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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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Chávez-García C, Karttunen M. Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases. J Chem Inf Model 2022; 62:668-677. [PMID: 35044757 DOI: 10.1021/acs.jcim.1c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homodimeric triosephosphate isomerases (TIMs) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have markedly similar amino-acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their reactivation speed after being denatured, have significant differences. The causes of these differences were explored with microsecond-scale molecular dynamics (MD) simulations of three different TIM proteins: TcTIM, TbTIM, and a chimeric protein, Mut1. We examined their electrostatic interactions and explored the impact of simulation length on them. The same salt bridge between catalytic residues Lys 14 and Glu 98 was observed in all three proteins, but key differences were found in other interactions that the catalytic amino acids form. In particular, a cation-π interaction between catalytic amino acids Lys 14 and His 96 and both a salt bridge and a hydrogen bond between catalytic Glu 168 and residue Arg 100 were only observed in TcTIM. Furthermore, although TcTIM forms less hydrogen bonds than TbTIM and Mut1, its hydrogen bond network spans almost the entire protein, connecting the residues in both monomers. This work provides new insight into the mechanisms that give rise to the different behavior of these proteins. The results also show the importance of long simulations.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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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: 0] [Impact Index Per Article: 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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Castro-Torres E, Jiménez-Sandoval P, Romero-Romero S, Fuentes-Pascacio A, López-Castillo LM, Díaz-Quezada C, Fernández-Velasco DA, Torres-Larios A, Brieba LG. Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:950-964. [PMID: 31034710 DOI: 10.1111/tpj.14375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Reactive oxidative species (ROS) and S-glutathionylation modulate the activity of plant cytosolic triosephosphate isomerases (cTPI). Arabidopsis thaliana cTPI (AtcTPI) is subject of redox regulation at two reactive cysteines that function as thiol switches. Here we investigate the role of these residues, AtcTPI-Cys13 and At-Cys218, by substituting them with aspartic acid that mimics the irreversible oxidation of cysteine to sulfinic acid and with amino acids that mimic thiol conjugation. Crystallographic studies show that mimicking AtcTPI-Cys13 oxidation promotes the formation of inactive monomers by reposition residue Phe75 of the neighboring subunit, into a conformation that destabilizes the dimer interface. Mutations in residue AtcTPI-Cys218 to Asp, Lys, or Tyr generate TPI variants with a decreased enzymatic activity by creating structural modifications in two loops (loop 7 and loop 6) whose integrity is necessary to assemble the active site. In contrast with mutations in residue AtcTPI-Cys13, mutations in AtcTPI-Cys218 do not alter the dimeric nature of AtcTPI. Therefore, modifications of residues AtcTPI-Cys13 and AtcTPI-Cys218 modulate AtcTPI activity by inducing the formation of inactive monomers and by altering the active site of the dimeric enzyme, respectively. The identity of residue AtcTPI-Cys218 is conserved in the majority of plant cytosolic TPIs, this conservation and its solvent-exposed localization make it the most probable target for TPI regulation upon oxidative damage by reactive oxygen species. Our data reveal the structural mechanisms by which S-glutathionylation protects AtcTPI from irreversible chemical modifications and re-routes carbon metabolism to the pentose phosphate pathway to decrease oxidative stress.
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Affiliation(s)
- Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Pedro Jiménez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Sergio Romero-Romero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Laura M López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - D Alejandro Fernández-Velasco
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, México City, 04510, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
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5
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Zhai X, Reinhardt CJ, Malabanan MM, Amyes TL, Richard JP. Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase. J Am Chem Soc 2018; 140:8277-8286. [PMID: 29862813 PMCID: PMC6037162 DOI: 10.1021/jacs.8b04367] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report pH rate profiles for kcat and Km for the
isomerization reaction
of glyceraldehyde 3-phosphate catalyzed by wildtype triosephosphate
isomerase (TIM) from three organisms and by ten mutants of TIM; and,
for Ki for inhibition of this reaction
by phosphoglycolate trianion (I3–). The pH profiles for Ki show
that the binding of I3– to TIM (E) to form EH·I3– is accompanied by
uptake of a proton by the carboxylate side-chain of E165, whose function
is to abstract a proton from substrate. The complexes for several
mutants exist mainly as E–·I3– at high pH, in which cases the pH profiles define the pKa for deprotonation of EH·I3–. The linear
free energy correlation, with slope of 0.73 (r2 = 0.96), between kcat/Km for TIM-catalyzed isomerization and the disassociation
constant of PGA trianion for TIM shows that EH·I3– and the
transition state are stabilized by similar interactions with the protein
catalyst. Values of pKa = 10–10.5
were estimated for deprotonation of EH·I3– for wildtype TIM.
This pKa decreases to as low as 6.3 for
the severely crippled Y208F mutant. There is a correlation between
the effect of several mutations on kcat/Km and on pKa for EH·I3–. The results support a model where the strong basicity of
E165 at the complex to the enediolate reaction intermediate is promoted
by side-chains from Y208 and S211, which serve to clamp loop 6 over
the substrate; I170, which assists in the creation of a hydrophobic
environment for E165; and P166, which functions in driving the carboxylate
side-chain of E165 toward enzyme-bound substrate.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
| | - Christopher J Reinhardt
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 S Mathews Avenue , Urbana , Illinois 61801 , United States
| | - M Merced Malabanan
- Department of Biochemistry , Vanderbilt University , 842 Robinson Research Building , Nashville , Tennessee 37205 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
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6
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Vázquez-Raygoza A, Cano-González L, Velázquez-Martínez I, Trejo-Soto PJ, Castillo R, Hernández-Campos A, Hernández-Luis F, Oria-Hernández J, Castillo-Villanueva A, Avitia-Domínguez C, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A. Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies. Molecules 2017; 22:molecules22122055. [PMID: 29186784 PMCID: PMC6149853 DOI: 10.3390/molecules22122055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023] Open
Abstract
Human African Trypanosomiasis (HAT), a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by Trypanosoma brucei. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, T. brucei depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM) is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds 1, 2 and 3) with an I50 value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM) activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.
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Affiliation(s)
- Alejandra Vázquez-Raygoza
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Lucia Cano-González
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Israel Velázquez-Martínez
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Pedro Josué Trejo-Soto
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Rafael Castillo
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Alicia Hernández-Campos
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Francisco Hernández-Luis
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Jesús Oria-Hernández
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Adriana Castillo-Villanueva
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Claudia Avitia-Domínguez
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Erick Sierra-Campos
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Mónica Valdez-Solana
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Alfredo Téllez-Valencia
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
- Correspondence: ; Tel./Fax: +52-618-812-1687
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Jimenez-Sandoval P, Vique-Sanchez JL, Hidalgo ML, Velazquez-Juarez G, Diaz-Quezada C, Arroyo-Navarro LF, Moran GM, Fattori J, Jessica Diaz-Salazar A, Rudiño-Pinera E, Sotelo-Mundo R, Figueira ACM, Lara-Gonzalez S, Benítez-Cardoza CG, Brieba LG. A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1423-1432. [DOI: 10.1016/j.bbapap.2017.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/07/2017] [Accepted: 07/24/2017] [Indexed: 11/30/2022]
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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9
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Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1696-1706. [PMID: 27614148 DOI: 10.1016/j.bbapap.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/17/2016] [Accepted: 09/03/2016] [Indexed: 01/12/2023]
Abstract
Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico; Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora 83000, Mexico
| | - Jesus S Carrasco-Miranda
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Claudia D Ramirez-Aguirre
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico; Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Av. Instituto Politécnico Nacional. s/n., 23096, La Paz, Baja California Sur 23096, Mexico; Cátedras CONACyT, Dirección Adjunta de Desarrollo Científico, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de Mexico, 03940, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico.
