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Wu RZ, Zhou HY, Song JF, Xia QH, Hu W, Mou XD, Li X. Chemotherapeutics for Toxoplasma gondii: Molecular Biotargets, Binding Modes, and Structure-Activity Relationship Investigations. J Med Chem 2021; 64:17627-17655. [PMID: 34894691 DOI: 10.1021/acs.jmedchem.1c01569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxoplasmosis, an infectious zoonotic disease caused by the apicomplexan parasite Toxoplasma gondii (T. gondii), is a major worldwide health problem. However, there are currently no effective options (chemotherapeutic drugs or prophylactic vaccines) for treating chronic latent toxoplasmosis infection. Accordingly, seeking more effective and safer chemotherapeutics for combating this disease remains a long-term and challenging objective. In this paper, we summarize possible molecular biotargets, with an emphasis on those that are druggable and promising, including, without limitation, calcium-dependent protein kinase 1, bifunctional thymidylate synthase-dihydrofolate reductase, and farnesyl diphosphate synthase. Meanwhile, as important components of medicinal chemistry, the binding modes and structure-activity relationship profiles of the corresponding inhibitors were also illuminated. We anticipate that this information will be helpful for further identification of more effective chemotherapeutic interventions to prevent and treat zoonotic infections caused by T. gondii.
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Affiliation(s)
- Rong-Zhen Wu
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China
| | - Huai-Yu Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, no. 44 Wenhua Xi Road, Ji'nan, Shandong 250012, PR China
| | - Jing-Feng Song
- School of Pharmaceutical Sciences and Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, no. 1168 Chunrong Xi Road, Kunming, Yunnan 650500, PR China
| | - Qiao-Hong Xia
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, no. 44 Wenhua Xi Road, Ji'nan, Shandong 250012, PR China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, no. 72 Binhai Road of JiMo, Qingdao, Shandong 266237, PR China
| | - Xiao-Dong Mou
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China
| | - Xun Li
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China.,Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100192, PR China
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Aygün C, Mutlu Ö. Computational characterisation of Toxoplasma gondii FabG (3-oxoacyl-[acyl-carrier-protein] reductase): a combined virtual screening and all-atom molecular dynamics simulation study. J Biomol Struct Dyn 2020; 40:1952-1969. [PMID: 33063633 DOI: 10.1080/07391102.2020.1834456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Toxoplasma gondii is an opportunistic obligate parasite, ubiquitous around the globe with seropositivity rates that range from 10% to 90% and infection by the parasite of pregnant women causes pre-natal death of the foetus in most cases and severe neurodegenerative syndromes in some. No vaccine is currently available, and since drug-resistance is common among T. gondii strains, discovering lead compounds for drug design using diverse tactics is necessary. In this study, the sole constituent isoform of an enzymatic 3-oxoacyl-[acyl-carrier-protein] reduction step in an apicoplast-located fatty acid biosynthesis pathway was chosen as a possible drug target. FASII is prokaryotic therefore, targeting it would pose fewer side-effects to human hosts. After a homology 3D modelling of TgFabG, a high-throughput virtual screening of 9867 compounds, the elimination of ligands was carried out by a flexible ligand molecular docking and 200 ns molecular dynamics simulations, with additional DCCM and PC plot analyses. Molecular Dynamics and related post-MD analyses of the top 3 TgFabG binders selected for optimal free binding energies, showed that L2 maintained strong H-bonds with TgFabG and facilitated structural reorientation expected of FabGs, namely an expansion of the Rossmann Fold and a flexible lid capping. The most flexible TgFabG sites were the α7 helix (the flexible lid region) and the β4-α4 and β5-α6 loops. For TgFabG-L2, the movements of these regions toward the active site enabled greater ligand stability. Thus, L2 ("Skimmine"; PubChem ID: 320361), was ultimately selected as the optimal candidate for the discovery of lead compounds for rational drug design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Can Aygün
- Faculty of Arts and Sciences, Biology Department, Marmara University, Istanbul, Turkey
| | - Özal Mutlu
- Faculty of Arts and Sciences, Biology Department, Marmara University, Istanbul, Turkey
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Roberts AD, Nair SC, Guerra AJ, Prigge ST. Development of a conditional localization approach to control apicoplast protein trafficking in malaria parasites. Traffic 2019; 20:571-582. [PMID: 31094037 DOI: 10.1111/tra.12656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023]
Abstract
Secretory proteins are of particular importance to apicomplexan parasites and comprise over 15% of the genomes of the human pathogens that cause diseases like malaria, toxoplasmosis and babesiosis as well as other diseases of agricultural significance. Here, we developed an approach that allows us to control the trafficking destination of secretory proteins in the human malaria parasite Plasmodium falciparum. Based on the unique structural requirements of apicoplast transit peptides, we designed three conditional localization domains (CLD1, 2 and 3) that can be used to control protein trafficking via the addition of a cell permeant ligand. Studies comparing the trafficking dynamics of each CLD show that CLD2 has the most optimal trafficking efficiency. To validate this system, we tested whether CLD2 could conditionally localize a biotin ligase called holocarboxylase synthetase 1 (HCS1) without interfering with the function of the enzyme. In a parasite line expressing CLD2-HCS1, we were able to control protein biotinylation in the apicoplast in a ligand-dependent manner, demonstrating the full functionality of the CLD tool. We have developed and validated a novel molecular tool that may be used in future studies to help elucidate the function of secretory proteins in malaria parasites.
