlying the relationship between vitamin B6 and genome integrity.
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Affiliation(s)
- Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy
| | - Victoria Bunik
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia.,Sechenov Medical University, Sechenov University, 119048 Moscow, Russia
| | - Angela Tramonti
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Pl.e A. Moro, 5, 00185 Roma, Italy
| | - Fiammetta Vernì
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Pl.e A. Moro, 5, 00185 Roma, Italy
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8
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020; 295:701-714. [PMID: 31767680 PMCID: PMC6970920 DOI: 10.1074/jbc.aw119.008150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Apicomplexa phylum comprises diverse parasitic organisms that have evolved from a free-living ancestor. These obligate intracellular parasites exhibit versatile metabolic capabilities reflecting their capacity to survive and grow in different hosts and varying niches. Determined by nutrient availability, they either use their biosynthesis machineries or largely depend on their host for metabolite acquisition. Because vitamins cannot be synthesized by the mammalian host, the enzymes required for their synthesis in apicomplexan parasites represent a large repertoire of potential therapeutic targets. Here, we review recent advances in metabolic reconstruction and functional studies coupled to metabolomics that unravel the interplay between biosynthesis and salvage of vitamins and cofactors in apicomplexans. A particular emphasis is placed on Toxoplasma gondii, during both its acute and latent stages of infection.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
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9
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49928-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Barile A, Tramonti A, di Salvo ML, Nogués I, Nardella C, Malatesta F, Contestabile R. Allosteric feedback inhibition of pyridoxine 5'-phosphate oxidase from Escherichia coli. J Biol Chem 2019; 294:15593-15603. [PMID: 31484724 DOI: 10.1074/jbc.ra119.009697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/02/2019] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the synthesis of pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, takes place through the so-called deoxyxylulose 5-phosphate-dependent pathway, whose last step is pyridoxine 5'-phosphate (PNP) oxidation to PLP, catalyzed by the FMN-dependent enzyme PNP oxidase (PNPOx). This enzyme plays a pivotal role in controlling intracellular homeostasis and bioavailability of PLP. PNPOx has been proposed to undergo product inhibition resulting from PLP binding at the active site. PLP has also been reported to bind tightly at a secondary site, apparently without causing PNPOx inhibition. The possible location of this secondary site has been indicated by crystallographic studies as two symmetric surface pockets present on the PNPOx homodimer, but this site has never been verified by other experimental means. Here, we demonstrate, through kinetic measurements, that PLP inhibition is actually of a mixed-type nature and results from binding of this vitamer at an allosteric site. This interpretation was confirmed by the characterization of a mutated PNPOx form, in which substrate binding at the active site is heavily hampered but PLP binding is preserved. Structural and functional connections between the active site and the allosteric site were indicated by equilibrium binding experiments, which revealed different PLP-binding stoichiometries with WT and mutant PNPOx forms. These observations open up new horizons on the mechanisms that regulate E. coli PNPOx, which may have commonalities with the mechanisms regulating human PNPOx, whose crucial role in vitamin B6 metabolism and epilepsy is well-known.
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Affiliation(s)
- Anna Barile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Angela Tramonti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy.,Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Isabel Nogués
- Istituto di Ricerca sugli Ecosistemi Terrestri, CNR, Via G. Marconi 2, 05010 Porano (TR), Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
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11
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Batista FA, Bosch SS, Butzloff S, Lunev S, Meissner KA, Linzke M, Romero AR, Wang C, Müller IB, Dömling ASS, Groves MR, Wrenger C. Oligomeric protein interference validates druggability of aspartate interconversion in Plasmodium falciparum. Microbiologyopen 2019; 8:e00779. [PMID: 30821109 PMCID: PMC6612543 DOI: 10.1002/mbo3.779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
The appearance of multi-drug resistant strains of malaria poses a major challenge to human health and validated drug targets are urgently required. To define a protein's function in vivo and thereby validate it as a drug target, highly specific tools are required that modify protein function with minimal cross-reactivity. While modern genetic approaches often offer the desired level of target specificity, applying these techniques is frequently challenging-particularly in the most dangerous malaria parasite, Plasmodium falciparum. Our hypothesis is that such challenges can be addressed by incorporating mutant proteins within oligomeric protein complexes of the target organism in vivo. In this manuscript, we provide data to support our hypothesis by demonstrating that recombinant expression of mutant proteins within P. falciparum leverages the native protein oligomeric state to influence protein function in vivo, thereby providing a rapid validation of potential drug targets. Our data show that interference with aspartate metabolism in vivo leads to a significant hindrance in parasite survival and strongly suggest that enzymes integral to aspartate metabolism are promising targets for the discovery of novel antimalarials.
