Effects of K444T, N460K, F490S, L452R, and T478R Mutations on the Solubility, Allergenicity, and Immunogenicity of SARS-CoV-2-based Spike Protein Vaccines In Silico Analysis of SARS-CoV-2 Spike Mutations
Journal of Pediatric Nephrology,
Vol. 11 No. 2 (2023),
7 February 2024
https://doi.org/10.22037/jpn.v12i2.43375
Abstract
Background and Aim: The spike glycoprotein is a prime focal point for vaccine development
due to its possession of numerous T-cell and B-cell epitopes. In this study, we investigated
the effects of some important mutations (K444T, N460K, F490S, L452R, and T478R) on the
immunogenicity of the spike protein in the Omicron variant. Additionally, we forecasted the
effects of these mutations on the spike protein’s solubility, allergenicity, and immunogenicity.
Methods: In this research, we obtained 100 SARS-CoV-2 spike sequences from two
databases, namely the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV and
NCBI. We conducted a comparative analysis between the wild-type spike protein (Wuhan
accession number: NC_045512.2) and the mutated spike proteins. The analysis focused on
solubility, allergenicity, and immunogenicity. It was carried out using various bioinformatics
servers, such as Dynamut, toxin pred, soluprot, Allertop, IEDB, and Vaxigen, as well as tools,
like Mega XI and Pymol II.V.II visualizer.
Results: According to the prediction of the IEDB server, the K444T mutation is likely to
decrease the humoral immune response. In addition, spike proteins in wild types and mutants
do not have allergenic properties, and these proteins are soluble and can be expressed in
Escherichia coli.
Conclusion: Vaccines formulated using spike protein design are effective. These findings
indicate the potential for developing pan-coronavirus vaccines that offer protection not only
against SARS-CoV-2 but also against a range of other coronaviruses in the future
- COVID-19
- Structural proteins
- Bioinformatics analysis
- Vaccine
How to Cite
References
Levin AT, Owusu-Boaitey N, Pugh S, Fosdick BK, Zwi AB,
Malani A, et al. Assessing the burden of COVID-19 in developing
countries: Systematic review, meta-analysis and public
policy implications. BMJ Glob Health. 2022; 7(5):e008477.
[DOI:10.1136/bmjgh-2022-008477] [PMID]
COVID-19 National Preparedness Collaborators. Pandemic
preparedness and COVID-19: An exploratory analysis of infection
and fatality rates, and contextual factors associated
with preparedness in 177 countries, from Jan 1, 2020, to Sept
, 2021. Lancet. 2022; 399(10334):1489-512.[DOI:10.1016/
S0140-6736(22)00172-6] [PMID]
Aghcheli B, Tahamtan A, Razavi Nikoo H, Bazi Z, Kalani
MR, Moradi A. Evaluation of mutations in SARS-CoV-2 N and
S genes on the proteins stability, immunogenicity, and pathogenicity
in Iranian patients from Golestan province. Int J Pediatr.
; 10(8):16486-97. [DOI:10.22038/ijp.2022.64880.4906]
Polatoğlu I, Oncu-Oner T, Dalman I, Ozdogan S. COVID-
in early 2023: Structure, replication mechanism, variants
of SARS-CoV-2, diagnostic tests, and vaccine & drug
development studies. MedComm (2020). 2023; 4(2):e228.
[DOI:10.1002/mco2.228] [PMID]
Pronker MF, Creutznacher R, Drulyte I, Hulswit RJG, Li Z,
van Kuppeveld FJM, et al. Sialoglycan binding triggers spike
opening in a human coronavirus. bioRxiv. Preprint. 2023;
-29. [DOI:10.1101/2023.04.20.536837]
Costello SM, Shoemaker SR, Hobbs HT, Nguyen AW, Hsieh
CL, Maynard JA, et al. The SARS-CoV-2 spike reversibly samples
an open-trimer conformation exposing novel epitopes.
Nat Struct Mol Biol. 2022; 29(3):229-38. [DOI:10.1038/s41594-
-00735-5] [PMID]
Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P,
Stilianakis NI, et al. The evolution of SARS-CoV-2. Nat Rev
Microbiol. 2023; 21(6):361-79. [DOI:10.1038/s41579-023-
-2] [PMID]
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes
J; COVID-19 Genomics UK Consortium, et al. SARS-CoV-2
variant biology: Immune escape, transmission and fitness.
