1
|
Angaitkar P, Ram Janghel R, Prasad Sahu T. An MCDM approach for Reverse vaccinology model to predict bacterial protective antigens. Vaccine 2024; 42:3874-3882. [PMID: 38704249 DOI: 10.1016/j.vaccine.2024.04.078] [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: 06/21/2023] [Revised: 01/26/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Reverse vaccinology (RV) is a significant step in sensible vaccine design. In recent years, many machine learning (ML) methods have been used to improve RV prediction accuracy. However, there are still issues with prediction accuracy and programme accessibility in ML-based RV. This paper presents a supervised ML-based method to classify bacterial protective antigens (BPAgs) and identify the model(s) that consistently perform well for the training dataset. Six ML classifiers are used for testing with physiochemical features extracted from a comprehensive training dataset. Selecting the best performing model from different performance metrics (accuracy, precision, recall, F1-score, and AUC-ROC) has not been easy, because all the metrics has the same importance to predict BPAgs. To fix this issue, we propose a soft and hard ranking model based on multi-criteria decision-making (MCDM) approach for selecting the best performing ML method that classifies BPAgs. First, our proposed model uses homologous proteins (positive and negative samples) from Protegen and Uniprot databases. Second, we applied four strategies of Synthetic Minority Oversampling Technique and Edited Nearest Neighbour (SMOTE-ENN) to handle the data imbalance problem and train the model using ML methods. Third, we consider MCDM-based technique for order preference by similarity to the ideal solution (TOPSIS) method integrated with soft and hard ranking model. The entropy is used to obtain weighted evaluation criteria for ranking the models. Our experimental evaluations show that the proposed method with best performing models (Random Forest and Extreme Gradient Boosting) outperforms compared to existing open-source RV methods using benchmark datasets.
Collapse
Affiliation(s)
- Pratik Angaitkar
- Department of Information Technology, National Institute of Technology, Raipur, G.E.Road Raipur, C.G. -492010, India.
| | - Rekh Ram Janghel
- Department of Information Technology, National Institute of Technology, Raipur, G.E.Road Raipur, C.G. -492010, India.
| | - Tirath Prasad Sahu
- Department of Information Technology, National Institute of Technology, Raipur, G.E.Road Raipur, C.G. -492010, India.
| |
Collapse
|
2
|
Mugunthan SP, Venkatesan D, Govindasamy C, Selvaraj D, Harish MC. Systems approach to design multi-epitopic peptide vaccine candidate against fowl adenovirus structural proteins for Gallus gallus domesticus. Front Cell Infect Microbiol 2024; 14:1351303. [PMID: 38881736 PMCID: PMC11177691 DOI: 10.3389/fcimb.2024.1351303] [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: 12/06/2023] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction Fowl adenovirus (FAdV) is a significant pathogen in poultry, causing various diseases such as hepatitis-hydropericardium, inclusion body hepatitis, and gizzard erosion. Different serotypes of FAdV are associated with specific conditions, highlighting the need for targeted prevention strategies. Given the rising prevalence of FAdV-related diseases globally, effective vaccination and biosecurity measures are crucial. In this study, we explore the potential of structural proteins to design a multi-epitope vaccine targeting FAdV. Methods We employed an in silico approach to design the multi-epitope vaccine. Essential viral structural proteins, including hexon, penton, and fiber protein, were selected as vaccine targets. T-cell and B-cell epitopes binding to MHC-I and MHC-II molecules were predicted using computational methods. Molecular docking studies were conducted to validate the interaction of the multi-epitope vaccine candidate with chicken Toll-like receptors 2 and 5. Results Our in silico methodology successfully identified potential T-cell and B-cell epitopes within the selected viral structural proteins. Molecular docking studies revealed strong interactions between the multi-epitope vaccine candidate and chicken Toll-like receptors 2 and 5, indicating the structural integrity and immunogenic potential of the designed vaccine. Discussion The designed multi-epitope vaccine presents a promising approach for combating FAdV infections in chickens. By targeting essential viral structural proteins, the vaccine is expected to induce a robust immunological response. The in silico methodology utilized in this study provides a rapid and cost-effective means of vaccine design, offering insights into potential vaccine candidates before experimental validation. Future studies should focus on in vitro and in vivo evaluations to further assess the efficacy and safety of the proposed vaccine.
Collapse
Affiliation(s)
| | | | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Dhivya Selvaraj
- Artificial Intelligence Laboratory, School of Computer Information and Communication Engineering, Kunsan National University, Gunsan, Republic of Korea
| | - Mani Chandra Harish
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, India
| |
Collapse
|
3
|
Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [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: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
Collapse
Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
| |
Collapse
|
4
|
Singh S, Sharma P, Pal N, Sarma DK, Tiwari R, Kumar M. Holistic One Health Surveillance Framework: Synergizing Environmental, Animal, and Human Determinants for Enhanced Infectious Disease Management. ACS Infect Dis 2024; 10:808-826. [PMID: 38415654 DOI: 10.1021/acsinfecdis.3c00625] [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] [Indexed: 02/29/2024]
Abstract
Recent pandemics, including the COVID-19 outbreak, have brought up growing concerns about transmission of zoonotic diseases from animals to humans. This highlights the requirement for a novel approach to discern and address the escalating health threats. The One Health paradigm has been developed as a responsive strategy to confront forthcoming outbreaks through early warning, highlighting the interconnectedness of humans, animals, and their environment. The system employs several innovative methods such as the use of advanced technology, global collaboration, and data-driven decision-making to come up with an extraordinary solution for improving worldwide disease responses. This Review deliberates environmental, animal, and human factors that influence disease risk, analyzes the challenges and advantages inherent in using the One Health surveillance system, and demonstrates how these can be empowered by Big Data and Artificial Intelligence. The Holistic One Health Surveillance Framework presented herein holds the potential to revolutionize our capacity to monitor, understand, and mitigate the impact of infectious diseases on global populations.
Collapse
Affiliation(s)
- Samradhi Singh
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Poonam Sharma
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Namrata Pal
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Rajnarayan Tiwari
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Manoj Kumar
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| |
Collapse
|
5
|
Koff WC, Anandkumar A, Poland GA. AI and the future of vaccine development. Vaccine 2024; 42:1407-1408. [PMID: 38296704 DOI: 10.1016/j.vaccine.2024.01.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
|
6
|
Gorki V, Medhi B. Use of artificial intelligence in vaccine development against pathogens: Challenges and future directions. Indian J Pharmacol 2024; 56:77-79. [PMID: 38687309 PMCID: PMC11161010 DOI: 10.4103/ijp.ijp_259_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Varun Gorki
- Department of Pharmacology, Experimental Pharmacological Laboratory, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Experimental Pharmacological Laboratory, PGIMER, Chandigarh, India
| |
Collapse
|
7
|
Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024; 11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.
Collapse
Affiliation(s)
- Doo Nam Kim
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Andrew D McNaughton
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| |
Collapse
|
8
|
Bravi B. Development and use of machine learning algorithms in vaccine target selection. NPJ Vaccines 2024; 9:15. [PMID: 38242890 PMCID: PMC10798987 DOI: 10.1038/s41541-023-00795-8] [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: 08/04/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024] Open
Abstract
Computer-aided discovery of vaccine targets has become a cornerstone of rational vaccine design. In this article, I discuss how Machine Learning (ML) can inform and guide key computational steps in rational vaccine design concerned with the identification of B and T cell epitopes and correlates of protection. I provide examples of ML models, as well as types of data and predictions for which they are built. I argue that interpretable ML has the potential to improve the identification of immunogens also as a tool for scientific discovery, by helping elucidate the molecular processes underlying vaccine-induced immune responses. I outline the limitations and challenges in terms of data availability and method development that need to be addressed to bridge the gap between advances in ML predictions and their translational application to vaccine design.
