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Fang XL, Cao XP, Xiao J, Hu Y, Chen M, Raza HK, Wang HY, He X, Gu JF, Zhang KJ. Overview of role of survivin in cancer: expression, regulation, functions, and its potential as a therapeutic target. J Drug Target 2024; 32:223-240. [PMID: 38252514 DOI: 10.1080/1061186x.2024.2309563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/11/2023] [Indexed: 01/24/2024]
Abstract
Survivin holds significant importance as a member of the inhibitor of apoptosis protein (IAP) family due to its predominant expression in tumours rather than normal terminally differentiated adult tissues. The high expression level of survivin in tumours is closely linked to chemotherapy resistance, heightened tumour recurrence, and increased tumour aggressiveness and serves as a negative prognostic factor for cancer patients. Consequently, survivin has emerged as a promising therapeutic target for cancer treatment. In this review, we delve into the various biological characteristics of survivin in cancers and its pivotal role in maintaining immune system homeostasis. Additionally, we explore different therapeutic strategies aimed at targeting survivin.
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Affiliation(s)
- Xian-Long Fang
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Xue-Ping Cao
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Jun Xiao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yun Hu
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Mian Chen
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Hafiz Khuram Raza
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Huai-Yuan Wang
- Institute of Smart Biomedical Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xu He
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jin-Fa Gu
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
| | - Kang-Jian Zhang
- Academician Expert Workstation of Fengxian District, Shanghai Yuansong Biotechnology Limited Company, Shanghai, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Institute of Smart Biomedical Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, China
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Usta S, Misura A, Rashedi I, Amitai I, Roos K, Jiang Y, Mangoff K, Klein G, Forward N, Stewart D, Mangel J, Tomlinson G, Tsui H, Berinstein NL. Intensity of survivin expression linked to features of aggressive relapsed/refractory diffuse large B-cell lymphoma. Leuk Lymphoma 2024:1-11. [PMID: 39328061 DOI: 10.1080/10428194.2024.2403668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 09/04/2024] [Accepted: 09/06/2024] [Indexed: 09/28/2024]
Abstract
SPiReL is a phase II clinical trial evaluating combination immunotherapy, pembrolizumab and cyclophosphamide, with maveropepimut-S, in survivin-expressing relapsed/refractory (R/R) Diffuse Large B Cell Lymphoma (DLBCL). We describe baseline tumor survivin expression and associations with clinico-pathological variables in 25 participants. The median number of survivin-expressing cells was 99%, and the intensity of survivin expression within tumors was heterogeneous by semi-quantitative immunohistochemistry assessment. Tumors with higher numbers of cells expressing 2+/3+ survivin were associated with characteristics of poor outcome, (Lactate dehydrogenase and cell-of-origin). Greater total baseline tumor area was associated with lower proportions of 1+ cells and greater proportions of 2+/3+ cells. High intensity survivin expression is associated with aggressive clinical features supporting a pathobiological role in R/R DLBCL. Future prognostic models incorporating survivin as a clinical biomarker require assessment of intensity, overall expression and should include potential threshold effects of survivin in DLBCL pathobiology.
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Affiliation(s)
- Sila Usta
- Sunnybrook Research Institute, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | | | | | - Irina Amitai
- Sunnybrook Health Sciences Centre, Toronto, Canada
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kim Roos
- Sunnybrook Research Institute, Toronto, Canada
| | - Yidi Jiang
- Sunnybrook Research Institute, Toronto, Canada
| | | | - Gail Klein
- Sunnybrook Research Institute, Toronto, Canada
| | | | | | - Joy Mangel
- Department of Medicine, London Health Sciences Centre, London, Canada
| | | | - Hubert Tsui
- Sunnybrook Research Institute, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Neil L Berinstein
- Sunnybrook Research Institute, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
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Bai Y, Zhou M, Wang N, Yang Y, Wang D. Designing a Candidate Multi-Epitope Vaccine against Transmissible Gastroenteritis Virus Based on Immunoinformatic and Molecular Dynamics. Int J Mol Sci 2024; 25:8828. [PMID: 39201514 PMCID: PMC11354480 DOI: 10.3390/ijms25168828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is an etiological agent of enteric disease that results in high mortality rates in piglets. The economic impact of the virus is considerable, causing significant losses to the pig industry. The development of an efficacious subunit vaccine to provide promising protection against TGEV is of the utmost importance. The viral antigen, spike glycoprotein (S), is widely regarded as one of the most effective antigenic components for vaccine research. In this study, we employed immunoinformatics and molecular dynamics approaches to develop an 'ideal' multi-epitope vaccine. Firstly, the dominant, non-toxic, highly antigenic T (Th, CTL) and B cell epitopes predicted from the TGEV S protein were artificially engineered in tandem to design candidate subunit vaccines. Molecular docking and dynamic simulation results demonstrate that it exhibits robust interactions with toll-like receptor 4 (TLR4). Of particular significance was the finding that the vaccine was capable of triggering an immune response in mammals, as evidenced by the immune simulation results. The humoral aspect is typified by elevated levels of IgG and IgM, whereas the cellular immune aspect is capable of eliciting the robust production of interleukins and cytokines (IFN-γ and IL-2). Furthermore, the adoption of E. coli expression systems for the preparation of vaccines will also result in cost savings. This study offers logical guidelines for the development of a secure and efficacious subunit vaccine against TGEV, in addition to providing a novel theoretical foundation and strategy to prevent associated CoV infections.
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Affiliation(s)
- Yihan Bai
- College of Biology, Hunan University, Changsha 410082, China;
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Mingxia Zhou
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Naidong Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Yi Yang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Dongliang Wang
- College of Biology, Hunan University, Changsha 410082, China;
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
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Oladejo M, Tijani AO, Puri A, Chablani L. Adjuvants in cutaneous vaccination: A comprehensive analysis. J Control Release 2024; 369:475-492. [PMID: 38569943 DOI: 10.1016/j.jconrel.2024.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Skin is the body's largest organ and serves as a protective barrier from physical, thermal, and mechanical environmental challenges. Alongside, the skin hosts key immune system players, such as the professional antigen-presenting cells (APCs) like the Langerhans cells in the epidermis and circulating macrophages in the blood. Further, the literature supports that the APCs can be activated by antigen or vaccine delivery via multiple routes of administration through the skin. Once activated, the stimulated APCs drain to the associated lymph nodes and gain access to the lymphatic system. This further allows the APCs to engage with the adaptive immune system and activate cellular and humoral immune responses. Thus, vaccine delivery via skin offers advantages such as reliable antigen delivery, superior immunogenicity, and convenient delivery. Several preclinical and clinical studies have demonstrated the significance of vaccine delivery using various routes of administration via skin. However, such vaccines often employ adjuvant/(s), along with the antigen of interest. Adjuvants augment the immune response to a vaccine antigen and improve the therapeutic efficacy. Due to these reasons, adjuvants have been successfully used with infectious disease vaccines, cancer immunotherapy, and immune-mediated diseases. To capture these developments, this review will summarize preclinical and clinical study results of vaccine delivery via skin in the presence of adjuvants. A focused discussion regarding the FDA-approved adjuvants will address the experiences of using such adjuvant-containing vaccines. In addition, the challenges and regulatory concerns with these adjuvants will be discussed. Finally, the review will share the prospects of adjuvant-containing vaccines delivered via skin.
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Affiliation(s)
- Mariam Oladejo
- Department of Immunotherapeutics and Biotechnology, Jerry H Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, TX 79601, USA
| | - Akeemat O Tijani
- Department of Pharmaceutical Sciences, Bill Gatton College of Pharmacy, East Tennessee State University, Johnson City, TN, USA
| | - Ashana Puri
- Department of Pharmaceutical Sciences, Bill Gatton College of Pharmacy, East Tennessee State University, Johnson City, TN, USA.
| | - Lipika Chablani
- Wegmans School of Pharmacy, St. John Fisher University, 3690 East Ave, Rochester, NY 14618, USA.
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Zhang G, Han L, Zhao Y, Li Q, Wang S, Shi H. Development and evaluation of a multi-epitope subunit vaccine against Mycoplasma synoviae infection. Int J Biol Macromol 2023; 253:126685. [PMID: 37666406 DOI: 10.1016/j.ijbiomac.2023.126685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Mycoplasma synoviae is an extremely significant avian pathogen, causing substantial financial harm to poultry farmers worldwide, and impacting both chicken and turkey production. Multi-epitope vaccines offer higher immunity and lower allergenicity compared to conventional vaccines. In this study, our objective is to develop a multi-epitope vaccine for M. synoviae (MSMV) and to evaluate the immune responses and protective efficacy of MSMV in chickens. We successfully identified a total of 14 B-cell, 5 MHC-I, and 16 MHC-II binding epitopes from the immunodominant proteins RS01790, BMP, GrpE, RS00900, and RS00275. Subsequently, we synthesized the multi-epitope vaccine by connecting all conserved epitopes using appropriate linkers. The resulting MSMV demonstrated notable antigenicity, non-allergenic properties, and stability. Notably, the MSMV effectively stimulated high levels of antibody production in chickens. Furthermore, MSMV the vaccine elicited a robust cellular immune response in chickens, characterized by a well-balanced Th1/Th2-type cytokine profile and enhanced lymphocyte proliferation. In immune protection experiments, the vaccinated chickens exhibited reduced air sac lesion scores and tracheal mucosal thickness compared to their non-vaccinated chickens. Additionally, vaccinated chickens displayed lower M. synoviae loads in throat swabs. These findings collectively suggested that the MSMV holds significant potential as a promising vaccine candidate for managing M. synoviae infections.
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Affiliation(s)
- Guihua Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Lejiabao Han
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yuying Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611-0880, USA.
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University (JIRLAAPS), Yangzhou, China.
