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González-Montero MC, Andrés-Rodríguez J, García-Fernández N, Pérez-Pertejo Y, Reguera RM, Balaña-Fouce R, García-Estrada C. Targeting Trypanothione Metabolism in Trypanosomatids. Molecules 2024; 29:2214. [PMID: 38792079 PMCID: PMC11124245 DOI: 10.3390/molecules29102214] [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: 04/11/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Infectious diseases caused by trypanosomatids, including African trypanosomiasis (sleeping sickness), Chagas disease, and different forms of leishmaniasis, are Neglected Tropical Diseases affecting millions of people worldwide, mainly in vulnerable territories of tropical and subtropical areas. In general, current treatments against these diseases are old-fashioned, showing adverse effects and loss of efficacy due to misuse or overuse, thus leading to the emergence of resistance. For these reasons, searching for new antitrypanosomatid drugs has become an urgent necessity, and different metabolic pathways have been studied as potential drug targets against these parasites. Considering that trypanosomatids possess a unique redox pathway based on the trypanothione molecule absent in the mammalian host, the key enzymes involved in trypanothione metabolism, trypanothione reductase and trypanothione synthetase, have been studied in detail as druggable targets. In this review, we summarize some of the recent findings on the molecules inhibiting these two essential enzymes for Trypanosoma and Leishmania viability.
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Affiliation(s)
- María-Cristina González-Montero
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
| | - Julia Andrés-Rodríguez
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
| | - Nerea García-Fernández
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Rosa M. Reguera
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (M.-C.G.-M.); (J.A.-R.); (N.G.-F.); (Y.P.-P.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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2
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Rubio-Hernández M, Alcolea V, Pérez-Silanes S. Potential of sulfur-selenium isosteric replacement as a strategy for the development of new anti-chagasic drugs. Acta Trop 2022; 233:106547. [PMID: 35667455 DOI: 10.1016/j.actatropica.2022.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
Abstract
Current treatment for Chagas disease is based on only two drugs: benznidazole and nifurtimox. Compounds containing sulfur (S) in their structure have shown promising results in vitro and in vivo against Trypanosoma cruzi, the parasite causing Chagas disease. Notably, some reports show that the isosteric replacement of S by selenium (Se) could be an interesting strategy for the development of new compounds for the treatment of Chagas disease. To date, the activity against T. cruzi of three Se- containing groups has been compared with their S counterparts: selenosemicarbazones, selenoquinones, and selenocyanates. More studies are needed to confirm the positive results of Se compounds. Therefore, we have investigated S compounds described in the literature tested against T. cruzi. We focused on those tested in vivo that allowed isosteric replacement to propose their Se counterparts as promising compounds for the future development of new drugs against Chagas disease.
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Lim KS, Reidenbach AG, Hua BK, Mason JW, Gerry CJ, Clemons PA, Coley CW. Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function. J Chem Inf Model 2022; 62:2316-2331. [PMID: 35535861 PMCID: PMC10830332 DOI: 10.1021/acs.jcim.2c00041] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-encoded library (DEL) screening and quantitative structure-activity relationship (QSAR) modeling are two techniques used in drug discovery to find novel small molecules that bind a protein target. Applying QSAR modeling to DEL selection data can facilitate the selection of compounds for off-DNA synthesis and evaluation. Such a combined approach has been done recently by training binary classifiers to learn DEL enrichments of aggregated "disynthons" in order to accommodate the sparse and noisy nature of DEL data. However, a binary classification model cannot distinguish between different levels of enrichment, and information is potentially lost during disynthon aggregation. Here, we demonstrate a regression approach to learning DEL enrichments of individual molecules, using a custom negative-log-likelihood loss function that effectively denoises DEL data and introduces opportunities for visualization of learned structure-activity relationships. Our approach explicitly models the Poisson statistics of the sequencing process used in the DEL experimental workflow under a frequentist view. We illustrate this approach on a DEL dataset of 108,528 compounds screened against carbonic anhydrase (CAIX), and a dataset of 5,655,000 compounds screened against soluble epoxide hydrolase (sEH) and SIRT2. Due to the treatment of uncertainty in the data through the negative-log-likelihood loss used during training, the models can ignore low-confidence outliers. While our approach does not demonstrate a benefit for extrapolation to novel structures, we expect our denoising and visualization pipeline to be useful in identifying structure-activity trends and highly enriched pharmacophores in DEL data. Further, this approach to uncertainty-aware regression modeling is applicable to other sparse or noisy datasets where the nature of stochasticity is known or can be modeled; in particular, the Poisson enrichment ratio metric we use can apply to other settings that compare sequencing count data between two experimental conditions.
