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  1. Article ; Online: Repurposing antiviral drugs against HTLV-1 protease by molecular docking and molecular dynamics simulation.

    Jahantigh, Hamidreza / Ahmadi, Nahid / Lovreglio, Piero / Stufano, Angela / Enayatkhani, Maryam / Shahbazi, Behzad / Ahmadi, Khadijeh

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 11, Page(s) 5057–5066

    Abstract: Human T-cell leukemia virus type I (HTLV-1) belongs to the delta retrovirus family and the etiological agent of adult T-cell leukemia (ATL(. While the current HTLV-1 therapy, relies on using Zidovudine plus IFN-γ, there is no FDA approved drugs against ... ...

    Abstract Human T-cell leukemia virus type I (HTLV-1) belongs to the delta retrovirus family and the etiological agent of adult T-cell leukemia (ATL(. While the current HTLV-1 therapy, relies on using Zidovudine plus IFN-γ, there is no FDA approved drugs against it.
    MeSH term(s) Humans ; Antiviral Agents/chemistry ; Molecular Docking Simulation ; Simeprevir ; Molecular Dynamics Simulation ; Saquinavir ; Atazanavir Sulfate ; Drug Repositioning ; Aspartic Acid Endopeptidases/chemistry ; Protease Inhibitors/chemistry
    Chemical Substances Antiviral Agents ; HTLV-1 protease (EC 3.4.23.-) ; Simeprevir (9WS5RD66HZ) ; Saquinavir (L3JE09KZ2F) ; Atazanavir Sulfate (4MT4VIE29P) ; Aspartic Acid Endopeptidases (EC 3.4.23.-) ; Protease Inhibitors
    Language English
    Publishing date 2022-05-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2022.2078411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  2. Article ; Online: In-silico identification of new inhibitors for Low-density lipoprotein receptor-related protein6 (LRP6).

    Enayatkhani, Maryam / Salimi, Mona / Azadmanesh, Kayhan / Teimoori-Toolabi, Ladan

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 10, Page(s) 4440–4450

    Abstract: Low-density lipoprotein receptor-related protein 6 (LRP6) is an important therapeutic target for diseases such as osteoporosis, Alzheimer, cancer, and neurodegenerative disease. Computational methods such as ligand-based and structure-based virtual ... ...

    Abstract Low-density lipoprotein receptor-related protein 6 (LRP6) is an important therapeutic target for diseases such as osteoporosis, Alzheimer, cancer, and neurodegenerative disease. Computational methods such as ligand-based and structure-based virtual screening have been introduced as an extremely efficient and accurate tool for finding new drug targets and candidates. In this study, we aimed to screen the National Cancer Institute (NCI) Diversity Set II and parts of the ZINC database by virtual screening to identify potential and safe compounds that can inhibit the LRP6 protein. By utilizing various screening methods such as rigid and flexible molecular docking and Lipinski's rule of five, we identified 10 potential compounds. Then, their validity was further tested by molecular dynamics simulation and MMPBSA binding free energy calculations. Eventually, it was concluded that ZINC03954520, ZINC01729523, ZINC03898665, ZINC13152226, ZINC26730911 and ZINC01069082 compounds can be potential drug compounds for inhibiting LRP6 protein. These compounds in complex with β-propeller domains of LRP6 showed that they are capable of altering the backbone of these domains and interfere with their structural dynamics which may lead to the inhibition of the signal transmission. Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Humans ; Lipoproteins, LDL ; Low Density Lipoprotein Receptor-Related Protein-6 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neurodegenerative Diseases ; Protein Binding
    Chemical Substances LRP6 protein, human ; Lipoproteins, LDL ; Low Density Lipoprotein Receptor-Related Protein-6
    Language English
    Publishing date 2020-12-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1857843
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Computational design of antagonist peptides based on the structure of secreted frizzled-related protein-1 (SFRP1) aiming to inhibit Wnt signaling pathway.

    Mafakher, Ladan / Rismani, Elham / Rahimi, Hamzeh / Enayatkhani, Maryam / Azadmanesh, Kayhan / Teimoori-Toolabi, Ladan

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 5, Page(s) 2169–2188

    Abstract: Aberrant activation of Wnt/β-catenin signaling pathway, due to the genetic or epigenetic changes, is responsible for tumorigenesis in epithelial cells of different types of cancer such as colorectal cancer. Secreted Frizzled-Related Protein-1 (SFRP1), as ...

    Abstract Aberrant activation of Wnt/β-catenin signaling pathway, due to the genetic or epigenetic changes, is responsible for tumorigenesis in epithelial cells of different types of cancer such as colorectal cancer. Secreted Frizzled-Related Protein-1 (SFRP1), as one of the antagonist proteins of this pathway, is hyper-methylated in colorectal cancer leading to the formation of Wnt-Fz-LRP and activation of Wnt/β-catenin signaling pathway. We aimed to design antagonist peptides based on SFRP1 structure against wingless-type 2 (Wnt2), a highly expressed ligand in different cancers like colorectal cancer, to inhibit the formation of the initial triple complex of Wnt-Fz-LRP. After homology modeling of SFRP1, molecular docking showed that Wnt2 and SFRP1 interact in the same mode of xWnt8-mFz8 and hWnt3-mFz8 through the thumb and finger binding sites. These binding sites were selected for designing peptides using either substitution or deep learning-based approaches. The efficiency of each designed peptide in interacting with Wnt2 was evaluated by molecular docking. Stability assessment of Wnt2-peptide complexes via molecular dynamic (MD) revealed that the designed peptides could effectively interact with Wnt2 binding sites during the simulation. However, the designed peptides against the thumb site had higher binding affinity and hydrogen bonds compared to the initial sequence. The secondary structure of the designed peptides indicated an alpha-helix structure which is a favorable structure for peptide drugs. Computing the physicochemical properties of peptides predicted a fairly acceptable structure which made them promising candidates in the treatment of cancers like CRC.
    MeSH term(s) Intracellular Signaling Peptides and Proteins/metabolism ; Molecular Docking Simulation ; Wnt Signaling Pathway ; beta Catenin/metabolism
    Chemical Substances Intracellular Signaling Peptides and Proteins ; WD repeat containing planar cell polarity effector ; beta Catenin
    Language English
    Publishing date 2020-11-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1835718
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an

