SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets.


Raghuvamsi PV(#)(1)(2), Tulsian NK(#)(1)(3), Samsudin F(2), Qian X(4), Purushotorman K(4), Yue G(4), Kozma MM(4), Hwa WY(5), Lescar J(5), Bond PJ(1)(2), MacAry PA(4), Anand GS(1)(6).
Author information:
(1)Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
(2)Bioinformatics Institute, Agency for Science, Technology, and Research
(A*STAR), Singapore, Singapore.
(3)Centre for Life Sciences, Department of Biochemistry, National University of Singapore, Singapore, Singapore.
(4)Life Sciences Institute, Centre for Life Sciences, National University of Singapore, Singapore, Singapore.
(5)School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
(6)Current address: Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics -Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, United States.
(#)Contributed equally


The spike (S) protein is the main handle for SARS-CoV-2 to enter host cells via surface angiotensin-converting enzyme 2 (ACE2) receptors. How ACE2 binding activates proteolysis of S protein is unknown. Here, using amide hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations, we have mapped the S:ACE2 interaction interface and uncovered long-range allosteric propagation of ACE2 binding to sites necessary for host-mediated proteolysis of S protein, critical for viral host entry. Unexpectedly, ACE2 binding enhances dynamics at a distal S1/S2 cleavage site and flanking protease docking site ~27 Å away while dampening dynamics of the stalk hinge (central helix and heptad repeat [HR]) regions ~130 Å away. This highlights that the stalk and proteolysis sites of the S protein are dynamic hotspots in the prefusion state. Our findings provide a dynamics map of the S:ACE2 interface in solution and also offer mechanistic insights into how ACE2 binding is allosterically coupled to distal proteolytic processing sites and viral-host membrane fusion. Thus, protease docking sites flanking the S1/S2 cleavage site represent alternate allosteric hotspot targets for potential therapeutic development.