1
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Ashton T, Calic PPS, Dans MG, Ooi ZK, Zhou Q, Palandri J, Loi K, Jarman KE, Qiu D, Lehane AM, Maity BC, De N, Giannangelo C, MacRaild CA, Creek DJ, Mao EY, Gancheva MR, Wilson DW, Chowdury M, de Koning-Ward TF, Famodimu MT, Delves MJ, Pollard H, Sutherland CJ, Baud D, Brand S, Jackson PF, Cowman AF, Sleebs BE. Property and Activity Refinement of Dihydroquinazolinone-3-carboxamides as Orally Efficacious Antimalarials that Target PfATP4. J Med Chem 2024; 67:14493-14523. [PMID: 39134060 PMCID: PMC11345840 DOI: 10.1021/acs.jmedchem.4c01241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024]
Abstract
To contribute to the global effort to develop new antimalarial therapies, we previously disclosed initial findings on the optimization of the dihydroquinazolinone-3-carboxamide class that targets PfATP4. Here we report on refining the aqueous solubility and metabolic stability to improve the pharmacokinetic profile and consequently in vivo efficacy. We show that the incorporation of heterocycle systems in the 8-position of the scaffold was found to provide the greatest attainable balance between parasite activity, aqueous solubility, and metabolic stability. Optimized analogs, including the frontrunner compound S-WJM992, were shown to inhibit PfATP4-associated Na+-ATPase activity, gave rise to a metabolic signature consistent with PfATP4 inhibition, and displayed altered activities against parasites with mutations in PfATP4. Finally, S-WJM992 showed appreciable efficacy in a malaria mouse model and blocked gamete development preventing transmission to mosquitoes. Importantly, further optimization of the dihydroquinazolinone class is required to deliver a candidate with improved pharmacokinetic and risk of resistance profiles.
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Affiliation(s)
- Trent
D. Ashton
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Petar P. S. Calic
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Madeline G. Dans
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Zi Kang Ooi
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Qingmiao Zhou
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Josephine Palandri
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Katie Loi
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Kate E. Jarman
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Deyun Qiu
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Adele M. Lehane
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | | | - Nirupam De
- TCG
Lifesciences, Kolkata, West Bengal 700091, India
| | - Carlo Giannangelo
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Christopher A. MacRaild
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Darren J. Creek
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Emma Y. Mao
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Maria R. Gancheva
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Danny W. Wilson
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mrittika Chowdury
- School
of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
- Institute
for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria 3216, Australia
| | - Tania F. de Koning-Ward
- School
of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
- Institute
for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria 3216, Australia
| | - Mufuliat T. Famodimu
- Department
of Infection Biology, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Michael J. Delves
- Department
of Infection Biology, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Harry Pollard
- Department
of Infection Biology, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Colin J. Sutherland
- Department
of Infection Biology, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Delphine Baud
- MMV Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, Geneva 1215, Switzerland
| | - Stephen Brand
- MMV Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, Geneva 1215, Switzerland
| | - Paul F. Jackson
- Emerging Science & Innovation, Discovery
Sciences, Janssen R&D LLC, La Jolla, California 92121, United States
| | - Alan F. Cowman
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Brad E. Sleebs
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
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2
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Simwela NV, Guiguemde WA, Straimer J, Regnault C, Stokes BH, Tavernelli LE, Yokokawa F, Taft B, Diagana TT, Barrett MP, Waters AP. A conserved metabolic signature associated with response to fast-acting anti-malarial agents. Microbiol Spectr 2023; 11:e0397622. [PMID: 37800971 PMCID: PMC10714989 DOI: 10.1128/spectrum.03976-22] [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: 10/02/2022] [Accepted: 01/27/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE In malaria drug discovery, understanding the mode of action of lead compounds is important as it helps in predicting the potential emergence of drug resistance in the field when these drugs are eventually deployed. In this study, we have employed metabolomics technologies to characterize the potential targets of anti-malarial drug candidates in the developmental pipeline at NITD. We show that NITD fast-acting leads belonging to spiroindolone and imidazothiadiazole class induce a common biochemical theme in drug-exposed malaria parasites which is similar to another fast-acting, clinically available drug, DHA. These biochemical features which are absent in a slower acting NITD lead (GNF17) point to hemoglobin digestion and inhibition of the pyrimidine pathway as potential action points for these drugs. These biochemical themes can be used to identify and inform on the mode of action of fast drug candidates of similar profiles in future drug discovery programs.
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Affiliation(s)
- Nelson V. Simwela
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | | | - Judith Straimer
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Clement Regnault
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Barbara H. Stokes
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Luis E. Tavernelli
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Fumiaki Yokokawa
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Benjamin Taft
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | | | - Michael P. Barrett
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Andrew P. Waters
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
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3
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Jonsdottir TK, Elsworth B, Cobbold S, Gabriela M, Ploeger E, Parkyn Schneider M, Charnaud SC, Dans MG, McConville M, Bullen HE, Crabb BS, Gilson PR. PTEX helps efficiently traffic haemoglobinases to the food vacuole in Plasmodium falciparum. PLoS Pathog 2023; 19:e1011006. [PMID: 37523385 PMCID: PMC10414648 DOI: 10.1371/journal.ppat.1011006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 08/10/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
A key element of Plasmodium biology and pathogenesis is the trafficking of ~10% of the parasite proteome into the host red blood cell (RBC) it infects. To cross the parasite-encasing parasitophorous vacuole membrane, exported proteins utilise a channel-forming protein complex termed the Plasmodium translocon of exported proteins (PTEX). PTEX is obligatory for parasite survival, both in vitro and in vivo, suggesting that at least some exported proteins have essential metabolic functions. However, to date only one essential PTEX-dependent process, the new permeability pathways, has been described. To identify other essential PTEX-dependant proteins/processes, we conditionally knocked down the expression of one of its core components, PTEX150, and examined which pathways were affected. Surprisingly, the food vacuole mediated process of haemoglobin (Hb) digestion was substantially perturbed by PTEX150 knockdown. Using a range of transgenic parasite lines and approaches, we show that two major Hb proteases; falcipain 2a and plasmepsin II, interact with PTEX core components, implicating the translocon in the trafficking of Hb proteases. We propose a model where these proteases are translocated into the PV via PTEX in order to reach the cytostome, located at the parasite periphery, prior to food vacuole entry. This work offers a second mechanistic explanation for why PTEX function is essential for growth of the parasite within its host RBC.
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Affiliation(s)
- Thorey K. Jonsdottir
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, Melbourne, Australia
| | - Brendan Elsworth
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
| | - Simon Cobbold
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Mikha Gabriela
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
- School of Medicine, Deakin University, Geelong, Australia
| | - Ellen Ploeger
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
| | | | - Sarah C. Charnaud
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
| | - Madeline G. Dans
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
| | - Malcolm McConville
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Hayley E. Bullen
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, Melbourne, Australia
| | - Brendan S. Crabb
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, Melbourne, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Paul R. Gilson
- Malaria Virulence and Drug Discovery Group, Burnet Institute, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, Melbourne, Australia
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4
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Ring-stage growth arrest: Metabolic basis of artemisinin tolerance in Plasmodium falciparum. iScience 2022; 26:105725. [PMID: 36579133 PMCID: PMC9791339 DOI: 10.1016/j.isci.2022.105725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
The emergence and spread of artemisinin-tolerant malaria parasites threatens malaria control programmes worldwide. Mutations in the propeller domain of the Kelch13 protein confer Plasmodium falciparum artemisinin resistance (ART-R). ART-R is linked to the reduced susceptibility of temporary growth-arrested ring-stage parasites, but the metabolic mechanisms remain elusive. We generated two PfKelch13 mutant lines via CRISPR-Cas9 gene editing which displayed a reduced susceptibility accompanied by an extended ring stage. The metabolome of ART-induced ring-stage growth arrest parasites carrying PfKelch13 mutations showed significant alterations in the tricarboxylic acid (TCA) cycle, glycolysis, and amino acids metabolism, pointing to altered energy and porphyrin metabolism with metabolic plasticity. The critical role of these pathways was further confirmed by altering metabolic flow or through chemical inhibition. Our findings uncover that the growth arrestment associated with ART-R is potentially attributed to the adaptative metabolic plasticity, indicating that the defined metabolic remodeling turns out to be the trigger for ART-R.
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5
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Recent metabolomic developments for antimalarial drug discovery. Parasitol Res 2022; 121:3351-3380. [PMID: 36194273 DOI: 10.1007/s00436-022-07673-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/14/2022] [Indexed: 10/10/2022]
Abstract
Malaria is a parasitic disease that remains a global health issue, responsible for a significant death and morbidity toll. Various factors have impacted the use and delayed the development of antimalarial therapies, such as the associated financial cost and parasitic resistance. In order to discover new drugs and validate parasitic targets, a powerful omics tool, metabolomics, emerged as a reliable approach. However, as a fairly recent method in malaria, new findings are timely and original practices emerge frequently. This review aims to discuss recent research towards the development of new metabolomic methods in the context of uncovering antiplasmodial mechanisms of action in vitro and to point out innovative metabolic pathways that can revitalize the antimalarial pipeline.
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6
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Looker O, Dans MG, Bullen HE, Sleebs BE, Crabb BS, Gilson PR. The Medicines for Malaria Venture Malaria Box contains inhibitors of protein secretion in
Plasmodium falciparum
blood stage parasites. Traffic 2022; 23:442-461. [PMID: 36040075 PMCID: PMC9543830 DOI: 10.1111/tra.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022]
Abstract
Plasmodium falciparum parasites which cause malaria, traffic hundreds of proteins into the red blood cells (RBCs) they infect. These exported proteins remodel their RBCs enabling host immune evasion through processes such as cytoadherence that greatly assist parasite survival. As resistance to all current antimalarial compounds is rising new compounds need to be identified and those that could inhibit parasite protein secretion and export would both rapidly reduce parasite virulence and ultimately lead to parasite death. To identify compounds that inhibit protein export we used transgenic parasites expressing an exported nanoluciferase reporter to screen the Medicines for Malaria Venture Malaria Box of 400 antimalarial compounds with mostly unknown targets. The most potent inhibitor identified in this screen was MMV396797 whose application led to export inhibition of both the reporter and endogenous exported proteins. MMV396797 mediated blockage of protein export and slowed the rigidification and cytoadherence of infected RBCs—modifications which are both mediated by parasite‐derived exported proteins. Overall, we have identified a new protein export inhibitor in P. falciparum whose target though unknown, could be developed into a future antimalarial that rapidly inhibits parasite virulence before eliminating parasites from the host.
