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Application of reverse vaccinology for designing of an mRNA vaccine against re-emerging marine birnavirus affecting fish species. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Du Y, Xu J. Engineered Bifunctional Proteins for Targeted Cancer Therapy: Prospects and Challenges. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103114. [PMID: 34585802 DOI: 10.1002/adma.202103114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/08/2021] [Indexed: 06/13/2023]
Abstract
Bifunctional proteins (BFPs) are a class of therapeutic agents produced through genetic engineering and protein engineering, and are increasingly used to treat various human diseases, including cancer. These proteins usually have two or more biological functions-specifically recognizing different molecular targets to regulate the related signaling pathways, or mediating effector molecules/cells to kill tumor cells. Unlike conventional small-molecule or single-target drugs, BFPs possess stronger biological activity but lower systemic toxicity. Hence, BFPs are considered to offer many benefits for the treatment of heterogeneous tumors. In this review, the authors briefly describe the unique structural feature of BFP molecules and innovatively divide them into bispecific antibodies, cytokine-based BFPs (immunocytokines), and protein toxin-based BFPs (immunotoxins) according to their mode of action. In addition, the latest advances in the development of BFPs are discussed and the potential limitations or problems in clinical applications are outlined. Taken together, future studies need to be centered on understanding the characteristics of BFPs for optimizing and designing more effective such drugs.
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Affiliation(s)
- Yue Du
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jian Xu
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20892, USA
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Xiong N, Xie D, Dong Y, Xue YP, Zheng YG. Efficient biosynthesis of 1-cyanocyclohexaneacetic acid using a highly soluble nitrilase by N-terminus modification of novel peptide tags. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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54
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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: 8] [Impact Index Per Article: 2.7] [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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55
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Aldakheel FM, Abrar A, Munir S, Aslam S, Allemailem KS, Khurshid M, Ashfaq UA. Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens. Vaccines (Basel) 2021; 9:1079. [PMID: 34696187 PMCID: PMC8539331 DOI: 10.3390/vaccines9101079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
C. perfringens is a highly versatile bacteria of livestock and humans, causing enteritis (a common food-borne illness in humans), enterotoxaemia (in which toxins are formed in the intestine which damage and destroy organs, i.e., the brain), and gangrene (wound infection). There is no particular cure for the toxins of C. perfringens. Supportive care (medical control of pain, intravenous fluids) is the standard treatment. Therefore, a multiple-epitope vaccine (MEV) should be designed to battle against C. perfringens infection. Furthermore, the main objective of this in silico investigation is to design an MEV that targets C. perfringens. For this purpose, we selected the top three proteins that were highly antigenic using immuno-informatics approaches, including molecular docking. B-cells, IFN-gamma, and T cells for target proteins were predicted and the most conserved epitopes were selected for further investigation. For the development of the final MEV, epitopes of LBL5, CTL17, and HTL13 were linked to GPGPG, AAY, and KK linkers. The vaccine N-end was joined to an adjuvant through an EAAK linker to improve immunogenicity. After the attachment of linkers and adjuvants, the final construct was 415 amino acids. B-cell and IFN-gamma epitopes demonstrate that the model structure is enhanced for humoral and cellular immune responses. To validate the immunogenicity and safety of the final construct, various physicochemical properties, and other properties such as antigenicity and non-allergens, were evaluated. Furthermore, molecular docking was carried out for verification of vaccine compatibility with the receptor, evaluated in silico. Also, in silico cloning was employed for the verification of the proper expression and credibility of the construct.
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Affiliation(s)
- Fahad M. Aldakheel
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11564, Saudi Arabia;
| | - Amna Abrar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Sehar Aslam
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad 38000, Pakistan;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
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56
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Zou J, Jing H, Zhang X, Liu Y, Zhao Z, Duan L, Yuan Y, Chen Z, Gou Q, Xiong Q, Li S, Yang F, Zeng H, Zou Q, Zhang J. α-Hemolysin-Aided Oligomerization of the Spike Protein RBD Resulted in Improved Immunogenicity and Neutralization Against SARS-CoV-2 Variants. Front Immunol 2021; 12:757691. [PMID: 34630436 PMCID: PMC8497984 DOI: 10.3389/fimmu.2021.757691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
The increase in confirmed COVID-19 cases and SARS-CoV-2 variants calls for the development of safe and broad cross-protective vaccines. The RBD of the spike protein was considered to be a safe and effective candidate antigen. However, the low immunogenicity limited its application in vaccine development. Herein, we designed and obtained an RBD heptamer (mHla-RBD) based on a carrier protein-aided assembly strategy. The molecular weight of mHla-RBD is up to 450 kDa, approximately 10 times higher than that of the RBD monomer. When formulated with alum adjuvant, mHla-RBD immunization significantly increased the immunogenicity of RBD, as indicated by increased titers of RBD-specific antibodies, neutralizing antibodies, Th2 cellular immune response, and pseudovirus neutralization activity, when compared to RBD monomer. Furthermore, we confirmed that RBD-specific antibodies predominantly target conformational epitopes, which was approximately 200 times that targeting linear epitopes. Finally, a pseudovirus neutralization assay revealed that neutralizing antibodies induced by mHla-RBD against different SARS-CoV-2 variants were comparable to those against the wild-type virus and showed broad-spectrum neutralizing activity toward different SARS-CoV-2 variants. Our results demonstrated that mHla-RBD is a promising candidate antigen for development of SARS-CoV-2 vaccines and the mHla could serve as a universal carrier protein for antigen design.
