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Article ; Online: Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity - an integrated experimental and bioinformatic approach.

Sam, Sohrab / Ofoghi, Hamideh / Farahmand, Behrokh

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–16

Abstract: In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an ...

Abstract	In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2302941
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Article: Fusion Protein Consisting of Hemagglutinin Small Subunit and Truncated Nucleoprotein as a Universal Influenza Vaccine Candidate: Starting In-Silico Evaluation Toward

Morshedi, Fatemeh / Nazeri, Elaheh / Saleh, Maryam / Farahmand, Behrokh

Journal of pharmacy & bioallied sciences

2023 Volume 15, Issue 1, Page(s) 57–62

Abstract: Background: Influenza virus is a respiratory pathogen, which causes high degree of mortality and morbidity during seasonal epidemics and sporadic pandemics. By selecting conserved antigenic proteins, for example, hemagglutinin small subunit (HA2) and ... ...

Abstract	Background: Influenza virus is a respiratory pathogen, which causes high degree of mortality and morbidity during seasonal epidemics and sporadic pandemics. By selecting conserved antigenic proteins, for example, hemagglutinin small subunit (HA2) and nucleoprotein (NP), we aimed to develop a vaccine based on a fusion protein leading to both cellular and humoral responses that are the most challenging aspects in designing a universal vaccine. Materials and methods: The bioinformatics analysis was performed for HA2-NP structure and function prediction. Primers for the antigenic part of NP were designed using bioinformatics tools. The desired product was amplified via polymerase chain reaction using the designed primers, which was then penetrated into T vector, followed by insertion into pET28a vector in order to construct pET28a/NP. The pET28a/HA2, previously generated in our lab, was digested with the same restriction enzymes as pET28a/NP (HindIII/Xhol). Then, NP was inserted to the downstream region of HA2 to construct pET28a/HA2. Results: The generated pET28a/HA2-NP was transformed into Conclusion: As currently available vaccines can cause some allergic reactions, using a chimer protein based on the bioinformatics analysis is continual, safe, and affordable, thus stimulating both cellular and humoral immunity systems. Our construct could potentially provide a basis for a universal vaccine candidate.
Language	English
Publishing date	2023-04-14
Publishing country	India
Document type	Journal Article
ZDB-ID	2573569-X
ISSN	0975-7406 ; 0976-4879
ISSN (online)	0975-7406
ISSN	0976-4879
DOI	10.4103/jpbs.JPBS_114_18
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Article ; Online: Phylogenetic analysis and docking study of neuraminidase gene of influenza A/H1N1 viruses circulating in Iran from 2010 to 2019.

Moeini, Sina / Mohebbi, Atefeh / Farahmand, Behrokh / Mehrbod, Parvaneh / Fotouhi, Fatemeh

Virus research

2023 Volume 334, Page(s) 199182

Abstract: Influenza A viruses (H1N1) have been consistently one of the most evolving viruses that escape from vaccine-induced immunity. Although there has been a rapid rise in human influenza virus knowledge since the 2009 pandemic, the molecular information about ...

Abstract	Influenza A viruses (H1N1) have been consistently one of the most evolving viruses that escape from vaccine-induced immunity. Although there has been a rapid rise in human influenza virus knowledge since the 2009 pandemic, the molecular information about Iranian strains is still inadequate. The aim of this study was to analyze the neuraminidase (NA) segment of the Iranian isolates in terms of phylogenetic, antiviral resistance, and vaccine efficiency. Ninety-three NA sequences collected among 1758 nasopharyngeal swab samples during the 2015-2016 influenza season were sequenced and submitted to NCBI. Moreover, all the submitted Iranian influenza H1N1 NA sequences since 2010 till 2019 were included in the study. Software including MEGA-X, MODELLER, UCSF ChimeraX, Auto-Dock 4.2, and other online tools were used to analyze the phylogenetic relationship, vaccine efficiency, and binding affinity to sialic acid of the selected NA proteins. Moreover, the information about antiviral drug resistance mutations of NA were gathered and compared to the Iranian NA segments to check the presence of antiviral drug-resistant strains. The phylogenetic study showed that most Iranian NA sequences (between 2015 and 2016) were located in a single clade and following years were located in its subclade by 3 major mutations (G77R/K, V81A, and J188T). Resistant mutations in drug targets of NA including I117M, D151E, I223V, and S247N were ascertained in 10 isolates during the 2015-2016 flu seasons. Investigation of vaccination effect revealed that Iranian isolates in 2017 and 2018 were best matched to A/Brisbane/02/2018 (H1N1), and in 2019 to A/Guangdong-Maonan/SWL1536/2019 (H1N1). Furthermore, we performed an in-silico analysis of NA enzymatic activity of all Iranian sequences by assessment of enzyme stability, ligand affinity, and active site availability. Overall, the enzyme activity of four Iranian strains (AUG84119, AUG84157, AUG84095, and AUG84100) was assumed as the maximum enzyme activity. This study highlighted the evolutionary trend of influenza A virus/H1N1 circulating in Iran, which provides a preliminary viewpoint for a better comprehension of new emerging strains' virulence and thus, more appropriate monitoring of influenza virus A/H1N1 during each outbreak season.
MeSH term(s)	Humans ; Antiviral Agents/pharmacology ; Drug Resistance, Viral/genetics ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Influenza A Virus, H1N1 Subtype ; Influenza, Human/epidemiology ; Iran/epidemiology ; Neuraminidase/genetics ; Phylogeny
Chemical Substances	Antiviral Agents ; Hemagglutinin Glycoproteins, Influenza Virus ; Neuraminidase (EC 3.2.1.18)
Language	English
Publishing date	2023-07-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2023.199182
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Article ; Online: In silico