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Affiliation(s)
| | - Madeline G. Dans
- Burnet Institute Melbourne Australia
- School of Medicine Deakin University Geelong Australia
| | - Hayley E. Bullen
- Burnet Institute Melbourne Australia
- Department of Immunology and Microbiology University of Melbourne Melbourne Australia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Brendan S. Crabb
- Burnet Institute Melbourne Australia
- Department of Immunology and Microbiology University of Melbourne Melbourne Australia
- Department of Immunology and Pathology Monash University Melbourne Australia
| | - Paul R. Gilson
- Burnet Institute Melbourne Australia
- Department of Immunology and Microbiology University of Melbourne Melbourne Australia
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7
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Bernard MM, Mohanty A, Rajendran V. Title: A Comprehensive Review on Classifying Fast-acting and Slow-acting Antimalarial Agents Based on Time of Action and Target Organelle of Plasmodium sp. Pathog Dis 2022; 80:6589403. [PMID: 35588061 DOI: 10.1093/femspd/ftac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/20/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The clinical resistance towards malarial parasites has rendered many antimalarials ineffective, likely due to a lack of understanding of time of action and stage specificity of all life stages. Therefore, to tackle this problem a more incisive comprehensive analysis of the fast and slow-acting profile of antimalarial agents relating to parasite time-kill kinetics and the target organelle on the progression of blood-stage parasites was carried out. It is evident from numerous findings that drugs targeting food vacuole, nuclear components, and endoplasmic reticulum mainly exhibit a fast-killing phenotype within 24h affecting first-cycle activity. Whereas drugs targeting mitochondria, apicoplast, microtubules, parasite invasion and egress exhibit a largely slow-killing phenotype within 96-120h, affecting second-cycle activity with few exemptions as moderately fast-killing. It is essential to understand the susceptibility of drugs on rings, trophozoites, schizonts, merozoites, and the appearance of organelle at each stage of 48h intraerythrocytic parasite cycle. Therefore, these parameters may facilitate the paradigm for understanding the timing of antimalarials action in deciphering its precise mechanism linked with time. Thus, classifying drugs based on the time of killing may promote designing new combination regimens against varied strains of P. falciparum and evaluating potential clinical resistance.
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Affiliation(s)
- Monika Marie Bernard
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Abhinab Mohanty
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
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8
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Rawat M, Kanyal A, Choubey D, Deshmukh B, Malhotra R, Mamatharani DV, Rao AG, Karmodiya K. Identification of Co-Existing Mutations and Gene Expression Trends Associated With K13-Mediated Artemisinin Resistance in Plasmodium falciparum. Front Genet 2022; 13:824483. [PMID: 35464842 PMCID: PMC9019836 DOI: 10.3389/fgene.2022.824483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum infects millions and kills thousands of people annually the world over. With the emergence of artemisinin and/or multidrug resistant strains of the pathogen, it has become even more challenging to control and eliminate the disease. Multiomics studies of the parasite have started to provide a glimpse into the confounding genetics and mechanisms of artemisinin resistance and identified mutations in Kelch13 (K13) as a molecular marker of resistance. Over the years, thousands of genomes and transcriptomes of artemisinin-resistant/sensitive isolates have been documented, supplementing the search for new genes/pathways to target artemisinin-resistant isolates. This meta-analysis seeks to recap the genetic landscape and the transcriptional deregulation that demarcate artemisinin resistance in the field. To explore the genetic territory of artemisinin resistance, we use genomic single-nucleotide polymorphism (SNP) datasets from 2,517 isolates from 15 countries from the MalariaGEN Network (The Pf3K project, pilot data release 4, 2015) to dissect the prevalence, geographical distribution, and co-existing patterns of genetic markers associated with/enabling artemisinin resistance. We have identified several mutations which co-exist with the established markers of artemisinin resistance. Interestingly, K13-resistant parasites harbor α-ß hydrolase and putative HECT domain-containing protein genes with the maximum number of SNPs. We have also explored the multiple, publicly available transcriptomic datasets to identify genes from key biological pathways whose consistent deregulation may be contributing to the biology of resistant parasites. Surprisingly, glycolytic and pentose phosphate pathways were consistently downregulated in artemisinin-resistant parasites. Thus, this meta-analysis highlights the genetic and transcriptomic features of resistant parasites to propel further exploratory studies in the community to tackle artemisinin resistance.
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Affiliation(s)
- Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Deepak Choubey
- Life Science Research Unit, Persistent Systems Limited, Pune, India
| | - Bhagyashree Deshmukh
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Rashim Malhotra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Anjani Gopal Rao
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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9
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Siddiqui G, Giannangelo C, De Paoli A, Schuh AK, Heimsch KC, Anderson D, Brown TG, MacRaild CA, Wu J, Wang X, Dong Y, Vennerstrom JL, Becker K, Creek DJ. Peroxide Antimalarial Drugs Target Redox Homeostasis in Plasmodium falciparum Infected Red Blood Cells. ACS Infect Dis 2022; 8:210-226. [PMID: 34985858 PMCID: PMC8762662 DOI: 10.1021/acsinfecdis.1c00550] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Plasmodium
falciparum causes the
most lethal form of malaria. Peroxide antimalarials based on artemisinin
underpin the frontline treatments for malaria, but artemisinin resistance
is rapidly spreading. Synthetic peroxide antimalarials, known as ozonides,
are in clinical development and offer a potential alternative. Here,
we used chemoproteomics to investigate the protein alkylation targets
of artemisinin and ozonide probes, including an analogue of the ozonide
clinical candidate, artefenomel. We greatly expanded the list of proteins
alkylated by peroxide antimalarials and identified significant enrichment
of redox-related proteins for both artemisinins and ozonides. Disrupted
redox homeostasis was confirmed by dynamic live imaging of the glutathione
redox potential using a genetically encoded redox-sensitive fluorescence-based
biosensor. Targeted liquid chromatography-mass spectrometry (LC-MS)-based
thiol metabolomics also confirmed changes in cellular thiol levels.
This work shows that peroxide antimalarials disproportionately alkylate
proteins involved in redox homeostasis and that disrupted redox processes
are involved in the mechanism of action of these important antimalarials.
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Affiliation(s)
- Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Amanda De Paoli
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Anna Katharina Schuh
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Kim C. Heimsch
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Timothy G. Brown
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Christopher A. MacRaild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Jianbo Wu
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Xiaofang Wang
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Yuxiang Dong
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Jonathan L. Vennerstrom
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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10
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Edgar RCS, Counihan NA, McGowan S, de Koning-Ward TF. Methods Used to Investigate the Plasmodium falciparum Digestive Vacuole. Front Cell Infect Microbiol 2022; 11:829823. [PMID: 35096663 PMCID: PMC8794586 DOI: 10.3389/fcimb.2021.829823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum malaria remains a global health problem as parasites continue to develop resistance to all antimalarials in use. Infection causes clinical symptoms during the intra-erythrocytic stage of the lifecycle where the parasite infects and replicates within red blood cells (RBC). During this stage, P. falciparum digests the main constituent of the RBC, hemoglobin, in a specialized acidic compartment termed the digestive vacuole (DV), a process essential for survival. Many therapeutics in use target one or multiple aspects of the DV, with chloroquine and its derivatives, as well as artemisinin, having mechanisms of action within this organelle. In order to better understand how current therapeutics and those under development target DV processes, techniques used to investigate the DV are paramount. This review outlines the involvement of the DV in therapeutics currently in use and focuses on the range of techniques that are currently utilized to study this organelle including microscopy, biochemical analysis, genetic approaches and metabolomic studies. Importantly, continued development and application of these techniques will aid in our understanding of the DV and in the development of new therapeutics or therapeutic partners for the future.
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Affiliation(s)
- Rebecca C. S. Edgar
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Natalie A. Counihan
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Monash University, Clayton, VIC, Australia
| | - Tania F. de Koning-Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
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11
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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12
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Lee WC, Russell B, Lee B, Chu CS, Phyo AP, Sriprawat K, Lau YL, Nosten F, Rénia L. Plasmodium falciparum rosetting protects schizonts against artemisinin. EBioMedicine 2021; 73:103680. [PMID: 34749300 PMCID: PMC8586750 DOI: 10.1016/j.ebiom.2021.103680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Background Artemisinin (ART) resistance in Plasmodium falciparum is thought to occur during the early stage of the parasite's erythrocytic cycle. Here, we identify a novel factor associated with the late stage parasite development that contributes to ART resistance. Methods Rosetting rates of clinical isolates pre- and post- brief (one hour) exposure to artesunate (AS, an ART derivative) were evaluated. The effects of AS-mediated rosetting on the post-AS-exposed parasite's replication and survival, as well as the extent of protection by AS-mediated rosetting on different parasite stages were investigated. The rosetting ligands, mechanisms, and gene mutations involved were studied. Findings Brief AS exposure stimulated rosetting, with AS-resistant isolates forming more rosettes in a more rapid manner. AS-mediated rosetting enabled infected erythrocytes (IRBC) to withstand AS exposure for several hours and protected the IRBC from phagocytosis. When their rosetting ability was blocked experimentally, the post-AS exposure survival advantage by the AS-resistant parasites was abrogated. Deletions in two genes coding for PfEMP1 exon 2 (PF3D7_0200300 and PF3D7_0223300) were found to be associated with AS-mediated rosetting, and these mutations were significantly selected through time in the parasite population under study, along with the K13 mutations, a molecular marker of ART-resistance. Interpretation Rapid ART parasite clearance is driven by the direct oxidative damages on IRBC by ART and the phagocytic destruction of the damaged IRBC. Rosetting serves as a rapid ‘buying time’ strategy that allows more parasites to complete schizont maturation, reinvasion and subsequent development into the intrinsically less ART-susceptible ring stage. Funding A*STAR, NMRC-OF-YIRG, HRC e-ASIA, Wellcome.
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Affiliation(s)
- Wenn-Chyau Lee
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network (SIgN), A*STAR, Singapore.
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A*STAR, Singapore
| | - Cindy S Chu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Laurent Rénia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network (SIgN), A*STAR, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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13
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Tewari SG, Rajaram K, Swift RP, Kwan B, Reifman J, Prigge ST, Wallqvist A. Inter-study and time-dependent variability of metabolite abundance in cultured red blood cells. Malar J 2021; 20:299. [PMID: 34215262 PMCID: PMC8254254 DOI: 10.1186/s12936-021-03780-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/24/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cultured human red blood cells (RBCs) provide a powerful ex vivo assay platform to study blood-stage malaria infection and propagation. In recent years, high-resolution metabolomic methods have quantified hundreds of metabolites from parasite-infected RBC cultures under a variety of perturbations. In this context, the corresponding control samples of the uninfected culture systems can also be used to examine the effects of these perturbations on RBC metabolism itself and their dependence on blood donors (inter-study variations). METHODS Time-course datasets from five independent studies were generated and analysed, maintaining uninfected RBCs (uRBC) at 2% haematocrit for 48 h under conditions originally designed for parasite cultures. Using identical experimental protocols, quadruplicate samples were collected at six time points, and global metabolomics were employed on the pellet fraction of the uRBC cultures. In total, ~ 500 metabolites were examined across each dataset to quantify inter-study variability in RBC metabolism, and metabolic network modelling augmented the analyses to characterize the metabolic state and fluxes of the RBCs. RESULTS To minimize inter-study variations unrelated to RBC metabolism, an internal standard metabolite (phosphatidylethanolamine C18:0/20:4) was identified with minimal variation in abundance over time and across all the samples of each dataset to normalize the data. Although the bulk of the normalized data showed a high degree of inter-study consistency, changes and variations in metabolite levels from individual donors were noted. Thus, a total of 24 metabolites were associated with significant variation in the 48-h culture time window, with the largest variations involving metabolites in glycolysis and synthesis of glutathione. Metabolic network analysis was used to identify the production of superoxide radicals in cultured RBCs as countered by the activity of glutathione oxidoreductase and synthesis of reducing equivalents via the pentose phosphate pathway. Peptide degradation occurred at a rate that is comparable with central carbon fluxes, consistent with active degradation of methaemoglobin, processes also commonly associated with storage lesions in RBCs. CONCLUSIONS The bulk of the data showed high inter-study consistency. The collected data, quantification of an expected abundance variation of RBC metabolites, and characterization of a subset of highly variable metabolites in the RBCs will help in identifying non-specific changes in metabolic abundances that may obscure accurate metabolomic profiling of Plasmodium falciparum and other blood-borne pathogens.
