Jeeraprapa Siriwaseree1, Kamonpan Sanachai2, Thitinan Aiebchun1, Lueacha Tabtimmai3, Buabarn Kuaprasert4, Kiattawee Choowongkomon1. 1. Faculty of Science, Department of Biochemistry, Kasetsart University, Bangkok 10900, Thailand. 2. Faculty of Science, Department of Biochemistry, Structural and Computational Biology Research Unit, Chulalongkorn University, Bangkok 10330, Thailand. 3. Faculty of Applied Science, Department of Biotechnology, King Mongkut's University of Technology of North Bangkok, Bangkok 10800, Thailand. 4. Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasrima 30000, Thailand.
Abstract
Janus kinase (JAK) deregulation of the JAK/signal transducers and activators of transcription pathway leads to myelofibrosis that can be treated by JAK inhibitors including Ruxolitinib and Tofacitinib. Even though both inhibitors are effective against myelofibrosis, each of them has a different mode of action in the cells. Ruxolitinib is an inhibitor for selective JAK1/2, and Tofacitinib is an inhibitor for JAK3. This study evaluated the chemical fingerprints of TF-1 cells after JAK inhibitor treatments by the synchrotron Fourier transform infrared microspectroscopy (S-FTIR) spectrum. Tofacitinib and Ruxolitinib treatments in TF-1 cells were applied with a chemical fingerprint approach in S-FTIR spectroscopy and in vitro cytotoxicity in a cell-based assay. Principal component analysis or PCA was utilized to classify three cell treatments with three biochemical alteration absorbances of lipid vibration by the C-H stretching, protein amide I that appeared from the C=O stretching, and a P=O phosphodiester bond from nucleic acids. The results showed that the inhibition effect of Ruxolitinib on the TF-1 cell lines was two-fold higher than Tofacitinib. PCA distinguishes untreated and drug-treated cells by detecting cellular biochemical alteration. The loading plots identify that proteins and nucleic acids were the different main components in disparate cell treatments. Tofacitinib was distinct from the others in lipid and nucleic acid. The second derivative spectra of the three molecular components had decreased lipid production and accumulation, changes in secondary structures in proteins, and a high level of RNA overexpression in cell treatment. The JAK inhibitors caused different spectroscopic biomarkers of the modifications of secondary protein conformation, stimulated cell lipid accumulation, and phosphorylation from untreated cells. The alteration of cellular biochemical components suggests that FTIR is a potential tool to analyze specific patterns of drug cellular responses at the molecular level.
Janus kinase (JAK) deregulation of the JAK/signal transducers and activators of transcription pathway leads to myelofibrosis that can be treated by JAK inhibitors including Ruxolitinib and Tofacitinib. Even though both inhibitors are effective against myelofibrosis, each of them has a different mode of action in the cells. Ruxolitinib is an inhibitor for selective JAK1/2, and Tofacitinib is an inhibitor for JAK3. This study evaluated the chemical fingerprints of TF-1 cells after JAK inhibitor treatments by the synchrotron Fourier transform infrared microspectroscopy (S-FTIR) spectrum. Tofacitinib and Ruxolitinib treatments in TF-1 cells were applied with a chemical fingerprint approach in S-FTIR spectroscopy and in vitro cytotoxicity in a cell-based assay. Principal component analysis or PCA was utilized to classify three cell treatments with three biochemical alteration absorbances of lipid vibration by the C-H stretching, protein amide I that appeared from the C=O stretching, and a P=O phosphodiester bond from nucleic acids. The results showed that the inhibition effect of Ruxolitinib on the TF-1 cell lines was two-fold higher than Tofacitinib. PCA distinguishes untreated and drug-treated cells by detecting cellular biochemical alteration. The loading plots identify that proteins and nucleic acids were the different main components in disparate cell treatments. Tofacitinib was distinct from the others in lipid and nucleic acid. The second derivative spectra of the three molecular components had decreased lipid production and accumulation, changes in secondary structures in proteins, and a high level of RNA overexpression in cell treatment. The JAK inhibitors caused different spectroscopic biomarkers of the modifications of secondary protein conformation, stimulated cell lipid accumulation, and phosphorylation from untreated cells. The alteration of cellular biochemical components suggests that FTIR is a potential tool to analyze specific patterns of drug cellular responses at the molecular level.
