2.1 Molecular docking:
The protein structures of the key proteins associated with NF-κB and JAK-STAT pathway were downloaded from the PDB database: IKK-α (5EBZ), IKK-β (4KIK), IκB- α (1IKN), p65 (1NFI), p50 (1SVC), p65-p50 heterodimer (1VKX), RelB (3DO7), NIK (4G3D), p52 (3DO7), JAK1 (6BBU), JAK2(6BBV), JAK3 (6DA4), STAT1(1YVL), STAT2 (5OEN), STAT3 (6TLC), STAT4(1BGF), STAT5A(1Y1U), TYK(6DBK). A total of 100 plant polyphenols were selected based on dietary intake consisting of flavonoids, non-flavonoids, and phenolic acid. SMILES of the chosen ligands were acquired from the PubChem database and transformed into conventional .pdbqt setup with the help of Open Babel software [40]. The molecular docking study of the identified ligands and the target proteins were carried out via AutoDock Vina and HADDOCK web server [41, 42]. For docking studies in AutoDock Vina, water molecules present in the target protein were detached, and polar hydrogens in addition to Kollman charges were affixed. The structures were next transformed to .pdbqt setup. The grid box was generated to help site-specific docking by locating binding points and the coordinates for x, y, z were fixed to 40, 40, and 40, respectively. For docking experiments of all 100 polyphenols, similar-sized grid box along with other similar parameters were employed, and the full set-up was performed to acquire the docked conformations. To determine the binding energy between proteins of the NF-κB and JAK-STAT pathway and the polyphenols, the best-fitted configuration with the lowermost root mean square deviation (RMSD) were chosen. The same protein and ligand structures were used to carry out docking studies in HADDOCK web server. Easy interface segment of HADDOCK web server was selected to upload the proteins and ligand structures as molecule-1 and molecule-2, respectively. The active sites of the protein critically involved in various interactions were specified. LigPlot+ was utilized to examine the interactions involved in the docked complexes containing the results from AutoDock and HADDOCK server [43].
2.2 MD simulation setup for the complexes:
The AMBER 20 Molecular Dynamics Package was used to simulate the docked p65 NF-κB-pinoresinol and STAT3-pinoresinol complexes [44]. The Amber LEaP module produced the topology and coordinate files necessary for MD simulation [45]. The protein was described using the ff99SB force field [46] and the generic Amber force field (GAFF) parameters for the ligand-protein complexes. The docked complex systems were solvated in a cubic periodic box using the explicit TIP3P (transferable intermolecular potential with 3 points) water model [47]. The requisite quantity of counter ions was added to the complicated systems to neutralize them, and the strong van der Waals was eliminated through energy reduction. The energy minimization dynamics are a part of the standard protocol for the Molecular Dynamics Simulations technique. We employed energy-minimized systems as a starting point for the succeeding MD stages. The above-mentioned constructed complex was subsequently put through an MD minimization run, which involves two steps of minimization: steepest descent and conjugate gradient. Following a nanosecond of NVT equilibration with the time step and NPT equilibration, the complicated structures were reduced using the steepest descent method for the picosecond. Structures were improved until the final RMS energy gradient was smaller than 0.1 Kcal/mol. Except as otherwise noted, the reduction was finished at each stage. The protein systems were equilibrated for one nanosecond under NPT conditions, which involve 300 K and one atm of pressure. The temperature, energy, and pressure graphs were plotted and examined to make sure the systems had successfully equilibrated. Subsequently, a 100 ns MD production run was conducted for the equilibrated structures of both systems using the Particle Mesh Ewald (PME) algorithm with a time step of 2 fs [48, 49]. During the simulation, nonbonding interactions (van der Waals and short-range electrostatic interactions) were handled with a cutoff of 8 Å, whereas the PME approach was used to tackle long-range electrostatic interactions. The SHAKE method was used to limit every bond in the systems [50]. The pressure and temperature (0.5 ps of heat bath and 0.2 ps of pressure relaxation) were maintained constant throughout the simulation process by the Berendsen weak coupling algorithm [51], and all the bonds that were present in the systems were constrained using the SHAKE algorithm [50].
2.3 Binding free energy calculations:
The binding free energies (BFE) of the p65 NF-κB-pinoresinol and STAT3-pinoresinol complexes in the presence of the pinoresinol molecule were calculated using the FastDRH (http://cadd.zju.edu.cn/fastdrh/) web server and Generalized-Born surface area continuum solvation (MM/GBSA) methods [52]. The total binding free energies (BFE) of the NF-κB-Pinoresinol and STAT3-Pinoresinol complex as well as the other derived components (VDW, ELE, GB, and SA) that contribute to the total BFE of the two complexes, were calculated.
2.4 Antibodies and reagents:
Pinoresinol, Phorbol-12-myristate- 13-acetate (PMA) and Type 1 Collagen were procured from Sigma-Aldrich, USA. Alexa Fluor 594 and IL-6 (human recombinant) protein were bought from Invitrogen, USA. RPMI-1640 medium was procured from Himedia, India. NE-PER™ Nuclear and Cytoplasmic Extraction Reagents, ProLong™ Gold Antifade Mountant, Halt™ Protease Inhibitor Cocktail, Halt™ Phosphatase Inhibitor Cocktail, and Verso cDNA synthesis kit were procured from Thermo Fisher Scientific, USA. Taq polymerase was obtained from BioBharati Life Science, India. Fetal bovine serum and penicillin/streptomycin were acquired from Life Technologies, Gibco, USA. The antibodies, mouse anti-TNF-α was obtained from Cloud-Clone Corp. and rabbit anti-β actin, mouse anti-STAT3, rabbit anti phospho STAT3 (Tyr705), mouse anti-NF-κB p65, rabbit anti-phospho NF-κB p65 (Ser536), rabbit anti-IKK, rabbit anti-phospho IKK (Ser176), rabbit anti-Ikβ-α, rabbit anti-phospho Ikβ- α (Ser32), rabbit anti-COX-2, rabbit anti-IL-1β, rabbit anti-MCP-1, rabbit anti-MMP-2, rabbit anti-MMP-9, rabbit anti-GAPDH, and rabbit anti-PARP were all procured from Cell Signaling Technology, USA.
