Domain server

Sugar-binding pockets in the N-terminal domain may increase the infectivity of SARS-CoV-2

The majority of research on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) focuses on the spike protein because it is crucial for viral entry and subsequent infection. In addition, special attention was paid to the spike protein receptor binding domain. However, another region called the N-terminal domain is also involved in viral entry into the host cell via binding to the sialic acid receptor.

The N-terminal domain has a fold that can bind sugar, and new research by Jonathan Lees of the University of Oxford Brookes found that the sugar-binding pockets near the N-terminal domain help increase sugar binding. viral infectivity. Additionally, the results show that the SARS-CoV-2 sugar binding pockets evolve with added loops seen in the pockets of new variants.

The SARS-CoV-2 variants of concern Gamma, Delta Plus, and Omicron have mutations in the N-terminal domain near the sugar-binding pockets and are associated with increased transmission. Understanding the structure of sugar binding pockets on the N-terminal domain could help create new antiviral drugs.

The study “Insertions in the N-Terminal Spike SARS-CoV-2 domain may aid in the transmission of COVID-19” was recently published on the website bioRxiv* preprint server.

To study: Insertions in the N-Terminal Spike SARS-CoV-2 domain may facilitate transmission of COVID-19. Image Credit: NIAID

Pockets in the N-terminal domain have strong sugar binding

The researchers analyzed four binding pockets in the N-terminal domain of SARS-CoV-2 as well as the N-terminal domain of other coronaviruses.

The results showed that the second and third pockets had greater sialic acid binding than the first sugar binding pocket.

The binding strength of the second pouch differed between all of the coronaviruses studied. However, the third pocket retained strong binding to sialic acid.

In addition, the insertions in the N-terminal domain contributed to more loops which extended the first pocket. The end result was increased contact and binding with sialic acid. Other regions of the N-terminal domain near the sugar binding pockets also enhanced sugar binding interactions.

Structure of the Spike SARS-CoV2 protein highlighting the different domains.  The RB domain is colored in blue, the NTD domain in purple, the SD1 domain in gray and the SD1 doma in black.  The trimer complex is represented in (A).  The S1 region of a Spike protein monomer is shown (B).  The interactions of NTDs with the SD1 and SD2 domains of the trimer of the Spike protein are presented in (C).  Structure of the 6VSB PDB.
Structure of the Spike SARS-CoV2 protein highlighting the different domains. The RB domain is colored in blue, the NTD domain in purple, the SD1 domain in gray and the SD1 domain in black. The trimer complex is represented in (A). The S1 region of a Spike protein monomer is shown (B). The interactions of the ATNs with the SD1 and SD2 domains of the trimer of the Spike protein are presented in (C). Structure of the 6VSB PDB.

Evolution of binding pockets in new coronavirus strains

Pockets 2 and 3 were more diverse in their structure. In addition, the emergence of the indel IR2 region – an area with a sugar binding motif for sialic acids – in the N-terminal domain is able to interact with pockets 2 and 3 due to the added loop. The results suggest that the SARS-CoV-2 virus evolves in these areas to improve sialic acid binding and increase infectivity.

Structural superposition of MTN Cov (SARS-CoV, PDB ID 6ACC, Pangolin CoV G PDB ID 7CN8, Pangolin-CoV-GD, PDB-ID 7BBH, Bat-Cov-RaTG13, PDB ID: 7CN4, SARS-Co 2, PDB ID 7C2L).  Structures are stained according to their secondary structural components (and proteins (different species / variants) (B).
Structural superposition of MTN Cov (SARS-CoV, PDB ID 6ACC, Pangolin CoV G PDB ID 7CN8, Pangolin-CoV-GD, PDB-ID 7BBH, Bat-Cov-RaTG13, PDB ID: 7CN4, SARS-Co 2, PDB ID 7C2L). Structures are stained according to their secondary structural components (and proteins (different species / variants) (B).

The researchers hypothesize that the SARS-CoV-2 virus could evolve specifically in these areas in response to specific changes in sugar in human cells. Indeed, studies on binding energy have shown that some worrisome variants of SARS-CoV-2 increased binding to sugars in pocket 3.

Pockets identified in the NTD domain of SARS-CoV-2 (A) and the NTD antigenic supersite SARS-CoV-2 shown in green (B).  For (A) we have colored pocket 1 yellow, pocket 2 blue, pocket 3 red and pocket 4 cyan.  Structures of APB 7C2L.  Supporting references: Behloul et al., 202 Fantini et al., 2020;  Baker et al., 2021;  Di Gaetano et al., 2021;  McCallum et al., 2021.
The pockets identified in the NTD domain of SARS-CoV-2 (A) and the NTD antigenic supersite SARS-CoV-2 are indicated in green (B). For (A) we have colored pocket 1 yellow, pocket 2 blue, pocket 3 red and pocket 4 cyan. Structures of APB 7C2L. Supporting references: Behloul et al., 202 Fantini et al., 2020; Baker et al., 2021; Di Gaetano et al., 2021; McCallum et al., 2021.

Sugar binding affinity differs among coronaviruses and SARS-CoV-2 variants of concern

The researchers performed a computer analysis to measure the binding energy of coronaviruses to sialic acid.

Their results revealed stronger binding activity in the N-terminal domain of SARS-CoV-2 compared to SARS-CoV. Specifically, the binding was strongest in binding pockets 1-3.

Compared to SARS-CoV and the original strain of SARS-CoV-2 identified in Wuhan, China, the Kappa variant with the E154K mutation had stronger binding in pocket 1. In addition, the Delta, Iota and Mu also had a stronger binding in pocket 3 when they had the T95I mutation.

Overlay of MTN CoV structure.  A) includes the 16 BCoV NTDs in the multipath sequence alignment (see Figure 5).  B) constitutes 24 BCoV NTD of the CATH family.  For and B), we used known structures and structural models (built using AlphaFold2).  We found a highly preserved bag (in the box) (score of 1838 - a highly positive DrugScore constitutes high processing ability) that could be a good target for coronavirus drugs.  C) illustrates this pocket prediction by CavityPlus in blue.  D) We calculated the structural conservation of the pockets by calculating t the mean SSAP score.
Overlay of MTN CoV structure. A) includes the 16 BCoV NTDs in the multipath sequence alignment (see Figure 5). B) constitutes 24 BCoV NTD of the CATH family. For and B), we used known structures and structural models (built using AlphaFold2). We found a highly preserved bag (in the box) (score of 1838 – a highly positive DrugScore constitutes high processing ability) that could be a good target for coronavirus drugs. C) illustrates this pocket prediction by CavityPlus in blue. D) We calculated the structural conservation of the pockets by calculating the mean SSAP score.

T95I mutations are one of the more recent mutations found in the Delta plus variant.

An interesting observation for the researchers is that the distance between the mutations of the sugar-binding pockets can influence the binding to other regions close to the pocket even if they do not bind directly to sialic acid.

The Gamma, Omicron, and Delta Plus variants have high binding energy in the binding pockets of the N-terminal domain 1 and 3. This may be related to the increased level of transmission observed with these worrisome variants.

“We offer continuous monitoring of mutations and indels of NTDs in the context of new emerging variants and their impacts on sugar binding,” the research team wrote. “For example, the Omicron variant has a rather unique 3 amino acid insert at position 214 which is near pocket 3.”

The high shelf life and drug nature of Bag 1 make it a suitable target for the development of drugs which would reduce or block binding to sialic acid. The researchers note that targeting galectins and sugar-binding pockets could help prevent host cell infectivity and influence the immune response against the virus.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behavior, or treated as established information.