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10
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Catucci G, Romagnolo A, Spina F, Varese GC, Gilardi G, Di Nardo G. Enzyme-substrate matching in biocatalysis: in silico studies to predict substrate preference of ten putative ene-reductases from Mucor circinelloides MUT44. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Krause M, Kiema TR, Neubauer P, Wierenga RK. Crystal structures of two monomeric triosephosphate isomerase variants identified via a directed-evolution protocol selecting for L-arabinose isomerase activity. Acta Crystallogr F Struct Biol Commun 2016; 72:490-9. [PMID: 27303904 PMCID: PMC4909251 DOI: 10.1107/s2053230x16007548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/05/2016] [Indexed: 11/10/2022] Open
Abstract
The crystal structures are described of two variants of A-TIM: Ma18 (2.7 Å resolution) and Ma21 (1.55 Å resolution). A-TIM is a monomeric loop-deletion variant of triosephosphate isomerase (TIM) which has lost the TIM catalytic properties. Ma18 and Ma21 were identified after extensive directed-evolution selection experiments using an Escherichia coli L-arabinose isomerase knockout strain expressing a randomly mutated A-TIM gene. These variants facilitate better growth of the Escherichia coli selection strain in medium supplemented with 40 mM L-arabinose. Ma18 and Ma21 differ from A-TIM by four and one point mutations, respectively. Ma18 and Ma21 are more stable proteins than A-TIM, as judged from CD melting experiments. Like A-TIM, both proteins are monomeric in solution. In the Ma18 crystal structure loop 6 is open and in the Ma21 crystal structure loop 6 is closed, being stabilized by a bound glycolate molecule. The crystal structures show only small differences in the active site compared with A-TIM. In the case of Ma21 it is observed that the point mutation (Q65L) contributes to small structural rearrangements near Asn11 of loop 1, which correlate with different ligand-binding properties such as a loss of citrate binding in the active site. The Ma21 structure also shows that its Leu65 side chain is involved in van der Waals interactions with neighbouring hydrophobic side-chain moieties, correlating with its increased stability. The experimental data suggest that the increased stability and solubility properties of Ma21 and Ma18 compared with A-TIM cause better growth of the selection strain when coexpressing Ma21 and Ma18 instead of A-TIM.
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Affiliation(s)
- Mirja Krause
- Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK 24, Berlin, Germany
| | - Tiila-Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland
| | - Peter Neubauer
- Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK 24, Berlin, Germany
| | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland
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12
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Hayward S, Kitao A. Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions. J Chem Theory Comput 2015; 11:3895-905. [DOI: 10.1021/acs.jctc.5b00215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven Hayward
- D’Arcy
Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Akio Kitao
- Institute
of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
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13
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Minini L, Álvarez G, González M, Cerecetto H, Merlino A. Molecular docking and molecular dynamics simulation studies of Trypanosoma cruzi triosephosphate isomerase inhibitors. Insights into the inhibition mechanism and selectivity. J Mol Graph Model 2015; 58:40-9. [DOI: 10.1016/j.jmgm.2015.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 11/22/2014] [Accepted: 02/12/2015] [Indexed: 02/05/2023]
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14
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Reyes A, Zhai X, Morgan KT, Reinhardt CJ, Amyes TL, Richard JP. The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture. J Am Chem Soc 2015; 137:1372-82. [PMID: 25555107 PMCID: PMC4311969 DOI: 10.1021/ja5123842] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/29/2022]
Abstract
The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO3(2-), FPO3(2-), S2O3(2-), SO4(2-) and HOPO3(2-). Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (E·S(‡)), with intrinsic oxydianion Gibbs binding free energies that range from -8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO3(2-) to -3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-β-d-erythrofuranosyl)orotic acid by HOPO3(2-). Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large -8.4 kcal/mol and small -3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO3(2-) and S2O3(2-), respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion -F and -S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits.
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Affiliation(s)
- Archie
C. Reyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Xiang Zhai
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Kelsey T. Morgan
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Christopher J. Reinhardt
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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15
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Richard JP, Zhai X, Malabanan MM. Reflections on the catalytic power of a TIM-barrel. Bioorg Chem 2014; 57:206-212. [PMID: 25092608 DOI: 10.1016/j.bioorg.2014.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/03/2014] [Accepted: 07/04/2014] [Indexed: 12/14/2022]
Abstract
The TIM-barrel fold is described and its propagation throughout the enzyme universe noted. The functions of the individual front loops of the eponymous TIM-barrel of triosephosphate isomerase are presented in a discussion of: (a) electrophilic catalysis, by amino acid side chains from loops 1 and 4, of abstraction of an α-carbonyl hydrogen from substrate dihydroxyacetone phosphate (DHAP) or d-glyceraldehyde 3-phosphate (DGAP). (b) The engineering of loop 3 to give the monomeric variant monoTIM and the structure and catalytic properties of this monomer. (c) The interaction between loops 6, 7 and 8 and the phosphodianion of DHAP or DGAP. (d) The mechanism by which a ligand-gated conformational change, dominated by motion of loops 6 and 7, activates TIM for catalysis of deprotonation of DHAP or DGAP. (e) The conformational plasticity of TIM, and the utilization of substrate binding energy to "mold" the distorted active site loops of TIM mutants into catalytically active enzymes. The features of the TIM-barrel fold that favor effective protein catalysis are discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States.
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States
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16
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Richard JP, Amyes TL, Goryanova B, Zhai X. Enzyme architecture: on the importance of being in a protein cage. Curr Opin Chem Biol 2014; 21:1-10. [PMID: 24699188 DOI: 10.1016/j.cbpa.2014.03.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/01/2014] [Indexed: 11/30/2022]
Abstract
Substrate binding occludes water from the active sites of many enzymes. There is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (KSI--small burden, substrate pKa=13), triosephosphate isomerase (TIM, substrate pKa≈18) and diaminopimelate epimerase (DAP epimerase, large burden, substrate pKa≈29) catalyzed reaction. KSI binds substrates at a surface cleft, TIM binds substrate at an exposed 'cage' formed by closure of flexible loops; and, DAP epimerase binds substrate in a tight cage formed by an 'oyster-like' clamping motion of protein domains. Directed evolution of a solvent-occluded active site at a designed protein catalyst of the Kemp elimination reaction is discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Bogdana Goryanova
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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17
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Smirlis D, Soares MBP. Selection of molecular targets for drug development against trypanosomatids. Subcell Biochem 2014; 74:43-76. [PMID: 24264240 DOI: 10.1007/978-94-007-7305-9_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Trypanosomatid parasites are a group of flagellated protozoa that includes the genera Leishmania and Trypanosoma, which are the causative agents of diseases (leishmaniases, sleeping sickness and Chagas disease) that cause considerable morbidity and mortality, affecting more than 27 million people worldwide. Today no effective vaccines for the prevention of these diseases exist, whereas current chemotherapy is ineffective, mainly due to toxic side effects of current drugs and to the emergence of drug resistance and lack of cost effectiveness. For these reasons, rational drug design and the search of good candidate drug targets is of prime importance. The search for drug targets requires a multidisciplinary approach. To this end, the completion of the genome project of many trypanosomatid species gives a vast amount of new information that can be exploited for the identification of good drug candidates with a prediction of "druggability" and divergence from mammalian host proteins. In addition, an important aspect in the search for good drug targets is the "target identification" and evaluation in a biological pathway, as well as the essentiality of the gene in the mammalian stage of the parasite, which is provided by basic research and genetic and proteomic approaches. In this chapter we will discuss how these bioinformatic tools and experimental evaluations can be integrated for the selection of candidate drug targets, and give examples of metabolic and signaling pathways in the parasitic protozoa that can be exploited for rational drug design.