Nat Rev Microbiol. 2023; 21(3):162-77. [DOI:10.1038/s41579-
-00841-7] [PMID]
Umitaibatin R, Harisna AH, Jauhar MM, Syaifie PH, Arda
AG, Nugroho DW, et al. Immunoinformatics study: Multi-
Epitope based vaccine design from SARS-CoV-2 spike glycoprotein.
Vaccines (Basel). 2023; 11(2):399. [DOI:10.3390/vaccines11020399]
[PMID]
Naz S, Aroosh A, Caner A, Şahar EA, Toz S, Ozbel Y, et al.
Immunoinformatics approach to design a multi-epitope vaccine
against Cutaneous Leishmaniasis. Vaccines (Basel). 2023;
(2):339. [DOI:10.3390/vaccines11020339] [PMID]
Sahu LK, Singh K. Cross-variant proof predictive vaccine
design based on SARS-CoV-2 spike protein using immunoinformatics
approach. Beni Suef Univ J Basic Appl Sci. 2023;
(1):5. [DOI:10.1186/s43088-023-00341-4] [PMID]
Evolution of SARS-CoV-2 Variants: Implications on immune
escape, vaccination, therapeutic and diagnostic strategies.
Viruses. 2023; 15(4):944. [DOI:10.3390/v15040944]
[PMID]
Thakur S, Sasi S, Pillai SG, Nag A, Shukla D, Singhal R,
et al. SARS-CoV-2 mutations and their impact on diagnostics,
therapeutics and vaccines. Front Med (Lausanne). 2022;
:815389. [DOI:10.3389/fmed.2022.815389] [PMID]
Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson
EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations
and immune escape. Nat Rev Microbiol. 2021; 19(7):409-
[DOI:10.1038/s41579-021-00573-0] [PMID]
Han W, Chen N, Xu X, Sahil A, Zhou J, Li Z, et al. Predicting
the antigenic evolution of SARS-COV-2 with deep learning.
Nat Commun. 2023; 14(1):3478. [DOI:10.1038/s41467-
-39199-6] [PMID]
Polatoğlu I, Oncu-Oner T, Dalman I, Ozdogan S. COVID-
in early 2023: Structure, replication mechanism, variants
of SARS-CoV-2, diagnostic tests, and vaccine & drug
development studies. MedComm (2020). 2023; 4(2):e228.----
[DOI:10.1002/mco2.228] [PMID]
Khamjan NA, Lohani M, Khan MF, Khan S, Algaissi A. Immunoinformatics
strategy to develop a novel universal multiple
epitope-based COVID-19 vaccine. Vaccines (Basel). 2023;
(6):1090. [DOI:10.3390/vaccines11061090] [PMID]
Qin J, Jeon JH, Xu J, Langston LK, Marasini R, Mou S, et
al. Design and preclinical evaluation of a universal SARSCoV-
mRNA vaccine. Front Immunol. 2023; 14:1126392.
[DOI:10.3389/fimmu.2023.1126392] [PMID]
Ojha R, Singh S, Gupta N, Kumar K, Padhi AK, Prajapati
VK. Multi-pathogen based chimeric vaccine to fight against
COVID-19 and concomitant coinfections. Biotechnol Lett.
; 45(7):779-97. [DOI:10.1007/s10529-023-03380-0] [PMID]
Moustafa RI, Faraag AHI, El-Shenawy R, Agwa MM, Elsayed
H. Harnessing immunoinformatics for developing a
multiple-epitope peptide-based vaccination approach against
SARS-CoV-2 spike protein. Saudi J Biol Sci. 2023; 30(6):103661.
[DOI:10.1016/j.sjbs.2023.103661] [PMID]
Islam MA, Shahi S, Marzan AA, Amin MR, Hasan MN,
Hoque MN, et al. Variant-specific deleterious mutations in
the SARS-CoV-2 genome reveal immune responses and potentials
for prophylactic vaccine development. Front Pharmacol.