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da Silva MK, Campos DMDO, Akash S, Akter S, Yee LC, Fulco UL, Oliveira JIN. Advances of Reverse Vaccinology for mRNA Vaccine Design against SARS-CoV-2: A Review of Methods and Tools. Viruses 2023; 15:2130. [PMID: 37896907 PMCID: PMC10611333 DOI: 10.3390/v15102130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
mRNA vaccines are a new class of vaccine that can induce potent and specific immune responses against various pathogens. However, the design of mRNA vaccines requires the identification and optimization of suitable antigens, which can be challenging and time consuming. Reverse vaccinology is a computational approach that can accelerate the discovery and development of mRNA vaccines by using genomic and proteomic data of the target pathogen. In this article, we review the advances of reverse vaccinology for mRNA vaccine design against SARS-CoV-2, the causative agent of COVID-19. We describe the steps of reverse vaccinology and compare the in silico tools used by different studies to design mRNA vaccines against SARS-CoV-2. We also discuss the challenges and limitations of reverse vaccinology and suggest future directions for its improvement. We conclude that reverse vaccinology is a promising and powerful approach to designing mRNA vaccines against SARS-CoV-2 and other emerging pathogens.
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Affiliation(s)
- Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Daniel Melo de Oliveira Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Sukrabad, Dhaka 1207, Bangladesh;
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka 1205, Bangladesh;
| | - Leow Chiuan Yee
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kota Bharu 11800, Kelantan, Malaysia;
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
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Mohammadzadeh Hosseini Moghri SAH, Ranjbar M, Hassannia H, Khakdan F. In silico analysis of the conserved surface-exposed epitopes to design novel multiepitope peptide vaccine for all variants of the SARS-CoV-2. J Biomol Struct Dyn 2023; 41:7603-7615. [PMID: 36124826 DOI: 10.1080/07391102.2022.2123395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to generic health. The SARS-CoV-2 spike (S) glycoprotein plays a fundamental role in binds and fusion to the angiotensin-converting enzyme 2 (ACE2). The multi-epitope peptide vaccines would be able to elicit both long-lasting humoral and cellular immune responses, resulting the eliminating SARS-CoV-2 infections as asymptomatic patients are in large numbers. Recently, the omicron variant of the SARS-CoV-2 became a variant of concern that contained just 15-point mutations in the receptor-binding domain of the spike protein. In order to eliminate new evidence on coronavirus variants of concern detected through epidemic intelligence, the conserved epitopes of the receptor-binding domain (RBD) and spike cleavage site is the most probable target for vaccine development to inducing binds and fusion inhibitors neutralizing antibodies respectively. In this study, we utilized bioinformatics tools for identifying and analyzing the spike (S) glycoprotein sequence, e.g. the prediction of the potential linear B-cell epitopes, B-cell multi‑epitope design, secondary and tertiary structures, physicochemical properties, solubility, antigenicity, allergenicity, the molecular docking and molecular dynamics simulation for the promising vaccine candidate against all variant of concern of SARS-CoV-2. Among the epitopes of the RBD region are surface-exposed epitopes SVYAWNRKRISNCV and ATRFASVYAWNRKR as the conserved sequences in all variants of concern can be a good candidate to induce an immune response.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Islamic Republic of Iran
| | - Hadi Hassannia
- Immunogenetic Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Tan C, Zhu F, Pan P, Wu A, Li C. Development of multi-epitope vaccines against the monkeypox virus based on envelope proteins using immunoinformatics approaches. Front Immunol 2023; 14:1112816. [PMID: 36993967 PMCID: PMC10040844 DOI: 10.3389/fimmu.2023.1112816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
BackgroundSince May 2022, cases of monkeypox, a zoonotic disease caused by the monkeypox virus (MPXV), have been increasingly reported worldwide. There are, however, no proven therapies or vaccines available for monkeypox. In this study, several multi-epitope vaccines were designed against the MPXV using immunoinformatics approaches.MethodsThree target proteins, A35R and B6R, enveloped virion (EV) form-derived antigens, and H3L, expressed on the mature virion (MV) form, were selected for epitope identification. The shortlisted epitopes were fused with appropriate adjuvants and linkers to vaccine candidates. The biophysical andbiochemical features of vaccine candidates were evaluated. The Molecular docking and molecular dynamics(MD) simulation were run to understand the binding mode and binding stability between the vaccines and Toll-like receptors (TLRs) and major histocompatibility complexes (MHCs). The immunogenicity of the designed vaccines was evaluated via immune simulation.ResultsFive vaccine constructs (MPXV-1-5) were formed. After the evaluation of various immunological and physicochemical parameters, MPXV-2 and MPXV-5 were selected for further analysis. The results of molecular docking showed that the MPXV-2 and MPXV-5 had a stronger affinity to TLRs (TLR2 and TLR4) and MHC (HLA-A*02:01 and HLA-DRB1*02:01) molecules, and the analyses of molecular dynamics (MD) simulation have further confirmed the strong binding stability of MPXV-2 and MPXV-5 with TLRs and MHC molecules. The results of the immune simulation indicated that both MPXV-2 and MPXV-5 could effectively induce robust protective immune responses in the human body.ConclusionThe MPXV-2 and MPXV-5 have good efficacy against the MPXV in theory, but further studies are required to validate their safety and efficacy.
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Affiliation(s)
- Caixia Tan
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
| | - Fei Zhu
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
| | - Pinhua Pan
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
| | - Anhua Wu
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
| | - Chunhui Li
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
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Survivin (BIRC5) Peptide Vaccine in the 4T1 Murine Mammary Tumor Model: A Potential Neoadjuvant T Cell Immunotherapy for Triple Negative Breast Cancer: A Preliminary Study. Vaccines (Basel) 2023; 11:vaccines11030644. [PMID: 36992227 DOI: 10.3390/vaccines11030644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
A triple negative breast cancer model using the murine 4T1 tumor cell line was used to explore the efficacy of an adjuvanted survivin peptide microparticle vaccine using tumor growth as the outcome metric. We first performed tumor cell dose titration studies to determine a tumor cell dose that resulted in sufficient tumor takes but allowed multiple serial measurements of tumor volumes, yet with minimal morbidity/mortality within the study period. Later, in a second cohort of mice, the survivin peptide microparticle vaccine was administered via intraperitoneal injection at the study start with a second dose given 14 days later. An orthotopic injection of 4T1 cells into the mammary tissue was performed on the same day as the administration of the second vaccine dose. The mice were followed for up to 41 days with subcutaneous measurements of tumor volume made every 3–4 days. Vaccination with survivin peptides was associated with a peptide antigen-specific gamma interferon enzyme-linked immunosorbent spot response in the murine splenocyte population but was absent from the control microparticle group. At the end of the study, we found that vaccination with adjuvanted survivin peptide microparticles resulted in statistically significant slower primary tumor growth rates in BALB/c mice challenged with 4T1 cells relative to the control peptideless vaccination group. These studies suggest that T cell immunotherapy specifically targeting survivin might be an applicable neoadjuvant immunotherapy therapy for triple negative breast cancer. More preclinical studies and clinical trials are needed to explore this concept further.
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Ullah A, Waqas M, Aziz S, Rahman SU, Khan S, Khalid A, Abdalla AN, Uddin J, Halim SA, Khan A, Al-Harrasi A. Bioinformatics and immunoinformatics approach to develop potent multi-peptide vaccine for coxsackievirus B3 capable of eliciting cellular and humoral immune response. Int J Biol Macromol 2023; 239:124320. [PMID: 37004935 DOI: 10.1016/j.ijbiomac.2023.124320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
Coxsackievirus B3 (CVB3) is a viral pathogen of various human disorders with no effective preventative interventions. Herein, we aimed to design a chimeric vaccine construct for CVB3 using reverse vaccinology and immunoinformatics approaches by screening the whole viral polyprotein sequence. Firstly, screening and mapping of viral polyprotein to predict 21 immunodominant epitopes (B-cell, CD8+ and CD4+ T-cell epitopes), fused with an adjuvant (Resuscitation-promoting factor), appropriate linkers, HIV-TAT peptide, Pan DR epitope, and 6His-tag to assemble a multi-epitope vaccine construct. The chimeric construct is predicted as probable antigen, non-allergen, stable, possess encouraging physicochemical features, and indicates a broader population coverage (98 %). The tertiary structure of the constructed vaccine was predicted and refined, and its interaction with the Toll-like receptor 4 (TLR4) was investigated through molecular docking and dynamics simulation. Computational cloning of the construct was carried out in pET28a (+) plasmid to guarantee the higher expression of the vaccine protein. Lastly, in silico immune simulation foreseen that humoral and cellular immune responses would be elicited in response to the administration of such a potent chimeric construct. Thus, the design constructed could vaccinate against CVB3 infection and various CVB serotypes. However, further in vitro/in vivo research must assess its safety and effectiveness.
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Motamedi H, Ari MM, Shahlaei M, Moradi S, Farhadikia P, Alvandi A, Abiri R. Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. BMC Bioinformatics 2023; 24:65. [PMID: 36829112 PMCID: PMC9951438 DOI: 10.1186/s12859-023-05197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage. METHODS In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4+ and CD8+) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy. RESULTS A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4+ T and CD8+ cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ. CONCLUSION Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.
