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 SARS-CoV-2 spike NTD harbors a dominant epitope, access to which can be controlled by an allosteric mechanism that is regulated through the recruitment of a metabolite.
Our data show that the NTD of SARS-CoV-2 harbors dominant epitope(s), responsible for a considerable fraction of spike antigenicity. It is well-established that viruses employ extensive glycosylation of their envelopes to shield antibody epitopes from recognition by humoral immunity. Here, we propose a novel mode of immune evasion via allostery, regulated through recruitment of a metabolite. In contrast to glycosylation, co-opting a metabolite may allow conditional unmasking, for example under acidic conditions within the endosomal compartment. Of note, a recent study proposed pH-dependent conformational masking of the epitopes on SARS-CoV-2 RBD.
Since the beginning of the COVID-19 pandemic, considerable effort was directed to monitoring the genetic changes within the virus. The biliverdin-binding cleft has remained intact in the dominant SARS-CoV-2 variants (such as B.1.1.7, B.1.351, and B.1.1.28). However, while this manuscript under review, R190S was reported in the emerging P.1 strain. It is currently unclear how widespread this mutation is, and it will be important to continue monitoring adaptation of the bat sarbecovirus to human host. Biliverdin levels in plasma of healthy individuals (0.9-6.9 μM) and more so under pathological conditions (>50 μM) greatly exceed the Kd of its interaction with the spike (~10 nM) and are therefore sufficient to impinge on SARS-CoV-2 antigenic properties and neutralization. Although SARS-CoV-2 spike bound bilirubin with lower affinity (fig. S3), this final product of haem catabolism accumulates at higher levels in vivo. Elevated bilirubin levels correlate with the symptoms and mortality among COVID-19 patients. Therefore, the tetrapyrroles may share a role in SARS-CoV-2 immune evasion. It is important to note that the binding of biliverdin and bilirubin to the spike is characterized by fast association and dissociation kinetics (fig. S3). The affinity of a typical antibody (10-200 pM) greatly exceeds that of the biliverdin-spike interaction. Accordingly, the metabolite is able to suppress antibody binding, because it can reach considerably higher molar concentrations. In addition, tetrapyrrole levels are likely to vary between anatomical locations and during the course of natural infection, explaining the emergence of the biliverdin sensitive antibody fraction.
Severe COVID-19 symptoms and death are associated with neutrophil infiltration in pulmonary capillaries and alveolar space. Indeed, nasopharyngeal swabs of COVID-19 patients are enriched in neutrophil myeloperoxidase, a highly abundant haem-containing protein responsible for coloration of mucus. Incidentally, host mechanisms to minimize inflammation in viral infections include the activation of haem oxygenase 1. Alongside extensive vascular damage, these symptoms provide rich source of haem catabolites, which may contribute to the inability to control the infection in severe cases. Although more work is required to validate this model, our results suggest that biliverdin binding may impair the sensitivity of SARS-CoV-2 immunoassays. Furthermore, it would be of interest to evaluate spike constructs deficient for the interaction with tetrapyrroles as vaccine candidates. Our results demonstrate a remarkable structural plasticity of the NTD and highlight the importance of this domain for antibody immunity against SARS-CoV-2.
Reference & source information : https://advances.sciencemag.org/
Read More on: