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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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Rastogi S, Chandra A. Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media. J Phys Chem B 2023; 127:8139-8149. [PMID: 37721415 DOI: 10.1021/acs.jpcb.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.
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Affiliation(s)
- Shreya Rastogi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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3
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Carter NS, Kawasaki Y, Nahata SS, Elikaee S, Rajab S, Salam L, Alabdulal MY, Broessel KK, Foroghi F, Abbas A, Poormohamadian R, Roberts SC. Polyamine Metabolism in Leishmania Parasites: A Promising Therapeutic Target. Med Sci (Basel) 2022; 10:24. [PMID: 35645240 PMCID: PMC9149861 DOI: 10.3390/medsci10020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania cause a variety of devastating and often fatal diseases in humans and domestic animals worldwide. The need for new therapeutic strategies is urgent because no vaccine is available, and treatment options are limited due to a lack of specificity and the emergence of drug resistance. Polyamines are metabolites that play a central role in rapidly proliferating cells, and recent studies have highlighted their critical nature in Leishmania. Numerous studies using a variety of inhibitors as well as gene deletion mutants have elucidated the pathway and routes of transport, revealing unique aspects of polyamine metabolism in Leishmania parasites. These studies have also shed light on the significance of polyamines for parasite proliferation, infectivity, and host-parasite interactions. This comprehensive review article focuses on the main polyamine biosynthetic enzymes: ornithine decarboxylase, S-adenosylmethionine decarboxylase, and spermidine synthase, and it emphasizes recent discoveries that advance these enzymes as potential therapeutic targets against Leishmania parasites.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sigrid C. Roberts
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR 97123, USA; (N.S.C.); (Y.K.); (S.S.N.); (S.E.); (S.R.); (L.S.); (M.Y.A.); (K.K.B.); (F.F.); (A.A.); (R.P.)
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4
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Sarkar D, Vijayan R, Gourinath S, Sau AK. A unique aromatic cluster near the active site of H. pylori CPA is essential for catalytic function. Biophys J 2022; 121:248-262. [PMID: 34932956 PMCID: PMC8790187 DOI: 10.1016/j.bpj.2021.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/16/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Polyamines are essential for cell growth and proliferation. In plants and many bacteria, including Helicobacter pylori, the parent polyamine putrescine is only produced through the metabolism of N-carbamoylputrescine by N-carbamoylputrescine amidase (CPA). Thus, CPA is a crucial intermediate enzyme. Moreover, the absence of CPA in humans makes its presence in H. pylori a potential target for the development of new therapeutics against this pathogen. Despite this enzyme's presence in plants and bacteria, its function is not completely explored. Using structure-guided biochemical and biophysical studies on H. pylori CPA, we discovered an aromatic cluster containing four conserved tryptophans near the catalytic site and elucidated its role. Mutational studies revealed that they are individually vital to enzyme function. Unlike wild-type, which forms a hexamer, the Trp to Ala mutants only formed dimers. Interestingly, two other conserved residues, Gln155 and Asp278, interact with the tryptophan cluster and perform similar roles. Our results indicate that aromatic-aromatic and H-bonding contacts between the residues (Trp156-Trp273, Trp196-Gln155, and Trp153-Asp278) play a crucial role in stimulating activity through hexamer formation. Additionally, Trp156 is essential to generating a catalytically efficient hexamer. These results suggest dual roles for the tryptophans; in hexamer formation and in generating its functionally active form, thereby providing a mechanistic understanding into the role of the cluster. We also elucidated the catalytic roles of Glu43, Lys115, and Cys152, which are present at the active site. Our findings highlight, for the first time, the importance of a tryptophan cluster in H. pylori CPA that can be exploited to design therapeutic inhibitors.
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Affiliation(s)
- Ditsa Sarkar
- National Institute of Immunology, New Delhi, India
| | | | | | - Apurba Kumar Sau
- National Institute of Immunology, New Delhi, India,Correspondence:
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Vicente-Barrueco A, Román ÁC, Ruiz-Téllez T, Centeno F. In Silico Research of New Therapeutics Rotenoids Derivatives against Leishmania amazonensis Infection. BIOLOGY 2022; 11:biology11010133. [PMID: 35053132 PMCID: PMC8772715 DOI: 10.3390/biology11010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
Abstract
Yearly, 1,500,000 cases of leishmaniasis are diagnosed, causing thousands of deaths. To advance in its therapy, we present an interdisciplinary protocol that unifies ethnobotanical knowledge of natural compounds and the latest bioinformatics advances to respond to an orphan disease such as leishmaniasis and specifically the one caused by Leishmania amazonensis. The use of ethnobotanical information serves as a basis for the development of new drugs, a field in which computer-aided drug design (CADD) has been a revolution. Taking this information from Amazonian communities, located in the area with a high prevalence of this disease, a protocol has been designed to verify new leads. Moreover, a method has been developed that allows the evaluation of lead molecules, and the improvement of their affinity and specificity against therapeutic targets. Through this approach, deguelin has been identified as a good lead to treat the infection due to its potential as an ornithine decarboxylase (ODC) inhibitor, a key enzyme in Leishmania development. Using an in silico-generated combinatorial library followed by docking approaches, we have found deguelin derivatives with better affinity and specificity against ODC than the original compound, suggesting that this approach could be adapted for developing new drugs against leishmaniasis.