Collapse
Affiliation(s)
- Barbara Bravi
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
9
|
Li C, Ye G, Jiang Y, Wang Z, Yu H, Yang M. Artificial Intelligence in battling infectious diseases: A transformative role. J Med Virol 2024; 96:e29355. [PMID: 38179882 DOI: 10.1002/jmv.29355] [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: 10/16/2023] [Revised: 12/01/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
It is widely acknowledged that infectious diseases have wrought immense havoc on human society, being regarded as adversaries from which humanity cannot elude. In recent years, the advancement of Artificial Intelligence (AI) technology has ushered in a revolutionary era in the realm of infectious disease prevention and control. This evolution encompasses early warning of outbreaks, contact tracing, infection diagnosis, drug discovery, and the facilitation of drug design, alongside other facets of epidemic management. This article presents an overview of the utilization of AI systems in the field of infectious diseases, with a specific focus on their role during the COVID-19 pandemic. The article also highlights the contemporary challenges that AI confronts within this domain and posits strategies for their mitigation. There exists an imperative to further harness the potential applications of AI across multiple domains to augment its capacity in effectively addressing future disease outbreaks.
Collapse
Affiliation(s)
- Chunhui Li
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Guoguo Ye
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Yinghan Jiang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Zhiming Wang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Haiyang Yu
- Hangzhou Yalla Information Technology Service Co., Ltd., Hangzhou, People's Republic of China
| | - Minghui Yang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, People's Republic of China
| |
Collapse
|
10
|
Zhang Y, Huffman A, Johnson J, He Y. Vaxign-DL: A Deep Learning-based Method for Vaccine Design and its Evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569096. [PMID: 38076796 PMCID: PMC10705428 DOI: 10.1101/2023.11.29.569096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Reverse vaccinology (RV) provides a systematic approach to identifying potential vaccine candidates based on protein sequences. The integration of machine learning (ML) into this process has greatly enhanced our ability to predict viable vaccine candidates from these sequences. We have previously developed a Vaxign-ML program based on the eXtreme Gradient Boosting (XGBoost). In this study, we further extend our work to develop a Vaxign-DL program based on deep learning techniques. Deep neural networks assemble non-linear models and learn multilevel abstraction of data using hierarchically structured layers, offering a data-driven approach in computational design models. Vaxign-DL uses a three-layer fully connected neural network model. Using the same bacterial vaccine candidate training data as used in Vaxign-ML development, Vaxign-DL was able to achieve an Area Under the Receiver Operating Characteristic of 0.94, specificity of 0.99, sensitivity of 0.74, and accuracy of 0.96. Using the Leave-One-Pathogen-Out Validation (LOPOV) method, Vaxign-DL was able to predict vaccine candidates for 10 pathogens. Our benchmark study shows that Vaxign-DL achieved comparable results with Vaxign-ML in most cases, and our method outperforms Vaxi-DL in the accurate prediction of bacterial protective antigens.
Collapse
Affiliation(s)
- Yuhan Zhang
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Justin Johnson
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Unit of Laboratory Animal Medicine and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
11
|
Mao Y, Xiao X, Zhang J, Mou X, Zhao W. Designing a multi-epitope vaccine against Peptostreptococcus anaerobius based on an immunoinformatics approach. Synth Syst Biotechnol 2023; 8:757-770. [PMID: 38099061 PMCID: PMC10720267 DOI: 10.1016/j.synbio.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/15/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Peptostreptococcus anaerobius is an anaerobic bacterium, which has been found selectively en-riched in the fecal and mucosal microbiota of colorectal cancer (CRC) patients. Emerging evidence suggest P. anaerobius may contribute to the development of CRC in human. In this study, we designed a multi-epitope chimeric vaccine against P. anaerobius PCWBR2, a recently identified adhesin that interacts directly with colon cell lines by binding α2/β1 integrin frequently overexpressed in human CRC tumors and cell lines. Immunoinformatics tools predicted six cytotoxic T lymphocyte epitopes, five helper T lymphocyte epitopes, and six linear B lymphocyte epitopes. The predicted epitopes were joined with AAY or GPGPG linkers and a previously reported TLR4 agonist was added to the vaccine construct's N terminal as an adjuvant using EAAAK linkers and the order of epitopes was optimized. Further in silico analysis revealed that the vaccine construct possesses satisfactory antigenicity, allergenicity, solubility, physicochemical properties, adjuvant-TLR4 molecular docking, and immune profile characteristics. Our study provided a promising design for vaccines against P. anaerobius.
Collapse
Affiliation(s)
- Yudan Mao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Xianzun Xiao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Jie Zhang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Xiangyu Mou
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Wenjing Zhao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| |
Collapse
|
12
|
Gupta Y, Baranwal M, Chudasama B. Immunoinformatics-Based Identification of the Conserved Immunogenic Peptides Targeting of Zika Virus Precursor Membrane Protein. Viral Immunol 2023; 36:503-519. [PMID: 37486711 DOI: 10.1089/vim.2023.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Zika virus infections lead to neurological complications such as congenital Zika syndrome and Guillain-Barré syndrome. Rising Zika infections in newborns and adults have triggered the need for vaccine development. In the current study, the precursor membrane (prM) protein of the Zika virus is explored for its functional importance and design of epitopes enriched conserved peptides with the usage of different immunoinformatics approach. Phylogenetic and mutational analyses inferred that the prM protein is highly conserved. Three conserved peptides containing multiple T and B cell epitopes were designed by employing different epitope prediction algorithms. IEDB population coverage analysis of selected peptides in six different continents has shown the population coverage of 60-99.8% (class I HLA) and 80-100% (class II HLA). Molecular docking of selected peptides/epitopes was carried out with each of class I and II HLA alleles using HADDOCK. A majority of peptide-HLA complex (pHLA) have HADDOCK scores found to be comparable and more than native-HLA complex representing the good binding interaction of peptides to HLA. Molecular dynamics simulation with best docked pHLA complexes revealed that pHLA complexes are stable with RMSD <5.5Å. Current work highlights the importance of prM as a strong antigenic protein and selected peptides have the potential to elicit humoral and cell-mediated immune responses.
Collapse
Affiliation(s)
- Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Bhupendra Chudasama
- School of Physics & Materials Science, Thapar Institute of Engineering and Technology, Patiala, India
| |
Collapse
|
13
|
Theodosiou AA, Read RC. Artificial intelligence, machine learning and deep learning: Potential resources for the infection clinician. J Infect 2023; 87:287-294. [PMID: 37468046 DOI: 10.1016/j.jinf.2023.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Artificial intelligence (AI), machine learning and deep learning (including generative AI) are increasingly being investigated in the context of research and management of human infection. OBJECTIVES We summarise recent and potential future applications of AI and its relevance to clinical infection practice. METHODS 1617 PubMed results were screened, with priority given to clinical trials, systematic reviews and meta-analyses. This narrative review focusses on studies using prospectively collected real-world data with clinical validation, and on research with translational potential, such as novel drug discovery and microbiome-based interventions. RESULTS There is some evidence of clinical utility of AI applied to laboratory diagnostics (e.g. digital culture plate reading, malaria diagnosis, antimicrobial resistance profiling), clinical imaging analysis (e.g. pulmonary tuberculosis diagnosis), clinical decision support tools (e.g. sepsis prediction, antimicrobial prescribing) and public health outbreak management (e.g. COVID-19). Most studies to date lack any real-world validation or clinical utility metrics. Significant heterogeneity in study design and reporting limits comparability. Many practical and ethical issues exist, including algorithm transparency and risk of bias. CONCLUSIONS Interest in and development of AI-based tools for infection research and management are undoubtedly gaining pace, although the real-world clinical utility to date appears much more modest.
Collapse
Affiliation(s)
- Anastasia A Theodosiou
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom.
| | - Robert C Read
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
| |
Collapse
|
14
|
Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [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: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
Collapse
Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| |
Collapse
|
15
|
Zhang G, Han L, Li Z, Chen Y, Li Q, Wang S, Shi H. Screening of immunogenic proteins and evaluation of vaccine candidates against Mycoplasma synoviae. NPJ Vaccines 2023; 8:121. [PMID: 37582795 PMCID: PMC10427712 DOI: 10.1038/s41541-023-00721-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
Mycoplasma synoviae (M. synoviae) is a serious avian pathogen that causes significant economic losses to chicken and turkey producers worldwide. The currently available live attenuated and inactivated vaccines provide limited protection. The objective of this study was to identify potential subunit vaccine candidates using immunoproteomics and reverse vaccinology analyses and to evaluate their preliminary protection. Twenty-four candidate antigens were identified, and five of them, namely RS01790 (a putative sugar ABC transporter lipoprotein), BMP (a substrate-binding protein of the BMP family ABC transporter), GrpE (a nucleotide exchange factor), RS00900 (a putative nuclease), and RS00275 (an uncharacterized protein), were selected to evaluate their immunogenicity and preliminary protection. The results showed that all five antigens had good immunogenicity, and they were localized on the M. synoviae cell membrane. The antigens induced specific humoral and cellular immune responses, and the vaccinated chickens exhibited significantly greater body weight gain and lower air sac lesion scores and tracheal mucosal thicknesses. Additionally, the vaccinated chickens had lower M. synoviae loads in throat swabs than non-vaccinated chickens. The protective effect of the RS01790, BMP, GrpE, and RS00900 vaccines was better than that of the RS00275 vaccine. In conclusion, our study demonstrates the potential of subunit vaccines as a new approach to developing M. synoviae vaccines, providing new ideas for controlling the spread of M. synoviae worldwide.
