|
1
|
Jiang D, Zhang J, Shen W, Sun Y, Wang Z, Wang J, Zhang J, Zhang G, Zhang G, Wang Y, Cai S, Zhang J, Wang Y, Liu R, Bai T, Sun Y, Yang S, Ma Z, Li Z, Li J, Ma C, Cheng L, Sun B, Yang K. DNA Vaccines Encoding HTNV GP-Derived Th Epitopes Benefited from a LAMP-Targeting Strategy and Established Cellular Immunoprotection. Vaccines (Basel) 2024; 12:928. [PMID: 39204051 PMCID: PMC11359959 DOI: 10.3390/vaccines12080928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Vaccines has long been the focus of antiviral immunotherapy research. Viral epitopes are thought to be useful biomarkers for immunotherapy (both antibody-based and cellular). In this study, we designed a novel vaccine molecule, the Hantaan virus (HTNV) glycoprotein (GP) tandem Th epitope molecule (named the Gnc molecule), in silico. Subsequently, computer analysis was used to conduct a comprehensive and in-depth study of the various properties of the molecule and its effects as a vaccine molecule in the body. The Gnc molecule was designed for DNA vaccines and optimized with a lysosomal-targeting membrane protein (LAMP) strategy. The effects of GP-derived Th epitopes and multiepitope vaccines were initially verified in animals. Our research has resulted in the design of two vaccines based on effective antiviral immune targets. The effectiveness of molecular therapies has also been preliminarily demonstrated in silico and in laboratory animals, which lays a foundation for the application of a vaccines strategy in the field of antivirals.
Collapse
Affiliation(s)
- Dongbo Jiang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China;
| | - Junqi Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Wenyang Shen
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yubo Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zhenjie Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jiawei Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jinpeng Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Guanwen Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Gefei Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yueyue Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Sirui Cai
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jiaxing Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yongkai Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Ruibo Liu
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Tianyuan Bai
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yuanjie Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Shuya Yang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zilu Ma
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zhikui Li
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jijin Li
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Chenjin Ma
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Linfeng Cheng
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China;
| | - Baozeng Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
- Yingtan Detachment, Jiangxi General Hospital, Chinese People’s Armed Police Force, Nanchang 330001, China
| | - Kun Yang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| |
Collapse
|
|
2
|
Biswas R, Swetha RG, Basu S, Roy A, Ramaiah S, Anbarasu A. Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines. Biologicals 2024; 87:101782. [PMID: 39003966 DOI: 10.1016/j.biologicals.2024.101782] [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: 12/06/2023] [Revised: 05/13/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024] Open
Abstract
Human cytomegalovirus (HCMV) is accountable for high morbidity in neonates and immunosuppressed individuals. Due to the high genetic variability of HCMV, current prophylactic measures are insufficient. In this study, we employed a pan-genome and reverse vaccinology approach to screen the target for efficient vaccine candidates. Four proteins, envelope glycoprotein M, UL41A, US23, and US28, were shortlisted based on cellular localization, high solubility, antigenicity, and immunogenicity. A total of 29 B-cell and 44 T-cell highly immunogenic and antigenic epitopes with high global population coverage were finalized using immunoinformatics tools and algorithms. Further, the epitopes that were overlapping among the finalized B-cell and T-cell epitopes were linked with suitable linkers to form various combinations of multi-epitopic vaccine constructs. Among 16 vaccine constructs, Vc12 was selected based on physicochemical and structural properties. The docking and molecular simulations of VC12 were performed, which showed its high binding affinity (-23.35 kcal/mol) towards TLR4 due to intermolecular hydrogen bonds, salt bridges, and hydrophobic interactions, and there were only minimal fluctuations. Furthermore, Vc12 eliciting a good response was checked for its expression in Escherichia coli through in silico cloning and codon optimization, suggesting it to be a potent vaccine candidate.
