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  1. Article ; Online: Peptide nanovaccine in melanoma immunotherapy.

    Dehghankhold, Mahvash / Sadat Abolmaali, Samira / Nezafat, Navid / Mohammad Tamaddon, Ali

    International immunopharmacology

    2024  Volume 129, Page(s) 111543

    Abstract: Melanoma is an especially fatal neoplasm resistant to traditional treatment. The advancement of novel therapeutical approaches has gained attention in recent years by shedding light on the molecular mechanisms of melanoma tumorigenesis and their powerful ...

    Abstract Melanoma is an especially fatal neoplasm resistant to traditional treatment. The advancement of novel therapeutical approaches has gained attention in recent years by shedding light on the molecular mechanisms of melanoma tumorigenesis and their powerful interplay with the immune system. The presence of many mutations in melanoma cells results in the production of a varied array of antigens. These antigens can be recognized by the immune system, thereby enabling it to distinguish between tumors and healthy cells. In the context of peptide cancer vaccines, generally, they are designed based on tumor antigens that stimulate immunity through antigen-presenting cells (APCs). As naked peptides often have low potential in eliciting a desirable immune reaction, immunization with such compounds usually necessitates adjuvants and nanocarriers. Actually, nanoparticles (NPs) can provide a robust immune response to peptide-based melanoma vaccines. They improve the directing of peptide vaccines to APCs and induce the secretion of cytokines to get maximum immune response. This review provides an overview of the current knowledge of the utilization of nanotechnology in peptide vaccines emphasizing melanoma, as well as highlights the significance of physicochemical properties in determining the fate of these nanovaccines in vivo, including their drainage to lymph nodes, cellular uptake, and influence on immune responses.
    MeSH term(s) Humans ; Melanoma ; Nanovaccines ; Peptides/therapeutic use ; Antigen-Presenting Cells ; Immunotherapy/methods
    Chemical Substances Nanovaccines ; Peptides
    Language English
    Publishing date 2024-01-31
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2043785-7
    ISSN 1878-1705 ; 1567-5769
    ISSN (online) 1878-1705
    ISSN 1567-5769
    DOI 10.1016/j.intimp.2024.111543
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  2. Article ; Online: Application of Cell Penetrating Peptides for Intracellular Delivery of Endostatin: A Computational Approach.

    Zamani, Mozhdeh / Nezafat, Navid / Mokarram, Pooneh / Kadkhodaei, Behnam

    Current computer-aided drug design

    2023  Volume 20, Issue 3, Page(s) 208–223

    Abstract: Background: Endostatin is an antiangiogenic compound with anticancer activity. The poor stability and low half-life of endostatin are the main barriers to the clinical use of this protein. Cell-penetrating peptides (CPPs) are extensively applied as ... ...

    Abstract Background: Endostatin is an antiangiogenic compound with anticancer activity. The poor stability and low half-life of endostatin are the main barriers to the clinical use of this protein. Cell-penetrating peptides (CPPs) are extensively applied as carrier in the delivery of drugs and different therapeutic agents. Therefore, they can be proper candidates to improve endostatin delivery to the target cells.
    Objective: In this study, we aim to computationally predict appropriate CPPs for the delivery of endostatin.
    Methods: Potential appropriate CPPs for protein delivery were selected based on the literature. The main parameters for detection of best CPP-endostatin fusions, including stability, hydrophobicity, antigenicity, and subcellular localization, were predicted using ProtParam, VaxiJen, and DeepLoc-1.0 servers, respectively. The 3D structures of the best CPP-Endostatin fusions were modeled by the I-TASSER server. The predicted models were validated using PROCHECK, ERRAT, Verify3D and ProSA-Web servers. The best models were visualized by the PyMol molecular graphics system.
    Results: Considering the principal parameters in the selection of best CPPs for endostatin delivery, endostatin fusions with four CPPs, including Cyt c-ss-MAP, TP-biot1, MPGα, and DPV1047, high stability and hydrophobicity, no antigenicity and extracellular localization were predicted as the best potential fusions for endostatin delivery. Four CPPs, including Cyt c-ss-MAP, TP-biot1, MPGα, and DPV1047, were predicted as the best potential candidates to improve endostatin delivery.
    Conclusion: Application of these CPPs may overcome the limitation of endostatin therapeutic applications, including poor stability and low half-life. Subsequent experimental studies will contribute to verifying these computational results.
    Language English
    Publishing date 2023-05-11
    Publishing country United Arab Emirates
    Document type Journal Article
    ISSN 1875-6697
    ISSN (online) 1875-6697
    DOI 10.2174/1573409919666230426093230
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  3. Article ; Online: Optimization of Spore Production in Bacillus coagulans Using Response Surface Methodology Approach.

