RSMD and RMSF plots of all complexes.
(A) Superimposed structure of pdbs of PPARα-Forasartan complex at 0-ns (dark slate grey) and 200-ns (Sienna) and closer view of conformational shifts. (B) 2D interaction of Forasartan-PPARα at 200-ns.Among all PPARα complexes, more fluctuations were observed in the Lanifibranor-PPARα complex. From zero ns to 87 ns, the fluctuations and random peaks were observed but afterward, the plot showed fewer fluctuations and more stability towards the very end of the simulation. The Lanifibranor-PPARα RSMD plot showed the highest peak at 192 ns of 2.78 Å. The variability in the RMSD of Lanifibranor-PPARα was detected due to the noteworthy movement of Lanifibranor in the docked pocket and inward movement of Ω-loop which brought Lanifibranor closer to the Helix-12 (H-12) of PPARα and developed new interactions with the residues (Pro262 and Gln265) of H-12 ((A) Superimposed structure of pdbs of PPARα-Lanifibranor complex at 0-ns (dark slate grey), 39-ns (dark magenta), 194-ns (green), and 200-ns (Sienna). A closer view of conformational changes occurred in PPARα during simulation and Movement of Lanifibranor towards H-12. (B) 2D interaction of Lanifibranor-PPARα at 200-ns.The RMSF was evaluated for residue-by-residue fluctuation of docked protein during simulation. The RMSF average value for APHM13, Forasartan, and Lanifibranor complex was 0.94 Å, 0.98 Å, and 1.18 Å, respectively. Among all PPARα complexes, the highest RMSF average value was observed for the Lanifibranor-PPARα complex as for the RMSD value, which indicates greater flexibility in the residues during simulation (