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Zhang X, Sicalo Gianechini L, Li K, Kaplan RM, Witola WH. Broad-Spectrum Inhibitors for Conserved Unique Phosphoethanolamine Methyltransferases in Parasitic Nematodes Possess Anthelmintic Efficacy. Antimicrob Agents Chemother 2023; 67:e0000823. [PMID: 37212658 PMCID: PMC10269165 DOI: 10.1128/aac.00008-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/20/2023] [Indexed: 05/23/2023] Open
Abstract
In humans, nematode infections are prevalent in developing countries, causing long-term ill health, particularly in children. Worldwide, nematode infections are prevalent in livestock and pets, affecting productivity and health. Anthelmintic drugs are the primary means of controlling nematodes, but there is now high prevalence of anthelmintic resistance, requiring urgent identification of new molecular targets for anthelmintics with novel mechanisms of action. Here, we identified orthologous genes for phosphoethanolamine methyltransferases (PMTs) in nematodes within the families Trichostrongylidae, Dictyocaulidae, Chabertiidae, Ancylostomatoidea, and Ascarididae. We characterized these putative PMTs and found that they possess bona fide PMT catalytic activities. By complementing a mutant yeast strain lacking the ability to synthesize phosphatidylcholine, the PMTs were validated to catalyze the biosynthesis of phosphatidylcholine. Using an in vitro phosphoethanolamine methyltransferase assay with PMTs as enzymes, we identified compounds with cross-inhibitory effects against the PMTs. Corroboratively, treatment of PMT-complemented yeast with the PMT inhibitors blocked growth of the yeast, underscoring the essential role of the PMTs in phosphatidylcholine synthesis. Fifteen of the inhibitors with the highest activity against complemented yeast were tested against Haemonchus contortus using larval development and motility assays. Among them, four were found to possess potent anthelmintic activity against both multiple drug-resistant and susceptible isolates of H. contortus, with IC50 values (95% confidence interval) of 4.30 μM (2.15-8.28), 4.46 μM (3.22-6.16), 28.7 μM (17.3-49.5), and 0.65 μM (0.21-1.88). Taken together, we have validated a molecular target conserved in a broad range of nematodes and identified its inhibitors that possess potent in vitro anthelmintic activity.
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Affiliation(s)
- Xuejin Zhang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | | | - Kun Li
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Traditional Chinese Veterinary Medicine, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ray M. Kaplan
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
- Pathobiology Department, School of Veterinary Medicine, St. George’s University, Grenada, West Indies
| | - William H. Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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2
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Bare A, Thomas J, Etoroma D, Lee SG. Functional analysis of phosphoethanolamine N-methyltransferase in plants and parasites: Essential S-adenosylmethionine-dependent methyltransferase in choline and phospholipid metabolism. Methods Enzymol 2023; 680:101-137. [PMID: 36710008 DOI: 10.1016/bs.mie.2022.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phospholipids play an essential role as a barrier between cell content and the extracellular environment and regulate various cell signaling processes. Phosphatidylcholine (PtdCho) is one of the most abundant phospholipids in plant, animal, and some prokaryote cell membranes. In plants and some parasites, the biosynthesis of PtdCho begins with the amino acid serine, followed mainly through a phosphoethanolamine N-methyltransferase (PMT)-mediated biosynthetic pathway to phosphocholine (pCho). Because the PMT-mediated pathway, referred to as the phosphobase methylation pathway, produces a series of important primary and specialized metabolites for plant development and stress response, understanding the PMT enzyme is a key aspect of engineering plants with improved stress tolerance and fortified nutrients. Importantly, given the very limited phylogenetic distribution of PMTs, functional analysis and the identification of inhibitors targeting PMTs have potential and positive impacts in humans and in veterinary and agricultural fields. Here, we describe detailed basic knowledge and practical research methods to enable the systematic study of the biochemical and biophysical functions of PMT. The research methods described in this chapter are also applicable to the studies of other ubiquitous S-adenosyl-l-methionine (SAM)-dependent methyltransferases in all kingdoms.