Jalalvand, Alireza / Fotouhi, Fatemeh / Bahramali, Golnaz / Bambai, Bijan / Farahmand, Behrokh

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–17

Abstract: Hemagglutinin (HA), a variable viral surface protein, is essential for influenza vaccine development. Annually, traditional trivalent vaccines containing influenza A/H1N1, A/H3N2 and B viruses are administered globally, which are not very effective for ... ...

Abstract	Hemagglutinin (HA), a variable viral surface protein, is essential for influenza vaccine development. Annually, traditional trivalent vaccines containing influenza A/H1N1, A/H3N2 and B viruses are administered globally, which are not very effective for the mutations in HA protein. The aim of this study was to design a multi-epitope vaccine containing epitopes of the HA protein of H1N1, H3N2 and B viruses using immunoinformatics methods. The HA protein epitope prediction was performed using Immune Epitope Database. Toxicity, antigenicity and conservancy of the epitopes were evaluated using ToxinPred, VaxiJen and Epitope Conservancy Analysis tools, respectively. Then, nontoxic, antigenic and high conserved epitopes with high prediction scores were selected. Their binding affinity was evaluated against human and mouse MHC class I and II molecules using the HPEPDOCK tool. Physicochemical properties and post-translational modifications were evaluated using ProtParam, SOLpro and MusiteDeep tools, respectively. Top selected epitopes were joined using linkers to produce the best effective recombinant trivalent vaccine candidate to elicit cellular and humoral immune responses in mouse and human host models. These sequences were modeled and verified. By evaluating the results of various analyses of all models and the most similarity to the native HA protein, model 5 was selected as the best model. Finally,
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2292293
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Article ; Online: An approach to the influenza chimeric subunit vaccine (3M2e-HA2-NP) provides efficient protection against lethal virus challenge.

Saleh, Maryam / Nowroozi, Jamileh / Farahmand, Behrokh / Fotouhi, Fatemeh

Biotechnology letters

2020 Volume 42, Issue 7, Page(s) 1147–1159

Abstract: Objectives: Vaccination is the most effective preventive strategy for influenza disease. As the virus undergoes high antigenic drift, it requires a constant reformulation to obtain high protection.: Results: Immunogenicity of a purified chimeric ... ...

