Computational Evaluation of Multitarget Capabilities of Phenylethanoid Glycosides Against SARS-CoV-2’s 3CLpro and PLpro

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Abstract
Background: The development of multitarget drugs capable of simultaneously inhibiting SARS-CoV-2 proteases—3CLpro and PLpro—may enhance therapeutic efficacy against COVID-19. Given the historical use of Traditional Chinese Medicine (TCM) in the management of respiratory diseases, phenylethanoid glycosides (PGs) represent an attractive and chemically diverse natural product scaffold for the discovery of antiviral agents. Objectives: This study aimed to identify promising candidates within this class capable of simultaneously inhibiting both target proteases. Methods: The PG structures described in the literature between 1950 and 2020 were gathered and curated to construct a dedicated database, which was subsequently subjected to virtual screening. In silico ADMETox predictions and 2D ligand–protein interaction analyses were then employed to evaluate the identified hit PGs. Ligand stability within the binding sites of the proteases was further assessed using free energy landscape (FEL) and MM/GBSA calculations, while enzymatic inhibition of the commercial PG was evaluated via FRET assays. Results: Virtual screening identified 22 PGs with multitarget potential, predominantly sourced from Asia, followed by the Americas and Europe. The hit compound magnoloside I is found in Magnolia officinalis, a species widely used in TCM for respiratory conditions and officially prescribed during the COVID-19 pandemic. A second hit, calceolarioside B, inhibited more than 90% of the enzymatic activity of both proteases in the FRET assay. Conclusions: Together, these findings highlight phenylethanoid glycosides as promising scaffolds for dual protease inhibition.
Funding Information
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (001)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (316186/2023-6)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (404646/2023-9)
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (211.398/2019)
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (E-26/211.717/2021)
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (E-26/211.285/2021)
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (E-26/210.713/2025)

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