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Heidari S, Hajjaran H, Mohebali M, Akhoundi B, Gharechahi J. Recognition of Immunoreactive Proteins in Leishmania infantum Amastigote-Like and Promastigote Using Sera of Visceral Leishmaniasis Patients: a Preliminary Study. Acta Parasitol 2024; 69:533-540. [PMID: 38227109 DOI: 10.1007/s11686-023-00764-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/22/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE Visceral leishmaniasis (VL) is a systemic and parasitic disease that is usually fatal if left untreated. VL is endemic in different parts of Iran and is caused mainly by Leishmania infantum. This study aimed to recognition immunoreactive proteins in amastigote-like and promastigote stages of L. infantum (Iranian strain) by antibodies present in the sera of VL patients. METHODS Total protein extract from amastigote-like and promastigote cells was separated by two-dimensional electrophoresis (2DE). To detect the immunoreactive proteins, 2DE immunoblotting method was performed using different pools of VL patients' sera. RESULTS Approximately 390 and 430 protein spots could be separated in 2DE profiles of L. infantum amastigote-like and promastigote stages, respectively. In immunoblotting method, approximately 295 and 135 immunoreactive proteins of amastigotes-like reacted with high antibody titer serum pool and low antibody titer serum pool, respectively. Approximately 120 and 85 immunoreactive proteins of promastigote extract were recognized using the high antibody titer sera pool and low antibody titer sera, respectively. CONCLUSION The present study has recognized a number of antigenic diversity proteins based on the molecular weight and pH in amastigote-like and promastigote stages of L. infantum. These results provide us a new concept for further analysis development in the field of diagnosis biomarkers and vaccine targets.
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Affiliation(s)
- Soudabeh Heidari
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
| | - Homa Hajjaran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran.
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
- Center for Research of Endemic Parasites of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnaz Akhoundi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Naveed M, Makhdoom SI, Abbas G, Safdari M, Farhadi A, Habtemariam S, Shabbir MA, Jabeen K, Asif MF, Tehreem S. The Virulent Hypothetical Proteins: The Potential Drug Target Involved in Bacterial Pathogenesis. Mini Rev Med Chem 2022; 22:2608-2623. [DOI: 10.2174/1389557522666220413102107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/01/2021] [Accepted: 01/21/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Hypothetical proteins (HPs) are non-predicted sequences that are identified only by open reading frames in sequenced genomes but their protein products remain uncharacterized by any experimental means. The genome of every species consists of HPs that are involved in various cellular processes and signaling pathways. Annotation of HPs is important as they play a key role in disease mechanisms, drug designing, vaccine production, antibiotic production, and host adaptation. In the case of bacteria, 25-50% of the genome comprises of HPs, which are involved in metabolic pathways and pathogenesis. The characterization of bacterial HPs helps to identify virulent proteins that are involved in pathogenesis. This can be done using in-silico studies, which provide sequence analogs, physiochemical properties, cellular or subcellular localization, structure and function validation, and protein-protein interactions. The most diverse types of virulent proteins are exotoxins, endotoxins, and adherent virulent factors that are encoded by virulent genes present on the chromosomal DNA of the bacteria. This review evaluates virulent HPs of pathogenic bacteria, such as Staphylococcus aureus, Chlamydia trachomatis, Fusobacterium nucleatum, and Yersinia pestis. The potential of these HPs as a drug target in bacteria-caused infectious diseases along with the mode of action and treatment approaches have been discussed.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Ghulam Abbas
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mohammadreza Safdari
- Department of Orthopedic Surgery, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amin Farhadi
- Kavian Institute of Higher Education, Mashhad, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services UK, University of Greenwich, Medway Campus-Science, Grenville Building (G102/G107), Central Avenue, Chatham-Maritime, Kent, ME4 4TB, UK
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Muhammad Farrukh Asif
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Sana Tehreem
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, Hubei, China
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Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes. BMC Genomics 2021; 22:733. [PMID: 34627149 PMCID: PMC8501643 DOI: 10.1186/s12864-021-08029-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Manual annotation efforts are time-consuming and complex; however, software can help reduce these drawbacks. Results We created Manual Annotation Studio (MAS) to improve the efficiency of the process of manual functional annotation prokaryotic and viral genomes. MAS allows users to upload unannotated genomes, provides an interface to edit and upload annotations, tracks annotation history and progress, and saves data to a relational database. MAS provides users with pertinent information through a simple point and click interface to execute and visualize results for multiple homology search tools (blastp, rpsblast, and HHsearch) against multiple databases (Swiss-Prot, nr, CDD, PDB, and an internally generated database). MAS was designed to accept connections over the local area network (LAN) of a lab or organization so multiple users can access it simultaneously. MAS can take advantage of high-performance computing (HPC) clusters by interfacing with SGE or SLURM and data can be exported from MAS in a variety of formats (FASTA, GenBank, GFF, and excel). Conclusions MAS streamlines and provides structure to manual functional annotation projects. MAS enhances the ability of users to generate, interpret, and compare results from multiple tools. The structure that MAS provides can improve project organization and reduce annotation errors. MAS is ideal for team-based annotation projects because it facilitates collaboration. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08029-8.
