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  1. Article ; Online: Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters.

    Hajji, Halima / Alaqarbeh, Marwa / Lakhlifi, Tahar / Ajana, Mohammed Aziz / Alsakhen, Nada / Bouachrine, Mohammed

    Computers in biology and medicine

    2022  Volume 150, Page(s) 106209

    Abstract: SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. ... ...

    Abstract SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. Efforts have been directed towards using medicinal plants as alternative medicines, as the active chemical compounds in them have been discovered as potential antiviral or anti-inflammatory agents. In this research, the potential of Saussurea costus (S. Costus) or QUST Al Hindi chemical consistent as potential antiviral agents was investigated by using computational methods such as Reverse Docking, ADMET, and Molecular Dynamics with different proteases COVID-19 such as PDB: 2GZ9; 6LU7; 7AOL, 6Y2E, 6Y84. The results of Reverse Docking the complex between 6LU7 proteases and Cynaropicrin compound being the best complex, as the same result, is achieved by molecular dynamics. Also, the toxicity testing result from ADMET method proved that the complex is the least toxic and the safest possible drug. In addition, 6LU7-Cynaropicrin complex obeyed Lipinski rule; it formed ≤5 H-bond donors and ≤10 H bond acceptors, MW < 500 Daltons, and octanol/water partition coefficient <5.
    MeSH term(s) Humans ; Molecular Dynamics Simulation ; Saussurea ; COVID-19 ; SARS-CoV-2 ; Peptide Hydrolases ; Molecular Docking Simulation ; Protease Inhibitors
    Chemical Substances cynaropicrin (M9233789I9) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Peptide Hydrolases (EC 3.4.-) ; Protease Inhibitors
    Language English
    Publishing date 2022-10-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2022.106209
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Computational analysis of bevacizumab binding with protein receptors for its potential anticancer activity.

    Alsakhen, Nada / Radwan, Enas S / Zafer, Imran / Abed Alfattah, Husam / Shamkh, Israa M / Rehman, Md Tabish / Shahwan, Moayad / Khan, Khalid Ali / Ahmed, Shimaa A

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–21

    Abstract: Breast cancer poses a significant global challenge, prompting researchers to explore novel approaches for potential treatments. In this study, we investigated the binding free energy ( ... ...

    Abstract Breast cancer poses a significant global challenge, prompting researchers to explore novel approaches for potential treatments. In this study, we investigated the binding free energy (Δ
    Language English
    Publishing date 2024-01-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2307445
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: In silico

    Belhassan, Assia / Chtita, Samir / Zaki, Hanane / Alaqarbeh, Marwa / Alsakhen, Nada / Almohtaseb, Firas / Lakhlifi, Tahar / Bouachrine, Mohammed

    Journal of molecular structure

    2022  Volume 1258, Page(s) 132652

    Abstract: COVID-19 is a new infectious disease caused by SARS-COV-2 virus of the coronavirus Family. The identification of drugs against this serious infection is a significant requirement due to the rapid rise in the positive cases and deaths around the world. ... ...

    Abstract COVID-19 is a new infectious disease caused by SARS-COV-2 virus of the coronavirus Family. The identification of drugs against this serious infection is a significant requirement due to the rapid rise in the positive cases and deaths around the world. With this concept, a molecular docking analysis for vitamins and their derivatives (28 molecules) with the active site of SARS-CoV-2 main protease was carried out. The results of molecular docking indicate that the structures with best binding energy in the binding site of the studied enzyme (lowest energy level) are observed for the compounds; Folacin, Riboflavin, and Phylloquinone oxide (Vitamin K1 oxide). A Molecular Dynamic simulation was carried out to study the binding stability for the selected vitamins with the active site of SARS-CoV-2 main protease enzyme. Molecular Dynamic shows that Phylloquinone oxide and Folacin are quite unstable in binding to SARS-CoV-2 main protease, while the Riboflavin is comparatively rigid. The higher fluctuations in Phylloquinone oxide and Folacin indicate that they may not fit very well into the binding site. As expected, the Phylloquinone oxide exhibits small number of H-bonds with protein and Folacin does not form a good interaction with protein. Riboflavin exhibits the highest number of Hydrogen bonds and forms consistent interactions with protein. Additionally, this molecule respect the conditions mentioned in Lipinski's rule and have acceptable ADMET proprieties which indicates that Riboflavin (Vitamin B2) could be interesting for the antiviral treatment of COVID-19.
    Language English
    Publishing date 2022-02-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 194476-9
    ISSN 0022-2860 ; 0377-046X
    ISSN 0022-2860 ; 0377-046X
    DOI 10.1016/j.molstruc.2022.132652
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Discovery of 1-(5-bromopyrazin-2-yl)-1-[3-(trifluoromethyl)benzyl]urea as a promising anticancer drug via synthesis, characterization, biological screening, and computational studies.

