Structural basis of measles virus polymerase inhibition by nonnucleoside inhibitor ERDRP-0519

Abstract

ERDRP-0519 is a potent nonnucleoside inhibitor active against measles virus (MeV) and other Morbilliviruses. Here we report cryo-EM structures of the compound bound to MeV polymerase complexes at 2.73 Å and 2.48 Å resolution, revealing a unique binding pocket in the RdRp palm subdomain that overlaps the catalytic GDN motif. These findings clarify the basis of resistance mutations, including W671, and provide a foundation for designing next-generation Paramyxovirus antivirals.

Fig. 1. Compound optimization and overall structures.

a Development of small-molecule inhibitors targeting MeV. b Chemical structure of the MeV RdRp lead compound ERDRP-0519 and its neutralization potency compared to other prodrugs. c Structures of the MeV polymerase complex with ERDRP-0519. The MeV L_core-P (left) and L_full-P-C (right) complexes are shown in cartoons with different subunit colors and ERDRP-0519 as magenta spheres. d The RdRp catalytic core is shown in cartoons: NTD (gray), fingers (blue), palm (lime), thumb (burlywood), and active site (red). ERDRP-0519 is represented as magenta sticks with transparent gray density. Zoom-in: Superimposition of the palm subdomain of the MeV L_full-P-C-ERDRP-0519 complex (lime) and apo-MeV L_full-P-C (gray). The active site loop (GDN) shifts upon compound binding (black arrow).

Fig. 2. Structural mechanisms of ERDRP-0519 inhibition.

a Interactions between the palm subdomain and ERDRP-0519, with the hydrogen bond to W671 shown as a dashed line. b List of residues interacting with ERDRP-0519’s functional groups. c Superimposition of MeV L_full-P-C-ERDRP-0519 and apo-MeV L_full-P-C (PDB: 9DUT), showing D773 displaced outward, forming a hydrophobic interaction with the compound. d Superimposition of MeV L_full-P-C-ERDRP-0519 and NiV L-P-RNA (PDB: 9GJU), with 3’ leader RNA shown as yellow sticks and the clash between ERDRP-0519 and RNA marked. The clip surface of MeV L protein (gray) displays the ERDRP-0519 binding pocket and the potential 3’ leader RNA channel.

Fig. 3. Conservation and functional validation of ERDRP-0519 binding.

a RdRp sequence alignment across Mononegavirales. MeV contact residues in red; conserved and non-conserved sites marked red and blue. Sequence sources: MeV (GenBank: K01711.1); CDV (KJ147057.1); HPIV3 (ARA15380.1); HPIV1 (ARB07783.1); NiV (AAY43917.1); MuV (AWI67642.1); HPIV5 (YP_138518.1); RSV (YP_009518860.1); HMPV (Q6WB93.1); VSV (Q98776.1); RABV (AAT48626.1); EBOV (NP_066251.1). b Dose-dependent inhibition of MeV polymerase by ERDRP-0519 (0, 1, 10, 100, 1000 nM) using the MeV NanoLuc minigenome assay. c Effect of ERDRP-0519 (100 nM) on MeV L mutants assessed by the MeV NanoLuc minigenome system. D773A serves as a negative control. Bars (b, c) show mean ± SD. Black circles indicate individual values (n   =   3). Significance by two-tailed unpaired t-test (*P  ≤  0.05, **P  ≤  0.01; ***P  ≤  0.001; ns, not significant). Source data are provided as a Source Data file.