When ATM molecules were merged with the SARS-CoV-2 spike protein, there was a very good fit for one particular pose at the tip of protein (Fig. 2 ). All other docking attempts on the NTD or the RBD of the spike protein were unsuccessful (Figure S2) as they did not satisfy the minimum cut-off values. Not surprisingly, their trajectories started destabilizing before 10 ns. In contrast, ATM #1 (coloured in yellow in Figure S2) remained bound to the spike protein throughout the simulation process (Fig. 3 ). Interestingly, a significant movement of the drug was observed from its docked pose to a stable MD pose (dock-to-MD transition), particularly during the first 10-ns of simulations (Figure S3). A stable complex association was then reached after 10 ns. Three amino acid residues, referred to as the “QFN triad”, exhibited significant conformational rearrangement during the binding process: Q-134, F-135 and N-137 (Fig. 3). The principal moves comprised a significant reorientation of the aromatic ring of F-135, from suboptimal stacking to stabilized T-shape CH-π interaction, and a concomitant retraction of the Q-134 side chain. Fluctuations during the 10 to 50 ns period did not affect the overall geometry of the complex, which converged to a mean energy of interaction of 92.4 ± 5.8 kJ.mol−1 as determined from triplicate MD simulations (Table S1). Schematically, the binding site is formed by two discontinuous regions of the protein, including the QFN triad with additional C-136, D-138, R-158 and S-161 residues (Fig. 4, Fig. 5 ). These seven amino acid residues accounted for almost 90% of the whole energy of interaction (Table S1 and Fig. 5).
Fig. 2 Molecular complex between the SARS-CoV-2 spike protein trimer and ATM. (a) Detailed view of ATM bound to the NTD tip of SARS-CoV-2 spike protein chain A, shown at two distinct magnifications and orientations (left and right panels). Note that the NTD tip displays a complementary landing surface for ATM (highlighted in red). The protein stretch 134-138, which contains the QFN triad, is highlighted in green. (b) The trimeric structure of the SARS-CoV-2 spike is represented in surface rendition with subunit (protein chain A, B and C) in cyan, yellow and purple, respectively. AMT (in red) is bound to the tip of the NTD domain of the A subunit (left panel). The ribbon structure of the cyan (chain A) subunit is shown in the right panel. (c) Above views of the spike-ATM complex. Note that the B and C subunits also display a fully accessible ATM binding site (red asterisk).
Fig. 3 Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex.
Fig. 4 Schematic of ATM interaction at the tip of the spike protein. Residues lining cavity under 3.5Å are shown. Hydrogen bonds and CH-π stacking interactions are indicated. Note that Q-134 (Gln-134) and S-161 (Ser-161) are linked by a hydrogen bond, which stabilizes the ATM-spike complex.
Fig. 5 Energy of interaction of spike protein-ATM and spike-GM1 complexes. Results are expressed by amino acid residue as mean ± SD of three distinct MD simulations (50 ns) with the same starting docking conditions. In the case of GM1, the simulations are done in presence of sphingomyelin and cholesterol to mimic a lipid raft plasma membrane domain. Each bar corresponds to a single amino acid residue, as indicated in the horizontal axis. Detailed values and statistics are shown in Table S1.