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  1. Article ; Online: In-silico design of a new multi-epitope vaccine candidate against SARS-CoV-2

    Abbas Alibakhshi / Armina Alagheband Bahrami / Elmira Mohammadi / Shahrzad Ahangarzadeh / Meysam Mobasheri

    Acta Virologica, Vol

    2024  Volume 67

    Abstract: Frequent, and sometimes more dangerous, mutations in SARS-CoV-2 indicate that a stronger strategy is needed to produce an effective vaccine—a vaccine that contains a wider range of virus factors and remains effective if one or more mutations have ... ...

    Abstract Frequent, and sometimes more dangerous, mutations in SARS-CoV-2 indicate that a stronger strategy is needed to produce an effective vaccine—a vaccine that contains a wider range of virus factors and remains effective if one or more mutations have occurred in a part of the genome. In this study, four important virus proteins were used to make a multi-epitope protein vaccine. For this purpose, antigenic determinant of 4 proteins were selected and a protein structure was designed using 4 domains containing epitopes. After examining its antigenic potential, its three-dimensional structure was designed and then docked with immune system receptors. Finally, using the dynamic molecular (MD) simulation, complexes and interactions were investigated and their interaction energies were measured. The results of the study showed that the designed structure has good relative stability and interacts well with its receptors and can be used as a vaccine candidate for further studies.
    Keywords SARS-CoV-2 ; COVID-19 ; multi-epitope ; vaccine ; dynamic molecular simulation ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
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  2. Article: Probiotic Potential, Antiproliferative, and Proapoptotic Activities of

    Shirvanian, Moein / Azimian Zavareh, Vajihe / Zamanzadeh, Zahra / Janghorban, Marjan / Mohammadi, Elmira / Ahangarzadeh, Shahrzad

    Advanced biomedical research

    2023  Volume 12, Page(s) 242

    Abstract: Background: Breast milk is always the best choice for infant's nutrition due to its useful compounds such as immune cells and molecules, oligosaccharides, as well as bacteria and their metabolites. We identified and characterized the isolated strain ... ...

    Abstract Background: Breast milk is always the best choice for infant's nutrition due to its useful compounds such as immune cells and molecules, oligosaccharides, as well as bacteria and their metabolites. We identified and characterized the isolated strain from human breast milk in this study.
    Materials and methods: A total of 20 lactating mothers aged 25 to 34 years were enrolled in our study. We collected the breast milk samples in sterile microtubes. 100 μl of each sample was spread on de Man-Rogosa-Sharpe (MRS) agar plates and incubated aerobically at 37°C for 48 hr. After identifying the isolated strain, initial tests (hemolysis inactivity and L-arginine hydrolysis, catalase), the acid tolerance, bile tolerance, and antibiotics susceptibility of the isolated strain were estimated. Furthermore, the antiproliferative and proapoptotic activities of heat-killed cells) HKC) and cell-free supernatant (CFS) of the strain on the HT-29 cell line were evaluated using MTT assay and flow cytometry analysis, respectively.
    Results: The isolated strain was Gram-positive, bacilli in shape, catalase-negative, non-hemolytic, and negative for L-arginine hydrolysis. By 16S rRNA gene sequencing, the isolated strain was
    Conclusion: Our findings suggest that this strain, despite the properties of probiotic bacteria, has potential antiproliferative and proapoptotic capabilities.
    Language English
    Publishing date 2023-10-28
    Publishing country India
    Document type Journal Article
    ZDB-ID 2672524-1
    ISSN 2277-9175
    ISSN 2277-9175
    DOI 10.4103/abr.abr_109_23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Molecular and Antigen Detection, Phylogenetics, and Immunoinformatics Study of the Zoonotic Coronavirus in Iranian Diarrheic Calves.

    Enayati, Soodeh / Ranjbar, Mohammad M / Hooshmandi, Soodeh / Ahangarzadeh, Shahrzad / Aboutalebian, Shima

    Advanced biomedical research

    2023  Volume 12, Page(s) 224

    Abstract: Background: Bovine coronaviruses (BCoVs) are zoonotic diseases that result in substantial economic losses due to mortality, impaired growth, and increased medication expenses in large animals. These viruses pose a risk to children who live beside ... ...

