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Rabaan AA, Alshahrani FS, Garout M, Alissa M, Mashraqi MM, Alshehri AA, Alsaleh AA, Alwarthan S, Sabour AA, Alfaraj AH, AlShehail BM, Alotaibi N, Abduljabbar WA, Aljeldah M, Alestad JH. Repositioning of anti-infective compounds against monkeypox virus core cysteine proteinase: a molecular dynamics study. Mol Divers 2024:10.1007/s11030-023-10802-8. [PMID: 38652365 DOI: 10.1007/s11030-023-10802-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 04/25/2024]
Abstract
Monkeypox virus (MPXV) core cysteine proteinase (CCP) is one of the major drug targets used to examine the inhibitory action of chemical moieties. In this study, an in silico technique was applied to screen 1395 anti-infective compounds to find out the potential molecules against the MPXV-CCP. The top five hits were selected after screening and processed for exhaustive docking based on the docked score of ≤ -9.5 kcal/mol. Later, the top three hits based on the exhaustive-docking score and interaction profile were selected to perform MD simulations. The overall RMSD suggested that two compounds, SC75741 and ammonium glycyrrhizinate, showed a highly stable complex with a standard deviation of 0.18 and 0.23 nm, respectively. Later, the MM/GBSA binding free energies of complexes showed significant binding strength with ΔGTOTAL from -21.59 to -15 kcal/mol. This report reported the potential inhibitory activity of SC75741 and ammonium glycyrrhizinate against MPXV-CCP by competitively inhibiting the binding of the native substrate.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Fatimah S Alshahrani
- Department of Internal Medicine, College of Medicine, King Saud University, 11362, Riyadh, Saudi Arabia
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, 11451, Riyadh, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Abdulmonem A Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, 34222, Dammam, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, 34212, Dammam, Saudi Arabia
| | - Amal A Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amal H Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, 33261, Abqaiq, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Nouf Alotaibi
- Clinical pharmacy Department, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Wesam A Abduljabbar
- Department of Medical laboratory sciences, Fakeeh College for Medical Science, 21134, Jeddah, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, 39831, Hafr Al Batin, Saudi Arabia
| | - Jeehan H Alestad
- Immunology and Infectious Microbiology Department, University of Glasgow, Glasgow, G1 1XQ, UK.
- Microbiology Department, Collage of Medicine, 46300, Jabriya, Kuwait.
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Ahmed N, Rabaan AA, Alwashmi ASS, Albayat H, Mashraqi MM, Alshehri AA, Garout M, Abduljabbar WA, Yusof NY, Yean CY. Immunoinformatic Execution and Design of an Anti-Epstein-Barr Virus Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses. Microorganisms 2023; 11:2448. [PMID: 37894106 PMCID: PMC10609278 DOI: 10.3390/microorganisms11102448] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
One of the most important breakthroughs in healthcare is the development of vaccines. The life cycle and its gene expression in the numerous virus-associated disorders must be considered when choosing the target vaccine antigen for Epstein-Barr virus (EBV). The vaccine candidate used in the current study will also be effective against all other herpesvirus strains, based on the conservancy study, which verified that the protein is present in all herpesviruses. From the screening, two B-cell epitopes, four MHC-I, and five MHC-II restricted epitopes were chosen for further study. The refined epitopes indicated 70.59% coverage of the population in Malaysia and 93.98% worldwide. After removing the one toxin (PADRE) from the original vaccine design, it was projected that the new vaccine would not be similar to the human host and would instead be antigenic, immunogenic, non-allergenic, and non-toxic. The vaccine construct was stable, thermostable, soluble, and hydrophilic. The immunological simulation projected that the vaccine candidate would be subject to a long-lasting active adaptive response and a short-lived active innate response. With IgM concentrations of up to 450 cells per mm3 and active B-cell concentrations of up to 400 cells per mm3, the B-cells remain active for a considerable time. The construct also discovered other conformational epitopes, improving its ability to stimulate an immune response. This suggests that, upon injection, the epitope will target the B-cell surface receptors and elicit a potent immune response. Furthermore, the discotope analysis confirmed that our conformational B-cell epitope was not displaced during the design. Lastly, the docking complex was stable and exhibited little deformability under heat pressure. These computational results are very encouraging for future testing of our proposed vaccine, which may potentially help in the management and prevention of EBV infections worldwide.
