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  1. Article ; Online: A Molecular Generative Model of COVID-19 Main Protease Inhibitors Using Long Short-Term Memory-Based Recurrent Neural Network.

    Mehrzadi, Arash / Rezaee, Elham / Gharaghani, Sajjad / Fakhar, Zeynab / Mirhosseini, Seyed Mohsen

    Journal of computational biology : a journal of computational molecular cell biology

    2023  Volume 31, Issue 1, Page(s) 83–98

    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19 ; Molecular Docking Simulation ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; Protease Inhibitors/chemistry ; Memory, Short-Term ; Molecular Dynamics Simulation ; Neural Networks, Computer
    Chemical Substances Protease Inhibitors
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2023.0064
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes.

    Khan, Shama / Fakhar, Zeynab / Ahmad, Aijaz

    Journal of molecular modeling

    2021  Volume 27, Issue 2, Page(s) 49

    Abstract: Ebola filovirus (EBOV) is one of the deadliest known infectious agents, and a cause of Western African epidemics from 2013 to 2016. The virus has infected nearly 3000 humans and almost 1900 have died. In the past few years, various small molecules have ... ...

    Abstract Ebola filovirus (EBOV) is one of the deadliest known infectious agents, and a cause of Western African epidemics from 2013 to 2016. The virus has infected nearly 3000 humans and almost 1900 have died. In the past few years, various small molecules have been discovered to display efficiency against EBOV and some of them have progressed towards clinical trials. Even though continuous attempts have been made to find antiEBOV therapeutics, no potential drugs are yet approved against this viral infection. The development of small antiviral inhibitors has gained tremendous attention in the attempt to overcome EVD. With this background, we seek to offer molecular insights into EBOV VP40 protein inhibition, using all atom molecular mechanics methodology and binding free energy calculations. We have selected five novel reported inhibitors against VP40 protein, namely Comp1, Comp2, Comp3, Comp4, and Comp5, and explored their binding against the same target. It was evident from the analysis that all the inhibitors displayed stability in complex with VP40 protein; however, Comp1 exhibited enhanced stability and compactness. Comp1 unveiled favorable binding, which accounted for positive correlation motions in the active site residues. Likewise, Comp1 revealed the most promising binding (ΔG
    MeSH term(s) Amino Acids/metabolism ; Humans ; Inhibitory Concentration 50 ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nucleoproteins/antagonists & inhibitors ; Nucleoproteins/chemistry ; Protein Stability ; RNA/chemistry ; RNA/metabolism ; Thermodynamics ; Viral Core Proteins/antagonists & inhibitors ; Viral Core Proteins/chemistry
    Chemical Substances Amino Acids ; Ligands ; Nucleoproteins ; Viral Core Proteins ; nucleoprotein VP40, Ebola virus ; RNA (63231-63-0)
    Language English
    Publishing date 2021-01-25
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-021-04682-8
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  3. Article ; Online: Discovery of novel heterocyclic amide-based inhibitors: an integrative

    Fakhar, Zeynab / Hejazi, Leila / Tabatabai, Sayyed Abbas / Munro, Orde Q

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 15, Page(s) 7114–7128

    Abstract: Inhibition of soluble epoxide hydrolase (sEH) is considered as an emerging druggable target to reduce blood pressure, improve insulin sensitivity, and decrease inflammation. Despite the availability of different classes of sEH small molecule inhibitors ... ...

    Abstract Inhibition of soluble epoxide hydrolase (sEH) is considered as an emerging druggable target to reduce blood pressure, improve insulin sensitivity, and decrease inflammation. Despite the availability of different classes of sEH small molecule inhibitors for the potential treatment of hypertension, only a few candidates have reached clinical trials, making the optimal control of blood pressure presently unattainable. This necessity motivated us to explore a series of novel quinazoline-4(3
    MeSH term(s) Amides/chemistry ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Epoxide Hydrolases ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Quinazolines ; Solubility
    Chemical Substances Amides ; Enzyme Inhibitors ; Quinazolines ; Epoxide Hydrolases (EC 3.3.2.-)
    Language English
    Publishing date 2021-03-02
    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 10.1080/07391102.2021.1894987
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Synthesis, Docking Study and Biological Evaluation of Amide-Based Soluble Epoxide Hydrolase Inhibitors with Novel Secondary Pharmacophore of Pyrimidin-2-ol.

    Hejazi, Leila / Ebadi, Abraham / Fakhar, Zeynab / Nazari, Maryam / Rezaee, Elham / Abbas Tabatabai, Sayyed

    Chemistry & biodiversity

    2022  Volume 19, Issue 11, Page(s) e202200231

    Abstract: Soluble epoxide hydrolase enzyme (sEH) is one of the most promising and emerging targets to develop drugs for multiple disease indications, including hypertension, diabetes, stroke, dyslipidemia, pain, etc. Most inhibitor scaffolds have a urea or amide ... ...

    Abstract Soluble epoxide hydrolase enzyme (sEH) is one of the most promising and emerging targets to develop drugs for multiple disease indications, including hypertension, diabetes, stroke, dyslipidemia, pain, etc. Most inhibitor scaffolds have a urea or amide moiety to mimic the active-site transition state. In this regard, we developed a series of amide sEH inhibitors with a pyrimidin-2-ol ring as a new secondary pharmacophore, which was subjected to in vitro evaluation. Compound 4w (4-chloro-N-{4-[6-(4-chlorophenyl)-2-hydroxypyrimidin-4-yl]phenyl}benzamide), which contains 4-chloro substituent in both terminal phenyl rings, exhibited the most inhibitory activity against sEH with an IC
    MeSH term(s) Epoxide Hydrolases/chemistry ; Epoxide Hydrolases/metabolism ; Amides/pharmacology ; Amides/chemistry ; Molecular Docking Simulation ; Structure-Activity Relationship ; Urea/pharmacology ; Urea/chemistry ; Enzyme Inhibitors/chemistry ; Solubility
    Chemical Substances Epoxide Hydrolases (EC 3.3.2.-) ; Amides ; Urea (8W8T17847W) ; Enzyme Inhibitors
    Language English
    Publishing date 2022-10-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2139001-0
    ISSN 1612-1880 ; 1612-1872
    ISSN (online) 1612-1880
    ISSN 1612-1872
    DOI 10.1002/cbdv.202200231
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  5. Article ; Online: Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic.