Janus
kinases (JAKs) are a family of intracellular and nonreceptor
tyrosine kinases including JAK1, JAK2, JAK3, and tyrosine kinase 2
(TYK2) that play a role in signal transductions due to cytokines and
growth factors.[1] These kinases are intermediaries
between the signal induction of cytokine and transcriptional factor
phosphorylation and signal transducers and activators of transcription
(STAT) passing through the JAK/STAT pathway. Therefore, JAK/STAT pathway
deregulation can initiate cancer inflammation and autoimmune diseases.[2,3]JAK1 related to mutated sites has been associated with acute
leukemia
or B-cell lymphoma. JAK2 mutation is also associated with thrombocytosis,
myelofibrosis, leukemia, and lymphoma, and increasing JAK3 signaling
can develop T-cell acute lymphocytic leukemia.[2,4] The
tyrosine kinase domain location is in the JH1 domain at the C-terminal
of the JAKs. This domain is controlled through a pseudokinase domain
or JH2 that lacks Asp residue for phosphotransfer in the His/Arg/Asp
motif of the catalytic loop in kinase activity. Hence, this domain
is assumed to regulate the JH1 domain catalytic activity.[5] Among the JAKs, JAK2 is a critical target for
the treatment of cancer disease. JAK2 inhibition can decrease the
risk of bone marrow cancer due to the prevention of JAK2 activation.Myelofibrosis cancer can be treated by JAK inhibition.[6] Ruxolitinib and Tofacitinib are two FDA-approved
drugs that are widely used in clinical treatment of this cancer. These
drugs interact in the ATP site of the JAKs and prevent JAK activation.
As a result, signal transduction cannot occur, and the risk of this
cancer is decreased. Ruxolitinib is selective for JAK1/2 (the half-maximal
inhibitory concentration (IC50) for JAK1 = 3.3 and for
JAK2 = 2.8 nM),[7] whereas Tofacitinib is
more selective for JAK3 (IC50 = 34 nM) than JAK1/2 (IC50 = 81 and 80 nM, respectively).[8] Ruxolitinib is effective for JAK1/2 inhibition, whereas Tofacitinib
can inhibit JAK1/3 more than JAK2. It is an interesting approach to
investigate the binding pattern of both drugs with JAKs.FTIR
is an effective tool for studying the biological systems by
considering the effect of molecular changes in cells on antitumor
drugs based on the FTIR spectrum.[9] Numerous
FTIR chemical fingerprints between cancer cells and drugs have been
reported. The leukemic cell lines (K562) treated with an Akt1/2 kinase
inhibitor (A6730) showed a noticeable change in the α-helix/β-strand
conformation ratio.[10] A previous report
revealed the capability of FTIR spectroscopy to evaluate the drug
sensitivity in cells as well as the interactions of different molecular
components of anti-cancer drugs.[11] TF-1
cell lines originate from erythroleukemia in humans. These cells’
proliferation is responsive to the granulocyte-macrophage colony-stimulating
factor (GM-CSF) or interleukin-3 (IL-3) through the JAK2/STAT signaling
pathway activation.[12] Understanding the
different inhibition patterns of drugs resulting from JAK2, based
on the FTIR spectrum in cells treated with drugs, is important to
better characterize the effect of JAK2 inhibition and the potential
explanation for differences in clinical effectiveness.In this
study, the objective was to assess the chemical fingerprints
of TF-1 cells after Tofacitinib and Ruxolitinib treatments. To achieve
this, we applied a chemical fingerprint approach, using the information
of both drugs from S-FTIR spectroscopy and in vitro cytotoxicity in a cell-based assay. These findings proposed that
S-FTIR can be used for analyzing distinct patterns of cellular responses
with drug treatments at the molecular level.