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Affiliation(s)
- Jintao Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Haiming Jing
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Xiaoli Zhang
- Department of Clinical Hematology, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Yiheng Liu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Zhuo Zhao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Lianli Duan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Yue Yuan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Zhifu Chen
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Qiang Gou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Qingshan Xiong
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Sisi Li
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Feng Yang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
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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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58
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Immunoinformatics Approach to Design Multi-Epitope- Subunit Vaccine against Bovine Ephemeral Fever Disease. Vaccines (Basel) 2021; 9:vaccines9080925. [PMID: 34452050 PMCID: PMC8402647 DOI: 10.3390/vaccines9080925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bovine ephemeral fever virus (BEFV) is an overlooked pathogen, recently gaining widespread attention owing to its associated enormous economic impacts affecting the global livestock industries. High endemicity with rapid spread and morbidity greatly impacts bovine species, demanding adequate attention towards BEFV prophylaxis. Currently, a few suboptimum vaccines are prevailing, but were confined to local strains with limited protection. Therefore, we designed a highly efficacious multi-epitope vaccine candidate targeted against the geographically distributed BEFV population. By utilizing immunoinformatics technology, all structural proteins were targeted for B- and T-cell epitope prediction against the entire allele population of BoLA molecules. Prioritized epitopes were adjoined by linkers and adjuvants to effectively induce both cellular and humoral immune responses in bovine. Subsequently, the in silico construct was characterized for its physicochemical parameters, high immunogenicity, least allergenicity, and non-toxicity. The 3D modeling, refinement, and validation of ligand (vaccine construct) and receptor (bovine TLR7) then followed molecular docking and molecular dynamic simulation to validate their stable interactions. Moreover, in silico cloning of codon-optimized vaccine construct in the prokaryotic expression vector (pET28a) was explored. This is the first time HTL epitopes have been predicted using bovine datasets. We anticipate that the designed construct could be an effective prophylactic remedy for the BEF disease that may pave the way for future laboratory experiments.
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59
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Wu M, Tao M, Wang Q, Lu X, Yuan H. Fusion proteins of biologic agents in the treatment of rheumatoid arthritis (RA): A network meta-analysis. Medicine (Baltimore) 2021; 100:e26350. [PMID: 34128886 PMCID: PMC8213327 DOI: 10.1097/md.0000000000026350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND To evaluate the efficacy of fusion proteins biologics (Etanercept (ETN), Anakinra (ANA), and Abatacept) combinations in the treatment of rheumatoid arthritis (RA) using network meta-analysis to rank those according to their performance medicines. The performance of these processes is ranked according to the results of the analysis and an explanatory study of the possible results is carried out. METHODS Multiple databases including PubMed, EMBASE, and Cochrane Library were used to identify applicable articles and collect relevant data to analyze using STATA (14.0) software. The literature included in this study was divided into a combination of a placebo, methotrexate (MTX), and an observation group (1 of the 3 drugs). The last search date was December 12, 2019. RESULTS A total of 19 eligible randomized controlled trials of fusion proteins biologics were identified, a total of 1109 papers were included, and the results showed that the ETN + MTX had the highest probability of being the most clinically efficacious intervention, with a surface under the cumulative ranking curve of 91.6, was significantly superior (P < .05). Patients who had received ETN or ETN + MTX or ANA had effective compared with patients who had received placebo (95% CI 1.28%-8.47%; 1.92%-19.18%; 1.06%-10.45%). CONCLUSIONS 1. The combination of ETN and MTX had the highest probability of optimal treatment compared to other drugs and 2. ENT, ENT + MTX, and ANA were effective in the treatment of RA compared to placebo.
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Affiliation(s)
- Mingcai Wu
- Department of Biochemistry and Molecular Biology
| | - Mengjun Tao
- Department of Epidemiology and Biostatistics
| | - Quanhai Wang
- Department of Biochemistry and Molecular Biology
| | - Xiaohua Lu
- Functional experiment and training center, School of Public Health, Wannan Medical College, Wuhu, China
| | - Hui Yuan
- Department of Epidemiology and Biostatistics
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Obaidullah AJ, Alanazi MM, Alsaif NA, Albassam H, Almehizia AA, Alqahtani AM, Mahmud S, Sami SA, Emran TB. Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. RSC Adv 2021; 11:18103-18121. [PMID: 35480208 PMCID: PMC9033181 DOI: 10.1039/d1ra02885e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a contagious respiratory tract infection that has become a global burden since the end of 2019. Notably, fewer patients infected with SARS-CoV-2 progress from acute disease onset to death compared with the progression rate associated with two other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Several research organizations and pharmaceutical industries have attempted to develop successful vaccine candidates for the prevention of COVID-19. However, increasing evidence indicates that the SARS-CoV-2 genome undergoes frequent mutation; thus, an adequate analysis of the viral strain remains necessary to construct effective vaccines. The current study attempted to design a multi-epitope vaccine by utilizing an approach based on the SARS-CoV-2 structural proteins. We predicted the antigenic T- and B-lymphocyte responses to four structural proteins after screening all structural proteins according to specific characteristics. The predicted epitopes were combined using suitable adjuvants and linkers, and a secondary structure profile indicated that the vaccine shared similar properties with the native protein. Importantly, the molecular docking analysis and molecular dynamics simulations revealed that the constructed vaccine possessed a high affinity for toll-like receptor 4 (TLR4). In addition, multiple descriptors were obtained from the simulation trajectories, including the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (R g), demonstrating the rigid nature and inflexibility of the vaccine and receptor molecules. In addition, codon optimization, based on Escherichia coli K12, was used to determine the GC content and the codon adaptation index (CAI) value, which further followed for the incorporation into the cloning vector pET28+(a). Collectively, these findings suggested that the constructed vaccine could be used to modulate the immune reaction against SARS-CoV-2.
