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<p>SARS-CoV-2 remains a critical global health concern due to its high transmissibility, evolving variants, and the absence of a universally effective treatment. Phytocompounds, known for their antiviral, anti-inflammatory, and immunomodulatory properties, continue to be explored as potential therapeutic agents. This study evaluated 20 phytocompounds and four approved antiviral drugs, Remdesivir, Favipiravir, Hydroxychloroquine, and Ivermectin, against nine SARS-CoV-2 spike glycoprotein structures, including five wild-type and four variants (Alpha, Beta, Delta, and Omicron). Molecular docking using two software platforms identified ursolic acid, betulinic acid, β-sitosterol, and ivermectin as top candidates, with binding affinities ranging from − 6.7 to − 9.6&#xa0;kcal/mol. These compounds also displayed favorable pharmacokinetic properties and druggability. 100&#xa0;ns molecular dynamics simulations were performed on the highest-affinity complexes to assess stability. Betulinic acid and β-sitosterol demonstrated stable binding interactions, with low RMSD values (~ 0.2–0.3&#xa0;nm) and consistent hydrogen bonding (1–3 bonds), suggesting structural stability. In contrast, ursolic acid and ivermectin showed unstable binding and higher structural fluctuations during simulation. Overall, the study highlights betulinic acid and β-sitosterol as presumptive SARS-CoV-2 inhibitors, warranting further experimental validation through in vitro and in vivo studies to confirm their therapeutic potential.</p>

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Uncovering potent natural phytochemicals targeting SARS-COV-2 spike protein variants: molecular dynamics insights

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月30日

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  • Tuba Sevimoglu,
  • Elif Kızılpınar,
  • Zihni Onur Çalışkaner,
  • İrem Nur Zengin

摘要

SARS-CoV-2 remains a critical global health concern due to its high transmissibility, evolving variants, and the absence of a universally effective treatment. Phytocompounds, known for their antiviral, anti-inflammatory, and immunomodulatory properties, continue to be explored as potential therapeutic agents. This study evaluated 20 phytocompounds and four approved antiviral drugs, Remdesivir, Favipiravir, Hydroxychloroquine, and Ivermectin, against nine SARS-CoV-2 spike glycoprotein structures, including five wild-type and four variants (Alpha, Beta, Delta, and Omicron). Molecular docking using two software platforms identified ursolic acid, betulinic acid, β-sitosterol, and ivermectin as top candidates, with binding affinities ranging from − 6.7 to − 9.6 kcal/mol. These compounds also displayed favorable pharmacokinetic properties and druggability. 100 ns molecular dynamics simulations were performed on the highest-affinity complexes to assess stability. Betulinic acid and β-sitosterol demonstrated stable binding interactions, with low RMSD values (~ 0.2–0.3 nm) and consistent hydrogen bonding (1–3 bonds), suggesting structural stability. In contrast, ursolic acid and ivermectin showed unstable binding and higher structural fluctuations during simulation. Overall, the study highlights betulinic acid and β-sitosterol as presumptive SARS-CoV-2 inhibitors, warranting further experimental validation through in vitro and in vivo studies to confirm their therapeutic potential.