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  1. Article ; Online: Development of a candidate multi-epitope vaccine against

    Alamri, Mubarak A

    Saudi medical journal

    2023  Volume 44, Issue 6, Page(s) 544–559

    Abstract: Objectives: To develop a candidate vaccine aginst the : Methods: Since there is currently no vaccine against this pathogen, we employed in-silico methods to extensively explore the outer membrane toxin-producing proteins found specifically in : ... ...

    Abstract Objectives: To develop a candidate vaccine aginst the
    Methods: Since there is currently no vaccine against this pathogen, we employed in-silico methods to extensively explore the outer membrane toxin-producing proteins found specifically in
    Results: TThe vaccine peptide comprises multiple linear and conformational B-cell epitopes, which have the potential to elicit humoral immunity. Projected B-cell- derived T-cell epitopes for outer membrane proteins are present in the produced protein. The docking and molecular dynamic simulation results indicating that the chimeric vaccine had adequate binding stability with TLR-4. Following the immunological simulation, significant levels of immune cell expression were observed as immunoglobulin (Ig) M and IgG, IgM, IgM1, and IgM2, and independently IgG1 and IgG2.
    Conclusion: The developed vaccine candidate is suitable for further testing and can assist experimental vaccinologists in developing an effective vaccine against
    MeSH term(s) Humans ; Vaccinology/methods ; Sphingobacterium ; Epitopes, B-Lymphocyte/chemistry ; Saudi Arabia
    Chemical Substances Epitopes, B-Lymphocyte
    Language English
    Publishing date 2023-06-21
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 392302-2
    ISSN 1658-3175 ; 0379-5284
    ISSN (online) 1658-3175
    ISSN 0379-5284
    DOI 10.15537/smj.2023.44.6.20220733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Bioinformatics and network pharmacology-based study to elucidate the multi-target pharmacological mechanism of the indigenous plants of Medina valley in treating HCV-related hepatocellular carcinoma.

    Alamri, Mubarak A

    Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society

    2023  Volume 31, Issue 6, Page(s) 1125–1138

    Abstract: The incidence of Hepatocellular Carcinoma (HCC) in Saudi Arabia is not surprising given the relatively high prevalence of hepatitis C virus (HCV) infection. Hepatitis C is also common in Saudi Arabia with a prevalence rate of 1% to 3% of the population, ... ...

    Abstract The incidence of Hepatocellular Carcinoma (HCC) in Saudi Arabia is not surprising given the relatively high prevalence of hepatitis C virus (HCV) infection. Hepatitis C is also common in Saudi Arabia with a prevalence rate of 1% to 3% of the population, which further increases the risk of HCC. The incidence of HCC has been increasing in recent years, with HCV-related HCC accounting for a significant proportion of cases. Traditional medicine has long been a part of Saudi Arabian culture, and many medicinal plants have been used for centuries to treat various ailments, including cancer. Following that, this study combines network pharmacology with bioinformatics approaches to potentially revolutionize HCV-related HCC treatment by identifying effective phytochemicals of indigenous plants of Medina valley. Eight indigenous plants including
    Language English
    Publishing date 2023-04-10
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 1378024-4
    ISSN 1319-0164
    ISSN 1319-0164
    DOI 10.1016/j.jsps.2023.04.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4758: Show issues Location:
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  3. Article ; Online: Network pharmacology and molecular dynamic simulation integrated strategy for the screening of active components and mechanisms of phytochemicals from

    Alamri, Mubarak A / Tahir Ul Qamar, Muhammad

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–17

    Abstract: Alzheimer's disease (AD) ranks as the most prevalent neurodegenerative disorder with dementia and it accounts for more than 70% of all cases. Despite extensive reporting on the experimental investigation ... ...

    Abstract Alzheimer's disease (AD) ranks as the most prevalent neurodegenerative disorder with dementia and it accounts for more than 70% of all cases. Despite extensive reporting on the experimental investigation of
    Language English
    Publishing date 2024-01-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2308756
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  4. Article: Network pharmacology based virtual screening of Flavonoids from

    Alamri, Mubarak A / Tahir Ul Qamar, Muhammad

    Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society

    2023  Volume 31, Issue 11, Page(s) 101802

    Abstract: Inflammation is a nonspecific immune response against injury caused by a harmful agent that strives to restore tissue function and homeostasis. ...