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Affiliation(s)
- Hamid Motamedi
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran ,grid.412112.50000 0001 2012 5829Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- grid.411746.10000 0004 4911 7066Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran ,grid.411746.10000 0004 4911 7066Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Shahlaei
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parisa Farhadikia
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhoushang Alvandi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Medical Technology Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Fertility and Infertility Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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12
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Ali Z, Cardoza JV, Basak S, Narsaria U, Singh VP, Isaac SP, França TCC, LaPlante SR, George SS. Computational design of candidate multi-epitope vaccine against SARS-CoV-2 targeting structural (S and N) and non-structural (NSP3 and NSP12) proteins. J Biomol Struct Dyn 2023; 41:13348-13367. [PMID: 36744449 DOI: 10.1080/07391102.2023.2173297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 virus has created a global damage and has exposed the vulnerable side of scientific research towards novel diseases. The intensity of the pandemic is huge, with mortality rates of more than 6 million people worldwide in a span of 2 years. Considering the gravity of the situation, scientists all across the world are continuously attempting to create successful therapeutic solutions to combat the virus. Various vaccination strategies are being devised to ensure effective immunization against SARS-CoV-2 infection. SARS-CoV-2 spreads very rapidly, and the infection rate is remarkably high than other respiratory tract viruses. The viral entry and recognition of the host cell is facilitated by S protein of the virus. N protein along with NSP3 is majorly responsible for viral genome assembly and NSP12 performs polymerase activity for RNA synthesis. In this study, we have designed a multi-epitope, chimeric vaccine considering the two structural (S and N protein) and two non-structural proteins (NSP3 and NSP12) of SARS-CoV-2 virus. The aim is to induce immune response by generating antibodies against these proteins to target the viral entry and viral replication in the host cell. In this study, computational tools were used, and the reliability of the vaccine was verified using molecular docking, molecular dynamics simulation and immune simulation studies in silico. These studies demonstrate that the vaccine designed shows steady interaction with Toll like receptors with good stability and will be effective in inducing a strong and specific immune response in the body.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, India
| | | | | | | | - Vijay Pratap Singh
- Department of Physiotherapy, Kasturba Medical College, Mangalore, Manipal academy of higher education, Mangalore, Manipal, India
| | | | - Tanos C C França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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Waqas M, Aziz S, Bushra A, Halim SA, Ali A, Ullah S, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Employing an immunoinformatics approach revealed potent multi-epitope based subunit vaccine for lymphocytic choriomeningitis virus. J Infect Public Health 2023; 16:214-232. [PMID: 36603375 DOI: 10.1016/j.jiph.2022.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/10/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lymphocytic choriomeningitis virus (LCMV) infects many individuals worldwide and causes severe infection in the immunosuppressant recipient, spontaneous abortion, and congenital disabilities in infants. OBJECTIVES There is no specific vaccine or therapeutics available to protect against LCMV infection; thus, there is a need to design a potential vaccine to combat the virus by developing immunity in the population. Herein, we attempted to design a potent multi-epitope vaccine for LCMV using immunoinformatics methods. METHODS The whole proteome of the virus was screened and mapped to extract immunodominant B-cell and T-cell epitopes which were fused with appropriate linkers (EAAAK, GGGS, AAY, GPGPG, and AAY), PADRE sequence (13aa) and an adjuvant (50 S ribosomal protein L7/L12) to formulate a multi-epitope vaccine ensemble. Codon adaptation and in silico cloning of the constructed vaccine were carried out using bioinformatics tools. The secondary and tertiary structure of the vaccine construct was predicted and refined. The physicochemical profile of the designed vaccine was analyzed, and the multi-epitope vaccine's potential to bind Toll-like receptors (TLR2 and TLR4) was evaluated through molecular docking and molecular dynamics simulations. Computational immune simulation of the designed vaccine antigen was performed using the C-ImmSim server. RESULTS The designed multi-epitope-based vaccine (613 aa) comprised 26 immunodominant (six B-cell, nine cytotoxic T lymphocytes, and 11 helper T lymphocytes) epitopes and is predicted antigenic, non-toxic, non-allergen, soluble, and topographically accessible with a suitable physicochemical profile. The designed vaccine is expected to cover a broad worldwide population (96.35 %) and stimulate a robust adaptive immune response against the virus upon administration. In silico cloning of the constructed vaccine in PET28a (+) vector ensured its optimal expression in the Escherichia coli system. Molecular docking, molecular dynamics simulation, and binding free energy estimation collectively support the stability and energetically favourable interaction of the modeled vaccine-TLR2/4 complexes. CONCLUSION The designed multi-epitope vaccine in the present study could serve as a potential vaccine candidate to protect against LMCV infection; however, the experimental validation and safety testing of the vaccine is warranted to validate the study's outcomes.
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Affiliation(s)
- Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman; Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Peshawar 25000, Pakistan
| | - Aiman Bushra
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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Mohammadzadeh Hosseini Moghri SAH, Mahmoodi Chalbatani G, Ranjbar M, Raposo C, Abbasian A. CD171 Multi-epitope peptide design based on immuno-informatics approach as a cancer vaccine candidate for glioblastoma. J Biomol Struct Dyn 2023; 41:1028-1040. [PMID: 36617427 DOI: 10.1080/07391102.2021.2020166] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glioblastoma (GB) is a common primary malignancy of the central nervous system, and one of the highly lethal brain tumors. GB cells can promote therapeutic resistance and tumor angiogenesis. The CD171 is an adhesion molecule in neuronal cells that is expressed in glioma cells as a regulator of brain development during the embryonic period. CD171 is one of the immunoglobulin-like CAMs (cell adhesion molecules) families that can be associated with prognosis in a variety of human tumors. The multi-epitope peptide vaccines are based on synthetic peptides with a combination of both B-cell epitopes and T-cell epitopes, which can induce specific humoral or cellular immune responses. Moreover, Cholera toxin subunit B (CTB), a novel TLR agonist was utilized in the final construct to polarize CD4+ T cells toward T-helper 1 to induce strong cytotoxic T lymphocytes (CTL) responses. In the present study, several immune-informatics tools were used for analyzing the CD171 sequence and studying the important characteristics of a designed vaccine. The results included molecular docking, molecular dynamics simulation, immune response simulation, prediction and validation of the secondary and tertiary structure, physicochemical properties, solubility, conservancy, toxicity as well as antigenicity and allergenicity of the promising candidate for a vaccine against CD171. The immuno-informatic analyze suggested 12 predicted multi-epitope peptides, whose construction consists of 582 residues long. Therewith, cloning adaptation of the designed vaccine was performed, and eventually sequence was inserted into pET30a (+) vector for the application of the anti-glioblastoma vaccine development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Mojtaba Ranjbar
- Faculty of Biotechnology, Department of Microbial Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Catarina Raposo
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arefeh Abbasian
- Faculty of Basic Sciences, Department of Biology, Semnan University, Semnan, Iran
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15
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Singhal A, Singh A, Shrivastava A, Khan R. Epitope imprinted polymeric materials: application in electrochemical detection of disease biomarkers. J Mater Chem B 2023; 11:936-954. [PMID: 36606445 DOI: 10.1039/d2tb02135h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epitope imprinting is a promising method for creating specialized recognition sites that resemble natural biorecognition elements. Epitope-imprinted materials have gained a lot of attention recently in a variety of fields, including bioanalysis, drug delivery, and clinical therapy. The vast applications of epitope imprinted polymers are due to the flexibility in choosing monomers, the simplicity in obtaining templates, specificity toward targets, and resistance to harsh environments along with being cost effective in nature. The "epitope imprinting technique," which uses only a tiny subunit of the target as the template during imprinting, offers a way around various drawbacks inherent to biomacromolecule systems i.e., traditional molecular imprinting techniques with regards to the large size of proteins, such as the size, complexity, accessibility, and conformational flexibility of the template. Electrochemical based sensors are proven to be promising tool for the quick, real-time monitoring of biomarkers. This review unravels epitope imprinting techniques, approaches, and strategies and highlights the applicability of these techniques for the electrochemical quantification of biomarkers for timely disease monitoring. In addition, some challenges are discussed along with future prospective developments.
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Affiliation(s)
- Ayushi Singhal
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Amrita Singh
- Department of Biotechnology, Barkatullah University, Habibganj, Bhopal, Madhya Pradesh 462026, India
| | - Apoorva Shrivastava
- Dr D. Y. Patil Biotechnology and Bioinformatics Institute, Dr D. Y. Patil Vidyapeeth, Sr. No. 87-88, Mumbai-Bangalore Highway, Tathawade, Pune, Maharashtra, 411033, India
| | - Raju Khan
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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16
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Waqas M, Aziz S, Liò P, Khan Y, Ali A, Iqbal A, Khan F, Almajhdi FN. Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets. Front Immunol 2023; 14:1091941. [PMID: 36776835 PMCID: PMC9908764 DOI: 10.3389/fimmu.2023.1091941] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The current monkeypox (MPX) outbreak, caused by the monkeypox virus (MPXV), has turned into a global concern, with over 59,000 infection cases and 23 deaths worldwide. Objectives Herein, we aimed to exploit robust immunoinformatics approach, targeting membrane-bound, enveloped, and extracellular proteins of MPXV to formulate a chimeric antigen. Such a strategy could similarly be applied for identifying immunodominant epitopes and designing multi-epitope vaccine ensembles in other pathogens responsible for chronic pathologies that are difficult to intervene against. Methods A reverse vaccinology pipeline was used to select 11 potential vaccine candidates, which were screened and mapped to predict immunodominant B-cell and T-cell epitopes. The finalized epitopes were merged with the aid of suitable linkers, an adjuvant (Resuscitation-promoting factor), a PADRE sequence (13 aa), and an HIV TAT sequence (11 aa) to formulate a multivalent epitope vaccine. Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. C-ImmSim server was implemented to examine the immune response against the designed multi-epitope antigen. Results and discussion The designed chimeric vaccine construct included 21 immunodominant epitopes (six B-cell, eight cytotoxic T lymphocyte, and seven helper T-lymphocyte) and is predicted non-allergen, antigenic, soluble, with suitable physicochemical features, that can promote cross-protection among the MPXV strains. The selected epitopes indicated a wide global population coverage (93.62%). Most finalized epitopes have 70%-100% sequence similarity with the experimentally validated immune epitopes of the vaccinia virus, which can be helpful in the speedy progression of vaccine design. Lastly, molecular docking and molecular dynamics simulation computed stable and energetically favourable interaction between the putative antigen and TLR4. Conclusion Our results show that the multi-epitope vaccine might elicit cellular and humoral immune responses and could be a potential vaccine candidate against the MPXV infection. Further experimental testing of the proposed vaccine is warranted to validate its safety and efficacy profile.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Yumna Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Faizullah Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Fahad Nasser Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Gul I, Hassan A, Muneeb JM, Akram T, Haq E, Shah RA, Ganai NA, Ahmad SM, Chikan NA, Shabir N. A multiepitope vaccine candidate against infectious bursal disease virus using immunoinformatics-based reverse vaccinology approach. Front Vet Sci 2023; 9:1116400. [PMID: 36713875 PMCID: PMC9880294 DOI: 10.3389/fvets.2022.1116400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Infectious bursal disease virus is the causative agent of infectious bursal disease (Gumboro disease), a highly contagious immunosuppressive disease of chicken with a substantial economic impact on small- and large-scale poultry industries worldwide. Currently, live attenuated vaccines are widely used to control the disease in chickens despite their issues with safety (immunosuppression and bursal atrophy) and efficiency (breaking through the maternally-derived antibody titer). To overcome the drawbacks, the current study has, for the first time, attempted to construct a computational model of a multiepitope based vaccine candidate against infectious bursal disease virus, which has the potential to overcome the safety and protection issues found in the existing live-attenuated vaccines. The current study used a reverse vaccinology based immunoinformatics approach to construct the vaccine candidate using major and minor capsid proteins of the virus, VP2 and VP3, respectively. The vaccine construct was composed of four CD8+ epitopes, seven CD4+ T-cell epitopes, 11 B-cell epitopes and a Cholera Toxin B adjuvant, connected using appropriate flexible peptide linkers. The vaccine construct was evaluated as antigenic with VaxiJen Score of 0.6781, immunogenic with IEDB score of 2.89887 and non-allergenic. The 55.64 kDa construct was further evaluated for its physicochemical characteristics, which revealed that it was stable with an instability index of 16.24, basic with theoretical pI of 9.24, thermostable with aliphatic index of 86.72 and hydrophilic with GRAVY score of -0.256. The docking and molecular dynamics simulation studies of the vaccine construct with Toll-like receptor-3 revealed fair structural interaction (binding affinity of -295.94 kcal/mol) and complex stability. Further, the predicted induction of antibodies and cytokines by the vaccine construct indicated the possible elicitation of the host's immune response against the virus. The work is a significant attempt to develop next-generation vaccines against the infectious bursal disease virus though further experimental studies are required to assess the efficacy and protectivity of the proposed vaccine candidate in vivo.
