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  1. Article: In silico

    Ahmed, Milad / Ahmed, Foeaz / Ahmed, Jamil / Akhand, Mst Rubaiat Nazneen / Azim, Kazi Faizul / Imran, Md Abdus Shukur / Hoque, Syeda Farjana / Hasan, Mahmudul

    Heliyon

    2021  Volume 7, Issue 4, Page(s) e06705

    Abstract: Corchorus capsularis, ...

    Abstract Corchorus capsularis,
    Language English
    Publishing date 2021-04-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e06705
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Molecular detection and analysis of virulence genes in multi-drug resistant

    Azim, Kazi Faizul / Somana, Saneya Risa / Hasan, Md Kamrul / Foysal, Md Javed / Ali, Md Hazrat / Chowdhury, Tanjia Afrin / Hossain, Md Nazmul

    Veterinary research forum : an international quarterly journal

    2021  Volume 12, Issue 4, Page(s) 505–510

    Abstract: Escherichia ... ...

    Abstract Escherichia coli
    Language English
    Publishing date 2021-12-15
    Publishing country Iran
    Document type Journal Article
    ISSN 2008-8140
    ISSN 2008-8140
    DOI 10.30466/vrf.2020.115921.2762
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy.

    Banik, Anik / Ahmed, Sheikh Rashel / Sajib, Emran Hossain / Deb, Anamika / Sinha, Shiuly / Azim, Kazi Faizul

    Molecular diversity

    2021  Volume 26, Issue 5, Page(s) 2473–2502

    Abstract: The deeper understanding of metastasis phenomenon and detection of drug targets could be a potential approach to minimize cancer mortality. In this study, attempts were taken to unmask novel therapeutics to prevent metastasis and cancer progression. ... ...

    Abstract The deeper understanding of metastasis phenomenon and detection of drug targets could be a potential approach to minimize cancer mortality. In this study, attempts were taken to unmask novel therapeutics to prevent metastasis and cancer progression. Initially, we explored the physiochemical, structural and functional insights of three metastasis tumor antigens (MTAs) and evaluated some plant-based bioactive compounds as potent MTA inhibitors. From 50 plant metabolites screened, isoflavone, gingerol, citronellal and asiatic acid showed maximum binding affinity with all three MTA proteins. The ADME analysis detected no undesirable toxicity that could reduce the drug likeness properties of top plant metabolites. Moreover, molecular dynamics studies revealed that the complexes were stable and showed minimum fluctuation at molecular level. We further performed ligand-based virtual screening to identify similar drug molecules using a large collection of 376,342 compounds from DrugBank. The results suggested that several structural analogs (e.g., tramadol, nabumetone, DGLA and hydrocortisone) may act as agonist to block the MTA proteins and inhibit cancer progression at early stage. The study could be useful to develop effective medications against cancer metastasis in future. Due to encouraging results, we highly recommend further in vitro and in vivo trials for the experimental validation of the findings.
    MeSH term(s) Antigens, Neoplasm/therapeutic use ; Humans ; Hydrocortisone/therapeutic use ; Isoflavones/therapeutic use ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nabumetone ; Neoplasms/drug therapy ; Pemetrexed/therapeutic use ; Tramadol/therapeutic use
    Chemical Substances Antigens, Neoplasm ; Isoflavones ; Ligands ; Pemetrexed (04Q9AIZ7NO) ; Tramadol (39J1LGJ30J) ; Nabumetone (LW0TIW155Z) ; Hydrocortisone (WI4X0X7BPJ)
    Language English
    Publishing date 2021-11-07
    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/s11030-021-10345-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Proteome Exploration of

    Khan, Md Tahsin / Mahmud, Araf / Hasan, Mahmudul / Azim, Kazi Faizul / Begum, Musammat Kulsuma / Rolin, Mohimenul Haque / Akter, Arzuba / Mondal, Shakhinur Islam

    Microbiology spectrum

    2022  Volume 10, Issue 4, Page(s) e0037322

    Abstract: Legionella pneumophila is the causative agent of a severe type of pneumonia (lung infection) called Legionnaires' disease. It is emerging as an antibiotic-resistant strain day by day. Hence, identifying novel drug targets and vaccine candidates is ... ...

