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Sarfraz A, Qurrat-Ul-Ain Fatima S, Shehroz M, Ahmad I, Zaman A, Nishan U, Tayyab M, Sheheryar, Moura AA, Ullah R, Ali EA, Shah M. Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis. Int Immunopharmacol 2024; 132:111952. [PMID: 38555818 DOI: 10.1016/j.intimp.2024.111952] [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: 01/03/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Yersinia pestis, the causative agent of plague, is a gram-negative bacterium that can be fatal if not treated properly. Three types of plague are currently known: bubonic, septicemic, and pneumonic plague, among which the fatality rate of septicemic and pneumonic plague is very high. Bubonic plague can be treated, but only if antibiotics are used at the initial stage of the infection. But unfortunately, Y. pestis has also shown resistance to certain antibiotics such as kanamycin, minocycline, tetracycline, streptomycin, sulfonamides, spectinomycin, and chloramphenicol. Despite tremendous progress in vaccine development against Y. pestis, there is no proper FDA-approved vaccine available to protect people from its infections. Therefore, effective broad-spectrum vaccine development against Y. pestis is indispensable. In this study, vaccinomics-assisted immunoinformatics techniques were used to find possible vaccine candidates by utilizing the core proteome prepared from 58 complete genomes of Y. pestis. Human non-homologous, pathogen-essential, virulent, and extracellular and membrane proteins are potential vaccine targets. Two antigenic proteins were prioritized for the prediction of lead epitopes by utilizing reverse vaccinology approaches. Four vaccine designs were formulated using the selected B- and T-cell epitopes coupled with appropriate linkers and adjuvant sequences capable of inducing potent immune responses. The HLA allele population coverage of the T-cell epitopes selected for vaccine construction was also analyzed. The V2 constructs were top-ranked and selected for further analysis on the basis of immunological, physicochemical, and immune-receptor docking interactions and scores. Docking and molecular dynamic simulations confirmed the stability of construct V2 interactions with the host immune receptors. Immune simulation analysis anticipated the strong immune profile of the prioritized construct. In silico restriction cloning ensured the feasible cloning ability of the V2 construct in the expression system of E. coli strain K12. It is anticipated that the designed vaccine construct may be safe, effective, and able to elicit strong immune responses against Y. pestis infections and may, therefore, merit investigation using in vitro and in vivo assays.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | | | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Muhammad Tayyab
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Pakistan
| | - Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan.
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Shahab M, Aiman S, Alshammari A, Alasmari AF, Alharbi M, Khan A, Wei DQ, Zheng G. Immunoinformatics-based potential multi-peptide vaccine designing against Jamestown Canyon Virus (JCV) capable of eliciting cellular and humoral immune responses. Int J Biol Macromol 2023; 253:126678. [PMID: 37666399 DOI: 10.1016/j.ijbiomac.2023.126678] [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: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Jamestown Canyon virus (JCV) is a deadly viral infection transmitted by various mosquito species. This mosquito-borne virus belongs to Bunyaviridae family, posing a high public health threat in the in tropical regions of the United States causing encephalitis in humans. Common symptoms of JCV include fever, headache, stiff neck, photophobia, nausea, vomiting, and seizures. Despite the availability of resources, there is currently no vaccine or drug available to combat JCV. The purpose of this study was to develop an epitope-based vaccine using immunoinformatics approaches. The vaccine aimed to be secure, efficient, bio-compatible, and capable of stimulating both innate and adaptive immune responses. In this study, the protein sequence of JCV was obtained from the NCBI database. Various bioinformatics methods, including toxicity evaluation, antigenicity testing, conservancy analysis, and allergenicity assessment were utilized to identify the most promising epitopes. Suitable linkers and adjuvant sequences were used in the design of vaccine construct. 50s ribosomal protein sequence was used as an adjuvant at the N-terminus of the construct. A total of 5 CTL, 5 HTL, and 5 linear B cell epitopes were selected based on non-allergenicity, immunological potential, and antigenicity scores to design a highly immunogenic multi-peptide vaccine construct. Strong interactions between the proposed vaccine and human immune receptors, i.e., TLR-2 and TLR-4, were revealed in a docking study using ClusPro software, suggesting their possible relevance in the immunological response to the vaccine. Immunological and physicochemical properties assessment ensured that the proposed vaccine demonstrated high immunogenicity, solubility and thermostability. Molecular dynamics simulations confirmed the strong binding affinities, as well as dynamic and structural stability of the proposed vaccine. Immune simulation suggest that the vaccine has the potential to effectively stimulate cellular and humoral immune responses to combat JCV infection. Experimental and clinical assays are required to validate the results of this study.
