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Francesconi V, Rizzo M, Schenone S, Carbone A, Tonelli M. State-of-the-art Review on the Antiparasitic Activity of Benzimidazolebased Derivatives: Facing Malaria, Leishmaniasis, and Trypanosomiasis. Curr Med Chem 2024; 31:1955-1982. [PMID: 37718524 PMCID: PMC11071657 DOI: 10.2174/0929867331666230915093928] [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: 05/09/2023] [Revised: 06/19/2023] [Accepted: 08/27/2023] [Indexed: 09/19/2023]
Abstract
Protozoan parasites represent a significant risk for public health worldwide, afflicting particularly people in more vulnerable categories and cause large morbidity and heavy economic impact. Traditional drugs are limited by their toxicity, low efficacy, route of administration, and cost, reflecting their low priority in global health management. Moreover, the drug resistance phenomenon threatens the positive therapy outcome. This scenario claims the need of addressing more adequate therapies. Among the diverse strategies implemented, the medicinal chemistry efforts have also focused their attention on the benzimidazole nucleus as a promising pharmacophore for the generation of new drug candidates. Hence, the present review provides a global insight into recent progress in benzimidazole-based derivatives drug discovery against important protozoan diseases, such as malaria, leishmaniasis and trypanosomiasis. The more relevant chemical features and structure-activity relationship studies of these molecules are discussed for the purpose of paving the way towards the development of more viable drugs for the treatment of these parasitic infections.
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Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Marco Rizzo
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
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Virtual Screening of Benzimidazole Derivatives as Potential Triose Phosphate Isomerase Inhibitors with Biological Activity against Leishmania mexicana. Pharmaceuticals (Basel) 2023; 16:ph16030390. [PMID: 36986489 PMCID: PMC10058926 DOI: 10.3390/ph16030390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Leishmania mexicana (L. mexicana) is a causal agent of cutaneous leishmaniasis (CL), a “Neglected disease”, for which the search for new drugs is a priority. Benzimidazole is a scaffold used to develop antiparasitic drugs; therefore, it is interesting molecule against L. mexicana. In this work, a ligand-based virtual screening (LBVS) of the ZINC15 database was performed. Subsequently, molecular docking was used to predict the compounds with potential binding at the dimer interface of triosephosphate isomerase (TIM) of L. mexicana (LmTIM). Compounds were selected on binding patterns, cost, and commercial availability for in vitro assays against L. mexicana blood promastigotes. The compounds were analyzed by molecular dynamics simulation on LmTIM and its homologous human TIM. Finally, the physicochemical and pharmacokinetic properties were determined in silico. A total of 175 molecules with docking scores between −10.8 and −9.0 Kcal/mol were obtained. Compound E2 showed the best leishmanicidal activity (IC50 = 4.04 µM) with a value similar to the reference drug pentamidine (IC50 = 2.23 µM). Molecular dynamics analysis predicted low affinity for human TIM. Furthermore, the pharmacokinetic and toxicological properties of the compounds were suitable for developing new leishmanicidal agents.
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Vázquez-Jiménez LK, Juárez-Saldivar A, Gómez-Escobedo R, Delgado-Maldonado T, Méndez-Álvarez D, Palos I, Bandyopadhyay D, Gaona-Lopez C, Ortiz-Pérez E, Nogueda-Torres B, Ramírez-Moreno E, Rivera G. Ligand-Based Virtual Screening and Molecular Docking of Benzimidazoles as Potential Inhibitors of Triosephosphate Isomerase Identified New Trypanocidal Agents. Int J Mol Sci 2022; 23:ijms231710047. [PMID: 36077439 PMCID: PMC9456061 DOI: 10.3390/ijms231710047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Trypanosoma cruzi (T. cruzi) is a parasite that affects humans and other mammals. T. cruzi depends on glycolysis as a source of adenosine triphosphate (ATP) supply, and triosephosphate isomerase (TIM) plays a key role in this metabolic pathway. This enzyme is an attractive target for the design of new trypanocidal drugs. In this study, a ligand-based virtual screening (LBVS) from the ZINC15 database using benzimidazole as a scaffold was accomplished. Later, a molecular docking on the interface of T. cruzi TIM (TcTIM) was performed and the compounds were grouped by interaction profiles. Subsequently, a selection of compounds was made based on cost and availability for in vitro evaluation against blood trypomastigotes. Finally, the compounds were analyzed by molecular dynamics simulation, and physicochemical and pharmacokinetic properties were determined using SwissADME software. A total of 1604 molecules were obtained as potential TcTIM inhibitors. BP2 and BP5 showed trypanocidal activity with half-maximal lytic concentration (LC50) values of 155.86 and 226.30 µM, respectively. Molecular docking and molecular dynamics simulation analyzes showed a favorable docking score of BP5 compound on TcTIM. Additionally, BP5 showed a low docking score (−5.9 Kcal/mol) on human TIM compared to the control ligand (−7.2 Kcal/mol). Both compounds BP2 and BP5 showed good physicochemical and pharmacokinetic properties as new anti-T. cruzi agents.
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Affiliation(s)
- Lenci K Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Alfredo Juárez-Saldivar
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Rogelio Gómez-Escobedo
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Timoteo Delgado-Maldonado
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Domingo Méndez-Álvarez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Isidro Palos
- Unidad Académica Multidisciplinaria Reynosa-Rodhe, Universidad Autónoma de Tamaulipas, Reynosa 88779, Mexico
| | - Debasish Bandyopadhyay
- Department of Chemistry and SEEMS, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Carlos Gaona-Lopez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Eyra Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Benjamín Nogueda-Torres
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México 07320, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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4
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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Chávez-García C, Karttunen M. Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases. J Chem Inf Model 2022; 62:668-677. [PMID: 35044757 DOI: 10.1021/acs.jcim.1c01501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homodimeric triosephosphate isomerases (TIMs) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have markedly similar amino-acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their reactivation speed after being denatured, have significant differences. The causes of these differences were explored with microsecond-scale molecular dynamics (MD) simulations of three different TIM proteins: TcTIM, TbTIM, and a chimeric protein, Mut1. We examined their electrostatic interactions and explored the impact of simulation length on them. The same salt bridge between catalytic residues Lys 14 and Glu 98 was observed in all three proteins, but key differences were found in other interactions that the catalytic amino acids form. In particular, a cation-π interaction between catalytic amino acids Lys 14 and His 96 and both a salt bridge and a hydrogen bond between catalytic Glu 168 and residue Arg 100 were only observed in TcTIM. Furthermore, although TcTIM forms less hydrogen bonds than TbTIM and Mut1, its hydrogen bond network spans almost the entire protein, connecting the residues in both monomers. This work provides new insight into the mechanisms that give rise to the different behavior of these proteins. The results also show the importance of long simulations.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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Betancourt-Conde I, Avitia-Domínguez C, Hernández-Campos A, Castillo R, Yépez-Mulia L, Oria-Hernández J, Méndez ST, Sierra-Campos E, Valdez-Solana M, Martínez-Caballero S, Hermoso JA, Romo-Mancillas A, Téllez-Valencia A. Benzimidazole Derivatives as New and Selective Inhibitors of Arginase from Leishmania mexicana with Biological Activity against Promastigotes and Amastigotes. Int J Mol Sci 2021; 22:ijms222413613. [PMID: 34948408 PMCID: PMC8705706 DOI: 10.3390/ijms222413613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
Leishmaniasis is a disease caused by parasites of the Leishmania genus that affects 98 countries worldwide, 2 million of new cases occur each year and more than 350 million people are at risk. The use of the actual treatments is limited due to toxicity concerns and the apparition of resistance strains. Therefore, there is an urgent necessity to find new drugs for the treatment of this disease. In this context, enzymes from the polyamine biosynthesis pathway, such as arginase, have been considered a good target. In the present work, a chemical library of benzimidazole derivatives was studied performing computational, enzyme kinetics, biological activity, and cytotoxic effect characterization, as well as in silico ADME-Tox predictions, to find new inhibitors for arginase from Leishmania mexicana (LmARG). The results show that the two most potent inhibitors (compounds 1 and 2) have an I50 values of 52 μM and 82 μM, respectively. Moreover, assays with human arginase 1 (HsARG) show that both compounds are selective for LmARG. According to molecular dynamics simulation studies these inhibitors interact with important residues for enzyme catalysis. Biological activity assays demonstrate that both compounds have activity against promastigote and amastigote, and low cytotoxic effect in murine macrophages. Finally, in silico prediction of their ADME-Tox properties suggest that these inhibitors support the characteristics to be considered drug candidates. Altogether, the results reported in our study suggest that the benzimidazole derivatives are an excellent starting point for design new drugs against leishmanisis.