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Affiliation(s)
- Katherine S Lim
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Connor W Coley
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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4
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Almeida FS, Sousa GLS, Rocha JC, Ribeiro FF, de Oliveira MR, de Lima Grisi TCS, Araújo DAM, de C Nobre MS, Castro RN, Amaral IPG, Keesen TSL, de Moura RO. In vitro anti-Leishmania activity and molecular docking of spiro-acridine compounds as potential multitarget agents against Leishmania infantum. Bioorg Med Chem Lett 2021; 49:128289. [PMID: 34311084 DOI: 10.1016/j.bmcl.2021.128289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Leishmaniasis is an infectious disease with several limitations regarding treatment schemes. This work reports the anti-Leishmania activity of spiroacridine compounds against the promastigote (IC50 = 1.1 to 6.0 µg / mL) and amastigote forms of the best compounds (EC50 = 4.9 and 0.9 µg / mL) inLeishmania (L.) infantumand proposes an in-silico study with possible selective therapeutic targets for L. infantum. The substituted dimethyl-amine compound (AMTAC 11) showed the best leishmanicidal activity in vitro, and was found to interact with TryRandLdTopoI. comparisons with standard inhibitors were performed, and its main interactions were elucidated. Based on the biological assessment and the structure-activity relationship study, the spiroacridine compounds appear to be promisinganti-leishmaniachemotherapeutic agents to be explored.
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Affiliation(s)
- Fernanda S Almeida
- Programa de Doutorado em Biotecnologia, Rede Nordeste de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil; Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Gleyton L S Sousa
- Programa de Doutorado em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ 23897-000, Brazil
| | - Juliana C Rocha
- Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Frederico F Ribeiro
- Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Márcia Rosa de Oliveira
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Joao Pessoa, Paraíba CEP 58059-900, Brazil
| | | | - Demetrius A M Araújo
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Michelangela S de C Nobre
- Programa de Doutorado em Ciências Farmacêuticas, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Rosane N Castro
- Programa de Doutorado em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ 23897-000, Brazil
| | - Ian P G Amaral
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Tatjana S L Keesen
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil; Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Ricardo Olímpio de Moura
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual da Paraíba, Campina Grande, PB 58429-500, Brazil.
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Saccoliti F, Di Santo R, Costi R. Recent Advancement in the Search of Innovative Antiprotozoal Agents Targeting Trypanothione Metabolism. ChemMedChem 2020; 15:2420-2435. [PMID: 32805075 DOI: 10.1002/cmdc.202000325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/13/2020] [Indexed: 01/28/2023]
Abstract
Leishmania and Trypanosoma parasites are responsible for the challenging neglected tropical diseases leishmaniases, Chagas disease, and human African trypanosomiasis, which account for up to 40,000 deaths annually mainly in developing countries. Current chemotherapy relies on drugs with significant limitations in efficacy and safety, prompting the urgent need to explore innovative approaches to improve the drug discovery pipeline. The unique trypanothione-based redox pathway, which is absent in human hosts, is vital for all trypanosomatids and offers valuable opportunities to guide the rational development of specific, broad-spectrum and innovative anti-trypanosomatid agents. Major efforts focused on the key metabolic enzymes trypanothione synthetase-amidase and trypanothione reductase, whose inhibition should affect the entire pathway and, finally, parasite survival. Herein, we will report and comment on the most recent studies in the search for enzyme inhibitors, underlining the promising opportunities that have emerged so far to drive the exploration of future successful therapeutic approaches.
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Affiliation(s)
- Francesco Saccoliti
- D3 PharmaChemistry, Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P. le Aldo Moro 5, 00185, Roma, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P. le Aldo Moro 5, 00185, Roma, Italy
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6
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Battista T, Colotti G, Ilari A, Fiorillo A. Targeting Trypanothione Reductase, a Key Enzyme in the Redox Trypanosomatid Metabolism, to Develop New Drugs against Leishmaniasis and Trypanosomiases. Molecules 2020; 25:E1924. [PMID: 32326257 PMCID: PMC7221613 DOI: 10.3390/molecules25081924] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
The protozoans Leishmania and Trypanosoma, belonging to the same Trypanosomatidae family, are the causative agents of Leishmaniasis, Chagas disease, and human African trypanosomiasis. Overall, these infections affect millions of people worldwide, posing a serious health issue as well as socio-economical concern. Current treatments are inadequate, mainly due to poor efficacy, toxicity, and emerging resistance; therefore, there is an urgent need for new drugs.
