1
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Giannangelo C, Challis MP, Siddiqui G, Edgar R, Malcolm TR, Webb CT, Drinkwater N, Vinh N, Macraild C, Counihan N, Duffy S, Wittlin S, Devine SM, Avery VM, De Koning-Ward T, Scammells P, McGowan S, Creek DJ. Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as an antimalarial strategy. eLife 2024; 13:RP92990. [PMID: 38976500 PMCID: PMC11230628 DOI: 10.7554/elife.92990] [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] [Indexed: 07/10/2024] Open
Abstract
New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum (PfA-M1) and Plasmodium vivax (PvA-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets PfA-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on PfA-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of PfA-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.
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Affiliation(s)
- Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew P Challis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Rebecca Edgar
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Tess R Malcolm
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Chaille T Webb
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Nyssa Drinkwater
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Natalie Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Christopher Macraild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Natalie Counihan
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Sandra Duffy
- Discovery Biology, Centre for Cellular Phenomics, Griffith University, Nathan, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Shane M Devine
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Vicky M Avery
- Discovery Biology, Centre for Cellular Phenomics, Griffith University, Nathan, Australia
- School of Environment and Science, Griffith University, Nathan, Australia
| | - Tania De Koning-Ward
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Peter Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Sheena McGowan
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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2
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Fraser M, Curtis B, Phillips P, Yates PA, Lam KS, Netzel O, van Dooren GG, Ingmundson A, Matuschewski K, McLeod MD, Maier AG. Harnessing cholesterol uptake of malaria parasites for therapeutic applications. EMBO Mol Med 2024; 16:1515-1532. [PMID: 38862600 DOI: 10.1038/s44321-024-00087-1] [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: 10/18/2023] [Revised: 05/14/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Parasites, such as the malaria parasite P. falciparum, are critically dependent on host nutrients. Interference with nutrient uptake can lead to parasite death and, therefore, serve as a successful treatment strategy. P. falciparum parasites cannot synthesise cholesterol, and instead source this lipid from the host. Here, we tested whether cholesterol uptake pathways could be 'hijacked' for optimal drug delivery to the intracellular parasite. We found that fluorescent cholesterol analogues were delivered from the extracellular environment to the intracellular parasite. We investigated the uptake and inhibitory effects of conjugate compounds, where proven antimalarial drugs (primaquine and artesunate) were attached to steroids that mimic the structure of cholesterol. These conjugated antimalarial drugs improved the inhibitory effects against multiple parasite lifecycle stages, multiple parasite species, and drug-resistant parasites, whilst also lowering the toxicity to human host cells. Steroids with introduced peroxides also displayed antimalarial activity. These results provide a proof-of-concept that cholesterol mimics can be developed as a drug delivery system against apicomplexan parasites with the potential to improve drug efficacy, increase therapeutic index, and defeat drug resistance.
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Affiliation(s)
- Merryn Fraser
- Research School of Biology, The Australian National University, Canberra, 2601, Australia
- Department of Molecular Parasitology, Institute of Biology, Humboldt University, Berlin, 10115, Germany
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Blake Curtis
- Research School of Chemistry, The Australian National University, Canberra, 2601, Australia
- Metabolism of Microbial Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Patrick Phillips
- Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Patrick A Yates
- Research School of Chemistry, The Australian National University, Canberra, 2601, Australia
| | - Kwong Sum Lam
- Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Otto Netzel
- Department of Molecular Parasitology, Institute of Biology, Humboldt University, Berlin, 10115, Germany
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Alyssa Ingmundson
- Department of Molecular Parasitology, Institute of Biology, Humboldt University, Berlin, 10115, Germany
| | - Kai Matuschewski
- Department of Molecular Parasitology, Institute of Biology, Humboldt University, Berlin, 10115, Germany
| | - Malcolm D McLeod
- Research School of Chemistry, The Australian National University, Canberra, 2601, Australia.
| | - Alexander G Maier
- Research School of Biology, The Australian National University, Canberra, 2601, Australia.
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3
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Mogire RM, Miruka SA, Juma DW, McNamara CW, Andagalu B, Burrows JN, Chenu E, Duffy J, Ogutu BR, Akala HM. Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum. J Cheminform 2024; 16:63. [PMID: 38831351 PMCID: PMC11145868 DOI: 10.1186/s13321-024-00856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it is possible to predict compounds' activity and identify their potential targets across diverse organisms. In this study, we aimed to assess the antiplasmodial activity of compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library using in vitro and bioinformatics approaches. We assessed the in vitro antiplasmodial activity of the compounds using blood-stage and liver-stage drug susceptibility assays. We used protein sequences of known targets of the ReFRAME compounds with high antiplasmodial activity (EC50 < 10 uM) to conduct a protein-pairwise search to identify similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) using NCBI protein BLAST. We further assessed the association between the compounds' in vitro antiplasmodial activity and level of similarity between their known and predicted P. falciparum target proteins using simple linear regression analyses. BLAST analyses revealed 735 P. falciparum proteins that were similar to the 226 known protein targets associated with the ReFRAME compounds. Antiplasmodial activity of the compounds was positively associated with the degree of similarity between the compounds' known targets and predicted P. falciparum protein targets (percentage identity, E value, and bit score), the number of the predicted P. falciparum targets, and their respective mutagenesis index and fitness scores (R2 between 0.066 and 0.92, P < 0.05). Compounds predicted to target essential P. falciparum proteins or those with a druggability index of 1 showed the highest antiplasmodial activity.
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Affiliation(s)
- Reagan M Mogire
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
| | - Silviane A Miruka
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Dennis W Juma
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicine, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Andagalu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
| | | | - Elodie Chenu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Bernhards R Ogutu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Hoseah M Akala
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya.
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4
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McLellan JL, Morales-Hernandez B, Saeger S, Hanson KK. A high content imaging assay for identification of specific inhibitors of native Plasmodium liver stage protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596519. [PMID: 38854116 PMCID: PMC11160711 DOI: 10.1101/2024.05.29.596519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Plasmodium parasite resistance to antimalarial drugs is a serious threat to public health in malaria-endemic areas. Compounds that target core cellular processes like translation are highly desirable, as they should be multistage actives, capable of killing parasites in the liver and blood, regardless of molecular target or mechanism. Assays that can identify these compounds are thus needed. Recently, specific quantification of native Plasmodium berghei liver stage protein synthesis as well as that of the hepatoma cells supporting parasite growth, was achieved via automated confocal feedback microscopy of the o-propargyl puromycin (OPP)-labeled nascent proteome, but this imaging modality is limited in throughput. Here, we developed and validated a miniaturized high content imaging (HCI) version of the OPP assay that increases throughput, before deploying this approach to screen the Pathogen Box. We identified only two hits, both of which are parasite-specific quinoline-4-carboxamides, and analogues of the clinical candidate and known inhibitor of blood and liver stage protein synthesis, DDD107498/cabamiquine. We further show that these compounds have strikingly distinct relationships between their antiplasmodial and translation inhibition efficacies. These results demonstrate the utility and reliability of the P. berghei liver stage OPP HCI assay for specific, single-well quantification of Plasmodium and human protein synthesis in the native cellular context, allowing identification of selective Plasmodium translation inhibitors with the highest potential for multistage activity.
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Affiliation(s)
- James L. McLellan
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Beatriz Morales-Hernandez
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Sarah Saeger
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K. Hanson
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
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5
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Sharma M, Pandey V, Poli G, Tuccinardi T, Lolli ML, Vyas VK. A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 1: triazolopyrimidine, isoxazolopyrimidine and pyrrole-based (DSM) compounds. Bioorg Chem 2024; 146:107249. [PMID: 38493638 DOI: 10.1016/j.bioorg.2024.107249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/10/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
One of the deadliest infectious diseases, malaria, still has a significant impact on global morbidity and mortality. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in de novo pyrimidine nucleotide biosynthesis and has been clinically validated as an innovative and promising target for the development of novel targeted antimalarial drugs. PfDHODH inhibitors have the potential to significantly slow down parasite growth at the blood and liver stages. Several PfDHODH inhibitors based on various scaffolds have been explored over the past two decades. Among them, triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based derivatives known as DSM compounds showed tremendous potential as novel antimalarial agents, and one of the triazolopyrimidine-based compounds (DSM265) was able to reach phase IIa clinical trials. DSM compounds were synthesized as PfDHODH inhibitors with various substitutions based on structure-guided medicinal chemistry approaches and further optimised as well. For the first time, this review provides an overview of all the synthetic approaches used for the synthesis, alternative synthetic routes, and novel strategies involving various catalysts and chemical reagents that have been used to synthesize DSM compounds. We have also summarized SAR study of all these PfDHODH inhibitors. In an attempt to assist readers, scientists, and researchers involved in the development of new PfDHODH inhibitors as antimalarials, this review provides accessibility of all synthetic techniques and SAR studies of the most promising triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based PfDHODH inhibitors.
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Affiliation(s)
- Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, India
| | - Vinita Pandey
- MIT College of Pharmacy, Ramganga Vihar, Phase-II, Moradabad, UP-244001, India
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Marco L Lolli
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 - Turin, Italy
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, India.
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6
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Matsuura Y, Fuse S. Rapid in situ generation of 2-(halomethyl)-5-phenylfuran and nucleophilic addition in a microflow reactor. Org Biomol Chem 2024; 22:3448-3452. [PMID: 38595317 DOI: 10.1039/d4ob00358f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
2,5-Disubstituted furans are frequently found in pharmaceuticals and bioactive natural products. Nucleophilic substitution reactions on the carbon atom adjacent to the furan ring are useful for producing various furan derivatives. However, the formation of 5-substituted 2-halomethylfuran and the subsequent nucleophilic substitution reactions are often limited by severe undesired reactions caused by the highly reactive halomethylfurans. This paper reports the successful rapid synthesis of various 2,5-disubstituted furans using microflow technology, which suppresses undesired reactions including dimerization and ring opening of the furans. We observed that Brønsted acids had a significant effect on the nucleophilic substitution reaction and the use of HBr and HI gave the best results. A plausible mechanism of the Brønsted acid-mediated nucleophilic substitutions in the developed approach was proposed.
