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  1. Article ; Online: Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study.

    Mahmoudi Gomari, Mohammad / Rostami, Neda / Omidi-Ardali, Hossein / Arab, Seyed Shahriar

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 12, Page(s) 5634–5642

    Abstract: Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the ... ...

    Abstract Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) COVID-19/genetics ; Humans ; Molecular Dynamics Simulation ; Mutation ; Point Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2021-01-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.1872418
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective.

    Mondeali, Mozhgan / Etemadi, Ali / Barkhordari, Khabat / Mobini Kesheh, Mina / Shavandi, Sara / Bahavar, Atefeh / Tabatabaie, Fatemeh Hosseini / Mahmoudi Gomari, Mohammad / Modarressi, Mohammad H

    Journal of cellular biochemistry

    2023  Volume 124, Issue 2, Page(s) 308–319

    Abstract: The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the ... ...

    Abstract The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein-protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.
    MeSH term(s) Humans ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; SARS-CoV-2 ; Mutation ; Protein Binding ; Molecular Dynamics Simulation
    Chemical Substances spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2023-01-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.30367
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Targeting siRNA in colorectal cancer therapy: Nanotechnology comes into view.

    Aghamiri, Shahin / Jafarpour, Ali / Malekshahi, Ziba Veisi / Mahmoudi Gomari, Mohammad / Negahdari, Babak

    Journal of cellular physiology

    2019  Volume 234, Issue 9, Page(s) 14818–14827

    Abstract: Colorectal cancer (CRC) is known as one of the most important causes of death and mortality worldwide. Although several efforts have been made for finding new therapies, no achievements have been made in this area. Multidrug resistance (MDR) mechanisms ... ...

    Abstract Colorectal cancer (CRC) is known as one of the most important causes of death and mortality worldwide. Although several efforts have been made for finding new therapies, no achievements have been made in this area. Multidrug resistance (MDR) mechanisms are one of the key factors that could lead to the failure of chemotherapy. Moreover, it has been shown that various chemotherapy drugs are associated with several side effects. Hence, it seems that finding new drugs or new therapeutic platforms is required. Among different therapeutic approaches, utilization of nanoparticles (NPs) for targeting a variety of molecules such as siRNAs are associated with good results for the treatment of CRC. Targeting siRNA-mediated NPs could turn off the effects of oncogenes and MDR-related genes. In the current study, we summarized various siRNAs targeted by NPs which could be used for the treatment of CRC. Moreover, we highlighted other routes such as liposome for targeting siRNAs in CRC therapy.
    Language English
    Publishing date 2019-03-28
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 3116-1
    ISSN 1097-4652 ; 0021-9541
    ISSN (online) 1097-4652
    ISSN 0021-9541
    DOI 10.1002/jcp.28281
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Newly Developed Targeted Therapies Against the Androgen Receptor in Triple-Negative Breast Cancer: A Review.

    Choupani, Edris / Mahmoudi Gomari, Mohammad / Zanganeh, Saeed / Nasseri, Sherko / Haji-Allahverdipoor, Kaveh / Rostami, Neda / Hernandez, Yaeren / Najafi, Safa / Saraygord-Afshari, Neda / Hosseini, Arshad

    Pharmacological reviews

    2022  Volume 75, Issue 2, Page(s) 309–327

    Abstract: Among different types of breast cancers (BC), triple-negative BC (TNBC) amounts to 15% to 20% of breast malignancies. Three principal characteristics of TNBC cells are (i) extreme aggressiveness, (ii) absence of hormones, and (iii) growth factor ... ...

    Abstract Among different types of breast cancers (BC), triple-negative BC (TNBC) amounts to 15% to 20% of breast malignancies. Three principal characteristics of TNBC cells are (i) extreme aggressiveness, (ii) absence of hormones, and (iii) growth factor receptors. Due to the lack or poor expression of the estrogen receptor, human epidermal growth factor receptor 2, and progesterone receptor, TNBC is resistant to hormones and endocrine therapies. Consequently, chemotherapy is currently used as the primary approach against TNBC. Expression of androgen receptor (AR) in carcinoma cells has been observed in a subset of patients with TNBC; therefore, inhibiting androgen signaling pathways holds promise for TNBC targeting. The new AR inhibitors have opened up new therapy possibilities for BC patients carrying AR-positive TNBC cells. Our group provides a comprehensive review of the structure and function of the AR and clinical evidence for targeting the cell's nuclear receptor in TNBC. We updated AR agonists, inhibitors, and antagonists. We also presented a new era of genetic manipulating CRISPR/Cas9 and nanotechnology as state-of-the-art approaches against AR to promote the efficiency of targeted therapy in TNBC. SIGNIFICANCE STATEMENT: The lack of effective treatment for triple-negative breast cancer is a health challenge. The main disadvantages of existing treatments are their side effects, due to their nonspecific targeting. Molecular targeting of cellular receptors, such as androgen receptors, increased expression in malignant tissues, significantly improving the survival rate of breast cancer patients.
    MeSH term(s) Humans ; Androgen Receptor Antagonists/pharmacology ; Androgen Receptor Antagonists/therapeutic use ; Hormones/therapeutic use ; Receptors, Androgen/genetics ; Receptors, Androgen/metabolism ; Treatment Outcome ; Triple Negative Breast Neoplasms/drug therapy ; Triple Negative Breast Neoplasms/genetics ; Triple Negative Breast Neoplasms/pathology
    Chemical Substances Androgen Receptor Antagonists ; Hormones ; Receptors, Androgen
    Language English
    Publishing date 2022-12-12
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 209898-2
    ISSN 1521-0081 ; 0031-6997
    ISSN (online) 1521-0081
    ISSN 0031-6997
    DOI 10.1124/pharmrev.122.000665
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry.

    Mahmoudi Gomari, Mohammad / Saraygord-Afshari, Neda / Farsimadan, Marziye / Rostami, Neda / Aghamiri, Shahin / Farajollahi, Mohammad M

    Biotechnology advances

    2020  Volume 45, Page(s) 107653

    Abstract: Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application ...

    Abstract Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
    MeSH term(s) Chromatography, Affinity ; Drug Industry ; Peptides ; Proteins ; Recombinant Fusion Proteins
    Chemical Substances Peptides ; Proteins ; Recombinant Fusion Proteins
    Language English
    Publishing date 2020-11-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 47165-3
    ISSN 1873-1899 ; 0734-9750
    ISSN (online) 1873-1899
    ISSN 0734-9750
    DOI 10.1016/j.biotechadv.2020.107653
    Database MEDical Literature Analysis and Retrieval System OnLINE

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