Unraveling the Mechanism of Action of Myricetin in the Inhibition of hUba1∼Ubiquitin Thioester Bond Formation via In Silico Molecular Modeling Techniques.

Ubiquitination is a crucial type of protein modification which helps to control substrate degradation and maintain cell homeostasis. Recent studies suggest that ubiquitination and deubiquitination are involved in regulating metabolic reprogramming in cancer cells and maintaining cancer stem cells. Uba1, a crucial protein in the ubiquitination cascade, can be targeted to develop effective inhibitors for cancer treatment. In previous work, we showed that myricetin (Myr) acts as a potential human Uba1 (hUba1) inhibitor. In this study, we have utilized computational modeling techniques to attempt to illustrate the mechanism of action of Myr. Through extra-precision docking, we confirmed that Myr binds to the adenosine triphosphate (ATP)-binding site of hUba1 (referred to as hotspot 1) with the highest binding affinity. The dynamics of this interaction revealed that hUba1 undergoes a conformational shift from open to closed upon binding of Myr. Myr also migrates outward to interact with the crossover loop simultaneously as the rotational shift of the ubiquitin fold domain (UFD) takes place, thereby blocking access to the ubiquitin binding interface of hUba1 and the crossover loop. The outward migration also explains the reversible nature of Myr binding to hUba1 in previous experiments. We hypothesize that Myr acts as an inhibitor of Uba1∼Ub thioester bond formation by causing a large domain shift toward a closed conformation. Few other analogues of Myr containing the same flavone skeleton showed promising docking scores against hUba1 and could be considered for further validation. We propose that Myr and some of its analogues reported in this study may be promising candidates for developing effective Uba1 inhibitors for cancer treatment.