Identifying
target
proteins
for
bioactive
molecules
is
essential
understanding
their
mechanisms,
developing
improved
derivatives,
and
minimizing
off-target
effects.
Despite
advances
in
identification
(target-ID)
technologies,
significant
challenges
remain,
impeding
drug
development.
Most
target-ID
methods
use
cell
lysates,
but
maintaining
an
intact
cellular
context
vital
capturing
specific
drug–protein
interactions,
such
as
those
with
transient
protein
complexes
membrane-associated
proteins.
To
address
these
limitations,
we
developed
POST-IT
(Pup-On-target
Small
molecule
Target
Identification
Technology),
a
non-diffusive
proximity
tagging
system
live
cells,
orthogonal
to
the
eukaryotic
system.
utilizes
engineered
fusion
of
proteasomal
accessory
factor
A
HaloTag
transfer
Pup
proximal
upon
directly
binding
small
molecule.
After
optimization
eliminate
self-pupylation
polypupylation,
minimize
depupylation,
optimize
chemical
linkers,
successfully
identified
known
targets
discovered
new
binder,
SEPHS2,
dasatinib,
VPS37C
hydroxychloroquine,
enhancing
our
drugs’
mechanisms
action.
Furthermore,
demonstrated
application
zebrafish
embryos,
highlighting
its
potential
broad
biological
research
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 15, 2025
Extracellular
proteins
play
pivotal
roles
in
both
intracellular
signaling
and
intercellular
communications
health
disease.
While
recent
advancements
proximity
labeling
(PL)
methods,
such
as
peroxidase-
photocatalyst-based
approaches,
have
facilitated
the
resolution
of
extracellular
proteomes,
their
vivo
compatibility
remains
limited.
Here,
we
report
TyroID,
an
vivo-compatible
PL
method
for
unbiased
mapping
with
high
spatiotemporal
resolution.
TyroID
employs
plant-
bacteria-derived
tyrosinases
to
produce
reactive
o-quinone
intermediates,
enabling
multiple
residues
on
endogenous
bioorthogonal
handles,
thereby
allowing
identification
via
chemical
proteomics.
We
validate
TyroID's
specificity
by
proteomes
HER2-neighboring
using
affibody-directed
recombinant
tyrosinases.
Demonstrating
its
superiority
over
other
enables
including
HER2-proximal
tumor
xenografts,
quantifying
turnover
plasma
hippocampal-specific
live
mouse
brains.
emerges
a
potent
tool
investigating
protein
localization
molecular
interactions
within
living
organisms.
is
that
maps
through
efficiently
labels
study
interactions.
ACS Central Science,
Год журнала:
2024,
Номер
10(6), С. 1135 - 1147
Опубликована: Июнь 12, 2024
The
proximitome
is
defined
as
the
entire
collection
of
biomolecules
spatially
in
proximity
a
biomolecule
interest.
More
broadly,
concept
can
be
extended
to
totality
cells
proximal
specific
cell
type.
Since
spatial
organization
and
essential
for
almost
all
biological
processes,
proximitomics
has
recently
emerged
an
active
area
scientific
research.
One
growing
strategies
leverages
reactive
species─which
are
generated
situ
confined,
chemically
tag
capture
systematic
analysis.
In
this
Outlook,
we
summarize
different
types
species
that
have
been
exploited
discuss
their
pros
cons
applications.
addition,
current
challenges
future
directions
exciting
field.
Science and Technology of Advanced Materials,
Год журнала:
2024,
Номер
25(1)
Опубликована: Июнь 28, 2024
Nanoarchitectonics,
as
a
technology
to
arrange
nano-sized
structural
units
such
molecules
in
desired
configuration,
requires
nano-organization,
which
usually
relies
on
intermolecular
interactions.
This
review
briefly
introduces
the
development
of
using
enzymatic
reactions
control
interactions
for
generating
artificial
nanoarchitectures
cellular
environment.
We
begin
discussion
with
early
examples
and
uniqueness
enzymatically
controlled
self-assembly.
Then,
we
describe
intracellular
nanostructures
their
relevant
applications.
Subsequently,
discuss
cases
forming
cell
surface
via
reactions.
Following
that,
highlight
use
creating
intercellular
nanostructures.