    Mohammed, Yasser Hussein Issa / Shamkh, Israa M / Alharthi, Nahed S / Shanawaz, Mohammed A / Alzahrani, Hind A / Jabbar, Basit / Beigh, Saba / Alghamdi, Saad / Alsakhen, Nada / Khidir, Elshiekh B / Alhuthali, Hayaa M / Karamalla, Taqwa Hafiz Elamin / Rabie, Amgad M

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 22824

    Abstract: Cancer and different types of tumors are still the most resistant diseases to available therapeutic agents. Finding a highly effective anticancer drug is the first target and concern of thousands of drug designers. In our attempts to address this concern, ...

    Abstract Cancer and different types of tumors are still the most resistant diseases to available therapeutic agents. Finding a highly effective anticancer drug is the first target and concern of thousands of drug designers. In our attempts to address this concern, a new pyrazine derivative, 1-(5-bromopyrazin-2-yl)-1-[3-(trifluoromethyl)benzyl]urea (BPU), was designed via structural optimization and synthesized to investigate its anticancer/antitumor potential. The in-vitro anticancer properties of BPU were evaluated by MTT assay using selected cell lines, including the Jurkat, HeLa, and MCF-7 cells. The Jurkat cells were chosen to study the effect of BPU on cell cycle analysis using flow cytometry technique. BPU exhibited an effective cytotoxic ability in all the three cell lines assessed. It was found to be more prominent with the Jurkat cell line (IC
    MeSH term(s) Humans ; Matrix Metalloproteinase 2/metabolism ; Matrix Metalloproteinase 9/metabolism ; Urea/pharmacology ; Antineoplastic Agents/chemistry ; MCF-7 Cells ; Drug Screening Assays, Antitumor ; Cell Proliferation ; Molecular Docking Simulation ; Cell Line, Tumor ; Structure-Activity Relationship ; Molecular Structure
    Chemical Substances Matrix Metalloproteinase 2 (EC 3.4.24.24) ; Matrix Metalloproteinase 9 (EC 3.4.24.35) ; Urea (8W8T17847W) ; Antineoplastic Agents
    Language English
    Publishing date 2023-12-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-44662-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: QSAR-driven screening uncovers and designs novel pyrimidine-4,6-diamine derivatives as potent JAK3 inhibitors.

    Faris, Abdelmoujoud / Ibrahim, Ibrahim M / Alnajjar, Radwan / Hadni, Hanine / Bhat, Mashooq Ahmad / Yaseen, Muhammad / Chakraborty, Souvik / Alsakhen, Nada / Shamkh, Israa M / Mabood, Fazal / M Naglah, Ahmed / Ullah, Ihsan / Ziedan, Noha / Elhallaoui, Menana

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–30

    Abstract: This study presents a robust and integrated methodology that harnesses a range of computational techniques to facilitate the design and prediction of new inhibitors targeting the JAK3/STAT pathway. This methodology encompasses several strategies, ... ...

    Abstract This study presents a robust and integrated methodology that harnesses a range of computational techniques to facilitate the design and prediction of new inhibitors targeting the JAK3/STAT pathway. This methodology encompasses several strategies, including QSAR analysis, pharmacophore modeling, ADMET prediction, covalent docking, molecular dynamics (MD) simulations, and the calculation of binding free energies (MM/GBSA). An efficacious QSAR model was meticulously crafted through the employment of multiple linear regression (MLR). The initial MLR model underwent further refinement employing an artificial neural network (ANN) methodology aimed at minimizing predictive errors. Notably, both MLR and ANN exhibited commendable performance, showcasing R2 values of 0.89 and 0.95, respectively. The model's precision was assessed via leave-one-out cross-validation (CV) yielding a Q2 value of 0.65, supplemented by rigorous Y-randomization. , The pharmacophore model effectively differentiated between active and inactive drugs, identifying potential JAK3 inhibitors, and demonstrated validity with an ROC value of 0.86. The newly discovered and designed inhibitors exhibited high inhibitory potency, ranging from 6 to 8, as accurately predicted by the QSAR models. Comparative analysis with FDA-approved Tofacitinib revealed that the new compounds exhibited promising ADMET properties and strong covalent docking (CovDock) interactions. The stability of the new discovered and designed inhibitors within the JAK3 binding site was confirmed through 500 ns MD simulations, while MM/GBSA calculations supported their binding affinity. Additionally, a retrosynthetic study was conducted to facilitate the synthesis of these potential JAK3/STAT inhibitors. The overall integrated approach demonstrates the feasibility of designing novel JAK3/STAT inhibitors with robust efficacy and excellent ADMET characteristics that surpass Tofacitinib by a significant margin.Communicated by Ramaswamy H. Sarma.
    Language English
    Publishing date 2023-12-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2283168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Camphor, Artemisinin and Sumac Phytochemicals as inhibitors against COVID-19: Computational approach.

    Belhassan, Assia / Zaki, Hanane / Chtita, Samir / Alaqarbeh, Marwa / Alsakhen, Nada / Benlyas, Mohamed / Lakhlifi, Tahar / Bouachrine, Mohammed

    Computers in biology and medicine

    2021  Volume 136, Page(s) 104758

    Abstract: Covid-19 is an emerging infectious disease caused by coronavirus SARS-CoV-2. Due to the rapid rise in deaths resulted from this infection all around the world, the identification of drugs against this new coronavirus is an important requirement. Among ... ...

