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Aguilera E, Sánchez C, Cruces ME, Dávila B, Minini L, Mosquillo F, Pérez-Díaz L, Serna E, Torres S, Schini A, Sanabria L, Vera de Bilbao NI, Yaluff G, Zolessi FR, Ceilas LF, Cerecetto H, Alvarez G. Preclinical Studies and Drug Combination of Low-Cost Molecules for Chagas Disease. Pharmaceuticals (Basel) 2022; 16:ph16010020. [PMID: 36678516 PMCID: PMC9863266 DOI: 10.3390/ph16010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chagas disease is caused by the protozoan Trypanosoma cruzi (T. cruzi). It remains the major parasitic disease in Latin America and is spreading worldwide, affecting over 10 million people. Hundreds of new compounds with trypanosomicidal action have been identified from different sources such as synthetic or natural molecules, but they have been deficient in several stages of drug development (toxicology, scaling-up, and pharmacokinetics). Previously, we described a series of compounds with simple structures, low cost, and environmentally friendly production with potent trypanosomicidal activity in vitro and in vivo. These molecules are from three different families: thiazolidenehydrazines, diarylideneketones, and steroids. From this collection, we explored their capacity to inhibit the triosephosphate isomerase and cruzipain of T. cruzi. Then, the mechanism of action was explored using NMR metabolomics and computational molecular dynamics. Moreover, the mechanism of death was studied by flow cytometry. Consequently, five compounds, 314, 793, 1018, 1019, and 1260, were pre-clinically studied and their pharmacologic profiles indicated low unspecific toxicity. Interestingly, synergetic effects of diarylideneketones 793 plus 1018 and 793 plus 1019 were evidenced in vitro and in vivo. In vivo, the combination of compounds 793 plus 1018 induced a reduction of more than 90% of the peak of parasitemia in the acute murine model of Chagas disease.
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Affiliation(s)
- Elena Aguilera
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Carina Sánchez
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - María Eugenia Cruces
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Belén Dávila
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Lucía Minini
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Florencia Mosquillo
- Laboratorio de Interacciones Moleculares, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Leticia Pérez-Díaz
- Laboratorio de Interacciones Moleculares, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Elva Serna
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Susana Torres
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Alicia Schini
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Luis Sanabria
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Ninfa I. Vera de Bilbao
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Gloria Yaluff
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 2169, Paraguay
| | - Flavio R. Zolessi
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República and Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | | | - Hugo Cerecetto
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
- Correspondence: (H.C.); (G.A.)
| | - Guzmán Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Rute 3 km 363, Paysandú 60000, Uruguay
- Correspondence: (H.C.); (G.A.)
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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Vázquez-Jiménez LK, Moreno-Herrera A, Juárez-Saldivar A, González-González A, Ortiz-Pérez E, Paz-González AD, Palos-Pizarro I, Ramírez-Moreno E, Rivera G. Recent Advances in the Development of Triose Phosphate Isomerase Inhibitors as Antiprotozoal Agents. Curr Med Chem 2021; 29:2504-2529. [PMID: 34517794 DOI: 10.2174/0929867328666210913090928] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/10/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Parasitic diseases caused by protozoa such as Chagas disease, leishmaniasis, malaria, African trypanosomiasis, amebiasis, trichomoniasis, and giardiasis are considered serious public health problems in developing countries. Drug-resistance among parasites justifies the search for new therapeutic drugs and the identification of new targets becomes a valuable approach. In this scenario, glycolysis pathway which consists of the conversion of glucose into pyruvate plays an important role in the protozoa energy supply and it is therefore considered as a promising target. In this pathway, triose phosphate isomerase (TIM) plays an essential role in efficient energy production. Furthermore, protozoa TIM show structural differences with human enzyme counterparts suggesting the possibility of obtaining selective inhibitors. Therefore, TIM is considered a valid approach to develop new antiprotozoal agents, inhibiting the glycolysis in the parasite. OBJECTIVE In this review, we discuss the drug design strategies, structure-activity relationship, and binding modes of outstanding TIM inhibitors against Trypanosoma cruzi, Trypanosoma brucei, Plasmodium falciparum, Giardia lamblia, Leishmania mexicana, Trichomonas vaginalis, and Entamoeba histolytica. RESULTS TIM inhibitors showed mainly aromatic systems and symmetrical structure, where the size and type of heteroatom are important for enzyme inhibition. This inhibition is mainly based on the interaction with i) the interfacial region of TIM inducing changes on the quaternary and tertiary structure or ii) with the TIM catalytic region were the main pathways that disabled the catalytic activity of the enzyme. CONCLUSION Benzothiazole, benzoxazole, benzimidazole, and sulfhydryl derivatives stand out as TIM inhibitors. In silico and in vitro studies demonstrate that the inhibitors bind mainly at the TIM dimer interface. In this review, the development of new TIM inhibitors as antiprotozoal drugs is demonstrated as an important pharmaceutical strategy that may lead to new therapies for these ancient parasitic diseases.