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Affiliation(s)
- Irene Betancourt-Conde
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango 34000, Mexico;
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango 34000, Mexico;
- Correspondence: (C.A.-D.); (A.T.-V.); Tel.: +52-618-812-1687 (A.T.-V.)
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (A.H.-C.); (R.C.)
| | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (A.H.-C.); (R.C.)
| | - Lilián Yépez-Mulia
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad-Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (J.O.-H.); (S.T.M.)
| | - Sara T. Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (J.O.-H.); (S.T.M.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Siseth Martínez-Caballero
- Departamento de Cristalografía y Biología Estructural, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain; (S.M.-C.); (J.A.H.)
| | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain; (S.M.-C.); (J.A.H.)
| | - Antonio Romo-Mancillas
- Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico;
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango 34000, Mexico;
- Correspondence: (C.A.-D.); (A.T.-V.); Tel.: +52-618-812-1687 (A.T.-V.)
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Vázquez-Jiménez LK, Moreno-Herrera A, Juárez-Saldivar A, González-González A, Ortiz-Pérez E, Paz-González AD, Palos-Pizarro I, Ramírez-Moreno E, Rivera G. Recent Advances in the Development of Triose Phosphate Isomerase Inhibitors as Antiprotozoal Agents. Curr Med Chem 2021; 29:2504-2529. [PMID: 34517794 DOI: 10.2174/0929867328666210913090928] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/10/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Parasitic diseases caused by protozoa such as Chagas disease, leishmaniasis, malaria, African trypanosomiasis, amebiasis, trichomoniasis, and giardiasis are considered serious public health problems in developing countries. Drug-resistance among parasites justifies the search for new therapeutic drugs and the identification of new targets becomes a valuable approach. In this scenario, glycolysis pathway which consists of the conversion of glucose into pyruvate plays an important role in the protozoa energy supply and it is therefore considered as a promising target. In this pathway, triose phosphate isomerase (TIM) plays an essential role in efficient energy production. Furthermore, protozoa TIM show structural differences with human enzyme counterparts suggesting the possibility of obtaining selective inhibitors. Therefore, TIM is considered a valid approach to develop new antiprotozoal agents, inhibiting the glycolysis in the parasite. OBJECTIVE In this review, we discuss the drug design strategies, structure-activity relationship, and binding modes of outstanding TIM inhibitors against Trypanosoma cruzi, Trypanosoma brucei, Plasmodium falciparum, Giardia lamblia, Leishmania mexicana, Trichomonas vaginalis, and Entamoeba histolytica. RESULTS TIM inhibitors showed mainly aromatic systems and symmetrical structure, where the size and type of heteroatom are important for enzyme inhibition. This inhibition is mainly based on the interaction with i) the interfacial region of TIM inducing changes on the quaternary and tertiary structure or ii) with the TIM catalytic region were the main pathways that disabled the catalytic activity of the enzyme. CONCLUSION Benzothiazole, benzoxazole, benzimidazole, and sulfhydryl derivatives stand out as TIM inhibitors. In silico and in vitro studies demonstrate that the inhibitors bind mainly at the TIM dimer interface. In this review, the development of new TIM inhibitors as antiprotozoal drugs is demonstrated as an important pharmaceutical strategy that may lead to new therapies for these ancient parasitic diseases.
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Affiliation(s)
- Lenci K Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Antonio Moreno-Herrera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alfredo Juárez-Saldivar
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alonzo González-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Eyra Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Isidro Palos-Pizarro
- Unidad Académica Multidisciplinaria Reynosa-Rodhe, Universidad Autónoma de Tamaulipas, 88779 Reynosa. Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, 07320 Ciudad de México. Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
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Esters of quinoxaline-7-carboxylate-1,4-di- N-oxide as Trichomonas vaginalis triosephosphate isomerase inhibitors. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2021; 71:485-495. [PMID: 36654088 DOI: 10.2478/acph-2021-0032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 01/20/2023]
Abstract
Trichomoniasis is a public health problem worldwide. Trichomoniasis treatment consists of the use of nitroimidazole derivatives; however, therapeutic ineffectiveness occurs in 5 to 20 % of the cases. Therefore, it is essential to propose new pharmacological agents against this disease. In this work, esters of quinoxaline-7-carboxylate-1,4-di-N-oxide (EQX-NO) were evaluated in in vitro assays as novel trichomonicidal agents. Additionally, an in vitro enzyme assay and molecular docking analysis against triosephosphate isomerase of Trichomonas vaginalis to confirm their mechanism of action were performed. Ethyl (compound 12) and n-propyl (compound 37) esters of quinoxaline-7-carboxy-late-1,4-di-N-oxide derivatives showed trichomonicidal activity comparable to nitazoxanide, whereas five methyl (compounds 5, 15, 19, 20 and 22), four isopropyl (compounds 28, 29, 30 and 34), three ethyl (compounds 4, 13 and 23) and one npropyl (compound 35) ester derivatives displayed activity comparable to albendazole. Compounds 6 and 20 decreased 100 % of the enzyme activity of recombinant protein triosephosphate isomerase.
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Vique-Sánchez JL, Jiménez-Pineda A, Benítez-Cardoza CG. Amoebicidal effect of 5,5'-[(4-nitrophenyl)methylene]bis-6-hydroxy-2-mercapto-3-methyl-4(3H)-pyrimidinone), a new drug against Entamoeba histolytica. Arch Pharm (Weinheim) 2020; 354:e2000263. [PMID: 33017058 DOI: 10.1002/ardp.202000263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023]
Abstract
Entamoeba histolytica is a cosmopolitan protozoan parasite that can produce infections in the intestine and some organs (liver, lungs, and brain), with worldwide prevalence. There are treatments against E. histolytica (antiparasitics), but as the drugs used in these treatments have presented some type of resistance and/or side effects, there are cases with complications of this disease. Therefore, it is necessary to develop new drugs aimed at a specific therapeutic target against this parasite. Here, we used the compound 5,5'-[(4-nitrophenyl)methylene]bis(6-hydroxy-2-mercapto-3-methyl-4(3H)-pyrimidinone) in the patenting process (called D4). D4 has a reported specific use against a glycolytic enzyme, the triosephosphate isomerase of Trichomonas vaginalis (TvTIM). We determined that D4 has an amoebicidal effect in in vitro cultures, with an IC50 value of 18.5 µM, and we proposed a specific site of interaction (Lys77, His110, Gln115, and Glu118) in the triosephosphate isomerase of E. histolytica (EhTIM). Furthermore, compound D4 has favorable experimental and theoretical toxicity results. Therefore, D4 should be further investigated as a potential drug against E. histolytica.
