1
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Zdrazil B, Felix E, Hunter F, Manners EJ, Blackshaw J, Corbett S, de Veij M, Ioannidis H, Lopez DM, Mosquera J, Magarinos M, Bosc N, Arcila R, Kizilören T, Gaulton A, Bento A, Adasme M, Monecke P, Landrum G, Leach A. The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Res 2024; 52:D1180-D1192. [PMID: 37933841 PMCID: PMC10767899 DOI: 10.1093/nar/gkad1004] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 and 2019 Nucleic Acids Research Database Issues. Since its introduction in 2009, ChEMBL's content has changed dramatically in size and diversity of data types. Through incorporation of multiple new datasets from depositors since the 2019 update, ChEMBL now contains slightly more bioactivity data from deposited data vs data extracted from literature. In collaboration with the EUbOPEN consortium, chemical probe data is now regularly deposited into ChEMBL. Release 27 made curated data available for compounds screened for potential anti-SARS-CoV-2 activity from several large-scale drug repurposing screens. In addition, new patent bioactivity data have been added to the latest ChEMBL releases, and various new features have been incorporated, including a Natural Product likeness score, updated flags for Natural Products, a new flag for Chemical Probes, and the initial annotation of the action type for ∼270 000 bioactivity measurements.
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Affiliation(s)
- Barbara Zdrazil
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eloy Felix
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Fiona Hunter
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James Blackshaw
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sybilla Corbett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Marleen de Veij
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Harris Ioannidis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David Mendez Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Juan F Mosquera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Maria Paula Magarinos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nicolas Bosc
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ricardo Arcila
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Tevfik Kizilören
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - A Patrícia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Melissa F Adasme
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Peter Monecke
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Gregory A Landrum
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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2
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Luo AP, Giannangelo C, Siddiqui G, Creek DJ. Promising antimalarial hits from phenotypic screens: a review of recently-described multi-stage actives and their modes of action. Front Cell Infect Microbiol 2023; 13:1308193. [PMID: 38162576 PMCID: PMC10757594 DOI: 10.3389/fcimb.2023.1308193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Over the last two decades, global malaria cases caused by Plasmodium falciparum have declined due to the implementation of effective treatments and the use of insecticides. However, the COVID-19 pandemic caused major disruption in the timely delivery of medical goods and diverted public health resources, impairing malaria control. The emergence of resistance to all existing frontline antimalarials underpins an urgent need for new antimalarials with novel mechanisms of action. Furthermore, the need to reduce malaria transmission and/or prevent malaria infection has shifted the focus of antimalarial research towards the discovery of compounds that act beyond the symptomatic blood stage and also impact other parasite life cycle stages. Phenotypic screening has been responsible for the majority of new antimalarial lead compounds discovered over the past 10 years. This review describes recently reported novel antimalarial hits that target multiple parasite stages and were discovered by phenotypic screening during the COVID-19 pandemic. Their modes of action and targets in blood stage parasites are also discussed.
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Affiliation(s)
| | | | - Ghizal Siddiqui
- 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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3
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Wilson C, Gardner JMF, Gray DW, Baragana B, Wyatt PG, Cookson A, Thompson S, Mendoza-Martinez C, Bodkin MJ, Gilbert IH, Tarver GJ. Design of the Global Health chemical diversity library v2 for screening against infectious diseases. PLoS Negl Trop Dis 2023; 17:e0011799. [PMID: 38150490 PMCID: PMC10752525 DOI: 10.1371/journal.pntd.0011799] [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: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
There is a need for novel chemical matter for phenotypic and target-based screens to find starting points for drug discovery programmes in neglected infectious diseases and non-hormonal contraceptives that disproportionately affect Low- and Middle-Income Countries (LMICs). In some disease areas multiple screens of corporate and other libraries have been carried out, giving rise to some valuable starting points and leading to preclinical candidates. Whilst in other disease areas, little screening has been carried out. Much screening against pathogens has been conducted phenotypically as there are few robustly validated protein targets. However, many of the active compound series identified share the same molecular targets. To address the need for new chemical material, in this article we describe the design of a new library, designed for screening in drug discovery programmes for neglected infectious diseases. The compounds have been selected from the Enamine REAL (REadily AccessibLe) library, a virtual library which contains approximately 4.5 billion molecules. The molecules theoretically can be synthesized quickly using commercially available intermediates and building blocks. The vast majority of these have not been prepared before, so this is a source of novel compounds. In this paper we describe the design of a diverse library of 30,000 compounds from this collection (graphical abstract). The new library will be made available to laboratories working in neglected infectious diseases, subject to a review process. The project has been supported by the Bill & Melinda Gates Foundation and the Wellcome Trust (Wellcome).
