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Edited by Richard Callaghan, Australian National University, Canberra, ACT, Australia, and accepted by Editorial Board Member Axel T. Brunger September 8, 2020 (received for review May 21, 2020)
Significance
ABCB1 is a membrane transport protein that protects cells from toxic compounds. At the same time, it limits the uptake of orally administered drugs and contributes to multidrug resistance in cancer cells. Small-molecule inhibitors of ABCB1 could alleviate these negative effects, but their development requires detailed insight into how such compounds interfere with ABCB1-catalyzed drug extrusion. Our study shows how ABCB1 inhibitors bind in pairs and can block the function of the transporter by interacting with structural features that are important for its transport function. Our results therefore provide insight into the mechanism of ABCB1 and will be valuable for the development of more effective inhibitors.
Abstract
ABCB1 detoxifies cells by exporting diverse xenobiotic compounds, thereby limiting drug disposition and contributing to multidrug resistance in cancer cells. Multiple small-molecule inhibitors and inhibitory antibodies have been developed for therapeutic applications, but the structural basis of their activity is insufficiently understood. We determined cryo-EM structures of nanodisc-reconstituted, human ABCB1 in complex with the Fab fragment of the inhibitory, monoclonal antibody MRK16 and bound to a substrate (the antitumor drug vincristine) or to the potent inhibitors elacridar, tariquidar, or zosuquidar. We found that inhibitors bound in pairs, with one molecule lodged in the central drug-binding pocket and a second extending into a phenylalanine-rich cavity that we termed the “access tunnel.” This finding explains how inhibitors can act as substrates at low concentration, but interfere with the early steps of the peristaltic extrusion mechanism at higher concentration. Our structural data will also help the development of more potent and selective ABCB1 inhibitors.
Footnotes
- ↵1To whom correspondence may be addressed. Email: locher{at}mol.biol.ethz.ch.
Author contributions: K.N. and K.P.L. designed research; K.N., K.R., R.N.I., J.K., and K.P.L. performed research; N.F. contributed new reagents/analytic tools; K.N., K.R., A.A., and K.P.L. analyzed data; and K.N. and K.P.L. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission. R.C. is a guest editor invited by the Editorial Board.
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2010264117/-/DCSupplemental.
Data Availability.
Data associated with this research have been deposited in the Electron Microscopy Data Bank (EMDB) (EMD-11666, EMD-11667, EMD-11670, EMD-11671, EMD-11672). Coordinates for deposited models are available at the Protein Data Bank with IDs: 7A65 (drug-free ABCB1–MRK16-Fab), 7A69 (vincristine-bound ABCB1–MRK16-Fab), 7A6C (elacridar-bound ABCB1–MRK16-Fab), 7A6E (tariquidar-bound ABCB1–MRK16-Fab), and 7A6F (zosuquidar-bound ABCB1–MRK16-Fab).
Published under the PNAS license.
References
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Cryo-EM structures reveal distinct mechanisms of inhibition of the human multidrug transporter ABCB1
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- Biophysics and Computational Biology
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