2. Academic Validation
  3. Design and Evaluation of Andrographolide Analogues as SARS-CoV-2 Main Protease Inhibitors: Molecular Modeling and in vitro Studies

Design and Evaluation of Andrographolide Analogues as SARS-CoV-2 Main Protease Inhibitors: Molecular Modeling and in vitro Studies

  • Drug Des Devel Ther. 2025 May 15:19:3907-3924. doi: 10.2147/DDDT.S514193.
Utid Suriya 1,  Pansachon Intamalee 2 3,  Rungnapha Saeeng 2 3,  Patcharin Wilasluck 4 5,  Peerapon Deetanya 4 5,  Kittikhun Wangkanont 4 5,  Phongthon Kanjanasirirat 6,  Chanikarn Wongwitayasombat 7,  Bodee Nutho 8
Affiliations

Affiliations

  • 1 Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
  • 2 Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand.
  • 3 The Research Unit in Synthetic Compounds and Synthetic Analogues from Natural Product for Drug Discovery (RSND), Burapha University, Chonburi, 20131, Thailand.
  • 4 Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
  • 5 Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
  • 6 Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
  • 7 Biomedical Science Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
  • 8 Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
PMID: 40391180 DOI: 10.2147/DDDT.S514193
Abstract

Background: The COVID-19 pandemic, caused by SARS-CoV-2, highlights the urgent need for novel Antiviral agents targeting key Viral Proteins. The main protease (Mpro) is a crucial enzyme for viral replication, making it an attractive drug target. Andrographolide, a natural compound with known Antiviral properties, serves as a promising scaffold for inhibitor development.

Objective: This study aimed to design, synthesize, and evaluate C-12 dithiocarbamate andrographolide analogues as potential SARS-CoV-2 Mpro inhibitors using computational and experimental approaches.

Methods: A structure-based drug design approach was employed to design andrographolide derivatives. Molecular dynamics simulations were conducted to assess binding interactions and stability. The hit compound was synthesized and evaluated using an enzyme inhibition assay against SARS-CoV-2 Mpro. Cytotoxicity was assessed in HepG2, HaCaT, and HEK293T cells to determine safety profiles.

Results: Among the designed compounds, compound 1, incorporating a 2,4,5-trifluorobenzene moiety, exhibited the strongest binding affinity and stable interactions with key Mpro residues (H41, M49 and M165). Enzyme inhibition assay confirmed ~70% inhibition at 100 µM, with moderate to low cytotoxicity (CC50 values comparable to andrographolide).

Conclusion: Compound 1 represents a promising non-covalent SARS-CoV-2 Mpro inhibitor. Further structural optimization is necessary to enhance potency, selectivity, and safety for therapeutic applications.

Keywords

COVID-19; MD simulations; SARS-CoV-2 main protease; andrographolide analogues; enzyme-based assay.

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