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Dang M, Wu LJ, Zhang SR, Zhu JR, Hu YZ, Yang CX, Zhang XY. MS2 Virus-like Particles as a Versatile Peptide Presentation Platform: Insights into the Deterministic Abilities for Accommodating Heterologous Peptide Lengths. ACS Synth Biol 2023; 12:3704-3715. [PMID: 37946498 PMCID: PMC10729756 DOI: 10.1021/acssynbio.3c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Virus-like particles (VLPs) are nanostructures with the potential to present heterologous peptides at high density, thereby triggering heightened immunogenicity. RNA bacteriophage MS2 VLPs are a compelling delivery platform among them. However, a notable hurdle arises from the immune response toward MS2 coat protein, swiftly eliminating subsequent vaccinations via the same vector. Although larger inserts effectively mask carrier epitopes, current research predominantly focuses on displaying short conserved peptides (<30 aa). A systematic evaluation regarding the deterministic ability of MS2 VLPs as a platform for presenting heterologous peptides remains a gap. In light of this, we employed the "single-chain dimer" paradigm to scrutinize the tolerance of MS2 VLPs for peptide/protein insertions. The results unveiled functional MS2 VLP assembly solely for inserts smaller than 91 aa. Particularly noteworthy is the largest insertion achieved on the MS2 VLPs to date: the RNA helicase A (RHA) dsRNA-binding domains (dsRBD1). Attempts to introduce additional linkers or empty coat subunits fail to augment the expression level or assembly of the MS2 VLPs displaying dsRBD1, affirming 91 aa as the upper threshold for exogenous protein presentation. By illuminating the precise confines of MS2 VLPs in accommodating distinct peptide lengths, our study informs the selection of appropriate peptide and protein dimensions. This revelation not only underscores the scope of MS2 VLPs but also establishes a pivotal reference point, facilitating the strategic manipulation of MS2 VLPs to design next-generation epitope/antibody-based therapeutics.
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Affiliation(s)
- Mei Dang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
- Department
of Biological Sciences, Faculty of Science, National University of Singapore, 10 Keng Ridge Crescent, 119260, Singapore
| | - Long J. Wu
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Si R. Zhang
- Xi’an
Middle School of Shaanxi Province, Fengcheng Wulu 69, Weiyang, Xi’an 710006, China
- Department
of Genetics, Stanford University, Palo Alto, California 94304, United States
- HSS,
Stanford University, Palo Alto, California 94305, United States
| | - Jian R. Zhu
- School of
Pharmacy, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yu Z. Hu
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Chen X. Yang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Xiao Y. Zhang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
- Centre
of Molecular & Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal
- Department
of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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2
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Jain M, Patil N, Gor D, Sharma MK, Goel N, Kaushik P. Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages. Proteomes 2022; 10:34. [PMID: 36278694 PMCID: PMC9624331 DOI: 10.3390/proteomes10040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The novel SARS-CoV-2 variant, Omicron (B.1.1.529), is being testified, and the WHO has characterized Omicron as a variant of concern due to its higher transmissibility and very contagious behavior, immunization breakthrough cases. Here, the comparative proteomic study has been conducted on spike-protein, hACE2 of five lineages (α, β, δ, γ and Omicron. The docking was performed on spike protein- hACE-2 protein using HADDOCK, and PRODIGY was used to analyze the binding energy affinity using a reduced Haddock score. Followed by superimposition in different variant-based protein structures and calculated the esteem root mean square deviation (RMSD). This study reveals that Omicron was seen generating a monophyletic clade. Further, as α variant is the principal advanced strain after Wuhan SARS-CoV-2, and that is the reason it was showing the least likeness rate with the Omicron and connoting Omicron has developed of late with the extreme number of mutations. α variant has shown the highest binding affinity with hACE2, followed by β strain, and followed with γ. Omicron showed a penultimate binding relationship, while the δ variant was seen as having the least binding affinity. This proteomic basis in silico analysis of variable spike proteins of variants will impart light on the development of vaccines and the identification of mutations occurring in the upcoming variants.