Results
Effect of Ruxolitinib and Tofacitinib on the
TF-1 Cell Lines
We used the TF-1 cells to investigate the
dose dependence of drug treatment using a PrestoBlue assay. At 72
h, the IC50 of Ruxolitinib was 14.47 ± 0.59 μM
and that of Tofacitinib was 30.29 ± 1.98 μM on TF-1 cells
(Figure ). These results
showed that drugs can inhibit the viability of TF-1 cells, and the
inhibitory effect indicated that Ruxolitinib can inhibit TF-1 cells
more than two-fold higher than Tofacitinib. However, the effect of
both drugs on the TF-1 cells was further evaluated to consider molecular
changes in cells by FTIR spectrum analysis.
Figure 1
TF-1 cell viability after
treatment with Ruxolitinib and Tofacitinib
at various concentrations.
TF-1 cell viability after
treatment with Ruxolitinib and Tofacitinib
at various concentrations.
Molecular Docking
To demonstrate
the interaction and binding mode of known drugs (Ruxolitinib and Tofacitinib)
with JAK1 and JAK2, both compounds were individually docked into the
binding pocket of the JAK1 and JAK2 proteins by using GOLD docking.
The docking scores of Ruxolitinib in complex with both proteins (59.40
kcal mol–1 for JAK1 and 57.81 kcal mol–1 for JAK2) were higher than Tofacitinib (50.91 kcal mol–1 for JAK1 and 51.88 kcal mol–1 for JAK2) (Figure S1). These results confirmed the previous
reports that the Ruxolitinib strongly interacts with JAK1 compared
to JAK2 whereas Tofacitinib strongly interact with JAK2 compared to
JAK1. Moreover, the binding pattern and 2D interactions of all systems
are illustrated in Figure . We found that Ruxolitinib and Tofacitinib bound at the binding
site with a similar pattern to JAK1/2; both compounds bound well with
the deazapurine ring and stabilized through other interactions such
as π-sulfur, π-alkyl, π-σ, and van der Waals
(Figures S2 and S3). Both drugs are effective
with JAK1 or JAK2 depending on the binding interactions and binding
position inward these proteins. Glu957 and Leu959 are important interactions
in the hinge region of JAK1,[13] and this
interaction is determined to be significant for the binding of inhibitors
within the kinase protein. Therefore, Ruxolitinib strongly binds with
JAK1 compared to Tofacitinib via the formation of two strong hydrogen
bonds. Moreover, the Glu930 and Leu932 residues in the hinge region
are unique to JAK2,[14] and we found that
Ruxolitinib strongly binds with JAK1 compared to Tofacitinib via the
formation of three strong hydrogen bonds.
Figure 2
2D interactions of Ruxolitinib
and Tofacitinib complexed with (A,
B) JAK1 and (C, D) JAK2.
2D interactions of Ruxolitinib
and Tofacitinib complexed with (A,
B) JAK1 and (C, D) JAK2.
FTIR
Analysis
To further investigate
if the different modes of action between both drugs could affect the
inhibition of the cell differently, FTIR was used to see differences
in the biochemical cell responses. The overall FTIR spectrum was obtained
from whole-cell lines between wavelength lengths 3800–1000
cm–1 in Figure A. The selected peaks at 2923, 1656, and 1238 cm–1 were assigned to the C–H stretch, C=O
stretch, and P=O stretch, respectively.[15] The selected spectral groups were adjusted using third
polynomial order, 11 smoothing points, and linear baseline correction
for finished Savitzky–Golay smoothing converted to second derivatives
and EMSC by Unscrambler X 10.4. For an additional detailed comparison
between different cell treatments, these average spectra were analyzed
by PCA.
Figure 3
(A) Average absorbance FTIR spectra of TF-1 cells under untreated
conditions (blue), Tofacitinib-treated cells (red), and Ruxolitinib-treated
cells (green). (B) Two-dimensional PCA score plot in PC1-2. (C) PCA
corresponding loading plot PC1-2 indicating all samples’ biomarker
differentiation.
