1
|
Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A. Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 2024; 14:176. [PMID: 38855144 PMCID: PMC11153438 DOI: 10.1007/s13205-024-04022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04022-6.
Collapse
Affiliation(s)
- Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, Odisha 761008 India
| | - Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| |
Collapse
|
2
|
Sobczak JM, Barkovska I, Balke I, Rothen DA, Mohsen MO, Skrastina D, Ogrina A, Martina B, Jansons J, Bogans J, Vogel M, Bachmann MF, Zeltins A. Identifying Key Drivers of Efficient B Cell Responses: On the Role of T Help, Antigen-Organization, and Toll-like Receptor Stimulation for Generating a Neutralizing Anti-Dengue Virus Response. Vaccines (Basel) 2024; 12:661. [PMID: 38932390 PMCID: PMC11209419 DOI: 10.3390/vaccines12060661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
T help (Th), stimulation of toll-like receptors (pathogen-associated molecular patterns, PAMPs), and antigen organization and repetitiveness (pathogen-associated structural patterns, PASPs) were shown numerous times to be important in driving B-cell and antibody responses. In this study, we dissected the individual contributions of these parameters using newly developed "Immune-tag" technology. As model antigens, we used eGFP and the third domain of the dengue virus 1 envelope protein (DV1 EDIII), the major target of virus-neutralizing antibodies. The respective proteins were expressed alone or genetically fused to the N-terminal fragment of the cucumber mosaic virus (CMV) capsid protein-nCMV, rendering the antigens oligomeric. In a step-by-step manner, RNA was attached as a PAMP, and/or a universal Th-cell epitope was genetically added for additional Th. Finally, a PASP was added to the constructs by displaying the antigens highly organized and repetitively on the surface of CMV-derived virus-like particles (CuMV VLPs). Sera from immunized mice demonstrated that each component contributed stepwise to the immunogenicity of both proteins. All components combined in the CuMV VLP platform induced by far the highest antibody responses. In addition, the DV1 EDIII induced high levels of DENV-1-neutralizing antibodies only if displayed on VLPs. Thus, combining multiple cues typically associated with viruses results in optimal antibody responses.
Collapse
Affiliation(s)
- Jan M. Sobczak
- Department of Immunology, University Clinic of Rheumatology and Immunology, Inselspital, CH-3010 Bern, Switzerland; (D.A.R.); (M.O.M.); (M.V.); (M.F.B.)
- Department of BioMedical Research, University of Bern, CH-3008 Bern, Switzerland
| | - Irena Barkovska
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Ina Balke
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Dominik A. Rothen
- Department of Immunology, University Clinic of Rheumatology and Immunology, Inselspital, CH-3010 Bern, Switzerland; (D.A.R.); (M.O.M.); (M.V.); (M.F.B.)
- Department of BioMedical Research, University of Bern, CH-3008 Bern, Switzerland
| | - Mona O. Mohsen
- Department of Immunology, University Clinic of Rheumatology and Immunology, Inselspital, CH-3010 Bern, Switzerland; (D.A.R.); (M.O.M.); (M.V.); (M.F.B.)
- Department of BioMedical Research, University of Bern, CH-3008 Bern, Switzerland
| | - Dace Skrastina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Anete Ogrina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Byron Martina
- Artemis Bioservices, 2629 JD Delft, The Netherlands;
- Protinhi Therapeutics, 6534 AT Nijmegen, The Netherlands
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Janis Bogans
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| | - Monique Vogel
- Department of Immunology, University Clinic of Rheumatology and Immunology, Inselspital, CH-3010 Bern, Switzerland; (D.A.R.); (M.O.M.); (M.V.); (M.F.B.)
- Department of BioMedical Research, University of Bern, CH-3008 Bern, Switzerland
| | - Martin F. Bachmann
- Department of Immunology, University Clinic of Rheumatology and Immunology, Inselspital, CH-3010 Bern, Switzerland; (D.A.R.); (M.O.M.); (M.V.); (M.F.B.)
- Department of BioMedical Research, University of Bern, CH-3008 Bern, Switzerland
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Andris Zeltins
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.B.); (I.B.); (D.S.); (A.O.); (J.J.); (J.B.); (A.Z.)
| |
Collapse
|
3
|
Alshabrmi FM, Alatawi EA. Subtractive proteomics-guided vaccine targets identification and designing of multi-epitopes vaccine for immune response instigation against Burkholderia pseudomallei. Int J Biol Macromol 2024; 270:132105. [PMID: 38710251 DOI: 10.1016/j.ijbiomac.2024.132105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
In this study, a methodical workflow using subtractive proteomics, vaccine designing, molecular simulation, and agent-based modeling approaches were used to annotate the whole proteome of Burkholderia pseudomallei (strain K96243) for vaccine designing. Among the total 5717 proteins in the whole proteome, 505 were observed to be essential for the pathogen's survival and pathogenesis predicted by the Database of Essential Genes. Among these, 23 vaccine targets were identified, of which fimbrial assembly chaperone (Q63UH5), Outer membrane protein (Q63UH1), and Hemolysin-like protein (Q63UE4) were selected for the subsequent analysis based on the systematic approaches. Using immunoinformatic approaches CTL (cytotoxic T lymphocytes), HTL (helper T lymphocytes), IFN-positive, and B cell epitopes were predicted for these targets. A total of 9 CTL epitopes were added using the GSS linker, 6 HTL epitopes using the GPGPG linker, and 6 B cell epitopes using the KK linker. An adjuvant was added for enhanced antigenicity, an HIV-TAT peptide for improved delivery, and a PADRE sequence was added to form a 466 amino acids long vaccine construct. The construct was classified as non-allergenic, highly antigenic, and experimentally feasible. Molecular docking results validated the robust interaction of MEVC with immune receptors such as TLR2/4. Furthermore, molecular simulation revealed stable dynamics and compact nature of the complexes. The binding free energy results further validated the robust binding. In silico cloning, results revealed GC contents of 50.73 % and a CIA value of 0.978 which shows proper downstream processing. Immune simulation results reported that after the three injections of the vaccine a robust secondary immune response, improved antigen clearance, and effective immune memory generation were observed highlighting its potential for effective and sustained immunity. Future directions should encompass experimental validations, animal model studies, and clinical trials to substantiate the vaccine's efficacy, safety, and immunogenicity.
Collapse
Affiliation(s)
- Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.
| | - Eid A Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia.
| |
Collapse
|
4
|
Abdulabbas HT, Mohammad Ali AN, Farjadfar A, Arabfard M, Najafipour S, Kouhpayeh A, Ghasemian A, Behmard E. Design of a novel multi-epitope vaccine candidate against Chlamydia trachomatis using structural and nonstructural proteins: an immunoinformatics study. J Biomol Struct Dyn 2024; 42:4356-4369. [PMID: 37288800 DOI: 10.1080/07391102.2023.2220812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
Chlamydia trachomatis (C. trachomatis) is an obligate intracellular bacterium which causes eye and sexually transmitted infections. During pregnancy, the bacterium is associated with preterm complications, low weight of neonates, fetal demise and endometritis leading to infertility. The aim of our study was design of a multi-epitope vaccine (MEV) candidate against C. trachomatis. After protein sequence adoption from the NCBI, potential epitopes toxicity, antigenicity, allergenicity, MHC-I and MHC-II binding, cytotoxic T lymphocytes (CTLs), Helper T lymphocytes (HTLs) and interferon-γ (IFN-γ)- induction were predicted. The adopted epitopes were fused together using appropriate linkers. In the next step, the MEV structural mapping and characterization, three-dimensional (3D) structure homology modeling and refinement were also performed. The MEV candidate interaction with the toll-like receptor 4 (TLR4) was also docked. The immune responses simulation was assessed using the C-IMMSIM server. Molecular dynamic (MD) simulation verified the structural stability of the TLR4-MEV complex. The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach demonstrated the MEV high affinity of binding to the TLR4, MHC-I and MHC-II. The MEV construct was also stable and water soluble and had enough antigenicity and lacked allergenicity with stimulation of T cells and B cells and INF-γ release. The immune simulation confirmed acceptable responses of both the humoral and cellular arms. It is proposed that in vitro and in vivo studies are needed to evaluate the findings of this study.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hussein T Abdulabbas
- Department of Medical Microbiology, Medical College, Al Muthanna University, Al Muthanna, Iraq
| | | | - Akbar Farjadfar
- Department of medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Amin Kouhpayeh
- Department of Pharmacology, Faculty of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
5
|
Moges Eskeziyaw B, Waihenya R, Maina N, Muuo Nzou S. Immunoinformatics-Based Designing of Novel and Potent Multi-Epitope PSA D15 and Cag11 Immunogens for Helicobacter pylori Immunodiagnostic Assay Development. Helicobacter 2024; 29:e13104. [PMID: 38923222 DOI: 10.1111/hel.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Helicobacter pylori (H. pylori) strain is the most genetically diverse pathogenic bacterium and now alarming serious human health concern ranging from chronic gastritis to gastric cancer and human death all over the world. Currently, the majority of commercially available diagnostic assays for H. pylori is a challenging task due to the heterogeneity of virulence factors in various geographical regions. In this concern, designing of universal multi-epitope immunogenic biomarker targeted for all H. pylori strains would be crucial to successfully immunodiagnosis assay and vaccine development for H. pylori infection. Hence, the present study aimed to explore the potential immunogenic epitopes of PSA D15 and Cag11 proteins of H. pylori, using immunoinformatics web tools in order to design novel immune-reactive multi-epitope antigens for enhanced immunodiagnosis in humans. Through an in silico immunoinformatics approach, high-ranked B-cell, MHC-I, and MHC-II epitopes of PSA D15 and Cag11 proteins were predicted, screened, and selected. Subsequently, a novel multi-epitope PSA D15 and Cag11 antigens were designed by fused the high-ranked B-cell, MHC-I, and MHC-II epitopes and 50S ribosomal protein L7/L12 adjuvant using linkers. The antigenicity, solubility, physicochemical properties, secondary and tertiary structures, 3D model refinement, and validations were carried. Furthermore, the designed multi-epitope antigens were subjected to codon adaptation and in silico cloning, immune response simulation, and molecular docking with receptor molecules. A novel, stable multi-epitope PSA D15 and Cag11 H. pylori antigens were developed and immune simulation of the designed antigens showed desirable levels of immunological response. Molecular docking of designed antigens with immune receptors (B-cell, MHC-I, MHC-II, and TLR-2/4) revealed robust interactions and stable binding affinity to the receptors. The codon optimized and in silico cloned showed that the designed antigens were successfully expressed (CAI value of 0.95 for PSA D15 and 1.0 for Cag11) after inserted into pET-32ba (+) plasmid of the E. coli K12 strain. In conclusion, this study revealed that the designed multi-epitope antigens have a huge immunological potential candidate biomarker and useful in developing immunodiagnostic assays and vaccines for H. pylori infection.