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Affiliation(s)
- José L Vique-Sánchez
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, Baja California, México
| | - Albertana Jiménez-Pineda
- Laboratorio de Investigación Bioquímica, ENMyH-Instituto Politécnico Nacional, Ciudad de México, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, ENMyH-Instituto Politécnico Nacional, Ciudad de México, México
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10
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Benítez‐Cardoza CG, Jiménez‐Pineda A, Angles‐Falconi SI, Fernández‐Velasco DA, Vique‐Sánchez JL. Potential Site to Direct Selective Compounds in the Triosephosphate Isomerase for the Development of New Drugs. ChemistrySelect 2020. [DOI: 10.1002/slct.202000820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Albertana Jiménez‐Pineda
- Laboratorio de Investigación BioquímicaENMyH-Instituto Politécnico Nacional Ciudad de México México
| | - Sergio I. Angles‐Falconi
- División Académica Multidisciplinaria de Jalpa de MéndezUniversidad Juárez Autónoma de Tabasco Jalpa de Méndez Tabasco, México
| | - Daniel A. Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de ProteínasDepartamento de BioquímicaFacultad de MedicinaUniversidad Nacional Autónoma de México México
| | - José L. Vique‐Sánchez
- Laboratorio de Investigación BioquímicaENMyH-Instituto Politécnico Nacional Ciudad de México México
- Facultad de MedicinaUniversidad Autónoma de Baja California Mexicali, BC, México
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11
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Benítez-Cardoza CG, Fernández-Velasco DA, Vique-Sánchez JL. Triosephosphate Isomerase Inhibitors as Potential Drugs against Clostridium perfringens. ChemistrySelect 2020. [DOI: 10.1002/slct.201904632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Daniel A. Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas; Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de; México México
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Novel and selective inactivators of Triosephosphate isomerase with anti-trematode activity. Sci Rep 2020; 10:2587. [PMID: 32054976 PMCID: PMC7018972 DOI: 10.1038/s41598-020-59460-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Trematode infections such as schistosomiasis and fascioliasis cause significant morbidity in an estimated 250 million people worldwide and the associated agricultural losses are estimated at more than US$ 6 billion per year. Current chemotherapy is limited. Triosephosphate isomerase (TIM), an enzyme of the glycolytic pathway, has emerged as a useful drug target in many parasites, including Fasciola hepatica TIM (FhTIM). We identified 21 novel compounds that selectively inhibit this enzyme. Using microscale thermophoresis we explored the interaction between target and compounds and identified a potent interaction between the sulfonyl-1,2,4-thiadiazole (compound 187) and FhTIM, which showed an IC50 of 5 µM and a Kd of 66 nM. In only 4 hours, this compound killed the juvenile form of F. hepatica with an IC50 of 3 µM, better than the reference drug triclabendazole (TCZ). Interestingly, we discovered in vitro inhibition of FhTIM by TCZ, with an IC50 of 7 µM suggesting a previously uncharacterized role of FhTIM in the mechanism of action of this drug. Compound 187 was also active against various developmental stages of Schistosoma mansoni. The low toxicity in vitro in different cell types and lack of acute toxicity in mice was demonstrated for this compound, as was demonstrated the efficacy of 187in vivo in F. hepatica infected mice. Finally, we obtained the first crystal structure of FhTIM at 1.9 Å resolution which allows us using docking to suggest a mechanism of interaction between compound 187 and TIM. In conclusion, we describe a promising drug candidate to control neglected trematode infections in human and animal health.
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A Fluorinated Phenylbenzothiazole Arrests the Trypanosoma cruzi Cell Cycle and Diminishes the Infection of Mammalian Host Cells. Antimicrob Agents Chemother 2020; 64:AAC.01742-19. [PMID: 31712204 DOI: 10.1128/aac.01742-19] [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] [Received: 08/27/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022] Open
Abstract
Chagas disease (CD) is a human infection caused by Trypanosoma cruzi CD was traditionally endemic to the Americas; however, due to migration it has spread to countries where it is not endemic. The current chemotherapy to treat CD induces several side effects, and its effectiveness in the chronic phase of the disease is controversial. In this contribution, substituted phenylbenzothiazole derivatives were synthesized and biologically evaluated as trypanocidal agents against Trypanosoma cruzi The trypanocidal activities of the most promising compounds were determined through systematic in vitro screening, and their modes of action were determined as well. The physicochemical-structural characteristics responsible for the trypanocidal effects were identified, and their possible therapeutic application in Chagas disease is discussed. Our results show that the fluorinated compound 2-methoxy-4-[5-(trifluoromethyl)-1,3-benzothiazol-2-yl] phenol (BT10) has the ability to inhibit the proliferation of epimastigotes [IC50(Epi) = 23.1 ± 1.75 μM] and intracellular forms of trypomastigotes [IC50(Tryp) = 8.5 ± 2.9 μM] and diminishes the infection index by more than 80%. In addition, BT10 has the ability to selectively fragment 68% of the kinetoplastid DNA compared with 5% of nucleus DNA. The mode of action for BT10 on T. cruzi suggests that the development of fluorinated phenylbenzothiazole with electron-withdrawing substituent is a promising strategy for the design of trypanocidal drugs.
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Castro-Torres E, Jimenez-Sandoval P, Fernández-de Gortari E, López-Castillo M, Baruch-Torres N, López-Hidalgo M, Peralta-Castro A, Díaz-Quezada C, Sotelo-Mundo RR, Benitez-Cardoza CG, Espinoza-Fonseca LM, Ochoa-Leyva A, Brieba LG. Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic Bacteria Synechocystis. Front Mol Biosci 2018; 5:103. [PMID: 30538993 PMCID: PMC6277545 DOI: 10.3389/fmolb.2018.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 11/05/2018] [Indexed: 11/18/2022] Open
Abstract
In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria Synechocystis (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α)8 fold. We found that oxidizing agents diamide (DA) and H2O2, as well as thiol-conjugating agents such as oxidized glutathione (GSSG) and methyl methanethiosulfonate (MMTS), do not inhibit the catalytic activity of SyTPI at concentrations required to inactivate plastidic and cytosolic TPIs from the plant model Arabidopsis thaliana (AtpdTPI and AtcTPI, respectively). The crystal structure of SyTPI revealed that each monomer contains three cysteines, C47, C127, and C176; however only the thiol group of C176 is solvent exposed. While AtcTPI and AtpdTPI are redox-regulated by chemical modifications of their accessible and reactive cysteines, we found that C176 of SyTPI is not sensitive to redox modification in vitro. Our data let us postulate that SyTPI was replaced by a eukaryotic TPI, because the latter contains redox-sensitive cysteines that may be subject to post-translational modifications required for modulating TPI's enzymatic activity.
