1.6  The function of S1-NTD
In at least some coronaviruses, S1-NTD is known to be involved in binding host proteins or glycans, but coronaviruses show great diversity in their binding which presumably underlies their ability to jump between very different host species. While the role of S1-NTD Compared with the current reasonably detailed knowledge of the remarkable mechanism of cell entry involving ACE2 and changes to the spike protein on cleavage, the specific function of S1-NTD of SARS-CoV-2 has not been elucidated (at least, not by the time of writing in April 2020). As noted above, S1 in SARS-CoV-2 is now well known to have a region which is the receptor binding domain to human ACE2 but also, significantly for what follows in the text below, SARS-like coronaviruses can bind CLEC4M/DC-SIGNR C-type lectin domains on host cells. See Ref. [12] for review of the diverse receptor recognition mechanisms of coronaviruses up to 2015, which represented the body of understanding until the COV-19 pandemic. Bovine coronavirus is an example of a coronavirus for which it seems clear that S1-NTD has an established glycan-binding function. Although the structure of a sugar-bound Bovine CoV S1-NTD was not available, some conclusions could be reached by researchers using structure-guided mutagenesis and comparisons with different coronaviruses. As well as evidence in 2008 linking hemagglutinin-esterase to the S1 domain of at least some coronaviruses [9], Zhang and Yap [13] had reported in 2004 a rational 3D model for S1 domain of SARS-CoV spike protein by fold recognition and molecular modeling techniques, and there they noted a suggestive structure similarity between S1 protein and influenza virus neuraminidase [14]. This opened up the possibility for those authors that existing anti-influenza virus inhibitors and anti-neuraminidase antibody could be used as a starting point for designing anti-SARS drugs, vaccines and antibodies [14].
Based on such observations and discussion so far, it is therefore reasonable to propose that S1-NTD could be important in the binding of certain alternative host cell surface receptors, or perhaps which aid in targeting the virus to ACE2, and so might provide a helpful therapeutic target (as well as candidate antigenic site for synthetic vaccine design). Nonetheless, such functions if present in SARS-CoV-2 could, a priori, reside in other domains at the virus surface. The challenge for research here is that the substantial knowledge concerning such matters in well-studied coronaviruses is not readily transferable. Variously throughout the coronaviruses, S1-NTD, CTD and S2 regions can recognize either protein or sugar receptors or both in various cases, and very similar coronavirus spike protein domains within the same genus may recognize different host cell receptors, while many very different coronaviruses may recognize the same host cell receptor. The studies mentioned above also suggested that at least some coronavirus S1-NTDs are evolutionarily related to human galectins, the term typically used for the lectins as carbohydrate-binding proteins that are specifically involved in inflammation, immune responses, cell migration, autophagy and signaling; however the viral domains derived from them have diverged with specificities for different sugar receptors [12]. Further review is given throughout Results Section 4 where appropriate. Another challenge discussed in Results Section 4 is that key regions for which an experimental 3D structure would help resolve the matter are disordered, and hence invisible, in current available spike protein structures.