Collapse
Affiliation(s)
- Biniam Moges Eskeziyaw
- Department of Molecular Biology & Biotechnology, Pan African University Institute for Basic Science, Technology and Innovation, Nairobi, Kenya
- Department of Biotechnology, Debre Berhan University, Debre Berhan, Ethiopia
| | - Rebecca Waihenya
- Zoology Department, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Naomi Maina
- Biochemistry Department, College of Health Science, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Samson Muuo Nzou
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| |
Collapse
|
6
|
Shahab M, Iqbal MW, Ahmad A, Alshabrmi FM, Wei DQ, Khan A, Zheng G. Immunoinformatics-driven In silico vaccine design for Nipah virus (NPV): Integrating machine learning and computational epitope prediction. Comput Biol Med 2024; 170:108056. [PMID: 38301512 DOI: 10.1016/j.compbiomed.2024.108056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
The Nipah virus (NPV) is a highly lethal virus, known for its significant fatality rate. The virus initially originated in Malaysia in 1998 and later led to outbreaks in nearby countries such as Bangladesh, Singapore, and India. Currently, there are no specific vaccines available for this virus. The current work employed the reverse vaccinology method to conduct a comprehensive analysis of the entire proteome of the NPV virus. The aim was to identify and choose the most promising antigenic proteins that could serve as potential candidates for vaccine development. We have also designed B and T cell epitopes-based vaccine candidate using immunoinformatics approach. We have identified a total of 5 novel Cytotoxic T Lymphocytes (CTL), 5 Helper T Lymphocytes (HTL), and 6 linear B-cell potential antigenic epitopes which are novel and can be used for further vaccine development against Nipah virus. Then we performed the physicochemical properties, antigenic, immunogenic and allergenicity prediction of the designed vaccine candidate against NPV. Further, Computational analysis indicated that these epitopes possessed highly antigenic properties and were capable of interacting with immune receptors. The designed vaccine were then docked with the human immune receptors, namely TLR-2 and TLR-4 showed robust interaction with the immune receptor. Molecular dynamics simulations demonstrated robust binding and good dynamics. After numerous dosages at varied intervals, computational immune response modeling showed that the immunogenic construct might elicit a significant immune response. In conclusion, the immunogenic construct shows promise in providing protection against NPV, However, further experimental validation is required before moving to clinical trials.
Collapse
Affiliation(s)
- Muhammad Shahab
- State key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Muhammad Waleed Iqbal
- State key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Abbas Ahmad
- Department of Biotechnology Abdul Wali Khan University Mardan, Pakistan
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia.
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, China; Center for Microbiome Research, School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Guojun Zheng
- State key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
7
|
Fatima I, Alshabrmi FM, Aziz T, Alamri AS, Alhomrani M, Alghamdi S, Alghuraybi RA, Babalghith AO, Bamagous GA, Alhindi Z, Dablool AS, Alhhazmi AA, Alruways MW. Revolutionizing and identifying novel drug targets in Citrobacter koseri via subtractive proteomics and development of a multi-epitope vaccine using reverse vaccinology and immuno-informatics. J Biomol Struct Dyn 2024:1-14. [PMID: 38407210 DOI: 10.1080/07391102.2024.2316762] [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: 11/16/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024]
Abstract
Citrobacter koseri is a gram-negative rod that has been linked to infections in people with significant comorbidities and immunocompromised immune systems. It is most commonly known to cause urinary tract infections. Thus, the development of an efficacious C. koseri vaccine is imperative, as the pathogen has acquired resistance to current antibiotics. Subtractive proteomics was employed during this research to identify potential antigenic proteins to design an effective vaccine against C. koseri. The pipeline identified two antigenic proteins as potential vaccine targets: DP-3-O-acyl-N-acetylglucosamine deacetylase and Arabinose 5-phosphate isomerase. B and T cell epitopes from the specific proteins were forecasted employing several immunoinformatic and bioinformatics resources. A vaccine was created using a combination of seven cytotoxic T cell lymphocytes (CTL), five helper T cell lymphocyte (HTL), and seven linear B cell lymphocyte (LBL) epitopes. An adjuvant (β-defensin) was added to the vaccine to enhance immunological responses. The created vaccine was stable for use in humans, highly antigenic, and non-allergenic. The vaccine's molecular and interactions binding affinity with the human immunological receptor TLR3 were studied using MMGBSA, molecular dynamics (MD) simulations, and molecular docking analyses. E. coli (strain-K12) plasmid vector pET-28a (+) was used to examine the ability of the vaccine to be expressed. The vaccine shows great promise in terms of developing protective immunity against diseases, based on the results of these computer experiments. However, in vitro and animal research are required to validate our findings.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Israr Fatima
- Department of Bioinformatics, College of Life Science, Northwest Agriculture and Forestry University, Yangling, China
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene, and Quality, Department of Agriculture, University of Ioannina, Arta, Greece
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Reem Ahmad Alghuraybi
- Laboratory and Blood Bank Department, Alnoor Specialist Hospital, Ministry of Health Makkah, Makkah, Saudi Arabia
| | - Ahmad O Babalghith
- Medical Genetics Department College of Medicine Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ghazi A Bamagous
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Zain Alhindi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Anas S Dablool
- Public health Department, Health Sciences College at Al-Leith، Umm Al-Qura University, Makkah, Saudi Arabia
| | - Areej A Alhhazmi
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Mashael W Alruways
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| |
Collapse
|
8
|
Roja B, Chellapandi P. Design and characterization of a multi-epitope vaccine against Clostridium botulinum A3 Loch Maree intoxication in humans. Gene 2024; 892:147865. [PMID: 37783297 DOI: 10.1016/j.gene.2023.147865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/03/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Clostridium botulinum Loch Maree expresses an extremely potent botulinum neurotoxin subtype, A3 causing botulism and several gastrointestinal disorders in mammals. Several recombinant vaccines have been developed for human botulism and no vaccine is currently available for the treatment of diseases caused by other virulence factors. Hence, we designed, constructed, and characterized a multi-epitope vaccine from new virulence proteins identified from this organism using an immunoinformatics approach. The vaccine construct used in this study was designed from 6B cell linear epitopes, 12 cytotoxic T cell lymphocyte epitopes, and 15 helper T cell lymphocyte epitopes, with a defensin adjuvant and adjusting linker sequences. A molecular modeling approach was used to model, refine, and validate the 3D structure of the vaccine construct. Molecular docking studies were performed to determine the stability of the molecular interactions between the vaccine construct and human toll-like receptor 7. The in silico molecular cloning was used to clone a codon-optimized synthetic vaccine gene in pCYB1 vector and expressed in Escherichia coli. The results of this study identified six new virulence proteins: peptidoglycan hydrolase, SCP-like extracellular protein, N-acetylmuramoyl-l-alanine amidase, putative membrane protein, drug/metabolite exporter, and bacillolysin. The top B-cell, cytotoxic T-cell lymphocyte, and helper T-lymphocyte epitopes were predicted from these virulence proteins with greater accuracy and reliability. HLA-A*02:01 and HLA-A*03:01 were identified as HLA-A-binding alleles for cytotoxic T-cell lymphocyte epitopes. DRB1*0110 and DRB1*0115 are the dominant alleles that bind to helper T-cell lymphocyte epitopes. The synthetic gene construct was highly expressed in a heterologous host and produced considerable amounts of antigenic protein. The multi-epitope vaccine is more conservative in the sequence-structure-function link, immunogenic with less allergenicity, and possibly provokes cellular and humoral immunity. The present study suggests that the designed multi-epitope vaccine is a promising prophylactic candidate for the virulence and intoxication caused by subtype A3 strains.
Collapse
Affiliation(s)
- B Roja
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - P Chellapandi
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
| |
Collapse
|
9
|
Firdaus ARR, Baroroh U, Ramdani Tohari T, Hardianto A, Subroto T, Yusuf M. Computational design of scFv anti-receptor binding domain of SARS-CoV-2 spike protein based on antibody S230 anti-SARS-CoV-1. J Biomol Struct Dyn 2024; 42:22-33. [PMID: 37880854 DOI: 10.1080/07391102.2023.2265485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 10/27/2023]
Abstract
Developing therapeutics such as neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is essential to halt the Covid-19 infection. However, antibody production is expensive and relatively inaccessible to many low-income countries. Therefore, a more efficient and smaller antibody fragment, such as a single-chain variable fragment (scFv), derived from a known neutralizing antibody structure, is of interest due to the lower cost of recombinant protein production and the ability to tailor scFvs against circulating viruses. In this study, we used computational design to create an scFv based on the structure of a known neutralizing antibody, S230, for SARS-CoV-1. By analyzing the interaction of S230 with the RBD of both SARS-CoV-1 and SARS-CoV-2, five mutations were introduced to improve the binding of the scFv to the RBD of SARS-CoV-2. These mutations were Ser32Thr, Trp99Val, Asn57Val, Lys65Glu, and Tyr106Ile. Molecular dynamics simulations were used to evaluate the stability and affinity of the designed scFv. Our results showed that the designed scFv improved binding to the RBD of SARS-CoV-2 compared to the original S230, as indicated by principal component analysis, distance analysis, and MM/GBSA interaction energy. Furthermore, a positive result in a spot test lateral flow assay of the expressed scFv against the RBD indicated that the mutations did not alter the protein's structure. The designed scFv showed a negative result when tested against human serum albumin as a negative control, indicating reasonable specificity. We hope that this study will be useful in designing a specific and low-cost therapeutic agent, particularly during early outbreaks when information on neutralizing antibodies is limited.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ade R R Firdaus
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Bandung, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Pharmacy, Sekolah Tinggi Farmasi Indonesia, Bandung, Indonesia
| | - Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Ari Hardianto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| |
Collapse
|
10
|
Shahab M, Aiman S, Alshammari A, Alasmari AF, Alharbi M, Khan A, Wei DQ, Zheng G. Immunoinformatics-based potential multi-peptide vaccine designing against Jamestown Canyon Virus (JCV) capable of eliciting cellular and humoral immune responses. Int J Biol Macromol 2023; 253:126678. [PMID: 37666399 DOI: 10.1016/j.ijbiomac.2023.126678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Jamestown Canyon virus (JCV) is a deadly viral infection transmitted by various mosquito species. This mosquito-borne virus belongs to Bunyaviridae family, posing a high public health threat in the in tropical regions of the United States causing encephalitis in humans. Common symptoms of JCV include fever, headache, stiff neck, photophobia, nausea, vomiting, and seizures. Despite the availability of resources, there is currently no vaccine or drug available to combat JCV. The purpose of this study was to develop an epitope-based vaccine using immunoinformatics approaches. The vaccine aimed to be secure, efficient, bio-compatible, and capable of stimulating both innate and adaptive immune responses. In this study, the protein sequence of JCV was obtained from the NCBI database. Various bioinformatics methods, including toxicity evaluation, antigenicity testing, conservancy analysis, and allergenicity assessment were utilized to identify the most promising epitopes. Suitable linkers and adjuvant sequences were used in the design of vaccine construct. 50s ribosomal protein sequence was used as an adjuvant at the N-terminus of the construct. A total of 5 CTL, 5 HTL, and 5 linear B cell epitopes were selected based on non-allergenicity, immunological potential, and antigenicity scores to design a highly immunogenic multi-peptide vaccine construct. Strong interactions between the proposed vaccine and human immune receptors, i.e., TLR-2 and TLR-4, were revealed in a docking study using ClusPro software, suggesting their possible relevance in the immunological response to the vaccine. Immunological and physicochemical properties assessment ensured that the proposed vaccine demonstrated high immunogenicity, solubility and thermostability. Molecular dynamics simulations confirmed the strong binding affinities, as well as dynamic and structural stability of the proposed vaccine. Immune simulation suggest that the vaccine has the potential to effectively stimulate cellular and humoral immune responses to combat JCV infection. Experimental and clinical assays are required to validate the results of this study.