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18
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Zaffagnini M, Michelet L, Sciabolini C, Di Giacinto N, Morisse S, Marchand CH, Trost P, Fermani S, Lemaire SD. High-resolution crystal structure and redox properties of chloroplastic triosephosphate isomerase from Chlamydomonas reinhardtii. MOLECULAR PLANT 2014; 7:101-20. [PMID: 24157611 DOI: 10.1093/mp/sst139] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Triosephosphate isomerase (TPI) catalyzes the interconversion of glyceraldehyde-3-phosphate to dihydroxyacetone phosphate. Photosynthetic organisms generally contain two isoforms of TPI located in both cytoplasm and chloroplasts. While the cytoplasmic TPI is involved in the glycolysis, the chloroplastic isoform participates in the Calvin-Benson cycle, a key photosynthetic process responsible for carbon fixation. Compared with its cytoplasmic counterpart, the functional features of chloroplastic TPI have been poorly investigated and its three-dimensional structure has not been solved. Recently, several studies proposed TPI as a potential target of different redox modifications including dithiol/disulfide interchanges, glutathionylation, and nitrosylation. However, neither the effects on protein activity nor the molecular mechanisms underlying these redox modifications have been investigated. Here, we have produced recombinantly and purified TPI from the unicellular green alga Chlamydomonas reinhardtii (Cr). The biochemical properties of the enzyme were delineated and its crystallographic structure was determined at a resolution of 1.1 Å. CrTPI is a homodimer with subunits containing the typical (β/α)8-barrel fold. Although no evidence for TRX regulation was obtained, CrTPI was found to undergo glutathionylation by oxidized glutathione and trans-nitrosylation by nitrosoglutathione, confirming its sensitivity to multiple redox modifications.
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Affiliation(s)
- Mirko Zaffagnini
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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19
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Aguirre Y, Cabrera N, Aguirre B, Pérez-Montfort R, Hernandez-Santoyo A, Reyes-Vivas H, Enríquez-Flores S, de Gómez-Puyou MT, Gómez-Puyou A, Sanchez-Ruiz JM, Costas M. Different contribution of conserved amino acids to the global properties of triosephosphate isomerases. Proteins 2013; 82:323-35. [DOI: 10.1002/prot.24398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/30/2013] [Accepted: 08/14/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Yolanda Aguirre
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | - Beatriz Aguirre
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | | | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética; Torre de Investigación, Instituto Nacional de Pediatría, Secretaría de Salud; 04530, México, D.F México
| | - Sergio Enríquez-Flores
- Laboratorio de Bioquímica-Genética; Torre de Investigación, Instituto Nacional de Pediatría, Secretaría de Salud; 04530, México, D.F México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México D.F México
| | - Jose M. Sanchez-Ruiz
- Departamento de Química Física; Facultad de Ciencias, Universidad de Granada; Granada Spain
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica; Facultad de Química, Universidad Nacional Autónoma de México; México D.F México
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20
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Malabanan MM, Nitsch-Velasquez L, Amyes TL, Richard JP. Magnitude and origin of the enhanced basicity of the catalytic glutamate of triosephosphate isomerase. J Am Chem Soc 2013; 135:5978-81. [PMID: 23560625 DOI: 10.1021/ja401504w] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glu-167 of triosephosphate isomerase from Trypanosoma brucei brucei (TbbTIM) acts as the base to deprotonate substrate to form an enediolate phosphate trianion intermediate. We report that there is a large ~6 pK unit increase in the basicity of the carboxylate side chain of Glu-167 upon binding of the inhibitor phosphoglycolate trianion (I(3-)), an analog of the enediolate phosphate intermediate, from pKEH ≈ 4 for the protonated free enzyme EH to pK(EHI) ≈ 10 for the protonated enzyme-inhibitor complex EH•I(3-). We propose that there is a similar increase in the basicity of this side chain when the physiological substrates are deprotonated by TbbTIM to form an enediolate phosphate trianion intermediate and that it makes an important contribution to the enzymatic rate acceleration. The affinity of wildtype TbbTIM for I(3-) increases 20,000-fold upon decreasing the pH from 9.3 to 4.9, because TbbTIM exists mainly in the basic form E over this pH range, while the inhibitor binds specifically to the rare protonated enzyme EH. This reflects the large increase in the basicity of the carboxylate side chain of Glu-167 upon binding of I(3-) to EH to give EH•I(3-). The I172A mutation at TbbTIM results in an ~100-fold decrease in the affinity of TbbTIM for I(3-) at pH < 6 and an ~2 pK unit decrease in the basicity of the carboxylate side chain of Glu-167 at the EH•I(3-) complex, to pK(EHI) = 7.7. Therefore, the hydrophobic side chain of Ile-172 plays a critical role in effecting the large increase in the basicity of the catalytic base upon the binding of substrate and/or inhibitors.
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Affiliation(s)
- M Merced Malabanan
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, USA
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21
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Mukherjee S, Roychowdhury A, Dutta D, Das AK. Crystal structures of triosephosphate isomerase from methicillin resistant Staphylococcus aureus MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop. Biochimie 2012; 94:2532-44. [PMID: 22813930 DOI: 10.1016/j.biochi.2012.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/04/2012] [Indexed: 10/28/2022]
Abstract
Staphylococcus aureus is one of the most dreaded pathogens worldwide and emergence of notorious antibiotic resistant strains have further exacerbated the present scenario. The glycolytic enzyme, triosephosphate isomerase (TIM) is one of the cell envelope proteins of the coccus and is involved in biofilm formation. It also plays an instrumental role in adherence and invasion of the bacteria into the host cell. To structurally characterize this important enzyme and analyze it's interaction with different inhibitors, substrate and transition state analogues, the present article describes several crystal structures of SaTIM alone and in complex with different ligands: glycerol-3-phosphate (G3P), glycerol-2-phosphate (G2P), 3-phosphoglyceric acid (3PG) and 2-phosphoglyceric acid (2PG). Unique conformations of the catalytic loop 6 (L6) has been observed in the different complexes. It is found to be in "almost closed" conformation in both subunits of the structure complexed to G3P. However L6 adopts the open conformation in presence of G2P and 2PG. The preference of the conformation of the catalytic loop can be correlated with the position of the phosphate group in the ligand. Novel modes of binding have been observed for G2P and 3PG for the very first time. The triose moiety is oriented away from the catalytic residues and occupies an entirely different position in some subunits. A completely new binding site for phosphate has also been identified in the complex with 2PG which differs substantially from the conventional phosphate binding site of the ligand in the crystal structures of TIM determined so far.