Collapse
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
| | - Zewei 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
| | - Yifei Chen
- 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.
| |
Collapse
|
16
|
Wong F, de la Fuente-Nunez C, Collins JJ. Leveraging artificial intelligence in the fight against infectious diseases. Science 2023; 381:164-170. [PMID: 37440620 PMCID: PMC10663167 DOI: 10.1126/science.adh1114] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023]
Abstract
Despite advances in molecular biology, genetics, computation, and medicinal chemistry, infectious disease remains an ominous threat to public health. Addressing the challenges posed by pathogen outbreaks, pandemics, and antimicrobial resistance will require concerted interdisciplinary efforts. In conjunction with systems and synthetic biology, artificial intelligence (AI) is now leading to rapid progress, expanding anti-infective drug discovery, enhancing our understanding of infection biology, and accelerating the development of diagnostics. In this Review, we discuss approaches for detecting, treating, and understanding infectious diseases, underscoring the progress supported by AI in each case. We suggest future applications of AI and how it might be harnessed to help control infectious disease outbreaks and pandemics.
Collapse
Affiliation(s)
- Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James J. Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| |
Collapse
|
17
|
Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
Collapse
Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
| |
Collapse
|
18
|
Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
Collapse
Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| |
Collapse
|
19
|
Ismail M, Bai B, Guo J, Bai Y, Sajid Z, Muhammad SA, Shaikh RS. Experimental Validation of MHC Class I and II Peptide-Based Potential Vaccine Candidates for Human Papilloma Virus Using Sprague-Dawly Models. Molecules 2023; 28:1687. [PMID: 36838675 PMCID: PMC9968051 DOI: 10.3390/molecules28041687] [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: 11/26/2022] [Revised: 01/09/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
Human papilloma virus (HPV) causes cervical and many other cancers. Recent trend in vaccine design is shifted toward epitope-based developments that are more specific, safe, and easy to produce. In this study, we predicted eight immunogenic peptides of CD4+ and CD8+ T-lymphocytes (MHC class I and II as M1 and M2) including early proteins (E2 and E6), major (L1) and minor capsid protein (L2). Male and female Sprague Dawly rats in groups were immunized with each synthetic peptide. L1M1, L1M2, L2M1, and L2M2 induced significant immunogenic response compared to E2M1, E2M2, E6M1 and E6M2. We observed optimal titer of IgG antibodies (>1.25 g/L), interferon-γ (>64 ng/L), and granzyme-B (>40 pg/mL) compared to control at second booster dose (240 µg/500 µL). The induction of peptide-specific IgG antibodies in immunized rats indicates the T-cell dependent B-lymphocyte activation. A substantial CD4+ and CD8+ cell count was observed at 240 µg/500 µL. In male and female rats, CD8+ cell count for L1 and L2 peptide is 3000 and 3118, and CD4+ is 3369 and 3484 respectively compared to control. In conclusion, we demonstrated that L1M1, L1M2, L2M1, L2M2 are likely to contain potential epitopes for induction of immune responses supporting the feasibility of peptide-based vaccine development for HPV.
Collapse
Affiliation(s)
- Mehreen Ismail
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Baogang Bai
- School of Information and Technology, Wenzhou Business College, Wenzhou 325015, China
- Engineering Research Center of Intelligent Medicine, Wenzhou 325000, China
- The 1st School of Medical, School of Information and Engineering, The 1st Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China
| | - Jinlei Guo
- School of Medical Engineering, Sanquan College of Xinxiang Medical University, Xinxiang 453513, China
| | - Yuhui Bai
- Department of Computer Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zureesha Sajid
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Rehan Sadiq Shaikh
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
- Centre for Applied Molecular Biology, University of the Punjab, Lahore 54000, Pakistan
| |
Collapse
|
20
|
Belov AA, Rodriguez Messan M, Yogurtcu ON, Schultz K, Maxfield K, Thompson L, Revell S, Warren-Henderson Y, Tegenge MA, Sauna ZE, Forshee RA. Summary of a Public FDA Workshop: Model Informed Drug Development Approaches for Immunogenicity Assessments. Clin Pharmacol Ther 2023; 113:221-225. [PMID: 35253213 DOI: 10.1002/cpt.2572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023]
Affiliation(s)
- Artur A Belov
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Marisabel Rodriguez Messan
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Osman N Yogurtcu
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Kimberly Schultz
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Kimberly Maxfield
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Laura Thompson
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Sherri Revell
- Office of Communication, Outreach and Development, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Yolonda Warren-Henderson
- Office of Communication, Outreach and Development, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Million A Tegenge
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Zuben E Sauna
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| | - Richard A Forshee
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
| |
Collapse
|
21
|
Preeti P, Nath SK, Arambam N, Sharma T, Choudhury PR, Choudhury A, Khanna V, Strych U, Hotez PJ, Bottazzi ME, Rawal K. Vaxi-DL: An Artificial Intelligence-Enabled Platform for Vaccine Development. Methods Mol Biol 2023; 2673:305-316. [PMID: 37258923 DOI: 10.1007/978-1-0716-3239-0_21] [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
Vaccine development is a complex and long process. It involves several steps, including computational studies, experimental analyses, animal model system studies, and clinical trials. This process can be accelerated by using in silico antigen screening to identify potential vaccine candidates. In this chapter, we describe a deep learning-based technique which utilizes 18 biological and 9154 physicochemical properties of proteins for finding potential vaccine candidates. Using this technique, a new web-based system, named Vaxi-DL, was developed which helped in finding new vaccine candidates from bacteria, protozoa, viruses, and fungi. Vaxi-DL is available at: https://vac.kamalrawal.in/vaxidl/ .
Collapse
Affiliation(s)
- P Preeti
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Swarsat Kaushik Nath
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Nevidita Arambam
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Trapti Sharma
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Priyanka Ray Choudhury
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Alakto Choudhury
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Vrinda Khanna
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India
| | - Ulrich Strych
- Department of Pediatrics, Division of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Peter J Hotez
- Department of Pediatrics, Division of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
| | - Maria Elena Bottazzi
- Department of Pediatrics, Division of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
| | - Kamal Rawal
- Centre for Computational Biology and Bioinformatics, AIB, Amity University, Noida, Uttar Pradesh, India.
| |
Collapse
|
22
|
Pang M, Tu T, Wang Y, Zhang P, Ren M, Yao X, Luo Y, Yang Z. Design of a multi-epitope vaccine against Haemophilus parasuis based on pan-genome and immunoinformatics approaches. Front Vet Sci 2022; 9:1053198. [PMID: 36644533 PMCID: PMC9835091 DOI: 10.3389/fvets.2022.1053198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022] Open
Abstract
Background Glässer's disease, caused by Haemophilus parasuis (HPS), is responsible for economic losses in the pig industry worldwide. However, the existing commercial vaccines offer poor protection and there are significant barriers to the development of effective vaccines. Methods In the current study, we aimed to identify potential vaccine candidates and design a multi-epitope vaccine against HPS by performing pan-genomic analysis of 121 strains and using a reverse vaccinology approach. Results The designed vaccine constructs consist of predicted epitopes of B and T cells derived from the outer membrane proteins of the HPS core genome. The vaccine was found to be highly immunogenic, non-toxic, and non-allergenic as well as have stable physicochemical properties. It has a high binding affinity to Toll-like receptor 2. In addition, in silico immune simulation results showed that the vaccine elicited an effective immune response. Moreover, the mouse polyclonal antibody obtained by immunizing the vaccine protein can be combined with different serotypes and non-typable Haemophilus parasuis in vitro. Conclusion The overall results of the study suggest that the designed multi-epitope vaccine is a promising candidate for pan-prophylaxis against different strains of HPS.