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Affiliation(s)
- Irfan Gul
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Amreena Hassan
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Jan Mohd Muneeb
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Towseef Akram
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Riaz Ahmad Shah
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Nazir Ahmad Ganai
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Syed Mudasir Ahmad
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Naveed Anjum Chikan
- Division of Computational Biology, Daskdan Innovations Pvt. Ltd., Srinagar, India
| | - Nadeem Shabir
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,*Correspondence: Nadeem Shabir ✉
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18
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Rahman MM, Masum MHU, Talukder A, Akter R. An in silico reverse vaccinology approach to design a novel multiepitope peptide vaccine for non-small cell lung cancers. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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19
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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20
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Campos DMDO, Silva MKD, Barbosa ED, Leow CY, Fulco UL, Oliveira JIN. Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants. Comput Biol Chem 2022; 101:107754. [PMID: 36037724 PMCID: PMC9385604 DOI: 10.1016/j.compbiolchem.2022.107754] [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] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
The current COVID-19 pandemic, an infectious disease caused by the novel coronavirus (SARS-CoV-2), poses a threat to global health because of its high rate of spread and death. Currently, vaccination is the most effective method to prevent the spread of this disease. In the present study, we developed a novel multiepitope vaccine against SARS-CoV-2 containing Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (BA.1) variants. To this end, we performed a robust immunoinformatics approach based on multiple epitopes of the four structural proteins of SARS-CoV-2 (S, M, N, and E) from 475 SARS-CoV-2 genomes sequenced from the regions with the highest number of registered cases, namely the United States, India, Brazil, France, Germany, and the United Kingdom. To investigate the best immunogenic epitopes for linear B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL), we evaluated antigenicity, allergenicity, conservation, immunogenicity, toxicity, human population coverage, IFN-inducing, post-translational modifications, and physicochemical properties. The tertiary structure of a vaccine prototype was predicted, refined, and validated. Through docking experiments, we evaluated its molecular coupling to the key immune receptor Toll-Like Receptor 3 (TLR3). To improve the quality of docking calculations, quantum mechanics/molecular mechanics calculations (QM/MM) were used, with the QM part of the simulations performed using the density functional theory formalism (DFT). Cloning and codon optimization were performed for the successful expression of the vaccine in E. coli. Finally, we investigated the immunogenic properties and immune response of our SARS-CoV-2 multiepitope vaccine. The results of the simulations show that administering our prototype three times significantly increases the antibody response and decreases the amount of antigens. The proposed vaccine candidate should therefore be tested in clinical trials for its efficacy in neutralizing SARS-CoV-2.
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Affiliation(s)
- Daniel Melo de Oliveira Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | | | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
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21
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Yousaf M, Ismail S, Ullah A, Bibi S. Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine. Front Immunol 2022; 13:1035924. [PMID: 36405737 PMCID: PMC9668073 DOI: 10.3389/fimmu.2022.1035924] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world’s population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.
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Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- *Correspondence: Maha Yousaf, ; Shabana Bibi,
| | - Saba Ismail
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, China
- *Correspondence: Maha Yousaf, ; Shabana Bibi,
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22
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Danazumi AU, Iliyasu Gital S, Idris S, BS Dibba L, Balogun EO, Górna MW. Immunoinformatic design of a putative multi-epitope vaccine candidate against Trypanosoma brucei gambiense. Comput Struct Biotechnol J 2022; 20:5574-5585. [PMID: 36284708 PMCID: PMC9576565 DOI: 10.1016/j.csbj.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/13/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022] Open
Abstract
Human African trypanosomiasis (HAT) is a neglected tropical disease that is caused by flagellated parasites of the genus Trypanosoma. HAT imposes a significant socio-economic burden on many countries in sub-Saharan Africa and its control is hampered by several drawbacks ranging from the ineffectiveness of drugs, complex dosing regimens, drug resistance, and lack of a vaccine. Despite more than a century of research and investigations, the development of a vaccine to tackle HAT is still challenging due to the complex biology of the pathogens. Advancements in computational modeling coupled with the availability of an unprecedented amount of omics data from different organisms have allowed the design of new generation vaccines that offer better antigenicity and safety profile. One of such new generation approaches is a multi-epitope vaccine (MEV) designed from a collection of antigenic peptides. A MEV can stimulate both cellular and humoral immune responses as well as avoiding possible allergenic reactions. Herein, we take advantage of this approach to design a MEV from conserved hypothetical plasma membrane proteins of Trypanosoma brucei gambiense, the trypanosome subspecies that is responsible for the west and central African forms of HAT. The designed MEV is 402 amino acids long (41.5 kDa). It is predicted to be antigenic, non-toxic, to assume a stable 3D conformation, and to interact with a key immune receptor. In addition, immune simulation foresaw adequate immune stimulation by the putative antigen and a lasting memory. Therefore, the designed chimeric vaccine represents a potential candidate that could be used to target HAT.
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Affiliation(s)
- Ammar Usman Danazumi
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland,Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
| | | | - Salisu Idris
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Department of Medical Laboratory Science, Kazaure School of Health Technology, Jigawa, Nigeria
| | - Lamin BS Dibba
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Department of Physical and Natural Sciences, School of Arts and Sciences, University of the Gambia, Brikama Campus. P.O Box 3530, Serrekunda, the Gambia
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
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23
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Samad A, Meghla NS, Nain Z, Karpiński TM, Rahman MS. Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: a molecular dynamics and immune simulation approaches. Cancer Immunol Immunother 2022; 71:2535-2548. [PMID: 35294591 PMCID: PMC8924353 DOI: 10.1007/s00262-022-03181-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022]
Abstract
Background Bovine leukemia virus (BLV) is an oncogenic delta-retrovirus causing bovine leucosis. Studies on BLV have shown the association with human breast cancer. However, the exact molecular mechanism is neither known nor their appropriate preventative measure to halt the disease initiation and progression. In this study, we designed a multi-epitope vaccine against BLV using a computational analyses.
Methods Following a rigorous assessment, the vaccine was constructed using the T-cell epitopes from each BLV-derived protein with suitable adjuvant and linkers. Both physicochemistry and immunogenic potency as well as the safeness of the vaccine candidate were assessed. Population coverage was done to evaluate the vaccine probable efficiency in eliciting the immune response worldwide. After homology modeling, the three-dimensional structure was refined and validated to determine the quality of the designed vaccine. The vaccine protein was then subjected to molecular docking with Toll-like receptor 3 (TLR3) to evaluate the binding efficiency followed by dynamic simulation for stable interaction. Results Our vaccine construct has the potential immune response and good physicochemical properties. The vaccine is antigenic and immunogenic, and has no allergenic or toxic effect on the human body. This novel vaccine contains a significant interactions and binding affinity with the TLR3 receptor. Conclusions The proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat BLV infections. However, experimental evaluations are essential to validate the exact safety and immunogenic profiling of this vaccine. Supplementary Information The online version contains supplementary material available at 10.1007/s00262-022-03181-w.
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Nigar Sultana Meghla
- Department of Microbiology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Zulkar Nain
- Department of Biochemistry, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
| | - Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
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24
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Soto LF, Romaní AC, Jiménez-Avalos G, Silva Y, Ordinola-Ramirez CM, Lopez Lapa RM, Requena D. Immunoinformatic analysis of the whole proteome for vaccine design: An application to Clostridium perfringens. Front Immunol 2022; 13:942907. [PMID: 36110855 PMCID: PMC9469472 DOI: 10.3389/fimmu.2022.942907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridium perfringens is a dangerous bacterium and known biological warfare weapon associated with several diseases, whose lethal toxins can produce necrosis in humans. However, there is no safe and fully effective vaccine against C. perfringens for humans yet. To address this problem, we computationally screened its whole proteome, identifying highly immunogenic proteins, domains, and epitopes. First, we identified that the proteins with the highest epitope density are Collagenase A, Exo-alpha-sialidase, alpha n-acetylglucosaminidase and hyaluronoglucosaminidase, representing potential recombinant vaccine candidates. Second, we further explored the toxins, finding that the non-toxic domain of Perfringolysin O is enriched in CTL and HTL epitopes. This domain could be used as a potential sub-unit vaccine to combat gas gangrene. And third, we designed a multi-epitope protein containing 24 HTL-epitopes and 34 CTL-epitopes from extracellular regions of transmembrane proteins. Also, we analyzed the structural properties of this novel protein using molecular dynamics. Altogether, we are presenting a thorough immunoinformatic exploration of the whole proteome of C. perfringens, as well as promising whole-protein, domain-based and multi-epitope vaccine candidates. These can be evaluated in preclinical trials to assess their immunogenicity and protection against C. perfringens infection.