Collapse
Affiliation(s)
- Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Rayapadi G Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, 761008, Odisha, India
| | - Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India.
| |
Collapse
|
|
3
|
Yaseen AR, Suleman M, Jabeen A, Nezami L, Qadri AS, Arif A, Arshad I, Iqbal K, Yaqoob T, Khan Z. Design and computational evaluation of a novel multi-epitope hybrid vaccine against monkeypox virus: Potential targets and immunogenicity assessment for pandemic preparedness. Biologicals 2024; 86:101770. [PMID: 38749079 DOI: 10.1016/j.biologicals.2024.101770] [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: 02/22/2024] [Revised: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Monkeypox is a type of DNA-enveloped virus that belongs to the orthopoxvirus family, closely related to the smallpox virus. It can cause an infectious disease in humans known as monkeypox disease. Although there are multiple drugs and vaccines designed to combat orthopoxvirus infections, with a primary focus on smallpox, the recent spread of the monkeypox virus to over 50 countries have ignited a mounting global concern. This unchecked viral proliferation has raised apprehensions about the potential for a pandemic corresponding to the catastrophic impact of COVID-19. This investigation explored the structural proteins of monkeypox virus as potential candidates for designing a novel hybrid multi-epitope vaccine. The epitopes obtained from the selected proteins were screened to ensure their non-allergenicity, non-toxicity, and antigenicity to trigger T and B-cell responses. The interaction of the vaccine with toll-like receptor-3 (TLR-3) and major histocompatibility complexes (MHCs) was assessed using Cluspro 2.0. To establish the reliability of the docked complexes, a comprehensive evaluation was conducted using Immune and MD Simulations and Normal Mode Analysis. However, to validate the computational results of this study, additional in-vitro and in-vivo research is essential.
Collapse
Affiliation(s)
- Allah Rakha Yaseen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Muhammad Suleman
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Aqsa Jabeen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Laiba Nezami
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan.
| | - Abdul Salam Qadri
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan; Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan.
| | - Ayesha Arif
- Centre for Applied Molecular biology (CAMB), University of the Punjab, Lahore, 54590, Pakistan.
| | - Iram Arshad
- Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.
| | - Khadija Iqbal
- Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.
| | - Tasuduq Yaqoob
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Zoha Khan
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan.
| |
Collapse
|
|
4
|
Elbehiry A, Al Shoaibi M, Alzahrani H, Ibrahem M, Moussa I, Alzaben F, Alsubki RA, Hemeg HA, Almutairi D, Althobaiti S, Alanazi F, Alotaibi SA, Almutairi H, Alzahrani A, Abu-Okail A. Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance. AMB Express 2024; 14:17. [PMID: 38329626 PMCID: PMC10853136 DOI: 10.1186/s13568-024-01675-7] [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: 11/23/2023] [Accepted: 01/27/2024] [Indexed: 02/09/2024] Open
Abstract
The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.
Collapse
Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, 52741, Al Bukayriyah, Saudi Arabia.
| | - Mansor Al Shoaibi
- Department of Support Service, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Hamzah Alzahrani
- Department of Preventive Medicine, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, 61421, Abha, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, 23311, Jeddah, Saudi Arabia
| | - Rousa A Alsubki
- Department of Clinical Laboratory Science, College of Applied Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Dakheel Almutairi
- Medical Transportation Administration of Prince Sultan Military Medical City, 12233, Riyadh, Saudi Arabia
| | - Saleh Althobaiti
- Pharmacy Department, Armed Forces Hospital in Jubail, 35517, Jubail, Saudi Arabia
| | - Fawaz Alanazi
- Supply Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, 35517, Jubail, Saudi Arabia
| | - Sultan A Alotaibi
- Medical Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, 35517, Jubail, Saudi Arabia
| | - Hamoud Almutairi
- Aviation Medicine, King Abdulaziz Medical City of National Guard, 14611, Riyadh, Saudi Arabia
| | - Ali Alzahrani
- Department of Preventive Medicine, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
| |
Collapse
|
|
5
|
Murtaza A, Hoa NT, Dieu-Huong D, Afzal H, Tariq MH, Cheng LT, Chung YC. Advancing PEDV Vaccination: Comparison between Inactivated and Flagellin N-Terminus-Adjuvanted Subunit Vaccines. Vaccines (Basel) 2024; 12:139. [PMID: 38400123 PMCID: PMC10892538 DOI: 10.3390/vaccines12020139] [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: 12/02/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Vaccinations can serve as an important preventive measure against the porcine epidemic diarrhea (PED) virus that currently threatens the swine industry. This study focuses on the development of a fusion protein vaccine, FliC99-mCOE, which combines the N-terminus of flagellin (FliC99) with a modified core neutralizing epitope (mCOE) of PEDV. In silico immunoinformatic analysis confirmed the construct's non-toxic, non-allergenic, and highly antigenic nature. Molecular docking and molecular dynamics (MD) simulations demonstrated FliC99-mCOE's strong binding to the TLR-5 immunological receptor. Repeated exposure simulations and immunological simulations suggested enhanced cell-mediated immunity. Both FliC99-mCOE and an inactivated PEDV vaccine were produced and tested in mice. The results from cell proliferation, ELISA, and neutralization assays indicated that FliC99-mCOE effectively stimulated cellular immunity and neutralized PEDV. We conclude that the FliC99-mCOE fusion protein may serve as a promising vaccine candidate against PEDV.