Collapse
Affiliation(s)
- Muhammad Shahab
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abbas Khan
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China; School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Dong-Qing Wei
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Guojun Zheng
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China.
| |
Collapse
|
11
|
Sura K, Rohilla H, Kumar D, Jakhar R, Ahlawat V, Kaushik D, Dangi M, Chhillar AK. Exploring structural antigens of yellow fever virus to design multi-epitope subunit vaccine candidate by utilizing an immuno-informatics approach. J Genet Eng Biotechnol 2023; 21:161. [PMID: 38051433 DOI: 10.1186/s43141-023-00621-7] [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: 04/21/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Yellow fever is a mosquito-borne viral hemorrhagic disease transmitted by several species of virus-infected mosquitoes endemic to tropical regions of Central and South America and Africa. Earlier in the twentieth century, mass vaccination integrated with mosquito control was implemented to eradicate the yellow fever virus. However, regular outbreaks occur in these regions which pose a threat to travelers and residents of Africa and South America. There is no specific antiviral therapy, but there can be an effective peptide-based vaccine candidate to combat infection caused by the virus. Therefore, the study aims to design a multi-epitope-based subunit vaccine (MESV) construct against the yellow fever virus to reduce the time and cost using reverse vaccinology (RV) approach. METHODS Yellow fever virus contains 10,233 nucleotides that encode for 10 proteins (C, prM, E, NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) including 3 structural and 7 non-structural proteins. Structural proteins-precursor membrane protein (prM) and envelope protein (E)-were taken as a target for B cell and T cell epitope screening. Further, various immunoinformatics approaches were employed to FASTA sequences of structural proteins to retrieve B cell and T cell epitopes. MESV was constructed from these epitopes based on allergenicity, antigenicity and immunogenicity, toxicity, conservancy, and population coverage followed by structure prediction. The efficacy of the MESV construct to bind with human TLR-3, TLR-4, and TLR-8 were evaluated using molecular docking and simulation studies. Finally, in-silico cloning of vaccine construct was performed withpBR322 Escherichia coli expression system using codon optimization. RESULTS Predicted epitopes evaluated and selected for MESV construction were found stable, non-allergenic, highly antigenic, and global population coverage of 68.03% according to in-silico analysis. However, this can be further tested in in-vitro and in-vivo investigations. Epitopes were sequentially merged to construct a MESV consisting of 393 amino acids using adjuvant and linkers. Molecular docking and simulation studies revealed stable and high-affinity interactions. Furthermore, in-silico immune response graphs showed effective immune response generation. Finally, higher CAI value ensured high gene expression of vaccine in the host cell. CONCLUSION The designed MESV construct in the present in-silico study can be effective in generating an immune response against the yellow fever virus. Therefore, to prevent yellow fever, it can be an effective vaccine candidate. However, further downstream, in-vitro study is required.
Collapse
Affiliation(s)
- Kiran Sura
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Himanshi Rohilla
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Dev Kumar
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Ritu Jakhar
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Vaishali Ahlawat
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
- Centre for Biotechnology, M.D. University, Rohtak, Haryana, India
| | | | - Mehak Dangi
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India.
| | | |
Collapse
|
12
|
Eltaib L, Alzain AA. Targeting the omicron variant of SARS-CoV-2 with phytochemicals from Saudi medicinal plants: molecular docking combined with molecular dynamics investigations. J Biomol Struct Dyn 2023; 41:9732-9744. [PMID: 36369836 DOI: 10.1080/07391102.2022.2146203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/05/2022] [Indexed: 11/14/2022]
Abstract
The new health crises caused by SARS-CoV-2 have resulted in millions of deaths worldwide. First discovered in November 2021, the omicron variant is more transmissible and is able to evade the immune system better than other previously identified SARS-CoV-2 variants, leading to a spike in cases. Great efforts have been made to discover inhibitors against SARS-CoV-2. Main protease (Mpro) inhibitors are considered promising anti-SARS-CoV-2 agents. The U.S. FDA has issued an Emergency Use Authorization for ritonavir-boosted nirmatrelvir. Nirmatrelvir is the first orally bioavailable inhibitor of SARS-CoV-2 Mpro. There is an urgent need to monitor the mutations and solve the problem of resistance, especially omicron Mpro, which contains one mutation - P132H. In the present study, 132,57 phytochemicals from 80 medicinal plants grown in Saudi Arabia were docked into the active site of Mpro omicron variant. Free binding energies were also calculated. This led to the discovery of five phytochemicals that showed better docking scores than the bound ligand nirmatrelvir. In addition, these molecules exhibited favorable free binding energies. The stability of compounds 1-5 with the protein was studied using molecular dynamics (MD) simulations. These compounds showed acceptable ADMET properties. The results were compared with the wild type. These candidates could be envisioned as new hits against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Lina Eltaib
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Arar, Saudi Arabia
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| |
Collapse
|
13
|
Alsubaiyel AM, Bukhari SI. Computational exploration and design of a multi-epitopes vaccine construct against Chlamydia psittaci. J Biomol Struct Dyn 2023:1-17. [PMID: 37897717 DOI: 10.1080/07391102.2023.2268173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Chlamydia psittaci is an intracellular pathogen and causes variety of deadly infections in humans. Antibiotics are effective against C. psittaci however high percentage of resistant strains have been reported in recent times. As there is no licensed vaccine, we used in-silico techniques to design a multi-epitopes vaccine against C. psittaci. Following a step-wise protocol, the proteome of available 26 strains was retrieved and filtered for subcellular localized proteins. Five proteins were selected (2 extracellular and 3 outer membrane) and were further analyzed for B-cell and T-cell epitopes prediction. Epitopes were further checked for antigenicity, solubility, stability, toxigenicity, allergenicity, and adhesive properties. Filtered epitopes were linked via linkers and the 3D structure of the designed vaccine construct was predicted. Binding of the designed vaccine with immune receptors: MHC-I, MHC-II, and TLR-4 was analyzed, which resulted in docking energy scores of -4.37 kcal/mol, -0.20 kcal/mol and -22.38 kcal/mol, respectively. Further, the docked complexes showed stable dynamics with a maximum value of vaccine-MHC-I complex (7.8 Å), vaccine-MHC-II complex (6.2 Å) and vaccine-TLR4 complex (5.2 Å). As per the results, the designed vaccine construct reported robust immune responses to protect the host against C. psittaci infections. In the study, the C. psittaci proteomes were considered in pan-genome analysis to extract core proteins. The pan-genome analysis was conducted using bacterial pan-genome analysis (BPGA) software. The core proteins were checked further for non-redundant proteins using a CD-Hit server. Surface localized proteins were investigated using PSORTb v 3.0. The surface proteins were BLASTp against Virulence Factor Data Base (VFDB) to predict virulent factors. Antigenicity prediction of the shortlisted proteins was further done using VAXIGEN v 2.0. The epitope mapping was done using the immune epitope database (IEDB). A multi-epitopes vaccine was built and a 3D structure was generated using 3Dprot online server. The docking analysis of the designed vaccine with immune receptors was carried out using PATCHDOCK. Molecular dynamics and post-simulation analyses were carried out using AMBER v20 to decipher the dynamics stability and intermolecular binding energies of the docked complexes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Sarah I Bukhari
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
14
|
Yusuf M, Destiarani W, Widayat W, Yosua Y, Gumilar G, Tanudireja AS, Rohmatulloh FG, Maulana FA, Baroroh U, Hardianto A, Maharani R, Nurainy N, Wijayadikusumah AR, Ristandi RB, Atmosukarto IIC, Subroto T. Coarse-grained molecular dynamics-guided immunoinformatics to explain the binder and non-binder classification of Cytotoxic T-cell epitope for SARS-CoV-2 peptide-based vaccine discovery. PLoS One 2023; 18:e0292156. [PMID: 37796941 PMCID: PMC10553366 DOI: 10.1371/journal.pone.0292156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Epitope-based peptide vaccine can elicit T-cell immunity against SARS-CoV-2 to clear the infection. However, finding the best epitope from the whole antigen is challenging. A peptide screening using immunoinformatics usually starts from MHC-binding peptide, immunogenicity, cross-reactivity with the human proteome, to toxicity analysis. This pipeline classified the peptides into three categories, i.e., strong-, weak-, and non-binder, without incorporating the structural aspect. For this reason, the molecular detail that discriminates the binders from non-binder is interesting to be investigated. In this study, five CTL epitopes against HLA-A*02:01 were identified from the coarse-grained molecular dynamics-guided immunoinformatics screening. The strong binder showed distinctive activities from the non-binder in terms of structural and energetic properties. Furthermore, the second residue from the nonameric peptide was most important in the interaction with HLA-A*02:01. By understanding the nature of MHC-peptide interaction, we hoped to improve the chance of finding the best epitope for a peptide vaccine candidate.
Collapse
Affiliation(s)
- Muhammad Yusuf
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Wanda Destiarani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Wahyu Widayat
- Faculty of Pharmacy, Pharmaceutical Biology Science, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Yosua Yosua
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, West Java, Indonesia
| | - Angelica Shalfani Tanudireja
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Fauzian Giansyah Rohmatulloh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Farhan Azhwin Maulana
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung, West Java, Indonesia
| | - Ari Hardianto
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Rani Maharani
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Neni Nurainy
- Department of Research and Development, PT Bio Farma, Bandung, West Java, Indonesia
| | | | - Ryan B. Ristandi
- West Java Provincial Reference Laboratory, Bandung, West Java, Indonesia
| | | | - Toto Subroto
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| |
Collapse
|
15
|
Liu S, Yu Q, Li S, Li M, Yang L, Wang Q, Tu Z, Tao F, Yang P, Kong L, Xin X. Expression and immunogenicity of recombinant porcine epidemic diarrhea virus Nsp9. Virology 2023; 587:109861. [PMID: 37572518 DOI: 10.1016/j.virol.2023.109861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) causes acute diarrhea, vomiting, dehydration, and high mortality in newborn piglets, which leads to significant economic losses. Coronavirus nonstructural protein 9 (Nsp9) is an essential RNA binding protein for coronavirus replication, which renders it a promising candidate for developing antiviral drugs and diagnosis targeting PEDV. In this study, PEDV Nsp9 protein fused with MBP protein and His-tag were expressed and purified in Escherichia coli. Furthermore, immunization of MBP-Nsp9 enhances both humoral and cellular immunity responses as compared with that of His-Nsp9 protein. Finally, the swine immunization showed that Nsp9 protein could stimulate the swine immunity system to carry out humoral immunity, and the generated antibody could inhibit the proliferation of PEDV in Vero cells. Altogether, our data provide direct evidence for the immunogenicity of PEDV Nsp9, which sheds light on the future developments of anti-PEDV drugs and vaccines for PED prevention.
