Machine learning-powered, high-affinity modification strategies for aptamers
Acta Materia Medica,
Год журнала:
2025,
Номер
4(1)
Опубликована: Янв. 1, 2025
The
binding
affinity
of
aptamers
to
targets
has
a
crucial
role
in
the
pharmaceutical
and
biosensing
effects.
Despite
diverse
post-systematic
evolution
ligands
by
exponential
enrichment
(post-SELEX)
modifications
explored
aptamer
optimization,
accurate
prediction
high-affinity
modification
strategies
remains
challenging.
Sclerostin,
which
antagonizes
Wnt
signaling
pathway,
negatively
regulates
bone
formation.
Our
screened
sclerostin
was
previously
shown
exert
anabolic
potential.
In
current
study,
an
interactive
methodology
involving
exchange
mutual
information
between
experimental
endeavors
machine
learning
initially
proposed
design
post-SELEX
strategy
for
aptamers.
After
four
rounds
training
(a
total
422
modified
aptamer-target
datasets
with
types
sites),
antifcial
intelligence
model
high
predictive
accuracy
correlation
coefficient
0.82
predicted
actual
affinities
obtained.
Notably,
learning-powered
selected
from
this
work
exhibited
105-fold
higher
(picomole
level
K
D
value)
3.2-folds
greater
Wnt-signal
re-activation
effect
compared
naturally
unmodified
This
approach
harnessed
power
predict
most
promising
Язык: Английский
Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern
Frontiers in Microbiology,
Год журнала:
2025,
Номер
16
Опубликована: Фев. 14, 2025
DNA
aptamers
with
high
binding
affinity
against
SARS-CoV-2
spike
proteins
have
been
selected
and
analyzed.
To
better
understand
the
affinities
between
(S-proteins)
of
relevant
variants
concerns
(VOCs),
in
silico
vitro
characterization
are
excellent
approaches
to
implement.
Here,
we
identified
generated
aptamer
sequences
targeting
S-protein
VOCs
through
systematic
evolution
ligands
by
exponential
enrichment
(SELEX).
In
,
prediction
was
conducted,
followed
a
step-by-step
workflow
for
secondary
tertiary
structures
determination,
modeling,
molecular
docking
target
S-protein.
The
strategy
limited
only
providing
predictions
possible
outcomes
based
on
scores,
ranking
complemented
analysis
using
direct
enzyme-linked
oligonucleotides
assay
(ELONA),
which
showed
dissociation
constants
(
K
d
)
within
32
nM–193
nM
range
across
three
significant
VOCs.
These
highly
specific
(Alpha
Apt,
Delta
Omicron
Apt)
can
be
further
studied
as
potential
candidates
both
diagnostic
therapeutic
applications.
Язык: Английский
Replication Features of SARS-CoV-2 and Advantages of Targeting S Protein with Aptamers to Block Viral Entry
ACS Omega,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 21, 2025
Severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
is
a
virus
of
the
coronaviridae
family.
The
enters
cell
through
binding
to
corresponding
receptor
angiotensin-converting
enzyme
(ACE2)
on
host
membrane
with
spike
protein
(S
protein)
its
envelope;
thus,
we
can
design
inhibitors
that
bind
S
block
entry
into
cells.
Aptamers
are
single
stranded
DNA
or
RNA
molecules
form
specific
three-dimensional
structures
and
their
target
high
affinity
specificity
thus
promising
candidates
for
inhibitors.
This
paper
reviews
replication
cycle
mechanisms
SARS-CoV-2
as
well
preparation
principle
characteristics
aptamers,
features
discussion
advantages
using
aptamers
prevent
from
infecting
cells,
finally
summarizes
research
progress
in
protein-blocking
aptamers.
Язык: Английский
A patent review of anti-coronavirus agents targeting the spike-ACE2 interaction (2019–present)
Expert Opinion on Therapeutic Patents,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 22, 2025
The
Angiotensin-converting
enzyme
2
(ACE2)
receptor,
crucial
for
coronavirus
recognition
of
host
cells,
is
a
key
target
therapeutic
intervention
against
SARS-CoV-2
and
related
coronaviruses.