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Affiliation(s)
- Fernando A. Batista
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Sabine Butzloff
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Sergey Lunev
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Kamila A. Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Atilio R. Romero
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Chao Wang
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Ingrid B. Müller
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Alexander S. S. Dömling
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Matthew R. Groves
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
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12
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Meissner KA, Kronenberger T, Maltarollo VG, Trossini GHG, Wrenger C. Targeting the Plasmodium falciparum plasmepsin V by ligand-based virtual screening. Chem Biol Drug Des 2018; 93:300-312. [PMID: 30320974 DOI: 10.1111/cbdd.13416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/05/2018] [Accepted: 06/09/2018] [Indexed: 12/16/2022]
Abstract
Malaria is a devastating disease depending only on chemotherapy as treatment. However, medication is losing efficacy, and therefore, there is an urgent need for the discovery of novel pharmaceutics. Recently, plasmepsin V, an aspartic protease anchored in the endoplasmaic reticulum, was demonstrated as responsible for the trafficking of parasite-derived proteins to the erythrocytic surface and further validated as a drug target. In this sense, ligand-based virtual screening has been applied to design inhibitors that target plasmepsin V of P. falciparum (PMV). After screening 5.5 million compounds, four novel plasmepsin inhibitors have been identified which were subsequently analyzed for the potency at the cellular level. Since PMV is membrane-anchored, the verification in vivo by using transgenic PMV overexpressing P. falciparum cells has been performed in order to evaluate drug efficacy. Two lead compounds, revealing IC50 values were 44.2 and 19.1 μm, have been identified targeting plasmepsin V in vivo and do not significantly affect the cell viability of human cells up to 300 μm. We herein report the use of the consensus of individual virtual screening as a new technique to design new ligands, and we propose two new lead compounds as novel protease inhibitors to target malaria.
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Affiliation(s)
- Kamila Anna Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Thales Kronenberger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Germany
| | - Vinícius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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13
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Xie F, Li G, Wang Y, Zhang Y, Zhou L, Wang C, Liu S, Liu S, Wang C. Pyridoxal phosphate synthases PdxS/PdxT are required for Actinobacillus pleuropneumoniae viability, stress tolerance and virulence. PLoS One 2017; 12:e0176374. [PMID: 28448619 PMCID: PMC5407770 DOI: 10.1371/journal.pone.0176374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/10/2017] [Indexed: 11/29/2022] Open
Abstract
Pyridoxal 5’-phosphate (PLP) is an essential cofactor for numerous enzymes involved in a diversity of cellular processes in living organisms. Previous analysis of the Actinobacillus pleuropneumoniae S-8 genome sequence revealed the presence of pdxS and pdxT genes, which are implicated in deoxyxylulose 5-phosphate (DXP)-independent pathway of PLP biosynthesis; however, little is known about their roles in A. pleuropneumoniae pathogenicity. Our data demonstrated that A. pleuropneumoniae could synthesize PLP by PdxS and PdxT enzymes. Disruption of the pdxS and pdxT genes rendered the pathogen auxotrophic for PLP, and the defective growth as a result of these mutants was chemically compensated by the addition of PLP, suggesting the importance of PLP production for A. pleuropneumoniae growth and viability. Additionally, the pdxS and pdxT deletion mutants displayed morphological defects as indicated by irregular and aberrant shapes in the absence of PLP. The reduced growth of the pdxS and pdxT deletion mutants under osmotic and oxidative stress conditions suggests that the PLP synthases PdxS/PdxT are associated with the stress tolerance of A. pleuropneumoniae. Furthermore, disruption of the PLP biosynthesis pathway led to reduced colonization and attenuated virulence of A. pleuropneumoniae in the BALB/c mouse model. The data presented in this study reveal the critical role of PLP synthases PdxS/PdxT in viability, stress tolerance, and virulence of A. pleuropneumoniae.