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Affiliation(s)
- Luis F. Soto
- Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ana C. Romaní
- Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Gabriel Jiménez-Avalos
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Yshoner Silva
- Departamento de Salud Pública, Facultad de Ciencias de la Salud, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru
| | - Carla M. Ordinola-Ramirez
- Departamento de Salud Pública, Facultad de Ciencias de la Salud, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru
| | - Rainer M. Lopez Lapa
- Departamento de Salud Pública, Facultad de Ciencias de la Salud, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru
- Instituto de Ganadería y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, United States
- *Correspondence: David Requena,
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25
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Alharbi N, Skwarczynski M, Toth I. The influence of component structural arrangement on peptide vaccine immunogenicity. Biotechnol Adv 2022; 60:108029. [PMID: 36028180 DOI: 10.1016/j.biotechadv.2022.108029] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
Peptide-based subunit vaccines utilise minimal immunogenic components (i.e. peptides) to generate highly specific immune responses, without triggering adverse reactions. However, strong adjuvants and/or effective delivery systems must be incorporated into such vaccines, as peptide antigens cannot induce substantial immune responses on their own. Unfortunately, many adjuvants are too weak or too toxic to be used in combination with peptide antigens. These shortcomings have been addressed by the conjugation of peptide antigens with lipidic/ hydrophobic adjuvanting moieties. The conjugates have shown promising safety profiles and improved immunogenicity without the help of traditional adjuvants and have been efficient in inducing desired immune responses following various routes of administration, including subcutaneous, oral and intranasal. However, not only conjugation per se, but also component arrangement influences vaccine efficacy. This review highlights the importance of influence of the vaccine chemical structure modification on the immune responses generated. It discusses a variety of factors that affect the immunogenicity of peptide conjugates, including: i) self-adjuvanting moiety length and number; ii) the orientation of epitopes and self-adjuvanting moieties in the conjugate; iii) the presence of spacers between conjugated components; iv) multiepitopic arrangement; and v) the effect of chirality on vaccine efficacy.
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Affiliation(s)
- Nedaa Alharbi
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; University of Jeddah, College of Science and Arts, Department of Chemistry, Jeddah, Saudi Arabia
| | - Mariusz Skwarczynski
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Istvan Toth
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; School of Pharmacy, The University of Queensland, Brisbane, QLD, 4102, Australia.
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26
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Jalal K, Khan K, Basharat Z, Abbas MN, Uddin R, Ali F, Khan SA, Hassan SSU. Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60035-60053. [PMID: 35414157 PMCID: PMC9005162 DOI: 10.1007/s11356-022-19979-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Sciences, HEJ Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Fawad Ali
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Saeed Ahmad Khan
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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27
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Yousaf M, Ullah A, Sarosh N, Abbasi SW, Ismail S, Bibi S, Hasan MM, Albadrani GM, Talaat Nouh NA, Abdulhakim JA, Abdel-Daim MM, Bin Emran T. Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach. Vaccines (Basel) 2022; 10:vaccines10081192. [PMID: 36016080 PMCID: PMC9414393 DOI: 10.3390/vaccines10081192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.
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Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan; (M.Y.); (N.S.)
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Nida Sarosh
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan; (M.Y.); (N.S.)
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan;
| | - Saba Ismail
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan;
- Correspondence: (S.I.); (S.B.)
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
- Correspondence: (S.I.); (S.B.)
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh;
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Nehal Ahmed Talaat Nouh
- Department of Microbiology, Medicine Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia;
- Inpatient Pharmacy, Mansoura University Hospitals, Mansoura 35516, Egypt
| | - Jawaher A. Abdulhakim
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu 46522, Saudi Arabia;
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia;
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
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28
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Khan K, Khan SA, Jalal K, Ul-Haq Z, Uddin R. Immunoinformatic approach for the construction of multi-epitopes vaccine against omicron COVID-19 variant. Virology 2022; 572:28-43. [PMID: 35576833 PMCID: PMC9087879 DOI: 10.1016/j.virol.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022]
Abstract
The newly discovered SARS-CoV-2 Omicron variant B.1.1.529 is a Variant of Concern (VOC) announced by the World Health Organization (WHO). It's becoming increasingly difficult to keep these variants from spreading over the planet. The fifth wave has begun in several countries because of Omicron variant, and it is posing a threat to human civilization. As a result, we need effective vaccination that can tackle Omicron SARS-CoV-2 variants that are bound to emerge. Therefore, the current study is an initiative to design a peptide-based chimeric vaccine that may potentially battle SARS-CoV-2 Omicron variant. As a result, the most relevant epitopes present in the mutagenic areas of Omicron spike protein were identified using a set of computational tools and immunoinformatic techniques to uncover common MHC-1, MHC-II, and B cell epitopes that may have the ability to influence the host immune mechanism. A final of three epitopes from CD8+ T-cell, CD4+ T-cell epitopes, and B-cell were shortlisted from spike protein, and that are highly antigenic, IFN-γ inducer, as well as overlapping for the construction of twelve vaccine models. As a result, the antigenic epitopes were coupled with a flexible and stable peptide linker, and the adjuvant was added at the N-terminal end to create a unique vaccine candidate. The structure of a 3D vaccine candidate was refined, and its quality was assessed by using web servers. However, the applied immunoinformatic study along with the molecular docking and simulation of 12 modeled vaccines constructs against six distinct HLAs, and TLRs (TLR2, and TLR4) complexes revealed that the V1 construct was non-allergenic, non-toxic, highly immunogenic, antigenic, and most stable. The vaccine candidate's stability was confirmed by molecular dynamics investigations. Finally, we studied the expression of the suggested vaccination using codon optimization and in-silico cloning. The current study proposed V1 Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that may help the scientific community to treat SARS-CoV-2 infections.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Salman Ali Khan
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Zaheer Ul-Haq
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Pakistan; Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
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29
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Islam E. Development of epitope-based chimeric protein as a vaccine against Lujo virus by utilizing immunoinformatic tools. Future Virol 2022. [DOI: 10.2217/fvl-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Lujo is a modern zoonotic virus that is potentially fatal and spreads by bodily fluids. In this research, immunoinformatic tools are used to build a vaccine. Methodology: The epitopes of cytotoxic T-lymphocytes, helper T-lymphocytes and linear B-lymphocytes were predicted from the most antigenic protein. The designed vaccine's physiochemical properties and 3D structure have been forecasted. Low free energy and strong binding affinity estimated in molecular docking against toll-like receptor 4 (TLR4) and dynamic simulation. Furthermore, in silico cloning in the Escherichia coli K12 host system was performed for high level of expression. Conclusion: Finally, immune simulation was used to determine immune responses to the vaccine that was formulated confirming the developed vaccine as a good candidate against Lujo virus.
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Affiliation(s)
- Enayetul Islam
- Department of Genetic Engineering & Biotechnology, University of Chittagong, Chittagong, Bangladesh
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Ullah N, Anwer F, Ishaq Z, Siddique A, Shah MA, Rahman M, Rahman A, Mao X, Jiang T, Lee BL, Bae T, Ali A. In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting multi-domain approach. J Immunol Methods 2022; 504:113264. [PMID: 35341759 PMCID: PMC9040383 DOI: 10.1016/j.jim.2022.113264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
The vaccine development strategies have evolved from using an entire organism as an immunogen to a single antigen and further towards an epitope. Since an epitope is a relatively tiny and immunologically relevant part of an antigen, it has the potential to stimulate more robust and specific immune responses while causing minimal adverse effects. As a result, the recent focus of vaccine development has been to develop multi-epitope vaccines that can target multiple virulence mechanisms. Accordingly, we designed multi-epitope vaccine candidates B (multi-B-cell epitope immunogen) and CTB-B (an adjuvant - cholera toxin subunit B (CTB) - attached to immunogen B) against S. aureus by employing immunoinformatics approaches. The designed vaccines are composed of B-cell epitope segments (20-mer) of the eight well-characterized S. aureus virulence factors, namely ClfB, FnbpA, Hla, IsdA, IsdB, LukE, SdrD, and SdrE connected in series. The designed vaccines were expressed, purified, and administered to C57BL/6 mice with Freund adjuvant to evaluate the immunogenicity and protective efficacy. The results revealed that the immunized mice showed high IgG titers for the immunogen, and the antibody titers increased significantly following the second immunization. However, the generated antibodies did not protect the mice from infection. The interaction of anti-B antibodies with source virulence factors showed that the generated antibodies have no binding affinity with any of the corresponding virulence factors. Our results demonstrate the limitation of the in silico designed B-cell multi-epitope vaccine and suggest that a protein domain carrying both linear and conformational B-cell epitopes might be a better choice for developing an effective multi-epitope vaccine against S. aureus.
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Affiliation(s)
- Nimat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan; Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, 3400 Broadway, Gary, Indiana 46408, USA
| | - Farha Anwer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan
| | - Zaara Ishaq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan
| | - Abubakar Siddique
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan
| | - Majid Ali Shah
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, 3400 Broadway, Gary, Indiana 46408, USA
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan
| | - Xinrui Mao
- Host Defense Protein Laboratory, College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - TingTing Jiang
- Host Defense Protein Laboratory, College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Bok Luel Lee
- Host Defense Protein Laboratory, College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, 3400 Broadway, Gary, Indiana 46408, USA.
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan.
