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Arif SM, Floto RA, Blundell TL. Using Structure-guided Fragment-Based Drug Discovery to Target Pseudomonas aeruginosa Infections in Cystic Fibrosis. Front Mol Biosci 2022; 9:857000. [PMID: 35433835 PMCID: PMC9006449 DOI: 10.3389/fmolb.2022.857000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) is progressive genetic disease that predisposes lungs and other organs to multiple long-lasting microbial infections. Pseudomonas aeruginosa is the most prevalent and deadly pathogen among these microbes. Lung function of CF patients worsens following chronic infections with P. aeruginosa and is associated with increased mortality and morbidity. Emergence of multidrug-resistant, extensively drug-resistant and pandrug-resistant strains of P. aeruginosa due to intrinsic and adaptive antibiotic resistance mechanisms has failed the current anti-pseudomonal antibiotics. Hence new antibacterials are urgently needed to treat P. aeruginosa infections. Structure-guided fragment-based drug discovery (FBDD) is a powerful approach in the field of drug development that has succeeded in delivering six FDA approved drugs over the past 20 years targeting a variety of biological molecules. However, FBDD has not been widely used in the development of anti-pseudomonal molecules. In this review, we first give a brief overview of our structure-guided FBDD pipeline and then give a detailed account of FBDD campaigns to combat P. aeruginosa infections by developing small molecules having either bactericidal or anti-virulence properties. We conclude with a brief overview of the FBDD efforts in our lab at the University of Cambridge towards targeting P. aeruginosa infections.
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Affiliation(s)
| | - R. Andres Floto
- Molecular Immunity Unit, Department of Medicine University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Tom L. Blundell,
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2
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Hsu D, Hwang T. Stereoselective Formal Synthesis of Platencin. ChemistrySelect 2022. [DOI: 10.1002/slct.202103794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Day‐Shin Hsu
- Department of Chemistry and Biochemistry National Chung Cheng University Minhsiung, Chiayi Taiwan 62102
| | - Tai‐Yun Hwang
- Department of Chemistry and Biochemistry National Chung Cheng University Minhsiung, Chiayi Taiwan 62102
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3
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Tomčala A, Michálek J, Schneedorferová I, Füssy Z, Gruber A, Vancová M, Oborník M. Fatty Acid Biosynthesis in Chromerids. Biomolecules 2020; 10:E1102. [PMID: 32722284 PMCID: PMC7464705 DOI: 10.3390/biom10081102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Fatty acids are essential components of biological membranes, important for the maintenance of cellular structures, especially in organisms with complex life cycles like protozoan parasites. Apicomplexans are obligate parasites responsible for various deadly diseases of humans and livestock. We analyzed the fatty acids produced by the closest phototrophic relatives of parasitic apicomplexans, the chromerids Chromera velia and Vitrella brassicaformis, and investigated the genes coding for enzymes involved in fatty acids biosynthesis in chromerids, in comparison to their parasitic relatives. Based on evidence from genomic and metabolomic data, we propose a model of fatty acid synthesis in chromerids: the plastid-localized FAS-II pathway is responsible for the de novo synthesis of fatty acids reaching the maximum length of 18 carbon units. Short saturated fatty acids (C14:0-C18:0) originate from the plastid are then elongated and desaturated in the cytosol and the endoplasmic reticulum. We identified giant FAS I-like multi-modular enzymes in both chromerids, which seem to be involved in polyketide synthesis and fatty acid elongation. This full-scale description of the biosynthesis of fatty acids and their derivatives provides important insights into the reductive evolutionary transition of a phototropic algal ancestor to obligate parasites.
