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Mortazavi B, Molaei A, Fard NA. Multi-epitopevaccines, from design to expression; an in silico approach. Hum Immunol 2024; 85:110804. [PMID: 38658216 DOI: 10.1016/j.humimm.2024.110804] [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: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The development of vaccines against a wide range of infectious diseases and pathogens often relies on multi-epitope strategies that can effectively stimulate both humoral and cellular immunity. Immunoinformatics tools play a pivotal role in designing such vaccines, enhancing immune response potential, and minimizing the risk of failure. This review presents a comprehensive overview of practical tools for epitope prediction and the associated immune responses. These immunoinformatics tools facilitate the selection of epitopes based on parameters such as antigenicity, absence of toxic and allergenic sequences, secondary and tertiary structures, sequence conservation, and population coverage. The chosen epitopes can be tailored for B-cells or T-cells, both of which require further assessments covered in this study. We offer a range of suitable linkers that effectively separate cytotoxic T lymphocyte and helper T lymphocyte epitopes while preserving their functionality. Additionally, we identify various adjuvants for specific purposes. We delve into the evaluation of MHC-epitope interactions, MHC clusters, and the simulation of final constructs through molecular docking techniques. We provide diverse linkers and adjuvants optimized for epitope functions to bolster immune responses through epitope attachment. By leveraging these comprehensive tools, the development of multi-epitope vaccines holds the promise of robust immunity and a significant reduction in experimental costs.
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Affiliation(s)
- Behnam Mortazavi
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Molaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Ahmad S, Demneh FM, Rehman B, Almanaa TN, Akhtar N, Pazoki-Toroudi H, Shojaeian A, Ghatrehsamani M, Sanami S. In silico design of a novel multi-epitope vaccine against HCV infection through immunoinformatics approaches. Int J Biol Macromol 2024; 267:131517. [PMID: 38621559 DOI: 10.1016/j.ijbiomac.2024.131517] [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: 11/11/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
Infection with the hepatitis C virus (HCV) is one of the causes of liver cancer, which is the world's sixth most prevalent and third most lethal cancer. The current treatments do not prevent reinfection; because they are expensive, their usage is limited to developed nations. Therefore, a prophylactic vaccine is essential to control this virus. Hence, in this study, an immunoinformatics method was applied to design a multi-epitope vaccine against HCV. The best B- and T-cell epitopes from conserved regions of the E2 protein of seven HCV genotypes were joined with the appropriate linkers to design a multi-epitope vaccine. In addition, cholera enterotoxin subunit B (CtxB) was included as an adjuvant in the vaccine construct. This study is the first to present this epitopes-adjuvant combination. The vaccine had acceptable physicochemical characteristics. The vaccine's 3D structure was predicted and validated. The vaccine's binding stability with Toll-like receptor 2 (TLR2) and TLR4 was confirmed using molecular docking and molecular dynamics (MD) simulation. The immune simulation revealed the vaccine's efficacy by increasing the population of B and T cells in response to vaccination. In silico expression in Escherichia coli (E. coli) was also successful.
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Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, P.O. Box 36, Lebanon; Department of Natural Sciences, Lebanese American University, Beirut, P.O. Box 36, Lebanon
| | - Fatemeh Mobini Demneh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Bushra Rehman
- Institute of Biotechnology and Microbiology, Bacha khan University, Charsadda, Pakistan
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Hamidreza Pazoki-Toroudi
- Department of Physiology & Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - 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.
| | - Samira Sanami
- Abnormal Uterine Bleeding Research Center, Semnan University of Medical Sciences, Semnan, Iran.
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Ganji M, Bakhshi S, Ahmadi K, Shoari A, Moeini S, Ghaemi A. Rational design of B-cell and T-cell multi epitope-based vaccine against Zika virus, an in silico study. J Biomol Struct Dyn 2024; 42:3426-3440. [PMID: 37190978 DOI: 10.1080/07391102.2023.2213339] [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: 09/01/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
The Zika virus (ZKV) is a single-stranded positive-sense, enveloped RNA virus. Zika infection during pregnancy can cause congenital microcephaly, Guillain-Barré syndrome, miscarriage, and other CNS abnormalities. The world needs safe and effective vaccinations to fight against ZIKV infection since vaccination is generally regarded as one of the most effective ways to prevent infectious diseases. In the present work, we used immunoinformatics and docking studies to construct a vaccine containing multi-epitopes using the structural and non-structural proteins of ZKV. The structural models of ZKV proteins (PrE, PrM, NS1, and NS2A) were constructed using Pyre2 and RaptorX servers. The epitopes of B-cell, T-cell (HTL and CTL), and IFN-γ were predicted, and each epitope's immunogenic nature and physiochemical properties were confirmed. As an adjuvant, the CPG-Oligodeoxynucleotide, an agonist of Toll-like receptor 9 (TLR9), is associated to cytotoxic T-lymphocytes (CTL) epitopes via PAPAP linker. To assess the binding affinity and the tendency of the designed vaccine to induce an immune response through TLR9, molecular docking was done. In the next step, molecular dynamics (MD) simulation to 100 nanoseconds (ns) was used to evaluate the stability of the interaction of the designed vaccine with TLR9. The designed vaccine is predicted to be highly antigenic, non-toxic, soluble, and stable with low flexibility in MD simulation. MD studies indicated that the finalized vaccine-TLR9 docked complex was stable during simulation time. The vaccine construct is able to stimulate both humoral and cellular immune responses. We suppose that our constructed model of the vaccine may have the ability to induce the host immune response against ZKV. Further studies, including in vitro and in vivo experimental analyses, are needed to prove the constructed vaccine's efficacy with multi-epitopes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shohreh Bakhshi
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Shoari
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Soheila Moeini
- Department of Surgery, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Tabll AA, Sohrab SS, Ali AA, Petrovic A, Steiner Srdarevic S, Siber S, Glasnovic M, Smolic R, Smolic M. Future Prospects, Approaches, and the Government's Role in the Development of a Hepatitis C Virus Vaccine. Pathogens 2023; 13:38. [PMID: 38251345 PMCID: PMC10820710 DOI: 10.3390/pathogens13010038] [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: 10/31/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Developing a safe and effective vaccine against the hepatitis C virus (HCV) remains a top priority for global health. Despite recent advances in antiviral therapies, the high cost and limited accessibility of these treatments impede their widespread application, particularly in resource-limited settings. Therefore, the development of the HCV vaccine remains a necessity. This review article analyzes the current technologies, future prospects, strategies, HCV genomic targets, and the governmental role in HCV vaccine development. We discuss the current epidemiological landscape of HCV infection and the potential of HCV structural and non-structural protein antigens as vaccine targets. In addition, the involvement of government agencies and policymakers in supporting and facilitating the development of HCV vaccines is emphasized. We explore how vaccine development regulatory channels and frameworks affect research goals, funding, and public health policy. The significance of international and public-private partnerships in accelerating the development of an HCV vaccine is examined. Finally, the future directions for developing an HCV vaccine are discussed. In conclusion, the review highlights the urgent need for a preventive vaccine to fight the global HCV disease and the significance of collaborative efforts between scientists, politicians, and public health organizations to reach this important public health goal.
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Affiliation(s)
- Ashraf A. Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Cairo 12622, Egypt
- Egypt Centre for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Sayed S. Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed A. Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo 12622, Egypt;
| | - Ana Petrovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Sabina Steiner Srdarevic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Stjepan Siber
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Marija Glasnovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Robert Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Martina Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
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Kumar KM, Karthik Y, Ramakrishna D, Balaji S, Skariyachan S, Murthy TPK, Sakthivel KM, Alotaibi BS, Shukry M, Sayed SM, Mushtaq M. Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2. Front Microbiol 2023; 14:1251716. [PMID: 37915849 PMCID: PMC10616776 DOI: 10.3389/fmicb.2023.1251716] [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: 07/02/2023] [Accepted: 09/12/2023] [Indexed: 11/03/2023] Open
Abstract
Many countries around the world are facing severe challenges due to the recently emerging variants of SARS-CoV-2. Over the last few months, scientists have been developing treatments, drugs, and vaccines to subdue the virus and prevent its transmission. In this context, a peptide-based vaccine construct containing pathogenic proteins of the virus known to elicit an immune response was constructed. An analysis of the spike protein-based epitopes allowed us to design an "epitope-based subunit vaccine" against coronavirus using the approaches of "reverse vaccinology" and "immunoinformatics." Computational experimentation and a systematic, comprehensive protocol were followed with an aim to develop and design a multi-epitope-based peptide (MEBP) vaccine candidate. Our study attempted to predict an MEBP vaccine by introducing mutations of SARS-CoV-2 (Delta, Lambda, Iota, Omicron, and Kappa) in Spike glycoprotein and predicting dual-purpose epitopes (B-cell and T-cell). This was followed by screening the selected epitopes based on antigenicity, allergenicity, and population coverage and constructing them into a vaccine by using linkers and adjuvants. The vaccine construct was analyzed for its physicochemical properties and secondary structure prediction, and a 3D structure was built, refined, and validated. Furthermore, the peptide-protein interaction of the vaccine construct with Toll-like receptor (TLR) molecules was performed. Immune profiling was performed to check the immune response. Codon optimization of the vaccine construct was performed to obtain the GC content before cloning it into the E. coli genome, facilitating its progression it into a vector. Finally, an in-silico simulation of the vaccine-protein complex was performed to comprehend its stability and conformational behavior.
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Affiliation(s)
- K. M. Kumar
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | - Yalpi Karthik
- Department of Studies and Research in Microbiology, Mangalore University, Chikka Aluvara, Kodagu, Karnataka, India
| | - D. Ramakrishna
- Biotechnology Department, Dayananda Sagar College of Engineering, Dr. C.D Sagar Centre for Life Sciences, Dayananda Sagar Institutions, Bengaluru, India
| | - S. Balaji
- Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Bengaluru, Karnataka, India
| | - Sinosh Skariyachan
- Department of Microbiology, St. Pius X College, Rajapuram, Kerala, India
| | - T. P. Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | | | - Badriyah S. Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mustafa Shukry
- Physiology Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Samy M. Sayed
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt
- Department of Science and Technology, University College-Ranyah, Taif University, Taif, Saudi Arabia
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
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Sher H, Sharif H, Zaheer T, Khan SA, Ali A, Javed H, Javed A. Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1). BMC Genomics 2023; 24:276. [PMID: 37226084 DOI: 10.1186/s12864-023-09330-4] [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: 10/19/2022] [Accepted: 04/24/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Despite being in the 21st century, the world has still not been able to vanquish the global AIDS epidemic, and the only foreseeable solution seems to be a safe and effective vaccine. Unfortunately, vaccine trials so far have returned unfruitful results, possibly due to their inability to induce effective cellular, humoral and innate immune responses. The current study aims to tackle these limitations and propose the desired vaccine utilizing immunoinformatic approaches that have returned promising results in designing vaccines against various rapidly mutating organisms. For this, all polyprotein and protein sequences of HIV-1 were retrieved from the LANL (Los Alamos National Laboratory) database. The consensus sequence was generated after alignment and used to predict epitopes. Conserved, antigenic, non-allergenic, T-cell inducing, B-cell inducing, IFN-ɣ inducing, non-human homologous epitopes were selected and combined to propose two vaccine constructs i.e., HIV-1a (without adjuvant) and HIV-1b (with adjuvant). RESULTS HIV-1a and HIV-1b were subjected to antigenicity, allergenicity, structural quality analysis, immune simulations, and MD (molecular dynamics) simulations. Both proposed multi-epitope vaccines were found to be antigenic, non-allergenic, stable, and induce cellular, humoral, and innate immune responses. TLR-3 docking and in-silico cloning of both constructs were also performed. CONCLUSION Our results indicate HIV-1b to be more promising than HIV-1a; experimental validations can confirm the efficacy and safety of both constructs and in-vivo efficacy in animal models.
