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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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2
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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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3
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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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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.
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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.)
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5
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Jimenez-Sandoval P, Castro-Torres E, González-González R, Díaz-Quezada C, Gurrola M, Camacho-Manriquez LD, Leyva-Navarro L, Brieba LG. Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites. PLoS Negl Trop Dis 2020; 14:e0007815. [PMID: 31923219 PMCID: PMC6980832 DOI: 10.1371/journal.pntd.0007815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/23/2020] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Triosephosphate isomerases (TPIs) from Taenia solium (TsTPI) and
Schistosoma mansoni (SmTPI) are potential vaccine and drug
targets against cysticercosis and schistosomiasis, respectively. This is due to
the dependence of parasitic helminths on glycolysis and because those proteins
elicit an immune response, presumably due to their surface localization. Here we
report the crystal structures of TsTPI and SmTPI in complex with
2-phosphoglyceric acid (2-PGA). Both TPIs fold into a dimeric (β-α)8
barrel in which the dimer interface consists of α-helices 2, 3, and 4, and
swapping of loop 3. TPIs from parasitic helminths harbor a region of three amino
acids knows as the SXD/E insert (S155 to E157 and S157 to D159 in TsTPI and
SmTPI, respectively). This insert is located between α5 and β6 and is proposed
to be the main TPI epitope. This region is part of a solvent-exposed
310–helix that folds into a hook-like structure. The crystal
structures of TsTPI and SmTPI predicted conformational epitopes that could be
used for vaccine design. Surprisingly, the epitopes corresponding to the SXD/E
inserts are not the ones with the greatest immunological potential. SmTPI, but
not TsTPI, habors a sole solvent exposed cysteine (SmTPI-S230) and alterations
in this residue decrease catalysis. The latter suggests that thiol-conjugating
agents could be used to target SmTPI. In sum, the crystal structures of SmTPI
and TsTPI are a blueprint for targeted schistosomiasis and cysticercosis drug
and vaccine development. Because of the worldwide prevalence of schistosomiasis and cysticercosis, it is
critical to develop drugs and vaccines against their causative agents. The
glycolytic enzyme triosephosphate isomerase (TPI) is a dual-edged sword against
diseases caused by parasitic helminths. This is because helminths heavily depend
on glycolysis for energy and because the surface localization exhibited by TPIs
that elicits an immune response against those organisms. Here we provide the
crystal structures TPIs from Taenia solium and
Schistosoma mansoni as a first step for vaccine and drug
design. As a proof of concept we found that modifications in the single solvent
exposed cysteine of TPI from S. mansoni
decreases catalysis, making this enzyme a novel target against
schistosomiasis.
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Affiliation(s)
- Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Rogelio González-González
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Misraim Gurrola
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Laura D. Camacho-Manriquez
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Lucia Leyva-Navarro
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
- * E-mail:
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Romero-Romero S, Becerril-Sesín LA, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Structure and conformational stability of the triosephosphate isomerase from Zea mays. Comparison with the chemical unfolding pathways of other eukaryotic TIMs. Arch Biochem Biophys 2018; 658:66-76. [PMID: 30261166 DOI: 10.1016/j.abb.2018.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/18/2018] [Accepted: 09/23/2018] [Indexed: 12/16/2022]
Abstract
We studied the structure, function and thermodynamic properties for the unfolding of the Triosephosphate isomerase (TIM) from Zea mays (ZmTIM). ZmTIM shows a catalytic efficiency close to the diffusion limit. Native ZmTIM is a dimer that dissociates upon dilution into inactive and unfolded monomers. Its thermal unfolding is irreversible with a Tm of 61.6 ± 1.4 °C and an activation energy of 383.4 ± 11.5 kJ mol-1. The urea-induced unfolding of ZmTIM is reversible. Transitions followed by catalytic activity and spectroscopic properties are monophasic and superimposable, indicating that ZmTIM unfolds/refolds in a two-state behavior with an unfolding ΔG°(H20) = 99.8 ± 5.3 kJ mol-1. This contrasts with most other studied TIMs, where folding intermediates are common. The three-dimensional structure of ZmTIM was solved at 1.8 Å. A structural comparison with other eukaryotic TIMs shows a similar number of intramolecular and intermolecular interactions. Interestingly the number of interfacial water molecules found in ZmTIM is lower than those observed in most TIMs that show folding intermediates. Although with the available data, there is no clear correlation between structural properties and the number of equilibrium intermediates in the unfolding of TIM, the identification of such structural properties should increase our understanding of folding mechanisms.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Luis A Becerril-Sesín
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Adela Rodríguez-Romero
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico.