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Affiliation(s)
- Alex Bare
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Jaime Thomas
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Etoroma
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Soon Goo Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States.
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Lee SG, Chung MS, DeMarsilis AJ, Holland CK, Jaswaney RV, Jiang C, Kroboth JHP, Kulshrestha K, Marcelo RZW, Meyyappa VM, Nelson GB, Patel JK, Petronio AJ, Powers SK, Qin PR, Ramachandran M, Rayapati D, Rincon JA, Rocha A, Ferreira JGRN, Steinbrecher MK, Yao K, Zhang EJ, Zou AJ, Gang M, Sparks M, Cascella B, Cruz W, Jez JM. Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus. Mol Biochem Parasitol 2020; 238:111291. [PMID: 32479776 DOI: 10.1016/j.molbiopara.2020.111291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022]
Abstract
In free-living and parasitic nematodes, the methylation of phosphoethanolamine to phosphocholine provides a key metabolite to sustain phospholipid biosynthesis for growth and development. Because the phosphoethanolamine methyltransferases (PMT) of nematodes are essential for normal growth and development, these enzymes are potential targets of inhibitor design. The pine wilt nematode (Bursaphelenchus xylophilus) causes extensive damage to trees used for lumber and paper in Asia. As a first step toward testing BxPMT1 as a potential nematicide target, we determined the 2.05 Å resolution x-ray crystal structure of the enzyme as a dead-end complex with phosphoethanolamine and S-adenosylhomocysteine. The three-dimensional structure of BxPMT1 served as a template for site-directed mutagenesis to probe the contribution of active site residues to catalysis and phosphoethanolamine binding using steady-state kinetic analysis. Biochemical analysis of the mutants identifies key residues on the β1d-α6 loop (W123F, M126I, and Y127F) and β1e-α7 loop (S155A, S160A, H170A, T178V, and Y180F) that form the phosphobase binding site and suggest that Tyr127 facilitates the methylation reaction in BxPMT1.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Michelle S Chung
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Antea J DeMarsilis
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Rohit V Jaswaney
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cherry Jiang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Jakob H P Kroboth
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kevin Kulshrestha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Raymundo Z W Marcelo
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Vidhya M Meyyappa
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Grant B Nelson
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Janki K Patel
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Alex J Petronio
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Samantha K Powers
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Peter R Qin
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Mythili Ramachandran
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Divya Rayapati
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - John A Rincon
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Andreia Rocha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | | | - Micah K Steinbrecher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kaisen Yao
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Eric J Zhang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Angela J Zou
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Margery Gang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Melanie Sparks
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States.
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Singh J, Mansuri R, Vijay S, Sahoo GC, Sharma A, Kumar M. Docking predictions based Plasmodium falciparum phosphoethanolamine methyl transferase inhibitor identification and in-vitro antimalarial activity analysis. BMC Chem 2019; 13:43. [PMID: 31384791 PMCID: PMC6661969 DOI: 10.1186/s13065-019-0551-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/08/2019] [Indexed: 11/10/2022] Open
Abstract
The increased multidrug resistance among antimalarial drugs produces the urgency of potent anti malarial to combat resistant malaria and the malaria burden worldwide. The protein which may prevent the growth or transmission of malaria parasite may be the great target for rational drug designing. Plasmodium falciparum phosphoethanolamine methyltransferase (Pfpmt) absent in human catalyzes triple methylation of ethanolamine into phosphocholine for phosphatidylcholine biosynthesis from serine decarboxylation phosphoethanolamine methyltransferase pathway for the membrane development at asexual as well as sexual stages of parasite. The Plasmodium requires production of membrane rapidly for growth and multiplication. Hence, the phosphoethanolamine methyltransferase of Plasmodium falciparum was selected as drug target for rational drug designing. Using Discovery studio 3.5 software the library of zinc compounds was screened against target and analyzed. The compounds with better druglike properties and docking affinity and binding interaction for target protein were procured for in vitro analysis against Plasmodium falciparum culture (IC50). Compounds ZINC02103914 and ZINC12882412 were found to have good druglike properties and affinity for Pfpmt also inhibited P. falciparum growth at very low µM IC50 concentration 3.0 µM and 2.1 µM respectively also found nontoxic in vitro against HEK-293 cells. Simulation study of best inhibitor revealed the specificity for the target protein. Hence, the compounds possessed the immense probability of being inhibitors of Pfpmt and may be optimized as antimalarial agent for combinational therapy to overcome the multidrug resistance and may also be used as template for optimization and rational drug designing.