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Raza A, Asif Rasheed M, Raza S, Tariq Navid M, Afzal A, Jamil F. Prediction and analysis of multi epitope based vaccine against Newcastle disease virus based on haemagglutinin neuraminidase protein. Saudi J Biol Sci 2022; 29:3006-3014. [PMID: 35531218 PMCID: PMC9073007 DOI: 10.1016/j.sjbs.2022.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
Newcastle disease virus (NDV), an avian orthoavulavirus, is a causative agent of Newcastle disease named (NDV), and can cause even the epidemics when disease is not treated. Previously several vaccines based on attenuated and inactivated viruses have been reported which are rendered useless with the passage of time due to versatile changes in viral genome. Therefore, we aimed to develop an effective multi-epitope vaccine against the haemagglutinin neuraminidase (HN) protein of 26 NDV strains from Pakistan through a modern immunoinformatic approaches. As a result, a vaccine chimaera was constructed by combining T-cell and B-cell epitopes with the appropriate linkers and adjuvant. The designed vaccine was highly immunogenic, non-allergen and antigenic; therefore, the potential 3D-structureof multi epitope vaccine was constructed, refined and validated. A molecular docking study of a multiepitope vaccine candidate with the chicken Toll-like receptor-4 indicated successful binding. An In silico immunological simulation was used to evaluate the candidate vaccine's ability to elicit an effective immune response. According to the computational studies, the proposed multiepitope vaccine is physically stable and may induce immune responses whichsuggested it a strong candidate against 26 Newcastle disease virus strains from Pakistan.
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Affiliation(s)
- Adnan Raza
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Muhammad Asif Rasheed
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Sohail Raza
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Tariq Navid
- Department of Biological Sciences, National University of Medical sciences, Rawalpindi 46000, Pakistan
| | - Amna Afzal
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Farrukh Jamil
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
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Rafi MO, Al-Khafaji K, Sarker MT, Taskin-Tok T, Rana AS, Rahman MS. Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. RSC Adv 2022; 12:4288-4310. [PMID: 35425433 PMCID: PMC8981096 DOI: 10.1039/d1ra06532g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/23/2022] [Indexed: 12/17/2022] Open
Abstract
A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, AL-Nisour University College Baghdad Iraq
| | - Md Takim Sarker
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Tugba Taskin-Tok
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University Gaziantep 27310 Turkey
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University Gaziantep Turkey
| | - Abdus Samad Rana
- School of Biotechnology, Jiangnan University Wuxi 214122 PR China
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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Mould RC, van Vloten JP, AuYeung AWK, Walsh SR, de Jong J, Susta L, Mutsaers AJ, Petrik JJ, Wood GA, Wootton SK, Karimi K, Bridle BW. Using a Prime-Boost Vaccination Strategy That Proved Effective for High Resolution Epitope Mapping to Characterize the Elusive Immunogenicity of Survivin. Cancers (Basel) 2021; 13:cancers13246270. [PMID: 34944889 PMCID: PMC8699342 DOI: 10.3390/cancers13246270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The generation of tumor-specific T cells remains a pillar of modern cancer immunotherapy. Exogenous vaccines often rely on targeting tumor-associated antigens. The anti-apoptotic protein survivin has been deemed a high priority target due to its overexpression in a wide variety of tumor types. To support the analysis of tumor-associated T cell responses, optimization of epitope mapping would be valuable. A heterologous prime-boost vaccination strategy was designed to target survivin to induce anti-tumor immune responses. However, survivin-specific T cell responses could not be detected in mice. Potential mechanisms to explain this failure were explored. To confirm the robustness of the vaccination platform, enhanced green fluorescent protein (eGFP) was targeted since it has been defined as a protein with relatively low immunogenicity. In this context the vaccination strategy uncovered novel T cell epitopes from eGFP in two strains of mice. This research highlighted the utility of the vaccine platform to triage potential target antigens based on their immunogenicity. Abstract Survivin is a member of the inhibitor of apoptosis family of proteins and has been reported to be highly expressed in a variety of cancer types, making it a high priority target for cancer vaccination. We previously described a heterologous prime-boost strategy using a replication-deficient adenovirus, followed by an oncolytic rhabdovirus that generates unprecedented antigen-specific T cell responses. We engineered each vector to express a mutated version of full-length murine survivin. We first sought to uncover the complete epitope map for survivin-specific T cell responses in C57BL/6 and BALB/c mice by flow cytometry. However, no T cell responses were detected by intracellular cytokine staining after re-stimulation of T cells. Survivin has been found to be expressed by activated T cells, which could theoretically cause T cell-mediated killing of activated T cells, known as fratricide. We were unable to recapitulate this phenomenon in experiments. Interestingly, the inactivated survivin construct has been previously shown to directly kill tumor cells in vitro. However, there was no evidence in our models of induction of death in antigen-presenting cells due to treatment with a survivin-expressing vector. Using the same recombinant virus-vectored prime-boost strategy targeting the poorly immunogenic enhanced green fluorescent protein proved to be a highly sensitive method for mapping T cell epitopes, particularly in the context of identifying novel epitopes recognized by CD4+ T cells. Overall, these results suggested there may be unusually robust tolerance to survivin in commonly used mouse strains that cannot be broken, even when using a particularly potent vaccination platform. However, the vaccination method shows great promise as a strategy for identifying novel and subdominant T cell epitopes.
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Affiliation(s)
- Robert C. Mould
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Jacob P. van Vloten
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Amanda W. K. AuYeung
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Scott R. Walsh
- McMaster Immunology Research Centre, McMaster University Hamilton, Hamilton, ON L8S 3L8, Canada;
| | - Jondavid de Jong
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Leonardo Susta
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Anthony J. Mutsaers
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (A.J.M.); (J.J.P.)
| | - James J. Petrik
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (A.J.M.); (J.J.P.)
| | - Geoffrey A. Wood
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Sarah K. Wootton
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Khalil Karimi
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
| | - Byram W. Bridle
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.C.M.); (J.P.v.V.); (A.W.K.A.); (J.d.J.); (L.S.); (G.A.W.); (S.K.W.); (K.K.)
- Correspondence: ; Tel.: +51-9824-4120 (ext. 54657)
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Al Zamane S, Nobel FA, Jebin RA, Amin MB, Somadder PD, Antora NJ, Hossain MI, Islam MJ, Ahmed K, Moni MA. Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches. INFORMATICS IN MEDICINE UNLOCKED 2021; 27:100781. [PMID: 34746365 PMCID: PMC8563510 DOI: 10.1016/j.imu.2021.100781] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/31/2023] Open
Abstract
The coronavirus family has been infecting the human population for the past two decades, but the ongoing coronavirus called SARS-CoV-2 has posed an enigmatic challenge to global public health security. Since last year, the mutagenic quality of this virus is causing changes to its genetic material. To prevent those situations, the FDA approved some emergency vaccines but there is no assurance that these will function properly in the complex human body system. In point of view, a short but efficient effort has made in this study to develop an immune epitope-based therapy for the rapid exploitation of SARS-CoV-2 by applying in silico structural biology and advancing immune information strategies. The antigenic epitopes were screened from the Surface, Membrane, Envelope proteins of SARS-CoV-2 and passed through several immunological filters to determine the best possible one. According to this, 7CD4+, 10CD8+ and 5 B-cell epitopes were found to be prominent, antigenic, immunogenic, and most importantly, highly conserved among 128 Bangladeshi and 110 other infected countries SARS-CoV-2 variants. After that, the selected epitopes and adjuvant were linked to finalize the multi-epitope vaccine by appropriate linkers. The immune simulation disclosed that the engineered vaccine could activate both humoral and innate immune responses. For the prediction of an effective binding, molecular docking was carried out between the vaccine and immunological receptors (TLRs). Strong binding affinity and good docking scores clarified the stringency of the vaccines. Furthermore, MD simulation was performed within the highest binding affinity complex to observe the stability. Codon optimization and other physicochemical properties revealed that the vaccine would be suitable for a higher expression at cloning level. So, monitoring the overall in silico assessment, we anticipated that our engineered vaccine would be a plausible prevention against COVID-19.
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Affiliation(s)
- Saad Al Zamane
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Fahim Alam Nobel
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Ruksana Akter Jebin
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Mohammed Badrul Amin
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, 1212, Bangladesh
| | - Pratul Dipta Somadder
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Nusrat Jahan Antora
- Department of Genetic Engineering and Biotechnology, Faculty of Sciences and Engineering, East West University, Aftabnagar, Dhaka, 1212, Bangladesh
| | - Md Imam Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Mohammod Johirul Islam
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Kawsar Ahmed
- Group of Biophotomatiχ, Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna University of Science and Technology, Pabna, 6600, Bangladesh
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Deb D, Basak S, Kar T, Narsaria U, Castiglione F, Paul A, Pandey A, Srivastava AP. Immunoinformatics based designing a multi-epitope vaccine against pathogenic Chandipura vesiculovirus. J Cell Biochem 2021; 123:322-346. [PMID: 34729821 DOI: 10.1002/jcb.30170] [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: 01/29/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/11/2022]
Abstract
Chandipura vesiculovirus (CHPV) is a rapidly emerging pathogen responsible for causing acute encephalitis. Due to its widespread occurrence in Asian and African countries, this has become a global threat, and there is an urgent need to design an effective and nonallergenic vaccine against this pathogen. The present study aimed to develop a multi-epitope vaccine using an immunoinformatics approach. The conventional method of vaccine design involves large proteins or whole organism which leads to unnecessary antigenic load with increased chances of allergenic reactions. In addition, the process is also very time-consuming and labor-intensive. These limitations can be overcome by peptide-based vaccines comprising short immunogenic peptide fragments that can elicit highly targeted immune responses, avoiding the chances of allergenic reactions, in a relatively shorter time span. The multi-epitope vaccine constructed using CTL, HTL, and IFN-γ epitopes was able to elicit specific immune responses when exposed to the pathogen, in silico. Not only that, molecular docking and molecular dynamics simulation studies confirmed a stable interaction of the vaccine with the immune receptors. Several physicochemical analyses of the designed vaccine candidate confirmed it to be highly immunogenic and nonallergic. The computer-aided analysis performed in this study suggests that the designed multi-epitope vaccine can elicit specific immune responses and can be a potential candidate against CHPV.
