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  1. Article ; Online: The computational analyses, molecular dynamics of fatty-acid transport mechanism to the CD36 receptor.

    Akachar, Jihane / Etchebest, Catherine / El Jaoudi, Rachid / Ibrahimi, Azeddine

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 23207

    Abstract: The transmembrane glycoprotein CD36, which is responsible of the metabolic disorders, and the elevated intake of fat induces lipid buildup, is a multifunctional scavenger receptor signaling those functions in high-affinity tissue uptake of long-chain ... ...

    Abstract The transmembrane glycoprotein CD36, which is responsible of the metabolic disorders, and the elevated intake of fat induces lipid buildup, is a multifunctional scavenger receptor signaling those functions in high-affinity tissue uptake of long-chain fatty acids. In this study, we used series of molecular dynamics simulations of the wild type and mutants types K164A CD36 protein interacting with one palmitic acid (PLM) besides simulations of the wild type interacting with the three PLM to find out the mechanism of the functioning of the complex CD36/Fatty acids and the unraveling of the role of the mutation. Additionally we determined whether Lys164, mostly exposed to protein surface, played important roles in fatty acid uptake. These simulations revealed, the conformational changes induced by Lys164 residue and the altered interactions induced by the mutagenesis of surface lysine that was badly influencing the folding, utility, solubility, and stability form of the variant. Furthermore, Lys164 residue provided the structural basis of forming an opening at the region of principal portal for the dissociation of palmitic acid. The results of our simulations revealed hole two fatty acids found in CD36 cavity structure and it was the most preferred to CD36 structure stabilization.
    MeSH term(s) Biological Transport ; CD36 Antigens/chemistry ; CD36 Antigens/genetics ; CD36 Antigens/metabolism ; Fatty Acids/metabolism ; Humans ; Molecular Dynamics Simulation ; Palmitic Acid/metabolism ; Point Mutation ; Protein Conformation
    Chemical Substances CD36 Antigens ; CD36 protein, human ; Fatty Acids ; Palmitic Acid (2V16EO95H1)
    Language English
    Publishing date 2021-12-01
    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/s41598-021-01373-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: In-silico

    Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Zouaidia, Fouad / Ibrahimi, Azeddine

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 11, Page(s) 5203–5210

    Abstract: Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with ... ...

    Abstract Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with the ligand binding domain (LBD) or agents inhibiting the production of estrogen. These strategies are limited by many factors that lead to constitutive activation of ERα and consequently, resistance to treatment. Targeting the DNA binding domain (DBD) of ERα instead of its LBD with small-molecule inhibitors could be an alternative to impair ERα's signalling pathway. For this purpose, we conducted a structure based virtual screening of DrugBank against the crystal structure of ERα-DBD (PDB ID: 1HCQ) using the Glide module in standard precision (SP) and extra precision (XP) mode of docking. Molecules with XP Gscore less than -8 kcal/mol were selected and visually inspected to keep only the reasonable docking poses. Subsequently, these molecules were clustered using structural interaction fingerprints analysis and the complexes of the top ranked molecules of each cluster based on XP Gscore were subjected to 200 ns molecular dynamics simulations followed by MM-GBSA binding free energy calculation for the last 100 ns of each complex. In this study, we identified three molecules from DrugBank namely DB03450, DB02593 and DB08001 showing significant stability and strong interaction with the key amino acids during MD simulation suggesting a potential inhibition of the target. These molecules could be used as promising lead compounds to impair the ERα signalisation in hormone therapy-resistant breast cancer.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Antineoplastic Agents/chemistry ; Binding Sites ; Breast Neoplasms/drug therapy ; DNA/metabolism ; Estrogen Receptor alpha/antagonists & inhibitors ; Estrogens ; Female ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding
    Chemical Substances Antineoplastic Agents ; Estrogen Receptor alpha ; Estrogens ; Ligands ; DNA (9007-49-2)
    Language English
    Publishing date 2021-01-06
    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 10.1080/07391102.2020.1869094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2093: Show issues Location:
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  3. Article ; Online: Synthesis, molecular docking, ADMET evaluation and

    Guerrab, Walid / Akachar, Jihane / Jemli, Meryem El / Abudunia, Abdul-Malik / Ouaabou, Rachida / Alaoui, Katim / Ibrahimi, Azeddine / Ramli, Youssef

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 10, Page(s) 4592–4600

    Abstract: Hydantoins comprise an important class of compounds which have long attracted attention due to their remarkable biological and pharmacological properties including antitumor and antiviral activities. As a continuation of our studies on hydantoins ... ...