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Affiliation(s)
- Shivendra G. Tewari
- grid.420210.50000 0001 0036 4726Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD USA ,grid.201075.10000 0004 0614 9826The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Krithika Rajaram
- grid.21107.350000 0001 2171 9311Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD USA
| | - Russell P. Swift
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA USA
| | - Bobby Kwan
- grid.21107.350000 0001 2171 9311Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD USA
| | - Jaques Reifman
- grid.420210.50000 0001 0036 4726Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD USA
| | - Sean T. Prigge
- grid.21107.350000 0001 2171 9311Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA.
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14
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Ullah I, Sharma R, Mete A, Biagini GA, Wetzel DM, Horrocks PD. The relative rate of kill of the MMV Malaria Box compounds provides links to the mode of antimalarial action and highlights scaffolds of medicinal chemistry interest. J Antimicrob Chemother 2021; 75:362-370. [PMID: 31665424 DOI: 10.1093/jac/dkz443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/04/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Rapid rate-of-kill (RoK) is a key parameter in the target candidate profile 1 (TCP1) for the next-generation antimalarial drugs for uncomplicated malaria, termed Single Encounter Radical Cure and Prophylaxis (SERCaP). TCP1 aims to rapidly eliminate the initial parasite burden, ideally as fast as artesunate, but minimally as fast as chloroquine. Here we explore whether the relative RoK of the Medicine for Malaria Venture (MMV) Malaria Box compounds is linked to their mode of action (MoA) and identify scaffolds of medicinal chemistry interest. METHODS We used a bioluminescence relative RoK (BRRoK) assay over 6 and 48 h, with exposure to equipotent IC50 concentrations, to compare the cytocidal effects of Malaria Box compounds with those of benchmark antimalarials. RESULTS BRRoK assay data demonstrate the following relative RoKs, from fast to slow: inhibitors of PfATP4>parasite haemoglobin catabolism>dihydrofolate reductase-thymidylate synthase (DHFR-TS)>dihydroorotate dehydrogenase (DHODH)>bc1 complex. Core-scaffold clustering analyses revealed intrinsic rapid cytocidal action for diamino-glycerols and 2-(aminomethyl)phenol, but slow action for 2-phenylbenz-imidazoles, 8-hydroxyquinolines and triazolopyrimidines. CONCLUSIONS This study provides proof of principle that a compound's RoK is related to its MoA and that the target's intrinsic RoK is also modified by factors affecting a drug's access to it. Our findings highlight that as we use medicinal chemistry to improve potency, we can also improve the RoK for some scaffolds. Our BRRoK assay provides the necessary throughput for drug discovery and a critical decision-making tool to support development campaigns. Finally, two scaffolds, diamino-glycerols and 2-phenylbenzimidazoles, exhibit fast cytocidal action, inviting medicinal chemistry improvements towards TCP1 candidates.
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Affiliation(s)
- Imran Ullah
- Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - Raman Sharma
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Antonio Mete
- Medsyndesign Ltd, Advanced Technology Innovation Centre, 5 Oakwood Drive, Loughborough, UK
| | - Giancarlo A Biagini
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Dawn M Wetzel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Paul D Horrocks
- Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
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15
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Cobbold SA, V Tutor M, Frasse P, McHugh E, Karnthaler M, Creek DJ, Odom John A, Tilley L, Ralph SA, McConville MJ. Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics. Mol Syst Biol 2021; 17:e10023. [PMID: 33821563 PMCID: PMC8022201 DOI: 10.15252/msb.202010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, proliferates rapidly in human erythrocytes by actively scavenging multiple carbon sources and essential nutrients from its host cell. However, a global overview of the metabolic capacity of intraerythrocytic stages is missing. Using multiplex 13 C-labelling coupled with untargeted mass spectrometry and unsupervised isotopologue grouping, we have generated a draft metabolome of P. falciparum and its host erythrocyte consisting of 911 and 577 metabolites, respectively, corresponding to 41% of metabolites and over 70% of the metabolic reaction predicted from the parasite genome. An additional 89 metabolites and 92 reactions were identified that were not predicted from genomic reconstructions, with the largest group being associated with metabolite damage-repair systems. Validation of the draft metabolome revealed four previously uncharacterised enzymes which impact isoprenoid biosynthesis, lipid homeostasis and mitochondrial metabolism and are necessary for parasite development and proliferation. This study defines the metabolic fate of multiple carbon sources in P. falciparum, and highlights the activity of metabolite repair pathways in these rapidly growing parasite stages, opening new avenues for drug discovery.
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Affiliation(s)
- Simon A Cobbold
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Philip Frasse
- Department of MedicineWashington University School of MedicineSt. LouisMOUSA
| | - Emma McHugh
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Markus Karnthaler
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Darren J Creek
- Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleVic.Australia
| | - Audrey Odom John
- The Children’s Hospital of PhiladelphiaUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Leann Tilley
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
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16
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Atypical Molecular Basis for Drug Resistance to Mitochondrial Function Inhibitors in Plasmodium falciparum. Antimicrob Agents Chemother 2021; 65:AAC.02143-20. [PMID: 33361312 DOI: 10.1128/aac.02143-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
The continued emergence of drug-resistant Plasmodium falciparum parasites hinders global attempts to eradicate malaria, emphasizing the need to identify new antimalarial drugs. Attractive targets for chemotherapeutic intervention are the cytochrome (cyt) bc 1 complex, which is an essential component of the mitochondrial electron transport chain (mtETC) required for ubiquinone recycling and mitochondrially localized dihydroorotate dehydrogenase (DHODH) critical for de novo pyrimidine synthesis. Despite the essentiality of this complex, resistance to a novel acridone class of compounds targeting cyt bc 1 was readily attained, resulting in a parasite strain (SB1-A6) that was panresistant to both mtETC and DHODH inhibitors. Here, we describe the molecular mechanism behind the resistance of the SB1-A6 parasite line, which lacks the common cyt bc 1 point mutations characteristic of resistance to mtETC inhibitors. Using Illumina whole-genome sequencing, we have identified both a copy number variation (∼2×) and a single-nucleotide polymorphism (C276F) associated with pfdhodh in SB1-A6. We have characterized the role of both genetic lesions by mimicking the copy number variation via episomal expression of pfdhodh and introducing the identified single nucleotide polymorphism (SNP) using CRISPR-Cas9 and assessed their contributions to drug resistance. Although both of these genetic polymorphisms have been previously identified as contributing to both DSM-1 and atovaquone resistance, SB1-A6 represents a unique genotype in which both alterations are present in a single line, suggesting that the combination contributes to the panresistant phenotype. This novel mechanism of resistance to mtETC inhibition has critical implications for the development of future drugs targeting the bc 1 complex or de novo pyrimidine synthesis that could help guide future antimalarial combination therapies and reduce the rapid development of drug resistance in the field.
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17
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Yu X, Feng G, Zhang Q, Cao J. From Metabolite to Metabolome: Metabolomics Applications in Plasmodium Research. Front Microbiol 2021; 11:626183. [PMID: 33505389 PMCID: PMC7829456 DOI: 10.3389/fmicb.2020.626183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023] Open
Abstract
Advances in research over the past few decades have greatly improved metabolomics-based approaches in studying parasite biology and disease etiology. This improves the investigation of varied metabolic requirements during life stages or when following transmission to their hosts, and fulfills the demand for improved diagnostics and precise therapeutics. Therefore, this review highlights the progress of metabolomics in malaria research, including metabolic mapping of Plasmodium vertebrate life cycle stages to investigate antimalarials mode of actions and underlying complex host-parasite interactions. Also, we discuss current limitations as well as make several practical suggestions for methodological improvements which could drive metabolomics progress for malaria from a comprehensive perspective.
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Affiliation(s)
- Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Medical College of Soochow University, Suzhou, China
| | - Gaoqian Feng
- Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Qingfeng Zhang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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18
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The Key Glycolytic Enzyme Phosphofructokinase Is Involved in Resistance to Antiplasmodial Glycosides. mBio 2020; 11:mBio.02842-20. [PMID: 33293381 PMCID: PMC7733947 DOI: 10.1128/mbio.02842-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, continues to be a devastating global health issue, causing 405,000 deaths and 228 million cases in 2018. Understanding key metabolic processes in malaria parasites is critical to the development of new drugs to combat this major infectious disease. The Plasmodium glycolytic pathway is essential to the malaria parasite, providing energy for growth and replication and supplying important biomolecules for other essential Plasmodium anabolic pathways. Despite this overreliance on glycolysis, no current drugs target glycolysis, and there is a paucity of information on critical glycolysis targets. Our work addresses this unmet need, providing new mechanistic insights into this key pathway. Plasmodium parasites rely heavily on glycolysis for ATP production and for precursors for essential anabolic pathways, such as the methylerythritol phosphate (MEP) pathway. Here, we show that mutations in the Plasmodium falciparum glycolytic enzyme, phosphofructokinase (PfPFK9), are associated with in vitro resistance to a primary sulfonamide glycoside (PS-3). Flux through the upper glycolysis pathway was significantly reduced in PS-3-resistant parasites, which was associated with reduced ATP levels but increased flux into the pentose phosphate pathway. PS-3 may directly or indirectly target enzymes in these pathways, as PS-3-treated parasites had elevated levels of glycolytic and tricarboxylic acid (TCA) cycle intermediates. PS-3 resistance also led to reduced MEP pathway intermediates, and PS-3-resistant parasites were hypersensitive to the MEP pathway inhibitor, fosmidomycin. Overall, this study suggests that PS-3 disrupts core pathways in central carbon metabolism, which is compensated for by mutations in PfPFK9, highlighting a novel metabolic drug resistance mechanism in P. falciparum.