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Affiliation(s)
- Lenci K Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Antonio Moreno-Herrera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alfredo Juárez-Saldivar
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alonzo González-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Eyra Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Isidro Palos-Pizarro
- Unidad Académica Multidisciplinaria Reynosa-Rodhe, Universidad Autónoma de Tamaulipas, 88779 Reynosa. Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, 07320 Ciudad de México. Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
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Cairo P, De Luca G, Tocci E, Drioli E. 110th Anniversary: Selective Recognition of 5-Fluorouracil with Molecular Imprinting Membranes: Molecular Details. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b02281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrizia Cairo
- Institute on Membrane Technology, ITM-CNR, Via P. Bucci 17/C, 87030 Rende (CS), Italy
| | - Giorgio De Luca
- Institute on Membrane Technology, ITM-CNR, Via P. Bucci 17/C, 87030 Rende (CS), Italy
| | - Elena Tocci
- Institute on Membrane Technology, ITM-CNR, Via P. Bucci 17/C, 87030 Rende (CS), Italy
| | - Enrico Drioli
- Institute on Membrane Technology, ITM-CNR, Via P. Bucci 17/C, 87030 Rende (CS), Italy
- Department of Chemical Engineering and Materials, University of Calabria, Via P. Bucci 44, 87030 Rende (CS), Italy
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- WCU Department of Energy Engineering, College of Engineering, Hanyang University, Seoul, 133-791, Korea
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Phenylpyrrole fungicides act on triosephosphate isomerase to induce methylglyoxal stress and alter hybrid histidine kinase activity. Sci Rep 2019; 9:5047. [PMID: 30911085 PMCID: PMC6433957 DOI: 10.1038/s41598-019-41564-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/06/2019] [Indexed: 01/03/2023] Open
Abstract
Fludioxonil, a natural product of pyrrolnitrin, is a potent fungicide used on crops worldwide. Drug action requires the presence of a group III hybrid histidine kinase (HHK) and the high osmolarity glycerol (HOG) pathway. We have reported that the drug does not act directly on HHK, but triggers the conversion of the kinase to a phosphatase, which dephosphorylates Ypd1 to constitutively activate HOG signaling. Still, the direct drug target remains unknown and mode of action ill defined. Here, we heterologously expressed a group III HHK, dimorphism-regulating kinase 1 (Drk1) in Saccharomyces cerevisae to delineate fludioxonil’s target and action. We show that the drug interferes with triosephosphate isomerase (TPI) causing release of methylglyoxal (MG). MG activates the group III HHK and thus the HOG pathway. Drug action involved Drk1 cysteine 392, as a C392S substitution increased drug resistance in vivo. Drug sensitivity was reversed by dimedone treatment, indicating Drk1 responds in vivo to an aldehydic stress. Fludioxonil treatment triggered elevated cytosolic methylglyoxal. Likewise, methylglyoxal treatment of Drk1-expressing yeast phenocopied treatment with fludioxonil. Fludioxonil directly inhibited TPI and also caused it to release methylglyoxal in vitro. Thus, TPI is a drug target of the phenylpyrrole class of fungicides, inducing elevated MG which alters HHK activity, likely converting the kinase to a phosphatase that acts on Ypd1 to trigger HOG pathway activation and fungal cell death.