Collapse
Affiliation(s)
- Asad Murtaza
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Nguyen-Thanh Hoa
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Do Dieu-Huong
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Haroon Afzal
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Muhammad Hamza Tariq
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates;
| | - Li-Ting Cheng
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Yao-Chi Chung
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| |
Collapse
|
|
6
|
Hossen MS, Hasan MN, Haque M, Al Arian T, Halder SK, Uddin MJ, Abdullah-Al-Mamun M, Shakil MS. Immunoinformatics-aided rational design of multiepitope-based peptide vaccine (MEBV) targeting human parainfluenza virus 3 (HPIV-3) stable proteins. J Genet Eng Biotechnol 2023; 21:162. [PMID: 38055114 DOI: 10.1186/s43141-023-00623-5] [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: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Human parainfluenza viruses (HPIVs) are common RNA viruses responsible for respiratory tract infections. Human parainfluenza virus 3 (HPIV-3) is particularly pathogenic, causing severe illnesses with no effective vaccine or therapy available. RESULTS The current study employed a systematic immunoinformatic/reverse vaccinology approach to design a multiple epitope-based peptide vaccine against HPIV-3 by analyzing the virus proteome. On the basis of a number of therapeutic features, all three stable and antigenic proteins with greater immunological relevance, namely matrix protein, hemagglutinin neuraminidase, and RNA-directed RNA polymerase L, were chosen for predicting and screening suitable T-cell and B-cell epitopes. All of our desired epitopes exhibited no homology with human proteins, greater population coverage (99.26%), and high conservancy among reported HPIV-3 isolates worldwide. All of the T- and B-cell epitopes are then joined by putative ligands, yielding a 478-amino acid-long final construct. Upon computational refinement, validation, and thorough screening, several programs rated our peptide vaccine as biophysically stable, antigenic, allergenic, and non-toxic in humans. The vaccine protein demonstrated sufficiently stable interaction as well as binding affinity with innate immune receptors TLR3, TLR4, and TLR8. Furthermore, codon optimization and virtual cloning of the vaccine sequence in a pET32a ( +) vector showed that it can be readily expressed in the bacterial system. CONCLUSION The in silico designed HPIV-3 vaccine demonstrated potential in evoking an effective immune response. This study paves the way for further preclinical and clinical evaluation of the vaccine, offering hope for a future solution to combat HPIV-3 infections.
Collapse
Affiliation(s)
- Md Sakib Hossen
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka, 1213, Bangladesh.
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
| | - Md Nazmul Hasan
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
| | - Munima Haque
- Biotechnology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, kha-208, 1 Bir Uttam Rafiqul Islam Ave, Dhaka, 1212, Bangladesh
| | - Tawsif Al Arian
- Department of Pharmacy, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Jasim Uddin
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - M Abdullah-Al-Mamun
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Salman Shakil
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh
- Microbiology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| |
Collapse
|
|
7
|
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] [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.