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19
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Yang T, Yeoh LM, Tutor MV, Dixon MW, McMillan PJ, Xie SC, Bridgford JL, Gillett DL, Duffy MF, Ralph SA, McConville MJ, Tilley L, Cobbold SA. Decreased K13 Abundance Reduces Hemoglobin Catabolism and Proteotoxic Stress, Underpinning Artemisinin Resistance. Cell Rep 2020; 29:2917-2928.e5. [PMID: 31775055 DOI: 10.1016/j.celrep.2019.10.095] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/08/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Increased tolerance of Plasmodium falciparum to front-line artemisinin antimalarials (ARTs) is associated with mutations in Kelch13 (K13), although the precise role of K13 remains unclear. Here, we show that K13 mutations result in decreased expression of this protein, while mislocalization of K13 mimics resistance-conferring mutations, pinpointing partial loss of function of K13 as the relevant molecular event. K13-GFP is associated with ∼170 nm diameter doughnut-shaped structures at the parasite periphery, consistent with the location and dimensions of cytostomes. Moreover, the hemoglobin-peptide profile of ring-stage parasites is reduced when K13 is mislocalized. We developed a pulse-SILAC approach to quantify protein turnover and observe less disruption to protein turnover following ART exposure when K13 is mislocalized. Our findings suggest that K13 regulates digestive vacuole biogenesis and the uptake/degradation of hemoglobin and that ART resistance is mediated by a decrease in heme-dependent drug activation, less proteotoxicity, and increased survival of parasite ring stages.
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Affiliation(s)
- Tuo Yang
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lee M Yeoh
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Matthew W Dixon
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paul J McMillan
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia; Biological Optical Microscopy Platform, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stanley C Xie
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jessica L Bridgford
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David L Gillett
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael F Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Simon A Cobbold
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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20
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Burns AL, Sleebs BE, Siddiqui G, De Paoli AE, Anderson D, Liffner B, Harvey R, Beeson JG, Creek DJ, Goodman CD, McFadden GI, Wilson DW. Retargeting azithromycin analogues to have dual-modality antimalarial activity. BMC Biol 2020; 18:133. [PMID: 32993629 PMCID: PMC7526119 DOI: 10.1186/s12915-020-00859-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/28/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Resistance to front-line antimalarials (artemisinin combination therapies) is spreading, and development of new drug treatment strategies to rapidly kill Plasmodium spp. malaria parasites is urgently needed. Azithromycin is a clinically used macrolide antibiotic proposed as a partner drug for combination therapy in malaria, which has also been tested as monotherapy. However, its slow-killing 'delayed-death' activity against the parasite's apicoplast organelle and suboptimal activity as monotherapy limit its application as a potential malaria treatment. Here, we explore a panel of azithromycin analogues and demonstrate that chemical modifications can be used to greatly improve the speed and potency of antimalarial action. RESULTS Investigation of 84 azithromycin analogues revealed nanomolar quick-killing potency directed against the very earliest stage of parasite development within red blood cells. Indeed, the best analogue exhibited 1600-fold higher potency than azithromycin with less than 48 hrs treatment in vitro. Analogues were effective against zoonotic Plasmodium knowlesi malaria parasites and against both multi-drug and artemisinin-resistant Plasmodium falciparum lines. Metabolomic profiles of azithromycin analogue-treated parasites suggested activity in the parasite food vacuole and mitochondria were disrupted. Moreover, unlike the food vacuole-targeting drug chloroquine, azithromycin and analogues were active across blood-stage development, including merozoite invasion, suggesting that these macrolides have a multi-factorial mechanism of quick-killing activity. The positioning of functional groups added to azithromycin and its quick-killing analogues altered their activity against bacterial-like ribosomes but had minimal change on 'quick-killing' activity. Apicoplast minus parasites remained susceptible to both azithromycin and its analogues, further demonstrating that quick-killing is independent of apicoplast-targeting, delayed-death activity. CONCLUSION We show that azithromycin and analogues can rapidly kill malaria parasite asexual blood stages via a fast action mechanism. Development of azithromycin and analogues as antimalarials offers the possibility of targeting parasites through both a quick-killing and delayed-death mechanism of action in a single, multifactorial chemotype.
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Affiliation(s)
- Amy L Burns
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3050, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3050, Australia
| | - Ghizal Siddiqui
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Amanda E De Paoli
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Dovile Anderson
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Benjamin Liffner
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Richard Harvey
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - James G Beeson
- Burnet Institute, Melbourne, Victoria, 3004, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Central Clinical School and Department of Microbiology, Monash University, Melbourne, Australia
| | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Christopher D Goodman
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Geoffrey I McFadden
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia.
- Burnet Institute, Melbourne, Victoria, 3004, Australia.
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21
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Riches A, Hart CJS, Trenholme KR, Skinner-Adams TS. Anti- Giardia Drug Discovery: Current Status and Gut Feelings. J Med Chem 2020; 63:13330-13354. [PMID: 32869995 DOI: 10.1021/acs.jmedchem.0c00910] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Giardia parasites are ubiquitous protozoans of global importance that impact a wide range of animals including humans. They are the most common enteric pathogen of cats and dogs in developed countries and infect ∼1 billion people worldwide. While Giardia infections can be asymptomatic, they often result in severe and chronic diseases. There is also mounting evidence that they are linked to postinfection disorders. Despite growing evidence of the widespread morbidity associated with Giardia infections, current treatment options are limited to compound classes with broad antimicrobial activity. Frontline anti-Giardia drugs are also associated with increasing drug resistance and treatment failures. To improve the health and well-being of millions, new selective anti-Giardia drugs are needed alongside improved health education initiatives. Here we discuss current treatment options together with recent advances and gaps in drug discovery. We also propose criteria to guide the discovery of new anti-Giardia compounds.
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Affiliation(s)
- Andrew Riches
- Commonwealth Scientific and Industrial Research Organization, Biomedical Manufacturing, Clayton, Victoria 3168, Australia
| | - Christopher J S Hart
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Katharine R Trenholme
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland 4029, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Tina S Skinner-Adams
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
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22
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Krishnan K, Ziniel P, Li H, Huang X, Hupalo D, Gombakomba N, Guerrero SM, Dotrang T, Lu X, Caridha D, Sternberg AR, Hughes E, Sun W, Bargieri DY, Roepe PD, Sciotti RJ, Wilkerson MD, Dalgard CL, Tawa GJ, Wang AQ, Xu X, Zheng W, Sanderson PE, Huang W, Williamson KC. Torin 2 Derivative, NCATS-SM3710, Has Potent Multistage Antimalarial Activity through Inhibition of P. falciparum Phosphatidylinositol 4-Kinase ( Pf PI4KIIIβ). ACS Pharmacol Transl Sci 2020; 3:948-964. [PMID: 33073193 DOI: 10.1021/acsptsci.0c00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Drug resistance is a constant threat to malaria control efforts making it important to maintain a good pipeline of new drug candidates. Of particular need are compounds that also block transmission by targeting sexual stage parasites. Mature sexual stages are relatively resistant to all currently used antimalarials except the 8-aminoquinolines that are not commonly used due to potential side effects. Here, we synthesized a new Torin 2 derivative, NCATS-SM3710 with increased aqueous solubility and specificity for Plasmodium and demonstrate potent in vivo activity against all P. berghei life cycle stages. NCATS-SM3710 also has low nanomolar EC50s against in vitro cultured asexual P. falciparum parasites (0.38 ± 0.04 nM) and late stage gametocytes (5.77 ± 1 nM). Two independent NCATS-SM3710/Torin 2 resistant P. falciparum parasite lines produced by growth in sublethal Torin 2 concentrations both had genetic changes in PF3D7_0509800, annotated as a phosphatidylinositol 4 kinase (Pf PI4KIIIβ). One line had a point mutation in the putative active site (V1357G), and the other line had a duplication of a locus containing Pf PI4KIIIβ. Both lines were also resistant to other Pf PI4K inhibitors. In addition NCATS-SM3710 inhibited purified Pf PI4KIIIβ with an IC50 of 2.0 ± 0.30 nM. Together the results demonstrate that Pf PI4KIIIβ is the target of Torin 2 and NCATS-SM3710 and provide new options for potent multistage drug development.
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Affiliation(s)
- Karthik Krishnan
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Peter Ziniel
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Hao Li
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Xiuli Huang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Daniel Hupalo
- Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Nita Gombakomba
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Sandra Mendoza Guerrero
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Thoai Dotrang
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Xiao Lu
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Diana Caridha
- Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Anna R Sternberg
- Departments of Chemistry and of Biochemistry, Cellular and Molecular Biology, Georgetown University, Washington, DC 20057, United States
| | - Emma Hughes
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wei Sun
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Daniel Y Bargieri
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, 05508, Brazil
| | - Paul D Roepe
- Departments of Chemistry and of Biochemistry, Cellular and Molecular Biology, Georgetown University, Washington, DC 20057, United States
| | - Richard J Sciotti
- Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Matthew D Wilkerson
- Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Gregory J Tawa
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Amy Q Wang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Xin Xu
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wei Zheng
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Philip E Sanderson
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wenwei Huang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Kim C Williamson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
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23
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Giannangelo C, Siddiqui G, De Paoli A, Anderson BM, Edgington-Mitchell LE, Charman SA, Creek DJ. System-wide biochemical analysis reveals ozonide antimalarials initially act by disrupting Plasmodium falciparum haemoglobin digestion. PLoS Pathog 2020; 16:e1008485. [PMID: 32589689 PMCID: PMC7347234 DOI: 10.1371/journal.ppat.1008485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/09/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023] Open
Abstract
Ozonide antimalarials, OZ277 (arterolane) and OZ439 (artefenomel), are synthetic peroxide-based antimalarials with potent activity against the deadliest malaria parasite, Plasmodium falciparum. Here we used a "multi-omics" workflow, in combination with activity-based protein profiling (ABPP), to demonstrate that peroxide antimalarials initially target the haemoglobin (Hb) digestion pathway to kill malaria parasites. Time-dependent metabolomic profiling of ozonide-treated P. falciparum infected red blood cells revealed a rapid depletion of short Hb-derived peptides followed by subsequent alterations in lipid and nucleotide metabolism, while untargeted peptidomics showed accumulation of longer Hb-derived peptides. Quantitative proteomics and ABPP assays demonstrated that Hb-digesting proteases were increased in abundance and activity following treatment, respectively. Ozonide-induced depletion of short Hb-derived peptides was less extensive in a drug-treated K13-mutant artemisinin resistant parasite line (Cam3.IIR539T) than in the drug-treated isogenic sensitive strain (Cam3.IIrev), further confirming the association between ozonide activity and Hb catabolism. To demonstrate that compromised Hb catabolism may be a primary mechanism involved in ozonide antimalarial activity, we showed that parasites forced to rely solely on Hb digestion for amino acids became hypersensitive to short ozonide exposures. Quantitative proteomics analysis also revealed parasite proteins involved in translation and the ubiquitin-proteasome system were enriched following drug treatment, suggestive of the parasite engaging a stress response to mitigate ozonide-induced damage. Taken together, these data point to a mechanism of action involving initial impairment of Hb catabolism, and indicate that the parasite regulates protein turnover to manage ozonide-induced damage.