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Affiliation(s)
- Jagbir Singh
- 1Division of Protein Biochemistry and Structural Biology, National Institute of Malaria Research (ICMR), Sector 8, Dwarka, New Delhi 110 077 India.,5Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, India
| | - Rani Mansuri
- 2School of Pharmaceutical Sciences, Apeejay Stya University, Gurugram, India
| | - Sonam Vijay
- Division of ECD, Indian Council of India, New Delhi, India
| | - Ganesh Chandra Sahoo
- 4Department of Biomedical Sciences, Rajendra Memorial Research Institute, Patna, India
| | - Arun Sharma
- 1Division of Protein Biochemistry and Structural Biology, National Institute of Malaria Research (ICMR), Sector 8, Dwarka, New Delhi 110 077 India
| | - Mahesh Kumar
- 5Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, India
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Antimalarial agents against both sexual and asexual parasites stages: structure-activity relationships and biological studies of the Malaria Box compound 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine (MMV019918) and analogues. Eur J Med Chem 2018; 150:698-718. [PMID: 29571157 DOI: 10.1016/j.ejmech.2018.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 01/31/2023]
Abstract
Therapies addressing multiple stages of Plasmodium falciparum life cycle are highly desirable for implementing malaria elimination strategies. MMV019918 (1, 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine) was selected from the MMV Malaria Box for its dual activity against both asexual stages and gametocytes. In-depth structure-activity relationship studies and cytotoxicity evaluation led to the selection of 25 for further biological investigation. The potential transmission blocking activity of 25 versus P. falciparum was confirmed through the standard membrane-feeding assay. Both 1 and 25 significantly prolonged atrioventricular conduction time in Langendorff-isolated rat hearts, and showed inhibitory activity of Ba2+ current through Cav1.2 channels. An in silico target-fishing study suggested the enzyme phosphoethanolamine methyltransferase (PfPMT) as a potential target. However, compound activity against PfPMT did not track with the antiplasmodial activity, suggesting the latter activity relies on a different molecular target. Nevertheless, 25 showed interesting activity against PfPMT, which could be an important starting point for the identification of more potent inhibitors active against both sexual and asexual stages of the parasite.