Abstract	Objectives: Vaccination is the most effective preventive strategy for influenza disease. As the virus undergoes high antigenic drift, it requires a constant reformulation to obtain high protection. Results: Immunogenicity of a purified chimeric protein containing conserved regions of influenza A/H1N1 viruses including the Hemagglutinin stalk domain, Nucleoprotein, and Matrix protein produced in a prokaryotic system was assessed in vitro and in vivo, alone or in combination with adjuvants by evaluating antibody responses, cytokine production, lymphocyte proliferative assay, and mortality rate after challenge. The animals that received the chimeric protein had specific antibody responses, elicited memory CD4 cells, cytokines of Th1 and Th2 cells and showed 75% protection against influenza virus lethal challenge. The animals injected with the chimeric protein supplemented with Alum showed improved immune responses, but they had 67% protection. In other words, although Alum adjuvant enriched the chimera specific immune responses potently, it could not enhance its protectivity. Conclusion: Regarding the immunogenicity and protectivity of the chimeric protein construct against influenza, findings of the study suggested that the chimeric protein could be considered as a promising influenza vaccine candidate.
MeSH term(s)	Animals ; Disease Models, Animal ; Dogs ; Female ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Humans ; Influenza Vaccines/administration & dosage ; Influenza Vaccines/immunology ; Madin Darby Canine Kidney Cells ; Mice ; Mice, Inbred BALB C ; Nucleocapsid Proteins/genetics ; Orthomyxoviridae Infections/immunology ; Orthomyxoviridae Infections/prevention & control ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/immunology ; Vaccination ; Vaccines, Subunit/administration & dosage ; Vaccines, Subunit/immunology
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; Influenza Vaccines ; Nucleocapsid Proteins ; Recombinant Fusion Proteins ; Vaccines, Subunit
Language	English
Publishing date	2020-03-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	423853-9
ISSN	1573-6776 ; 0141-5492
ISSN (online)	1573-6776
ISSN	0141-5492
DOI	10.1007/s10529-020-02822-3
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Article: An approach to the influenza chimeric subunit vaccine (3M2e-HA2-NP) provides efficient protection against lethal virus challenge

Saleh, Maryam / Nowroozi, Jamileh / Farahmand, Behrokh / Fotouhi, Fatemeh

Biotechnology letters. 2020 July, v. 42, no. 7

2020

Abstract: OBJECTIVES: Vaccination is the most effective preventive strategy for influenza disease. As the virus undergoes high antigenic drift, it requires a constant reformulation to obtain high protection. RESULTS: Immunogenicity of a purified chimeric protein ... ...

Abstract	OBJECTIVES: Vaccination is the most effective preventive strategy for influenza disease. As the virus undergoes high antigenic drift, it requires a constant reformulation to obtain high protection. RESULTS: Immunogenicity of a purified chimeric protein containing conserved regions of influenza A/H1N1 viruses including the Hemagglutinin stalk domain, Nucleoprotein, and Matrix protein produced in a prokaryotic system was assessed in vitro and in vivo, alone or in combination with adjuvants by evaluating antibody responses, cytokine production, lymphocyte proliferative assay, and mortality rate after challenge. The animals that received the chimeric protein had specific antibody responses, elicited memory CD4 cells, cytokines of Th1 and Th2 cells and showed 75% protection against influenza virus lethal challenge. The animals injected with the chimeric protein supplemented with Alum showed improved immune responses, but they had 67% protection. In other words, although Alum adjuvant enriched the chimera specific immune responses potently, it could not enhance its protectivity. CONCLUSION: Regarding the immunogenicity and protectivity of the chimeric protein construct against influenza, findings of the study suggested that the chimeric protein could be considered as a promising influenza vaccine candidate.
Keywords	CD4-positive T-lymphocytes ; Orthomyxoviridae ; adjuvants ; alum ; antibodies ; antigenic variation ; biotechnology ; cytokines ; hemagglutinins ; immunogenicity ; influenza ; influenza vaccines ; mortality ; nucleoproteins ; recombinant fusion proteins ; subunit vaccines ; vaccination ; viruses
Language	English
Dates of publication	2020-07
Size	p. 1147-1159.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	423853-9
ISSN	1573-6776 ; 0141-5492
ISSN (online)	1573-6776
ISSN	0141-5492
DOI	10.1007/s10529-020-02822-3
Database	NAL-Catalogue (AGRICOLA)

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Article: Synthesis of Ni

Shariati, Alireza / Hosseinzadeh, Sara Ali / Barghi, Zahra / Mortazavi, Sogand Sadat / Atarod, Kosar / Shariati, Fatemeh Sadat / Farahmand, Behrokh

AMB Express

2023 Volume 13, Issue 1, Page(s) 112

Abstract: Facilitated purification of proteins, at a low cost and a short time, is one of the key steps in the industrial production of recombinant proteins. In the current study, polydopamine nanoparticles (PDA-NPs) are considered in the synthesis of magnetic ... ...

Abstract	Facilitated purification of proteins, at a low cost and a short time, is one of the key steps in the industrial production of recombinant proteins. In the current study, polydopamine nanoparticles (PDA-NPs) are considered in the synthesis of magnetic beads for purifying recombinant proteins due to advantages such as biocompatibility/ biodegradability, easy synthesis, as well as the ability to directly chelate metal ions. They were synthesized in Tris buffer (pH: 8:5), then chelated with Fe
Language	English
Publishing date	2023-10-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2621432-5
ISSN	2191-0855
ISSN	2191-0855
DOI	10.1186/s13568-023-01613-z
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Article ; Online: Induction of Homosubtypic and Heterosubtypic Immunity to Influenza Viruses Using a Conserved Internal and External Proteins.