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Affiliation(s)
- Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Eli Fernández-de Gortari
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States
| | - Margarita López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico
| | - L Michel Espinoza-Fonseca
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
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15
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Wu M, Yan M, Xu J, Yin X, Dong X, Wang N, Gu X, Xie Y, Lai W, Jing B, Peng X, Yang G. Molecular characterization of triosephosphate isomerase from Echinococcus granulosus. Parasitol Res 2018; 117:3169-3176. [PMID: 30027383 DOI: 10.1007/s00436-018-6015-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 07/12/2018] [Indexed: 11/26/2022]
Abstract
Cystic echinococcosis (CE) is a zoonosis that can be caused by the larvae of Echinococcus granulosus; this disease occurs worldwide and is highly endemic in China. E. granulosus can produce energy by glycolysis as well as both aerobic and anaerobic respirations. Triosephosphate isomerase is a glycolytic enzyme present in a wide range of organisms and plays an important role in glycolysis. However, there has been little research on triosephosphate isomerase from E. granulosus (Eg-TIM). Here, we present a bioinformatic characterization and the experimentally determined tissue distribution characteristics of Eg-TIM. We also explored its potential value for diagnosing CE in sheep using indirect enzyme-linked immunosorbent assay (ELISA). Native Eg-TIM was located in the neck and hooks of protoscoleces (PSCs), as well as the tegument and parenchyma tissue of adult worms. The entire germinal layer was also Eg-TIM positive. Western blots showed that recombinant Eg-TIM (rEg-TIM) reacts with positive serum from sheep and had good immunogenicity. Indirect ELISA exhibited low specificity (53.6%) and low sensitivity (87.5%) and cross-reacted with both Taenia multiceps and Taenia hydatigena. Our results suggest that TIM may take part in the growth and development of E. granulosus. Furthermore, we determined that rEg-TIM is not a suitable serodiagnostic antigen for CE in sheep.
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Affiliation(s)
- Maodi Wu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Min Yan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxiao Yin
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaowei Dong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ning Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weimin Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Ya'an, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
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Díaz-Mazariegos S, Cabrera N, Perez-Montfort R. Three unrelated and unexpected amino acids determine the susceptibility of the interface cysteine to a sulfhydryl reagent in the triosephosphate isomerases of two trypanosomes. PLoS One 2018; 13:e0189525. [PMID: 29342154 PMCID: PMC5771576 DOI: 10.1371/journal.pone.0189525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/27/2017] [Indexed: 11/23/2022] Open
Abstract
Proteins with great sequence similarity usually have similar structure, function and other physicochemical properties. But in many cases, one or more of the physicochemical or functional characteristics differ, sometimes very considerably, among these homologous proteins. To better understand how critical amino acids determine quantitative properties of function in proteins, the responsible residues must be located and identified. This can be difficult to achieve, particularly in cases where multiple amino acids are involved. In this work, two triosephosphate isomerases with very high similarity from two related human parasites were used to address one such problem. We demonstrate that a seventy-fold difference in the reactivity of an interface cysteine to the sulfhydryl reagent methylmethane sulfonate in these two enzymes depends on three amino acids located far away from this critical residue and which could not have been predicted using other current methods. Starting from previous observations with chimeric proteins involving these two triosephosphate isomerases, we developed a strategy involving additive mutant enzymes and selected site directed mutants to locate and identify the three amino acids. These three residues seem to induce changes in the interface cysteine in reactivity by increasing (or decreasing) its apparent pKa. Some enzymes with four to seven mutations also exhibited altered reactivity. This study completes a strategy for identifying key residues in the sequences of proteins that can have applications in future protein structure-function studies.
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Affiliation(s)
- Selma Díaz-Mazariegos
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ruy Perez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail:
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17
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Vázquez-Raygoza A, Cano-González L, Velázquez-Martínez I, Trejo-Soto PJ, Castillo R, Hernández-Campos A, Hernández-Luis F, Oria-Hernández J, Castillo-Villanueva A, Avitia-Domínguez C, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A. Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies. Molecules 2017; 22:molecules22122055. [PMID: 29186784 PMCID: PMC6149853 DOI: 10.3390/molecules22122055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023] Open
Abstract
Human African Trypanosomiasis (HAT), a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by Trypanosoma brucei. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, T. brucei depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM) is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds 1, 2 and 3) with an I50 value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM) activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.
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Affiliation(s)
- Alejandra Vázquez-Raygoza
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Lucia Cano-González
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Israel Velázquez-Martínez
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Pedro Josué Trejo-Soto
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Rafael Castillo
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Alicia Hernández-Campos
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Francisco Hernández-Luis
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Jesús Oria-Hernández
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Adriana Castillo-Villanueva
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Claudia Avitia-Domínguez
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Erick Sierra-Campos
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Mónica Valdez-Solana
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Alfredo Téllez-Valencia
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
- Correspondence: ; Tel./Fax: +52-618-812-1687
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18
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Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1696-1706. [PMID: 27614148 DOI: 10.1016/j.bbapap.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/17/2016] [Accepted: 09/03/2016] [Indexed: 01/12/2023]
Abstract
Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico; Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora 83000, Mexico
| | - Jesus S Carrasco-Miranda
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Claudia D Ramirez-Aguirre
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico; Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Av. Instituto Politécnico Nacional. s/n., 23096, La Paz, Baja California Sur 23096, Mexico; Cátedras CONACyT, Dirección Adjunta de Desarrollo Científico, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de Mexico, 03940, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico.
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19
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Synthesis and trypanocidal activity of novel benzimidazole derivatives. Bioorg Med Chem Lett 2016; 26:4377-81. [DOI: 10.1016/j.bmcl.2015.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 01/01/2023]
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20
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López-Castillo LM, Jiménez-Sandoval P, Baruch-Torres N, Trasviña-Arenas CH, Díaz-Quezada C, Lara-González S, Winkler R, Brieba LG. Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1817. [PMID: 27999583 PMCID: PMC5138414 DOI: 10.3389/fpls.2016.01817] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/18/2016] [Indexed: 05/04/2023]
Abstract
In plants triosephosphate isomerase (TPI) interconverts glyceraldehyde 3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) during glycolysis, gluconeogenesis, and the Calvin-Benson cycle. The nuclear genome of land plants encodes two tpi genes, one gene product is located in the cytoplasm and the other is imported into the chloroplast. Herein we report the crystal structures of the TPIs from the vascular plant Arabidopsis thaliana (AtTPIs) and address their enzymatic modulation by redox agents. Cytoplasmic TPI (cTPI) and chloroplast TPI (pdTPI) share more than 60% amino acid identity and assemble as (β-α)8 dimers with high structural homology. cTPI and pdTPI harbor two and one accessible thiol groups per monomer respectively. cTPI and pdTPI present a cysteine at an equivalent structural position (C13 and C15 respectively) and cTPI also contains a specific solvent accessible cysteine at residue 218 (cTPI-C218). Site directed mutagenesis of residues pdTPI-C15, cTPI-C13, and cTPI-C218 to serine substantially decreases enzymatic activity, indicating that the structural integrity of these cysteines is necessary for catalysis. AtTPIs exhibit differential responses to oxidative agents, cTPI is susceptible to oxidative agents such as diamide and H2O2, whereas pdTPI is resistant to inhibition. Incubation of AtTPIs with the sulfhydryl conjugating reagents methylmethane thiosulfonate (MMTS) and glutathione inhibits enzymatic activity. However, the concentration necessary to inhibit pdTPI is at least two orders of magnitude higher than the concentration needed to inhibit cTPI. Western-blot analysis indicates that residues cTPI-C13, cTPI-C218, and pdTPI-C15 conjugate with glutathione. In summary, our data indicate that AtTPIs could be redox regulated by the derivatization of specific AtTPI cysteines (cTPI-C13 and pdTPI-C15 and cTPI-C218). Since AtTPIs have evolved by gene duplication, the higher resistance of pdTPI to redox agents may be an adaptive consequence to the redox environment in the chloroplast.
