Multi-Target Computational Screening Identifies Robinin as a Potential Natural Broad-Spectrum ATP-Competitive Candidate for ABC Transporters Associated with Multidrug Resistance

Background: Several ATP-binding cassette (ABC) transporters are associated with multidrug resistance (MDR) in cancers and pathogens. Targeting their nucleotide-binding domains (NBDs), which drive ATP hydrolysis, is a promising strategy to overcome MDR. This study aimed to identify natural ATP-competitive modulators with reported anticancer and MDR-modulating activities, targeting the NBDs of the major MDR-associated transporters ABCB1, ABCC1, and ABCG2. Methods: A total of 71 natural compounds were docked with the isolated NBDs of the three transporters. The top five hit compounds were further evaluated for structural stability, hydrogen-bond networks, residue-contact frequencies, and binding affinity using GROMACS MD simulations and MM/PBSA free-energy analysis. Results: Five compounds—(–)-catechingallate, limonin, naringin, rhoifolin, and robinin—identified through molecular docking exhibit favorable docking scores for the ATP-binding pockets of all three transporters (ranging from −6.57 ± 0.21 to −8.63 ± 0.32 kcal/mol). MD simulations revealed that robinin demonstrated the greatest structural stability, sustained hydrogen-bonding networks (averaging 5.35 per frame; range 3.04–7.48), high residue-contact frequencies (up to 60 contacts per frame), and consistently low minimum distances (approximately 0.17 nm) within the ATP-binding site across all transporters. Free-energy analysis additionally indicated that all five compounds exhibited energetically favorable interactions, with robinin demonstrating the most favorable and reliable binding free energy (−24.41 to −48.0 kcal/mol). Conclusions: Our findings suggest that robinin is a promising predicted candidate that may act as an ATP-competitive modulator of MDR-associated ABC transporters. Additional experimental validation is required to confirm direct binding and therapeutic potential in overcoming drug resistance.