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Affiliation(s)
- Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Amanda De Paoli
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Bethany M. Anderson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Laura E. Edgington-Mitchell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Maxillofacial Surgery, College of Dentistry, New York University, New York, New York, United States of America
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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24
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Brown AC, Moore CC, Guler JL. Cholesterol-dependent enrichment of understudied erythrocytic stages of human Plasmodium parasites. Sci Rep 2020; 10:4591. [PMID: 32165667 PMCID: PMC7067793 DOI: 10.1038/s41598-020-61392-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/26/2020] [Indexed: 01/01/2023] Open
Abstract
For intracellular pathogens, the host cell provides needed protection and nutrients. A major challenge of intracellular parasite research is collection of high parasite numbers separated from host contamination. This situation is exemplified by the malaria parasite, which spends a substantial part of its life cycle inside erythrocytes as rings, trophozoites, and schizonts, before egress and reinvasion. Erythrocytic Plasmodium parasite forms refractory to enrichment remain understudied due to high host contamination relative to low parasite numbers. Here, we present a method for separating all stages of Plasmodium-infected erythrocytes through lysis and removal of uninfected erythrocytes. The Streptolysin O-Percoll (SLOPE) method is effective on previously inaccessible forms, including circulating rings from malaria-infected patients and artemisinin-induced quiescent parasites. SLOPE can be used on multiple parasite species, under multiple media formulations, and lacks measurable impacts on parasite viability. We demonstrate erythrocyte membrane cholesterol levels modulate the preferential lysis of uninfected host cells by SLO, and therefore modulate the effectiveness of SLOPE. Targeted metabolomics of SLOPE-enriched ring stage samples confirms parasite-derived metabolites are increased and contaminating host material is reduced compared to non-enriched samples. Due to consumption of cholesterol by other intracellular bacteria and protozoa, SLOPE holds potential for improving research on organisms beyond Plasmodium.
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Affiliation(s)
- Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, VA, USA. .,Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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25
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Tewari SG, Swift RP, Reifman J, Prigge ST, Wallqvist A. Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite. Malar J 2020; 19:94. [PMID: 32103749 PMCID: PMC7045481 DOI: 10.1186/s12936-020-03174-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Background Human blood cells (erythrocytes) serve as hosts for the malaria parasite Plasmodium falciparum during its 48-h intraerythrocytic developmental cycle (IDC). Established in vitro protocols allow for the study of host–parasite interactions during this phase and, in particular, high-resolution metabolomics can provide a window into host–parasite interactions that support parasite development. Methods Uninfected and parasite-infected erythrocyte cultures were maintained at 2% haematocrit for the duration of the IDC, while parasitaemia was maintained at 7% in the infected cultures. The parasite-infected cultures were synchronized to obtain stage-dependent information of parasite development during the IDC. Samples were collected in quadruplicate at six time points from the uninfected and parasite-infected cultures and global metabolomics was used to analyse cell fractions of these cultures. Results In uninfected and parasite-infected cultures during the IDC, 501 intracellular metabolites, including 223 lipid metabolites, were successfully quantified. Of these, 19 distinct metabolites were present only in the parasite-infected culture, 10 of which increased to twofold in abundance during the IDC. This work quantified approximately five times the metabolites measured in previous studies of similar research scope, which allowed for more detailed analyses. Enrichment in lipid metabolism pathways exhibited a time-dependent association with different classes of lipids during the IDC. Specifically, enrichment occurred in sphingolipids at the earlier stages, and subsequently in lysophospholipid and phospholipid metabolites at the intermediate and end stages of the IDC, respectively. In addition, there was an accumulation of 18-, 20-, and 22-carbon polyunsaturated fatty acids, which produce eicosanoids and promote gametocytogenesis in infected erythrocyte cultures. Conclusions The current study revealed a number of heretofore unidentified metabolic components of the host–parasite system, which the parasite may exploit in a time-dependent manner to grow over the course of its development in the blood stage. Notably, the analyses identified components, such as precursors of immunomodulatory molecules, stage-dependent lipid dynamics, and metabolites, unique to parasite-infected cultures. These conclusions are reinforced by the metabolic alterations that were characterized during the IDC, which were in close agreement with those known from previous studies of blood-stage infection.
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Affiliation(s)
- Shivendra G Tewari
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA. .,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, MD, USA.
| | - Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA.
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26
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Birrell GW, Challis MP, De Paoli A, Anderson D, Devine SM, Heffernan GD, Jacobus DP, Edstein MD, Siddiqui G, Creek DJ. Multi-omic Characterization of the Mode of Action of a Potent New Antimalarial Compound, JPC-3210, Against Plasmodium falciparum. Mol Cell Proteomics 2020; 19:308-325. [PMID: 31836637 PMCID: PMC7000111 DOI: 10.1074/mcp.ra119.001797] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/17/2019] [Indexed: 01/22/2023] Open
Abstract
The increasing incidence of antimalarial drug resistance to the first-line artemisinin combination therapies underpins an urgent need for new antimalarial drugs, ideally with a novel mode of action. The recently developed 2-aminomethylphenol, JPC-3210, (MMV 892646) is an erythrocytic schizonticide with potent in vitro antimalarial activity against multidrug-resistant Plasmodium falciparum lines, low cytotoxicity, potent in vivo efficacy against murine malaria, and favorable preclinical pharmacokinetics including a lengthy plasma elimination half-life. To investigate the impact of JPC-3210 on biochemical pathways within P. falciparum-infected red blood cells, we have applied a "multi-omics" workflow based on high resolution orbitrap mass spectrometry combined with biochemical approaches. Metabolomics, peptidomics and hemoglobin fractionation analyses revealed a perturbation in hemoglobin metabolism following JPC-3210 exposure. The metabolomics data demonstrated a specific depletion of short hemoglobin-derived peptides, peptidomics analysis revealed a depletion of longer hemoglobin-derived peptides, and the hemoglobin fractionation assay demonstrated decreases in hemoglobin, heme and hemozoin levels. To further elucidate the mechanism responsible for inhibition of hemoglobin metabolism, we used in vitro β-hematin polymerization assays and showed JPC-3210 to be an intermediate inhibitor of β-hematin polymerization, about 10-fold less potent then the quinoline antimalarials, such as chloroquine and mefloquine. Further, quantitative proteomics analysis showed that JPC-3210 treatment results in a distinct proteomic signature compared with other known antimalarials. While JPC-3210 clustered closely with mefloquine in the metabolomics and proteomics analyses, a key differentiating signature for JPC-3210 was the significant enrichment of parasite proteins involved in regulation of translation. These studies revealed that the mode of action for JPC-3210 involves inhibition of the hemoglobin digestion pathway and elevation of regulators of protein translation. Importantly, JPC-3210 demonstrated rapid parasite killing kinetics compared with other quinolones, suggesting that JPC-3210 warrants further investigation as a potentially long acting partner drug for malaria treatment.
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Affiliation(s)
- Geoffrey W Birrell
- Australian Defense Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Matthew P Challis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Amanda De Paoli
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Dovile Anderson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Shane M Devine
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | | | - Michael D Edstein
- Australian Defense Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Ghizal Siddiqui
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.
| | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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27
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Srivastava A, Creek DJ. Using the IDEOM Workflow for LCMS-Based Metabolomics Studies of Drug Mechanisms. Methods Mol Biol 2020; 2104:419-445. [PMID: 31953829 DOI: 10.1007/978-1-0716-0239-3_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid advancements in metabolomics technologies have allowed for application of liquid chromatography mass spectrometry (LCMS)-based metabolomics to investigate a wide range of biological questions. In addition to an important role in studies of cellular biochemistry and biomarker discovery, an exciting application of metabolomics is the elucidation of mechanisms of drug action (Creek et al., Antimicrob Agents Chemother 60:6650-6663, 2016; Allman et al., Antimicrob Agents Chemother 60:6635-6649, 2016). Although it is a very useful technique, challenges in raw data processing, extracting useful information out of large noisy datasets, and identifying metabolites with confidence, have meant that metabolomics is still perceived as a highly specialized technology. As a result, metabolomics has not yet achieved the anticipated extent of uptake in laboratories around the world as genomics or transcriptomics. With a view to bring metabolomics within reach of a nonspecialist scientist, here we describe a routine workflow with IDEOM, which is a graphical user interface within Microsoft Excel, which almost all researchers are familiar with. IDEOM consists of custom built algorithms that allow LCMS data processing, automatic noise filtering and identification of metabolite features (Creek et al., Bioinformatics 28:1048-1049, 2012). Its automated interface incorporates advanced LCMS data processing tools, mzMatch and XCMS, and requires R for complete functionality. IDEOM is freely available for all researchers and this chapter will focus on describing the IDEOM workflow for the nonspecialist researcher in the context of studies designed to elucidate mechanisms of drug action.
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Affiliation(s)
- Anubhav Srivastava
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.
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28
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The Metabolite Repair Enzyme Phosphoglycolate Phosphatase Regulates Central Carbon Metabolism and Fosmidomycin Sensitivity in Plasmodium falciparum. mBio 2019; 10:mBio.02060-19. [PMID: 31822583 PMCID: PMC6904873 DOI: 10.1128/mbio.02060-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The malaria parasite has a voracious appetite, requiring large amounts of glucose and nutrients for its rapid growth and proliferation inside human red blood cells. The host cell is resource rich, but this is a double-edged sword; nutrient excess can lead to undesirable metabolic reactions and harmful by-products. Here, we demonstrate that the parasite possesses a metabolite repair enzyme (PGP) that suppresses harmful metabolic by-products (via substrate dephosphorylation) and allows the parasite to maintain central carbon metabolism. Loss of PGP leads to the accumulation of two damaged metabolites and causes a domino effect of metabolic dysregulation. Accumulation of one damaged metabolite inhibits an essential enzyme in the pentose phosphate pathway, leading to substrate accumulation and secondary inhibition of glycolysis. This work highlights how the parasite coordinates metabolic flux by eliminating harmful metabolic by-products to ensure rapid proliferation in its resource-rich niche. Members of the haloacid dehalogenase (HAD) family of metabolite phosphatases play an important role in regulating multiple pathways in Plasmodium falciparum central carbon metabolism. We show that the P. falciparum HAD protein, phosphoglycolate phosphatase (PGP), regulates glycolysis and pentose pathway flux in asexual blood stages via detoxifying the damaged metabolite 4-phosphoerythronate (4-PE). Disruption of the P. falciparumpgp gene caused accumulation of two previously uncharacterized metabolites, 2-phospholactate and 4-PE. 4-PE is a putative side product of the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase, and its accumulation inhibits the pentose phosphate pathway enzyme, 6-phosphogluconate dehydrogenase (6-PGD). Inhibition of 6-PGD by 4-PE leads to an unexpected feedback response that includes increased flux into the pentose phosphate pathway as a result of partial inhibition of upper glycolysis, with concomitant increased sensitivity to antimalarials that target pathways downstream of glycolysis. These results highlight the role of metabolite detoxification in regulating central carbon metabolism and drug sensitivity of the malaria parasite.
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29
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A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites. Cell Host Microbe 2019; 26:385-399.e9. [DOI: 10.1016/j.chom.2019.08.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/24/2019] [Accepted: 08/15/2019] [Indexed: 01/08/2023]
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30
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Hennig K, Abi-Ghanem J, Bunescu A, Meniche X, Biliaut E, Ouattara AD, Lewis MD, Kelly JM, Braillard S, Courtemanche G, Chatelain E, Béquet F. Metabolomics, lipidomics and proteomics profiling of myoblasts infected with Trypanosoma cruzi after treatment with different drugs against Chagas disease. Metabolomics 2019; 15:117. [PMID: 31440849 DOI: 10.1007/s11306-019-1583-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/17/2019] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Chagas disease, the most important parasitic infection in Latin America, is caused by the intracellular protozoan Trypanosoma cruzi. To treat this disease, only two nitroheterocyclic compounds with toxic side effects exist and frequent treatment failures are reported. Hence there is an urgent need to develop new drugs. Recently, metabolomics has become an efficient and cost-effective strategy for dissecting drug mode of action, which has been applied to bacteria as well as parasites, such as different Trypanosome species and forms. OBJECTIVES We assessed if the metabolomics approach can be applied to study drug action of the intracellular amastigote form of T. cruzi in a parasite-host cell system. METHODS We applied a metabolic fingerprinting approach (DI-MS and NMR) to evaluate metabolic changes induced by six different (candidate) drugs in a parasite-host cell system. In a second part of our study, we analyzed the impact of two drugs on polar metabolites, lipid and proteins to evaluate if affected pathways can be identified. RESULTS Metabolic signatures, obtained by the fingerprinting approach, resulted in three different clusters. Two can be explained by already known of mode actions, whereas the three experimental drugs formed a separate cluster. Significant changes induced by drug action were observed in all the three metabolic fractions (polar metabolites, lipids and proteins). We identified a general impact on the TCA cycle, but no specific pathways could be attributed to drug action, which might be caused by a high percentage of common metabolome between a eukaryotic host cell and a eukaryotic parasite. Additionally, ion suppression effects due to differences in abundance between host cells and parasites may have occurred. CONCLUSION We validated the metabolic fingerprinting approach to a complex host-cell parasite system. This technique can potentially be applied in the early stage of drug discovery and could help to prioritize early leads or reconfirmed hits for further development.
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Affiliation(s)
- K Hennig
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - J Abi-Ghanem
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - A Bunescu
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - X Meniche
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - E Biliaut
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - A D Ouattara
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - M D Lewis
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - J M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - S Braillard
- Drugs for Neglected Diseases Initiative (DNDi), 15 Chemin Louis-Dunant, 1202, Geneva, Switzerland
| | | | - E Chatelain
- Drugs for Neglected Diseases Initiative (DNDi), 15 Chemin Louis-Dunant, 1202, Geneva, Switzerland
| | - F Béquet
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France.
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31
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Sexton AE, Doerig C, Creek DJ, Carvalho TG. Post-Genomic Approaches to Understanding Malaria Parasite Biology: Linking Genes to Biological Functions. ACS Infect Dis 2019; 5:1269-1278. [PMID: 31243988 DOI: 10.1021/acsinfecdis.9b00093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plasmodium species are evolutionarily distant from model eukaryotes, and as a consequence they exhibit many non-canonical cellular processes. In the post-genomic era, functional "omics" disciplines (transcriptomics, proteomics, and metabolomics) have accelerated our understanding of unique aspects of the biology of malaria parasites. Functional "omics" tools, in combination with genetic manipulations, have offered new opportunities to investigate the function of previously uncharacterized genes. Knowledge of basic parasite biology is fundamental to understanding drug modes of action, mechanisms of drug resistance, and relevance of vaccine candidates. This Perspective highlights recent "omics"-based discoveries in basic biology and gene function of the most virulent human malaria parasite, Plasmodium falciparum.
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Affiliation(s)
- Anna E. Sexton
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Christian Doerig
- Centre for Chronic, Inflammatory and Infectious Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia
| | - Darren J. Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Teresa G. Carvalho
- Molecular Parasitology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Kingsbury Drive, Bundoora, VIC 3086, Australia
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Kennedy K, Cobbold SA, Hanssen E, Birnbaum J, Spillman NJ, McHugh E, Brown H, Tilley L, Spielmann T, McConville MJ, Ralph SA. Delayed death in the malaria parasite Plasmodium falciparum is caused by disruption of prenylation-dependent intracellular trafficking. PLoS Biol 2019; 17:e3000376. [PMID: 31318858 PMCID: PMC6667170 DOI: 10.1371/journal.pbio.3000376] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/30/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023] Open
Abstract
Apicomplexan parasites possess a plastid organelle called the apicoplast. Inhibitors that selectively target apicoplast housekeeping functions, including DNA replication and protein translation, are lethal for the parasite, and several (doxycycline, clindamycin, and azithromycin) are in clinical use as antimalarials. A major limitation of such drugs is that treated parasites only arrest one intraerythrocytic development cycle (approximately 48 hours) after treatment commences, a phenotype known as the ‘delayed death’ effect. The molecular basis of delayed death is a long-standing mystery in parasitology, and establishing the mechanism would aid rational clinical implementation of apicoplast-targeted drugs. Parasites undergoing delayed death transmit defective apicoplasts to their daughter cells and cannot produce the sole, blood-stage essential metabolic product of the apicoplast: the isoprenoid precursor isopentenyl-pyrophosphate. How the isoprenoid precursor depletion kills the parasite remains unknown. We investigated the requirements for the range of isoprenoids in the human malaria parasite Plasmodium falciparum and characterised the molecular and morphological phenotype of parasites experiencing delayed death. Metabolomic profiling reveals disruption of digestive vacuole function in the absence of apicoplast derived isoprenoids. Three-dimensional electron microscopy reveals digestive vacuole fragmentation and the accumulation of cytostomal invaginations, characteristics common in digestive vacuole disruption. We show that digestive vacuole disruption results from a defect in the trafficking of vesicles to the digestive vacuole. The loss of prenylation of vesicular trafficking proteins abrogates their membrane attachment and function and prevents the parasite from feeding. Our data show that the proximate cause of delayed death is an interruption of protein prenylation and consequent cellular trafficking defects. After treatment with drugs that target apicoplast functions, malaria parasites are initially superficially healthy and go on to infect new erythrocytes. This cell biology study shows that the parasites subsequently die in their second cycle due to trafficking defects caused by depletion of prenyl groups.
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Affiliation(s)
- Kit Kennedy
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Simon A. Cobbold
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Eric Hanssen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
- Advanced Microscopy Facility, Bio21 Molecular Science and Biotechnology Institute, Victoria, Australia
| | - Jakob Birnbaum
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Natalie J. Spillman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Emma McHugh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Hannah Brown
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Tobias Spielmann
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Malcolm J. McConville
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Stuart A. Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
- * E-mail:
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Cobbold SA, McConville MJ. Determining the Mode of Action of Antimalarial Drugs Using Time-Resolved LC-MS-Based Metabolite Profiling. Methods Mol Biol 2019; 1859:225-239. [PMID: 30421232 DOI: 10.1007/978-1-4939-8757-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Methods for assessing the mode of action of new antimalarial compounds identified in high throughput phenotypic screens are needed to triage and facilitate lead compound development and to anticipate potential resistance mechanisms that might emerge. Here we describe a mass spectrometry-based approach for detecting metabolic changes in asexual erythrocytic stages of Plasmodium falciparum induced by antimalarial compounds. Time-resolved or concentration-resolved measurements are used to discriminate between putative targets of the compound and nonspecific and/or downstream secondary metabolic effects. These protocols can also be coupled with 13C-stable-isotope tracing experiments under nonequilibrative (or nonstationary) conditions to measure metabolic dynamics following drug exposure. Time-resolved 13C-labeling studies greatly increase confidence in target assignment and provide a more comprehensive understanding of the metabolic perturbations induced by small molecule inhibitors. The protocol provides details on the experimental design, Plasmodium falciparum culture, sample preparation, analytical approaches, and data analysis used in either targeted (pathway focused) or untargeted (all detected metabolites) analysis of drug-induced metabolic perturbations.
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Affiliation(s)
- Simon A Cobbold
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, 3010, Victoria, Australia.
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Ozonide Antimalarial Activity in the Context of Artemisinin-Resistant Malaria. Trends Parasitol 2019; 35:529-543. [PMID: 31176584 DOI: 10.1016/j.pt.2019.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/02/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
Abstract
The ozonides are one of the most advanced drug classes in the antimalarial development pipeline and were designed to improve on limitations associated with current front-line artemisinin-based therapies. Like the artemisinins, the pharmacophoric peroxide bond of ozonides is essential for activity, and it appears that these antimalarials share a similar mode of action, raising the possibility of cross-resistance. Resistance to artemisinins is associated with Plasmodium falciparum mutations that allow resistant parasites to escape short-term artemisinin-mediated damage (elimination half-life ~1 h). Importantly, some ozonides (e.g., OZ439) have a sustained in vivo drug exposure profile, providing a major pharmacokinetic advantage over the artemisinin derivatives. Here, we describe recent progress made towards understanding ozonide antimalarial activity and discuss ozonide utility within the context of artemisinin resistance.
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35
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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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36
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Husna AU, Wang N, Cobbold SA, Newton HJ, Hocking DM, Wilksch JJ, Scott TA, Davies MR, Hinton JC, Tree JJ, Lithgow T, McConville MJ, Strugnell RA. Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium. J Biol Chem 2018; 293:9506-9519. [PMID: 29720401 PMCID: PMC6005444 DOI: 10.1074/jbc.ra118.002592] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/28/2018] [Indexed: 11/06/2022] Open
Abstract
Methionine (Met) is an amino acid essential for many important cellular and biosynthetic functions, including the initiation of protein synthesis and S-adenosylmethionine–mediated methylation of proteins, RNA, and DNA. The de novo biosynthetic pathway of Met is well conserved across prokaryotes but absent from vertebrates, making it a plausible antimicrobial target. Using a systematic approach, we examined the essentiality of de novo methionine biosynthesis in Salmonella enterica serovar Typhimurium, a bacterial pathogen causing significant gastrointestinal and systemic diseases in humans and agricultural animals. Our data demonstrate that Met biosynthesis is essential for S. Typhimurium to grow in synthetic medium and within cultured epithelial cells where Met is depleted in the environment. During systemic infection of mice, the virulence of S. Typhimurium was not affected when either de novo Met biosynthesis or high-affinity Met transport was disrupted alone, but combined disruption in both led to severe in vivo growth attenuation, demonstrating a functional redundancy between de novo biosynthesis and acquisition as a mechanism of sourcing Met to support growth and virulence for S. Typhimurium during infection. In addition, our LC-MS analysis revealed global changes in the metabolome of S. Typhimurium mutants lacking Met biosynthesis and also uncovered unexpected interactions between Met and peptidoglycan biosynthesis. Together, this study highlights the complexity of the interactions between a single amino acid, Met, and other bacterial processes leading to virulence in the host and indicates that disrupting the de novo biosynthetic pathway alone is likely to be ineffective as an antimicrobial therapy against S. Typhimurium.
