Targeting mTOR Kinase with Natural Compounds: Potent ATP-Competitive Inhibition Through Enhanced Binding Mechanisms

Abstract

Background/Objectives: The mammalian target of the rapamycin (mTOR) signaling pathway is a central regulator of cell growth, proliferation, metabolism, and survival. Dysregulation of mTOR signaling contributes to many human diseases, including cancer, diabetes, and obesity. Therefore, inhibitors against mTOR's catalytic kinase domain (KD) have been developed and have shown significant antitumor activities, making it a promising therapeutic target. The ATP-KD interaction is particularly important for mTOR to exert its cellular functions, and such inhibitors have demonstrated efficient attenuation of overall mTOR activity. Methods: In this study, we screened the Traditional Chinese Medicine (TCM) database, which enlists natural products that capture the relationships between drugs targets and diseases. Our aim was to identify potential ATP-competitive agonists that target the mTOR-KD and compete with ATP to bind the mTOR-KD serving as potential potent mTOR inhibitors. Results: We identified two compounds that demonstrated interatomic interactions similar to those of ATP-mTOR. The conformational stability and dynamic features of the mTOR-KD bound to the selected compounds were tested by subjecting each complex to 200 ns molecular dynamic (MD) simulations and molecular mechanics/generalized Born surface area (MM/GBSA) to extract free binding energies. We show the effectiveness of both compounds in forming stable complexes with the mTOR-KD, which is more effective than the mTOR-KD-ATP complex with more robust binding affinities. Conclusions: This study implies that both compounds could serve as potential therapeutic inhibitors of mTOR, regulating its function and, therefore, mitigating human disease progression.

Keywords: ATP; kinase domain; mTOR; mTOR inhibitors; molecular simulation; natural compounds.

Figure 1

The structural organization of mTOR and its ATP binding sites. A schematic representation of the four mTOR domains; FAT, FRB, kinase domain (KD), and FATC. The 3D structure of the KD is depicted in orange, bound to ATP (green). The 2D schematic of ATP interatomic interactions with the KD residues formed H-bonds (red), electrostatic interactions (magenta), and pi-bonds (orange). mTOR, mammalian target of rapamycin; HEAT, huntingtin, elongation factor 3, PP2A, and TOR1; FAT, FRAP, ATM, and TRAP; FRB, FKBP–rapamycin binding; KD, kinase domain; FATC, C-terminal FAT.

Figure 2

Validation of the protocol using experimental ligands. (A) The superimposed binding of 2-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-1H-indol-5-ol (PDB ID: 4JT5) (lavender) and the docked ligand (magenta); (B) the binding of 3-(4-morpholin-4-ylpyrido[3′,2′:4,5]furo[3,2-d]pyrimidin-2-yl)phenol (PDB: ID 4JT6) (purple) and the docked ligand (red).

Figure 3

The interaction patterns of Compounds A and B with the mTOR-KD. (A) The right panel shows a 3D representation of the mTOR-KD (orange) bound to Compound A (teal), and the left panel depicts a 2D representation of the Compound A-mTOR-KD interaction. (B) The right panel shows a 3D representation of the mTOR-KD (orange) bound to Compound B (blue), and the left panel depicts a 2D representation of the Compound B-mTOR-KD interaction. The H-bonds are represented by red dashed lines, and magenta dashed lines indicate electrostatic interactions.

Figure 4

Dynamic stability and compactness assessment of ligands bound to the mTOR-KD. (A) RMSD and Rg of Compound A (teal) in complex with the mTOR-KD. (B) RMSD and Rg of Compound B (blue) in complex with the mTOR-KD. The dynamic stability of Compounds A and B were compared with the RMSD and Rg of ATP in complex the mTOR-KD (green).

Figure 5

Residue flexibility assessment of the mTOR-KD ligand complexes. Residual flexibility of the mTOR-KD in complex with ATP (green), Compound A (teal), and Compound B (blue).