Collapse
Affiliation(s)
- Shiguo Liu
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qijia Yu
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sha Li
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mingzhi Li
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Li Yang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Quansheng Wang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zewen Tu
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Feifei Tao
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Pingping Yang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lingbao Kong
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiu Xin
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
16
|
Ahmad S, Nazarian S, Alizadeh A, Pashapour Hajialilou M, Tahmasebian S, Alharbi M, Alasmari AF, Shojaeian A, Ghatrehsamani M, Irfan M, Pazoki-Toroudi H, Sanami S. Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins. J Biomol Struct Dyn 2023:1-18. [PMID: 37713338 DOI: 10.1080/07391102.2023.2258403] [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: 05/15/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Sciences, Virginia Tech, Blacksburg, VA, USA
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Shahin Nazarian
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Akram Alizadeh
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Maryam Pashapour Hajialilou
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| |
Collapse
|
17
|
Zhang C, Li M, Yu T. Bioinformatics analysis of Muscovy duck parvovirus REP and VP1 proteins. J Biomol Struct Dyn 2023; 41:7174-7189. [PMID: 36065642 DOI: 10.1080/07391102.2022.2118170] [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: 05/09/2022] [Accepted: 08/20/2022] [Indexed: 10/14/2022]
Abstract
This article was aimed at analyzing the sequence, structure, and function of the two Muscovy duck parvovirus proteins, including REP and VP1. The antigenicity, physical and chemical properties, transmembrane regions, phosphorylation sites, glycosylation sites, three-dimensional structure, and linear epitope of VP1 and REP were predicted and analyzed through bioinformatics methods. A multi-epitope vaccine was also constructed based on the screened epitopes, and the vaccine was characterized, modeled, molecularly docked and molecularly cloned. The epitopes were screened according to the criteria of antigenicity, non-allergenicity and non-toxicity, and 12 epitope fragments were obtained. The B cell epitopes were analyzed according to four scales: β-turn, hydrophilicity, surface accessibility and antigenicity. Combined with the epitope prediction results based on structure, the final epitope prediction results were obtained. The multi-epitope vaccine used an EAAAK-linked adjuvant, a GPGPG-linked T-cell epitope, and a KK-linked B-cell epitope. The analysis showed that the vaccine was stable hydrophilic, antigenic, conserved and non-allergenic. Based on molecular docking it was shown that good interactions between the vaccine and the immune receptor were generated and were essential to generate an immune response. The final vaccine was reverse translated into cDNA and the DNA vaccine was designed by codon optimization and molecular cloning. Further trials are still needed to demonstrate the immunogenicity and other aspects of vaccine efficacy.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Chi Zhang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Ming Li
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Tianfei Yu
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| |
Collapse
|
18
|
Mohammadzadeh Hosseini Moghri SAH, Ranjbar M, Hassannia H, Khakdan F. In silico analysis of the conserved surface-exposed epitopes to design novel multiepitope peptide vaccine for all variants of the SARS-CoV-2. J Biomol Struct Dyn 2023; 41:7603-7615. [PMID: 36124826 DOI: 10.1080/07391102.2022.2123395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to generic health. The SARS-CoV-2 spike (S) glycoprotein plays a fundamental role in binds and fusion to the angiotensin-converting enzyme 2 (ACE2). The multi-epitope peptide vaccines would be able to elicit both long-lasting humoral and cellular immune responses, resulting the eliminating SARS-CoV-2 infections as asymptomatic patients are in large numbers. Recently, the omicron variant of the SARS-CoV-2 became a variant of concern that contained just 15-point mutations in the receptor-binding domain of the spike protein. In order to eliminate new evidence on coronavirus variants of concern detected through epidemic intelligence, the conserved epitopes of the receptor-binding domain (RBD) and spike cleavage site is the most probable target for vaccine development to inducing binds and fusion inhibitors neutralizing antibodies respectively. In this study, we utilized bioinformatics tools for identifying and analyzing the spike (S) glycoprotein sequence, e.g. the prediction of the potential linear B-cell epitopes, B-cell multi‑epitope design, secondary and tertiary structures, physicochemical properties, solubility, antigenicity, allergenicity, the molecular docking and molecular dynamics simulation for the promising vaccine candidate against all variant of concern of SARS-CoV-2. Among the epitopes of the RBD region are surface-exposed epitopes SVYAWNRKRISNCV and ATRFASVYAWNRKR as the conserved sequences in all variants of concern can be a good candidate to induce an immune response.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Islamic Republic of Iran
| | - Hadi Hassannia
- Immunogenetic Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | |
Collapse
|
19
|
Paul B, Alam J, Hossain MMK, Hoque SF, Bappy MNI, Akter H, Ahmed N, Akter M, Ali Zinnah M, Das S, Mia MM, Parvej MS, Sarkar S, Ghosh H, Hasan M, Ashour HM, Rahman MM. Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections. Biomedicines 2023; 11:2180. [PMID: 37626677 PMCID: PMC10452229 DOI: 10.3390/biomedicines11082180] [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: 05/31/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Canine parvovirus (CPV-2) is one of the most important pathogens of dogs of all ages, causing pandemic infections that are characterized by fatal hemorrhagic enteritis. The CPV-2 vaccine is recommended as a core vaccine for pet animals. Despite the intensive practice of active immunization, CPV-2 remains a global threat. In this study, a multi-epitope vaccine against CPV-2 was designed, targeting the highly conserved capsid protein (VP2) via in silico approaches. Several immunoinformatics methods, such as epitope screening, molecular docking, and simulation were used to design a potential vaccine construct. The partial protein sequences of the VP2 gene of CPV-2 and protein sequences retrieved from the NCBI were screened to predict highly antigenic proteins through antigenicity, trans-membrane-topology screening, an allergenicity assessment, and a toxicity analysis. Homologous VP2 protein sequences typically linked to the disease were identified using NCBI BLAST, in which four conserved regions were preferred. Overall, 10 epitopes, DPIGGKTGI, KEFDTDLKP, GTDPDDVQ, GGTNFGYIG, GTFYFDCKP, NRALGLPP, SGTPTN, LGLPPFLNSL, IGGKTG, and VPPVYPN, were selected from the conserved regions to design the vaccine construct. The molecular docking demonstrated the higher binding affinity of these epitopes with dog leukocyte antigen (DLA) molecules. The selected epitopes were linked with Salmonella enterica flagellin FliC adjuvants, along with the PADRE sequence, by GGS linkers to construct a vaccine candidate with 272 nucleotides. The codon adaptation and in silico cloning showed that the generated vaccine can be expressed by the E. coli strain, K12, and the sequence of the vaccine construct showed no similarities with dog protein. Our results suggest that the vaccine construct might be useful in preventing canine parvoviral enteritis (CPE) in dogs. Further in vitro and in vivo experiments are needed for the validation of the vaccine candidate.
Collapse
Affiliation(s)
- Bashudeb Paul
- Department of Anatomy and Histology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka 1349, Bangladesh
| | | | - Syeda Farjana Hoque
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Md. Nazmul Islam Bappy
- Department of Animal and Fish Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hafsa Akter
- Department of Biochemistry and Chemistry, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Margia Akter
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Ali Zinnah
- Department of Microbiology and Public Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Shobhan Das
- Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30458, USA
| | - Md. Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | | | - Sonjoy Sarkar
- Department of Anatomy and Histology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hiren Ghosh
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL 33701, USA
| | - Md. Masudur Rahman
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- ABEx Bio-Research Center, Dhaka 1230, Bangladesh
| |
Collapse
|
20
|
Tabibzadeh A, Karbalaie Niya MH, Keyvani H, Karampoor S, Yousefi P, Razizadeh MH, Mousavizadeh L, Esghaei M. A survey of ORF8 sequence and immunoinformatics features during alpha, delta, and wild type peaks of the SARS-CoV-2 pandemic in Iran. Malawi Med J 2023; 35:101-105. [PMID: 38264170 PMCID: PMC10731532 DOI: 10.4314/mmj.v35i2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Background The Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and epitope features of these substitutions in the various SARS-CoV-2 outbreaks including delta, alpha, and wild type variants in Iran from 2020 to 2022. In addition, we evaluate B cell, HLA I and II epitopes, by in-silico approach to ORF8 binding site prediction. Methods The samples were collected from patients diagnosed with SARS-CoV-2 infection via a real-time PCR assay. Then, a conventional PCR was carried out for ORF8 mutations analysis and further Sanger sequencing. Possible important alterations in epitope features of the ORF8 were evaluated by epitope mapping. B cell, HLA class I and II epitopes, evaluated by online databases ABCpred, NetMHCpan-4.1, and NetMHCIIpan-3.2, respectively. Results The current study results could not represent novel variations in seven full-length ORF8 sequences or major ORF8 deletions in 80 evaluated samples. In addition, we could not find any ORF8 A382 during each outbreak of variants. Epitope mapping represents differences between the Alpha and other variants, especially in B cell potential epitopes and HLA I. Conclusion The immunoinformatic evaluation of ORF8 suggested epitopes represent major differences for the Alpha variant in comparison with other variants. In addition, having mild pathogenesis of the Omicron variant does not seem to be associated with ORF8 alteration by phylogenetic evaluation. Future in-vitro studies for a clear conclusion about the epitope features of ORF8 are required.
Collapse
Affiliation(s)
- Alireza Tabibzadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Karbalaie Niya
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parastoo Yousefi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Leila Mousavizadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
21
|
Sanami S, Nazarian S, Ahmad S, Raeisi E, Tahir Ul Qamar M, Tahmasebian S, Pazoki-Toroudi H, Fazeli M, Ghatreh Samani M. In silico design and immunoinformatics analysis of a universal multi-epitope vaccine against monkeypox virus. PLoS One 2023; 18:e0286224. [PMID: 37220125 DOI: 10.1371/journal.pone.0286224] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Monkeypox virus (MPXV) outbreaks have been reported in various countries worldwide; however, there is no specific vaccine against MPXV. In this study, therefore, we employed computational approaches to design a multi-epitope vaccine against MPXV. Initially, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), linear B lymphocytes (LBL) epitopes were predicted from the cell surface-binding protein and envelope protein A28 homolog, both of which play essential roles in MPXV pathogenesis. All of the predicted epitopes were evaluated using key parameters. A total of 7 CTL, 4 HTL, and 5 LBL epitopes were chosen and combined with appropriate linkers and adjuvant to construct a multi-epitope vaccine. The CTL and HTL epitopes of the vaccine construct cover 95.57% of the worldwide population. The designed vaccine construct was found to be highly antigenic, non-allergenic, soluble, and to have acceptable physicochemical properties. The 3D structure of the vaccine and its potential interaction with Toll-Like receptor-4 (TLR4) were predicted. Molecular dynamics (MD) simulation confirmed the vaccine's high stability in complex with TLR4. Finally, codon adaptation and in silico cloning confirmed the high expression rate of the vaccine constructs in strain K12 of Escherichia coli (E. coli). These findings are very encouraging; however, in vitro and animal studies are needed to ensure the potency and safety of this vaccine candidate.
Collapse
Affiliation(s)
- Samira Sanami
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Shahin Nazarian
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, United States of America
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Elham Raeisi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Fazeli
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Ghatreh Samani
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| |
Collapse
|
22
|
Westphal T, Mader M, Karsten H, Cords L, Knapp M, Schulte S, Hermanussen L, Peine S, Ditt V, Grifoni A, Addo MM, Huber S, Sette A, Lütgehetmann M, Pischke S, Kwok WW, Sidney J, Schulze zur Wiesch J. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4 + T-cell response with pre-primed responses directed against common cold coronaviruses. Front Immunol 2023; 14:1182504. [PMID: 37215095 PMCID: PMC10196118 DOI: 10.3389/fimmu.2023.1182504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction The nonstructural protein 12 (NSP12) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has a high sequence identity with common cold coronaviruses (CCC). Methods Here, we comprehensively assessed the breadth and specificity of the NSP12-specific T-cell response after in vitro T-cell expansion with 185 overlapping 15-mer peptides covering the entire SARS-CoV-2 NSP12 at single-peptide resolution in a cohort of 27 coronavirus disease 2019 (COVID-19) patients. Samples of nine uninfected seronegative individuals, as well as five pre-pandemic controls, were also examined to assess potential cross-reactivity with CCCs. Results Surprisingly, there was a comparable breadth of individual NSP12 peptide-specific CD4+ T-cell responses between COVID-19 patients (mean: 12.82 responses; range: 0-25) and seronegative controls including pre-pandemic samples (mean: 12.71 responses; range: 0-21). However, the NSP12-specific T-cell responses detected in acute COVID-19 patients were on average of a higher magnitude. The most frequently detected CD4+ T-cell peptide specificities in COVID-19 patients were aa236-250 (37%) and aa246-260 (44%), whereas the peptide specificities aa686-700 (50%) and aa741-755 (36%), were the most frequently detected in seronegative controls. In CCC-specific peptide-expanded T-cell cultures of seronegative individuals, the corresponding SARS-CoV-2 NSP12 peptide specificities also elicited responses in vitro. However, the NSP12 peptide-specific CD4+ T-cell response repertoire only partially overlapped in patients analyzed longitudinally before and after a SARS-CoV-2 infection. Discussion The results of the current study indicate the presence of pre-primed, cross-reactive CCC-specific T-cell responses targeting conserved regions of SARS-CoV-2, but they also underline the complexity of the analysis and the limited understanding of the role of the SARS-CoV-2 specific T-cell response and cross-reactivity with the CCCs.
