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Aiman S, Ali Y, Malik A, Alkholief M, Ahmad A, Akhtar S, Ali S, Khan A, Li C, Shams S. Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus. J Biomol Struct Dyn 2024; 42:6292-6306. [PMID: 37424185 DOI: 10.1080/07391102.2023.2233627] [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: 02/17/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Monkeypox virus (MPXV) is an orthopoxvirus, causing zoonotic infections in humans with smallpox-like symptoms. The WHO reported MPXV cases in May 2022 and the outbreak caused significant morbidity threats to immunocompromised individuals and children. Currently, no clinically validated therapies are available against MPXV infections. The present study is based on immunoinformatics approaches to design mRNA-based novel vaccine models against MPXV. Three proteins were prioritized based on high antigenicity, low allergenicity, and toxicity values to predict T- and B-cell epitopes. Lead T- and B-cell epitopes were used to design vaccine constructs, linked with epitope-specific linkers and adjuvant to enhance immune responses. Additional sequences, including Kozak sequence, MITD sequence, tPA sequence, Goblin 5', 3' UTRs, and a poly(A) tail were added to design stable and highly immunogenic mRNA vaccine construct. High-quality structures were predicted by molecular modeling and 3D-structural validation of the vaccine construct. Population coverage and epitope-conservancy speculated broader protection of designed vaccine model against multiple MPXV infectious strains. MPXV-V4 was eventually prioritized based on its physicochemical and immunological parameters and docking scores. Molecular dynamics and immune simulations analyses predicted significant structural stability and binding affinity of the top-ranked vaccine model with immune receptors to elicit cellular and humoral immunogenic responses against the MPXV. The pursuance of experimental and clinical follow-up of these prioritized constructs may lay the groundwork to develop safe and effective vaccine against MPXV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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2
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Ponne S, Kumar R, Vanmathi SM, Brilhante RSN, Kumar CR. Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens. Vaccine 2024; 42:2503-2518. [PMID: 38523003 DOI: 10.1016/j.vaccine.2024.02.087] [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: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain viruses is challenging due to various factors, notably the inability to culture certain viruses in cell cultures and the wide-ranging diversity of MHC profiles in humans. Fortunately, reverse vaccinology (RV) efficiently overcomes these limitations and has simplified the identification of epitopes from antigenic proteins across the entire proteome, streamlining the vaccine development process. Furthermore, it enables the creation of multiepitope vaccines that can effectively account for the variations in MHC profiles within the human population. The RV approach offers numerous advantages in developing precise and effective vaccines against viral pathogens, including extensive proteome coverage, accurate epitope identification, cross-protection capabilities, and MHC compatibility. With the introduction of RV, there is a growing emphasis among researchers on creating multiepitope-based vaccines aiming to stimulate the host's immune responses against multiple serotypes, as opposed to single-component monovalent alternatives. Regardless of how promising the RV-based vaccine candidates may appear, they must undergo experimental validation to probe their protection efficacy for real-world applications. The time, effort, and resources allocated to the laborious epitope identification process can now be redirected toward validating vaccine candidates identified through the RV approach. However, to overcome failures in the RV-based approach, efforts must be made to incorporate immunological principles and consider targeting the epitope regions involved in disease pathogenesis, immune responses, and neutralizing antibody maturation. Integrating multi-omics and incorporating artificial intelligence and machine learning-based tools and techniques in RV would increase the chances of developing an effective vaccine. This review thoroughly explains the RV approach, ideal RV-based vaccine construct components, RV-based vaccines designed to combat viral pathogens, its challenges, and future perspectives.
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Affiliation(s)
- Saravanaraman Ponne
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (Deemed to be University), Kirumampakkam, Puducherry 607402, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 106 91, Sweden
| | - S M Vanmathi
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India
| | - Raimunda Sâmia Nogueira Brilhante
- Medical Mycology Specialized Center, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Chinnadurai Raj Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India.
