Structural and mechanistic insights into the inhibition of respiratory syncytial virus polymerase by a non-nucleoside inhibitor
Xiaodi Yu, Pravien Abeywickrema, Brecht Bonneux, Ishani Behera, Brandon J. Anson, Edgar Jacoby, Amy Fung, Suraj Adhikary, A. Bhaumik, Rodrigo J. Carbajo, Suzanne De Bruyn, Robyn Miller, Aaron Patrick, Quyen Pham, Madison Piassek, Nick Verheyen, Afzaal Shareef, Priscila Sutto‐Ortiz, Nina Ysebaert, Herman van Vlijmen, Tim H. M. Jonckers, Florence Herschke, Jason S. McLellan, Étienne Decroly, Rachel Fearns, Sandrine Grosse, Dirk Roymans, Sujata Sharma, Peter Rigaux, Zhinan Jin
Abstract
The respiratory syncytial virus polymerase complex, consisting of the polymerase (L) and phosphoprotein (P), catalyzes nucleotide polymerization, cap addition, and cap methylation via the RNA dependent RNA polymerase, capping, and Methyltransferase domains on L. Several nucleoside and non-nucleoside inhibitors have been reported to inhibit this polymerase complex, but the structural details of the exact inhibitor-polymerase interactions have been lacking. Here, we report a non-nucleoside inhibitor JNJ-8003 with sub-nanomolar inhibition potency in both antiviral and polymerase assays. Our 2.9 Å resolution cryo-EM structure revealed that JNJ-8003 binds to an induced-fit pocket on the capping domain, with multiple interactions consistent with its tight binding and resistance mutation profile. The minigenome and gel-based de novo RNA synthesis and primer extension assays demonstrated that JNJ-8003 inhibited nucleotide polymerization at the early stages of RNA transcription and replication. Our results support that JNJ-8003 binding modulates a functional interplay between the capping and RdRp domains, and this molecular insight could accelerate the design of broad-spectrum antiviral drugs.