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Affiliation(s)
- Aleah D Roberts
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sethu C Nair
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alfredo J Guerra
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Afanador GA, Tomchick DR, Phillips MA. Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs. Structure 2018; 26:1499-1512.e5. [PMID: 30197036 DOI: 10.1016/j.str.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
Trypanosoma brucei is a neglected tropical disease endemic to Africa. The polyamine spermidine is essential for post-translational hypusine modification of eukaryotic initiation factor 5A (eIF5A), which is catalyzed by deoxyhypusine synthase (TbDHS). In trypanosomatids, deoxyhypusine synthase (DHS) activity is dependent on heterotetramer formation between two paralogs, DHSc and DHSp, both with minimal activity on their own due to missing catalytic residues. We determined the X-ray structure of TbDHS showing a single functional shared active site is formed at the DHSc/DHSp heterodimer interface, with deficiencies in one subunit complemented by the other. Each heterodimer contains two NAD+ binding sites, one housed in the functional catalytic site and the second bound in a remnant dead site that lacks key catalytic residues. Functional analysis of these sites by site-directed mutagenesis identified long-range contributions to the catalytic site from the dead site. Differences between trypanosomatid and human DHS that could be exploited for drug discovery were identified.
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Affiliation(s)
- Gustavo A Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Afanador GA, Guerra AJ, Swift RP, Rodriguez RE, Bartee D, Matthews KA, Schön A, Freire E, Freel Meyers CL, Prigge ST. A novel lipoate attachment enzyme is shared by Plasmodium and Chlamydia species. Mol Microbiol 2017; 106:439-451. [PMID: 28836704 DOI: 10.1111/mmi.13776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/22/2022]
Abstract
Lipoate is an essential cofactor for enzymes that are important for central metabolism and other processes. In malaria parasites, scavenged lipoate from the human host is required for survival. The Plasmodium falciparum mitochondrion contains two enzymes (PfLipL1 and PfLipL2) that are responsible for activating mitochondrial proteins through the covalent attachment of lipoate (lipoylation). Lipoylation occurs via a novel redox-gated mechanism that remains poorly understood. We show that PfLipL1 functions as a redox switch that determines which downstream proteins will be activated. Based on the lipoate redox state, PfLipL1 either functions as a canonical lipoate ligase or as a lipoate activating enzyme which works in conjunction with PfLipL2. We demonstrate that PfLipL2 is a lipoyltransferase and is a member of a novel clade of lipoate attachment enzymes. We show that a LipL2 enzyme from Chlamydia trachomatis has similar activity, demonstrating conservation between intracellular pathogens from different phylogenetic kingdoms and supporting the hypothesis that an early ancestor of malaria parasites once contained a chlamydial endosymbiont. Redox-dependent lipoylation may regulate processes such as central metabolism and oxidative defense pathways.
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Affiliation(s)
- Gustavo A Afanador
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alfredo J Guerra
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ryan E Rodriguez
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Krista A Matthews
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Zitko J, Doležal M. Enoyl acyl carrier protein reductase inhibitors: an updated patent review (2011 – 2015). Expert Opin Ther Pat 2016; 26:1079-94. [DOI: 10.1080/13543776.2016.1211112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Jordan CA, Sandoval BA, Serobyan MV, Gilling DH, Groziak MP, Xu HH, Vey JL. Crystallographic insights into the structure-activity relationships of diazaborine enoyl-ACP reductase inhibitors. Acta Crystallogr F Struct Biol Commun 2015; 71:1521-30. [PMID: 26625295 PMCID: PMC4666481 DOI: 10.1107/s2053230x15022098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/18/2015] [Indexed: 05/28/2024] Open
Abstract
Enoyl-ACP reductase, the last enzyme of the fatty-acid biosynthetic pathway, is the molecular target for several successful antibiotics such as the tuberculosis therapeutic isoniazid. It is currently under investigation as a narrow-spectrum antibiotic target for the treatment of several types of bacterial infections. The diazaborine family is a group of boron heterocycle-based synthetic antibacterial inhibitors known to target enoyl-ACP reductase. Development of this class of molecules has thus far focused solely on the sulfonyl-containing versions. Here, the requirement for the sulfonyl group in the diazaborine scaffold was investigated by examining several recently characterized enoyl-ACP reductase inhibitors that lack the sulfonyl group and exhibit additional variability in substitutions, size and flexibility. Biochemical studies are reported showing the inhibition of Escherichia coli enoyl-ACP reductase by four diazaborines, and the crystal structures of two of the inhibitors bound to E. coli enoyl-ACP reductase solved to 2.07 and 2.11 Å resolution are reported. The results show that the sulfonyl group can be replaced with an amide or thioamide without disruption of the mode of inhibition of the molecule.
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Affiliation(s)
- Cheryl A. Jordan
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA
| | - Braddock A. Sandoval
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA
| | - Mkrtich V. Serobyan
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA
| | - Damian H. Gilling
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Michael P. Groziak
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542-3089, USA
| | - H. Howard Xu
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Jessica L. Vey
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA
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Fatty acid metabolism in the Plasmodium apicoplast: Drugs, doubts and knockouts. Mol Biochem Parasitol 2015; 199:34-50. [DOI: 10.1016/j.molbiopara.2015.03.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/25/2022]
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