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Srivastava S, Kolbe M. Novel "GaEl Antigenic Patches" Identified by a "Reverse Epitomics" Approach to Design Multipatch Vaccines against NIPAH Infection, a Silent Threat to Global Human Health. ACS OMEGA 2023; 8:31698-31713. [PMID: 37692250 PMCID: PMC10483669 DOI: 10.1021/acsomega.3c01909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Nipah virus (NiV) is a zoonotic virus that causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. Several NiV outbreaks have been reported since 1999 with nearly annual occurrences in Bangladesh. The outbreaks had high mortality rates ranging from 40 to 90%. No specific vaccine has yet been reported against NiV. Recently, several vaccine candidates and different designs of vaccines composed of epitopes against NiV were proposed. Most of the vaccines target single protein or protein complex subunits of the pathogen. The multiepitope vaccines proposed also cover a largely limited number of epitopes, and hence, their efficiency is still uncertain. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have utilized the "reverse epitomics" approach ("overlapping-epitope-clusters-to-patches" method) to identify "antigenic patches" (Ag-Patches) and utilize them as immunogenic composition for multipatch vaccine (MPV) design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties, and interaction with Toll-like receptor 3 ectodomain. In total, 30 CTL (cytotoxic T lymphocyte) and 27 HTL (helper T lymphocyte) antigenic patches were identified from the entire NiV proteome based on the clusters of overlapping epitopes. These identified Ag-Patches cover a total of discrete 362 CTL and 414 HTL epitopes from the entire proteome of NiV. The antigenic patches were utilized as immunogenic composition for the design of two CTL and two HTL multipatch vaccines. The 57 antigenic patches utilized here cover 776 overlapping epitopes targeting 52 different HLA class I and II alleles, providing a global ethnically distributed human population coverage of 99.71%. Such large number of epitope coverage resulting in large human population coverage cannot be reached with single-protein/subunit or multiepitope based vaccines. The reported antigenic patches also provide potential immunogenic composition for early detection diagnostic kits for NiV infection. Further, all the MPVs and Toll-like receptor ectodomain complexes show a stable nature of molecular interaction with numerous hydrogen bonds, salt bridges, and nonbounded contact formation and acceptable root mean square deviation and fluctuation. The cDNA analysis shows a favorable large-scale expression of the MPV constructs in a human cell line. By utilizing the novel "reverse epitomics" approach, highly immunogenic novel "GaEl antigenic patches" (GaEl Ag-Patches), a synonym term for "antigenic patches", were identified and utilized as immunogenic composition to design four MPVs against NiV. We conclude that the novel multipatch vaccines are potential candidates to combat NiV, with greater effectiveness, high specificity, and large human population coverage worldwide.
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Affiliation(s)
- Sukrit Srivastava
- Infection
Biology Group, Indian Foundation for Fundamental
Research Trust, Raebareli, Uttar Pradesh 229316, India
- Department
for Structural Infection Biology, Centre
for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection
Research, Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Kolbe
- Department
for Structural Infection Biology, Centre
for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection
Research, Notkestraße 85, 22607 Hamburg, Germany
- Faculty
of Mathematics, Informatics and Natural Sciences, University of Hamburg, Rothenbaumchaussee 19, 20148 Hamburg, Germany
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Srivastava S, Verma S, Kamthania M, Saxena AK, Pandey KC, Pande V, Kolbe M. Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health. PLoS One 2023; 18:e0282580. [PMID: 36920996 PMCID: PMC10016716 DOI: 10.1371/journal.pone.0282580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Nipah virus (NiV) is an emerging zoonotic virus that caused several serious outbreaks in the south asian region with high mortality rates ranging from 40 to 90% since 2001. NiV infection causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. No specific and effective vaccine has yet been reported against NiV. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have designed two Multi-Epitope Vaccines (MEVs) composed of 33 Cytotoxic T lymphocyte (CTL) epitopes and 38 Helper T lymphocyte (HTL) epitopes. Out of those CTL and HTL combined 71 epitopes, 61 novel epitopes targeting nine different NiV proteins were not used before for vaccine design. Codon optimization for the cDNA of both the designed MEVs might ensure high expression potential in the human cell line as stable proteins. Both MEVs carry potential B cell linear epitope overlapping regions, B cell discontinuous epitopes as well as IFN-γ inducing epitopes. Additional criteria such as sequence consensus amongst CTL, HTL and B Cell epitopes was implemented for the design of final constructs constituting MEVs. Hence, the designed MEVs carry the potential to elicit cell-mediated as well as humoral immune response. Selected overlapping CTL and HTL epitopes were validated for their stable molecular interactions with HLA class I and II alleles and in case of CTL epitopes with human Transporter Associated with antigen Processing (TAP) cavity. The structure based epitope cross validation for interaction with TAP cavity was used as another criteria choosing final epitopes for NiV MEVs. Finally, human Beta-defensin 2 and Beta-defensin 3 were used as adjuvants to enhance the immune response of both the MEVs. Molecular dynamics simulation studies of MEVs-TLR3 ectodomain (Human Toll-Like Receptor 3) complex indicated the stable molecular interaction. We conclude that the MEVs designed and in silico validated here could be highly potential vaccine candidates to combat NiV infections, with great effectiveness, high specificity and large human population coverage worldwide.