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Affiliation(s)
- Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hussam Albassam
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University Abha 62529 Saudi Arabia
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi Rajshahi 6205 Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong Chittagong 4331 Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh Chittagong 4381 Bangladesh
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61
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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: 74] [Impact Index Per Article: 24.7] [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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Han YY, Yue HY, Zhang XY, Lyu YM, Liu L, Voglmeir J. Construction and Evaluation of Peptide-Linked Lactobacillus brevis β-Galactosidase Heterodimers. Protein Pept Lett 2021; 28:221-228. [PMID: 32798366 DOI: 10.2174/0929866527666200813201242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND β-galactosidases are enzymes that are utilized to hydrolyze lactose into galactose and glucose, and are is widely used in the food industry. OBJECTIVE We describe the recombinant expression of an unstudied, heterodimeric β-galactosidase originating from Lactobacillus brevis ATCC 367 in Escherichia coli. Furthermore, six different constructs, in which the two protein subunits were fused with different peptide linkers, were also investigated. METHODS The heterodimeric subunits of the β-galactosidase were cloned in expressed in various expression constructs, by using either two vectors for the independent expression of each subunit, or using a single Duet vector for the co-expression of the two subunits. RESULTS The co-expression in two independent expression vectors only resulted in low β-galactosidase activities, whereas the co-expression in a single Duet vector of the independent and fused subunits increased the β-galactosidase activity significantly. The recombinant β-galactosidase showed comparable hydrolyzing properties towards lactose, N-acetyllactosamine, and pNP-β-D-galactoside. CONCLUSION The usability of the recombinant L. brevis β-galactosidase was further demonstrated by the hydrolysis of human, bovine, and goat milk samples. The herein presented fused β-galactosidase constructs may be of interest for analytical research as well as in food- and biotechnological applications.
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Affiliation(s)
- Yuan-Yuan Han
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hai-Yun Yue
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yang Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yong-Mei Lyu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Almofti YA, Abd-Elrahman KA, Eltilib EEM. Vaccinomic approach for novel multi epitopes vaccine against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). BMC Immunol 2021; 22:22. [PMID: 33765919 PMCID: PMC7992937 DOI: 10.1186/s12865-021-00412-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/10/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The spread of a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in China and other countries is of great concern worldwide with no effective vaccine. This study aimed to design a novel vaccine construct against SARS-CoV-2 from the spike S protein and orf1ab polyprotein using immunoinformatics tools. The vaccine was designed from conserved epitopes interacted against B and T lymphocytes by the combination of highly immunogenic epitopes with suitable adjuvant and linkers. RESULTS The proposed vaccine composed of 526 amino acids and was shown to be antigenic in Vaxigen server (0.6194) and nonallergenic in Allertop server. The physiochemical properties of the vaccine showed isoelectric point of 10.19. The instability index (II) was 31.25 classifying the vaccine as stable. Aliphatic index was 84.39 and the grand average of hydropathicity (GRAVY) was - 0.049 classifying the vaccine as hydrophilic. Vaccine tertiary structure was predicted, refined and validated to assess the stability of the vaccine via Ramachandran plot and ProSA-web servers. Moreover, solubility of the vaccine construct was greater than the average solubility provided by protein sol and SOLpro servers indicating the solubility of the vaccine construct. Disulfide engineering was performed to reduce the high mobile regions in the vaccine to enhance stability. Docking of the vaccine construct with TLR4 demonstrated efficient binding energy with attractive binding energy of - 338.68 kcal/mol and - 346.89 kcal/mol for TLR4 chain A and chain B respectively. Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells and INF-γ. Upon cloning, the vaccine protein was reverse transcribed into DNA sequence and cloned into pET28a(+) vector to ensure translational potency and microbial expression. CONCLUSION A unique vaccine construct from spike S protein and orf1ab polyprotein against B and T lymphocytes was generated with potential protection against the pandemic. The present study might assist in developing a suitable therapeutics protocol to combat SARSCoV-2 infection.
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Affiliation(s)
- Yassir A Almofti
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan.
| | - Khoubieb Ali Abd-Elrahman
- Department of Pharmaceutical Technology, College of Pharmacy, University of Medical Science and Technology (MUST), Khartoum, Sudan
| | - Elsideeq E M Eltilib
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
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64
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Dzayee SA, Khudhur PK, Mahmood A, Markov A, Maseleno A, Ebrahimpour Gorji A. Computational design of a new multi-epitope vaccine using immunoinformatics approach against mastitis disease. Anim Biotechnol 2021; 33:1359-1370. [PMID: 33761829 DOI: 10.1080/10495398.2021.1899937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mastitis disease causes significant economic losses in dairy farms by reducing milk production, increasing production costs, and reducing milk quality. Streptococcus agalactiae continues to be a major cause of mastitis in dairy cattle. To date, there has been no approved multi-epitope vaccine against this pathogen in the market. In the present study, an efficient multi-epitope vaccine against S. agalactiae, the causative agent of mastitis, was designed using various immonoinformtics approaches. Potential epitopes were selected from Sip protein to improve vaccine immunogenicity. The designed vaccine is more antigenic in nature. Then, linkers and profilin adjuvant were added to enhance the immunity of vaccines. The designed vaccine was evaluated in terms of molecular weight, PI, immunogenicity, Toxicity, and allergenicity. Prediction of three-dimensional (3 D) structure of multi-epitope vaccine, followed by refinement and validation, was conducted to obtain a high-quality 3 D structure of the designed multi-epitope vaccine. The designed vaccine was then subjected to molecular docking with Toll-like receptor 11 (TLR11) receptor to evaluate its binding efficiency followed by dynamic simulation for stable interaction. In silico cloning approach was carried out to improve the expression of the vaccine construct. These analyses indicate that the designed multi-epitope vaccine may produce particular immune responses against S. agalactiae and may be further helpful to control mastitis after in vitro and in vivo immunological assays.