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Affiliation(s)
- Laura M. López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
- Departamento de Biotecnología y Bioquímica, CINVESTAV Unidad IrapuatoIrapuato Guanajuato, Mexico
| | - Pedro Jiménez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
| | - Samuel Lara-González
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C.San Luis Potosí, Mexico
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, CINVESTAV Unidad IrapuatoIrapuato Guanajuato, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato Guanajuato, Mexico
- *Correspondence: Luis G. Brieba
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Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015; 109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022] Open
Abstract
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Doga Findik
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
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22
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Álvarez G, Martínez J, Varela J, Birriel E, Cruces E, Gabay M, Leal SM, Escobar P, Aguirre-López B, Cabrera N, Tuena de Gómez-Puyou M, Gómez Puyou A, Pérez-Montfort R, Yaluff G, Torres S, Serna E, Vera de Bilbao N, González M, Cerecetto H. Development of bis-thiazoles as inhibitors of triosephosphate isomerase from Trypanosoma cruzi. Identification of new non-mutagenic agents that are active in vivo. Eur J Med Chem 2015; 100:246-56. [PMID: 26094151 DOI: 10.1016/j.ejmech.2015.06.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 06/05/2015] [Accepted: 06/06/2015] [Indexed: 10/23/2022]
Abstract
The neglected disease American trypanosomiasis is one of the major health problems in Latin America. Triosephosphate isomerase from Trypanosoma cruzi (TcTIM), the etiologic agent of this disease, has been proposed as a druggable target. Some bis-benzothiazoles have been described as irreversible inhibitors of this enzyme. On the other hand, new bioactive furane-containing thiazoles have been described as excellent in vivo anti-T. cruzi agents. This encouraged us to design and develop new bis-thiazoles with potential use as drugs for American trypanosomiasis. The bis-thiazol 5, 3,3'-allyl-2,2'-bis[3-(2-furyl)-2-propenylidenehydrazono]-2,2',3,3'-tetrahydro-4,4'-bisthiazole, showed the best in vitro anti-T. cruzi profile with a higher selectivity index than the reference drugs Nifurtimox and Benznidazole against amastigote form of the parasite. This derivative displayed marginal activity against TcTIM however the bis-thiazol 14, 3-allyl-2-[3-(2-furyl)-2-propenylidenehydrazono]-3'-phenyl-2'-(3-phenyl-2-propenylidenehydrazono]-2,2',3,3'-tetrahydro-4,4'-bisthiazole, was an excellent inhibitor of the enzyme of the parasite. The absence of both in vitro mutagenic and in vivo toxicity effects, together with the activity of bis-thiazol 5in vivo, suggests that this compound is a promising anti-T. cruzi agent surpassing the "hit-to-lead" stage in the drug development process.
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Affiliation(s)
- Guzmán Álvarez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Jennyfer Martínez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Javier Varela
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Estefania Birriel
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Eugenia Cruces
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Martín Gabay
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Sandra M Leal
- Centro de Investigaciones de Enfermedades Tropicales, Departamento de Ciencias Básicas, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Patricia Escobar
- Centro de Investigaciones de Enfermedades Tropicales, Departamento de Ciencias Básicas, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, México
| | - Armando Gómez Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, México
| | - Gloria Yaluff
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - Susana Torres
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - Elva Serna
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - Ninfa Vera de Bilbao
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - Mercedes González
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
| | - Hugo Cerecetto
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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23
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Minini L, Álvarez G, González M, Cerecetto H, Merlino A. Molecular docking and molecular dynamics simulation studies of Trypanosoma cruzi triosephosphate isomerase inhibitors. Insights into the inhibition mechanism and selectivity. J Mol Graph Model 2015; 58:40-9. [DOI: 10.1016/j.jmgm.2015.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 11/22/2014] [Accepted: 02/12/2015] [Indexed: 02/05/2023]
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Kryshchyshyn A, Kaminskyy D, Grellier P, Lesyk R. Trends in research of antitrypanosomal agents among synthetic heterocycles. Eur J Med Chem 2014; 85:51-64. [DOI: 10.1016/j.ejmech.2014.07.092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 12/18/2022]
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25
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Zinsser VL, Hoey EM, Trudgett A, Timson DJ. Biochemical characterisation of triose phosphate isomerase from the liver fluke Fasciola hepatica. Biochimie 2013; 95:2182-9. [DOI: 10.1016/j.biochi.2013.08.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/07/2013] [Indexed: 11/29/2022]
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26
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Zinsser VL, Farnell E, Dunne DW, Timson DJ. Triose phosphate isomerase from the blood flukeSchistosoma mansoni: Biochemical characterisation of a potential drug and vaccine target. FEBS Lett 2013; 587:3422-7. [DOI: 10.1016/j.febslet.2013.09.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/04/2013] [Accepted: 09/11/2013] [Indexed: 11/26/2022]
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27
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Saucedo-Mendiola ML, Salas-Pacheco JM, Nájera H, Rojo-Domínguez A, Yépez-Mulia L, Avitia-Domínguez C, Téllez-Valencia A. Discovery of Entamoeba histolytica hexokinase 1 inhibitors through homology modeling and virtual screening. J Enzyme Inhib Med Chem 2013; 29:325-32. [PMID: 23534932 DOI: 10.3109/14756366.2013.779265] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Entamoeba histolytica, the parasite which causes amebiasis is responsible for 110,000 deaths a year. Entamoeba histolytica depends on glycolysis to obtain ATP for cellular work. According to metabolic flux studies, hexokinase exerts the highest flux control of this metabolic pathway; therefore, it is an excellent target in the search of new antiamebic drugs. To this end, a tridimensional model of E. histolytica hexokinase 1 (EhHK1) was constructed and validated by homology modeling. After virtual screening of 14,400 small molecules, the 100 with the best docking scores were selected, purchased and assessed in their inhibitory capacity. The results showed that three molecules (compounds 2921, 11275 and 2755) inhibited EhHK1 with an I50 of 48, 91 and 96 µM, respectively. Thus, we found the first inhibitors of EhHK1 that can be used in the search of new chemotherapeutic agents against amebiasis.