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Li M, Yu M, Yuan Y, Li D, Ye D, Zhao M, Lin Z, Shi L. Designing a conjugate vaccine targeting Klebsiella pneumoniae ST258 and ST11. Heliyon 2024; 10:e27417. [PMID: 38486755 PMCID: PMC10938132 DOI: 10.1016/j.heliyon.2024.e27417] [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: 09/22/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a common bacterium that can cause iatrogenic infection. Recently, the rise of antibiotic resistance among K. pneumoniae strains is one key factor associated with antibiotic treatment failure. Hencefore, there is an urgent need for effective K. pneumoniae vaccines. This study aimed to design a multi-epitope vaccine (MEV) candidate against K. pneumonia by utilizing an immunoinformatics method. In this study, we obtained 15 cytotoxic T lymphocyte epitopes, 10 helper T lymphocyte epitopes, 6 linear B-cell epitopes, and 2 conformational B-cell epitopes for further research. Then, we designed a multi-epitope vaccine composed of a total of 743 amino acids, containing the epitopes linked by GPGPG flexible links and an EAAAK linker to the Cholera Toxin Subunit B coadjuvant. The observed properties of the MEV, including non-allergenicity, high antigenicity, and hydrophilicity, are noteworthy. The improvements in the tertiary structure through structural refinement and disulfide bonding, coupled with promising molecular interactions revealed by molecular dynamics simulations with TLR4, position the MEV as a strong candidate for further investigation against K. pneumoniae.
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Affiliation(s)
- Min Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Mingkai Yu
- School of Life Science and Technology, Southeast University, Xinjiekou Street, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Yigang Yuan
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Danyang Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Daijiao Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Min Zhao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Zihan Lin
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Liuzhi Shi
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Albutti A. An integrated multi-pronged reverse vaccinology and biophysical approaches for identification of potential vaccine candidates against Nipah virus. Saudi Pharm J 2023; 31:101826. [PMID: 38028215 PMCID: PMC10651679 DOI: 10.1016/j.jsps.2023.101826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Nipah virus, a paramyxovirus linked to Hendra virus that first appeared in Malaysia and is the etiological agent of viral lethal encephalitis, has emerged as a strong threat to the health community in recent decades. Viral infections are seriously affecting global health. Since there are now no efficient therapeutic options, it will take considerable effort to develop appropriate therapeutic management for the Nipah virus. The main purpose of this study was to design a messenger RNA-based multi-epitope vaccine construct against Nipah virus. This purpose was achieved through multiple immunogenic epitopes prediction using Nipah virus antigenic protein using the immune epitope database and analysis resource (IEDB) followed by the vaccine construction and processing. As in multi-epitopes vaccine construction we selected immunogenic potential fragments of viral proteins, therefore in host immune stimulation we observed proper immune responses toward a multi-epitopes vaccine. In this study, the Nipah virus V protein was used to identify immunodominant epitopes utilizing several reverse vaccinology, immunoinformatics and biophysical methods. The potential antigenic predicted epitopes were further analyzed for immunoinformatics analysis and only selected probable antigenic and non-toxic epitopes were used in designing a multi-epitope mRNA based in silico vaccine against the target pathogen. In vaccine designing a total number of 03B cell epitopes, 09 Cytotoxic T lymphocytes (CTLs) and 01 Helper T lymphocytes (HTL) were prioritized as a good vaccine candidate. In the vaccine construction phase, the selected epitopes were linked together using EAAAK, GPGPG, KK, and AAY linkers, and B-defensin (adjuvant), and MITD sequences were also added to the vaccine construct to increase the potency. After vaccine construction, the physiochemical properties of the vaccine construct were evaluated which predicted that the vaccine construct comprises 320 amino acids with 34.29 kDa (kDa) molecular weight. The instability index was 36.55 proving its stability with the aliphatic index of 82.88. Furthermore, 9.0 theoretical pI and -0.317, GRAVY (Grand Average of Hydropathy) values were predicted in physicochemical properties analysis. A solubility check was applied against the vaccine