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Lee SG, Jez JM. Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation. J Biol Chem 2017; 292:21690-21702. [PMID: 29084845 DOI: 10.1074/jbc.ra117.000106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/20/2017] [Indexed: 01/05/2023] Open
Abstract
Phosphocholine (pCho) is a precursor for phosphatidylcholine and osmoprotectants in plants. In plants, de novo synthesis of pCho relies on the phosphobase methylation pathway. Phosphoethanolamine methyltransferase (PMT) catalyzes the triple methylation of phosphoethanolamine (pEA) to pCho. The plant PMTs are di-domain methyltransferases that divide the methylation of pEA in one domain from subsequent methylations in the second domain. To understand the molecular basis of this architecture, we examined the biochemical properties of three Arabidopsis thaliana PMTs (AtPMT1-3) and determined the X-ray crystal structures of AtPMT1 and AtPMT2. Although each isoform synthesizes pCho from pEA, their physiological roles differ with AtPMT1 essential for normal growth and salt tolerance, whereas AtPMT2 and AtPMT3 overlap functionally. The structures of AtPMT1 and AtPMT2 reveal unique features in each methyltransferase domain, including active sites that use different chemical mechanisms for phosphobase methylation. These structures also show how rearrangements in both the active sites and the di-domain linker form catalytically competent active sites and provide insight on the evolution of the PMTs in plants, nematodes, and apicomplexans. Connecting conformational changes with catalysis in modular enzymes, like the PMT, provides new insights on interdomain communication in biosynthetic systems.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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Witola WH, Cooks-Fagbodun S, Ordonez AR, Matthews K, Abugri DA, McHugh M. Knockdown of phosphoethanolamine transmethylation enzymes decreases viability of Haemonchus contortus. Vet Parasitol 2016; 223:1-6. [PMID: 27198768 DOI: 10.1016/j.vetpar.2016.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/19/2023]
Abstract
The phosphobase methylation pathway, in which phosphoethanolamine N-methyltransferases (PMTs) successively catalyze the methylation of phosphoethanolamine to phosphocholine, is essential in the free-living nematode Caenorhabditis elegans. Two PMT-encoding genes (HcPMT1 and HcPMT2) cloned from Haemonchus contortus have been shown, by in vitro assays, to possess enzymatic characteristics similar to those of C. elegans PMTs, but their physiological significance in H. contortus is yet to be elucidated. Therefore, in this study, we endeavored to determine the importance of HcPMT1 and HcPMT2 in the survival of H. contortus by adapting the use of phosphorodiamidate morpholino oligomers (PPMO) antisense approach to block the translation of HcPMT1 and HcPMT2 in the worms. We found that PPMOs targeting HcPMT1 and HcPMT2 down-regulated the expression of HcPMT1 and HcPMT2 proteins in adult H. contortus. Analysis of the effect of HcPMT1 and HcPMT2 knockdown showed that it significantly decreased worm motility and viability, thus validating HcPMT1 and HcPMT2 as essential enzymes for survival of H. contortus. Studies of gene function in H. contortus have been constrained by limited forward and reverse genetic technologies for use in H. contortus. Thus, our success in adaptation of use of PPMO antisense approach in H. contortus provides an important reverse genetic technological advance for studying this parasitic nematode of veterinary significance.
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Affiliation(s)
- William H Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, USA.
| | - Sheritta Cooks-Fagbodun
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
| | - Adriana Reyes Ordonez
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
| | - Kwame Matthews
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
| | - Daniel A Abugri
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
| | - Mark McHugh
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
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Witola WH, Matthews K, McHugh M. In vitro anthelmintic efficacy of inhibitors of phosphoethanolamine Methyltransferases in Haemonchus contortus. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2016; 6:44-53. [PMID: 27054063 PMCID: PMC4805780 DOI: 10.1016/j.ijpddr.2016.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 12/03/2022]
Abstract
The essential phosphobase methylation pathway for synthesis of phosphocholine is unique to nematodes, protozoa and plants, and thus an attractive antiparasitic molecular target. Herein, we screened compounds from the National Cancer Institute (Developmental Therapeutics Program Open Chemical Repository) for specific inhibitory activity against Haemonchus contortus phosphoethanolamine methyltransferases (HcPMT1 and HcPMT2), and tested candidate compounds for anthelmintic activity against adult and third-stage larvae of H. contortus. We identified compound NSC-641296 with IC50 values of 8.3 ± 1.1 μM and 5.1 ± 1.8 μM for inhibition of the catalytic activity of HcPMT1 alone and HcPMT1/HcPMT2 combination, respectively. Additionally we identified compound NSC-668394 with inhibitory IC50 values of 5.9 ± 0.9 μM and 2.8 ± 0.6 μM for