Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production

Abstract

SARS-CoV-2 contains four structural proteins, two of which, the spike and nucleocapsid, are commonly used for the standardization of novel methods for antibody detection; however, some limitations in their use have been observed due to the homology of this virus with other phylogenetically-related viruses. We performed in silico analysis to search for novel immunogenic and antigenic peptides. A total of twenty-five peptides were preliminarily selected, located in the 3D structure of both proteins. Finally, eight peptides were selected: one located in the N protein and seven in the S1 domain of the spike protein. Additionally, the localization of selected peptides in 2D structures and possible changes in the sequences of these peptides in SARS-CoV-2 variants of concern were analyzed. All peptides were synthetized in MAP8 format, and recombinant S (trimer and RBD) and N proteins were used as antigens to search for antibodies in serum samples derived from COVID-19 patients, and for antibody response in New Zealand rabbits. Results showed high recognition of the serum derived from COVID-19 patients to all selected peptides; however, only the RBD3 peptide induced antibody production. In conclusion, this work provides evidence for a new strategy in peptide selection and its use for antibody detection or antibody production in animals.

Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

“…For example, in SARS-CoV , the N-protein has been shown to adhere to viral RNA and assemble it into RNP complexes. The packed RNPs particles are found on the viral membrane's internal face, generating a distinct layer from the envelope proteins M, E, and S. Moreover, the association between N and the C-terminus of the M-protein may facilitate RNP localization 50 , 51 . Numerous mutations at the nucleotide and amino acid positions in the N-protein of SARS-CoV-2 have been discerned ( Table 3 ).…”

Immunized mice naturally process in silico-derived peptides from the nucleocapsid of SARS-CoV-2

“…Whole proteome screening and immunoinformatic analysis of SARS-CoV-2 revealed 21 epitopes from 7 different proteins of SARS-CoV-2; the best epitopes were from S (ATSRTLSYY) and N (KAYNVTQAF) proteins [ 14 ]. Recently, we used immunoinformatic analysis to identify immunogenic and antigenic peptides in S and N proteins of SARS-CoV-2 and reported a list of peptides for both proteins [ 15 ].…”

Nanotechnology meets immunology towards a rapid diagnosis solution: the COVID-19 outbreak challenge

“…Thus, simpler and less-expensive tests based on antigen–antibody affinity are highly demanded and have been intensively researched. 14–16…”

“…Thus, simpler and less-expensive tests based on antigen-antibody affinity are highly demanded and have been intensively researched. [14][15][16] Many studies have focused their primary efforts on searching antigenic sites in SARS-CoV-2 for immunogenic responses using bioinformatic tools to design novel methods for virus or antibody detection of infected patients that can also be applied later for developing effective vaccines to prevent new infections. Various advanced bioinformatics tools have remarkably improved the search for immunogenic peptides.…”

“…The in silico analysis and simulation have been applied to identify novel immunogenic epitopes that could be used to develop novel synthetic antigenic peptides for the development of antibody/ antigen-based diagnostic tests for detecting SARS-CoV-2. 16 The in silico research has focused on the four main structural proteins of the SARS-CoV-2 virus, namely, spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. These proteins facilitate several pivotal biological functions, such as binding the virus to the host cell receptors, the fusion of virus envelop to the host cell, the fusion of viral RNA inside the host cell, and virus replication.…”