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Affiliation(s)
- Muhammad Shahab
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abbas Khan
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China; School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Dong-Qing Wei
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Guojun Zheng
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China.
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Aiman S, Ahmad A, Khan A, Ali Y, Malik A, Alkholief M, Akhtar S, Khan RS, Li C, Jalil F, Ali Y. Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella Sonnei: Immunoinformatics and chemoinformatics approaches. PLoS One 2023; 18:e0289773. [PMID: 37992050 PMCID: PMC10664945 DOI: 10.1371/journal.pone.0289773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/25/2023] [Indexed: 11/24/2023] Open
Abstract
Shigella sonnei is a gram-negative bacterium and is the primary cause of shigellosis in advanced countries. An exceptional rise in the prevalence of the disease has been reported in Asia, the Middle East, and Latin America. To date, no preventive vaccine is available against S. sonnei infections. This pathogen has shown resistances towards both first- and second-line antibiotics. Therefore, an effective broad spectrum vaccine development against shigellosis is indispensable. In the present study, vaccinomics-aided immunoinformatics strategies were pursued to identify potential vaccine candidates from the S. sonnei whole proteome data. Pathogen essential proteins that are non-homologous to human and human gut microbiome proteome set, are feasible candidates for this purpose. Three antigenic outer membrane proteins were prioritized to predict lead epitopes based on reverse vaccinology approach. Multi-epitope-based chimeric vaccines was designed using lead B- and T-cell epitopes combined with suitable linker and adjuvant peptide sequences to enhance immune responses against the designed vaccine. The SS-MEVC construct was prioritized based on multiple physicochemical, immunological properties, and immune-receptors docking scores. Immune simulation analysis predicted strong immunogenic response capability of the designed vaccine construct. The Molecular dynamic simulations analysis ensured stable molecular interactions of lead vaccine construct with the host receptors. In silico restriction and cloning analysis predicted feasible cloning capability of the SS-MEVC construct within the E. coli expression system. The proposed vaccine construct is predicted to be more safe, effective and capable of inducing robust immune responses against S. sonnei infections and may be worthy of examination via in vitro/in vivo assays.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Raham Sher Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Ali
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Hong Kong
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Aiman S, Ahmad A, Khan AA, Alanazi AM, Samad A, Ali SL, Li C, Ren Z, Khan A, Khattak S. Vaccinomics-based next-generation multi-epitope chimeric vaccine models prediction against Leishmania tropica - a hierarchical subtractive proteomics and immunoinformatics approach. Front Immunol 2023; 14:1259612. [PMID: 37781384 PMCID: PMC10540849 DOI: 10.3389/fimmu.2023.1259612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Leishmania tropica is a vector-borne parasitic protozoa that is the leading cause of leishmaniasis throughout the global tropics and subtropics. L. tropica is a multidrug-resistant parasite with a diverse set of serological, biochemical, and genomic features. There are currently no particular vaccines available to combat leishmaniasis. The present study prioritized potential vaccine candidate proteins of L. tropica using subtractive proteomics and vaccinomics approaches. These vaccine candidate proteins were downstream analyzed to predict B- and T-cell epitopes based on high antigenicity, non-allergenic, and non-toxic characteristics. The top-ranked overlapping MHC-I, MHC-II, and linear B-cell epitopes were prioritized for model vaccine designing. The lead epitopes were linked together by suitable linker sequences to design multi-epitope constructs. Immunogenic adjuvant sequences were incorporated at the N-terminus of the model vaccine constructs to enhance their immunological potential. Among different combinations of constructs, four vaccine designs were selected based on their physicochemical and immunological features. The tertiary structure models of the designed vaccine constructs were predicted and verified. The molecular docking and molecular dynamic (MD) simulation analyses indicated that the vaccine design V1 demonstrated robust and stable molecular interactions with toll-like receptor 4 (TLR4). The top-ranked vaccine construct model-IV demonstrated significant expressive capability in the E. coli expression system during in-silico restriction cloning analysis. The results of the present study are intriguing; nevertheless, experimental bioassays are required to validate the efficacy of the predicted model chimeric vaccine.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Syed Luqman Ali