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Affiliation(s)
- Shireen Ahmed Dzayee
- Medical Microbiology Unit, Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq
| | - Pinar Khalid Khudhur
- Medical Microbiology Unit, Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq
| | - Arshad Mahmood
- School of Management, University Sains Malaysia, Penang, Malaysia
| | - Alexander Markov
- Department of Medical Prevention and Rehabilitation, Institute of Continuing Professional Education Tyumen State Medical University, Tyumen, Russian Federation
| | - Andino Maseleno
- Department of Information Systems, STMIK Pringsewu, Lampung, Indonesia
| | - Abdolvahab Ebrahimpour Gorji
- Department of Fisheries, Faculty of Animal Sciences and Fisheries, Sari Agricultural and Natural Resources University, Sari, Iran
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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: 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: 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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66
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Abass OA, Timofeev VI, Sarkar B, Onobun DO, Ogunsola SO, Aiyenuro AE, Aborode AT, Aigboje AE, Omobolanle BN, Imolele AG, Abiodun AA. Immunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria. J Biomol Struct Dyn 2021; 40:7283-7302. [PMID: 33719908 DOI: 10.1080/07391102.2021.1896387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lassa mammarenavirus (LASMV) is responsible for a specific type of acute viral hemorrhagic fever known as Lassa fever. Lack of effective treatments and counter-measures against the virus has resulted in a high mortality rate in its endemic regions. Therefore, in this study, a novel epitope-based vaccine has been designed using the methods of immunoinformatics targeting the glycoprotein and nucleoprotein of the virus. After numerous robust analyses, two CTL epitopes, eight HTL epitopes and seven B-cell epitopes were finally selected for constructing the vaccine. All these most promising epitopes were found to be antigenic, non-allergenic, nontoxic and non-human homolog, which made them suitable for designing the subunit vaccine. Furthermore, the selected T-cell epitopes which were found to be fully conserved across different isolates of the virus, were also considered for final vaccine construction. After that, numerous validation experiments, i.e. molecular docking, molecular dynamics simulation and immune simulation were conducted, which predicted that our designed vaccine should be stable within the biological environment and effective in combating the LASMV infection. In the end, codon adaptation and in silico cloning studies were performed to design a recombinant plasmid for producing the vaccine industrially. However, further in vitro and in vivo assessments should be done on the constructed vaccine to finally confirm its safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ohilebo Abdulateef Abass
- Department of Bioinformatics & Computational Biology, Centre for BioCode, Benin, Nigeria.,Department of Biochemistry, Faculty of Life Sciences, Ambrose Alli University, Ekpoma, Nigeria
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Bishajit Sarkar
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Desmond Odiamehi Onobun
- Department of Bioinformatics & Computational Biology, Centre for BioCode, Benin, Nigeria.,Department of Biochemistry, Faculty of Life Sciences, Ambrose Alli University, Ekpoma, Nigeria
| | | | | | - Abdullahi Tunde Aborode
- Research & Development, Shaping Women in STEM (SWIS) Africa, Lagos, Nigeria.,Research & Development, Healthy Africans Platform, Ibadan, Nigeria
| | | | | | | | - Alade Adebowale Abiodun
- Bio-Computing Research Unit, Molecular Biology & Simulations (Mols & Sims) Centre, Ado-Ekiti, Nigeria
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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: 14] [Impact Index Per Article: 4.7] [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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68
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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: 76] [Impact Index Per Article: 19.0] [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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69
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Li D, Ren J, Ji F, Peng Q, Teng H, Jia L. Peptide Linker Affecting the Activity Retention Rate of VHH in Immunosorbents. Biomolecules 2020; 10:biom10121610. [PMID: 33261088 PMCID: PMC7760621 DOI: 10.3390/biom10121610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
VHH-based immunosorbents are an emerging and promising tool for the removal of toxic substances from plasma. However, the small size of VHHs is a double-edged sword, bringing both benefits and drawbacks to the immunosorbent. The small size of the VHH allows a higher coupling density, while the closer distance to the resin might create steric hindrance for paratope access. The latter could be avoided by inserting a linker between the VHH and the gel attachment site. Here, we report an approach to improve the activity retention of the immobilized VHH by selecting suitable linkers between the VHH and the site-specific immobilization site on the resin. Seven peptide linkers differing in length and flexibility were fused to the VHH and contained the formylglycine generating enzyme (FGE) recognition sequence. These constructs were expressed in the cytoplasm of bacteria and purified, the VHH production yield and affinity for its cognate antigen was measured. Furthermore, the fGly conversion, the immobilization of the aldehyde-containing nanobodies, the immobilization on resin and the antigen binding activity of the VHH-based immunoadsorbents was monitored. The VHH with longer and rigid, proline-rich linkers exhibited good expression yield of approximately 160 mg/L of culture, a fGly conversion of up to 100%, and the highest activity retention rate of more than 68%. This study unveiled two suitable linkers for the preparation of VHH-based immunosorbents that will assist the development of their clinical application.