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Affiliation(s)
- Yuma Matsuura
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Shinichiro Fuse
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan.
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7
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Creek D, Giannangelo C, Challis M, Siddiqui G, Edgar R, Malcolm T, Webb C, Drinkwater N, Vinh N, MacRaild C, Counihan N, Duffy S, Wittlin S, Devine S, Avery V, de Koning-Ward T, Scammells P, McGowan S. Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as an antimalarial strategy. RESEARCH SQUARE 2024:rs.3.rs-3251230. [PMID: 38746424 PMCID: PMC11092810 DOI: 10.21203/rs.3.rs-3251230/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum ( Pf A-M1) and Plasmodium vivax ( Pv A-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets Pf A-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on Pf A-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of Pf A-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.
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8
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Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
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Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
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9
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Nguyen W, Boulet C, Dans MG, Loi K, Jarman KE, Watson GM, Tham WH, Fairhurst KJ, Yeo T, Fidock DA, Wittlin S, Chowdury M, de Koning-Ward TF, Chen G, Yan D, Charman SA, Baud D, Brand S, Jackson PF, Cowman AF, Gilson PR, Sleebs BE. Activity refinement of aryl amino acetamides that target the P. falciparum STAR-related lipid transfer 1 protein. Eur J Med Chem 2024; 270:116354. [PMID: 38554474 DOI: 10.1016/j.ejmech.2024.116354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/01/2024]
Abstract
Malaria is a devastating disease that causes significant morbidity worldwide. The development of new antimalarial chemotypes is urgently needed because of the emergence of resistance to frontline therapies. Independent phenotypic screening campaigns against the Plasmodium asexual parasite, including our own, identified the aryl amino acetamide hit scaffold. In a prior study, we identified the STAR-related lipid transfer protein (PfSTART1) as the molecular target of this antimalarial chemotype. In this study, we combined structural elements from the different aryl acetamide hit subtypes and explored the structure-activity relationship. It was shown that the inclusion of an endocyclic nitrogen, to generate the tool compound WJM-715, improved aqueous solubility and modestly improved metabolic stability in rat hepatocytes. Metabolic stability in human liver microsomes remains a challenge for future development of the aryl acetamide class, which was underscored by modest systemic exposure and a short half-life in mice. The optimized aryl acetamide analogs were cross resistant to parasites with mutations in PfSTART1, but not to other drug-resistant mutations, and showed potent binding to recombinant PfSTART1 by biophysical analysis, further supporting PfSTART1 as the likely molecular target. The optimized aryl acetamide analogue, WJM-715 will be a useful tool for further investigating the druggability of PfSTART1 across the lifecycle of the malaria parasite.
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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
| | - 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
| | - Gabrielle M Watson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University, Irving Medical Center, New York, 10032, NY, USA
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University, Irving Medical Center, New York, 10032, NY, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University, Irving Medical Center, New York, 10032, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University, Irving Medical Center, New York, 10032, NY, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwi, Switzerland; University of Basel, 4003, Basel, Switzerland
| | - 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
| | - Gong Chen
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Dandan Yan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Susan A Charman
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Delphine Baud
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Paul F Jackson
- Global Public Health, Janssen R&D LLC, La Jolla, 92121, USA
| | - 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
| | - Paul R Gilson
- Burnet Institute, Melbourne, Victoria, 3004, 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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10
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Lindblom JR, Zhang X, Lehane AM. A pH Fingerprint Assay to Identify Inhibitors of Multiple Validated and Potential Antimalarial Drug Targets. ACS Infect Dis 2024; 10:1185-1200. [PMID: 38499199 PMCID: PMC11019546 DOI: 10.1021/acsinfecdis.3c00588] [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: 10/31/2023] [Revised: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
New drugs with novel modes of action are needed to safeguard malaria treatment. In recent years, millions of compounds have been tested for their ability to inhibit the growth of asexual blood-stage Plasmodium falciparum parasites, resulting in the identification of thousands of compounds with antiplasmodial activity. Determining the mechanisms of action of antiplasmodial compounds informs their further development, but remains challenging. A relatively high proportion of compounds identified as killing asexual blood-stage parasites show evidence of targeting the parasite's plasma membrane Na+-extruding, H+-importing pump, PfATP4. Inhibitors of PfATP4 give rise to characteristic changes in the parasite's internal [Na+] and pH. Here, we designed a "pH fingerprint" assay that robustly identifies PfATP4 inhibitors while simultaneously allowing the detection of (and discrimination between) inhibitors of the lactate:H+ transporter PfFNT, which is a validated antimalarial drug target, and the V-type H+ ATPase, which was suggested as a possible target of the clinical candidate ZY19489. In our pH fingerprint assays and subsequent secondary assays, ZY19489 did not show evidence for the inhibition of pH regulation by the V-type H+ ATPase, suggesting that it has a different mode of action in the parasite. The pH fingerprint assay also has the potential to identify protonophores, inhibitors of the acid-loading Cl- transporter(s) (for which the molecular identity(ies) remain elusive), and compounds that act through inhibition of either the glucose transporter PfHT or glycolysis. The pH fingerprint assay therefore provides an efficient starting point to match a proportion of antiplasmodial compounds with their mechanisms of action.
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Affiliation(s)
| | | | - Adele M. Lehane
- Research School of Biology, Australian National University, Canberra, Australian Capital
Territory 2600, Australia
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11
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Alves-Rosa MF, Tayler NM, Dorta D, Coronado LM, Spadafora C. P. falciparum Invasion and Erythrocyte Aging. Cells 2024; 13:334. [PMID: 38391947 PMCID: PMC10887143 DOI: 10.3390/cells13040334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Plasmodium parasites need to find red blood cells (RBCs) that, on the one hand, expose receptors for the pathogen ligands and, on the other hand, maintain the right geometry to facilitate merozoite attachment and entry into the red blood cell. Both characteristics change with the maturation of erythrocytes. Some Plasmodia prefer younger vs. older erythrocytes. How does the life evolution of the RBC affect the invasion of the parasite? What happens when the RBC ages? In this review, we present what is known up until now.
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Affiliation(s)
| | | | | | | | - Carmenza Spadafora
- Center of Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicio de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City 0843-01103, Panama; (M.F.A.-R.); (N.M.T.); (D.D.); (L.M.C.)
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12
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Le Berre M, Tubiana T, Reuterswärd Waldner P, Lazar N, Li de la Sierra I, Santos JM, Llinás M, Nessler S. Structural characterization of the ACDC domain from ApiAP2 proteins of the malaria parasite. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579679. [PMID: 38370614 PMCID: PMC10871335 DOI: 10.1101/2024.02.09.579679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The Apicomplexan AP2 (ApiAP2) proteins are the best characterized family of DNA-binding proteins in the malaria parasite. Apart from the AP2 DNA-binding domain, there is little sequence similarity between ApiAP2 proteins and no other functional domains have been extensively characterized. One protein domain, which is present in a subset of the ApiAP2 proteins, is the conserved AP2-coincident domain mostly at the C-terminus (ACDC domain). Here we solved for the first time the crystal structure of the ACDC domain from two distinct Plasmodium falciparum ApiAP2 proteins and one orthologue from P. vivax , revealing a non-canonical four-helix bundle. Despite little sequence conservation between the ACDC domains from the two proteins, the structures are remarkably similar and do not resemble that of any other known protein domains. Due to their unique protein architecture and lack of homologues in the human genome, we performed in silico docking calculations against a library of known antimalarial compounds and we identified a small molecule that can potentially bind to any Apicomplexan ACDC domain within a pocket highly conserved amongst ApiAP2 proteins. Inhibitors based on this compound would disrupt the function of the ACDC domain and thus of the ApiAP2 proteins containing it, providing a new therapeutic window for targeting the malaria parasite and other Apicomplexans.
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13
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Berhe H, Kumar Cinthakunta Sridhar M, Zerihun M, Qvit N. The Potential Use of Peptides in the Fight against Chagas Disease and Leishmaniasis. Pharmaceutics 2024; 16:227. [PMID: 38399281 PMCID: PMC10892537 DOI: 10.3390/pharmaceutics16020227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Chagas disease and leishmaniasis are both neglected tropical diseases that affect millions of people around the world. Leishmaniasis is currently the second most widespread vector-borne parasitic disease after malaria. The World Health Organization records approximately 0.7-1 million newly diagnosed leishmaniasis cases each year, resulting in approximately 20,000-30,000 deaths. Also, 25 million people worldwide are at risk of Chagas disease and an estimated 6 million people are infected with Trypanosoma cruzi. Pentavalent antimonials, amphotericin B, miltefosine, paromomycin, and pentamidine are currently used to treat leishmaniasis. Also, nifurtimox and benznidazole are two drugs currently used to treat Chagas disease. These drugs are associated with toxicity problems such as nephrotoxicity and cardiotoxicity, in addition to resistance problems. As a result, the discovery of novel therapeutic agents has emerged as a top priority and a promising alternative. Overall, there is a need for new and effective treatments for Chagas disease and leishmaniasis, as the current drugs have significant limitations. Peptide-based drugs are attractive due to their high selectiveness, effectiveness, low toxicity, and ease of production. This paper reviews the potential use of peptides in the treatment of Chagas disease and leishmaniasis. Several studies have demonstrated that peptides are effective against Chagas disease and leishmaniasis, suggesting their use in drug therapy for these diseases. Overall, peptides have the potential to be effective therapeutic agents against Chagas disease and leishmaniasis, but more research is needed to fully investigate their potential.