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Affiliation(s)
- Adrián Vicente-Barrueco
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Ángel Carlos Román
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
- Correspondence: (Á.C.R.); (F.C.)
| | - Trinidad Ruiz-Téllez
- Departamento de Biología Vegetal, Ecología y Ciencias de la Tierra, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Francisco Centeno
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
- Correspondence: (Á.C.R.); (F.C.)
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Osman MS, Shantier SW, Awad TA, Garelnabi EA. In vitro evaluation, in silico studies and toxicological assay of some xanthones as potential Leishmania donovani inhibitors. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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7
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Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane. Biochem J 2021; 478:4137-4149. [PMID: 34796899 DOI: 10.1042/bcj20210647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022]
Abstract
Ornithine decarboxylase (ODC) is the rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are oncometabolites that are required for proliferation, and pharmaceutical ODC inhibition is pursued for the treatment of hyperproliferative diseases, including cancer and infectious diseases. The most potent ODC inhibitor is 1-amino-oxy-3-aminopropane (APA). A previous crystal structure of an ODC-APA complex indicated that APA non-covalently binds ODC and its cofactor pyridoxal 5-phosphate (PLP) and functions by competing with the ODC substrate ornithine for binding to the catalytic site. We have revisited the mechanism of APA binding and ODC inhibition through a new crystal structure of APA-bound ODC, which we solved at 2.49 Å resolution. The structure unambiguously shows the presence of a covalent oxime between APA and PLP in the catalytic site, which we confirmed in solution by mass spectrometry. The stable oxime makes extensive interactions with ODC but cannot be catabolized, explaining APA's high potency in ODC inhibition. In addition, we solved an ODC/PLP complex structure with citrate bound at the substrate-binding pocket. These two structures provide new structural scaffolds for developing more efficient pharmaceutical ODC inhibitors.
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Herrera-Acevedo C, Dos Santos Maia M, Cavalcanti ÉBVS, Coy-Barrera E, Scotti L, Scotti MT. Selection of antileishmanial sesquiterpene lactones from SistematX database using a combined ligand-/structure-based virtual screening approach. Mol Divers 2021; 25:2411-2427. [PMID: 32909084 DOI: 10.1007/s11030-020-10139-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/30/2020] [Indexed: 12/20/2022]
Abstract
Leishmaniasis refers to a complex of diseases, caused by the intracellular parasitic protozoans belonging to the genus Leishmania. Among the three types of disease manifestations, the most severe type is visceral leishmaniasis, which is caused by Leishmania donovani, and is diagnosed in more than 20,000 cases annually, worldwide. Because the current therapeutic options for disease treatment are associated with several limitations, the identification of new potential leads/drugs remains necessary. In this study, a combined approach was used, based on two different virtual screening (VS) methods, which were designed to select promising antileishmanial agents from among the entire sesquiterpene lactone (SL) dataset registered in SistematX, a web interface for managing a secondary metabolite database that is accessible by multiple platforms on the Internet. Thus, a ChEMBL dataset, including 3159 and 1569 structures that were previously tested against L. donovani amastigotes and promastigotes in vitro, respectively, was used to develop two random forest models, which performed with greater than 74% accuracy in both the cross-validation and test sets. Subsequently, a ligand-based VS assay was performed against the 1306 SistematX-registered SLs. In parallel, the crystal structures of three L. donovani target proteins, N-myristoyltransferase, ornithine decarboxylase, and mitogen-activated protein kinase 3, and a homology model of pteridine reductase 1 were used to perform a structure-based VS, using molecular docking, of the entire SistematX SL dataset. The consensus analysis of these two VS approaches resulted in the normalization of probability scores and identified 13 promising, enzyme-targeting, antileishmanial SLs from SistematX that may act against L. donovani. A combined approach based on two different virtual screening methods (structure-based and ligand-based) was performed using an in-house dataset composed of 1306 sesquiterpene lactones to identify potential antileishmanial (Leishmania donovani) structures.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Mayara Dos Santos Maia
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
| | | | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil.
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Bojarska J, New R, Borowiecki P, Remko M, Breza M, Madura ID, Fruziński A, Pietrzak A, Wolf WM. The First Insight Into the Supramolecular System of D,L-α-Difluoromethylornithine: A New Antiviral Perspective. Front Chem 2021; 9:679776. [PMID: 34055746 PMCID: PMC8155678 DOI: 10.3389/fchem.2021.679776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022] Open
Abstract
Targeting the polyamine biosynthetic pathway by inhibiting ornithine decarboxylase (ODC) is a powerful approach in the fight against diverse viruses, including SARS-CoV-2. Difluoromethylornithine (DFMO, eflornithine) is the best-known inhibitor of ODC and a broad-spectrum, unique therapeutical agent. Nevertheless, its pharmacokinetic profile is not perfect, especially when large doses are required in antiviral treatment. This article presents a holistic study focusing on the molecular and supramolecular structure of DFMO and the design of its analogues toward the development of safer and more effective formulations. In this context, we provide the first deep insight into the supramolecular system of DFMO supplemented by a comprehensive, qualitative and quantitative survey of non-covalent interactions via Hirshfeld surface, molecular electrostatic potential, enrichment ratio and energy frameworks analysis visualizing 3-D topology of interactions in order to understand the differences in the cooperativity of interactions involved in the formation of either basic or large synthons (Long-range Synthon Aufbau Modules, LSAM) at the subsequent levels of well-organized supramolecular self-assembly, in comparison with the ornithine structure. In the light of the drug discovery, supramolecular studies of amino acids, essential constituents of proteins, are of prime importance. In brief, the same amino-carboxy synthons are observed in the bio-system containing DFMO. DFT calculations revealed that the biological environment changes the molecular structure of DFMO only slightly. The ADMET profile of structural modifications of DFMO and optimization of its analogue as a new promising drug via molecular docking are discussed in detail.