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Gontijo VS, Colombo FA, Ferreira Espuri P, Freitas PGD, Nunes JB, Alves LB, Veloso MP, Alves RB, Freitas RP, Marques MJ. In vivo evaluation of anti-Leishmania activity of alkyltriazoles and alkylphosphocholines by oral route. Exp Parasitol 2021; 226-227:108123. [PMID: 34144040 DOI: 10.1016/j.exppara.2021.108123] [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: 06/02/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
The failures in the treatment of leishmaniasis is an increasing problem around the world, especially related to resistance. Thus, we describe the synthesis and in vivo anti-Leishmania activity of alkylphosphocholine and alkyltriazoles; besides, their likely action mechanisms stem from some eventual inhibition of parasite enzymes using computational tools. These compounds were tested in an in vivo hamster model infected with Leishmania Leishmania infantum chagasi. Fifty days after parasite inoculation, the two compounds 12-azidedodecylphosphocholine (3) and 3-(1-(12-fluorododecyl)-1H-1,2,3-triazol-1-yl)propano-1-ol (9), were separately administered once a day as oral suspensions (25 and 12.5 mg/kg/day, respectively) during ten days, and their efficacy was compared to the reference compound pentavalent antimonial Glucantime (GLU). Compound 3 significantly reduced the number of parasites in the spleen (4.93 × 102 amastigotes/g) and liver (4.52 × 103 amastigotes/g). Compound 9 reduced the number of amastigotes in the spleen to 1.30 × 104 and 1.36 × 103 amastigotes/g in the liver. GLU was the most effective overall treatment (7.50 × 101 and 2.28 × 102 amastigotes/g in the spleen and liver, respectively). The high activity levels of these compounds in vivo may stem from their high in vitro leishmanicidal activity and lipophilicity. The in silico absorption, distribution, metabolism, and excretion studies also showed some anti-Leishmania potential. Compound 9 had more lipophilic characteristics than those of compound 3. In silico studies of the nine enzymes of compounds 3 and 9 showed significant evidence of interactions with nicotimidase and tyrosine aminotransferase, demonstrating possible inhibition enzymes present in L. (L.) infantum chagasi. These compounds could be a promising template for developing a new class of leishmanicidal agents, by oral route, and deserve further investigation to explore different therapeutic regimens.
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Affiliation(s)
- Vanessa Silva Gontijo
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
| | - Fabio Antônio Colombo
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Patrícia Ferreira Espuri
- Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Poliany Graziella de Freitas
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Juliana Barbosa Nunes
- Laboratório de Patologia de Moléstias Infecciosas, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, Av. Dr. Arnaldo, 455. Cerqueira César, São Paulo, 01246-903, São Paulo, SP, Brazil
| | - Levy Bueno Alves
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Márcia Paranho Veloso
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Rosemeire Brondi Alves
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Rossimiriam Pereira Freitas
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcos José Marques
- Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil.