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Affiliation(s)
| | | | | | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed 1311502, Israel; (H.B.); (M.K.C.S.); (M.Z.)
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14
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Schäfer TM, Pessanha de Carvalho L, Inoue J, Kreidenweiss A, Held J. The problem of antimalarial resistance and its implications for drug discovery. Expert Opin Drug Discov 2024; 19:209-224. [PMID: 38108082 DOI: 10.1080/17460441.2023.2284820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
INTRODUCTION Malaria remains a devastating infectious disease with hundreds of thousands of casualties each year. Antimalarial drug resistance has been a threat to malaria control and elimination for many decades and is still of concern today. Despite the continued effectiveness of current first-line treatments, namely artemisinin-based combination therapies, the emergence of drug-resistant parasites in Southeast Asia and even more alarmingly the occurrence of resistance mutations in Africa is of great concern and requires immediate attention. AREAS COVERED A comprehensive overview of the mechanisms underlying the acquisition of drug resistance in Plasmodium falciparum is given. Understanding these processes provides valuable insights that can be harnessed for the development and selection of novel antimalarials with reduced resistance potential. Additionally, strategies to mitigate resistance to antimalarial compounds on the short term by using approved drugs are discussed. EXPERT OPINION While employing strategies that utilize already approved drugs may offer a prompt and cost-effective approach to counter antimalarial drug resistance, it is crucial to recognize that only continuous efforts into the development of novel antimalarial drugs can ensure the successful treatment of malaria in the future. Incorporating resistance propensity assessment during this developmental process will increase the likelihood of effective and enduring malaria treatments.
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Affiliation(s)
| | | | - Juliana Inoue
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research (DZIF), Tübingen, Germany
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15
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [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: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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16
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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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17
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Morales-Luna L, Vázquez-Bautista M, Martínez-Rosas V, Rojas-Alarcón MA, Ortega-Cuellar D, González-Valdez A, Pérez de la Cruz V, Arreguin-Espinosa R, Rodríguez-Bustamante E, Rodríguez-Flores E, Hernández-Ochoa B, Gómez-Manzo S. Fused Enzyme Glucose-6-Phosphate Dehydrogenase::6-Phosphogluconolactonase (G6PD::6PGL) as a Potential Drug Target in Giardia lamblia, Trichomonas vaginalis, and Plasmodium falciparum. Microorganisms 2024; 12:112. [PMID: 38257939 PMCID: PMC10819308 DOI: 10.3390/microorganisms12010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Several microaerophilic parasites such as Giardia lamblia, Trichomonas vaginalis, and Plasmodium falciparum are major disease-causing organisms and are responsible for spreading infections worldwide. Despite significant progress made in understanding the metabolism and molecular biology of microaerophilic parasites, chemotherapeutic treatment to control it has seen limited progress. A current proposed strategy for drug discovery against parasitic diseases is the identification of essential key enzymes of metabolic pathways associated with the parasite's survival. In these organisms, glucose-6-phosphate dehydrogenase::6-phosphogluconolactonase (G6PD:: 6PGL), the first enzyme of the pentose phosphate pathway (PPP), is essential for its metabolism. Since G6PD:: 6PGL provides substrates for nucleotides synthesis and NADPH as a source of reducing equivalents, it could be considered an anti-parasite drug target. This review analyzes the anaerobic energy metabolism of G. lamblia, T. vaginalis, and P. falciparum, with a focus on glucose metabolism through the pentose phosphate pathway and the significance of the fused G6PD:: 6PGL enzyme as a therapeutic target in the search for new drugs.
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Affiliation(s)
- Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Montserrat Vázquez-Bautista
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Miriam Abigail Rojas-Alarcón
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Verónica Pérez de la Cruz
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico;
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
| | - Eduardo Rodríguez-Bustamante
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey 64849, Mexico
| | - Eden Rodríguez-Flores
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City 06720, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
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18
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Lisauskaitė M, Nixon GL, Woodley CM, Berry NG, Coninckx A, Qie LC, Leung SC, Taramelli D, Basilico N, Parapini S, Ward SA, Vadas O, Soldati-Favre D, Hong WD, O'Neill PM. Design, synthesis and modelling of photoreactive chemical probes for investigating target engagement of plasmepsin IX and X in Plasmodium falciparum. RSC Chem Biol 2024; 5:19-29. [PMID: 38179191 PMCID: PMC10763550 DOI: 10.1039/d3cb00109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/27/2023] [Indexed: 01/06/2024] Open
Abstract
The emergence of Plasmodium parasite resistance to current front-line antimalarial treatments poses a serious threat to global malaria control and highlights the necessity for the development of therapeutics with novel targets and mechanisms of action. Plasmepsins IX and X (PMIX/PMX) have been recognised as highly promising targets in Plasmodium due to their contribution to parasite's pathogenicity. Recent research has demonstrated that dual PMIX/PMX inhibition results in the impairment of multiple parasite's life cycle stages, which is an important feature in drug resistance prevention. Herein we report novel hydroxyethylamine photoaffinity labelling (PAL) probes, designed for PMIX/PMX target engagement and proteomics experiments in Plasmodium parasites. The prepared probes have both a photoreactive group (diazirine or benzophenone) for covalent attachment to target proteins, and a terminal alkyne handle allowing their use in bioorthogonal ligation. One of the synthesised benzophenone probes was shown to be highly promising as demonstrated by its outstanding antimalarial potency (IC50 = 15 nM versus D10 P. falciparum) and its inhibitory effect against PfPMX in an enzymatic assay. Molecular docking and molecular dynamics studies show that the inclusion of the benzophenone and alkyne handle does not alter the binding mode compared to the parent compound. The photoaffinity probe can be used in future chemical proteomics studies to allow hydroxyethylamine drug scaffold target identification and validation in Plasmodium. We expect our findings to act as a tool for future investigations on PMIX/PMX inhibition in antimalarial drug discovery.
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Affiliation(s)
| | - Gemma L Nixon
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | | | - Neil G Berry
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Andy Coninckx
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - L Charlie Qie
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Suet C Leung
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Donatella Taramelli
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DISFEB), Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Nicoletta Basilico
- Dipartimento di Scienze Biomediche, Chirurgiche e Odontoiatriche, Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Silvia Parapini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Stephen A Ward
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine Liverpool L3 5QA UK
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet CH-1211 Genève 4 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet CH-1211 Genève 4 Switzerland
| | - W David Hong
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
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19
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Chung Z, Lin J, Wirjanata G, Dziekan JM, El Sahili A, Preiser PR, Bozdech Z, Lescar J. Identification and structural validation of purine nucleoside phosphorylase from Plasmodium falciparum as a target of MMV000848. J Biol Chem 2024; 300:105586. [PMID: 38141766 PMCID: PMC10911062 DOI: 10.1016/j.jbc.2023.105586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/25/2023] Open
Abstract
About 247 million cases of malaria occurred in 2021 with Plasmodium falciparum accounting for the majority of 619,000 deaths. In the absence of a widely available vaccine, chemotherapy remains crucial to prevent, treat, and contain the disease. The efficacy of several drugs currently used in the clinic is likely to suffer from the emergence of resistant parasites. A global effort to identify lead compounds led to several initiatives such as the Medicine for Malaria Ventures (MMV), a repository of compounds showing promising efficacy in killing the parasite in cell-based assays. Here, we used mass spectrometry coupled with cellular thermal shift assay to identify putative protein targets of MMV000848, a compound with an in vitro EC50 of 0.5 μM against the parasite. Thermal shift assays showed a strong increase of P. falciparum purine nucleoside phosphorylase (PfPNP) melting temperature by up to 15 °C upon incubation with MMV000848. Binding and enzymatic assays returned a KD of 1.52 ± 0.495 μM and an IC50 value of 21.5 ± 2.36 μM. The inhibition is competitive with respect to the substrate, as confirmed by a cocrystal structure of PfPNP bound with MMV000848 at the active site, determined at 1.85 Å resolution. In contrast to transition states inhibitors, MMV000848 specifically inhibits the parasite enzyme but not the human ortholog. An isobologram analysis shows subadditivity with immucillin H and with quinine respectively, suggesting overlapping modes of action between these compounds. These results point to PfPNP as a promising antimalarial target and suggest avenues to improve inhibitor potency.
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Affiliation(s)
- Zara Chung
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jerzy M Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore.
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20
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Li Y, Cardoso-Silva J, Kelly JM, Delves MJ, Furnham N, Papageorgiou LG, Tsoka S. Optimisation-based modelling for explainable lead discovery in malaria. Artif Intell Med 2024; 147:102700. [PMID: 38184363 DOI: 10.1016/j.artmed.2023.102700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/17/2023] [Accepted: 10/29/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND The search for new antimalarial treatments is urgent due to growing resistance to existing therapies. The Open Source Malaria (OSM) project offers a promising starting point, having extensively screened various compounds for their effectiveness. Further analysis of the chemical space surrounding these compounds could provide the means for innovative drugs. METHODS We report an optimisation-based method for quantitative structure-activity relationship (QSAR) modelling that provides explainable modelling of ligand activity through a mathematical programming formulation. The methodology is based on piecewise regression principles and offers optimal detection of breakpoint features, efficient allocation of samples into distinct sub-groups based on breakpoint feature values, and insightful regression coefficients. Analysis of OSM antimalarial compounds yields interpretable results through rules generated by the model that reflect the contribution of individual fingerprint fragments in ligand activity prediction. Using knowledge of fragment prioritisation and screening of commercially available compound libraries, potential lead compounds for antimalarials are identified and evaluated experimentally via a Plasmodium falciparum asexual growth inhibition assay (PfGIA) and a human cell cytotoxicity assay. CONCLUSIONS Three compounds are identified as potential leads for antimalarials using the methodology described above. This work illustrates how explainable predictive models based on mathematical optimisation can pave the way towards more efficient fragment-based lead discovery as applied in malaria.