Collapse
Affiliation(s)
- Maonan Pang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Teng Tu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Yin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China,*Correspondence: Yin Wang
| | - Pengfei Zhang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Meishen Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Xueping Yao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Yan Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Zexiao Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| |
Collapse
|
23
|
Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
Collapse
Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
| | | |
Collapse
|
24
|
Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes. Nat Commun 2022; 13:6075. [PMID: 36241641 PMCID: PMC9562072 DOI: 10.1038/s41467-022-33721-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screen for Listeria peptides presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detect 68 Listeria immunopeptides from 42 different bacterial proteins, including several known antigens. Peptides presented on different cell lines are often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations results in specific CD8+ T-cell responses and induces protection in vaccination challenge experiments in mice. Our results can serve as a starting point for the development of a clinical mRNA vaccine against Listeria and aid to improve attenuated Listeria vaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.
Collapse
|
25
|
Huffman A, Ong E, Hur J, D’Mello A, Tettelin H, He Y. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Brief Bioinform 2022; 23:bbac190. [PMID: 35649389 PMCID: PMC9294427 DOI: 10.1093/bib/bbac190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
Collapse
Affiliation(s)
- Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202, USA
| | - Adonis D’Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
26
|
Sharma A, Virmani T, Pathak V, Sharma A, Pathak K, Kumar G, Pathak D. Artificial Intelligence-Based Data-Driven Strategy to Accelerate Research, Development, and Clinical Trials of COVID Vaccine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7205241. [PMID: 35845955 PMCID: PMC9279074 DOI: 10.1155/2022/7205241] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5-15 years to 1-2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
Collapse
Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Vipluv Pathak
- GL Bajaj Institute of Technology and Management, Greater Noida, Uttar Pradesh, India
| | | | - Kamla Pathak
- Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh 206001, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Devender Pathak
- Rajiv Academy for Pharmacy, NH. #2, Mathura Delhi Road P.O, Chhatikara, Mathura, Uttar Pradesh 281001, India
| |
Collapse
|
27
|
Dawood AA. Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants. VACUNAS 2022; 23:S18-S31. [PMID: 35702697 PMCID: PMC9181368 DOI: 10.1016/j.vacun.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/20/2022] [Indexed: 12/05/2022]
Abstract
Background The new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19. Aim The study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools. Methods To create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated. Results The designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations. Conclusions We advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.
Collapse
Affiliation(s)
- Ali Adel Dawood
- Dept. of Medical Biology, College of Medicine, University of Mosul, Mosul, Iraq
| |
Collapse
|
28
|
Omoniyi AA, Adebisi SS, Musa SA, Nzalak JO, Bauchi ZM, Bako KW, Olatomide OD, Zachariah R, Nyengaard JR. In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. Sci Rep 2022; 12:8736. [PMID: 35610299 PMCID: PMC9127496 DOI: 10.1038/s41598-022-12651-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/12/2022] [Indexed: 12/16/2022] Open
Abstract
Crimean Congo Hemorrhagic Fever virus (CCHFV) is a deadly human pathogen that causes an emerging zoonotic disease with a broad geographic spread, especially in Africa, Asia, and Europe, and the second most common viral hemorrhagic fever and widely transmitted tick-borne viral disease. Following infection, the patients are presented with a variety of clinical manifestations and a fatality rate of 40%. Despite the high fatality rate, there are unmet clinical interventions, as no antiviral drugs or vaccines for CCHF have been approved. Immunoinformatics pipeline and reverse vaccinology were used in this study to design a multi-epitope vaccine that may elicit a protective humoral and cellular immune response against Crimean-Congo hemorrhagic fever virus infection. Three essential virulent and antigenic proteins (S, M, and L) were used to predict seven CTL and 18 HTL epitopes that were non-allergenic, antigenic, IFN-γ inducing, and non-toxic. The epitopes were connected using linkers and 50S ribosomal protein L7/L12 was used as an adjuvant and raised a multi-epitope vaccine (MEV) that is 567 amino acids long. Molecular docking and simulation of the predicted 3D structure of the MEV with the toll-like (TLR2, TLR3, and TLR4) receptors and major histocompatibility complex (MCH-I and MCH-II) indicate high interactions and stability of the complexes, MM-GBSA free binding energy calculation revealed a favourable protein-protein complex. Maximum MEV expression was achieved with a CAI value of 0.98 through in silico cloning in the Drosophila melanogaster host. According to the immune simulation, IgG1, T-helper cells, T-cytotoxic cells, INF-γ, and IL-2 were predicted to be significantly elevated. These robust computational analyses demonstrated that the proposed MEV is effective in preventing CCHFV infections. However, it is still necessary to conduct both in vitro and in vivo experiments to validate the potential of the vaccine.
Collapse
Affiliation(s)
- Akinyemi Ademola Omoniyi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria.
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark.
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.
| | - Samuel Sunday Adebisi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Sunday Abraham Musa
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - James Oliver Nzalak
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Zainab Mahmood Bauchi
- Department of Human Anatomy, Faculty of Basic Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Kerkebe William Bako
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Oluwasegun Davis Olatomide
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Richard Zachariah
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Jens Randel Nyengaard
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
29
|
Wang H, Zhang K, Wu L, Qin Q, He Y. Prediction of Pathogenic Factors in Dysbiotic Gut Microbiomes of Colorectal Cancer Patients Using Reverse Microbiomics. Front Oncol 2022; 12:882874. [PMID: 35574378 PMCID: PMC9091335 DOI: 10.3389/fonc.2022.882874] [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: 02/24/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Gut microbiome plays a crucial role in the formation and progression of colorectal cancer (CRC). To better identify the underlying gene-level pathogenic mechanisms of microbiome-associated CRC, we applied our newly developed Reverse Microbiomics (RM) to predict potential pathogenic factors using the data of microbiomes in CRC patients. Results Our literature search first identified 40 bacterial species enriched and 23 species depleted in the guts of CRC patients. These bacteria were systematically modeled and analyzed using the NCBI Taxonomy ontology. Ten species, including 6 enriched species (e.g., Bacteroides fragilis, Fusobacterium nucleatum and Streptococcus equinus) and 4 depleted species (e.g., Bacteroides uniformis and Streptococcus thermophilus) were chosen for follow-up comparative genomics analysis. Vaxign was used to comparatively analyze 47 genome sequences of these ten species. In total 18 autoantigens were predicted to contribute to CRC formation, six of which were reported with experimental evidence to be correlated with drug resistance and/or cell invasiveness of CRC. Interestingly, four human homology proteins (EDK89078.1, EDK87700.1, EDK89777.1, and EDK89145.1) are conserved among all enriched strains. Furthermore, we predicted 76 potential virulence factors without homology to human proteins, including two riboflavin synthase proteins, three ATP-binding cassettes (ABC) transporter protein family proteins, and 12 outer membrane proteins (OMPs). Riboflavin synthase is present in all the enriched strains but not in depleted species. The critical role of riboflavin synthase in CRC development was further identified from its hub role in our STRING-based protein-protein interaction (PPI) network analysis and from the finding of the riboflavin metabolism as the most significantly enriched pathway in our KEGG pathway analysis. A novel model of the CRC pathogenesis involving riboflavin synthase and other related proteins including TpiA and GrxC was further proposed. Conclusions The RM strategy was used to predict 18 autoantigens and 76 potential virulence factors from CRC-associated microbiome data. In addition to many of these autoantigens and virulence factors experimentally verified as reported in the literature, our study predicted many new pathogenetic factors and developed a new model of CRC pathogenesis involving the riboflavin synthase from the enriched colorectal bacteria and other associated proteins.