Collapse
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
| |
Collapse
|
|
8
|
Ahmad S, Nazarian S, Alizadeh A, Pashapour Hajialilou M, Tahmasebian S, Alharbi M, Alasmari AF, Shojaeian A, Ghatrehsamani M, Irfan M, Pazoki-Toroudi H, Sanami S. Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins. J Biomol Struct Dyn 2023:1-18. [PMID: 37713338 DOI: 10.1080/07391102.2023.2258403] [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: 05/15/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Sciences, Virginia Tech, Blacksburg, VA, USA
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Shahin Nazarian
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Akram Alizadeh
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Maryam Pashapour Hajialilou
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| |
Collapse
|
|
9
|
Yaseen AR, Suleman M, Qadri AS, Asghar A, Arshad I, Khan DM. Development of conserved multi-epitopes based hybrid vaccine against SARS-CoV-2 variants: an immunoinformatic approach. In Silico Pharmacol 2023; 11:18. [PMID: 37519944 PMCID: PMC10374517 DOI: 10.1007/s40203-023-00156-2] [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: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
The world has faced unprecedented disruptions like global quarantine and the COVID-19 pandemic due to SARS-CoV-2. To combat these unsettling situations, several effective vaccines have been developed and are currently being used. However, the emergence of new variants due to the high mutation rate of SARS-CoV-2 challenges the efficacy of existing vaccines and has highlighted the need for novel vaccines that will be effective against various SARS-CoV-2 variants. In this study, we exploited the four structural proteins of SARS-CoV-2 to execute a potential multi-epitope vaccine against SARS-CoV-2 and its variants. The vaccine was designed by utilizing the antigenic, non-toxic, and non-allergenic B-cell and T-cell epitopes, which were selected from conserved regions of viral proteins. To build a vaccine construct, epitopes were connected through different linkers and an adjuvant was also attached at the start of the construct to enhance the immunogenicity and specificity of the epitopes. The vaccine construct was then screened through the aforementioned filters and it scored 0.6019 against the threshold of 0.4 on VexiJen 2.0 which validates its antigenicity. Toll-like receptors (i.e., TLR2, TLR3, TLR4, TLR5, and TLR8) and vaccine construct were docked by Cluspro 2.0, and TLR8 showed strong interaction with construct having a maximum negative binding energy of - 1577.1 kCal/mole. C-IMMSIM's immune simulations over three doses of the vaccine and iMODS' molecular dynamic simulations were executed to assess the reliability of the docked complexes. The stability of the vaccine construct was evaluated through the physicochemical analyses and the findings suggested that the manufactured vaccine is stable under a wide range of circumstances and can trigger immune responses against various SARS-CoV-2 variants (due to conserved epitopes). However, to strengthen the formulation of the vaccine and assess its safety and effectiveness, additional investigations and studies are required to support the computational data of this research at in-vitro and in-vivo levels. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00156-2.