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Affiliation(s)
- Theo Battista
- Department of Biochemical Sciences, Sapienza University, P.le A.Moro 5, 00185 Rome, Italy;
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, IBPM-CNR, c/o Department of Biochemical Sciences, Sapienza University, P.le A.Moro 5, 00185 Rome, Italy; (G.C.); (A.I.)
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, Italian National Research Council, IBPM-CNR, c/o Department of Biochemical Sciences, Sapienza University, P.le A.Moro 5, 00185 Rome, Italy; (G.C.); (A.I.)
| | - Annarita Fiorillo
- Department of Biochemical Sciences, Sapienza University, P.le A.Moro 5, 00185 Rome, Italy;
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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De Gasparo R, Halgas O, Harangozo D, Kaiser M, Pai EF, Krauth‐Siegel RL, Diederich F. Targeting a Large Active Site: Structure‐Based Design of Nanomolar Inhibitors of
Trypanosoma brucei
Trypanothione Reductase. Chemistry 2019; 25:11416-11421. [DOI: 10.1002/chem.201901664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Raoul De Gasparo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Ondrej Halgas
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - Dora Harangozo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute Socinstrasse 57 4002 Basel Switzerland
- University of Basel Petersplatz 1 4003 Basel Switzerland
| | - Emil F. Pai
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - R. Luise Krauth‐Siegel
- Biochemie-Zentrum Heidelberg (BZH)Universität Heidelberg Im Neuenheimer Feld 328 69120 Heidelberg Germany
| | - François Diederich
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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Quantitative Structure-Activity Relationships for Structurally Diverse Chemotypes Having Anti- Trypanosoma cruzi Activity. Int J Mol Sci 2019; 20:ijms20112801. [PMID: 31181717 PMCID: PMC6600563 DOI: 10.3390/ijms20112801] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Small-molecule compounds that have promising activity against macromolecular targets from Trypanosoma cruzi occasionally fail when tested in whole-cell phenotypic assays. This outcome can be attributed to many factors, including inadequate physicochemical and pharmacokinetic properties. Unsuitable physicochemical profiles usually result in molecules with a poor ability to cross cell membranes. Quantitative structure-activity relationship (QSAR) analysis is a valuable approach to the investigation of how physicochemical characteristics affect biological activity. In this study, artificial neural networks (ANNs) and kernel-based partial least squares regression (KPLS) were developed using anti-T. cruzi activity data for broadly diverse chemotypes. The models exhibited a good predictive ability for the test set compounds, yielding q2 values of 0.81 and 0.84 for the ANN and KPLS models, respectively. The results of this investigation highlighted privileged molecular scaffolds and the optimum physicochemical space associated with high anti-T. cruzi activity, which provided important guidelines for the design of novel trypanocidal agents having drug-like properties.
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10
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Tiwari N, Tanwar N, Munde M. Molecular insights into trypanothione reductase-inhibitor interaction: A structure-based review. Arch Pharm (Weinheim) 2018; 351:e1700373. [DOI: 10.1002/ardp.201700373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Neha Tiwari
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
| | - Neetu Tanwar
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
| | - Manoj Munde
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
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11
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De Gasparo R, Brodbeck-Persch E, Bryson S, Hentzen NB, Kaiser M, Pai EF, Krauth-Siegel RL, Diederich F. Biological Evaluation and X-ray Co-crystal Structures of Cyclohexylpyrrolidine Ligands for Trypanothione Reductase, an Enzyme from the Redox Metabolism of Trypanosoma. ChemMedChem 2018; 13:957-967. [PMID: 29624890 DOI: 10.1002/cmdc.201800067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Indexed: 01/02/2023]
Abstract
The tropical diseases human African trypanosomiasis, Chagas disease, and the various forms of leishmaniasis are caused by parasites of the family of trypanosomatids. These protozoa possess a unique redox metabolism based on trypanothione and trypanothione reductase (TR), making TR a promising drug target. We report the optimization of properties and potency of cyclohexylpyrrolidine inhibitors of TR by structure-based design. The best inhibitors were freely soluble and showed competitive inhibition constants (Ki ) against Trypanosoma (T.) brucei TR and T. cruzi TR and in vitro activities (half-maximal inhibitory concentration, IC50 ) against these parasites in the low micromolar range, with high selectivity against human glutathione reductase. X-ray co-crystal structures confirmed the binding of the ligands to the hydrophobic wall of the "mepacrine binding site" with the new, solubility-providing vectors oriented toward the surface of the large active site.
