Elucidation of the Binding Modes of Known Potent Inhibitors at Mycobacterial FOF1-ATP Synthase Subunits c and ε

The FOF1-adenosine triphosphate (ATP) synthase is a classical anti-tubercular target that has led to Bedaquiline (BDQ), marketed as Sirturo® in 2012 for the treatment of tuberculosis (TB). A co-crystal structure of BDQ bound within the c subunit of the rotary ring of Mycobacterium phlei FOF1-ATP synthase was reported in 2015. Meanwhile, a hypothesis was made for its potential binding at another site in the ε subunit of ATP synthase that needs further exploration. In view of the rapidly emerging drug resistance cases, a molecule targeting multiple sites of ATP synthase is highly desirable to cope with drug resistance. In fact, a thorough understanding of the FOF1-ATP synthase structure, various binding sites, and structural insights useful for the design of new potent inhibitors are much desired. Therefore, we performed a systematic assessment of the recently resolved structures of subunits c and ε of mycobacterial ATP synthase and explored the binding characteristics of few known potent FOF1-ATP synthase inhibitors at the BDQ binding site (i.e., rotary ring, subunit c) and the hypothesized druggable subunit ε site. At the subunit c site, we observed the importance of GLU65, TYR68, LEU63, and PHE69 amino acids of protein that were in direct or water-mediated contacts with the known inhibitors, e.g., the hydroxyl and NH groups of BDQ showed hydrogen bonding and salt-bridge interactions that corroborated well with the X-ray-based information. Alongside, other inhibitors fitted well at the subunit c site and showed a combination of hydrophobic and hydrophilic interactions similar to BDQ but with different affinities. On the other hand, at the subunit ε site, we delineated the novel potential binding characteristics of these known inhibitors. Here, in the case of subunit ε site 1, ARG26, GLU31, and ARG115 were found to be important residues that were involved in either H-bond or salt-bridge interactions. Overall, the structural insights gained in this study may be useful in the design of new small molecule inhibitors targeting these two sites of the mycobacterial F-type ATP synthase enzyme.