    Enayatkhani, Maryam / Hasaniazad, Mehdi / Faezi, Sobhan / Gouklani, Hamed / Davoodian, Parivash / Ahmadi, Nahid / Einakian, Mohammad Ali / Karmostaji, Afsaneh / Ahmadi, Khadijeh

    Journal of biomolecular structure & dynamics

    2020  Volume 39, Issue 8, Page(s) 2857–2872

    Abstract: At present, ... ...

    Abstract At present, novel
    MeSH term(s) COVID-19 ; Computational Biology ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte/genetics ; Humans ; Molecular Docking Simulation ; SARS-CoV-2 ; Vaccines, Subunit ; Vaccinology
    Chemical Substances Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Vaccines, Subunit
    Keywords covid19
    Language English
    Publishing date 2020-05-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1756411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2093: Show issues Location:
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  5. Article ; Online: Comparative study of the immune responses to the HMS-based fusion protein and capsule-based conjugated molecules as vaccine candidates in a mouse model of Staphylococcus aureus systemic infection.

    Ahmadi, Khadijeh / Hasaniazad, Mehdi / Kalani, Mehdi / Faezi, Sobhan / Ahmadi, Nahid / Enayatkhani, Maryam / Mahdavi, Mehdi / Pouladfar, Gholamreza

    Microbial pathogenesis

    2020  Volume 150, Page(s) 104656

    Abstract: Staphylococcus aureus is a powerful pathogen that causes a wide range of infectious diseases and results in a high mortality rate in humans. Treating S. aureus-related infections is extremely difficult because of its ability to resist many antibiotics; ... ...

    Abstract Staphylococcus aureus is a powerful pathogen that causes a wide range of infectious diseases and results in a high mortality rate in humans. Treating S. aureus-related infections is extremely difficult because of its ability to resist many antibiotics; therefore, developing an effective vaccine against this infection can be an alternative and promising approach. In this study, we evaluated the protective effects of a Hla-MntC-SACOL0723 multi-epitope protein (HMS) compared with HMS conjugated to polysaccharides 5 and 8 (CP5 and CP8) of S. aureus and CP5 and CP8 in a mouse sepsis model. To evaluate the type of induced immune response, specific IgG, and antibody isotypes (IgG1 and IgG2a) were determined using the ELISA method. The functional activity of these vaccine candidates was assessed by opsonophagocytosis. Mice were infected with S. aureus COL strain and evaluated for bacterial load in the kidney and spleen homogenates. Th1, Th2, and Th17-related cytokines in the spleen cell supernatants were assessed by flow cytometry. The therapeutic effect of specific anti-HMS protein IgG antibodies against S. aureus COL strain infection was evaluated by passive immunization. HMS recombinant protein induced a higher level of Th1, Th2, and Th17-related cytokines compared with conjugated molecules. Also, mice immunized with the HMS protein reduced the bacterial load in the kidney and spleen more than the one that received the conjugated molecules. Our study suggests that the HMS fusion protein and conjugate molecule vaccine candidates could be suitable candidates for the removal of S. aureus in the mouse sepsis model but HMS protein can be a more effective candidate.
    MeSH term(s) Animals ; Antibodies, Bacterial ; Immunity ; Mice ; Mice, Inbred BALB C ; Recombinant Proteins ; Staphylococcal Infections/prevention & control ; Staphylococcus aureus ; Vaccines, Conjugate
    Chemical Substances Antibodies, Bacterial ; Recombinant Proteins ; Vaccines, Conjugate
    Language English
    Publishing date 2020-11-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 632772-2
    ISSN 1096-1208 ; 0882-4010
    ISSN (online) 1096-1208
    ISSN 0882-4010
    DOI 10.1016/j.micpath.2020.104656
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2136: Show issues Location:
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  6. Article ; Online: Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19

    Enayatkhani, Maryam / Hasaniazad, Mehdi / Faezi, Sobhan / Gouklani, Hamed / Davoodian, Parivash / Ahmadi, Nahid / Einakian, Mohammad Ali / Karmostaji, Afsaneh / Ahmadi, Khadijeh

    Journal of Biomolecular Structure and Dynamics

    an in silico study

    2020  , Page(s) 1–16

    Keywords Molecular Biology ; Structural Biology ; General Medicine ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1756411
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Zs.A 2093: Show issues Location:
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  7. Article: Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study

    Enayatkhani, Maryam / Hasaniazad, Mehdi / Faezi, Sobhan / Guklani, Hamed / Davoodian, Parivash / Ahmadi, Nahid / Einakian, Mohammad Ali / Karmostaji, Afsaneh / Ahmadi, Khadijeh

    J Biomol Struct Dyn

    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 ... ...

    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.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #66327
    Database COVID19

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