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Affiliation(s)
- Caroline Wilson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - J. Mark F. Gardner
- AMG Consultants Ltd, Discovery Park House, Ramsgate Road, Sandwich, Kent, United Kingdom
| | - David W. Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Beatriz Baragana
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Paul G. Wyatt
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Alex Cookson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Stephen Thompson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Cesar Mendoza-Martinez
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Michael J. Bodkin
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Ian H. Gilbert
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Gary J. Tarver
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
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4
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Green SR, Wilson C, Eadsforth TC, Punekar AS, Tamaki FK, Wood G, Caldwell N, Forte B, Norcross NR, Kiczun M, Post JM, Lopez-Román EM, Engelhart CA, Lukac I, Zuccotto F, Epemolu O, Boshoff HIM, Schnappinger D, Walpole C, Gilbert IH, Read KD, Wyatt PG, Baragaña B. Identification and Optimization of Novel Inhibitors of the Polyketide Synthase 13 Thioesterase Domain with Antitubercular Activity. J Med Chem 2023; 66:15380-15408. [PMID: 37948640 PMCID: PMC10683028 DOI: 10.1021/acs.jmedchem.3c01514] [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: 08/16/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
There is an urgent need for new tuberculosis (TB) treatments, with novel modes of action, to reduce the incidence/mortality of TB and to combat resistance to current treatments. Through both chemical and genetic methodologies, polyketide synthase 13 (Pks13) has been validated as essential for mycobacterial survival and as an attractive target for Mycobacterium tuberculosis growth inhibitors. A benzofuran series of inhibitors that targeted the Pks13 thioesterase domain, failed to progress to preclinical development due to concerns over cardiotoxicity. Herein, we report the identification of a novel oxadiazole series of Pks13 inhibitors, derived from a high-throughput screening hit and structure-guided optimization. This new series binds in the Pks13 thioesterase domain, with a distinct binding mode compared to the benzofuran series. Through iterative rounds of design, assisted by structural information, lead compounds were identified with improved antitubercular potencies (MIC < 1 μM) and in vitro ADMET profiles.
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Affiliation(s)
- Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Thomas C. Eadsforth
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Avinash S. Punekar
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio K. Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Gavin Wood
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Barbara Forte
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Neil R. Norcross
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Michael Kiczun
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - John M. Post
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Medicines R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Iva Lukac
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, QC H4A 3J1, Canada
| | - Ian H. Gilbert
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Beatriz Baragaña
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
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5
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van Heerden A, Turon G, Duran-Frigola M, Pillay N, Birkholtz LM. Machine Learning Approaches Identify Chemical Features for Stage-Specific Antimalarial Compounds. ACS OMEGA 2023; 8:43813-43826. [PMID: 38027377 PMCID: PMC10666252 DOI: 10.1021/acsomega.3c05664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
Efficacy data from diverse chemical libraries, screened against the various stages of the malaria parasite Plasmodium falciparum, including asexual blood stage (ABS) parasites and transmissible gametocytes, serve as a valuable reservoir of information on the chemical space of compounds that are either active (or not) against the parasite. We postulated that this data can be mined to define chemical features associated with the sole ABS activity and/or those that provide additional life cycle activity profiles like gametocytocidal activity. Additionally, this information could provide chemical features associated with inactive compounds, which could eliminate any future unnecessary screening of similar chemical analogs. Therefore, we aimed to use machine learning to identify the chemical space associated with stage-specific antimalarial activity. We collected data from various chemical libraries that were screened against the asexual (126 374 compounds) and sexual (gametocyte) stages of the parasite (93 941 compounds), calculated the compounds' molecular fingerprints, and trained machine learning models to recognize stage-specific active and inactive compounds. We were able to build several models that predict compound activity against ABS and dual activity against ABS and gametocytes, with Support Vector Machines (SVM) showing superior abilities with high recall (90 and 66%) and low false-positive predictions (15 and 1%). This allowed the identification of chemical features enriched in active and inactive populations, an important outcome that could be mined for essential chemical features to streamline hit-to-lead optimization strategies of antimalarial candidates. The predictive capabilities of the models held true in diverse chemical spaces, indicating that the ML models are therefore robust and can serve as a prioritization tool to drive and guide phenotypic screening and medicinal chemistry programs.
