Construction of Peptide Vaccine Candidate Based on β-Cell Epitopes of Indonesian Monkeypox Virus (MPXV) Virulence Protein:A Reverse Vaccinology
Viol Dhea Kharisma1,2, A. N. M. Ansori3, Ahmad Affan Ali Murtadlo2,
Muhammad Hermawan Widyananda4, Md. Emdad Ullah5, Sin War Naw6,
Vikash Jakhmola7, Kiran Dobhal7, Tarun Parashar7, Maksim Rebezov8,9,10,
Rahadian Zainul11,12*
1Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.
2Computational Virology Research Unit, Division of Molecular Biology and Genetics,
Generasi Biologi Indonesia Foundation, Gresik, Indonesia.
3Professor Nidom Foundation, Surabaya, Indonesia.
4Department of Biology, Faculty of Mathematics and Natural Sciences,
Universitas Brawijaya, Malang, Indonesia.
5Department of Chemistry,Mississippi State University, Mississippi, United States.
6Department of Chemistry, Myitkyina University, Myitkyina, Myanmar.
7Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Uttarakhand, Dehradun, India.
8Department of Scientific Research, Russian State Agrarian University –
Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation.
9Faculty of Biotechnology and Food Engineering, Ural State Agrarian University,
Yekaterinburg, Russian Federation.
10Department of Scientific Research, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation.
11Department of Chemistry, Faculty of Mathematics and Natural Sciences,
Universitas Negeri Padang, Padang, Indonesia.
12Center for Advanced Material Processing, Artificial Intelligence, and Biophysic Informatics, Universitas Negeri Padang, Padang, Indonesia.
*Corresponding Author E-mail: rahadianzmsiphd@fmipa.unp.ac.id
ABSTRACT:
Infection with a DNA virus called monkeypox virus (MPXV) in humans has been identified in the Congo since 1970. Antiviral drugs are not effective for preventing MPXV infection. MPXV infection cases in Indonesia are very low but MPXV has the potential to become a global pandemic so it is very important to do prevention such as vaccine development. This study aims to construct a B cell epitope-based peptide vaccine candidate in Indonesian MPXV through an in silico approach.The development of the MPXV vaccine can be performed through a computational approach for preliminary studies. In silico-based construction of vaccines using B cell epitopes, antigenicity, allergenicity, docking, and molecular dynamics analysis have been used by researchers and scientists in solving viral infection cases. We recommend Pep A and Pep D as vaccine candidates because they allow recognition by B cells, antigenic peptides, non-allergenic and non-toxin. Peptide vaccine candidate can trigger B-cell activation to produce IgM isotype-specific antibodies through BCR interaction. In summary, the results of this study can be used for an initial study of MPXV vaccine development in Indonesia.
KEYWORDS: B-cell Epitope, Bioinformatics, MPXV, PeptideVaccine.
INTRODUCTION:
Infection with a DNA virus called monkeypox virus (MPXV) in humans has been identified in the Congo since 1970.1 Research has continued to date, in May 2022 several cases of MPXV infection appeared in the world, scientists worried that an MPXV pandemic would threaten the world's human population.2 MPXV can be spread from person to person through closed communication, skin lesions, and droplets.3 Scientific evidence of MPXV transmission through sexual contact such as vaginal or seminal fluids has not been identified.4 MPXV drug treatment has been used in various health facilities in the United Kingdom, but the use of antiviral drugs is not effective for preventing MPXV infection.5 MPXV infection cases in Indonesia are very low but MPXV has the potential to become a global pandemic so it is very important to do prevention such as vaccine development.6
Vaccine is the right solution for prevention of MPXV infection continuity.7 Production of traditional vaccines takes a long time and is expensive8. The development of the MPXV vaccine can be performed through a computational approach for preliminary studies. In silico-based construction of vaccines using B cell epitopes, antigenicity, allergenicity, docking, and molecular dynamics analysis have been used by researchers and scientists in solving viral infection cases.9,10 This study aims to construct a B cell epitope-based peptide vaccine candidate in Indonesian MPXV through an in silico approach.