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Affiliation(s)
- Hamza Sher
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hafsa Sharif
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tahreem Zaheer
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Sarmad Ahmad Khan
- German Cancer Research Center (DFKZ), German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Amjad Ali
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hasnain Javed
- Advanced Diagnostic Lab BSL-3, Punjab AIDS Control Program, Primary and Secondary Healthcare Department, Government of the Punjab, Lahore, Pakistan
| | - Aneela Javed
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
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Usman M, Ayub A, Habib S, Rana MS, Rehman Z, Zohaib A, Jamal SB, Jaiswal AK, Andrade BS, de Carvalho Azevedo V, Faheem M, Javed A. Vaccinomics Approach for Multi-Epitope Vaccine Design against Group A Rotavirus Using VP4 and VP7 Proteins. Vaccines (Basel) 2023; 11:726. [PMID: 37112638 PMCID: PMC10144065 DOI: 10.3390/vaccines11040726] [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: 01/20/2023] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Rotavirus A is the most common cause of Acute Gastroenteritis globally among children <5 years of age. Due to a segmented genome, there is a high frequency of genetic reassortment and interspecies transmission which has resulted in the emergence of novel genotypes. There are concerns that monovalent (Rotarix: GlaxoSmithKline Biologicals, Rixensart, Belgium) and pentavalent (RotaTeq: MERCK & Co., Inc., Kenilworth, NJ, USA) vaccines may be less effective against non-vaccine strains, which clearly shows the demand for the design of a vaccine that is equally effective against all circulating genotypes. In the present study, a multivalent vaccine was designed from VP4 and VP7 proteins of RVA. Epitopes were screened for antigenicity, allergenicity, homology with humans and anti-inflammatory properties. The vaccine contains four B-cell, three CTL and three HTL epitopes joined via linkers and an N-terminal RGD motif adjuvant. The 3D structure was predicted and refined preceding its docking with integrin. Immune simulation displayed promising results both in Asia and worldwide. In the MD simulation, the RMSD value varied from 0.2 to 1.6 nm while the minimum integrin amino acid fluctuation (0.05-0.1 nm) was observed with its respective ligand. Codon optimization was performed with an adenovirus vector in a mammalian expression system. The population coverage analysis showed 99.0% and 98.47% in South Asia and worldwide, respectively. These computational findings show potential against all RVA genotypes; however, in-vitro/in-vivo screening is essential to devise a meticulous conclusion.
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Affiliation(s)
- Muhammad Usman
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
- Department of Virology, National Institute of Health, Islamabad 45500, Pakistan
| | - Aaima Ayub
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Sabahat Habib
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | | | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad 45500, Pakistan
| | - Ali Zohaib
- Department of Microbiology, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur 63100, Pakistan
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan (M.F.)
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Bahia 45083-900, Brazil
| | - Vasco de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan (M.F.)
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
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Masalova OV, Lesnova EI, Andreev SM, Shershakova NN, Kozlov VV, Permyakova KY, Demidova NA, Valuev-Elliston VT, Turetskiy EA, Ivanov AV, Nikolaeva TN, Khaitov MR, Pronin AV, Kushch AA. [Adjuvant effect of dispersed fullerene C60 on the immune response to constructs harboring amino acid and nucleotide sequences of hepatitis C virus nonstructural NS5B protein]. Vopr Virusol 2023; 67:516-526. [PMID: 37264841 DOI: 10.36233/0507-4088-149] [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: 12/26/2022] [Indexed: 06/03/2023]
Abstract
INTRODUCTION A vaccine against hepatitis C has not yet been developed. Recombinant proteins and plasmids encoding hepatitis C virus (HCV) proteins, the components of candidate vaccines, induce a weak immune response and require the use of adjuvants. The aim of the work was to study the adjuvant action of an aqueous solution of fullerene C60 during immunization of mice with HCV recombinant protein NS5B (rNS5B) that is an RNA-dependent RNA polymerase, or with NS5B-encoding pcNS5B plasmid. MATERIALS AND METHODS An aqueous solution of dispersed fullerene (dnC60) was obtained by ultrafiltration. C57BL/6 mice were immunized with rNS5B subcutaneously, pcNS5B intramuscularly mixed with different doses of dnC60 three times, then the humoral and cellular response to HCV was evaluated. RESULTS Mice immunization with rNS5B in a mixture with dnC60 at doses of 250 g/mouse significantly induced humoral response: a dose-dependent increase in IgG1 antibody titers was 720 times higher than in the absence of fullerene. There was no increase in the cellular response to rNS5B when administered with dnC60. The humoral response to DNA immunization was weak in mice of all groups receiving pcNS5B. The cellular response was suppressed when the plasmid was injected in a mixture with dnC60. CONCLUSIONS Dispersed fullerene dnC60 is a promising adjuvant for increasing the immunostimulating activity of weakly immunogenic proteins including surface and other HCV proteins, important for a protective response. Further research is needed to enhance the ability of dnC60 to boost the cellular immune response to the components of the candidate vaccine.
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Affiliation(s)
- O V Masalova
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | - E I Lesnova
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | | | | | - V V Kozlov
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | - K Y Permyakova
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
- Federal State Budgetary Educational Institution of Higher Education «Moscow State Academy of Veterinary Medicine and Biotechnology - MVA by K.I. Skryabin»
| | - N A Demidova
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | | | - E A Turetskiy
- NRC Institute of Immunology FMBA of Russia
- Sechenov First Moscow State Medical University (Sechenov University)
| | - A V Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
| | - T N Nikolaeva
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | - M R Khaitov
- NRC Institute of Immunology FMBA of Russia
- Pirogov Russian National Research Medical University
| | - A V Pronin
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
| | - A A Kushch
- Gamaleya NRC of Epidemiology and Microbiology, Ministry of Health of the Russian Federation
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The CD8+ and CD4+ T Cell Immunogen Atlas of Zika Virus Reveals E, NS1 and NS4 Proteins as the Vaccine Targets. Viruses 2022; 14:v14112332. [PMID: 36366430 PMCID: PMC9696057 DOI: 10.3390/v14112332] [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: 09/21/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 02/01/2023] Open
Abstract
Zika virus (ZIKV)-specific T cells are activated by different peptides derived from virus structural and nonstructural proteins, and contributed to the viral clearance or protective immunity. Herein, we have depicted the profile of CD8+ and CD4+ T cell immunogenicity of ZIKV proteins in C57BL/6 (H-2b) and BALB/c (H-2d) mice, and found that featured cellular immunity antigens were variant among different murine alleles. In H-2b mice, the proteins E, NS2, NS3 and NS5 are recognized as immunodominant antigens by CD8+ T cells, while NS4 is dominantly recognized by CD4+ T cells. In contrast, in H-2d mice, NS1 and NS4 are the dominant CD8+ T cell antigen and NS4 as the dominant CD4+ T cell antigen, respectively. Among the synthesized 364 overlapping polypeptides spanning the whole proteome of ZIKV, we mapped 91 and 39 polypeptides which can induce ZIKV-specific T cell responses in H-2b and H-2d mice, respectively. Through the identification of CD8+ T cell epitopes, we found that immunodominant regions E294-302 and NS42351-2360 are hotspots epitopes with a distinct immunodominance hierarchy present in H-2b and H-2d mice, respectively. Our data characterized an overall landscape of the immunogenic spectrum of the ZIKV polyprotein, and provide useful insight into the vaccine development.
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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11
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Sankar S. In silico design of a multi-epitope Chimera from Aedes aegypti salivary proteins OBP 22 and OBP 10: A promising candidate vaccine. J Vector Borne Dis 2022; 59:327-336. [PMID: 36751764 DOI: 10.4103/0972-9062.353271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES The emergence and re-emergence of arboviruses such as dengue, Chikungunya and Zika viruses causing morbidity and mortality around the globe are of serious concern. A safe and effective vaccine is essential to control viral transmission. The salivary proteins of the mosquito that aid in blood probing, feeding and development are immunogenic. We aimed to report a multi-epitope candidate vaccine chimera from Aedes aegyptii mosquito salivary proteins OBP 22 and OBP 10 that could confer protection against all pathogens transmitted by the vector. METHODS Linear and conformation B-cell epitopes and MHC class-I and class-II binding T- cell epitopes were predicted using bioinformatic tools. Selected B- and T-cell epitopes were chosen for designing a multiepitope vaccine construct. The chimeric construct was analyzed for its immunogenicity, TAP and proteasomal cleavage, allergenicity, and structural validation for its suitability to be used as a candidate vaccine. Molecular docking was carried out to analyze the binding interactions with TLRs molecules. RESULTS A chimeric multiepitope vaccine was designed with the best-selected combination of immunogenic B-cell epitope, cytotoxic and helper T-cell and gamma interferon inducing epitopes with suitable adjuvant and linkers. The interacting residues between the candidate vaccine and the TLR molecules have been identified. INTERPRETATION & CONCLUSION The proposed multiepitope candidate vaccine was designed from the mosquito salivary protein OBP 22 and OBP 10. The candidate vaccine was found promising for the protection against arboviruses. Further clinical validation is warranted to prove its efficacy, safety and immunogenicity for its potential use.
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Affiliation(s)
- Sathish Sankar
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India
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Behmard E, Abdulabbas HT, Abdalkareem Jasim S, Najafipour S, Ghasemian A, Farjadfar A, Barzegari E, Kouhpayeh A, Abdolmaleki P. Design of a novel multi-epitope vaccine candidate against hepatitis C virus using structural and nonstructural proteins: An immunoinformatics approach. PLoS One 2022; 17:e0272582. [PMID: 36040967 PMCID: PMC9426923 DOI: 10.1371/journal.pone.0272582] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus (HCV) infects the liver and causes chronic infection. Several mutations in the viral genome have been associated with drug resistance development. Currently, there is no approved vaccine against the HCV. The employment of computational biology is the primary and crucial step for vaccine design or antiviral therapy which can substantially reduce the duration and cost of studies. Therefore, in this study, we designed a multi-epitope vaccine using various immunoinformatics tools to elicit the efficient human immune responses against the HCV. Initially, various potential (antigenic, immunogenic, non-toxic and non-allergenic) epitope segments were extracted from viral structural and non-structural protein sequences using multiple screening methods. The selected epitopes were linked to each other properly. Then, toll-like receptors (TLRs) 3 and 4 agonists (50S ribosomal protein L7/L12 and human β-defensin 2, respectively) were added to the N-terminus of the final vaccine sequence to increase its immunogenicity. The 3D structure of the vaccine was modeled. Molecular dynamics simulations studies verified the high stability of final free vaccines and in complex with TLR3 and TLR4. These constructs were also antigenic, non-allergenic, nontoxic and immunogenic. Although the designed vaccine traits were promising as a potential candidate against the HCV infection, experimental studies and clinical trials are required to verify the protective traits and safety of the designed vaccine.
