mTOR–mLST8 interaction: hot spot identification through quantum biochemistry calculations

Abstract

The characterization of protein–protein interactions (PPIs) is an important step toward the development of therapeutic strategies. In this regard, the use of quantum calculations combined with protein fragmentation schemes can offer an opportunity to obtain high quality data and identify key interactions. The mechanistic target of rapamycin (mTOR) protein assembles with partner proteins, such as mLST8, to form two complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), with distinct roles in the coordination of cellular metabolism, growth and survival. Imbalances in this pathway is highly related to cancer risk and recent reports have linked mLST8 upregulation with colon, prostate and liver cancers, demonstrating that the knockout of mLST8 genes in these cells makes them more vulnerable than healthy ones. Such upregulation seems to affect preferentially tumour cells, making this mechanism a pathway for emerging therapeutic strategies. In this work in silico approaches were employed to describe the interaction energy between each amino acid residue at the mTOR–mLST8 interface. PPI calculations were performed at the quantum level, within the density functional theory (DFT) framework, to identify hotspots at the interface side of both proteins. The calculated relative total interaction energy is −195.2 (−179.5) kcal mol⁻¹ for the crystallographic (MD) structure, with the strongest contribution from a portion at the C-terminal lobe, which is known for forming the binding site for mLST8. Calculated interactions identified the main residues at the mTOR interface as Met2281, Met2271, Glu2285, Glu2288 and His2277, whilst the main residues at the mLST8 interface are Tyr20, Tyr222 and Trp272. This work identifies for the first time, using quantum calculations, the key residues controlling the interaction between mTOR and its partner protein mLST8 and may represent the first step towards designing and probing new compounds to treat cancer through the disruption/modulation of mTOR interactions.