    Mirmajidi, Seyedeh Habibeh / Irajie, Cambyz / Savardashtaki, Amir / Nezafat, Navid / Morowvat, Mohammad Hossein / Ghasemi, Younes

    Applied biochemistry and biotechnology

    2024  

    Abstract: Due to its spore-forming ability, Bacillus coagulans has advantages over the other non-spore-forming probiotics. Among them, survival and stability during food processing and storage, resistance to acid pH, and digestive enzymes are important. However, ... ...

    Abstract Due to its spore-forming ability, Bacillus coagulans has advantages over the other non-spore-forming probiotics. Among them, survival and stability during food processing and storage, resistance to acid pH, and digestive enzymes are important. However, there are few studies on the quality and amount of sporulation in B. coagulans. This study investigated the spore densities and formation efficiency of B. coagulans. The optimal medium formulation consisted of yeast extract (1.00 g L
    Language English
    Publishing date 2024-03-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392344-7
    ISSN 1559-0291 ; 0273-2289
    ISSN (online) 1559-0291
    ISSN 0273-2289
    DOI 10.1007/s12010-024-04934-2
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  4. Article: A structural vaccinology approach for in silico designing of a potential self-assembled nanovaccine against Leishmania infantum

    Vakili, Bahareh / Nezafat, Navid / Negahdaripour, Manica / Ghasemi, Younes

    Experimental parasitology. 2022 Aug., v. 239

    2022  

    Abstract: Visceral leishmaniasis (VL) remains a major public health problem across 98 countries. To date, VL has no effective drug. Vaccines, as the most successful breakthroughs in medicine, can promise an effective strategy to fight various diseases. More ... ...

    Abstract Visceral leishmaniasis (VL) remains a major public health problem across 98 countries. To date, VL has no effective drug. Vaccines, as the most successful breakthroughs in medicine, can promise an effective strategy to fight various diseases. More recently, self-assembled peptide nanoparticles (SAPNs) have attracted considerable attention in the field of vaccine design due to their multivalency. In this study, a SAPN nanovaccine was designed using various immunoinformatics methods. High-ranked epitopes were chosen from a number of antigens, including Leishmania-specific hypothetical protein (LiHy), Leishmania-specific antigenic protein (LSAP), histone H1, and sterol 24-c-methyltransferase (SMT). To facilitate the oligomerization process, pentameric and trimeric coiled-coil domains were employed. RpfE, a resuscitation-promoting factor of Mycobacterium tuberculosis, was added to induce strong immune responses. Pentameric and trimeric coiled-coil domains as well as eight immunodominant epitopes from antigenic proteins of Leishmania infantum, the causative agent of VL, were joined together using appropriate linkers. High-quality 3D structure of monomeric and oligomeric structures followed by refinement and validation processes demonstrated that the designed nanovaccine could be considered to be a promising medication against the parasite; however, experimental validation is essential to confirm the effectiveness of the nanovaccine.
    Keywords Leishmania infantum ; Mycobacterium tuberculosis ; computer simulation ; drug therapy ; etiological agents ; histones ; immunodominant epitopes ; immunoinformatics ; medicine ; oligomerization ; parasites ; parasitology ; peptides ; public health ; sterols ; vaccine development ; visceral leishmaniasis
    Language English
    Dates of publication 2022-08
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 391089-1
    ISSN 1090-2449 ; 0014-4894
    ISSN (online) 1090-2449
    ISSN 0014-4894
    DOI 10.1016/j.exppara.2022.108295
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  5. Article ; Online: Proteome Exploration of Human Coronaviruses for Identifying Novel Vaccine Candidate: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach.

