1
|
Cláudia Marinho da Silva A, Lima Amaral CM, Maestre Herazo MA, Nattaly Nobre Santos E, Petterson Viana Pereira E, Paula Silva da Costa H, Rodrigues Freitas E, Renata Figueiredo Gadelha C, Izabel Florindo Guedes M, Fraga van Tilburg M. Production and characterization of egg yolk antibodies against the ZIKV NS2B expressed in Nicotiana benthamiana. Int Immunopharmacol 2023; 125:111088. [PMID: 37925945 DOI: 10.1016/j.intimp.2023.111088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/23/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
The emergence of Zika virus (ZIKV) and its associated neonatal and congenital complications pose a threat to global health, particularly in tropical and subtropical regions with co-circulation of related flaviviruses and intense vector proliferation. Diagnosis of ZIKV by RT-PCR is limited to the viraemic phase and is not always accessible in low-income tropical settings, while serological tests often show cross-reactivity with other flaviviruses. Given the similarity of ZIKV symptoms to those of other arboviruses, but the different prognosis and risks, it is important to develop specific and accessible diagnostic tools. Egg yolk antibodies (IgY) were obtained from Leghorn laying hens immunized with recombinant ZIKV NS2B protein produced in agroinfiltrated Nicotiana benthamiana. After three immunizations, total IgY was recovered from the eggs by the 20% ammonium sulfate precipitation method. After characterisation by SDS-PAGE, dot blotting and ELISA, the IgY was adsorbed to dengue virus (DENV) from cell culture supernatants and tested for its ability to specifically detect ZIKV-positive sera samples. High yield and purity were observed on SDS-PAGE for polyclonal IgY, which reacted with NS2B at high titres in ELISA and detected both NS2B and ZIKV in dot blotting. However, a cross-reaction with DENV was observed and the anti-NS2B IgY was unable to discriminate ZIKV from DENV positive sera samples, even after adsorption with DENV. This is probably due to the phylogenetic relationship of the viruses and the shared identity of their proteins.
Collapse
Affiliation(s)
- Ana Cláudia Marinho da Silva
- Northeast Biotechnology Network, Graduate Program of Biotechnology, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil; Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| | - Cícero Matheus Lima Amaral
- Northeast Biotechnology Network, Graduate Program of Biotechnology, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil; Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| | - Mario A Maestre Herazo
- Northeast Biotechnology Network, Graduate Program of Biotechnology, Federal University of Ceará, Campus do Pici, 60020-181 Fortaleza, Ceará, Brazil
| | - Eduarda Nattaly Nobre Santos
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| | - Eric Petterson Viana Pereira
- Superior Institute of Biomedical Sciences, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil.
| | - Helen Paula Silva da Costa
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| | | | | | - Maria Izabel Florindo Guedes
- Northeast Biotechnology Network, Graduate Program of Biotechnology, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil; Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| | - Mauricio Fraga van Tilburg
- Northeast Biotechnology Network, Graduate Program of Biotechnology, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil; Biotechnology and Molecular Biology Laboratory, State University of Ceará, Campus do Itaperi, 60714-903 Fortaleza, Ceará, Brazil
| |
Collapse
|
2
|
Pereira EPV, da Silva Felipe SM, de Freitas RM, da Cruz Freire JE, Oliveira AER, Canabrava N, Soares PM, van Tilburg MF, Guedes MIF, Grueter CE, Ceccatto VM. Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways. Pathogens 2023; 12:1373. [PMID: 38003837 PMCID: PMC10674242 DOI: 10.3390/pathogens12111373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets.
Collapse
Affiliation(s)
- Eric Petterson Viana Pereira
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Stela Mirla da Silva Felipe
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Raquel Martins de Freitas
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - José Ednésio da Cruz Freire
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | | | - Natália Canabrava
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Paula Matias Soares
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Mauricio Fraga van Tilburg
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Maria Izabel Florindo Guedes
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Chad Eric Grueter
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Vânia Marilande Ceccatto
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| |
Collapse
|
3
|
de Paula Junior VF, van Tilburg MF, Morais PA, Júnior FFM, Lima EG, Oliveira VTDS, Guedes MIF, Caetano EWS, Freire VN. Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket. Int J Mol Sci 2022; 23:ijms231710088. [PMID: 36077486 PMCID: PMC9456192 DOI: 10.3390/ijms231710088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.
Collapse
Affiliation(s)
- Valdir Ferreira de Paula Junior
- Biotechnology & Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, Brazil
- Correspondence: ; Tel.: +55-859-8541-8255
| | | | - Pablo Abreu Morais
- Federal Institute of Education, Science and Technology of Ceará, Campus Horizonte, Horizonte 62884-105, Brazil
| | - Francisco Franciné Maia Júnior
- Departamento de Ciências Naturais, Matemática e Estatística, Universidade Federal Rural do Semi-Árido, Mossoró 59625-900, Brazil
| | - Elza Gadelha Lima
- Laboratório Central de Saúde Pública do Ceará (LACEN), Fortaleza 60120-002, Brazil
| | | | | | | | | |
Collapse
|
4
|
van Tilburg MF, Sousa SD, Ferreira de Melo RB, Moreno FB, Monteiro-Moreira AC, Moreira RA, de Alencar Moura A. Proteome of the rete testis fluid from tropically-adapted Morada Nova rams. Anim Reprod Sci 2016; 176:20-31. [PMID: 27908670 DOI: 10.1016/j.anireprosci.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/06/2016] [Accepted: 11/17/2016] [Indexed: 01/25/2023]
Abstract
The rete testis has a close relationship with sperm development and may have other functions besides serving as an intercalated channel. The aim of this study was to identify and characterize the proteins of rete testis fluid (RTF) from tropically-adapted Morada Nova rams. Testicles obtained from six Morada Nova rams were dissected and the head of the epididymis was separated to access the efferent ducts. Rete testis fluid was obtained by gentle massage of the testis. The fluid was centrifuged to remove cell debris and sperm. RTF samples (containing 400μg protein) were separated by 2-D SDS-PAGE and gels, analyzed using PDQuest software (Bio Rad, USA). Proteins were identified using tandem mass spectrometry. Gene ontology and protein network were analyzed using the software tool for searching annotations of proteins (STRAP) and STRING database. Gels had, on average, 227±13.5 spots and 51% of the proteins were found above 40kDa, corresponding to 65% of the intensity of all spots detected. Based on gene ontology analysis, the most common biological processes associated with RTF proteins were regulation (24.3%) and cellular process (23.3%). Binding (27.3%) and catalytic activity (19.3%) corresponded to the most frequent molecular functions. Albumin, clusterin, serotransferrin, immunoglobulin gamma-1 chain and alpha-2-HS-glycoprotein were the most abundant proteins in the ram rete testis fluid. In conclusion, proteins identified in the ram rete testis fluid are linked to several physiological processes associated with sperm protection and spermatogenesis.
Collapse
Affiliation(s)
| | | | | | - Frederico B Moreno
- Department of Pharmacy, The University of Fortaleza, Fortaleza, Ceará, Brazil
| | | | - Renato A Moreira
- Department of Pharmacy, The University of Fortaleza, Fortaleza, Ceará, Brazil
| | | |
Collapse
|