SARS-CoV-2 entry into the host cells has been reported to follow a direct fusion mechanism soon after the cleavage at the second cleavage site in the spike protein by the activated protease of TMPRSS2 (Wang & Xiang, 2020). Despite this, literature evidences suggest that endocytosis pathway for viral entry cantnot be completely ruled out (Burkard et al., 2018; Yap et al., 2015). Taking cue from the fact that S2’ cleavage by the activated serine protease domain which is tethered to the hNECD by a disulfide bond between Cys244 And Cys365, positions the hNECD and the primed VS2’ at a distance proximal enough for their possible binding with each other. Our modelling followed by docking studies presented in this communication are the attempts toward giving a model of this possible interaction. We propose that the hNECD binds to primed Spike protein and results in SRCR/LDLRA domain mediated endocytosis of SARS-CoV-2 into the host cells. Till now, protein-protein Interaction between the serine protease domain of TMPRSS2 and spike protein has only been investigated to understand their molecular interactions involved in the cleavage of spike protein at S1/S2 and S2 cleavage sites (Mushtaq Hussain et al., 2020). However, the interaction between hNECD and VS2’ has not yet been captured or reported. This may perhaps be due to the inability of the methods, i.e., affinity-purification mass spectrometry, to detect the interactions involving membrane-bound proteins (Gordon et al., 2020)
We have used interaction interface of hNECD from hNECD-VS2’ complex for virtual screening of FDA approved drugs and druggable phytochemical compounds derived from Indian medicinal plants database and identified top10 potential drugs and top10 potential phytochemical compounds that could inhibit the interaction between hNECD and VS2’ and thereby SARS-CoV-2 virus entry mediated by hNECD into host cells. We mapped known mutations of concern and mutations of interest in SARS-CoV-2 spike protein and observed none of these mutations mapped at interaction interface of VS2’ with hNECD and therefore we can consider this hNECD-VS2’ interaction as a potential therapeutic target for targeting the current SARS-CoV-2 variant of concerns.
Our virtual screening of FDA approved drugs has identified Dutasteride as one of the hits. This drug has undergone a clinical trial for males with mild COVID-19 symptoms with a promising benefit (Cadegiani, McCoy, Gustavo Wambier, & Goren, 2021). Maraviroc which is known to block HIV entry into the host cells has also been shown by in vitro studies to inhibit early infection of SARS-CoV-2 (preprint Kenneth et al., 2020). In the light of our model, further studies could be carried to investigate the efficacy of these drugs in patients with COVID-19. Our studies have also identified some phytochemical compounds to initiate target i.e, hNECD-VS2’ interaction-based studies. It is known that the medicinal plant Gamhar shows antiviral activity however its active compound and its possible target have not been well studied and in this light, our study can be used as the testable hypothesis to conduct further studies to check efficacy of these phytochemical compounds for the treatment of COVID-19.
Mapping of known mutations of concern and mutations of interest onto the interaction interface of S2’
Mutations with evidence of increasing transmissibility or virulence or decreasing therapeutic/vaccine efficacy are classified as Mutations of Concern (MC), and the mutations suspected of causing a change in transmissibility or virulence or therapeutic/vaccine efficacy are classified as Mutations of Interest (MI) (https://outbreak.info/situation-reports).
Mutation E484K has been classified as an MC and the mutations L18F, K417N, K417T, N439K, L452R, S477N, S494P, N501Y, P681H, P681R have been classified as MIs. It is interesting to find that none of these mutations (both MC and Mis) map on to the interaction interface of S2’ and hNECD.
Delta variant has one mutation D950N in the S2’ region and this mutation is not present at interaction interface of S2’ with hNECD. Omicron strain has four mutations N856K, Q954H, N969K, and L981F in the S2’ region. Out of these four mutations, two mutations N856K and L981F are at the interaction interface of S2’ with hNECD. Stealth Omicron (BA.2) has only two mutations Q954H and N969K, in the S2 region and none of these mutations are at the interaction interface of S2’ with hNECD. Mutations mapped on spike protein corresponding to the variants of concern are listed in the Table 3.
Table 3: Five Variants of concern SARS-CoV-2 strains and their respective mutations.
Variant of concern
|
Mutations in spike protein
|
Mutations at the interaction interface of S2’
|
Delta
|
T19R, E156G, DEL157/158, L452R, T478K,
D614G, P681R, D950N
|
NA
|
Omicron
|
A67V, DEL69/70, T95I, G142D, DEL143/145, N211I, DEL212/212,G339D, S371L, S373P, S375F, S477N, T478K,E484A,Q493R,N501Y,Y505H, T547K, D614G, H655Y, N679K, P681H, N764K,D796Y,N856K,Q954H, N969K,L981F
|
N856K, L981F
|
Alpha
|
DEL69/70,DEL144/144,N501Y,A570D,D614G,P681H,
T716I,S982A,D1118H
|
S982A
|
Beta
|
D80A,D215G,DEL241/243,K417N,E484K,N501Y,
D614G,A701V
|
NA
|
Gamma
|
L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y
D614G,H655Y,T1027I,V1176F
|
NA
|
It is to be noted that an attempt was made to investigate interaction between hNECD and VS2' by expressing the synthetic genes corresponding to the hNECD and VS2' in E.coli using the standard pull down assays. This study could not identify interaction between the engineered proteins (Dayananda Siddavattam, Private communication). This result could be considered as a false-negative due to the following reason. The proteins of the synthetic genes correspond to the truncated domains devoid of their membrane anchoring parts and other domains. It is very likely that these unanchored isolated proteins do not fold into the required 3D structures under the experimental conditions. Needless to mention the folded structures are quintessential for protein-protein interactions.