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Affiliation(s)
- Debashrito Deb
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Srijita Basak
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Tamalika Kar
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Utkarsh Narsaria
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Via dei Taurini, Rome, Italy
| | - Abhirup Paul
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Ashutosh Pandey
- Plant Metabolic Engineering, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Anurag P Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
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Identification of immunodominant epitopes in allelic variants VK210 and VK247 of Plasmodium Vivax Circumsporozoite immunogen. INFECTION GENETICS AND EVOLUTION 2021; 96:105120. [PMID: 34655808 DOI: 10.1016/j.meegid.2021.105120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax-induced malaria is among the leading causes of morbidity and mortality in sub-tropical and tropical regions and infect 2.85 billion people globally. The continual rise and propagation of resistance against anti-malarial drugs is a prerequisite to develop a potent vaccine candidate for Plasmodium vivax (P. vivax). Circumsporozoite protein (CSP) is an important immunogen of malaria parasite that has the conserved CSP structure as an immune dominant B-cell epitope. In current study, we focused on designing multi-epitope vaccines (MEVs) using various immunoinformatics tools against Pakistani based allelic variants VK210 and VK247 of P. vivax CSP (PvCSP) gene. Antigenicity, allergic potential and physicochemical parameters of both PvCSP variants were assessed for the designed MEVs and they were within acceptable range suitable for post experimental investigations. The three-dimensional structures of both MEVs have been predicted ab initio, optimized, and validated by using different online servers. The both MEVs candidates were stable and free from aggregation-prone regions. The stability of both MEVs had been improved by a disulfide engineering approach. To estimate the binding energy and stability of the MEVs, molecular docking simulation and binding free energy calculations with TLR-4 immune receptor have been conducted. The docking score of PvCSP210 and PvCSP247 for TLR-4 was -6.34 kJ/mol and - 2.3 kJ/mol, respectively. For PvCSP210-TLR4 system, mean RMSD was 4.96 Å while PvCSP247-TLR4 system, average RMSD was 4.49 Å. The binding free energy of PvCSP210-TLR4 complex and PvCSP247-TLR4 complex was -50.49/-117.15 kcal/mol (MMGBSA/MMPSA) and -52.94/-96.26 kcal/mol (MMGBSA/MMPSA), respectively. The expression of both MEVs produced in Escherichia coli K12 expression system by in silico cloning was significant. Immune simulation revealed that the proposed MEVs induce strong humoral and cellular immunological responses, in addition to significant production of interleukins and cytokines. In conclusions, we believed that the MEVs proposed in current research, using combine approach of immunoinformatics, structural biology and biophysical approaches, could induce protective and effective immune responses against P. vivax and the experimental validation of our findings could contribute to the development of potential malaria vaccine.
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Mahmud S, Rafi MO, Paul GK, Promi MM, Shimu MSS, Biswas S, Emran TB, Dhama K, Alyami SA, Moni MA, Saleh MA. Designing a multi-epitope vaccine candidate to combat MERS-CoV by employing an immunoinformatics approach. Sci Rep 2021; 11:15431. [PMID: 34326355 PMCID: PMC8322212 DOI: 10.1038/s41598-021-92176-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/21/2021] [Indexed: 01/26/2023] Open
Abstract
Currently, no approved vaccine is available against the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes severe respiratory disease. The spike glycoprotein is typically considered a suitable target for MERS-CoV vaccine candidates. A computational strategy can be used to design an antigenic vaccine against a pathogen. Therefore, we used immunoinformatics and computational approaches to design a multi-epitope vaccine that targets the spike glycoprotein of MERS-CoV. After using numerous immunoinformatics tools and applying several immune filters, a poly-epitope vaccine was constructed comprising cytotoxic T-cell lymphocyte (CTL)-, helper T-cell lymphocyte (HTL)-, and interferon-gamma (IFN-γ)-inducing epitopes. In addition, various physicochemical, allergenic, and antigenic profiles were evaluated to confirm the immunogenicity and safety of the vaccine. Molecular interactions, binding affinities, and the thermodynamic stability of the vaccine were examined through molecular docking and dynamic simulation approaches, during which we identified a stable and strong interaction with Toll-like receptors (TLRs). In silico immune simulations were performed to assess the immune-response triggering capabilities of the vaccine. This computational analysis suggested that the proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat viral infections; however, experimental evaluations remain necessary to verify the exact safety and immunogenicity profile of this vaccine.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Mst Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Salem A Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Faculty of Medicine, WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh.
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Akbay B, Abidi SH, Ibrahim MAA, Mukhatayev Z, Ali S. Multi-Subunit SARS-CoV-2 Vaccine Design Using Evolutionarily Conserved T- and B- Cell Epitopes. Vaccines (Basel) 2021; 9:702. [PMID: 34206865 PMCID: PMC8310312 DOI: 10.3390/vaccines9070702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
The SARS-CoV-2 pandemic has created a public health crisis worldwide. Although vaccines against the virus are efficiently being rolled out, they are proving to be ineffective against certain emerging SARS-CoV-2 variants. The high degree of sequence similarity between SARS-CoV-2 and other human coronaviruses (HCoV) presents the opportunity for designing vaccines that may offer protection against SARS-CoV-2 and its emerging variants, with cross-protection against other HCoVs. In this study, we performed bioinformatics analyses to identify T and B cell epitopes originating from spike, membrane, nucleocapsid, and envelope protein sequences found to be evolutionarily conserved among seven major HCoVs. Evolutionary conservation of these epitopes indicates that they may have critical roles in viral fitness and are, therefore, unlikely to mutate during viral replication thus making such epitopes attractive candidates for a vaccine. Our designed vaccine construct comprises of twelve T and six B cell epitopes that are conserved among HCoVs. The vaccine is predicted to be soluble in water, stable, have a relatively long half-life, and exhibit low allergenicity and toxicity. Our docking results showed that the vaccine forms stable complex with toll-like receptor 4, while the immune simulations predicted that the vaccine may elicit strong IgG, IgM, and cytotoxic T cell responses. Therefore, from multiple perspectives, our multi-subunit vaccine design shows the potential to elicit a strong immune-protective response against SARS-CoV-2 and its emerging variants while carrying minimal risk for causing adverse effects.
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Affiliation(s)
- Burkitkan Akbay
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Zhussipbek Mukhatayev
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
| | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (B.A.); (Z.M.)
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Tay BQ, Wright Q, Ladwa R, Perry C, Leggatt G, Simpson F, Wells JW, Panizza BJ, Frazer IH, Cruz JLG. Evolution of Cancer Vaccines-Challenges, Achievements, and Future Directions. Vaccines (Basel) 2021; 9:vaccines9050535. [PMID: 34065557 PMCID: PMC8160852 DOI: 10.3390/vaccines9050535] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/06/2023] Open
Abstract
The development of cancer vaccines has been intensively pursued over the past 50 years with modest success. However, recent advancements in the fields of genetics, molecular biology, biochemistry, and immunology have renewed interest in these immunotherapies and allowed the development of promising cancer vaccine candidates. Numerous clinical trials testing the response evoked by tumour antigens, differing in origin and nature, have shed light on the desirable target characteristics capable of inducing strong tumour-specific non-toxic responses with increased potential to bring clinical benefit to patients. Novel delivery methods, ranging from a patient’s autologous dendritic cells to liposome nanoparticles, have exponentially increased the abundance and exposure of the antigenic payloads. Furthermore, growing knowledge of the mechanisms by which tumours evade the immune response has led to new approaches to reverse these roadblocks and to re-invigorate previously suppressed anti-tumour surveillance. The use of new drugs in combination with antigen-based therapies is highly targeted and may represent the future of cancer vaccines. In this review, we address the main antigens and delivery methods used to develop cancer vaccines, their clinical outcomes, and the new directions that the vaccine immunotherapy field is taking.
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Affiliation(s)
- Ban Qi Tay
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Quentin Wright
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia;
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
| | - Christopher Perry
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
- Department of Otolaryngology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | - Graham Leggatt
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Fiona Simpson
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - James W. Wells
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Benedict J. Panizza
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
- Department of Otolaryngology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | - Ian H. Frazer
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Jazmina L. G. Cruz
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
- Correspondence: ; Tel.: +61-0478912737
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Forner M, Cañas-Arranz R, Defaus S, de León P, Rodríguez-Pulido M, Ganges L, Blanco E, Sobrino F, Andreu D. Peptide-Based Vaccines: Foot-and-Mouth Disease Virus, a Paradigm in Animal Health. Vaccines (Basel) 2021; 9:vaccines9050477. [PMID: 34066901 PMCID: PMC8150788 DOI: 10.3390/vaccines9050477] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/19/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccines are considered one of the greatest global health achievements, improving the welfare of society by saving lives and substantially reducing the burden of infectious diseases. However, few vaccines are fully effective, for reasons ranging from intrinsic limitations to more contingent shortcomings related, e.g., to cold chain transport, handling and storage. In this context, subunit vaccines where the essential antigenic traits (but not the entire pathogen) are presented in rationally designed fashion have emerged as an attractive alternative to conventional ones. In particular, this includes the option of fully synthetic peptide vaccines able to mimic well-defined B- and T-cell epitopes from the infectious agent and to induce protection against it. Although, in general, linear peptides have been associated to low immunogenicity and partial protection, there are several strategies to address such issues. In this review, we report the progress towards the development of peptide-based vaccines against foot-and-mouth disease (FMD) a highly transmissible, economically devastating animal disease. Starting from preliminary experiments using single linear B-cell epitopes, recent research has led to more complex and successful second-generation vaccines featuring peptide dendrimers containing multiple copies of B- and T-cell epitopes against FMD virus or classical swine fever virus (CSFV). The usefulness of this strategy to prevent other animal and human diseases is discussed.