MATERIAL AND METHODS:
MPXV virulence protein genome sequence (EPI_ISL_14615579) obtained from GISAID (https://gisaid.org/).The amino acid sequence in this study was obtained through a seq genomic modification process via MEGA 11 software, target sequence is saved in FASTA format on Notepad software.11,12
3D Modeling and Validation:
The 3D structure of MPXV virulence protein was modeled via SWISS-MODEL (https://swissmodel.expasy.org/)with the homology modeling method. Assessment of the target 3D structure model was performed with the Ramachandran plot, 3D model visualized through PyMol v2.5 with structural selection.13,14
B-cell Epitope Mapping:
The prediction of B-cell epitope mapping in this study is based on linear epitope prediction using the IEDB Analysis Resource (http://tools.iedb.org/bcell/). B cell linear epitope prediction works with the HMMs method and a trend scale to produce probability values. Input sample MPXV virulence protein in AA format for analysis running. Peptides from potential epitopes were obtained through this simulation.15,16
Antigenicity, Allergenicity, and Toxicity Prediction:
This study uses VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/ VaxiJen/VaxiJen.html), AllerTop v.0.2 (https://www.ddg-pharmfac.net/AllerTOP/),and ToxiPred (https://webs.iiitd.edu.in/raghava/toxinpred/design.php)for the prediction of antigenicity, allergenicity, and toxicity to obtain antigenic peptides with low probability values as allergens and non-toxic.17,18
Peptide Stability:
Antigenic peptide stability in this study was identified through PortParam (https://web.expasy.org/protparam/) with reference to physicochemical parameters consisting of amino acids number, molecular weight, theoretical pI, instability index, and grand average of hydropathicity (GRAVY).19,20
Peptide-Protein Docking:
Molecular interaction simulation in this study was performed using the peptide-protein docking method through ClusPro v2.0 (https://cluspro.bu.edu/login.php). The antigenic peptide of MPXV virulence protein acts as a ligand and the target is the B-cell receptor. Docking in this study aims to simulate antigen recognition through the direct pathway by B cells. Visualization of docking results is done through PyMol v2.5 with structural and color selection.21
Interactions fluctuative in this study was identified through molecular dynamics simulations on CABS-flex 2.0 (http://biocomp.chem.uw.edu.pl/CABSflex2/index). Molecular dynamic parameters consist of restraints, rigidity, global c-alpha, number of cycles, temperature, and RNG seed. The output data is RMSF as a determinant of interaction stability.22,23
Immune Simulation:
Simulation of the immune response in B cells was identified through C-ImmSim (https://kraken.iac.rm.cnr.it/C-IMMSIM/index.php?page=1) to simulate the type of antibody produced by B cells when injecting a vaccine into the body. Simulation parameters consisting of random seed: 12345, simulation volume: 10, and simulation steps: 100 are used in this study.24,25
RESULTS AND DISCUSSION:
MPXV Sample Information:
Monkeypox virus (MPXV) is a zoonotic virus from the genus Orthopoxvirus, they have dsDNA as a genome, WHO explains that MPXV has the potential to trigger an epidemic or pandemic. This virus is 250nm in size, enveloped, brick-shaped, and can bind to glycosaminoglycans to enter the host. MPXV vaccine construction allows for the handling and prevention of viral infections.26 This study used a sample of MPXV virulence protein as a target of vaccine design from GISAID (https://gisaid.org/)with the following information virus name: hMpxV/Indonesia/JK-NIHRD-MP0024/2022, accession ID: EPI_ISL_14615579, host: human, collection date: 2022-08-18, clade/lineage: IIb B.1, location: Asia/Indonesia/Jakarta, originating lab: RSUPN dr. Cipto Mangunkusumo, submitting lab: National Institute of Health Research and Development, specimen source: lesion swab. The MPXV virulence protein protein sequence obtained was 190-mer ('MTIYGLIAYLIFVTSSIASPLYIPVIPPISEDKSFNSVEVLVSLFPDDQKDYTVTSQFNNYTIGTKDWTINVLSTPDGLDIPLTNITYWSRFTIGRALFKSESEDIFQKKMSILGVSIECKKPSTLLTFLTVRKMTRVFNRFPDMAYYRGDCLEAVYVTMTYKNTKTGETDYTYLSNGGLPAYYRNGVDG').
3D Model of MPXV Virulence Protein:
MPXV virulence protein was modeled using the SWISS-MODEL homology modeling method (https://swissmodel.expasy.org/). Homology modeling works for the construction of template-based homologous models with a minimum similarity value of >20%.27 Model validation analysis was carried out through the Ramachandran plot referring to the value of the favoured region which must be >80% with 0 bad bonds. MPXV virulence protein has a similarity value of 21.71% similar to the template, favoured region of 89.55%, and no bad bonds were found referring to the Ramachandran Plot. 3D visualization with transparent surfaces, and color selection (Figure 1).
Revealing of Peptide Vaccine Candidate Against MPXV Infection:
Epitope mapping prediction aims to determine the position of potential epitopes as targets for vaccine design.28 B-cell epitope mapping consists of various method parameters for epitope classification such as BepiPred 2, Emini Surfaces Accessibility, Karplus and Schulz Flexibility, and Parker Hydrophilicity. All methods are used for prediction of B cell epitopes through the physicochemical properties of amino acids, surface position, hydrophilic properties, propensity scales, and Hidden Markov Models (HMMs) calculations.29 The results of B-cell epitope mapping analysis in this study showed four peptide candidates from potential epitopes that could be recognized by B cells were shown in the plot (Figure 2). The epitope must act as an antigen, non-allergen, and non-toxin. Peptides consisting of Pep A and Pep D have followed these three categories (antigenic peptide, non-allergenic, and non-toxin) (Table 1). Peptide stability refers to physicochemical properties such as theoretical pI, instability index, GRAVY, and molecular weight used in this study. The stability prediction results show that Pep A and Pep D are classified as stable peptides (Table 2).
Figure 1. MPXV virulence protein model. (A) 3D visualization (B) Plot Ramachandran.