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Affiliation(s)
- María Leticia Saucedo-Mendiola
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinaria S/N Circuito Universitario , Durango , México
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28
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Alvarez G, Martínez J, Aguirre-López B, Cabrera N, Pérez-Díaz L, Gómez-Puyou MTD, Gómez-Puyou A, Pérez-Montfort R, Garat B, Merlino A, González M, Cerecetto H. New chemotypes as Trypanosoma cruzi triosephosphate isomerase inhibitors: a deeper insight into the mechanism of inhibition. J Enzyme Inhib Med Chem 2013; 29:198-204. [DOI: 10.3109/14756366.2013.765415] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guzmán Alvarez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República
MontevideoUruguay
| | - Jennyfer Martínez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República
MontevideoUruguay
| | - Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
Mexico DF.Mexico
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
Mexico DF.Mexico
| | - Leticia Pérez-Díaz
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República
MontevideoUruguay
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
Mexico DF.Mexico
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
Mexico DF.Mexico
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
Mexico DF.Mexico
| | - Beatriz Garat
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República
MontevideoUruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República
MontevideoUruguay
| | - Mercedes González
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República
MontevideoUruguay
| | - Hugo Cerecetto
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República
MontevideoUruguay
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29
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Alvarez G, Aguirre-López B, Cabrera N, Marins EB, Tinoco L, Batthyány CI, de Gómez-Puyou MT, Puyou AG, Pérez-Montfort R, Cerecetto H, González M. 1,2,4-thiadiazol-5(4H)-ones: a new class of selective inhibitors of Trypanosoma cruzi triosephosphate isomerase. Study of the mechanism of inhibition. J Enzyme Inhib Med Chem 2012; 28:981-9. [PMID: 22803666 DOI: 10.3109/14756366.2012.700928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CONTEXT Triosephosphate isomerase (TIM) is a ubiquitous enzyme that has been targeted for the discovery of small molecular weight compounds with potential use against Trypanosoma cruzi, the causative agent of Chagas disease. We have identified a new selective inhibitor chemotype of TIM from T. cruzi (TcTIM), 1,2,4-thiadiazol-5(4H)-one. OBJECTIVE Study the mechanism of TcTIM inhibition by a 1,2,4-thiadiazol derivative. METHODS We performed the biochemical characterization of the interaction of the 1,2,4-thiadiazol derivative with the wild-type and mutant TcTIMs, using DOSY-NMR and MS experiments. Studies of T. cruzi growth inhibition were additionally carried out. RESULTS AND CONCLUSION At low micromolar concentrations, the compound induces highly selective irreversible inactivation of TcTIM through non-covalent binding. Our studies indicate that it interferes with the association of the two monomers of the dimeric enzyme. We also show that it inhibits T. cruzi growth in culture.
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Affiliation(s)
- Guzmán Alvarez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República , Uruguay
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30
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Kurkcuoglu Z, Ural G, Demet Akten E, Doruker P. Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human. Mol Inform 2011; 30:986-95. [PMID: 27468153 DOI: 10.1002/minf.201100109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/12/2011] [Indexed: 11/06/2022]
Abstract
We aim to uncover the binding modes of benzothiazoles, which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM), by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings, the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits, whereas non-inhibitors mostly choose other sites. In contrast, TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site, which may explain its relatively higher inhibition effect on hTIM.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - Gulgun Ural
- Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - E Demet Akten
- Department of Information Technologies, Kadir Has University, Cibali, 34083, Istanbul, Turkey.
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey. .,Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
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Romo-Mancillas A, Téllez-Valencia A, Yépez-Mulia L, Hernández-Luis F, Hernández-Campos A, Castillo R. The design and inhibitory profile of new benzimidazole derivatives against triosephosphate isomerase from Trypanosoma cruzi: a problem of residue motility. J Mol Graph Model 2011; 30:90-9. [PMID: 21798779 DOI: 10.1016/j.jmgm.2011.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/18/2011] [Accepted: 06/21/2011] [Indexed: 10/17/2022]
Abstract
To develop a new set of compounds with inhibitory activity against the triosephosphate isomerase of Trypanosoma cruzi (TcTIM), a group of benzimidazole derivatives was studied using four different docking procedures. These docking procedures differ in the number and type of mobile residues considered in the analysis. As a result of this methodology, a clustered analysis of plausible candidate structures was produced. A different set of previously synthesized compounds was used to validate this analysis. The validation showed that the best results correspond to the docking procedure in which the residues near the hydrophobic pocket of the protein's interface were considered mobile. A binding site for the best candidates was identified. Residues Tyr103, Glu105 and Lys113, among others, are important for the binding of this kind of compound. Residue Tyr103 is different in the human TIM, thus establishing a key feature for the future design of selective inhibitors.
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Affiliation(s)
- Antonio Romo-Mancillas
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México DF 04510, Mexico
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32
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Moraes J, Arreola R, Cabrera N, Saramago L, Freitas D, Masuda A, da Silva Vaz I, Tuena de Gomez-Puyou M, Perez-Montfort R, Gomez-Puyou A, Logullo C. Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 41:400-409. [PMID: 21396445 DOI: 10.1016/j.ibmb.2011.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 02/17/2011] [Accepted: 02/28/2011] [Indexed: 05/30/2023]
Abstract
Triosephosphate isomerase (TIM) is an enzyme with a role in glycolysis and gluconeogenesis by catalyzing the interconversion between glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This enzyme has been used as a target in endoparasite drug development. In this work we cloned, expressed, purified and studied kinetic and structural characteristics of TIM from tick embryos, Rhipicephalus (Boophilus) microplus (BmTIM). The Km and Vmax of the recombinant BmTIM with glyceraldehyde 3-phosphate as substrate, were 0.47 mM and 6031 μmol min⁻¹ mg protein⁻¹, respectively. The resolution of the diffracted crystal was estimated to be 2.4 Å and the overall data showed that BmTIM is similar to other reported dimeric TIMs. However, we found that, in comparison to other TIMs, BmTIM has the highest content of cysteine residues (nine cysteine residues per monomer). Only two cysteines could make disulfide bonds in monomers of BmTIM. Furthermore, BmTIM was highly sensitive to the action of the thiol reagents dithionitrobenzoic acid and methyl methane thiosulfonate, suggesting that there are five cysteines exposed in each dimer and that these residues could be employed in the development of species-specific inhibitors.
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Affiliation(s)
- Jorge Moraes
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal-RJ, CBB, UENF, Avenida Alberto Lamego 2000, Horto, Campos dos Goytacazes, RJ, CEP 28015-620, Brazil
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33
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García-Torres I, Cabrera N, Torres-Larios A, Rodríguez-Bolaños M, Díaz-Mazariegos S, Gómez-Puyou A, Perez-Montfort R. Identification of amino acids that account for long-range interactions in two triosephosphate isomerases from pathogenic trypanosomes. PLoS One 2011; 6:e18791. [PMID: 21533154 PMCID: PMC3078909 DOI: 10.1371/journal.pone.0018791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 03/18/2011] [Indexed: 11/18/2022] Open
Abstract
For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.
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Affiliation(s)
- Itzhel García-Torres
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Mónica Rodríguez-Bolaños
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Selma Díaz-Mazariegos
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
| | - Ruy Perez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México DF, Mexico
- * E-mail:
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Hassan N, Gárate MP, Sandoval T, Espinoza L, Piñeiro Á, Ruso JM. On the self-assembly of a highly selective benzothiazole-based TIM inhibitor in aqueous solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:16681-16689. [PMID: 20949959 DOI: 10.1021/la102916x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Benzothiazole is a common scaffold on which many bioactive structures, including protein inhibitors and biosensors, are based. The potential self-aggregation of such molecules to form nanoparticles is relevant for a number of practical applications. 3-(2-Benzothiazolylthio)-propanesulfonic acid (BTS) has been reported as a powerful and selective inhibitor of triosephosphate isomerase from Trypanosoma cruzi, the parasite that causes the Chagas' disease. Electrical conductivity, sound velocity, density, and nuclear magnetic resonance experiments as a function of temperature and of NaCl concentration have been performed in the present work to provide a comprehensive physicochemical description of this compound in aqueous solution. Molecular dynamics simulations of the same system were also performed to characterize the structure and dynamic behavior of the corresponding aggregates at several concentrations of BTS.
