Using Pymol to Visualize how Rapamycin works to Inhibit MTOR Complex 1

Mechanistic/Mammalian Target of Rapamycin (MTOR), is a protein kinase that plays a vital role in cellular processes such as growth, proliferation, metabolism, apoptosis, and autophagy. It is an evolutionarily conserved protein found in all eukaryotes and is a central regulator of cellular homeostasis. MTOR is an attractive target for drug development because of its role in various diseases, including cancer, diabetes, and neurological disorders.

Why does MTOR matter for our longevity?

The direct impact that MTOR has on autophagy is what makes it such an effective longevity pathway. Autophagy is the process in which old cells in the body are broken down and reused to maintain efficient body operations. So ideally, want this process to operate as consistently as possible.

Although MTOR activation is essential for vital processes such as protein synthesis, an upregulation of MTOR negatively impacts autophagy in our body’s cells. Therefore, we need to downregulate the MTOR longevity pathway to optimize our cell’s recycling processes.

So how can we do this?

First, we need to understand that MTOR exists in two distinct complexes, MTORC1 and MTORC2. These two complexes differ in their composition, regulation, and downstream effects. MTOR Complex 1 is activated by nutrients such as amino acids, energy status, and growth factors, and regulates cell growth, protein synthesis, and autophagy. MTOR Complex 2, on the other hand, is activated by growth factors and regulates cell survival, metabolism, and cytoskeletal organization.

MTOR Complex 1 and 2 signaling network pathways.

Although both complexes are important for our longevity because of their impact on autophagy and metabolism, only MTOR Complex 1 can be effectively targeted with a drug called rapamycin to downregulate the protein.

NOTE: Rapamycin alone cannot inhibit MTOR but must bond with a protein called FKBP12 to form FKBP12-Rapamycin. Only then is MTOR complex 1 actually inhibited.

You may be wondering “What makes MTOR complex 1 so much more effective as a target for rapamycin compared to MTOR complex 2?” The reason MTOR complex 1 is a more effective target for rapamycin compared to MTOR complex 2 lies in the structures between these two complexes. The binding site for FKBP12-Rapamycin on the MTOR protein is present in MTOR complex 1 but hidden in MTOR complex 2.

As seen in the right side of the image above, the red parts of MTOR complex 1 show the binding sites available for FKBP12-Rapamycin. As seen on the left side of the image above, binding sites (red parts) are not as readily avaliable in MTOR complex 2.

Well, now we know that MTOR complex 1 can be effectively bonded with the FKBP12-Rapamycin, but how does this explain how rapamycin actually downregulates (inhibits) the MTOR longevity pathway?

To understand this concept further, I used PYMOL to visualize how FKBP12-Rapamycin structurally bonds to MTOR complex 1.

Here is the image of that visualization:

FKBP!2- Rapamycin bound to MTOR Complex 1 (through PYMOL)

The yellow enzyme in this image (FKBP12-Rapamycin) is being bonded to the purple part of the MTOR protein (FKBP12-Rapamycin binding site). When these two parts are bonded it helps to bridge the gap between the pink (MTOR catalytic cleft) and the purple (binding sites for FKBP12-Rapamycin) parts of the MTOR protein.

When the gap between the pink and purple parts are bridged, a lid is formed to reduce the activity of substrates to the MTOR active sites. Basically, this “lid” reduces the activation of MTOR complex 1 because fewer enzymes have access to MTOR active sites to react with MTOR! If rapamycin alone were to be bound to MTOR complex 1, no “lid” would be formed because it’s the protein FKBP12-Rapamycin that physically bridges the gap. This explains why rapamycin alone can’t inhibit MTOR!

From all of this, MTOR has been successfully downregulated to encourage cellular autophagy and increase our longevity!

Key takeaways:

• MTOR is an essential protein kinase that plays a crucial role in regulating cellular processes. MTOR exists in two complexes, MTORC1 and MTORC2, which have distinct functions and regulation.
• Rapamycin bonded with FKBP12 to form FKBP12-Rapamycin is a potent inhibitor of MTORC1 and is used as a means of increasing human longevity (due to autophagy).
• The differential inhibition of MTORC1 and MTORC2 by rapamycin suggests that more specific inhibitors of these complexes could be developed for therapeutic purposes too!
• Sounds like tons of potential for the longevity industry!