Open Journal of Philosophy,
Год журнала:
2024,
Номер
14(02), С. 448 - 480
Опубликована: Янв. 1, 2024
In
accordance
with
current
philosophical
opinions,
four
classical
and
one
more
recently
proposed
types
of
methods
frequently
used
in
theoretical
natural
science
are
specified
here
together
the
corresponding
sources
inspiration.
More
precisely,
abstract
models,
thought
experiments,
mathematical
hypotheses
metaphors
dealt
as
methods,
whereas
hybrids
experiments
represent
recent
methodic
group.
addition,
this
paper
describes
relationships
introduced
to
(i)
three-floor
hierarchy
scientific
theories,
(ii)
examples
ancient
or
discoveries
(iii)
usage
computers.
Frontiers in Microbiology,
Год журнала:
2023,
Номер
14
Опубликована: Июнь 28, 2023
Mosquitoes
are
the
primary
vector
for
West
Nile
virus,
a
flavivirus.
The
virus’s
ability
to
infiltrate
and
establish
itself
in
increasing
numbers
of
nations
has
made
it
persistent
threat
public
health
worldwide.
Despite
widespread
occurrence
this
potentially
fatal
disease,
no
effective
treatment
options
currently
on
market.
As
result,
there
is
an
immediate
need
research
development
novel
pharmaceuticals.
To
begin,
molecular
docking
was
performed
two
possible
virus
target
proteins
using
panel
twelve
natural
chemicals,
including
Apigenin,
Resveratrol,
Hesperetin,
Fungisterol,
Lucidone,
Ganoderic
acid,
Curcumin,
Kaempferol,
Cholic
Chlorogenic
Pinocembrin,
Sanguinarine.
methyltransferase
(PDB
ID:
2OY0)
binding
affinities
varied
from
−7.4
−8.3
kcal/mol,
whereas
envelope
glycoprotein
ranged
−6.2
−8.1
kcal/mol
2I69).
Second,
substances
with
larger
weights
less
likely
be
unhappy
Lipinski
rule.
Hence,
additional
carried
out
without
regard
weight.
In
addition,
compounds
01,
02,
03,
05,
06,
07,
08,
09,
10
11
more
soluble
water
than
compound
04
is.
Besides,
based
maximum
affinity,
best
three
(Apigenin,
Acid)
been
dynamic
simulation
(MDs)
at
100
ns
determine
their
stability.
MDs
data
also
reported
that
these
mentioned
molecules
highly
stable.
Finally,
advanced
principal
component
analysis
(PCA),
dynamics
cross-correlation
matrices
(DCCM)
analysis,
free
energy
cross
correlation
matrix
theoretical
study
included
established
phytochemical
as
potential
drug
candidate.
Research
indicated
aforementioned
may
tool
battle
against
dangerous
virus.
This
aims
locate
bioactive
might
used
pharmaceutical.
Viruses,
Год журнала:
2023,
Номер
15(8), С. 1739 - 1739
Опубликована: Авг. 15, 2023
The
Ebola
virus
and
its
close
relative,
the
Marburg
virus,
both
belong
to
family
Filoviridae
are
highly
hazardous
contagious
viruses.
With
a
mortality
rate
ranging
from
23%
90%,
depending
on
specific
outbreak,
development
of
effective
antiviral
interventions
is
crucial
for
reducing
fatalities
mitigating
impact
outbreaks.
In
this
investigation,
virtual
screening
approach
was
employed
evaluate
2042
natural
compounds
their
potential
interactions
with
VP35
protein
virus.
Average
worst
binding
energies
were
calculated
all
20
poses,
that
exhibited
<−6
kcal/mol
in
criteria
selected
further
analysis.
Based
energies,
only
six
(Estradiol
benzoate,
INVEGA
(paliperidone),
Isosilybin,
Protopanaxadiol,
Permethrin,
Bufalin)
subsequent
investigations,
focusing
interaction
Among
these
compounds,
Estradiol
Isosilybin
showed
strong
hydrogen
bonds,
while
others
did
not.
study,
Myricetin,
benzoate
subjected
molecular
dynamics
(MD)
simulation
free
energy
calculation
using
MM/GBSA
reference
component
Myricetin
served
as
control.
most
stable
consistent
root-mean-square
deviation
(RMSD)
values,
whereas
significant
fluctuations
RMSD.
compound
lowest
ΔG
(−22.89
kcal/mol),
surpassing
control
compound’s
(−9.29
kcal/mol).
Overall,
investigation
suggested
possesses
favorable
indicating
inhibitory
mechanism
against
study
proposes
could
serve
therapeutic
option
preventing
infection.
However,
experimental
validation
required
corroborate
findings.
