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Schwarzer E, Skorokhod O. Post-Translational Modifications of Proteins of Malaria Parasites during the Life Cycle. Int J Mol Sci 2024; 25:6145. [PMID: 38892332 PMCID: PMC11173270 DOI: 10.3390/ijms25116145] [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: 05/01/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Post-translational modifications (PTMs) are essential for regulating protein functions, influencing various fundamental processes in eukaryotes. These include, but are not limited to, cell signaling, protein trafficking, the epigenetic control of gene expression, and control of the cell cycle, as well as cell proliferation, differentiation, and interactions between cells. In this review, we discuss protein PTMs that play a key role in the malaria parasite biology and its pathogenesis. Phosphorylation, acetylation, methylation, lipidation and lipoxidation, glycosylation, ubiquitination and sumoylation, nitrosylation and glutathionylation, all of which occur in malarial parasites, are reviewed. We provide information regarding the biological significance of these modifications along all phases of the complex life cycle of Plasmodium spp. Importantly, not only the parasite, but also the host and vector protein PTMs are often crucial for parasite growth and development. In addition to metabolic regulations, protein PTMs can result in epitopes that are able to elicit both innate and adaptive immune responses of the host or vector. We discuss some existing and prospective results from antimalarial drug discovery trials that target various PTM-related processes in the parasite or host.
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Affiliation(s)
- Evelin Schwarzer
- Department of Oncology, University of Turin, Via Santena 5 bis, 10126 Turin, Italy;
| | - Oleksii Skorokhod
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, 10123 Turin, Italy
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2
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Mahanta PJ, Lhouvum K. Plasmodium falciparum proteases as new drug targets with special focus on metalloproteases. Mol Biochem Parasitol 2024; 258:111617. [PMID: 38554736 DOI: 10.1016/j.molbiopara.2024.111617] [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: 10/17/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Malaria poses a significant global health threat particularly due to the prevalence of Plasmodium falciparum infection. With the emergence of parasite resistance to existing drugs including the recently discovered artemisinin, ongoing research seeks novel therapeutic avenues within the malaria parasite. Proteases are promising drug targets due to their essential roles in parasite biology, including hemoglobin digestion, merozoite invasion, and egress. While exploring the genomic landscape of Plasmodium falciparum, it has been revealed that there are 92 predicted proteases, with only approximately 14 of them having been characterized. These proteases are further distributed among 26 families grouped into five clans: aspartic proteases, cysteine proteases, metalloproteases, serine proteases, and threonine proteases. Focus on metalloprotease class shows further role in organelle processing for mitochondria and apicoplasts suggesting the potential of metalloproteases as viable drug targets. Holistic understanding of the parasite intricate life cycle and identification of potential drug targets are essential for developing effective therapeutic strategies against malaria and mitigating its devastating global impact.
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Affiliation(s)
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
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3
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Wang UTT, Tian X, Liou YH, Lee SP, Hu HT, Lu CH, Lin PT, Cheng YJ, Chen P, Chen BC. Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging. Sci Rep 2023; 13:21922. [PMID: 38081848 PMCID: PMC10713663 DOI: 10.1038/s41598-023-48959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
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Affiliation(s)
- Ueh-Ting Tim Wang
- Affiliated Senior High School of National Taiwan Normal University, Taipei, 106348, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taipei, 11529, Taiwan
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Po-Ting Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ya-Jen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Neuroscience Program, NPAS, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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Thornton LB, Key M, Micchelli C, Stasic AJ, Kwain S, Floyd K, Moreno SN, Dominy BN, Whitehead DC, Dou Z. A cathepsin C-like protease mediates the post-translation modification of Toxoplasma gondii secretory proteins for optimal invasion and egress. mBio 2023; 14:e0017423. [PMID: 37326431 PMCID: PMC10470614 DOI: 10.1128/mbio.00174-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/01/2023] [Indexed: 06/17/2023] Open
Abstract
Microbial pathogens use proteases for their infections, such as digestion of proteins for nutrients and activation of their virulence factors. As an obligate intracellular parasite, Toxoplasma gondii must invade host cells to establish its intracellular propagation. To facilitate invasion, the parasites secrete invasion effectors from microneme and rhoptry, two unique organelles in apicomplexans. Previous work has shown that some micronemal invasion effectors experience a series of proteolytic cleavages within the parasite's secretion pathway for maturation, such as the aspartyl protease (TgASP3) and the cathepsin L-like protease (TgCPL), localized within the post-Golgi compartment and the endolysosomal system, respectively. Furthermore, it has been shown that the precise maturation of micronemal effectors is critical for Toxoplasma invasion and egress. Here, we show that an endosome-like compartment (ELC)-residing cathepsin C-like protease (TgCPC1) mediates the final trimming of some micronemal effectors, and its loss further results in defects in the steps of invasion, egress, and migration throughout the parasite's lytic cycle. Notably, the deletion of TgCPC1 completely blocks the activation of subtilisin-like protease 1 (TgSUB1) in the parasites, which globally impairs the surface-trimming of many key micronemal invasion and egress effectors. Additionally, we found that Toxoplasma is not efficiently inhibited by the chemical inhibitor targeting the malarial CPC ortholog, suggesting that these cathepsin C-like orthologs are structurally different within the apicomplexan phylum. Collectively, our findings identify a novel function of TgCPC1 in processing micronemal proteins within the Toxoplasma parasite's secretory pathway and expand the understanding of the roles of cathepsin C protease. IMPORTANCE Toxoplasma gondii is a microbial pathogen that is well adapted for disseminating infections. It can infect virtually all warm-blooded animals. Approximately one-third of the human population carries toxoplasmosis. During infection, the parasites sequentially secrete protein effectors from the microneme, rhoptry, and dense granule, three organelles exclusively found in apicomplexan parasites, to help establish their lytic cycle. Proteolytic cleavage of these secretory proteins is required for the parasite's optimal function. Previous work has revealed that two proteases residing within the parasite's secretory pathway cleave micronemal and rhoptry proteins, which mediate parasite invasion and egress. Here, we demonstrate that a cathepsin C-like protease (TgCPC1) is involved in processing several invasion and egress effectors. The genetic deletion of TgCPC1 prevented the complete maturation of some effectors in the parasites. Strikingly, the deletion led to a full inactivation of one surface-anchored protease, which globally impaired the trimming of some key micronemal proteins before secretion. Therefore, this finding represents a novel post-translational mechanism for the processing of virulence factors within microbial pathogens.