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Affiliation(s)
- Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Hussein T. Abdulabbas
- Department of Medical Laboratory Techniques, Faculty of Health and Medical Techniques, Imam Ja’afar Al-Sadiq University, Al Muthanna, Iraq
| | | | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
- * E-mail: (PA); (AK); (AG)
| | - Akbar Farjadfar
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Kouhpayeh
- Department of Pharmacology, Fasa University of Medical Sciences, Fasa, Iran
- * E-mail: (PA); (AK); (AG)
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (PA); (AK); (AG)
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Imran MA, Islam MR, Saha A, Ferdousee S, Mishu MA, Ghosh A. Development of Multi-epitope Based Subunit Vaccine Against Crimean-Congo Hemorrhagic Fever Virus Using Reverse Vaccinology Approach. Int J Pept Res Ther 2022; 28:124. [PMID: 35789799 PMCID: PMC9244561 DOI: 10.1007/s10989-022-10430-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Md. Ashik Imran
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Md. Rubiath Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Akash Saha
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Shahida Ferdousee
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Moshiul Alam Mishu
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
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Aslam S, Ashfaq UA, Zia T, Aslam N, Alrumaihi F, Shahid F, Noor F, Qasim M. Proteome based mapping and reverse vaccinology techniques to contrive multi-epitope based subunit vaccine (MEBSV) against Streptococcus pyogenes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105259. [PMID: 35231667 DOI: 10.1016/j.meegid.2022.105259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Streptococcus pyogenes is a root cause of human infection like pharyngitis, tonsillitis, scarlet fever, impetigo, and respiratory tract infections. About 11 million individuals in the US suffer from pharyngitis every year. Unfortunately, no vaccine against S. pyogenes is available yet. The purpose of this study is to create a multiepitope-based subunit vaccine (MEBSV) targeting S. pyogenes top four highly antigenic proteins by using a combination of immunological techniques and molecular docking to tackle term group A streptococcal (GAS) infections. T-cell (HTL & CTL), B-cell, and IFN-γ of target proteins were forecasted and epitopes having high antigenic properties being selected for subsequent research. For designing of final vaccine, 5LBL, 9CTL, and 4HTL epitopes were joined by the KK, AAY, and GPGPG linkers. To enhance the immune response, the N-end of the vaccine was linked by adjuvant (Cholera enterotoxin subunit B) with a linker named EAAAK. With the addition of adjuvants and linkers, the construct size was 421 amino acids. IFN-γ and B-cell epitopes illustrate that the modeled construct is optimized for cell-mediated immune or humoral responses. The developed MEBSV structure was assessed to be highly antigenic, non-toxic, and non-allergenic. Moreover, disulphide engineering further enhanced the stability of the final vaccine protein. Molecular docking of the MEBSV with toll-like receptor 4 (TLR4) was conducted to check the vaccine's compatibility with the receptor. Besides, in-silico cloning has been carried out for credibility validation and proper expression of vaccine construct. These findings suggested that the multi-epitope vaccine produced might be a potential immunogenic against Group A streptococcus infections but further experimental testing is required to validate this study.
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Affiliation(s)
- Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Tuba Zia
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Nosheen Aslam
- Department of Biochemistry, Government College University Faisalabad, Pakistan
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan.
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Khan A, Nawaz M, Ullah S, Rehman IU, Khan A, Saleem S, Zaman N, Shinwari ZK, Ali M, Wei DQ. Core amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines. J Biomol Struct Dyn 2022; 40:3753-3768. [PMID: 33246391 DOI: 10.1080/07391102.2020.1850353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV), which infected 71 million worldwide and about 5%-6% are from Pakistan, is an ssRNA virus, responsible for end-stage liver disease. To date, no effective therapy is available to cure this disease. Hence, it is important to study the most prevalent genotypes infecting human population and design novel vaccine or small molecule inhibitors to control the infections associated with HCV. Therefore, in this study clinical samples (n = 35; HCV-3a) from HCV patients were subjected to Sanger sequencing method. The sequencing of the core gene, which is generally considered as conserved, involved in the detection, quantitation and genotyping of HCV was performed. Multiple mutations, that is, R46C, R70Q, L91C, G60E, N/S105A, P108A, N110I, S116V, G90S, A77G and G145R that could be linked with response to antiviral therapies were detected. Phylogenetic analysis suggests emerging viral isolates are circulating in Pakistan. Using ab initio modelling technique, we predicted the 3D structure of core protein and subjected to molecular dynamics simulation to extract the most stable conformation of the structure for further analysis. Immunoinformatic approaches were used to propose a multi-epitopes vaccine against HCV by using core protein. The vaccine constructs consist of nine CTL and three HTL epitopes joined by different linkers were docked against the two reported Toll-like receptors (TLR-3 and TLR-8). Docking of vaccine construct with TLR-3 and TLR-8 shows proper binding and in silico expression of the vaccine resulted in a CAI value of 0.93. These analyses suggest that specific immune responses may be produced by the proposed vaccine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayyaz Khan
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Mehboob Nawaz
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Saeed Ullah
- Saidu Group of Teaching Hospital, Swat, Pakistan
| | - Irshad Ur Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Nasib Zaman
- Center of Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China
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Sana M, Javed A, Babar Jamal S, Junaid M, Faheem M. Development of multivalent vaccine targeting M segment of Crimean Congo Hemorrhagic Fever Virus (CCHFV) using immunoinformatic approaches. Saudi J Biol Sci 2022; 29:2372-2388. [PMID: 35531180 PMCID: PMC9072894 DOI: 10.1016/j.sjbs.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/25/2021] [Accepted: 12/04/2021] [Indexed: 01/23/2023] Open
Abstract
Crimean-Congo Hemorrhagic Fever (CCHF) is a tick-borne viral infection with no licensed vaccine or therapeutics available for its treatment. In the present study we have developed the first multi-epitope subunit vaccine effective against all the seven genotypes of CCHF virus (CCHFV). The vaccine contains five B-cell, two MHC-II (HTL), and three MHC-I (CTL) epitopes screened from two structural glycoproteins (Gc and Gn in M segment) of CCHFV with an N-terminus human β-defensin as an adjuvant, as well as an N-terminus EAAAK sequence. The epitopes were rigorously investigated for their antigenicity, allergenicity, IFN gamma induction, anti-inflammatory responses, stability, and toxicity. The three-dimensional structure of the vaccine was predicted and docked with TLR-3, TLR-8, and TLR-9 receptors to find the strength of the binding complexes via molecular dynamics simulation. After codon adaptation, the subunit vaccine construct was developed in a pDual-GC plasmid and has population coverage of 98.47% of the world's population (HLA-I & II combined). The immune simulation studies were carried out on the C-ImmSim in-silico interface showing a marked increase in the production of cellular and humoral response (B-cell and T-cell) as well as TGFβ, IL-2, IL-10, and IL-12 indicating that the proposed vaccine would be able to sufficiently provoke both humoral and cell-mediated immune responses. Thus, making it a new and promising vaccine candidate against CCHFV.
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Affiliation(s)
- Maaza Sana
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Syed Babar Jamal
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
| | - Muhammad Junaid
- Precision Medicine Laboratory, Rehman Medical Institute, Hayatabad, Peshawar, KPK, 25000, Pakistan
| | - Muhammad Faheem
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
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In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting multi-domain approach. J Immunol Methods 2022; 504:113264. [PMID: 35341759 PMCID: PMC9040383 DOI: 10.1016/j.jim.2022.113264] [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: 11/16/2021] [Revised: 01/24/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
The vaccine development strategies have evolved from using an entire organism as an immunogen to a single antigen and further towards an epitope. Since an epitope is a relatively tiny and immunologically relevant part of an antigen, it has the potential to stimulate more robust and specific immune responses while causing minimal adverse effects. As a result, the recent focus of vaccine development has been to develop multi-epitope vaccines that can target multiple virulence mechanisms. Accordingly, we designed multi-epitope vaccine candidates B (multi-B-cell epitope immunogen) and CTB-B (an adjuvant - cholera toxin subunit B (CTB) - attached to immunogen B) against S. aureus by employing immunoinformatics approaches. The designed vaccines are composed of B-cell epitope segments (20-mer) of the eight well-characterized S. aureus virulence factors, namely ClfB, FnbpA, Hla, IsdA, IsdB, LukE, SdrD, and SdrE connected in series. The designed vaccines were expressed, purified, and administered to C57BL/6 mice with Freund adjuvant to evaluate the immunogenicity and protective efficacy. The results revealed that the immunized mice showed high IgG titer for the immunogen, and the antibody titer increased significantly following the second immunization. However, the generated antibodies did not protect mice from infection. The interaction of anti-B antibodies with source virulence factors showed that the generated antibodies have no binding affinity with any of the corresponding virulence factors. Our results demonstrate the limitation of in silico designed B-cell multi-epitope vaccine and suggest that a protein domain carrying both linear and conformational B-cell epitopes might be a better choice for developing an effective multi-epitope vaccine against S. aureus.
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Aghamirza Moghim Aliabadi H, Eivazzadeh‐Keihan R, Beig Parikhani A, Fattahi Mehraban S, Maleki A, Fereshteh S, Bazaz M, Zolriasatein A, Bozorgnia B, Rahmati S, Saberi F, Yousefi Najafabadi Z, Damough S, Mohseni S, Salehzadeh H, Khakyzadeh V, Madanchi H, Kardar GA, Zarrintaj P, Saeb MR, Mozafari M. COVID-19: A systematic review and update on prevention, diagnosis, and treatment. MedComm (Beijing) 2022; 3:e115. [PMID: 35281790 PMCID: PMC8906461 DOI: 10.1002/mco2.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 01/09/2023] Open
Abstract
Since the rapid onset of the COVID-19 or SARS-CoV-2 pandemic in the world in 2019, extensive studies have been conducted to unveil the behavior and emission pattern of the virus in order to determine the best ways to diagnosis of virus and thereof formulate effective drugs or vaccines to combat the disease. The emergence of novel diagnostic and therapeutic techniques considering the multiplicity of reports from one side and contradictions in assessments from the other side necessitates instantaneous updates on the progress of clinical investigations. There is also growing public anxiety from time to time mutation of COVID-19, as reflected in considerable mortality and transmission, respectively, from delta and Omicron variants. We comprehensively review and summarize different aspects of prevention, diagnosis, and treatment of COVID-19. First, biological characteristics of COVID-19 were explained from diagnosis standpoint. Thereafter, the preclinical animal models of COVID-19 were discussed to frame the symptoms and clinical effects of COVID-19 from patient to patient with treatment strategies and in-silico/computational biology. Finally, the opportunities and challenges of nanoscience/nanotechnology in identification, diagnosis, and treatment of COVID-19 were discussed. This review covers almost all SARS-CoV-2-related topics extensively to deepen the understanding of the latest achievements (last updated on January 11, 2022).
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Affiliation(s)
- Hooman Aghamirza Moghim Aliabadi
- Protein Chemistry LaboratoryDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
- Advance Chemical Studies LaboratoryFaculty of ChemistryK. N. Toosi UniversityTehranIran
| | | | - Arezoo Beig Parikhani
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | - Ali Maleki
- Department of ChemistryIran University of Science and TechnologyTehranIran
| | | | - Masoume Bazaz
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | | | - Saman Rahmati
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Fatemeh Saberi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Yousefi Najafabadi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Shadi Damough
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Sara Mohseni
- Non‐metallic Materials Research GroupNiroo Research InstituteTehranIran
| | | | - Vahid Khakyzadeh
- Department of ChemistryK. N. Toosi University of TechnologyTehranIran
| | - Hamid Madanchi
- School of MedicineSemnan University of Medical SciencesSemnanIran
- Drug Design and Bioinformatics UnitDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
| | - Gholam Ali Kardar
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Payam Zarrintaj
- School of Chemical EngineeringOklahoma State UniversityStillwaterOklahomaUSA
| | - Mohammad Reza Saeb
- Department of Polymer TechnologyFaculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative MedicineIran University of Medical SciencesTehranIran
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Immunomodulatory and Allergenic Properties of Antimicrobial Peptides. Int J Mol Sci 2022; 23:ijms23052499. [PMID: 35269641 PMCID: PMC8910669 DOI: 10.3390/ijms23052499] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
With the growing problem of the emergence of antibiotic-resistant bacteria, the search for alternative ways to combat bacterial infections is extremely urgent. While analyzing the effect of antimicrobial peptides (AMPs) on immunocompetent cells, their effect on all parts of the immune system, and on humoral and cellular immunity, is revealed. AMPs have direct effects on neutrophils, monocytes, dendritic cells, T-lymphocytes, and mast cells, participating in innate immunity. They act on B-lymphocytes indirectly, enhancing the induction of antigen-specific immunity, which ultimately leads to the activation of adaptive immunity. The adjuvant activity of AMPs in relation to bacterial and viral antigens was the reason for their inclusion in vaccines and made it possible to formulate the concept of a “defensin vaccine” as an innovative basis for constructing vaccines. The immunomodulatory function of AMPs involves their influence on cells in the nearest microenvironment, recruitment and activation of other cells, supporting the response to pathogenic microorganisms and completing the inflammatory process, thus exhibiting a systemic effect. For the successful use of AMPs in medical practice, it is necessary to study their immunomodulatory activity in detail, taking into account their pleiotropy. The degree of maturity of the immune system and microenvironment can contribute to the prevention of complications and increase the effectiveness of therapy, since AMPs can suppress inflammation in some circumstances, but aggravate the response and damage of organism in others. It should also be taken into account that the real functions of one or another AMP depend on the types of total regulatory effects on the target cell, and not only on properties of an individual peptide. A wide spectrum of biological activity, including direct effects on pathogens, inactivation of bacterial toxins and influence on immunocompetent cells, has attracted the attention of researchers, however, the cytostatic activity of AMPs against normal cells, as well as their allergenic properties and low stability to host proteases, are serious limitations for the medical use of AMPs. In this connection, the tasks of searching for compounds that selectively affect the target and development of an appropriate method of application become critically important. The scope of this review is to summarize the current concepts and newest advances in research of the immunomodulatory activity of natural and synthetic AMPs, and to examine the prospects and limitations of their medical use.