HcPMT1 alone and HcPMT1/HcPMT2 combination, respectively. Of the two compounds, NSC-641296 depicted significant anthelmintic activity against third-stage larvae (IC50 = 15 ± 2.9 μM) and adult stages (IC50 = 7 ± 2.9 μM) of H. contortus, with optimal effective in vitro concentrations being 2-fold and 4-fold, respectively, lower than its cytotoxic IC50 (29 ± 2.1 μM) in a mammalian cell line. Additionally, we identified two compounds, NSC-158011 and NSC-323241, with low inhibitory activity against the combined activity of HcPMT1 and HcPMT2, but both compounds did not show any anthelmintic activity against H. contortus. The identification of NSC-641296 that specifically inhibits a unique biosynthetic pathway in H. contortus and has anthelmintic activity against both larval and adult stages of H. contortus, provides impetus for the development of urgently needed new efficacious anthelmintics to address the prevailing problem of anthelmintic-resistant H. contortus. NSC-641296 and NSC-668394 inhibit HcPMT1 and HcPMT2 enzymes in Haemonchus contortus. NSC-641296 has in vitro anthelmintic activity against larvae and adult H. contortus. H. contortus HcPMT1 and HcPMT2 are two unique targets for anthelmintic development.
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Affiliation(s)
- William H Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana-Champaign, USA.
| | - Kwame Matthews
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
| | - Mark McHugh
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA
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Saen-Oon S, Lee SG, Jez JM, Guallar V. An alternative mechanism for the methylation of phosphoethanolamine catalyzed by Plasmodium falciparum phosphoethanolamine methyltransferase. J Biol Chem 2014; 289:33815-25. [PMID: 25288796 DOI: 10.1074/jbc.m114.611319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The phosphobase methylation pathway catalyzed by the phosphoethanolamine methyltransferase in Plasmodium falciparum (PfPMT), the malaria parasite, offers an attractive target for anti-parasitic drug development. PfPMT methylates phosphoethanolamine (pEA) to phosphocholine for use in membrane biogenesis. Quantum mechanics and molecular mechanics (QM/MM) calculations tested the proposed reaction mechanism for methylation of pEA involving the previously identified Tyr-19-His-132 dyad, which indicated an energetically unfavorable mechanism. Instead, the QM/MM calculations suggested an alternative mechanism involving Asp-128. The reaction coordinate involves the stepwise transfer of a proton to Asp-128 via a bridging water molecule followed by a typical Sn2-type methyl transfer from S-adenosylmethionine to pEA. Functional analysis of the D128A, D128E, D128Q, and D128N PfPMT mutants shows a loss of activity with pEA but not with the final substrate of the methylation pathway. X-ray crystal structures of the PfPMT-D128A mutant in complex with S-adenosylhomocysteine and either pEA or phosphocholine reveal how mutation of Asp-128 disrupts a hydrogen bond network in the active site. The combined QM/MM, biochemical, and structural studies identify a key role for Asp-128 in the initial step of the phosphobase methylation pathway in Plasmodium and provide molecular insight on the evolution of multiple activities in the active site of the PMT.
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Affiliation(s)
- Suwipa Saen-Oon
- From the Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program, Carrer de Jordi Girona 29, 08034 Barcelona, Spain
| | - Soon Goo Lee
- the Department of Biology, Washington University, St. Louis, Missouri 63130, and
| | - Joseph M Jez
- the Department of Biology, Washington University, St. Louis, Missouri 63130, and
| | - Victor Guallar
- From the Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program, Carrer de Jordi Girona 29, 08034 Barcelona, Spain, the Catalan Institution for Research and Advanced Studies, Barcelona 08010, Spain
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Abstract
Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
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Lee SG, Jez JM. Nematode phospholipid metabolism: an example of closing the genome-structure-function circle. Trends Parasitol 2014; 30:241-50. [PMID: 24685202 DOI: 10.1016/j.pt.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 01/03/2023]
Abstract
Parasitic nematodes that infect humans, animals, and plants cause health problems, livestock and agricultural losses, and economic damage worldwide and are important targets for drug development. The growing availability of nematode genomes supports the discovery of new pathways that differ from host organisms and are a starting point for structural and functional studies of novel antiparasitic targets. As an example of how genome data, structural biology, and biochemistry integrate into a research cycle targeting parasites, we summarize the discovery of the phosphobase methylation pathway for phospholipid synthesis in nematodes and compare the phosphoethanolamine methyltransferases (PMTs) from nematodes, plants, and Plasmodium. Crystallographic and biochemical studies of the PMTs in this pathway provide a foundation that guides the next steps that close the genome-structure-function circle.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA.