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhiguang Ren
- The First Affiliated Hospital, Henan University, Kaifeng, China
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
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Angaitkar P, Aljrees T, Kumar Pandey S, Kumar A, Janghel RR, Sahu TP, Singh KU, Singh T. Inferring linear-B cell epitopes using 2-step metaheuristic variant-feature selection using genetic algorithm. Sci Rep 2023; 13:14593. [PMID: 37670007 PMCID: PMC10480427 DOI: 10.1038/s41598-023-41179-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
Linear-B cell epitopes (LBCE) play a vital role in vaccine design; thus, efficiently detecting them from protein sequences is of primary importance. These epitopes consist of amino acids arranged in continuous or discontinuous patterns. Vaccines employ attenuated viruses and purified antigens. LBCE stimulate humoral immunity in the body, where B and T cells target circulating infections. To predict LBCE, the underlying protein sequences undergo a process of feature extraction, feature selection, and classification. Various system models have been proposed for this purpose, but their classification accuracy is only moderate. In order to enhance the accuracy of LBCE classification, this paper presents a novel 2-step metaheuristic variant-feature selection method that combines a linear support vector classifier (LSVC) with a Modified Genetic Algorithm (MGA). The feature selection model employs mono-peptide, dipeptide, and tripeptide features, focusing on the most diverse ones. These selected features are fed into a machine learning (ML)-based parallel ensemble classifier. The ensemble classifier combines correctly classified instances from various classifiers, including k-Nearest Neighbor (kNN), random forest (RF), logistic regression (LR), and support vector machine (SVM). The ensemble classifier came up with an impressively high accuracy of 99.3% as a result of its work. This accuracy is superior to the most recent models that are considered to be state-of-the-art for linear B-cell classification. As a direct consequence of this, the entire system model can now be utilised effectively in real-time clinical settings.
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Affiliation(s)
- Pratik Angaitkar
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India
| | - Turki Aljrees
- College of Computer Science and Engineering, University of Hafr Al Batin, 39524, Hafar Al Batin, Saudi Arabia
| | - Saroj Kumar Pandey
- Department of Computer Engineering & Applications, GLA University, Mathura, India
| | - Ankit Kumar
- Department of Computer Engineering & Applications, GLA University, Mathura, India.
| | - Rekh Ram Janghel
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India
| | - Tirath Prasad Sahu
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India
| | | | - Teekam Singh
- Department of Computer Science and Engineering, Graphic Era Deemed to be University, Dehradun, 248002, Uttarakhand, India
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Gaiya DD, Muhammad A, Aimola IA, Udu SK, Balarabe SA, Auta R, Ekpa E, Sheyin A. Potential of Onchocerca ochengi inosine-5'-monophosphate dehydrogenase (IMPDH) and guanosine-5'-monophosphate oxidoreductase (GMPR) as druggable and vaccine candidates: immunoinformatics screening. J Biomol Struct Dyn 2023; 41:14832-14848. [PMID: 36866624 DOI: 10.1080/07391102.2023.2184171] [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: 08/29/2022] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Abstract
Onchocerciasis is a vector-borne disease caused by the filarial nematode Onchocerca volvulus, which is responsible for most of the visual impairments recorded in Africa, Asia and the Americas. It is known that O. volvulus has similar molecular and biological characteristics as Onchocerca ochengi in cattle. This study was designed to screen for immunogenic epitopes and binding pockets of O. ochengi IMPDH and GMPR ligands using immunoinformatic approaches. In this study, a total of 23 B cell epitopes for IMPDH and 7 B cell epitopes for GMPR were predicted using ABCpred tool, Bepipred 2.0 and Kolaskar and Tongaonkar methods. The CD4+ Th computational results showed 16 antigenic epitopes from IMPDH with strong binding affinity for DRB1_0301, DRB3_0101, DRB1_0103 and DRB1_1501 MHC II alleles while 8 antigenic epitopes from GMPR were predicted to bind DRB1_0101 and DRB1_0401 MHC II alleles, respectively. For the CD8+ CTLs analysis, 8 antigenic epitopes from IMPDH showed strong binding affinity to human leukocyte antigen HLA-A*26:01, HLA-A*03:01, HLA-A*24:02 and HLA-A*01:01 MHC I alleles while 2 antigenic epitopes from GMPR showed strong binding affinity to HLA-A*01:01 allele, respectively. The immunogenic B cell and T cell epitopes were further evaluated for antigenicity, non-alllergernicity, toxicity, IFN-gamma, IL4 and IL10. The docking score revealed favorable binding free energy with IMP and MYD scoring the highest binding affinity at -6.6 kcal/mol with IMPDH and -8.3 kcal/mol with GMPR. This study provides valuable insight on IMPDH and GMPR as potential drug targets and for the development of multiple epitope vaccine candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Danladi Gaiya