(A) Average absorbance FTIR spectra of TF-1 cells under untreated
conditions (blue), Tofacitinib-treated cells (red), and Ruxolitinib-treated
cells (green). (B) Two-dimensional PCA score plot in PC1-2. (C) PCA
corresponding loading plot PC1-2 indicating all samples’ biomarker
differentiation.
PCA Distinguishes
Untreated and Drug-Treated
Cells by Detecting Cellular Biochemical Alteration
The goal
was to distinguish the different cell treatments with biochemical
alteration by PCA. PCA is a dimensionality-reduction method that uses
multivariate exploratory analysis techniques allowing identification
of the significant variables or wavenumbers describing differences
between samples. PCA could be achieved and could represent two types
of information, namely, plot scores indicating class separation and
loading plots for identification of the variables, providing clustering
for the responsible information.[15] The
2D score plots in Figure B distinctly show the three samples; PC-1 was sufficient to
separate the TF-1 drug treatment from the untreated cells with an
accuracy of 83% while PC-2 explained 5% total variance in the model.
From Figure C, the
loading plots identify various biochemical components by PC-1 and
PC-2. The major components in the different treatment cells were differentiated
at around 1700–1500 cm–1 for protein; it
was reported that JAK inhibitor-treated cells compared to untreated
cells by PC-1 had higher signals for amide I.[16] Previous research indicated that the range was around 3000–2800
cm–1 for the CH2 and CH3 asymmetric/symmetric
stretching in lipids, fatty acids, and proteins and 1300–1000
cm–1 for the PO2– asymmetric
stretching of DNA and RNA in PC-2.[17] PC-2
loading scores showed that Tofacitinib was distinct from the others
with less lipid and a higher level of nucleic acid accumulation. For
further detailed analysis, the secondary derivative spectra were created
and overlapped for comparison.
Cellular
Biochemical Identification and Differentiation
Detected by S-FTIR
The average FTIR absorbance spectra of
the three samples were subsequently transformed to a second derivative
to reduce baseline slopes and cover every single band in the unrefined
spectra of samples. To identify the band and sub-band components,
the spectra after the second derivative process of the three major
molecular components, namely, lipid, protein, and nucleic acid, are
presented in Figures –6. The peak areas
were assigned to the molecular vibrations in individual wavenumbers
or IR frequencies that are summarized in Table .
Figure 4
Average of second derivative FTIR spectra characterizing
the lipid
regions in the wavelengths from 3000 to 2800 cm–1: 60 spectra of untreated TF-1 cells (blue), 100 spectra of cells
treated with 30.28 μM Tofacitinib (red), and 42 spectra of cells
treated with 14.47 μM Ruxolitinib (green) after incubation for
72 h.
Figure 6
Average second derivative FTIR spectra characterizing nucleic acids
regions in wavelength from 1300 to 1000 cm–1: 60
spectra of untreated TF-1 cells (blue), 100 spectra of 30.28 μM
Tofacitinib-treated cells (red), and 42 spectra of 14.47 μM
Ruxolitinib-treated cells (green) after incubation for 72 h.