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Machado JM, Costa LE, Dias DS, Ribeiro PAF, Martins VT, Lage DP, Carvalho GB, Franklin ML, Tavares GSV, Oliveira-da-Silva JA, Machado AS, Ramos LS, Nogueira LM, Mariano RMS, Moura HB, Silva ES, Teixeira-Neto RG, Campos-da-Paz M, Galdino AS, Coelho EAF. Diagnostic markers selected by immunoproteomics and phage display applied for the serodiagnosis of canine leishmaniosis. Res Vet Sci 2019; 126:4-8. [PMID: 31415928 DOI: 10.1016/j.rvsc.2019.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 11/24/2022]
Abstract
Canine leishmaniosis (CanL) is one of the most important parasitic diseases found in several countries worldwide. Dogs are considered important domestic reservoirs of the parasites, being relevant in the maintenance of transmission cycle of the disease between sandflies and humans. However, the prevalence of asymptomatic infection is considerably higher than that of apparent clinical illness in the infected animals; thus making promptly necessary to diagnose the infection in these animals, which could help to allow to the adoption of more efficient control measures against disease. Parasitological tests, which are considered as gold standard to demonstrate the infection and diagnose the disease, present problems related with their sensitivity. Also, the sample´s collect is considered invasive. As consequence, serological tests could be applied as an additional tool to detect the asymptomatic and symptomatic CanL. For this purpose, distinct recombinant antigens have been studied; however, problems in their sensitivity and/or specificity have been still registered. The present review focus in advances in the identification of new diagnostic targets applied for the CanL diagnose, represented here by recombinant single, combined or chimeric proteins, as well as by peptides that mimic epitopes (mimotopes); which were selected by means of immunoproteomics and phage display.
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Affiliation(s)
- Juliana M Machado
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Lourena E Costa
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Daniel S Dias
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Patricia A F Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Vívian T Martins
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Daniela P Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Gerusa B Carvalho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Michelle L Franklin
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Grasiele S V Tavares
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - João A Oliveira-da-Silva
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Amanda S Machado
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Luana S Ramos
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Lais M Nogueira
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Reysla M S Mariano
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Henrique B Moura
- Infectious Parasitic Diseases Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Eduardo S Silva
- Infectious Parasitic Diseases Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Rafael G Teixeira-Neto
- Infectious Parasitic Diseases Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Mariana Campos-da-Paz
- Nanobiotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Alexsandro S Galdino
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, 35501-296 Divinópolis, Minas Gerais, Brazil
| | - Eduardo A F Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, 30130-100 Belo Horizonte, Minas Gerais, Brazil.
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Identifying miltefosine-resistant key genes in protein-protein interactions network and experimental verification in Iranian Leishmania major. Mol Biol Rep 2019; 46:5371-5388. [PMID: 31385238 DOI: 10.1007/s11033-019-04992-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/19/2019] [Indexed: 12/23/2022]
Abstract
Drug resistance is a complex phenomenon during leishmaniasis chemotherapy. In this study, the genes and pathways involved in miltefosine (MIL)-resistant Leishmania were identified using microarray data and in silico approaches. GSE30685 and GSE45496 were obtained from GEO database and analyzed with GEO2R tool to identify genes involved in MIL-resistant Leishmania. 177 differentially expressed genes (DEGs) were selected from these GSEs, which about half of them were uncharacterized/hypothetical proteins. The interactions between DEGs were investigated using STRING database and protein-protein interaction (PPI) networks. Five hub nodes were found in the PPI network. The gene ontology (GO) analysis of the resulting network revealed that DNA replication (GO:0006260) and ATP hydrolysis coupled proton transport (GO:0015991) were the most enriched GO term. Iranian MIL-resistant Leishmania major (L. major) parasites were generated by exposure of wild-type isolates to the increasing concentrations of MIL over a period of 5 months. Proof of mRNA expression levels of the obtained hub genes was assessed in Iranian wild-type and acquired resistant L. major parasites by real-time PCR. A significant higher expression level of LDBPK_150170 (encoding protein phosphatase 2C, PP2C), was only observed in Iranian L. major parasites resistance to MIL. Moreover, the RT-PCR results showed that the expression of metacyclic marker (small hydrophilic endoplasmic reticulum-associated protein, SHERP) and MIL-resistant marker (Leishmania MIL-transporter, LMT) was significantly increased and decreased, respectively, in Iranian MIL-resistant L. major parasites. Taken together, these data suggested that PP2C as well as SHERP and LMT genes may be prospective targets for the treatment of MIL-resistant Leishmania.