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Affiliation(s)
- Asma Ul Husna
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Nancy Wang
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia,
| | - Simon A Cobbold
- the Department of Biochemistry and Molecular Biology, University of Melbourne at the Bio21 Institute, Parkville, Victoria 3052, Australia
| | - Hayley J Newton
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Dianna M Hocking
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Jonathan J Wilksch
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Timothy A Scott
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Mark R Davies
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Jay C Hinton
- the Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jai J Tree
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia.,the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia, and
| | - Trevor Lithgow
- the Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Malcolm J McConville
- the Department of Biochemistry and Molecular Biology, University of Melbourne at the Bio21 Institute, Parkville, Victoria 3052, Australia
| | - Richard A Strugnell
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia,
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37
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Influential Parameters for the Analysis of Intracellular Parasite Metabolomics. mSphere 2018; 3:3/2/e00097-18. [PMID: 29669882 PMCID: PMC5907652 DOI: 10.1128/msphere.00097-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Molecular characterization of pathogens such as the malaria parasite can lead to improved biological understanding and novel treatment strategies. However, the distinctive biology of the Plasmodium parasite, including its repetitive genome and the requirement for growth within a host cell, hinders progress toward these goals. Untargeted metabolomics is a promising approach to learn about pathogen biology. By measuring many small molecules in the parasite at once, we gain a better understanding of important pathways that contribute to the parasite’s response to perturbations such as drug treatment. Although increasingly popular, approaches for intracellular parasite metabolomics and subsequent analysis are not well explored. The findings presented in this report emphasize the critical need for improvements in these areas to limit misinterpretation due to host metabolites and to standardize biological interpretation. Such improvements will aid both basic biological investigations and clinical efforts to understand important pathogens. Metabolomics is increasingly popular for the study of pathogens. For the malaria parasite Plasmodium falciparum, both targeted and untargeted metabolomics have improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular pathogens have not been explored. Here, we purified in vitro-grown ring-stage intraerythrocytic P. falciparum parasites for untargeted metabolomics studies; the small size of this developmental stage amplifies the challenges associated with metabolomics studies as the ratio between host and parasite biomass is maximized. Following metabolite identification and data preprocessing, we explored multiple confounding factors that influence data interpretation, including host contamination and normalization approaches (including double-stranded DNA, total protein, and parasite numbers). We conclude that normalization parameters have large effects on differential abundance analysis and recommend the thoughtful selection of these parameters. However, normalization does not remove the contribution from the parasite’s extracellular environment (culture media and host erythrocyte). In fact, we found that extraparasite material is as influential on the metabolome as treatment with a potent antimalarial drug with known metabolic effects (artemisinin). Because of this influence, we could not detect significant changes associated with drug treatment. Instead, we identified metabolites predictive of host and medium contamination that could be used to assess sample purification. Our analysis provides the first quantitative exploration of the effects of these factors on metabolomics data analysis; these findings provide a basis for development of improved experimental and analytical methods for future metabolomics studies of intracellular organisms. IMPORTANCE Molecular characterization of pathogens such as the malaria parasite can lead to improved biological understanding and novel treatment strategies. However, the distinctive biology of the Plasmodium parasite, including its repetitive genome and the requirement for growth within a host cell, hinders progress toward these goals. Untargeted metabolomics is a promising approach to learn about pathogen biology. By measuring many small molecules in the parasite at once, we gain a better understanding of important pathways that contribute to the parasite’s response to perturbations such as drug treatment. Although increasingly popular, approaches for intracellular parasite metabolomics and subsequent analysis are not well explored. The findings presented in this report emphasize the critical need for improvements in these areas to limit misinterpretation due to host metabolites and to standardize biological interpretation. Such improvements will aid both basic biological investigations and clinical efforts to understand important pathogens.
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38
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The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes. PLoS Biol 2018; 16:e2004328. [PMID: 29529020 PMCID: PMC5864071 DOI: 10.1371/journal.pbio.2004328] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/22/2018] [Accepted: 02/16/2018] [Indexed: 01/13/2023] Open
Abstract
Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to-or is selected by-this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to-or are selected by-the host environment in severe malaria.
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Parasite-Mediated Degradation of Synthetic Ozonide Antimalarials Impacts In Vitro Antimalarial Activity. Antimicrob Agents Chemother 2018; 62:AAC.01566-17. [PMID: 29263074 DOI: 10.1128/aac.01566-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/16/2017] [Indexed: 01/05/2023] Open
Abstract
The peroxide bond of the artemisinins inspired the development of a class of fully synthetic 1,2,4-trioxolane-based antimalarials, collectively known as the ozonides. Similar to the artemisinins, heme-mediated degradation of the ozonides generates highly reactive radical species that are thought to mediate parasite killing by damaging critical parasite biomolecules. We examined the relationship between parasite dependent degradation and antimalarial activity for two ozonides, OZ277 (arterolane) and OZ439 (artefenomel), using a combination of in vitro drug stability and pulsed-exposure activity assays. Our results showed that drug degradation is parasite stage dependent and positively correlates with parasite load. Increasing trophozoite-stage parasitemia leads to substantially higher rates of degradation for both OZ277 and OZ439, and this is associated with a reduction in in vitro antimalarial activity. Under conditions of very high parasitemia (∼90%), OZ277 and OZ439 were rapidly degraded and completely devoid of activity in trophozoite-stage parasite cultures exposed to a 3-h drug pulse. This study highlights the impact of increasing parasite load on ozonide stability and in vitro antimalarial activity and should be considered when investigating the antimalarial mode of action of the ozonide antimalarials under conditions of high parasitemia.
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40
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Li J, Hou L, Wang C, Jia X, Qin X, Wu C. Short Term Intrarectal Administration of Sodium Propionate Induces Antidepressant-Like Effects in Rats Exposed to Chronic Unpredictable Mild Stress. Front Psychiatry 2018; 9:454. [PMID: 30319461 PMCID: PMC6170646 DOI: 10.3389/fpsyt.2018.00454] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 01/12/2023] Open
Abstract
Depression has been correlated with metabolic disorders, and the gut microbiota and its metabolites have been reported to be key factors affecting metabolic disorders. Several metabolites generated by the gut microbiota have been reported to exert antidepressant-like effects, including the short chain fatty acid (SCFA) butyrate. However, recent work has suggested that the abundance of butyrate is not significantly changed in neither human nor experimental animals with depression, and butyrate has been reported to decrease upon the administration of prebiotics with antidepressant-like effects. Supplementation of endogenous metabolites that are unchanged in depression may induce additional metabolic disorders and may lead to poorer clinical outcomes. However, the endogenous metabolites that are imbalanced in depression may include several antidepressant candidates that could circumvent these problems. In this study, we used GC-MS spectrometry to study the fecal metabolome of rats under Chronic Unpredictable Mild Stress (CUMS). We carried out static and dynamic metabolomics analyses to identify the differential metabolites between the CUMS rats and control rats. We identified propionic acid, rather than butyric acid, as a differential metabolite of the CUMS rats. Consistent with this, a 1-week intrarectal administration of sodium propionate (NaP, the salt form of propionic acid) induced antidepressant-like effects and partially rebalanced the plasma metabolome. The antidepressant-like effects of NaP were correlated with differential rescue of neurotransmitters in the prefrontal cortex, which may be achieved through the reduction of catabolism of noradrenaline, tryptophan and dopamine, rather than serotonin. These findings support NaP as a potential candidate in fighting depression by administering an endogenous metabolite.
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Affiliation(s)
- Jianguo Li
- Laboratory for Microbiome Sciences, Institute of Biomedical Sciences, Shanxi University, Taiyuan, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Luwen Hou
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Cui Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Xueyang Jia
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Xuemei Qin
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China.,Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Changxin Wu
- Laboratory for Microbiome Sciences, Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
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41
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Donnelly S, Huston WM, Johnson M, Tiberti N, Saunders B, O'Brien B, Burke C, Labbate M, Combes V. Targeting the master regulator mTOR: a new approach to prevent the neurological of consequences of parasitic infections? Parasit Vectors 2017; 10:581. [PMID: 29162126 PMCID: PMC5697405 DOI: 10.1186/s13071-017-2528-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
Abstract
A systematic analysis of 240 causes of death in 2013 revealed that parasitic diseases were responsible for more than one million deaths. The vast majority of these fatalities resulted from protozoan infections presenting with neurological sequelae. In the absence of a vaccine, development of effective therapies is essential to improving global public health. In 2015, an intriguing strategy to prevent cerebral malaria was proposed by Gordon et al. 2015 mBio, 6:e00625. Their study suggested that inhibition of the mammalian target of rapamycin prevented experimental cerebral malaria by blocking the damage to the blood brain barrier and stopping the accumulation of parasitized red blood cells and T cells in the brain. Here, we hypothesize that the same therapeutic strategy could be adopted for other protozoan infections with a brain tropism, to prevent cerebral parasitosis by limiting pathogen replication and preventing immune mediated destruction of brain tissue.
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Affiliation(s)
- Sheila Donnelly
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Wilhelmina M Huston
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Michael Johnson
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Natalia Tiberti
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Bernadette Saunders
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Bronwyn O'Brien
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Catherine Burke
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Maurizio Labbate
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Valery Combes
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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42
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Burgess SL, Gilchrist CA, Lynn TC, Petri WA. Parasitic Protozoa and Interactions with the Host Intestinal Microbiota. Infect Immun 2017; 85:e00101-17. [PMID: 28584161 PMCID: PMC5520446 DOI: 10.1128/iai.00101-17] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Parasitic protozoan infections represent a major health burden in the developing world and contribute significantly to morbidity and mortality. These infections are often associated with considerable variability in clinical presentation. An emerging body of work suggests that the intestinal microbiota may help to explain some of these differences in disease expression. The objective of this minireview is to synthesize recent progress in this rapidly advancing field. Studies of humans and animals and in vitro studies of the contribution of the intestinal microbiota to infectious disease are discussed. We hope to provide an understanding of the human-protozoal pathogen-microbiome interaction and to speculate on how that might be leveraged for treatment.
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Affiliation(s)
- Stacey L Burgess
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Carol A Gilchrist
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Tucker C Lynn
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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43
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Carey MA, Papin JA, Guler JL. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance. BMC Genomics 2017; 18:543. [PMID: 28724354 PMCID: PMC5518114 DOI: 10.1186/s12864-017-3905-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Background Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. Results Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P. falciparum parasite to expand our understanding of metabolic changes that support resistance. We identified 11 metabolic tasks to evaluate iPfal17 performance. Flux balance analysis and simulation of gene knockouts and enzyme inhibition predict candidate drug targets unique to resistant parasites. Moreover, integration of clinical parasite transcriptomes into the iPfal17 reconstruction reveals patterns associated with antimalarial resistance. These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites, including folate and polyamines. Our findings are consistent with experimental literature, while generating novel hypotheses about artemisinin resistance and parasite biology. We detect evidence that resistant parasites maintain greater metabolic flexibility, perhaps representing an incomplete transition to the metabolic state most appropriate for nutrient-rich blood. Conclusion Using this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. This perspective allows us to more productively analyze and interpret clinical expression data for the identification of candidate drug targets for the treatment of resistant parasites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3905-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA.
