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<p>Ginger is an important plant for its economic, nutritional and pharmaceutical values around the world. The consistency of viable seed stock is an important factor for sustainable food production. Nevertheless, the fungal diseases damage the total production of ginger as a result of huge economic losses. The effective treatment of ginger plant diseases is considerably reliant on the usage of agrochemicals but no effective anti-fungal drugs have been developed that can block the diseases. It was observed that (Nep1)-like proteins (NLPs) are secreted from the <i>Pythium aphanidermatum</i> and play an important role by triggering necrosis in various monocot plants (<i>Azadirachta indica</i>) upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Blocking the protein may inhibit the initiation of necrosis and may be discovered as a potential anti-fungal drug&#xa0;alternative&#xa0;against fungal infections. The rapid progress in computational and bioinformatics tools has opened new avenues for selected small molecules as drug candidates. Fifty-five phytochemical components from the plant were screened out through the molecular docking study. Three compounds, specifically Quercetin (CID5280343), Nicotiflorin (CID5318767), and Rutin (CID5280805) were designated based on their binding affinities such as − 7.7&#xa0;kcal/mol, − 7.6&#xa0;kcal/mol, and − 7.4&#xa0;kcal/mol. The ADME (Absorption, Distribution, Metabolism, and Excretion) properties and toxicity were evaluated for further confirmation of the selected compound. In addition, Molecular dynamics (MD) simulation and MM-GBSA were used to validate the binding stability and determine the free energy associated with ligand and receptor. Consequently, this in silico drug design will not only afford new evidence about the <i>P. aphanidermatum</i> insights into the fungal pathogen of ginger but also will facilitate to combat of the financial losses in the plants in a significant and worthwhile way.</p>

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Identification of natural antifungal drug candidate against ginger soft rot disease: computational drug design approaches

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月31日

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  • Mohammad Rashedul Islam,
  • Dhafer A. Alzahrani,
  • Enas J. Albokhari,
  • Mohammad Habibur Rahman Molla,
  • Ahmed Mohammed Shater

摘要

Ginger is an important plant for its economic, nutritional and pharmaceutical values around the world. The consistency of viable seed stock is an important factor for sustainable food production. Nevertheless, the fungal diseases damage the total production of ginger as a result of huge economic losses. The effective treatment of ginger plant diseases is considerably reliant on the usage of agrochemicals but no effective anti-fungal drugs have been developed that can block the diseases. It was observed that (Nep1)-like proteins (NLPs) are secreted from the Pythium aphanidermatum and play an important role by triggering necrosis in various monocot plants (Azadirachta indica) upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Blocking the protein may inhibit the initiation of necrosis and may be discovered as a potential anti-fungal drug alternative against fungal infections. The rapid progress in computational and bioinformatics tools has opened new avenues for selected small molecules as drug candidates. Fifty-five phytochemical components from the plant were screened out through the molecular docking study. Three compounds, specifically Quercetin (CID5280343), Nicotiflorin (CID5318767), and Rutin (CID5280805) were designated based on their binding affinities such as − 7.7 kcal/mol, − 7.6 kcal/mol, and − 7.4 kcal/mol. The ADME (Absorption, Distribution, Metabolism, and Excretion) properties and toxicity were evaluated for further confirmation of the selected compound. In addition, Molecular dynamics (MD) simulation and MM-GBSA were used to validate the binding stability and determine the free energy associated with ligand and receptor. Consequently, this in silico drug design will not only afford new evidence about the P. aphanidermatum insights into the fungal pathogen of ginger but also will facilitate to combat of the financial losses in the plants in a significant and worthwhile way.