Molecular basis of receptor binding and antibody neutralization of Omicron

Abstract

The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading rapidly worldwide. Understanding the structural basis of the high transmissibility and enhanced immune evasion of Omicron is of high importance. Here, using cryo-electron microscopy, we present both the closed and the open states of the Omicron spike (S) protein, which appear more compact than the counterparts of the G614 strain 1 , potentially related to enhanced inter-protomer and S1-S2 interactions induced by Omicron residue substitution. The closed state showing dominant population may indicate a conformational masking mechanism for the immune evasion of Omicron. Moreover, we captured three states for the Omicron S-ACE2 complex, revealing that the substitutions on the Omicron RBM result in new salt bridges and hydrogen bonds, more favourable electrostatic surface properties, and an overall strengthened S-ACE2 interaction, in line with the observed higher ACE2 affinity of Omicron S than of G614. Furthermore, we determined the structures of Omicron S in complex with the Fab of S3H3, an antibody that is able to cross-neutralize major variants of concern including Omicron, elucidating the structural basis for S3H3-mediated broad-spectrum neutralization. Our findings shed light on the receptor engagement and antibody neutralization or evasion of Omicron and may also inform the design of broadly effective vaccines against SARS-CoV-2.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone considerable evolution since its initial discovery, leading to the emergence of several variants of concern (VOCs) including Alpha 2-6 , Beta 5-10 , Gamma 11 and Delta 12,13 . These variants that have multiple mutations on their S protein show enhanced transmissibility and resistance to antibody neutralization 13 . Recently, a new variant named Omicron (B.1.1.529), which was first reported in South Africa in November 2021, was classified as the fifth VOC by the World Health Organization (WHO) 14 . Omicron bears 37 mutations in its S protein relative to the original SARS-CoV-2 strain 15,16 . As a consequence, Omicron has been observed to extensively escape neutralization by previously developed neutralizing monoclonal antibodies (mAbs) or sera from vaccinated or convalescent individuals 15,[17][18][19][20][21][22] . Among all of the Omicron S mutations, 15 are present in the receptor-binding domain (RBD) that mediates binding of the virus to its host cell receptor, angiotensin-converting enzyme 2 (ACE2), which is also a major target for neutralizing antibodies [23][24][25][26][27] . However, Omicron still uses ACE2 as its entry receptor 22 . Moreover, the Omicron S appears to have an increased binding affinity to ACE2 relative to the wild-type (WT) S 15,16,28 .The high transmissibility and greatly enhanced resistance to antibody neutralization observed for Omicron makes this VOC particularly threatening. Therefore, further understanding of the nature of Omicron is of substantial importance and may help in developing countermeasures ag...

Hierarchical Computational Modeling and Dynamic Network Analysis of Allosteric Regulation in the SARS-CoV-2 Spike Omicron Trimer Structures: Omicron Mutations Cooperate to Allosterically Control Balance of Protein Stability and Conformational Adaptability

“…54 The cryo-EM structural analysis of the Omicron variant in the unbound form and in the complex with ACE2 revealed that the mutations Q493R, G496S, Q498R and N501Y can enhance the ACE2 binding strength and offset some loss of affinity caused by other RBD mutations. 55 Biophysical experiments studies suggested that the Omicron variant may have evolved to mediate diverse neutralization escape via multiple mutations while enhancing binding affinity with ACE2 using mutational changes in several key energy hotspots. 55 The cryo-EM analysis of the Omicron S trimers showed that Omicron substitutions in the S2 subunit can strengthen the interaction network between neighboring protomers and subunits in the closed state which may be important for regulatory functions of the S protein.…”

“…55 Biophysical experiments studies suggested that the Omicron variant may have evolved to mediate diverse neutralization escape via multiple mutations while enhancing binding affinity with ACE2 using mutational changes in several key energy hotspots. 55 The cryo-EM analysis of the Omicron S trimers showed that Omicron substitutions in the S2 subunit can strengthen the interaction network between neighboring protomers and subunits in the closed state which may be important for regulatory functions of the S protein. 56 At the same time, another group of Omicron RBM mutations Q493R, and Q498R, G496S and Y505H can mediate the improved binding with the ACE2 receptor.…”

“…81 Computer simulations of the S Omicron RBD structures and complexes with ACE2 detailed the molecular determinants of the enhanced interfacial interactions mediated by the Omicron mutational sites. 82, 83 Recent insightful evolutionary analysis 84 suggested that the mechanisms underlying emergence of the Omicron variant involves multiple fitness trade-offs including balancing between immune escape 85–87 and binding affinity for ACE2 proteins 33, 55, 56 and between the requirements to switch to the RBD-up configuration for ACE2 recognition and the increased stabilization of the closed form that prevents binding of neutralizing antibodies. 59–88…”

“…55 The cryo-EM analysis of the Omicron S trimers showed that Omicron substitutions in the S2 subunit can strengthen the interaction network between neighboring protomers and subunits in the closed state which may be important for regulatory functions of the S protein. 56 At the same time, another group of Omicron RBM mutations Q493R, and Q498R, G496S and Y505H can mediate the improved binding with the ACE2 receptor. 56 These structural insights suggested that Omicron mutations can be important in modulating both local and longrange interactions in the S protein, providing a diverse range of modulation functions through a carefully orchestrated cooperation between mutated positions.…”

“…56 At the same time, another group of Omicron RBM mutations Q493R, and Q498R, G496S and Y505H can mediate the improved binding with the ACE2 receptor. 56 These structural insights suggested that Omicron mutations can be important in modulating both local and longrange interactions in the S protein, providing a diverse range of modulation functions through a carefully orchestrated cooperation between mutated positions. The cryo-EM structures of the SARS-CoV-2 Omicron S ectodomain trimer bound to S309 and S2L20 antibodies and the X-ray crystal structure of the Omicron RBD in complex with human ACE2 further elucidated structural basis of Omicron-induced immune evasion and receptor engagement mechanisms 57 .…”