Table 1
Second Derivative FTIR Spectra Band
Assignments for the Vibration of Functional Groups That Are Found
in Untreated and Drug-Treated TF-1 Cells
regions
second derivative
spectra (cm–1) band
band assignments
lipid
2963
C–H
asymmetric stretching
(CH3) in fatty acids, lipids, and proteins[17]
2923
C–H
asymmetric stretching
(CH2) in fatty acids, lipids, and proteins[17]
2874
C–H
symmetric stretching
(CH3) in fatty acids, lipids, and proteins[17]
2852
C–H
symmetric stretching
(CH2) in fatty acids, lipids, and proteins[17]
protein
1656–1650
α-helix structure
of amide I[17]
1639–1633
β-sheet structure
of amide I[17]
nucleic acid
1243–1238
PO–2 asymmetric and symmetric stretching (phosphate I) nucleic
acids, phosphorylated proteins, and phospholipids)[17,19]
1226–1216
PO–2 asymmetric stretching (phosphate I)[17]
1191
amide III band region[17]
Average of second derivative FTIR spectra characterizing
the lipid
regions in the wavelengths from 3000 to 2800 cm–1: 60 spectra of untreated TF-1 cells (blue), 100 spectra of cells
treated with 30.28 μM Tofacitinib (red), and 42 spectra of cells
treated with 14.47 μM Ruxolitinib (green) after incubation for
72 h.Average second derivative FTIR spectra characterizing
the protein
regions in wavelengths from 1700 to 1600 cm–1: 60
spectra of untreated TF-1 cells (blue), 100 spectra of Tofacitinib-treated
(30.28 μM) cells (red), and 42 spectra of Ruxolitinib-treated
(14.47 μM) cells (green) after incubation for 72 h.Average second derivative FTIR spectra characterizing nucleic acids
regions in wavelength from 1300 to 1000 cm–1: 60
spectra of untreated TF-1 cells (blue), 100 spectra of 30.28 μM
Tofacitinib-treated cells (red), and 42 spectra of 14.47 μM
Ruxolitinib-treated cells (green) after incubation for 72 h.
FTIR Spectra of Treated Cells Display Lipid
Alteration
The spectra in the region of 3000–2800
cm–1 detected vibrations of the C–H groups
CH2 in lipids and CH3 from fatty acids, lipids,
and proteins using symmetric/asymmetric parameters. The average of
the three samples’ second derivative spectra exhibited high
absorbance at 2963, 2923, and 2852 cm–1 (Figure ). Untreated cells
were stronger than the others for high lipid accumulation. After treatment
with Tofacitinib and Ruxolitinib, the result clearly shows that both
drug treatments decrease lipid production and accumulation. However,
the absorbance of the C–H symmetric stretching of CH3 at 2874 cm–1 was increased after drug treatment.
FTIR Spectra Display Treated Cell Changes
of Secondary Structures in Proteins
The most apparent measurable
differences of second derivatives are the fact that they were surrounded
by reflecting vibrations of protein amide I in 1700–1600 cm–1 (Figure ). The major absorptions of the amide I band from the C=O
stretching of the backbone and the peptide backbone vibrations of
the N–H bending and C–N stretching were detected and
assigned vibrations revealing the secondary structure change in proteins.
On this basis, infrared bands in the 1660–1650 cm–1 range were defined to be the α-helix structure, β-sheets
were imposed in the wavelengths of 1640–1620 cm–1, and β-turn and β-sheet structures were determined in
the 1695–1660 cm–1 region. Furthermore, the
1650–1620 cm–1 region was defined to be the
unordered structures.[16,18] All the sample results showed
that the absorption peaks exhibited the α-helix (1656 cm–1) and β-sheet (1639 cm–1)
in the amide I. Although Tofacitinib- and Ruxolitinib-treated cells
had remarkably reduced α-helix absorbance, they exhibited an
increase in the β-sheet peak at 1639–1633 cm–1. Particularly, the aggregated peak at 1630–1620 cm–1 was increased in Tofacitinib-treated cells. This implies that the
intramolecular β-sheet structures collapsed into aggregated
forms.
Figure 5
Average second derivative FTIR spectra characterizing
the protein
regions in wavelengths from 1700 to 1600 cm–1: 60
spectra of untreated TF-1 cells (blue), 100 spectra of Tofacitinib-treated
(30.28 μM) cells (red), and 42 spectra of Ruxolitinib-treated
(14.47 μM) cells (green) after incubation for 72 h.
High Levels of RNA Overexpression in Cell
Treatment
The average second derivative FTIR spectra characterizing
nucleic acid regions in wavelengths from 1300 to 1000 cm–1 are shown in Figure . Treated cells exhibited high synthesized nucleic acid levels at
1243–1238 cm–1 peaks together with 1226–1216
cm–1 related to the asymmetrical stretching of PO2– in the phosphodiester backbone of DNA or RNA and
also the high absorption of amide III band region at 1191 cm–1. In previous publications, the FTIR application establishes biomarkers
for early screening of B-cell precursor lymphoblastic leukemia (BCP-ALL).