    Abstract Background: Bovine coronaviruses (BCoVs) are zoonotic diseases that result in substantial economic losses due to mortality, impaired growth, and increased medication expenses in large animals. These viruses pose a risk to children who live beside infected animal, as they can cause diarrhea. This study was dedicated to molecular and antigen detections and phylogenetic and immunoinformatics analysis of zoonotic coronavirus (CoV) in Iran.
    Materials and methods: A total of 77 diarrheic samples were collected from Holstein dairy herds in selected provinces of Iran. Samples were tested by capture antibody enzyme-linked immunosorbent assay (ELISA) to detect CoV and reverse transcriptase-polymerase chain reaction (RT-PCR) for verification of detection and also genotyping of spike glycoprotein in CoV-positive samples. After statistical analysis, nucleotide sequence alignment, and nucleotide and protein phylogenetic tree construction, the centralized sequence for vaccine strains was obtained using computationally optimized broadly reactive antigen (COBRA)'s center-of-the-tree (COT) method.
    Results: Twenty-two (28.5%) and eight (10.3%) of 77 samples were positive according to RT-PCR and ELISA, respectively. (Basic Local Alignment Search Tool) BLAST and phylogenetic analysis revealed that most similar sequences to the Iranian CoV sequence were for European countries. Furthermore, there were strong correlations to other CoVs in humans and wild and domesticated animals. As CoV has variable COT, the most recent strains and COBRA vaccine strains were obtained.
    Conclusion: Based on the high prevalence of this viral disease in calves and its economic impact on the breeding industry, as well as the potential transmission to humans and correlation with World Health Organization (WHO) One Health approach guidelines, the study emphasizes the importance of implementing preventive strategies such as animal vaccination.
    Language English
    Publishing date 2023-09-27
    Publishing country India
    Document type Journal Article
    ZDB-ID 2672524-1
    ISSN 2277-9175
    ISSN 2277-9175
    DOI 10.4103/abr.abr_422_22
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  4. Article: The effect of mutation on neurotoxicity reduction of new chimeric reteplase, a computational study.

    Pour, Pardis Mohammadi / Mahnam, Karim / Taherzadeh, Mahsa / Ahangarzadeh, Shahrzad / Alibakhshi, Abbas / Mohammadi, Elmira

    Research in pharmaceutical sciences

    2023  Volume 18, Issue 4, Page(s) 404–412

    Abstract: Background and purpose: Excitotoxicity in nerve cells is a type of neurotoxicity in which excessive stimulation of receptors (such as N-methyl-d-aspartate glutamate receptors (NMDAR)) leads to the influx of high-level calcium ions into cells and finally ...

    Abstract Background and purpose: Excitotoxicity in nerve cells is a type of neurotoxicity in which excessive stimulation of receptors (such as N-methyl-d-aspartate glutamate receptors (NMDAR)) leads to the influx of high-level calcium ions into cells and finally cell damage or death. This complication can occur after taking some of the plasminogen activators like tissue plasminogen activator and reteplase. The interaction of the kringle2 domain in such plasminogen activator with the amino-terminal domain (ATD) of the NR1 subunit of NMDAR finally leads to excitotoxicity. In this study, we assessed the interaction of two new chimeric reteplase, mutated in the kringle2 domain, with ATD and compared the interaction of wild-type reteplase with ATD, computationally.
    Experimental approach: Homology modeling, protein docking, molecular dynamic simulation, and molecular dynamics trajectory analysis were used for the assessment of this interaction.
    Findings/results: The results of the free energy analysis between reteplase and ATD (wild reteplase: -2127.516 ± 0.0, M1-chr: -1761.510 ± 0.0, M2-chr: -521.908 ± 0.0) showed lower interaction of this chimeric reteplase with ATD compared to the wild type.
    Conclusion and implications: The decreased interaction between two chimeric reteplase and ATD of NR1 subunit in NMDAR which leads to lower neurotoxicity related to these drugs, can be the start of a way to conduct more tests and if the results confirm this feature, they can be considered potential drugs in acute ischemic stroke treatment.
    Language English
    Publishing date 2023-06-01
    Publishing country Iran
    Document type Journal Article
    ZDB-ID 2400156-9
    ISSN 1735-9414 ; 1735-5362
    ISSN (online) 1735-9414
    ISSN 1735-5362
    DOI 10.4103/1735-5362.378087
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Acetate Kinase a Antisense Delivery by PAMAM Dendrimer for Decreasing Acetate Production and Increasing the Production of Recombinant Albumin in

