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
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PARP1 hyperactivity leading to cell stress or
death associated with many diseases, eg. cardiovascular disease, several common
neurodegenerative disorders
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Clinical inhibitors
o
Bind to the same location
o
Catalytic site
o
Blocking the binding of substrate NAD+
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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
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Molecular roots of PARP1 trapping on DNA remain
poorly understood
What they do the study
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Examining a panel of PARPi
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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
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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
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HD is effected in distinct ways depending on
particular PARPi inhibitors binding to the active site, which is adjacent to HD
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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
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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
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Type I; allosteric pro-retention on DNA
o
PARPi contact helix aF -- > initiate
allosteric chain reaction -- > increase DNA binding
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Type II; non-allosteric
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Type-III; allosteric prerelease from DNA
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