Finally,
provide
summary
outlook
promises
future
direction
this
strategy.
Our
aim
is
give
an
updated
introduction
reaction
regulating
interactions,
phenomenon
ubiquitous
biology
but
relatively
less
explored
by
chemists
materials
scientists.
goal
stimulate
new
developments
simple
versatile
approach
addressing
societal
needs.
Biochemical Society Transactions,
Год журнала:
2025,
Номер
53(01)
Опубликована: Фев. 12, 2025
Protein–protein
interactions
(PPIs)
in
the
brain
play
critical
roles
across
all
aspects
of
central
nervous
system,
from
synaptic
transmission,
glial
development,
myelination,
to
cell-to-cell
communication,
and
more.
Understanding
these
is
crucial
for
deciphering
neurological
mechanisms
underlying
biochemical
machinery
affected
disorders.
Recently,
advances
proteomics
techniques
have
significantly
enhanced
our
ability
study
among
proteins
expressed
brain.
Here,
we
review
some
high-throughput
studies
characterizing
PPIs,
using
affinity
purification,
proximity
labeling,
co-fractionation,
chemical
cross-linking
mass
spectrometry
methods,
as
well
yeast
two-hybrid
assays.
We
present
current
state
field,
discuss
challenges,
highlight
promising
future
directions.
Journal of the American Chemical Society,
Год журнала:
2025,
Номер
147(9), С. 7305 - 7316
Опубликована: Фев. 24, 2025
Peroxynitrite
(ONOO–),
the
product
of
diffusion-controlled
reaction
superoxide
(O2•–)
with
nitric
oxide
(NO•),
plays
a
crucial
role
in
oxidative
and
nitrative
stress
modulates
key
physiological
processes
such
as
redox
signaling.
While
biological
ONOO–
is
conventionally
analyzed
using
3-nitrotyrosine
antibodies
fluorescent
sensors,
probes
lack
specificity
sensitivity,
making
high-throughput
comprehensive
profiling
ONOO–-associated
proteins
challenging.
In
this
study,
we
used
conditional
proteomics
approach
to
investigate
homeostasis
by
identifying
its
protein
neighbors
cells.
We
developed
Peroxynitrite-responsive
Labeling
reagents
(Porp-L)
and,
for
first
time,
discovered
2,6-dichlorophenol
an
ideal
moiety
that
can
be
selectively
rapidly
activated
labeling
proximal
proteins.
The
Porp-L
generated
several
short-lived
reactive
intermediates
modify
Tyr,
His,
Lys
residues
on
surface.
have
demonstrated
Porp-L-based
immune-stimulated
macrophages,
which
indeed
identified
known
involved
generation
modification
revealed
endoplasmic
reticulum
(ER)
hot
spot.
Moreover,
previously
unknown
Ero1a,
ER-resident
protein,
formation
ONOO–.
Overall,
represent
promising
research
tool
advancing
our
understanding
roles
Melanoma
is
one
of
the
most
aggressive
forms
skin
cancer.
Accurate
and
early
diagnosis
melanoma
crucial
for
improving
patient
outcomes.
This
study
develops
two
TYR-activatable
molecular
probes,
Mn-TyrEDTA
Al-18F-TyrEDTA,
selective
detection
in
vivo.
In
vitro
studies
reveal
that
exhibits
TYR
activity-dependent
relaxivity
enhancement,
undergoing
TYR-mediated
oxidative
polymerization,
resulting
formation
paramagnetic
oligomers.
UV-vis
analysis
supports
this
mechanism,
showing
time-
concentration-dependent
increases
broad
band
absorbance
region,
specifically
around
475
nm,
due
to
o-quinone
intermediates
melanin-like
HPLC
further
confirmed
presence
polar
oligomeric
products
solutions
incubated
with
TYR/O2.
MRI
demonstrate
Mn-TyrEDTA's
retention
signal
enhancement
TYR-expressing
tissues.
Furthermore,
PET
imaging
Al-18F-TyrEDTA
conducted
using
a
dual-xenograft
mouse
model
reveals
significantly
higher
uptake
compared
TYR-negative
tumors.
could
be
attributed
proximity
labeling
where
highly
reactive
quinones
form
covalent
bonds
nearby
tumor
proteins.
summary,
our
findings
establish
as
promising
offering
novel
strategy
prognosis
melanoma.