; 14:1090717. [DOI:10.3389/fphar.2023.1090717]
[PMID]
Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P,
Stilianakis NI, et al. The evolution of SARS-CoV-2. Nat Rev
Microbiol. 2023; 21(6):361-79.---- [DOI:10.1038/s41579-023-
-2] [PMID]
Gili R, Burioni R. SARS-CoV-2 before and after Omicron:
Two different viruses and two different diseases? J Transl
Med. 2023; 21(1):251. [DOI:10.1186/s12967-023-04095-6]
[PMID]
Arduini A, Laprise F, Liang C. SARS-CoV-2 ORF8: A rapidly
evolving immune and viral modulator in COVID-19. Viruses.
; 15(4):871. [DOI:10.3390/v15040871] [PMID]
Alquraan L, Alzoubi KH, Rababa'h SY. Mutations of
SARS-CoV-2 and their impact on disease diagnosis and severity.
Inform Med Unlocked. 2023; 39:101256. [DOI:10.1016/j.
imu.2023.101256] [PMID]
Focosi D, Quiroga R, McConnell S, Johnson MC, Casadevall
A. Convergent evolution in SARS-CoV-2 spike creates a
variant soup from which new COVID-19 waves emerge. Int J
Mol Sci. 2023; 24(3):2264. [DOI:10.3390/ijms24032264] [PMID]
Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary
Genetics Analysis Version 11. Mol Biol Evol. 2021;
(7):3022-7. [DOI:10.1093/molbev/msab120] [PMID]
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G,
Gumienny R, et al. SWISS-MODEL: Homology modelling of
protein structures and complexes. Nucleic Acids Res. 2018;
(W1):W296-303. [DOI:10.1093/nar/gky427] [PMID]
Laskowski RA, MacArthur MW, Moss DS, Thornton JM.
PROCHECK: A program to check the stereochemical quality
of protein structures. J Appl Crystallogr. 1993; 26:283-91.
[DOI:10.1107/S0021889892009944]
Rodrigues CH, Pires DE, Ascher DB. DynaMut: Predicting
the impact of mutations on protein conformation, flexibility
and stability. Nucleic Acids Res. 2018; 46(W1):W350-5.
[DOI:10.1093/nar/gky300] [PMID]
Fleri W, Paul S, Dhanda SK, Mahajan S, Xu X, Peters B, et
al. The immune epitope database and analysis resource in
epitope discovery and synthetic vaccine design. Front Immunol.
; 8:278. [DOI:10.3389/fimmu.2017.00278] [PMID]
Doytchinova IA, Flower DR. VaxiJen: A server for prediction
of protective antigens, tumour antigens and subunit
vaccines. BMC Bioinformatics. 2007; 8:4. [DOI:10.1186/1471-
-8-4] [PMID]
Hon J, Marusiak M, Martinek T, Kunka A, Zendulka J,
Bednar D, et al. SoluProt: Prediction of soluble protein expression
in Escherichia coli. Bioinformatics. 2021; 37(1):23-8.
[DOI:10.1093/bioinformatics/btaa1102] [PMID]
Dimitrov I, Bangov I, Flower DR, Doytchinova I. AllerTOP
v.2--a server for in silico prediction of allergens. J Mol Model.
; 20(6):2278. [DOI:10.1007/s00894-014-2278-5] [PMID]
Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R;
Open Source Drug Discovery Consortium, et al. In silico approach
for predicting toxicity of peptides and proteins. PLoS
One. 2013; 8(9):e73957. [DOI:10.1371/journal.pone.0073957]
[PMID]
COVID-19 Forecasting Team. Past SARS-CoV-2 infection
protection against re-infection: A systematic review and
meta-analysis. Lancet. 2023; 401(10379):833-42. [DOI:10.1016/
S0140-6736(22)02465-5] [PMID]
Tan ST, Kwan AT, Rodríguez-Barraquer I, Singer BJ, Park
HJ, Lewnard JA, et al. Infectiousness of SARS-CoV-2 breakthrough
infections and reinfections during the Omicron
wave. Nat Med. 2023; 29(2):358-65. [DOI:10.1038/s41591-022-
-x] [PMID]
Vicentini M, Venturelli F, Mancuso P, Bisaccia E, Zerbini A,
Massari M, et al. Risk of SARS-CoV-2 reinfection by vaccination
status, predominant variant and time from prior infection:
A cohort study, Reggio Emilia province, Italy, February
to February 2022. Euro Surveill. 2023; 28(13):2200494.