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Affiliation(s)
- Ashleigh van Heerden
- Department
of Biochemistry, Genetics and Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Gemma Turon
- Ersilia
Open Source Initiative, 28 Belgrave Road, Cambridge CB1 3DE, U.K.
| | | | - Nelishia Pillay
- Department
of Computer Science, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Lyn-Marié Birkholtz
- Department
of Biochemistry, Genetics and Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
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6
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Siqueira-Neto JL, Wicht KJ, Chibale K, Burrows JN, Fidock DA, Winzeler EA. Antimalarial drug discovery: progress and approaches. Nat Rev Drug Discov 2023; 22:807-826. [PMID: 37652975 PMCID: PMC10543600 DOI: 10.1038/s41573-023-00772-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 09/02/2023]
Abstract
Recent antimalarial drug discovery has been a race to produce new medicines that overcome emerging drug resistance, whilst considering safety and improving dosing convenience. Discovery efforts have yielded a variety of new molecules, many with novel modes of action, and the most advanced are in late-stage clinical development. These discoveries have led to a deeper understanding of how antimalarial drugs act, the identification of a new generation of drug targets, and multiple structure-based chemistry initiatives. The limited pool of funding means it is vital to prioritize new drug candidates. They should exhibit high potency, a low propensity for resistance, a pharmacokinetic profile that favours infrequent dosing, low cost, preclinical results that demonstrate safety and tolerability in women and infants, and preferably the ability to block Plasmodium transmission to Anopheles mosquito vectors. In this Review, we describe the approaches that have been successful, progress in preclinical and clinical development, and existing challenges. We illustrate how antimalarial drug discovery can serve as a model for drug discovery in diseases of poverty.
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Affiliation(s)
| | - Kathryn J Wicht
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | | | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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7
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Nguyen W, Dans MG, Currie I, Awalt JK, Bailey BL, Lumb C, Ngo A, Favuzza P, Palandri J, Ramesh S, Penington J, Jarman KE, Mukherjee P, Chakraborty A, Maier AG, van Dooren GG, Papenfuss T, Wittlin S, Churchyard A, Baum J, Winzeler EA, Baud D, Brand S, Jackson PF, Cowman AF, Sleebs BE. 7- N-Substituted-3-oxadiazole Quinolones with Potent Antimalarial Activity Target the Cytochrome bc1 Complex. ACS Infect Dis 2023; 9:668-691. [PMID: 36853190 PMCID: PMC10012268 DOI: 10.1021/acsinfecdis.2c00607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The development of new antimalarials is required because of the threat of resistance to current antimalarial therapies. To discover new antimalarial chemotypes, we screened the Janssen Jumpstarter library against the P. falciparum asexual parasite and identified the 7-N-substituted-3-oxadiazole quinolone hit class. We established the structure-activity relationship and optimized the antimalarial potency. The optimized analog WJM228 (17) showed robust metabolic stability in vitro, although the aqueous solubility was limited. Forward genetic resistance studies uncovered that WJM228 targets the Qo site of cytochrome b (cyt b), an important component of the mitochondrial electron transport chain (ETC) that is essential for pyrimidine biosynthesis and an established antimalarial target. Profiling against drug-resistant parasites confirmed that WJM228 confers resistance to the Qo site but not Qi site mutations, and in a biosensor assay, it was shown to impact the ETC via inhibition of cyt b. Consistent with other cyt b targeted antimalarials, WJM228 prevented pre-erythrocytic parasite and male gamete development and reduced asexual parasitemia in a P. berghei mouse model of malaria. Correcting the limited aqueous solubility and the high susceptibility to cyt b Qo site resistant parasites found in the clinic will be major obstacles in the future development of the 3-oxadiazole quinolone antimalarial class.