    Abstract Inflammation is a nonspecific immune response against injury caused by a harmful agent that strives to restore tissue function and homeostasis.
    Language English
    Publishing date 2023-09-28
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 1378024-4
    ISSN 1319-0164
    ISSN 1319-0164
    DOI 10.1016/j.jsps.2023.101802
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4758: Show issues Location:
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  5. Article: Adamantane-derived scaffolds targeting the sigma-2 receptor; an

    Alamri, Mohammed A / Alamri, Mubarak A

    Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society

    2021  Volume 29, Issue 10, Page(s) 1166–1172

    Abstract: Novel adamantane-based compounds were synthesized and assessed as potential sigma-2 receptor ligands. Molecular docking and 50 ns molecular dynamic simulation were carried out to determine the binding modes, mechanism of interaction, and stability of ... ...

    Abstract Novel adamantane-based compounds were synthesized and assessed as potential sigma-2 receptor ligands. Molecular docking and 50 ns molecular dynamic simulation were carried out to determine the binding modes, mechanism of interaction, and stability of these compounds within the active site of the sigma-2 receptor. In addition, the ADME-T properties have been explored. The cytotoxicity in cancer cell lines that express sigma-2 receptors was also examined. In addition, the in silico and cytotoxicity data for the new compounds were compared to a reference sigma-2 receptor ligand with high receptor-binding affinity and selectivity. The data suggests that the new compounds interact with the sigma-2 receptor in a comparable manner to the reference compound, and that adamantane can be used as a scaffold to synthesize sigma-2 receptor ligands with useful functional groups that can be used to conjugate moieties for tumor-imaging or cytotoxic cargo delivery.
    Language English
    Publishing date 2021-08-29
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 1378024-4
    ISSN 1319-0164
    ISSN 1319-0164
    DOI 10.1016/j.jsps.2021.08.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target.

    Alawam, Abdullah S / M Alneghery, Lina / Alwethaynani, Maher S / Alamri, Mubarak A

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–11

    Abstract: The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell wall polymers cross linking during typhoid toxin release, ... ...

    Abstract The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell wall polymers cross linking during typhoid toxin release, β-lactam resistance and outer membrane defect rescue. These observations have been recorded in different bacterial pathogens such as
    Language English
    Publishing date 2024-02-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2322619
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
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  7. Article ; Online: Flavonoids as potential KRAS inhibitors: DFT, molecular docking, molecular dynamics simulation and ADMET analyses.

    Prinsa / Saha, Supriyo / Bulbul, Md Zahidul Haque / Ozeki, Yasuhiro / Alamri, Mubarak A / Kawsar, Sarkar M A

    Journal of Asian natural products research

    2024  , Page(s) 1–38

    Abstract: KRAS mutations linked with cancer. Flavonoids were docked against KRAS G12C and G12D receptors. Abyssinone III, alpha naphthoflavone, beta naphthoflavone, abyssinone I, abyssinone II and beta naphthoflavone, genistin, daidzin showed good docking scores ... ...

    Abstract KRAS mutations linked with cancer. Flavonoids were docked against KRAS G12C and G12D receptors. Abyssinone III, alpha naphthoflavone, beta naphthoflavone, abyssinone I, abyssinone II and beta naphthoflavone, genistin, daidzin showed good docking scores against KRAS G12C and G12D receptors, respectively. The MD simulation data revealed that Rg, RMSD, RMSF, and SASA values were within acceptable limits. Alpha and beta naphthoflavone showed good binding energies with KRAS G12C and G12D receptors. DFT and MEP analysis highlighted the nucleophilic and electrophilic zones of best-docked flavonoids. A novel avenue for the control of KRAS G12C and G12D mutations is made possible by flavonoids.
    Language English
    Publishing date 2024-04-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 2077926-4
    ISSN 1477-2213 ; 1028-6020
    ISSN (online) 1477-2213
    ISSN 1028-6020
    DOI 10.1080/10286020.2024.2343821
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies.