2.5 Cell culture and treatment:
THP-1 cell line derived from human monocytes was procured from the American Type Culture Collection (ATCC, USA). Cells were maintained in RPMI-1640 enriched with 10% FBS as well as penicillin/streptomycin at 370C in 5% CO2. The culture was passaged in fresh medium every 2-3 days. For gene and protein expression studies, around 1.5 X 106-2.5 X 106 THP-1 monocytes were differentiated to THP-1 macrophages by treatment with 5 ng/ml PMA for a period of 48 hours. The differentiated cells underwent pre-treatment with Pinoresinol at two dosages, 50 μM and 100 μM, for a duration of 4 hours in 1% FBS-containing RPMI media (without antibiotics) and then induced with IL-6 (50 ng/ml) for another 2 hours. Cells were subsequently harvested for protein and gene expression.
2.6 Cell viability assay:
Around 10,000 THP-1 cells in a 96-well plate were differentiated as described above. After 24 hours of rest, cells were subjected to either IL-6 (50ng/ml) alone or with a range of pinoresinol concentrations (12.5-200 μM). Following treatment, the cells were incubated for 24 hours. Upon adding 15μl of 5 mg/ml MTT to each well after 24 hours, absorbance was measured at 590 nm.
2.7 Semi-quantitative PCR:
Total cellular RNA was extracted using TriZol reagent and reverse transcribed with Verso cDNA synthesis kit (Thermo Scientific, USA) following manufacturer’s protocol. Semi-quantitative PCR reactions were performed using the cDNA samples as templates with gene-specific primers (Supplementary Table 3).
2.8 Cell fractionation studies:
3 X 106 THP-1 monocytes were seeded and subsequently differentiated by PMA treatment (5ng/ml). Cells were subjected to pinoresinol (50μM and 100μM) treatment for 4 hours prior to incubation with IL-6 (50ng/ml) for 2 hours. Cells were harvested, washed with ice-cold 1XPBS and subjected to centrifugation at 500 x g (5 minutes). NE-PER™ Nuclear and Cytoplasmic Extraction Kit (Thermo Fisher Scientific), was used to prepare the nuclear and cytoplasmic fractions following manufacturer’s protocol.
2.9 Western blotting:
Cells underwent treatment, as previously described, and harvested with RIPA buffer containing phosphatase and protease inhibitors for western blot studies. SDS-PAGE was carried out to resolve the proteins from whole-cell lysate samples, which were then transferred to PVDF membranes. After washing, the membranes were subjected to primary antibody incubation at 4oC overnight, followed by incubation with secondary antibody (HRP-linked) for an hour at room temperature. The blots were then exposed to a chemiluminescence substrate (Clarity Western ECL Substrate, Bio-Rad). The images were captured with the help of the ChemiDocXRS + system (Bio-Rad, USA). The protein bands were assessed and quantified using ImageJ software [53].
2.10. Adhesion Assay:
A 96-well plate was coated with 75 μl of 40 μg/ml type 1 collagen, sealed, and incubated overnight at 4ºC. The following day, 0.5 x 106 cells were loaded onto a 6-well cell culture plate. Cells were treated with pinoresinol and IL-6 as described earlier. The collagen-coated plate from 4ºC incubation was kept at room temperature for 2 hours, excess collagen was removed and then placed in CO2 incubator. Post-treatment, cells were transferred to microfuge tubes, centrifuged (2000 rpm, 5 mins) and the cell pellet was resuspended in incomplete RPMI medium. The collagen-coated wells were rinsed with incomplete RPMI medium, and 100 μl of cell preparations from every sample were dispensed into the wells, followed by 1-hour incubation for adhesion. Post incubation, medium was withdrawn, adhered cells were fixed by 5% glutaraldehyde treatment for 20-30 min at room temperature. After couple of washes, cell were incubated with 2% crystal violet for 5 minutes followed by imaging 10X objective. Cells were then solubilized with 10% acetic acid and absorbance were measured at 580 nm.
2.11 Migration Assay:
Differentiated THP-1 macrophages (0.25 x 106/well) were seeded in the lower chamber of a 24-well plate. Cells were pretreated with two pinoresinol concentrations (50 μM and 100 μM) followed by 2-hour stimulation with IL-6 (50 ng/ml) as described earlier. Post-treatment, the cells were washed twice with 1X DPBS and incomplete media was added. Transwell inserts with 5μm pore size (Corning, USA) loaded with THP-1 monocytes (0.2-2 x 106/well) were placed in upper chamber in a serum-deficient medium. Migrated monocytic cells beneath the insert were fixed at room temperature using 3.7% formaldehyde in PBS. After washing, cells were permeabilized with 100% methanol for 20 minutes and stained with Giemsa for 15 minutes. The stain was removed, followed by washing with PBS, and observed under a 10X objective on a bright-field microscope.
2.12 Statistical analysis:
Data were collected from mean ± SEM from a minimum of three distinct experiments. ImageJ software was used for densitometric analysis of bands acquired from Western blotting and PCR experiments. One-way ANOVA were performed to compare the distinct sets of data. We considered statistical significance at a P-value equal to or below 0.05.