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Affiliation(s)
- Joanna Bojarska
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Roger New
- Faculty of Science & Technology, Middlesex University, London, United Kingdom
| | - Paweł Borowiecki
- Faculty of Chemistry, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformation, Warsaw University of Technology, Warsaw, Poland
| | | | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Bratislava, Slovakia
| | - Izabela D. Madura
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Andrzej Fruziński
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Anna Pietrzak
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Wojciech M. Wolf
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
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10
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Herrera-Acevedo C, Perdomo-Madrigal C, Muratov EN, Scotti L, Scotti MT. Discovery of Alternative Chemotherapy Options for Leishmaniasis through Computational Studies of Asteraceae. ChemMedChem 2021; 16:1234-1245. [PMID: 33336460 DOI: 10.1002/cmdc.202000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a complex disease caused by over 20 Leishmania species that primarily affects populations with poor socioeconomic conditions. Currently available drugs for treating leishmaniasis include amphotericin B, paromomycin, and pentavalent antimonials, which have been associated with several limitations, such as low efficacy, the development of drug resistance, and high toxicity. Natural products are an interesting source of new drug candidates. The Asteraceae family includes more than 23 000 species worldwide. Secondary metabolites that can be found in species from this family have been widely explored as potential new treatments for leishmaniasis. Recently, computational tools have become more popular in medicinal chemistry to establish experimental designs, identify new drugs, and compare the molecular structures and activities of novel compounds. Herein, we review various studies that have used computational tools to examine various compounds identified in the Asteraceae family in the search for potential drug candidates against Leishmania.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Camilo Perdomo-Madrigal
- School of Science, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 n° 55-37, Bogotá D.C., Colombia
| | - Eugene N Muratov
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
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11
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Northover DE, Shank SD, Liberles DA. Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. BMC Evol Biol 2020; 20:24. [PMID: 32046633 PMCID: PMC7011509 DOI: 10.1186/s12862-020-1585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 01/16/2020] [Indexed: 11/21/2022] Open
Abstract
Background Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is possible to make inferences about the evolutionary events that have given rise to species-specific diversification. Here we characterize the evolutionary trends found in chordate species using The Adaptive Evolution Database (TAED). TAED is a database of phylogenetically indexed gene families designed to detect episodes of directional or diversifying selection across chordates. Gene families within the database have been assessed for lineage-specific estimates of dN/dS and have been reconciled to the chordate species to identify retained duplicates. Gene families have also been mapped to the functional pathways and amino acid changes which occurred on high dN/dS lineages have been mapped to protein structures. Results An analysis of this exhaustive database has enabled a characterization of the processes of lineage-specific diversification in chordates. A pathway level enrichment analysis of TAED determined that pathways most commonly found to have elevated rates of evolution included those involved in metabolism, immunity, and cell signaling. An analysis of protein fold presence on proteins, after normalizing for frequency in the database, found common folds such as Rossmann folds, Jelly Roll folds, and TIM barrels were overrepresented on proteins most likely to undergo directional selection. A set of gene families which experience increased numbers of duplications within short evolutionary times are associated with pathways involved in metabolism, olfactory reception, and signaling. An analysis of protein secondary structure indicated more relaxed constraint in β-sheets and stronger constraint on alpha Helices, amidst a general preference for substitutions at exposed sites. Lastly a detailed analysis of the ornithine decarboxylase gene family, a key enzyme in the pathway for polyamine synthesis, revealed lineage-specific evolution along the lineage leading to Cetacea through rapid sequence evolution in a duplicate gene with amino acid substitutions causing active site rearrangement. Conclusion Episodes of lineage-specific evolution are frequent throughout chordate species. Both duplication and directional selection have played large roles in the evolution of the phylum. TAED is a powerful tool for facilitating this understanding of lineage-specific evolution.
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Affiliation(s)
- David E Northover
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Stephen D Shank
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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12
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Olin-Sandoval V, Yu JSL, Miller-Fleming L, Alam MT, Kamrad S, Correia-Melo C, Haas R, Segal J, Peña Navarro DA, Herrera-Dominguez L, Méndez-Lucio O, Vowinckel J, Mülleder M, Ralser M. Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism. Nature 2019; 572:249-253. [PMID: 31367038 PMCID: PMC6774798 DOI: 10.1038/s41586-019-1442-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 06/28/2019] [Indexed: 11/25/2022]
Abstract
Both single and multicellular organisms depend on anti-stress mechanisms that enable them to deal with sudden changes in the environment, including exposure to heat and oxidants. Central to the stress response are dynamic changes in metabolism, such as the transition from the glycolysis to the pentose phosphate pathway-a conserved first-line response to oxidative insults1,2. Here we report a second metabolic adaptation that protects microbial cells in stress situations. The role of the yeast polyamine transporter Tpo1p3-5 in maintaining oxidant resistance is unknown6. However, a proteomic time-course experiment suggests a link to lysine metabolism. We reveal a connection between polyamine and lysine metabolism during stress situations, in the form of a promiscuous enzymatic reaction in which the first enzyme of the polyamine pathway, Spe1p, decarboxylates lysine and forms an alternative polyamine, cadaverine. The reaction proceeds in the presence of extracellular lysine, which is taken up by cells to reach concentrations up to one hundred times higher than those required for growth. Such extensive harvest is not observed for the other amino acids, is dependent on the polyamine pathway and triggers a reprogramming of redox metabolism. As a result, NADPH-which would otherwise be required for lysine biosynthesis-is channelled into glutathione metabolism, leading to a large increase in glutathione concentrations, lower levels of reactive oxygen species and increased oxidant tolerance. Our results show that nutrient uptake occurs not only to enable cell growth, but when the nutrient availability is favourable it also enables cells to reconfigure their metabolism to preventatively mount stress protection.