Collapse
Affiliation(s)
- Haihe Wang
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Kaibo Zhang
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Lin Wu
- Center of Computer Experiment, Lishui University, Lishui, China
| | - Qian Qin
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States.,Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| |
Collapse
|
30
|
Rawal K, Sinha R, Nath SK, Preeti P, Kumari P, Gupta S, Sharma T, Strych U, Hotez P, Bottazzi ME. Vaxi-DL: A web-based deep learning server to identify potential vaccine candidates. Comput Biol Med 2022; 145:105401. [PMID: 35381451 DOI: 10.1016/j.compbiomed.2022.105401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/19/2022]
Abstract
The development of a new vaccine is a challenging exercise involving several steps including computational studies, experimental work, and animal studies followed by clinical studies. To accelerate the process, in silico screening is frequently used for antigen identification. Here, we present Vaxi-DL, web-based deep learning (DL) software that evaluates the potential of protein sequences to serve as vaccine target antigens. Four different DL pathogen models were trained to predict target antigens in bacteria, protozoa, fungi, and viruses that cause infectious diseases in humans. Datasets containing antigenic and non-antigenic sequences were derived from known vaccine candidates and the Protegen database. Biological and physicochemical properties were computed for the datasets using publicly available bioinformatics tools. For each of the four pathogen models, the datasets were divided into training, validation, and testing subsets and then scaled and normalised. The models were constructed using Fully Connected Layers (FCLs), hyper-tuned, and trained using the training subset. Accuracy, sensitivity, specificity, precision, recall, and AUC (Area under the Curve) were used as metrics to assess the performance of these models. The models were benchmarked using independent datasets of known target antigens against other prediction tools such as VaxiJen and Vaxign-ML. We also tested Vaxi-DL on 219 known potential vaccine candidates (PVC) from 37 different pathogens. Our tool predicted 175 PVCs correctly out of 219 sequences. We also tested Vaxi-DL on different datasets obtained from multiple resources. Our tool has demonstrated an average sensitivity of 93% and will thus be a useful tool for prioritising PVCs for preclinical studies.
Collapse
Affiliation(s)
- Kamal Rawal
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Robin Sinha
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | | | - P Preeti
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Priya Kumari
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Srijanee Gupta
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Trapti Sharma
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Ulrich Strych
- Texas Children's Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Peter Hotez
- Texas Children's Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Biology, Baylor University, Waco, TX, USA.
| | - Maria Elena Bottazzi
- Texas Children's Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Biology, Baylor University, Waco, TX, USA.
| |
Collapse
|
31
|
Alyasseri ZAA, Al‐Betar MA, Doush IA, Awadallah MA, Abasi AK, Makhadmeh SN, Alomari OA, Abdulkareem KH, Adam A, Damasevicius R, Mohammed MA, Zitar RA. Review on COVID-19 diagnosis models based on machine learning and deep learning approaches. EXPERT SYSTEMS 2022; 39:e12759. [PMID: 34511689 PMCID: PMC8420483 DOI: 10.1111/exsy.12759] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
COVID-19 is the disease evoked by a new breed of coronavirus called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, COVID-19 has become a pandemic by infecting more than 152 million people in over 216 countries and territories. The exponential increase in the number of infections has rendered traditional diagnosis techniques inefficient. Therefore, many researchers have developed several intelligent techniques, such as deep learning (DL) and machine learning (ML), which can assist the healthcare sector in providing quick and precise COVID-19 diagnosis. Therefore, this paper provides a comprehensive review of the most recent DL and ML techniques for COVID-19 diagnosis. The studies are published from December 2019 until April 2021. In general, this paper includes more than 200 studies that have been carefully selected from several publishers, such as IEEE, Springer and Elsevier. We classify the research tracks into two categories: DL and ML and present COVID-19 public datasets established and extracted from different countries. The measures used to evaluate diagnosis methods are comparatively analysed and proper discussion is provided. In conclusion, for COVID-19 diagnosing and outbreak prediction, SVM is the most widely used machine learning mechanism, and CNN is the most widely used deep learning mechanism. Accuracy, sensitivity, and specificity are the most widely used measurements in previous studies. Finally, this review paper will guide the research community on the upcoming development of machine learning for COVID-19 and inspire their works for future development. This review paper will guide the research community on the upcoming development of ML and DL for COVID-19 and inspire their works for future development.
Collapse
Affiliation(s)
- Zaid Abdi Alkareem Alyasseri
- Center for Artificial Intelligence Technology, Faculty of Information Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
- ECE Department‐Faculty of EngineeringUniversity of KufaNajafIraq
| | - Mohammed Azmi Al‐Betar
- Artificial Intelligence Research Center (AIRC)Ajman UniversityAjmanUnited Arab Emirates
- Department of Information TechnologyAl‐Huson University College, Al‐Balqa Applied UniversityIrbidJordan
| | - Iyad Abu Doush
- Computing Department, College of Engineering and Applied SciencesAmerican University of KuwaitSalmiyaKuwait
- Computer Science DepartmentYarmouk UniversityIrbidJordan
| | - Mohammed A. Awadallah
- Artificial Intelligence Research Center (AIRC)Ajman UniversityAjmanUnited Arab Emirates
- Department of Computer ScienceAl‐Aqsa UniversityGazaPalestine
| | - Ammar Kamal Abasi
- Artificial Intelligence Research Center (AIRC)Ajman UniversityAjmanUnited Arab Emirates
- School of Computer SciencesUniversiti Sains MalaysiaPenangMalaysia
| | - Sharif Naser Makhadmeh
- Artificial Intelligence Research Center (AIRC)Ajman UniversityAjmanUnited Arab Emirates
- Faculty of Information TechnologyMiddle East UniversityAmmanJordan
| | | | | | - Afzan Adam
- Center for Artificial Intelligence Technology, Faculty of Information Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
| | | | - Mazin Abed Mohammed
- College of Computer Science and Information TechnologyUniversity of AnbarAnbarIraq
| | - Raed Abu Zitar
- Sorbonne Center of Artificial IntelligenceSorbonne University‐Abu DhabiAbu DhabiUnited Arab Emirates
| |
Collapse
|
32
|
Michalik M, Djahanschiri B, Leo JC, Linke D. An Update on "Reverse Vaccinology": The Pathway from Genomes and Epitope Predictions to Tailored, Recombinant Vaccines. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2412:45-71. [PMID: 34918241 DOI: 10.1007/978-1-0716-1892-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this chapter, we review the computational approaches that have led to a new generation of vaccines in recent years. There are many alternative routes to develop vaccines based on the concept of reverse vaccinology. They all follow the same basic principles-mining available genome and proteome information for antigen candidates, and recombinantly expressing them for vaccine production. Some of the same principles have been used successfully for cancer therapy approaches. In this review, we focus on infectious diseases, describing the general workflow from bioinformatic predictions of antigens and epitopes down to examples where such predictions have been used successfully for vaccine development.
Collapse
Affiliation(s)
| | - Bardya Djahanschiri
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Jack C Leo
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
33
|
Bali A, Bali N. Role of artificial intelligence in fast-track drug discovery and vaccine development for COVID-19. NOVEL AI AND DATA SCIENCE ADVANCEMENTS FOR SUSTAINABILITY IN THE ERA OF COVID-19 2022. [PMCID: PMC9069021 DOI: 10.1016/b978-0-323-90054-6.00006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
COVID-19 is a global pandemic spread across more than 200 countries and several measures are being taken to control it. Researchers in pharmaceutical academia/industry are incessantly targeting this disease through vaccine and drug development protocols. Artificial intelligence is being extensively explored for surveillance, diagnostics, contact tracing, and for clinical management of COVID-19. The most common application has been for repurposing of existing drugs through various AI tools. Successful training of artificial neural networks based on identification of specific patterns in binding of known antiviral drugs with protein sequences from diverse virus species have generated models giving good predictions for molecules against SARS-CoV-2 virus, in sync with clinical studies. ML tools have also been used to investigate immunogenic components of the virus to be exploited as vaccine candidates. In this chapter, the utilization of artificial intelligence to accelerate drug-design and vaccine design research for COVID-19 has been reviewed.