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70
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Improved linalool production in Saccharomyces cerevisiae by combining directed evolution of linalool synthase and overexpression of the complete mevalonate pathway. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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71
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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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72
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Samad A, Ahammad F, Nain Z, Alam R, Imon RR, Hasan M, Rahman MS. Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach. J Biomol Struct Dyn 2020; 40:14-30. [PMID: 32677533 PMCID: PMC7441805 DOI: 10.1080/07391102.2020.1792347] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ongoing COVID-19 outbreak has raised a drastic challenge to global public health
security. Most of the patients with COVID-19 suffer from mild flu-like illnesses such as
cold and fever; however, few percentages of the patients progress from severe illness to
death, mostly in an immunocompromised individual. The causative agent of COVID-19 is an
RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite
these debilitating conditions, no medication to stop the disease progression or
vaccination is available till now. Therefore, we aimed to formulate a multi-epitope
vaccine against SARS-CoV-2 by utilizing an immunoinformatics approach. For this purpose,
we used the SARS-CoV-2 spike glycoprotein to determine the immunodominant T- and B-cell
epitopes. After rigorous assessment, we designed a vaccine construct using four potential
epitopes from each of the three epitope classes such as cytotoxic T-lymphocytes, helper
T-lymphocyte, and linear B-lymphocyte epitopes. The designed vaccine was antigenic,
immunogenic, and non-allergenic with suitable physicochemical properties and has higher
solubility. More importantly, the predicted vaccine structure was similar to the native
protein. Further investigations indicated a strong and stable binding interaction between
the vaccine and the toll-like receptor (TLR4). Strong binding stability and structural
compactness were also evident in molecular dynamics simulation. Furthermore, the
computer-generated immune simulation showed that the vaccine could trigger real-life-like
immune responses upon administration into humans. Finally, codon optimization based on
Escherichia coli K12 resulted in optimal GC content and
higher CAI value followed by incorporating it into the cloning vector pET28+(a). Overall,
these results suggest that the designed peptide vaccine can serve as an excellent
prophylactic candidate against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Foysal Ahammad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Rahat Alam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Raihan Rahman Imon
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mahadi Hasan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Ghavimi R, Mohammadi E, Akbari V, Shafiee F, Jahanian-Najafabadi A. In silico design of two novel fusion proteins, p28-IL-24 and p28-M4, targeted to breast cancer cells. Res Pharm Sci 2020; 15:200-208. [PMID: 32582360 PMCID: PMC7306244 DOI: 10.4103/1735-5362.283820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/20/2020] [Accepted: 04/18/2020] [Indexed: 01/29/2023] Open
Abstract
Background and purpose: An anticancer peptide P28, has shown to be cytolethal on various cancer cells including breast cancer. Moreover, p28 can be also used as a targeting moiety in the structure of fusion proteins. IL-24 (or its truncated form, M4) is a cytokine with anticancer activity against a wide range of tumor cells. We aimed at production of a fusion protein consisted of p28 and either IL-24 or M4 to target breast cancer. However, selection of a proper linker to join the two moieties without intervening each other’s function is a key factor in the construction of fusion proteins. In the present study, the impact of different linkers on construction of the two chimeric proteins (p28-IL-24 and p28-M4) was assessed in silico. Experimental approach: After selection of some linkers with different lengths and characteristics, a small library of the chimeric proteins was created and assessed. Furthermore, following selection of the most suitable linker, the three-dimensional structures and dynamic behavior of both fusion proteins were evaluated by homology modeling and molecular dynamic simulation, respectively. Findings / Results: Based on the results, a rigid linker having the peptide sequences of AEAAAKEAAAKA showed highest freedom of action for both moieties. Conclusion and implications: Between the p28-IL-24 and p28-M4 fusion proteins, the former showed better stability as well as solubility and might show stronger anticancer effects in vitro and in vivo, because its peptide moieties showed to exert their activities freely.
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Affiliation(s)
- Reza Ghavimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Elmira Mohammadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Fatemeh Shafiee
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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Jing H, Zhang X, Zou J, Yuan Y, Chen Z, Liu D, Wu W, Yang F, Lu D, Zou Q, Zhang J. Oligomerization of IC43 resulted in improved immunogenicity and protective efficacy against Pseudomonas aeruginosa lung infection. Int J Biol Macromol 2020; 159:174-182. [PMID: 32413471 DOI: 10.1016/j.ijbiomac.2020.05.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022]
Abstract
IC43, a truncate form of outer membrane proteins OprF190-342 and OprI21-83 from Pseudomonas aeruginosa, is a promising candidate antigen and exists as monomer in solution. In this study, we generated the heptamer of IC43 by carrier protein aided oligomerization, which was confirmed by gel-filtration and chemical cross-linking analysis. The carrier protein naturally exists as a homo-heptamer, and IC43 was displayed on the surface of the carrier protein in the fusion protein. Immunization with this fusion protein resulted in increased level of antigen specific IgG antibodies and higher survival rate after infection. The improved efficacy was correlated with lower bacteria burden, inflammation and tissue damage in the lungs of immunized mice. Further studies revealed that immunization with this fusion protein resulted in increased levels of IL-4 and antigen specific IgG1, suggesting a stronger Th2 immune response was induced. The improved immunogenicity may be attributed to the exposure of more epitopes on the antigen, which was confirmed by results from immune-dominant peptide mapping and passive immunization. These results demonstrated a possible strategy to improve the immunogenicity of an antigen by carrier protein aided oligomerization.
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Affiliation(s)
- Haiming Jing
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Xiaoli Zhang
- Department of Clinical Hematology, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Jintao Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Yue Yuan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Zhifu Chen
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Dong Liu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Weiru Wu
- Department of Clinical Hematology, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Feng Yang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Dongshui Lu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China
| | - Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, PR China.
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Sayed SB, Nain Z, Khan MSA, Abdulla F, Tasmin R, Adhikari UK. Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses. Int J Pept Res Ther 2020; 26:2089-2107. [PMID: 32421065 PMCID: PMC7223894 DOI: 10.1007/s10989-019-10003-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Lassa virus (LASV) is responsible for a type of acute viral haemorrhagic fever referred to as Lassa fever. Lack of adequate treatment and preventive measures against LASV resulted in a high mortality rate in its endemic regions. In this study, a multi-epitope vaccine was designed using immunoinformatics as a prophylactic agent against the virus. Following a rigorous assessment, the vaccine was built using T-cell (NCTL = 8 and NHTL = 6) and B-cell (NLBL = 4) epitopes from each LASV-derived protein in addition with suitable linkers and adjuvant. The physicochemistry, immunogenic potency and safeness of the designed vaccine (~ 68 kDa) were assessed. In addition, chosen CTL and HTL epitopes of our vaccine showed 97.37% worldwide population coverage. Besides, disulphide engineering also improved the stability of the chimeric vaccine. Molecular docking of our vaccine protein with toll-like receptor 2 (TLR2) showed binding efficiency followed by dynamics simulation for stable interaction. Furthermore, higher levels of cell-mediated immunity and rapid antigen clearance were suggested by immune simulation and repeated-exposure simulation, respectively. Finally, the optimized codons were used in in silico cloning to ensure higher expression within E. coli K12 bacterium. With further assessment both in vitro and in vivo, we believe that our proposed peptide-vaccine would be potential immunogen against Lassa fever.