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Idowu Asegame Aimola
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Stella Kuyet Udu
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Sallau Abdullahi Balarabe
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Richard Auta
- Department of Biochemistry, Faculty of Science, Kaduna State University, Kaduna, Kaduna State, Nigeria
| | - Emmanuel Ekpa
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Abraham Sheyin
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
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Khan A, Wei DQ, Suleman M. Computational Vaccine Design for Poxviridae Family Viruses. Methods Mol Biol 2023; 2673:475-485. [PMID: 37258933 DOI: 10.1007/978-1-0716-3239-0_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The computational approach to designing vaccines has several useful characteristics over traditional vaccine development, such as being highly specific, less time-consuming and less expensive. Thus, this chapter describes an immunoinformatics workflow to design a vaccine against a member of the Poxviridae family known as Monkeypox virus. The immunoinformatics approach uses several online servers to select highly antigenic and non-allergenic CTL, HTL, and B cell epitopes. Then, it links the predicted epitopes through linkers and submit them for 3D structure modeling. Afterward, the modeled vaccine is docked with TLRs to check the induction of the immune system. Finally, immune simulations are performed to check the level of several immune factors like IgG, IgM, cytokines and interleukins, among others, upon the injection of the constructed vaccine. This approach can be used to successfully design novel and effective vaccine candidates against emerging species from the Poxviridae family.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, People's Republic of China.
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, People's Republic of China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
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Shahab M, Hayat C, Sikandar R, Zheng G, Akter S. In silico designing of a multi-epitope vaccine against Burkholderia pseudomallei: reverse vaccinology and immunoinformatics. J Genet Eng Biotechnol 2022; 20:100. [PMID: 35821357 PMCID: PMC9275536 DOI: 10.1186/s43141-022-00379-4] [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: 04/13/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Burkholderia pseudomallei is an infectious agent causing severe disease melioidosis resulting in pneumonia, fever, and acute septicemia in humans. B. pseudomallei show resistance to drugs. No such FDA-approved vaccine is available against B. pseudomallei, and treatment is limited to therapy. Therefore, the scientific study was designed to develop a vaccine for B. pseudomallei. The protein sequence of B. pseudomallei was retrieved from NCBI. B-cell and T-cell epitopes were identified and further screened for allergenicity, antigenicity docking, and simulation. RESULTS Here, in this study, in silico approach was applied to design a multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of proteins considered to be potential novel vaccine candidates. Peptide epitopes were joined by adjuvant and EAAAK, CPGPG, and AAY linkers. This constructed vaccine was subjected to in silico immune simulations by C-ImmSim. The protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using SnapGene. CONCLUSION The designed multi-epitope vaccine was analyzed for its physicochemical, structural, and immunological characteristics, and it was found to be antigenic, soluble, stable, nonallergenic, and have a high affinity to its target receptor. The immune simulation studies were carried out on the C-ImmSim showing increased production of cellular and humoral responses indicating that the constructed vaccine proved effective and able to provoke humoral and cell-mediated response immune responses. In silico study could be a breakthrough in designing effective vaccines to eradicate B. pseudomallei globally.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chandni Hayat
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Ramin Sikandar
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research, Dhaka, 1205, Bangladesh.
