Cryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery
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.
Authors
- Michael DiDonato (ORCID: https://orcid.org/0000-0002-9074-7284)
- Judith Straimer
- Glen Spraggon (ORCID: https://orcid.org/0000-0001-7880-8454)
- James Hunt (ORCID: https://orcid.org/0000-0003-2884-5622)
- Cosmo Z. Buffalo (ORCID: https://orcid.org/0000-0002-8187-4660)
- Matthew C. Clifton (ORCID: https://orcid.org/0000-0003-2658-2654)
- Lili Xie (ORCID: https://orcid.org/0000-0001-7604-2037)
- Colin Deniston (ORCID: https://orcid.org/0000-0002-0204-0466)
- Debjani Patra (ORCID: https://orcid.org/0000-0003-4343-4645)
- Bo Liang (ORCID: https://orcid.org/0000-0002-5617-9228)
- Ahmed Rohaim (ORCID: https://orcid.org/0000-0001-7339-1637)
- Dongdong Cao (ORCID: https://orcid.org/0000-0002-2031-9321)
- Debapriya Sengupta (ORCID: https://orcid.org/0000-0002-4192-6227)
- Jaquelin P. Dudley (ORCID: https://orcid.org/0000-0002-1581-1098)
- Tiffany Tsang (ORCID: https://orcid.org/0000-0002-2324-4978)
- Zhenhang Chen (ORCID: https://orcid.org/0000-0001-5803-9491)
- Lan Wen (ORCID: https://orcid.org/0009-0007-6676-7123)
- Nadine Jarrousse
Institutions
- Genomics Institute of the Novartis Research Foundation (US)
- Emory University (US)
- Novartis (China) (CN)
- Novartis (United States) (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-07-19
- DOI
- https://doi.org/10.1038/s41467-025-61764-4
- Citations
- 1
- Primary Topic
- Virology and Viral Diseases
- Type
- article
- Field-Weighted Citation Impact
- 1.35
Funders
- GlaxoSmithKline
- Purdue University
- Emory University
- National Institutes of Health
- National Institute of General Medical Sciences
- National Institute of Allergy and Infectious Diseases
- Common Fund