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Affiliation(s)
- William Nguyen
- 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
| | - Iain Currie
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Jon Kyle Awalt
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Brodie L Bailey
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Chris Lumb
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Anna Ngo
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Paola Favuzza
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, 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
| | - Saishyam Ramesh
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Jocelyn Penington
- 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
| | | | | | - Alexander G Maier
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Tony Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ U.K
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ U.K.,School of Biomedical Sciences, University of New South Wales, Sydney 2031, Australia
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego, 9500 Gilman Drive 0760, La Jolla, California 92093, United States
| | - Delphine Baud
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Paul F Jackson
- Global Public Health, 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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8
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Reader J, Opperman DFL, van der Watt ME, Theron A, Leshabane M, da Rocha S, Turner J, Garrabrant K, Piña I, Mills C, Woster PM, Birkholtz L. New Transmission-Selective Antimalarial Agents through Hit-to-Lead Optimization of 2-([1,1'-Biphenyl]-4-carboxamido)benzoic Acid Derivatives. Chembiochem 2022; 23:e202200427. [PMID: 36106425 PMCID: PMC10946866 DOI: 10.1002/cbic.202200427] [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: 07/27/2022] [Revised: 09/14/2022] [Indexed: 11/12/2022]
Abstract
Malaria elimination requires multipronged approaches, including the application of antimalarial drugs able to block human-to-mosquito transmission of malaria parasites. The transmissible gametocytes of Plasmodium falciparum seem to be highly sensitive towards epidrugs, particularly those targeting demethylation of histone post-translational marks. Here, we report exploration of compounds from a chemical library generated during hit-to-lead optimization of inhibitors of the human histone lysine demethylase, KDM4B. Derivatives of 2-([1,1'-biphenyl]-4-carboxamido) benzoic acid, around either the amide or a sulfonamide linker backbone (2-(arylcarboxamido)benzoic acid, 2-carboxamide (arylsulfonamido)benzoic acid and N-(2-(1H-tetrazol-5-yl)phenyl)-arylcarboxamide), showed potent activity towards late-stage gametocytes (stage IV/V) of P. falciparum, with the most potent compound reaching single digit nanomolar activity. Structure-activity relationship trends were evident and frontrunner compounds also displayed microsomal stability and favourable solubility profiles. Simplified synthetic routes support further derivatization of these compounds for further development of these series as malaria transmission-blocking agents.
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Affiliation(s)
- Janette Reader
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Daniel F. L. Opperman
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Mariëtte E. van der Watt
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
- School of Health Systems and Public HealthUniversity of Pretoria, HatfieldPretoria0028South Africa
| | - Anjo Theron
- Next Generation HealthCouncil for Scientific and Industrial ResearchPretoria0001South Africa
| | - Meta Leshabane
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Shanté da Rocha
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Jonathan Turner
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Kathleen Garrabrant
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Ivett Piña
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Catherine Mills
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Patrick M. Woster
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Lyn‐Marié Birkholtz
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
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9
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Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs. Nat Commun 2022; 13:5992. [PMID: 36220877 PMCID: PMC9552147 DOI: 10.1038/s41467-022-33736-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/30/2022] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis is a major global cause of both mortality and financial burden mainly in low and middle-income countries. Given the significant and ongoing rise of drug-resistant strains of Mycobacterium tuberculosis within the clinical setting, there is an urgent need for the development of new, safe and effective treatments. Here the development of a drug-like series based on a fused dihydropyrrolidino-pyrimidine scaffold is described. The series has been developed against M. tuberculosis lysyl-tRNA synthetase (LysRS) and cellular studies support this mechanism of action. DDD02049209, the lead compound, is efficacious in mouse models of acute and chronic tuberculosis and has suitable physicochemical, pharmacokinetic properties and an in vitro safety profile that supports further development. Importantly, preliminary analysis using clinical resistant strains shows no pre-existing clinical resistance towards this scaffold.
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10
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Reader J, van der Watt ME, Birkholtz LM. Streamlined and Robust Stage-Specific Profiling of Gametocytocidal Compounds Against Plasmodium falciparum. Front Cell Infect Microbiol 2022; 12:926460. [PMID: 35846744 PMCID: PMC9282888 DOI: 10.3389/fcimb.2022.926460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 12/29/2022] Open
Abstract
Malaria elimination is dependent on the ability to target both the pathogenic and transmissible stages of the human malaria parasite, Plasmodium falciparum. These forms of the parasite are differentiated by unique developmental stages, each with their own biological mechanisms and processes. These individual stages therefore also respond differently to inhibitory compounds, and this complicates the discovery of multistage active antimalarial agents. The search for compounds with transmission-blocking activity has focused on screening for activity on mature gametocytes, with only limited descriptions available for the activity of such compounds on immature stage gametocytes. This therefore poses a gap in the profiling of antimalarial agents for pan-reactive, multistage activity to antimalarial leads. Here, we optimized an effective and robust strategy for the simple and cost-effective description of the stage-specific action of gametocytocidal antimalarial compounds.