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Affiliation(s)
- Raoul De Gasparo
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Elke Brodbeck-Persch
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Steve Bryson
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Medical Sciences Building, #5358, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,The Campbell Family Institute for Cancer Research, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nina B Hentzen
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Emil F Pai
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Medical Sciences Building, #5358, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,The Campbell Family Institute for Cancer Research, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - R Luise Krauth-Siegel
- Biochemie-Zentrum Heidelberg (BZH), Universität Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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12
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Rodríguez-Becerra J, Cáceres-Jensen L, Hernández-Ramos J, Barrientos L. Identification of potential trypanothione reductase inhibitors among commercially available
$$\upbeta $$
β
-carboline derivatives using chemical space, lead-like and drug-like filters, pharmacophore models and molecular docking. Mol Divers 2017; 21:697-711. [DOI: 10.1007/s11030-017-9747-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/16/2017] [Indexed: 10/19/2022]
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13
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Leroux AE, Krauth-Siegel RL. Thiol redox biology of trypanosomatids and potential targets for chemotherapy. Mol Biochem Parasitol 2016; 206:67-74. [DOI: 10.1016/j.molbiopara.2015.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/09/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
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O’Sullivan MC, Durham TB, Valdes HE, Dauer KL, Karney NJ, Forrestel AC, Bacchi CJ, Baker JF. Dibenzosuberyl substituted polyamines and analogs of clomipramine as effective inhibitors of trypanothione reductase; molecular docking, and assessment of trypanocidal activities. Bioorg Med Chem 2015; 23:996-1010. [DOI: 10.1016/j.bmc.2015.01.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/04/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
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15
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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17
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Reguera RM, Calvo-Álvarez E, Alvarez-Velilla R, Balaña-Fouce R. Target-based vs. phenotypic screenings in Leishmania drug discovery: A marriage of convenience or a dialogue of the deaf? INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:355-7. [PMID: 25516847 PMCID: PMC4266804 DOI: 10.1016/j.ijpddr.2014.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drug discovery programs sponsored by public or private initiatives pursue the same ambitious goal: a crushing defeat of major Neglected Tropical Diseases (NTDs) during this decade. Both target-based and target-free screenings have pros and cons when it comes to finding potential small-molecule leads among chemical libraries consisting of myriads of compounds. Within the target-based strategy, crystals of pathogen recombinant-proteins are being used to obtain three-dimensional (3D) structures in silico for the discovery of structure-based inhibitors. On the other hand, genetically modified parasites expressing easily detectable reporters are in the pipeline of target-free (phenotypic) screenings. Furthermore, lead compounds can be scaled up to in vivo preclinical trials using rodent models of infection monitoring parasite loads by means of cutting-edge bioimaging devices. As such, those preferred are fluorescent and bioluminescent readouts due to their reproducibility and rapidity, which reduces the number of animals used in the trials and allows for an earlier stage detection of the infective process as compared with classical methods. In this review, we focus on the current differences between target-based and phenotypic screenings in Leishmania, as an approach that leads to the discovery of new potential drugs against leishmaniasis.
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Affiliation(s)
- Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Estefanía Calvo-Álvarez
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Raquel Alvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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18
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Structural insights into the enzymes of the trypanothione pathway: targets for antileishmaniasis drugs. Future Med Chem 2014; 5:1861-75. [PMID: 24144416 DOI: 10.4155/fmc.13.146] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Leishmaniasis is a neglected disease that kills 60,000 people worldwide, and which is caused by the protozoa Leishmania. The enzymes of the trypanothione pathway: trypanothione synthetase-amidase, trypanothione reductase (TR) and tryparedoxin-dependent peroxidase are absent in human hosts, and are essential for parasite survival and druggable. The most promising target is trypanothione synthetase-amidase, which has been also chemically validated. However, the structural data presented in this review show that TR also should be considered as a good target. Indeed, it is strongly inhibited by silver- and gold-containing compounds, which are active against Leishmania parasites and can be used for the development of novel antileishmanial agents. Moreover, TR trypanothione-binding site is not featureless but contains a sub-pocket where inhibitors bind, potentially useful for the design of new lead compounds.
