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TitleCryo-EM structures of Nipah virus polymerases and high-throughput RdRp assay development enable anti-NiV drug discovery.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6655, Year 2025
Publish dateJul 19, 2025
AuthorsZhenhang 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 /
PubMed AbstractTranscription 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, ...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.
External linksNat Commun / PubMed:40683863 / PubMed Central
MethodsEM (single particle)
Resolution2.92 - 2.99 Å
Structure data

45782

9cok

EMDB-45782, PDB-9cok:
Cryo-EM structure of the Nipah virus (Malaysia Strain) L:P complex
Method: EM (single particle) / Resolution: 2.92 Å

45896

9mzh

EMDB-45896: cryo-EM structure of the Nipah virus polymerase containing the connecting domain
PDB-9mzh: Cryo-EM structure of the Nipah virus polymerase containing the connecting domain
Method: EM (single particle) / Resolution: 2.99 Å

48649

9muw

EMDB-48649, PDB-9muw:
Cryo-EM structure of a truncated Nipah virus (Malaysia Strain) L:P complex
Method: EM (single particle) / Resolution: 2.99 Å

Source
  • henipavirus nipahense
KeywordsVIRAL PROTEIN / TRANSFERASE / RNA dependent RNA polymerase / Nipah virus / LP complex / polymerase / connecting domain

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