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7
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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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8
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Rodríguez-Bolaños M, Cabrera N, Perez-Montfort R. Identification of the critical residues responsible for differential reactivation of the triosephosphate isomerases of two trypanosomes. Open Biol 2017; 6:rsob.160161. [PMID: 27733588 PMCID: PMC5090059 DOI: 10.1098/rsob.160161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
The reactivation of triosephosphate isomerase (TIM) from unfolded monomers induced by guanidine hydrochloride involves different amino acids of its sequence in different stages of protein refolding. We describe a systematic mutagenesis method to find critical residues for certain physico-chemical properties of a protein. The two similar TIMs of Trypanosoma brucei and Trypanosoma cruzi have different reactivation velocities and efficiencies. We used a small number of chimeric enzymes, additive mutants and planned site-directed mutants to produce an enzyme from T. brucei with 13 mutations in its sequence, which reactivates fast and efficiently like wild-type (WT) TIM from T. cruzi, and another enzyme from T. cruzi, with 13 slightly altered mutations, which reactivated slowly and inefficiently like the WT TIM of T. brucei. Our method is a shorter alternative to random mutagenesis, saturation mutagenesis or directed evolution to find multiple amino acids critical for certain properties of proteins.
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Affiliation(s)
- Monica Rodríguez-Bolaños
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Ruy Perez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
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9
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Olivares-Illana V, Riveros-Rosas H, Cabrera N, Tuena de Gómez-Puyou M, Pérez-Montfort R, Costas M, Gómez-Puyou A. A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Proteins 2017; 85:1190-1211. [PMID: 28378917 DOI: 10.1002/prot.25299] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
Triosephosphate isomerase (TIM) is a ubiquitous enzyme, which appeared early in evolution. TIM is responsible for obtaining net ATP from glycolysis and producing an extra pyruvate molecule for each glucose molecule, under aerobic and anaerobic conditions. It is placed in a metabolic crossroad that allows a quick balance of the triose phosphate aldolase produced by glycolysis, and is also linked to lipid metabolism through the alternation of glycerol-3-phosphate and the pentose cycle. TIM is one of the most studied enzymes with more than 199 structures deposited in the PDB. The interest for this enzyme stems from the fact that it is involved in glycolysis, but also in aging, human diseases and metabolism. TIM has been a target in the search for chemical compounds against infectious diseases and is a model to study catalytic features. Until February 2017, 62% of all residues of the protein have been studied by mutagenesis and/or using other approaches. Here, we present a detailed and comprehensive recompilation of the reported effects on TIM catalysis, stability, druggability and human disease produced by each of the amino acids studied, contributing to a better understanding of the properties of this fundamental protein. The information reviewed here shows that the role of the noncatalytic residues depend on their molecular context, the delicate balance between the short and long-range interactions in concerted action determining the properties of the protein. Each protein should be regarded as a unique entity that has evolved to be functional in the organism to which it belongs. Proteins 2017; 85:1190-1211. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer. Instituto de Física, Universidad Autónoma de San Luis Potosí, SLP, 78290, México
| | - Hector Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
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10
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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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11
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Costa EP, Campos E, de Andrade CP, Façanha AR, Saramago L, Masuda A, da Silva Vaz I, Fernandez JH, Moraes J, Logullo C. Partial characterization of an atypical family I inorganic pyrophosphatase from cattle tick Rhipicephalus (Boophilus) microplus. Vet Parasitol 2012; 184:238-47. [DOI: 10.1016/j.vetpar.2011.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/18/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
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12
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Enríquez-Flores S, Rodríguez-Romero A, Hernández-Alcántara G, Oria-Hernández J, Gutiérrez-Castrellón P, Pérez-Hernández G, de la Mora-de la Mora I, Castillo-Villanueva A, García-Torres I, Méndez ST, Gómez-Manzo S, Torres-Arroyo A, López-Velázquez G, Reyes-Vivas H. Determining the molecular mechanism of inactivation by chemical modification of triosephosphate isomerase from the human parasite Giardia lamblia: a study for antiparasitic drug design. Proteins 2011; 79:2711-24. [PMID: 21786322 DOI: 10.1002/prot.23100] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 05/17/2011] [Accepted: 05/27/2011] [Indexed: 11/06/2022]