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Fatima I, Ahmad S, Abbasi SW, Ashfaq UA, Shahid F, Tahir Ul Qamar M, Rehman A, Allemailem KS. Designing of a multi-epitopes-based peptide vaccine against rift valley fever virus and its validation through integrated computational approaches. Comput Biol Med 2021; 141:105151. [PMID: 34942394 DOI: 10.1016/j.compbiomed.2021.105151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 01/23/2023]
Abstract
Since its discovery, the Rift Valley Fever virus (RVFV) has been the source of numerous outbreaks in the Arab Peninsulas and Africa, wreaking havoc on humans and animals. The lack of therapeutics or licensed human vaccines limits the options for controlling RVFV outbreaks. Therefore, RVFV has been prioritized for rapid research and innovation of prevention strategies to control and prevent its outbreaks. The purpose of this study was to design a multi-epitope-based peptide vaccine (MEBPV) against RVFV. Bioinformatics approaches were used to design a potent MEBPV that can potentially activate both CD8+ and CD4+ T-cell immune responses, and several computational tools were employed to investigate its biological activities. Three antigenic proteins (Nucleocapsid (N), Glycoprotein C (GC), and Glycoprotein N (GN)) from the RVFV were chosen and potential immunogenic T- and B -cell epitopes were predicted from them. Based on in silico analysis, a MEBPV based on highly scored T and B-cell epitopes (6 CTL, 5 HTL, and 4 LBL) combined with linkers and adjuvants was developed. The finest predicted model was used for docking studies with Toll-like receptors (TLR3 and TLR8) and MHC molecules (MHC I and MHC II) after predicting and analyzing the tertiary structure of MEBPV. The designed MEBPV was then tested for stability with TLR3 and TLR8 receptors using molecular dynamics (MD) simulation and MMGBSA analysis. The MEBPV -TLR3, MEBPV -TLR8, MEBPV-MHC I and MEBPV -MHC II docked models were found stable during simulation time in MD and MMGBSA studies. In silico analysis revealed that the constructed vaccine could elicit both cell-mediated and humoral immune responses simultaneously. The proposed MEBPV could be a strong candidate against RVFV, but it will need to be tested in the laboratory to guarantee its safety and immunogenicity.
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Affiliation(s)
- Israr Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan.
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan.
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | | | - Abdur Rehman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.
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Hasanshahi Z, Hashempour A, Ghasabi F, Moayedi J, Musavi Z, Dehghani B, Sharafi H, Joulaei H. First report on molecular docking analysis and drug resistance substitutions to approved HCV NS5A and NS5B inhibitors amongst Iranian patients. BMC Gastroenterol 2021; 21:443. [PMID: 34819046 PMCID: PMC8612383 DOI: 10.1186/s12876-021-01988-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background NS5A and NS5B proteins of hepatitis C virus (HCV) are the main targets of compounds that directly inhibit HCV infections. However, the emergence of resistance-associated substitutions (RASs) may cause substantial reductions in susceptibility to inhibitors. Methods Viral load and genotyping were determined in eighty-seven naïve HCV-infected patients, and the amplified NS5A and NS5B regions were sequenced by Sanger sequencing. In addition, physicochemical properties, structural features, immune epitopes, and inhibitors-protein interactions of sequences were analyzed using several bioinformatics tools. Results Several amino acid residue changes were found in NS5A and NS5B proteins; however, we did not find any mutations related to resistance to the treatment in NS5B. Different phosphorylation and few glycosylation sites were assessed. Disulfide bonds were identified in both proteins that had a significant effect on the function and structure of HCV proteins. Applying reliable software to predict B-cell epitopes, 3 and 5 regions were found for NS5A and NS5B, respectively, representing a considerable potential to induce the humoral immune system. Docking analysis determined amino acids involved in the interaction of inhibitors and mentioned proteins may not decrease the drug efficiency. Conclusions Strong interactions between inhibitors, NS5A and NS5B proteins and the lack of efficient drug resistance mutations in the analyzed sequences may confirm the remarkable ability of NS5A and NS5B inhibitors to control HCV infection amongst Iranian patients. The results of bioinformatics analysis could unveil all features of both proteins, which can be beneficial for further investigations on HCV drug resistance and designing novel vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01988-y.
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Affiliation(s)
- Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Musavi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Hassan Joulaei
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Tariq MH, Bhatti R, Ali NF, Ashfaq UA, Shahid F, Almatroudi A, Khurshid M. Rational design of chimeric Multiepitope Based Vaccine (MEBV) against human T-cell lymphotropic virus type 1: An integrated vaccine informatics and molecular docking based approach. PLoS One 2021; 16:e0258443. [PMID: 34705829 PMCID: PMC8550388 DOI: 10.1371/journal.pone.0258443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/27/2021] [Indexed: 01/03/2023] Open
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is an infectious virus that has been linked to adult T cell leukemia /lymphoma, aggressive CD4-T cell malignancy and many other immune-related medical illnesses. So far, no effective vaccine is known to combat HTLV-1, hence, the current research work was performed to design a potential multi-epitope-based subunit vaccine (MEBV) by adopting the latest methodology of reverse vaccinology. Briefly, three highly antigenic proteins (Glycoprotein, Accessory protein, and Tax protein) with no or minimal (<37%) similarity with human proteome were sorted out and potential B- and T-cell epitopes were forecasted from them. Highly antigenic, immunogenic, non-toxic, non-allergenic and overlapping epitopes were short-listed for vaccine development. The chosen T-cell epitopes displayed a strong binding affinity with their corresponding Human Leukocyte Antigen alleles and demonstrated 95.8% coverage of the world's population. Finally, nine Cytotoxic T Lymphocytes, six Helper T Lymphocytes and five Linear B Lymphocytes epitopes, joint through linkers and adjuvant, were exploited to design the final MEBV construct, comprising of 382 amino acids. The developed MEBV structure showed highly antigenic properties while being non-toxic, soluble, non-allergenic, and stable in nature. Moreover, disulphide engineering further enhanced the stability of the final vaccine protein. Additionally, Molecular docking analysis and Molecular Dynamics (MD) simulations confirmed the strong association between MEBV construct and human pathogenic immune receptor TLR-3. Repeated-exposure simulations and Immune simulations ensured the rapid antigen clearance and higher levels of cell-mediated immunity, respectively. Furthermore, MEBV codon optimization and in-silico cloning was carried out to confirm its augmented expression. Results of our experiments suggested that the proposed MEBV could be a potential immunogenic against HTLV-1; nevertheless, additional wet lab experiments are needed to elucidate our conclusion.
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Affiliation(s)
- Muhammad Hamza Tariq
- Atta ur Rehman School of Applied Bioscience, National University of Science and Technology, Islamabad, Pakistan
| | - Rashid Bhatti
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nida Fatima Ali
- Atta ur Rehman School of Applied Bioscience, National University of Science and Technology, Islamabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
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Echeverría N, Comas V, Aldunate F, Perbolianachis P, Moreno P, Cristina J. In the era of rapid mRNA-based vaccines: Why is there no effective hepatitis C virus vaccine yet? World J Hepatol 2021; 13:1234-1268. [PMID: 34786164 PMCID: PMC8568586 DOI: 10.4254/wjh.v13.i10.1234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/14/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is responsible for no less than 71 million people chronically infected and is one of the most frequent indications for liver transplantation worldwide. Despite direct-acting antiviral therapies fuel optimism in controlling HCV infections, there are several obstacles regarding treatment accessibility and reinfection continues to remain a possibility. Indeed, the majority of new HCV infections in developed countries occur in people who inject drugs and are more plausible to get reinfected. To achieve global epidemic control of this virus the development of an effective prophylactic or therapeutic vaccine becomes a must. The coronavirus disease 19 (COVID-19) pandemic led to auspicious vaccine development against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, which has renewed interest on fighting HCV epidemic with vaccination. The aim of this review is to highlight the current situation of HCV vaccine candidates designed to prevent and/or to reduce HCV infectious cases and their complications. We will emphasize on some of the crossroads encountered during vaccine development against this insidious virus, together with some key aspects of HCV immunology which have, so far, hampered the progress in this area. The main focus will be on nucleic acid-based as well as recombinant viral vector-based vaccine candidates as the most novel vaccine approaches, some of which have been recently and successfully employed for SARS-CoV-2 vaccines. Finally, some ideas will be presented on which methods to explore for the design of live-attenuated vaccines against HCV.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Victoria Comas
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | - Fabián Aldunate
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Paula Perbolianachis
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
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Sufyan M, Shahid F, Irshad F, Javaid A, Qasim M, Ashfaq UA. Implementation of Vaccinomics and In-Silico Approaches to Construct Multimeric Based Vaccine Against Ovarian Cancer. Int J Pept Res Ther 2021; 27:2845-2859. [PMID: 34690620 PMCID: PMC8524215 DOI: 10.1007/s10989-021-10294-w] [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] [Accepted: 09/28/2021] [Indexed: 11/03/2022]
Abstract
One of the most common gynecologic cancers is ovarian cancer and ranked third after the other two most common cancers: cervical and uterine. The highest mortality rate has been observed in the case of ovarian cancer. To treat ovarian cancer, an immune-informatics approach was used to design a multi-epitope vaccine (MEV) structure. Epitopes prediction of the cancer testis antigens (NY-ESO-1), A-Kinase anchor protein (AKAP4), Acrosin binding protein (ACRBP), Piwi-like protein (PIWIL3), and cancer testis antigen 2 (LAGE-1) was done. Non-toxic, highly antigenic, non-allergenic, and overlapping epitopes were shortlisted for vaccine construction. Chosen T-cell epitopes displayed a robust binding attraction with their corresponding Human Leukocyte Antigen (HLA) alleles demonstrated 97.59% of population coverage. The vaccine peptide was established by uniting three key constituents, comprising the 14 epitopes of CD8 + cytotoxic T lymphocytes (CTLs), 5 helper epitopes, and the adjuvant. For the generation of the effective response of CD4 + cells towards the T-helper cells, granulocyte–macrophage-colony-stimulating factor (GM-CSF) was applied. With the addition of adjuvants and linkers, the construct size was 547 amino acids. The developed MEV structure was predicted to be antigenic, non-toxic, non-allergenic, and firm in nature. I-tasser anticipated the 3D construction of MEV. Moreover, disulfide engineering further enhanced the stability of the final vaccine protein. In-silico cloning and vaccine codon optimization were done to analyze the up-regulation of its expression. The outcomes established the vaccine’s immunogenicity and safety profile, besides its aptitude to encourage both humoral and cellular immune responses. The offered vaccine, grounded on our in-silico investigation, may be considered for ovarian cancer immunotherapy.
