Supercomputing Multi-Ligand Modeling, Simulation, Wavelet Analysis and Surface Plasmon Resonance to Develop Novel Combination Drugs: A Case Study of Arbidol and Baicalein Against Main Protease of SARS-CoV-2.

Publication date: Jul 17, 2025

Background/Objectives: Combination therapies using traditional Chinese medicine and Western drugs have gained attention for their enhanced therapeutic effects and reduced side effects. Toujie Quwen Granules (TQG), known for its antiviral properties, particularly against respiratory viruses, could offer new treatment strategies when combined with antiviral drugs like arbidol, especially for diseases such as Coronavirus disease. This study investigates the synergistic mechanisms between arbidol and components from TQG against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M). Methods: We identified compounds from TQG via existing data. Multi-ligand molecular docking, pharmacokinetic/toxicity screening, and preliminary simulations were performed to assess potential synergistic compounds with arbidol. UPLC-Q-Exactive Orbitrap-MS verified the presence of these compounds. Extended simulations and in vitro assays, including Luciferase and surface plasmon resonance, validated the findings. Results: Five compounds interacted with arbidol in synergy based on docking and preliminary dynamics simulation results. Only Baicalein (HQA004) could be identified in the herbal remedy by untargeted metabolomics, with ideal pharmacokinetic properties, and as a non-toxic compound. Extended simulations revealed that HQA004 enhanced arbidol’s antiviral activity via a “Far” Addition Mechanism #2, with an optimal 2:1 arbidol:HQA004 ratio. The movements of arbidol (diffusion and intramolecular conformational shifts) in the system were significantly reduced by HQA004, which may be the main reason for the synergism that occurred. In vitro experiments confirmed an increased inhibition of M by the combination. Conclusions: HQA004 demonstrated synergistic potential with arbidol in inhibiting M. The development of combination therapies integrating Western and herbal medicine is supported by these findings for effective antiviral treatments.

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Concepts Keywords
Chinese COVID-19
Coronavirus synergism
Increased Toujie Quwen Granules
Luciferase umifenovir
Pharmaceuticals

Semantics

Type Source Name
pathway KEGG Coronavirus disease
drug DRUGBANK Coenzyme M
drug DRUGBANK L-Valine
drug DRUGBANK Umifenovir
disease MESH COVID 19
disease MESH infections
disease MESH syndrome
drug DRUGBANK Ritonavir
disease IDO assay
disease MESH sore throat
disease MESH asymptomatic infection
disease MESH chronic conditions
disease MESH high blood pressure
drug DRUGBANK Ribavirin
disease MESH influenza
disease MESH hepatitis
drug DRUGBANK Oseltamivir
drug DRUGBANK Lopinavir
disease IDO replication
disease MESH severe acute respiratory syndrome
disease IDO symptom
drug DRUGBANK Water
pathway REACTOME Metabolism
drug DRUGBANK Spinosad

Original Article

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