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Affiliation(s)
- Sukrit Srivastava
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- * E-mail: (SS); (MK)
| | - Sonia Verma
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Kailash C. Pandey
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Kumaun University, Bheemtal, Nainital, Uttarakhand, India
| | - Michael Kolbe
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
- * E-mail: (SS); (MK)
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Srivastava S, Verma S, Kamthania M, Agarwal D, Saxena AK, Kolbe M, Singh S, Kotnis A, Rathi B, Nayar SA, Shin HJ, Vashisht K, Pandey KC. Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide. J Biomol Struct Dyn 2022; 40:2369-2388. [PMID: 33155524 PMCID: PMC7651196 DOI: 10.1080/07391102.2020.1838329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, 'overlapping-epitope-clusters-to-patches' method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as 'Ag-Patch or Ag-Patches', for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sukrit Srivastava
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Sonia Verma
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Deepa Agarwal
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Michael Kolbe
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bhopal, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Bhopal, India
| | - Brijesh Rathi
- Laboratory For Translational Chemistry and Drug Discovery, Hansraj College, University of Delhi, New Delhi, India
| | - Seema A. Nayar
- Department of Microbiology, Government Medical College, Trivandrum, India
- Department of Microbiology, Sree Gokulam Medical College, Trivandrum, India
| | - Ho-Joon Shin
- Department of Microbiology, School of Medicine, Ajou University, Suwon, South Korea
| | - Kapil Vashisht
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Kailash C. Pandey
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
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Srivastava S, Chatziefthymiou SD, Kolbe M. Vaccines Targeting Numerous Coronavirus Antigens, Ensuring Broader Global Population Coverage: Multi-epitope and Multi-patch Vaccines. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2410:149-175. [PMID: 34914046 DOI: 10.1007/978-1-0716-1884-4_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronaviruses are causative agents of different zoonosis including SARS, MERS, or COVID-19 in humans. The high transmission rate of coronaviruses, the time-consuming development of efficient anti-infectives and vaccines, the possible evolutionary adaptation of the virus to conventional vaccines, and the challenge to cover broad human population worldwide are the major reasons that made it challenging to avoid coronaviruses outbreaks. Although, a plethora of different approaches are being followed to design and develop vaccines against coronaviruses, most of them target subunits, full-length single, or only a very limited number of proteins. Vaccine targeting multiple proteins or even the entire proteome of the coronavirus is yet to come. In the present chapter, we will be discussing multi-epitope vaccine (MEV) and multi-patch vaccine (MPV) approaches to design and develop efficient and sustainably successful strategies against coronaviruses. MEV and MPV utilize highly conserved, potentially immunogenic epitopes and antigenic patches, respectively, and hence they have the potential to target large number of coronavirus proteins or even its entire proteome, allowing us to combat the challenge of its evolutionary adaptation. In addition, the large number of human leukocyte antigen (HLA) alleles targeted by the chosen specific epitopes enables MEV and MPV to cover broader global population.
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Affiliation(s)
- Sukrit Srivastava
- Infection Biology Group, Indian Foundation for Fundamental Research, Raebareli, Uttar Pradesh, India.
| | - Spyros D Chatziefthymiou
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany
| | - Michael Kolbe
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany. .,MIN-Faculty University Hamburg, Hamburg, Germany.
