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Azevedo LG, Sosa E, de Queiroz ATL, Barral A, Wheeler RJ, Nicolás MF, Farias LP, Do Porto DF, Ramos PIP. High-throughput prioritization of target proteins for development of new antileishmanial compounds. Int J Parasitol Drugs Drug Resist 2024; 25:100538. [PMID: 38669848 PMCID: PMC11068527 DOI: 10.1016/j.ijpddr.2024.100538] [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: 10/18/2023] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Leishmaniasis, a vector-borne disease, is caused by the infection of Leishmania spp., obligate intracellular protozoan parasites. Presently, human vaccines are unavailable, and the primary treatment relies heavily on systemic drugs, often presenting with suboptimal formulations and substantial toxicity, making new drugs a high priority for LMIC countries burdened by the disease, but a low priority in the agenda of most pharmaceutical companies due to unattractive profit margins. New ways to accelerate the discovery of new, or the repositioning of existing drugs, are needed. To address this challenge, our study aimed to identify potential protein targets shared among clinically-relevant Leishmania species. We employed a subtractive proteomics and comparative genomics approach, integrating high-throughput multi-omics data to classify these targets based on different druggability metrics. This effort resulted in the ranking of 6502 ortholog groups of protein targets across 14 pathogenic Leishmania species. Among the top 20 highly ranked groups, metabolic processes known to be attractive drug targets, including the ubiquitination pathway, aminoacyl-tRNA synthetases, and purine synthesis, were rediscovered. Additionally, we unveiled novel promising targets such as the nicotinate phosphoribosyltransferase enzyme and dihydrolipoamide succinyltransferases. These groups exhibited appealing druggability features, including less than 40% sequence identity to the human host proteome, predicted essentiality, structural classification as highly druggable or druggable, and expression levels above the 50th percentile in the amastigote form. The resources presented in this work also represent a comprehensive collection of integrated data regarding trypanosomatid biology.
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Affiliation(s)
- Lucas G Azevedo
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
| | - Ezequiel Sosa
- Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Artur T L de Queiroz
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
| | - Aldina Barral
- Laboratório de Medicina e Saúde Pública de Precisão (MeSP2), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil.
| | - Richard J Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil.
| | - Leonardo P Farias
- Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil; Laboratório de Medicina e Saúde Pública de Precisão (MeSP2), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil.
| | | | - Pablo Ivan P Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
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Docampo R. Advances in the cellular biology, biochemistry, and molecular biology of acidocalcisomes. Microbiol Mol Biol Rev 2024; 88:e0004223. [PMID: 38099688 PMCID: PMC10966946 DOI: 10.1128/mmbr.00042-23] [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] [Indexed: 02/04/2024] Open
Abstract
SUMMARYAcidocalcisomes are organelles conserved during evolution and closely related to the so-called volutin granules of bacteria and archaea, to the acidocalcisome-like vacuoles of yeasts, and to the lysosome-related organelles of animal species. All these organelles have in common their acidity and high content of polyphosphate and calcium. They are characterized by a variety of functions from storage of phosphorus and calcium to roles in Ca2+ signaling, osmoregulation, blood coagulation, and inflammation. They interact with other organelles through membrane contact sites or by fusion, and have several enzymes, pumps, transporters, and channels.
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Affiliation(s)
- Roberto Docampo
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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Pal J, Sharma V, Khanna A, Saha S. The SET7 protein of Leishmania donovani moderates the parasite's response to a hostile oxidative environment. J Biol Chem 2024; 300:105720. [PMID: 38311179 PMCID: PMC10907163 DOI: 10.1016/j.jbc.2024.105720] [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: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
SET domain proteins methylate specific lysines on proteins, triggering stimulation or repression of downstream processes. Twenty-nine SET domain proteins have been identified in Leishmania donovani through sequence annotations. This study initiates the first investigation into these proteins. We find LdSET7 is predominantly cytosolic. Although not essential, set7 deletion slows down promastigote growth and hypersensitizes the parasite to hydroxyurea-induced G1/S arrest. Intriguingly, set7-nulls survive more proficiently than set7+/+ parasites within host macrophages, suggesting that LdSET7 moderates parasite response to the inhospitable intracellular environment. set7-null in vitro promastigote cultures are highly tolerant to hydrogen peroxide (H2O2)-induced stress, reflected in their growth pattern, and no detectable DNA damage at H2O2 concentrations tested. This is linked to reactive oxygen species levels remaining virtually unperturbed in set7-nulls in response to H2O2 exposure, contrasting to increased reactive oxygen species in set7+/+ cells under similar conditions. In analyzing the cell's ability to scavenge hydroperoxides, we find peroxidase activity is not upregulated in response to H2O2 exposure in set7-nulls. Rather, constitutive basal levels of peroxidase activity are significantly higher in these cells, implicating this to be a factor contributing to the parasite's high tolerance to H2O2. Higher levels of peroxidase activity in set7-nulls are coupled to upregulation of tryparedoxin peroxidase transcripts. Rescue experiments using an LdSET7 mutant suggest that LdSET7 methylation activity is critical to the modulation of the cell's response to oxidative environment. Thus, LdSET7 tunes the parasite's behavior within host cells, enabling the establishment and persistence of infection without eradicating the host cell population it needs for survival.
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Affiliation(s)
- Jyoti Pal
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Varshni Sharma
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Arushi Khanna
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.
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Lukeš J, Speijer D, Zíková A, Alfonzo JD, Hashimi H, Field MC. Trypanosomes as a magnifying glass for cell and molecular biology. Trends Parasitol 2023; 39:902-912. [PMID: 37679284 DOI: 10.1016/j.pt.2023.08.004] [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: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023]
Abstract
The African trypanosome, Trypanosoma brucei, has developed into a flexible and robust experimental model for molecular and cellular parasitology, allowing us to better combat these and related parasites that cause worldwide suffering. Diminishing case numbers, due to efficient public health efforts, and recent development of new drug treatments have reduced the need for continued study of T. brucei in a disease context. However, we argue that this pathogen has been instrumental in revolutionary discoveries that have widely informed molecular and cellular biology and justifies continuing research as an experimental model. Ongoing work continues to contribute towards greater understanding of both diversified and conserved biological features. We discuss multiple examples where trypanosomes pushed the boundaries of cell biology and hope to inspire researchers to continue exploring these remarkable protists as tools for magnifying the inner workings of cells.
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Affiliation(s)
- Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| | - Dave Speijer
- Medical Biochemistry, University of Amsterdam, AMC, Amsterdam, The Netherlands
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Juan D Alfonzo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Mark C Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; School of Life Sciences, University of Dundee, Dundee, UK
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