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Affiliation(s)
- Naveed Ahmed
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Wesam A. Abduljabbar
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Sciences, Jeddah 21461, Saudi Arabia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia
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Rabaan AA, Alfaraj AH, Alshengeti A, Alawfi A, Alwarthan S, Alhajri M, Al-Najjar AH, Al Fares MA, Najim MA, Almuthree SA, AlShurbaji ST, Alofi FS, AlShehail BM, AlYuosof B, Alynbiawi A, Alzayer SA, Al Kaabi N, Abduljabbar WA, Bukhary ZA, Bueid AS. Antibodies to Combat Fungal Infections: Development Strategies and Progress. Microorganisms 2023; 11:microorganisms11030671. [PMID: 36985244 PMCID: PMC10051215 DOI: 10.3390/microorganisms11030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
The finding that some mAbs are antifungal suggests that antibody immunity may play a key role in the defense of the host against mycotic infections. The discovery of antibodies that guard against fungi is a significant advancement because it gives rise to the possibility of developing vaccinations that trigger protective antibody immunity. These vaccines might work by inducing antibody opsonins that improve the function of non-specific (such as neutrophils, macrophages, and NK cells) and specific (such as lymphocyte) cell-mediated immunity and stop or aid in eradicating fungus infections. The ability of antibodies to defend against fungi has been demonstrated by using monoclonal antibody technology to reconsider the function of antibody immunity. The next step is to develop vaccines that induce protective antibody immunity and to comprehend the mechanisms through which antibodies mediate protective effects against fungus.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
- Correspondence:
| | - Amal H. Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, Abqaiq 33261, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Amal H. Al-Najjar
- Drug & Poison Information Center, Pharmacy Department, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia
| | - Mustafa A. Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
| | - Souad A. Almuthree
- Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
| | - Sultan T. AlShurbaji
- Outpatient Pharmacy, Dr. Sulaiman Alhabib Medical Group, Diplomatic Quarter, Riyadh 91877, Saudi Arabia
| | - Fadwa S. Alofi
- Department of Infectious Diseases, King Fahad Hospital, Madinah 42351, Saudi Arabia
| | - Bashayer M. AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Buthina AlYuosof
- Directorate of Public Health, Dammam Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Ahlam Alynbiawi
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Suha A. Alzayer
- Parasitology Laboratory Department, Qatif Comprehensive Inspection Center, Qatif 31911, Saudi Arabia
| | - Nawal Al Kaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi 51900, United Arab Emirates
| | - Wesam A. Abduljabbar
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Zakiyah A. Bukhary
- Department of Internal Medicine, King Fahad General Hospital, Jeddah 23325, Saudi Arabia
| | - Ahmed S. Bueid
- Microbiology Laboratory, King Faisal General Hospital, Al-Ahsa 31982, Saudi Arabia
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Rabaan AA, Al-Ahmed SH, Albayat H, Alwarthan S, Alhajri M, Najim MA, AlShehail BM, Al-Adsani W, Alghadeer A, Abduljabbar WA, Alotaibi N, Alsalman J, Gorab AH, Almaghrabi RS, Zaidan AA, Aldossary S, Alissa M, Alburaiky LM, Alsalim FM, Thakur N, Verma G, Dhawan M. Variants of SARS-CoV-2: Influences on the Vaccines' Effectiveness and Possible Strategies to Overcome Their Consequences. Medicina (Kaunas) 2023; 59:507. [PMID: 36984508 PMCID: PMC10051174 DOI: 10.3390/medicina59030507] [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] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
The immune response elicited by the current COVID-19 vaccinations declines with time, especially among the immunocompromised population. Furthermore, the emergence of novel SARS-CoV-2 variants, particularly the Omicron variant, has raised serious concerns about the efficacy of currently available vaccines in protecting the most vulnerable people. Several studies have reported that vaccinated people get breakthrough infections amid COVID-19 cases. So far, five variants of concern (VOCs) have been reported, resulting in successive waves of infection. These variants have shown a variable amount of resistance towards the neutralising antibodies (nAbs) elicited either through natural infection or the vaccination. The spike (S) protein, membrane (M) protein, and envelope (E) protein on the viral surface envelope and the N-nucleocapsid protein in the core of the ribonucleoprotein are the major structural vaccine target proteins against COVID-19. Among these targets, S Protein has been extensively exploited to generate effective vaccines against COVID-19. Hence, amid the emergence of novel variants of SARS-CoV-2, we have discussed their impact on currently available vaccines. We have also discussed the potential roles of S Protein in the development of novel vaccination approaches to contain the negative consequences of the variants' emergence and acquisition of mutations in the S Protein of SARS-CoV-2. Moreover, the implications of SARS-CoV-2's structural proteins were also discussed in terms of their variable potential to elicit an effective amount of immune response.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Shamsah H. Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif 32654, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mustafa A. Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
| | - Bashayer M. AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Wasl Al-Adsani
- Department of Medicine, Infectious Diseases Hospital, Kuwait City 63537, Kuwait
- Department of Infectious Diseases, Hampton Veterans Administration Medical Center, Hampton, VA 23667, USA
| | - Ali Alghadeer
- Department of Anesthesia, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Wesam A. Abduljabbar
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Nouf Alotaibi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Jameela Alsalman
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 435, Bahrain
| | - Ali H. Gorab
- Al Kuzama Primary Health Care Center, Al Khobar Health Network, Eastern Health Cluster, Al Khobar 34446, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ali A. Zaidan
- Gastroenterology Department, King Fahad Armed Forces Hospital, Jeddah 23831, Saudi Arabia
| | - Sahar Aldossary
- Pediatric Infectious Diseases, Women and Children’s Health Institute, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Lamees M. Alburaiky
- Pediatric Department, Safwa General Hospital, Eastern Health Cluster, Safwa 31921, Saudi Arabia
| | - Fatimah Mustafa Alsalim
- Department of Family Medicine, Primary Health Care, Qatif Health Cluster, Qatif 32434, Saudi Arabia
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Geetika Verma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India
- Trafford College, Altrincham, Manchester WA14 5PQ, UK
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