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Affiliation(s)
- Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Faiza Irshad
- Environment Biotechnology Lab, Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Anam Javaid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
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Chand Y, Singh S. Prioritization of potential vaccine candidates and designing a multiepitope-based subunit vaccine against multidrug-resistant Salmonella Typhi str. CT18: A subtractive proteomics and immunoinformatics approach. Microb Pathog 2021; 159:105150. [PMID: 34425197 DOI: 10.1016/j.micpath.2021.105150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Salmonella enterica serovar Typhi (S. Typhi), a causative agent of typhoid fever, is a Gram-negative, human-restricted pathogen that causes significant morbidity and mortality, particularly in developing countries. The currently available typhoid vaccines are not recommended to children below six years of age and have poor long-term efficacy. Due to these limitations and the emerging threat of multidrug-resistance (MDR) strains, the development of a new vaccine is urgently needed. The present study aims to design a multiepitope-based subunit vaccine (MESV) against MDR S. Typhi str. CT18 using a computational-based approach comprising subtractive proteomics and immunoinformatics. Firstly, we investigated the proteome of S. Typhi str. CT18 using subtractive proteomics and identified twelve essential, virulent, host non-homologous, and antigenic outer membrane proteins (OMPs) as potential vaccine candidates with low transmembrane helices (≤1) and molecular weight (≤110 kDa). The OMPs were mapped for cytotoxic T lymphocyte(CTL) epitopes, helper T lymphocyte (HTL) epitopes, and linear B lymphocyte (LBL) epitopes using various immunoinformatics tools and servers. A total of 6, 12, and 11 CTL, HTL, and LBL epitopes were shortlisted, respectively, based on their immunogenicity, antigenicity, allergenicity, toxicity, and hydropathicity potential. Four MESV constructs (MESVCs), MESVC-1, MESVC-2, MESVC-3, and MESVC-4, were designed by linking the CTL, HTL, and LBL epitopes with immune-modulating adjuvants, linkers, and PADRE (Pan HLA DR-binding epitope) sequences. The MESVCs were evaluated for their physicochemical properties, allergenicity, antigenicity, toxicity, and solubility potential to ensure their safety and immunogenic behavior. Secondary and tertiary structures of shortlisted MESVCs (MESVC-1, MESVC-3, and MESVC-4) were predicted, modeled, refined, validated, and then docked with various MHC I, MHC II, and TLR4/MD2 complex. Molecular dynamics (MD) simulation of the final selected MESVC-4 with TLR4/MD2 complex confirms its binding affinity and stability. Codon optimization and in silico cloning verified the translation efficiency and successful expression of MESVC-4 in E. coli str. K12. Finally, the efficiency of MESVC-4 to trigger an effective immune response was assessed by an in silico immune simulation. In conclusion, our findings show that the designed MESVC-4 can elicit humoral and cellular immune responses, implying that it may be used for prophylactic or therapeutic purposes. Therefore, it should be subjected to further experimental validations.
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Affiliation(s)
- Yamini Chand
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Sachidanand Singh
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India; Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, 522213, Andhra Pradesh, India.
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Akbay B, Abidi SH, Ibrahim MAA, Mukhatayev Z, Ali S. Multi-Subunit SARS-CoV-2 Vaccine Design Using Evolutionarily Conserved T- and B- Cell Epitopes. Vaccines (Basel) 2021; 9:702. [PMID: 34206865 PMCID: PMC8310312 DOI: 10.3390/vaccines9070702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
The SARS-CoV-2 pandemic has created a public health crisis worldwide. Although vaccines against the virus are efficiently being rolled out, they are proving to be ineffective against certain emerging SARS-CoV-2 variants. The high degree of sequence similarity between SARS-CoV-2 and other human coronaviruses (HCoV) presents the opportunity for designing vaccines that may offer protection against SARS-CoV-2 and its emerging variants, with cross-protection against other HCoVs. In this study, we performed bioinformatics analyses to identify T and B cell epitopes originating from spike, membrane, nucleocapsid, and envelope protein sequences found to be evolutionarily conserved among seven major HCoVs. Evolutionary conservation of these epitopes indicates that they may have critical roles in viral fitness and are, therefore, unlikely to mutate during viral replication thus making such epitopes attractive candidates for a vaccine. Our designed vaccine construct comprises of twelve T and six B cell epitopes that are conserved among HCoVs. The vaccine is predicted to be soluble in water, stable, have a relatively long half-life, and exhibit low allergenicity and toxicity. Our docking results showed that the vaccine forms stable complex with toll-like receptor 4, while the immune simulations predicted that the vaccine may elicit strong IgG, IgM, and cytotoxic T cell responses. Therefore, from multiple perspectives, our multi-subunit vaccine design shows the potential to elicit a strong immune-protective response against SARS-CoV-2 and its emerging variants while carrying minimal risk for causing adverse effects.
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Affiliation(s)
- Burkitkan Akbay
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Zhussipbek Mukhatayev
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
| | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
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Naqvi STQ, Yasmeen M, Ismail M, Muhammad SA, Nawazish-i-Husain S, Ali A, Munir F, Zhang Q. Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9940010. [PMID: 34136576 PMCID: PMC8177976 DOI: 10.1155/2021/9940010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 05/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) infection is a public health epidemic, leading to around 3 million hospitalization and about 66,000 deaths each year. It is a life-threatening condition exclusive to children with no effective treatment. METHODS In this study, we used system-level and vaccinomics approaches to design a polyvalent vaccine for RSV, which could stimulate the immune components of the host to manage this infection. Our framework involves data accession, antigenicity and subcellular localization analysis, T cell epitope prediction, proteasomal and conservancy evaluation, host-pathogen-protein interactions, pathway studies, and in silico binding affinity analysis. RESULTS We found glycoprotein (G), fusion protein (F), and small hydrophobic protein (SH) of RSV as potential vaccine candidates. Of these proteins (G, F, and SH), we found 9 epitopes for multiple alleles of MHC classes I and II bear significant binding affinity. These potential epitopes were linked to form a polyvalent construct using AAY, GPGPG linkers, and cholera toxin B adjuvant at N-terminal with a 23.9 kDa molecular weight of 224 amino acid residues. The final construct was a stable, immunogenic, and nonallergenic protein containing cleavage sites, TAP transport efficiency, posttranslation shifts, and CTL epitopes. The molecular docking indicated the optimum binding affinity of RSV polyvalent construct with MHC molecules (-12.49 and -10.48 kcal/mol for MHC classes I and II, respectively). This interaction showed that a polyvalent construct could manage and control this disease. CONCLUSION Our vaccinomics and system-level investigation could be appropriate to trigger the host immune system to prevent RSV infection.
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Affiliation(s)
| | - Mamoona Yasmeen
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | - Mehreen Ismail
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | | | - Amjad Ali
- ASAB, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Fahad Munir
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
- Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - QiYu Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
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Tahir Ul Qamar M, Ahmad S, Fatima I, Ahmad F, Shahid F, Naz A, Abbasi SW, Khan A, Mirza MU, Ashfaq UA, Chen LL. Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches. Comput Biol Med 2021; 132:104389. [PMID: 33866250 DOI: 10.1016/j.compbiomed.2021.104389] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/27/2021] [Accepted: 04/07/2021] [Indexed: 01/28/2023]
Abstract
Staphylococcus aureus is a deadly human bacterial pathogen that causes a wide variety of clinical manifestations. Invasive S. aureus infections in hospitals and the community are one of the main causes of mortality and morbidity, as virulent and multi-drug-resistant strains have evolved. There is an unmet and urgent clinical need for immune-based non-antibiotic approaches to treat these infections as the growing antibiotic resistance poses a significant public health danger. Subtractive proteomics assisted reverse vaccinology-based immunoinformatics pipeline was used in this study to target the suitable antigenic proteins for the development of multi-epitope vaccine (MEV). Three essential virulent and antigenic proteins were identified including Glycosyltransferase, Elastin Binding Protein, and Staphylococcal secretory antigen. A variety of immunoinformatics tools have been used to forecast T-cell and B-cell epitopes from target proteins. Seven CTL, five HTL, and eight LBL epitopes, connected through suitable linkers and adjuvant, were employed to design 444 amino acids long MEV construct. The vaccine was paired with the TLR4 agonist 50S ribosomal protein L7/L12 adjuvant to enhance the immune response towards the vaccine. The predicted MEV structure was assessed to be highly antigenic, non-toxic, non-allergenic, flexible, stable, and soluble. Molecular docking simulation of the MEV with the human TLR4 (toll-like receptor 4) and major histocompatibility complex molecules (MHCI and MHCII) was performed to validate the interactions with the receptors. Molecular dynamics (MD) simulation and MMGBSA binding free energy analyses were carried out for the stability evaluation and binding of the MEV docked complexes with TLR4, MHCI and MHCII. To achieve maximal vaccine protein expression with optimal post-translational modifications, MEV was reverse translated, its mRNA structure was analyzed, and finally in silico cloning was performed into E. coli expression host. These rigorous computational analyses supported the effectivity of proposed MEV in protection against infections associated with S. aureus. However, further experimental validations are required to fully evaluate the potential of proposed vaccine candidate.
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Affiliation(s)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Israr Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Faisal Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, PR China.
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Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design. Vaccines (Basel) 2021; 9:vaccines9030293. [PMID: 33801143 PMCID: PMC8004085 DOI: 10.3390/vaccines9030293] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) causes chronic and acute hepatitis infections. As there is extreme variability in the HCV genome, no approved HCV vaccine has been available so far. An effective polypeptide vaccine based on the functionally conserved epitopes will be greatly helpful in curing disease. For this purpose, an immuno-informatics study is performed based on the published HCV subtype-3a from Pakistan. First, the virus genome was translated to a polyprotein followed by a subsequent prediction of T-cell epitopes. Non-allergenic, IFN-γ producer, and antigenic epitopes were shortlisted, including 5 HTL epitopes and 4 CTL, which were linked to the final vaccine by GPGPG and AAY linkers, respectively. Beta defensin was included as an adjuvant through the EAAAK linker to improve the immunogenicity of the polypeptide. To ensure its safety and immunogenicity profile, antigenicity, allergenicity, and various physiochemical attributes of the polypeptide were evaluated. Molecular docking was conducted between TLR4 and vaccine to evaluate the binding affinity and molecular interactions. For stability assessment and binding of the vaccine-TLR4 docked complex, molecular dynamics (MD) simulation and MMGBSA binding free-energy analyses were conducted. Finally, the candidate vaccine was cloned in silico to ensure its effectiveness. The current vaccine requires future experimental confirmation to validate its effectiveness. The vaccine construct produced might be useful in providing immune protection against HCV-related infections.
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Mahmood M, Javaid A, Shahid F, Ashfaq UA. Rational design of multimeric based subunit vaccine against Mycoplasma pneumonia: Subtractive proteomics with immunoinformatics framework. INFECTION GENETICS AND EVOLUTION 2021; 91:104795. [PMID: 33667723 DOI: 10.1016/j.meegid.2021.104795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/14/2021] [Accepted: 02/27/2021] [Indexed: 02/06/2023]
Abstract
Mycoplasma pneumoniae is the prevalent cause of acquired respiratory infections around the globe. A multi-epitope vaccine (MEV) must be developed to combat infections of M. pneumoniae because there is no specific disease-modifying treatment or vaccination is present. The objective of this research is to design a vaccine that targets M. pneumoniae top five highly antigenic proteins using a combination of immunological techniques and molecular docking. T-cell (HTL & CTL), B-cell, and IFN-γ of target proteins were forecasted and highly conservative epitopes were chosen for further study. For designing of final vaccine, 4LBL, 7CTL, and 5HTL epitopes were joined by linkers of KK, AAY, and GPGPG. The N-end of the vaccine was linked to an adjuvant (Cholera enterotoxin subunit B) with a linker named EAAAK to enhance immunogenicity. After the addition of adjuvants and linkers, the size of the construct was 395 amino acids. The epitopes of IFN-γ and B-cells illustrate that the model construct is optimized for cell-mediated immune or humoral responses. To ensure that the final design is safer and immunogenic, properties like non-allergens, antigenicity, and various physicochemical properties were evaluated. Molecular docking of the vaccine with the toll-like receptor 4 (TLR4) was conducted to check the compatibility of the vaccine with the receptor. Besides, in-silico cloning was utilized for validation of the credibility and proper expression of the vaccine. Furthermore, to confirm that the multi-epitope vaccine created is protective and immunogenic, this research requires experimental validation.