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Affiliation(s)
- Janette Reader
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Mariette E. van der Watt
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- *Correspondence: Lyn-Marié Birkholtz,
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11
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Bansal M, Upadhyay C, Poonam, Kumar S, Rathi B. Phthalimide analogs for antimalarial drug discovery. RSC Med Chem 2021; 12:1854-1867. [PMID: 34825184 DOI: 10.1039/d1md00244a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/03/2021] [Indexed: 11/21/2022] Open
Abstract
Malaria remains one of the world's most life-threatening diseases and, thus, it is a major public health concern all around the world. The disease can become devastating if not treated with proper medication in a timely manner. Currently, the number of viable treatment therapies is in continuous decline due to compromised effectiveness, probably owing to the complex life cycle of Plasmodium falciparum. The factors responsible for the unclear status of malaria eradication programmes include ever-developing parasite resistance to the most effective treatments used on the frontline (i.e., artemisinin derivatives) and the paucity of new effective therapeutics. Due to these circumstances, the development of novel effective drug candidates with unique modes of action is essential for overcoming the listed obstacles. As such, the discovery of novel chemical compounds based on validated pharmacophores remains an unmet need in the field of medicinal chemistry. In this area, functionalized phthalimide (Pht) analogs have been explored as potential candidates against various diseases, including malaria. Pht presents a promising bioactive scaffold that can be easily functionalized and thus utilized as a starting point for the development of new antimalarial candidates suitable for preclinical and clinical studies. In this short review, we highlight a wide range of Pht analogs that have been investigated for their activity against various strains of Plasmodium falciparum.
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Affiliation(s)
- Meenakshi Bansal
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India .,Department of Chemistry, Deenbandhu Chhotu Ram University of Science and Technology Murthal Sonepat-131039 Haryana India
| | - Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Sumit Kumar
- Department of Chemistry, Deenbandhu Chhotu Ram University of Science and Technology Murthal Sonepat-131039 Haryana India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India
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12
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Niemand J, van Biljon R, van der Watt M, van Heerden A, Reader J, van Wyk R, Orchard L, Chibale K, Llinás M, Birkholtz LM. Chemogenomic Fingerprints Associated with Stage-Specific Gametocytocidal Compound Action against Human Malaria Parasites. ACS Infect Dis 2021; 7:2904-2916. [PMID: 34569223 DOI: 10.1021/acsinfecdis.1c00373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kinase-focused inhibitors previously revealed compounds with differential activity against different stages of Plasmodium falciparum gametocytes. MMV666810, a 2-aminopyrazine, is more active on late-stage gametocytes, while a pyrazolopyridine, MMV674850, preferentially targets early-stage gametocytes. Here, we probe the biological mechanisms underpinning this differential stage-specific killing using in-depth transcriptome fingerprinting. Compound-specific chemogenomic profiles were observed with MMV674850 treatment associated with biological processes shared between asexual blood stage parasites and early-stage gametocytes but not late-stage gametocytes. MMV666810 has a distinct profile with clustered gene sets associated primarily with late-stage gametocyte development, including Ca2+-dependent protein kinases (CDPK1 and 5) and serine/threonine protein kinases (FIKK). Chemogenomic profiling therefore highlights essential processes in late-stage gametocytes, on a transcriptional level. This information is important to prioritize compounds that preferentially compromise late-stage gametocytes for further development as transmission-blocking antimalarials.
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Affiliation(s)
- Jandeli Niemand
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Riëtte van Biljon
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Mariëtte van der Watt
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Ashleigh van Heerden
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Roelof van Wyk
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Lindsey Orchard
- Department of Biochemistry & Molecular Biology and the Huck Centre for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African Medical Research Council, Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and the Huck Centre for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
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13
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Forte B, Ottilie S, Plater A, Campo B, Dechering KJ, Gamo FJ, Goldberg DE, Istvan ES, Lee M, Lukens AK, McNamara CW, Niles JC, Okombo J, Pasaje CFA, Siegel MG, Wirth D, Wyllie S, Fidock DA, Baragaña B, Winzeler EA, Gilbert IH. Prioritization of Molecular Targets for Antimalarial Drug Discovery. ACS Infect Dis 2021; 7:2764-2776. [PMID: 34523908 PMCID: PMC8608365 DOI: 10.1021/acsinfecdis.1c00322] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
There is a shift
in antimalarial drug discovery from phenotypic
screening toward target-based approaches, as more potential drug targets
are being validated in Plasmodium species. Given
the high attrition rate and high cost of drug discovery, it is important
to select the targets most likely to deliver progressible drug candidates.