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Screening diagnostic candidates from Leishmania infantum proteins for human visceral leishmaniasis using an immunoproteomics approach. Parasitology 2019; 146:1467-1476. [PMID: 31142384 DOI: 10.1017/s0031182019000714] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There is no suitable vaccine against human visceral leishmaniasis (VL) and available drugs are toxic and/or present high cost. In this context, diagnostic tools should be improved for clinical management and epidemiological evaluation of disease. However, the variable sensitivity and/or specificity of the used antigens are limitations, showing the necessity to identify new molecules to be tested in a more sensitive and specific serology. In the present study, an immunoproteomics approach was performed in Leishmania infantum promastigotes and amastigotes employing sera samples from VL patients. Aiming to avoid undesired cross-reactivity in the serological assays, sera from Chagas disease patients and healthy subjects living in the endemic region of disease were also used in immunoblottings. The most reactive spots for VL samples were selected, and 29 and 21 proteins were identified in the promastigote and amastigote extracts, respectively. Two of them, endonuclease III and GTP-binding protein, were cloned, expressed, purified and tested in ELISA experiments against a large serological panel, and results showed high sensitivity and specificity values for the diagnosis of disease. In conclusion, the identified proteins could be considered in future studies as candidate antigens for the serodiagnosis of human VL.
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Calarco L, Ellis J. Annotating the ‘hypothetical’ in hypothetical proteins: In-silico analysis of uncharacterised proteins for the Apicomplexan parasite, Neospora caninum. Vet Parasitol 2019; 265:29-37. [DOI: 10.1016/j.vetpar.2018.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
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Subramanian A, Sarkar RR. Perspectives on Leishmania Species and Stage-specific Adaptive Mechanisms. Trends Parasitol 2018; 34:1068-1081. [DOI: 10.1016/j.pt.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/10/2018] [Accepted: 09/21/2018] [Indexed: 12/23/2022]
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10
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Chávez-Fumagalli MA, Lage DP, Tavares GSV, Mendonça DVC, Dias DS, Ribeiro PAF, Ludolf F, Costa LE, Coelho VTS, Coelho EAF. In silico Leishmania proteome mining applied to identify drug target potential to be used to treat against visceral and tegumentary leishmaniasis. J Mol Graph Model 2018; 87:89-97. [PMID: 30522092 DOI: 10.1016/j.jmgm.2018.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/12/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]
Abstract
New therapeutic strategies against leishmaniasis are desirable, since the treatment against disease presents problems, such as the toxicity, high cost and/or parasite resistance. As consequence, new antileishmanial compounds are necessary to be identified, as presenting high activity against Leishmania, but low toxicity in mammalian hosts. In the present study, a Leishmania proteome mining strategy was developed, in order to select new drug targets with low homology to human proteins, but that are considered relevant for the parasite' survival. Results showed a hypothetical protein, which was functionally annotated as a glucosidase-like protein, as presenting such characteristics. This protein was associated with the metabolic network of the N-Glycan biosynthesis pathway in Leishmania, and two specific inhibitors - acarbose and miglitol - were predicted to be potential targets against it. In this context, miglitol [1-(2-Hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol] was tested against stationary promastigotes and axenic amastigotes of the Leishmania amazonensis and L. infantum species, and results showed high values of antileishmanial inhibition against both parasite species. Miglitol showed also efficacy in the treatment of Leishmania-infected macrophages; thus denoting its potential use as an antileishmanial candidate. In conclusion, this work presents a new drug target identified by a proteome mining strategy associated with bioinformatics tools, and suggested its use as a possible candidate to be applied in the treatment against disease.
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Affiliation(s)
- Miguel A Chávez-Fumagalli
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela P Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Grasiele S V Tavares
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora V C Mendonça
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel S Dias
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia A F Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Ludolf
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lourena E Costa
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicio T S Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo A F Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling. Int J Biol Macromol 2018; 123:350-362. [PMID: 30445075 DOI: 10.1016/j.ijbiomac.2018.11.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism. Some of them are responsible for stress-response mechanisms and cell cycle, membrane transport, and regulatory processes. The genome-neighborhood analysis found five important gene clusters (dsr, ehb, kaiC, cmr, and gas) involving in the energetic metabolism and defense systems. MTH operome contains 223 enzymes with 15 metabolic subsystems, 15 cell cycle proteins, 17 transcriptional regulators and 33 binding proteins. Functional annotation of its operome is thus more fundamental to a profound understanding of the molecular and cellular machinery at systems-level.
