1
|
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.
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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]
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
The role of imidazole and benzimidazole heterocycles in Chagas disease: A review. Eur J Med Chem 2020; 206:112692. [PMID: 32818869 DOI: 10.1016/j.ejmech.2020.112692] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/02/2023]
Abstract
The haemoflagellate protozoan Trypanosoma cruzi (T. cruzi) is the causative agent of Chagas disease (CD), a potentially life-threatening disease. Little by little, remarkable progress has been achieved against CD, although it is still not enough. In the absence of effective chemotherapy, many research groups, organizations and pharmaceutical companies have focused their efforts on the search for compounds that could become viable drugs against CD. Within the wide variety of reported derivatives, this review summarizes and provides a global vision of the situation of those compounds that include broadly studied heterocycles in their structures due to their applications in medicinal chemistry: imidazole and benzimidazole rings. Therefore, the intention of this work is to present a compilation, as much as possible, of all the reported information, regarding these imidazole and benzimidazole derivatives against T. cruzi, as a starting point for future researchers in this field.
Collapse
|
6
|
Enríquez-Flores S, Flores-López LA, García-Torres I, de la Mora-de la Mora I, Cabrera N, Gutiérrez-Castrellón P, Martínez-Pérez Y, López-Velázquez G. Deamidated Human Triosephosphate Isomerase is a Promising Druggable Target. Biomolecules 2020; 10:E1050. [PMID: 32679775 PMCID: PMC7407242 DOI: 10.3390/biom10071050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/04/2020] [Accepted: 07/10/2020] [Indexed: 12/27/2022] Open
Abstract
Therapeutic strategies for the treatment of any severe disease are based on the discovery and validation of druggable targets. The human genome encodes only 600-1500 targets for small-molecule drugs, but posttranslational modifications lead to a considerably larger druggable proteome. The spontaneous conversion of asparagine (Asn) residues to aspartic acid or isoaspartic acid is a frequent modification in proteins as part of the process called deamidation. Triosephosphate isomerase (TIM) is a glycolytic enzyme whose deamidation has been thoroughly studied, but the prospects of exploiting this phenomenon for drug design remain poorly understood. The purpose of this study is to demonstrate the properties of deamidated human TIM (HsTIM) as a selective molecular target. Using in silico prediction, in vitro analyses, and a bacterial model lacking the tim gene, this study analyzed the structural and functional differences between deamidated and nondeamidated HsTIM, which account for the efficacy of this protein as a druggable target. The highly increased permeability and loss of noncovalent interactions of deamidated TIM were found to play a central role in the process of selective enzyme inactivation and methylglyoxal production. This study elucidates the properties of deamidated HsTIM regarding its selective inhibition by thiol-reactive drugs and how these drugs can contribute to the development of cell-specific therapeutic strategies for a variety of diseases, such as COVID-19 and cancer.
Collapse
Affiliation(s)
- Sergio Enríquez-Flores
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de EIMyT, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.A.F.-L.); (I.G.-T.); (I.d.l.M.-d.l.M.)
| | - Luis Antonio Flores-López
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de EIMyT, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.A.F.-L.); (I.G.-T.); (I.d.l.M.-d.l.M.)
- CONACYT-Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Itzhel García-Torres
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de EIMyT, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.A.F.-L.); (I.G.-T.); (I.d.l.M.-d.l.M.)
| | - Ignacio de la Mora-de la Mora
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de EIMyT, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.A.F.-L.); (I.G.-T.); (I.d.l.M.-d.l.M.)
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | | | - Yoalli Martínez-Pérez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Gabriel López-Velázquez
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de EIMyT, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.A.F.-L.); (I.G.-T.); (I.d.l.M.-d.l.M.)
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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]
|
9
|
Fluorine-containing benzothiazole as a novel trypanocidal agent: design, in silico study, synthesis and activity evaluation. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1475-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
10
|
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]
|
11
|
Triosephosphate isomerase is dispensable in vitro yet essential for Mycobacterium tuberculosis to establish infection. mBio 2014; 5:e00085. [PMID: 24757211 PMCID: PMC3994511 DOI: 10.1128/mbio.00085-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Triosephosphate isomerase (TPI) catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P). This reaction is required for glycolysis and gluconeogenesis, and tpi has been predicted to be essential for growth of Mycobacterium tuberculosis. However, when studying a conditionally regulated tpi knockdown mutant, we noticed that depletion of TPI reduced growth of M. tuberculosis in media containing a single carbon source but not in media that contained both a glycolytic and a gluconeogenic carbon source. We used such two-carbon-source media to isolate a tpi deletion (Δtpi) mutant. The Δtpi mutant did not survive with single carbon substrates but grew like wild-type (WT) M. tuberculosis in the presence of both a glycolytic and a gluconeogenic carbon source. 13C metabolite tracing revealed the accumulation of TPI substrates in Δtpi and the absence of alternative triosephosphate isomerases and metabolic bypass reactions, which confirmed the requirement of TPI for glycolysis and gluconeogenesis in M. tuberculosis. The Δtpi strain was furthermore severely attenuated in the mouse model of tuberculosis, suggesting that M. tuberculosis cannot simultaneously access sufficient quantities of glycolytic and gluconeogenic carbon substrates to establish infection in mice. The importance of central carbon metabolism for the pathogenesis of M. tuberculosis has recently been recognized, but the consequences of depleting specific metabolic enzymes remain to be identified for many enzymes. We investigated triosephosphate isomerase (TPI) because it is central to both glycolysis and gluconeogenesis and had been predicted to be essential for growth of M. tuberculosis. This work identified metabolic conditions that make TPI dispensable for M. tuberculosis growth in culture and proved that M. tuberculosis relies on a single TPI enzyme and has no metabolic bypass for the TPI-dependent interconversion of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate in glycolysis and gluconeogenesis. Finally, we demonstrate that TPI is essential for growth of the pathogen in mouse lungs.
Collapse
|
12
|
Fei F, Zhou Z. New substituted benzimidazole derivatives: a patent review (2010 – 2012). Expert Opin Ther Pat 2013; 23:1157-79. [DOI: 10.1517/13543776.2013.800857] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
13
|
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.
Collapse
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.
| |
Collapse
|