Abstract
Giardiasis, the most prevalent intestinal parasitosis in humans, is caused by Giardia lamblia. Current drug therapies have adverse effects on the host, and resistant strains against these drugs have been reported, demonstrating an urgent need to design more specific antigiardiasic drugs. ATP production in G. lamblia depends mainly on glycolysis; therefore, all enzymes of this pathway have been proposed as potential drug targets. We previously demonstrated that the glycolytic enzyme triosephosphate isomerase from G. lamblia (GlTIM), could be completely inactivated by low micromolar concentrations of thiol-reactive compounds, whereas, in the same conditions, the activity of human TIM (HuTIM) was almost unaltered. We found that the chemical modification (derivatization) of at least one Cys, of the five Cys residues per monomer in GlTIM, causes this inactivation. In this study, structural and functional studies were performed to describe the molecular mechanism of GlTIM inactivation by thiol-reactive compounds. We found that the Cys222 derivatization is responsible for GlTIM inactivation; this information is relevant because HuTIM has a Cys residue in an equivalent position (Cys217). GlTIM inactivation is associated with a decrease in ligand affinity, which affects the entropic component of ligand binding. In summary, this work describes a mechanism of inactivation that has not been previously reported for TIMs from other parasites and furthermore, we show that the difference in reactivity between the Cys222 in GlTIM and the Cys217 in HuTIM, indicates that the surrounding environment of each Cys residue has unique structural differences that can be exploited to design specific antigiardiasic drugs.
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Affiliation(s)
- Sergio Enríquez-Flores
- Laboratorio de Bioquímica-Genética, Torre de Investigación, Instituto Nacional de Pediatría, Secretaría de Salud, 04530, México, D.F
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13
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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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14
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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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15
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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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16
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Banerjee M, Balaram H, Joshi NV, Balaram P. Engineered dimer interface mutants of triosephosphate isomerase: the role of inter-subunit interactions in enzyme function and stability. Protein Eng Des Sel 2011; 24:463-72. [DOI: 10.1093/protein/gzr005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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17
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Nolan MJ, Hofmann A, Jex AR, Gasser RB. A theoretical study to establish the relationship between the three-dimensional structure of triose-phosphate isomerase of Giardia duodenalis and point mutations in the respective gene. Mol Cell Probes 2010; 24:281-5. [DOI: 10.1016/j.mcp.2010.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/01/2010] [Accepted: 06/03/2010] [Indexed: 11/15/2022]
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18
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Alves-Ferreira M, Guimarães ACR, Capriles PVDSZ, Dardenne LE, Degrave WM. A new approach for potential drug target discovery through in silico metabolic pathway analysis using Trypanosoma cruzi genome information. Mem Inst Oswaldo Cruz 2009; 104:1100-10. [DOI: 10.1590/s0074-02762009000800006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 10/28/2009] [Indexed: 11/22/2022] Open
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19
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Zárate-Pérez F, Chánez-Cárdenas ME, Arreola R, Torres-Larios A, Vázquez-Contreras E. Different catalytic properties of two highly homologous triosephosphate isomerase monomers. Biochem Biophys Res Commun 2009; 382:626-30. [PMID: 19303397 DOI: 10.1016/j.bbrc.2009.03.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 03/16/2009] [Indexed: 11/26/2022]
Abstract
It is assumed that amino acid sequence differences in highly homologous enzymes would be found at the peripheral level, subtle changes that would not necessarily affect catalysis. Here, we demonstrate that, using the same set of mutations at the level of the interface loop 3, the activity of a triosephosphate isomerase monomeric enzyme is ten times higher than that of a homologous enzyme with 74% identity and 86% similarity, whereas the activity of the native, dimeric enzymes is essentially the same. This is an example of how the dimeric biological unit evolved to compensate for the intrinsic differences found at the monomeric species level. Biophysical techniques of size exclusion chromatography, dynamic light scattering, X-ray crystallography, fluorescence and circular dichroism, as well as denaturation/renaturation assays with guanidinium hydrochloride and ANS binding, allowed us to fully characterize the properties of the new monomer.