    Abstract Legionella pneumophila is the causative agent of a severe type of pneumonia (lung infection) called Legionnaires' disease. It is emerging as an antibiotic-resistant strain day by day. Hence, identifying novel drug targets and vaccine candidates is essential to fight against this pathogen. Here, attempts were taken through a subtractive genomics approach on the complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total of 2,930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human nonhomologous and pathogen-specific essential proteins, druggability and "anti-target" analysis, subcellular localization prediction, human microbiome nonhomology screening, and protein-protein interaction studies to find out effective drug and vaccine targets. Only three fulfilled these criteria and were proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as a potential vaccine target with a better antigenicity score. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis, and a molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes, along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different major histocompatibility complex (MHC) molecules and human immune TLR-2 receptors with minimum deformability at the molecular level. The present study aids the development of novel therapeutics and vaccine candidates for efficient treatment and prevention of L. pneumophila infections. However, further wet-lab-based phenotypic and genomic investigations and
    MeSH term(s) Anti-Bacterial Agents ; Epitopes ; Genomics ; Humans ; Legionella pneumophila/genetics ; Legionnaires' Disease/drug therapy ; Legionnaires' Disease/prevention & control ; Molecular Docking Simulation ; Proteome ; Toll-Like Receptor 2 ; Vaccinology
    Chemical Substances Anti-Bacterial Agents ; Epitopes ; Proteome ; Toll-Like Receptor 2
    Language English
    Publishing date 2022-07-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00373-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family

    Azim, Kazi Faizul / Lasker, Tahera / Akter, Rahima / Hia, Mantasha Mahmud / Bhuiyan, Omar Faruk / Hasan, Mahmudul / Hossain, Md Nazmul

    Heliyon. 2021 May, v. 7, no. 5

    2021  

    Abstract: Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, ...

    Abstract Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, the study was employed to design a highly immunogenic cross-reactive vaccine against Arenaviridae family using reverse vaccinology approach. The whole proteome of Lassa virus (LASV), Lymphocytic Choriomeningitis virus (LCMV), Lujo virus and Guanarito virus were retrieved and assessed to determine the most antigenic viral proteins. Both T-cell and B-cell epitopes were predicted and screened based on transmembrane topology, antigenicity, allergenicity, toxicity and molecular docking analysis. The final constructs were designed using different adjuvants, top epitopes, PADRE sequence and respective linkers and were assessed for the efficacy, safety, stability and molecular cloning purposes. The proposed epitopes were highly conserved (84%–100%) and showed greater cumulative population coverage. Moreover, T cell epitope GWPYIGSRS was conserved in Junin virus (Argentine mammarenavirus) and Sabia virus (Brazilian mammarenavirus), while B cell epitope NLLYKICLSG was conserved in Machupo virus (Bolivian mammarenavirus) and Sabia virus, indicating the possibility of final vaccine construct to confer a broad range immunity in the host. Docking analysis of the refined vaccine with different MHC molecules and human immune receptors were biologically significant. The vaccine-receptor (V1-TLR3) complex showed minimal deformability at molecular level and was compatible for cloning into pET28a(+) vector of E. coli strain K12. The study could be helpful in developing vaccine to combat arenaviral infections in the future. However, further in vitro and in vivo trials using model animals are highly recommended for the experimental validation of our findings.
    Keywords Argentinian mammarenavirus ; B-lymphocytes ; Brazilian mammarenavirus ; Escherichia coli ; Guanarito mammarenavirus ; Lassa mammarenavirus ; Lymphocytic choriomeningitis mammarenavirus ; Machupo mammarenavirus ; T-lymphocytes ; allergenicity ; epitopes ; humans ; immunity ; nucleoproteins ; proteome ; therapeutics ; topology ; toxicity ; vaccine development ; vaccines ; viruses
    Language English
    Dates of publication 2021-05
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e07022
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Genomic attributes and recent advances in detection of white spot syndrome virus in shrimp: a review

    Hossain, Md Nazmul / Chowdhury, Tanjia Afrin / Hasan, Mahmudul / Azim, Kazi Faizul / Jenny, Sayadatunnasa / Rabbee, Muhammad Fazie / Rahman, Md. Mahbubur / Somana, Saneya Risa

    Marine biology research

    2021  Volume 17, Issue 9/10, Page(s) 794

    Language English
    Document type Article
    ZDB-ID 2168764-X
    ISSN 1745-1000
    Database Current Contents Nutrition, Environment, Agriculture

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  7. Book ; Online: Screening and Druggability Analysis of Some Plant Metabolites Against SARS-CoV-2

    Kazi Faizul Azim / Sheikh Rashel Ahmed / Anik Banik / Md. Mostafigur Rahman Khan / Anamika Deb

    2020  

    Abstract: The sudden outbreak of novel corona virus at the end of 2019 has caused a global threat to mankind due to its extreme infection rate and mortality. Despite extensive research, still there is no an approved drug or vaccine to combat SARS-CoV-2 infections. ...

