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Inhibiting the transcription and replication of Ebola viruses by disrupting the nucleoprotein and VP30 protein interaction with small molecules

Yan-hong Ma1, Xu Hong2, Fang Wu1, Xin-feng Xu1, Rui Li1, Jin Zhong3, Yao-qi Zhou2, Shu-wen Liu1, Jian Zhan2, Wei Xu1,4
1 NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
2 Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518038, China
3 Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200031, China
4 Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
Correspondence to: Yao-qi Zhou: zhouyq@szbl.ac.cn, Shu-wen Liu: liusw@smu.edu.cn, Jian Zhan: zhanjian@szbl.ac.cn, Wei Xu: xuwei3322@smu.edu.cn,
DOI: 10.1038/s41401-023-01055-0
Received: 16 September 2022
Accepted: 10 January 2023
Advance online: 9 February 2023

Abstract

Ebola virus (EBOV) causes hemorrhagic fever in humans with high morbidity and fatality. Although over 45 years have passed since the first EBOV outbreak, small molecule drugs are not yet available. Ebola viral protein VP30 is a unique RNA synthesis cofactor, and the VP30/NP interaction plays a critical role in initiating the transcription and propagation of EBOV. Here, we designed a high- throughput screening technique based on a competitive binding assay to bind VP30 between an NP-derived peptide and a chemical compound. By screening a library of 8004 compounds, we obtained two lead compounds, Embelin and Kobe2602. The binding of these compounds to the VP30-NP interface was validated by dose-dependent competitive binding assay, surface plasmon resonance, and thermal shift assay. Moreover, the compounds were confirmed to inhibit the transcription and replication of the Ebola genome by a minigenome assay. Similar results were obtained for their two respective analogs (8-gingerol and Kobe0065). Interestingly, these two structurally different molecules exhibit synergistic binding to the VP30/NP interface. The antiviral efficacy (EC50) increased from 1 μM by Kobe0065 alone to 351 nM when Kobe0065 and Embelin were combined in a 4:1 ratio. The synergistic anti-EBOV effect provides a strong incentive for further developing these lead compounds in future studies.
Keywords: Ebola; VP30; minigenome; high-throughput screening; drug synergy

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