BPR3P0128, a non-nucleoside RNA-dependent RNA polymerase inhibitor, inhibits SARS-CoV-2 variants of concern and exerts synergistic antiviral activity in combination with remdesivir

Wen Fang Tang, Yu Hsiu Chang, Cheng Chin Lin, Jia Rong Jheng, Chung Fan Hsieh, Yuan Fan Chin, Tein Yao Chang, Jin Ching Lee, Po Huang Liang, Chia Yi Lin, Guan Hua Lin, Jie Yun Cai, Yu Li Chen, Yuan Siao Chen, Shan Ko Tsai, Ping Cheng Liu, Chuen Mi Yang, Tolou Shadbahr, Jing Tang, Yu Lin HsuChih Heng Huang, Ling Yu Wang, Cheng Cheung Chen, Jyh Hwa Kau, Yi Jen Hung, Hsin Yi Lee, Wen Chieh Wang, Hui Ping Tsai*, Jim Tong Horng*

*Corresponding author for this work

Research output: Contribution to journalJournal Article peer-review

1 Scopus citations


Viral RNA-dependent RNA polymerase (RdRp), a highly conserved molecule in RNA viruses, has recently emerged as a promising drug target for broad-acting inhibitors. Through a Vero E6-based anti-cytopathic effect assay, we found that BPR3P0128, which incorporates a quinoline core similar to hydroxychloroquine, outperformed the adenosine analog remdesivir in inhibiting RdRp activity (EC50 = 0.66 μM and 3 μM, respectively). BPR3P0128 demonstrated broad-spectrum activity against various severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. When introduced after viral adsorption, BPR3P0128 significantly decreased SARS-CoV-2 replication; however, it did not affect the early entry stage, as evidenced by a time-of-drug-addition assay. This suggests that BPR3P0128's primary action takes place during viral replication. We also found that BPR3P0128 effectively reduced the expression of proinflammatory cytokines in human lung epithelial Calu-3 cells infected with SARS-CoV-2. Molecular docking analysis showed that BPR3P0128 targets the RdRp channel, inhibiting substrate entry, which implies it operates differently - but complementary - with remdesivir. Utilizing an optimized cell-based minigenome RdRp reporter assay, we confirmed that BPR3P0128 exhibited potent inhibitory activity. However, an enzyme-based RdRp assay employing purified recombinant nsp12/nsp7/nsp8 failed to corroborate this inhibitory activity. This suggests that BPR3P0128 may inhibit activity by targeting host-related RdRp-associated factors. Moreover, we discovered that a combination of BPR3P0128 and remdesivir had a synergistic effect - a result likely due to both drugs interacting with separate domains of the RdRp. This novel synergy between the two drugs reinforces the potential clinical value of the BPR3P0128-remdesivir combination in combating various SARS-CoV-2 variants of concern.

Original languageEnglish
Pages (from-to)e0095623
JournalAntimicrobial Agents and Chemotherapy
Issue number4
StatePublished - 03 04 2024

Bibliographical note

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Copyright © 2024 American Society for Microbiology. All Rights Reserved.


  • antiviral
  • BPR3P0128
  • broad-spectrum antiviral
  • RdRp reporter assay
  • remdesivir
  • SARS-CoV-2
  • synergistic effect
  • SARS-CoV-2/metabolism
  • Quinolines
  • COVID-19 Drug Treatment
  • Alanine/analogs & derivatives
  • Antiviral Agents/chemistry
  • Pyrazoles
  • Humans
  • RNA-Dependent RNA Polymerase/metabolism
  • COVID-19
  • Adenosine Monophosphate/analogs & derivatives
  • Molecular Docking Simulation


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