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Affiliation(s)
- Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
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22
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Malabanan MM, Koudelka AP, Amyes TL, Richard JP. Mechanism for activation of triosephosphate isomerase by phosphite dianion: the role of a hydrophobic clamp. J Am Chem Soc 2012; 134:10286-98. [PMID: 22583393 DOI: 10.1021/ja303695u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of the hydrophobic side chains of Ile-172 and Leu-232 in catalysis of the reversible isomerization of R-glyceraldehyde 3-phosphate (GAP) to dihydroxyacetone phosphate (DHAP) by triosephosphate isomerase (TIM) from Trypanosoma brucei brucei (Tbb) has been investigated. The I172A and L232A mutations result in 100- and 6-fold decreases in k(cat)/K(m) for the isomerization reaction, respectively. The effect of the mutations on the product distributions for the catalyzed reactions of GAP and of [1-(13)C]-glycolaldehyde ([1-(13)C]-GA) in D(2)O is reported. The 40% yield of DHAP from wild-type Tbb TIM-catalyzed isomerization of GAP with intramolecular transfer of hydrogen is found to decrease to 13% and to 4%, respectively, for the reactions catalyzed by the I172A and L232A mutants. Likewise, the 13% yield of [2-(13)C]-GA from isomerization of [1-(13)C]-GA in D(2)O is found to decrease to 2% and to 1%, respectively, for the reactions catalyzed by the I172A and L232A mutants. The decrease in the yield of the product of intramolecular transfer of hydrogen is consistent with a repositioning of groups at the active site that favors transfer of the substrate-derived hydrogen to the protein or the oxygen anion of the bound intermediate. The I172A and L232A mutations result in (a) a >10-fold decrease (I172A) and a 17-fold increase (L232A) in the second-order rate constant for the TIM-catalyzed reaction of [1-(13)C]-GA in D(2)O, (b) a 170-fold decrease (I172A) and 25-fold increase (L232A) in the third-order rate constant for phosphite dianion (HPO(3)(2-)) activation of the TIM-catalyzed reaction of GA in D(2)O, and (c) a 1.5-fold decrease (I172A) and a larger 16-fold decrease (L232A) in K(d) for activation of TIM by HPO(3)(2-) in D(2)O. The effects of the I172A mutation on the kinetic parameters for the wild-type TIM-catalyzed reactions of the whole substrate and substrate pieces are consistent with a decrease in the basicity of the carboxylate side chain of Glu-167 for the mutant enzyme. The data provide striking evidence that the L232A mutation leads to a ca. 1.7 kcal/mol stabilization of a catalytically active loop-closed form of TIM (E(C)) relative to an inactive open form (E(O)).
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Affiliation(s)
- M Merced Malabanan
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260-3000, USA
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Richard JP. A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase. Biochemistry 2012; 51:2652-61. [PMID: 22409228 DOI: 10.1021/bi300195b] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triosephosphate isomerase (TIM) catalyzes the stereospecific 1,2-proton shift at dihydroxyacetone phosphate (DHAP) to give (R)-glyceraldehyde 3-phosphate through a pair of isomeric enzyme-bound cis-enediolate phosphate intermediates. The chemical transformations that occur at the active site of TIM were well understood by the early 1990s. The mechanism for enzyme-catalyzed isomerization is similar to that for the nonenzymatic reaction in water, but the origin of the catalytic rate acceleration is not understood. We review the results of experimental work that show that a substantial fraction of the large 12 kcal/mol intrinsic binding energy of the nonreacting phosphodianion fragment of TIM is utilized to activate the active site side chains for catalysis of proton transfer. Evidence is presented that this activation is due to a phosphodianion-driven conformational change, the most dramatic feature of which is closure of loop 6 over the dianion. The kinetic data are interpreted within the framework of a model in which activation is due to the stabilization by the phosphodianion of a rare, desolvated, loop-closed form of TIM. The dianion binding energy is proposed to drive the otherwise thermodynamically unfavorable desolvation of the solvent-exposed active site. This reduces the effective local dielectric constant of the active site, to enhance stabilizing electrostatic interactions between polar groups and the anionic transition state, and increases the basicity of the carboxylate side chain of Glu-165 that functions to deprotonate the bound carbon acid substrate. A rebuttal is presented to the recent proposal [Samanta, M., Murthy, M. R. N., Balaram, H., and Balaram, P. (2011) ChemBioChem 12, 1886-1895] that the cationic side chain of K12 functions as an active site electrophile to protonate the carbonyl oxygen of DHAP.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States.
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Kumar K, Bhargava P, Roy U. Cloning, overexpression and characterization of Leishmania donovani triosephosphate isomerase. Exp Parasitol 2012; 130:430-6. [PMID: 22342510 DOI: 10.1016/j.exppara.2012.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 11/19/2022]
Abstract
Triosephosphate isomerase (TIM) is a major enzyme in the glycolytic pathway, which catalyzes the interconversion of glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. Here, we report cloning, expression and purification of a catalytically active recombinant TIM of Leishmania donovani (LdTIM). The recombinant LdTIM had a pH optimum in the range of 7.2-9.0, found stable at 25°C for 30 min and K(m) and V(max) for the substrate glyceraldehyde 3-phosphate was 0.328±0.02mM and 10.05mM/min/mg, respectively. The cysteine-reactive agent methylmethane thiosulphonate (MMTS) was used as probe, in order to test its effect on enzyme activity. The MMTS induced 75% enzyme inactivation within 15 min at 250 μM concentration. The biochemical characterization of LdTIM described in this work is the essential step towards deeper understanding of its role in parasite survival. The purification of LdTIM in bioactive form provides important tools for further functional and structural studies.
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Affiliation(s)
- Kishore Kumar
- Division of Biochemistry, CSIR - Central Drug Research Institute, Lucknow 226001, UP, India
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25
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Venkatesan R, Alahuhta M, Pihko PM, Wierenga RK. High resolution crystal structures of triosephosphate isomerase complexed with its suicide inhibitors: the conformational flexibility of the catalytic glutamate in its closed, liganded active site. Protein Sci 2011; 20:1387-97. [PMID: 21633986 PMCID: PMC3189524 DOI: 10.1002/pro.667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 05/19/2011] [Indexed: 01/07/2023]
Abstract
The key residue of the active site of triosephosphate isomerase (TIM) is the catalytic glutamate, which is proposed to be important (i) as a catalytic base, for initiating the reaction, as well as (ii) for the subsequent proton shuttling steps. The structural properties of this glutamate in the liganded complex have been investigated by studying the high resolution crystal structures of typanosomal TIM, complexed with three suicide inhibitors: (S)-glycidol phosphate ((S)-GOP, at 0.99 Å resolution), (R)-glycidol phosphate, ((R)-GOP, at 1.08 Å resolution), and bromohydroxyacetone phosphate (BHAP, at 1.97 Å resolution). The structures show that in the (S)-GOP active site this catalytic glutamate is in the well characterized, competent conformation. However, an unusual side chain conformation is observed in the (R)-GOP and BHAP complexes. In addition, Glu97, salt bridged to the catalytic lysine in the competent active site, adopts an unusual side chain conformation in these two latter complexes. The higher chemical reactivity of (S)-GOP compared with (R)-GOP, as known from solution studies, can be understood: the structures indicate that in the case of (S)-GOP, Glu167 can attack the terminal carbon of the epoxide in a stereoelectronically favored, nearly linear OCO arrangement, but this is not possible for the (R)-GOP isomer. These structures confirm the previously proposed conformational flexibility of the catalytic glutamate in its closed, liganded state. The importance of this conformational flexibility for the proton shuttling steps in the TIM catalytic cycle, which is apparently achieved by a sliding motion of the side chain carboxylate group above the enediolate plane, is also discussed.