    Abstract Covid-19 is an emerging infectious disease caused by coronavirus SARS-CoV-2. Due to the rapid rise in deaths resulted from this infection all around the world, the identification of drugs against this new coronavirus is an important requirement. Among the drugs that can fight this type of infection; natural products are substances that serve as sources of beneficial chemical molecules for the development of effective therapies. In this study, Camphor, Artemisinin and 14 Sumac phytochemicals were docked in the active site of SARS-CoV-2 main protease (PDB code: 6LU7). We have also performed molecular dynamic simulation at 100 ns with MM-GBSA/PBSA analysis for the structures with the best affinity in the binding site of the studied enzyme (Hinokiflavone and Myricetin) after docking calculations to consider parameters like RMSD, covariance, PCA, radius of gyration, potential energy, temperature and pressure. The result indicates that Hinokiflavone and Myricetin are the structures with best affinity and stability in the binding site of the studied enzyme and they respect the conditions mentioned in Lipinski's rule and have acceptable ADMET proprieties; so, these compounds have important pharmacokinetic properties and bioavailability, and they could have more potent antiviral treatment of COVID-19 than the other studied compounds.
    MeSH term(s) Artemisinins ; COVID-19 ; Camphor ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Phytochemicals/pharmacology ; Protease Inhibitors ; Rhus ; SARS-CoV-2
    Chemical Substances Artemisinins ; Phytochemicals ; Protease Inhibitors ; Camphor (76-22-2)
    Language English
    Publishing date 2021-08-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2021.104758
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Isoform switching leads to downregulation of cytokine producing genes in estrogen receptor positive breast cancer.

    Khan, Mohammad Shahbaz / Hanif, Waqar / Alsakhen, Nada / Jabbar, Basit / Shamkh, Israa M / Alsaiari, Ahad Amer / Almehmadi, Mazen / Alghamdi, Saad / Shakoori, Afnan / Al Farraj, Dunia A / Almutairi, Saeedah Musaed / Hussein Issa Mohammed, Yasser / Abouzied, Amr S / Rehman, Aziz-Ur / Huwaimel, Bader

    Frontiers in genetics

    2023  Volume 14, Page(s) 1230998

    Abstract: Objective: ...

    Abstract Objective:
    Language English
    Publishing date 2023-10-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1230998
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  8. Article ; Online: In silico identification of 1,2,4-triazoles as potential Candida Albicans inhibitors using 3D-QSAR, molecular docking, molecular dynamics simulations, and ADMET profiling.

    Bouamrane, Soukaina / Khaldan, Ayoub / Hajji, Halima / El-Mernissi, Reda / Alaqarbeh, Marwa / Alsakhen, Nada / Maghat, Hamid / Ajana, Mohammed Aziz / Sbai, Abdelouahid / Bouachrine, Mohammed / Lakhlifi, Tahar

    Molecular diversity

    2022  Volume 27, Issue 5, Page(s) 2111–2132

    Abstract: Fluconazole and Voriconazole are individual antifungal inhibitors broadly adopted for treating fungal infections, including Candida Albicans. Unfortunately, these medicines clinically used have significant side effects. Consequently, the improvement of ... ...

    Abstract Fluconazole and Voriconazole are individual antifungal inhibitors broadly adopted for treating fungal infections, including Candida Albicans. Unfortunately, these medicines clinically used have significant side effects. Consequently, the improvement of safer and better therapy became more indispensable. In this study, a set of 27 1,2,4-triazole compounds have been tested as potential Candida Albicans inhibitors by using different theoretical methods. The created comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) contour maps significantly impacted the development of novel Candida Albicans inhibitors with valuable activities. The mode of interactions between the 1,2,4-triazole inhibitors and the targeted receptor was studied by molecular docking simulation. The proposed new molecule P1 showed satisfied stability in the active pocket of the targeted receptor compared to the more active molecule in the dataset compared to Fluconazole medication. Meanwhile, the binding energy obtained by molecular docking for molecule P1 is - 9.3 kcal/mol compared with - 6.7 kcal/mol for Fluconazole medication. Also, MM/GBSA value obtained by molecular dynamics simulations at 100 ns for molecule P1 is - 33.34 kcal/mol compared with - 15.85 kcal/mol for Fluconazole medication. In addition, molecule P1 showed good oral bioavailability and was non-toxic according to ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties. Therefore, the results indicated compound P1 might be a future inhibitor of Candida Albicans infection.
    MeSH term(s) Molecular Dynamics Simulation ; Molecular Docking Simulation ; Triazoles/pharmacology ; Candida albicans ; Fluconazole/pharmacology ; Quantitative Structure-Activity Relationship
    Chemical Substances Triazoles ; Fluconazole (8VZV102JFY)
    Language English
    Publishing date 2022-10-14
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-022-10546-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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