    Alabbas, Alhumaidi B / Alamri, Mubarak A

    Saudi journal of biological sciences

    2021  Volume 29, Issue 1, Page(s) 526–533

    Abstract: The continuous and rapid development of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern especially with the emergence of numerous variants and mutations worldwide. As with other RNA viruses, SARS-CoV-2 has ... ...

    Abstract The continuous and rapid development of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern especially with the emergence of numerous variants and mutations worldwide. As with other RNA viruses, SARS-CoV-2 has a genetically high mutation rate. These mutations have an impact on the virus characteristics, including transmissibility, antigenicity and development of drug and vaccine resistance. This work was pursued to identify the differences that exist in the papain-like protease (PL
    Language English
    Publishing date 2021-09-17
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 2515206-3
    ISSN 2213-7106 ; 1319-562X
    ISSN (online) 2213-7106
    ISSN 1319-562X
    DOI 10.1016/j.sjbs.2021.09.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Pharmacoinformatics and molecular dynamic simulation studies to identify potential small-molecule inhibitors of WNK-SPAK/OSR1 signaling that mimic the RFQV motifs of WNK kinases

    Mubarak A. Alamri

    Arabian Journal of Chemistry, Vol 13, Iss 4, Pp 5107-

    2020  Volume 5117

    Abstract: The WNK-SPAK/OSR1 signaling is a complex of serine and threonine protein kinases that involves in the regulation of human blood pressure. The WNK kinases phosphorylate and activate SPAK and OSR1 kinases through the interaction of RFQV motifs of WNK ... ...

    Abstract The WNK-SPAK/OSR1 signaling is a complex of serine and threonine protein kinases that involves in the regulation of human blood pressure. The WNK kinases phosphorylate and activate SPAK and OSR1 kinases through the interaction of RFQV motifs of WNK kinases with the C-terminal domains of SPAK and OSR1. Upon phosphorylation, SPAK and OSR1 phosphorylate key ion co-transporters such as Na+-[K+]-2Cl− (NKCC1-2) and K+-Cl− (KCC1-4), which are essential for electrolytes balance and blood pressure regulation. Targeting the binding site of the RFQV motifs of WNK kinases on the C-terminal domain (CTD) of SPAK and OSR1 has emerged as a valuable approach to inhibit the WNK-SPAK/OSR1 signaling pathway. Herein, an effort has been intended to pinpoint non-peptidic small-molecules that could disrupt the binding of SPAK/OSR1 to WNK kinases, hence, inhibit the SPAK and OSR1 phosphorylation and activation by WNK kinases through pharmacoinformatics and molecular dynamic simulation methodologies. A sequential structure-based virtual screening of a focus protein-protein interaction chemical library composed of 11,870 compounds lead to the identification of three compounds having good lead-compound properties with respect to their predicted inhibitory constants, pharmacophore fit scores, binding affinities, ADME-T parameters, drug-likeness properties and ligand efficiency metrics. The mechanism of interaction and binding stability of these compounds to OSR1-CTD were confirmed using molecular docking and dynamic simulation studies. Hence, the identified compounds may have therapeutic potential as novel antihypertensive agents subjected to experimental validation. Keywords: Pharmacophore, MD simulation, SPAK, OSR1, Virtual screening, WNK
    Keywords Chemistry ; QD1-999
    Subject code 540 ; 571
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Prospective virtual screening combined with bio-molecular simulation enabled identification of new inhibitors for the KRAS drug target.

    Ajmal, Amar / Alkhatabi, Hind A / Alreemi, Roaa M / Alamri, Mubarak A / Khalid, Asaad / Abdalla, Ashraf N / Alotaibi, Bader S / Wadood, Abdul

    BMC chemistry

    2024  Volume 18, Issue 1, Page(s) 57

    Abstract: Lung cancer is a disease with a high mortality rate and it is the number one cause of cancer death globally. Approximately 12-14% of non-small cell lung cancers are caused by mutations in ... ...

    Abstract Lung cancer is a disease with a high mortality rate and it is the number one cause of cancer death globally. Approximately 12-14% of non-small cell lung cancers are caused by mutations in KRAS
    Language English
    Publishing date 2024-03-25
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2661-801X
    ISSN (online) 2661-801X
    DOI 10.1186/s13065-024-01152-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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