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Affiliation(s)
- Mukul Jain
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
- Lab 209—Cell & Developmental Biology, Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Nil Patil
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
- Lab 209—Cell & Developmental Biology, Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Darshil Gor
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
| | - Mohit Kumar Sharma
- School of Molecular Medicine, Medical University of Warsaw, ul. Żwirki i Wigury 61, 02-091 Warsaw, Poland;
- Malopolska Center of Biotechnology, 30-387 Krakow, Poland
| | - Neha Goel
- Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
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3
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Shishir TA, Jannat T, Naser IB. An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant. PLoS One 2022; 17:e0266844. [PMID: 35446879 PMCID: PMC9022835 DOI: 10.1371/journal.pone.0266844] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 01/16/2023] Open
Abstract
The emergence of Omicron (B.1.1.529), a new Variant of Concern in the COVID-19 pandemic, while accompanied by the ongoing Delta variant infection, has once again fueled fears of a new infection wave and global health concern. In the Omicron variant, the receptor-binding domain (RBD) of its spike glycoprotein is heavily mutated, a feature critical for the transmission rate of the virus by interacting with hACE2. In this study, we used a combination of conventional and advanced neural network-based in silico approaches to predict how these mutations would affect the spike protein. The results demonstrated a decrease in the electrostatic potentials of residues corresponding to receptor recognition sites, an increase in the alkalinity of the protein, a change in hydrophobicity, variations in functional residues, and an increase in the percentage of alpha-helix structure. Moreover, several mutations were found to modulate the immunologic properties of the potential epitopes predicted from the spike protein. Our next step was to predict the structural changes of the spike and their effect on its interaction with the hACE2. The results revealed that the RBD of the Omicron variant had a higher affinity than the reference. Moreover, all-atom molecular dynamics simulations concluded that the RBD of the Omicron variant exhibits a more dispersed interaction network since mutations resulted in an increased number of hydrophobic interactions and hydrogen bonds with hACE2.
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Affiliation(s)
- Tushar Ahmed Shishir
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
- Rangamati General Hospital, Chattogram, Bangladesh
| | - Taslimun Jannat
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Iftekhar Bin Naser
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
- * E-mail:
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4
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Gerstweiler L, Bi J, Middelberg APJ. Virus-like particle preparation is improved by control over capsomere-DNA interactions during chromatographic purification. Biotechnol Bioeng 2021; 118:1707-1720. [PMID: 33484156 DOI: 10.1002/bit.27687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022]
Abstract
Expression of viral capsomeres in bacterial systems and subsequent in vitro assembly into virus-like particles is a possible pathway for affordable future vaccines. However, purification is challenging as viral capsomeres show poor binding to chromatography media. In this study, the behavior of capsomeres in unfractionated bacterial lysate was compared with that for purified capsomeres, with or without added microbial DNA, to better understand reasons for poor bioprocess behavior. We show that aggregates or complexes form through the interaction between viral capsomeres and DNA, especially in bacterial lysates rich in contaminating DNA. The formation of these complexes prevents the target protein capsomeres from accessing the pores of chromatography media. We find that protein-DNA interactions can be modulated by controlling the ionic strength of the buffer and that at elevated ionic strengths the protein-DNA complexes dissociate. Capsomeres thus released show enhanced bind-elute behavior on salt-tolerant chromatography media. DNA could therefore be efficiently removed. We believe this is the first report of the use of an optimized salt concentration that dissociates capsomere-DNA complexes yet enables binding to salt-tolerant media. Post purification, assembly experiments indicate that DNA-protein interactions can play a negative role during in vitro assembly, as DNA-protein complexes could not be assembled into virus-like particles, but formed worm-like structures. This study reveals that the control over DNA-protein interaction is a critical consideration during downstream process development for viral vaccines.