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Affiliation(s)
- Viridiana Olin-Sandoval
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Nutrition Physiology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jason Shu Lim Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Leonor Miller-Fleming
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Stephan Kamrad
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Haas
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Joanna Segal
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Oscar Méndez-Lucio
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jakob Vowinckel
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Biognosys AG, Schlieren, Switzerland
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité University Medicine, Berlin, Germany.
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Vijayakumar S, Das P. Recent progress in drug targets and inhibitors towards combating leishmaniasis. Acta Trop 2018; 181:95-104. [PMID: 29452111 DOI: 10.1016/j.actatropica.2018.02.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/24/2018] [Accepted: 02/11/2018] [Indexed: 12/22/2022]
Abstract
Lesihmaniasis is one of the major neglected tropical disease caused by the parasite of the genus Leishmania. The disease has more than one clinical forms and the visceral form is considered fatal. With the lack of potential vaccine, chemotherapy is the major treatment source considered for the control of the disease in the infected people. Drugs including amphotericin B and miltefosine are widely used for the treatment, however, development of resistance by the parasite towards the administered drug and high-toxicity of the drug are of major concern. Hence, more attention has been shown on identifying new targets, effective inhibitors, and better drug delivery system against the disease. This review deals with recent studies on drug targets and exploring their essentiality for the survival of Leishmania. Further, new inhibitors for those targets, novel anti-leishmanial peptides and vaccines against leishmaniasis were discussed. We believe that this pool of information will ease the researchers to gain knowledge and help in choosing right targets and design of new inhibitors against Leishmaniasis.
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Sivashanmugam M, K N S, V U. Virtual screening of natural inhibitors targeting ornithine decarboxylase with pharmacophore scaffolding of DFMO and validation by molecular dynamics simulation studies. J Biomol Struct Dyn 2018; 37:766-780. [PMID: 29436980 DOI: 10.1080/07391102.2018.1439772] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ornithine decarboxylase (ODC) is an enzyme that initiates polyamine synthesis in human. Polyamines play key roles in cell-cell adhesion, cell motility and cell cycle regulation. Higher synthesis of polyamines also occurs in rapidly proliferating cancer cells are mediated by ODC. As per earlier studies, di-flouro-methyl-orninthine (DFMO) is a proven efficient inhibitor ODC targeting the catalytic activity, however, its usage is limited due to side effects. Targeting ODC is considered as a potential therapeutic modality in the treatment of cancer. In this study, it is attempted to use DFMO scaffold to build a ligand-based pharmocophore query using MOE to screen similar active compounds from Universal Natural Products Database with better ADMET properties. The identified compounds were virtually screened against the active cavity of ODC using Glide. Further, potential natural hits targeting ODC were shortlisted based on Molecular Mechanics/Generalized-Born/Surface Area (MM-GBSA) score. Finally, molecular dynamics simulations were performed for the natural molecule hit and DFMO in complex with ODC using Desmond. Among the hits shortlisted, 2-amino-5, 9, 13, 17-tetramethyloctadeca-8, 16-diene-1, 3, 14-triol (UNPD208110) was found to be highly potential, as it showed a higher binding affinity in terms of interactions with key active cavity residues, and also showed better ADMET property, HUMO-LUMO gap energy and more stable complex formation with ODC compared to DFMO. Hence, the proposed molecule (UNPD208110) shall be favourably considered as a potential natural inhibitor targeting ODC-mediated disease conditions.
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Affiliation(s)
- Muthukumaran Sivashanmugam
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation , Chennai , India.,b School of Chemical and Biotechnology , SASTRA University , Thanjavur , India
| | - Sulochana K N
- c R.S. Mehta Jain Department of Biochemistry and Cell Biology , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation , Chennai , India
| | - Umashankar V
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation , Chennai , India
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15
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Nilam M, Gribbon P, Reinshagen J, Cordts K, Schwedhelm E, Nau WM, Hennig A. A Label-Free Continuous Fluorescence-Based Assay for Monitoring Ornithine Decarboxylase Activity with a Synthetic Putrescine Receptor. SLAS DISCOVERY 2017; 22:906-914. [PMID: 28346093 DOI: 10.1177/2472555216689288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Polyamines play an important role in cell growth, differentiation, and cancer development, and the biosynthetic pathway of polyamines is established as a drug target for the treatment of parasitic diseases, neoplasia, and cancer chemoprevention. The key enzyme in polyamine biosynthesis is ornithine decarboxylase (ODC). We report herein an analytical method for the continuous fluorescence monitoring of ODC activity based on the supramolecular receptor cucurbit[6]uril (CB6) and the fluorescent dye trans-4-[4-(dimethylamino)styryl]-1-methylpyridinium iodide (DSMI). CB6 has a significantly higher binding constant to the ODC product putrescine (>107 M-1) than to the substrate L-ornithine (340 M-1). This enables real-time monitoring of the enzymatic reaction through a continuous fluorescence change caused by dye displacement from the macrocycle by the formed product, which allowed a straightforward determination of enzyme kinetic parameters ( kcat = 0.12 s-1 and KM = 24 µM) and inhibition constants of the two ODC inhibitors α-difluoromethylornithine (DFMO) and epigallocatechin gallate (EGCG). The potential for high-throughput screening (HTS) was demonstrated by excellent Z' factors (>0.9) in a microplate reader format, and the sensitivity of the assay is comparable to or better than most established complementary methods, which invariably have the disadvantage of not being compatible with direct implementation and upscaling to HTS format in the drug discovery process.