The control group peak area at 1241 cm–1 was identified
as the asymmetric/symmetric stretching of PO2– (nucleic
acids, phosphorylated proteins, and phospholipids).[19] This correlates with the peak result of the treated cells,
which exhibited high synthesized nucleic acid levels at 1243–1238
cm–1. As a result of both type I inhibitor effect
mechanisms, Ruxolitinib decreased signaling can be associated with
the accumulation of activation loop phosphorylation for preventing
JAK2 dephosphorylation and ubiquitination.[20]
Discussion
The JAK–STAT
pathway is related to cellular processes such
as cell division, proliferation, cell death, tumor formation, and
immunity. The pathway information from the chemical signals outside
to the nucleus of the cell results in the initiation of genes through
a process called transcription.[21] Ruxolitinib
and Tofacitinib are first-generation and type I kinase inhibitors,
which are competitive ATP binding sites and repress the enzyme activity
of JAK kinases; thus, the effect of inhibitors is silencing the signal
transduction and action of cytokine. As a result, signal transduction
cannot occur, and the risk of this cancer is decreased. Therefore,
FTIR is an effective tool to study biological systems and consider
the molecular change of cells subjected to antitumor drugs based on
the FTIR spectrum.[9]This study evaluates
the chemical fingerprints of TF-1 cells after
Tofacitinib and Ruxolitinib treatments. The TF-1 cells have proliferative
responses to IL-3 or GM-CSF that can result in activation of the JAK2/STAT
signaling pathway. Both JAK inhibitor drugs are selective JAK inhibitors,
but Ruxolitinib is effective for JAK1/2 inhibition, whereas Tofacitinib
causes a higher inhibition of JAK1/3 than JAK2.[22] This result corresponds to the higher inhibition of TF-1
cells by Ruxolitinib than Tofacitinib.From the binding mode
analysis of known drugs (Ruxolitinib and
Tofacitinib) with JAK1 and JAK2, we found that the docking scores
of Ruxolitinib in complex with both proteins were higher than Tofacitinib
(Figure S1). These results suggested that
Ruxolitinib fits better with both proteins than Tofacitinib due to
the fact that Ruxolitinib is a dual inhibitor against JAK1/2, whereas
Tofacitinib is a dual inhibitor for JAK1/3.[23] Additionally, 2D interactions and the binding pattern bound well
with the deazapurine ring at the ATP binding site (Figure S2). In JAK1, the nitrogen atoms on the deazapurine
ring of Ruxolitinib formed two hydrogen bonds (H-bonds) with Glu957
and Leu959, while Tofacitinib formed H-bonds with Leu959. For JAK2,
we found that nitrogen atoms on the deazapurine ring and nitrile group
formed H-bonds with Lys882, Glu930, and Leu932 for Ruxolitinib and
Leu932 and Arg980 for Tofacitinib (Figure ). Apart from that, all compounds are stabilized
through other interactions such as π-sulfur, π-σ,
π-alkyl, and van der Waals interaction; these interactions are
called hydrophobic interactions (Figure S3).The goal was to evaluate the chemical fingerprints of TF-1
cells
after Tofacitinib and Ruxolitinib treatments. FTIR analysis was performed
and determined from the absorption (or transmission) versus wavelength
(or frequency) of infrared radiation associated with the vibrations
of functional groups within the molecule and chemical bonds between
atoms undergoing various forms.[24] The second
derivative spectra of the three major molecular components, namely,
lipid, protein, and nucleic acid, are presented. (1) Part of the lipid
region is allocated for the phospholipid bilayer and organelle membranes
of the cell. This consists of the fatty acid side chains that have
repeated moieties of CH2– and CH3–
stretching vibration. (2) The protein region is designated to the
amide bonds of amino acid binding in proteins and the peptide bond
that provides the stretching vibration of amide I and bending vibration
of amide II. (3) The region of nucleic acid is given for phosphodiester
bond binding to form DNA/RNA. Accordingly, the sensitized TF-1 cells
of Ruxolitinib compared to Tofacitinib in the JAK/STAT pathway control
can be observed and represent the FTIR spectrum. Biologically, the
JAK/STAT pathway controls crucial cellular processes.[25] Ruxolitinib withdrew phosphorylated STAT3, stimulated caspase-3
cleaving, enhanced apoptosis, and inhibited tumor growth.[26] The inhibitors induced autophagosome accumulation
and reduced the IL-6, IL-18, JAK2, TYK2, and AKT gene expression in
multiple myeloma cells.[27] In a previous
publication, Han et al. provided the Western blot results of Ruxolitinib
treatment using ovarian cancer cells and explained the inhibition
of STAT3 phosphorylation.[28] For Tofacitinib,
the drug effect in JAK/STAT signaling inhibition is anti-myeloma therapeutic.