Collapse
Affiliation(s)
- Tim Westphal
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Maria Mader
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marc Lütgehetmann
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Pischke
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| |
Collapse
|
23
|
Joshi A, Akhtar N, Sharma NR, Kaushik V, Borkotoky S. MERS virus spike protein HTL-epitopes selection and multi-epitope vaccine design using computational biology. J Biomol Struct Dyn 2023; 41:12464-12479. [PMID: 36935104 DOI: 10.1080/07391102.2023.2191137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/03/2023] [Indexed: 03/20/2023]
Abstract
MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more cost-effective strategy to design potential vaccine candidates. In this work, the spike proteins from different strains of MERS-CoV were selected to predict HTL-epitopes that show affinity for T-helper MHC-class II HTL allelic determinant (HLA-DRB1:0101). The antigenicity and conservation of these epitopes among the selected spike protein variants in different MERS-CoV strains were analyzed. The analysis identified five epitopes with high antigenicity: QSIFYRLNGVGITQQ, DTIKYYSIIPHSIRS, PEPITSLNTKYVAPQ, INGRLTTLNAFVAQQ and GDMYVYSAGHATGTT. Then, a multi-epitope vaccine candidate was designed using linkers and adjuvant molecules. Finally, the vaccine construct was subjected to molecular docking with TLR5 (Toll-like receptor-5). The proposed vaccine construct had strong binding energy of -32.3 kcal/mol when interacting with TLR5.Molecular dynamics simulation analysis showed that the complex of the vaccine construct and TLR5 is stable. Analysis using in silico immune simulation also showed that the prospective multi-epitope vaccine design had the potential to elicit a response within 70 days, with the immune system producing cytokines and immunoglobulins. Finally, codon adaptation and in silico cloning analysis showed that the candidate vaccine could be expressed in the Escherichia coli K12 strain. Here we also designed support vaccine construct MEV-2 by using B-cell and CD8+ CTL epitopes to generate the complete immunogenic effect. This study opens new avenues for the extension of research on MERS vaccine development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Amit Joshi
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
- Department of Biochemistry, Kalinga University, Raipur, India
| | - Nahid Akhtar
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Neeta Raj Sharma
- Domain of Bioinformatics, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Vikas Kaushik
- Domain of Bioinformatics, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Subhomoi Borkotoky
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| |
Collapse
|
24
|
Rahimnahal S, Yousefizadeh S, Mohammadi Y. Novel multi-epitope vaccine against bovine brucellosis: approach from immunoinformatics to expression. J Biomol Struct Dyn 2023; 41:15460-15484. [PMID: 36927475 DOI: 10.1080/07391102.2023.2188962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
Brucellosis is a zoonotic caused by the Brucella which is a well-known infectious disease agent in domestic animals and if transmitted, it can cause infection in humans. Because brucellosis is contagious, its control depends on the eradication of the animal disease in farms. There are two vaccines based on the killed and/or weakened bacteria against B. melitensis and B. abortus, but no recombinant vaccine is available for preventing the disease. The present study was designed to develop a multi-epitope vaccine against of B. melitensis and B. abortus using virB10, Omp31 and Omp16 antigens by the prediction of T lymphocytes, T cell cytotoxicity and IFN-γ epitopes. 50S L7/L12 Ribosomal protein from Mycobacterium tuberculosis was used as a bovine TLR4 and TLR9 agonist. GPGPG, AAY and KK linkers were used as a linker. Brucella construct was well-integrated in the pET-32a Shuttle vector with BamHI and HindIII restriction enzymes. The final construct contained 769 amino acids, that it was soluble protein of about ∼82 kDa after expression in the Escherichia coli SHuffle host. Modeled protein analysis based on the tertiary structure validation, molecular docking studies, molecular dynamics simulations results like RMSD, Gyration and RMSF as well as MM/PBSA analysis showed that this protein has a stable construct and is capable being in interaction with bovine TLR4 and TLR9. Analysis of the data obtained suggests that the proposed vaccine can induce the immune response by stimulating T- and B-cells, and may be used for prevention and remedial purposes, against B. melitensis and B. abortus.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Somayyeh Rahimnahal
- Department of Animal Science, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Shahnaz Yousefizadeh
- Department of Laboratory and Clinical Sciences, Faculty of Para-Veterinary, Ilam University, Ilam, Iran
| | - Yahya Mohammadi
- Department of Animal Science, Faculty of Agriculture, Ilam University, Ilam, Iran
| |
Collapse
|
25
|
Raoufi E, Hosseini F, Onagh B, Salehi-Shadkami M, Mehrali M, Mohsenzadegan M, Ho JQ, Bigdelou B, Sepand MR, Webster TJ, Zanganeh S, Farajollahi MM. Designing and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples. Clin Chim Acta 2023; 542:117279. [PMID: 36871661 PMCID: PMC9985519 DOI: 10.1016/j.cca.2023.117279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND More than 3 y into the coronavirus 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to undergo mutations. In this context, the Receptor Binding Domain (RBD) is the most antigenic region among the SARS-CoV-2 Spike protein and has emerged as a promising candidate for immunological development. We designed an IgG-based indirect enzyme-linked immunoassay (ELISA) kit based on recombinant RBD, which was produced from the laboratory to 10 L industry scales in Pichia pastoris. METHODS A recombinant-RBD comprising 283 residues (31 kDa) was constructed after epitope analyses. The target gene was initially cloned into an Escherichia coli TOP10 genotype and transformed into Pichia pastoris CBS7435 muts for protein production. Production was scaled up in a 10 L fermenter after a 1 L shake-flask cultivation. The product was ultrafiltered and purified using ion-exchange chromatography. IgG-positive human sera for SARS-CoV-2 were employed by an ELISA test to evaluate the antigenicity and specific binding of the produced protein. RESULTS Bioreactor cultivation yielded 4 g/l of the target protein after 160 h of fermentation, and ion-exchange chromatography indicated a purity > 95%. A human serum ELISA test was performed in 4 parts, and the ROC area under the curve (AUC) was > 0.96 for each part. The mean specificity and sensitivity of each part was 100% and 91.5%, respectively. CONCLUSION A highly specific and sensitive IgG-based serologic kit was developed for improved diagnostic purposes in patients with COVID-19 after generating an RBD antigen in Pichia pastoris at laboratory and 10 L fermentation scales.
Collapse
Affiliation(s)
- Ehsan Raoufi
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Hosseini
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Onagh
- Department of Biochemistry, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Marjan Mehrali
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Iran University of Medical Sciences, Tehran, Iran
| | - Jim Q Ho
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Banafsheh Bigdelou
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Mohammad Reza Sepand
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Thomas J Webster
- School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, China; School of Engineering, Saveetha University, Chennai, India; Program in Materials Science, UFPI, Teresina, Brazil
| | - Steven Zanganeh
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States.
| | | |
Collapse
|
26
|
Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
Collapse
Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
| |
Collapse
|
27
|
Pandya N, Kumar A. Immunoinformatics analysis for design of multi-epitope subunit vaccine by using heat shock proteins against Schistosoma mansoni. J Biomol Struct Dyn 2023; 41:1859-1878. [PMID: 35040367 DOI: 10.1080/07391102.2021.2025430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The development of T cell and B cell that able provide long-term immune response against the schistosomiasisis to the people belongs to the epidemic area. Heat Shock Proteins (HSPs) are up-regulated in schistosomes as their environment changes owing to the developmental cycle, assisting the parasite in living with the adverse circumstances related with its life cycle. Schistosomiasis is still a severe health problem in the people of many countries in worldwide. In this work, to develop a chimeric antigen, we used an advanced and powerful immunoinformatics technique that targeted Schistosoma mansoni (S. mansoni) Heat shock protein (HSPs). Antigenicity, immunogenicity, allergenicity, and physicochemical characteristics were all assessed in silico for the developed subunit vaccine. The 3D structure of the vaccine was constructed and the stability of the vaccine construct was increased by using disulphide engineering. The protein-protein docking and simulation were performed between the vaccine construct and Toll-like receptor-4. The antigenicity probability value obtained for the vaccine construct was 0.93, which indicates that vaccine is non-allergenic and safe for human consumption. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| |
Collapse
|
28
|
Ali Z, Cardoza JV, Basak S, Narsaria U, Singh VP, Isaac SP, França TCC, LaPlante SR, George SS. Computational design of candidate multi-epitope vaccine against SARS-CoV-2 targeting structural (S and N) and non-structural (NSP3 and NSP12) proteins. J Biomol Struct Dyn 2023; 41:13348-13367. [PMID: 36744449 DOI: 10.1080/07391102.2023.2173297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 virus has created a global damage and has exposed the vulnerable side of scientific research towards novel diseases. The intensity of the pandemic is huge, with mortality rates of more than 6 million people worldwide in a span of 2 years. Considering the gravity of the situation, scientists all across the world are continuously attempting to create successful therapeutic solutions to combat the virus. Various vaccination strategies are being devised to ensure effective immunization against SARS-CoV-2 infection. SARS-CoV-2 spreads very rapidly, and the infection rate is remarkably high than other respiratory tract viruses. The viral entry and recognition of the host cell is facilitated by S protein of the virus. N protein along with NSP3 is majorly responsible for viral genome assembly and NSP12 performs polymerase activity for RNA synthesis. In this study, we have designed a multi-epitope, chimeric vaccine considering the two structural (S and N protein) and two non-structural proteins (NSP3 and NSP12) of SARS-CoV-2 virus. The aim is to induce immune response by generating antibodies against these proteins to target the viral entry and viral replication in the host cell. In this study, computational tools were used, and the reliability of the vaccine was verified using molecular docking, molecular dynamics simulation and immune simulation studies in silico. These studies demonstrate that the vaccine designed shows steady interaction with Toll like receptors with good stability and will be effective in inducing a strong and specific immune response in the body.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, India
| | | | | | | | - Vijay Pratap Singh
- Department of Physiotherapy, Kasturba Medical College, Mangalore, Manipal academy of higher education, Mangalore, Manipal, India
| | | | - Tanos C C França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | | |
Collapse
|
29
|
Rahman S, Sarkar K, Das AK. Exploring staphylococcal superantigens to design a potential multi-epitope vaccine against Staphylococcus aureus: an in-silico reverse vaccinology approach. J Biomol Struct Dyn 2023; 41:13098-13112. [PMID: 36729064 DOI: 10.1080/07391102.2023.2171138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
Staphylococcus aureus is a horrifying bacteria capable of causing millions of deaths yearly across the globe. A major contribution to the success of S. aureus as an ESKAPE pathogen is the abundance of virulence factors that can manipulate the innate and adaptive immune system of the individual. Currently, no vaccine is available to treat S. aureus-mediated infections. In this study, we present in-silico approaches to design a stable, safe and immunogenic vaccine that could help to control the infections associated with the bacteria. Three vital pathogenic secreted toxins of S. aureus, such as staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB), Toxic-shock syndrome toxin (TSST-1), were selected using the reverse vaccinology approach to design the multi-epitope vaccine (MEV). Linear B-lymphocyte, cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. For designing the multi-epitope vaccine (MEV), B-cell epitopes were joined with the KK linker, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Finally, to increase the immune response to the vaccine, a human β-defensin-3 (hBD-3) adjuvant was added to the N-terminus of the MEV construct. The final MEV was found to be antigenic and non-allergen in nature. In-silico immune simulation and cloning analysis predicted the immune-stimulating potential of the designed MEV construct along with the cloning feasibility in the pET28a(+) vector with the E. coli expression system. This immunoinformatics study provides a platform for designing a suitable, safe and effective vaccine against S. aureus.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Kasturi Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| |
Collapse
|
30
|
Jiang F, Liu Y, Xue Y, Cheng P, Wang J, Lian J, Gong W. Developing a multiepitope vaccine for the prevention of SARS-CoV-2 and monkeypox virus co-infection: A reverse vaccinology analysis. Int Immunopharmacol 2023; 115:109728. [PMID: 36652758 PMCID: PMC9832108 DOI: 10.1016/j.intimp.2023.109728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and monkeypox virus (MPXV) severely threaten human health; however, currently, no vaccine can prevent a co-infection with both viruses. METHODS Five antigens were selected to predict dominant T and B cell epitopes screened for immunogenicity, antigenicity, toxicity, and sensitization. After screening, all antigens joined in the construction of a novel multiepitope vaccine. The physicochemical and immunological characteristics, and secondary and tertiary structures of the vaccine were predicted and analyzed using bio- and immunoinformatics. Finally, codon optimization and cloning in-silico were performed. RESULTS A new multiepitope vaccine, named S7M8, was constructed based on four helper T lymphocyte (HTL) epitopes, six cytotoxic T lymphocyte (CTL) epitopes, five B cell epitopes, as well as Toll-like receptor (TLR) agonists. The antigenicity and immunogenicity scores of the S7M8 vaccine were 0.907374 and 0.6552, respectively. The S7M8 vaccine was comprised of 26.96% α-helices, the optimized Z-value of the tertiary structure was -5.92, and the favored area after majorization in the Ramachandran plot was 84.54%. Molecular docking showed that the S7M8 vaccine could tightly bind to TLR2 (-1100.6 kcal/mol) and TLR4 (-950.3 kcal/mol). In addition, the immune stimulation prediction indicated that the S7M8 vaccine could activate T and B lymphocytes to produce high levels of Th1 cytokines and antibodies. CONCLUSION S7M8 is a promising biomarker with good antigenicity, immunogenicity, non-toxicity, and non-sensitization. The S7M8 vaccine can trigger significantly high levels of Th1 cytokines and antibodies and may be a potentially powerful tool in preventing SARS-CoV-2 and MPXV.