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Affiliation(s)
- Francisco Zárate-Pérez
- Instituto de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de Mexico, Circuito Exterior, Mexico, DF 04510, Mexico
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20
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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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21
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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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22
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Zomosa-Signoret V, Aguirre-López B, Hernández-Alcántara G, Pérez-Montfort R, de Gómez-Puyou MT, Gómez-Puyou A. Crosstalk between the subunits of the homodimeric enzyme triosephosphate isomerase. Proteins 2007; 67:75-83. [PMID: 17221869 DOI: 10.1002/prot.21242] [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: 11/06/2022]
Abstract
Homodimeric triosephosphate isomerase (TIM) from Trypanosoma cruzi (TcTIM) and T. brucei (TbTIM) are markedly similar in amino acid sequence and three-dimensional structure. In their dimer interfaces, each monomer has a Cys15 that is surrounded by loop3 of the adjoining subunit. Perturbation of Cys15 by methylmethane thiosulfonate (MMTS) induces abolition of catalysis and structural changes. In the two TIMs, the structural arrangements of their Cys15 are almost identical. Nevertheless, the susceptibility of TcTIM to MMTS is nearly 100-fold higher than in TbTIM. To ascertain the extent to which the characteristics of the interface Cys depend on the dynamics of its own monomer or on those of the adjacent monomer, we studied MMTS action on mutants of TcTIM that had the interface residues of TbTIM, and hybrids that have only one interfacial Cys15 (C15ATcTIM-wild type TbTIM). We found that the solvent exposure of the interfacial Cys depends predominantly on the characteristics of the adjoining monomer. The maximal inhibition of activity induced by perturbation of the sole interface Cys in the C15ATcTIM-TbTIM hybrid is around 60%. Hybrids formed with C15ATcTIM monomers and catalytically inert TbTIM monomers (E168DTbTIM) were also studied. Their activity drops by nearly 50% when the only interfacial Cys is perturbed. These results in conjunction with those on C15ATcTIM-wild type TbTIM hybrid indicate that about half of the activity of each monomer depends on the integrity of each of the two Cys15-loop3 portions of the interface. This could be another reason of why TIM is an obligatory dimer.
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Affiliation(s)
- Viviana Zomosa-Signoret
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70243, 04510 México, D. F., Mexico
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23
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Rodríguez-Romero A, Hernández-Santoyo A, del Pozo Yauner L, Kornhauser A, Fernández-Velasco DA. Structure and inactivation of triosephosphate isomerase from Entamoeba histolytica. J Mol Biol 2002; 322:669-75. [PMID: 12270704 DOI: 10.1016/s0022-2836(02)00809-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Triosephosphate isomerase (TIM) has been proposed as a target for drug design. TIMs from several parasites have a cysteine residue at the dimer interface, whose derivatization with thiol-specific reagents induces enzyme inactivation and aggregation. TIMs lacking this residue, such as human TIM, are less affected. TIM from Entamoeba histolytica (EhTIM) has the interface cysteine residue and presents more than ten insertions when compared with the enzyme from other pathogens. To gain further insight into the role that interface residues play in the stability and reactivity of these enzymes, we determined the high-resolution structure and characterized the effect of methylmethane thiosulfonate (MMTS) on the activity and conformational properties of EhTIM. The structure of this enzyme was determined at 1.5A resolution using molecular replacement, observing that the dimer is not symmetric. EhTIM is completely inactivated by MMTS, and dissociated into stable monomers that possess considerable secondary structure. Structural and spectroscopic analysis of EhTIM and comparison with TIMs from other pathogens reveal that conformational rearrangements of the interface after dissociation, as well as intramonomeric contacts formed by the inserted residues, may contribute to the unusual stability of the derivatized EhTIM monomer.