Collapse
|
34
|
A step toward better sample management of COVID-19: On-spot detection by biometric technology and artificial intelligence. COVID-19 AND THE SUSTAINABLE DEVELOPMENT GOALS 2022. [PMCID: PMC9334987 DOI: 10.1016/b978-0-323-91307-2.00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
35
|
Ong E, He Y. Vaccine Design by Reverse Vaccinology and Machine Learning. Methods Mol Biol 2022; 2414:1-16. [PMID: 34784028 DOI: 10.1007/978-1-0716-1900-1_1] [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] [Indexed: 04/04/2024]
Abstract
Reverse vaccinology (RV) is the state-of-the-art vaccine development strategy that starts with predicting vaccine antigens by bioinformatics analysis of the whole genome of a pathogen of interest. Vaxign is the first web-based RV vaccine prediction method based on calculating and filtering different criteria of proteins. Vaxign-ML is a new Vaxign machine learning (ML) method that predicts vaccine antigens based on extreme gradient boosting with the advance of new technologies and cumulation of protective antigen data. Using a benchmark dataset, Vaxign-ML showed superior performance in comparison to existing open-source RV tools. Vaxign-ML is also implemented within the web-based Vaxign platform to support easy and intuitive access. Vaxign-ML is also available as a command-based software package for more advanced and customizable vaccine antigen prediction. Both Vaxign and Vaxign-ML have been applied to predict SARS-CoV-2 (cause of COVID-19) and Brucella vaccine antigens to demonstrate the integrative approach to analyze and select vaccine candidates using the Vaxign platform.
Collapse
Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- GlaxoSmithKline Vaccines, Rixensart, Belgium
| | - Yongqun He
- Center of Computational Medicine and Bioinformatics, Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
36
|
Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants. VACUNAS (ENGLISH EDITION) 2022; 23:S18-S31. [PMCID: PMC9683844 DOI: 10.1016/j.vacune.2022.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2023]
Abstract
Background The new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19. Aim The study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools. Methods To create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated. Results The designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations. Conclusions We advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.
Collapse
|
37
|
Huang PC, Goru R, Huffman A, Yu Lin A, Cooke MF, He Y. Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base. Vaccine X 2021; 10:100139. [PMID: 34981039 PMCID: PMC8716025 DOI: 10.1016/j.jvacx.2021.100139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/09/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
The development of SARS-CoV-2 vaccines during the COVID-19 pandemic has prompted the emergence of COVID-19 vaccine data. Timely access to COVID-19 vaccine information is crucial to researchers and public. To support more comprehensive annotation, integration, and analysis of COVID-19 vaccine information, we have developed Cov19VaxKB, a knowledge-focused COVID-19 vaccine database (http://www.violinet.org/cov19vaxkb/). Cov19VaxKB features comprehensive lists of COVID-19 vaccines, vaccine formulations, clinical trials, publications, news articles, and vaccine adverse event case reports. A web-based query interface enables comparison of product information and host responses among various vaccines. The knowledge base also includes a vaccine design tool for predicting vaccine targets and a statistical analysis tool that identifies enriched adverse events for FDA-authorized COVID-19 vaccines based on VAERS case report data. To support data exchange, Cov19VaxKB is synchronized with Vaccine Ontology and the Vaccine Investigation and Online Information Network (VIOLIN) database. The data integration and analytical features of Cov19VaxKB can facilitate vaccine research and development while also serving as a useful reference for the public.
Collapse
Key Words
- AE, adverse event
- CDC, Centers for Disease Control and Prevention
- COVID-19
- COVID-19 vaccine
- COVID-19, Coronavirus disease 2019
- Cov19VaxKB
- FDA, Food and Drug Administration
- MERS-CoV, Middle Eastern Respiratory Syndrome
- NCBI, National Center for Biotechnology Information
- OWL, Web Ontology Language
- PMID, PubMed identification number
- PRR, Proportional Reporting Ratio
- SARS-CoV, Severe Acute Respiratory Syndrome Coronavirus
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- VAERS
- VAERS, Vaccine Adverse Event Reporting System
- VIOLIN, Vaccine Investigation and Online Information Network
- VO, Vaccine Ontology
- WHO, World Health Organization
- adverse event
- bioinformatics
- database
- knowledge base
- ontology
- vaccine
Collapse
Affiliation(s)
- Philip C. Huang
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Goru
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asiyah Yu Lin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael F. Cooke
- School of Information, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
38
|
Liu CH, Lu CH, Lin LT. Pandemic strategies with computational and structural biology against COVID-19: A retrospective. Comput Struct Biotechnol J 2021; 20:187-192. [PMID: 34900126 PMCID: PMC8650801 DOI: 10.1016/j.csbj.2021.11.040] [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: 07/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic, has dominated all aspects of life since of 2020. Research studies on the virus and exploration of therapeutic and preventive strategies has been moving at rapid rates to control the pandemic. In the field of bioinformatics or computational and structural biology, recent research strategies have used multiple disciplines to compile large datasets to uncover statistical correlations and significance, visualize and model proteins, perform molecular dynamics simulations, and employ the help of artificial intelligence and machine learning to harness computational processing power to further the research on COVID-19, including drug screening, drug design, vaccine development, prognosis prediction, and outbreak prediction. These recent developments should help us better understand the viral disease and develop the much-needed therapies and strategies for the management of COVID-19.
Collapse
Affiliation(s)
- Ching-Hsuan Liu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Cheng-Hua Lu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Liang-Tzung Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
39
|
Mugunthan SP, Mani Chandra H. A Computational Reverse Vaccinology Approach for the Design and Development of Multi-Epitopic Vaccine Against Avian Pathogen Mycoplasma gallisepticum. Front Vet Sci 2021; 8:721061. [PMID: 34765664 PMCID: PMC8577832 DOI: 10.3389/fvets.2021.721061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/21/2021] [Indexed: 01/28/2023] Open
Abstract
Avian mycoplasma is a bacterial disease causing chronic respiratory disease (CRD) in poultry industries with high economic losses. The eradication of this disease still remains as a challenge. A multi-epitope prophylactic vaccine aiming the antigenic proteins of Mycoplasma gallisepticum can be a capable candidate to eradicate this infection. The present study is focused to design a multi-epitope vaccine candidate consisting of cytotoxic T-cell (CTL), helper T-cell (HTL), and B-cell epitopes of antigenic proteins, using immunoinformatics strategies. The multi-epitopic vaccine was designed, and its tertiary model was predcited, which was further refined and validated by computational tools. After initial validation, molecular docking was performed between multi-epitope vaccine construct and chicken TLR-2 and 5 receptors, which predicted effective binding. The in silico results specify the structural stability, precise specificity, and immunogenic response of the designed multi-epitope vaccine, and it could be an appropriate vaccine candidate for the M. gallisepticum infection.
Collapse
Affiliation(s)
| | - Harish Mani Chandra
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, India
| |
Collapse
|
40
|
Teahan B, Ong E, Yang Z. Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach. Vaccines (Basel) 2021; 9:vaccines9101098. [PMID: 34696207 PMCID: PMC8538456 DOI: 10.3390/vaccines9101098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death of any single infectious agent, having led to 1.4 million deaths in 2019 alone. Moreover, an estimated one-quarter of the global population is latently infected with Mycobacterium tuberculosis (MTB), presenting a huge pool of potential future disease. Nonetheless, the only currently licensed TB vaccine fails to prevent the activation of latent TB infections (LTBI). These facts together illustrate the desperate need for a more effective TB vaccine strategy that can prevent both primary infection and the activation of LTBI. In this study, we employed a machine learning-based reverse vaccinology approach to predict the likelihood that each protein within the proteome of MTB laboratory reference strain H37Rv would be a protective antigen (PAg). The proteins predicted most likely to be a PAg were assessed for their belonging to a protein family of previously established PAgs, the relevance of their biological processes to MTB virulence and latency, and finally the immunogenic potential that they may provide in terms of the number of promiscuous epitopes within each. This study led to the identification of 16 proteins with the greatest vaccine potential for further in vitro and in vivo studies. It also demonstrates the value of computational methods in vaccine development.
Collapse
Affiliation(s)
- Blaine Teahan
- Epidemiology Department, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Zhenhua Yang
- Epidemiology Department, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA;
- Correspondence:
| |
Collapse
|
41
|
Hatmal MM, Abuyaman O, Taha M. Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study. Comput Struct Biotechnol J 2021; 19:4790-4824. [PMID: 34426763 PMCID: PMC8373588 DOI: 10.1016/j.csbj.2021.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 01/10/2023] Open
Abstract
In the present work we introduce the use of multiple docked poses for bootstrapping machine learning-based QSAR modelling. Ligand-receptor contact fingerprints are implemented as descriptor variables. We implemented this method for the discovery of potential inhibitors of the serine protease enzyme TMPRSS2 involved the infectivity of coronaviruses. Several machine learners were scanned, however, Xgboost, support vector machines (SVM) and random forests (RF) were the best with testing set accuracies reaching 90%. Three potential hits were identified upon using the method to scan known untested FDA approved drugs against TMPRSS2. Subsequent molecular dynamics simulation and covalent docking supported the results of the new computational approach.