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Affiliation(s)
- Natalia Hassan
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
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Chávez-Calvillo R, Costas M, Hernández-Trujillo J. Theoretical analysis of intermolecular interactions of selected residues of triosephosphate isomerase from Trypanosoma cruzi with its inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid. Phys Chem Chem Phys 2010; 12:2067-74. [DOI: 10.1039/b918104k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gayosso-De-Lucio J, Torres-Valencia M, Rojo-Domínguez A, Nájera-Peña H, Aguirre-López B, Salas-Pacheco J, Avitia-Domínguez C, Téllez-Valencia A. Selective inactivation of triosephosphate isomerase from Trypanosoma cruzi by brevifolin carboxylate derivatives isolated from Geranium bellum Rose. Bioorg Med Chem Lett 2009; 19:5936-9. [PMID: 19733070 DOI: 10.1016/j.bmcl.2009.08.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 02/06/2023]
Abstract
In the search of molecules that can serve as leads in the design of a new drug for the treatment of Chagas' disease, we found that some brevifolin carboxylate derivatives isolated from Geranium bellum Rose, inactivate triosephosphate isomerase from Trypanosoma cruzi (TcTIM) in a species-specific manner. After spectroscopic characterization, these compounds were identified as methylbrevifolin carboxylate (1), ethylbrevifolin carboxylate (2), butylbrevifolin carboxylate (3) and the methylated derivate methyl tri-O-methylbrevifolin carboxylate (4). The concentrations required to inactivate fifty percent the activity of TcTIM were 6.5, 8 and 14 microM of 1, 2 and 3, respectively, while compound 4 had no inhibitory effect. Molecular docking simulations of 1 on the structure of TcTIM showed that residues of both monomers interact with the compound. These compounds are very selective with respect to the parasite enzyme, since they showed no effect on the activity of human TIM at concentrations as high as 1mM. In conclusion, the brevifolin carboxylate derivatives described here are excellent leads in the search of a new chemotherapy for the treatment of this disease.
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Affiliation(s)
- Juan Gayosso-De-Lucio
- Area Académica de Farmacia, Universidad Autónoma del Estado de Hidalgo, Exhacienda La Concepción, Tilcuautla, Hidalgo 42160, Mexico
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37
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Expression and activity of glycogen synthase kinase during vitellogenesis and embryogenesis of Rhipicephalus (Boophilus) microplus. Vet Parasitol 2009; 161:261-9. [PMID: 19285806 DOI: 10.1016/j.vetpar.2009.01.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 01/12/2009] [Accepted: 01/26/2009] [Indexed: 11/24/2022]
Abstract
Glycogen synthase kinase 3 (GSK-3) is classically described as a key enzyme involved in glycogen metabolism in mammals. GSK-3 belongs to a highly conserved family of serine/threonine protein kinases, whose members are involved in hormonal regulation, nuclear signaling, and cell fate determination in higher eukaryotes. We have cloned and characterized the RmGSK-3 gene from Rhipicephalus (Boophilus) microplus tick embryos. DNA and protein sequence analysis depicted high similarity to the corresponding enzyme, from both vertebrate and invertebrate animals. In addition, the mRNA transcription profile identified during embryogenesis was analyzed. We observed that the RmGSK-3 mRNA rapidly decreases from the 1st to 3rd day of development, and increases from the 3rd to 15th day. After the 15th day of development, we observed a near 50% reduction in RmGSK-3 mRNA transcription in comparison to the 1st day. We detected the GSK-3beta isoform in egg homogenates throughout embryogenesis using Western blot analysis. RmGSK-3 mRNA was present in fat body, midgut and ovary from partially and fully engorged adult female ticks. The highest mRNA level was observed in ovaries from both developmental stages and in first-day eggs. Furthermore, RmGSK-3 activity correlated with glycogen content variation. Finally, kinase activity in egg homogenates was inhibited by the specific inhibitor, SB-216763. These data suggest that RmGSK-3beta may be involved in glycogen metabolism regulation during R. microplus embryogenesis.
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38
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Díaz-Vergara N, Piñeiro Á. Molecular Dynamics Study of Triosephosphate Isomerase from Trypanosoma cruzi in Water/Decane Mixtures. J Phys Chem B 2008; 112:3529-39. [DOI: 10.1021/jp7102275] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norma Díaz-Vergara
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
| | - Ángel Piñeiro
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
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39
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Cabrera N, Hernández-Alcántara G, Mendoza-Hernández G, Gómez-Puyou A, Perez-Montfort R. Key Residues of Loop 3 in the Interaction with the Interface Residue at Position 14 in Triosephosphate Isomerase from Trypanosoma brucei. Biochemistry 2008; 47:3499-506. [DOI: 10.1021/bi702439r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nallely Cabrera
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70242, 04510 México DF, Mexico, Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, 04530 México DF, Mexico, and Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México DF, Mexico
| | - Gloria Hernández-Alcántara
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70242, 04510 México DF, Mexico, Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, 04530 México DF, Mexico, and Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México DF, Mexico
| | - Guillermo Mendoza-Hernández
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70242, 04510 México DF, Mexico, Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, 04530 México DF, Mexico, and Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México DF, Mexico
| | - Armando Gómez-Puyou
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70242, 04510 México DF, Mexico, Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, 04530 México DF, Mexico, and Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México DF, Mexico
| | - Ruy Perez-Montfort
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70242, 04510 México DF, Mexico, Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, 04530 México DF, Mexico, and Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México DF, Mexico
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41
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Mixcoha-Hernández E, Moreno-Vargas LM, Rojo-Domínguez A, Benítez-Cardoza CG. Thermal-unfolding Reaction of Triosephosphate Isomerase from Trypanosoma cruzi. Protein J 2007; 26:491-8. [PMID: 17763928 DOI: 10.1007/s10930-007-9090-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Thermal denaturation of triosephosphate isomerase from Trypanosoma cruzi was studied by circular dicrhoism and fluorescence spectroscopies. The unfolding transition was found to be highly irreversible even at the very early stages of the reaction. Kinetic studies, allowed us to identify consecutive reactions. Firstly, only the tryptophan environment is altered. Next, changes on the secondary structure and hydrophobic surface exposure measured by 1-anilino-8-naphthalenesulfonate (ANS) binding were observed. Further conformational changes imply additional modifications on the secondary and tertiary structures and release of the hydrophobic dye leading to the formation of the unfolded state that is prone to aggregate.
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Affiliation(s)
- Edgar Mixcoha-Hernández
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
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42
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Espinoza-Fonseca LM, Trujillo-Ferrara JG. Toward a rational design of selective multi-trypanosomatid inhibitors: a computational docking study. Bioorg Med Chem Lett 2006; 16:6288-92. [PMID: 16997551 DOI: 10.1016/j.bmcl.2006.09.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 09/05/2006] [Accepted: 09/07/2006] [Indexed: 11/18/2022]
Abstract
Compound V7, a benzothiazole which was recently found as selective inhibitor of trypanosomal TIMs, was docked into TIMs from Trypanosoma cruzi, Trypanosoma brucei, Entamoeba histolytica, Plasmodium falciparum, yeast, and human. Structural analyses revealed the importance of the accessibility to the two aromatic clusters located at the dimer's interface for the selective inhibition of trypanosomal TIMs. Thus, it was found that different accessibilities of the protein interface of TIMs plays an important role in the inhibitory activity of benzothiazoles. These findings will contribute to the rational development and improvement of benzothiazoles to be used as multi-trypanosomatid inhibitors.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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43
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Olivares-Illana V, Pérez-Montfort R, López-Calahorra F, Costas M, Rodríguez-Romero A, Tuena de Gómez-Puyou M, Gómez Puyou A. Structural differences in triosephosphate isomerase from different species and discovery of a multitrypanosomatid inhibitor. Biochemistry 2006; 45:2556-60. [PMID: 16489748 DOI: 10.1021/bi0522293] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the interfaces of homodimeric triosephosphate isomerase (TIM) from eight different species. The crystal structures of the enzymes showed that a portion of the interface is markedly similar in TIMs from Trypanosoma cruzi (TcTIM), Trypanosoma brucei, and Leishmania mexicana and significantly different from that of TIMs from human, yeast, chicken, Plasmodium falciparum, and Entamoeba histolytica. Since this interfacial region is central in the stability of TcTIM, we hypothesized that it would be possible to find agents that selectively affect the stability of TIMs from the three trypanosomatids. We found that 6,6'-bisbenzothiazole-2,2' diamine in the low micromolar range causes a desirable irreversible inactivation of the enzymes from the three trypanosomatids and has no effect on the other five TIMs. Thus, the data indicate that it is possible to find compounds that induce selective inactivation of the enzymes from three different trypanosomatids.