Collapse
Affiliation(s)
- Fan Jiang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China,The Second Brigade of Cadet, Basic Medical Science Academy of Air Force Medical University, Xi’an, China,Department of Infectious Diseases, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yinping Liu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Peng Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jianqi Lian
- Department of Infectious Diseases, Tangdu Hospital, Air Force Medical University, Xi'an, China.
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China.
| |
Collapse
|
31
|
Mohammadzadeh Hosseini Moghri SAH, Mahmoodi Chalbatani G, Ranjbar M, Raposo C, Abbasian A. CD171 Multi-epitope peptide design based on immuno-informatics approach as a cancer vaccine candidate for glioblastoma. J Biomol Struct Dyn 2023; 41:1028-1040. [PMID: 36617427 DOI: 10.1080/07391102.2021.2020166] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glioblastoma (GB) is a common primary malignancy of the central nervous system, and one of the highly lethal brain tumors. GB cells can promote therapeutic resistance and tumor angiogenesis. The CD171 is an adhesion molecule in neuronal cells that is expressed in glioma cells as a regulator of brain development during the embryonic period. CD171 is one of the immunoglobulin-like CAMs (cell adhesion molecules) families that can be associated with prognosis in a variety of human tumors. The multi-epitope peptide vaccines are based on synthetic peptides with a combination of both B-cell epitopes and T-cell epitopes, which can induce specific humoral or cellular immune responses. Moreover, Cholera toxin subunit B (CTB), a novel TLR agonist was utilized in the final construct to polarize CD4+ T cells toward T-helper 1 to induce strong cytotoxic T lymphocytes (CTL) responses. In the present study, several immune-informatics tools were used for analyzing the CD171 sequence and studying the important characteristics of a designed vaccine. The results included molecular docking, molecular dynamics simulation, immune response simulation, prediction and validation of the secondary and tertiary structure, physicochemical properties, solubility, conservancy, toxicity as well as antigenicity and allergenicity of the promising candidate for a vaccine against CD171. The immuno-informatic analyze suggested 12 predicted multi-epitope peptides, whose construction consists of 582 residues long. Therewith, cloning adaptation of the designed vaccine was performed, and eventually sequence was inserted into pET30a (+) vector for the application of the anti-glioblastoma vaccine development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Mojtaba Ranjbar
- Faculty of Biotechnology, Department of Microbial Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Catarina Raposo
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arefeh Abbasian
- Faculty of Basic Sciences, Department of Biology, Semnan University, Semnan, Iran
| |
Collapse
|
32
|
Sharma S, Solanki V, Tiwari V. Reverse vaccinology approach to design a vaccine targeting membrane lipoproteins of Salmonella typhi. J Biomol Struct Dyn 2023; 41:954-969. [PMID: 34939517 DOI: 10.1080/07391102.2021.2015443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Typhoid fever caused by Salmonella is one of the major health issues worldwide, resulting in millions of cases and has very high rates of morbidities. The therapeutic approaches need to be updated for the effective elimination of the bacterial pathogen. The designing of the multiepitope vaccine against Salmonella using comparative proteomics and reverse vaccinology has covered up all the epitopes that induce sufficient immune responses in the host body. Out of the 4293 proteins, 15 outer membrane proteins have been selected based on their antigenicity, low transmembrane helix (<1), and virulence-associated factors. With the help of the reverse vaccinology approach, the epitopes of MHC Class I, Class II, and B-cell with antigenic, low toxicity, and that have the potential to generate immunogenic response have been identified. Based on the comparative analysis of all the epitopes, a multiepitope-based construct has been designed. Based on physicochemical properties and docking scores for HLA and TLR4, the VC5 construct has been selected, and the molecular dynamic simulation studies have confirmed their interaction. The dissociation constant of the VC5 and TLR4 was found to be 3.1 x 10-9. Different immune cell activation has been analyzed, representing the potentiality of the VC5 construct as an effective vaccine target. In silico cloning of VC5 in pET28a has also been performed, which requires experimental validation. Therefore, the present study designs a multi-epitope vaccine VC5 targeted to the membrane lipoproteins of Salmonella typhi.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Saroj Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vandana Solanki
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
33
|
Reverse vaccinology assisted design of a novel multi-epitope vaccine to target Wuchereria bancrofti cystatin: An immunoinformatics approach. Int Immunopharmacol 2023; 115:109639. [PMID: 36586276 DOI: 10.1016/j.intimp.2022.109639] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
Proteases are the critical mediators of immunomodulation exerted by the filarial parasites to bypass and divert host immunity. Cystatin is a small (∼15 kDa) immunomodulatory filarial protein and known to contribute in the immunomodulation strategy by inducing anti-inflammatory response through alternative activation of macrophages. Recently, Wuchereria bancrofti cystatin has been discovered as a ligand of human toll-like receptor 4 which is key behind the cystatin-induced anti-inflammatory response in major human antigen-presenting cells. Considering the pivotal role of cystatin in the immunobiology of filariasis, cystatin could be an efficacious target for developing vaccine. Herein, we present the design and in-silico analyses of a multi-epitope-based peptide vaccine to target W. bancrofti cystatin through immune-informatics approaches. The 262 amino acid long antigen construct comprises 9 MHC-I epitopes and MHC-II epitopes linked together by GPGPG peptide alongside an adjuvant (50S ribosomal protein L7/L12) at N terminus and 6 His tags at C terminus. Molecular docking study reveals that the peptide could trigger TLR4-MD2 to induce protective innate immune responses while the induced adaptive responses were found to be mediated by IgG, IgM and Th1 mediated responses. Notably, the designed vaccine exhibits high stability and no allergenicity in-silico. Furthermore, the muti epitope-vaccine was also predicted for its RNA structure and cloned in pET30ax for further experimental validation. Taken together, this study presents a novel multi-epitope peptide vaccine for triggering efficient innate and adaptive immune responses against W. bancrofti to intervene LF through immunotherapy.
Collapse
|
34
|
Designing multi-epitope mRNA construct as a universal influenza vaccine candidate for future epidemic/pandemic preparedness. Int J Biol Macromol 2023; 226:885-899. [PMID: 36521707 DOI: 10.1016/j.ijbiomac.2022.12.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Despite the availability of prevention and treatment strategies and advancing immunization approaches, the influenza virus remains a global threat that continues to plague humanity with unpredictable pandemics. Due to the unusual genetic variability and segmented genome, the reassortment between different strains of influenza is facilitated and the viruses continuously evolve and adapt to the host cell's immunity. This underlies the seasonal vaccine mismatches that decrease the vaccine efficacy and increase the risk of outbreaks. Thus, the development of a universal vaccine covering all the influenza A and B strains would reduce the pervasiveness of the influenza virus. In the current study, a potentially universal influenza multi-epitope vaccine was designed based on the experimentally tested conserved T cell and B cell epitopes of hemagglutinin (HA), neuraminidase (NA), nucleoprotein (NP), and matrix-2 proton channel (M2) of the virus. The immune simulation and molecular docking of the vaccine construct with TLR2, TLR3, and TLR4 elicited the favorable immunogenicity of the vaccine and the formation of stable complexes, respectively. Ultimately, based on the immunoinformatics analysis, the universal mRNA multi-epitope vaccine designed in this study might have a protection potential against the various subtypes of influenza A and B.
Collapse
|
35
|
Bayani F, Safaei Hashkavaei N, Karamian MR, Uskoković V, Sefidbakht Y. In silico design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:11748-11762. [PMID: 36703619 DOI: 10.1080/07391102.2023.2170470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/22/2022] [Indexed: 01/28/2023]
Abstract
Computational studies can comprise an effective approach to treating and preventing viral infections. Since 2019, the world has been dealing with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most important achievement in this short period of time in the effort to reduce morbidity and mortality was the production of vaccines and effective antiviral drugs. Although the virus has been significantly suppressed, it continues to evolve, spread, and evade the host's immune system. Recently, researchers have turned to immunoinformatics tools to reduce side effects and save the time and cost of traditional vaccine production methods. In the present study, an attempt has been made to design a multi-epitope vaccine with humoral and cellular immune response stimulation against the Omicron variant of SARS-CoV-2 by investigating new mutations in spike (S) and nucleocapsid (N) proteins. The population coverage of the vaccine was evaluated as appropriate compared to other studies. The results of molecular dynamics simulation and molecular mechanics/generalized Born surface area (MM/GBSA) calculations predict the stability and proper interaction of the vaccine with Toll-like receptor 4 (TLR-4) as an innate immune receptor. The results of the immune simulation show a significant increase in the coordinated response of IgM and IgG after the third injection of the vaccine. Also, in the continuation of the research, spike proteins from BA.4 and BA.5 lineages were screened by immunoinformatics filters and effective epitopes were suggested for vaccine design. Despite the high precision of computational studies, in-vivo and in-vitro research is needed for final confirmation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Mohammad Reza Karamian
- Department of Cell and Molecular Biology, Faculty of Science, Kharazmi University, Tehran, Iran
| | - Vuk Uskoković
- TardigradeNano LLC, Irvine, CA, USA
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| |
Collapse
|
36
|
Mahmoudvand S, Esmaeili Gouvarchin Ghaleh H, Jalilian FA, Farzanehpour M, Dorostkar R. Design of a multi-epitope-based vaccine consisted of immunodominant epitopes of structural proteins of SARS-CoV-2 using immunoinformatics approach. Biotechnol Appl Biochem 2023:10.1002/bab.2431. [PMID: 36577011 PMCID: PMC9880719 DOI: 10.1002/bab.2431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown rapid global spread and has resulted in a significant death toll worldwide. In this study, we aimed to design a multi-epitope vaccine against SARS-CoV-2 based on structural proteins S, M, N, and E. We identified B- and T-cell epitopes and then the antigenicity, toxicity, allergenicity, and similarity of predicted epitopes were analyzed. T-cell epitopes were docked with corresponding HLA alleles. Consequently, the selected T- and B-cell epitopes were included in the final construct. All selected epitopes were connected with different linkers and flagellin and pan-HLA DR binding epitopes (PADRE) as an adjuvant were used in the vaccine construct. Furthermore, molecular docking was used to evaluate the complex between the final vaccine construct and two alleles, HLA-A*02:01 and HLA-DRB1*01:01. Finally, codons were optimized for in silico cloning into pET28a(+) vector using SnapGene. The final vaccine construct comprised 11 CTL, HTL, and B-cell epitopes corresponding to 394 amino acid residues. In silico evaluation showed that the designed vaccine might potentially promote an immune response. Further in vivo preclinical and clinical testing is required to determine the safety and efficacy of the designed vaccine.