Collapse
Affiliation(s)
- Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Omar Abuyaman
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Mutasem Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
| |
Collapse
|
42
|
Prasad K, Kumar V. Artificial intelligence-driven drug repurposing and structural biology for SARS-CoV-2. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100042. [PMID: 34870150 PMCID: PMC8317454 DOI: 10.1016/j.crphar.2021.100042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
It has been said that COVID-19 is a generational challenge in many ways. But, at the same time, it becomes a catalyst for collective action, innovation, and discovery. Realizing the full potential of artificial intelligence (AI) for structure determination of unknown proteins and drug discovery are some of these innovations. Potential applications of AI include predicting the structure of the infectious proteins, identifying drugs that may be effective in targeting these proteins, and proposing new chemical compounds for further testing as potential drugs. AI and machine learning (ML) allow for rapid drug development including repurposing existing drugs. Algorithms were used to search for novel or approved antiviral drugs capable of inhibiting SARS-CoV-2. This paper presents a survey of AI and ML methods being used in various biochemistry of SARS-CoV-2, from structure to drug development, in the fight against the deadly COVID-19 pandemic. It is envisioned that this study will provide AI/ML researchers and the wider community an overview of the current status of AI applications particularly in structural biology, drug repurposing, and development, and motivate researchers in harnessing AI potentials in the fight against COVID-19.
Collapse
Affiliation(s)
- Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
| |
Collapse
|
43
|
Ong E, Cooke MF, Huffman A, Xiang Z, Wong MU, Wang H, Seetharaman M, Valdez N, He Y. Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res 2021; 49:W671-W678. [PMID: 34009334 PMCID: PMC8218197 DOI: 10.1093/nar/gkab279] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/29/2021] [Accepted: 04/15/2021] [Indexed: 01/12/2023] Open
Abstract
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-based vaccine design program using reverse vaccinology with machine learning. Vaxign2 is a comprehensive web server for rational vaccine design, consisting of predictive and computational workflow components. The predictive part includes the original Vaxign filtering-based method and a new machine learning-based method, Vaxign-ML. The benchmarking results using a validation dataset showed that Vaxign-ML had superior prediction performance compared to other RV tools. Besides the prediction component, Vaxign2 implemented various post-prediction analyses to significantly enhance users' capability to refine the prediction results based on different vaccine design rationales and considerably reduce user time to analyze the Vaxign/Vaxign-ML prediction results. Users provide proteome sequences as input data, select candidates based on Vaxign outputs and Vaxign-ML scores, and perform post-prediction analysis. Vaxign2 also includes precomputed results from approximately 1 million proteins in 398 proteomes of 36 pathogens. As a demonstration, Vaxign2 was used to effectively analyse SARS-CoV-2, the coronavirus causing COVID-19. The comprehensive framework of Vaxign2 can support better and more rational vaccine design. Vaxign2 is publicly accessible at http://www.violinet.org/vaxign2.
Collapse
Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael F Cooke
- School of Information, University of Michigan, Ann Arbor, MI 48109, USA
- Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zuoshuang Xiang
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mei U Wong
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Haihe Wang
- Department of Pathogenobiology, Daqing Branch of Harbin Medical University, Daqing, Helongjiang, China
| | - Meenakshi Seetharaman
- Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ninotchka Valdez
- Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
44
|
Genomic Analysis of Pasteurella atlantica Provides Insight on Its Virulence Factors and Phylogeny and Highlights the Potential of Reverse Vaccinology in Aquaculture. Microorganisms 2021; 9:microorganisms9061215. [PMID: 34199775 PMCID: PMC8226905 DOI: 10.3390/microorganisms9061215] [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: 05/07/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022] Open
Abstract
Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology of the bacteria involved and in devising an efficient preventive strategy. The genomes of two clinical Pasteurella atlantica isolates were sequenced (≈2.3 Mbp), and phylogenetic analysis confirmed their position as a novel species within the Pasteurellaceae. In silico analyses revealed 11 genomic islands and 5 prophages, highlighting the potential of mobile elements as driving forces in the evolution of this species. The previously documented pathogenicity of P. atlantica is strongly supported by the current study, and 17 target genes were recognized as putative primary drivers of pathogenicity. The expression level of a predicted vaccine target, an uncharacterized adhesin protein, was significantly increased in both broth culture and following the exposure of P. atlantica to lumpsucker head kidney leucocytes. Based on in silico and functional analyses, the strongest gene target candidates will be prioritized in future vaccine development efforts to prevent future pasteurellosis outbreaks.
Collapse
|
45
|
Hwang W, Lei W, Katritsis NM, MacMahon M, Chapman K, Han N. Current and prospective computational approaches and challenges for developing COVID-19 vaccines. Adv Drug Deliv Rev 2021; 172:249-274. [PMID: 33561453 PMCID: PMC7871111 DOI: 10.1016/j.addr.2021.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019 and is a coronavirus which is zoonotic in origin. As it spread around the world there has been an unprecedented effort in developing effective vaccines. Computational methods can be used to speed up the long and costly process of vaccine development. Antigen selection, epitope prediction, and toxicity and allergenicity prediction are areas in which computational tools have already been applied as part of reverse vaccinology for SARS-CoV-2 vaccine development. However, there is potential for computational methods to assist further. We review approaches which have been used and highlight additional bioinformatic approaches and PK modelling as in silico methods which may be useful for SARS-CoV-2 vaccine design but remain currently unexplored. As more novel viruses with pandemic potential are expected to arise in future, these techniques are not limited to application to SARS-CoV-2 but also useful to rapidly respond to novel emerging viruses.
Collapse
Affiliation(s)
- Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
46
|
Xie J, Zi W, Li Z, He Y. Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development. Curr Pharm Des 2021; 27:900-910. [PMID: 33238868 DOI: 10.2174/1381612826666201125112131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
Vaccination is one of the most important innovations in human history. It has also become a hot research area in a new application - the development of new vaccines against non-infectious diseases such as cancers. However, effective and safe vaccines still do not exist for many diseases, and where vaccines exist, their protective immune mechanisms are often unclear. Although licensed vaccines are generally safe, various adverse events, and sometimes severe adverse events, still exist for a small population. Precision medicine tailors medical intervention to the personal characteristics of individual patients or sub-populations of individuals with similar immunity-related characteristics. Precision vaccinology is a new strategy that applies precision medicine to the development, administration, and post-administration analysis of vaccines. Several conditions contribute to make this the right time to embark on the development of precision vaccinology. First, the increased level of research in vaccinology has generated voluminous "big data" repositories of vaccinology data. Secondly, new technologies such as multi-omics and immunoinformatics bring new methods for investigating vaccines and immunology. Finally, the advent of AI and machine learning software now makes possible the marriage of Big Data to the development of new vaccines in ways not possible before. However, something is missing in this marriage, and that is a common language that facilitates the correlation, analysis, and reporting nomenclature for the field of vaccinology. Solving this bioinformatics problem is the domain of applied biomedical ontology. Ontology in the informatics field is human- and machine-interpretable representation of entities and the relations among entities in a specific domain. The Vaccine Ontology (VO) and Ontology of Vaccine Adverse Events (OVAE) have been developed to support the standard representation of vaccines, vaccine components, vaccinations, host responses, and vaccine adverse events. Many other biomedical ontologies have also been developed and can be applied in vaccine research. Here, we review the current status of precision vaccinology and how ontological development will enhance this field, and propose an ontology-based precision vaccinology strategy to support precision vaccine research and development.