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Bahiri-Elitzur S, Tuller T. Codon-based indices for modeling gene expression and transcript evolution. Comput Struct Biotechnol J 2021; 19:2646-2663. [PMID: 34025951 PMCID: PMC8122159 DOI: 10.1016/j.csbj.2021.04.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 11/21/2022] Open
Abstract
Codon usage bias (CUB) refers to the phenomena that synonymous codons are used in different frequencies in most genes and organisms. The general assumption is that codon biases reflect a balance between mutational biases and natural selection. Today we understand that the codon content is related and can affect all gene expression steps. Starting from the 1980s, codon-based indices have been used for answering different questions in all biomedical fields, including systems biology, agriculture, medicine, and biotechnology. In general, codon usage bias indices weigh each codon or a small set of codons to estimate the fitting of a certain coding sequence to a certain phenomenon (e.g., bias in codons, adaptation to the tRNA pool, frequencies of certain codons, transcription elongation speed, etc.) and are usually easy to implement. Today there are dozens of such indices; thus, this paper aims to review and compare the different codon usage bias indices, their applications, and advantages. In addition, we perform analysis that demonstrates that most indices tend to correlate even though they aim to capture different aspects. Due to the centrality of codon usage bias on different gene expression steps, it is important to keep developing new indices that can capture additional aspects that are not modeled with the current indices.
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Affiliation(s)
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
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Srivastava S, Verma S, Kamthania M, Kaur R, Badyal RK, Saxena AK, Shin HJ, Kolbe M, Pandey KC. Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2020; 1:e19371. [PMID: 32776022 PMCID: PMC7370533 DOI: 10.2196/19371] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND The novel coronavirus disease (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to the ongoing 2019-2020 pandemic. SARS-CoV-2 is a positive-sense single-stranded RNA coronavirus. Effective countermeasures against SARS-CoV-2 infection require the design and development of specific and effective vaccine candidates. OBJECTIVE To address the urgent need for a SARS-CoV-2 vaccine, in the present study, we designed and validated one cytotoxic T lymphocyte (CTL) and one helper T lymphocyte (HTL) multi-epitope vaccine (MEV) against SARS-CoV-2 using various in silico methods. METHODS Both designed MEVs are composed of CTL and HTL epitopes screened from 11 Open Reading Frame (ORF), structural and nonstructural proteins of the SARS-CoV-2 proteome. Both MEVs also carry potential B-cell linear and discontinuous epitopes as well as interferon gamma-inducing epitopes. To enhance the immune response of our vaccine design, truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 was used as an adjuvant at the N termini of both MEVs. The tertiary models for both the designed MEVs were generated, refined, and further analyzed for stable molecular interaction with toll-like receptor 3. Codon-biased complementary DNA (cDNA) was generated for both MEVs and analyzed in silico for high level expression in a mammalian (human) host cell line. RESULTS In the present study, we screened and shortlisted 38 CTL, 33 HTL, and 12 B cell epitopes from the 11 ORF protein sequences of the SARS-CoV-2 proteome. Moreover, the molecular interactions of the screened epitopes with their respective human leukocyte antigen allele binders and the transporter associated with antigen processing (TAP) complex were positively validated. The shortlisted screened epitopes were utilized to design two novel MEVs against SARS-CoV-2. Further molecular models of both MEVs were prepared, and their stable molecular interactions with toll-like receptor 3 were positively validated. The codon-optimized cDNAs of both MEVs were also positively analyzed for high levels of overexpression in a human cell line. CONCLUSIONS The present study is highly significant in terms of the molecular design of prospective CTL and HTL vaccines against SARS-CoV-2 infection with potential to elicit cellular and humoral immune responses. The epitopes of the designed MEVs are predicted to cover the large human population worldwide (96.10%). Hence, both designed MEVs could be tried in vivo as potential vaccine candidates against SARS-CoV-2.