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Persch E, Bryson S, Todoroff NK, Eberle C, Thelemann J, Dirdjaja N, Kaiser M, Weber M, Derbani H, Brun R, Schneider G, Pai EF, Krauth-Siegel RL, Diederich F. Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase. ChemMedChem 2014; 9:1880-91. [PMID: 24788386 DOI: 10.1002/cmdc.201402032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 01/16/2023]
Abstract
The causative agents of the parasitic disease human African trypanosomiasis belong to the family of trypanosomatids. These parasitic protozoa exhibit a unique thiol redox metabolism that is based on the flavoenzyme trypanothione reductase (TR). TR was identified as a potential drug target and features a large active site that allows a multitude of possible ligand orientations, which renders rational structure-based inhibitor design highly challenging. Herein we describe the synthesis, binding properties, and kinetic analysis of a new series of small-molecule inhibitors of TR. The conjunction of biological activities, mutation studies, and virtual ligand docking simulations led to the prediction of a binding mode that was confirmed by crystal structure analysis. The crystal structures revealed that the ligands bind to the hydrophobic wall of the so-called "mepacrine binding site". The binding conformation and potency of the inhibitors varied for TR from Trypanosoma brucei and T. cruzi.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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20
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Abstract
The potential of flavoproteins as targets of pharmacological treatments is immense. In this review we present an overview of the current research progress on medical interventions based on flavoproteins with a special emphasis on cancer, infectious diseases, and neurological disorders.
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Affiliation(s)
- Esther Jortzik
- Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
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21
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Toro MA, Sánchez-Murcia PA, Moreno D, Ruiz-Santaquiteria M, Alzate JF, Negri A, Camarasa MJ, Gago F, Velázquez S, Jiménez-Ruiz A. Probing the dimerization interface of Leishmania infantum trypanothione reductase with site-directed mutagenesis and short peptides. Chembiochem 2013; 14:1212-7. [PMID: 23744811 DOI: 10.1002/cbic.201200744] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/22/2013] [Indexed: 11/07/2022]
Abstract
Binding at the interface: We tested the inhibitory activity of a set of peptide sequences derived from an α-helix of the dimeric trypanothione reductase from Leishmania infantum. Replacement of a glutamic acid residue with a lysine promoted monomer dissociation and enzyme inhibition.
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Affiliation(s)
- Miguel A Toro
- Departamento de Biología de Sistemas, Unidad Asociada de I+D+I al CSIC, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
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22
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Kumari P, Sahal D, Jain SK, Chauhan VS. Bioactivity guided fractionation of leaves extract of Nyctanthes arbor tristis (Harshringar) against P falciparum. PLoS One 2012; 7:e51714. [PMID: 23300557 PMCID: PMC3530506 DOI: 10.1371/journal.pone.0051714] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/05/2012] [Indexed: 11/30/2022] Open
Abstract
Background Nyctanthes arbor-tristis (Harshringar, Night Jasmine) has been traditionally used in Ayurveda, Unani and other systems of medicine in India. The juice of its leaves has been used by various tribal populations of India in treatment of fevers resembling malaria. Aim of the study This work reports the antiplasmodial activity guided fractionation of Harshringar leaves extract. Methodology Crude ethanolic Harshringar leaves extract and its RPHPLC purified fractions were studied for antiplasmodial potency against 3D7 (CQ sensitive) and Dd2 (CQ resistant) strains of P.falciparum and subsequently subjected to bioassay guided fractionation using reverse phase chromatography to pursue the isolation of active fractions. Principal Findings Harshringar crude leaves extract and some of its RPHPLC purified fractions exhibited promising antiplasmodial potency against 3D7 and Dd2 strains of P.falciparum. Conclusions The present study has provided scientific validity to the traditional use of leaves extract of Harshringar against malaria leading to the conclusion that this plant holds promise with respect to antimalarial phytotherapy. This is the first scientific report of antiplasmodial activity of RPHPLC fractions of Harshringar leaves extract against P.falciparum strains.