    Fakhar, Zeynab / Faramarzi, Bahar / Pacifico, Severina / Faramarzi, Shadab

    Journal of biomolecular structure & dynamics

    2020  Volume 39, Issue 16, Page(s) 6171–6183

    Abstract: A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To treat the patients with coronavirus disease (COVID-19), currently no effective ... ...

    Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To treat the patients with coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds based natural products targeting main protease (M
    MeSH term(s) Anthocyanins ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19 ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pandemics ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2
    Chemical Substances Anthocyanins ; Antiviral Agents ; Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
    Keywords covid19
    Language English
    Publishing date 2020-08-03
    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 10.1080/07391102.2020.1801510
    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)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article: Investigating the Antituberculosis Activity of Selected Commercial Essential Oils and Identification of Active Constituents Using a Biochemometrics Approach and In Silico Modeling.

    Boussamba-Digombou, Katyna J / Sandasi, Maxleene / Kamatou, Guy P / van Vuuren, Sandy / Sawicki, Rafal / Fakhar, Zeynab / Viljoen, Alvaro M

    Antibiotics (Basel, Switzerland)

    2022  Volume 11, Issue 7

    Abstract: Tuberculosis (TB) is a disease caused ... ...

    Abstract Tuberculosis (TB) is a disease caused by
    Language English
    Publishing date 2022-07-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics11070948
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  7. Article ; Online: Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease

    Fakhar, Zeynab / Faramarzi, Bahar / Pacifico, Severina / Faramarzi, Shadab

    Journal of Biomolecular Structure and Dynamics

    An in-silico perspective of therapeutic targets against COVID-19 pandemic

    2020  , Page(s) 1–13

    Keywords Molecular Biology ; Structural Biology ; General Medicine ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1801510
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19.

    Fakhar, Zeynab / Khan, Shama / AlOmar, Suliman Y / Alkhuriji, Afrah / Ahmad, Aijaz

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 234

    Abstract: A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine ... ...

    Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds by considering drug repurposing approach targeting main protease (M
    MeSH term(s) Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/virology ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; Protein Binding ; Pyridines/pharmacology ; Pyridines/therapeutic use ; Pyrroles/pharmacology ; Pyrroles/therapeutic use ; SARS-CoV-2/drug effects ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Protease Inhibitors ; Pyridines ; Pyrroles ; ABBV-744 (9MX546E2SF)
    Language English
    Publishing date 2021-01-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-79918-3
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  9. Article ; Online: ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19

    Zeynab Fakhar / Shama Khan / Suliman Y. AlOmar / Afrah Alkhuriji / Aijaz Ahmad

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or ...

    Abstract Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds by considering drug repurposing approach targeting main protease (Mpro) enzyme of SARS-CoV-2. This enzyme considered to be an attractive drug target as it contributes significantly in mediating viral replication and transcription. Herein, comprehensive computational investigations were performed to identify potential inhibitors of SARS-CoV-2 Mpro enzyme. The structure-based pharmacophore modeling was developed based on the co-crystallized structure of the enzyme with its biological active inhibitor. The generated hypotheses were applied for virtual screening based PhaseScore. Docking based virtual screening workflow was used to generate hit compounds using HTVS, SP and XP based Glide GScore. The pharmacological and physicochemical properties of the selected lead compounds were characterized using ADMET. Molecular dynamics simulations were performed to explore the binding affinities of the considered lead compounds. Binding energies revealed that compound ABBV-744 binds to the Mpro with strong affinity (ΔG bind −45.43 kcal/mol), and the complex is more stable in comparison with other protein–ligand complexes. Our study classified three best compounds which could be considered as promising inhibitors against main protease SARS-CoV-2 virus.
    Keywords Medicine ; R ; Science ; Q
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic

    Fakhar, Zeynab / Faramarzi, Bahar / Pacifico, Severina / Faramarzi, Shadab

    J Biomol Struct Dyn

    Abstract: A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To treat the patients with coronavirus disease (COVID-19), currently no effective ... ...

    Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To treat the patients with coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds based natural products targeting main protease (Mpro) enzyme of SARS-CoV-2. The Mpro enzyme plays a key role in mediating viral replication and transcription and thus being considered as an attractive drug target. Herein, comprehensive computational investigations were performed to identify new lead compounds against main protease enzyme. In this study, the candidate anthocyanin-derived compounds from PubChem database were filtered considering antiviral characteristics of anthocyanins. The structure-based pharmacophore modeling was developed based on the co-crystallized structure of the enzyme with its biological active inhibitor. The generated hypotheses were applied for virtual screening-based PHASE Screen Score. Docking based virtual screening work flow was used to generate hit compounds using HTVS, SP and XP based Glide Gscore. The obtained hit compounds were filtered using ADMET pharmacological and physicochemical properties screening. Molecular dynamics simulations were performed to explore the binding affinities of the considered compounds. Our study identified six best anthocyanin-derived natural compounds which could be used as promising lead compounds against main protease SARS-CoV-2 virus. Communicated by Ramaswamy H. Sarma.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #691959
    Database COVID19

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