Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics

Considerations
of binding pocket dynamics are one of the crucial
aspects of the rational design of binders. Identification of alternative
conformational states or cryptic subpockets could lead to the discovery
of completely novel groups of the ligands. However, experimental characterization
of pocket dynamics, besides being expensive, may not be able to elucidate
all of the conformational states relevant for drug discovery projects.
In this study, we propose the protocol for computational simulations
of sirtuin 2 (SIRT2) binding pocket dynamics and its integration into
the structure-based virtual screening (SBVS) pipeline. Initially,
unbiased molecular dynamics simulations of SIRT2:inhibitor complexes
were performed using optimized force field parameters of SIRT2 inhibitors.
Time-lagged independent component analysis (tICA) was used to design
pocket-related collective variables (CVs) for enhanced sampling of
SIRT2 pocket dynamics. Metadynamics simulations in the tICA eigenvector
space revealed alternative conformational states of the SIRT2 binding
pocket and the existence of a cryptic subpocket. Newly identified
SIRT2 conformational states outperformed experimentally resolved states
in retrospective SBVS validation. After performing prospective SBVS,
compounds from the under-represented portions of the SIRT2 inhibitor
chemical space were selected for in vitro evaluation.
Two compounds, NDJ18 and NDJ85, were identified as potent and selective
SIRT2 inhibitors, which validated the in silico protocol
and opened up the possibility for generalization and broadening of
its application. The anticancer effects of the most potent compound
NDJ18 were examined on the triple-negative breast cancer cell line.
Results indicated that NDJ18 represents a promising structure suitable
for further evaluation.