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Bustamante C, Díez-Mejía AF, Arbeláez N, Soares MJ, Robledo SM, Ochoa R, Varela-M. RE, Marín-Villa M. In Silico, In Vitro, and Pharmacokinetic Studies of UBMC-4, a Potential Novel Compound for Treating against Trypanosoma cruzi. Pathogens 2022; 11:pathogens11060616. [PMID: 35745470 PMCID: PMC9229894 DOI: 10.3390/pathogens11060616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 12/10/2022] Open
Abstract
The lack of therapeutic alternatives for the treatment of Chagas disease, a neglected disease, drives the discovery of new drugs with trypanocidal activity. Consequently, we conducted in vitro studies using UBMC-4, a potential Trypanosoma cruzi AKT-like pleckstrin homology (PH) domain inhibitory compound found using bioinformatics tools. The half effective concentration (EC50) on intracellular amastigotes was determined at 1.85 ± 1 μM showing low cytotoxicity (LC50) > 40 μM on human cell lines tested. In order to study the lethal effect caused by the compound on epimastigotes, morphological changes were assessed by scanning and transmission electron microscopy. Progressive alterations such as flagellum inactivation, cell size reduction, nuclear structure alteration, condensation of chromatin towards the nuclear periphery, vacuole formation, and mitochondrial swelling with kinetoplast integrity loss were evidenced. In addition, apoptosis-like markers in T. cruzi were assessed by flow cytometry, demonstrating that the effect of UBMC-4 on T. cruzi AKT-like kinase reduced the tolerance to nutritional stress-triggered, apoptosis-like events, including DNA fragmentation, mitochondrial damage, and loss of plasma membrane integrity. After this, UBMC-4 was formulated for oral administration and pharmacokinetics were analyzed in a mouse model. Finally, upon oral administration of 200 mg/kg in mice, we found that a UBMC-4 plasma concentration remaining in circulation beyond 24 h after administration is well described by the two-compartment model. We conclude that UBMC-4 has an effective trypanocidal activity in vitro at low concentrations and this effect is evident in T. cruzi cell structures. In mice, UBMC-4 was well absorbed and reached plasma concentrations higher than the EC50, showing features that would aid in developing a new drug to treat Chagas disease.
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Affiliation(s)
- Christian Bustamante
- PECET-Programa de Estudio y Control de Enfermedades Tropicales, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia; (A.F.D.-M.); (N.A.); (S.M.R.)
- Correspondence: (C.B.); (M.M.-V.)
| | - Andrés Felipe Díez-Mejía
- PECET-Programa de Estudio y Control de Enfermedades Tropicales, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia; (A.F.D.-M.); (N.A.); (S.M.R.)
| | - Natalia Arbeláez
- PECET-Programa de Estudio y Control de Enfermedades Tropicales, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia; (A.F.D.-M.); (N.A.); (S.M.R.)
| | - Maurilio José Soares
- Cell Biology Laboratory, Carlos Chagas Institute/Fiocruz, Curitiba 81350-010, Paraná, Brazil;
| | - Sara M. Robledo
- PECET-Programa de Estudio y Control de Enfermedades Tropicales, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia; (A.F.D.-M.); (N.A.); (S.M.R.)
| | - Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Rubén E. Varela-M.
- Grupo (QUIBIO), School of Basic Sciences, Universidad Santiago de Cali, Cali 760032, Colombia;
| | - Marcel Marín-Villa
- PECET-Programa de Estudio y Control de Enfermedades Tropicales, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia; (A.F.D.-M.); (N.A.); (S.M.R.)
- Correspondence: (C.B.); (M.M.-V.)
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Bosch SS, Lunev S, Batista FA, Linzke M, Kronenberger T, Dömling ASS, Groves MR, Wrenger C. Molecular Target Validation of Aspartate Transcarbamoylase from Plasmodium falciparum by Torin 2. ACS Infect Dis 2020; 6:986-999. [PMID: 32129597 DOI: 10.1021/acsinfecdis.9b00411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Malaria is a tropical disease that kills about half a million people around the world annually. Enzymatic reactions within pyrimidine biosynthesis have been proven to be essential for Plasmodium proliferation. Here we report on the essentiality of the second enzymatic step of the pyrimidine biosynthesis pathway, catalyzed by aspartate transcarbamoylase (ATC). Crystallization experiments using a double mutant ofPlasmodium falciparum ATC (PfATC) revealed the importance of the mutated residues for enzyme catalysis. Subsequently, this mutant was employed in protein interference assays (PIAs), which resulted in inhibition of parasite proliferation when parasites transfected with the double mutant were cultivated in medium lacking an excess of nutrients, including aspartate. Addition of 5 or 10 mg/L of aspartate to the minimal medium restored the parasites' normal growth rate. In vitro and whole-cell assays in the presence of the compound Torin 2 showed inhibition of specific activity and parasite growth, respectively. In silico analyses revealed the potential binding mode of Torin 2 to PfATC. Furthermore, a transgenic ATC-overexpressing cell line exhibited a 10-fold increased tolerance to Torin 2 compared with control cultures. Taken together, our results confirm the antimalarial activity of Torin 2, suggesting PfATC as a target of this drug and a promising target for the development of novel antimalarials.
