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Trabelsi K, Ben Khalaf N, Ramadan AR, Elsharkawy A, Ashoor D, Chlif S, Boussoffara T, Ben-Ahmed M, Kumar M, Fathallah MD. A novel approach to designing viral precision vaccines applied to SARS-CoV-2. Front Cell Infect Microbiol 2024; 14:1346349. [PMID: 38628551 PMCID: PMC11018900 DOI: 10.3389/fcimb.2024.1346349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.
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Affiliation(s)
- Khaled Trabelsi
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddin Ben Khalaf
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Amany Elsharkawy
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - Dana Ashoor
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Thouraya Boussoffara
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Melika Ben-Ahmed
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - M-Dahmani Fathallah
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Ashoor D, Marzouq M, Trabelsi K, Chlif S, Abotalib N, Khalaf NB, Ramadan AR, Fathallah MD. How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system. Front Cell Infect Microbiol 2022; 12:868205. [PMID: 36034694 PMCID: PMC9399656 DOI: 10.3389/fcimb.2022.868205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus’ major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic.
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Affiliation(s)
- Dana Ashoor
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Maryam Marzouq
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Khaled Trabelsi
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Nasser Abotalib
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddine Ben Khalaf
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - M-Dahmani Fathallah
- Department of Life Sciences, Health Biotechnology Program - King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
- *Correspondence: M-Dahmani Fathallah,
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Ashoor D, Ben Khalaf N, Marzouq M, Jarjanazi H, Chlif S, Fathallah MD. A Computational Approach to Evaluate the Combined Effect of SARS-CoV-2 RBD Mutations and ACE2 Receptor Genetic Variants on Infectivity: The COVID-19 Host-Pathogen Nexus. Front Cell Infect Microbiol 2021; 11:707194. [PMID: 34434902 PMCID: PMC8381355 DOI: 10.3389/fcimb.2021.707194] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 01/21/2023] Open
Abstract
SARS-CoV-2 infectivity is largely determined by the virus Spike protein binding to the ACE2 receptor. Meanwhile, marked infection rate differences were reported between populations and individuals. To understand the disease dynamic, we developed a computational approach to study the implications of both SARS-CoV-2 RBD mutations and ACE2 polymorphism on the stability of the virus-receptor complex. We used the 6LZG PDB RBD/ACE2 3D model, the mCSM platform, the LigPlot+ and PyMol software to analyze the data on SARS-CoV-2 mutations and ACE variants retrieved from GISAID and Ensembl/GnomAD repository. We observed that out of 351 RBD point mutations, 83% destabilizes the complex according to free energy (ΔΔG) differences. We also spotted variations in the patterns of polar and hydrophobic interactions between the mutations occurring in 15 out of 18 contact residues. Similarly, comparison of the effect on the complex stability of different ACE2 variants showed that the pattern of molecular interactions and the complex stability varies also according to ACE2 polymorphism. We infer that it is important to consider both ACE2 variants and circulating SARS-CoV-2 RBD mutations to assess the stability of the virus-receptor association and evaluate infectivity. This approach might offers a good molecular ground to mitigate the virus spreading.
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Affiliation(s)
- Dana Ashoor
- Department of Life Sciences, Health Biotechnology Program # King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddine Ben Khalaf
- Department of Life Sciences, Health Biotechnology Program # King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Maryam Marzouq
- Department of Life Sciences, Health Biotechnology Program # King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Hamdi Jarjanazi
- Department of Life Sciences, Health Biotechnology Program # King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
- Environmental Monitoring and Reporting Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, Canada
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - M. Dahmani Fathallah
- Department of Life Sciences, Health Biotechnology Program # King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Marzouq M, Nairouz A, Ben Khalaf N, Bourguiba-Hachemi S, Quaddorah R, Ashoor D, Fathallah MD. Genetic variants of the EGFR ligand-binding domain and their association with structural alterations in Arab cancer patients. BMC Res Notes 2021; 14:146. [PMID: 33874989 PMCID: PMC8054381 DOI: 10.1186/s13104-021-05559-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/08/2021] [Indexed: 01/03/2023] Open
Abstract
Objective This study aimed to identify novel genetic variants in the CR2 extracellular domain of the epidermal growth factor receptor (EGFR) in healthy individuals and patients with six different types of adenocarcinoma, in Arabian peninsula populations. It also aimed to investigate the effects of these variants on the EGFR structure and their eventual relevance to tumorigenesis. Results We detected seven new EGFR genetic variants in 168 cancer patients and 114 controls. A SNP rs374670788 was more frequent in bladder cancer but not significantly associated to. However, a missense mutation (V550M) was significantly associated to colon, ovary, lung, bladder and thyroid cancer samples (p < 0.05). Three mutations (H590R, E602K and T605T) were found in the heterozygous form only in colon cancer patients. Genomic analysis of the synonymous mutation (G632G) showed that the T/A genotype could be associated to thyroid cancer in Arab patients (p < 0.05). An additional novel SNP rs571064657 was observed in control individuals. Computational analysis of the genetic variants revealed a reduction in the stabilization of the EGFR tethered form for both V550M and the common R521K variant with low energetic state (− ∆∆G). Molecular interactions analysis suggested that these mutations might affect the receptor’s function and promote tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05559-y.
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Affiliation(s)
- Maryam Marzouq
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - Ali Nairouz
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - Noureddine Ben Khalaf
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - Sonia Bourguiba-Hachemi
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - Raed Quaddorah
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - Dana Ashoor
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain
| | - M Dahmani Fathallah
- Department of Life Sciences, Health Biotechnology Program, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain. .,King Fahad Chair for Health Biotechnology, College of Graduate Studies, Arabian Gulf University, PO Box 26671, Manama, Kingdom of Bahrain.
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