Table 1: B-cell epitope prediction assessment
Peptide Label |
Position |
B-cell Epitope Seq Candidate |
Length (mer) |
Antigenic, Allergenic, and Toxicity Prediction |
||
Vaxi Jen v2.0 |
Aller Top v.0.2 |
Toxi Pred |
||||
Pep A |
48-64 |
DQKDYTVTSQFNNYTIG |
17 |
Antigenic |
Non-Allergen |
Non-Toxin |
Pep B |
100-109 |
KSESEDIFQK |
10 |
Non-Antigenic |
- |
- |
Pep C |
137-149 |
RVFNRFPDMAYYR |
13 |
Non-Antigenic |
- |
- |
Pep D |
175-187 |
LSNGGLPAYYRNG |
13 |
Antigenic |
Non-Allergen |
Non-Toxin |
Table 2: Peptide molecular stability
Peptide Label |
Amino Acids Number |
Molecular Weight |
Theoretical pI |
Formula |
Instability Index |
GRAVY |
Classifies |
Pep A |
17 |
1994.10 |
4.21 |
C87H128N22O32 |
1.32 |
-1.135 |
Stable |
Pep D |
13 |
1381.51 |
8.59 |
C61H92N18O19 |
31.21 |
-0.638 |
Stable |
Figure 2: The result of B-cell epitope predictions. (A)BepiPred 2, (B) Emini Surfaces Accessibility, (C) Karplus and Schulz Flexibility, (D) Parker Hydrophilicity.
Molecular Interaction and Stability of Peptide Vaccine Candidate:
The 3D model of Pep A and Pep D was obtained from PEP-FOLD v3.5 (https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/)through the folding modeling method. The method works by indenting specific points in the primary structure of the protein and then forming a secondary structure or final model. Visualization of vaccine candidate peptide models was carried out using PyMol v2.5 with transparent surfaces, cartoons, and color selection (Figure 3). Peptide interactions with B cell receptors (BCR) were carried out through docking simulations with the molecular superimposed method on ClusPro v2.0 (https://cluspro.bu.edu/login.php). The energy resulting from the docking consists of the center/lowest pose chosen as the most negative and balanced. Pep A_BCR has a more negative docking energy in cluster 8 members 34 which is -539.8 kJ, Pep D_BCR has a more negative docking energy of -652.4 kJ in cluster 8 and members 55 (Table 3). This energy is needed to form a stable complex and trigger a B-cell response via the BCR to produce specific antibodies to tackle MPXV infection. The 3D structure of the docking results is displayed in PyMol v2.5 with surfaces, cartoons, sticks and color selection structures (Figure 4). Pep A_BCR and Pep D_BCR identified the stability of molecular interactions formed by molecular dynamic simulations. The RMSF value of Pep A_BCR and Pep D_BCR indicated by the P1 label on the plot has <3 Å, the RMSF value produced by the two vaccine candidate peptides is stable (Figure 5).
Table 3: The result of peptide-protein docking simulation
Molecular Complex |
Cluster |
Members |
Cluspro Docking Energy (kJ) |
|
Center |
Lowest |
|||
PepA_BCR |
8 |
34 |
-539.8 |
-539.8 |
11 |
11 |
-519.1 |
-519.1 |
|
13 |
1 |
-482.7 |
-482.7 |
|
Pep D_BCR |
8 |
55 |
-652.4 |
-652.4 |
9 |
34 |
-641.5 |
-641.5 |
|
12 |
11 |
-616.3 |
-616.3 |
Figure 3: Structural visualization of peptide vaccine candidate. (A) Pep A, (B) Pep D.
Figure 4: Molecular interaction of peptide vaccine candidate with BCR. . (A) Pep A_BCR (B) Pep D_BCR.
Figure 5: Structural conformation and RMSF plot. (A) Pep A_BCR (B) Pep D_BCR.
Prediction of B-cell Immune Response:
Pep A and Pep B sequences were then simulated via C-Imm Sim (https://kraken.iac.rm.cnr.it/C-IMMSIM/index.php?page=1) to identify the antibody isotype. The immune response of B cells through the direct antigen recognition pathway can trigger the formation of IgM isotype antibodies for the neutralization process.30 The simulation results showed that the production of IgM isotype antibodies detected on the fifth day increased to the fifteenth day with a B cell population of 450 - 500 cells per mm3 (Figure 6).
Figure 6: The result of immune simulation analysis.
CONCLUSION:
We recommend Pep A and Pep D as vaccine candidates because they allow recognition by B cells, antigenic peptides, non-allergenic and non-toxin. Peptide vaccine candidate can trigger B-cell activation to produce IgM isotype-specific antibodies through BCR interaction. The results of this study can be used for an initial study of MPXV vaccine development in Indonesia.
CONFLICT OF INTEREST:
The authors declare that there is no conflict of interest.
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Received on 20.01.2023 Modified on 30.03.2023
Accepted on 04.05.2023 © RJPT All right reserved
Research J. Pharm. and Tech 2024; 17(1):291-296.
DOI: 10.52711/0974-360X.2024.00045