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, USA. .,Division of Infectious Diseases and International Health, University of Virginia, School of Medicine, Charlottesville, USA.
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Hapuarachchi SV, Cobbold SA, Shafik SH, Dennis ASM, McConville MJ, Martin RE, Kirk K, Lehane AM. The Malaria Parasite's Lactate Transporter PfFNT Is the Target of Antiplasmodial Compounds Identified in Whole Cell Phenotypic Screens. PLoS Pathog 2017; 13:e1006180. [PMID: 28178359 PMCID: PMC5298231 DOI: 10.1371/journal.ppat.1006180] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/11/2017] [Indexed: 11/19/2022] Open
Abstract
In this study the ‘Malaria Box’ chemical library comprising 400 compounds with antiplasmodial activity was screened for compounds that perturb the internal pH of the malaria parasite, Plasmodium falciparum. Fifteen compounds induced an acidification of the parasite cytosol. Two of these did so by inhibiting the parasite’s formate nitrite transporter (PfFNT), which mediates the H+-coupled efflux from the parasite of lactate generated by glycolysis. Both compounds were shown to inhibit lactate transport across the parasite plasma membrane, and the transport of lactate by PfFNT expressed in Xenopus laevis oocytes. PfFNT inhibition caused accumulation of lactate in parasitised erythrocytes, and swelling of both the parasite and parasitised erythrocyte. Long-term exposure of parasites to one of the inhibitors gave rise to resistant parasites with a mutant form of PfFNT that showed reduced inhibitor sensitivity. This study provides the first evidence that PfFNT is a druggable antimalarial target. The emergence and spread of Plasmodium falciparum strains resistant to leading antimalarial drugs has intensified the need to discover and develop drugs that kill the parasite via new mechanisms. Here we screened compounds that are known to inhibit P. falciparum growth for their effects on the pH inside the parasite. We identified fifteen compounds that decrease the pH inside the parasite, and determined the mechanism by which two of these, MMV007839 and MMV000972, disrupt pH and kill the parasite. The two compounds were found to inhibit the P. falciparum formate nitrite transporter (PfFNT), a transport protein that is located on the parasite surface and that serves to remove the waste product lactic acid from the parasite. The compounds inhibited both the H+-coupled transport of lactate across the parasite plasma membrane and the transport of lactate by PfFNT expressed in Xenopus oocytes. In addition to disrupting pH, PfFNT inhibition led to a build-up of lactate in the parasite-infected red blood cell and the swelling of both the parasite and the infected red blood cell. Exposing parasites to MMV007839 over a prolonged time period gave rise to resistant parasites with a mutant form of PfFNT that was less sensitive to the compound. This study validates PfFNT as a novel antimalarial drug target.
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Affiliation(s)
| | - Simon A Cobbold
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adelaide S M Dennis
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Rowena E Martin
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adele M Lehane
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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Dickerman BK, Elsworth B, Cobbold SA, Nie CQ, McConville MJ, Crabb BS, Gilson PR. Identification of inhibitors that dually target the new permeability pathway and dihydroorotate dehydrogenase in the blood stage of Plasmodium falciparum. Sci Rep 2016; 6:37502. [PMID: 27874068 PMCID: PMC5118696 DOI: 10.1038/srep37502] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Plasmodium parasites are responsible for the devastating disease malaria that affects hundreds of millions of people each year. Blood stage parasites establish new permeability pathways (NPPs) in infected red blood cell membranes to facilitate the uptake of nutrients and removal of parasite waste products. Pharmacological inhibition of the NPPs is expected to lead to nutrient starvation and accumulation of toxic metabolites resulting in parasite death. Here, we have screened a curated library of antimalarial compounds, the MMV Malaria Box, identifying two compounds that inhibit NPP function. Unexpectedly, metabolic profiling suggested that both compounds also inhibit dihydroorotate dehydrogense (DHODH), which is required for pyrimidine synthesis and is a validated drug target in its own right. Expression of yeast DHODH, which bypasses the need for the parasite DHODH, increased parasite resistance to these compounds. These studies identify two potential candidates for therapeutic development that simultaneously target two essential pathways in Plasmodium, NPP and DHODH.
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Affiliation(s)
| | - Brendan Elsworth
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
| | - Simon A. Cobbold
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Malcolm J. McConville
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Brendan S. Crabb
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Paul R. Gilson
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
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Metabolomics-Based Screening of the Malaria Box Reveals both Novel and Established Mechanisms of Action. Antimicrob Agents Chemother 2016; 60:6650-6663. [PMID: 27572396 DOI: 10.1128/aac.01226-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/16/2016] [Indexed: 12/22/2022] Open
Abstract
High-throughput phenotypic screening of chemical libraries has resulted in the identification of thousands of compounds with potent antimalarial activity, although in most cases, the mechanism(s) of action of these compounds remains unknown. Here we have investigated the mode of action of 90 antimalarial compounds derived from the Malaria Box collection using high-coverage, untargeted metabolomics analysis. Approximately half of the tested compounds induced significant metabolic perturbations in in vitro cultures of Plasmodium falciparum In most cases, the metabolic profiles were highly correlated with known antimalarials, in particular artemisinin, the 4-aminoquinolines, or atovaquone. Select Malaria Box compounds also induced changes in intermediates in essential metabolic pathways, such as isoprenoid biosynthesis (i.e., 2-C-methyl-d-erythritol 2,4-cyclodiphosphate) and linolenic acid metabolism (i.e., traumatic acid). This study provides a comprehensive database of the metabolic perturbations induced by chemically diverse inhibitors and highlights the utility of metabolomics for triaging new lead compounds and defining specific modes of action, which will assist with the development and optimization of new antimalarial drugs.
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Metabolomic Profiling of the Malaria Box Reveals Antimalarial Target Pathways. Antimicrob Agents Chemother 2016; 60:6635-6649. [PMID: 27572391 DOI: 10.1128/aac.01224-16] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/16/2016] [Indexed: 12/11/2022] Open
Abstract
The threat of widespread drug resistance to frontline antimalarials has renewed the urgency for identifying inexpensive chemotherapeutic compounds that are effective against Plasmodium falciparum, the parasite species responsible for the greatest number of malaria-related deaths worldwide. To aid in the fight against malaria, a recent extensive screening campaign has generated thousands of lead compounds with low micromolar activity against blood stage parasites. A subset of these leads has been compiled by the Medicines for Malaria Venture (MMV) into a collection of structurally diverse compounds known as the MMV Malaria Box. Currently, little is known regarding the activity of these Malaria Box compounds on parasite metabolism during intraerythrocytic development, and a majority of the targets for these drugs have yet to be defined. Here we interrogated the in vitro metabolic effects of 189 drugs (including 169 of the drug-like compounds from the Malaria Box) using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention and offer a critical blueprint for selecting and advancing lead compounds as next-generation antimalarial drugs. Our results reveal several major classes of metabolic disruption, which allow us to predict the mode of action (MoA) for many of the Malaria Box compounds. We anticipate that future combination therapies will be greatly informed by these results, allowing for the selection of appropriate drug combinations that simultaneously target multiple metabolic pathways, with the aim of eliminating malaria and forestalling the expansion of drug-resistant parasites in the field.
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48
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Edwards RL, Odom John AR. Muddled mechanisms: recent progress towards antimalarial target identification. F1000Res 2016; 5:2514. [PMID: 27803804 PMCID: PMC5070598 DOI: 10.12688/f1000research.9477.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 01/06/2023] Open
Abstract
In the past decade, malaria rates have plummeted as a result of aggressive infection control measures and the adoption of artemisinin-based combination therapies (ACTs). However, a potential crisis looms ahead. Treatment failures to standard antimalarial regimens have been reported in Southeast Asia, and devastating consequences are expected if resistance spreads to the African continent. To prevent a potential public health emergency, the antimalarial arsenal must contain therapeutics with novel mechanisms of action (MOA). An impressive number of high-throughput screening (HTS) campaigns have since been launched, identifying thousands of compounds with activity against one of the causative agents of malaria,
Plasmodium falciparum. Now begins the difficult task of target identification, for which studies are often tedious, labor intensive, and difficult to interpret. In this review, we highlight approaches that have been instrumental in tackling the challenges of target assignment and elucidation of the MOA for hit compounds. Studies that apply these innovative techniques to antimalarial target identification are described, as well as the impact of the data in the field.
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Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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Woodrow CJ, White NJ. The clinical impact of artemisinin resistance in Southeast Asia and the potential for future spread. FEMS Microbiol Rev 2016; 41:34-48. [PMID: 27613271 PMCID: PMC5424521 DOI: 10.1093/femsre/fuw037] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/11/2016] [Accepted: 07/31/2016] [Indexed: 11/25/2022] Open
Abstract
Artemisinins are the most rapidly acting of currently available antimalarial drugs. Artesunate has become the treatment of choice for severe malaria, and artemisinin-based combination therapies (ACTs) are the foundation of modern falciparum malaria treatment globally. Their safety and tolerability profile is excellent. Unfortunately, Plasmodium falciparum infections with mutations in the ‘K13’ gene, with reduced ring-stage susceptibility to artemisinins, and slow parasite clearance in patients treated with ACTs, are now widespread in Southeast Asia. We review clinical efficacy data from the region (2000–2015) that provides strong evidence that the loss of first-line ACTs in western Cambodia, first artesunate-mefloquine and then DHA-piperaquine, can be attributed primarily to K13 mutated parasites. The ring-stage activity of artemisinins is therefore critical for the sustained efficacy of ACTs; once it is lost, rapid selection of partner drug resistance and ACT failure are inevitable consequences. Consensus methods for monitoring artemisinin resistance are now available. Despite increased investment in regional control activities, ACTs are failing across an expanding area of the Greater Mekong subregion. Although multiple K13 mutations have arisen independently, successful multidrug-resistant parasite genotypes are taking over and threaten to spread to India and Africa. Stronger containment efforts and new approaches to sustaining long-term efficacy of antimalarial regimens are needed to prevent a global malaria emergency. Artemisinin resistance in Plasmodium falciparum malaria is causing failure of artemisinin-based combination therapies across an expanding area of Southeast Asia, undermining control and elimination efforts. The potential global consequences can only be avoided by new approaches that ensure sustained efficacy for antimalarial regimens in malaria affected populations.
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Affiliation(s)
- Charles J Woodrow
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6, Rajvithi Road, Bangkok 10400, Thailand
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6, Rajvithi Road, Bangkok 10400, Thailand
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