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Affiliation(s)
- Pinky Kumari
- Malaria Research Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Dinkar Sahal
- Malaria Research Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - S. K. Jain
- Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Virander S. Chauhan
- Malaria Research Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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23
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Flohé L. The trypanothione system and its implications in the therapy of trypanosomatid diseases. Int J Med Microbiol 2012; 302:216-20. [PMID: 22889611 DOI: 10.1016/j.ijmm.2012.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biosynthesis and the use of trypanothione, a redox metabolite of parasitic trypanosomatids, are reviewed here with special emphasis on the development of trypanocidal drugs. This metabolic system is unique to and essential for the protozoal parasites. Selective inhibition of key elements of trypanothione metabolism, therefore, promises eradication of the parasites without affecting the host. Considering the metabolic importance and drugability of system components, inhibition of the enzymes for regeneration and de novo synthesis of trypanothione is rated as the most promising approach, while related peroxidases and redoxins are disregarded as targets because of limited chances to achieve selective inhibition. The organizational need to exploit the accumulating knowledge of trypanosomatid metabolism for medical practice is briefly addressed.
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Affiliation(s)
- Leopold Flohé
- Department of Chemistry, Otto-von-Guericke-Universität, Universitätsplatz 2, 39106 Magdeburg, Germany.
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Abstract
Drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein–ligand interactions. Structure- (SBDD) and ligand-based drug design (LBDD) approaches bring together the most powerful concepts in modern chemistry and biology, linking medicinal chemistry with structural biology. The definition and assessment of both chemical and biological space have revitalized the importance of exploring the intrinsic complementary nature of experimental and computational methods in drug design. Major challenges in this field include the identification of promising hits and the development of high-quality leads for further development into clinical candidates. It becomes particularly important in the case of neglected tropical diseases (NTDs) that affect disproportionately poor people living in rural and remote regions worldwide, and for which there is an insufficient number of new chemical entities being evaluated owing to the lack of innovation and R&D investment by the pharmaceutical industry. This perspective paper outlines the utility and applications of SBDD and LBDD approaches for the identification and design of new small-molecule agents for NTDs.
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Fueller F, Jehle B, Putzker K, Lewis JD, Krauth-Siegel RL. High throughput screening against the peroxidase cascade of African trypanosomes identifies antiparasitic compounds that inactivate tryparedoxin. J Biol Chem 2012; 287:8792-802. [PMID: 22275351 DOI: 10.1074/jbc.m111.338285] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In African trypanosomes, the detoxification of broad spectrum hydroperoxides relies on a unique cascade composed of trypanothione (T(SH)(2)), trypanothione reductase, tryparedoxin (Tpx), and nonselenium glutathione peroxidase-type enzymes. All three proteins are essential for Trypanosoma brucei. Here, we subjected the complete system to a high throughput screening approach with nearly 80,000 chemicals. Twelve compounds inhibited the peroxidase system. All but one carried chloroalkyl substituents. The detailed kinetic analysis showed that two compounds weakly inhibited trypanothione reductase, but none of them specifically interacted with the peroxidase. They proved to be time-dependent inhibitors of Tpx-modifying Cys-40, the first cysteine of its active site WCPPC motif. Importantly, gel shift assays verified Tpx as a target in the intact parasites. T(SH)(2), present in the in vitro assays and in the cells in high molar excess, did not interfere with Tpx inactivation. The compounds inhibited the proliferation of bloodstream T. brucei with EC(50) values down to <1 μM and exerted up to 83-fold lower toxicity toward HeLa cells. Irreversible inhibitors are traditionally regarded as unfavorable. However, a large number of antimicrobials and anticancer therapeutics acts covalently with their target protein. The compounds identified here also interacted with recombinant human thioredoxin, a distant relative of Tpx. This finding might even be exploited for thioredoxin-based anticancer drug development approaches reported recently. The fact that the T(SH)(2)/Tpx couple occupies a central position within the trypanosomal thiol metabolism and delivers electrons also for the synthesis of DNA precursors renders the parasite-specific oxidoreductase an attractive drug target molecule.
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Affiliation(s)
- Florian Fueller
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
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