Collapse
Affiliation(s)
- Shahab Mahmoudvand
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Farid Azizi Jalilian
- Department of Medical VirologyFaculty of MedicineHamadan University of Medical SciencesHamadanIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| |
Collapse
|
37
|
Mahmoodi S, Amirzakaria JZ, Ghasemian A. In silico design and validation of a novel multi-epitope vaccine candidate against structural proteins of Chikungunya virus using comprehensive immunoinformatics analyses. PLoS One 2023; 18:e0285177. [PMID: 37146081 PMCID: PMC10162528 DOI: 10.1371/journal.pone.0285177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/16/2023] [Indexed: 05/07/2023] Open
Abstract
Chikungunya virus (CHIKV) is an emerging viral infectious agent with the potential of causing pandemic. There is neither a protective vaccine nor an approved drug against the virus. The aim of this study was design of a novel multi-epitope vaccine (MEV) candidate against the CHIKV structural proteins using comprehensive immunoinformatics and immune simulation analyses. In this study, using comprehensive immunoinformatics approaches, we developed a novel MEV candidate using the CHIKV structural proteins (E1, E2, 6 K, and E3). The polyprotein sequence was obtained from the UniProt Knowledgebase and saved in FASTA format. The helper and cytotoxic T lymphocytes (HTLs and CTLs respectively) and B cell epitopes were predicted. The toll-like receptor 4 (TLR4) agonist RS09 and PADRE epitope were employed as promising immunostimulatory adjuvant proteins. All vaccine components were fused using proper linkers. The MEV construct was checked in terms of antigenicity, allergenicity, immunogenicity, and physicochemical features. The docking of the MEV construct and the TLR4 and molecular dynamics (MD) simulation were also performed to assess the binding stability. The designed construct was non-allergen and was immunogen which efficiently stimulated immune responses using the proper synthetic adjuvant. The MEV candidate exhibited acceptable physicochemical features. Immune provocation included prediction of HTL, B cell, and CTL epitopes. The docking and MD simulation confirmed the stability of the docked TLR4-MEV complex. The high-level protein expression in the Escherichia coli (E. coli) host was observed through in silico cloning. The in vitro, in vivo, and clinical trial investigations are required to verify the findings of the current study.
Collapse
Affiliation(s)
- Shirin Mahmoodi
- Department of Medical Biotechnology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Javad Zamani Amirzakaria
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
38
|
Sethi G, Varghese RP, Krishna R. Identification and design of a multi-epitope subunit vaccine against the opportunistic pathogen Staphylococcus epidermidis: An immunoinformatics approach. J Biomol Struct Dyn 2022; 40:13859-13871. [PMID: 34726118 DOI: 10.1080/07391102.2021.1997819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Staphylococcus epidermidis is one of the major causes of nosocomial infections around the globe that leads to a high rate of mortality and morbidity in both immunocompromised patients and preterm infants. Despite the alarming increase in multi-drug resistance, no promising vaccines are readily available against this pathogen. Thus, the present study is focused on designing a multi-epitope subunit vaccine using five antigenic proteins of S. epidermidis through an immunoinformatics approach. The final vaccine comprised B-cell, HTL, and CTL binding epitopes followed by Lipoprotein LprA adjuvant added at N-terminal to augment the immunogenicity. Physicochemical assessment of the vaccine reveals the antigenic and non-allergic nature. The vaccine structure was designed, refined, validated, and disulfide engineered to obtain the best model. Molecular docking and dynamics simulation of the proposed vaccine with toll-like receptors (TLR-2 and TLR-4) showed strong and stable interactions. MM-PBSA analysis was implemented as an efficient tool to determine the intermolecular binding free energies of the system. The vaccine was subjected to immune simulation to predict its immunogenic profile. In silico cloning suggested that the proposed vaccine can be expressed efficiently in E.coli. Furthermore, in vivo animal experiment is needed to determine the effectiveness of the in silico designed vaccine.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Guneswar Sethi
- Centre for Bioinformatics, Pondicherry University, Puducherry, India
| | | | - Ramadas Krishna
- Centre for Bioinformatics, Pondicherry University, Puducherry, India
| |
Collapse
|
39
|
Susithra Priyadarshni M, Isaac Kirubakaran S, Harish MC. In silico approach to design a multi-epitopic vaccine candidate targeting the non-mutational immunogenic regions in envelope protein and surface glycoprotein of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:12948-12963. [PMID: 34528491 PMCID: PMC8477437 DOI: 10.1080/07391102.2021.1977702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The novel corona virus (COVID-19) is a causative agent for severe acute respiratory syndrome (SARS-CoV-2) and responsible for the current human pandemic situation which has caused global social and economic commotion. The currently available vaccines use whole viruses whereas there is scope for peptide based vaccines. Thus, the global raise in statistics of this infection at an alarming rate evoked us to determine a novel and effective vaccine candidate against SARS-CoV-2. To find the potential vaccine candidate targets, immunoinformatics approaches were used to analyze the mutations in the envelope protein and surface glycoprotein and determine the conserved region; further specific T-cell epitopes VSLVKPSFY, SLVKPSFYV, RVKNLNSSR, SEETGTLIV, LVKPSFYVY, LTDEMIAQY, YLQPRTFLL, RLFRKSNLK, SPRRARSVA, AEIRASANL, TLLALHRSY, YSRVKNLNS and FELLHAPAT and B-cells epitopes TLAILTALRLCAYCCN and AGTITSGWTFGAGAAL were identified. The 3 D structure of epitope was predicted, refined and validated. The molecular docking analysis of multi-epitope vaccine candidates with TLR receptors, predicted effective binding. Overall, using bioinformatics approach this multi-epitopic target facilitates the proof of concept for SARS-CoV-2 conserved epitopic vaccine design.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - S. Isaac Kirubakaran
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Kansas Medical Center, KS, USA
| | - M. C. Harish
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, India,CONTACT M. C. Harish Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore632115, India
| |
Collapse
|
40
|
Mahapatra SR, Dey J, Kushwaha GS, Puhan P, Mohakud NK, Panda SK, Lata S, Misra N, Suar M. Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars. J Biomol Struct Dyn 2022; 40:11809-11821. [PMID: 34463211 DOI: 10.1080/07391102.2021.1964600] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Overcoming multi drug resistance is one of the crucial challenges to control enteric typhoid fever caused by Salmonella typhi and Salmonella paratyphi. Overexpression of efflux pumps predominantly causes drug resistance in microorganisms. Therefore, immunotherapy targeting the various efflux pumps antigens could be a promising strategy to increase the success of vaccines. An immunoinformatic approach was employed to design a Salmonellosis multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of multidrug resistance protein families including ATP Binding Cassette (ABC), major facilitator superfamily (MFS), resistance nodulation cell division (RND), small multidrug resistance (SMR), and multidrug and toxin extrusion (MATE). The selected epitopes exhibited conservation in both S. typhi and S. paratyphi and thus could be helpful for cross-protection. Further, the final vaccine construct encompassing the peptides, adjuvants and specific linker sequences showed high immunogenicity, solubility, non-allergenic, nontoxic, and wide population coverage due to strong binding affinity to maximum HLA alleles. The three-dimensional structure was predicted, and validated using various structure validation tools. Additionally, protein-protein docking of the chimeric vaccine construct with the TLR-2 protein and molecular dynamics demonstrated stable and efficient binding. Conclusively, the immunoinformatic study showed that the novel multi epitopic vaccine construct can simulate the both T-cell and B-cell immune responses in typhoidal Salmonella serovars and could potentially be used for prophylactic or therapeutic applications.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Gajraj Singh Kushwaha
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puspasree Puhan
- Science and Technology Department, Government of Odisha, Bhubaneswar, India
| | - Nirmal Kumar Mohakud
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - Santosh Kumar Panda
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - S Lata
- Kalinga Institute of Dental Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| |
Collapse
|
41
|
Mohanty R, Manoswini M, Dhal AK, Ganguly N. In silico analysis of a novel protein in CAR T- cell therapy for the treatment of hematologic cancer through molecular modelling, docking, and dynamics approach. Comput Biol Med 2022; 151:106285. [PMID: 36395593 DOI: 10.1016/j.compbiomed.2022.106285] [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: 01/04/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Cellular therapy has emerged as a key tool in the treatment of hematological malignancies. An advanced cell therapy known as chimeric antigen receptor T cell therapy (CAR T-cell therapy) has been approved by the United States Food and Drug Administration (FDA) as KYMRIAH by Novartis and YESCARTA by Gilead/Kite pharma in the year 2017. A chimeric receptor is composed of an extracellular antigen recognition site along with some co-stimulating and signalling domains. On the whole, it turns out to be one of the most potent receptors on T cells targeting a specific type of cancer cell based on its antigenic marker. CD19 CAR T-cell therapy is the first clinically approved therapy for lymphoma with remarkable results in complete remission of B cell lymphoblastic leukemia up to 90%. The high rate of effectiveness of the CAR T-cell therapy against B-ALL justifies the investigation and application of this therapy for fatal diseases like all types of hematological malignancies. The most critical aspect of chimeric receptor therapy is designing and building an artificial receptor that is specific to a given type of cancer. For this reason, the in silico technique is an appropriate model to investigate the integrity and effectiveness of the engineered chimeric receptor prior to commencing in vitro experiments followed by clinical trials. This computerized experimental study aids in predicting the molecular mechanism of chimeric protein and how it interacts with both ligands. We have anticipated various features of the chimeric protein in terms of qualitative analysis (structure, protein modelling, physiological properties) and functional analysis (antigenicity, allergenicity, its receptor-ligand binding ability, involving signalling pathways). Furthermore, the reliability and validation of the binding mode of the chimeric protein against receptors were performed through a complex molecular dynamics simulation for a 100 ns timeframe in an aqueous environment. The obtained simulation study showed that CD30 was a better approachable marker as compared to CD20 due to its better binding energy score and also binding conformations stability.
Collapse
Affiliation(s)
- Rimjhim Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India.
| | - Manoswini Manoswini
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India
| | - Ajit Kumar Dhal
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India
| | - Niladri Ganguly
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India.
| |
Collapse
|
42
|
Özcengiz E, Keser D, Özcengiz G, Çelik G, Özkul A, İnçeh FN. Two formulations of coronavirus disease-19 recombinant subunit vaccine candidate made up of S1 fragment protein P1, S2 fragment protein P2, and nucleocapsid protein elicit strong immunogenicity in mice. Immun Inflamm Dis 2022; 10:e748. [PMID: 36444622 PMCID: PMC9695085 DOI: 10.1002/iid3.748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/09/2022] [Accepted: 10/29/2022] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Coronavirus disease (COVID-19) is ongoing as a global epidemic and there is still a need to develop much safer and more effective new vaccines that can also be easily adapted to important variants of the pathogen. In the present study in this direction, we developed a new COVID-19 vaccine, composed of two critical antigenic fragments of the S1 and S2 region of severe acute respiratory syndrome coronavirus 2 as well as the whole nucleocapsid protein (N), which was formulated with either alum or alum plus monophosphoryl lipid A (MPLA) adjuvant combinations. METHODS From within the spike protein S1 region, a fragmented protein P1 (MW:33 kDa) which includes the receptor-binding domain (RBD), another fragment protein P2 (MW:17.6) which contains important antigenic epitopes within the spike protein S2 region, and N protein (MW:46 kDa) were obtained after recombinant expression of the corresponding gene regions in Escherichia coli BL21. For use in immunization studies, three proteins were adsorbed with aluminum hydroxide gel and with the combination of aluminum hydroxide gel plus MPLA. RESULTS Each of the three protein antigens produced strong reactions in enzyme-linked immunosorbent assays and Western blot analysis studies performed with convalescent COVID-19 patient sera. In mice, these combined protein vaccine candidates elicited high titer anti-P1, anti-P2, and anti-N IgG and IgG2a responses. These also induced highly neutralizing antibodies and elicited significant cell-mediated immunity as demonstrated by enhanced antigen-specific levels of interferon-γ (INF-γ) in the splenocytes of immunized mice. CONCLUSION The results of this study showed that formulations of the three proteins with Alum or Alum + MPLA are effective in terms of humoral and cellular responses. However, since the Alum + MPLA formulation appears to be superior in Th1 response, this vaccine candidate may be recommended mainly for the elderly and immunocompromised individuals. We also believe that the alum-only formulation will provide great benefits for adults, young adolescents, and children.
