Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery
Abstract Transcription and replication of the Nipah virus (NiV) are driven by the large protein (L) together with its essential co-factor phosphoprotein (P). L encodes all the viral enzymatic functions, including RNA-dependent RNA polymerase (RdRp) activity, while the tetrameric P is multi-modular....
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-07-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61764-4 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849331627445977088 |
|---|---|
| author | Zhenhang Chen Jeanne Quirit Dudley Colin Deniston Cosmo Z. Buffalo Debjani Patra Dongdong Cao Julia Hunt Ahmed Rohaim Debapriya Sengupta Lan Wen Tiffany Tsang Lili Xie Michael DiDonato Glen Spraggon Matthew C. Clifton Nadine Jarrousse Judith Straimer Bo Liang |
| author_facet | Zhenhang Chen Jeanne Quirit Dudley Colin Deniston Cosmo Z. Buffalo Debjani Patra Dongdong Cao Julia Hunt Ahmed Rohaim Debapriya Sengupta Lan Wen Tiffany Tsang Lili Xie Michael DiDonato Glen Spraggon Matthew C. Clifton Nadine Jarrousse Judith Straimer Bo Liang |
| author_sort | Zhenhang Chen |
| collection | DOAJ |
| description | Abstract Transcription and replication of the Nipah virus (NiV) are driven by the large protein (L) together with its essential co-factor phosphoprotein (P). L encodes all the viral enzymatic functions, including RNA-dependent RNA polymerase (RdRp) activity, while the tetrameric P is multi-modular. Here, we investigate the molecular mechanism of the NiV polymerase and build tools for anti-NiV drug discovery. We analyze and compare multiple cryo-EM structures of both full-length and truncated NiV polymerases from the Malaysia and Bangladesh strains. We identify two conserved loops in the polyribonucleotidyltransferase (PRNTase) domain of L and the binding between RdRp-PRNTase and CD domains. To further assess the mechanism of NiV polymerase activity, we establish a highly sensitive radioactive-labeled RNA synthesis assay and identify a back-priming activity in the NiV polymerase as well as a fluorescence and luminescent-based non-radioactive polymerase assay to enable high-throughput screening for L protein inhibitors. The combination of structural analysis and the development of both high-sensitive and high-throughput biochemical assays will enable the identification of new direct-acting antiviral candidates for treating highly pathogenic henipaviruses. |
| format | Article |
| id | doaj-art-13d22cf3bbe346f6a326d2c4b97666be |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-13d22cf3bbe346f6a326d2c4b97666be2025-08-20T03:46:28ZengNature PortfolioNature Communications2041-17232025-07-0116111410.1038/s41467-025-61764-4Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discoveryZhenhang Chen0Jeanne Quirit Dudley1Colin Deniston2Cosmo Z. Buffalo3Debjani Patra4Dongdong Cao5Julia Hunt6Ahmed Rohaim7Debapriya Sengupta8Lan Wen9Tiffany Tsang10Lili Xie11Michael DiDonato12Glen Spraggon13Matthew C. Clifton14Nadine Jarrousse15Judith Straimer16Bo Liang17Department of Biochemistry, Emory University School of MedicineBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisDepartment of Biochemistry, Emory University School of MedicineDepartment of Biochemistry, Emory University School of MedicineBiomedical Research, NovartisBiomedical Research, NovartisDepartment of Biochemistry, Emory University School of MedicineBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisBiomedical Research, NovartisDepartment of Biochemistry, Emory University School of MedicineAbstract Transcription and replication of the Nipah virus (NiV) are driven by the large protein (L) together with its essential co-factor phosphoprotein (P). L encodes all the viral enzymatic functions, including RNA-dependent RNA polymerase (RdRp) activity, while the tetrameric P is multi-modular. Here, we investigate the molecular mechanism of the NiV polymerase and build tools for anti-NiV drug discovery. We analyze and compare multiple cryo-EM structures of both full-length and truncated NiV polymerases from the Malaysia and Bangladesh strains. We identify two conserved loops in the polyribonucleotidyltransferase (PRNTase) domain of L and the binding between RdRp-PRNTase and CD domains. To further assess the mechanism of NiV polymerase activity, we establish a highly sensitive radioactive-labeled RNA synthesis assay and identify a back-priming activity in the NiV polymerase as well as a fluorescence and luminescent-based non-radioactive polymerase assay to enable high-throughput screening for L protein inhibitors. The combination of structural analysis and the development of both high-sensitive and high-throughput biochemical assays will enable the identification of new direct-acting antiviral candidates for treating highly pathogenic henipaviruses.https://doi.org/10.1038/s41467-025-61764-4 |
| spellingShingle | Zhenhang Chen Jeanne Quirit Dudley Colin Deniston Cosmo Z. Buffalo Debjani Patra Dongdong Cao Julia Hunt Ahmed Rohaim Debapriya Sengupta Lan Wen Tiffany Tsang Lili Xie Michael DiDonato Glen Spraggon Matthew C. Clifton Nadine Jarrousse Judith Straimer Bo Liang Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery Nature Communications |
| title | Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery |
| title_full | Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery |
| title_fullStr | Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery |
| title_full_unstemmed | Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery |
| title_short | Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery |
| title_sort | cryo em structures of nipah virus polymerases and high throughput rdrp assay development enable anti niv drug discovery |
| url | https://doi.org/10.1038/s41467-025-61764-4 |
| work_keys_str_mv | AT zhenhangchen cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT jeannequiritdudley cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT colindeniston cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT cosmozbuffalo cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT debjanipatra cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT dongdongcao cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT juliahunt cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT ahmedrohaim cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT debapriyasengupta cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT lanwen cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT tiffanytsang cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT lilixie cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT michaeldidonato cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT glenspraggon cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT matthewcclifton cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT nadinejarrousse cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT judithstraimer cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery AT boliang cryoemstructuresofnipahviruspolymerasesandhighthroughputrdrpassaydevelopmentenableantinivdrugdiscovery |