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Affiliation(s)
- Aleš Tomčala
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia, Husova 458/102, 370 05 České Budějovice, Czech Republic
| | - Jan Michálek
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Ivana Schneedorferová
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Ansgar Gruber
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Marie Vancová
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Miroslav Oborník
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
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4
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Affiliation(s)
- Day-Shin Hsu
- Department of Chemistry and Biochemistry; National Chung Cheng University; 621 Minhsiung Taiwan
| | - Tai-Yu Hwang
- Department of Chemistry and Biochemistry; National Chung Cheng University; 621 Minhsiung Taiwan
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5
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Ghosh S, Pathak S, Sonawat HM, Sharma S, Sengupta A. Metabolomic changes in vertebrate host during malaria disease progression. Cytokine 2018; 112:32-43. [PMID: 30057363 DOI: 10.1016/j.cyto.2018.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/24/2022]
Abstract
Metabolomics refers to top-down systems biological analysis of metabolites in biological specimens. Phenotypic proximity of metabolites makes them interesting candidates for studying biomarkers of environmental stressors such as parasitic infections. Moreover, the host-parasite interaction directly impinges upon metabolic pathways since the parasite uses the host metabolite pool as a biosynthetic resource. Malarial infection, although not recognized as a classic metabolic disorder, often leads to severe metabolic changes such as hypoglycemia and lactic acidosis. Thus, metabolomic analysis of the infection has become an invaluable tool for promoting a better understanding of the host-parasite interaction and for the development of novel therapeutics. In this review, we summarize the current knowledge obtained from metabolomic studies of malarial infection in rodent models and human patients. Metabolomic analysis of experimental rodent malaria has provided significant insights into the mechanisms of disease progression including utilization of host resources by the parasite, sexual dimorphism in metabolic phenotypes, and cellular changes in host metabolism. Moreover, these studies also provide proof of concept for prediction of cerebral malaria. On the other hand, metabolite analysis of patient biofluids generates extensive data that could be of use in identifying biomarkers of infection severity and in monitoring disease progression. Through the use of metabolomic datasets one hopes to assess crucial infection-specific issues such as clinical severity, drug resistance, therapeutic targets, and biomarkers. Also discussed are nascent or newly emerging areas of metabolomics such as pre-erythrocytic stages of the infection and the host immune response. This review is organized in four broad sections-methodologies for metabolomic analysis, rodent infection models, studies of human clinical specimens, and potential of immunometabolomics. Data summarized in this review should serve as a springboard for novel hypothesis testing and lead to a better understanding of malarial infection and parasite biology.
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Affiliation(s)
- Soumita Ghosh
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
| | - Sulabha Pathak
- Department of Biological Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Mumbai 400005, India
| | - Haripalsingh M Sonawat
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Mumbai 400005, India
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Mumbai 400005, India
| | - Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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Abstract
The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.
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Affiliation(s)
| | - John Parkinson
- a Program in Molecular Structure and Function , Hospital for Sick Children , Toronto , Ontario , Canada
- b Departments of Biochemistry, Molecular Genetics and Computer Science , University of Toronto , Toronto , Ontario , Canada
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7
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Abstract
Chemical genetics has emerged as a powerful approach to dissect biological processes, based on the utilization of small molecules disturbing the function of specific target proteins. By analogy with classical genetics, 'reverse chemical genetics' refers to the utilization of drugs acting on a known target, enabling its functional characterization at the levels of the cells, tissues and organisms. Likewise, 'direct chemical genetics' refers to the utilization of a drug of unknown mode of action, but triggering a phenotype of interest. In that case, one has to identify the target(s) possibly blocked (or possibly activated) by the small molecule. This chapter illustrates both approaches, like the analysis of the elongation of fatty acids, the biosynthesis of galactoglycerolipids or the catabolism of phosphoglycerolipids by reverse chemical genetics or the study of the membrane glycerolipid remodeling triggered upon phosphate starvation, by direct chemical genetics.
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8
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Cukier CD, Hope AG, Elamin AA, Moynie L, Schnell R, Schach S, Kneuper H, Singh M, Naismith JH, Lindqvist Y, Gray DW, Schneider G. Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa. ACS Chem Biol 2013; 8:2518-27. [PMID: 24015914 PMCID: PMC3833349 DOI: 10.1021/cb4005063] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis. Here, we report gene deletion experiments that support the essentiality of this gene in P. aeruginosa and the identification of a number of small molecule FabG inhibitors with IC50 values in the nanomolar to low micromolar range and good physicochemical properties. Structural characterization of 16 FabG-inhibitor complexes by X-ray crystallography revealed that the compounds bind at a novel allosteric site located at the FabG subunit-subunit interface. Inhibitor binding relies primarily on hydrophobic interactions, but specific hydrogen bonds are also observed. Importantly, the binding cavity is formed upon complex formation and therefore would not be recognized by virtual screening approaches. The structure analysis further reveals that the inhibitors act by inducing conformational changes that propagate to the active site, resulting in a displacement of the catalytic triad and the inability to bind NADPH.