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Affiliation(s)
- Yutong Li
- Department of Informatics, King's College London, Bush House, London, WC2B 4BG, UK
| | - Jonathan Cardoso-Silva
- Data Science Institute, London School of Economics and Political Science, Houghton St, London, WC2A 2AE, UK
| | - John M Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Michael J Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Lazaros G Papageorgiou
- The Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
| | - Sophia Tsoka
- Department of Informatics, King's College London, Bush House, London, WC2B 4BG, UK.
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21
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Ong HW, de Silva C, Avalani K, Kwarcinski F, Mansfield CR, Chirgwin M, Truong A, Derbyshire ER, Zutshi R, Drewry DH. Characterization of 2,4-Dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. ACS Med Chem Lett 2023; 14:1774-1784. [PMID: 38116430 PMCID: PMC10726455 DOI: 10.1021/acsmedchemlett.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Plasmodium kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (1) as an inhibitor of five P. falciparum kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase were discovered. We identified common and divergent SAR trends across all five kinases, highlighting substituents in each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the P. falciparum blood stage. Eight submicromolar inhibitors were discovered, of which 37 demonstrated potent antiplasmodial activity (EC50 = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts toward novel antimalarials.
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Affiliation(s)
- Han Wee Ong
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chandi de Silva
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Krisha Avalani
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Frank Kwarcinski
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Christopher R. Mansfield
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| | - Michael Chirgwin
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Anna Truong
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Reena Zutshi
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - David H. Drewry
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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22
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Bosc N, Felix E, Gardner JMF, Mills J, Timmerman M, Asveld D, Rensen K, Mukherjee P, Das R, Chenu E, Besson D, Burrows JN, Duffy J, Laleu B, Guantai EM, Leach AR. MAIP: An Open-Source Tool to Enrich High-Throughput Screening Output and Identify Novel, Druglike Molecules with Antimalarial Activity. ACS Med Chem Lett 2023; 14:1733-1741. [PMID: 38116432 PMCID: PMC10726451 DOI: 10.1021/acsmedchemlett.3c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023] Open
Abstract
Efforts to tackle malaria must continue for a disease that threatens half of the global population. Parasite resistance to current therapies requires new chemotypes that are able to demonstrate effectiveness and safety. Previously, we developed a machine-learning-based approach to predict compound antimalarial activity, which was trained on the compound collections of several organizations. The resulting prediction platform, MAIP, was made freely available to the scientific community and offers a solution to prioritize molecules of interest in virtual screening and hit-to-lead optimization. Here, we experimentally validate MAIP and demonstrate how the approach was used in combination with a robust compound selection workflow and a recently introduced innovative high-throughput screening (HTS) cascade to select and purchase compounds from a public library for subsequent experimental screening. We observed a 12-fold enrichment compared with a randomly selected set of molecules, and the eight hits we ultimately selected exhibit good potency and absorption, distribution, metabolism, and excretion (ADME) profiles.
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Affiliation(s)
- Nicolas Bosc
- European
Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Eloy Felix
- European
Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - J. Mark F. Gardner
- AMG
Consultants Ltd, Discovery
Park House, Discovery Park, Sandwich, Kent CT13 9ND, United Kingdom
| | - James Mills
- Sandexis
Medicinal Chemistry Ltd, Innovation House, Discovery Park, Sandwich, Kent CT13 9FF, United Kingdom
| | - Martijn Timmerman
- Pivot
Park Screening Centre, Pivot Park (Frederick Banting Building), Kloosterstraat 9, 5349 AB Oss, The Netherlands
| | - Dennis Asveld
- Pivot
Park Screening Centre, Pivot Park (Frederick Banting Building), Kloosterstraat 9, 5349 AB Oss, The Netherlands
| | - Kim Rensen
- Pivot
Park Screening Centre, Pivot Park (Frederick Banting Building), Kloosterstraat 9, 5349 AB Oss, The Netherlands
| | - Partha Mukherjee
- TCG
Life Sciences, Bengal Intelligent Park Limited, Block EP & GP, Salt Lake Electronics
Complex, Sector V, Kolkata, West Bengal 700091, India
| | - Rishi Das
- TCG
Life Sciences, Bengal Intelligent Park Limited, Block EP & GP, Salt Lake Electronics
Complex, Sector V, Kolkata, West Bengal 700091, India
| | - Elodie Chenu
- Medicines
for Malaria Ventures, 1215 Geneva, Switzerland
| | | | | | - James Duffy
- Medicines
for Malaria Ventures, 1215 Geneva, Switzerland
| | - Benoît Laleu
- Medicines
for Malaria Ventures, 1215 Geneva, Switzerland
| | - Eric M. Guantai
- Department
of Pharmacy, Faculty of Health Sciences, University of Nairobi, 00202 Nairobi, Kenya
| | - Andrew R. Leach
- European
Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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23
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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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24
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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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25
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Tomaz KCP, Tavella TA, Borba JVB, Salazar-Alvarez LC, Levandoski JE, Mottin M, Sousa BKP, Moreira-Filho JT, Almeida VM, Clementino LC, Bourgard C, Massirer KB, Couñago RM, Andrade CH, Sunnerhagen P, Bilsland E, Cassiano GC, Costa FTM. Identification of potential inhibitors of casein kinase 2 alpha of Plasmodium falciparum with potent in vitro activity. Antimicrob Agents Chemother 2023; 67:e0058923. [PMID: 37819090 PMCID: PMC10649021 DOI: 10.1128/aac.00589-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/11/2023] [Indexed: 10/13/2023] Open
Abstract
Drug resistance to commercially available antimalarials is a major obstacle in malaria control and elimination, creating the need to find new antiparasitic compounds with novel mechanisms of action. The success of kinase inhibitors for oncological treatments has paved the way for the exploitation of protein kinases as drug targets in various diseases, including malaria. Casein kinases are ubiquitous serine/threonine kinases involved in a wide range of cellular processes such as mitotic checkpoint signaling, DNA damage response, and circadian rhythm. In Plasmodium, it is suggested that these protein kinases are essential for both asexual and sexual blood-stage parasites, reinforcing their potential as targets for multi-stage antimalarials. To identify new putative PfCK2α inhibitors, we utilized an in silico chemogenomic strategy involving virtual screening with docking simulations and quantitative structure-activity relationship predictions. Our investigation resulted in the discovery of a new quinazoline molecule (542), which exhibited potent activity against asexual blood stages and a high selectivity index (>100). Subsequently, we conducted chemical-genetic interaction analysis on yeasts with mutations in casein kinases. Our chemical-genetic interaction results are consistent with the hypothesis that 542 inhibits yeast Cka1, which has a hinge region with high similarity to PfCK2α. This finding is in agreement with our in silico results suggesting that 542 inhibits PfCK2α via hinge region interaction.
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Affiliation(s)
- Kaira C. P. Tomaz
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
| | - Tatyana A. Tavella
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
| | - Joyce V. B. Borba
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Luis C. Salazar-Alvarez
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
| | - João E. Levandoski
- Department of Materials and Bioprocesses Engineering, School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | - Melina Mottin
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Bruna K. P. Sousa
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - José T. Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Vitor M. Almeida
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética(CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Leandro C. Clementino
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
| | - Catarina Bourgard
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Katlin B. Massirer
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética(CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética(CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina H. Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás (UFG), Goiânia, Brazil
- Center for Research and Advancement of Fragments and Molecular Targets (CRAFT), University of São Paulo, São Paulo, Brazil
- Center for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elizabeth Bilsland
- Department of Structural and Functional Biology, Synthetic Biology Laboratory, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Gustavo C. Cassiano
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Fabio T. M. Costa
- Laboratory of Tropical Diseases (LDT), Institute of Biology, University of Campinas, Campinas, Brazil
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Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
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Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
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27
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Miljkovic M, Lozano S, Castellote I, de Cózar C, Villegas-Moreno AI, Gamallo P, Jimenez-Alfaro Martinez D, Fernández-Álvaro E, Ballell L, Garcia GA. Novel inhibitors that target bacterial virulence identified via HTS against intra-macrophage survival of Shigella flexneri. mSphere 2023; 8:e0015423. [PMID: 37565760 PMCID: PMC10597453 DOI: 10.1128/msphere.00154-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 08/12/2023] Open
Abstract
Shigella flexneri is a facultative intracellular pathogen that causes shigellosis, a human diarrheal disease characterized by the destruction of the colonic epithelium. Novel antimicrobial compounds to treat infections are urgently needed due to the proliferation of bacterial antibiotic resistance and lack of new effective antimicrobials in the market. Our approach to find compounds that block the Shigella virulence pathway has three potential advantages: (i) resistance development should be minimized due to the lack of growth selection pressure, (ii) no resistance due to environmental antibiotic exposure should be developed since the virulence pathways are not activated outside of host infection, and (iii) the normal intestinal microbiota, which do not have the targeted virulence pathways, should be unharmed. We chose to utilize two phenotypic assays, inhibition of Shigella survival in macrophages and Shigella growth inhibition (minimum inhibitory concentration), to interrogate the 1.7 M compound screening collection subset of the GlaxoSmithKline drug discovery chemical library. A number of secondary assays on the hit compounds resulting from the primary screens were conducted, which, in combination with chemical, structural, and physical property analyses, narrowed the final hit list to 44 promising compounds for further drug discovery efforts. The rapid development of antibiotic resistance is a critical problem that has the potential of returning the world to a "pre-antibiotic" type of environment, where millions of people will die from previously treatable infections. One relatively newer approach to minimize the selection pressures for the development of resistance is to target virulence pathways. This is anticipated to eliminate any resistance selection pressure in environmental exposure to virulence-targeted antibiotics and will have the added benefit of not affecting the non-virulent microbiome. This paper describes the development and application of a simple, reproducible, and sensitive assay to interrogate an extensive chemical library in high-throughput screening format for activity against the survival of Shigella flexneri 2457T-nl in THP-1 macrophages. The ability to screen very large numbers of compounds in a reasonable time frame (~1.7 M compounds in ~8 months) distinguishes this assay as a powerful tool in further exploring new compounds with intracellular effect on S. flexneri or other pathogens with similar pathways of pathogenesis. The assay utilizes a luciferase reporter which is extremely rapid, simple, relatively inexpensive, and sensitive and possesses a broad linear range. The assay also utilized THP-1 cells that resemble primary monocytes and macrophages in morphology and differentiation properties. THP-1 cells have advantages over human primary monocytes or macrophages because they are highly plastic and their homogeneous genetic background minimizes the degree of variability in the cell phenotype (1). The intracellular and virulence-targeted selectivity of our methodology, determined via secondary screening, is an enormous advantage. Our main interest focuses on hits that are targeting virulence, and the most promising compounds with adequate physicochemical and drug metabolism and pharmacokinetic (DMPK) properties will be progressed to a suitable in vivo shigellosis model to evaluate the therapeutic potential of this approach. Additionally, compounds that act via a host-directed mechanism could be a promising source for further research given that it would allow a whole new, specific, and controlled approach to the treatment of diseases caused by some pathogenic bacteria.
