Allostery of PARP1 - a very nice story which could lead to 4th PARPi

Note for: Structural basis for allosteric PARP-1 retention on DNA breaks_2020

Doi: 10.1126/science.aax6367

Overview

-       PARP1 hyperactivity leading to cell stress or death associated with many diseases, eg. cardiovascular disease, several common neurodegenerative disorders

-       Clinical inhibitors

o   Bind to the same location

o   Catalytic site

o   Blocking the binding of substrate NAD+

-       More evident revealed the potency is related to the ability of PARP1 trapping to DNA damage site which caused more damages and becoming toxic to the cells, esp. cells defect in DNA strand breaks

Rational

-       Molecular roots of PARP1 trapping on DNA remain poorly understood

What they do the study

-       Examining a panel of PARPi

-       Using biophysical and biochemical approaches

o   Hydrogen/deuterium exchange mass spectrometry (HXMS)

o   X-crystallography

o   Biochemical assay

o   Cell survival assay

§  Using CAPAN-1 and SUM149T cells

-       Structure-guided modification of PARPi

o   To studied the trapping ability using the chromatin fractionation (observe PARP1 binding to DNA -- > no inhibitor vs various inhibitors)

o   Site-directed mutagenesis -- > disrupt the helix aF-PARPi contact

o   There was a case reporting mutation of PARP1 allosteric site -- > de novo PARPi-resistant patient with OV cancer

Founding

-       HD is effected in distinct ways depending on particular PARPi inhibitors binding to the active site, which is adjacent to HD

-       PARPi

o   Destabilize specific HD regions

§  Increase PARP1 affinity for DNA

§  Retained PARP1 on DNA breaks

o   No effect on HD

o   Stabilized HD

§  Decreased PARP1 affinity for DNA breaks

Classification of PARPi based on DNA binding capability

-       Observation from the experiment

o   PARPi contact with HD element -- > helix alphaF

o   Contacting with helix alphaF -- > used for discriminating factor between types of PARPi

-       Type I; allosteric pro-retention on DNA

o   PARPi contact helix aF -- > initiate allosteric chain reaction -- > increase DNA binding

-       Type II; non-allosteric

-       Type-III; allosteric prerelease from DNA