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  1. Article: Subtractive genomics study for the identification of therapeutic targets against

    Ahammad, Ishtiaque / Bushra Lamisa, Anika / Sharmin, Sadia / Bhattacharjee, Arittra / Mahmud Chowdhury, Zeshan / Ahamed, Tanvir / Uzzal Hossain, Mohammad / Chandra Das, Keshob / Salimullah, Md / Ara Keya, Chaman

    Heliyon

    2024  Volume 10, Issue 9, Page(s) e30332

    Abstract: Cronobacter ... ...

    Abstract Cronobacter sakazakii
    Language English
    Publishing date 2024-04-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e30332
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice.

    Ahammad, Ishtiaque / Jamal, Tabassum Binte / Lamisa, Anika Bushra / Bhattacharjee, Arittra / Zinan, Nayeematul / Hasan Chowdhury, Md Zahid / Naimul Islam, Shah Mohammad / Faruque, Kazi Md Omar / Mahmud Chowdhury, Zeshan / Uzzal Hossain, Mohammad / Chandra Das, Keshob / Ara Keya, Chaman / Salimullah, Md

    Journal, genetic engineering & biotechnology

    2024  Volume 22, Issue 1, Page(s) 100353

    Abstract: Background: Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental ...

    Abstract Background: Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against X. oryzae pv. oryzae, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants.
    Results: The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in Xoo proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time.
    Conclusion: Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by X. oryzae pv. oryzae. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from in silico studies should be validated through further in vitro and in vivo investigation before approval.
    Language English
    Publishing date 2024-01-23
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2637420-1
    ISSN 2090-5920 ; 1687-157X ; 2090-5920
    ISSN (online) 2090-5920
    ISSN 1687-157X ; 2090-5920
    DOI 10.1016/j.jgeb.2024.100353
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database.

    Hossain, Mohammad Uzzal / Ahammad, Ishtiaque / Moniruzzaman, Md / Akter Lubna, Mahbuba / Bhattacharjee, Arittra / Mahmud Chowdhury, Zeshan / Ahmed, Istiak / Hosen, Md Billal / Biswas, Shourov / Chandra Das, Keshob / Keya, Chaman Ara / Salimullah, Md

    Cancer reports (Hoboken, N.J.)

    2023  Volume 6, Issue 12, Page(s) e1906

    Abstract: Background: Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer ... ...

    Abstract Background: Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression.
    Aim: The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts.
    Methods and results: A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers.
    Conclusion: The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.
    MeSH term(s) Humans ; Stomach Neoplasms/genetics ; Molecular Docking Simulation ; Germ-Line Mutation ; Polymerase Chain Reaction ; Germ Cells
    Language English
    Publishing date 2023-10-22
    Publishing country United States
    Document type Journal Article
    ISSN 2573-8348
    ISSN (online) 2573-8348
    DOI 10.1002/cnr2.1906
    Database MEDical Literature Analysis and Retrieval System OnLINE

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