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Virtual Screening of Benzimidazole Derivatives as Potential Triose Phosphate Isomerase Inhibitors with Biological Activity against Leishmania mexicana. Pharmaceuticals (Basel) 2023; 16:ph16030390. [PMID: 36986489 PMCID: PMC10058926 DOI: 10.3390/ph16030390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Leishmania mexicana (L. mexicana) is a causal agent of cutaneous leishmaniasis (CL), a “Neglected disease”, for which the search for new drugs is a priority. Benzimidazole is a scaffold used to develop antiparasitic drugs; therefore, it is interesting molecule against L. mexicana. In this work, a ligand-based virtual screening (LBVS) of the ZINC15 database was performed. Subsequently, molecular docking was used to predict the compounds with potential binding at the dimer interface of triosephosphate isomerase (TIM) of L. mexicana (LmTIM). Compounds were selected on binding patterns, cost, and commercial availability for in vitro assays against L. mexicana blood promastigotes. The compounds were analyzed by molecular dynamics simulation on LmTIM and its homologous human TIM. Finally, the physicochemical and pharmacokinetic properties were determined in silico. A total of 175 molecules with docking scores between −10.8 and −9.0 Kcal/mol were obtained. Compound E2 showed the best leishmanicidal activity (IC50 = 4.04 µM) with a value similar to the reference drug pentamidine (IC50 = 2.23 µM). Molecular dynamics analysis predicted low affinity for human TIM. Furthermore, the pharmacokinetic and toxicological properties of the compounds were suitable for developing new leishmanicidal agents.
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Guerrero-Hernández J, Bobes RJ, García-Varela M, Castellanos-Gonzalez A, Laclette JP. Identification and functional characterization of the siRNA pathway in Taenia crassiceps by silencing Enolase A. Acta Trop 2022; 225:106197. [PMID: 34688628 DOI: 10.1016/j.actatropica.2021.106197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/01/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022]
Abstract
A gene silencing procedure on cysticerci of the taeniid cestode Taenia crassiceps is described. This is the first time this technique is reported in this species that is widely used as an animal model for human cysticercosis. Genome database searches were performed in order to find out if relevant genes involved in gene silencing and non-coding RNA processing, Argonaute and Dicer (AGO and Dcr) are present in T. crassiceps. We found three AGO and two Dcr orthologues that were designed TcAGO1, Tc2 and Tc3, as well as TcDcr1 and TcDcr2. In order to elucidate the evolutionary relationships of T. crassiceps TcAGO and TcDcr genes, separate phylogenetic analyses were carried out for each, including AGO and Dcr orthologues of other 20 platyhelminthes. Our findings showed a close phylogenetic relationship of TcAGO and TcDcr with those previously described for Echinococcus spp. Our RT-PCR studies demonstrated expression of all TcAGO and TcDcr orthologues. Our results show that the gene silencing machinery in T. crassiceps is functionally active by inducing silencing of TcEnoA (∼90%). These results clearly show that gene silencing using siRNAs can be used as a molecular methodology to study gene function in taeniid cestodes.
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Affiliation(s)
- Julio Guerrero-Hernández
- Biomedical Research Institute. Universidad Nacional Autónoma de México, México, 04510, Coyoacán, Cd. de México, México
| | - Raúl J Bobes
- Biomedical Research Institute. Universidad Nacional Autónoma de México, México, 04510, Coyoacán, Cd. de México, México
| | - Martín García-Varela
- Biology Institute. Universidad Nacional Autónoma de México, 04510, Coyoacán, Cd. de México, México
| | - Alejandro Castellanos-Gonzalez
- Division of Infectious Diseases, University of Texas Medical Branch, United States; Center for Tropical Diseases, University of Texas Medical Branch, United States..
| | - Juan P Laclette
- Biomedical Research Institute. Universidad Nacional Autónoma de México, México, 04510, Coyoacán, Cd. de México, México.
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Vique-Sánchez JL, Jiménez-Pineda A, Benítez-Cardoza CG. Amoebicidal effect of 5,5'-[(4-nitrophenyl)methylene]bis-6-hydroxy-2-mercapto-3-methyl-4(3H)-pyrimidinone), a new drug against Entamoeba histolytica. Arch Pharm (Weinheim) 2020; 354:e2000263. [PMID: 33017058 DOI: 10.1002/ardp.202000263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023]
Abstract
Entamoeba histolytica is a cosmopolitan protozoan parasite that can produce infections in the intestine and some organs (liver, lungs, and brain), with worldwide prevalence. There are treatments against E. histolytica (antiparasitics), but as the drugs used in these treatments have presented some type of resistance and/or side effects, there are cases with complications of this disease. Therefore, it is necessary to develop new drugs aimed at a specific therapeutic target against this parasite. Here, we used the compound 5,5'-[(4-nitrophenyl)methylene]bis(6-hydroxy-2-mercapto-3-methyl-4(3H)-pyrimidinone) in the patenting process (called D4). D4 has a reported specific use against a glycolytic enzyme, the triosephosphate isomerase of Trichomonas vaginalis (TvTIM). We determined that D4 has an amoebicidal effect in in vitro cultures, with an IC50 value of 18.5 µM, and we proposed a specific site of interaction (Lys77, His110, Gln115, and Glu118) in the triosephosphate isomerase of E. histolytica (EhTIM). Furthermore, compound D4 has favorable experimental and theoretical toxicity results. Therefore, D4 should be further investigated as a potential drug against E. histolytica.