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Affiliation(s)
- Cyprian D. Cukier
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | - Ayssar A. Elamin
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | - Lucile Moynie
- Biomedical
Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, U.K
| | - Robert Schnell
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Susanne Schach
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | | | - Mahavir Singh
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | - James H. Naismith
- Biomedical
Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, U.K
| | - Ylva Lindqvist
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | - Gunter Schneider
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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9
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Cell biology of chromerids: autotrophic relatives to apicomplexan parasites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 306:333-69. [PMID: 24016529 DOI: 10.1016/b978-0-12-407694-5.00008-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chromerida are algae possessing a complex plastid surrounded by four membranes. Although isolated originally from stony corals in Australia, they seem to be globally distributed. According to their molecular phylogeny, morphology, ultrastructure, structure of organellar genomes, and noncanonical pathway for tetrapyrrole synthesis, these algae are thought to be the closest known phototrophic relatives to apicomplexan parasites. Here, we summarize the current knowledge of cell biology and evolution of this novel group of algae, which contains only two formally described species, but is apparently highly diverse and virtually ubiquitous in marine environments.
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10
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Botté CY, Dubar F, McFadden GI, Maréchal E, Biot C. Plasmodium falciparum apicoplast drugs: targets or off-targets? Chem Rev 2011; 112:1269-83. [PMID: 22026508 DOI: 10.1021/cr200258w] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Cyrille Y Botté
- Laboratoire de Physiologie Cellulaire Végétale, UMR 5168, CNRS, CEA, INRA, Université Joseph Fourier, Grenoble, France
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11
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Yoshimitsu T, Nojima S, Hashimoto M, Tanaka T. Total Synthesis of (±)-Platencin. Org Lett 2011; 13:3698-701. [DOI: 10.1021/ol2013439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takehiko Yoshimitsu
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoji Nojima
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Hashimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuaki Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Hung SS, Parkinson J. Post-genomics resources and tools for studying apicomplexan metabolism. Trends Parasitol 2011; 27:131-40. [DOI: 10.1016/j.pt.2010.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/03/2010] [Accepted: 11/10/2010] [Indexed: 11/26/2022]
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13
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Louie T, Goodman CD, Holloway GA, McFadden GI, Mollard V, Watson KG. Dimeric cyclohexane-1,3-dione oximes inhibit wheat acetyl-CoA carboxylase and show anti-malarial activity. Bioorg Med Chem Lett 2010; 20:4611-3. [PMID: 20580556 DOI: 10.1016/j.bmcl.2010.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 06/01/2010] [Indexed: 11/18/2022]
Abstract
A series of dimeric 1,3-cyclohexanedione oxime ethers were synthesized and found to have significant antiplasmodial activity with IC(50)'s in the range 3-12 microM. The most active dimer was tested in the Plasmodium berghei mouse model of malaria and at a dose of 48 mg/kg gave a 45% reduction in parasitaemia. Several commercial herbicides, all known to be inhibitors of maize acetyl-CoA carboxylase, were also tested for antimalarial activity, but were essentially inactive with the exception of butroxydim which gave an IC(50) of 10 microM.
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Affiliation(s)
- Theola Louie
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Victoria, Australia
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14
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Keeling PJ. The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci 2010; 365:729-48. [PMID: 20124341 DOI: 10.1098/rstb.2009.0103] [Citation(s) in RCA: 373] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.
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Affiliation(s)
- Patrick J Keeling
- Botany Department, Canadian Institute for Advanced Research, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4.
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15
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Hunter WN. Structure-based ligand design and the promise held for antiprotozoan drug discovery. J Biol Chem 2008; 284:11749-53. [PMID: 19103598 PMCID: PMC2673241 DOI: 10.1074/jbc.r800072200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The development of the pharmaceutical industry, driven by progress in
chemistry, biology, and technology, ranks as one of the most successful of
human endeavors. However, serious health problems persist, among which are
diseases caused by protozoan parasites, largely ignored in modern times.
Advances in genomic sciences, molecular and structural biology, and
computational and medicinal chemistry now set the scene for a renewed assault
on such infections. A structure-centric approach to support discovery of
antiparasitic compounds promises much. Current strategies and benefits of a
structure-based approach to support early stage drug discovery will be
described.
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Affiliation(s)
- William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom.
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