Fig 1.
The vision of an alphavirus and the arrangement of its genome this image shows the nucleocapsid of an alphavirus virion, composed of a 42S RNA genome (red) in plus-sense orientation and capsid proteins (sky blue). Virus glycoproteins E1 and E2 heterodimers (grey) are embedded in a lipid bilayer (green) surrounding the nucleocapsid, enclosed by a lipid bilayer.
Fig 2.
Table 1.
Screening of phytochemicals based on their best binding energy.
Fig 3.
Best docked pose of Lupenone with 2ALA displaying 2D interaction plot on the left panel.
Pink dashed lines indicate the Pi-Alkyl bond and residues embedded in the light green sphere, indicating involvement in Van der Waals interactions. On the center panel, surface view of 2ALA displaying binding cavity of Lupenone and right panel displays the zoomed out binding pocket having amino acid residues at 3Å surrounding the Lupenone molecule.
Fig 4.
A. MD simulation trajectory analysis of Root Mean Square Divisions (RMSD) of 92158 (Lupenone) bound with 2ALA, i.e. Spike E1 200 ns time frame in triplicate displayed: R1 (replicate 1) RMSD plot of 92158 bound 2ALA (red) with control 2ALA (light green); R2 (replicate 2) RMSD plot of 92158 bound 2ALA (dark maroon) with control 2ALA (juniper green); R3 (replicate 3) RMSD plot of 92158 bound 2FLU (yellow) with control 2ALA (cyan); B. MD simulation trajectory analysis of Root Mean Square Fluctuations (RMSF) of 92158 (Lupenone) bound with 2ALA, i.e. Spike E1 200 ns time frame in triplicate displayed: R1 (replicate 1) RMSF plot of 92158 bound 2ALA (red) with control 2ALA (black); R2 (replicate 2) RMSF plot of 92158 bound 2ALA (maroon) with control 2ALA (cyan); R3 (replicate 3) RMSF plot of 92158 bound 2FLU (yellow) with control 2ALA (pickle green); C. MD simulation trajectory analysis of Radius of gyration (Rg) of 92158 (Lupenone) bound with 2ALA, i.e. Spike E1 200 ns time frame in triplicate displayed: R1 (replicate 1) Rg plot of 92158 bound 2ALA (red) with control 2ALA (light green); R2 (replicate 2) Rg plot of 92158 bound 2ALA (porcelain) with control 2ALA (dark green); R3 (replicate 3) Rg plot of 92158 bound 2FLU (black) with control 2ALA (Prussian blue); D. MD simulation trajectory analysis of Hydrogen Bonding (H-Bonds) of 92158 (Lupenone) bound with 2ALA, i.e. Spike E1 200 ns time frame in triplicate displayed: R1 (replicate 1) H-Bond plot of 92158 bound 2ALA (red); R2 (replicate 2) H-Bond plot of 92158 bound 2ALA (black); R3 (replicate 3) H-Bond plot of 92158 bound 2FLU (light green).
Fig 5.
Stepwise trajectory analysis for every 25 ns displaying the protein and ligand conformation during 200 ns of simulation.
Fig 6.
MMGBSA trajectory (0 ns, before simulation and 200 ns, after simulation) exhibited conformational changes of Lupenone upon binding with the protein 2ALA.
The arrows indicating the overall positional variation (movement and pose) of Lupenone at the binding site cavity.
Fig 7.
A. Free Energy Landscape displaying the achievement of global minima (ΔG, kj/mol) of (P) 2ALA in presence of Lupenone with respect to their RMSD (nm) and Radius of gyration (Rg, nm); B. SASA of bound and unbound state.
Fig 8.
Decomposition of the binding free energy on a per-residue basis into contributions of 2ALA residues with Lupenone.
Table 2.
Binding energy calculation of Lupenone with 2ALA and non-bonded interaction energies from MMGBSA trajectories.
Fig 9.
A. Dynamic Cross Correlation matrix (DCCM) of 2ALA and correlated amino acids conformed into secondary structural domains (colored) and non-correlated domains (grey) of 2ALA; B. PCA of 2ALA-Lupenone showing a stable configuration; C. Energy plot of protein 2ALA and Lupenone complex system during the entire simulation event of 200 ns. The total energy (dark green), van der Waal’s energy (cyan) and coulomb energy (red) of the entire system indicate the stability of the individual systems bound to Lupenone molecule.