    Abstract The sudden outbreak of novel corona virus at the end of 2019 has caused a global threat to mankind due to its extreme infection rate and mortality. Despite extensive research, still there is no an approved drug or vaccine to combat SARS-CoV-2 infections. Hence, the study was designed to evaluate some plant-based active compounds for drug candidacy against SARS-CoV-2 by using virtual screening methods and various computational analysis. A total of 27 plant metabolites were screened against SARS-Cov-2 main protease proteins (MPP), Nsp9 RNA binding protein, spike receptor binding domain, spike ecto-domain and HR2 domain using molecular docking approach. Four metabolites i.e. asiatic acid, avicularin, guajaverin and withaferin showed maximum binding affinity with all key proteins in terms of lowest global binding energy. The top candidates were further employed for ADME ( absorption , distribution , metabolism , and excretion ) analysis to investigate their drug profiles. Results suggest that none of the compounds render any undesirable consequences that could reduce their drug likeness properties. The analysis of toxicity pattern revealed no significant tumorigenic, mutagenic, irritating or reproductive effects by the compounds. However, witheferin was comparatively toxic among the top four candidates with considerable cytotoxicity and immunotoxicity. Most of the target class by top drug candidates belonged to enzyme groups (e.g. oxidoreductases hydrolases, phosphatases). Moreover, results of drug similarity prediction identified two approved structural analogs of Asiatic acid from DrugBank, Hydrocortisone (DB00741) (previously used for SARS-CoV-1 and MERS) and Dinoprost-tromethamine (DB01160). In addition, two other biologically active compounds, Mupirocin (DB00410) and Simvastatin (DB00641) could be an alternative choice to witheferin for the treatment of viral infections. The study may pave the way to develop effective medications and preventive measure against SARS-CoV-2 in the future. However, the results were based solely on computational tools and algorithms. Due to the encouraging results, we highly recommend further in vivo trials for the experimental validation of our findings.
    Keywords Bioinformatics and Computational Biology ; SARS-CoV-2 ; Plant Metabolites ; main protease proteins ; molecular docking ; ADME analysis ; drug target ; covid19
    Subject code 540
    Publishing date 2020-05-05T12:30:08Z
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family.

    Azim, Kazi Faizul / Lasker, Tahera / Akter, Rahima / Hia, Mantasha Mahmud / Bhuiyan, Omar Faruk / Hasan, Mahmudul / Hossain, Md Nazmul

    Heliyon

    2021  Volume 7, Issue 5, Page(s) e07022

    Abstract: Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, ...

    Abstract Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, the study was employed to design a highly immunogenic cross-reactive vaccine against Arenaviridae family using reverse vaccinology approach. The whole proteome of Lassa virus (LASV), Lymphocytic Choriomeningitis virus (LCMV), Lujo virus and Guanarito virus were retrieved and assessed to determine the most antigenic viral proteins. Both T-cell and B-cell epitopes were predicted and screened based on transmembrane topology, antigenicity, allergenicity, toxicity and molecular docking analysis. The final constructs were designed using different adjuvants, top epitopes, PADRE sequence and respective linkers and were assessed for the efficacy, safety, stability and molecular cloning purposes. The proposed epitopes were highly conserved (84%-100%) and showed greater cumulative population coverage. Moreover, T cell epitope GWPYIGSRS was conserved in Junin virus (Argentine mammarenavirus) and Sabia virus (Brazilian mammarenavirus), while B cell epitope NLLYKICLSG was conserved in Machupo virus (Bolivian mammarenavirus) and Sabia virus, indicating the possibility of final vaccine construct to confer a broad range immunity in the host. Docking analysis of the refined vaccine with different MHC molecules and human immune receptors were biologically significant. The vaccine-receptor (V1-TLR3) complex showed minimal deformability at molecular level and was compatible for cloning into pET28a(+) vector of
    Language English
    Publishing date 2021-05-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e07022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Identification and host response interaction study of SARS-CoV-2 encoded miRNA-like sequences: an in silico approach.

    Roy, Sawrab / Sharma, Binayok / Mazid, Md Ishtiaque / Akhand, Rubaiat Nazneen / Das, Moumita / Marufatuzzahan, Marufatuzzahan / Chowdhury, Tanjia Afrin / Azim, Kazi Faizul / Hasan, Mahmudul

    Computers in biology and medicine

    2021  Volume 134, Page(s) 104451

    Abstract: COVID-19, a global pandemic caused by an RNA virus named SARS-CoV-2 has brought the world to a standstill in terms of infectivity, casualty, and commercial plummet. RNA viruses can encode microRNAs (miRNAs) capable of modulating host gene expression, and ...