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Affiliation(s)
- L. Brock Thornton
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Melanie Key
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Chiara Micchelli
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Andrew J. Stasic
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Katherine Floyd
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Silvia N.J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Brian N. Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Daniel C. Whitehead
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, USA
| | - Zhicheng Dou
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, USA
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5
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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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6
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Thornton LB, Key M, Micchelli C, Stasic AJ, Kwain S, Floyd K, Moreno SNJ, Dominy BN, Whitehead DC, Dou Z. A cathepsin C-like protease post-translationally modifies Toxoplasma gondii secretory proteins for optimal invasion and egress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.21.525043. [PMID: 36712013 PMCID: PMC9882377 DOI: 10.1101/2023.01.21.525043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial pathogens use proteases for their infections, such as digestion of proteins for nutrients and activation of their virulence factors. As an obligate intracellular parasite, Toxoplasma gondii must invade host cells to establish its intracellular propagation. To facilitate invasion, the parasites secrete invasion effectors from microneme and rhoptry, two unique organelles in apicomplexans. Previous work has shown that some micronemal invasion effectors experience a series of proteolytic cleavages within the parasite's secretion pathway for maturation, such as the aspartyl protease (TgASP3) and the cathepsin L-like protease (TgCPL), localized within the post-Golgi compartment (1) and the endolysosomal system (2), respectively. Furthermore, it has been shown that the precise maturation of micronemal effectors is critical for Toxoplasma invasion and egress (1). Here, we show that an endosome-like compartment (ELC)-residing cathepsin C-like protease (TgCPC1) mediates the final trimming of some micronemal effectors, and its loss further results in defects in the steps of invasion, egress, and migration throughout the parasite's lytic cycle. Notably, the deletion of TgCPC1 completely blocks the activation of subtilisin-like protease 1 (TgSUB1) in the parasites, which globally impairs the surface-trimming of many key micronemal invasion and egress effectors. Additionally, we found that TgCPC1 was not efficiently inhibited by the chemical inhibitor targeting its malarial ortholog, suggesting that these cathepsin C-like orthologs are structurally different within the apicomplexan phylum. Taken together, our findings identify a novel function of TgCPC1 in the processing of micronemal proteins within the secretory pathway of Toxoplasma parasites and expand the understanding of the roles of cathepsin C protease. IMPORTANCE Toxoplasma gondii is a microbial pathogen that is well adapted for disseminating infections. It can infect virtually all warm-blooded animals. Approximately one-third of the human population carries toxoplasmosis. During infection, the parasites sequentially secrete protein effectors from the microneme, rhoptry, and dense granule, three organelles exclusively found in apicomplexan parasites, to help establish their lytic cycle. Proteolytic cleavage of these secretory proteins is required for the parasite's optimal function. Previous work has revealed that two proteases residing within the parasite's secretory pathway cleave micronemal and rhoptry proteins, which mediate parasite invasion and egress. Here, we demonstrate that a cathepsin C-like protease (TgCPC1) is involved in processing several invasion and egress effectors. The genetic deletion of TgCPC1 prevented the complete maturation of some effectors in the parasites. Strikingly, the deletion led to a full inactivation of one surface-anchored protease, which globally impaired the trimming of some key micronemal proteins before secretion. Therefore, this finding represents a novel post-translational mechanism for the processing of virulence factors within microbial pathogens.
