SARS-CoV-2 recruits a haem metabolite to evade antibody immunity

Abstract

The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of haem metabolism, with nanomolar affinity. Using cryo-electron microscopy and X-ray crystallography we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope and demonstrate the remarkable structural plasticity of the NTD.

Linking COVID-19 and heme-driven pathophysiologies: A combined computational-experimental approach

“…In the past, heme-binding studies on the level of protein-derived peptides as a tool for the evaluation of motifs derived from proteins was successful to characterize heme binding, as can be exempli ed with IL-36α and APC [82,83]. In addition, heme binding to the S1 subunit of the S protein has been analyzed with surface plasmon resonance spectroscopy recently, which revealed a binding a nity of ~ 7 nM [86]. The study focused on bilirubin binding to the S protein, yet lacked information about heme-binding sites, stoichiometry and functional consequences of heme binding.…”

SARS-CoV-2-specific memory B cells can persist in the elderly despite loss of neutralising antibodies

“…S1c). This highlights the importance of the RBD as the major target for neutralising antibodies, whilst also underscoring the contribution of antibodies targeting regions outside of the RBD (for example the NTD of the spike protein 15,[29][30][31] ) to the neutralising antibody response, at the 5 month timepoint in this cohort. These data therefore revealed the persistence of detectable, albeit reduced, MBC specific for both spike and RBD in most people whose nAb titres against live virus had fallen below the threshold of detection.…”

“…Recombinant S1 protein constructs spanning SARS-CoV-2 residues 1-530 for ELISpot were produced as previously described. 28,30 Briefly, codon-optimised DNA fragments were cloned into mammalian expression vector pQ-3C-2xStrep to create plasmids, which were then transfected into Expi293F cells growing at 37 in 5% CO2 atmosphere using ExpiFectamine reagent (Thermofisher Scientific). Proteins were purified by strep-tag affinity and subsequently size exclusion chromatography.…”

Linking COVID-19 and Heme-Driven Pathophysiologies: A Combined Computational–Experimental Approach

“…In the past, heme-binding studies on the level of protein-derived peptides as a tool for the evaluation of motifs derived from proteins were successful in characterizing heme binding, as can be exemplified with IL-36α and APC [83,84]. In addition, heme binding to the S1 subunit of the S protein was recently analyzed with surface plasmon resonance spectroscopy, which revealed a binding affinity of~7 nM [87]. The study focused on bilirubin binding to the S protein, yet lacked information about heme-binding sites, stoichiometry, and the functional consequences of heme binding.…”