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Affiliation(s)
- Rajaram Venkatesan
- Biocenter Oulu and Department of Biochemistry, FIN 90014, University of OuluFinland
| | - Markus Alahuhta
- Biocenter Oulu and Department of Biochemistry, FIN 90014, University of OuluFinland
| | - Petri M Pihko
- Department of Chemistry and Nanoscience Center, University of Jyväskylä, FIN 40014, University of JyväskyläFinland
| | - Rik K Wierenga
- Biocenter Oulu and Department of Biochemistry, FIN 90014, University of OuluFinland,*Correspondence to: Rik K. Wierenga, Biocenter Oulu and Department of Biochemistry, P.O. Box 3000, FIN 90014, University of Oulu, Finland. E-mail:
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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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Carpenter RA, Xiong J, Robbins JM, Ellis HR. Functional Role of a Conserved Arginine Residue Located on a Mobile Loop of Alkanesulfonate Monooxygenase. Biochemistry 2011; 50:6469-77. [DOI: 10.1021/bi200429d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Russell A. Carpenter
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jingyuan Xiong
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - John M. Robbins
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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Malabanan MM, Go MK, Amyes TL, Richard JP. Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion. Biochemistry 2011; 50:5767-79. [PMID: 21553855 DOI: 10.1021/bi2005416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Product yields for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D2O at pD 7.9 catalyzed by wildtype triosephosphate isomerase from Trypanosoma brucei brucei (Tbb TIM) and a monomeric variant (monoTIM) of this wildtype enzyme were determined by (1)H NMR spectroscopy and were compared with the yields determined in earlier work for the reactions catalyzed by TIM from rabbit and chicken muscle [O'Donoghue, A. C., Amyes, T. L., and Richard, J. P. (2005), Biochemistry 44, 2610 - 2621]. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen, d-DHAP from isomerization with incorporation of deuterium from D2O into C-1 of DHAP, and d-GAP from incorporation of deuterium from D2O into C-2 of GAP. The yield of DHAP formed by intramolecular transfer of hydrogen decreases from 49% for the muscle enzymes to 40% for wildtype Tbb TIM to 34% for monoTIM. There is no significant difference in the ratio of the yields of d-DHAP and d-GAP for wildtype TIM from muscle sources and Trypanosoma brucei brucei, but partitioning of the enediolate intermediate of the monoTIM reaction to form d-DHAP is less favorable ((k(C1))(D)/(k(C2))(D) = 1.1) than for the wildtype enzyme ((k(C1))(D)/(k(C2))(D) = 1.7). Product yields for the wildtype Tbb TIM and monoTIM-catalyzed reactions of glycolaldehyde labeled with carbon-13 at the carbonyl carbon ([1-(13)C]-GA) at pD 7.0 in the presence of phosphite dianion and in its absence were determined by (1)H NMR spectroscopy [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778]. There is no detectable difference in the yields of the products of wildtype muscle and Tbb TIM-catalyzed reactions of [1-(13)C]-GA in D2O. The kinetic parameters for phosphite dianion activation of the reactions of [1-(13)C]-GA catalyzed by wildtype Tbb TIM are similar to those reported for the enzyme from rabbit muscle [Amyes, T. L. and Richard, J. P. (2007) Biochemistry 46, 5841-5854], but there is no detectable dianion activation of the reaction catalyzed by monoTIM. The engineered disruption of subunit contacts at monoTIM causes movement of the essential side chains of Lys-13 and His-95 away from the catalytic active positions. We suggest that this places an increased demand that the intrinsic binding energy of phosphite dianion be utilized to drive the change in the conformation of monoTIM back to the active structure for wildtype TIM.
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Affiliation(s)
- M Merced Malabanan
- Department of Chemistry, University at Buffalo, The State University of New York (SUNY), Buffalo, New York 14260-3000, USA
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29
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Malabanan MM, Amyes TL, Richard JP. A role for flexible loops in enzyme catalysis. Curr Opin Struct Biol 2010; 20:702-10. [PMID: 20951028 DOI: 10.1016/j.sbi.2010.09.005] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 09/09/2010] [Accepted: 09/10/2010] [Indexed: 11/29/2022]
Abstract
Triosephosphate isomerase (TIM), glycerol 3-phosphate dehydrogenase, and orotidine 5'-monophosphate decarboxylase each use the binding energy from the interaction of phosphite dianion with a flexible phosphate gripper loop to activate a second, phosphodianion-truncated, substrate towards enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation, respectively. Studies on TIM suggest that the most important general effect of loop closure over the substrate phosphodianion, and the associated conformational changes, is to extrude water from the enzyme active site. This should cause a decrease in the effective active-site dielectric constant, and an increase in transition state stabilization from enhanced electrostatic interactions with polar amino acid side chains. The most important specific effect of these conformational changes is to increase the basicity of the carboxylate side chain of the active site glutamate base by its placement in a 'hydrophobic cage'.
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Affiliation(s)
- M Merced Malabanan
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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30
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Chawla B, Madhubala R. Drug targets in Leishmania. J Parasit Dis 2010; 34:1-13. [PMID: 21526026 DOI: 10.1007/s12639-010-0006-3] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 06/22/2010] [Indexed: 02/03/2023] Open
Abstract
Leishmaniasis is a major public health problem and till date there are no effective vaccines available. The control strategy relies solely on chemotherapy of the infected people. However, the present repertoire of drugs is limited and increasing resistance towards them has posed a major concern. The first step in drug discovery is to identify a suitable drug target. The genome sequences of Leishmania major and Leishmania infantum has revealed immense amount of information and has given the opportunity to identify novel drug targets that are unique to these parasites. Utilization of this information in order to come up with a candidate drug molecule requires combining all the technology and using a multi-disciplinary approach, right from characterizing the target protein to high throughput screening of compounds. Leishmania belonging to the order kinetoplastidae emerges from the ancient eukaryotic lineages. They are quite diverse from their mammalian hosts and there are several cellular processes that we are getting to know of, which exist distinctly in these parasites. In this review, we discuss some of the metabolic pathways that are essential and could be used as potential drug targets in Leishmania.
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Affiliation(s)
- Bhavna Chawla
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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31
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Salin M, Kapetaniou EG, Vaismaa M, Lajunen M, Casteleijn MG, Neubauer P, Salmon L, Wierenga RK. Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:934-44. [PMID: 20693693 DOI: 10.1107/s0907444910025710] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 06/30/2010] [Indexed: 11/10/2022]
Abstract
Crystallographic binding studies have been carried out to probe the active-site binding properties of a monomeric variant (A-TIM) of triosephosphate isomerase (TIM). These binding studies are part of a structure-based directed-evolution project aimed towards changing the substrate specificity of monomeric TIM and are therefore aimed at finding binders which are substrate-like molecules. A-TIM has a modified more extended binding pocket between loop-7 and loop-8 compared with wild-type TIM. The A-TIM crystals were grown in the presence of citrate, which is bound in the active site of each of the two molecules in the asymmetric unit. In this complex, the active-site loops loop-6 and loop-7 adopt the closed conformation, similar to that observed in liganded wild-type TIM. Extensive crystal-soaking protocols have been developed to flush the bound citrate out of the active-site pocket of both molecules and the crystal structure shows that the unliganded open conformation of the A-TIM active site is the same as in unliganded wild-type TIM. It is also shown that sulfonate compounds corresponding to the transition-state analogue 2-phosphoglycolate bind in the active site, which has a closed conformation. It is also shown that the new binding pocket of A-TIM can bind 3-phosphoglycerate (3PGA; an analogue of a C4-sugar phosphate) and 4-phospho-D-erythronohydroxamic acid (4PEH; an analogue of a C5-sugar phosphate). Therefore, these studies have provided a rationale for starting directed-evolution experiments aimed at generating the catalytic properties of a C5-sugar phosphate isomerase on the A-TIM framework.