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Affiliation(s)
- Fang Xie
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Gang Li
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yalei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Yanhe Zhang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Long Zhou
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Chengcheng Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Shuanghong Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Chunlai Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- * E-mail:
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14
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Tramonti A, Milano T, Nardella C, di Salvo ML, Pascarella S, Contestabile R. Salmonella typhimurium PtsJ is a novel MocR-like transcriptional repressor involved in regulating the vitamin B 6 salvage pathway. FEBS J 2017; 284:466-484. [PMID: 27987384 DOI: 10.1111/febs.13994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022]
Abstract
The vitamin B6 salvage pathway, involving pyridoxine 5'-phosphate oxidase (PNPOx) and pyridoxal kinase (PLK), recycles B6 vitamers from nutrients and protein turnover to produce pyridoxal 5'-phosphate (PLP), the catalytically active form of the vitamin. Regulation of this pathway, widespread in living organisms including humans and many bacteria, is very important to vitamin B6 homeostasis but poorly understood. Although some information is available on the enzymatic regulation of PNPOx and PLK, little is known on their regulation at the transcriptional level. In the present work, we identified a new MocR-like regulator, PtsJ from Salmonella typhimurium, which controls the expression of the pdxK gene encoding one of the two PLKs expressed in this organism (PLK1). Analysis of pdxK expression in a ptsJ knockout strain demonstrated that PtsJ acts as a transcriptional repressor. This is the first case of a MocR-like regulator acting as repressor of its target gene. Expression and purification of PtsJ allowed a detailed characterisation of its effector and DNA-binding properties. PLP is the only B6 vitamer acting as effector molecule for PtsJ. A DNA-binding region composed of four repeated nucleotide sequences is responsible for binding of PtsJ to its target promoter. Analysis of binding stoichiometry revealed that protein subunits/DNA molar ratio varies from 4 : 1 to 2 : 1, depending on the presence or absence of PLP. Structural characteristics of DNA transcriptional factor-binding sites suggest that PtsJ binds DNA according to a different model with respect to other characterised members of the MocR subgroup.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.,Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
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15
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Lee H, Park MJ, Sun SH, Choi DH, Lee YH, Park KW, Chun BW. Ascorbic acid and vitamin C-containing beverages delay the leucomalachite green reaction to detect latent bloodstains. Leg Med (Tokyo) 2016; 23:79-85. [PMID: 27890109 DOI: 10.1016/j.legalmed.2016.10.003] [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: 07/24/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022]
Abstract
The leucomalachite green (LMG) test is one of catalytic tests for the detection of latent bloodstains and generally used in forensic field because of convenience and cost/time-effectiveness. However, contamination of latent bloodstains at crime scenes can interfere with the LMG reaction, resulting in false-negative or false-positive decisions. Herein, we examined if ascorbic acid and vitamin C (l-ascorbic acid or ascorbate)-containing beverages affect the LMG reaction. Ascorbic acid showed the inhibitory activities on the LMG reaction in a dose-dependent manner. Similarly, vitamin C-containing beverages also inhibited the LMG reaction and the inhibitory effects were proportional to the concentrations of vitamin C in beverages. It was also identified that as incubation time after adding LMG reagent to the mixtures of blood and ascorbic acid or beverages was increased, the inhibitory effects of ascorbic acid vitamin C-containing beverages on LMG test were disappeared. These results suggest that the LMG reaction is delayed but not stopped by ascorbic acid and vitamin C-containing beverages. Neither incubation at room temperature around 20-25°C nor the addition of acetic acid affects the inhibitory activity of ascorbic acid on LMG reaction. We also showed that ascorbic acid does not affect DNA stability, allowing us to obtain full short tandem repeat (STR) profiles through amplification of DNA using commercial STR kits. In conclusion, ascorbic acid and vitamin C-containing beverages delayed the LMG reaction, suggesting that it should be considered that negative results of LMG test could be false negative due to contamination of bloodstains with inhibitory factors on LMG test.