    Dorosti, Hesam / Zarei, Mahboubeh / Nezafat, Navid

    Recent patents on biotechnology

    2022  Volume 17, Issue 2, Page(s) 163–175

    Abstract: Background: The SARS-CoV-2 has been responsible for infecting more than 613,615,658 people in 222 countries by September 11, 2022, of which 6,516,076 have died. COVID-19 was introduced by World Health Organization as a global concern and a pandemic ... ...

    Abstract Background: The SARS-CoV-2 has been responsible for infecting more than 613,615,658 people in 222 countries by September 11, 2022, of which 6,516,076 have died. COVID-19 was introduced by World Health Organization as a global concern and a pandemic disease due to its prevalence.
    Objective: Developing preventive or therapeutic medications against 2019-nCoV is an urgent need, and has been deemed as a high priority among scientific societies; in this regard, the production of effective vaccines is one of the most significant and high-priority requirements. Because of costly and time-consuming process of vaccine design, different immunoinformatics methods have been developed.
    Methods: At the beginning of vaccine design, the proteome study is essential. In this investigation, the whole human coronavirus proteome was evaluated using the proteome subtraction strategy. Out of 5945 human coronavirus proteins, five new antigenic proteins were selected by analyzing the hierarchical proteome subtraction, and then their various physicochemical and immunological properties were investigated bioinformatically.
    Results: All five protein sequences are antigenic and non-allergenic proteins; moreover, the spike protein group, including spike glycoprotein (E2) (Peplomer protein), spike fragment and spike glycoprotein fragment, showed acceptable stability, which can be used to design new vaccines against human coronaviruses.
    Conclusion: The selected peptides and the other proteins introduced in this study (HE, orf7a, SARS_X4 domain-containing protein and protein 8) can be employed as a suitable candidate for developing a novel prophylactic or therapeutic vaccine against human coronaviruses.
    MeSH term(s) Humans ; COVID-19/prevention & control ; SARS-CoV-2/genetics ; Proteome/genetics ; COVID-19 Vaccines/genetics ; Vaccinology ; Patents as Topic ; Vaccines ; Genomics ; Glycoproteins
    Chemical Substances Proteome ; COVID-19 Vaccines ; Vaccines ; Glycoproteins
    Language English
    Publishing date 2022-05-12
    Publishing country United Arab Emirates
    Document type Journal Article
    ISSN 2212-4012
    ISSN (online) 2212-4012
    DOI 10.2174/1872208316666220504234800
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  6. Article ; Online: Exosome-based vaccines and their position in next generation vaccines.

    Negahdaripour, Manica / Vakili, Bahare / Nezafat, Navid

    International immunopharmacology

    2022  Volume 113, Issue Pt A, Page(s) 109265

    Abstract: Extracellular vesicles (EVs), which include exosomes as a subset, are generated by most cell types and play crucial roles in intercellular communication. Exosomes offer intriguing tools as potential vaccines due to their ability to deliver a wide range ... ...