In this paper, we describe the criteria that we consider important
for selecting targets for antimalarial drug discovery. We describe
the analysis of a number of drug targets in the Malaria Drug Accelerator
(MalDA) pipeline, which has allowed us to prioritize targets that
are ready to enter the drug discovery process. This selection process
has also highlighted where additional data are required to inform
target progression or deprioritization of other targets. Finally,
we comment on how additional drug targets may be identified.
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Affiliation(s)
- Barbara Forte
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Andrew Plater
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | | | - Daniel E. Goldberg
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Eva S. Istvan
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Marcus Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Amanda K. Lukens
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Case W. McNamara
- Calibr, a Division of The Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge Massachusetts 02139-4307, United States
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Charisse Flerida A. Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge Massachusetts 02139-4307, United States
| | | | - Dyann Wirth
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Beatriz Baragaña
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Ian H. Gilbert
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, United Kingdom
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14
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van Heerden A, van Wyk R, Birkholtz LM. Machine Learning Uses Chemo-Transcriptomic Profiles to Stratify Antimalarial Compounds With Similar Mode of Action. Front Cell Infect Microbiol 2021; 11:688256. [PMID: 34268139 PMCID: PMC8277430 DOI: 10.3389/fcimb.2021.688256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/04/2021] [Indexed: 11/26/2022] Open
Abstract
The rapid development of antimalarial resistance motivates the continued search for novel compounds with a mode of action (MoA) different to current antimalarials. Phenotypic screening has delivered thousands of promising hit compounds without prior knowledge of the compounds’ exact target or MoA. Whilst the latter is not initially required to progress a compound in a medicinal chemistry program, identifying the MoA early can accelerate hit prioritization, hit-to-lead optimization and preclinical combination studies in malaria research. The effects of drug treatment on a cell can be observed on systems level in changes in the transcriptome, proteome and metabolome. Machine learning (ML) algorithms are powerful tools able to deconvolute such complex chemically-induced transcriptional signatures to identify pathways on which a compound act and in this manner provide an indication of the MoA of a compound. In this study, we assessed different ML approaches for their ability to stratify antimalarial compounds based on varied chemically-induced transcriptional responses. We developed a rational gene selection approach that could identify predictive features for MoA to train and generate ML models. The best performing model could stratify compounds with similar MoA with a classification accuracy of 76.6 ± 6.4%. Moreover, only a limited set of 50 biomarkers was required to stratify compounds with similar MoA and define chemo-transcriptomic fingerprints for each compound. These fingerprints were unique for each compound and compounds with similar targets/MoA clustered together. The ML model was specific and sensitive enough to group new compounds into MoAs associated with their predicted target and was robust enough to be extended to also generate chemo-transcriptomic fingerprints for additional life cycle stages like immature gametocytes. This work therefore contributes a new strategy to rapidly, specifically and sensitively indicate the MoA of compounds based on chemo-transcriptomic fingerprints and holds promise to accelerate antimalarial drug discovery programs.
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Affiliation(s)
- Ashleigh van Heerden
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.,University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Roelof van Wyk
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.,University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.,University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, South Africa
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15
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Rangel GW, Llinás M. Re-Envisioning Anti-Apicomplexan Parasite Drug Discovery Approaches. Front Cell Infect Microbiol 2021; 11:691121. [PMID: 34178727 PMCID: PMC8226314 DOI: 10.3389/fcimb.2021.691121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Parasites of the phylum Apicomplexa impact humans in nearly all parts of the world, causing diseases including to toxoplasmosis, cryptosporidiosis, babesiosis, and malaria. Apicomplexan parasites have complex life cycles comprised of one or more stages characterized by rapid replication and biomass amplification, which enables accelerated evolutionary adaptation to environmental changes, including to drug pressure. The emergence of drug resistant pathogens is a major looming and/or active threat for current frontline chemotherapies, especially for widely used antimalarial drugs. In fact, resistant parasites have been reported against all modern antimalarial drugs within 15 years of clinical introduction, including the current frontline artemisinin-based combination therapies. Chemotherapeutics are a major tool in the public health arsenal for combatting the onset and spread of apicomplexan diseases. All currently approved antimalarial drugs have been discovered either through chemical modification of natural products or through large-scale screening of chemical libraries for parasite death phenotypes, and so far, none have been developed through a gene-to-drug pipeline. However, the limited duration of efficacy of these drugs in the field underscores the need for new and innovative approaches to discover drugs that can counter rapid resistance evolution. This review details both historical and current antimalarial drug discovery approaches. We also highlight new strategies that may be employed to discover resistance-resistant drug targets and chemotherapies in order to circumvent the rapid evolution of resistance in apicomplexan parasites.