    Ahangarzadeh, Shahrzad / Moghimi, Hamidreza / Bandehpour, Mojgan / Ranjbari, Javad

    Iranian journal of biotechnology

    2021  Volume 19, Issue 1, Page(s) e2617

    Abstract: Background: Acetate accumulation in the culture medium is known as an inhibitor in recombinant protein production in Escherichia coli. Various approaches have been proposed and evaluated to overcome this challenge and reduce the concentration of acetate. ...

    Abstract Background: Acetate accumulation in the culture medium is known as an inhibitor in recombinant protein production in Escherichia coli. Various approaches have been proposed and evaluated to overcome this challenge and reduce the concentration of acetate. In this study, we examined the effect of acetate kinase A antisense on acetate production rate in
    Objective: This study aimed to decrease acetate production as a by-product using an antisense-dendrimer complex to increase mass cell and subsequently recombinant Albumin production in
    Materials and methods: Here, to study the effect of this treatment on recombinant protein production, we used pET22b/HAS construct. The ackA gene expression was inhibited by designed antisense to reduce acetate concentration in culture medium. AckA antisense was transferred to
    Results: Our data showed, designed antisense lead to reduction of acetate kinase gene expression and subsequently acetate concentration in the culture medium. Finally, acetate concentration reduction and cell mass increase result in enhanced recombinant Alb production in the treated group (1.25 mg.mL
    Conclusions: Reduction of acetate in
    Language English
    Publishing date 2021-01-01
    Publishing country Iran
    Document type Journal Article
    ZDB-ID 2223669-7
    ISSN 2322-2921 ; 1728-3043
    ISSN (online) 2322-2921
    ISSN 1728-3043
    DOI 10.30498/IJB.2021.2617
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  6. Article: Comparative Analysis and Identification of Spike Mutations in Iranian COVID-19 Samples from the First Three Waves of Disease.

    Shoaei, Parisa / Ranjbar, Mohammad M / Tokhanbigli, Samaneh / Ataei, Behrouz / Alibakhshi, Abbas / Haghjooy Javanmard, Shaghayegh / Ahangarzadeh, Shahrzad

    Advanced biomedical research

    2023  Volume 12, Page(s) 153

    Abstract: Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the ... ...

    Abstract Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical target for vaccine and therapeutics development. In the current research, we analyzed the variability and mutations of the spike glycoprotein isolated from 72 COVID-19-positive patients from Iran's first three waves of disease.
    Materials and methods: The RNA was extracted from nasopharyngeal samples of confirmed COVID-19 cases and served as a template for cDNA synthesis and reverse transcriptase polymerase chain reaction. The reverse transcriptase polymerase chain reaction products of each sample were assembled and sequenced.
    Results: After analysis of 72 sequences, we obtained 46 single nucleotide polymorphisms, including 23 that produce amino acid changes. Our analysis showed that the most frequent mutation was the D614G (in the samples of the second and third waves).
    Conclusions: Our findings suggest that developing effective vaccines requires identifying the predominant variants of SARS-CoV-2 in each community.
    Language English
    Publishing date 2023-06-28
    Publishing country India
    Document type Journal Article
    ZDB-ID 2672524-1
    ISSN 2277-9175
    ISSN 2277-9175
    DOI 10.4103/abr.abr_171_22
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  7. Article: Evaluation of Specific IgG Antibody in Subjects Who Had Been Previously Infected with SARS-CoV-2.

