SuperNatural inhibitors to reverse multidrug resistance emerged by ABCB1 transporter: Database mining, lipid-mediated molecular dynamics, and pharmacokinetics study

• DOI: 10.1371/journal.pone.0288919
• Publication Date: 2023-07-26T18:32:53Z
• Authors: Mahmoud A. A. Ibr...; Khlood A. A. Abde...; Alaa H. M. Abdelr...; Mahmoud M. H. Abd...; Mohamed Ahmed Naeem; Gamal A. H. Mekhemer; Peter A. Sidhom; Shaban R. M. Sayed; Paul W. Paré; Mohamed-Elamir F....
• Keywords: Pharmacology, Toxicology and Pharmaceutics; Computational chemistry; ATP Binding Cassette Transporter, Subfamily B; Docking (animal); Pharmaceutical Science; Multiple drug resistance; Nursing; Molecular Dynamics Simulation; FOS: Health sciences; P-glycoprotein; Molecular dynamics; Transporter; POPC; Biochemistry; Gene; Lipid bilayer; Drug Delivery Systems; In vitro; Copper and Zinc in Health and Disease; Antibiotics; Cell Line, Tumor; Health Sciences; In vivo; ATP-binding cassette transporter; Genetics; Pharmacokinetics; Biology; Pharmacology; Nutrition and Dietetics; Mechanisms of Multidrug Resistance in Cancer; In silico; Membrane; Life Sciences; ATP-dependent Transporters; Lipids; Drug Resistance, Multiple; 3. Good health; Molecular Docking Simulation; Chemistry; Oncology; Drug Resistance, Neoplasm; Lipinski's rule of five; FOS: Biological sciences; Medicine; Multidrug Resistance; Research Article

An effective approach to reverse multidrug resistance (MDR) is P-glycoprotein (P-gp, ABCB1) transport inhibition. To identify such molecular regulators, the SuperNatural II database, which comprises > 326,000 compounds, was virtually screened for ABCB1 transporter inhibitors. The Lipinski rule was utilized to initially screen the SuperNatural II database, identifying 128,126 compounds. Those natural compounds were docked against the ABCB1 transporter, and those with docking scores less than zosuquidar (ZQU) inhibitor were subjected to molecular dynamics (MD) simulations. Based on MM-GBA binding energy (ΔGbinding) estimations, UMHSN00009999 and UMHSN00097206 demonstrated ΔGbinding values of –68.3 and –64.1 kcal/mol, respectively, compared to ZQU with a ΔGbinding value of –49.8 kcal/mol. For an investigation of stability, structural and energetic analyses for UMHSN00009999- and UMHSN00097206-ABCB1 complexes were performed and proved the high steadiness of these complexes throughout 100 ns MD simulations. Pharmacokinetic properties of the identified compounds were also predicted. To mimic the physiological conditions, MD simulations in POPC membrane surroundings were applied to the UMHSN00009999- and UMHSN00097206-ABCB1 complexes. These results demonstrated that UMHSN00009999 and UMHSN00097206 are promising ABCB1 inhibitors for reversing MDR in cancer and warrant additional in-vitro/in-vivo studies.