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Khan T, Abdullah M, Toor TF, Almajhdi FN, Suleman M, Iqbal A, Ali L, Khan A, Waheed Y, Wei DQ. Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria. Front Med (Lausanne) 2022; 8:825876. [PMID: 35186980 PMCID: PMC8854494 DOI: 10.3389/fmed.2021.825876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/29/2021] [Indexed: 02/05/2023] Open
Abstract
Achromobacter xylosoxidans is a rod-shaped Gram-negative bacterium linked with causing several infections which mostly includes hematological malignancies. It has been recently reported to be associated with the development and progression of lung cancer and is an emerging respiratory disease-causing bacterium. The treatment of individuals infected with A. xylosoxidans bacteremia is difficult due to the fact that this pathogen has both intrinsic and acquired resistance mechanisms, typically resulting in a phenotype of multidrug resistance (MDR). Efforts are needed to design effective therapeutic strategies to curtail the emergence of this bacterium. Computational vaccine designing has proven its effectiveness, specificity, safety, and stability compared to conventional approaches of vaccine development. Therefore, the whole proteome of A. xylosoxidans was screened for the characterization of potential vaccine targets through subtractive proteomics pipeline for therapeutics design. Annotation of the whole proteome confirmed the three immunogenic vaccine targets, such as (E3HHR6), (E3HH04), and (E3HWA2), which were used to map the putative immune epitopes. The shortlisted epitopes, specific against Cytotoxic T Lymphocytes, Helper T-cell Lymphocytes, and linear B-Cell, were used to design the mRNA and multi-epitopes vaccine (MEVC). Initial validations confirmed the antigenic and non-allergenic properties of these constructs, followed by docking with the immune receptor, TLR-5, which resulted in robust interactions. The interaction pattern that followed in the docking complex included formation of 5 hydrogen bonds, 2 salt bridges, and 165 non-bonded contacts. This stronger binding affinity was also assessed through using the mmGBSA approach, showing a total of free binding energy of -34.64 kcal/mol. Further validations based on in silico cloning revealed a CAI score of 0.98 and an optimal percentage of GC contents (54.4%) indicated a putatively higher expression of the vaccine construct in Escherichia coli. Moreover, immune simulation revealed strong antibodies production upon the injection of the designed MEVC that resulted in the highest peaks of IgM+ IgG production (>3,500) between 10 and 15 days. In conclusion the current study provide basis for vaccine designing against the emerging A. xylosoxidans, which demands further experimental studies for in vitro and in vivo validations.
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Affiliation(s)
- Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Fahad N. Almajhdi
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Pakistan
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Pakistan
| | - Liaqat Ali
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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Haq AU, Khan A, Khan J, Irum S, Waheed Y, Ahmad S, Nizam-Uddin N, Albutti A, Zaman N, Hussain Z, Ali SS, Waseem M, Kanwal F, Wei DQ, Wang Q. Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against Yersinia pestis through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach. Vaccines (Basel) 2021; 9:vaccines9111327. [PMID: 34835260 PMCID: PMC8625334 DOI: 10.3390/vaccines9111327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023] Open
Abstract
Yersinia pestis is responsible for plague and major pandemics in Asia and Europe. This bacterium has shown resistance to an array of drugs commonly used for the treatment of plague. Therefore, effective therapeutics measurements, such as designing a vaccine that can effectively and safely prevent Y. pestis infection, are of high interest. To fast-track vaccine development against Yersinia pestis, herein, proteome-wide vaccine target annotation was performed, and structural vaccinology-assisted epitopes were predicted. Among the total 3909 proteins, only 5 (rstB, YPO2385, hmuR, flaA1a, and psaB) were shortlisted as essential vaccine targets. These targets were then subjected to multi-epitope vaccine design using different linkers. EAAK, AAY, and GPGPG as linkers were used to link CTL, HTL, and B-cell epitopes, and an adjuvant (beta defensin) was also added at the N-terminal of the MEVC. Physiochemical characterization, such as determination of the instability index, theoretical pI, half-life, aliphatic index, stability profiling, antigenicity, allergenicity, and hydropathy of the ensemble, showed that the vaccine is highly stable, antigenic, and non-allergenic and produces multiple interactions with immune receptors upon docking. In addition, molecular dynamics simulation confirmed the stable binding and good dynamic properties of the vaccine-TLR complex. Furthermore, in silico and immune simulation of the developed MEVC for Y. pestis showed that the vaccine triggered strong immune response after several doses at different intervals. Neutralization of the antigen was observed at the third day of injection. Conclusively, the vaccine designed here for Y. pestis produces an immune response; however, further immunological testing is needed to unveil its real efficacy.