Collapse
Affiliation(s)
- Allah Rakha Yaseen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590 Pakistan
| | - Muhammad Suleman
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590 Pakistan
| | - Abdul Salam Qadri
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000 Pakistan
| | - Ali Asghar
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000 Pakistan
| | - Iram Arshad
- Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000 Pakistan
| | - Daulat Munaza Khan
- Institute of Molecular Biology and Biotechnology, Faculty of Life Sciences, University of Lahore, Lahore, 54000 Pakistan
| |
Collapse
|
|
10
|
Girija ASS, Gunasekaran S, Habib S, Aljeldah M, Al Shammari BR, Alshehri AA, Alwashmi ASS, Turkistani SA, Alawfi A, Alshengeti A, Garout M, Alwarthan S, Alsubki RA, Moustafa NM, Rabaan AA. Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in Acinetobacter baumannii Using an In Silico Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59020343. [PMID: 36837545 PMCID: PMC9959147 DOI: 10.3390/medicina59020343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Background and Objectives: The BaeR protein is involved in the adaptation system of A. baumannii and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope peptides for the design of vaccines against BaeR protein, using an immune-informatic approach. Materials and Methods: FASTA sequences of BaeR from five different strains of A. baumannii were retrieved from the UNIPROT database and evaluated for their antigenicity, allergenicity and vaccine properties using BepiPred, Vaxijen, AlgPred, AntigenPro and SolPro. Their physio-chemical properties were assessed using the Expasy Protparam server. Immuno-dominant B-cell and T-cell epitope peptides were predicted using the IEDB database and MHC cluster server with a final assessment of their interactions with TLR-2. Results: A final selection of two peptide sequences (36aa and 22aa) was made from the 38 antigenic peptides. E1 was considered a soluble, non-allergenic antigen, and possessed negative GRAVY values, substantiating the hydrophilic nature of the proteins. Further analysis on the T-cell epitopes, class I immunogenicity and HLA allele frequencies yielded T-cell immuno-dominant peptides. The protein-peptide interactions of the TLR-2 receptor showed good similarity scores in terms of the high number of hydrogen bonds compared to other protein-peptide interactions. Conclusions: The two epitopes predicted from BaeR in the present investigation are promising vaccine candidates for targeting the TCS of A. baumannii in systemic and nosocomial infections. This study also demonstrates an alternative strategy to tackling and mitigating MDR strains of A. baumannii and provides a useful reference for the design and construction of novel vaccine candidates against this bacteria.
Collapse
Affiliation(s)
- A. S. Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. Road, Chennai 600077, India
- Correspondence: (A.S.S.G.); (A.A.R.)
| | - Shoba Gunasekaran
- Department of Biotechnology, DG Vaishnav College, Chennai 600106, India
| | - Saman Habib
- Department of Medical Education, King Edward Medical University, Lahore 54000, Pakistan
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Safaa A. Turkistani
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, 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
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Nouran M. Moustafa
- Basic Medical Science Department, College of Medicine, Dar Al Uloom University, Riyadh 12922, Saudi Arabia
- Medical Microbiology & Immunology Department, Faculty of Medicine, Ain Shams University, Cairo 1181, Egypt
| | - 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: (A.S.S.G.); (A.A.R.)
| |
Collapse
|
|
11
|
Designing Novel Multi-Epitope Vaccine Construct against Prevotella intermedia-Interpain A: An Immunoinformatics Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59020302. [PMID: 36837503 PMCID: PMC9966096 DOI: 10.3390/medicina59020302] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/19/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Background and Objectives: Periodontitis is a chronic multifactorial inflammatory infectious disease marked by continuous degradation of teeth and surrounding parts. One of the most important periodontal pathogens is P. intermedia, and with its interpain A proteinase, it leads to an increase in lethal infection. Materials and Methods: The current study was designed to create a multi-epitope vaccine using an immunoinformatics method that targets the interpain A of P. intermedia. For the development of vaccines, P. intermedia peptides InpA were found appropriate. To create a multi-epitope vaccination design, interpain A, B, and T-cell epitopes were found and assessed depending on the essential variables. The vaccine construct was evaluated based on its stability, antigenicity, and allergenicity. Results: The vaccine construct reached a more significant population and was able to bind to both the binding epitopes of major histocompatibility complex (MHC)-I and MHC-II. Through the C3 receptor complex route, P. intermedia InpA promotes an immunological subunit. Utilizing InpA-C3 and vaccination epitopes as the receptor and ligand, the molecular docking and dynamics were performed using the ClusPro 2.0 server. Conclusion: The developed vaccine had shown good antigenicity, solubility, and stability. Molecular docking indicated the vaccine's 3D structure interacts strongly with the complement C3. The current study describes the design for vaccine, and steady interaction with the C3 immunological receptor to induce a good memory and an adaptive immune response against Interpain A of P. intermedia.