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García-Ortiz AL, Domínguez-González R, Romero-Ávila M, Flores-Pérez B, Guillén L, Castro M, Barba-Behrens N. The role of weak interactions in self-assembly of supramolecular associations of benzothiazole derivatives and their coordination compounds. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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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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Han D, Su M, Tan J, Li C, Zhang X, Wang C. Structure–activity relationship and binding mode studies for a series of diketo-acids as HIV integrase inhibitors by 3D-QSAR, molecular docking and molecular dynamics simulations. RSC Adv 2016. [DOI: 10.1039/c6ra00713a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We explored the main factors affecting the activity of compounds by different statistical and computational methods.
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Affiliation(s)
- Dan Han
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Min Su
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Jianjun Tan
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Chunhua Li
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Xiaoyi Zhang
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Cunxin Wang
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- China
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Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015; 109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022] Open
Abstract
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Doga Findik
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
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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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Wang H, Zhang H, Zou Y, Mi Y, Lin S, Xie Z, Yan Y, Zhang H. Structural Insight into the Tetramerization of an Iterative Ketoreductase SiaM through Aromatic Residues in the Interfaces. PLoS One 2014; 9:e97996. [PMID: 24901639 PMCID: PMC4046962 DOI: 10.1371/journal.pone.0097996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/23/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Hua Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huaidong Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanling Mi
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhixiong Xie
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Houjin Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail:
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Flores Sandoval CA, Cuevas Hernández RI, Correa Basurto J, Beltrán Conde HI, Padilla Martínez II, Farfán García JN, Nogueda Torres B, Trujillo Ferrara JG. Synthesis and theoretic calculations of benzoxazoles and docking studies of their interactions with triosephosphate isomerase. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0264-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Kurkcuoglu Z, Ural G, Demet Akten E, Doruker P. Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human. Mol Inform 2011; 30:986-95. [PMID: 27468153 DOI: 10.1002/minf.201100109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/12/2011] [Indexed: 11/06/2022]
Abstract
We aim to uncover the binding modes of benzothiazoles, which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM), by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings, the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits, whereas non-inhibitors mostly choose other sites. In contrast, TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site, which may explain its relatively higher inhibition effect on hTIM.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - Gulgun Ural
- Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - E Demet Akten
- Department of Information Technologies, Kadir Has University, Cibali, 34083, Istanbul, Turkey.
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey. .,Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
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14
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Romo-Mancillas A, Téllez-Valencia A, Yépez-Mulia L, Hernández-Luis F, Hernández-Campos A, Castillo R. The design and inhibitory profile of new benzimidazole derivatives against triosephosphate isomerase from Trypanosoma cruzi: a problem of residue motility. J Mol Graph Model 2011; 30:90-9. [PMID: 21798779 DOI: 10.1016/j.jmgm.2011.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/18/2011] [Accepted: 06/21/2011] [Indexed: 10/17/2022]
Abstract
To develop a new set of compounds with inhibitory activity against the triosephosphate isomerase of Trypanosoma cruzi (TcTIM), a group of benzimidazole derivatives was studied using four different docking procedures. These docking procedures differ in the number and type of mobile residues considered in the analysis. As a result of this methodology, a clustered analysis of plausible candidate structures was produced. A different set of previously synthesized compounds was used to validate this analysis. The validation showed that the best results correspond to the docking procedure in which the residues near the hydrophobic pocket of the protein's interface were considered mobile. A binding site for the best candidates was identified. Residues Tyr103, Glu105 and Lys113, among others, are important for the binding of this kind of compound. Residue Tyr103 is different in the human TIM, thus establishing a key feature for the future design of selective inhibitors.
