Overall, these molecular modelling studies are consistent with the notion that ATM might inhibit SARS-CoV-2 infection through direct binding to the virus spike and subsequent neutralization of the infection process, which requires spike protein recognition and attachment to gangliosides. This mechanism of action is illustrated in Fig. 8 . Comparing the models in Figs. 8a and 8b shows that both ATM and gangliosides bind to the same site of the spike protein, centred on the QFN triad. Thus, in the presence of ATM, the virus spike would not reach gangliosides on the host plasma membrane (Fig. 8c). To the best of our knowledge, it is the first time that such a mechanism of action is proposed to explain the antiviral effect of ATM.
Fig. 8 CLQ-OH/ATM combination therapy at the molecular level. (a) ATM bound to the SARS-CoV-2 spike protein trimer. (b) Ganglioside dimer (two symmetrically arranged GM1 molecules in a typical chalice-like shape, just like the one observed in lipid raft simulations) bound to SARS-CoV-2 spike protein trimer. Note that both ATM and gangliosides share the same binding region. (c) ATM prevents ganglioside binding to the SARS-CoV-2 spike protein trimer. CLQ-OH, once bound to gangliosides (blue and orange surfaces), also prevents any interaction with the viral spike. (d) 4 CLQ-OH molecules bound to a ganglioside dimer. Each GM1 molecule is blocked by two CLQ-OH molecules (blue and orange surfaces), which wrap around the saccharide part. (e) Detail of the 134-138 SARS-CoV-2 spike protein stretch bound to GM1. Note that the ganglioside interacts with Q-134 and F-135, but not with D-138. (f) Detail of the 134-138 SARS-CoV-2 spike protein stretch bound to ATM. In this case, the binding site includes D-138 in addition to Q-134 and F-135. Note that N-137, which interacts with both ATM and GM1, is not visible in these representations as it is located behind.