    Rostami, Soodabeh / Ahangarzadeh, Shahrzad / Zamani Moghaddam, Ali / Nokhodian, Zary / Modaresifar, Hossein / Roustaei, Amirsaman / Shoaei, Parisa / Rowzati, Mohsen / Tahvilian, Zohreh / Nazari, Alireza / Kassaian, Nazila / Haghjooy Javanmard, Shaghayegh / Ataei, Behrooz

    Advanced biomedical research

    2023  Volume 12, Page(s) 171

    Language English
    Publishing date 2023-06-30
    Publishing country India
    Document type Journal Article
    ZDB-ID 2672524-1
    ISSN 2277-9175
    ISSN 2277-9175
    DOI 10.4103/abr.abr_195_22
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  8. Article ; Online: Comparative analysis and identification of spike mutations in Iranian COVID-19 samples from the first three waves of disease

    Parisa Shoaei / Mohammad M Ranjbar / Samaneh Tokhanbigli / Behrouz Ataei / Abbas Alibakhshi / Shaghayegh Haghjooy Javanmard / Shahrzad Ahangarzadeh

    Advanced Biomedical Research, Vol 12, Iss 1, Pp 153-

    2023  Volume 153

    Abstract: Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical ...

    Abstract Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical target for vaccine and therapeutics development. In the current research, we analyzed the variability and mutations of the spike glycoprotein isolated from 72 COVID-19–positive patients from Iran's first three waves of disease. Materials and Methods: The RNA was extracted from nasopharyngeal samples of confirmed COVID-19 cases and served as a template for cDNA synthesis and reverse transcriptase polymerase chain reaction. The reverse transcriptase polymerase chain reaction products of each sample were assembled and sequenced. Results: After analysis of 72 sequences, we obtained 46 single nucleotide polymorphisms, including 23 that produce amino acid changes. Our analysis showed that the most frequent mutation was the D614G (in the samples of the second and third waves). Conclusions: Our findings suggest that developing effective vaccines requires identifying the predominant variants of SARS-CoV-2 in each community.
    Keywords mutation ; sars-cov-2 ; spike glycoprotein ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Herbal Medicines as Potential Inhibitors of SARS-CoV-2 Infection.

    Rostami, Soodabeh / Gharibi, Shima / Yaghoobi, Hajar / Nokhodian, Zary / Shoaei, Parisa / Bahrami, Armina Alagheband / Ahangarzadeh, Shahrzad / Alibakhshi, Abbas

    Current pharmaceutical design

    2022  Volume 28, Issue 29, Page(s) 2375–2386

    Abstract: Coronavirus disease 2019 (COVID-19) is the result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding molecular pathogenesis is an essential factor for the allocation of effective preventive measures and the ... ...

    Abstract Coronavirus disease 2019 (COVID-19) is the result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding molecular pathogenesis is an essential factor for the allocation of effective preventive measures and the development of targeted therapeutics against COVID-19. The genome of SARS-CoV-2 encodes structural and nonstructural proteins, which can be targets for compounds with potential therapeutic ability. On the other hand, the virus life cycle has stages susceptible to targeting by drug compounds. Many natural antiviral compounds have been studied and evaluated at the cellular and molecular levels with antiviral potential. Meanwhile, many studies over the past few months have shown that plant polysaccharides have a good ability to target proteins and stages of the virus life cycle. In this regard, in this review study, the virus specifications and infectious process and structural and functional components of SARSCoV- 2 will be reviewed, and then the latest studies on the effect of plant compounds with more focus on polysaccharides on viral targets and their inhibitory potential on the infectious process of COVID-19 will be discussed.
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Humans ; Plants, Medicinal/metabolism ; SARS-CoV-2
    Chemical Substances Antiviral Agents
    Language English
    Publishing date 2022-08-04
    Publishing country United Arab Emirates
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1304236-1
    ISSN 1873-4286 ; 1381-6128
    ISSN (online) 1873-4286
    ISSN 1381-6128
    DOI 10.2174/1381612828666220802121014
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  10. Article ; Online: Evaluation of specific IgG antibody in subjects who had been previously infected with SARS-CoV-2

    Soodabeh Rostami / Shahrzad Ahangarzadeh / Ali Zamani Moghaddam / Zary Nokhodian / Hossein Modaresifar / Amirsaman Roustaei / Parisa Shoaei / Mohsen Rowzati / Zohreh Tahvilian / Alireza Nazari / Nazila Kassaian / Shaghayegh Haghjooy Javanmard / Behrooz Ataei

    Advanced Biomedical Research, Vol 12, Iss 1, Pp 171-

    2023  Volume 171

    Keywords Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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