Enhanced Sampling Protocol to Elucidate Fusion Peptide Opening of SARS-CoV-2 Spike Protein

Remington, Jacob M.; McKay, Kyle T.; Ferrell, Jonathon B.; Schneebeli, Severin T.; Li, Jianing

Large-scale conformational transitions in the spike protein S2 domain are required during host cell infection of the SARS-CoV-2 virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes due to the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a novel selection algorithm, and Markov state models to interrogate the dynamics of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a sub-microsecond timescale following cleavage at the S2’ site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof-of-principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.