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  1. Article: Views on Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease by Dai et al. (2020).

    Odhar, Hasanain Abdulhameed

    Bioinformation

    2020  Volume 16, Issue 5, Page(s) 435–437

    Keywords covid19
    Language English
    Publishing date 2020-05-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630016435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Molecular docking and dynamics simulation analysis of the human FXIIa with compounds from the Mcule database.

    Odhar, Hasanain Abdulhameed / Hashim, Ahmed Fadhil / Ahjel, Salam Waheed / Humadi, Suhad Sami

    Bioinformation

    2023  Volume 19, Issue 2, Page(s) 160–166

    Abstract: The human factor XIIa is a serine protease enzyme that is implicated in the pathological thrombosis. This coagulation factor represents an interesting molecular target to design safer antithrombotic agents without adversely influencing physiological ... ...

    Abstract The human factor XIIa is a serine protease enzyme that is implicated in the pathological thrombosis. This coagulation factor represents an interesting molecular target to design safer antithrombotic agents without adversely influencing physiological hemostasis. Therefore, it is of interest to virtually screen the human factor XIIa crystal with millions of compounds in Mcule database in order to identify potential inhibitors. For this purpose, both molecular docking and dynamics simulation were employed to identify potential hits. Also, various predictive approaches were utilized to estimate chemical, pharmacokinetics and toxicological features for the top hits. As such, we report here that compound 4 (1-(4-benzylpiperazin-1-yl)-2-[5-(3,5-dimethylpyrazol-1-yl)-1,2,3, 4-tetrazol-2-yl]ethanone) may be a potential ligand against the human factor XIIa for further consideration in the design and development of novel antithrombotic agents.
    Language English
    Publishing date 2023-02-28
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630019160
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Molecular docking and dynamics simulation analysis of nucleoprotein from the Crimea-Congo hemorrhagic fever virus strain Baghdad-12 with FDA approved drugs.

    Hashim, Ahmed Fadhil / Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed

    Bioinformation

    2022  Volume 18, Issue 5, Page(s) 442–449

    Abstract: Crimea-Congo hemorrhagic fever virus is considered a potential public health threat due to the high case fatality ratio of the disease hemorrhagic phase and absence of approved vaccines or antiviral agents. Therefore, it is of interest to screen FDA ... ...

    Abstract Crimea-Congo hemorrhagic fever virus is considered a potential public health threat due to the high case fatality ratio of the disease hemorrhagic phase and absence of approved vaccines or antiviral agents. Therefore, it is of interest to screen FDA approved drugs against the nucleoprotein crystal of Crimea-Congo hemorrhagic fever virus strain Baghdad-12 by using molecular docking and dynamics simulation. Hence, we report that the beta receptor blocker Nebivolol and the antihistamine Loratadine may bind to RNA binding region on nucleoprotein for further consideration in drug design and development.
    Language English
    Publishing date 2022-05-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630018442
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Towards the design of epitope candidates for Coronavirus 2.

    Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed / Humadi, Suhad Sami

    Bioinformation

    2020  Volume 16, Issue 5, Page(s) 375–386

    Abstract: The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress ... ...

    Abstract The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress into acute respiratory distress syndrome especially in elderly patients with comorbidities. Therefore, it is of interest to design and develop candidates for treatment, therapy and prevention. The spike glycoprotein of the virus known to potentially interact with angiotensin converting enzyme 2 as a cell entry receptor is a suitable candidate for further consideration as vaccine and treatment candidate. Hence, we screened the spike protein of coronavirus-2 for potential B-cell and T-cell epitopes for further deliberation. Thus, we document several peptides on the spike protein with predicted high antigenicity, low allergenicity and good stability against selected proteases. The linear B-cell epitope with sequence 'GFNCYFPLQSYGF' is of particular interest in this context towards the design and development of short peptide vaccine candidates for combat and care against the virus.
    Keywords covid19
    Language English
    Publishing date 2020-05-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630016375
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: Potential Trends for COVID-19 Fighting

    Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed

    An Immuno-informatics Overview

    2020  

    Abstract: Public health care capacity is currently overwhelmed by pandemic outbreak of coronavirus disease 2019. This respiratory disease is a real threat especially for those elderly people with comorbidities. The disease can progress into acute respiratory ... ...

    Abstract Public health care capacity is currently overwhelmed by pandemic outbreak of coronavirus disease 2019. This respiratory disease is a real threat especially for those elderly people with comorbidities. The disease can progress into acute respiratory distress syndrome which can be fatal. No vaccine or drug had been developed against any human coronaviruses due to cessation of previous epidemics and withdrawal of assigned funds. Currently, humanity is in a real challenge to accelerate the development of effective drug and vaccine against severe acute respiratory syndrome coronavirus 2. Till now, computational approaches have played a substantial role for analysis of viral structure and also development of both drug and vaccine candidates in an accelerated pace. Some of these therapeutic designs have found their way into clinical trials. Here, we will overview different immuno-informatics attempts, targets and ideas as possible trends to counteract coronavirus disease 2019.
    Keywords covid19
    Publisher Center for Open Science
    Publishing country us
    Document type Book ; Online
    DOI 10.31219/osf.io/d63mp
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article ; Online: Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2

    Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed / Humadi, Suhad Sami

    bioRxiv

    Abstract: Coronavirus disease 2019 is a current pandemic health threat especially for elderly patients with comorbidities. This respiratory disease is caused by a beta coronavirus known as severe acute respiratory syndrome coronavirus 2. The disease can progress ... ...