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A biosynthetic enzyme worms its way out of a conserved mechanism. Structure 2013; 21:1719-20. [PMID: 24119669 DOI: 10.1016/j.str.2013.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee SG, Jez JM. Evolution of structure and mechanistic divergence in di-domain methyltransferases from nematode phosphocholine biosynthesis. Structure 2013; 21:1778-87. [PMID: 24012478 PMCID: PMC3797223 DOI: 10.1016/j.str.2013.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/25/2013] [Accepted: 07/28/2013] [Indexed: 10/26/2022]
Abstract
The phosphobase methylation pathway is the major route for supplying phosphocholine to phospholipid biosynthesis in plants, nematodes, and Plasmodium. In this pathway, phosphoethanolamine N-methyltransferase (PMT) catalyzes the sequential methylation of phosphoethanolamine to phosphocholine. In the PMT, one domain (MT1) catalyzes methylation of phosphoethanolamine to phosphomonomethylethanolamine and a second domain (MT2) completes the synthesis of phosphocholine. The X-ray crystal structures of the di-domain PMT from the parasitic nematode Haemonchus contortus (HcPMT1 and HcPMT2) reveal that the catalytic domains of these proteins are structurally distinct and allow for selective methylation of phosphobase substrates using different active site architectures. These structures also reveal changes leading to loss of function in the vestigial domains of the nematode PMT. Divergence of function in the two nematode PMTs provides two distinct antiparasitic inhibitor targets within the same essential metabolic pathway. The PMTs from nematodes, plants, and Plasmodium also highlight adaptable metabolic modularity in evolutionarily diverse organisms.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
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Lee SG, Alpert TD, Jez JM. Crystal structure of phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with amodiaquine. Bioorg Med Chem Lett 2012; 22:4990-3. [PMID: 22771008 PMCID: PMC3401361 DOI: 10.1016/j.bmcl.2012.06.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/05/2012] [Accepted: 06/11/2012] [Indexed: 11/16/2022]
Abstract
Phosphoethanolamine N-methyltransferase (PMT) is essential for phospholipid biogenesis in the malarial parasite Plasmodium falciparum. PfPMT catalyzes the triple methylation of phosphoethanolamine to produce phosphocholine, which is then used for phosphatidylcholine synthesis. Here we describe the 2.0Å resolution X-ray crystal structure of PfPMT in complex with amodiaquine. To better characterize inhibition of PfPMT by amodiaquine, we determined the IC(50) values of a series of aminoquinolines using a direct radiochemical assay. Both structural and functional analyses provide a possible approach for the development of new small molecule inhibitors of PfPMT.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Lee SG, Kim Y, Alpert TD, Nagata A, Jez JM. Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target. J Biol Chem 2012; 287:1426-34. [PMID: 22117061 PMCID: PMC3256908 DOI: 10.1074/jbc.m111.315267] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/07/2011] [Indexed: 01/19/2023] Open
Abstract
In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19-1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a "catalytic" latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Youngchang Kim
- the Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Tara D. Alpert
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Akina Nagata
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Department of Biology, Knox College, Galesburg, Illinois 61401
| | - Joseph M. Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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