The result of Western blotting demonstrates a decrease in STAT3 phosphorylation
after treatment with 1 μM Tofacitinib.[29]In vivo, Tofacitinib represses JAK–STAT
pathways by downregulating the phosphorylation of STAT1, STAT3, STAT4,
and STAT5, which also decreases the expression of interferon-regulated
and metalloproteinase genes in rheumatoid arthritis disease.[30]
Conclusions
The
study revealed that FTIR microspectroscopy and PCA analysis
represent methods for classifying the biochemical pattern of untreated
and treated TF-1 cells. The absorbance spectra of C–H lipids,
C=O amide I protein, and the P=O phosphodiester bond
from nucleic acids were detected. Possibly, Ruxolitinib- and Tofacitinib-treated
cells induced the modifications of secondary protein conformation,
stimulated lipid accumulation, and induced protein phosphorylation.
These conclusions imply that FTIR can be a prospective tool for analyzing
individual cellular response patterns in drug-treated cells at the
molecular level.
Materials and Methods
Cell Culture of TF-1 Cell Lines
The
human erythroleukemia TF-1 cells (ATCC CRL-2003, Manassas, VA, USA)
were grown in a complete RPMI-1640 medium (Gibco, Thermo Fisher Scientific
Inc., Waltham, Massachusetts, USA) supplemented with fetal bovine
serum (FBS) (10% v/v) (Gibco), penicillin (100 U/mL), streptomycin
(100 μg/mL) (Gibco), and GM-CSF (2 ng/mL) (Sigma-Aldrich, Merck
KGaA, Darmstadt, Germany). Cells were incubated at 37 °C in a
humidified incubator containing CO2 (5% v/v) and air (95%
v/v).
Cytotoxicity
Tofacitinib and Ruxolitinib
(Sigma-Aldrich) in dimethyl sulfoxide (DMSO) (Sigma-Aldrich) toward
the TF-1 cells were determined using the PrestoBlue assay. The cell
suspensions with a density of 50,000 cells/well were prepared by a
96-well microplate seeding and incubation overnight at 37 °C.
After treatment with the drugs, the cells were incubated for 72 h.
Subsequently, the cells were added to the PrestoBlue reagent (10 μL)
(Invitrogen, Thermo Fisher Scientific Inc., Waltham, Massachusetts,
USA) and incubated at 37 °C for 1 h. Finally, the absorbance
of Resorufin was measured at 570 nm and compared to the vehicle control
by a microplate reader (Infinite M200 microplate reader, Tecan, Männedorf,
Switzerland). The experiment was performed in triplicate independent
experiments (n = 9).
Molecular
Docking
The crystal structures
of JAK1 (PDB ID: 3EYG) and JAK2 (PDB ID: 3FUP)[14,31] were obtained from the Protein Data Bank
(PDB). The 3D structures of the drugs (Ruxolitinib and Tofacitinib)
were downloaded in SDF format from the ZINC database. All docking
tests were performed by GOLD docking software version 2020.1. The
docking protocols of each system were set as 12 Å for sphere
docking and GOLD score and ChemScore (rescore) for the scoring function.
