Molecular basis of V-ATPase inhibition by bafilomycin A1

Rong Wang,Xiao-Song Xie,Xiaochun Li,Chia-Hsueh Lee,Jin Wang,Abdirahman Hassan

doi:10.1038/s41467-021-22111-5

Abstract

Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7’-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.

Highlights

Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses
The transmembrane helix 0 (TM0) of subunit c′′ along with the TMs of PRR and Ac45 constitutes the core of the Vo domain (Supplementary Fig. 1a, b)
To validate the potency of bafilomycin A1 to inhibit the V-ATPase activity, we measured the inhibitory effect of bafilomycin A1 on the proton translocation activity of V-ATPase which would be an assay for completely coupled enzyme

Summary

Introduction

Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin, a member of the pleomacrolides family, was identified as the first specific V-ATPase inhibitor in the 1980s (Fig. 1a). This molecule can inhibit V-ATPases from a broad range of organisms including yeast and mammals at nanomolar concentrations[15]. Many other V-ATPase inhibitors such as concanamycin, archazolid, and the plant toxin pea albumin 1 subunit b (PA1b) (Supplementary Fig. 2) show some overlap with the bafilomycin’s binding sites, indicating a common mechanism of inhibition[16]. Most available inhibitors of V-ATPase exhibit cellular toxicity due to a lack of tissue specificity[22] These inhibitors represent complex chemical structures, and their synthetic modification is challenging. The molecular basis for how they inhibit the V-ATPase will provide valuable insights necessary for understanding the physiological role of V-ATPases and for facilitating the rational design of potential drugs

Methods

Results

Conclusion