Maleki, Mahnoosh / Hosseini, Seyed Masoud / Farahmand, Behrokh / Saleh, Maryam / Shokouhi, Hadiseh / Torabi, Ali / Fotouhi, Fatemeh

Current microbiology

2023 Volume 80, Issue 6, Page(s) 212

Abstract: The immunogenicity and protective properties of the designed recombinant fusion peptide of 3M2e and truncated nucleoprotein (trNP), originating from Influenza A virus, were investigated in the BALB/c mice model in comparison with the Mix protein (3M2e + ... ...

Abstract	The immunogenicity and protective properties of the designed recombinant fusion peptide of 3M2e and truncated nucleoprotein (trNP), originating from Influenza A virus, were investigated in the BALB/c mice model in comparison with the Mix protein (3M2e + trNP). The results were evaluated by antibody response, cytokine production, lymphocyte proliferation assay, and mortality rate after challenge with homologous (H1N1) and heterologous (H3N2) influenza viruses in BALB/c mice. The animals that received the chimer protein with or without adjuvant had more specific antibody responses and elicited memory CD4 T cells, and cytokines of Th1 and Th2 cells compared to the Mix protein. Moreover, the Mix protein, like the recombinant chimer protein, provided equal and effective protection against both homologous and heterologous challenges in mice. Nevertheless, the chimer protein demonstrated superior immune protection compared to the Mix protein. The percentage of survived animals in the adjuvanted protein group (78.4%) was less than the non-adjuvanted one (85.7%). However, the Mix protein plus Alum could induce protective immunity in only 57.1% and 42.8% of homologous and heterologous virus-challenged mice, respectively. Regarding the sufficient immunogenicity and protectivity of the chimer protein construct against influenza viruses, the findings of the study suggest that the chimer protein without a requirement of adjuvant can be used as an adequate vaccine formulation to protect against a broad spectrum of influenza viruses.
MeSH term(s)	Animals ; Mice ; Humans ; Influenza A Virus, H3N2 Subtype ; Influenza A Virus, H1N1 Subtype ; Antibodies, Viral ; Influenza, Human ; Influenza Vaccines ; Adjuvants, Immunologic/pharmacology ; Mice, Inbred BALB C
Chemical Substances	Antibodies, Viral ; Influenza Vaccines ; Adjuvants, Immunologic
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-023-03331-y
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Article ; Online: Computational peptide engineering approach for selection of the new C05 antibody-driven peptide with potency to blocking influenza a virus attachment; from

Gholami, Shima / Mafakher, Ladan / Fotouhi, Fatemeh / Bambai, Bijan / Cohan, Reza Ahangari / Mehrbod, Parvaneh / Shokouhi, Hadiseh / Farahmand, Behrokh

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–17

Abstract: Antiviral drugs are currently used to prevent or treat viral infections like influenza A Virus (IAV). Nonetheless, annual genetic mutations of influenza viruses make them resistant to efficient treatment by current medications. Antiviral peptides have ... ...

Abstract	Antiviral drugs are currently used to prevent or treat viral infections like influenza A Virus (IAV). Nonetheless, annual genetic mutations of influenza viruses make them resistant to efficient treatment by current medications. Antiviral peptides have recently attracted researchers' attention and can potentially supplant the current medications. This study aimed to design peptides against IAV propagation. For this purpose, P2 and P3 peptides were computationally designed based on the HCDR3 region of the C05 antibody (a monoclonal antibody that neutralizes influenza HA protein and inhibits the virus attachment). The synthesized peptides were tested against the influenza A virus (A/Puerto Rico/8/34 (H1N1))
Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2241554
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Article: Computational Design and Analysis of a Multi-epitope Against Influenza A virus.

Rostaminia, Samaneh / Aghaei, Seyed Soheil / Farahmand, Behrokh / Nazari, Raziye / Ghaemi, Amir

International journal of peptide research and therapeutics

2021 Volume 27, Issue 4, Page(s) 2625–2638

Abstract: Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. ...

Abstract	Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.
Language	English
Publishing date	2021-09-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2192632-3
ISSN	1573-3904 ; 1573-3149
ISSN (online)	1573-3904
ISSN	1573-3149
DOI	10.1007/s10989-021-10278-w
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