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Affiliation(s)
- José L Vique-Sánchez
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, Baja California, México
| | - Albertana Jiménez-Pineda
- Laboratorio de Investigación Bioquímica, ENMyH-Instituto Politécnico Nacional, Ciudad de México, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, ENMyH-Instituto Politécnico Nacional, Ciudad de México, México
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Benítez‐Cardoza CG, Jiménez‐Pineda A, Angles‐Falconi SI, Fernández‐Velasco DA, Vique‐Sánchez JL. Potential Site to Direct Selective Compounds in the Triosephosphate Isomerase for the Development of New Drugs. ChemistrySelect 2020. [DOI: 10.1002/slct.202000820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Albertana Jiménez‐Pineda
- Laboratorio de Investigación BioquímicaENMyH-Instituto Politécnico Nacional Ciudad de México México
| | - Sergio I. Angles‐Falconi
- División Académica Multidisciplinaria de Jalpa de MéndezUniversidad Juárez Autónoma de Tabasco Jalpa de Méndez Tabasco, México
| | - Daniel A. Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de ProteínasDepartamento de BioquímicaFacultad de MedicinaUniversidad Nacional Autónoma de México México
| | - José L. Vique‐Sánchez
- Laboratorio de Investigación BioquímicaENMyH-Instituto Politécnico Nacional Ciudad de México México
- Facultad de MedicinaUniversidad Autónoma de Baja California Mexicali, BC, México
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Benítez-Cardoza CG, Fernández-Velasco DA, Vique-Sánchez JL. Triosephosphate Isomerase Inhibitors as Potential Drugs against Clostridium perfringens. ChemistrySelect 2020. [DOI: 10.1002/slct.201904632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Daniel A. Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas; Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de; México México
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Jimenez-Sandoval P, Castro-Torres E, González-González R, Díaz-Quezada C, Gurrola M, Camacho-Manriquez LD, Leyva-Navarro L, Brieba LG. Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites. PLoS Negl Trop Dis 2020; 14:e0007815. [PMID: 31923219 PMCID: PMC6980832 DOI: 10.1371/journal.pntd.0007815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/23/2020] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Triosephosphate isomerases (TPIs) from Taenia solium (TsTPI) and
Schistosoma mansoni (SmTPI) are potential vaccine and drug
targets against cysticercosis and schistosomiasis, respectively. This is due to
the dependence of parasitic helminths on glycolysis and because those proteins
elicit an immune response, presumably due to their surface localization. Here we
report the crystal structures of TsTPI and SmTPI in complex with
2-phosphoglyceric acid (2-PGA). Both TPIs fold into a dimeric (β-α)8
barrel in which the dimer interface consists of α-helices 2, 3, and 4, and
swapping of loop 3. TPIs from parasitic helminths harbor a region of three amino
acids knows as the SXD/E insert (S155 to E157 and S157 to D159 in TsTPI and
SmTPI, respectively). This insert is located between α5 and β6 and is proposed
to be the main TPI epitope. This region is part of a solvent-exposed
310–helix that folds into a hook-like structure. The crystal
structures of TsTPI and SmTPI predicted conformational epitopes that could be
used for vaccine design. Surprisingly, the epitopes corresponding to the SXD/E
inserts are not the ones with the greatest immunological potential. SmTPI, but
not TsTPI, habors a sole solvent exposed cysteine (SmTPI-S230) and alterations
in this residue decrease catalysis. The latter suggests that thiol-conjugating
agents could be used to target SmTPI. In sum, the crystal structures of SmTPI
and TsTPI are a blueprint for targeted schistosomiasis and cysticercosis drug
and vaccine development. Because of the worldwide prevalence of schistosomiasis and cysticercosis, it is
critical to develop drugs and vaccines against their causative agents. The
glycolytic enzyme triosephosphate isomerase (TPI) is a dual-edged sword against
diseases caused by parasitic helminths. This is because helminths heavily depend
on glycolysis for energy and because the surface localization exhibited by TPIs
that elicits an immune response against those organisms. Here we provide the
crystal structures TPIs from Taenia solium and
Schistosoma mansoni as a first step for vaccine and drug
design. As a proof of concept we found that modifications in the single solvent
exposed cysteine of TPI from S. mansoni
decreases catalysis, making this enzyme a novel target against
schistosomiasis.
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Affiliation(s)
- Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Rogelio González-González
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Misraim Gurrola
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Laura D. Camacho-Manriquez
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Lucia Leyva-Navarro
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
- * E-mail:
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Rodríguez-Lima O, García-Gutierrez P, Jiménez L, Zarain-Herzberg Á, Lazzarini R, Landa A. Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes. PLoS One 2015; 10:e0141818. [PMID: 26529408 PMCID: PMC4631506 DOI: 10.1371/journal.pone.0141818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH2-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH2 and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH2-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene.
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Affiliation(s)
- Oscar Rodríguez-Lima
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | | | - Lucía Jiménez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Roberto Lazzarini
- Departamento de Biología Experimental, Universidad Autónoma Metropolitana–Iztapalapa, México D.F., México
| | - Abraham Landa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
- * E-mail:
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Zhou J, Liao H, Li S, Zhou C, Huang Y, Li X, Liang C, Yu X. Molecular identification, immunolocalization, and characterization of Clonorchis sinensis triosephosphate isomerase. Parasitol Res 2015; 114:3117-24. [DOI: 10.1007/s00436-015-4530-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 01/05/2023]
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