Therefore,
thoroughly
investigating
the
interaction
mechanism
between
ACE2
Spike
protein
(S
protein),
as
well
developing
targeted
inhibitors
based
on
this
mechanism,
vital
effectively
controlling
spread
preventing
potential
future
pandemics
caused
by
other
This
article
comprehensively
reviews
mechanisms
underlying
ACE2-S
that
facilitates
entry
into
cells.
It
also
analyzes
patent
landscape
regarding
targeting
interface
since
2019.
In
five
years
outbreak
SARS-CoV-2,
numerous
methods
design
strategies
have
been
employed
to
develop
innovative
therapeutics
Among
these
approaches,
both
receptor
S
gained
significant
interest
due
their
in
blocking
various
Despite
facing
challenges
similar
protein-protein
inhibitors,
progress
has
made
through
virtual
screening,
covalent
binding,
peptide
modification
strategies.
However,
obstacles
persist
clinical
translation,
necessitating
multidisciplinary
strategy
integrates
state-of-the-art
methodologies
optimize
S-ACE2
interface-targeted
drug
discovery.
Язык: Английский
Aptamer-engaged nanotherapeutics against SARS-CoV-2
Discover Nano,
Год журнала:
2025,
Номер
20(1)
Опубликована: Апрель 27, 2025
The
COVID-19
pandemic,
caused
by
the
virus
SARS-CoV-2
infection,
has
underscored
critical
importance
of
rapid
and
accurate
therapeutics.
neutralization
is
paramount
in
controlling
spread
impact
COVID-19.
In
this
context,
integration
aptamers
aptamer-related
nanotherapeutics
presents
a
valuable
scientifically
significant
approach.
Despite
potential,
current
reviews
area
are
often
not
comprehensive
specific
enough
to
encapsulate
full
scope
therapeutic
principles,
strategies,
advancements,
challenges.
This
review
aims
fill
that
gap
providing
an
in-depth
examination
role
their
related
molecular
medicine
We
first
introduce
unique
properties,
selection,
recognition
mechanism
bind
with
high
affinity
various
targets.
Next,
we
delve
into
potential
aptamers,
focusing
on
ability
inhibit
viral
entry
replication,
as
well
modulate
host
immune
response.
nucleic
acid
nanomedicine
explored.
Finally,
address
challenges
future
perspectives
aptamer
therapeutics,
including
issues
stability,
delivery,
manufacturing
scalability.
conclude
underscoring
continued
research
development
field
meet
ongoing
posed
pandemics.
Our
will
be
resource
for
researchers
clinicians
interested
latest
developments
at
intersection
biology,
nanotechnology,
infectious
disease
management.
Язык: Английский
Analyzing aptamer structure and interactions: in silico modelling and instrumental methods
Biophysical Reviews,
Год журнала:
2024,
Номер
16(6), С. 685 - 700
Опубликована: Ноя. 20, 2024
Язык: Английский
Aptamer-decorated nanocarriers for viral adsorption: A special look at COVID-19
Molecular Therapy — Nucleic Acids,
Год журнала:
2024,
Номер
35(3), С. 102310 - 102310
Опубликована: Авг. 15, 2024
Viral
infections
are
one
of
the
leading
causes
death
in
world.
One
main
challenge
fighting
against
these
diseases
is
unavailability
effective
eradicating
drugs
and
specific
treatments.
Nanocarriers
aptamer-decorated
nanocarriers
designed
to
attach
many
targets,
including
viral
particles.
By
lowering
infectivity
attachment
capability,
they
add
therapeutic
values
even
without
containing
antiviral
drugs.
Nevertheless,
nanoparticles
(NPs)
with
encapsulated
can
display
extra
effects.
Furthermore,
it
has
been
shown
that
aptamers
bind
particles
nanocarriers,
presenting
promising
approaches
for
identification
viruses
treatment
infections.
Although
there
no
satisfying
literature
revealing
strong
potential
nanotechnology
COVID-19,
following
information
provide
new
perspectives
upcoming
investigations
pertaining
developing
aptamer-nanocarrier
agents
COVID-19.
Язык: Английский