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Affiliation(s)
- Antonio Romo-Mancillas
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México DF 04510, Mexico
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15
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Massive screening yields novel and selective Trypanosoma cruzi triosephosphate isomerase dimer-interface-irreversible inhibitors with anti-trypanosomal activity. Eur J Med Chem 2010; 45:5767-72. [PMID: 20889239 DOI: 10.1016/j.ejmech.2010.09.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 11/22/2022]
Abstract
Triosephosphate isomerase from Trypanosoma cruzi (TcTIM), an enzyme in the glycolytic pathway that exhibits high catalytic rates of glyceraldehyde-3-phosphate- and dihydroxyacetone-phosphate-isomerization only in its dimeric form, was screened against an in-house chemical library containing nearly 230 compounds belonging to different chemotypes. After secondary screening, twenty-six compounds from eight different chemotypes were identified as screening positives. Four compounds displayed selectivity for TcTIM over TIM from Homo sapiens and, concomitantly, in vitro activity against T. cruzi.
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16
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Chávez-Calvillo R, Costas M, Hernández-Trujillo J. Theoretical analysis of intermolecular interactions of selected residues of triosephosphate isomerase from Trypanosoma cruzi with its inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid. Phys Chem Chem Phys 2010; 12:2067-74. [DOI: 10.1039/b918104k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Espinoza-Fonseca LM, Trujillo-Ferrara JG. Toward a rational design of selective multi-trypanosomatid inhibitors: a computational docking study. Bioorg Med Chem Lett 2006; 16:6288-92. [PMID: 16997551 DOI: 10.1016/j.bmcl.2006.09.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 09/05/2006] [Accepted: 09/07/2006] [Indexed: 11/18/2022]
Abstract
Compound V7, a benzothiazole which was recently found as selective inhibitor of trypanosomal TIMs, was docked into TIMs from Trypanosoma cruzi, Trypanosoma brucei, Entamoeba histolytica, Plasmodium falciparum, yeast, and human. Structural analyses revealed the importance of the accessibility to the two aromatic clusters located at the dimer's interface for the selective inhibition of trypanosomal TIMs. Thus, it was found that different accessibilities of the protein interface of TIMs plays an important role in the inhibitory activity of benzothiazoles. These findings will contribute to the rational development and improvement of benzothiazoles to be used as multi-trypanosomatid inhibitors.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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18
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Wongsantichon J, Ketterman A. An intersubunit lock-and-key 'clasp' motif in the dimer interface of Delta class glutathione transferase. Biochem J 2006; 394:135-44. [PMID: 16225458 PMCID: PMC1386011 DOI: 10.1042/bj20050915] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Structural investigations of a GST (glutathione transferase), adGSTD4-4, from the malaria vector Anopheles dirus show a novel lock-and-key 'Clasp' motif in the dimer interface of the Delta class enzyme. This motif also appears to be highly conserved across several insect GST classes, but differs from a previously reported mammalian lock-and-key motif. The aromatic 'key' residue not only inserts into a hydrophobic pocket, the 'lock', of the neighbouring subunit, but also acts as part of the 'lock' for the other subunit 'key'. The 'key' residues from both subunits show aromatic ring stacking with each other in a pi-pi interaction, generating a 'Clasp' in the middle of the subunit interface. Enzyme catalytic and structural characterizations revealed that single amino acid replacements in this 'Clasp' motif impacted on catalytic efficiencies, substrate selectivity and stability. Substitutions to the 'key' residue create strong positive co-operativity for glutathione binding, with a Hill coefficient approaching 2. The lock-and-key motif in general and especially the 'Clasp' motif with the pi-pi interaction appear to play a pivotal role in subunit communication between active sites, as well as in stabilizing the quaternary structure. Evidence of allosteric effects suggests an important role for this particular intersubunit architecture in regulating catalytic activity through conformational transitions of subunits. The observation of co-operativity in the mutants also implies that glutathione ligand binding and dimerization are linked. Quaternary structural changes of all mutants suggest that subunit assembly or dimerization basically manipulates subunit communication.
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Affiliation(s)
- Jantana Wongsantichon
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Phutthamonthol Road 4, Salaya, Nakhon Pathom 73170, Thailand
| | - Albert J. Ketterman
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Phutthamonthol Road 4, Salaya, Nakhon Pathom 73170, Thailand
- To whom correspondence should be addressed (email )
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