In this section, we present important allosteric mechanisms in the main protease of SARS-CoV-2. Using our ensemble-based methods, we were able to reliably recognise allosteric modulations hitherto unknown. We elucidate binding cooperativity between RQN and LZE ligands such that the presence of LZE affects the binding interactions of RQN at its active site and vice-versa. Such modulations also provide an explanation for the inhibitory effect of LZE. Thanks to our ensemble approach, we are able to confidently state that such effects do not affect RQN's binding affinity. In addition, we also discovered an unknown mechanism of Figure : ∆G values obtained from different free energy protocols: ∆G direct compared against ∆G ESM ACS using both the standard ESMACS protocol as well as that using bound conformations extracted from "long" trajectories. "corr" denotes the Pearson's correlation coefficient. Dashed lines denote the best fit lines for each plot. All values are in kcal/mol. action of RQN ligand which has been shown to act by binding at the substrate binding site.