Biophysical Society Conference | Estes Park 2023

Membrane Budding and Fusion

Poster Abstracts

26-POS Board 9 STRUCTURE-BASED DESIGN OF SARS-COV-2 MEMBRANE FUSION INHIBITORS Kailu Yang 1 ; Chuchu Wang 1 ; Alex Kreutzberger 2 ; Ravi Ojha 3 ; Suvi Kuivanen 3 ; Sergio Couoh-Cardel 1 ; Serena Muratcioglu 4 ; Timothy Eisen 4 ; Ian White 1 ; Richard Pfuetzner 1 ; John Kuriyan 4 ; Olli Vapalahti 3 ; Giuseppe Balistreri 3 ; Tomas Kirchhausen 2 ; Axel Brunger 1 ;

1 Stanford University, Stanford, CA, USA 2 Harvard Medical School, Boston, MA, USA 3 University of Helsinki, Helsinki, Finland 4 University of California, Berkeley, Berkeley, CA, USA

Membrane fusion is a critical process employed by SARS-CoV-2 to deliver its genetic material into host cells. The viral spike protein (S) facilitates this fusion process. Following receptor binding and proteolytic activation, the S protein undergoes dissociation into two subunits: S1 and S2. Notably, the S2 subunit undergoes substantial conformational changes, leading to membrane fusion. In the postfusion state, the heptad repeat 1 (HR1) and 2 (HR2) domains of the S2 subunit, initially distant in the primary sequence and prefusion structure, form a 6-helix bundle that contributes energy to overcome the kinetic barrier of membrane fusion. To efficiently determine high-resolution bundle structures, we developed a molecular scaffolding and cryogenic electron microscopy-based method. Leveraging this approach, we identified an HR2-based peptide inhibitor named longHR2_42, which exhibits potent inhibition against wildtype SARS-CoV-2 and many variants, with an IC50 of approximately 1 nM. However, longHR2_42 demonstrated reduced efficacy against the Omicron variant. Further investigation revealed that a single mutation, N969K, in the Omicron variant induced significant displacement of the HR2 backbone within the HR1HR2 bundle. Based on this structural observation, we designed an Omicron specific inhibitor, 42G, which successfully restored the inhibitory activity of longHR2_42 against the Omicron variant. Our findings highlight the importance of structure-based design in developing effective inhibitors against SARS-CoV-2 infection.

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