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Affiliation(s)
- Azaz Ul Haq
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Jafar Khan
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Shamaila Irum
- Department of Zoology, University of Gujrat, Punjab 50700, Pakistan;
| | - Yasir Waheed
- Multidisciplinary Department, Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan;
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - N. Nizam-Uddin
- Biomedical Engineering Department, HITEC University, Taxila 47080, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Nasib Zaman
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad 46000, Pakistan;
| | - Fariha Kanwal
- Med-X Research Institute, School of Biomedical Engineering, Shanghai Jiaotong University, Shanghai 200240, China;
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Correspondence: (D.-Q.W.); (Q.W.)
| | - Qian Wang
- Department of Medicine, Nanjing Medical University, No. 140, Hanzhong Road, Nanjing 210029, China
- Correspondence: (D.-Q.W.); (Q.W.)
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Magez S, Li Z, Nguyen HTT, Pinto Torres JE, Van Wielendaele P, Radwanska M, Began J, Zoll S, Sterckx YGJ. The History of Anti-Trypanosome Vaccine Development Shows That Highly Immunogenic and Exposed Pathogen-Derived Antigens Are Not Necessarily Good Target Candidates: Enolase and ISG75 as Examples. Pathogens 2021; 10:pathogens10081050. [PMID: 34451514 PMCID: PMC8400590 DOI: 10.3390/pathogens10081050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Salivarian trypanosomes comprise a group of extracellular anthroponotic and zoonotic parasites. The only sustainable method for global control of these infection is through vaccination of livestock animals. Despite multiple reports describing promising laboratory results, no single field-applicable solution has been successful so far. Conventionally, vaccine research focusses mostly on exposed immunogenic antigens, or the structural molecular knowledge of surface exposed invariant immunogens. Unfortunately, extracellular parasites (or parasites with extracellular life stages) have devised efficient defense systems against host antibody attacks, so they can deal with the mammalian humoral immune response. In the case of trypanosomes, it appears that these mechanisms have been perfected, leading to vaccine failure in natural hosts. Here, we provide two examples of potential vaccine candidates that, despite being immunogenic and accessible to the immune system, failed to induce a functionally protective memory response. First, trypanosomal enolase was tested as a vaccine candidate, as it was recently characterized as a highly conserved enzyme that is readily recognized during infection by the host antibody response. Secondly, we re-addressed a vaccine approach towards the Invariant Surface Glycoprotein ISG75, and showed that despite being highly immunogenic, trypanosomes can avoid anti-ISG75 mediated parasitemia control.
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Affiliation(s)
- Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Correspondence:
| | - Zeng Li
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Hang Thi Thu Nguyen
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
| | - Joar Esteban Pinto Torres
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark Zwijnaarde 71, 9000 Ghent, Belgium
| | - Jakub Began
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Sebastian Zoll
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
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12
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Washah HN, Salifu EY, Soremekun O, Elrashedy AA, Munsamy G, Olotu FA, Soliman ME. Integrating Bioinformatics Strategies in Cancer Immunotherapy: Current and Future Perspectives. Comb Chem High Throughput Screen 2020; 23:687-698. [DOI: 10.2174/1386207323666200427113734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/21/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023]
Abstract
For the past few decades, the mechanisms of immune responses to cancer have been
exploited extensively and significant attention has been given into utilizing the therapeutic
potential of the immune system. Cancer immunotherapy has been established as a promising
innovative treatment for many forms of cancer. Immunotherapy has gained its prominence through
various strategies, including cancer vaccines, monoclonal antibodies (mAbs), adoptive T cell cancer
therapy, and immune checkpoint therapy. However, the full potential of cancer immunotherapy is yet
to be attained. Recent studies have identified the use of bioinformatics tools as a viable option to help
transform the treatment paradigm of several tumors by providing a therapeutically efficient method of
cataloging, predicting and selecting immunotherapeutic targets, which are known bottlenecks in the
application of immunotherapy. Herein, we gave an insightful overview of the types of
immunotherapy techniques used currently, their mechanisms of action, and discussed some
bioinformatics tools and databases applied in the immunotherapy of cancer. This review also provides
some future perspectives in the use of bioinformatics tools for immunotherapy.