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Affiliation(s)
- Sifat Bin Sayed
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Zulkar Nain
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Md Shakil Ahmed Khan
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Faruq Abdulla
- 2Department of Statistics, Faculty of Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Rubaia Tasmin
- 3Department of Pharmacy, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Utpal Kumar Adhikari
- 4School of Medicine, Western Sydney University, Campbelltown, NSW 2560 Australia
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76
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Ojha R, Pareek A, Pandey RK, Prusty D, Prajapati VK. Strategic Development of a Next-Generation Multi-Epitope Vaccine To Prevent Nipah Virus Zoonotic Infection. ACS OMEGA 2019; 4:13069-13079. [PMID: 31460434 PMCID: PMC6705194 DOI: 10.1021/acsomega.9b00944] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/26/2019] [Indexed: 05/23/2023]
Abstract
Nipah virus (NiV) is an emerging zoonotic pathogen, reported for the recent severe outbreaks of encephalitis and respiratory illness in humans and animals, respectively. Many antiviral drugs have been discovered to inhibit this pathogen, but none of them were that much efficient. To overcome the complications associated with this severe pathogenic virus, we have designed a multi-epitope subunit vaccine using computational immunology strategies. Identification of structural and nonstructural proteins of Nipah virus assisted in the vaccine designing. The selected proteins are known to be involved in the survival of the virus. The antigenic binders (B-cell, HTL, and CTL) from the selected proteins were prognosticated. These antigenic binders will be able to generate the humoral as well as cell-mediated immunity. All the epitopes were united with the help of suitable linkers and with an adjuvant at the N-terminal of the vaccine, for the enhancement of immunogenicity. The physiological characterization, along with antigenicity and allergenicity of the designed vaccine candidates, was estimated. The 3D structure prediction and its validation were performed. The validated vaccine model was then docked and simulated with the TLR-3 receptor to check the stability of the docked complex. This next-generation approach will provide a new vision for the development of a high immunogenic vaccine against the NiV.
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Affiliation(s)
- Rupal Ojha
- Department of Biochemistry,
School of Life Sciences, Central University
of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Aditi Pareek
- Department of Biochemistry,
School of Life Sciences, Central University
of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Rajan K. Pandey
- Department of Biochemistry,
School of Life Sciences, Central University
of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Dhaneswar Prusty
- Department of Biochemistry,
School of Life Sciences, Central University
of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Vijay K. Prajapati
- Department of Biochemistry,
School of Life Sciences, Central University
of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
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77
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Sun X, Tang X, Hu R, Luo M, Hill P, Fang B, Xu C. Biosynthetic bifunctional enzyme complex with high-efficiency luciferin-recycling to enhance the bioluminescence imaging. Int J Biol Macromol 2019; 130:705-714. [PMID: 30849466 DOI: 10.1016/j.ijbiomac.2019.03.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
Firefly luciferase is a prominent reporter on molecular imaging with the advantage of longer wavelength on light emission and the ATP linear correlation, which makes it useful in most of current bioluminescence imaging model. However, the utility of this biomaterial was limited by the signal intensity and stability which are respectively affected by enzyme activity and substrate consumption. This study demonstrated a series of novel synthetic bifunctional enzyme complex of Firefly luciferase (Fluc) and Luciferin-regenerating enzyme (LRE). A peptide linker library was constructed for the fusion strategy on biosynthesis. The findings of both experimental data and structural simulation demonstrated that the intervention of fused LRE remarkably improve the stability of in vitro bioluminescence signal through luciferin recycling; and revealed the competitive relationship of Fluc and LRE on luciferin binding: Fluc performed higher activity with one copy number of rigid linker (EAAAK) at the C terminal while LRE acted more efficiently with two copy numbers of flexible linker (GGGGS) at the N terminal. With the advantage of signal intensity and stability, this fused bifunctional enzyme complex may expand the application of firefly luciferase to in vitro bioluminescence imaging.
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Affiliation(s)
- Xiaohui Sun
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Xu Tang
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Rui Hu
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Man Luo
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Philip Hill
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Sutton Bonington, Loughbrough LE12 5RD, UK
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Chang'an Xu
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China.
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78
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Shih TC, Ho LP, Wu JL, Chou HY, Pai TW. A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family. BMC Bioinformatics 2019; 20:192. [PMID: 31074372 PMCID: PMC6509842 DOI: 10.1186/s12859-019-2736-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily Results The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily Conclusions Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
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Affiliation(s)
- Tao-Chuan Shih
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Li-Ping Ho
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Jen-Leih Wu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yiu Chou
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan. .,Department of Aquaculture, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan.
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan. .,Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan.