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Sharma R, Terrão MC, Castro FF, Breitling R, Faça V, Oliveira EB, Cruz AK. Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major. PLoS One 2018; 13:e0203369. [PMID: 30208112 PMCID: PMC6135404 DOI: 10.1371/journal.pone.0203369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/20/2018] [Indexed: 11/29/2022] Open
Abstract
The N-end rule pathway leads to regulated proteolysis as an adaptive response to external stress and is ubiquitous from bacteria to mammals. In this study, we investigated a gene coding for a putative core enzyme of this post-translational regulatory pathway in Leishmania major, which may be crucial during cytodifferentiation and the environment adaptive responses of the parasite. Leucyl, phenylalanyl-tRNA protein transferase and arginyl-tRNA protein transferase are key components of this pathway in E. coli and eukaryotes, respectively. They catalyze the specific conjugation of leucine, phenylalanine or arginine to proteins containing exposed N-terminal amino acid residues, which are recognized by the machinery for the targeted proteolysis. Here, we characterized a conserved hypothetical protein coded by the LmjF.21.0725 gene in L. major. In silico analysis suggests that the LmjF.21.0725 protein is highly conserved among species of Leishmania and might belong to the Acyl CoA-N-acyltransferases (NAT) superfamily of proteins. Immunofluorescence cell imaging indicates that the cytosolic localization of the studied protein and the endogenous levels of the protein in promastigotes are barely detectable by western blotting assay. The knockout of the two alleles of LmjF.21.0725 by homologous recombination was only possible in the heterozygous transfectant expressing LmjF.21.0725 as a transgene from a plasmid. Moreover, the kinetics of loss of the plasmid in the absence of drug pressure suggests that maintenance of the gene is essential for promastigote survival. Here, evidence is provided that this putative aminoacyl tRNA-protein transferase is essential for parasite survival. The enzyme activity and corresponding post-translational regulatory pathway are yet to be investigated.
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Affiliation(s)
- Rohit Sharma
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Monica Cristina Terrão
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Felipe Freitas Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Vitor Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Eduardo Brandt Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- * E-mail:
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Sundar S, Singh B. Understanding Leishmania parasites through proteomics and implications for the clinic. Expert Rev Proteomics 2018; 15:371-390. [PMID: 29717934 PMCID: PMC5970101 DOI: 10.1080/14789450.2018.1468754] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Leishmania spp. are causative agents of leishmaniasis, a broad-spectrum neglected vector-borne disease. Genomic and transcriptional studies are not capable of solving intricate biological mysteries, leading to the emergence of proteomics, which can provide insights into the field of parasite biology and its interactions with the host. Areas covered: The combination of genomics and informatics with high throughput proteomics may improve our understanding of parasite biology and pathogenesis. This review analyses the roles of diverse proteomic technologies that facilitate our understanding of global protein profiles and definition of parasite development, survival, virulence and drug resistance mechanisms for disease intervention. Additionally, recent innovations in proteomics have provided insights concerning the drawbacks associated with conventional chemotherapeutic approaches and Leishmania biology, host-parasite interactions and the development of new therapeutic approaches. Expert commentary: With progressive breakthroughs in the foreseeable future, proteome profiles could provide target molecules for vaccine development and therapeutic intervention. Furthermore, proteomics, in combination with genomics and informatics, could facilitate the elimination of several diseases. Taken together, this review provides an outlook on developments in Leishmania proteomics and their clinical implications.