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Affiliation(s)
- Mikko Salin
- Department of Biochemistry, PO Box 3000, 90014 University of Oulu, Finland
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Xu Y, Lorieau J, McDermott AE. Triosephosphate isomerase: 15N and 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy. J Mol Biol 2010; 397:233-48. [PMID: 19854202 PMCID: PMC5512891 DOI: 10.1016/j.jmb.2009.10.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 11/21/2022]
Abstract
Microcrystalline uniformly (13)C,(15)N-enriched yeast triosephosphate isomerase (TIM) is sequentially assigned by high-resolution solid-state NMR (SSNMR). Assignments are based on intraresidue and interresidue correlations, using dipolar polarization transfer methods, and guided by solution NMR assignments of the same protein. We obtained information on most of the active-site residues involved in chemistry, including some that were not reported in a previous solution NMR study, such as the side-chain carbons of His95. Chemical shift differences comparing the microcrystalline environment to the aqueous environment appear to be mainly due to crystal packing interactions. Site-specific perturbations of the enzyme's chemical shifts upon ligand binding are studied by SSNMR for the first time. These changes monitor proteinwide conformational adjustment upon ligand binding, including many of the sites probed by solution NMR and X-ray studies. Changes in Gln119, Ala163, and Gly210 were observed in our SSNMR studies, but were not reported in solution NMR studies (chicken or yeast). These studies identify a number of new sites with particularly clear markers for ligand binding, paving the way for future studies of triosephosphate isomerase dynamics and mechanism.
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Affiliation(s)
- Yimin Xu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Justin Lorieau
- National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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Galland N, de Walque S, Voncken FGJ, Verlinde CLMJ, Michels PAM. An internal sequence targets Trypanosoma brucei triosephosphate isomerase to glycosomes. Mol Biochem Parasitol 2010; 171:45-9. [PMID: 20138091 DOI: 10.1016/j.molbiopara.2010.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 01/08/2010] [Accepted: 01/18/2010] [Indexed: 12/01/2022]
Abstract
In kinetoplastid protists, glycolysis is compartmentalized in glycosomes, organelles belonging to the peroxisome family. The Trypanosoma brucei glycosomal enzyme triosephosphate isomerase (TPI) does not contain either of the two established peroxisome-targeting signals, but we identified a 22 amino acids long fragment, present at an internal position of the polypeptide, that has the capacity to route a reporter protein to glycosomes in transfected trypanosomes, as demonstrated by cell-fractionation experiments and corroborating immunofluorescence studies. This polypeptide-internal routing information seems to be unique for the sequence of the trypanosome enzyme: a reporter protein fused to a Saccharomyces cerevisiae peptide containing the sequence corresponding to the 22-residue fragment of the T. brucei enzyme, was not targeted to glycosomes. In yeasts, as in most other organisms, TPI is indeed exclusively present in the cytosol. These results suggest that it may be possible to develop new trypanocidal drugs by targeting specifically the glycosome import mechanism of TPI.
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Affiliation(s)
- Nathalie Galland
- Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium
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Thakur SS, Deepalakshmi P, Gayathri P, Banerjee M, Murthy M, Balaram P. Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase. Protein Eng Des Sel 2009; 22:289-304. [DOI: 10.1093/protein/gzp005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kurochkina N. Specific sequence combinations at parallel and antiparallel helix-helix interfaces. J Theor Biol 2008; 255:188-98. [PMID: 18786547 DOI: 10.1016/j.jtbi.2008.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 08/12/2008] [Accepted: 08/19/2008] [Indexed: 11/17/2022]
Abstract
Orientation of helices at parallel and antiparallel helix-helix interfaces in proteins depends on interacting amino acids from both helices. Particularly important are amino acids at positions analogous to a and d in GCN4 leucine zipper nomenclature, which form hydrophobic core. In this work repeating sequence combinations at a and d positions characteristic for both parallel and antiparallel packing are shown. Layer packing of hydrophobic groups is compared for possible combinations of aliphatic amino acids at all four positions. Correlation between specific position of methyl groups and interhelical angle is found for parallel and antiparallel types of packing.
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Affiliation(s)
- N Kurochkina
- Department of Biophysics, School of Theoretical Modeling, P.O. Box 15676, Chevy Chase, MD 20825, USA.
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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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Olivares-Illana V, Rodríguez-Romero A, Becker I, Berzunza M, García J, Pérez-Montfort R, Cabrera N, López-Calahorra F, de Gómez-Puyou MT, Gómez-Puyou A. Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi. PLoS Negl Trop Dis 2007; 1:e1. [PMID: 17989778 PMCID: PMC2041813 DOI: 10.1371/journal.pntd.0000001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/07/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM), and tested if they kill the parasite. METHODOLOGY/PRINCIPAL FINDINGS Dithiodianiline (DTDA) at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM). It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 A resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture. CONCLUSIONS/SIGNIFICANCE By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.
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Affiliation(s)
- Vanesa Olivares-Illana
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Ingeborg Becker
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Berzunza
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juventino García
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ruy Pérez-Montfort
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Nallely Cabrera
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Armando Gómez-Puyou
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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39
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Kim KH. Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers? J Comput Aided Mol Des 2007; 21:421-35. [PMID: 17646926 DOI: 10.1007/s10822-007-9126-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 06/13/2007] [Indexed: 11/25/2022]
Abstract
Structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies play an important role in a lead optimization of drug discovery research. When there is a lack of ligand-bound protein structural information, one of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. In such studies, outliers have often been observed, especially in QSAR. However, most of these studies have focused their attention on the development of QSAR and left outliers unattended. We searched ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results showed the possibility of conformational changes in a flexible binding site as one possible source of outliers.
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Affiliation(s)
- Ki Hwan Kim
- Hope Drug Discovery Research Laboratory, Vernon Hills, IL 60061, USA.
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40
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Amyes TL, Richard JP. Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Biochemistry 2007; 46:5841-54. [PMID: 17444661 PMCID: PMC2556868 DOI: 10.1021/bi700409b] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
More than 80% of the rate acceleration for enzymatic catalysis of the aldose-ketose isomerization of (R)-glyceraldehyde 3-phosphate (GAP) by triosephosphate isomerase (TIM) can be attributed to the phosphodianion group of GAP [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. We examine here the necessity of the covalent connection between the phosphodianion and triose sugar portions of the substrate by "carving up" GAP into the minimal neutral two-carbon sugar glycolaldehyde and phosphite dianion pieces. This "two-part substrate" preserves both the alpha-hydroxycarbonyl and oxydianion portions of GAP. TIM catalyzes proton transfer from glycolaldehyde in D2O, resulting in deuterium incorporation that can be monitored by 1H NMR spectroscopy, with kcat/Km = 0.26 M-1 s-1. Exogenous phosphite dianion results in a very large increase in the observed second-order rate constant (kcat/Km)obsd for turnover of glycolaldehyde, and the dependence of (kcat/Km)obsd on [HPO32-] exhibits saturation. The data give kcat/Km = 185 M-1 s-1 for turnover of glycolaldehyde by TIM that is saturated with phosphite dianion so that the separate binding of phosphite dianion to TIM results in a 700-fold acceleration of proton transfer from carbon. The binding of phosphite dianion to the free enzyme (Kd = 38 mM) is 700-fold weaker than its binding to the fleeting complex of TIM with the altered substrate in the transition state (Kd = 53 muM); the total intrinsic binding energy of phosphite dianion in the transition state is 5.8 kcal/mol. We propose a physical model for catalysis by TIM in which the intrinsic binding energy of the substrate phosphodianion group is utilized to drive closing of the "mobile loop" and a protein conformational change that leads to formation of an active site environment that is optimally organized for stabilization of the transition state for proton transfer from alpha-carbonyl carbon.