Collapse
Affiliation(s)
| | - Duygu Keser
- Vaccine R&DPharmada PharmaceuticalsAnkaraTurkey
| | - Gülay Özcengiz
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTurkey
| | - Gözde Çelik
- Vaccine R&DPharmada PharmaceuticalsAnkaraTurkey
| | - Aykut Özkul
- Department of Virology, School of Veterinary MedicineAnkara UniversityAnkaraTurkey
| | | |
Collapse
|
43
|
Immunoinformatics-Aided Design of a Peptide Based Multiepitope Vaccine Targeting Glycoproteins and Membrane Proteins against Monkeypox Virus. Viruses 2022; 14:v14112374. [PMID: 36366472 PMCID: PMC9693848 DOI: 10.3390/v14112374] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The disease has a case fatality ratio of 3-6% and, recently, a multi-country outbreak of the disease has occurred. The currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges of safety and efficacy in chronic infections. In this study, we have used an immunoinformatics-aided design of a multi-epitope vaccine (MEV) candidate by targeting monkeypox virus (MPXV) glycoproteins and membrane proteins. From these proteins, seven epitopes (two T-helper cell epitopes, four T-cytotoxic cell epitopes and one linear B cell epitopes) were finally selected and predicted as antigenic, non-allergic, interferon-γ activating and non-toxic. These epitopes were linked to adjuvants to design a non-allergic and antigenic candidate MPXV-MEV. Further, molecular docking and molecular dynamics simulations predicted stable interactions between predicted MEV and human receptor TLR5. Finally, the immune-simulation analysis showed that the candidate MPXV-MEV could elicit a human immune response. The results obtained from these in silico experiments are promising but require further validation through additional in vivo experiments.
Collapse
|
44
|
Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines (Basel) 2022; 10:vaccines10101729. [PMID: 36298594 PMCID: PMC9611379 DOI: 10.3390/vaccines10101729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies.
Collapse
|
45
|
Fernández-Lainez C, de la Mora-de la Mora I, Enríquez-Flores S, García-Torres I, Flores-López LA, Gutiérrez-Castrellón P, de Vos P, López-Velázquez G. The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors. Int J Mol Sci 2022; 23:ijms231911552. [PMID: 36232855 PMCID: PMC9569872 DOI: 10.3390/ijms231911552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Beyond the problem in public health that protist-generated diseases represent, understanding the variety of mechanisms used by these parasites to interact with the human immune system is of biological and medical relevance. Giardia lamblia is an early divergent eukaryotic microorganism showing remarkable pathogenic strategies for evading the immune system of vertebrates. Among various multifunctional proteins in Giardia, arginine deiminase is considered an enzyme that plays multiple regulatory roles during the life cycle of this parasite. One of its most important roles is the crosstalk between the parasite and host. Such a molecular "chat" is mediated in human cells by membrane receptors called Toll-like receptors (TLRs). Here, we studied the importance of the 3D structure of giardial arginine deiminase (GlADI) to immunomodulate the human immune response through TLRs. We demonstrated the direct effect of GlADI on human TLR signaling. We predicted its mode of interaction with TLRs two and four by using the AlphaFold-predicted structure of GlADI and molecular docking. Furthermore, we showed that the immunomodulatory capacity of this virulent factor of Giardia depends on the maintenance of its 3D structure. Finally, we also showed the influence of this enzyme to exert specific responses on infant-like dendritic cells.
Collapse
Affiliation(s)
- Cynthia Fernández-Lainez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatria, Ciudad de México 04530, Mexico
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Center Groningen, 9700 Groningen, The Netherlands
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | | | - Sergio Enríquez-Flores
- Laboratorio de Biomoleculas y Salud Infantil, Instituto Nacional de Pediatria, Ciudad de México 04530, Mexico
| | - Itzhel García-Torres
- Laboratorio de Biomoleculas y Salud Infantil, Instituto Nacional de Pediatria, Ciudad de México 04530, Mexico
| | - Luis A. Flores-López
- Laboratorio de Biomoleculas y Salud Infantil, Instituto Nacional de Pediatria, Ciudad de México 04530, Mexico
- CONACYT-Instituto Nacional de Pediatria, Secretaria de Salud, Ciudad de México 04530, Mexico
| | | | - Paul de Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Center Groningen, 9700 Groningen, The Netherlands
| | - Gabriel López-Velázquez
- Laboratorio de Biomoleculas y Salud Infantil, Instituto Nacional de Pediatria, Ciudad de México 04530, Mexico
- Correspondence: ; Tel.: +52-5510840900 (ext. 1726)
| |
Collapse
|
46
|
Vaccinomics to Design a Multiepitope Vaccine against Legionella pneumophila. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4975721. [PMID: 36164443 PMCID: PMC9509222 DOI: 10.1155/2022/4975721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
Legionella pneumophila is found in the natural aquatic environment and can resist a wide range of environmental conditions. There are around fifty species of Legionella, at least twenty-four of which are directly linked to infections in humans. L. pneumophila is the cause of Legionnaires' disease, a potentially lethal form of pneumonia. By blocking phagosome-lysosome fusion, L. pneumophila lives and proliferates inside macrophages. For this disease, there is presently no authorized multiepitope vaccine available. For the multi-epitope-based vaccine (MEBV), the best antigenic candidates were identified using immunoinformatics and subtractive proteomic techniques. Several immunoinformatics methods were utilized to predict B and T cell epitopes from vaccine candidate proteins. To construct an in silico vaccine, epitopes (07 CTL, 03 HTL, and 07 LBL) were carefully selected and docked with MHC molecules (MHC-I and MHC-II) and human TLR4 molecules. To increase the immunological response, the vaccine was combined with a 50S ribosomal adjuvant. To maximize vaccine protein expression, MEBV was cloned and reverse-translated in Escherichia coli. To prove the MEBV's efficacy, more experimental validation is required. After its development, the resulting vaccine is greatly hoped to aid in the prevention of L. pneumophila infections.
Collapse
|
47
|
Sun Q, Huang Z, Yang S, Li Y, Ma Y, Yang F, Zhang Y, Xu F. Bioinformatics-based SARS-CoV-2 epitopes design and the impact of Spike protein mutants on epitope humoral immunities. Immunobiology 2022; 227:152287. [PMID: 36244092 PMCID: PMC9516880 DOI: 10.1016/j.imbio.2022.152287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/10/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022]
Abstract
Background Epitope selection is the key to peptide vaccines development. Bioinformatics tools can efficiently improve the screening of antigenic epitopes and help to choose the right ones. Objective To predict, synthesize and testify peptide epitopes at spike protein, assess the effect of mutations on epitope humoral immunity, thus provide clues for the design and development of epitope peptide vaccines against SARS-CoV-2. Methods Bioinformatics servers and immunological tools were used to identify the helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes on the S protein of SARS-CoV-2. Physicochemical properties of candidate epitopes were analyzed using IEDB, VaxiJen, and AllerTOP online software. Three candidate epitopes were synthesized and their antigenic responses were evaluated by binding antibody detection. Results A total of 20 antigenic, non-toxic and non-allergenic candidate epitopes were identified from 1502 epitopes, including 6 helper T-cell epitopes, 13 cytotoxic T-cell epitopes, and 1 linear B cell epitope. After immunization with antigen containing candidate epitopes S206-221, S403-425, and S1157-1170 in rabbits, the binding titers of serum antibody to the corresponding peptide, S protein, receptor-binding domain protein were (415044, 2582, 209.3), (852819, 45238, 457767) and (357897, 10528, 13.79), respectively. The binding titers to Omicron S protein were 642, 12,878 and 7750, respectively, showing that N211L, DEL212 and K417N mutations cause the reduction of the antibody binding activity. Conclusions Bioinformatic methods are effective in peptide epitopes design. Certain mutations of the Omicron would lead to the loss of antibody affinity to Omicron S protein.
Collapse
Affiliation(s)
- Qi Sun
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Zhuanqing Huang
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Sen Yang
- Medical School of Chinese PLA, Beijing, China; Chinese People's Armed Police Force Hospital of Beijing, Beijing, China
| | - Yuanyuan Li
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Yue Ma
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Fei Yang
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Ying Zhang
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China
| | - Fenghua Xu
- Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China.
| |
Collapse
|
48
|
The Correlation between Subolesin-Reactive Epitopes and Vaccine Efficacy. Vaccines (Basel) 2022; 10:vaccines10081327. [PMID: 36016215 PMCID: PMC9414912 DOI: 10.3390/vaccines10081327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccination is an environmentally-friendly alternative for tick control. The tick antigen Subolesin (SUB) has shown protection in vaccines for the control of multiple tick species in cattle. Additionally, recent approaches in quantum vaccinomics have predicted SUB-protective epitopes and the peptide sequences involved in protein−protein interactions in this tick antigen. Therefore, the identification of B-cell−reactive epitopes by epitope mapping using a SUB peptide array could be essential as a novel strategy for vaccine development. Subolesin can be used as a model to evaluate the effectiveness of these approaches for the identification of protective epitopes related to vaccine protection and efficacy. In this study, the mapping of B-cell linear epitopes of SUB from three different tick species common in Uganda (Rhipicephalus appendiculatus, R. decoloratus, and Amblyomma variegatum) was conducted using serum samples from two cattle breeds immunized with SUB-based vaccines. The results showed that in cattle immunized with SUB from R. appendiculatus (SUBra) all the reactive peptides (Z-score > 2) recognized by IgG were also significant (Z-ratio > 1.96) when compared to the control group. Additionally, some of the reactive peptides recognized by IgG from the control group were also recognized in SUB cocktail−immunized groups. As a significant result, cattle groups that showed the highest vaccine efficacy were Bos indicus immunized with a SUB cocktail (92%), and crossbred cattle were immunized with SUBra (90%) against R. appendiculatus ticks; the IgG from these groups recognized overlapping epitopes from the peptide SPTGLSPGLSPVRDQPLFTFRQVGLICERMMKERESQIRDEYDHVLSAKLAEQYDTFVKFTYDQKRFEGATPSYLS (Z-ratio > 1.96), which partially corresponded to a Q38 peptide and the SUB protein interaction domain. These identified epitopes could be related to the protection and efficacy of the SUB-based vaccines, and new chimeras containing these protective epitopes could be designed using this new approach.
Collapse
|
49
|
Kaushik V, Jain P, Akhtar N, Joshi A, Gupta LR, Grewal RK, Oliva R, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics-Aided Design and In Vivo Validation of a Peptide-Based Multiepitope Vaccine Targeting Canine Circovirus. ACS Pharmacol Transl Sci 2022. [DOI: 10.1021/acsptsci.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Pankaj Jain
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Nahid Akhtar
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
50
|
Huffman A, Ong E, Hur J, D’Mello A, Tettelin H, He Y. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Brief Bioinform 2022; 23:bbac190. [PMID: 35649389 PMCID: PMC9294427 DOI: 10.1093/bib/bbac190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
Collapse
Affiliation(s)
- Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202, USA
| | - Adonis D’Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| |
Collapse
|