    Abstract Extracellular vesicles (EVs), which include exosomes as a subset, are generated by most cell types and play crucial roles in intercellular communication. Exosomes offer intriguing tools as potential vaccines due to their ability to deliver a wide range of antigens and immunomodulatory properties. Exosome-based vaccines have demonstrated promising results against different types of infectious diseases as well as cancers, both in vitro and in vivo. In this review, a number of studies on exosome-based vaccines are highlighted and relevant clinical trials are discussed.
    MeSH term(s) Exosomes/metabolism ; Extracellular Vesicles ; Vaccines ; Cell Communication ; Immunity
    Chemical Substances Vaccines
    Language English
    Publishing date 2022-10-14
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2043785-7
    ISSN 1878-1705 ; 1567-5769
    ISSN (online) 1878-1705
    ISSN 1567-5769
    DOI 10.1016/j.intimp.2022.109265
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  7. Article ; Online: A structural vaccinology approach for in silico designing of a potential self-assembled nanovaccine against Leishmania infantum.

    Vakili, Bahareh / Nezafat, Navid / Negahdaripour, Manica / Ghasemi, Younes

    Experimental parasitology

    2022  Volume 239, Page(s) 108295

    Abstract: Visceral leishmaniasis (VL) remains a major public health problem across 98 countries. To date, VL has no effective drug. Vaccines, as the most successful breakthroughs in medicine, can promise an effective strategy to fight various diseases. More ... ...

    Abstract Visceral leishmaniasis (VL) remains a major public health problem across 98 countries. To date, VL has no effective drug. Vaccines, as the most successful breakthroughs in medicine, can promise an effective strategy to fight various diseases. More recently, self-assembled peptide nanoparticles (SAPNs) have attracted considerable attention in the field of vaccine design due to their multivalency. In this study, a SAPN nanovaccine was designed using various immunoinformatics methods. High-ranked epitopes were chosen from a number of antigens, including Leishmania-specific hypothetical protein (LiHy), Leishmania-specific antigenic protein (LSAP), histone H1, and sterol 24-c-methyltransferase (SMT). To facilitate the oligomerization process, pentameric and trimeric coiled-coil domains were employed. RpfE, a resuscitation-promoting factor of Mycobacterium tuberculosis, was added to induce strong immune responses. Pentameric and trimeric coiled-coil domains as well as eight immunodominant epitopes from antigenic proteins of Leishmania infantum, the causative agent of VL, were joined together using appropriate linkers. High-quality 3D structure of monomeric and oligomeric structures followed by refinement and validation processes demonstrated that the designed nanovaccine could be considered to be a promising medication against the parasite; however, experimental validation is essential to confirm the effectiveness of the nanovaccine.
    MeSH term(s) Antigens, Protozoan ; Epitopes ; Humans ; Leishmania infantum ; Leishmaniasis, Visceral/parasitology ; Peptides ; Vaccinology
    Chemical Substances Antigens, Protozoan ; Epitopes ; Peptides
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 391089-1
    ISSN 1090-2449 ; 0014-4894
    ISSN (online) 1090-2449
    ISSN 0014-4894
    DOI 10.1016/j.exppara.2022.108295
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  8. Article ; Online: Computational Elucidation of Phylogenetic, Functional and Structural Features of Methioninase from Pseudomonas, Escherichia, Clostridium and Citrobacter Strains.

    Irajie, Cambyz / Mohkam, Milad / Vakili, Bahareh / Nezafat, Navid

    Recent patents on biotechnology

    2021  Volume 15, Issue 4, Page(s) 286–301

    Abstract: Background: L-Methioninase (EC 4.4.1.11; MGL) is a pyridoxal phosphate (PLP)-dependent enzyme that is produced by a variety of bacteria, fungi, and plants. L-methioninase, especially from Pseudomonas and Citrobacter sp., is considered as the efficient ... ...