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Affiliation(s)
- Gabriel W. Rangel
- Department of Biochemistry and Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, United States
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
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16
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High-content approaches to anthelmintic drug screening. Trends Parasitol 2021; 37:780-789. [PMID: 34092518 DOI: 10.1016/j.pt.2021.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 11/23/2022]
Abstract
Most anthelmintics were discovered through in vivo screens using animal models of infection. Developing in vitro assays for parasitic worms presents several challenges. The lack of in vitro life cycle culture protocols requires harvesting worms from vertebrate hosts or vectors, limiting assay throughput. Once worms are removed from the host environment, established anthelmintics often show no obvious phenotype - raising concerns about the predictive value of many in vitro assays. However, with recent progress in understanding how anthelmintics subvert host-parasite interactions, and breakthroughs in high-content imaging and machine learning, in vitro assays have the potential to discern subtle cryptic parasite phenotypes. These may prove better endpoints than conventional in vitro viability assays.
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17
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Yang T, Ottilie S, Istvan ES, Godinez-Macias KP, Lukens AK, Baragaña B, Campo B, Walpole C, Niles JC, Chibale K, Dechering KJ, Llinás M, Lee MCS, Kato N, Wyllie S, McNamara CW, Gamo FJ, Burrows J, Fidock DA, Goldberg DE, Gilbert IH, Wirth DF, Winzeler EA. MalDA, Accelerating Malaria Drug Discovery. Trends Parasitol 2021; 37:493-507. [PMID: 33648890 PMCID: PMC8261838 DOI: 10.1016/j.pt.2021.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of new chemically and biologically validated targets, as well as future scientific directions.
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Affiliation(s)
- Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Eva S Istvan
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Karla P Godinez-Macias
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Beatriz Baragaña
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - Chris Walpole
- Structural Genomics Consortium, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Building 56-341, 77 Massachusetts Avenue, Cambridge MA 02139-4307, USA
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16082, USA
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nobutaka Kato
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Susan Wyllie
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Jeremy Burrows
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel E Goldberg
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Ian H Gilbert
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
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18
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Lawong A, Gahalawat S, Okombo J, Striepen J, Yeo T, Mok S, Deni I, Bridgford JL, Niederstrasser H, Zhou A, Posner B, Wittlin S, Gamo FJ, Crespo B, Churchyard A, Baum J, Mittal N, Winzeler E, Laleu B, Palmer MJ, Charman SA, Fidock DA, Ready JM, Phillips MA. Novel Antimalarial Tetrazoles and Amides Active against the Hemoglobin Degradation Pathway in Plasmodium falciparum. J Med Chem 2021; 64:2739-2761. [PMID: 33620219 DOI: 10.1021/acs.jmedchem.0c02022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Malaria control programs continue to be threatened by drug resistance. To identify new antimalarials, we conducted a phenotypic screen and identified a novel tetrazole-based series that shows fast-kill kinetics and a relatively low propensity to develop high-level resistance. Preliminary structure-activity relationships were established including identification of a subseries of related amides with antiplasmodial activity. Assaying parasites with resistance to antimalarials led us to test whether the series had a similar mechanism of action to chloroquine (CQ). Treatment of synchronized Plasmodium falciparum parasites with active analogues revealed a pattern of intracellular inhibition of hemozoin (Hz) formation reminiscent of CQ's action. Drug selections yielded only modest resistance that was associated with amplification of the multidrug resistance gene 1 (pfmdr1). Thus, we have identified a novel chemical series that targets the historically druggable heme polymerization pathway and that can form the basis of future optimization efforts to develop a new malaria treatment.