    Abstract Hydantoins comprise an important class of compounds which have long attracted attention due to their remarkable biological and pharmacological properties including antitumor and antiviral activities. As a continuation of our studies on hydantoins derivatives we report the successful synthesis of hydantoins derivatives. These synthesized compounds were evaluated for their cytotoxic activity against
    MeSH term(s) Animals ; Humans ; Chlorocebus aethiops ; Methotrexate/pharmacology ; Molecular Docking Simulation ; Phenytoin/pharmacology ; Vero Cells ; Structure-Activity Relationship ; Antineoplastic Agents/pharmacology ; Cell Line ; Rhabdomyosarcoma/drug therapy ; Drug Screening Assays, Antitumor ; Molecular Structure ; Cell Proliferation ; Cell Line, Tumor
    Chemical Substances Methotrexate (YL5FZ2Y5U1) ; Phenytoin (6158TKW0C5) ; Antineoplastic Agents
    Language English
    Publishing date 2022-05-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2022.2069865
    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:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2

    Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Belyamani, Lahcen / Ibrahimi, Azeddine

    3 Biotech. 2020 Nov., v. 10, no. 11

    2020  

    Abstract: SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ... ...

    Abstract SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an in silico approach to predict the potential animals range with high susceptibility to SARS-CoV-2 by modelling and studying the Spike–ACE2 interaction of 22 domestic and wild animals. Our results showed that all studied animals are potentially susceptible to SARS-CoV-2 infection with a slight difference in the binding affinity and stability of their ACE2–RBD complexes. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. These results may help to provide important insights into SARS-CoV-2 host range which will make it possible to control the spread of the virus and identify animal models that could be used for screening antiviral drugs or vaccine candidates against SARS-CoV-2.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; computer simulation ; histidine ; host range ; pneumonia ; tyrosine ; vaccines ; viruses
    Language English
    Dates of publication 2020-11
    Size p. 483.
    Publishing place Springer International Publishing
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-020-02471-3
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach

    Akachar, Jihane / Bouricha, El Mehdi / Hakmi, Mohammed / Belyamani, Lahcen / El Jaoudi, Rachid / Ibrahimi, Azeddine

    Heliyon. 2020 Dec., v. 6, no. 12 p.e05739-

    2020  

    Abstract: The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million ... ...

    Abstract The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antiviral properties ; bioavailability ; computer simulation ; epitopes ; humans ; molecular dynamics ; peptides ; vaccines ; Coronavirus 19 ; Molecular docking ; Peptide-based drugs ; Spike protein ; Cluster of differentiation ; Computer science ; Engineering ; Physics ; Chemistry ; Biological sciences
    Language English
    Dates of publication 2020-12
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Use and reproduction
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e05739
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: In silico

    Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Belyamani, Lahcen / Ibrahimi, Azeddine

    3 Biotech

    2020  Volume 10, Issue 11, Page(s) 483

    Abstract: SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ... ...

    Abstract SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an
    Keywords covid19
    Language English
    Publishing date 2020-10-21
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-020-02471-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  7. Article: Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an

    Akachar, Jihane / Bouricha, El Mehdi / Hakmi, Mohammed / Belyamani, Lahcen / El Jaoudi, Rachid / Ibrahimi, Azeddine

    Heliyon

    2020  Volume 6, Issue 12, Page(s) e05739

    Abstract: The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million ... ...

    Abstract The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
    Language English
    Publishing date 2020-12-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e05739
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2.