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Affiliation(s)
- Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Fernando A. Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Alexander S. S. Dömling
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Matthew R. Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
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Fresh insights into the pyrimidine metabolism in the trypanosomatids. Parasit Vectors 2018; 11:87. [PMID: 29422065 PMCID: PMC5803862 DOI: 10.1186/s13071-018-2660-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/18/2018] [Indexed: 11/26/2022] Open
Abstract
The trypanosomatid parasites continue their killing spree resulting in significant annual mortality due to the lack of effective treatments and the prominence of these diseases in poorer countries. These dimorphic parasites thrive unchecked in the host system, outsmarting the immune mechanisms. An understanding of biology of these parasitic forms will help in the management and elimination of these fatal diseases. Investigation of various metabolic pathways in these parasites has shed light in the understanding of the unique biology of the trypansomatids. An understanding of these pathways have helped in tracing the soft targets in the metabolic pathways, which could be used as effective drug targets which would further impact the therupeutic implications. Pyrimidine pathway is a vital metabolic pathway which yields in the formation of pyrimidines, which are then integrated in nucleic acids (DNA and RNA) in sugars (UDP sugars) and lipids (CDP lipids). A wealth of data and information has been generated in the past decades by in-depth analyses of pyrimidine pathway in the trypanosomatid parasites, which can aid in the identification of anomalies between the parasitic and host counterpart which could be further harnessed to develop therapeutic interventions for the treatment of parasitic diseases. This review presents an updated and comprehensive detailing of the pyrimidine metabolism in the trypansomatids, their uniqueness and their distinctions, and its possible outcomes that would aid in the eradication of these parasitic diseases.
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Lunev S, Bosch SS, Batista FDA, Wrenger C, Groves MR. Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum. Acta Crystallogr F Struct Biol Commun 2016; 72:523-33. [PMID: 27380369 PMCID: PMC4933002 DOI: 10.1107/s2053230x16008475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/25/2016] [Indexed: 11/10/2022] Open
Abstract
The de novo pyrimidine-biosynthesis pathway of Plasmodium falciparum is a promising target for antimalarial drug discovery. The parasite requires a supply of purines and pyrimidines for growth and proliferation and is unable to take up pyrimidines from the host. Direct (or indirect) inhibition of de novo pyrimidine biosynthesis via dihydroorotate dehydrogenase (PfDHODH), the fourth enzyme of the pathway, has already been shown to be lethal to the parasite. In the second step of the plasmodial pyrimidine-synthesis pathway, aspartate and carbamoyl phosphate are condensed to N-carbamoyl-L-aspartate and inorganic phosphate by aspartate transcarbamoylase (PfATC). In this paper, the 2.5 Å resolution crystal structure of PfATC is reported. The space group of the PfATC crystals was determined to be monoclinic P21, with unit-cell parameters a = 87.0, b = 103.8, c = 87.1 Å, α = 90.0, β = 117.7, γ = 90.0°. The presented PfATC model shares a high degree of homology with the catalytic domain of Escherichia coli ATC. There is as yet no evidence of the existence of a regulatory domain in PfATC. Similarly to E. coli ATC, PfATC was modelled as a homotrimer in which each of the three active sites is formed at the oligomeric interface. Each active site comprises residues from two adjacent subunits in the trimer with a high degree of evolutional conservation. Here, the activity loss owing to mutagenesis of the key active-site residues is also described.
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Affiliation(s)
- Sergey Lunev
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Fernando de Assis Batista
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Matthew R. Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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Nara T, Hashimoto M, Hirawake H, Liao CW, Fukai Y, Suzuki S, Tsubouchi A, Morales J, Takamiya S, Fujimura T, Taka H, Mineki R, Fan CK, Inaoka DK, Inoue M, Tanaka A, Harada S, Kita K, Aoki T. Molecular interaction of the first 3 enzymes of the de novo pyrimidine biosynthetic pathway of Trypanosoma cruzi. Biochem Biophys Res Commun 2012; 418:140-3. [DOI: 10.1016/j.bbrc.2011.12.148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 01/18/2023]
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