Collapse
|
|
12
|
Identification of B-Cell Epitopes on Capsid Protein Reveals Two Potential Neutralization Mechanisms in Red-Spotted Grouper Nervous Necrosis Virus. J Virol 2023; 97:e0174822. [PMID: 36633407 PMCID: PMC9888288 DOI: 10.1128/jvi.01748-22] [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: 01/13/2023] Open
Abstract
Nervous necrosis virus (NNV), a formidable pathogen in marine and freshwater fish, has inflicted enormous financial tolls on the aquaculture industry worldwide. Although capsid protein (CP) is the sole structural protein with pathogenicity and antigenicity, public information on immunodominant regions remains extremely scarce. Here, we employed neutralizing monoclonal antibodies (MAbs) specific for red-spotted grouper NNV (RGNNV) CNPgg2018 in combination with partially overlapping truncated proteins and peptides to identify two minimal B-cell epitope clusters on CP, 122GYVAGFL128 and 227SLYNDSL233. Site-directed mutational analysis confirmed residues Y123, G126, and L128 and residues L228, Y229, N230, D231, and L233 as the critical residues responsible for the direct interaction with ligand, respectively. According to homologous modeling and bioinformatic evaluation, 122GYVAGFL128 is harbored at the groove of the CP junction with strict conservation among all NNV isolates, while 227SLYNDSL233 is localized in proximity to the tip of a viral protrusion having relatively high evolutionary dynamics in different genotypes. Additionally, 227SLYNDSL233 was shown to be a receptor-binding site, since the corresponding polypeptide could moderately suppress RGNNV multiplication by impeding virion entry. In contrast, 122GYVAGFL128 seemed dedicated only to stabilizing viral native conformation and not to assisting initial virus attachment. Altogether, these findings contribute to a novel understanding of the antigenic distribution pattern of NNV and the molecular basis for neutralization, thus advancing the development of biomedical products, especially epitope-based vaccines, against NNV. IMPORTANCE NNV is a common etiological agent associated with neurological virosis in multiple aquatic organisms, causing significant hazards to the host. However, licensed drugs or vaccines to combat NNV infection are very limited to date. Toward the advancement of broad-spectrum prophylaxis and therapeutics against NNV, elucidating the diversity of immunodominant regions within it is undoubtedly essential. Here, we identified two independent B-cell epitopes on NNV CP, followed by the confirmation of critical amino acid residues participating in direct interaction. These two sites were distributed on the shell and protrusion domains of the virion, respectively, and mediated the neutralization exerted by MAbs via drastically distinct mechanisms. Our work promotes new insights into NNV antigenicity as well as neutralization and, more importantly, offers promising targets for the development of antiviral countermeasures.
Collapse
|
|
13
|
Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines (Basel) 2022; 10:vaccines10101729. [PMID: 36298594 PMCID: PMC9611379 DOI: 10.3390/vaccines10101729] [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: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies.
Collapse
|
|
14
|
Hammed-Akanmu M, Mim M, Osman AY, Sheikh AM, Behmard E, Rabaan AA, Suppain R, Hajissa K. Designing a Multi-Epitope Vaccine against Toxoplasma gondii: An Immunoinformatics Approach. Vaccines (Basel) 2022; 10:vaccines10091389. [PMID: 36146470 PMCID: PMC9505382 DOI: 10.3390/vaccines10091389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 08/16/2022] [Indexed: 12/25/2022] Open
Abstract
Infection with the intracellular apicomplexan parasite Toxoplasma gondii causes serious clinical outcomes in both human and veterinary settings worldwide. Although approximately one-third of the world’s population is infected with T. gondii, an effective human vaccine for this disease remains unavailable. We aimed to design a potential T. gondii vaccine candidate that consisted of the B- and T-lymphocyte epitopes of three parasite immunogenic antigens. Firstly, the immunodominant epitopes expressed within the ROP2, MIC3, and GRA7 proteins of T. gondii were identified. Subsequently, six B-cell epitopes, five CTL epitopes, and five HTL epitopes were combined to generate a multi-epitope vaccine, and the 50S ribosomal protein L7/L12 was added as an adjuvant to boost the vaccine’s immunogenicity. All these epitopes were found to be antigenic, nonallergenic, nontoxic, and nonhuman homologs. The designed vaccine construct has a molecular weight of 51 kDa, an antigenicity score of 0.6182, and a solubility of 0.903461. Likewise, the candidate vaccine was immunogenic, nonallergenic, and stable. Molecular docking analysis revealed stable interactions between the vaccine construct and the TLR-4 immune receptor. Meanwhile, the stability of the developed vaccine was validated using molecular dynamics simulation. In silico, the vaccine construct was able to trigger primary immune responses. However, further laboratory-based assessments are needed to confirm its efficacy and safety.