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Affiliation(s)
- Houda N. Washah
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Elliasu Y. Salifu
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Opeyemi Soremekun
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Ahmed A. Elrashedy
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Geraldene Munsamy
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A. Olotu
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E.S. Soliman
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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Hasan MM, Khatun MS, Kurata H. iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:593-600. [PMID: 33099033 PMCID: PMC8377379 DOI: 10.1016/j.gpb.2019.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/13/2019] [Accepted: 04/19/2019] [Indexed: 12/17/2022]
Abstract
Linear B-cell epitopes are critically important for immunological applications, such as vaccine design, immunodiagnostic test, and antibody production, as well as disease diagnosis and therapy. The accurate identification of linear B-cell epitopes remains challenging despite several decades of research. In this work, we have developed a novel predictor, Identification of Linear B-cell Epitope (iLBE), by integrating evolutionary and sequence-based features. The successive feature vectors were optimized by a Wilcoxon-rank sum test. Then the random forest (RF) algorithm using the optimal consecutive feature vectors was applied to predict linear B-cell epitopes. We combined the RF scores by the logistic regression to enhance the prediction accuracy. iLBE yielded an area under curve score of 0.809 on the training dataset and outperformed other prediction models on a comprehensive independent dataset. iLBE is a powerful computational tool to identify the linear B-cell epitopes and would help to develop penetrating diagnostic tests. A web application with curated datasets for iLBE is freely accessible at http://kurata14.bio.kyutech.ac.jp/iLBE/.
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Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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Design of an Epitope-Based Vaccine Ensemble for Animal Trypanosomiasis by Computational Methods. Vaccines (Basel) 2020; 8:vaccines8010130. [PMID: 32188062 PMCID: PMC7157688 DOI: 10.3390/vaccines8010130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/29/2020] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
African animal trypanosomiasis is caused by vector-transmitted parasites of the genus Trypanosoma. T. congolense and T. brucei brucei are predominant in Africa; T. evansi and T. vivax in America and Asia. They have in common an extracellular lifestyle and livestock tropism, which provokes huge economic losses in regions where vectors are endemic. There are licensed drugs to treat the infections, but adherence to treatment is poor and appearance of resistances common. Therefore, the availability of a prophylactic vaccine would represent a major breakthrough towards the management and control of the disease. Selection of the most appropriate antigens for its development is a bottleneck step, especially considering the limited resources allocated. Herein we propose a vaccine strategy based on multiple epitopes from multiple antigens to counteract the parasites´ biological complexity. Epitopes were identified by computer-assisted genome-wide screenings, considering sequence conservation criteria, antigens annotation and sub-cellular localization, high binding affinity to antigen presenting molecules, and lack of cross-reactivity to proteins in cattle and other breeding species. We ultimately provide 31 B-cell, 8 CD4 T-cell, and 15 CD8 T-cell epitope sequences from 30 distinct antigens for the prospective design of a genetic ensemble vaccine against the four trypanosome species responsible for African animal trypanosomiasis.
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Sunita, Sajid A, Singh Y, Shukla P. Computational tools for modern vaccine development. Hum Vaccin Immunother 2020; 16:723-735. [PMID: 31545127 PMCID: PMC7227725 DOI: 10.1080/21645515.2019.1670035] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/28/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Vaccines play an essential role in controlling the rates of fatality and morbidity. Vaccines not only arrest the beginning of different diseases but also assign a gateway for its elimination and reduce toxicity. This review gives an overview of the possible uses of computational tools for vaccine design. Moreover, we have described the initiatives of utilizing the diverse computational resources by exploring the immunological databases for developing epitope-based vaccines, peptide-based drugs, and other resources of immunotherapeutics. Finally, the applications of multi-graft and multivalent scaffolding, codon optimization and antibodyomics tools in identifying and designing in silico vaccine candidates are described.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi
| | - Andaleeb Sajid
- National Institutes of Health, National Cancer Institute, Bethesda, MD, USA
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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