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Affiliation(s)
- L. Brock Thornton
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Melanie Key
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Chiara Micchelli
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Andrew J. Stasic
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Katherine Floyd
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Brian N. Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Daniel C. Whitehead
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Zhicheng Dou
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
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Activity-Based Protein Profiling of Human and Plasmodium Serine Hydrolases and Interrogation of Potential Antimalarial Targets. iScience 2022; 25:104996. [PMID: 36105595 PMCID: PMC9464883 DOI: 10.1016/j.isci.2022.104996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Malaria remains a global health issue requiring the identification of novel therapeutic targets to combat drug resistance. Metabolic serine hydrolases are druggable enzymes playing essential roles in lipid metabolism. However, very few have been investigated in malaria-causing parasites. Here, we used fluorophosphonate broad-spectrum activity-based probes and quantitative chemical proteomics to annotate and profile the activity of more than half of predicted serine hydrolases in P. falciparum across the erythrocytic cycle. Using conditional genetics, we demonstrate that the activities of four serine hydrolases, previously annotated as essential (or important) in genetic screens, are actually dispensable for parasite replication. Of importance, we also identified eight human serine hydrolases that are specifically activated at different developmental stages. Chemical inhibition of two of them blocks parasite replication. This strongly suggests that parasites co-opt the activity of host enzymes and that this opens a new drug development strategy against which the parasites are less likely to develop resistance. P. falciparum has 48 predicted metabolic SHs. Many react with the ABP, FP-N3 The activity of 25 PfSHs and 8 HsSHs was profiled throughout the asexual life cycle Catalytic mutants of 4 PfSHs (formerly held essential) had no parasite growth effect Selective inhibitors for 2 HsSHs (APEH and LPLA2) affected parasite growth
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Abugri J, Ayariga J, Sunwiale SS, Wezena CA, Gyamfi JA, Adu-Frimpong M, Agongo G, Dongdem JT, Abugri D, Dinko B. Targeting the Plasmodium falciparum proteome and organelles for potential antimalarial drug candidates. Heliyon 2022; 8:e10390. [PMID: 36033316 PMCID: PMC9398786 DOI: 10.1016/j.heliyon.2022.e10390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/12/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022] Open
Abstract
There is an unmet need to unearth alternative treatment options for malaria, wherein this quest is more pressing in recent times due to high morbidity and mortality data arising mostly from the endemic countries coupled with partial diversion of attention from the disease in view of the SARS-Cov-2 pandemic. Available therapeutic options for malaria have been severely threatened with the emergence of resistance to almost all the antimalarial drugs by the Plasmodium falciparum parasite in humans, which is a worrying situation. Artemisinin combination therapies (ACT) that have so far been the mainstay of malaria have encountered resistance by malaria parasite in South East Asia, which is regarded as a notorious ground zero for the emergence of resistance to antimalarial drugs. This review analyzes a few key druggable targets for the parasite and the potential of specific inhibitors to mitigate the emerging antimalarial drug resistance problem by providing a concise assessment of the essential proteins of the malaria parasite that could serve as targets. Moreover, this work provides a summary of the advances made in malaria parasite biology and the potential to leverage these findings for antimalarial drug production.
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Affiliation(s)
- James Abugri
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Joseph Ayariga
- The Biomedical Engineering Programme, Alabama State University, Montgomery, AL, 36104, USA
| | - Samuel Sunyazi Sunwiale
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Cletus Adiyaga Wezena
- Department of Microbiology, School of Biosciences, University for Development Studies (UDS), Nyankpala Campus, Tamale, Ghana
| | - Julien Agyemang Gyamfi
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Michael Adu-Frimpong
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Julius Tieroyaare Dongdem
- Department of Biochemistry and Molecular Medicine. School of Medicine. University for Development Studies (UDS), Tamale-Campus, Ghana
| | - Daniel Abugri
- Department of Biological Sciences, Microbiology PhD Programme, Laboratory of Ethnomedicine, Parasitology, and Drug Discovery, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, USA
| | - Bismarck Dinko
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho. Ghana
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Roy M, Rawat A, Kaushik S, Jyoti A, Srivastava VK. Endogenous cysteine protease inhibitors in upmost pathogenic parasitic protozoa. Microbiol Res 2022; 261:127061. [DOI: 10.1016/j.micres.2022.127061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
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10
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Bingxiang W, Ningning Z, Yakun W, Lingyu S, Hongmei L, Zhang X, Zhao X. Characterization of the Eimeria tenella rhoptry protein with a nuclear localization sequence (EtROP30). Parasitol Res 2022; 121:1507-1516. [PMID: 35314894 PMCID: PMC8938219 DOI: 10.1007/s00436-022-07499-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/16/2022] [Indexed: 01/25/2023]
Abstract
Rhoptry proteins (ROPs), secreted by specific rhoptry organelles of apicomplexan parasites, are determinants of parasite pathogenesis and sources of vaccine candidates. Twenty-eight ROPs of Eimeria tenella have been predicted by genomic approaches, and in the present study, E. tenella rhoptry protein 30 (EtROP30) was characterized. Subcellular localizations of EtROP30 in sporozoites and merozoites were in the apical complex and rhoptry-like bulb, suggesting that EtROP30 is a member of ROPs in E. tenella. Sequence analysis showed that EtROP30 contained an N-terminal secretory signal, a protein kinase domain with eight E. tenella-specific rhoptry kinase 1 subfamily (ROPK-Eten1) motifs, and a C-terminal nuclear localization sequence (NLS), making EtROP30 the only ROP that contains both a secretory signal and an NLS in E. tenella. Subsequent experiments showed that EtROP30 was a secreted protein in the sporozoite stage, relying on NLS for migration to the host nucleus. In addition, EtROP30 showed significantly higher expression levels in the parasite merozoite stage, indicating that EtROP30 plays a critical role during parasite reinvasion and development and may be a viable option as a vaccine candidate for anti-parasitic infection. The immunization protection efficacies of EtROP30 were evaluated. Significant improvements in mean body weight gain, reduction of cecum lesion score, and number of oocysts excreted were observed, indicating that EtROP30 has good immunogenicity against E. tenella. In the present study, a ROP of E. tenella with secretory and nuclear localization characteristics has been identified, and proved to be an effective vaccine candidate against this parasite.