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Affiliation(s)
- Tina L Amyes
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, USA
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41
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Kurochkina N. Amino acid composition of parallel helix-helix interfaces. J Theor Biol 2007; 247:110-21. [PMID: 17379252 DOI: 10.1016/j.jtbi.2007.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 01/10/2007] [Accepted: 02/05/2007] [Indexed: 11/27/2022]
Abstract
Amino acids at helix-helix parallel interfaces influence arrangement of helices and interhelical angles. Parallel interfaces in 79 proteins were considered. Location of amino acids at the positions analogous to a and d in GCN4 leucine zipper nomenclature shows that certain combinations of amino acids characteristic for parallel packing occur more often than could be expected by chance. Repeating sequence combinations occur at a and d positions of parallel helix-helix interfaces with similar values of interhelical angles not only in homologous proteins but also within the same protein and in nonhomologous proteins. Within each group of observed combinations correlation exists between the size of amino acid and magnitude of the interhelical angle.
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Affiliation(s)
- N Kurochkina
- Department of Biophysics, The School of Theoretical Modeling, P.O. Box 15676, Chevy Chase, MD 20825, USA.
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42
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Casteleijn MG, Alahuhta M, Groebel K, El-Sayed I, Augustyns K, Lambeir AM, Neubauer P, Wierenga RK. Functional role of the conserved active site proline of triosephosphate isomerase. Biochemistry 2006; 45:15483-94. [PMID: 17176070 DOI: 10.1021/bi061683j] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of the fully conserved active site proline, Pro168, for the reaction mechanism of triosephosphate isomerase (TIM) has been investigated by studying the enzymatic and crystallographic properties of the P168A variant of trypanosomal TIM. In TIM, Pro168 follows the key catalytic residue Glu167, situated at the beginning of the flexible active site loop (loop 6). Turnover numbers of the P168A variant for its substrates are reduced approximately 50-fold, whereas the Km values are approximately 2 times lower. The affinity of the P168A variant for the transition state analogue 2-phosphoglycolate (2PG) is reduced 5-fold. The crystal structures of unliganded and liganded (2PG) P168A show that the phosphate moiety of 2PG is bound similarly as in wild-type TIM, whereas the interactions of the carboxylic acid moiety with the side chain of the catalytic Glu167 differ. The unique properties of the proline side chain at position 168 are required to transmit ligand binding to the conformational change of Glu167: the side chain of Glu167 flips from the inactive swung-out to the active swung-in conformation on ligand binding in wild-type TIM, whereas in the mutant this conformational change does not occur. Further structural comparisons show that in the wild-type enzyme the concerted movement of loop 6 and loop 7 from unliganded-open to liganded-closed appears to be facilitated by the interactions of the phosphate moiety with loop 7. Apparently, the rotation of 90 degrees of the Gly211-Gly212 peptide plane of loop 7 plays a key role in this concerted movement.
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Affiliation(s)
- Marco G Casteleijn
- Department of Process and Environmental Engineering and Bioprocess Engineering Laboratory, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
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43
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Reyes-Vivas H, Diaz A, Peon J, Mendoza-Hernandez G, Hernandez-Alcantara G, De la Mora-De la Mora I, Enriquez-Flores S, Dominguez-Ramirez L, Lopez-Velazquez G. Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity. J Mol Biol 2006; 365:752-63. [PMID: 17095008 DOI: 10.1016/j.jmb.2006.10.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 10/12/2006] [Accepted: 10/17/2006] [Indexed: 11/25/2022]
Abstract
Triosephosphate isomerase from the mesophile Giardia lamblia (GlTIM) is the only known TIM with natural disulfide bridges. We previously found that oxidized and reduced thiol states of GlTIM are involved in the interconversion between native dimers and higher oligomeric species, and in the regulation of enzymatic activity. Here, we found that trophozoites and cysts have different oligomeric species of GlTIM and complexes of GlTIM with other proteins. Our data indicate that the internal milieu of G. lamblia is favorable for the formation of disulfide bonds. Enzyme mutants of the three most solvent exposed Cys of GlTIM (C202A, C222A, and C228A) were prepared to ascertain their contribution to oligomerization and activity. The data show that the establishment of a disulfide bridge between two C202 of two dimeric GlTIMs accounts for multimerization. In addition, we found that the establishment of an intramonomeric disulfide bond between C222 and C228 abolishes catalysis. Multimerization and inactivation are both reversed by reducing conditions. The 3D structure of the C202A GlTIM was solved at 2.1 A resolution, showing that the environment of the C202 is prone to hydrophobic interactions. Molecular dynamics of an in silico model of GlTIM when the intramonomeric disulfide bond is formed, showed that S216 is displaced 4.6 A from its original position, causing loss of hydrogen bonds with residues of the active-site loop. This suggests that this change perturb the conformational state that aligns the catalytic center with the substrate, inducing enzyme inactivation.
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Affiliation(s)
- Horacio Reyes-Vivas
- Laboratorio de Bioquimica Genetica, Instituto Nacional de Pediatria, 04530 Mexico, D.F
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44
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Donnini S, Groenhof G, Wierenga RK, Juffer AH. The planar conformation of a strained proline ring: a QM/MM study. Proteins 2006; 64:700-10. [PMID: 16741995 DOI: 10.1002/prot.21006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
QM and QM/MM energy calculations have been carried out on an atomic resolution structure of liganded triosephosphate isomerase (TIM) that has an active site proline (Pro168) in a planar conformation. The origin of the planarity of this proline has been identified. Steric interactions between the atoms of the proline ring and a tyrosine ring (Tyr166) on one side of the proline prevent the ring from adopting the up pucker (chi1 is approximately -30 degrees), while the side chain of a nearby alanine (Ala171) forbids the down pucker (chi1 is approximately +30 degrees). To obtain a proline conformation that is in agreement with the experimentally observed planar state, a quantum system of sufficient size is required and should at least include the nearby side chains of Tyr166, Ala171, and Glu129 to provide enough stabilization. It is argued that the current force fields for structure optimization do not describe strained protein fragments correctly. The proline is part of a catalytic loop that closes upon ligand binding. Comparison of the proline conformation in different TIM X-ray structures, indicates that in the closed conformation of TIM the proline is planar or nearly planar, while in the open conformation it is down puckered. This suggests that the planarity possibly plays a role in the overall catalytic cycle of TIM, presumable acting as a reservoir of energy that becomes available upon loop opening.
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Affiliation(s)
- Serena Donnini
- The Biocenter and the Department of Biochemistry, University of Oulu, FIN-90014 University of Oulu, Finland
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45
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Celotto AM, Frank AC, Seigle JL, Palladino MJ. Drosophila model of human inherited triosephosphate isomerase deficiency glycolytic enzymopathy. Genetics 2006; 174:1237-46. [PMID: 16980388 PMCID: PMC1667072 DOI: 10.1534/genetics.106.063206] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Heritable mutations, known as inborn errors of metabolism, cause numerous devastating human diseases, typically as a result of a deficiency in essential metabolic products or the accumulation of toxic intermediates. We have isolated a missense mutation in the Drosophila sugarkill (sgk) gene that causes phenotypes analogous to symptoms of triosephosphate isomerase (TPI) deficiency, a human familial disease, characterized by anaerobic metabolic dysfunction resulting from pathological missense mutations affecting the encoded TPI protein. In Drosophila, the sgk gene encodes the glycolytic enzyme TPI. Our analysis of sgk mutants revealed TPI impairment associated with reduced longevity, progressive locomotor deficiency, and neural degeneration. Biochemical studies demonstrate that mutation of this glycolytic enzyme gene does not result in a bioenergetic deficit, suggesting an alternate cause of enzymopathy associated with TPI impairment.
