Background:PARP1 (poly ADP-ribose polymerase 1, also known as ADPRT1) plays a
significant role in DNA repair and has become an attractive target for treating PARP1-related diseases,
such as cancer.Objective:This study aimed to discover inhibitors targeting PARP1 from the phytochemicals of
Huangbai (Phellodendron chinense Schneid.), Baixianpi (Dictamnus dasycarpus Turcz.), and
Shechuangzi (Cnidium monnieri (L.) Spreng.).Methods:The chemical compositions of Huangbai, Baixianpi, and Shechuangzi were extracted
from the HERB database. Next, a combination of molecular docking and PARP1 enzyme assay was
used to identify PARP1 inhibitors from these chemical components. Finally, molecular dynamics
simulation and binding free energy calculation were used to explore the detailed interaction mode
of these inhibitors with PARP1.Results:A total of 507 chemical constituents of Huangbai, Baixianpi, and Shechuangzi were collected
from the HERB database. Four potential PARP1 inhibitors were screened based on molecular
docking and PARP1 enzyme assay. Demethyleneberberine exhibited strong PARP1 inhibitory
activity with an IC50 value of 2.0 ± 0.8 μM. The IC50 values of the inhibitory activities of 8-hydroxy
dictanmnine, meranzin hydrate, and osthol on PARP1 ranged from 44 μM to 76 μM. Molecular
dynamics simulation and binding free energy calculation suggested that the nonpolar interaction
energies of HIS862, GLY863, TYR889, TYR896, PHE897, and TYR907 played a primary role in
the binding of inhibitors to PARP1.Conclusion:Integrating molecular simulation and bioactivity testing was found to be an effective
approach for the rapid discovery of targeted PARP1 inhibitors. Demethyleneberberine demonstrated
strong PRAP1 inhibitory activity and has a good prospect for development.