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Affiliation(s)
- Marvah Mahmood
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Anam Javaid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
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Mahdevar E, Safavi A, Abiri A, Kefayat A, Hejazi SH, Miresmaeili SM, Iranpur Mobarakeh V. Exploring the cancer-testis antigen BORIS to design a novel multi-epitope vaccine against breast cancer based on immunoinformatics approaches. J Biomol Struct Dyn 2021; 40:6363-6380. [PMID: 33599191 DOI: 10.1080/07391102.2021.1883111] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recently, cancer immunotherapy has gained lots of attention to replace the current chemoradiation approaches and multi-epitope cancer vaccines are manifesting as the next generation of cancer immunotherapy. Therefore, in this study, we used multiple immunoinformatics approaches along with other computational approaches to design a novel multi-epitope vaccine against breast cancer. The most immunogenic regions of the BORIS cancer-testis antigen were selected according to the binding affinity to MHC-I and II molecules as well as containing multiple cytotoxic T lymphocyte (CTL) epitopes by multiple immunoinformatics servers. The selected regions were linked together by GPGPG linker. Also, a T helper epitope (PADRE) and the TLR-4/MD-2 agonist (L7/L12 ribosomal protein from mycobacterium) were incorporated by A(EAAAK)3A linker to form the final vaccine construct. Then, its physicochemical properties, cleavage sites, TAP transport efficiency, B cell epitopes, IFN-γ inducing epitopes and population coverage were predicted. The final vaccine construct was reverse translated, codon-optimized and inserted into pcDNA3.1 to form the DNA vaccine. The final vaccine construct was a stable, immunogenic and non-allergenic protein that contained numerous CTL epitopes, IFN-γ inducing epitopes and several linear and conformational B cell epitopes. Also, the final vaccine construct formed stable and significant interactions with TLR-4/MD-2 complex according to molecular docking and dynamics simulations. Moreover, its world population coverage for HLA-I and HLA-II were about 93% and 96%, respectively. Taking together, these preliminary results can be used as an appropriate platform for further experimental investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Mohsen Miresmaeili
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
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Ashfaq UA, Saleem S, Masoud MS, Ahmad M, Nahid N, Bhatti R, Almatroudi A, Khurshid M. Rational design of multi epitope-based subunit vaccine by exploring MERS-COV proteome: Reverse vaccinology and molecular docking approach. PLoS One 2021; 16:e0245072. [PMID: 33534822 PMCID: PMC7857617 DOI: 10.1371/journal.pone.0245072] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Middle East respiratory syndrome (MERS-COV), first identified in Saudi Arabia, was caused by a novel strain of coronavirus. Outbreaks were recorded from different regions of the world, especially South Korea and the Middle East, and were correlated with a 35% mortality rate. MERS-COV is a single-stranded, positive RNA virus that reaches the host by binding to the receptor of dipeptidyl-peptides. Because of the unavailability of the vaccine available for the protection from MERS-COV infection, the rapid case detection, isolation, infection prevention has been recommended to combat MERS-COV infection. So, vaccines for the treatment of MERS-COV infection need to be developed urgently. A possible antiviral mechanism for preventing MERS-CoV infection has been considered to be MERS-CoV vaccines that elicit unique T-cell responses. In the present study, we incorporated both molecular docking and immunoinformatic approach to introduce a multiepitope vaccine (MEP) against MERS-CoV by selecting 15 conserved epitopes from seven viral proteins such as three structural proteins (envelope, membrane, and nucleoprotein) and four non-structural proteins (ORF1a, ORF8, ORF3, ORF4a). The epitopes, which were examined for non-homologous to host and antigenicity, were selected on the basis of conservation between T-cell, B-cell, and IFN-γ epitopes. The selected epitopes were then connected to the adjuvant (β-defensin) at the N-terminal through an AAY linker to increase the immunogenic potential. Structural modelling and physiochemical characteristic were applied to the vaccine construct developed. Afterwards the structure has been successfully docked with antigenic receptor, Toll-like receptor 3 (TLR-3) and in-silico cloning ensures that its expression efficiency is legitimate. Nonetheless the MEP presented needs tests to verify its safety and immunogenic profile.
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Affiliation(s)
- Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- * E-mail:
| | - Saman Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Rashid Bhatti
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan
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Shabani SH, Kardani K, Milani A, Bolhassani A. In Silico and in Vivo Analysis of HIV-1 Rev Regulatory Protein for Evaluation of a Multiepitope-based Vaccine Candidate. Immunol Invest 2021; 51:1-28. [PMID: 33416004 DOI: 10.1080/08820139.2020.1867163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In silico-designed multiepitope conserved regions of human immunodeficiency virus 1 (HIV-1) proteins would be a beneficial strategy for antigen design which induces effective anti-HIV-1 T-cell responses. The conserved multiple HLA-DR-binding epitopes of Rev protein were identified using IEDB MHC-I prediction tools and SYFPEITHI webserver to screen potential T-cell epitopes. We analyzed toxicity, allergenicity, immunogenicity, hemolytic activity, cross-reactivity, cell-penetrating peptide (CPP) potency, and molecular docking of the candidate epitopes using several immune-informatics tools. Afterward, we designed a novel multiepitope construct based on non-toxic and non-allergenic Rev, Nef, Gp160 and P24-derived cytotoxic T cell (CTL) and T-helper cell (HTL) epitopes. Next, the designed construct (Nef-Rev-Gp160-P24) was subjected to three B-cell epitope prediction webservers, ProtParam and Protein-Sol to obtain the physicochemical features. Then, the recombinant multiepitope DNA and polypeptide constructs were complexed with different CPPs for nanoparticle formation and pass them via the cell membranes. Finally, the immunogenicity of multiepitope constructs in a variety of modalities was evaluated in mice. The results demonstrated that groups immunized with heterologous DNA+ MPG or HR9 CPP prime/rNef-Rev-Gp160-P24 polypeptide + LDP-NLS CPP boost regimens could significantly produce higher levels of IFN-γ and Granzyme B, and lower amounts of IL-10 than other groups. Moreover, higher levels of IgG2a and IgG2b were observed in all heterologous prime-boost regimens than homologous DNA or polypeptide regimens. Altogether, the present findings indicated that the Nef-Rev-Gp160-P24 polypeptide meets the criteria to be potentially useful as a multiepitope-based vaccine candidate against HIV-1 infection.
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Affiliation(s)
- Samaneh H Shabani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Kimia Kardani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Alireza Milani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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A comprehensive screening of the whole proteome of hantavirus and designing a multi-epitope subunit vaccine for cross-protection against hantavirus: Structural vaccinology and immunoinformatics study. Microb Pathog 2020; 150:104705. [PMID: 33352214 DOI: 10.1016/j.micpath.2020.104705] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/18/2020] [Accepted: 12/10/2020] [Indexed: 11/23/2022]
Abstract
Hantaviruses are an emerging zoonotic group of rodent-borne viruses that are having serious implications on global public health due to the increase in outbreaks. Since there is no permanent cure, there is increasing interest in developing a vaccine against the hantavirus. This research aimed to design a robust cross-protective subunit vaccine using a novel immunoinformatics approach. After careful evaluation, the best predicted cytotoxic & helper T-cell and B-cell epitopes from nucleocapsid proteins, glycoproteins, RdRp proteins, and non-structural proteins were considered as potential vaccine candidates. Among the four generated vaccine models with different adjuvant, the model with toll-like receptor-4 (TLR-4) agonist adjuvant was selected because of its high antigenicity, non-allergenicity, and structural quality. The selected model was 654 amino acids long and had a molecular weight of 70.5 kDa, which characterizes the construct as a good antigenic vaccine candidate. The prediction of the conformational B-lymphocyte (CBL) epitope secured its ability to induce the humoral response. Thereafter, disulfide engineering improved vaccine stability. Afterwards, the molecular docking confirmed a good binding affinity of -1292 kj/mol with considered immune receptor TLR-4 and the dynamics simulation showed high stability of the vaccine-receptor complex. Later, the in silico cloning confirmed the better expression of the constructed vaccine protein in E. coli K12. Finally, in in silico immune simulation, significantly high levels of immunoglobulin M (IgM), immunoglobulin G1 (IgG1), cytotoxic & helper T lymphocyte (CTL & HTL) populations, and numerous cytokines such as interferon-γ (IFN-γ), interleukin-2 (IL-2) etc. were found as coherence with actual immune response and also showed faster antigen clearance for repeated exposures. Nonetheless, experimental validation can demonstrate the safety and cross-protective ability of the proposed vaccine to fight against hantavirus infection.
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Tahir ul Qamar M, Rehman A, Tusleem K, Ashfaq UA, Qasim M, Zhu X, Fatima I, Shahid F, Chen LL. Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. PLoS One 2020; 15:e0244176. [PMID: 33351863 PMCID: PMC7755200 DOI: 10.1371/journal.pone.0244176] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/04/2020] [Indexed: 01/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory coronavirus 2 (SARS-COV-2) is a significant threat to global health security. Till date, no completely effective drug or vaccine is available to cure COVID-19. Therefore, an effective vaccine against SARS-COV-2 is crucially needed. This study was conducted to design an effective multiepitope based vaccine (MEV) against SARS-COV-2. Seven highly antigenic proteins of SARS-COV-2 were selected as targets and different epitopes (B-cell and T-cell) were predicted. Highly antigenic and overlapping epitopes were shortlisted. Selected epitopes indicated significant interactions with the HLA-binding alleles and 99.93% coverage of the world's population. Hence, 505 amino acids long MEV was designed by connecting 16 MHC class I and eleven MHC class II epitopes with suitable linkers and adjuvant. MEV construct was non-allergenic, antigenic, stable and flexible. Furthermore, molecular docking followed by molecular dynamics (MD) simulation analyses, demonstrated a stable and strong binding affinity of MEV with human pathogenic toll-like receptors (TLR), TLR3 and TLR8. Finally, MEV codons were optimized for its in silico cloning into Escherichia coli K-12 system, to ensure its increased expression. Designed MEV in present study could be a potential candidate for further vaccine production process against COVID-19. However, to ensure its safety and immunogenic profile, the proposed MEV needs to be experimentally validated.
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Affiliation(s)
| | - Abdur Rehman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Xitong Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Israr Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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Behmard E, Soleymani B, Najafi A, Barzegari E. Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2. Sci Rep 2020; 10:20864. [PMID: 33257716 PMCID: PMC7704662 DOI: 10.1038/s41598-020-77547-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an acute pneumonic disease, with no prophylactic or specific therapeutical solution. Effective and rapid countermeasure against the spread of the disease’s associated virus, SARS-CoV-2, requires to incorporate the computational approach. In this study, we employed various immunoinformatics tools to design a multi-epitope vaccine polypeptide with the highest potential for activating the human immune system against SARS-CoV-2. The initial epitope set was extracted from the whole set of viral structural proteins. Potential non-toxic and non-allergenic T-cell and B-cell binding and cytokine inducing epitopes were then identified through a priori prediction. Selected epitopes were bound to each other with appropriate linkers, followed by appending a suitable adjuvant to increase the immunogenicity of the vaccine polypeptide. Molecular modelling of the 3D structure of the vaccine construct, docking, molecular dynamics simulations and free energy calculations confirmed that the vaccine peptide had high affinity for Toll-like receptor 3 binding, and that the vaccine-receptor complex was highly stable. As our vaccine polypeptide design captures the advantages of structural epitopes and simultaneously integrates precautions to avoid relevant side effects, it is suggested to be promising for elicitation of an effective and safe immune response against SARS-CoV-2 in vivo.
