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Ahmadi K, Zahedifard F, Mafakher L, Einakian MA, Ghaedi T, Kavousipour S, Faezi S, Karmostaji A, Sharifi-Sarasiabi K, Gouklani H, Hassaniazad M. Active site-based analysis of structural proteins for drug targets in different human Coronaviruses. Chem Biol Drug Des 2021; 99:585-602. [PMID: 34914204 DOI: 10.1111/cbdd.14004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Seven types of Coronaviruses (CoVs) have been identified that can cause infection in humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, HCoV-MERS, and SARS-CoV-2. In this study, we investigated the genetic structure, the homology of the structural protein sequences, as well as the investigation of the active site of structural proteins. The active site of structural proteins was determined based on the previous studies, and the homology of their amino acid sequences and structure was compared. Multiple sequence alignment of Spike protein of HCoVs showed that the receptor-binding domain of SARS-CoV-2, SARS-CoV, and MERS-CoV was located at a similar site to the S1 subunit. The binding motif of PDZ (postsynaptic density- 95/discs large/zona occludens-1) of the envelope protein, was conserved in SARS-CoV and SARS-CoV-2 according to multiple sequence alignment but showed different changes in the other HCoVs. Overall, Spike protein showed the most variation in its active sites, but the other structural proteins were highly conserved. In this study, for the first time, the active site of all structural proteins of HCoVs as a drug target was investigated. The binding site of these proteins can be suitable targets for drugs or vaccines among HCoVs.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farnaz Zahedifard
- Drug discovery and Evaluation unit, Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tayebeh Ghaedi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khojasteh Sharifi-Sarasiabi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Ghaedi T, Davoodian P, Hassaniazad M, Eftekhar E, Faezi S, Abparvar AA, Einakian MA, Ahmadi K. Protective efficacy of Hla-MntC-SACOL0723 fusion protein adjuvanted in alum and MPL against Staphylococcus aureus sepsis infection in mice. J Immunol Methods 2021; 494:113055. [PMID: 33857474 DOI: 10.1016/j.jim.2021.113055] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
To develop a suitable and effective vaccine against Staphylococcus aureus (S. aureus), we selected the Hla-MntC-SACOL0723 (HMS) recombinant protein with two different formulations of alum and Monophosphoryl lipid A (MPL) adjuvants. In this study, we aimed to evaluate the potentials of alum and MPL adjuvants in stimulating the immune response of HMS vaccine candidate against S. aureus. To evaluate the type of induced immune response, anti-HMS total IgG, IgG1, IgG2a, and IFN-γ, IL-2, IL-4, and IL-17 cytokines were determined after vaccination of mice with HMS-alum, HMS-MPL candidates. Mice were challenged with Methicillin-resistant Staphylococcus aureus (MRSA) was isolated from pressure sores and evaluated for bacterial load in the kidney homogenates and survival rate. It was observed that total IgG and isotypes (IgG1 and IgG2a), IL-4, and IL-17 were significantly increased in the group that received HMS-alum vaccine compared with the group that received HMS-MPL formulation. On the other hand, the levels of IFN-γ and IL-2 cytokines in the group that received HMS-MPL were higher than the group that received HMS-alum formulation. Bacterial load in the mice who received HMS protein formulated with alum adjuvant was reduced more than the mice who received HMS protein formulated with MPL adjuvant. Histopathological analysis showed more pathological changes in kidney tissues of the group received of HMS-MPL compared with the HMS-alum formulation. The survival rate was equal in both groups of immunized with HMS-alum and HMS-MPL formulations. Finally, it could be concluded that both adjuvants of alum and MPL are suitable immune response enhancers to HMS vaccine candidate.
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Affiliation(s)
- Tayebeh Ghaedi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Parivash Davoodian
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ali Atash Abparvar
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Enayatkhani M, Hasaniazad M, Faezi S, Gouklani H, Davoodian P, Ahmadi N, Einakian MA, Karmostaji A, Ahmadi K. Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study. J Biomol Struct Dyn 2020; 39:2857-2872. [PMID: 32295479 PMCID: PMC7196925 DOI: 10.1080/07391102.2020.1756411] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [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] [Indexed: 01/22/2023]
Abstract
At present, novel Coronavirus (2019-nCoV, the causative agent of COVID-19) has caused worldwide social and economic disruption. The disturbing statistics of this infection promoted us to develop an effective vaccine candidate against the COVID-19. In this study, bioinformatics approaches were employed to design and introduce a novel multi-epitope vaccine against 2019-nCoV that can potentially trigger both CD4+ and CD8+ T-cell immune responses and investigated its biological activities by computational tools. Three known antigenic proteins (Nucleocapsid, ORF3a, and Membrane protein, hereafter called NOM) from the virus were selected and analyzed for prediction of the potential immunogenic B and T-cell epitopes and then validated using bioinformatics tools. Based on in silico analysis, we have constructed a multi-epitope vaccine candidate (NOM) with five rich-epitopes domain including highly scored T and B-cell epitopes. After predicting and evaluating of the third structure of the protein candidate, the best 3 D predicted model was applied for docking studies with Toll-like receptor 4 (TLR4) and HLA-A*11:01. In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of the designed fusion protein with TLR4 and HLA-A*11:01 receptors. MD studies demonstrated that the NOM-TLR4 and NOM-HLA-A*11:01 docked models were stable during simulation time. In silico evaluation showed that the designed chimeric protein could simultaneously elicit humoral and cell-mediated immune responses. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maryam Enayatkhani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hasaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Parivash Davoodian
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Nahid Ahmadi
- Department of pharmaceutical chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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