## 3 Results and Discussion
### Docking Simulations of SARS-CoV-1 S Protein-ACE2 Complex  
The docking simulations allowed investigation of emodin, promazine and anthraquinone capacities fitting within the aforementioned surface pocket. Although docking simulations reliably allow investigation of ligand-protein interaction [22; 26], a fit-for-purpose feasibility assessment was performed by comparing docking scores and experimental outcomes previously reported for emodin, promazine and anthraquinone [7]. The lack of further background data did not allow a wider system validation to be performed. Nonetheless, the results collected supported the model reliability. Indeed, emodin, promazine and anthraquinone recorded \(64.8\pm 0.4\), \(73.9\pm 0.1\) and \(53.5\pm 0.6\) GOLDScore units, respectively. Docking scores, which may correlate with the binding capacity of molecules within the pocket (the higher GOLDScore scoring, the higher the ligand-pocket match), were significantly different for the three compounds (\(p<0.001\), [PERSON]'s LSD post hoc test) and reflected the potency rank described by [PERSON] (i.e., promazine \(>\) emodine \(>\) anthraquinone) [7]. This result reinforced our hypothesis on differences in binding capacity for the three compounds at the protein-protein interface as the basis of their diverse inhibition of SARS-CoV-1 S protein-ACE2 interaction. With regard to binding architectures, emodin, promazine and anthraquinone showed similar pocket occupancy (Figure 3). Emodin engaged through polar contacts the side chain of Tyr169 and the peptidic nitrogen of Lys68 with the hydroxyl group in position 8 and the keto group in position 10, respectively (Figure 3A). Anthraquinone engaged only Lys68 with the keto group in position 10 (Figure 3B), while promazine interacted with the pocket mainly via hydrophobic contacts (Figure 3C).  
The comparison between the docking poses and the pharmacapohoric fingerprint of the pocket provided a rationale for the score differences recorded. Anthraquinone satisfied the hydrophobic requirements and, in addition, fitted the keto group in a region able to receive a hydrogen-bond acceptor group forming a polar contact (Figure 3D). Conversely, emodin maintained the same matches of anthraquinone along with the involvement of 6-methyl and 3-hydroxyl groups arranged in a region able to receive hydrophobic and hydrogen-bond donor groups, respectively (Figure 3E). These additional pharmacapohoric matches show that the structure of emodin satisfies pocket requirements better than anthraquinone. Promazine matched the hydrophobic requirements in similar fashion to anthraquinone and emodin, adding a wide pocket match with the branched chain (propan-1-ammine group), which matched both hydrophobic and polar requirements of the pocket (Figure 3F). Promazine capacity to expand interactions outside the inner part of the pocket with a good pharmacapohoric match provided a rationale for the higher computational score compared to emodin and promazine.  
Overall, docking results and pharmacophoric analysis supported the model reliability and it was assumed that the extent of ligand-pocket match is a crucial pre-requisite to stably interact at the protein-protein interface to disrupt the complex stability. Also, the agreement between computational scores and experimental outcomes reinforced the hypothesis that such interface pocket provides a relevant site of interaction for small molecules enabling the inhibition of the complex formation.