Chemical Reviews,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 3, 2025
The
cell
surface
proteome,
or
surfaceome,
is
the
hub
for
cells
to
interact
and
communicate
with
outside
world.
Many
disease-associated
changes
are
hard-wired
within
yet
approved
drugs
target
less
than
50
proteins.
In
past
decade,
proteomics
community
has
made
significant
strides
in
developing
new
technologies
tailored
studying
surfaceome
all
its
complexity.
this
review,
we
first
dive
into
unique
characteristics
functions
of
emphasizing
necessity
specialized
labeling,
enrichment,
proteomic
approaches.
An
overview
surfaceomics
methods
provided,
detailing
techniques
measure
protein
expression
how
leads
novel
discovery.
Next,
highlight
advances
proximity
labeling
(PLP),
showcasing
various
enzymatic
photoaffinity
can
map
protein-protein
interactions
membrane
complexes
on
surface.
We
then
review
role
extracellular
post-translational
modifications,
focusing
glycosylation,
proteolytic
remodeling,
secretome.
Finally,
discuss
identifying
tumor-specific
peptide
MHC
they
have
shaped
therapeutic
development.
This
emerging
field
neo-protein
epitopes
constantly
evolving,
where
targets
identified
at
proteome
level
encompass
defined
PTMs,
complexes,
dysregulated
cellular
tissue
locations.
Given
functional
importance
biology
therapy,
view
as
a
critical
piece
quest
neo-epitope
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 13, 2024
ABSTRACT
Cell-Cell
interactions
are
fundamental
in
biology
for
maintaining
physiological
conditions,
with
direct
contact
being
the
most
straightforward
mode
of
interaction.
Recent
advancements
have
led
to
development
various
chemical
tools
detecting
or
identifying
these
interactions.
However,
use
exogenous
cues,
such
as
toxic
reagents,
bulky
probes,
and
light
irradiations,
can
disrupt
normal
cell
physiology.
For
example,
toxicity
hydrogen
peroxide
(H
2
O
)
limits
applications
peroxidases
proximity
labeling
field.
In
this
study,
we
aimed
address
limitation
by
demonstrating
that
membrane-localized
Horseradish
Peroxidase
(HRP-TM)
efficiently
utilizes
endogenously
generated
extracellular
H
.
By
harnessing
endogenous
,
observed
HRP-TM-expressing
cells
effectively
label
contacting
without
need
treatment.
Furthermore,
confirmed
HRP-TM
labels
proximal
an
interaction-dependent
manner.
These
findings
offer
a
novel
approach
studying
cell-cell
under
more
confounding
effects
stimuli.
Our
study
contributes
elucidating
interaction
networks
model
organisms,
providing
valuable
insights
into
dynamic
interplay
between
their
native
network.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 8, 2024
Abstract
Identifying
target
proteins
for
bioactive
molecules
is
essential
understanding
their
mechanisms,
developing
improved
derivatives,
and
minimizing
off-target
effects.
Despite
advances
in
identification
(target-ID)
technologies,
significant
challenges
remain,
impeding
drug
development.
Most
target-ID
methods
use
cell
lysates,
but
maintaining
an
intact
cellular
context
vital
capturing
specific
drug-protein
interactions,
such
as
those
with
transient
protein
complexes
membrane-associated
proteins.
To
address
these
limitations,
we
developed
POST-IT
(Pup-On-target
Small
molecule
Target
Identification
Technology),
a
non-diffusive
proximity
tagging
system
live
cells,
orthogonal
to
the
eukaryotic
system.
utilizes
engineered
fusion
of
proteasomal
accessory
factor
A
(PafA)
HaloTag
transfer
Pup
proximal
upon
directly
binding
small
molecule.
After
optimization
eliminate
self-pupylation
polypupylation,
minimize
depupylation,
optimize
chemical
linkers,
successfully
identified
known
targets
discovered
new
binder,
SEPHS2,
dasatinib,
VPS37C
hydroxychloroquine,
enhancing
our
drugs’
mechanisms
action.
Furthermore,
demonstrated
application
zebrafish
embryos,
highlighting
its
potential
broad
biological
research