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Affiliation(s)
- Wang Bingxiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Zhao Ningning
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Wang Yakun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Sun Lingyu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Li Hongmei
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Xiao Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China.
| | - Xiaomin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China. .,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China. .,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China.
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11
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Abstract
All intracellular pathogens must escape (egress) from the confines of their host cell to disseminate and proliferate. The malaria parasite only replicates in an intracellular vacuole or in a cyst, and must undergo egress at four distinct phases during its complex life cycle, each time disrupting, in a highly regulated manner, the membranes or cyst wall that entrap the parasites. This Cell Science at a Glance article and accompanying poster summarises our current knowledge of the morphological features of egress across the Plasmodium life cycle, the molecular mechanisms that govern the process, and how researchers are working to exploit this knowledge to develop much-needed new approaches to malaria control. ![]()
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Affiliation(s)
- Michele S Y Tan
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, UK .,Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
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12
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Singh V, Hada RS, Uddin A, Aneja B, Abid M, Pandey KC, Singh S. Inhibition of Hemoglobin Degrading Protease Falcipain-2 as a Mechanism for Anti-Malarial Activity of Triazole-Amino Acid Hybrids. Curr Top Med Chem 2020; 20:377-389. [PMID: 32000644 DOI: 10.2174/1568026620666200130162347] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/20/2019] [Accepted: 10/20/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Novel drug development against malaria parasite over old conventional antimalarial drugs is essential due to rapid and indiscriminate use of drugs, which led to the emergence of resistant strains. METHODS In this study, previously reported triazole-amino acid hybrids (13-18) are explored against Plasmodium falciparum as antimalarial agents. Among six compounds, 15 and 18 exhibited antimalarial activity against P. falciparum with insignificant hemolytic activity and cytotoxicity towards HepG2 mammalian cells. In molecular docking studies, both compounds bind into the active site of PfFP-2 and block its accessibility to the substrate that leads to the inhibition of target protein further supported by in vitro analysis. RESULTS Antimalarial half-maximal inhibitory concentration (IC50) of 15 and 18 compounds were found to be 9.26 μM and 20.62 μM, respectively. Blood stage specific studies showed that compounds, 15 and 18 are effective at late trophozoite stage and block egress pathway of parasites. Decreased level of free monomeric heme was found in a dose dependent manner after the treatment with compounds 15 and 18, which was further evidenced by the reduction in percent of hemoglobin hydrolysis. Compounds 15 and 18 hindered hemoglobin degradation via intra- and extracellular cysteine protease falcipain-2 (PfFP-2) inhibitory activity both in in vitro and in vivo in P. falciparum. CONCLUSION We report antimalarial potential of triazole-amino acid hybrids and their role in the inhibition of cysteine protease PfFP-2 as its mechanistic aspect.
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Affiliation(s)
- Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rahul Singh Hada
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar UP, 201314, India
| | - Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Babita Aneja
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.,Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Kailash C Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi 110077, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
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13
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Smith NA, Clarke OB, Lee M, Hodder AN, Smith BJ. Structure of the Plasmodium falciparum PfSERA5 pseudo-zymogen. Protein Sci 2020; 29:2245-2258. [PMID: 32955133 PMCID: PMC7586913 DOI: 10.1002/pro.3956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022]
Abstract
PfSERA5, a significantly abundant protein present within the parasitophorous vacuole (PV) and essential for normal growth during the blood-stage life cycle of the malaria parasite Plasmodium falciparum, displays structural similarity to many other cysteine proteases. However, PfSERA5 does not exhibit any detectable protease activity and therefore the role of the PfSERA5 papain-like domain (PfSERA5E), thought to remain bound to its cognate prodomain, remains unknown. In this study, we present a revised structure of the central PfSERA5E domain at a resolution of 1.2 Å, and the first structure of the "zymogen" of this papain-like domain including its cognate prodomain (PfSERA5PE) to 2.2 Å resolution. PfSERA5PE is somewhat structurally similar to that of other known proenzymes, retaining the conserved overall folding and orientation of the prodomain through, and occluding, the archetypal papain-like catalytic triad "active-site" cleft, in the same reverse direction as conventional prodomains. Our findings are congruent with previously identified structures of PfSERA5E and of similar "zymogens" and provide a foundation for further investigation into the function of PfSERA5.
