Mutational analysis reveals the importance of residues of the access tunnel inhibitor site to human P‐glycoprotein (ABCB1)‐mediated transport

• Published in: Protein science 2024-09, Vol.33 (9), p.e5155-n/a
• Main Authors: Salazar, Paula B., Murakami, Megumi, Ranganathan, Nandhini, Durell, Stewart R., Ambudkar, Suresh V.
• Format: Article
• Language: English
• Subjects: ABC transporter; ABCB1; access‐tunnel; Adenosine triphosphate; Alanine; Antineoplastic drugs; ATP; ATP Binding Cassette Transporter, Subfamily B - antagonists & inhibitors; ATP Binding Cassette Transporter, Subfamily B - chemistry; ATP Binding Cassette Transporter, Subfamily B - genetics; ATP Binding Cassette Transporter, Subfamily B - metabolism; ATPase; Binding; Binding Sites; Chemotherapy; Drug resistance; drug‐binding pocket; Efflux; elacridar; Electron microscopy; Glycoproteins; Helices; Humans; Inhibitors; L‐site; Models, Molecular; Molecular docking; Mutagenesis; Mutants; Mutation; Nucleotides; P‐glycoprotein; Quinolines - chemistry; Quinolines - metabolism; Quinolines - pharmacology; Residues; Substrate inhibition; Substrates; tariquidar; transport; Tunnels; zosuquidar
• ISSN: 0961-8368; 1469-896X; 1469-896X
• DOI: 10.1002/pro.5155

Human P‐glycoprotein (P‐gp) utilizes energy from ATP hydrolysis for the efflux of chemically dissimilar amphipathic small molecules and plays an important role in the development of resistance to chemotherapeutic agents in most cancers. Efforts to overcome drug resistance have focused on inhibiting P‐gp‐mediated drug efflux. Understanding the features distinguishing P‐gp inhibitors from substrates is critical. Cryo‐electron microscopy has revealed distinct binding patterns, emphasizing the role of the L‐site or access tunnel in inhibition. We substituted 5–9 residues of the L‐site with alanine to investigate whether the binding of a second inhibitor molecule to the L‐site is required for inhibiting drug efflux. We reveal, for the first time, that mutations in the L‐site affect the drug efflux activity of P‐gp, despite their distance from the substrate‐binding pocket (SBP). Surprisingly, after the mutations were introduced, inhibitors such as tariquidar and zosuquidar still inhibited drug efflux by mutant P‐gps. Communication between the transmembrane helices (TMHs) and nucleotide‐binding domains (NBDs) was evaluated using the ATPase assay, revealing distinct modulation patterns by inhibitors for the mutants, with zosuquidar exhibiting substrate‐like stimulation of ATPase. Furthermore, L‐site mutations abolished ATP‐dependent thermal stabilization. In silico molecular docking studies corroborated the altered inhibitor binding due to mutations in the L‐site residues, shedding light on their critical role in substrate transport and inhibitor interactions with P‐gp. These findings suggest that inhibitors bind either to the SBP alone, and/or to alternate site(s) when the L‐site is disabled by mutagenesis.