    Abstract COVID-19, a global pandemic caused by an RNA virus named SARS-CoV-2 has brought the world to a standstill in terms of infectivity, casualty, and commercial plummet. RNA viruses can encode microRNAs (miRNAs) capable of modulating host gene expression, and with that notion, we aimed to predict viral miRNA like sequences of MERS-CoV, SARS-CoV and SARS-CoV-2, analyze sequence reciprocity and investigate SARS-CoV-2 encoded potential miRNA-human genes interaction using bioinformatics tools. In this study, we retrieved 206 SARS-CoV-2 genomes, executed phylogenetic analysis, and the selected reference genome (MT434792.1) exhibited about 99% similarities among the retrieved genomes. We predicted 402, 137, and 85 putative miRNAs of MERS-CoV (NC_019843.3), SARS-CoV (NC_004718.3), and SARS-CoV-2 (MT434792.1) genome, respectively. Sequence similarity was analyzed among 624 miRNAs which revealed that the predicted miRNAs of SARS-CoV-2 share a cluster with the clad of miRNAs from MERS-CoV and SARS-CoV. Only SARS-CoV-2 derived 85 miRNAs were encountered for target prediction and 29 viral miRNAs seemed to target 119 human genes. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis suggested the involvement of respective genes in various pathways and biological processes. Finally, we focused on eight putative miRNAs influencing 14 genes that are involved in the adaptive hypoxic response, neuroinvasion and hormonal regulation, and tumorigenic progression in patients with COVID-19. SARS-CoV-2 encoded miRNAs may cause misexpression of some critical regulators and facilitate viral neuroinvasion, altered hormonal axis, and tumorigenic events in the human host. However, these propositions need validation from future studies.
    Language English
    Publishing date 2021-04-27
    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.2021.104451
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Major Insights in Dynamics of Host Response to SARS-CoV-2: Impacts and Challenges.

    Hakim, Al / Hasan, Md Mahbub / Hasan, Mahmudul / Lokman, Syed Mohammad / Azim, Kazi Faizul / Raihan, Topu / Chowdhury, Parveen Afroz / Azad, Abul Kalam

    Frontiers in microbiology

    2021  Volume 12, Page(s) 637554

    Abstract: The coronavirus disease 2019 (COVID-19), a pandemic declared by the World Health Organization on March 11, 2020, is caused by the infection of highly transmissible species of a novel coronavirus called severe acute respiratory syndrome coronavirus-2 ( ... ...

    Abstract The coronavirus disease 2019 (COVID-19), a pandemic declared by the World Health Organization on March 11, 2020, is caused by the infection of highly transmissible species of a novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). As of July 25, 2021, there are 194,372,584 cases and 4,167,937 deaths with high variability in clinical manifestations, disease burden, and post-disease complications among different people around the globe. Overall, COVID-19 is manifested as mild to moderate in almost 90% of the cases and only the rest 10% of the cases need hospitalization. However, patients with older age and those having different comorbidities have made worst the pandemic scenario. The variability of pathological consequences and clinical manifestations of COVID-19 is associated with differential host-SARS-CoV-2 interactions, which are influenced by the factors that originated from the SARS-CoV-2 and the host. These factors usually include the genomic attributes and virulent factors of the SARS-CoV-2, the burden of coinfection with other viruses and bacteria, age and gender of the individuals, different comorbidities, immune suppressions/deficiency, genotypes of major histocompatibility complex, and blood group antigens and antibodies. We herein retrieved and reviewed literatures from PubMed, Scopus, and Google relevant to clinical complications and pathogenesis of COVID-19 among people of different age, sex, and geographical locations; genomic characteristics of SARS-CoV-2 including its variants, host response under different variables, and comorbidities to summarize the dynamics of the host response to SARS-CoV-2 infection; and host response toward approved vaccines and treatment strategies against COVID-19. After reviewing a large number of published articles covering different aspects of host response to SARS-CoV-2, it is clear that one aspect from one region is not working with the scenario same to others, as studies have been done separately with a very small number of cases from a particular area/region of a country. Importantly, to combat such a pandemic as COVID-19, a conclusive understanding of the disease dynamics is required. This review emphasizes on the identification of the factors influencing the dynamics of host responses to SARS-CoV-2 and offers a future perspective to explore the molecular insights of COVID-19.
    Language English
    Publishing date 2021-08-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.637554
    Database MEDical Literature Analysis and Retrieval System OnLINE

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