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Adessi TG, Cantero J, Ballesteros-Casallas A, García ME, Nicotra VE, Paulino M. Identification of potential biological target for trypanocidal sesquiterpene lactones derivatives. J Biomol Struct Dyn 2023; 41:14510-14523. [PMID: 36856082 DOI: 10.1080/07391102.2023.2183031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
Sesquiterpene lactones are natural products of the Asteraceae family that have shown trypanocidal activity against Trypanosoma cruzi, even exceeding the effectiveness of drugs used in the treatment of American trypanosomiasis. However, there is no agreement on their mechanism of action and their specificity to interact with parasite proteins. For this reason, we aimed to find biological targets that can interact with these compounds by reverse virtual screening with ligand pharmacophores and putative binding sites and the use of bioinformatic databases. Therefore, 41 possible biological targets were found, and four of them (with crystallized proteins), interfering directly or indirectly in the trypanosomatid redox system, were studied in detail. As a first approach, we focused on the study of trypanothione reductase, and protein-ligand interaction fingerprint analyses were performed to find binding site determinants that promote a possible inhibition of the enzyme. This study contributes to the understanding of one of the putative mechanisms of action of sesquiterpene lactones on one of the numerous suggested targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tonino G Adessi
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Jorge Cantero
- Centro de Investigaciones Médicas, Facultad de Ciencias de la Salud, Universidad Nacional del Este, Minga Guazu, Paraguay
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
| | | | - Manuela E García
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Viviana E Nicotra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Margot Paulino
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
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Halder AK, Dias Soeiro Cordeiro MN. Advanced in Silico Methods for the Development of Anti- Leishmaniasis and Anti-Trypanosomiasis Agents. Curr Med Chem 2020; 27:697-718. [DOI: 10.2174/0929867325666181031093702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/24/2018] [Accepted: 09/19/2018] [Indexed: 11/22/2022]
Abstract
Leishmaniasis and trypanosomiasis occur primarily in undeveloped countries and account
for millions of deaths and disability-adjusted life years. Limited therapeutic options, high toxicity of
chemotherapeutic drugs and the emergence of drug resistance associated with these diseases demand
urgent development of novel therapeutic agents for the treatment of these dreadful diseases. In the last
decades, different in silico methods have been successfully implemented for supporting the lengthy and
expensive drug discovery process. In the current review, we discuss recent advances pertaining to in
silico analyses towards lead identification, lead modification and target identification of antileishmaniasis
and anti-trypanosomiasis agents. We describe recent applications of some important in
silico approaches, such as 2D-QSAR, 3D-QSAR, pharmacophore mapping, molecular docking, and so
forth, with the aim of understanding the utility of these techniques for the design of novel therapeutic
anti-parasitic agents. This review focuses on: (a) advanced computational drug design options; (b) diverse
methodologies - e.g.: use of machine learning tools, software solutions, and web-platforms; (c)
recent applications and advances in the last five years; (d) experimental validations of in silico predictions;
(e) virtual screening tools; and (f) rationale or justification for the selection of these in silico
methods.
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Affiliation(s)
- Amit Kumar Halder
- LAQV@ REQUIMTE/Department of Chemistry and Biochemistry, University of Porto, Porto 4169-007, Portugal
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da Silva AD, Dos Santos JA, Machado PA, Alves LA, Laque LC, de Souza VC, Coimbra ES, Capriles PVSZ. Insights about resveratrol analogs against trypanothione reductase of Leishmania braziliensis: Molecular modeling, computational docking and in vitro antileishmanial studies. J Biomol Struct Dyn 2018; 37:2960-2969. [PMID: 30058445 DOI: 10.1080/07391102.2018.1502096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this work, we combined molecular modeling, computational docking and in vitro analysis to explore the antileishmanial effect of some resveratrol analogs (ResAn), focusing on their pro-oxidant effect. The molecular target was the trypanothione reductase of Leishmania braziliensis (LbTryR), an essential component of the antioxidant defenses in trypanosomatid parasites. Three-dimensional structures of LbTryR were modeled and molecular docking studies of ResAn1-5 compounds showed the following affinity: ResAn1 > ResAn2 > ResAn4 > ResAn5 > ResAn3. Positive correlation was observed between these compounds' affinity to the LbTryR and the IC50 values against Leishmania sp (ResAn1 < ResAn2 < ResAn4), which allows for TryR being considered an important target for them. As the compound ResAn1 showed the best antileishmanial activity, and docking studies showed its high affinity for NADP binding site (NS) of TryR, plus having been able to induce ROS production in L. braziliensis promastigotes treated, ResAn1 probably occupies NS interfering in the electron transfer processes responsible for the catalytic reaction. The in silico prediction of ADMET properties suggests that ResAn1 may be a promising drug candidate with properties to cross biological membranes and high gastrointestinal absorption, not violating Lipinski's rules. Ultimately, the antileishmanial effect of ResAn can be associated with a pro-oxidant effect which, in turn, can be exploited as an antimicrobial agent. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adilson D da Silva