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79
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Wu X, Fraser K, Zha J, Dordick JS. Flexible Peptide Linkers Enhance the Antimicrobial Activity of Surface-Immobilized Bacteriolytic Enzymes. ACS APPLIED MATERIALS & INTERFACES 2018; 10:36746-36756. [PMID: 30281274 DOI: 10.1021/acsami.8b14411] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Chemical linkers are frequently used in enzyme immobilization to improve enzyme flexibility and activity, whereas peptide linkers, although ubiquitous in protein engineering, are much less explored in enzyme immobilization. Here, we report peptide-linker-assisted noncovalent immobilization of the bacteriolytic enzyme lysostaphin (Lst) to generate anti- Staphylococcus aureus surfaces. Lst was immobilized through affinity tags onto a silica surface (glass slides) and nickel nitrilotriacetic acid (NiNTA) agarose beads via silica-binding peptides (SiBPs) or a hexahistidine tag (His-tag) fused at the C-terminus of Lst, respectively. By inserting specific peptide linkers upstream of the SiBP or His-tag, the immobilized enzymes killed >99.5% of S. aureus ATCC 6538 cells (108 CFU/mL) within 3 h in buffer and could be reused multiple times without significant loss of activity. In contrast, immobilized Lst without a peptide linker was less active/stable. Molecular modeling of Lst-linker-affinity tag constructs illustrated that the presence of the peptide linkers enhanced the molecular flexibility of the proximal Lst binding domain, which interacts with the bacterial substrate, and such increased flexibility correlated with increased antimicrobial activity. We further show that Lst immobilized onto NiNTA beads retained the ability to kill ∼99% of a 108 CFU/mL microbial challenge even in the presence of 1% of a commercial anionic surfactant, C12-14 alcohol EO 3:1 sodium sulfate, when the Lst construct contained a decapeptide linker containing glycine, serine, and alanine residues. This linker-assisted immobilization strategy could be extended to an unrelated lytic enzyme, the endolysin PlyPH, to target Bacillus anthracis Sterne cells either in buffer or in the presence of anionic surfactants. Our approach, therefore, provides a facile route to the use of antimicrobial enzymes on surfaces.
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80
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Gonçalves F, Silva C, Ribeiro A, Cavaco-Paulo A. 1-Aminoanthracene Transduction into Liposomes Driven by Odorant-Binding Protein Proximity. ACS APPLIED MATERIALS & INTERFACES 2018; 10:27531-27539. [PMID: 30040883 DOI: 10.1021/acsami.8b10158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, the anchorage of pig odorant binding protein (OBP-I) into liposomal membrane was promoted by the fusion of OBP-I with the anchor SP-DS3 peptide and with the (GQ)20 spacer. The presence of the (GQ)20 spacer in the construct confers flexibility to the protein and increases the distance between the OBP binding site and the liposomal surface. The engineered proteins, OBP::SP-DS3 and OBP::(GQ)20::SP-DS3, were produced in Escherichia coli BL21(DE3) and characterized by circular dichroism spectroscopy and MALDI-TOF. The functionalization of liposomes with the OBP proteins was performed through ethanol injection, and similar liposomal anchorage (∼92-97%) was found for both OBP constructs. The effect of OBPs' proximity to the liposomes membrane on 1-aminoanthracene (1-AMA, model ligand) transduction was evaluated by measuring the amount of 1-AMA transduced into liposomes by fluorescence spectroscopy. While protein flexibility, given by the presence of the (GQ)20 spacer, seems to influence the binding efficiency, ∼45% for OBP::(GQ)20::SP-DS3 and ∼29% for OBP::SP-DS3, the distance between the proteins' binding site and the liposomal membrane determines their ability to transduce the 1-AMA into the liposomes (∼23% for OBP::SP-DS3 and ∼19% for OBP::(GQ)20::SP-DS3). The anchorage capacity and proximity effect were confirmed by an experimental control where the wild-type (wt) OBP was added to the liposomes, resulting in low 1-AMA transduction (∼3.5%) and low binding to OBPwt (∼9%). These findings evidence the effect of anchorage, carrier protein's flexibility, and proximity as key features for the entrapment of molecules into the liposomal membrane. The developed OBP-based devices are thus promising anchorage systems for the capture and storage of odors with potential applications in textile and cosmetic industries.
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Affiliation(s)
- Filipa Gonçalves
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 Braga , Portugal
| | - Carla Silva
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 Braga , Portugal
| | - Artur Ribeiro
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 Braga , Portugal
| | - Artur Cavaco-Paulo
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 Braga , Portugal
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81
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Caparco AA, Bommarius AS, Champion JA. Effect of peptide linker length and composition on immobilization and catalysis of leucine zipper‐enzyme fusion proteins. AIChE J 2018. [DOI: 10.1002/aic.16150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Adam A. Caparco
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Julie A. Champion
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
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82
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Shamriz S, Ofoghi H. Engineering the chloroplast of Chlamydomonas reinhardtii to express the recombinant PfCelTOS-Il2 antigen-adjuvant fusion protein. J Biotechnol 2018; 266:111-117. [DOI: 10.1016/j.jbiotec.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/25/2017] [Accepted: 12/17/2017] [Indexed: 12/23/2022]
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83
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Pinheiro AM, Carreira A, Ferreira RB, Monteiro S. Fusion proteins towards fungi and bacteria in plant protection. MICROBIOLOGY (READING, ENGLAND) 2018; 164:11-19. [PMID: 29239714 PMCID: PMC5892777 DOI: 10.1099/mic.0.000592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
Abstract
In agriculture, although fungi are considered the foremost problem, infections by bacteria also cause significant economical losses. The presence of different diseases in crops often leads to a misuse of the proper therapeutic, or the combination of different diseases forces the use of more than one pesticide. This work concerns the development of a 'super-Blad': a chimeric protein consisting of Blad polypeptide, the active ingredient of a biological fungicide already on the market, and two selected peptides, SP10-5 and Sub5, proven to possess biological potential as antibacterial agents. The resulting chimeric protein obtained from the fusion of Blad with SP10-5 not only maintained strong antibacterial activity, especially against Xanthomonas spp. and Pseudomonas syringae, but was also able to retain the ability to inhibit the growth of both yeast and filamentous fungi. However, the antibacterial activity of Sub5 was considerably diminished when fused with Blad, which seems to indicate that not all fusion proteins behave equally. These newly designed drugs can be considered promising compounds for use in plant protection. A deeper and focused development of an appropriate formulation may result in a potent biopesticide that can replace, per se, two conventional chemistries with less impact on the environment.