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Affiliation(s)
- Sukrit Srivastava
- Infection Biology Group, Department of Biotechnology, Mangalayatan University, Aligarh, India
- Molecular Medicine Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Sonia Verma
- Parasite-Host Biology Group, Protein Biochemistry and Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Department of Biotechnology, Institute of Applied Medicines and Research, Ghaziabad, India
| | - Rupinder Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar, India
| | | | - Ajay Kumar Saxena
- Molecular Medicine Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Ho-Joon Shin
- Department of Microbiology, School of Medicine, Ajou University, Suwon, Gyeonggi-do, Republic of Korea
| | - Michael Kolbe
- Centre for Structural Systems Biology, Department for Structural Infection Biology, Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Kailash C Pandey
- Parasite-Host Biology Group, Protein Biochemistry and Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
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Srivastava S, Kamthania M, Kumar Pandey R, Kumar Saxena A, Saxena V, Kumar Singh S, Kumar Sharma R, Sharma N. Design of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics. J Biomol Struct Dyn 2019; 37:4345-4360. [PMID: 30457455 DOI: 10.1080/07391102.2018.1548977] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Severe acute respiratory syndrome (SARS) is endemic in South China and is continuing to spread worldwide since the 2003 outbreak, affecting human population of 37 countries till present. SARS is caused by the severe acute respiratory syndrome Coronavirus (SARS-CoV). In the present study, we have designed two multi-epitope vaccines (MEVs) composed of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell epitopes overlap, bearing the potential to elicit cellular as well as humoral immune response. We have used truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 as molecular adjuvants at N-terminal of both the MEVs. Selected overlapping epitopes of both the MEVs were further validated for stable molecular interactions with their respective human leukocyte antigen class I and II allele binders. Moreover, CTL epitopes were further studied for their molecular interaction with transporter associated with antigen processing. Furthermore, after tertiary structure modelling, both the MEVs were validated for their stable molecular interaction with Toll-like receptors 2 and 4. Codon-optimized cDNA of both the MEVs was analysed for their potential high level of expression in the mammalian cell line (Human) needed for their further in vivo testing. Overall, the present study proposes in silico validated design of two MEVs against SARS composed of specific epitopes with the potential to cause a high level of SARS-CoV specific cellular as well as humoral immune response. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sukrit Srivastava
- Department of Biotechnology, Mangalayatan University , Aligarh , India.,Molecular Medicine Lab, School of Life Science, Jawaharlal Nehru University , New Delhi , India
| | - Mohit Kamthania
- Department of Biotechnology, Mangalayatan University , Aligarh , India.,Department of Biotechnology, Faculty of Life Sciences, Institute of Applied Medicines and Research , Ghaziabad , India
| | - Rajesh Kumar Pandey
- Center of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University , Varanasi , India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab, School of Life Science, Jawaharlal Nehru University , New Delhi , India
| | - Vaishali Saxena
- Molecular Medicine Lab, School of Life Science, Jawaharlal Nehru University , New Delhi , India
| | - Santosh Kumar Singh
- Center of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University , Varanasi , India
| | | | - Nishi Sharma
- Department of Biotechnology, Mangalayatan University , Aligarh , India
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Srivastava S, Kamthania M, Singh S, Saxena AK, Sharma N. Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach. Infect Drug Resist 2018; 11:2377-2391. [PMID: 30538505 PMCID: PMC6254671 DOI: 10.2147/idr.s175114] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Middle East respiratory syndrome (MERS) is caused by MERS coronavirus (MERS-CoV). Thus
far, MERS outbreaks have been reported from Saudi Arabia (2013 and 2014) and South Korea
(2015). No specific vaccine has yet been reported against MERS. Purpose To address the urgent need for an MERS vaccine, in the present study, we have designed
two multi-epitope vaccines (MEVs) against MERS utilizing several in silico methods and
tools. Methods The design of both the multi-epitope vaccines (MEVs) are composed of cytotoxic T
lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes, screened form thirteen
different proteins of MERS-CoV. Both the MEVs also carry potential B-cell linear epitope
regions, B-cell discontinuous epitopes as well as interferon-γ-inducing
epitopes. Human β-defensin-2 and β-defensin-3 were used as adjuvants to
enhance the immune response of MEVs. To design the MEVs, short peptide molecular linkers
were utilized to link screened most potential CTL epitopes, HTL epitopes and the
adjuvants. Tertiary models for both the MEVs were generated, refined, and further
studied for their molecular interaction with toll-like receptor 3. The cDNAs of both
MEVs were generated and analyzed in silico for their expression in a mammalian host cell
line (human). Results Screened CTL and HTL epitopes were found to have high propensity for stable molecular
interaction with HLA alleles molecules. CTL epitopes were also found to have favorable
molecular interaction within the cavity of transporter associated with antigen
processing. The selected CTL and HTL epitopes jointly cover upto 94.0% of worldwide
human population. Both the CTL and HTL MEVs molecular models have shown to have stable
binding and complex formation propensity with toll-like receptor 3. The cDNA analysis of
both the MEVs have shown high expression tendency in mammalian host cell line
(human). Conclusion After multistage in silico analysis, both the MEVs are predicted to elicit humoral as
well as cell mediated immune response. Epitopes of the designed MEVs are predicted to
cover large human population worldwide. Hence both the designed MEVs could be tried in
vivo as potential vaccine candidates against MERS.