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Affiliation(s)
- Shyam Sundar
- a Department of Medicine, Institute of Medical Sciences , Banaras Hindu University , Varanasi , India
| | - Bhawana Singh
- a Department of Medicine, Institute of Medical Sciences , Banaras Hindu University , Varanasi , India
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A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:6813467. [PMID: 29785196 PMCID: PMC5896251 DOI: 10.1155/2018/6813467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/25/2018] [Indexed: 12/11/2022]
Abstract
Background The development of new therapeutic strategies to treat patients for leishmaniasis has become a priority. The antileishmanial activity of the strychnobiflavone flavonoid was recently demonstrated against Leishmania amazonensis and Leishmania infantum amastigotes and promastigotes. The biological effect of this molecule was identified due to its capacity to interfere in the parasite mitochondrial membrane; however, the underlying molecular mechanism remains unclear. Methods and Results In this study, a computational approach using bioinformatics was performed to screen biological targets of strychnobiflavone in L. infantum. Computational programs, such as the target fishing approach and molecular docking assays, were used. Results showed that the putative pathway targeted by strychnobiflavone in L. infantum is the methylglyoxal degradation superpathway, and one hydrolase-like protein was predicted to be the molecular target of this flavonoid in the parasites. Conclusion In this context, this study provides the basis for understanding the mechanism of action of strychnobiflavone in L. infantum and presents a strategy based on bioinformatics programs to screen targets of other molecules with biological action against distinct pathogens.
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Oliveira MP, Martins VT, Santos TTO, Lage DP, Ramos FF, Salles BCS, Costa LE, Dias DS, Ribeiro PAF, Schneider MS, Machado-de-Ávila RA, Teixeira AL, Coelho EAF, Chávez-Fumagalli MA. Small Myristoylated Protein-3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis. Int J Mol Sci 2018; 19:E129. [PMID: 29301342 PMCID: PMC5796078 DOI: 10.3390/ijms19010129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/14/2017] [Accepted: 12/25/2017] [Indexed: 11/23/2022] Open
Abstract
In a proteomics approach conducted with Leishmania amazonensis, parasite proteins showed either an increase or a decrease in their expression content during extensive in vitro cultivation, and were related to the survival and the infectivity of the parasites, respectively. In the current study, a computational screening was performed to predict virulence factors among these molecules. Three proteins were selected, one of which presented no homology to human proteins. This candidate, namely small myristoylated protein-3 (SMP-3), was cloned, and its recombinant version (rSMP-3) was used to stimulate peripheral blood mononuclear cells (PBMCs) from healthy subjects living in an endemic area of leishmaniasis and from visceral leishmaniasis patients. Results showed high interferon-γ (IFN-γ) production and low levels of interleukin 10 (IL-10) in the cell supernatants. An in vivo experiment was then conducted on BALB/c mice, which were immunized with rSMP-3/saponin and later challenged with Leishmania infantum promastigotes. The rSMP-3/saponin combination induced high production of protein-specific IFN-γ, IL-12, and granulocyte-macrophage colony-stimulating factor (GM-CSF) by the spleen cells of the immunized mice. This pattern was associated with protection, which was characterized by a significant reduction in the parasite load in distinct organs of the animals. Altogether, these results have revealed that this new virulence factor is immunogenic in both mice and humans, and have proven its protective efficacy against visceral leishmaniasis in a murine model.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/metabolism
- Computational Biology
- Cytokines/metabolism
- Epitopes, T-Lymphocyte/metabolism
- Humans
- Immunity, Cellular
- Immunity, Humoral
- Leishmania/pathogenicity
- Leishmania infantum
- Leishmaniasis, Visceral/immunology
- Leishmaniasis, Visceral/parasitology
- Leishmaniasis, Visceral/prevention & control
- Leukocytes, Mononuclear/metabolism
- Linear Models
- Mice, Inbred BALB C
- Molecular Sequence Annotation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- Reproducibility of Results
- Structural Homology, Protein
- Virulence Factors/metabolism
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Affiliation(s)
- Marcelo P Oliveira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Vívian T Martins
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Thaís T O Santos
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Daniela P Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Fernanda F Ramos
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Beatriz C S Salles
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Lourena E Costa
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Daniel S Dias
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Patrícia A F Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Mônica S Schneider
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Ricardo A Machado-de-Ávila
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil.
| | - Antônio L Teixeira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Neuropsychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Road, Houston, TX 77041, USA.
| | - Eduardo A F Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Departamento de Patologia Clínica, do Colégio Técnico (COLTEC), Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Miguel A Chávez-Fumagalli
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
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