- a Departamento de Química , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Juliana A Dos Santos
- a Departamento de Química , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Patrícia A Machado
- b Departamento de Parasitologia, Microbiologia e Imunologia , I.C.B. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Lara A Alves
- c Programa de Pós-graduação em Modelagem Computacional, Departamento de Ciência da Computação , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Larissa C Laque
- c Programa de Pós-graduação em Modelagem Computacional, Departamento de Ciência da Computação , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Vinícius C de Souza
- c Programa de Pós-graduação em Modelagem Computacional, Departamento de Ciência da Computação , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Elaine S Coimbra
- b Departamento de Parasitologia, Microbiologia e Imunologia , I.C.B. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
| | - Priscila V S Z Capriles
- c Programa de Pós-graduação em Modelagem Computacional, Departamento de Ciência da Computação , I.C.E. Universidade Federal de Juiz de Fora , Juiz de Fora , Brazil
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Silva DG, Rocha JR, Sartori GR, Montanari CA. Highly predictive hologram QSAR models of nitrile-containing cruzain inhibitors. J Biomol Struct Dyn 2016; 35:3232-3249. [DOI: 10.1080/07391102.2016.1252282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Daniel Gedder Silva
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Josmar Rodrigues Rocha
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Carlos Alberto Montanari
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
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Vera B, Vázquez K, Mascayano C, Tapia RA, Espinosa V, Soto-Delgado J, Salas CO, Paulino M. Structural analysis and molecular docking of trypanocidal aryloxy-quinones in trypanothione and glutathione reductases: a comparison with biochemical data. J Biomol Struct Dyn 2016; 35:1785-1803. [PMID: 27232454 DOI: 10.1080/07391102.2016.1195283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A set of aryloxy-quinones, previously synthesized and evaluated against Trypanosoma cruzi epimastigotes cultures, were found more potent and selective than nifurtimox. One of the possible mechanisms of the trypanocidal activity of these quinones could be inhibition of trypanothione reductase (TR). Considering that glutathione reductase (GR) is the equivalent of TR in humans, biochemical, kinetic, and molecular docking studies in TR and GR were envisaged and compared with the trypanocidal and cytotoxic data of a set of aryloxy-quinones. Biochemical assays indicated that three naphthoquinones (Nq-h, Nq-g, and Nq-d) selectively inhibit TR and the TR kinetic analyses indicated that Nq-h inhibit TR in a noncompetitive mechanism. Molecular dockings were performed in TR and GR in the following three putative binding sites: the catalytic site, the dimer interface, and the nicotinamide adenine dinucleotide phosphate-binding site. In TR and GR, the aryloxy-quinones were found to exhibit high affinity for a site near it cognate-binding site in a place in which the noncompetitive kinetics could be justified. Taking as examples the three compounds with TR specificity (TRS) (Nq-h, Nq-g, and Nq-d), the presence of a network of contacts with the quinonic ring sustained by the triad of Lys62, Met400', Ser464' residues, seems to contribute hardly to the TRS. Compound Nq-b, a naphthoquinone with nitrophenoxy substituent, proved to be the best scaffold for the design of trypanocidal compounds with low toxicity. However, the compound displayed only a poor and non-selective effect toward TR indicating that TR inhibition is not the main reason for the antiparasitic activity of the aryloxy-quinones.
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Affiliation(s)
- Brenda Vera
- a Centro de Bioinformática estructural, DETEMA, Facultad de Química , UdelaR , Montevideo , Uruguay
| | - Karina Vázquez
- b Facultad de Química , Pontificia Universidad Católica de Chile , Santiago , Chile.,c Campus de Ciencias Agropecuarias, Facultad de Medicina Veterinaria y Zootecnia , Universidad Autónoma de Nuevo León , Nuevo León , Mexico
| | - Carolina Mascayano
- d Departamento de Ciencias del Ambiente, Facultad de Química y Biología , Universidad de Santiago, Chile , Santiago , Chile
| | - Ricardo A Tapia
- b Facultad de Química , Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Victoria Espinosa
- e Centro de investigaciones biomédicas y aplicadas, Escuela de Medicina, Facultad de Ciencias Médicas , Universidad de Santiago, Chile , Santiago , Chile
| | - Jorge Soto-Delgado
- f Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andrés Bello , Quillota 980, Viña del Mar , Chile
| | - Cristian O Salas
- b Facultad de Química , Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Margot Paulino
- a Centro de Bioinformática estructural, DETEMA, Facultad de Química , UdelaR , Montevideo , Uruguay
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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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