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Affiliation(s)
- Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jessica L Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Hanspeter Niederstrasser
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Anwu Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Benigno Crespo
- Medicines Development Campus, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Jake Baum
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Nimisha Mittal
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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19
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Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box. Nat Commun 2021; 12:269. [PMID: 33431834 PMCID: PMC7801607 DOI: 10.1038/s41467-020-20629-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022] Open
Abstract
Chemical matter is needed to target the divergent biology associated with the different life cycle stages of Plasmodium. Here, we report the parallel de novo screening of the Medicines for Malaria Venture (MMV) Pandemic Response Box against Plasmodium asexual and liver stage parasites, stage IV/V gametocytes, gametes, oocysts and as endectocides. Unique chemotypes were identified with both multistage activity or stage-specific activity, including structurally diverse gametocyte-targeted compounds with potent transmission-blocking activity, such as the JmjC inhibitor ML324 and the antitubercular clinical candidate SQ109. Mechanistic investigations prove that ML324 prevents histone demethylation, resulting in aberrant gene expression and death in gametocytes. Moreover, the selection of parasites resistant to SQ109 implicates the druggable V-type H+-ATPase for the reduced sensitivity. Our data therefore provides an expansive dataset of compounds that could be redirected for antimalarial development and also point towards proteins that can be targeted in multiple parasite life cycle stages. Here, Reader et al. screen the Medicines for Malaria Venture Pandemic Response Box in parallel against Plasmodiumasexual and liver stage parasites, stage IV/V gametocytes, gametes, oocysts and as endectocides. They identify two potent transmission-blocking drugs: a histone demethylase inhibitor ML324 and the antitubercular SQ109.
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20
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de Koning-Ward TF, Boddey JA, Fowkes FJI. Molecular approaches to Malaria 2020. Cell Microbiol 2020; 23:e13289. [PMID: 33197142 DOI: 10.1111/cmi.13289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022]
Abstract
Twenty years ago the Molecular Approaches to Malaria conference was conceived as a forum to present the very latest advances in malaria research and to consolidate and forge new collaborative links between international researchers. The 6th MAM conference, held in February 2020 in Australia, provided 5 days of stimulating scientific exchange and highlighted the incredible malaria research conducted globally that is providing the critical knowledge and cutting-edge technological tools needed to control and ultimately eliminate malaria.
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Affiliation(s)
| | - Justin A Boddey
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Freya J I Fowkes
- The Burnet Institute, Melbourne, Australia.,Department of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.,Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Australia
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21
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Sahu SK, Behera PK, Choudhury P, Panda S, Rout L. Strategy and Problems for Synthesis of Antimalaria Artemisinin (Qinghaosu). ChemistrySelect 2020. [DOI: 10.1002/slct.202002885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Santosh Kumar Sahu
- Department of Chemistry Berhampur University Bhanjabihar Ganjam Odisha 760007
| | | | | | - Subhalaxmi Panda
- Department of Chemistry Berhampur University Bhanjabihar Ganjam Odisha 760007
| | - Laxmidhar Rout
- Department of Chemistry Berhampur University Bhanjabihar Ganjam Odisha 760007
- Adjunct Faculty Department of Chemical Science IISER Berhampur Odisha
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22
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Moyo P, Mugumbate G, Eloff JN, Louw AI, Maharaj VJ, Birkholtz LM. Natural Products: A Potential Source of Malaria Transmission Blocking Drugs? Pharmaceuticals (Basel) 2020; 13:E251. [PMID: 32957668 PMCID: PMC7558993 DOI: 10.3390/ph13090251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The ability to block human-to-mosquito and mosquito-to-human transmission of Plasmodium parasites is fundamental to accomplish the ambitious goal of malaria elimination. The WHO currently recommends only primaquine as a transmission-blocking drug but its use is severely restricted by toxicity in some populations. New, safe and clinically effective transmission-blocking drugs therefore need to be discovered. While natural products have been extensively investigated for the development of chemotherapeutic antimalarial agents, their potential use as transmission-blocking drugs is comparatively poorly explored. Here, we provide a comprehensive summary of the activities of natural products (and their derivatives) of plant and microbial origins against sexual stages of Plasmodium parasites and the Anopheles mosquito vector. We identify the prevailing challenges and opportunities and suggest how these can be mitigated and/or exploited in an endeavor to expedite transmission-blocking drug discovery efforts from natural products.
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Affiliation(s)
- Phanankosi Moyo
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Private Bag, 7724 Chinhoyi, Zimbabwe;
| | - Jacobus N. Eloff
- Phytomedicine Programme, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Private Bag x04, Onderstepoort 0110 Pretoria, South Africa;
| | - Abraham I. Louw
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Vinesh J. Maharaj
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
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