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Affiliation(s)
- Haeyong Lee
- DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul 158-707, Republic of Korea.
| | - Myung Jin Park
- DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul 158-707, Republic of Korea.
| | - Seol Hee Sun
- DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul 158-707, Republic of Korea.
| | - Dong-Ho Choi
- DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul 158-707, Republic of Korea.
| | - Yang-Han Lee
- Forensic DNA Division, National Forensic Service, Wonju 220-170, Republic of Korea.
| | - Ki-Won Park
- Forensic DNA Division, National Forensic Service, Wonju 220-170, Republic of Korea.
| | - Byung Won Chun
- Forensic DNA Division, National Forensic Service, Wonju 220-170, Republic of Korea.
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16
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Kronenberger T, Lunev S, Wrenger C, Groves MR. Purification, crystallization and preliminary X-ray diffraction analysis of pyridoxal kinase from Plasmodium falciparum (PfPdxK). ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1550-5. [PMID: 25372829 DOI: 10.1107/s2053230x14019864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/02/2014] [Indexed: 11/10/2022]
Abstract
Pyridoxal kinases (PdxK) catalyze the phosphorylation of vitamin B6 precursors. Thus, these enzymes are an essential part of many metabolic processes in all organisms. The protozoan parasite Plasmodium falciparum (the main causative agent of Malaria tropica) possesses a unique de novo B6-biosynthesis pathway in addition to a interconversion pathway based on the activity of plasmodial PdxK (PfPdxK). The role of PdxK in B6 salvage has prompted previous authors to suggest PdxK as a promising target for structure-based antimalarial drug design. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis of PfPdxK are reported. PfPdxK crystals have been grown in space group P2₁, with unit-cell parameters a=52.7, b=62.0, c=93.7 Å, β=95°. A data set has been collected to 2 Å resolution and an initial molecular-replacement solution is described.
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Affiliation(s)
- Thales Kronenberger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of Saõ Paulo, Avenida Professor Lineu Prestes 1374, Saõ Paulo-SP 05508-000, Brazil
| | - Sergey Lunev
- Department of Drug Design, Groningen Research Institute of Pharmacy (GRIP), Rijksuniversiteit Groningen (RUG), Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of Saõ Paulo, Avenida Professor Lineu Prestes 1374, Saõ Paulo-SP 05508-000, Brazil
| | - Matthew R Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy (GRIP), Rijksuniversiteit Groningen (RUG), Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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17
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Moccand C, Boycheva S, Surriabre P, Tambasco-Studart M, Raschke M, Kaufmann M, Fitzpatrick TB. The pseudoenzyme PDX1.2 boosts vitamin B6 biosynthesis under heat and oxidative stress in Arabidopsis. J Biol Chem 2014; 289:8203-16. [PMID: 24505140 DOI: 10.1074/jbc.m113.540526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Vitamin B6 is an indispensable compound for survival, well known as a cofactor for numerous central metabolic enzymes and more recently for playing a role in several stress responses, particularly in association with oxidative stress. Regulatory aspects for the use of the vitamin in these roles are not known. Here we show that certain plants carry a pseudoenzyme (PDX1.2), which is involved in regulating vitamin B6 biosynthesis de novo under stress conditions. Specifically, we demonstrate that Arabidopsis PDX1.2 enhances the activity of its catalytic paralogs by forming a heterododecameric complex. PDX1.2 is strongly induced by heat as well as singlet oxygen stress, concomitant with an enhancement of vitamin B6 production. Analysis of pdx1.2 knockdown lines demonstrates that boosting vitamin B6 content is dependent on PDX1.2, revealing that this pseudoenzyme acts as a positive regulator of vitamin B6 biosynthesis during such stress conditions in plants.
