New nanobodies target SARS-CoV-2 replication protein

Published online 9 November 2021

Two new nanobodies might inhibit a protein crucial for SARS-CoV-2 replication.

Rieko Kawabata

The team mapped specific nanobody contacts (cyan) on the SARS-CoV-2 Nsp9 tetramer using NMR spectroscopy.
The team mapped specific nanobody contacts (cyan) on the SARS-CoV-2 Nsp9 tetramer using NMR spectroscopy.
Piergiorgio Percipalle and Gennaro Esposito
A multinational team of researchers has identified two nanobodies that are capable of specifically blocking SARS-CoV-2 replication. 

Nanobodies are antibody fragments derived from llamas and other camelids and are increasingly viewed as promising therapeutic proteins. Several studies have focused on nanobodies that target the SARS-CoV-2 spike protein. However, in a bid to widen the range of nanobodies that may have potential use in diagnostics and treatment, researchers have turned their attention to Nsp9, a key RNA-binding protein in the SARS-CoV-2 replication transcription complex (RTC).   

To initiate replication, a viral enzyme subcomponent, called NiRAN, adds a nucleoside monophosphate to Nsp9. Researchers led by Piergiorgio Percipalle, of New York University Abu Dhabi (NYUAD), aimed to block this part of the viral replication process.

By conducting a series of enzyme-linked immunosorbent assay (ELISA) tests, the team identified 136 nanobodies that are capable of targeting Nsp9. Two of these nanobodies, called 2NSP23 and 2NSP90, were tested and found to specifically recognize even low concentrations of Nsp9. The finding suggests they could lead to the development of highly sensitive, cost-effective diagnostic tools. 

Importantly, the two nanobodies were able to bind to Nsp9 in saliva samples from patients infected with COVID-19. 

Further analysis using nuclear magnetic resonance (NMR) spectroscopy showed that 2NSP23 and 2NSP90 affect Nsp9 in a way that appears to disrupt the RTC and effectively block viral replication.

Percipalle and co-author Gennaro Esposito at NYUAD say that 2NSP23 and 2NSP90 may serve as possible Nsp9 inhibitors, negatively impacting on SARS-CoV-2 replication by disturbing the protein’s transition into its stable form. 

Percipalle adds that the study identifies Nsp9 as “a novel druggable target”, implying that the findings could lead to new treatment options. “We hope that our research will produce a new generation of antivirals specific for SARS-CoV-2 but also for other variants and other members of the coronavirus family, given that Nsp9 is highly conserved among them,” he says.

“In addition to providing insights into new strategies to test for and treat COVID-19 infections, the report highlights the strengths of applying solution NMR spectroscopy to study biophysical properties of proteins, and the recent drug discovery focus on protein-protein interactions,” says physical biochemist, Garry Buchko at Pacific Northwest National Laboratory, in the United States, who was not involved in the study. 


Esposito, G. et al. NMR-based analysis of nanobodies to SARS-CoV-2 Nsp9 reveals a possible antiviral strategy against COVID-19. Adv. Biology (2021).