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Affiliation(s)
- Marija Miljkovic
- Department of Medical Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- GSK Global Health Unit, Madrid, Spain
| | | | | | | | | | | | | | | | | | - George A. Garcia
- Department of Medical Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
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28
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Tsebriy O, Khomiak A, Miguel-Blanco C, Sparkes PC, Gioli M, Santelli M, Whitley E, Gamo FJ, Delves MJ. Machine learning-based phenotypic imaging to characterise the targetable biology of Plasmodium falciparum male gametocytes for the development of transmission-blocking antimalarials. PLoS Pathog 2023; 19:e1011711. [PMID: 37801466 PMCID: PMC10584170 DOI: 10.1371/journal.ppat.1011711] [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: 05/08/2023] [Revised: 10/18/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Preventing parasite transmission from humans to mosquitoes is recognised to be critical for achieving elimination and eradication of malaria. Consequently developing new antimalarial drugs with transmission-blocking properties is a priority. Large screening campaigns have identified many new transmission-blocking molecules, however little is known about how they target the mosquito-transmissible Plasmodium falciparum stage V gametocytes, or how they affect their underlying cell biology. To respond to this knowledge gap, we have developed a machine learning image analysis pipeline to characterise and compare the cellular phenotypes generated by transmission-blocking molecules during male gametogenesis. Using this approach, we studied 40 molecules, categorising their activity based upon timing of action and visual effects on the organisation of tubulin and DNA within the cell. Our data both proposes new modes of action and corroborates existing modes of action of identified transmission-blocking molecules. Furthermore, the characterised molecules provide a new armoury of tool compounds to probe gametocyte cell biology and the generated imaging dataset provides a new reference for researchers to correlate molecular target or gene deletion to specific cellular phenotype. Our analysis pipeline is not optimised for a specific organism and could be applied to any fluorescence microscopy dataset containing cells delineated by bounding boxes, and so is potentially extendible to any disease model.
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Affiliation(s)
| | | | | | - Penny C. Sparkes
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | | | | | - Edgar Whitley
- Department of Management, London School of Economics and Political Science, London, United Kingdom
| | | | - Michael J. Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
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29
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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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30
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Li B, Lin M, Chen T, Wang L. FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction. Brief Bioinform 2023; 24:bbad398. [PMID: 37930026 DOI: 10.1093/bib/bbad398] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/25/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023] Open
Abstract
Artificial intelligence-based molecular property prediction plays a key role in molecular design such as bioactive molecules and functional materials. In this study, we propose a self-supervised pretraining deep learning (DL) framework, called functional group bidirectional encoder representations from transformers (FG-BERT), pertained based on ~1.45 million unlabeled drug-like molecules, to learn meaningful representation of molecules from function groups. The pretrained FG-BERT framework can be fine-tuned to predict molecular properties. Compared to state-of-the-art (SOTA) machine learning and DL methods, we demonstrate the high performance of FG-BERT in evaluating molecular properties in tasks involving physical chemistry, biophysics and physiology across 44 benchmark datasets. In addition, FG-BERT utilizes attention mechanisms to focus on FG features that are critical to the target properties, thereby providing excellent interpretability for downstream training tasks. Collectively, FG-BERT does not require any artificially crafted features as input and has excellent interpretability, providing an out-of-the-box framework for developing SOTA models for a variety of molecule (especially for drug) discovery tasks.
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Affiliation(s)
- Biaoshun Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Mujie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Tiegen Chen
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Room 109, Building C, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong, 528400, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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31
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Ling DB, Nguyen W, Looker O, Razook Z, McCann K, Barry AE, Scheurer C, Wittlin S, Famodimu MT, Delves MJ, Bullen HE, Crabb BS, Sleebs BE, Gilson PR. A Pyridyl-Furan Series Developed from the Open Global Health Library Block Red Blood Cell Invasion and Protein Trafficking in Plasmodium falciparum through Potential Inhibition of the Parasite's PI4KIIIB Enzyme. ACS Infect Dis 2023; 9:1695-1710. [PMID: 37639221 PMCID: PMC10496428 DOI: 10.1021/acsinfecdis.3c00138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 08/29/2023]
Abstract
With the resistance increasing to current antimalarial medicines, there is an urgent need to discover new drug targets and to develop new medicines against these targets. We therefore screened the Open Global Health Library of Merck KGaA, Darmstadt, Germany, of 250 compounds against the asexual blood stage of the deadliest malarial parasite Plasmodium falciparum, from which eight inhibitors with low micromolar potency were found. Due to its combined potencies against parasite growth and inhibition of red blood cell invasion, the pyridyl-furan compound OGHL250 was prioritized for further optimization. The potency of the series lead compound (WEHI-518) was improved 250-fold to low nanomolar levels against parasite blood-stage growth. Parasites selected for resistance to a related compound, MMV396797, were also resistant to WEHI-518 as well as KDU731, an inhibitor of the phosphatidylinositol kinase PfPI4KIIIB, suggesting that this kinase is the target of the pyridyl-furan series. Inhibition of PfPI4KIIIB blocks multiple stages of the parasite's life cycle and other potent inhibitors are currently under preclinical development. MMV396797-resistant parasites possess an E1316D mutation in PfPKI4IIIB that clusters with known resistance mutations of other inhibitors of the kinase. Building upon earlier studies that showed that PfPI4KIIIB inhibitors block the development of the invasive merozoite parasite stage, we show that members of the pyridyl-furan series also block invasion and/or the conversion of merozoites into ring-stage intracellular parasites through inhibition of protein secretion and export into red blood cells.
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Affiliation(s)
- Dawson B. Ling
- Burnet Institute,
Melbourne, Victoria3004, Australia
- Department of Microbiology and Immunology,
University of Melbourne, Melbourne, Victoria3010,
Australia
| | - William Nguyen
- The Walter and Eliza Hall Institute of
Medical Research, Melbourne, Victoria3052,
Australia
- Department of Medical Biology, The
University of Melbourne, Parkville, Victoria3010,
Australia
| | - Oliver Looker
- Burnet Institute,
Melbourne, Victoria3004, Australia
| | - Zahra Razook
- Burnet Institute,
Melbourne, Victoria3004, Australia
- School of Medicine and Institute for Mental and
Physical Health and Clinical Translation, Deakin University,
Waurn Ponds, Victoria3216, Australia
| | - Kirsty McCann
- Burnet Institute,
Melbourne, Victoria3004, Australia
- School of Medicine and Institute for Mental and
Physical Health and Clinical Translation, Deakin University,
Waurn Ponds, Victoria3216, Australia
| | - Alyssa E. Barry
- Burnet Institute,
Melbourne, Victoria3004, Australia
- School of Medicine and Institute for Mental and
Physical Health and Clinical Translation, Deakin University,
Waurn Ponds, Victoria3216, Australia
| | - Christian Scheurer
- Swiss Tropical and Public Health
Institute, Allschwil, 4123Switzerland
- University of Basel, Basel,
4001Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health
Institute, Allschwil, 4123Switzerland
- University of Basel, Basel,
4001Switzerland
| | - Mufuliat Toyin Famodimu
- Department of Infection Biology, Faculty of Infectious
Diseases, London School of Hygiene and Tropical Medicine, Kepel
Street, London, WC1E 7HT, U.K.
| | - Michael J Delves
- Department of Infection Biology, Faculty of Infectious
Diseases, London School of Hygiene and Tropical Medicine, Kepel
Street, London, WC1E 7HT, U.K.
| | - Hayley E. Bullen
- Burnet Institute,
Melbourne, Victoria3004, Australia
- Department of Microbiology and Immunology,
University of Melbourne, Melbourne, Victoria3010,
Australia
| | - Brendan S. Crabb
- Burnet Institute,
Melbourne, Victoria3004, Australia
- Department of Microbiology and Immunology,
University of Melbourne, Melbourne, Victoria3010,
Australia
- Department of Immunology and Pathology,
Monash University, Melbourne, Victoria3800,
Australia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of
Medical Research, Melbourne, Victoria3052,
Australia
- Department of Medical Biology, The
University of Melbourne, Parkville, Victoria3010,
Australia
| | - Paul R. Gilson
- Burnet Institute,
Melbourne, Victoria3004, Australia
- Department of Microbiology and Immunology,
University of Melbourne, Melbourne, Victoria3010,
Australia
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32
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da Silva G, Luz AFS, Duarte D, Fontinha D, Silva VLM, Almeida Paz FA, Madureira AM, Simões S, Prudêncio M, Nogueira F, Silva AMS, Moreira R. Facile Access to Structurally Diverse Antimalarial Indoles Using a One-Pot A 3 Coupling and Domino Cyclization Approach. ChemMedChem 2023; 18:e202300264. [PMID: 37392377 DOI: 10.1002/cmdc.202300264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/03/2023]
Abstract
A multistep and diversity-oriented synthetic route aiming at the A3 coupling/domino cyclization of o-ethynyl anilines, aldehydes and s-amines is described. The preparation of the corresponding precursors included a series of transformations, such as haloperoxidation and Sonogashira cross-coupling reactions, amine protection, desilylation and amine reduction. Some products of the multicomponent reaction underwent further detosylation and Suzuki coupling. The resulting library of structurally diverse compounds was evaluated against blood and liver stage malaria parasites, which revealed a promising lead with sub-micromolar activity against intra-erythrocytic forms of Plasmodium falciparum. The results from this hit-to-lead optimization are hereby reported for the first time.
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Affiliation(s)
- Gustavo da Silva
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - André F S Luz
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Denise Duarte
- GHTM - Global Health and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira n° 100, 1349-008, Lisboa, Portugal
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Vera L M Silva
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Filipe A Almeida Paz
- Department of Chemistry & CICECO -, Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana M Madureira
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Sandra Simões
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Fátima Nogueira
- GHTM - Global Health and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira n° 100, 1349-008, Lisboa, Portugal
| | - Artur M S Silva
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- GHTM - Global Health and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira n° 100, 1349-008, Lisboa, Portugal
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33
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Kovada V, Withers-Martinez C, Bobrovs R, Ce̅rule H, Liepins E, Grinberga S, Hackett F, Collins CR, Kreicberga A, Jiménez-Díaz MB, Angulo-Barturen I, Rasina D, Suna E, Jaudzems K, Blackman MJ, Jirgensons A. Macrocyclic Peptidomimetic Plasmepsin X Inhibitors with Potent In Vitro and In Vivo Antimalarial Activity. J Med Chem 2023; 66:10658-10680. [PMID: 37505188 PMCID: PMC10424242 DOI: 10.1021/acs.jmedchem.3c00812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 07/29/2023]
Abstract
The Plasmodium falciparum aspartic protease plasmepsin X (PMX) is essential for the egress of invasive merozoite forms of the parasite. PMX has therefore emerged as a new potential antimalarial target. Building on peptidic amino alcohols originating from a phenotypic screening hit, we have here developed a series of macrocyclic analogues as PMX inhibitors. Incorporation of an extended linker between the S1 phenyl group and S3 amide led to a lead compound that displayed a 10-fold improved PMX inhibitory potency and a 3-fold improved half-life in microsomal stability assays compared to the acyclic analogue. The lead compound was also the most potent of the new macrocyclic compounds in in vitro parasite growth inhibition. Inhibitor 7k cleared blood-stage P. falciparum in a dose-dependent manner when administered orally to infected humanized mice. Consequently, lead compound 7k represents a promising orally bioavailable molecule for further development as a PMX-targeting antimalarial drug.
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Affiliation(s)
- Vadims Kovada
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | - Raitis Bobrovs
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Hele̅na Ce̅rule
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Edgars Liepins
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | - Fiona Hackett
- Malaria
Biochemistry Laboratory, The Francis Crick
Institute, London NW1 1AT, United
Kingdom
| | - Christine R. Collins
- Malaria
Biochemistry Laboratory, The Francis Crick
Institute, London NW1 1AT, United
Kingdom
| | | | - María Belén Jiménez-Díaz
- The
Art of Discovery SL, Biscay Science and Technology Park, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Iñigo Angulo-Barturen
- The
Art of Discovery SL, Biscay Science and Technology Park, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Dace Rasina
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Edgars Suna
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | - Michael J. Blackman
- Malaria
Biochemistry Laboratory, The Francis Crick
Institute, London NW1 1AT, United
Kingdom
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
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34
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Rosenthal MR, Ng CL. High-content imaging as a tool to quantify and characterize malaria parasites. CELL REPORTS METHODS 2023; 3:100516. [PMID: 37533635 PMCID: PMC10391350 DOI: 10.1016/j.crmeth.2023.100516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 01/18/2023] [Accepted: 06/02/2023] [Indexed: 08/04/2023]
Abstract
In 2021, Plasmodium falciparum was responsible for 619,000 reported malaria-related deaths. Resistance has been detected to every clinically used antimalarial, urging the development of novel antimalarials with uncompromised mechanisms of actions. High-content imaging allows researchers to collect and quantify numerous phenotypic properties at the single-cell level, and machine learning-based approaches enable automated classification and clustering of cell populations. By combining these technologies, we developed a method capable of robustly differentiating and quantifying P. falciparum asexual blood stages. These phenotypic properties also allow for the quantification of changes in parasite morphology. Here, we demonstrate that our analysis can be used to quantify schizont nuclei, a phenotype that previously had to be enumerated manually. By monitoring stage progression and quantifying parasite phenotypes, our method can discern stage specificity of new compounds, thus providing insight into the compound's mode of action.
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Affiliation(s)
- Melissa R. Rosenthal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Caroline L. Ng
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biology, University of Omaha, Omaha, NE 68182, USA
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35
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Wu Y, Ni X, Wang Z, Feng W. Enhancing drug property prediction with dual-channel transfer learning based on molecular fragment. BMC Bioinformatics 2023; 24:293. [PMID: 37479969 PMCID: PMC10360281 DOI: 10.1186/s12859-023-05413-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Accurate prediction of molecular property holds significance in contemporary drug discovery and medical research. Recent advances in AI-driven molecular property prediction have shown promising results. Due to the costly annotation of in vitro and in vivo experiments, transfer learning paradigm has been gaining momentum in extracting general self-supervised information to facilitate neural network learning. However, prior pretraining strategies have overlooked the necessity of explicitly incorporating domain knowledge, especially the molecular fragments, into model design, resulting in the under-exploration of the molecular semantic space. RESULTS We propose an effective model with FRagment-based dual-channEL pretraining (FREL). Equipped with molecular fragments, FREL comprehensively employs masked autoencoder and contrastive learning to learn intra- and inter-molecule agreement, respectively. We further conduct extensive experiments on ten public datasets to demonstrate its superiority over state-of-the-art models. Further investigations and interpretations manifest the underlying relationship between molecular representations and molecular properties. CONCLUSIONS Our proposed model FREL achieves state-of-the-art performance on the benchmark datasets, emphasizing the importance of incorporating molecular fragments into model design. The expressiveness of learned molecular representations is also investigated by visualization and correlation analysis. Case studies indicate that the learned molecular representations better capture the drug property variation and fragment semantics.
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Affiliation(s)
- Yue Wu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xinran Ni
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhihao Wang
- College of Intelligence and Information Engineering, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Weike Feng
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China.
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36
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Hayward JA, Makota FV, Cihalova D, Leonard RA, Rajendran E, Zwahlen SM, Shuttleworth L, Wiedemann U, Spry C, Saliba KJ, Maier AG, van Dooren GG. A screen of drug-like molecules identifies chemically diverse electron transport chain inhibitors in apicomplexan parasites. PLoS Pathog 2023; 19:e1011517. [PMID: 37471441 PMCID: PMC10403144 DOI: 10.1371/journal.ppat.1011517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/04/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Apicomplexans are widespread parasites of humans and other animals, and include the causative agents of malaria (Plasmodium species) and toxoplasmosis (Toxoplasma gondii). Existing anti-apicomplexan therapies are beset with issues around drug resistance and toxicity, and new treatment options are needed. The mitochondrial electron transport chain (ETC) is one of the few processes that has been validated as a drug target in apicomplexans. To identify new inhibitors of the apicomplexan ETC, we developed a Seahorse XFe96 flux analyzer approach to screen the 400 compounds contained within the Medicines for Malaria Venture 'Pathogen Box' for ETC inhibition. We identified six chemically diverse, on-target inhibitors of the ETC in T. gondii, at least four of which also target the ETC of Plasmodium falciparum. Two of the identified compounds (MMV024937 and MMV688853) represent novel ETC inhibitor chemotypes. MMV688853 belongs to a compound class, the aminopyrazole carboxamides, that were shown previously to target a kinase with a key role in parasite invasion of host cells. Our data therefore reveal that MMV688853 has dual targets in apicomplexans. We further developed our approach to pinpoint the molecular targets of these inhibitors, demonstrating that all target Complex III of the ETC, with MMV688853 targeting the ubiquinone reduction (Qi) site of the complex. Most of the compounds we identified remain effective inhibitors of parasites that are resistant to Complex III inhibitors that are in clinical use or development, indicating that they could be used in treating drug resistant parasites. In sum, we have developed a versatile, scalable approach to screen for compounds that target the ETC in apicomplexan parasites, and used this to identify and characterize novel inhibitors.
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Affiliation(s)
- Jenni A. Hayward
- Research School of Biology, Australian National University, Canberra, Australia
| | - F. Victor Makota
- Research School of Biology, Australian National University, Canberra, Australia
| | - Daniela Cihalova
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rachel A. Leonard
- Research School of Biology, Australian National University, Canberra, Australia
| | - Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australia
| | - Soraya M. Zwahlen
- Research School of Biology, Australian National University, Canberra, Australia
| | - Laura Shuttleworth
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ursula Wiedemann
- Research School of Biology, Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, Australian National University, Canberra, Australia
| | - Kevin J. Saliba
- Research School of Biology, Australian National University, Canberra, Australia
| | - Alexander G. Maier
- Research School of Biology, Australian National University, Canberra, Australia
| | - Giel G. van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
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Acquah FA, Mooers BHM. Targeting RNA Structure to Inhibit Editing in Trypanosomes. Int J Mol Sci 2023; 24:10110. [PMID: 37373258 PMCID: PMC10298474 DOI: 10.3390/ijms241210110] [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: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.