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Affiliation(s)
- Esmaeil Behmard
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Zakariya Razi Blvd., Kermanshah, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bijan Soleymani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Zakariya Razi Blvd., Kermanshah, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Zakariya Razi Blvd., Kermanshah, Iran.
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Soria ME, García-Crespo C, Martínez-González B, Vázquez-Sirvent L, Lobo-Vega R, de Ávila AI, Gallego I, Chen Q, García-Cehic D, Llorens-Revull M, Briones C, Gómez J, Ferrer-Orta C, Verdaguer N, Gregori J, Rodríguez-Frías F, Buti M, Esteban JI, Domingo E, Quer J, Perales C. Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection. J Clin Microbiol 2020; 58:JCM.01985-20. [PMID: 32999010 PMCID: PMC7685896 DOI: 10.1128/jcm.01985-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide resistance-associated substitutions (RAS), from 220 patients who failed therapy. They were present frequently in basal and posttreatment virus of patients who failed different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. They also have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value for treatment response, are discussed.
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Affiliation(s)
- María Eugenia Soria
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Brenda Martínez-González
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Qian Chen
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Damir García-Cehic
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Meritxell Llorens-Revull
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Astrobiología (CAB, CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L., Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
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Safavi A, Kefayat A, Mahdevar E, Abiri A, Ghahremani F. Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. Vaccine 2020; 38:7612-7628. [PMID: 33082015 PMCID: PMC7546226 DOI: 10.1016/j.vaccine.2020.10.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes a severe respiratory disease called COVID-19. Currently, global health is facing its devastating outbreak. However, there is no vaccine available against this virus up to now. In this study, a novel multi-epitope vaccine against SARS-CoV-2 was designed to provoke both innate and adaptive immune responses. The immunodominant regions of six non-structural proteins (nsp7, nsp8, nsp9, nsp10, nsp12 and nsp14) of SARS-CoV-2 were selected by multiple immunoinformatic tools to provoke T cell immune response. Also, immunodominant fragment of the functional region of SARS-CoV-2 spike (400-510 residues) protein was selected for inducing neutralizing antibodies production. The selected regions' sequences were connected to each other by furin-sensitive linker (RVRR). Moreover, the functional region of β-defensin as a well-known agonist for the TLR-4/MD complex was added at the N-terminus of the vaccine using (EAAAK)3 linker. Also, a CD4 + T-helper epitope, PADRE, was used at the C-terminal of the vaccine by GPGPG and A(EAAAK)2A linkers to form the final vaccine construct. The physicochemical properties, allergenicity, antigenicity, functionality and population coverage of the final vaccine construct were analyzed. The final vaccine construct was an immunogenic, non-allergen and unfunctional protein which contained multiple CD8 + and CD4 + overlapping epitopes, IFN-γ inducing epitopes, linear and conformational B cell epitopes. It could form stable and significant interactions with TLR-4/MD according to molecular docking and dynamics simulations. Global population coverage of the vaccine for HLA-I and II were estimated 96.2% and 97.1%, respectively. At last, the final vaccine construct was reverse translated to design the DNA vaccine. Although the designed vaccine exhibited high efficacy in silico, further experimental validation is necessary.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak School of Paramedicine, Arak University of Medical Sciences, Arak, Iran.
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Oladipo EK, Ajayi AF, Ariyo OE, Onile SO, Jimah EM, Ezediuno LO, Adebayo OI, Adebayo ET, Odeyemi AN, Oyeleke MO, Oyewole MP, Oguntomi AS, Akindiya OE, Olamoyegun BO, Aremu VO, Arowosaye AO, Aboderin DO, Bello HB, Senbadejo TY, Awoyelu EH, Oladipo AA, Oladipo BB, Ajayi LO, Majolagbe ON, Oyawoye OM, Oloke JK. Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100438. [PMID: 33043110 PMCID: PMC7533051 DOI: 10.1016/j.imu.2020.100438] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/27/2020] [Indexed: 01/07/2023] Open
Abstract
Stimulation and generation of T and B cell-mediated long-term immune response are essential for the curbing of a deadly virus such as SAR-CoV-2 (Severe Acute Respiratory Corona Virus 2). Immunoinformatics approach in vaccine design takes advantage of antigenic and non-allergenic epitopes present on the spike glycoprotein of SARS-CoV-2 to elicit immune responses. T cells and B cells epitopes were predicted, and the selected residues were subjected to allergenicity, antigenicity and toxicity screening which were linked by appropriate linkers to form a multi-epitope subunit vaccine. The physiochemical properties of the vaccine construct were analyzed, and the molecular weight, molecular formula, theoretical isoelectric point value, half-life, solubility score, instability index, aliphatic index and GRAVY were predicted. The vaccine structure was constructed, refined, validated, and disulfide engineered to get the best model. Molecular binding simulation and molecular dynamics simulation were carried out to predict the stability and binding affinity of the vaccine construct with TLRs. Codon acclimatization and in silico cloning were performed to confirm the vaccine expression and potency. Results obtained indicated that this novel vaccine candidate is non-toxic, capable of initiating the immunogenic response and will not induce an allergic reaction. The highest binding energy was observed in TLR4 (Toll-like Receptor 4) (−1398.1), and the least is TLR 2 (−1479.6). The steady rise in Th (T-helper) cell population with memory development was noticed, and IFN-g (Interferon gamma) was provoked after simulation. At this point, the vaccine candidate awaits animal trial to validate its efficacy and safety for use in the prevention of the novel COVID-19 (Coronavirus Disease 2019) infections.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Ayodeji Folorunsho Ajayi
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olumuyiwa Elijah Ariyo
- Department of Medicine, Infectious Diseases and Tropical Medicine Unit, Federal Teaching Hospital, Ido-Ekiti, Ekiti State, Nigeria
| | | | - Esther Moradeyo Jimah
- Department of Medical Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Oluwadunsin Iyanuoluwa Adebayo
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Emmanuel Tayo Adebayo
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Aduragbemi Noah Odeyemi
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Marvellous Oluwaseun Oyeleke
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | | | - Olawumi Elizabeth Akindiya
- Microbiology Programme, Department of Biological Science, Olusegun Agagu University of Science and Technology, Okitipupa, Ondo State, Nigeria
| | | | - Victoria Oyetayo Aremu
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Abiola O Arowosaye
- Department of Virology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | | | - Elukunbi Hilda Awoyelu
- Department of Natural Sciences, Precious Conerstone University, Ibadan, Oyo State, Nigeria
| | - Adio Abayomi Oladipo
- Department of Haematology and Blood Grouping Serology, Obafemi Awolowo Teaching Hospital Complex, Ile-Ife Wesley Guild Hospital Wing, Osun State, Nigeria
| | - Bukola Bisola Oladipo
- Department of Clinical Nursing, Bowen University Teaching Hospital, Ogbomoso, Oyo State, Nigeria
| | | | - Olusola Nathaniel Majolagbe
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olubukola Monisola Oyawoye
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Julius Kola Oloke
- Department of Natural Sciences, Precious Conerstone University, Ibadan, Oyo State, Nigeria
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Ismail S, Ahmad S, Azam SS. Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine. J Mol Liq 2020; 314:113612. [PMID: 32834259 PMCID: PMC7297697 DOI: 10.1016/j.molliq.2020.113612] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/14/2020] [Accepted: 06/14/2020] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health emergency of international concern and thus calling for the development of effective and safe therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for a vaccine, antibodies, and inhibitors development because of the many roles it plays in attachment, fusion and entry into the host cell. In the present investigation, we characterized the SARS-CoV-2 spike glycoprotein by immunoinformatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in aqueous milieu aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel axial frequency distribution (AFD) analytical tool. Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus could be considered in experimental studies.
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Affiliation(s)
- Saba Ismail
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
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Bhuiyan MA, Quayum ST, Ahammad F, Alam R, Samad A, Nain Z. Discovery of potential immune epitopes and peptide vaccine design - a prophylactic strategy against Rift Valley fever virus. F1000Res 2020. [DOI: 10.12688/f1000research.24975.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Rift Valley fever virus (RVFV) is an emerging arbovirus infecting both animals and humans. Any form of direct contact with body fluids, blood or tissue of infected animals is the mode of transmission of this pathogen. Despite being an emerging virus, no proper vaccinations are yet available for the public. Our objective is to compose a multiepitope vaccine utilizing immuno-bioinformatics as a strategy against RVFV. Methods: To identify immunodominant epitopes and design a potent vaccine candidate, we applied a series of immunoinformatic approaches with molecular dynamics and immune response simulation frameworks. Results: A glycoprotein with the highest antigenicity was selected and employed for determining promising epitopes. We selected T cell epitopes based on their immunological potencies and cytokine inducing properties, while B cell epitopes were selected based on their antigenic features. Finally, we selected four cytotoxic T-lymphocyte, two helper T-lymphocyte, and three linear B-lymphocyte epitopes that were arranged into a vaccine construct with appropriate adjuvants and linkers. The chimera protein was modeled, refined, and validated prior to docking against toll-like receptor 4. Docking studies suggest strong binding interactions while dynamics simulation revealed the stable nature of the docked complex. Furthermore, the immune simulation showed robust and prolonged immune responses with rapid antigen clearance. Finally, codon optimization and cloning conducted with Escherichia coli K12 suggests high translation efficiency within the host system. Conclusion: We believe that our designed multiepitope vaccine is a promising prophylactic candidate against RVFV pathogenesis.
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Designing an HCV diagnostic kit for common genotypes of the virus in Iran based on conserved regions of core, NS3-protease, NS4A/B, and NS5A/B antigens: an in silico approach. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00566-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kardani K, Bolhassani A, Namvar A. An overview of in silico vaccine design against different pathogens and cancer. Expert Rev Vaccines 2020; 19:699-726. [PMID: 32648830 DOI: 10.1080/14760584.2020.1794832] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Due to overcome the hardness of the vaccine design, computational vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing analysis, antigenicity analysis, population coverage, conservancy analysis, allergenicity assessment, toxicity prediction, and protein-peptide docking are important steps in the process of designing and developing potent vaccines against various viruses and cancers. In order to perform all of the analyses, several bioinformatics tools and online web servers have been developed. Scientists must take the decision to apply more suitable and precise servers for each part based on their accuracy. AREAS COVERED In this review, a wide-range list of different bioinformatics tools and online web servers has been provided. Moreover, some studies were proposed to show the importance of various bioinformatics tools for predicting and developing efficient vaccines against different pathogens including viruses, bacteria, parasites, and fungi as well as cancer. EXPERT OPINION Immunoinformatics is the best way to find potential vaccine candidates against different pathogens. Thus, the selection of the most accurate tools is necessary to predict and develop potent preventive and therapeutic vaccines. To further evaluation of the computational and in silico vaccine design, in vitro/in vivo analyses are required to develop vaccine candidates.