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Affiliation(s)
- Lukas Gerstweiler
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia, Australia
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Saeng‐chuto K, Jermsutjarit P, Stott CJ, Vui DT, Tantituvanont A, Nilubol D. Retrospective study, full-length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in Vietnam. Transbound Emerg Dis 2020; 67:183-198. [PMID: 31469947 PMCID: PMC7168546 DOI: 10.1111/tbed.13339] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 12/16/2022]
Abstract
Increased evidence of porcine deltacoronavirus (PDCoV) causing diarrhoea in pigs has been reported in several countries worldwide. The virus has currently evolved into three separated groups including US, China and Southeast Asia (SEA) groups. In Vietnam, PDCoV was first reported in 2015. Based on phylogenetic analyses of spike, membrane and nucleocapsid genes, it is suggested that Vietnam PDCoV is chimeric virus. In the present study, we retrospectively investigated the presence of PDCoV in Vietnam and the full-length genomes of six PDCoV isolates identified in 2014-2016 were further characterized. The results demonstrated that Vietnam PDCoV was first detected as early as 2014. All six Vietnam PDCoV are in the SEA group and further divided into two separated subgroups including SEA-1 and SEA-2. Vietnam PDCoV in SEA-2 was closely related to Thai and Lao PDCoV. Recombination analysis demonstrated that three isolates in SEA-1 were a chimeric virus of which P12_14_VN_0814, the first Vietnam isolate, and US PDCoV isolates were major and minor parents, respectively. The recombination was further evaluated by phylogenetic construction based on 3 recombinant fragments. The first and third fragments, closely related to P12_14_VN_0814, were associated with ORF1a/1b and N genes, respectively. The second fragment, associated with S, E, and M genes, was closely related to US PDCoV isolates. High antigenic and hydrophobic variations were detected in S1 protein. Three-day-old pigs challenged with the chimeric virus displayed clinical diseases and villus atrophy. In conclusion, Vietnam PDCoV is genetically diverse influenced by an external introduction from neighbouring countries. The chimeric Vietnam PDCoV can induce a disease similar to Thai PDCoV.
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Affiliation(s)
- Kepalee Saeng‐chuto
- Department of Veterinary MicrobiologyFaculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
| | - Patumporn Jermsutjarit
- Department of Veterinary MicrobiologyFaculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
| | - Christopher J. Stott
- Department of Veterinary MicrobiologyFaculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
| | - Dam Thi Vui
- Virology SectionDepartment of Animal HealthNational Center for Veterinary DiagnosisHanoiVietnam
| | - Angkana Tantituvanont
- Department of Pharmaceutics and Industrial PharmacyFaculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand
| | - Dachrit Nilubol
- Department of Veterinary MicrobiologyFaculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
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6
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Balke I, Zeltins A. Use of plant viruses and virus-like particles for the creation of novel vaccines. Adv Drug Deliv Rev 2019; 145:119-129. [PMID: 30172923 DOI: 10.1016/j.addr.2018.08.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 07/24/2018] [Accepted: 08/27/2018] [Indexed: 12/15/2022]
Abstract
In recent decades, the development of plant virology and genetic engineering techniques has resulted in the construction of plant virus-based vaccines for protection against different infectious agents, cancers and autoimmune diseases in both humans and animals. Interaction studies between plant viruses and mammalian organisms have suggested that plant viruses and virus-like particles (VLPs) are safe and noninfectious to humans and animals. Plant viruses with introduced antigens are powerful vaccine components due to their strongly organized, repetitive spatial structure; they can elicit strong immune responses similar to those observed with infectious mammalian viruses. The analysis of published data demonstrated that at least 73 experimental vaccines, including 61 prophylactic and 12 therapeutic vaccines, have been constructed using plant viruses as a carrier structure for presentation of different antigens. This information clearly demonstrates that noninfectious viruses are also applicable as vaccine carriers. Moreover, several plant viruses have been used for platform development, and corresponding vaccines are currently being tested in human and veterinary clinical trials. This review therefore discusses the main principles of plant VLP vaccine construction, emphasizing the physical, chemical, genetic and immunological aspects. Results of the latest studies suggest that several plant virus-based vaccines will join the list of approved human and animal vaccines in the near future.
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Affiliation(s)
- Ina Balke
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia
| | - Andris Zeltins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia.
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Shi W, Zhao L, Xu Y, Xu G, Zeng Y. Identification of mimotope of Mycoplasma pneumoniae P1 protein and its potential value in serodiagnosis. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1638299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Wenyuan Shi
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Lanhua Zhao
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, PR China
| | - Yujuan Xu
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Guizhen Xu
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, PR China
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