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Affiliation(s)
- Ana Margarida Pinheiro
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Alexandra Carreira
- CEV, SA, Parque Industrial de Cantanhede/Biocant-Park, lote 120, 3060-197 Cantanhede, Portugal
| | - Ricardo B. Ferreira
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Sara Monteiro
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
- CEV, SA, Parque Industrial de Cantanhede/Biocant-Park, lote 120, 3060-197 Cantanhede, Portugal
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Wang J, Zheng W, Liu F, Wang Y, He Y, Zheng L, Fan Q, Luo E, Cao Y, Cui L. Characterization of Pb51 in Plasmodium berghei as a malaria vaccine candidate targeting both asexual erythrocytic proliferation and transmission. Malar J 2017; 16:458. [PMID: 29132428 PMCID: PMC5683326 DOI: 10.1186/s12936-017-2107-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background A vaccine that targets multiple developmental stages of malaria parasites would be an effective tool for malaria control and elimination. Methods A conserved gene in Plasmodium, the Plasmodium berghei gene (PBANKA_020570) encoding a 51 kDa protein (pb51 gene), was identified through search of the PlasmoDB database using a combination of expression and protein localization criteria. A partial domain of the Pb51 protein was expressed in a prokaryotic expression system (rPb51) and used for immunization in mice. The protein expression profile and localization were studied by Western blot and indirect immunofluorescence assay (IFA), respectively. The inhibitory effect of the anti-rPb51 antibodies on parasite proliferation was evaluated in erythrocytes in vivo. The transmission-blocking activity of the immune sera was determined by in vitro ookinete conversion assay and by direct mosquito feeding assay (DFA). Results The rPb51 elicited specific antibodies in mice. Western blot confirmed Pb51 expression in schizonts, gametocytes and ookinetes. IFA showed localization of Pb51 on the outer membranes of schizonts, gametocytes, zygotes, retorts, ookinetes and sporozoites of P. berghei. Mice immunized with the rPb51 protein significantly reduced parasite proliferation and gametocyte conversion in vivo. Moreover, the rPb51 antisera also significantly reduced the in vitro ookinete conversion when added into the ookinete culture medium. In DFA, mice immunized with the rPb51 reduced the prevalence of mosquito infection by 21.3% and oocyst density by 54.8%. Conclusions In P. berghei, P51 was expressed in both asexual erythrocytic and sexual stages and localized on the surface of these stages with the exception of the ring stage. The anti-rPb51 antibodies inhibited both P. berghei proliferation in mice and transmission of the parasite to mosquitoes. Electronic supplementary material The online version of this article (10.1186/s12936-017-2107-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Wenqi Zheng
- Laboratory of Surgery, The Affiliated Hospital, Inner Mongolia Medical University, Hohhot, 010050, China
| | - Fei Liu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Yaru Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Yiwen He
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Li Zheng
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Qi Fan
- Dalian Institute of Biotechnology, Dalian, Liaoning, China
| | - Enjie Luo
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China.
| | - Liwang Cui
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, Liaoning, China.,Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
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Vishnu US, Sankarasubramanian J, Gunasekaran P, Rajendhran J. Identification of potential antigens from non-classically secreted proteins and designing novel multitope peptide vaccine candidate against Brucella melitensis through reverse vaccinology and immunoinformatics approach. INFECTION GENETICS AND EVOLUTION 2017; 55:151-158. [PMID: 28919551 DOI: 10.1016/j.meegid.2017.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/01/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
Brucella melitensis is an intracellular pathogen resides in the professional and non-professional phagocytes of the host, causing zoonotic disease brucellosis. The stealthy nature of the Brucella makes it's highly pathogenic, and it is hard to eliminate the bacteria completely from the infected host. Hitherto, no licensed vaccines are available for human brucellosis. In this study, we identified potential antigens for vaccine development from non-classically secreted proteins through reverse vaccinology approach. Based on the systemic screening of non-classically secreted proteins of B. melitensis 16M, we identified nine proteins as potential vaccine candidates. Among these, Omp31 and Omp22 are known immunogens, and its role in the virulence of Brucella is known. Roles of other proteins in the pathogenesis are yet to be studied. From the nine proteins, we identified six novel antigenic epitopes that can elicit both B-cell and T-cell immune responses. Among the nine proteins, the epitopes were predicted from Omp31 immunogenic protein precursor, Omp22 protein precursor, extracellular serine protease, hypothetical membrane-associated protein, iron-regulated outer membrane protein FrpB. Further, we designed a multitope vaccine using Omp31 immunogenic protein precursor, Omp22 protein precursor, extra cellular serine protease, iron-regulated outer membrane protein FrpB, hypothetical membrane-associated protein, and LPS-assembly protein LptD and polysaccharide export protein identified in the previous study. Epitopes were joined using amino acid linkers such as EAAAK and GPGPG. Cholera toxin subunit B, the nontoxic part of cholera toxin, was used as an adjuvant and it was linked to the N-terminal of the multitope vaccine candidate. The designed vaccine candidate was modeled, validated and the physicochemical properties were analyzed. Results revealed that the vaccine candidate is soluble, stable, non-allergenic, antigenic and 87% of residues of the designed vaccine candidate is located in the favored region. In conclusion, the computational analysis showed that the newly designed multitope protein could be used to develop a promising vaccine for human brucellosis.
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Affiliation(s)
- Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Jagadesan Sankarasubramanian
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
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The potential roles of Pinto bean (Phaseolus vulgaris cv. Pinto) bioactive peptides in regulating physiological functions: Protease activating, lipase inhibiting and bile acid binding activities. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.03.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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Meza B, Ascencio F, Sierra-Beltrán AP, Torres J, Angulo C. A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: An in silico approach. INFECTION GENETICS AND EVOLUTION 2017; 49:309-317. [DOI: 10.1016/j.meegid.2017.02.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/02/2017] [Accepted: 02/05/2017] [Indexed: 02/07/2023]
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