    Abstract Background: L-Methioninase (EC 4.4.1.11; MGL) is a pyridoxal phosphate (PLP)-dependent enzyme that is produced by a variety of bacteria, fungi, and plants. L-methioninase, especially from Pseudomonas and Citrobacter sp., is considered as the efficient therapeutic enzyme, particularly in cancers such as glioblastomas, medulloblastoma, and neuroblastoma that are more sensitive to methionine starvation.
    Objective: The low stability is one of the main drawbacks of the enzyme; in this regard, in the current study, different features of the enzyme, including phylogenetic, functional, and structural from Pseudomonas, Escherichia, Clostridium, and Citrobacter strains were evaluated to find the best bacterial L-Methioninase.
    Methods: After the initial screening of L-Methioninase sequences from the above-mentioned bacterial strains, the three-dimensional structures of enzymes from Escherichia fergusonii, Pseudomonas fluorescens, and Clostridium homopropionicum were determined through homology modeling via GalaxyTBM server and refined by GalaxyRefine server.
    Results and conclusion: Afterwards, PROCHECK, verify 3D, and ERRAT servers were used for verification of the obtained models. Moreover, antigenicity, allergenicity, and physico-chemical analysis of enzymes were also carried out. In order to get insight into the interaction of the enzyme with other proteins, the STRING server was used. The secondary structure of the enzyme is mainly composed of random coils and alpha-helices. However, these outcomes should further be validated by wet-lab investigations.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/chemistry ; Carbon-Sulfur Lyases/genetics ; Citrobacter/enzymology ; Citrobacter/genetics ; Clostridium/enzymology ; Clostridium/genetics ; Escherichia/enzymology ; Escherichia/genetics ; Patents as Topic ; Phylogeny ; Pseudomonas/enzymology ; Pseudomonas/genetics
    Chemical Substances Bacterial Proteins ; Carbon-Sulfur Lyases (EC 4.4.-) ; L-methionine gamma-lyase (EC 4.4.1.11)
    Language English
    Publishing date 2021-09-27
    Publishing country United Arab Emirates
    Document type Journal Article
    ISSN 2212-4012
    ISSN (online) 2212-4012
    DOI 10.2174/1872208315666210910091438
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  9. Article ; Online: A versatile theranostic magnetic polydopamine iron oxide NIR laser-responsive nanosystem containing doxorubicin for chemo-photothermal therapy of melanoma.

    Dehghankhold, Mahvash / Ahmadi, Fatemeh / Nezafat, Navid / Abedi, Mehdi / Iranpour, Pooya / Dehghanian, Amirreza / Koohi-Hosseinabadi, Omid / Akbarizadeh, Amin Reza / Sobhani, Zahra

    Biomaterials advances

    2024  Volume 159, Page(s) 213797

    Abstract: Theranostics nanoparticles (NPs) have recently received much attention in cancer imaging and treatment. This study aimed to develop a multifunctional nanosystem for the targeted delivery of photothermal and chemotherapy agents. ... ...

    Abstract Theranostics nanoparticles (NPs) have recently received much attention in cancer imaging and treatment. This study aimed to develop a multifunctional nanosystem for the targeted delivery of photothermal and chemotherapy agents. Fe
    MeSH term(s) Humans ; Melanoma/drug therapy ; Photothermal Therapy ; Precision Medicine ; Phototherapy/methods ; Doxorubicin/pharmacology ; Doxorubicin/therapeutic use ; Lasers ; Ferric Compounds ; Indoles ; Polymers
    Chemical Substances polydopamine ; ferric oxide (1K09F3G675) ; Doxorubicin (80168379AG) ; Ferric Compounds ; Indoles ; Polymers
    Language English
    Publishing date 2024-02-12
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2772-9508
    ISSN (online) 2772-9508
    DOI 10.1016/j.bioadv.2024.213797
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  10. Article ; Online: The potential of intrinsically disordered regions in vaccine development.

    Ameri, Mehrdad / Nezafat, Navid / Eskandari, Sedigheh

    Expert review of vaccines

    2021  Volume 21, Issue 1, Page(s) 1–3

    MeSH term(s) Humans ; Protein Binding ; Protein Conformation ; Vaccine Development
    Language English
    Publishing date 2021-11-15
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2181284-6
    ISSN 1744-8395 ; 1476-0584
    ISSN (online) 1744-8395
    ISSN 1476-0584
    DOI 10.1080/14760584.2022.1997600
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