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Affiliation(s)
- Mohamed Nilam
- 1 Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | | | - Kathrin Cordts
- 3 Institute of Clinical Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- 4 German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Edzard Schwedhelm
- 3 Institute of Clinical Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- 4 German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Werner M Nau
- 1 Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Andreas Hennig
- 1 Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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Abstract
In trypanosomatids, polyamine and trypanothione pathways can be considered as a whole unique metabolism, where most enzymes are essential for parasitic survival and infectivity. Leishmania parasites and all the other members of the Trypanosomatids family depend on polyamines for growth and survival: the enzymes involved in the synthesis and utilization of spermidine and trypanothione, i.e., arginase, ornithine decarboxylase, S-adenosylmethionine decarboxylase, spermidine synthase and in particular trypanothione synthetase-amidase, trypanothione reductase and tryparedoxin-dependent peroxidase are promising targets for drug development. This review deals with recent structure-based studies on these enzymes, aimed at the discovery of inhibitors of this pathway.
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17
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Sivashanmugam M, J J, V U, K N S. Ornithine and its role in metabolic diseases: An appraisal. Biomed Pharmacother 2016; 86:185-194. [PMID: 27978498 DOI: 10.1016/j.biopha.2016.12.024] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/16/2016] [Accepted: 12/04/2016] [Indexed: 11/28/2022] Open
Abstract
Ornithine is a non-essential amino acid produced as an intermediate molecule in urea cycle. It is a key substrate for the synthesis of proline, polyamines and citrulline. Ornithine also plays an important role in the regulation of several metabolic processes leading to diseases like hyperorithinemia, hyperammonemia, gyrate atrophy and cancer in humans. However, the mechanism of action behind the multi-faceted roles of ornithine is yet to be unraveled completely. Several types of cancers are also characterized by excessive polyamine synthesis from ornithine by different rate limiting enzymes. Hence, in this review we aim to provide extensive insights on potential roles of ornithine in many of the disease related cellular processes and also on the structural features of ornithine interacting proteins, enabling development of therapeutic modalities.
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Affiliation(s)
- Muthukumaran Sivashanmugam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India; School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Jaidev J
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India
| | - Umashankar V
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
| | - Sulochana K N
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
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18
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Bunsupa S, Hanada K, Maruyama A, Aoyagi K, Komatsu K, Ueno H, Yamashita M, Sasaki R, Oikawa A, Saito K, Yamazaki M. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis. PLANT PHYSIOLOGY 2016; 171:2432-44. [PMID: 27303024 PMCID: PMC4972286 DOI: 10.1104/pp.16.00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/09/2016] [Indexed: 05/03/2023]
Abstract
Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer's disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase.
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Affiliation(s)
- Somnuk Bunsupa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kousuke Hanada
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Maruyama
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kaori Aoyagi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kana Komatsu
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Hideki Ueno
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Madoka Yamashita
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Ryosuke Sasaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Oikawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
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Structural basis of Ornithine Decarboxylase inactivation and accelerated degradation by polyamine sensor Antizyme1. Sci Rep 2015; 5:14738. [PMID: 26443277 PMCID: PMC4595762 DOI: 10.1038/srep14738] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/07/2015] [Indexed: 11/18/2022] Open
Abstract
Ornithine decarboxylase (ODC) catalyzes the first and rate-limiting step of polyamine biosynthesis in humans. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. Excessive accumulation of polyamines has a cytotoxic effect on cells and elevated level of ODC activity is associated with cancer development. To maintain normal cellular proliferation, regulation of polyamine synthesis is imposed by Antizyme1 (AZ1). The expression of AZ1 is induced by a ribosomal frameshifting mechanism in response to increased intracellular polyamines. AZ1 regulates polyamine homeostasis by inactivating ODC activity and enhancing its degradation. Here, we report the structure of human ODC in complex with N-terminally truncated AZ1 (cAZ1). The structure shows cAZ1 binding to ODC, which occludes the binding of a second molecule of ODC to form the active homodimer. Consequently, the substrate binding site is disrupted and ODC is inactivated. Structural comparison shows that the binding of cAZ1 to ODC causes a global conformational change of ODC and renders its C-terminal region flexible, therefore exposing this region for degradation by the 26S proteasome. Our structure provides the molecular basis for the inactivation of ODC by AZ1 and sheds light on how AZ1 promotes its degradation.