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Affiliation(s)
- Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S, Park H, Uhlemann AC, Jana GP, Maity BC, Laleu B, Chenu E, Duffy J, Moliner Cubel S, Franco V, Gomez-Lorenzo MG, Gamo FJ, Winzeler EA, Fidock DA, Chookajorn T, Lee MCS. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. Nat Commun 2023; 14:3059. [PMID: 37244916 DOI: 10.1038/s41467-023-38774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.
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Affiliation(s)
- Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, USA
| | - Theerarat Kochakarn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Benoît Laleu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - Elodie Chenu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | | | - Virginia Franco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Thanat Chookajorn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
- Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
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Muema JM, Mutunga JM, Obonyo MA, Getahun MN, Mwakubambanya RS, Akala HM, Cheruiyot AC, Yeda RA, Juma DW, Andagalu B, Johnson JL, Roth AL, Bargul JL. Isoliensinine from Cissampelos pariera rhizomes exhibits potential gametocytocidal and anti-malarial activities against Plasmodium falciparum clinical isolates. Malar J 2023; 22:161. [PMID: 37208735 DOI: 10.1186/s12936-023-04590-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The unmet demand for effective malaria transmission-blocking agents targeting the transmissible stages of Plasmodium necessitates intensive discovery efforts. In this study, a bioactive bisbenzylisoquinoline (BBIQ), isoliensinine, from Cissampelos pariera (Menispermaceae) rhizomes was identified and characterized for its anti-malarial activity. METHODS Malaria SYBR Green I fluorescence assay was performed to evaluate the in vitro antimalarial activity against D6, Dd2, and F32-ART5 clones, and immediate ex vivo (IEV) susceptibility for 10 freshly collected P. falciparum isolates. To determine the speed- and stage-of-action of isoliensinine, an IC50 speed assay and morphological analyses were performed using synchronized Dd2 asexuals. Gametocytocidal activity against two culture-adapted gametocyte-producing clinical isolates was determined using microscopy readouts, with possible molecular targets and their binding affinities deduced in silico. RESULTS Isoliensinine displayed a potent in vitro gametocytocidal activity at mean IC50gam values ranging between 0.41 and 0.69 µM for Plasmodium falciparum clinical isolates. The BBIQ compound also inhibited asexual replication at mean IC50Asexual of 2.17 µM, 2.22 µM, and 2.39 µM for D6, Dd2 and F32-ART5 respectively, targeting the late-trophozoite to schizont transition. Further characterization demonstrated a considerable immediate ex vivo potency against human clinical isolates at a geometric mean IC50IEV = 1.433 µM (95% CI 0.917-2.242). In silico analyses postulated a probable anti-malarial mechanism of action by high binding affinities for four mitotic division protein kinases; Pfnek1, Pfmap2, Pfclk1, and Pfclk4. Additionally, isoliensinine was predicted to possess an optimal pharmacokinetics profile and drug-likeness properties. CONCLUSION These findings highlight considerable grounds for further exploration of isoliensinine as an amenable scaffold for malaria transmission-blocking chemistry and target validation.
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Affiliation(s)
- Jackson M Muema
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya.
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya.
| | - James M Mutunga
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- Department of Biological Sciences, School of Pure and Applied Sciences, Mount Kenya University, Thika, Kenya
- School of Engineering Design, Technology and Professional Programs, Pennsylvania State University, University Park, PA, 16802, USA
| | - Meshack A Obonyo
- Department of Biochemistry and Molecular Biology, Egerton University, Egerton, Kenya
| | - Merid N Getahun
- International Centre of Insect Physiology and Ecology (Icipe), Nairobi, Kenya
| | | | - Hoseah M Akala
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Agnes C Cheruiyot
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Redemptah A Yeda
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Dennis W Juma
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Ben Andagalu
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Jaree L Johnson
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Amanda L Roth
- U.S. Army Medical Research Directorate-Africa (USAMRD-A), Centre for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya.
- International Centre of Insect Physiology and Ecology (Icipe), Nairobi, Kenya.
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40
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Müller J, Hemphill A. Toxoplasma gondii infection: novel emerging therapeutic targets. Expert Opin Ther Targets 2023; 27:293-304. [PMID: 37212443 PMCID: PMC10330558 DOI: 10.1080/14728222.2023.2217353] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
INTRODUCTION Toxoplasmosis constitutes a challenge for public health, animal production, and welfare. So far, only a limited panel of drugs has been marketed for clinical applications. In addition to classical screening, the investigation of unique targets of the parasite may lead to the identification of novel drugs. AREAS COVERED Herein, the authors describe the methodology to identify novel drug targets in Toxoplasma gondii and review the literature with a focus on the last two decades. EXPERT OPINION Over the last two decades, the investigation of essential proteins of T. gondii as potential drug targets has fostered the hope of identifying novel compounds for the treatment of toxoplasmosis. Despite good efficacies in vitro, only a few classes of these compounds are effective in suitable rodent models, and none has cleared the hurdle to applications in humans. This shows that target-based drug discovery is in no way better than classical screening approaches. In both cases, off-target effects and adverse side effects in the hosts must be considered. Proteomics-driven analyses of parasite- and host-derived proteins that physically bind drug candidates may constitute a suitable tool to characterize drug targets, irrespectively of the drug discovery methods.
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Affiliation(s)
- Joachim Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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41
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Ong HW, Adderley J, Tobin AB, Drewry DH, Doerig C. Parasite and host kinases as targets for antimalarials. Expert Opin Ther Targets 2023; 27:151-169. [PMID: 36942408 DOI: 10.1080/14728222.2023.2185511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION The deployment of Artemisinin-based combination therapies and transmission control measures led to a decrease in the global malaria burden over the recent decades. Unfortunately, this trend is now reversing, in part due to resistance against available treatments, calling for the development of new drugs against untapped targets to prevent cross-resistance. AREAS COVERED In view of their demonstrated druggability in noninfectious diseases, protein kinases represent attractive targets. Kinase-focussed antimalarial drug discovery is facilitated by the availability of kinase-targeting scaffolds and large libraries of inhibitors, as well as high-throughput phenotypic and biochemical assays. We present an overview of validated Plasmodium kinase targets and their inhibitors, and briefly discuss the potential of host cell kinases as targets for host-directed therapy. EXPERT OPINION We propose priority research areas, including (i) diversification of Plasmodium kinase targets (at present most efforts focus on a very small number of targets); (ii) polypharmacology as an avenue to limit resistance (kinase inhibitors are highly suitable in this respect); and (iii) preemptive limitation of resistance through host-directed therapy (targeting host cell kinases that are required for parasite survival) and transmission-blocking through targeting sexual stage-specific kinases as a strategy to protect curative drugs from the spread of resistance.
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Affiliation(s)
- Han Wee Ong
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC USA
| | - Jack Adderley
- Department of Laboratory Medicine, School of Health and Biomedical Sciences, Rmit University, Bundoora VIC Australia
| | - Andrew B Tobin
- Advanced Research Centre, University of Glasgow, Glasgow, UK
| | - David H Drewry
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC USA
| | - Christian Doerig
- Department of Laboratory Medicine, School of Health and Biomedical Sciences, Rmit University, Bundoora VIC Australia
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42
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Bopp S, Pasaje CFA, Summers RL, Magistrado-Coxen P, Schindler KA, Corpas-Lopez V, Yeo T, Mok S, Dey S, Smick S, Nasamu AS, Demas AR, Milne R, Wiedemar N, Corey V, Gomez-Lorenzo MDG, Franco V, Early AM, Lukens AK, Milner D, Furtado J, Gamo FJ, Winzeler EA, Volkman SK, Duffey M, Laleu B, Fidock DA, Wyllie S, Niles JC, Wirth DF. Potent acyl-CoA synthetase 10 inhibitors kill Plasmodium falciparum by disrupting triglyceride formation. Nat Commun 2023; 14:1455. [PMID: 36927839 PMCID: PMC10020447 DOI: 10.1038/s41467-023-36921-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Identifying how small molecules act to kill malaria parasites can lead to new "chemically validated" targets. By pressuring Plasmodium falciparum asexual blood stage parasites with three novel structurally-unrelated antimalarial compounds (MMV665924, MMV019719 and MMV897615), and performing whole-genome sequence analysis on resistant parasite lines, we identify multiple mutations in the P. falciparum acyl-CoA synthetase (ACS) genes PfACS10 (PF3D7_0525100, M300I, A268D/V, F427L) and PfACS11 (PF3D7_1238800, F387V, D648Y, and E668K). Allelic replacement and thermal proteome profiling validates PfACS10 as a target of these compounds. We demonstrate that this protein is essential for parasite growth by conditional knockdown and observe increased compound susceptibility upon reduced expression. Inhibition of PfACS10 leads to a reduction in triacylglycerols and a buildup of its lipid precursors, providing key insights into its function. Analysis of the PfACS11 gene and its mutations point to a role in mediating resistance via decreased protein stability.