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Affiliation(s)
- Sukrit Srivastava
- Department of Biotechnology, Mangalayatan University, Aligarh, India, .,Molecular Medicine Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India,
| | - Mohit Kamthania
- Department of Biotechnology, Mangalayatan University, Aligarh, India, .,Department of Biotechnology, Faculty of Life Sciences, Institute of Applied Medicines and Research, Ghaziabad, Uttar Pradesh, India
| | - Soni Singh
- Department of Biotechnology, Mangalayatan University, Aligarh, India,
| | - Ajay K Saxena
- Molecular Medicine Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India,
| | - Nishi Sharma
- Department of Biotechnology, Mangalayatan University, Aligarh, India,
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9
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Liu A, Feng R, Liang B. Microbial surface displaying formate dehydrogenase and its application in optical detection of formate. Enzyme Microb Technol 2016; 91:59-65. [DOI: 10.1016/j.enzmictec.2016.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 01/15/2023]
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10
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Gaunt E, Wise HM, Zhang H, Lee LN, Atkinson NJ, Nicol MQ, Highton AJ, Klenerman P, Beard PM, Dutia BM, Digard P, Simmonds P. Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection. eLife 2016; 5:e12735. [PMID: 26878752 PMCID: PMC4798949 DOI: 10.7554/elife.12735] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/15/2016] [Indexed: 01/09/2023] Open
Abstract
Previously, we demonstrated that frequencies of CpG and UpA dinucleotides profoundly influence the replication ability of echovirus 7 (Tulloch et al., 2014). Here, we show that that influenza A virus (IAV) with maximised frequencies of these dinucleotides in segment 5 showed comparable attenuation in cell culture compared to unmodified virus and a permuted control (CDLR). Attenuation was also manifested in vivo, with 10-100 fold reduced viral loads in lungs of mice infected with 200PFU of CpG-high and UpA-high mutants. However, both induced powerful inflammatory cytokine and adaptive (T cell and neutralising antibody) responses disproportionate to their replication. CpG-high infected mice also showed markedly reduced clinical severity, minimal weight loss and reduced immmunopathology in lung, yet sterilising immunity to lethal dose WT challenge was achieved after low dose (20PFU) pre-immunisation with this mutant. Increasing CpG dinucleotide frequencies represents a generic and potentially highly effective method for generating safe, highly immunoreactive vaccines.
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Affiliation(s)
- Eleanor Gaunt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen M Wise
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Huayu Zhang
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Lian N Lee
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicky J Atkinson
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Marlynne Quigg Nicol
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew J Highton
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Philippa M Beard
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernadette M Dutia
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Digard
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Tulloch F, Atkinson NJ, Evans DJ, Ryan MD, Simmonds P. RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies. eLife 2014; 3:e04531. [PMID: 25490153 PMCID: PMC4383024 DOI: 10.7554/elife.04531] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.
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Affiliation(s)
- Fiona Tulloch
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Nicky J Atkinson
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin D Ryan
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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Han HW, Bae SH, Jung YH, Moon J. Genome-wide characterization of the relationship between essential and TATA-containing genes. FEBS Lett 2013; 587:444-51. [DOI: 10.1016/j.febslet.2012.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/18/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022]
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Diene SM, Merhej V, Henry M, El Filali A, Roux V, Robert C, Azza S, Gavory F, Barbe V, La Scola B, Raoult D, Rolain JM. The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle. Mol Biol Evol 2012; 30:369-83. [PMID: 23071100 DOI: 10.1093/molbev/mss236] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepancies of this bacterium and show that its core genome originates from another genus, Klebsiella. Atypical characteristics of this bacterium (i.e., motility, presence of ornithine decarboxylase, and lack of urease activity) are attributed to genomic mosaicism, by acquisition of additional genes, such as the complete 60,582 bp flagellar assembly operon acquired "en bloc" from the genus Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative plasmid shows that it is a chimera of transposons and integrative conjugative elements from various bacterial origins, resembling a rhizome. Moreover, we demonstrate biologically that a G53S mutation in the pmrA gene results in colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA operons and 87 cognate tRNAs that have the ability to translate transferred genes that use different codons, as exemplified by the significantly different codon usage between genes from the core genome and the "mobilome." On the basis of our findings, the evolution of this bacterium to become a "killer bug" with new genomic repertoires was from three criteria that are "opportunity, power, and usage" to indicate a sympatric lifestyle: "opportunity" to meet other bacteria and exchange foreign sequences since this bacteria was similar to sympatric bacteria; "power" to integrate these foreign sequences such as the acquisition of several mobile genetic elements (plasmids, integrative conjugative element, prophages, transposons, flagellar assembly system, etc.) found in his genome; and "usage" to have the ability to translate these sequences including those from rare codons to serve as a translator of foreign languages.
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Affiliation(s)
- Seydina M Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UMR7278 CNRS-IRD-INSERM, IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
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