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20
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Screening of potential targets in Plasmodium falciparum using stage-specific metabolic network analysis. Mol Divers 2015; 19:991-1002. [PMID: 26303382 DOI: 10.1007/s11030-015-9632-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 01/29/2023]
Abstract
The Apicomplexa parasite Plasmodium is a major cause of death in developing countries which are less equipped to bring new medicines to the market. Currently available drugs used for treatment of malaria are limited either by inadequate efficacy, toxicity and/or increased resistance. Availability of the genome sequence, microarray data and metabolic profile of Plasmodium parasite offers an opportunity for the identification of stage-specific genes important to the organism's lifecycle. In this study, microarray data were analysed for differential expression and overlapped onto metabolic pathways to identify differentially regulated pathways essential for transition to successive erythrocytic stages. The results obtained indicate that S-adenosylmethionine decarboxylase/ornithine decarboxylase, a bifunctional enzyme required for polyamine synthesis, is important for the Plasmodium cell growth in the absence of exogenous polyamines. S-adenosylmethionine decarboxylase/ornithine decarboxylase is a valuable target for designing therapeutically useful inhibitors. One such inhibitor, [Formula: see text]-difluoromethyl ornithine, is currently in use for the treatment of African sleeping sickness caused by Trypanosoma brucei. Structural studies of ornithine decarboxylase along with known inhibitors and their analogues were carried out to screen drug databases for more effective and less toxic compounds.
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21
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Khomutov MA, Weisell J, Hyvönen M, Keinänen TA, Vepsäläinen J, Alhonen L, Khomutov AR, Kochetkov SN. Hydroxylamine derivatives for regulation of spermine and spermidine metabolism. BIOCHEMISTRY. BIOKHIMIIA 2013; 78:1431-46. [PMID: 24490733 DOI: 10.1134/s0006297913130051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biogenic polyamines spermine, spermidine, and their precursor putrescine are present in micro-to-millimolar concentrations in all cell types and are vitally important for their normal growth. High intracellular content of spermine and spermidine determines the multiplicity of the cellular functions of the polyamines. Many of these functions are not well characterized at the molecular level, ensuring the ongoing development of this field of biochemistry. Tumor cells have elevated polyamine level if compared with normal cells, and this greatly stimulates the search for new opportunities to deplete the intracellular pool of spermine and spermidine resulting in decrease in cell growth and even cell death. O-Substituted hydroxylamines occupy their own place among chemical regulators of the activity of the enzymes of polyamine metabolism. Varying the structure of the alkyl substituent made it possible to obtain within one class of chemical compounds highly effective inhibitors and regulators of the activity of all the enzymes of putrescine, spermine and spermidine metabolism (with the exception of FAD-dependent spermine oxidase and acetylpolyamine oxidase), effectors of the polyamine transport system, and even actively transported in cells "proinhibitor" of ornithine decarboxylase. Some principles for the design of specific inhibitors of these enzymes as well as the peculiarities of cellular effects of corresponding O-substituted hydroxylamines are discussed.
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Affiliation(s)
- M A Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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Aminooxy analog of histamine is an efficient inhibitor of mammalian l-histidine decarboxylase: combined in silico and experimental evidence. Amino Acids 2013; 46:621-31. [DOI: 10.1007/s00726-013-1589-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/27/2013] [Indexed: 12/20/2022]
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Structural insight into DFMO resistant ornithine decarboxylase from Entamoeba histolytica: an inkling to adaptive evolution. PLoS One 2013; 8:e53397. [PMID: 23326423 PMCID: PMC3543441 DOI: 10.1371/journal.pone.0053397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Background Polyamine biosynthetic pathway is a validated therapeutic target for large number of infectious diseases including cancer, giardiasis and African sleeping sickness, etc. α-Difluoromethylornithine (DFMO), a potent drug used for the treatment of African sleeping sickness is an irreversible inhibitor of ornithine decarboxylase (ODC), the first rate limiting enzyme of polyamine biosynthesis. The enzyme ODC of E. histolytica (EhODC) has been reported to exhibit resistance towards DFMO. Methodology/Principal Finding The basis for insensitivity towards DFMO was investigated by structural analysis of EhODC and conformational modifications at the active site. Here, we report cloning, purification and crystal structure determination of C-terminal truncated Entamoeba histolytica ornithine decarboxylase (EhODCΔ15). Structure was determined by molecular replacement method and refined to 2.8 Å resolution. The orthorhombic crystal exhibits P212121 symmetry with unit cell parameters a = 76.66, b = 119.28, c = 179.28 Å. Functional as well as evolutionary relations of EhODC with other ODC homologs were predicted on the basis of sequence analysis, phylogeny and structure. Conclusions/Significance We determined the tetrameric crystal structure of EhODCΔ15, which exists as a dimer in solution. Insensitivity towards DFMO is due to substitution of key substrate binding residues in active site pocket. Additionally, a few more substitutions similar to antizyme inhibitor (AZI), a non-functional homologue of ODCs, were identified in the active site. Here, we establish the fact that EhODC sequence has conserved PLP binding residues; in contrast few substrate binding residues are mutated similar to AZI. Further sequence analysis and structural studies revealed that EhODC may represent as an evolutionary bridge between active decarboxylase and inactive AZI.