    Abstract Coronavirus disease 2019 is a current pandemic health threat especially for elderly patients with comorbidities. This respiratory disease is caused by a beta coronavirus known as severe acute respiratory syndrome coronavirus 2. The disease can progress into acute respiratory distress syndrome that can be fatal. Currently, no specific drug or vaccine are available to combat this pandemic outbreak. Social distancing and lockdown have been enforced in many places worldwide. The spike protein of coronavirus 2 is essential for viral entry into host target cells via interaction with angiotensin converting enzyme 2. This viral protein is considered a potential target for design and development of a drug or vaccine. Previously, we have reported several potential epitopes on coronavirus 2 spike protein with high antigenicity, low allergenicity and good stability against specified proteases. In the current study, we have constructed and evaluated a peptide vaccine from these potential epitopes by using in silico approach. This construct is predicted to have a protective immunogenicity, low allergenicity and good stability with minor structural flaws in model build. The population coverage of the used T-cells epitopes is believed to be high according to the employed restricted alleles. The vaccine construct can elicit efficient and long-lasting immune response as appeared through simulation analysis. This multiepitope-based peptide vaccine may represent a potential candidate against coronavirus 2. However, further in vitro and in vivo verification are required.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.07.07.186122
    Database COVID19

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    Inter-library loan at ZB MED

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  8. Article: Towards the design of epitope candidates for Coronavirus 2

    Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed / Humadi, Suhad Sami

    Bioinformation

    Abstract: The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress ... ...

    Abstract The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress into acute respiratory distress syndrome especially in elderly patients with comorbidities. Therefore, it is of interest to design and develop candidates for treatment, therapy and prevention. The spike glycoprotein of the virus known to potentially interact with angiotensin converting enzyme 2 as a cell entry receptor is a suitable candidate for further consideration as vaccine and treatment candidate. Hence, we screened the spike protein of coronavirus-2 for potential B-cell and T-cell epitopes for further deliberation. Thus, we document several peptides on the spike protein with predicted high antigenicity, low allergenicity and good stability against selected proteases. The linear B-cell epitope with sequence 'GFNCYFPLQSYGF' is of particular interest in this context towards the design and development of short peptide vaccine candidates for combat and care against the virus.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #729740
    Database COVID19

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    Inter-library loan at ZB MED

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  9. Article: Molecular docking enabled updated screening of the matrix protein VP40 from Ebola virus with millions of compounds in the MCULE database for potential inhibitors.

    Odhar, Hasanain Abdulhameed / Rayshan, Ali Mahmood / Ahjel, Salam Waheed / Hashim, Alaa Abduljabbar / Albeer, Ali A Mohammed Ali

    Bioinformation

    2019  Volume 15, Issue 9, Page(s) 627–632

    Abstract: Ebola virus is known for several outbreaks of hemorrhagic fever in West Africa. This RNA virus is linked to high fatality and easy transmission. Recently, an effective vaccine and a monoclonal antibody cocktail have been introduced to combat Ebola virus ... ...

    Abstract Ebola virus is known for several outbreaks of hemorrhagic fever in West Africa. This RNA virus is linked to high fatality and easy transmission. Recently, an effective vaccine and a monoclonal antibody cocktail have been introduced to combat Ebola virus infection. The matrix protein VP40 of Ebola virus is a known drug target and it is essential for viral life cycle through participation in RNA transcription as well as for the budding of the mature virus. It is known that residues phenylalanine 125 and arginine 134 of VP40 are involved in the interaction with RNA. Therefore, it is of interest to screen VP40 with millions of compounds at the mcule.com database for potential inhibitors. The output hits were ranked according to their minimum binding energy to matrix protein VP40. We further calculated the pharmacokinetics and toxicology properties for the best five hits using several predictive ADME analysis web tools. We report a candidate lead (compound #5: ((10R)-10-(4-hydroxyphenyl)-11,12,14,16-tetraazatetracyclo[7.7.0.02,7.011,15] hexadeca-1(16), 2(7),3,5,8,12,14-heptaen-8-ol)) with high drug-likeness score, promising lead-likeness behaviour and high median lethal dose. The candidate lead compound #5 engages in hydrogen bonding and hydrophobic interactions with VP40 active site residues. Thus, the lead compound #5 is recommended for further in vitro and in vivo validations for further consideration.
    Language English
    Publishing date 2019-10-08
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630015627
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus.

    Odhar, Hasanain Abdulhameed / Ahjel, Salam Waheed / Albeer, Ali A Mohammed Ali / Hashim, Ahmed Fadhil / Rayshan, Ali Mahmood / Humadi, Suhad Sami

    Bioinformation

    2020  Volume 16, Issue 3, Page(s) 236–244

    Abstract: Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having ... ...

    Abstract Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding pocket of main protease during simulation. However, these data need further in vitro and in vivo evaluation to repurpose these two drugs against 2019-nCoV.
    Keywords covid19
    Language English
    Publishing date 2020-03-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630016236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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