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Affiliation(s)
- Nicholas A. Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
| | - Oliver B. Clarke
- Department of AnesthesiologyColumbia UniversityNew YorkNew YorkUSA
- Department of Physiology and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
| | - Anthony N. Hodder
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Brian J. Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
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14
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Efange NM, Lobe MMM, Keumoe R, Ayong L, Efange SMN. Spirofused tetrahydroisoquinoline-oxindole hybrids as a novel class of fast acting antimalarial agents with multiple modes of action. Sci Rep 2020; 10:17932. [PMID: 33087791 PMCID: PMC7578093 DOI: 10.1038/s41598-020-74824-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/07/2020] [Indexed: 11/15/2022] Open
Abstract
Molecular hybridization of privileged scaffolds may generate novel antiplasmodial chemotypes that display superior biological activity and delay drug resistance. In the present study, we describe the in vitro activities and mode of action of 3′,4′-dihydro-2′H-spiro[indoline-3,1′-isoquinolin]-2-ones, a novel class of spirofused tetrahydroisoquinoline–oxindole hybrids, as novel antimalarial agents. Whole cell phenotypic screening of these compounds identified (14b), subsequently named (±)-moxiquindole, as the most potent compound in the current series with equipotent antiplasmodial activity against both chloroquine sensitive and multidrug resistant parasite strains with good selectivity. The compound was active against all asexual stages of the parasite including inhibition of merozoite egress. Additionally, (±)-moxiquindole exhibited significant inhibitory effects on hemoglobin degradation, and disrupted vacuolar lipid dynamics. Taken together, our data confirm the antiplasmodial activity of (±)-moxiquindole, and identify 3′4′-dihydro-2′H-spiro[indoline-3,1′-isoquinolin]-2-ones as a novel class of antimalarial agents with multiple modes of action.
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Affiliation(s)
- Noella M Efange
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, Cameroon.,Centre Pasteur du Cameroon, Yaoundé, Cameroon
| | - Maloba M M Lobe
- Department of Chemistry, University of Buea, P.O. Box 63, Buea, Cameroon
| | | | | | - Simon M N Efange
- Department of Chemistry, University of Buea, P.O. Box 63, Buea, Cameroon.
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15
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Uddin A, Singh V, Irfan I, Mohammad T, Singh Hada R, Imtaiyaz Hassan M, Abid M, Singh S. Identification and structure-activity relationship (SAR) studies of carvacrol derivatives as potential anti-malarial against Plasmodium falciparum falcipain-2 protease. Bioorg Chem 2020; 103:104142. [PMID: 32763521 DOI: 10.1016/j.bioorg.2020.104142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/30/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023]
Abstract
In an effort to develop a potent anti-malarial agent against Plasmodium falciparum, a structure-guided virtual screening using an in-house library comprising 652 compounds was performed. By docking studies, we identified two compounds (JMI-105 and JMI-346) which formed significant non-covalent interactions and fit well in the binding pocket of PfFP-2. We affirmed this observation by MD simulation studies. As evident by the biochemical analysis, such as enzyme inhibition assay, Surface Plasmon Resonance (SPR), live-cell imaging and hemozoin inhibition, JMI-105 and JMI-346 at 25 µM concentration showed an inhibitory effect on purified PfFP-2. JMI-105 and JMI-346 inhibited the growth of CQS (3D7; IC50 = 8.8 and 13 µM) and CQR (RKL-9; IC50 = 14.3 and 33 µM) strains of P. falciparum. Treatment with compounds resulted in defect in parasite growth and development. No significant hemolysis or cytotoxicity towards human cells was observed suggesting that these molecules are non-toxic. We pursued, structural optimization on JMI-105 and in the process, SAR oriented derivatives (5a-5l) were synthesized and evaluated for growth inhibition potential. JMI-105 significantly decreased parasitemia and prolonged host survival in a murine model with P. berghei ANKA infection. The compounds (JMI-105 and JMI-346) against PfFP-2 have the potential to be used as an anti-malarial agent.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Iram Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rahul Singh Hada
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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16
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Tan QW, Mutwil M. Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species. Nucleic Acids Res 2020; 48:D768-D775. [PMID: 31372645 PMCID: PMC6943069 DOI: 10.1093/nar/gkz662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/04/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria is a tropical parasitic disease caused by the Plasmodium genus, which resulted in an estimated 219 million cases of malaria and 435 000 malaria-related deaths in 2017. Despite the availability of the Plasmodium falciparum genome since 2002, 74% of the genes remain uncharacterized. To remedy this paucity of functional information, we used transcriptomic data to build gene co-expression networks for two Plasmodium species (P. falciparum and P. berghei), and included genomic data of four other Plasmodium species, P. yoelii, P. knowlesi, P. vivax and P. cynomolgi, as well as two non-Plasmodium species from the Apicomplexa, Toxoplasma gondii and Theileria parva. The genomic and transcriptomic data were incorporated into the resulting database, malaria.tools, which is preloaded with tools that allow the identification and cross-species comparison of co-expressed gene neighbourhoods, clusters and life stage-specific expression, thus providing sophisticated tools to predict gene function. Moreover, we exemplify how the tools can be used to easily identify genes relevant for pathogenicity and various life stages of the malaria parasite. The database is freely available at www.malaria.tools.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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17
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Koussis K, Withers-Martinez C, Baker DA, Blackman MJ. Simultaneous multiple allelic replacement in the malaria parasite enables dissection of PKG function. Life Sci Alliance 2020; 3:e201900626. [PMID: 32179592 PMCID: PMC7081069 DOI: 10.26508/lsa.201900626] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 01/28/2023] Open
Abstract
Over recent years, a plethora of new genetic tools has transformed conditional engineering of the malaria parasite genome, allowing functional dissection of essential genes in the asexual and sexual blood stages that cause pathology or are required for disease transmission, respectively. Important challenges remain, including the desirability to complement conditional mutants with a correctly regulated second gene copy to confirm that observed phenotypes are due solely to loss of gene function and to analyse structure-function relationships. To meet this challenge, here we combine the dimerisable Cre (DiCre) system with the use of multiple lox sites to simultaneously generate multiple recombination events of the same gene. We focused on the Plasmodium falciparum cGMP-dependent protein kinase (PKG), creating in parallel conditional disruption of the gene plus up to two allelic replacements. We use the approach to demonstrate that PKG has no scaffolding or adaptor role in intraerythrocytic development, acting solely at merozoite egress. We also show that a phosphorylation-deficient PKG is functionally incompetent. Our method provides valuable new tools for analysis of gene function in the malaria parasite.