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Affiliation(s)
- Cyril Moccand
- From the Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
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18
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Vitamin B6-dependent enzymes in the human malaria parasite Plasmodium falciparum: a druggable target? BIOMED RESEARCH INTERNATIONAL 2014; 2014:108516. [PMID: 24524072 PMCID: PMC3912857 DOI: 10.1155/2014/108516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 10/24/2013] [Accepted: 11/28/2013] [Indexed: 11/17/2022]
Abstract
Malaria is a deadly infectious disease which affects millions of people each year in tropical regions. There is no effective vaccine available and the treatment is based on drugs which are currently facing an emergence of drug resistance and in this sense the search for new drug targets is indispensable. It is well established that vitamin biosynthetic pathways, such as the vitamin B6 de novo synthesis present in Plasmodium, are excellent drug targets. The active form of vitamin B6, pyridoxal 5-phosphate, is, besides its antioxidative properties, a cofactor for a variety of essential enzymes present in the malaria parasite which includes the ornithine decarboxylase (ODC, synthesis of polyamines), the aspartate aminotransferase (AspAT, involved in the protein biosynthesis), and the serine hydroxymethyltransferase (SHMT, a key enzyme within the folate metabolism).
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19
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Chemical and genetic validation of thiamine utilization as an antimalarial drug target. Nat Commun 2013; 4:2060. [PMID: 23804074 DOI: 10.1038/ncomms3060] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/28/2013] [Indexed: 11/08/2022] Open
Abstract
Thiamine is metabolized into an essential cofactor for several enzymes. Here we show that oxythiamine, a thiamine analog, inhibits proliferation of the malaria parasite Plasmodium falciparum in vitro via a thiamine-related pathway and significantly reduces parasite growth in a mouse malaria model. Overexpression of thiamine pyrophosphokinase (the enzyme that converts thiamine into its active form, thiamine pyrophosphate) hypersensitizes parasites to oxythiamine by up to 1,700-fold, consistent with oxythiamine being a substrate for thiamine pyrophosphokinase and its conversion into an antimetabolite. We show that parasites overexpressing the thiamine pyrophosphate-dependent enzymes oxoglutarate dehydrogenase and pyruvate dehydrogenase are up to 15-fold more resistant to oxythiamine, consistent with the antimetabolite inactivating thiamine pyrophosphate-dependent enzymes. Our studies therefore validate thiamine utilization as an antimalarial drug target and demonstrate that a single antimalarial can simultaneously target several enzymes located within distinct organelles.
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20
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Targeting the vitamin biosynthesis pathways for the treatment of malaria. Future Med Chem 2013; 5:769-79. [PMID: 23651091 DOI: 10.4155/fmc.13.43] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The most severe form of malaria is Malaria tropica, caused by Plasmodium falciparum. There are more than 1 billion people that are exposed to malaria parasites leading to more than 500,000 deaths annually. Vaccines are not available and the increasing drug resistance of the parasite prioritizes the need for novel drug targets and chemotherapeutics, which should be ideally designed to target selectively the parasite. In this sense, parasite-specific pathways, such as the vitamin biosyntheses, represent perfect drug-target characteristics because they are absent in humans. In the past, the vitamin B9 (folate) metabolism has been exploited by antifolates to treat infections caused by malaria parasites. Recently, two further vitamin biosynthesis pathways - for the vitamins B6 (pyridoxine) and B1 (thiamine) - have been identified in Plasmodium and analyzed for their suitability to discover new drugs. In this review, the current status of the druggability of plasmodial vitamin biosynthesis pathways is summarized.
