1
|
Gao Y, Wei C, Luo L, Tang Y, Yu Y, Li Y, Xing J, Pan X. Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein. Front Mol Biosci 2024; 11:1364494. [PMID: 38560519 PMCID: PMC10979361 DOI: 10.3389/fmolb.2024.1364494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.
Collapse
Affiliation(s)
- Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Tang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongzhen Yu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yaling Li
- Department of Pharmacy, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|