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Affiliation(s)
| | | | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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18
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Garcia-Longoria L, Palinauskas V, Ilgūnas M, Valkiūnas G, Hellgren O. Differential gene expression of Plasmodium homocircumflexum (lineage pCOLL4) across two experimentally infected passerine bird species. Genomics 2020; 112:2857-2865. [PMID: 32234432 DOI: 10.1016/j.ygeno.2020.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/28/2022]
Abstract
Plasmodium parasites are present in a wide range of host species, some of which tend to be more susceptible than others, potentially as an outcome of evolved tolerance or resistance. Common starlings seem to cope with malaria infection while common crossbills are more susceptible to the same infections. That raises the question if the parasites rely on the same molecular mechanisms regardless of host species or do Plasmodium parasites change gene-expressions in accordance to the environment different hosts might provide? We used RNA-sequencing from starlings and crossbills, experimentally infected with Plasmodium homocircumflexum (lineage pCOLL4). The assembled transcriptome contained a total of 26,733 contigs. Parasite expression patterns differed between bird species. Parasites had higher expression of cell-invasion genes when infecting crossbills compared to starlings whereas in starlings genes related to apoptosis or/and oxidative stress showed higher expression levels. This article reveals how a Plasmodium parasite might adjust its expression and gene function depending on the host species infected.
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Affiliation(s)
- L Garcia-Longoria
- Department of Biology, Lund University, Lund, Sweden; Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, E-506071 Badajoz, Spain.
| | | | - M Ilgūnas
- Nature Research Centre, Vilnius, Lithuania
| | | | - O Hellgren
- Department of Biology, Lund University, Lund, Sweden
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19
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Tan MSY, Davison D, Sanchez MI, Anderson BM, Howell S, Snijders A, Edgington-Mitchell LE, Deu E. Novel broad-spectrum activity-based probes to profile malarial cysteine proteases. PLoS One 2020; 15:e0227341. [PMID: 31923258 PMCID: PMC6953825 DOI: 10.1371/journal.pone.0227341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/17/2019] [Indexed: 11/18/2022] Open
Abstract
Clan CA cysteine proteases, also known as papain-like proteases, play important roles throughout the malaria parasite life cycle and are therefore potential drug targets to treat this disease and prevent its transmission. In order to study the biological function of these proteases and to chemically validate some of them as viable drug targets, highly specific inhibitors need to be developed. This is especially challenging given the large number of clan CA proteases present in Plasmodium species (ten in Plasmodium falciparum), and the difficulty of designing selective inhibitors that do not cross-react with other members of the same family. Additionally, any efforts to develop antimalarial drugs targeting these proteases will also have to take into account potential off-target effects against the 11 human cysteine cathepsins. Activity-based protein profiling has been a very useful tool to determine the specificity of inhibitors against all members of an enzyme family. However, current clan CA proteases broad-spectrum activity-based probes either target endopeptidases or dipeptidyl aminopeptidases, but not both subfamilies efficiently. In this study, we present a new series of dipeptydic vinyl sulfone probes containing a free N-terminal tryptophan and a fluorophore at the P1 position that are able to label both subfamilies efficiently, both in Plasmodium falciparum and in mammalian cells, thus making them better broad-spectrum activity-based probes. We also show that some of these probes are cell permeable and can therefore be used to determine the specificity of inhibitors in living cells. Interestingly, we show that the choice of fluorophore greatly influences the specificity of the probes as well as their cell permeability.
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Affiliation(s)
| | - Dara Davison
- The Francis Crick Institute, London, United Kingdom
| | - Mateo I. Sanchez
- Department of Genetics, Stanford School of Medicine, Stanford, California, United States of America
| | - Bethany M. Anderson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville Victoria, Australia
| | | | | | - Laura E. Edgington-Mitchell
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville Victoria, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Maxillofacial Surgery, College of Dentistry, New York University, New York, New York, United States of America
| | - Edgar Deu
- The Francis Crick Institute, London, United Kingdom
- * E-mail:
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20
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Sanchez MI, de Vries LE, Lehmann C, Lee JT, Ang KK, Wilson C, Chen S, Arkin MR, Bogyo M, Deu E. Identification of Plasmodium dipeptidyl aminopeptidase allosteric inhibitors by high throughput screening. PLoS One 2019; 14:e0226270. [PMID: 31851699 PMCID: PMC6919601 DOI: 10.1371/journal.pone.0226270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/22/2019] [Indexed: 12/04/2022] Open
Abstract
Dipeptidyl aminopeptidases (DPAPs) are cysteine proteases that cleave dipeptides from the N-terminus of protein substrates and have been shown to play important roles in many pathologies including parasitic diseases such as malaria, toxoplasmosis and Chagas's disease. Inhibitors of the mammalian homologue cathepsin C have been used in clinical trials as potential drugs to treat chronic inflammatory disorders, thus proving that these enzymes are druggable. In Plasmodium species, DPAPs play important functions at different stages of parasite development, thus making them potential antimalarial targets. Most DPAP inhibitors developed to date are peptide-based or peptidomimetic competitive inhibitors. Here, we used a high throughput screening approach to identify novel inhibitor scaffolds that block the activity of Plasmodium falciparum DPAP1. Most of the hits identified in this screen also inhibit Plasmodium falciparum DPAP3, cathepsin C, and to a lesser extent other malarial clan CA proteases, indicating that these might be general DPAP inhibitors. Interestingly, our mechanism of inhibition studies indicate that most hits are allosteric inhibitors, which opens a completely new strategy to inhibit these enzymes, study their biological function, and potentially develop new inhibitors as starting points for drug development.