construct depicting that the vaccine construct is soluble with its calculated value of 0.6. Additionally, after prediction the 3D structure was modeled and refined for docking analysis, the refined 3D structure of the vaccine candidate was further checked for binding affinity with immune cell receptors through docking analysis, in the docking analysis we observed that the vaccine construct has a good binding affinity with immune cells receptor and can induce a proper immune response in host cells. As we predicted effective binding of the designed vaccine construct, hence it can further facilitate the development of vaccine formulation against the Nipah virus. Additionally, molecular dynamic simulation was done using the AMBER v20 package for analysis of the dynamic behaviour of the docked complexes and we observed proper binding stability of the vaccine with target receptor. In C-immune simulation, different humoral and cellular antibody titer was observed in response to the vaccine. Overall using bioinformatics, immunoinformatics, and biophysical approaches we observed that this mRNA base epitopes vaccine construct could facilitate the proof of concept for the formation of the experimental base vaccine against the Nipah virus, as the in silico predictions indicated that the vaccine is highly promising in terms of developing protective immunity. However experimental validation is required to disclose the real immune-protective efficacy of the vaccine.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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5
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Jahangirian E, Zargan J, Rabbani H, Zamani J. Investigating the inhibitory and penetrating properties of three novel anticancer and antimicrobial scorpion peptides via molecular docking and molecular dynamic simulation. J Biomol Struct Dyn 2023; 41:15354-15385. [PMID: 36927377 DOI: 10.1080/07391102.2023.2188956] [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: 12/01/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
The two types of bladder cancer, muscle invasive and non-muscle invasive (NMIBC), are among the most prevalent cancers worldwide. Despite this, even though muscle-invasive bladder cancer is more deadly, NMIBC requires more therapy due to a greater recurrence rate and more extended and expensive care. Immunotherapy, intravesical chemotherapy, cystoscopy, and transurethral resection (TUR) are among the treatments available. Crude scorpion venomand purified proteins and peptides, can suppress cancer metastasis in an in vitro or in vivo context, suppress cancer growth, halt the cell cycle, and cause cell apoptosis, according to an increasing number of experimental and preclinical studies. In this research, three novels discovered peptides (P2, P3 and P4. ProteomeXchange: PXD036231) from Buthotus saulcyi and, Odontobuthus doriae scorpions were used along with a peptide called pantinin (as a control). The phylogenetic tree showed that the peptides belong to Chaperonin HSP60, Chrysophsin2 and Pheromone-binding protein2, respectively. These peptides were docked with four known antigens, BAGE, BLCAP, PRAME and ROR1 related to bladder cancer and three bacterial antigens FliC, FliD and FimH to investigate their antimicrobial and anticancer properties. The results showed that peptides 2 and 3 have the best binding rate. The MD simulation results also confirmed the binding of peptides 2 and 3 to antigens. The penetration power of peptides 2 and 3 in the membrane of cancer cells and bacterial cells was also simulated, and the results of RMSD and PD confirmed it. QSAR suggests that peptides 2 and 3 can act as anti-cancer and anti-microbial peptides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ehsan Jahangirian
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Jamil Zargan
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Hodjattallah Rabbani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Javad Zamani
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Ishwarlall TZ, Adeleke VT, Maharaj L, Okpeku M, Adeniyi AA, Adeleke MA. Identification of potential candidate vaccines against Mycobacterium ulcerans based on the major facilitator superfamily transporter protein. Front Immunol 2022; 13:1023558. [PMID: 36426350 PMCID: PMC9679648 DOI: 10.3389/fimmu.2022.1023558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023] Open
Abstract