[DOI:10.2807/1560-7917.ES.2023.28.13.2200494] [PMID]
Rouet R, Henry JY, Johansen MD, Sobti M, Balachandran
H, Langley DB, et al. Broadly neutralizing SARS-CoV-2 antibodies
through epitope-based selection from convalescent
patients. Nat Commun. 2023; 14(1):687. [DOI:10.1038/s41467-
-36295-5] [PMID]
Park SW, Dushoff J, Grenfell BT, Weitz JS. Intermediate
levels of asymptomatic transmission can lead to the highest
epidemic fatalities. PNAS Nexus. 2023; 2(4):pgad106.
[DOI:10.1093/pnasnexus/pgad106] [PMID]
Sterlin D, Mathian A, Miyara M, Mohr A, Anna F, Claër L,
et al. IgA dominates the early neutralizing antibody response
to SARS-CoV-2. Sci Transl Med. 2021; 13(577):eabd2223.
[DOI:10.1126/scitranslmed.abd2223] [PMID]
Contreras M, Vicente J, Cerón JJ, Martinez Subiela S, Urra
JM, Rodríguez-Del-Río FJ, et al. Antibody isotype epitope
mapping of SARS-CoV-2 Spike RBD protein: Targets for
COVID-19 symptomatology and disease control. Eur J Immunol.
; 53(4):e2250206. [DOI:10.1002/eji.202250206]
[PMID]
Yerukala Sathipati S, Shukla SK, Ho SY. Tracking the amino
acid changes of spike proteins across diverse host species
of severe acute respiratory syndrome coronavirus 2. iScience.
; 25(1):103560. [DOI:10.1016/j.isci.2021.103560] [PMID]
Olukitibi TA, Ao Z, Warner B, Unat R, Kobasa D, Yao X.
Significance of conserved regions in Coronavirus spike protein
for developing a novel vaccine against SARS-CoV-2 infection.
Vaccines (Basel). 2023; 11(3):545. [DOI:10.3390/vaccines11030545]
[PMID]
Yang LQ, Sang P, Tao Y, Fu YX, Zhang KQ, Xie YH, et al.
Protein dynamics and motions in relation to their functions:
Several case studies and the underlying mechanisms. J Bio mol Struct Dyn. 2014; 32(3):372-93. [DOI:10.1080/07391102.2
770372] [PMID]
Barthe M, Hertereau L, Lamghari N, Osman-Ponchet H,
Braud VM. Receptors and cofactors that contribute to SARSCoV-
entry: Can skin be an alternative route of entry? Int J
Mol Sci. 2023; 24(7):6253. [DOI:10.3390/ijms24076253] [PMID]
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, et al. Omicron
SARS-CoV-2 mutations stabilize spike up-RBD conformation
and lead to a non-RBM-binding monoclonal antibody
escape. Nat Commun. 2022; 13(1):4958. [DOI:10.1038/s41467-
-32665-7] [PMID]
Lee WS, Wheatley AK, Kent SJ, DeKosky BJ. Antibodydependent
enhancement and SARS-CoV-2 vaccines and
therapies. Nat Microbiol. 2020; 5(10):1185-91. [DOI:10.1038/
s41564-020-00789-5] [PMID]
Dormeshkin D, Katsin M, Stegantseva M, Golenchenko
S, Shapira M, Dubovik S, et al. Design and immunogenicity
of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion
protein. Vaccines (Basel). 2023; 11(6):1014. [DOI:10.3390/vaccines11061014]
[PMID]
Hou XC, Xu HF, Liu Y, Sun P, Ding LW, Yue JJ, et al. A
Vaccine with multiple receptor-binding domain subunit mutations
induces broad-spectrum immune response against
SARS-CoV-2 variants of concern. Vaccines (Basel). 2022;
(10):1653. [DOI:10.3390/vaccines10101653] [PMID]
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