Frontiers in Pharmacology,
Год журнала:
2023,
Номер
14
Опубликована: Апрель 19, 2023
During
the
second
phase
of
SARS-CoV-2,
an
unknown
fungal
infection,
identified
as
black
fungus,
was
transmitted
to
numerous
people
among
hospitalized
COVID-19
patients
and
increased
death
rate.
The
fungus
is
associated
with
Mycolicibacterium
smegmatis,
Mucor
lusitanicus,
Rhizomucor
miehei
microorganisms.
At
same
time,
other
pathogenic
diseases,
such
Monkeypox
virus
Marburg
virus,
impacted
global
health.
Policymakers
are
concerned
about
these
pathogens
due
their
severe
capabilities
rapid
spread.
However,
no
standard
therapies
available
manage
treat
those
conditions.
Since
coptisine
has
significant
antimicrobial,
antiviral,
antifungal
properties;
therefore,
current
investigation
been
designed
by
modifying
identify
effective
drug
molecule
against
Black
Monkeypox,
virus.
After
designing
derivatives
coptisine,
they
have
optimized
get
a
stable
molecular
structure.
These
ligands
were
then
subjected
docking
study
two
vital
proteins
obtained
from
pathogens:
(PDB
ID:
4WTP)
smegmatis
ID
7D6X),
found
in
4QWO)
4OR8).
Following
docking,
computational
investigations,
ADMET,
QSAR,
drug-likeness,
quantum
calculation
dynamics,
also
performed
determine
potentiality
antiviral
inhibitors.
score
reported
that
strong
affinities
Then,
dynamic
simulation
conducted
stability
durability
physiological
system
water
at
100
ns,
which
documented
mentioned
drugs
over
simulated
time.
Thus,
our
silico
provides
preliminary
report
safe
potentially
Hence,
may
be
prospective
candidate
for
developing
viruses.
Molecules,
Год журнала:
2023,
Номер
28(14), С. 5320 - 5320
Опубликована: Июль 10, 2023
The
COVID-19
pandemic
has
caused
severe
health
threat
globally,
and
novel
SARS-Cov-2
inhibitors
are
urgently
needed
for
antiviral
treatment.
main
protease
(Mpro)
of
the
virus
is
one
most
effective
conserved
targets
anti-SARS-CoV-2
drug
development.
In
this
study,
we
utilized
a
molecular
docking-based
virtual
screening
approach
against
catalytic
site
to
identify
small-molecule
SARS-CoV-2
Mpro.
Further
biological
evaluation
helped
us
two
compounds,
AF-399/40713777
AI-942/42301830,
with
moderate
inhibitory
activity.
Besides
that,
in
silico
data,
including
dynamics
(MD)
simulation,
binding
free
energy
calculations,
AMDET
profiles,
suggested
that
these
hits
could
serve
as
starting
point
future
development
intervention
treatments.
Medicine in Novel Technology and Devices,
Год журнала:
2024,
Номер
21, С. 100286 - 100286
Опубликована: Янв. 23, 2024
Mycobacterium
tuberculosis
(Mtb)
is
responsible
for
the
spread
of
(TB).
The
current
study
employed
virtual
screening
2569
natural
compounds
against
DNA-directed
RNA
polymerase
(RNAP)
Mtb
to
identify
possible
binders
that
can
inhibit
its
function.
in-silico
methodology
included
molecular
docking
compounds,
further,
stability
and
flexibility
best
complexes
were
studied
using
dynamics
simulation,
MM/GBSA
binding
free
energy
technique
with
decomposition,
PCA,
FEL,
steered
MD
umbrella
sampling.
Individual
screenings
conducted
five
RNAP
subunits
(chains
A,
B,
C,
D,
E)
a
compound
capable
inhibiting
oligomerization.
A
promising
compound,
isoestradiol
3-benzoate,
exhibited
low
score
(−7.28
kcal/mol
−8.21
kcal/mol)
showed
ability
all
protein.
Thus,
3-benzoate
selected
simulation
analysis.
Furthermore,
RMSD
bound
chain
E
lowest
0.49
nm,
while
chains
B
it
had
most
stable
consistent
conformations
1.75
nm
1.2
respectively.
H-bond
between
C
highest
occupancy
(58.27
%,
45.33
50.80
42.25
11.75
%).
Moreover,
MMPBSA
strong
association
(ΔGbind
=
−126.25
±
2.03
−129.27
2.25).
Additionally,
FEL-steered
sampling
also
performed
validate
ligand
Isoestradiol
binds
strongly
E;
therefore,
should
be
considered
as
viable
candidate
formation
protein
complex,
concluded
in
this
study.