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Affiliation(s)
- Kimia Kardani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences , Tehran, Iran.,Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center , Tehran, Iran
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Zaheer T, Waseem M, Waqar W, Dar HA, Shehroz M, Naz K, Ishaq Z, Ahmad T, Ullah N, Bakhtiar SM, Muhammad SA, Ali A. Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences. PeerJ 2020; 8:e9541. [PMID: 32832263 PMCID: PMC7409810 DOI: 10.7717/peerj.9541] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The coronavirus SARS-CoV-2 is a member of the Coronaviridae family that has caused a global public health emergency. Currently, there is no approved treatment or vaccine available against it. The current study aimed to cover the diversity of SARS-CoV-2 strains reported from all over the world and to design a broad-spectrum multi-epitope vaccine using an immunoinformatics approach. METHODS For this purpose, all available complete genomes were retrieved from GISAID and NGDC followed by genome multiple alignments to develop a global consensus sequence to compare with the reference genome. Fortunately, comparative genomics and phylogeny revealed a significantly high level of conservation between the viral strains. All the Open Reading Frames (ORFs) of the reference sequence NC_045512.2 were subjected to epitope mapping using CTLpred and HLApred, respectively. The predicted CTL epitopes were then screened for antigenicity, immunogenicity and strong binding affinity with HLA superfamily alleles. HTL predicted epitopes were screened for antigenicity, interferon induction potential, overlapping B cell epitopes and strong HLA DR binding potential. The shortlisted epitopes were arranged into two multi-epitope sequences, Cov-I-Vac and Cov-II-Vac, and molecular docking was performed with Toll-Like Receptor 8 (TLR8). RESULTS The designed multi-epitopes were found to be antigenic and non-allergenic. Both multi-epitopes were stable and predicted to be soluble in an Escherichia coli expression system. The molecular docking with TLR8 also demonstrated that they have a strong binding affinity and immunogenic potential. These in silico analyses suggest that the proposed multi-epitope vaccine can effectively evoke an immune response.
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Affiliation(s)
- Tahreem Zaheer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Maaz Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Walifa Waqar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hamza Arshad Dar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Shehroz
- Department of Biotechnology, Virtual University of Pakistan, Peshawar, Pakistan
| | - Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Zaara Ishaq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tahir Ahmad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nimat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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Dong R, Chu Z, Yu F, Zha Y. Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches. Front Immunol 2020; 11:1784. [PMID: 32849643 PMCID: PMC7399176 DOI: 10.3389/fimmu.2020.01784] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/03/2020] [Indexed: 01/10/2023] Open
Abstract
COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1-14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded, positive (+) sense RNA beta coronavirus. The development of a vaccine for SARS-CoV-2 is an urgent need worldwide. Immunoinformatics approaches are both cost-effective and convenient, as in silico predictions can reduce the number of experiments needed. In this study, with the aid of immunoinformatics tools, we tried to design a multi-epitope vaccine that can be used for the prevention and treatment of COVID-19. The epitopes were computed by using B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) base on the proteins of SARS-CoV-2. A vaccine was devised by fusing together the B cell, HTL, and CTL epitopes with linkers. To enhance the immunogenicity, the β-defensin (45 mer) amino acid sequence, and pan-HLA DR binding epitopes (13aa) were adjoined to the N-terminal of the vaccine with the help of the EAAAK linker. To enable the intracellular delivery of the modeled vaccine, a TAT sequence (11aa) was appended to C-terminal. Linkers play vital roles in producing an extended conformation (flexibility), protein folding, and separation of functional domains, and therefore, make the protein structure more stable. The secondary and three-dimensional (3D) structure of the final vaccine was then predicted. Furthermore, the complex between the final vaccine and immune receptors (toll-like receptor-3 (TLR-3), major histocompatibility complex (MHC-I), and MHC-II) were evaluated by molecular docking. Lastly, to confirm the expression of the designed vaccine, the mRNA of the vaccine was enhanced with the aid of the Java Codon Adaptation Tool, and the secondary structure was generated from Mfold. Then we performed in silico cloning. The final vaccine requires experimental validation to determine its safety and efficacy in controlling SARS-CoV-2 infections.
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Affiliation(s)
- Rong Dong
- Department of Biomedicine, Guizhou University School of Medicine, Guiyang, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
| | - Zhugang Chu
- Department of Urinary Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Fuxun Yu
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
| | - Yan Zha
- Department of Biomedicine, Guizhou University School of Medicine, Guiyang, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
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Computational design of a potential multi-epitope subunit vaccine using immunoinformatics to fight Ebola virus. INFECTION GENETICS AND EVOLUTION 2020; 85:104464. [PMID: 32681997 DOI: 10.1016/j.meegid.2020.104464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/23/2020] [Accepted: 07/12/2020] [Indexed: 01/11/2023]
Abstract
Ebola virus (EBOV) is a rare but fatal disease that has been a burden to mankind for over 40 years. EBOV exhibits several symptoms including severe bleeding, organ failure and if left untreated causes death. It is assumed that fruit bats of the Pteropodidae family are natural hosts for the virus. Over the years, there has been no effective vaccine that can confer immunity to this virus. Considering the necessity of a vaccine against EBOV, this study to develop a multi-epitope subunit vaccine for the EBOV using the immunoinformatics approach was conducted. The construct was designed using structural and non-structural proteins of EBOV. Class I and Class II MHC epitopes were predicted and linked along with β defensin and compatible linkers. B-cell linear epitopes were also assessed and the physiological parameters of the vaccine were determined. The vaccine was capable of administration to humans and also is capable of an immune response. The vaccine was modeled further and affinity towards the TLR4 receptor was studied by docking and simulation for 20 ns. The trajectory analysis high affinity between the vaccine and the construct with an average hydrogen bond of 18. For ease of purification, the vaccine construct was ligated into pET28a(+) vector with His-tag. Concluding from the results, the vaccine construct has the potentiality to help develop immunity against the Ebola virus. Furthermore, experimental and immunological investigations will be required to verify the feasibility of the multi-epitope subunit construct as a commercial vaccine.
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Khalid H, Ashfaq UA. Exploring HCV genome to construct multi-epitope based subunit vaccine to battle HCV infection: Immunoinformatics based approach. J Biomed Inform 2020; 108:103498. [PMID: 32621883 DOI: 10.1016/j.jbi.2020.103498] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 05/03/2020] [Accepted: 06/25/2020] [Indexed: 01/16/2023]
Abstract
Hepatitis C Virus (HCV) infection is a major cause of chronic liver disease, hepatocellular carcinoma, and the single most common indication for liver transplantation. HCV vaccines eliciting specific T-cell responses, have been considered as potent method to prevent HCV infection. Despite several reports on progress of vaccine, these vaccine failed in mediating clinical relevance activity against HCV in humans. In this study we integrated both immunoinformatic and molecular docking approach to present a multiepitope vaccine against HCV by designating 17 conserved epitopes from eight viral proteins such as Core protein, E1, E2, NS2, NS34A, NS4B, NS5A, and NS5B. The epitopes were prioritized based on conservation among epitopes of T cell, B cell and IFN-γ that were then scanned for non-homologous to host and antigenicity. The prioritized epitopes were then linked together by AAY linker and adjuvant (β-defensin) were attached at N-terminal to enhance immunogenic potential. The construct thus formed were subjected to structural modeling and physiochemical characteristics. The modeled structure were successfully docked to antigenic receptor TLR-3 and In-silico cloning confers the authenticity of its expression efficiency. However, the proposed construct need to be validate experimentally to ensure its safety and immunogenic profile.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
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El-Tahan RR, Ghoneim AM, Zaghloul H. Dissection of two drug-targeted regions of Hepatitis C virus subtype 4a infecting Egyptian patients. Virus Genes 2020; 56:564-581. [PMID: 32572756 PMCID: PMC7307947 DOI: 10.1007/s11262-020-01776-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Recently, treatment of HCV infection has been improved after the development of direct acting antivirals (DAAs) which target different viral proteins (NS3-4A, NS5A and NS5B). The activity and effectiveness of these DAAs are affected by the presence of resistance associated substitutions (RASs). This study aimed to characterize HCV genotypes circulating among Egyptian HCV patients, to dissect the full sequences of HCV NS3-4A and NS5B regions, and to characterize RASs associated with NS3-4A and NS5B inhibitors in HCV treatment-naïve patients. Genotyping of 80 HCV samples from treatment-naïve patients was done using restriction fragment length polymorphism and phylogenetic analysis based on some full NS5B sequences. Results showed the prevalence of HCV subtype 4a. Twenty four new full sequences of NS3-4A and NS5B regions of subtype 4a were deposited in the GenBank database. In general, the substitutions associated with NS3-4A-targeting drugs were absent predicting possible responsiveness of Egyptian HCV patients to these drugs. In addition, the absence of amino acid substitutions associated with resistance to Sofosbuvir may predict good response to treatment with Sofosbuvir. Some amino acid substitutions associated with resistance to different classes of non-nucleoside inhibitors were detected. Further investigations on treated Egyptian HCV patients may evaluate the effectiveness of the massively used drugs. Many predicted T-cell-binding epitopes in NS3-4A and NS5B regions were found to be highly conserved in the currently studied isolates; a finding that might be important for HCV vaccine development. We demonstrated potential NS3 epitopes that could be used in engineering T cells against HCV epitopes.
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Affiliation(s)
- Radwa R El-Tahan
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt
| | - Ahmed M Ghoneim
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt.
| | - Hosam Zaghloul
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Sepulveda-Crespo D, Resino S, Martinez I. Innate Immune Response against Hepatitis C Virus: Targets for Vaccine Adjuvants. Vaccines (Basel) 2020; 8:vaccines8020313. [PMID: 32560440 PMCID: PMC7350220 DOI: 10.3390/vaccines8020313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Despite successful treatments, hepatitis C virus (HCV) infections continue to be a significant world health problem. High treatment costs, the high number of undiagnosed individuals, and the difficulty to access to treatment, particularly in marginalized susceptible populations, make it improbable to achieve the global control of the virus in the absence of an effective preventive vaccine. Current vaccine development is mostly focused on weakly immunogenic subunits, such as surface glycoproteins or non-structural proteins, in the case of HCV. Adjuvants are critical components of vaccine formulations that increase immunogenic performance. As we learn more information about how adjuvants work, it is becoming clear that proper stimulation of innate immunity is crucial to achieving a successful immunization. Several hepatic cell types participate in the early innate immune response and the subsequent inflammation and activation of the adaptive response, principally hepatocytes, and antigen-presenting cells (Kupffer cells, and dendritic cells). Innate pattern recognition receptors on these cells, mainly toll-like receptors, are targets for new promising adjuvants. Moreover, complex adjuvants that stimulate different components of the innate immunity are showing encouraging results and are being incorporated in current vaccines. Recent studies on HCV-vaccine adjuvants have shown that the induction of a strong T- and B-cell immune response might be enhanced by choosing the right adjuvant.
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Affiliation(s)
| | - Salvador Resino
- Correspondence: (S.R.); (I.M.); Tel.: +34-91-8223266 (S.R.); +34-91-8223272 (I.M.); Fax: +34-91-5097919 (S.R. & I.M.)
| | - Isidoro Martinez
- Correspondence: (S.R.); (I.M.); Tel.: +34-91-8223266 (S.R.); +34-91-8223272 (I.M.); Fax: +34-91-5097919 (S.R. & I.M.)
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Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets. Vaccines (Basel) 2020; 8:vaccines8020290. [PMID: 32526960 PMCID: PMC7350000 DOI: 10.3390/vaccines8020290] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/23/2022] Open
Abstract
A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design. Computational prediction of potential epitopes might significantly reduce the time required to screen peptide libraries as part of emergent vaccine design. In our present study, we used an extensive immunoinformatics-based approach to predict conserved immunodominant epitopes from the proteome of SARS-CoV-2. Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective antigens, and (iii) they were completely identical to experimentally validated epitopes of SARS-CoV. Further, structural and molecular docking analyses were performed in order to understand the binding interactions of the identified immunodominant epitopes with human major histocompatibility complexes (MHC). Our study provides a set of potential immunodominant epitopes that could enable the generation of both antibody- and cell-mediated immunity. This could contribute to developing peptide vaccine-based adaptive immunotherapy against SARS-CoV-2 infections and prevent future pandemic outbreaks.
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