Buruli ulcer is a neglected tropical disease that is characterized by non-fatal lesion development. The causative agent is Mycobacterium ulcerans (M. ulcerans). There are no known vectors or transmission methods, preventing the development of control methods. There are effective diagnostic techniques and treatment routines; however, several socioeconomic factors may limit patients' abilities to receive these treatments. The Bacillus Calmette-Guérin vaccine developed against tuberculosis has shown limited efficacy, and no conventionally designed vaccines have passed clinical trials. This study aimed to generate a multi-epitope vaccine against M. ulcerans from the major facilitator superfamily transporter protein using an immunoinformatics approach. Twelve M. ulcerans genome assemblies were analyzed, resulting in the identification of 11 CD8+ and 7 CD4+ T-cell epitopes and 2 B-cell epitopes. These conserved epitopes were computationally predicted to be antigenic, immunogenic, non-allergenic, and non-toxic. The CD4+ T-cell epitopes were capable of inducing interferon-gamma and interleukin-4. They successfully bound to their respective human leukocyte antigens alleles in in silico docking studies. The expected global population coverage of the T-cell epitopes and their restricted human leukocyte antigens alleles was 99.90%. The population coverage of endemic regions ranged from 99.99% (Papua New Guinea) to 21.81% (Liberia). Two vaccine constructs were generated using the Toll-like receptors 2 and 4 agonists, LprG and RpfE, respectively. Both constructs were antigenic, non-allergenic, non-toxic, thermostable, basic, and hydrophilic. The DNA sequences of the vaccine constructs underwent optimization and were successfully in-silico cloned with the pET-28a(+) plasmid. The vaccine constructs were successfully docked to their respective toll-like receptors. Molecular dynamics simulations were carried out to analyze the binding interactions within the complex. The generated binding energies indicate the stability of both complexes. The constructs generated in this study display severable favorable properties, with construct one displaying a greater range of favorable properties. However, further analysis and laboratory validation are required.
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Affiliation(s)
- Tamara Z. Ishwarlall
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Victoria T. Adeleke
- Department of Chemical Engineering, Mangosuthu University of Technology, Durban, South Africa
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Adebayo A. Adeniyi
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
- Department of Industrial Chemistry, Federal University Oye Ekiti, Oye-Ekiti, Ekiti State, Nigeria
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
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Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB. A novel vaccine based on SARS-CoV-2 CD4 + and CD8 + T cell conserved epitopes from variants Alpha to Omicron. Sci Rep 2022; 12:16731. [PMID: 36202985 PMCID: PMC9537284 DOI: 10.1038/s41598-022-21207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/23/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 caused, as of September, 1rst, 2022, 599,825,400 confirmed cases, including 6,469,458 deaths. Currently used vaccines reduced severity and mortality but not virus transmission or reinfection by different strains. They are based on the Spike protein of the Wuhan reference virus, which although highly antigenic suffered many mutations in SARS-CoV-2 variants, escaping vaccine-generated immune responses. Multiepitope vaccines based on 100% conserved epitopes of multiple proteins of all SARS-CoV-2 variants, rather than a single highly mutating antigen, could offer more long-lasting protection. In this study, a multiepitope multivariant vaccine was designed using immunoinformatics and in silico approaches. It is composed of highly promiscuous and strong HLA binding CD4+ and CD8+ T cell epitopes of the S, M, N, E, ORF1ab, ORF 6 and ORF8 proteins. Based on the analysis of one genome per WHO clade, the epitopes were 100% conserved among the Wuhan-Hu1, Alpha, Beta, Gamma, Delta, Omicron, Mµ, Zeta, Lambda and R1 variants. An extended epitope-conservancy analysis performed using GISAID metadata of 3,630,666 SARS-CoV-2 genomes of these variants and the additional genomes of the Epsilon, Lota, Theta, Eta, Kappa and GH490 R clades, confirmed the high conservancy of the epitopes. All but one of the CD4 peptides showed a level of conservation greater than 97% among all genomes. All but one of the CD8 epitopes showed a level of conservation greater than 96% among all genomes, with the vast majority greater than 99%. A multiepitope and multivariant recombinant vaccine was designed and it was stable, mildly hydrophobic and non-toxic. The vaccine has good molecular docking with TLR4 and promoted, without adjuvant, strong B and Th1 memory immune responses and secretion of high levels of IL-2, IFN-γ, lower levels of IL-12, TGF-β and IL-10, and no IL-6. Experimental in vivo studies should validate the vaccine’s further use as preventive tool with cross-protective properties.