Collapse
Affiliation(s)
- Jiangan Xie
- Chongqing Engineering Research Center of Medical Electronics and Information Technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Wenrui Zi
- Chongqing engineering research center of medical electronics and information technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Zhangyong Li
- Chongqing engineering research center of medical electronics and information technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yongqun He
- Unit of Laboratory Animal Medicine, Development of Microbiology and Immunology, Center of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States
| |
Collapse
|
47
|
Wang H, Ong E, Kao JY, Sun D, He Y. Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients. Front Microbiol 2021; 12:633732. [PMID: 33717026 PMCID: PMC7947680 DOI: 10.3389/fmicb.2021.633732] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Alterations in the gut microbiome have been associated with various human diseases. Most existing gut microbiome studies stopped at the stage of identifying microbial alterations between diseased or healthy conditions. As inspired by reverse vaccinology (RV), we developed a new strategy called Reverse Microbiomics (RM) that turns this process around: based on the identified microbial alternations, reverse-predicting the molecular mechanisms underlying the disease and microbial alternations. Our RM methodology starts by identifying significantly altered microbiota profiles, performing bioinformatics analysis on the proteomes of the microbiota identified, and finally predicting potential virulence or protective factors relevant to a microbiome-associated disease. As a use case study, this reverse methodology was applied to study the molecular pathogenesis of rheumatoid arthritis (RA), a common autoimmune and inflammatory disease. Those bacteria differentially associated with RA were first identified and annotated from published data and then modeled and classified using the Ontology of Host-Microbiome Interactions (OHMI). Our study identified 14 species increased and 9 species depleted in the gut microbiota of RA patients. Vaxign was used to comparatively analyze 15 genome sequences of the two pairs of species: Gram-negative Prevotella copri (increased) and Prevotella histicola (depleted), as well as Gram-positive Bifidobacterium dentium (increased) and Bifidobacterium bifidum (depleted). In total, 21 auto-antigens were predicted to be related to RA, and five of them were previously reported to be associated with RA with experimental evidence. Furthermore, we identified 94 potential adhesive virulence factors including 24 microbial ABC transporters. While eukaryotic ABC transporters are key RA diagnosis markers and drug targets, we identified, for the first-time, RA-associated microbial ABC transporters and provided a novel hypothesis of RA pathogenesis. Our study showed that RM, by broadening the scope of RV, is a novel and effective strategy to study from bacterial level to molecular level factors and gain further insight into how these factors possibly contribute to the development of microbial alterations under specific diseases.
Collapse
Affiliation(s)
- Haihe Wang
- Department of Pathogen Biology, Harbin Medical University (Daqing), Daqing, China.,Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John Y Kao
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States.,Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
48
|
Santus E, Marino N, Cirillo D, Chersoni E, Montagud A, Santuccione Chadha A, Valencia A, Hughes K, Lindvall C. Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development. J Med Internet Res 2021; 23:e22453. [PMID: 33560998 PMCID: PMC7958975 DOI: 10.2196/22453] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/07/2020] [Accepted: 01/31/2021] [Indexed: 01/07/2023] Open
Abstract
Artificial intelligence (AI) technologies can play a key role in preventing, detecting, and monitoring epidemics. In this paper, we provide an overview of the recently published literature on the COVID-19 pandemic in four strategic areas: (1) triage, diagnosis, and risk prediction; (2) drug repurposing and development; (3) pharmacogenomics and vaccines; and (4) mining of the medical literature. We highlight how AI-powered health care can enable public health systems to efficiently handle future outbreaks and improve patient outcomes.
Collapse
Affiliation(s)
- Enrico Santus
- Division of Decision Science and Advanced Analytics, Bayer Pharmaceuticals, Whippany, NJ, United States
- The Women's Brain Project, Zurich, Switzerland
| | - Nicola Marino
- The Women's Brain Project, Zurich, Switzerland
- Department of Medical and Surgical Sciences, Università degli Studi di Foggia, Foggia, Italy
| | - Davide Cirillo
- The Women's Brain Project, Zurich, Switzerland
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Emmanuele Chersoni
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong, China (Hong Kong)
| | | | | | - Alfonso Valencia
- Barcelona Supercomputing Center, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Kevin Hughes
- Massachusetts General Hospital, Boston, MA, United States
| | - Charlotta Lindvall
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| |
Collapse
|
49
|
Yang Z, Bogdan P, Nazarian S. An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study. Sci Rep 2021; 11:3238. [PMID: 33547334 PMCID: PMC7865008 DOI: 10.1038/s41598-021-81749-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical therapy, vaccines are urgently needed to avoid the spread of this disease. In this study, we propose an in silico deep learning approach for prediction and design of a multi-epitope vaccine (DeepVacPred). By combining the in silico immunoinformatics and deep neural network strategies, the DeepVacPred computational framework directly predicts 26 potential vaccine subunits from the available SARS-CoV-2 spike protein sequence. We further use in silico methods to investigate the linear B-cell epitopes, Cytotoxic T Lymphocytes (CTL) epitopes, Helper T Lymphocytes (HTL) epitopes in the 26 subunit candidates and identify the best 11 of them to construct a multi-epitope vaccine for SARS-CoV-2 virus. The human population coverage, antigenicity, allergenicity, toxicity, physicochemical properties and secondary structure of the designed vaccine are evaluated via state-of-the-art bioinformatic approaches, showing good quality of the designed vaccine. The 3D structure of the designed vaccine is predicted, refined and validated by in silico tools. Finally, we optimize and insert the codon sequence into a plasmid to ensure the cloning and expression efficiency. In conclusion, this proposed artificial intelligence (AI) based vaccine discovery framework accelerates the vaccine design process and constructs a 694aa multi-epitope vaccine containing 16 B-cell epitopes, 82 CTL epitopes and 89 HTL epitopes, which is promising to fight the SARS-CoV-2 viral infection and can be further evaluated in clinical studies. Moreover, we trace the RNA mutations of the SARS-CoV-2 and ensure that the designed vaccine can tackle the recent RNA mutations of the virus.
Collapse
MESH Headings
- Allergens
- COVID-19/prevention & control
- COVID-19 Vaccines/adverse effects
- COVID-19 Vaccines/chemistry
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/toxicity
- Codon Usage
- Computational Biology
- Deep Learning
- Drug Design
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/immunology
- Humans
- Immunogenicity, Vaccine
- Models, Molecular
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Mutation
- Protein Conformation
- RNA, Viral
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Solubility
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Helper-Inducer/immunology
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
Collapse
Affiliation(s)
- Zikun Yang
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Shahin Nazarian
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| |
Collapse
|
50
|
Malik JA, Mulla AH, Farooqi T, Pottoo FH, Anwar S, Rengasamy KRR. Targets and strategies for vaccine development against SARS-CoV-2. Biomed Pharmacother 2021; 137:111254. [PMID: 33550049 PMCID: PMC7843096 DOI: 10.1016/j.biopha.2021.111254] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 01/03/2021] [Indexed: 12/16/2022] Open
Abstract
The SARS-CoV-2, previously called a novel coronavirus, that broke out in the Wuhan city of China caused a significant number of morbidity and mortality in the world. It is spreading at peak levels since the first case reported and the need for vaccines is in immense demand globally. Numerous treatment and vaccination strategies that were previously employed for other pathogens including coronaviruses are now being been adopted to guide the formulation of new SARS-CoV-2 vaccines. Several vaccine targets can be utilized for the development of the SARS-CoV-2 vaccine. In this review, we highlighted the potential of various antigenic targets and other modes for formulating an effective vaccine against SARS-CoV-2. There are a varying number of challenges encountered during developing the most effective vaccines, and measures for tackling such challenges will assist in fast pace development of vaccines. This review will give a concise overview of various aspects of the vaccine development process against SARS-CoV-2, including 1) potential antigen targets 2) different vaccination strategies from conventional to novel platforms, 3) ongoing clinical trials, 4) varying challenges encountered during developing the most effective vaccine and the futuristic approaches.
Collapse
Affiliation(s)
- Jonaid Ahmad Malik
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India; Department of Biomedical Engineering, Indian Institute of Technology (IIT), Ropar, Punjab, India
| | | | - Tahmeena Farooqi
- Department of Pharmacology and Toxicology National Institute of Pharmaceutical Education and Research, Hyderabad Telangana, India
| | - Faheem Hyder Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, P.O.BOX 1982, Dammam, 31441, Saudi Arabia.
| | - Sirajudheen Anwar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
| | - Kannan R R Rengasamy
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Viet Nam; Faculty of Environment and Chemical Engineering, Duy Tan University, Da Nang, 550000, Viet Nam; Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2745, North West Province, South Africa.
| |
Collapse
|