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Affiliation(s)
- Adela Rodríguez-Romero
- Laboratorio Universitario de Estructura de Proteínas and Departamento de Bioquímica, Instituto de Química, Universidad Nacional Autónoma de México, DF, Mexico.
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24
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Maithal K, Ravindra G, Balaram H, Balaram P. Inhibition of plasmodium falciparum triose-phosphate isomerase by chemical modification of an interface cysteine. Electrospray ionization mass spectrometric analysis of differential cysteine reactivities. J Biol Chem 2002; 277:25106-14. [PMID: 12006590 DOI: 10.1074/jbc.m202419200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum triose-phosphate isomerase, a homodimeric enzyme, contains four cysteine residues at positions 13, 126, 196, and 217 per subunit. Among these, Cys-13 is present at the dimer interface and is replaced by methionine in the corresponding human enzyme. We have investigated the effect of sulfhydryl labeling on the parasite enzyme, with a view toward developing selective covalent inhibitors by targeting the interface cysteine residue. Differential labeling of the cysteine residues by iodoacetic acid and iodoacetamide has been followed by electrospray ionization mass spectrometry and positions of the labels determined by analysis of tryptic fragments. The rates of labeling follows the order Cys-196 > Cys-13 Cys-217/Cys-126, which correlates well with surface accessibility calculations based on the enzyme crystal structure. Iodoacetic acid labeling leads to a soluble, largely inactive enzyme, whereas IAM labeling leads to precipitation. Carboxyl methylation of Cys-13 results in formation of monomeric species detectable by gel filtration. Studies with an engineered C13D mutant permitted elucidation of the effects of introducing a negative charge at the interface. The C13D mutant exhibits a reduced stability to denaturants and 7-fold reduction in the enzymatic activity even under the concentrations in which dimeric species are observed.
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Affiliation(s)
- Kapil Maithal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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25
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Maithal K, Ravindra G, Nagaraj G, Singh SK, Balaram H, Balaram P. Subunit interface mutation disrupting an aromatic cluster in Plasmodium falciparum triosephosphate isomerase: effect on dimer stability. Protein Eng Des Sel 2002; 15:575-84. [PMID: 12200540 DOI: 10.1093/protein/15.7.575] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A mutation at the dimer interface of Plasmodium falciparum triosephosphate isomerase (PfTIM) was created by mutating a tyrosine residue at position 74, at the subunit interface, to glycine. Tyr74 is a critical residue, forming a part of an aromatic cluster at the interface. The resultant mutant, Y74G, was found to have considerably reduced stability compared with the wild-type protein (TIMWT). The mutant was found to be much less stable to denaturing agents such as urea and guanidinium chloride. Fluorescence and circular dichroism studies revealed that the Y74G mutant and TIMWT have similar spectroscopic properties, suggestive of similar folded structures. Further, the Y74G mutant also exhibited a concentration-dependent loss of enzymatic activity over the range 0.1-10 microM. In contrast, the wild-type enzyme did not show a concentration dependence of activity in this range. Fluorescence quenching of intrinsic tryptophan emission was much more efficient in case of Y74G than TIMWT, suggestive of greater exposure of Trp11, which lies adjacent to the dimer interface. Analytical gel filtration studies revealed that in Y74G, monomeric and dimeric species are in dynamic equilibrium, with the former predominating at low protein concentration. Spectroscopic studies established that the monomeric form of the mutant is largely folded. Low concentrations of urea also drive the equilibrium towards the monomeric form. These studies suggest that the replacement of tyrosine with a small residue at the interface of triosephosphate isomerase weakens the subunit-subunit interactions, giving rise to structured, but enzymatically inactive, monomers at low protein concentration.