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21
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Exploring inhibition of Pdx1, a component of the PLP synthase complex of the human malaria parasite Plasmodium falciparum. Biochem J 2013; 449:175-87. [PMID: 23039077 DOI: 10.1042/bj20120925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Malaria tropica is a devastating infectious disease caused by Plasmodium falciparum. This parasite synthesizes vitamin B6 de novo via the PLP (pyridoxal 5'-phosphate) synthase enzymatic complex consisting of PfPdx1 and PfPdx2 proteins. Biosynthesis of PLP is largely performed by PfPdx1, ammonia provided by PfPdx2 subunits is condensed together with R5P (D-ribose 5-phosphate) and G3P (DL-glyceraldehyde 3-phosphate). PfPdx1 accommodates both the R5P and G3P substrates and intricately co-ordinates the reaction mechanism, which is composed of a series of imine bond formations, leading to the production of PLP. We demonstrate that E4P (D-erythrose 4-phosphate) inhibits PfPdx1 in a dose-dependent manner. We propose that the acyclic phospho-sugar E4P, with a C1 aldehyde group similar to acyclic R5P, could interfere with R5P imine bond formations in the PfPdx1 reaction mechanism. Molecular docking and subsequent screening identified the E4P hydrazide analogue 4PEHz (4-phospho-D-erythronhydrazide), which selectively inhibited PfPdx1 with an IC50 of 43 μM. PfPdx1 contained in the heteromeric PLP synthase complex was shown to be more sensitive to 4PEHz and was inhibited with an IC50 of 16 μM. Moreover, the compound had an IC50 value of 10 μM against cultured P. falciparum intraerythrocytic parasites. To analyse further the selectivity of 4PEHz, transgenic cell lines overexpressing PfPdx1 and PfPdx2 showed that additional copies of the protein complex conferred protection against 4PEHz, indicating that the PLP synthase is directly affected by 4PEHz in vivo. These PfPdx1 inhibitors represent novel lead scaffolds which are capable of targeting PLP biosynthesis, and we propose this as a viable strategy for the development of new therapeutics against malaria.
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22
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Panwar B, Gupta S, Raghava GPS. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information. BMC Bioinformatics 2013; 14:44. [PMID: 23387468 PMCID: PMC3577447 DOI: 10.1186/1471-2105-14-44] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 01/31/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. RESULTS In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL). It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i) vitamin interacting residues (VIRs), (ii) vitamin-A interacting residues (VAIRs), (iii) vitamin-B interacting residues (VBIRs) and (iv) pyridoxal-5-phosphate (vitamin B6) interacting residues (PLPIRs) have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM) features of protein sequences. Finally, we selected best performing SVM modules and obtained highest MCC of 0.53, 0.48, 0.61, 0.81 for VIRs, VAIRs, VBIRs, PLPIRs respectively, using PSSM-based evolutionary information. All the modules developed in this study have been trained and tested on non-redundant datasets and evaluated using five-fold cross-validation technique. The performances were also evaluated on the balanced and different independent datasets. CONCLUSIONS This study demonstrates that it is possible to predict VIRs, VAIRs, VBIRs and PLPIRs from evolutionary information of protein sequence. In order to provide service to the scientific community, we have developed web-server and standalone software VitaPred (http://crdd.osdd.net/raghava/vitapred/).
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Affiliation(s)
- Bharat Panwar
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
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23
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Butzloff S, Groves MR, Wrenger C, Müller IB. Cytometric quantification of singlet oxygen in the human malaria parasite Plasmodium falciparum. Cytometry A 2012; 81:698-703. [DOI: 10.1002/cyto.a.22081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/13/2012] [Accepted: 05/21/2012] [Indexed: 12/30/2022]
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