Structural insights into measles virus RNA synthesis regulation and pan-paramyxoviral polymerase inhibition by ERDRP-0519

Figures

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  Fig. 1.. Overview of the cryo-EM maps and models of MeV RdRP complexes. (A) Overall architecture of the apo L–P complex showing well-resolved RdRp (light blue) and PRNTase (pink) cores, together with four P protomers (salmon, lime, wheat, and limon). (B and C) Cryo-EM map and model of the MeV L–P complex reveals two bound C protomers (marine and slate) interacting with L domains, with visible CD (yellow), MTase (orange), and CTD (red). (D) Cross-sectional view of the cryo-EM map of the L–P complex bound to ERDRP-0519 (highlighted in yellow). (E) The ERDRP-0519 density in the cryo-EM map superimposed with the fitted atomic model. (F) Superposition of the MeV RdRP complex models: apo L–P (pink), LPE (blue), and LPC (light green). The C-terminal functional domains and C protein dimers are shown in the same colors as in B and C. (G) Schematic domain organization of the MeV L, P, and C proteins. Conserved regions I–VI (CR I–VI) in the L protein are labeled based on sequence alignment across paramyxoviruses. Catalytic residues within the RdRp, PRNTase, and MTase domains are annotated. Gray boxes with solid outlines indicate unresolved regions in the structures, while gray boxes with dashed…

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  Fig. 2.. Conformation of the C-terminal region in MeV LPC complex and functional role of MeV C protein. The RdRp and PRNTase cores are shown as light blue and pink surfaces. Priming and intrusion loops are in green and dark blue, respectively. C-terminal functional domains of MeV L (CD, MTase, CTD) are depicted as yellow, orange, and red cartoons, with P tetramers in gray. Top–down views mark CD, MTase, and CTD by colored circles (yellow, orange, red), with arrows indicating their spatial rearrangements. (A) MeV LPC complex with open RNA exit channel. Two possible RNA exit routes toward the MTase are indicated: route 1 (magenta), route 2 (green). (B) Visualization of the product RNA exit channel in the MeV LPC complex, the CD-MTase-CTD module, and C dimer is hidden for clarity. (C) Conformational comparison of CD, MTase, and CTD between PIV5 (PDB: 6V85) and MeV polymerase. PIV5 domains are shown in green (CD), brown (MTase), and salmon (CTD), with arrows indicating domain rotation angles. For clarity, the superimposed PIV5 core structure is omitted. (D) MST analysis of full-length C protein binding to different forms of N proteins, including the monomeric apo N protein, N protein bound to…

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  Fig. 3.. Molecular mechanism of ERDRP-0519 recognition and inhibition of MeV RNA polymerase. (A) Spatial localization of ERDRP-0519 (yellow sticks) within the MeV L RdRp. (B) Close-up view of the ERDRP-0519 binding pocket in the palm and fingers, with cryo-EM density as magenta mesh. (C) Detailed interactions of ERDRP-0519 with palm (magenta) and fingers (cyan) residues (sticks); polar contacts shown as red dashed lines. (D) Structural superposition of the ERDRP-0519 binding pocket in the apo and LPE complexes, showing clashes, conformational changes in motifs C (yellow) and E (dark blue), and apo conformation (light blue). (E) Main/side chain differences of key residues between apo (slate) and bound (cyan), with Y667 densities in light blue (apo) and salmon (bound). (F) Resistance mutations mapped onto the pocket: MeV (black dots) and CDV (black squares) shown as cyan sticks; surrounding residues in slate. (G and H) Surface representation of the ERDRP-0519 binding pocket, spatial location of the pocket (G), sequence conservation calculated using the ConSurf server (H) (52). (I) Structure-based partial sequence alignment of representative paramyxoviral L proteins spanning motifs A–D;…

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  Fig. 4.. Mechanistic insights into ERDRP-0519 binding to and the inhibition of NiV polymerase. (A) Cross-sectional view of NiV L–P bound to ERDRP-0519; RdRp (blue), PRNTase (pink), P protomers in light orange, wheat, limon, lime, and ERDRP-0519 in yellow. (B) Zoomed-in view with atomic model overlaid. (C) Comparison of ERDRP-0519 localization in MeV (yellow) and NiV (salmon) RdRp; NiV subdomains: NTD (gray), fingers (light slate), palm (light pink), thumb (limon). (D) Close-up view of the ERDRP-0519 binding pocket with ERDRP-0519 density (dark blue mesh). (E) Detailed interactions of ERDRP-0519 with palm (magenta) and fingers (light slate) residues; polar contacts shown as red and blue dashed lines. (F) Superposition of apo (yellow, PDB: 9BDQ) and inhibitor-bound (light pink) NiV RdRp shows clashes (red arrows) and conformational rearrangements in the palm subdomain. (G) Side chain differences of key binding residues between apo (limon sticks) and inhibitor-bound (magenta sticks) structures. (H) Superposition of dsRNA-bound (limon, PDB: 9GJU) and inhibitor-bound (light pink) NiV L–P complexes highlights clashes (red arrows) and palm conformational changes. (I) Steric hindrance between…

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  Fig. 5.. Dynamics of ERDRP-0519 in representative paramyxoviral polymerase complexes. MD simulations and docking analyses of ERDRP-0519 bound to the L–P complex structures of MeV (A, this study), NiV (B, this study), PIV5 (C, docking model), HPIV3 (D, docking model), MuV (E, docking model), and NDV (F, docking model). Three independent 200-ns simulations were conducted for each system. Left panels: RMSD plots of ERDRP-0519 over time across the three replicates, illustrating the stability of the compound within the binding pocket. Right panels: Representative structural snapshots extracted at 20-ns intervals throughout the simulations. Key conserved residues (e.g., G741, W747) mediating ERDRP-0519 binding are shown as green sticks. ERDRP-0519 is depicted in salmon, highlighting its consistent binding pose across different Paramyxoviridae RdRp domains.