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Affiliation(s)
- Iam Palatnik-de-Sousa
- Department of Electrical Engeneering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stephany Christiny Cavalcante
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Paula Fonseca Ribeiro
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Antônio Barbosa Martins Silva
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ciro Cavalcante
- Department of Pharmacy, Campus Professor Antônio Garcia Filho, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Global Virus Network, Baltimore, MD, USA
| | - Clarisa Beatriz Palatnik-de-Sousa
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. .,Institute for Immunological Investigation (III), INCT, National Council for Scientific and Technological Development (CNPq), São Paulo, Brazil.
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8
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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9
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Oluwagbemi OO, Oladipo EK, Dairo EO, Ayeni AE, Irewolede BA, Jimah EM, Oyewole MP, Olawale BM, Adegoke HM, Ogunleye AJ. Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100845. [PMID: 35071728 PMCID: PMC8760845 DOI: 10.1016/j.imu.2022.100845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/28/2021] [Accepted: 01/01/2022] [Indexed: 12/19/2022] Open
Abstract
The discovery of a new SARS-CoV-2 virus strain in South Africa presents a major public health threat, therefore contributing to increased infections and transmission rates during the second wave of the global pandemic. This study lays the groundwork for the development of a novel subunit vaccine candidate from the circulating strains of South African SARS-CoV-2 and provides an understanding of the molecular epidemiological trend of the circulating strains. A total of 475 whole-genome nucleotide sequences from South Africa submitted between December 1, 2020 and February 15, 2021 available at the GISAID database were retrieved based on its size, coverage level and hosts. To obtain the distribution of the clades and lineages of South African SARS-CoV-2 circulating strains, the metadata of the sequence retrieved were subjected to an epidemiological analysis. There was a prediction of the cytotoxic T lymphocytes (CTL), Helper T cells (HTL) and B-cell epitopes. Furthermore, there was allergenicity, antigenicity and toxicity predictions on the epitopes. The analysis of the physicochemical properties of the vaccine construct was performed; the secondary structure, tertiary structure and B-cell 3D conformational structure of the vaccine construct were predicted. Also, molecular binding simulations and dynamics simulations were adopted in the prediction of the vaccine construct's stability and binding affinity with TLRs. Result obtained from the metadata analysis indicated lineage B.1.351 to be in higher circulation among various circulating strains of SARS-CoV-2 in South Africa and GH has the highest number of circulating clades. The construct of the novel vaccine was antigenic, non-allergenic and non-toxic. The Instability index (II) score and aliphatic index were estimated as 41.74 and 78.72 respectively. The computed half-life in mammalian reticulocytes was 4.4 h in vitro, for yeast and in E. coli was >20 h and >10 h in vivo respectively. The grand average of hydropathicity (GRAVY) score is estimated to be -0.129, signifying the hydrophilic nature of the protein. The molecular docking indicates that the vaccine construct has a high binding affinity towards the TLRs with TLR 3 having the highest binding energy (-1203.2 kcal/mol) and TLR 9 with the lowest (-1559.5 kcal/mol). These results show that the vaccine construct is promising and should be evaluated using animal model.
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Affiliation(s)
- Olugbenga Oluseun Oluwagbemi
- Department of Computer Science and Information Technology, Sol Plaatje University, 8301, Kimberley, South Africa
- Department of Mathematical Sciences, Stellenbosch University, 7602, Matieland, South Africa
- National Institute of Theoretical and Computational Sciences (NiTheCS), South Africa
| | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Emmanuel Oluwatobi Dairo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Ayodele Eugene Ayeni
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Esther Moradeyo Jimah
- Department of Medical Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Moyosoluwa Precious Oyewole
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife Mary Olawale
- Reproduction and Bioinformatics Unit, Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adewale Joseph Ogunleye
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Oblast, Russian Federation
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Ferreira CS, Martins YC, Souza RC, Vasconcelos ATR. EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes. PeerJ 2021; 9:e12548. [PMID: 34909278 PMCID: PMC8641484 DOI: 10.7717/peerj.12548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.
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Affiliation(s)
- Cristina S. Ferreira
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Yasmmin C. Martins
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Rangel Celso Souza
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Ana Tereza R. Vasconcelos
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
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