    Hakmi, Mohammed / Bouricha, E L Mehdi / Akachar, Jihane / Lmimouni, Badreddine / El Harti, Jaouad / Belyamani, Lahcen / Ibrahimi, Azeddine

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 4, Page(s) 1546–1557

    Abstract: The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development ... ...

    Abstract The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the virus entry into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 100
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; COVID-19 ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation, alpha-Helical ; SARS-CoV-2/drug effects ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Keywords covid19
    Language English
    Publishing date 2020-10-07
    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 10.1080/07391102.2020.1830175
    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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  9. Article ; Online: The displacement study of

    Chemlal, Laila / Akachar, Jihane / Makram, Sanaa / Zoubir, Brahim / Cherrah, Yahia / Eljaoudi, Rachid / Ibrahimi, Azeddine / Faouzi, Mly A

    IUBMB life

    2019  Volume 71, Issue 12, Page(s) 2003–2009

    Abstract: ... ...

    Abstract The
    MeSH term(s) Binding, Competitive ; Dialysis ; Furosemide/chemistry ; Furosemide/pharmacokinetics ; Humans ; Hydrogen Bonding ; Metformin/chemistry ; Metformin/pharmacokinetics ; Molecular Docking Simulation ; Serum Albumin, Human/chemistry ; Serum Albumin, Human/metabolism ; Technetium Tc 99m Pentetate/chemistry ; Technetium Tc 99m Pentetate/metabolism
    Chemical Substances Furosemide (7LXU5N7ZO5) ; Metformin (9100L32L2N) ; Technetium Tc 99m Pentetate (VW78417PU1) ; Serum Albumin, Human (ZIF514RVZR)
    Language English
    Publishing date 2019-10-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1492141-8
    ISSN 1521-6551 ; 1521-6543
    ISSN (online) 1521-6551
    ISSN 1521-6543
    DOI 10.1002/iub.2167
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Design, synthesis, structural and molecular characterization, toxicity, psychotropic activity and molecular docking evaluation of a novel phenytoin derivative: 3-decyl-5,5-diphenylimidazolidine-2,4-dione.

    Guerrab, Walid / El Jemli, Meryem / Akachar, Jihane / Demirtaş, Güneş / Mague, Joel T / Taoufik, Jamal / Ibrahimi, Azeddine / Ansar, M'Hammed / Alaoui, Katim / Ramli, Youssef

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 19, Page(s) 8765–8782

    Abstract: The hydantoin scaffold is of substantial importance and it is commonly used in drug discovery. Herein, we report the synthesis of a novel phenytoine (a hydantoin derivative) with high yield by the reaction of phenytoin with 1-bromodecyl agent. Namely, 3- ... ...

    Abstract The hydantoin scaffold is of substantial importance and it is commonly used in drug discovery. Herein, we report the synthesis of a novel phenytoine (a hydantoin derivative) with high yield by the reaction of phenytoin with 1-bromodecyl agent. Namely, 3-decyl-5,5- diphenylimidazolidine-2,4-dione (3DDID). The optimized geometry of the compound was calculated using density functional theory (DFT) method by B3LYP with 6-311++G(d,p) basis set. For this calculation, the X-ray data were used as initial values. Molecular electrostatic potential (MEP) surface and Frontier molecular orbitals (FOMs) were prepared for the compound. The crystal structure of the title compound contains intermolecular N-H···O, C-H···O hydrogen bonds and weak C-H···π interactions. Hirshfeld surface analysis and 2D fingerprint plots of the molecule aid comparison of intermolecular interactions and these analysis reveals that two close contacts are associated with intermolecular hydrogen bonds. The psychotropic activity evaluation of the synthesized compound was further explored using hole bored test for exploratory behaviors, dark//light box test for anxiolytic activity and Rota-road, traction, chimney testes were used to assess the myrelaxant effect. In addition, molecular modeling study was also conducted to rationalize the potential as neurotherapeutic drugs of our synthesized compound by predicting their binding modes, binding affinities and optimal orientation at the active site of the GABA-A receptor and Na
    Language English
    Publishing date 2021-05-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.1922096
    Database MEDical Literature Analysis and Retrieval System OnLINE

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