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Affiliation(s)
- Kapil Maithal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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26
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Singh SK, Maithal K, Balaram H, Balaram P. Synthetic peptides as inactivators of multimeric enzymes: inhibition of Plasmodium falciparum triosephosphate isomerase by interface peptides. FEBS Lett 2001; 501:19-23. [PMID: 11457449 DOI: 10.1016/s0014-5793(01)02606-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic peptides corresponding to two distinct segments of the subunit interface of the homodimeric enzyme triosephosphate isomerase (residues 9-18, ANWKCNGTLE, peptide I; residues 68-79, KFGNGSYTGEVS, peptide II) from Plasmodium falciparum (PfTIM) have been investigated for their ability to act as inhibitors by interfering with the quaternary structure of the enzyme. An analog of peptide II containing cysteine at the site corresponding to position 74 and tyrosine at position 69 in the protein sequence KYGNGSCTGEVS (peptide III) was also investigated. A substantial fall in enzyme activity was observed following incubation of the enzyme with peptide II, whereas peptide I did not show any appreciable inhibition. The inhibitory effect was more pronounced on two mutants of PfTIM (Y74C and Y74G), both of which have reduced stability compared to the wild-type protein due to an interface cavity. The IC50 value determined for peptide II is in the range of 0.6-0.8 microM. This study suggests that interface peptides of oligomeric enzymes can be used to inhibit dimeric enzymes by disrupting their native multimeric states and may provide lead structures for potential inhibitor design.
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Affiliation(s)
- S K Singh
- Molecular Biophysics Unit, indian Institute of Science, Bangalore
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27
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Saab-Rincón G, Juárez VR, Osuna J, Sánchez F, Soberón X. Different strategies to recover the activity of monomeric triosephosphate isomerase by directed evolution. PROTEIN ENGINEERING 2001; 14:149-55. [PMID: 11342710 DOI: 10.1093/protein/14.3.149] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A monomeric version of triosephosphate isomerase from Trypanosoma brucei, MonoTIM, has very low activity, and the same is true for all of the additional monomeric variants so far constructed. Here, we subjected MonoTIM to directed evolution schemes to achieve an activity improvement. The construction of a suitable strain for genetic selection provided an effective way to obtain active catalysts from a diverse population of protein variants. We used this tool to identify active mutants from two different strategies of mutagenesis: random mutagenesis of the whole gene and randomization of loop 2. Both strategies converged in the isolation of mutations Ala43 to Pro and Thr44 to either Ala or Ser, when randomizing the entire gene or to Arg in the case of randomization of loop 2. The kinetic characterization of the two more active mutants showed an increase of 11-fold in k(cat) and a reduction of 4-fold in K(m) for both of them, demonstrating the sensitivity of the selection method. A small difference in growth rate is observed when both mutant genes are compared, which seems to be attributable to a difference in solubility of the expressed proteins.
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Affiliation(s)
- G Saab-Rincón
- Instituto de Biotecnología, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 62271, México
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28
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Verlinde CL, Hannaert V, Blonski C, Willson M, Périé JJ, Fothergill-Gilmore LA, Opperdoes FR, Gelb MH, Hol WG, Michels PA. Glycolysis as a target for the design of new anti-trypanosome drugs. Drug Resist Updat 2001; 4:50-65. [PMID: 11512153 DOI: 10.1054/drup.2000.0177] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Glycolysis is perceived as a promising target for new drugs against parasitic trypanosomatid protozoa because this pathway plays an essential role in their ATP supply. Trypanosomatid glycolysis is unique in that it is compartmentalized, and many of its enzymes display unique structural and kinetic features. Structure- and catalytic mechanism-based approaches are applied to design compounds that inhibit the glycolytic enzymes of the parasites without affecting the corresponding proteins of the human host. For some trypanosomatid enzymes, potent and selective inhibitors have already been developed that affect only the growth of cultured trypanosomatids, and not mammalian cells.
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Affiliation(s)
- C L Verlinde
- Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, USA
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29
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Gao XG, Maldonado E, Pérez-Montfort R, Garza-Ramos G, de Gómez-Puyou MT, Gómez-Puyou A, Rodríguez-Romero A. Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane. Proc Natl Acad Sci U S A 1999; 96:10062-7. [PMID: 10468562 PMCID: PMC17842 DOI: 10.1073/pnas.96.18.10062] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2-A resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 A from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.
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Affiliation(s)
- X G Gao
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 México D. F., Mexico
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