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Grover A, Katiyar SP, Jeyakanthan J, Dubey VK, Sundar D. Mechanistic insights into the dual inhibition strategy for checking Leishmaniasis. J Biomol Struct Dyn 2012; 30:474-87. [DOI: 10.1080/07391102.2012.682212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Abhinav Grover
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi , Hauz Khas, New Delhi, 110016, India
| | - Shashank Prakash Katiyar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi , Hauz Khas, New Delhi, 110016, India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University , Karaikudi, Tamil Nadu, 630003, India
| | - Vikash Kumar Dubey
- Department of Biotechnology, Indian Institute of Technology (IIT) Guwahati , Guwahati, 781039, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi , Hauz Khas, New Delhi, 110016, India
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Chakraborty D, Saravanan P, Patra S, Dubey VK. Studies on ornithine decarboxylase of Leishmania donovani: structure modeling and inhibitor docking. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0035-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bunsupa S, Katayama K, Ikeura E, Oikawa A, Toyooka K, Saito K, Yamazaki M. Lysine decarboxylase catalyzes the first step of quinolizidine alkaloid biosynthesis and coevolved with alkaloid production in leguminosae. THE PLANT CELL 2012; 24:1202-16. [PMID: 22415272 PMCID: PMC3336119 DOI: 10.1105/tpc.112.095885] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 05/03/2023]
Abstract
Lysine decarboxylase (LDC) catalyzes the first-step in the biosynthetic pathway of quinolizidine alkaloids (QAs), which form a distinct, large family of plant alkaloids. A cDNA of lysine/ornithine decarboxylase (L/ODC) was isolated by differential transcript screening in QA-producing and nonproducing cultivars of Lupinus angustifolius. We also obtained L/ODC cDNAs from four other QA-producing plants, Sophora flavescens, Echinosophora koreensis, Thermopsis chinensis, and Baptisia australis. These L/ODCs form a phylogenetically distinct subclade in the family of plant ornithine decarboxylases. Recombinant L/ODCs from QA-producing plants preferentially or equally catalyzed the decarboxylation of L-lysine and L-ornithine. L. angustifolius L/ODC (La-L/ODC) was found to be localized in chloroplasts, as suggested by the transient expression of a fusion protein of La-L/ODC fused to the N terminus of green fluorescent protein in Arabidopsis thaliana. Transgenic tobacco (Nicotiana tabacum) suspension cells and hairy roots produced enhanced levels of cadaverine-derived alkaloids, and transgenic Arabidopsis plants expressing (La-L/ODC) produced enhanced levels of cadaverine, indicating the involvement of this enzyme in lysine decarboxylation to form cadaverine. Site-directed mutagenesis and protein modeling studies revealed a structural basis for preferential LDC activity, suggesting an evolutionary implication of L/ODC in the QA-producing plants.
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Affiliation(s)
- Somnuk Bunsupa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan
| | - Kae Katayama
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan
| | - Emi Ikeura
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan
| | - Akira Oikawa
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kiminori Toyooka
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Kawaguchi 332-0012, Japan
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Kappes B, Tews I, Binter A, Macheroux P. PLP-dependent enzymes as potential drug targets for protozoan diseases. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1814:1567-76. [PMID: 21884827 DOI: 10.1016/j.bbapap.2011.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 07/01/2011] [Accepted: 07/18/2011] [Indexed: 11/20/2022]
Abstract
The chemical properties of the B(6) vitamers are uniquely suited for wide use as cofactors in essential reactions, such as decarboxylations and transaminations. This review addresses current efforts to explore vitamin B(6) dependent enzymatic reactions as drug targets. Several current targets are described that are found amongst these enzymes. The focus is set on diseases caused by protozoan parasites. Comparison across a range of these organisms allows insight into the distribution of potential targets, many of which may be of interest in the development of broad range anti-protozoan drugs. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Barbara Kappes
- University Hospital Heidelberg, Department of Infectious Diseases, Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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Abstract
New drugs are urgently needed for the treatment of tropical and subtropical parasitic diseases, such as African sleeping sickness, Chagas' disease, leishmaniasis and malaria. Enzymes in polyamine biosynthesis and thiol metabolism, as well as polyamine transporters, are potential drug targets within these organisms. In the present review, the current knowledge of unique properties of polyamine metabolism in these parasites is outlined. These properties include prozyme regulation of AdoMetDC (S-adenosylmethionine decarboxylase) activity in trypanosomatids, co-expression of ODC (ornithine decarboxylase) and AdoMetDC activities in a single protein in plasmodia, and formation of trypanothione, a unique compound linking polyamine and thiol metabolism in trypanosomatids. Particularly interesting features within polyamine metabolism in these parasites are highlighted for their potential in selective therapeutic strategies.
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Oliveira EF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes. J Am Chem Soc 2011; 133:15496-505. [DOI: 10.1021/ja204229m] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Eduardo F. Oliveira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | | | - Pedro A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5′-Phosphate-Requiring Enzymes. J Chem Theory Comput 2011; 7:1356-68. [DOI: 10.1021/ct1002219] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - P. A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - M. J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
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31
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Lignin-derived oak phenolics: a theoretical examination of additional potential health benefits of red wine. J Mol Model 2010; 17:1841-5. [DOI: 10.1007/s00894-010-0893-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/31/2010] [Indexed: 10/18/2022]
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Colotti G, Ilari A. Polyamine metabolism in Leishmania: from arginine to trypanothione. Amino Acids 2010; 40:269-85. [PMID: 20512387 DOI: 10.1007/s00726-010-0630-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 05/13/2010] [Indexed: 12/20/2022]
Abstract
Polyamines (PAs) are essential metabolites in eukaryotes, participating in a variety of proliferative processes, and in trypanosomatid protozoa play an additional role in the synthesis of the critical thiol trypanothione. The PAs are synthesized by a metabolic process which involves arginase (ARG), which catalyzes the enzymatic hydrolysis of L-arginine (L-Arg) to L-ornithine and urea, and ornithine decarboxylase (ODC), which catalyzes the enzymatic decarboxylation of L-ornithine in putrescine. The S-adenosylmethionine decarboxylase (AdoMetDC) catalyzes the irreversible decarboxylation of S-adenosylmethionine (AdoMet), generating the decarboxylated S-adenosylmethionine (dAdoMet), which is a substrate, together with putrescine, for spermidine synthase (SpdS). Leishmania parasites and all the other members of the trypanosomatid family depend on spermidine for growth and survival. They can synthesize PAs and polyamine precursors, and also scavenge them from the microenvironment, using specific transporters. In addition, Trypanosomatids have a unique thiol-based metabolism, in which trypanothione (N1-N8-bis(glutathionyl)spermidine, T(SH)(2)) and trypanothione reductase (TR) replace many of the antioxidant and metabolic functions of the glutathione/glutathione reductase (GR) and thioredoxin/thioredoxin reductase (TrxR) systems present in the host. Trypanothione synthetase (TryS) and TR are necessary for the protozoa survival. Consequently, enzymes involved in spermidine synthesis and its utilization, i.e. ARG, ODC, AdoMetDC, SpdS and, in particular, TryS and TR, are promising targets for drug development.
