Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design

Targeted protein degradation (TPD) is emerging as a promising
therapeutic
approach for cancer and other diseases, with an increasing number
of programs demonstrating its efficacy in human clinical trials. One
notable method for TPD is Proteolysis Targeting Chimeras (PROTACs)
that selectively degrade a protein of interest (POI) through E3-ligase
induced ubiquitination followed by proteasomal degradation. PROTACs
utilize a warhead-linker-ligand architecture to bring the POI (bound
to the warhead) and the E3 ligase (bound to the ligand) into proximity.
The resulting non-native protein–protein interactions (PPIs)
formed between the POI and E3 ligase lead to the formation of a stable
ternary complex, enhancing cooperativity for TPD. A significant challenge
in PROTAC design is the screening of the linkers to induce favorable
non-native PPIs between POI and E3 ligase. Here, we present a physics-based
computational protocol to predict noncanonical and metastable PPI
interfaces between an E3 ligase and a given POI, aiding in the design
of linkers to stabilize the ternary complex and enhance degradation.
Specifically, we build the non-Markovian dynamic model using the Integrative
Generalized Master equation (IGME) method from ∼1.5 ms all-atom
molecular dynamics simulations of linker-less encounter complex, to
systematically explore the inherent PPIs between the oncogene homologue
protein and the von Hippel-Lindau E3 ligase. Our protocol revealed
six metastable states each containing a different PPI interface. We
selected three of these metastable states containing promising PPIs
for linker design. Our selection criterion included thermodynamic
and kinetic stabilities of PPIs and the accessibility between the
solvent-exposed sites on the warheads and E3 ligand. One selected
PPIs closely matches a recent cocrystal PPI interface structure induced
by an experimentally designed PROTAC with potent degradation efficacy.
We anticipate that our protocol has significant potential for widespread
application in predicting metastable POI-ligase interfaces that can
enable rational design of PROTACs.