Collapse
Affiliation(s)
- Mutiat Hammed-Akanmu
- Department of Biomedicine, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Maria Mim
- Department of Biomedicine, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Abdinasir Yusuf Osman
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
| | - Abdulrahman M. Sheikh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - 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
| | - Rapeah Suppain
- Department of Biomedicine, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: (R.S.); (K.H.)
| | - Khalid Hajissa
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
- Department of Zoology, Faculty of Science and Technology, Omdurman Islamic University, Omdurman P.O. Box 382, Sudan
- Correspondence: (R.S.); (K.H.)
| |
Collapse
|
|
15
|
Naveed M, Jabeen K, Naz R, Mughal MS, Rabaan AA, Bakhrebah MA, Alhoshani FM, Aljeldah M, Shammari BRA, Alissa M, Sabour AA, Alaeq RA, Alshiekheid MA, Garout M, Almogbel MS, Halwani MA, Turkistani SA, Ahmed N. Regulation of Host Immune Response against Enterobacter cloacae Proteins via Computational mRNA Vaccine Design through Transcriptional Modification. Microorganisms 2022; 10:1621. [PMID: 36014038 PMCID: PMC9415879 DOI: 10.3390/microorganisms10081621] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 12/13/2022] Open
Abstract
Enterobacter cloacae is mainly responsible for sepsis, urethritis, and respiratory tract infections. These bacteria may affect the transcription of the host and particularly their immune system by producing changes in their epigenetics. In the present study, four proteins of Enterobacter cloacae were used to predict the epitopes for the construction of an mRNA vaccine against Enterobacter cloacae infections. In order to generate cellular and humoral responses, various immunoinformatic-based approaches were used for developing the vaccine. The molecular docking analysis was performed for predicting the interaction among the chosen epitopes and corresponding MHC alleles. The vaccine was developed by combining epitopes (thirty-three total), which include the adjuvant Toll-like receptor-4 (TLR4). The constructed vaccine was analyzed and predicted to cover 99.2% of the global population. Additionally, in silico immunological modeling of the vaccination was also carried out. When it enters the cytoplasm of the human (host), the codon is optimized to generate the translated mRNA efficiently. Moreover, the peptide structures were analyzed and docked with TLR-3 and TLR-4. A dynamic simulation predicted the stability of the binding complex. The assumed construct was considered to be a potential candidate for a vaccine against Enterobacter cloacae infections. Hence, the proposed construct is suitable for in vitro analyses to validate its effectiveness.
Collapse
Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Sciences and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Sciences and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Rubina Naz
- Corona Intensive Care Units, District Headquarter Teaching Hospital, Dera Ghazi Khan 33000, Punjab, Pakistan
| | - Muhammad Saad Mughal
- Department of Biotechnology, Faculty of Sciences and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - 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
| | - Muhammed A. Bakhrebah
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Fahad M. Alhoshani
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Amal A. Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rana A. Alaeq
- Department of Medical Laboratories Technology, Faculty of Applied Medical Science, Taibah University, Al Madinah Al Munawarh 344, Saudi Arabia
| | - Maha A. Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammed S. Almogbel
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 4030, Saudi Arabia
| | - Muhammad A. Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha 4781, Saudi Arabia
| | - Safaa A. Turkistani
- Department of Medical Laboratory, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Naveed Ahmed
- Department of Biotechnology, Faculty of Sciences and Technology, University of Central Punjab, Lahore 54590, Pakistan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| |
Collapse
|