Researchers identified several antibodies to the nucleocapsid protein from a convalescent COVID-19 patient. Tests found some can inhibit complement hyperactivation and could potentially lead to new therapeutics.
Approximately half of all patients with severe COVID-19 disease develop acute respiratory distress, which can be fatal. Some patients also have symptoms similar to acute respiratory distress syndrome (ARDS). Studies have suggested that a hyperactive complement system, a part of the immune system that increases the ability of antibodies to fight infections, predisposes patients to adverse COVID-19 outcomes. Hyperactivation of the complement system, which usually helps with immunity, can lead to tissue injury.
The nucleocapsid protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of several proteins in the virus that perform numerous functions.
Although several monoclonal antibodies against the SARS-CoV-2 spike protein have been developed and clinically tested, little is known about antibodies to the nucleocapsid protein. In a paper published recently in the journal Nature Communications, researchers report a human monoclonal antibody that targets the nucleocapsid protein.
Antibodies to the nucleocapsid protein
The team collected samples from six patients in China about 7–25 days after symptom onset. Through serological analysis, they found that the antibody levels against the nucleocapsid protein were higher than the antibody levels against the virus spike protein in most patients.
The team found that the characteristics of the nucleocapsid antibodies recovered were different from those of spike antibodies during early recovery, suggesting sample collection time is critical in identifying the different immune responses to different viral proteins. These findings are consistent with those of other studies, some of which report antibodies to nucleocapsid protein developing earlier than spike antibodies and higher levels of nucleocapsid antibodies in patients requiring intensive hospital care.
From the sample of one patient, who completely recovered within nine days of symptom onset, they found 32 monoclonal antibodies that reacted to the nucleocapsid protein, which included 20 antibodies from plasma cells and 12 from memory B cells. In contrast, they found only eight monoclonal antibodies to the spike protein.
Of the antibodies that bind to the nucleocapsid protein, 13 bound to the N-terminal domain and one to the C-terminal domain. The team also determined the crystal structure for the complex with the nucleocapsid protein with one of the antibodies. The main interaction was found in the residues between 159 and 172 of SARS-CoV-2.
The binding of the antibody causes several conformational changes in the N-terminal domain, leading to the binding pocket becoming bigger and partial unfolding of the basic palm region.
Since some of the residues are conserved in all betacoronaviruses, this antibody may likely cross-react with other coronavirus nucleocapsid proteins. The authors confirmed this with binding studies, which showed that this antibody could also react with MERS-CoV.
Inhibiting complement hyperactivation
The authors also developed a method to study levels of complement activation in the presence of the SARS-CoV-2 nucleocapsid protein. They found that the nucleocapsid protein induces hyperactivation of MASP-2 proteases, enzymes used in complement activation. Addition of a nucleocapsid antibody identified before reduced the rate of reaction of the complement hyperactivation. This inhibition was also seen with three other nucleocapsid protein antibodies identified. However, the exact interaction of the virus with protease is still unknown.
There is growing evidence that severely ill COVID-19 patients benefit from the use of complement inhibitors, with several clinical trials underway. One of the nucleocapsid antibodies isolated has high binding to the protein and may potentially also inhibit complement hyperactivation.
For the other antibodies identified, the team was unable to express the nucleocapsid protein regions they attach to separately as they belonged to disordered to flexible parts of the protein. The N- and C-terminal domains of the protein are involved in several key viral functions, and in the future, they plan to focus on antibodies binding to these regions.
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