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Affiliation(s)
- Mateo I. Sanchez
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Laura E. de Vries
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
| | - Christine Lehmann
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
| | - Jeong T. Lee
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Kenny K. Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Christopher Wilson
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Steven Chen
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, United States of America
| | - Matthew Bogyo
- Departments of Pathology and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, United States of America
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Lab, The Francis Crick Institute, London, United Kingdom
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21
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Das D, Krishnan SR, Roy A, Bulusu G. A network-based approach reveals novel invasion and Maurer's clefts-related proteins in Plasmodium falciparum. Mol Omics 2019; 15:431-441. [PMID: 31631203 DOI: 10.1039/c9mo00124g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Malaria continues to be a major concern in developing countries despite continuous efforts to find a cure for the disease. Understanding the pathogenesis mechanism is necessary to identify more effective drug targets against malaria. Many years of experimental research have generated a large amount of data for the malarial parasite, Plasmodium falciparum. These data are useful to understand the importance of certain parasite proteins, but it often remains unclear how these proteins come together, interact with other proteins and carry out their function. Identification of all proteins involved in pathogenesis is an important step towards understanding the molecular mechanism of pathogenesis. In this study, dynamic stage-specific protein-protein interaction networks were created based on gene expression data during the parasite's intra-erythrocytic stages and static protein-protein interaction data. Using previously known proteins of a biological event as seed proteins, the random walk with restart (RWR) method was used on the dynamic protein-protein interaction networks to identify novel proteins related to that event. Two screening procedures namely, permutation test and GO enrichment test were performed to increase the reliability of the RWR predictions. The proposed method was first validated on Plasmodium falciparum proteins related to invasion, where it could reproduce the existing knowledge from a small set of seed proteins. It was then used to identify novel Maurer's clefts resident proteins, where it could identify 152 parasite proteins. We show that the current approach can annotate conserved proteins with unknown function. The predicted proteins can help build a mechanistic model for disease pathogenesis, which will be useful in identifying new drug targets.
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Affiliation(s)
- Dibyajyoti Das
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India.
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22
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de Vries LE, Sanchez MI, Groborz K, Kuppens L, Poreba M, Lehmann C, Nevins N, Withers-Martinez C, Hirst DJ, Yuan F, Arastu-Kapur S, Horn M, Mares M, Bogyo M, Drag M, Deu E. Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies differences in amino acid preferences between peptide-based substrates and covalent inhibitors. FEBS J 2019; 286:3998-4023. [PMID: 31177613 PMCID: PMC6851853 DOI: 10.1111/febs.14953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
Abstract
Malarial dipeptidyl aminopeptidases (DPAPs) are cysteine proteases important for parasite development thus making them attractive drug targets. In order to develop inhibitors specific to the parasite enzymes, it is necessary to map the determinants of substrate specificity of the parasite enzymes and its mammalian homologue cathepsin C (CatC). Here, we screened peptide-based libraries of substrates and covalent inhibitors to characterize the differences in specificity between parasite DPAPs and CatC, and used this information to develop highly selective DPAP1 and DPAP3 inhibitors. Interestingly, while the primary amino acid specificity of a protease is often used to develop potent inhibitors, we show that equally potent and highly specific inhibitors can be developed based on the sequences of nonoptimal peptide substrates. Finally, our homology modelling and docking studies provide potential structural explanations of the differences in specificity between DPAP1, DPAP3, and CatC, and between substrates and inhibitors in the case of DPAP3. Overall, this study illustrates that focusing the development of protease inhibitors solely on substrate specificity might overlook important structural features that can be exploited to develop highly potent and selective compounds.
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Affiliation(s)
- Laura E de Vries
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mateo I Sanchez
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Katarzyna Groborz
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Laurie Kuppens
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Marcin Poreba
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Christine Lehmann
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Neysa Nevins
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - David J Hirst
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Stevenage, UK
| | - Fang Yuan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirin Arastu-Kapur
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Michael Mares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcin Drag
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
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23
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Biguanide is a modifiable pharmacophore for recruitment of endogenous Zn 2+ to inhibit cysteinyl cathepsins: review and implications. Biometals 2019; 32:575-593. [PMID: 31044334 PMCID: PMC6647370 DOI: 10.1007/s10534-019-00197-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/13/2019] [Indexed: 01/28/2023]
Abstract
Excessive activities of cysteinyl cathepsins (CysCts) contribute to the progress of many diseases; however, therapeutic inhibition has been problematic. Zn2+ is a natural inhibitor of proteases with CysHis dyads or CysHis(Xaa) triads. Biguanide forms bidentate metal complexes through the two imino nitrogens. Here, it is discussed that phenformin (phenylethyl biguanide) is a model for recruitment of endogenous Zn2+ to inhibit CysHis/CysHis(X) peptidolysis. Phenformin is a Zn2+-interactive, anti-proteolytic agent in bioassay of living tissue. Benzoyl-L-arginine amide (BAA) is a classical substrate of papain-like proteases; the amide bond is scissile. In this review, the structures of BAA and the phenformin-Zn2+ complex were compared in silico. Their chemistry and dimensions are discussed in light of the active sites of papain-like proteases. The phenyl moieties of both structures bind to the "S2" substrate-binding site that is typical of many proteases. When the phenyl moiety of BAA binds to S2, then the scissile amide bond is directed to the position of the thiolate-imidazolium ion pair, and is then hydrolyzed. However, when the phenyl moiety of phenformin binds to S2, then the coordinated Zn2+ is directed to the identical position; and catalysis is inhibited. Phenformin stabilizes a "Zn2+ sandwich" between the drug and protease active site. Hundreds of biguanide derivatives have been synthesized at the 1 and 5 nitrogen positions; many more are conceivable. Various substituent moieties can register with various arrays of substrate-binding sites so as to align coordinated Zn2+ with catalytic partners of diverse proteases. Biguanide is identified here as a modifiable pharmacophore for synthesis of therapeutic CysCt inhibitors with a wide range of potencies and specificities. Phenformin-Zn2+ Complex.
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Aroonsri A, Posayapisit N, Kongsee J, Siripan O, Vitsupakorn D, Utaida S, Uthaipibull C, Kamchonwongpaisan S, Shaw PJ. Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target. PeerJ 2019; 7:e6713. [PMID: 31024761 PMCID: PMC6475138 DOI: 10.7717/peerj.6713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/20/2022] Open
Abstract
Background Hypusination is an essential post-translational modification in eukaryotes. The two enzymes required for this modification, namely deoxyhypusine synthase (DHS) and deoxyhypusine hydrolase are also conserved. Plasmodium falciparum human malaria parasites possess genes for both hypusination enzymes, which are hypothesized to be targets of antimalarial drugs. Methods Transgenic P. falciparum parasites with modification of the PF3D7_1412600 gene encoding PfDHS enzyme were created by insertion of the glmS riboswitch or the M9 inactive variant. The PfDHS protein was studied in transgenic parasites by confocal microscopy and Western immunoblotting. The biochemical function of PfDHS enzyme in parasites was assessed by hypusination and nascent protein synthesis assays. Gene essentiality was assessed by competitive growth assays and chemogenomic profiling. Results Clonal transgenic parasites with integration of glmS riboswitch downstream of the PfDHS gene were established. PfDHS protein was present in the cytoplasm of transgenic parasites in asexual stages. The PfDHS protein could be attenuated fivefold in transgenic parasites with an active riboswitch, whereas PfDHS protein expression was unaffected in control transgenic parasites with insertion of the riboswitch-inactive sequence. Attenuation of PfDHS expression for 72 h led to a significant reduction of hypusinated protein; however, global protein synthesis was unaffected. Parasites with attenuated PfDHS expression showed a significant growth defect, although their decline was not as rapid as parasites with attenuated dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) expression. PfDHS-attenuated parasites showed increased sensitivity to N 1-guanyl-1,7-diaminoheptane, a structural analog of spermidine, and a known inhibitor of DHS enzymes. Discussion Loss of PfDHS function leads to reduced hypusination, which may be important for synthesis of some essential proteins. The growth defect in parasites with attenuated Pf DHS expression suggests that this gene is essential. However, the slower decline of PfDHS mutants compared with PfDHFR-TS mutants in competitive growth assays suggests that PfDHS is less vulnerable as an antimalarial target. Nevertheless, the data validate PfDHS as an antimalarial target which can be inhibited by spermidine-like compounds.
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Affiliation(s)
- Aiyada Aroonsri
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Navaporn Posayapisit
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jindaporn Kongsee
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand
| | - Onsiri Siripan
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Danoo Vitsupakorn
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sugunya Utaida
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand
| | - Chairat Uthaipibull
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Philip J Shaw
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Mishra M, Singh V, Singh S. Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets. Front Microbiol 2019; 10:394. [PMID: 30891019 PMCID: PMC6411711 DOI: 10.3389/fmicb.2019.00394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/14/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria, caused by protozoan of genus Plasmodium, remains one of the highest mortality infectious diseases. Malaria parasites have a complex life cycle, easily adapt to their host’s immune system and have evolved with an arsenal of unique proteases which play crucial roles in proliferation and survival within the host cells. Owing to the existing knowledge of enzymatic mechanisms, 3D structures and active sites of proteases, they have been proven to be opportune for target based drug development. Here, we discuss in depth the crucial roles of essential proteases in Plasmodium life cycle and particularly focus on highlighting the atypical “structural signatures” of key parasite proteases which have been exploited for drug development. These features, on one hand aid parasites pathogenicity while on the other hand could be effective in designing targeted and very specific inhibitors for counteracting them. We conclude that Plasmodium proteases are suitable as multistage targets for designing novel drugs with new modes of action to combat malaria.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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