Fig 1.
Flow chart of the current work.
Table 1.
Negative logarithm values of the biological activity concerning the 33 compounds.
Table 2.
Descriptors showing correlation coefficients higher than 0.1 with the activity.
Table 3.
K-means clustering results.
Table 4.
Multi-collinearity statistics.
Fig 2.
Correlation of observed and predicted activities (training set in blue and test set in red).
Table 5.
Descriptors’ computed values and predicted activities as well of the test set compounds using the MLR model generated.
Fig 3.
Williams plot of standardized residual versus leverage for the MLR model (with: h* = 0.45 and residual limits = ± 2.5); training samples are designed in black color and test samples in red color.
Fig 4.
Chemical structure of the new proposed drug (C27H32N6O4S).
Table 6.
Physicochemical properties.
Fig 5.
4LL3-Structure downloaded from PDB.
Fig 6.
3TTP-Structure downloaded from PDB.
Fig 7.
New drug candidate optimized using Gaussian.
Fig 8.
3D structure of DRV.
Fig 9.
2D-binding interactions in the active site of the wild type protease (WT-ND).
Fig 10.
2D-binding interactions in the active site of the mutant type protease (MT-ND).
Fig 11.
2D-binding interactions in the active site of the wild type protease (WT-Darunavir).
Fig 12.
2D-binding interactions in the active site of the mutant type protease (MT-Darunavir).
Fig 13.
3D-binding interactions in the active site of the wild type protease (WT-ND).
Fig 14.
3D-binding interactions in the active site of the mutant type protease (MT-ND).
Fig 15.
3D structure of complex compound with WT protease (WT-DRV).
Fig 16.
3D structure of complex compound with MT protease (MT-DRV).
Table 7.
Complex compounds’ affinity values and the number of different interaction types.
Fig 17.
The root means square deviation (RMSD) plots of MT and WT proteases virgin as with ligands (ND and DRV) during 100ns of molecular dynamics simulation.
Fig 18.
The root means square fluctuation (RMSF) plots of MT (chain (A) and chain (B)) and WT (chain (A) and chain (B)) proteases without and with ligands (ND and DRV) during the period of simulation.
Fig 19.
Graphs representing the Radius of gyration (Rg) values for MT and WT proteases without as with ligands (ND and DRV) during the period of simulation.
Fig 20.
Graphs showing the number of hydrogen bonds (at every 20 ns) along with the simulation time for complex compounds containing MT and WT proteases.
Fig 21.
Graphs showing the number of hydrophobic interactions (at every 20 ns) along with the simulation time for complex compounds containing MT and WT proteases.
Fig 22.
Time evolution (at every 20 ns) of solvent accessible surface area (SASA) or of the wild type and the mutant type proteases along with DRV and the ND.
Table 8.
Average MM-PBSA free energies for proteins (WT and MT) and ligands (DRV and ND).