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Affiliation(s)
- Gianni Colotti
- Institute of Biology and Molecular Pathology, CNR, c/o Department of Biochemical Sciences, University Sapienza, P.le A. Moro 5, 00185, Rome, Italy.
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Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: A molecular docking analysis. J Mol Model 2009; 16:311-26. [DOI: 10.1007/s00894-009-0547-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 06/11/2009] [Indexed: 11/25/2022]
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Khomutov AR, Keinanen TA, Grigorenko NA, Hyvonen MT, Uimari A, Pietila M, Cerrada-Gimenez M, Simonian AR, Khomutov MA, Vepsalainen J, Alhonen L, Janne J. Methylated analogs of spermine and spermidine as tools to investigate cellular functions of polyamines and enzymes of their metabolism. Mol Biol 2009. [DOI: 10.1134/s0026893309020083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
Cofactors are organic molecules, most of them originating from vitamins, that bind to enzymes making them able to catalyze defined reactions. A cofactor-based chemogenomics approach exploits the presence of a cofactor-binding domain to develop compound scaffolds tailored to mimic the cofactor and to replace it within target enzyme classes. As a result, a loss of function is observed. An expansion of the cofactor scaffold to include structural/chemical features derived from the substrate, that usually binds at cofactor adjacent sites, increases the specificity of the enzyme fishing. This approach has been so far applied only to NAD(P)(+)-dependent enzymes. However, it is suitable for all other cofactors, with difficulties, for some of them, originated by very tight binding. In the case of cofactors covalently bound to the enzyme, the competition between the natural cofactor and the cofactor scaffold mimic can only occur during enzyme folding.
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Affiliation(s)
- Ratna Singh
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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36
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Wu F, Gehring H. Structural requirements for novel coenzyme‐substrate derivatives to inhibit intracellular ornithine decarboxylase and cell proliferation. FASEB J 2008; 23:565-74. [DOI: 10.1096/fj.08-115121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fang Wu
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
- Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne EPFLCH‐1015LausanneSwitzerland
| | - Heinz Gehring
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
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37
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Wanasen N, Soong L. L-arginine metabolism and its impact on host immunity against Leishmania infection. Immunol Res 2008; 41:15-25. [PMID: 18040886 DOI: 10.1007/s12026-007-8012-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Leishmaniasis is a vector-borne disease found in many countries worldwide. The causative agent of the disease, Leishmania spp., lives as an obligate intracellular parasite within mammalian hosts. Since tissue macrophages are major target cells for parasite replication, the outcome of infection depends largely on the activation status of these cells. L-arginine is a crucial amino acid required for both nitric oxide (NO)-mediated parasite killing and polyamine-mediated parasite replication. This review highlights the significance of L-arginine as a factor determining the outcomes of Leishmania infection in vitro and its influences on host immune responses in vivo. Various therapeutic approaches targeting L-arginine metabolic pathways during infections with Leishmania are also discussed.
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Affiliation(s)
- Nanchaya Wanasen
- Department of Microbiology, Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infections, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
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38
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Hu T, Wu D, Chen J, Ding J, Jiang H, Shen X. The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis. J Biol Chem 2008; 283:21284-93. [PMID: 18508763 PMCID: PMC3258949 DOI: 10.1074/jbc.m801823200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/22/2008] [Indexed: 11/06/2022] Open
Abstract
The meso-diaminopimelate decarboxylase (DAPDC, EC 4.1.1.20) catalyzes the final step of L-lysine biosynthesis in bacteria and is regarded as a target for the discovery of antibiotics. Here we report the 2.3A crystal structure of DAPDC from Helicobacter pylori (HpDAPDC). The structure, in which the product L-lysine forms a Schiff base with the cofactor pyridoxal 5'-phosphate, provides structural insight into the substrate specificity and catalytic mechanism of the enzyme, and implies that the carboxyl to be cleaved locates at the si face of the cofactor. To our knowledge, this might be the first reported external aldimine of DAPDC. Moreover, the active site loop of HpDAPDC is in a "down" conformation and shields the ligand from solvent. Mutations of Ile(148) from the loop greatly impaired the catalytic efficiency. Combining the structural analysis of the I148L mutant, we hypothesize that HpDAPDC adopts an induced-fit catalytic mechanism in which this loop cycles through "down" and "up" conformations to stabilize intermediates and release product, respectively. Our work is expected to provide clues for designing specific inhibitors of DAPDC.
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Affiliation(s)
- Tiancen Hu
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dalei Wu
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Chen
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianping Ding
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hualiang Jiang
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xu Shen
- Drug Discovery and Design
Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203 and
State Key Laboratory of Molecular
Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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