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Affiliation(s)
- Vanesa Olivares-Illana
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D. F., México
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44
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Fonvielle M, Mariano S, Therisod M. New inhibitors of rabbit muscle triose-phosphate isomerase. Bioorg Med Chem Lett 2005; 15:2906-9. [PMID: 15911278 DOI: 10.1016/j.bmcl.2005.03.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 03/08/2005] [Accepted: 03/17/2005] [Indexed: 10/25/2022]
Abstract
We describe the synthesis and evaluation of three new competitive inhibitors of triose-phosphate isomerase. One of them (phosphoglycoloamidoxime: K(i) = 4.5 microM) is among the best reversible inhibitors so far reported for this enzyme.
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Affiliation(s)
- M Fonvielle
- LCBB, ICMMO, Bat. 420, Université Paris-Sud, Orsay, France
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45
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Espinoza-Fonseca LM, Trujillo-Ferrara JG. Structural considerations for the rational design of selective anti-trypanosomal agents: the role of the aromatic clusters at the interface of triosephosphate isomerase dimer. Biochem Biophys Res Commun 2005; 328:922-8. [PMID: 15707966 DOI: 10.1016/j.bbrc.2005.01.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Indexed: 11/30/2022]
Abstract
Seven benzothiazoles were successfully docked into the interface of both human and trypanosomal triosephosphate isomerases, and the binding free energies of each complex were calculated using the program AutoDock. Structural and energetical analysis of the complexes showed that large benzothiazoles could form more stable complexes with trypanosomal triosephosphate isomerase than with human triosephosphate isomerase. Thus, we hypothesize that the distribution of the residues forming the aromatic clusters at the enzyme's interface and the size of the inhibitors might play a crucial role in the selective inhibition of TcTIM. Following the findings here presented, it is possible to better determine the structural elements involved in the origin of the selectivity at the trypanosomal triosephosphate isomerase interface, and to enable efficient anti-trypanosomal drug design strategies.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Physical Chemistry, FNS, Comenius University, Mlynská dolina, Bratislava 84215, Slovakia.
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46
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Blanchard JE, Elowe NH, Huitema C, Fortin PD, Cechetto JD, Eltis LD, Brown ED. High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase. ACTA ACUST UNITED AC 2005; 11:1445-53. [PMID: 15489171 PMCID: PMC7134594 DOI: 10.1016/j.chembiol.2004.08.011] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Revised: 07/20/2004] [Accepted: 08/10/2004] [Indexed: 11/24/2022]
Abstract
The causative agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus, SARS-CoV. The main proteinase of SARS-CoV, 3CLpro, is an attractive target for therapeutics against SARS owing to its fundamental role in viral replication. We sought to identify novel inhibitors of 3CLpro to advance the development of appropriate therapies in the treatment of SARS. 3CLpro was cloned, expressed, and purified from the Tor2 isolate. A quenched fluorescence resonance energy transfer assay was developed for 3CLpro to screen the proteinase against 50,000 drug-like small molecules on a fully automated system. The primary screen identified 572 hits; through a series of virtual and experimental filters, this number was reduced to five novel small molecules that show potent inhibitory activity (IC50 = 0.5-7 microM) toward SARS-CoV 3CLpro.
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Affiliation(s)
- Jan E Blanchard
- McMaster High Throughput Screening Laboratory, Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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47
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Espinoza-Fonseca LM, Trujillo-Ferrara JG. Exploring the possible binding sites at the interface of triosephosphate isomerase dimer as a potential target for anti-tripanosomal drug design. Bioorg Med Chem Lett 2005; 14:3151-4. [PMID: 15149664 DOI: 10.1016/j.bmcl.2004.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Revised: 04/02/2004] [Accepted: 04/07/2004] [Indexed: 10/26/2022]
Abstract
To explore the possible binding sites at the interface of tripanosomal triosephosphate isomerase, fully flexible benzothiazoles were docked onto the dimer interface. Docking studies revealed that the most favorable interactions occur in the aromatic clusters of the dimeric form. Hence is purposed that the dimer disruption is not via Cys 15, as presented in last studies, but it could be carried out through the unstabilization of pi-pi interactions of two aromatic clusters present in the interface. These studies enable a novel alternative for rational structure-based anti-tripanosomal drug design.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Departamento de Bioquímica, Escuela Superior de Medicina del Instituto Politécnico Nacional, Apartado Postal 42-161, C.P. 11340, Mexico City, Mexico.
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48
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Téllez-Valencia A, Olivares-Illana V, Hernández-Santoyo A, Pérez-Montfort R, Costas M, Rodríguez-Romero A, López-Calahorra F, Tuena De Gómez-Puyou M, Gómez-Puyou A. Inactivation of triosephosphate isomerase from Trypanosoma cruzi by an agent that perturbs its dimer interface. J Mol Biol 2004; 341:1355-65. [PMID: 15321726 DOI: 10.1016/j.jmb.2004.06.056] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 06/10/2004] [Accepted: 06/14/2004] [Indexed: 11/17/2022]
Abstract
We characterized by crystallographic, calorimetric and biochemical methods the action of a low molecular weight compound, 3-(2-benzothiazolylthio)-1-propanesulfonic acid (compound 8) that binds to the dimer interface of triosephosphate isomerase from Trypanosoma cruzi (TcTIM) and thereby abolishes its function with a high level of selectivity. The kinetics of TcTIM inactivation by the agent and isothermal titration calorimetry experiments showed that the binding of two molecules of the compound per enzyme is needed for inactivation. The binding of the first molecule is endothermic, and that of the second exothermic. Crystals of TcTIM in complex with one molecule of the inactivating agent that diffracted to a resolution of 2A were obtained. The compound is at the dimer interface at less than 4A from residues of the two subunits. Compound 8 is more effective at low than at high protein concentrations, indicating that it perturbs the association between the two TcTIM monomers. Calorimetric and kinetic data of experiments in which TcTIM was added to a solution of the inactivating agent showed that at low concentrations of the compound, inactivation is limited by binding, whereas at high concentrations of the agent, the events that follow binding become rate-limiting. The portion of the interface of TcTIM that binds the benzothiazole derivative and its equivalent region in human TIM differs in amino acid composition and hydrophobic packing. Thus, we show that by focusing on protein-protein interfaces, it is possible to discover low molecular weight compounds that are selective for enzymes from parasites.
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Affiliation(s)
- Alfredo Téllez-Valencia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., 04510 México
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