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Affiliation(s)
- Alicia M Celotto
- Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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46
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Massi F, Wang C, Palmer AG. Solution NMR and Computer Simulation Studies of Active Site Loop Motion in Triosephosphate Isomerase†. Biochemistry 2006; 45:10787-94. [PMID: 16953564 DOI: 10.1021/bi060764c] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution NMR spin relaxation experiments and classical MD simulations are used to study the dynamics of triosephosphate isomerase (TIM) in complex with glycerol 3-phosphate (G3P). Three regions in TIM exhibit conformational transitions on the micros-ms time scale as detected by chemical exchange broadening effects in NMR spectroscopy: residue Lys 84 on helix C, located at the dimeric interface; active site loop 6; and helix G. The results indicate that the conformational exchange process affecting the residues of loop 6 is the correlated opening and closing of the loop. Distinct processes are responsible for the chemical exchange linebroadening observed in the other regions of TIM. MD simulations confirm that motions of individual residues within the active site loop are correlated and suggest that the chemical exchange processes observed for residues in helix G arise from transitions between 3(10)- and alpha-helical structures. The results of the joint NMR and MD study provide global insight into the role of conformational dynamic processes in the function of TIM.
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Affiliation(s)
- Francesca Massi
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
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47
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Olivares-Illana V, Pérez-Montfort R, López-Calahorra F, Costas M, Rodríguez-Romero A, Tuena de Gómez-Puyou M, Gómez Puyou A. Structural differences in triosephosphate isomerase from different species and discovery of a multitrypanosomatid inhibitor. Biochemistry 2006; 45:2556-60. [PMID: 16489748 DOI: 10.1021/bi0522293] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the interfaces of homodimeric triosephosphate isomerase (TIM) from eight different species. The crystal structures of the enzymes showed that a portion of the interface is markedly similar in TIMs from Trypanosoma cruzi (TcTIM), Trypanosoma brucei, and Leishmania mexicana and significantly different from that of TIMs from human, yeast, chicken, Plasmodium falciparum, and Entamoeba histolytica. Since this interfacial region is central in the stability of TcTIM, we hypothesized that it would be possible to find agents that selectively affect the stability of TIMs from the three trypanosomatids. We found that 6,6'-bisbenzothiazole-2,2' diamine in the low micromolar range causes a desirable irreversible inactivation of the enzymes from the three trypanosomatids and has no effect on the other five TIMs. Thus, the data indicate that it is possible to find compounds that induce selective inactivation of the enzymes from three different trypanosomatids.
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Affiliation(s)
- Vanesa Olivares-Illana
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D. F., México
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48
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Chánez-Cárdenas ME, Pérez-Hernández G, Sánchez-Rebollar BG, Costas M, Vázquez-Contreras E. Reversible Equilibrium Unfolding of Triosephosphate Isomerase from Trypanosoma cruzi in Guanidinium Hydrochloride Involves Stable Dimeric and Monomeric Intermediates. Biochemistry 2005; 44:10883-92. [PMID: 16086591 DOI: 10.1021/bi047687a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reversible guanidinium hydrochloride-induced unfolding of Trypanosoma cruzi triosephosphate isomerase (TcTIM) was characterized under equilibrium conditions. The catalytic activity was followed as a native homodimeric functional probe. Circular dichroism, intrinsic fluorescence, and size-exclusion chromatography were used as secondary, tertiary, and quaternary structural probes, respectively. The change in ANS fluorescence intensity with increasing denaturant concentrations was also determined. The results show that two stable intermediates exist in the transition from the homodimeric native enzyme to the unfolded monomers: one (N(2*)) is a slightly more expanded, non-native, and active dimer, and the other is a partially expanded monomer (M) that binds ANS. Spectroscopic and activity data were used to reach a thermodynamic characterization. The results indicate that the Gibbs free energies for the partial reactions are 4.5 (N(2) <==> N(2*)), 65.8 (N(2*) <==> 2M), and 17.8 kJ/mol (M <==> U). It appears that TcTIM monomers are more stable than those found for other TIM species (except yeast TIM), where monomer stability is only marginal. These results are compared with those for the guanidinium hydrochloride-induced denaturation of TIM from different species, where despite the functional and three-dimensional similarities, a remarkable heterogeneity exists in the unfolding pathways.
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Affiliation(s)
- María Elena Chánez-Cárdenas
- Laboratorio de Patología Vascular Cerebral, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, México, DF, Mexico
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Moyersoen J, Choe J, Fan E, Hol WGJ, Michels PAM. Biogenesis of peroxisomes and glycosomes: trypanosomatid glycosome assembly is a promising new drug target. FEMS Microbiol Rev 2005; 28:603-43. [PMID: 15539076 DOI: 10.1016/j.femsre.2004.06.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 06/14/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022] Open
Abstract
In trypanosomatids (Trypanosoma and Leishmania), protozoa responsible for serious diseases of mankind in tropical and subtropical countries, core carbohydrate metabolism including glycolysis is compartmentalized in peculiar peroxisomes called glycosomes. Proper biogenesis of these organelles and the correct sequestering of glycolytic enzymes are essential to these parasites. Biogenesis of glycosomes in trypanosomatids and that of peroxisomes in other eukaryotes, including the human host, occur via homologous processes involving proteins called peroxins, which exert their function through multiple, transient interactions with each other. Decreased expression of peroxins leads to death of trypanosomes. Peroxins show only a low level of sequence conservation. Therefore, it seems feasible to design compounds that will prevent interactions of proteins involved in biogenesis of trypanosomatid glycosomes without interfering with peroxisome formation in the human host cells. Such compounds would be suitable as lead drugs against trypanosomatid-borne diseases.
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Affiliation(s)
- Juliette Moyersoen
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, ICP-TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium
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50
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de Paula da Silva CHT, Sanches SM, Taft CA. A molecular modeling and QSAR study of suppressors of the growth of Trypanosoma cruzi epimastigotes. J Mol Graph Model 2004; 23:89-97. [PMID: 15331057 DOI: 10.1016/j.jmgm.2004.03.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Revised: 03/04/2004] [Accepted: 03/05/2004] [Indexed: 11/17/2022]
Abstract
In this work, we have used molecular modeling and QSAR tools to study 18 dithiocarbamate suppressors of the growth of Trypanosoma cruzi epimastigotes, which have been reported in the literature as superoxide dismutase (SOD) inhibitors. The principal component analysis (PCA) showed that the descriptors superficial area, heat of formation, logarithm of the partition coefficient, charge of the nitrogen atom from the dithiocarbamate group and Charges of the two carbon atoms adjacent to that nitrogen are responsible for the classification between the higher and lower trypanomicid activity. Using multiple linear regression (MLR) and docking methods it was possible to identify the probable bioactive isomers that suppress of the growth of T. cruzi epimastigotes. Our best partial least square (PLS) model obtained with these six descriptors yields a good correlation between experimental and predicted biological activities and compares two different SODs as possible target for interaction with the dithiocarbamates.
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