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Affiliation(s)
- Selina Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | | | - Robert L Summers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Pamela Magistrado-Coxen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Victoriano Corpas-Lopez
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Smick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Armiyaw S Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allison R Demas
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Rachel Milne
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Natalie Wiedemar
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Victoria Corey
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Maria De Gracia Gomez-Lorenzo
- Tres Cantos Medicines Research and Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Virginia Franco
- Tres Cantos Medicines Research and Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Danny Milner
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Jeremy Furtado
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Francisco-Javier Gamo
- Tres Cantos Medicines Research and Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Elizabeth A Winzeler
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA
| | | | - Benoît Laleu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
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Istvan ES, Guerra F, Abraham M, Huang KS, Rocamora F, Zhao H, Xu L, Pasaje C, Kumpornsin K, Luth MR, Cui H, Yang T, Diaz SP, Gomez-Lorenzo MG, Qahash T, Mittal N, Ottilie S, Niles J, Lee MCS, Llinas M, Kato N, Okombo J, Fidock DA, Schimmel P, Gamo FJ, Goldberg DE, Winzeler EA. Cytoplasmic isoleucyl tRNA synthetase as an attractive multistage antimalarial drug target. Sci Transl Med 2023; 15:eadc9249. [PMID: 36888694 PMCID: PMC10286833 DOI: 10.1126/scitranslmed.adc9249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
Development of antimalarial compounds into clinical candidates remains costly and arduous without detailed knowledge of the target. As resistance increases and treatment options at various stages of disease are limited, it is critical to identify multistage drug targets that are readily interrogated in biochemical assays. Whole-genome sequencing of 18 parasite clones evolved using thienopyrimidine compounds with submicromolar, rapid-killing, pan-life cycle antiparasitic activity showed that all had acquired mutations in the P. falciparum cytoplasmic isoleucyl tRNA synthetase (cIRS). Engineering two of the mutations into drug-naïve parasites recapitulated the resistance phenotype, and parasites with conditional knockdowns of cIRS became hypersensitive to two thienopyrimidines. Purified recombinant P. vivax cIRS inhibition, cross-resistance, and biochemical assays indicated a noncompetitive, allosteric binding site that is distinct from that of known cIRS inhibitors mupirocin and reveromycin A. Our data show that Plasmodium cIRS is an important chemically and genetically validated target for next-generation medicines for malaria.
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Affiliation(s)
- Eva S. Istvan
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Francisco Guerra
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Matthew Abraham
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | | | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | | | - Lan Xu
- The Global Health Drug Discovery Institute, Tsinghua University 30 Shuangqing Rd, Haidian District, Beijing, China
| | - Charisse Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sara Palomo Diaz
- Global Health Medicines, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | | | - Tarrick Qahash
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Jacquin Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Manuel Llinas
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Nobutaka Kato
- The Global Health Drug Discovery Institute, Tsinghua University 30 Shuangqing Rd, Haidian District, Beijing, China
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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Ong HW, Truong A, Kwarcinski F, de Silva C, Avalani K, Havener TM, Chirgwin M, Galal KA, Willis C, Krämer A, Liu S, Knapp S, Derbyshire ER, Zutshi R, Drewry DH. Discovery of potent Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors with a type II inhibitor pharmacophore. Eur J Med Chem 2023; 249:115043. [PMID: 36736152 PMCID: PMC10052868 DOI: 10.1016/j.ejmech.2022.115043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 01/01/2023]
Abstract
Malaria is a devastating disease that causes significant global morbidity and mortality. The rise of drug resistance against artemisinin-based combination therapy demonstrates the necessity to develop alternative antimalarials with novel mechanisms of action. We report the discovery of Ki8751 as an inhibitor of essential kinase PfPK6. 79 derivatives were designed, synthesized and evaluated for PfPK6 inhibition and antiplasmodial activity. Using group efficiency analyses, we established the importance of key groups on the scaffold consistent with a type II inhibitor pharmacophore. We highlight modifications on the tail group that contribute to antiplasmodial activity, cumulating in the discovery of compound 67, a PfPK6 inhibitor (IC50 = 13 nM) active against the P. falciparum blood stage (EC50 = 160 nM), and compound 79, a PfPK6 inhibitor (IC50 < 5 nM) with dual-stage antiplasmodial activity against P. falciparum blood stage (EC50 = 39 nM) and against P. berghei liver stage (EC50 = 220 nM).
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna Truong
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Frank Kwarcinski
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Chandi de Silva
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Krisha Avalani
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Tammy M Havener
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael Chirgwin
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Kareem A Galal
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Caleb Willis
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Andreas Krämer
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, 27599-3420, USA; Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599-3420, USA
| | - Stefan Knapp
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC, 27710, USA.
| | - Reena Zutshi
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA.
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Elsworth B, Keroack C, Rezvani Y, Paul A, Barazorda K, Tennessen J, Sack S, Moreira C, Gubbels MJ, Meyers M, Zarringhalam K, Duraisingh M. Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases. RESEARCH SQUARE 2023:rs.3.rs-2553721. [PMID: 36909484 PMCID: PMC10002801 DOI: 10.21203/rs.3.rs-2553721/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Apicomplexan egress from host cells is fundamental to the spread of infection and is poorly characterized in Babesia spp., parasites of veterinary importance and emerging zoonoses. Through the use of video microscopy, transcriptomics and chemical genetics, we have implicated signaling, proteases and gliding motility as key drivers of egress by Babesia divergens. We developed reverse genetics to perform a knockdown screen of putative mediators of egress, identifying kinases and proteases involved in distinct steps of egress (ASP3, PKG and CDPK4) and invasion (ASP2, ASP3 and PKG). Inhibition of egress leads to continued intracellular replication, indicating exit from the replication cycle is uncoupled from egress. Chemical genetics validated PKG, ASP2 and ASP3 as druggable targets in Babesia spp. All taken together, egress in B. divergens more closely resembles T. gondii than the more evolutionarily-related Plasmodium spp. We have established a molecular framework for biological and translational studies of B. divergens egress.
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Structure-based development of potent Plasmodium falciparum M1 and M17 aminopeptidase selective and dual inhibitors via S1'-region optimisation. Eur J Med Chem 2023; 248:115051. [PMID: 36634455 DOI: 10.1016/j.ejmech.2022.115051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Malaria remains a global health threat and growing resistance to artemisinin-based therapies calls for therapeutic agents with novel mechanisms of action. The Plasmodium spp M1 and M17 metalloaminopeptidases have been identified as attractive new antimalarial drug targets as inhibition of these enzymes results in antiplasmodial activity. Previously identified novel hydroxamic acid 2 as a moderate inhibitor of PfA-M1 and PfA-M17 and a potent inhibitor of P. falciparum. This study has sought to improve the enzymatic inhibitory properties in addition to increasing the drug-likeness of this scaffold by introducing polar moieties into the S1' region of the active site. Structural biology studies on the co-crystallised structures of potent dual-inhibitor 9aa bound to PfA-M1 and PfA-M17 have revealed that there are few direct interactions between the inhibitor and the S1' domain of these enzymes. Structure-based compound design led to the identification of a variety of novel hydroxamic acids that show improved inhibitory activity against PfA-M1 and PfA-M17, in addition to displaying antiplasmodial activity. Notably, compounds with substitutions on the aniline ring resulted in a loss of potency (Ki > 500 nM) toward PfA-M1 and PfA-M17. ioisosteric replacement of the S1-region biaryl ring system with a bromophenyl moiety resulted in increased potency compared to parent 9aa. Elaboration of 9aa to bioisosterically replace the S1 moiety with an aryl bromide, combined with substituted anilines has resulted in potent selective PfA-M1 inhibitors which show strong activity against Pf-3D7, with meta- and para-fluoroaniline groups of 15ag and 15ah forming hydrogen-bonds with residues within the active site. These findings establish the importance of the previously under-utilised S1' domain and will aid the design of future PfA-M1 and PfA-M17 inhibitors.
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Identifying inhibitors of β-haematin formation with activity against chloroquine-resistant Plasmodium falciparum malaria parasites via virtual screening approaches. Sci Rep 2023; 13:2648. [PMID: 36788274 PMCID: PMC9929333 DOI: 10.1038/s41598-023-29273-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
The biomineral haemozoin, or its synthetic analogue β-haematin (βH), has been the focus of several target-based screens for activity against Plasmodium falciparum parasites. Together with the known βH crystal structure, the availability of this screening data makes the target amenable to both structure-based and ligand-based virtual screening. In this study, molecular docking and machine learning techniques, including Bayesian and support vector machine classifiers, were used in sequence to screen the in silico ChemDiv 300k Representative Compounds library for inhibitors of βH with retained activity against P. falciparum. We commercially obtained and tested a prioritised set of inhibitors and identified the coumarin and iminodipyridinopyrimidine chemotypes as potent in vitro inhibitors of βH and whole cell parasite growth.
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Liu Y, Zhang T, Chen SB, Cui YB, Wang SQ, Zhang HW, Shen HM, Chen JH. Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s. Front Microbiol 2023; 14:1071689. [PMID: 36846776 PMCID: PMC9948256 DOI: 10.3389/fmicb.2023.1071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction In malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China. Methods The samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection. Results China's inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades. Discussion Our data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.
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Affiliation(s)
- Ying Liu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shu-Qi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hong-Wei Zhang
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Hai-Mo Shen, ✉
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jun-Hu Chen, ✉
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Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
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Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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50
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Martins LS, Kruger HG, Naicker T, Alves CN, Lameira J, Araújo Silva JR. Computational insights for predicting the binding and selectivity of peptidomimetic plasmepsin IV inhibitors against cathepsin D. RSC Adv 2022; 13:602-614. [PMID: 36605626 PMCID: PMC9773328 DOI: 10.1039/d2ra06246a] [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: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Plasmepsins (Plms) are aspartic proteases involved in the degradation of human hemoglobin by P. falciparum and are essential for the survival and growth of the parasite. Therefore, Plm enzymes are reported as an important antimalarial drug target. Herein, we have applied molecular docking, molecular dynamics (MD) simulations, and binding free energy with the Linear Interaction Energy (LIE) approach to investigate the binding of peptidomimetic PlmIV inhibitors with a particular focus on understanding their selectivity against the human Asp protease cathepsin D (CatD). The residual decomposition analysis results suggest that amino acid differences in the subsite S3 of PlmIV and CatD are responsible for the higher selectivity of the 5a inhibitor. These findings yield excellent agreement with experimental binding data and provide new details regarding van der Waals and electrostatic interactions of subsite residues as well as structural properties of the PlmIV and CatD systems.
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Affiliation(s)
- Lucas Sousa Martins
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | | | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu-NatalDurban 4000South Africa
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - José Rogério Araújo Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
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