The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor

Esther S. Brielle; Dina Schneidman-Duhovny; Michal Linial

Experimental affinity measurements (e.g. surface plasmon resonance, SPR) confirm the high affinity of SARS-2002 RBD-ACE2 binding, with an equilibrium dissociation constant (KD) of ~15 mM (18) (19) (20) (21) , similar to the binding affinity of ACE2 and the COVID-19 RBD (22, 23) . Our MD based calculation is consistent with SARS-2002 displaying a similar but slightly higher affinity relative to COVID-19 (Fig. 1A, Fig. S2 and Table S2 ). Binding affinity is achieved through a combination of interface contact optimization and protein stability (Fig. 3E) . While the RBD-ACE2 complex can be resolved at high-resolution by cryo-EM (17, 23) , MD simulations provide orthogonal information about the interaction dynamics on a nanosecond timescale. In the case of CoVs, MD simulations reveal an exceptional versatility of viral receptor binding strategies (Fig. 3E) . COVID-19 adopted a different strategy for achieving comparable affinity to SARS-2002: the interface of COVID-19 is significantly larger than that of SARS-2002 (1204Ã… vs. 998Ã…) with a remarkable number of interacting residues (ACE2: 30 vs. 24, Fig. 1C) . In contrast, SARS-2002 is more flexible in its interaction with ACE2, interacting through fewer contacts that serve as "hot spots". Therefore, we predict that SARS-2002 RBD neutralizing antibodies will not be effective for COVID-19. The failure of several of these antibodies to neutralize the binding of COVID-19 RBD to its receptor is consistent with our findings (20, 23) . The fluctuation from high-to low-affinity conformations in SARS-2002 leads to an increased . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.10.986398 doi: bioRxiv preprint efficacy for inhibiting peptides (24) and high-affinity antibodies (25) compared to COVID-19. This implies a therapeutic challenge is attributed to the enhanced rigidity of the COVID-19 RBD relative to that of the SARS-2002. The geometric and physicochemical properties of RBD-ACE2 interfaces resemble those of antibody-antigen interactions. In both cases the interface benefits from long loop plasticity, bulky aromatic side chains as anchoring sites, and the stabilization of the complex by distributed . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.10.986398 doi: bioRxiv preprint electrostatic interactions (26) . Both COVID-19 and SARS-2002 interfaces contain long flexible loops and nine aromatic residues (Tyr, Trp, Phe) in the interface with ACE2 ( Fig. 2A) . Moreover, in the SARS designed variant (SARS-des (11)), the addition of an aromatic residue (L486F substitution) significantly improved the interaction scores and interface stability (Fig. 3, B and D) . Our findings shed light on the accelerated evolution of spike protein binding to the ACE2 receptor similar to the rapid evolution along the antibody-antigen affinity maturation process.