Then, docking into the ATP-binding pocket with 100 docking poses occurred.
The binding between proteins and drugs was visualized using the Discovery
Studio 2020 (Accelrys Inc.) and the UCSF Chimera package.
Sample Preparation for S-FTIR
The
TF-1 cells with a density of 300,000 cells/well were seeded in a 24-well
microplate and incubated overnight at 37 °C. Afterward, the cells
were replenished with a medium without drugs or a medium containing
2-fold concentrations of Tofacitinib or Ruxolitinib for a half-inhibitory
concentration. After incubation for 72 h, cells were harvested by
centrifugation at 300g for 5 min. The pelleted cells
were suspended and washed in NaCl (0.9% w/v) two times, and then cells
were fixed with formaldehyde (4% v/v) at 25 °C for 30 min. After
decanting with formaldehyde, cells were washed three times and re-suspended
with sterile distilled water (20 μL). The resuspended cells
(2 μL) were dropped onto 22 m-diameter × 1 mm-thickness
calcium fluoride IR (CaF2) windows for monolayer formation,
then vacuum-dried, and stored in a desiccator until spectra were acquired
from FTIR analysis.
The S-FTIR experiments were accomplished
at the BL4.1 Infrared
Spectroscopy and Imaging (ISI), Synchrotron Light Research Institute
(SLRI), Nakhon Ratchasima, Thailand. Samples were examined in the
transmission mode of measurement using a photon energy range of 0.01–0.5
eV with a 36× Schwarzschild Objective, a Bruker Vertex 70 spectrometer
coupled to a Bruker Hyperion 2000 microscope (Bruker Optics Ltd.,
Ettlingen, Germany), and a 100-micron narrow band mercury-cadmium-telluride
(MCT) detector cooled with liquid nitrogen. The infrared spectra of
the samples were collected in the spectral range between 3800 and
1000 cm–1 using a 10 × 10 μm square aperture
with a spectral resolution of 6 cm–1 in 40 to 100
scans. The instrument control and spectral achievement were performed
by OPUS 7.2 software (Bruker Optics Ltd., Ettlingen, Germany) and
evaluated in the spectral ranges of 3000–2800 and 1800–1000
cm–1 for each sample group for PCA by Unscrambler
10.4 software (CAMO, Oslo, Norway). The absorbance of molecules of
interest during vibrational modes was identified by spectral secondary
derivative analysis. The absorbances of the C–H stretching
of lipids were detected between 3000 and 2800 cm–1. The absorbances between 1700 and 1500 cm–1 from
the C=O stretching protein amide I and P=O phosphodiester
bond from nucleic acids were detected in the absorbance of 1300–1000
cm–1.
Statistical Analysis
The IC50 values data are presented as mean ± standard
error of the mean
(SEM). In the cytotoxicity experiments, significant differences were
determined by comparing each treatment with an independent T-test. P < 0.05 was indicative of a
statistically significant difference.
Authors: Jun Li; Margaret Favata; Jennifer A Kelley; Eian Caulder; Beth Thomas; Xiaoming Wen; Richard B Sparks; Ari Arvanitis; James D Rogers; Andrew P Combs; Kris Vaddi; Kimberly A Solomon; Peggy A Scherle; Robert Newton; Jordan S Fridman Journal: Neoplasia Date: 2010-01 Impact factor: 5.715
Authors: Denis Tvorogov; Daniel Thomas; Nicholas P D Liau; Mara Dottore; Emma F Barry; Maya Lathi; Winnie L Kan; Timothy R Hercus; Frank Stomski; Timothy P Hughes; Vinay Tergaonkar; Michael W Parker; David M Ross; Ravindra Majeti; Jeffrey J Babon; Angel F Lopez Journal: Sci Adv Date: 2018-11-28 Impact factor: 14.136