bc0c00062_si_001.pdf (739.52 kB)
Rational Design of Small Molecules to Enhance Genome Editing Efficiency by Selectively Targeting Distinct Functional States of CRISPR-Cas12a
journal contribution
posted on 2020-03-06, 18:11 authored by Wenqing Li, Chun Chan, Chunxi Zeng, Rolf Turk, Mark A. Behlke, Xiaolin Cheng, Yizhou DongCRISPR-Cas12a, a
type-V CRISPR-Cas endonuclease, is an effective
genome editing platform. To improve the gene editing efficiency of
Cas12a, we rationally designed small molecule enhancers through a
combined computational approach. First, we used extensive molecular
dynamics (MD) simulations to explore the conformational landscape
of Cas12a from Acidaminococcus (AsCas12a), revealing
distinct conformational states that could be targeted by small molecules
to modulate its genome editing function. We then identified 57 compounds
that showed different binding behavior and stabilizing effects on
these distinct conformational states using molecular docking. After
experimental testing 6 of these 57 compounds, compound 1, quinazoline-2,4(1H,3H)-dione,
was found particularly promising in enhancing the AsCas12a-mediated
genome editing efficiency in human cells. Compound 1 was
shown to act like a molecular “glue” at the interface
between AsCas12a and crRNA near the 5′-handle region, thus
specifically stabilizing the enzyme–crRNA complex. These results
provide a new paradigm for future design of small molecules to modulate
the genome editing of the CRISPR-Cas systems.