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Affiliation(s)
- Mar Forner
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (M.F.); (S.D.)
| | - Rodrigo Cañas-Arranz
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.R.-P.)
| | - Sira Defaus
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (M.F.); (S.D.)
| | - Patricia de León
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.R.-P.)
| | - Miguel Rodríguez-Pulido
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.R.-P.)
| | - Llilianne Ganges
- Centre de Recerca en Sanitat Animal (CReSA), OIE Reference Laboratory for Classical Swine Fever, Institute of Agrifood Research and Technology, 08193 Barcelona, Spain;
| | - Esther Blanco
- Centro de Investigación en Sanidad Animal (CISA-INIA), 28130 Valdeolmos, Spain;
| | - Francisco Sobrino
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.R.-P.)
- Correspondence: (F.S.); (D.A.)
| | - David Andreu
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (M.F.); (S.D.)
- Correspondence: (F.S.); (D.A.)
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HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas. Genes (Basel) 2021; 12:genes12010120. [PMID: 33477943 PMCID: PMC7833434 DOI: 10.3390/genes12010120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter. This gene pair synergistically promoted the development of non-small cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remains obscure. In the present study, we first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from The Cancer Genome Atlas (TCGA) database using the correlation analysis of gene expression and gene set enrichment analysis (GSEA), which revealed that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited the Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected using RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2, and BUB1, was involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with the shorter overall survival of LSCC patients. Taken together, our results indicate that GLI1/2 mediates the expression of the PRR11-SKA2-centric gene set that serves as an unfavorable prognostic indicator for LSCC patients, potentializing new combinatorial diagnostic and therapeutic strategies in LSCC.
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Tsai SJ, Amerman A, Jewell CM. Altering Antigen Charge to Control Self-Assembly and Processing of Immune Signals During Cancer Vaccination. Front Immunol 2021; 11:613830. [PMID: 33488621 PMCID: PMC7815530 DOI: 10.3389/fimmu.2020.613830] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Biomaterial delivery systems offer unique potential to improve cancer vaccines by offering targeted delivery and modularity to address disease heterogeneity. Here, we develop a simple platform using a conserved human melanoma peptide antigen (Trp2) modified with cationic arginine residues that condenses an anionic toll-like receptor agonist (TLRa), CpG, into polyplex-like nanoparticles. We reasoned that these structures could offer several useful features for immunotherapy – such as tunable loading, co-delivery of immune cues, and cargo protection – while eliminating the need for synthetic polymers or other complicating delivery systems. We demonstrate that Trp2/CpG polyplexes can readily form over a range of Trp2:CpG ratios and improve antigen uptake by primary antigen presenting cells. We show antigen loading can be tuned by interchanging Trp2 peptides with defined charges and numbers of arginine residues. Notably, these polyplexes with greater antigen loading enhance the functionality of Trp-2 specific T cells and in a mouse melanoma model, decrease tumor burden and improve survival. This work highlights opportunities to control the biophysical properties of nanostructured materials built from immune signals to enhance immunotherapy, without the added complexity or background immune effects often associated with synthetic carriers.
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Affiliation(s)
- Shannon J Tsai
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, United States
| | - Allie Amerman
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, United States
| | - Christopher M Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, United States.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, United States.,United States Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD, United States.,Department of Microbiology and Immunology, University of Maryland Medical School, Baltimore, MD, United States.,Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, United States
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43
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Designing a multi-epitope vaccine against the Lassa virus through reverse vaccinology, subtractive proteomics, and immunoinformatics approaches. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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44
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Hossain MS, Hossan MI, Mizan S, Moin AT, Yasmin F, Akash AS, Powshi SN, Hasan AR, Chowdhury AS. Immunoinformatics approach to designing a multi-epitope vaccine against Saint Louis Encephalitis Virus. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2020.100500] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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45
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Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, Bhinder MA. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. BIOLOGY 2020; 9:E296. [PMID: 32962156 PMCID: PMC7563440 DOI: 10.3390/biology9090296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Mian Azhar Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
- Department of Health, Government of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Sarfraz Ahmad
- Drug Design and Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan;
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia;
| | - Muhammad Shahbaz Aslam
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan;
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
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Kar T, Narsaria U, Basak S, Deb D, Castiglione F, Mueller DM, Srivastava AP. A candidate multi-epitope vaccine against SARS-CoV-2. Sci Rep 2020; 10:10895. [PMID: 32616763 PMCID: PMC7331818 DOI: 10.1038/s41598-020-67749-1] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022] Open
Abstract
In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
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Affiliation(s)
- Tamalika Kar
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Utkarsh Narsaria
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Srijita Basak
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Debashrito Deb
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Via dei Taurini, Rome, Italy
| | - David M Mueller
- Center for Genetic Diseases, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, USA
| | - Anurag P Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
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Hanif A, Lee S, Gupta M, Chander A, Kannisto ED, Punnanitinont A, Fenstermaker R, Ciesielski M, Attwood K, Qiu J, Yendamuri S, Iyer R. Exploring the role of survivin in neuroendocrine neoplasms. Oncotarget 2020; 11:2246-2258. [PMID: 32577168 PMCID: PMC7289533 DOI: 10.18632/oncotarget.27631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Neuroendocrine tumors (NETs) are a heterogenous group of tumors. While most NETs have excellent prognosis, certain subsets have aggressive biology and have limited treatment options. We explored the role of survivin in NET as a prognostic and potentially therapeutic marker. Tissue microarrays of 132 patients were stained for survivin using immunohistochemistry (IHC) and correlated with outcomes. Using genomic database, we then correlated survivin (BIRC5) mRNA expression with radiosensitivity index (RSI) in 52 samples of NET. Finally, we studied the effect of radiation on survivin expression in human cell lines and the impact of knock-down of BIRC5 on cell proliferation and radiation sensitivity. We found that survivin positivity by IHC correlated with a shorter survival (overall survival 8.5 years vs. 18.3 years, p < 0.001). There was a positive correlation between BIRC5 expression and RSI (r = 0.234, p < 0.0001). Radiation exposure increased BIRC5 gene expression in a human carcinoid cell line. Knockout of BIRC5 using siRNA reduced proliferation of neuroendocrine cells but did not increase radiation sensitivity. We conclude that survivin expression in NET correlates with an inferior survival and survivin expression in human carcinoid cell lines increases after exposure to ionizing radiation.
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Affiliation(s)
- Ahmad Hanif
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sunyoung Lee
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Medhavi Gupta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Ankush Chander
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Eric D Kannisto
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Achamaporn Punnanitinont
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Robert Fenstermaker
- Department of Neurosurgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Michael Ciesielski
- Department of Neurosurgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Kristopher Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Jingxin Qiu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Renuka Iyer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans—An integrated vaccinomics approach. Mol Immunol 2020; 120:146-163. [DOI: 10.1016/j.molimm.2020.02.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 12/29/2022]
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Bernardo PS, Lemos LGT, de Moraes GN, Maia RC. Unraveling survivin expression in chronic myeloid leukemia: Molecular interactions and clinical implications. Blood Rev 2020; 43:100671. [PMID: 32107072 DOI: 10.1016/j.blre.2020.100671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the BCR-ABL oncoprotein, known to drive leukemogenesis by orchestrating multiple signaling pathways ultimately involved in cell survival. Despite successful response rates of CML patients to tyrosine kinase inhibitors (TKIs), resistance eventually arises due to BCR-ABL-dependent and independent mechanisms. Survivin is an inhibitor of apoptosis protein acting in the interface between apoptosis deregulation and cell cycle progression. In CML, high levels of survivin have been associated with late stages of disease and therapy resistance. In this review, we provide an overview of important aspects concerning survivin subcellular localization and expression pattern in CML patients and cell lines. Moreover, we highlight the relevance of molecular networks involving survivin for disease progression and treatment resistance. Finally, we discuss the mechanisms accounting for survivin overexpression, as well as novel therapeutic interventions that have been designed to counteract survivin-associated malignancy in CML.
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Affiliation(s)
- Paula Sabbo Bernardo
- Laboratory of Cellular and Molecular Hemato-Oncology, Program of Molecular Hemato-Oncology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Lauana Greicy Tonon Lemos
- Laboratory of Cellular and Molecular Hemato-Oncology, Program of Molecular Hemato-Oncology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Gabriela Nestal de Moraes
- Laboratory of Cellular and Molecular Hemato-Oncology, Program of Molecular Hemato-Oncology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Raquel Ciuvalschi Maia
- Laboratory of Cellular and Molecular Hemato-Oncology, Program of Molecular Hemato-Oncology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil.
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50
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Li F, Aljahdali I, Ling X. Cancer therapeutics using survivin BIRC5 as a target: what can we do after over two decades of study? JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:368. [PMID: 31439015 PMCID: PMC6704566 DOI: 10.1186/s13046-019-1362-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
Survivin (also named BIRC5) is a well-known cancer therapeutic target. Since its discovery more than two decades ago, the use of survivin as a target for cancer therapeutics has remained a central goal of survivin studies in the cancer field. Many studies have provided intriguing insight into survivin's functional role in cancers, thus providing promise for survivin as a cancer therapeutic target. Despite this, moving survivin-targeting agents into and through the clinic remains a challenge. In order to address this challenge, we may need to rethink current strategies in order to develop a new mindset for targeting survivin. In this Review, we will first summarize the current survivin mechanistic studies, and then review the status of survivin cancer therapeutics, which is classified into five categories: (i) survivin-partner protein interaction inhibitors, (ii) survivin homodimerization inhibitors, (iii) survivin gene transcription inhibitors, (iv) survivin mRNA inhibitors and (v) survivin immunotherapy. We will then provide our opinions on cancer therapeutics using survivin as a target, with the goal of stimulating discussion that might facilitate translational research for discovering improved strategies and/or more effective anticancer agents that target survivin for cancer therapy.
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Affiliation(s)
- Fengzhi Li
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA. .,Developmental Therapeutics Program, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA.
| | - Ieman Aljahdali
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA.,Department of Cellular & Molecular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA
| | - Xiang Ling
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA.,Canget BioTekpharma LLC, Buffalo, New York, USA
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