Article Figures & Data
Figures
- Figure 1
- A 3D structure-based pharmacophore features generated by the knowledge of molecular interactions between gp120 and BMS-488043. The H-bond acceptor features are shown in purple color, Aromatic features are shown in green color while H-bond donor and hydrophobic features are shown in blue color. BMS-488043 mapped on the pharmacophore features are shown in yellow color.
- Figure 2
- Structures of 22 retrieved hits from ZINC and Cambridge database.
- Figure 3
- Pharmacophore mapping and binding interactions of selected compounds. The upper panel of A), b), c) and d) showed the binding interactions of compound 8,12,13, and 4, respectively. The lower panel of A), b), c) and d) showed the pharmacophore mapping of compound 8,12,13, and 4, respectively.
- Figure 4
- Dynamic analysis of simulated complexes. A) RMSD of BMS-488043, Cambridge14695864 and ZINC06893293 in complex with gp120 during the 100ns of simulation. B) RMSF of gp120 residues after binding of BMS-488043, Cambridge14695864 and ZINC06893293 during the 100ns of simulation. C) Dynamics cross‐correlation matrix of (a) gp120/BMS-488043, (b) gp120/Cambridge14695864, and (c) gp120/ZINC06893293.
Tables
- Table 1
- Results of molecular docking studies and physiochemical properties of the hit compounds from Chembridge and ZINC database.
S. No Compound ID Docking score (S) Binding energy (kcal/mol) Binding Affinity (kcal/mol) Physiochemical properties Mol. weight Log P Donor Acceptor Log S 1 ZINC72027118 -7.43 -13.81 -5.66 364.405 4.74 1 4 -5.59 2 ZINC06893293 -9.65 -18.82 -7.24 400.455 2.03 1 5 -3.82 3 ZINC78871949 -9.56 -18.36 -7.05 390.487 3.45 2 3 -5.63 4 ZINC10271817 -9.76 -17.34 -7.30 469.494 0.43 4 7 -4.14 5 ZINC28082519 -8.26 -16.07 -6.56 388.448 2.61 2 5 -3.57 6 ZINC04543426 -8.59 -26.06 -7.94 404.415 0.75 2 5 -3.35 7 ZINC72014953 -9.05 -22.35 -6.72 428.439 5.14 1 5 -5.74 8 ZINC79193975 -11.12 -19.24 -8.12 487.505 1.15 5 9 -2.82 9 ChemBridge14695864 -9.21 -27.59 -7.83 381.411 2.27 2 4 -5.11 10 ChemBridge16586658 -8.75 -23.02 -8.12 407.514 3.19 2 4 -4.62 11 ChemBridge16610636 -9.30 -23.41 -7.73 448.485 5.10 2 4 -4.55 12 ChemBridge17115705 -11.05 -19.28 -7.27 474.557 4.27 2 5 -6.39 13 ChemBridge18573235 -10.08 -23.57 -8.05 448.947 3.74 2 6 -4.36 14 ChemBridge31483125 -8.18 -12.49 -5.49 340.427 2.43 2 5 -1.98 15 ChemBridge32351948 -7.86 -15.72 -5.58 398.507 2.27 2 5 -2.84 16 ChemBridge36158778 -7.41 -15.17 -7.44 312.353 2.71 2 5 -3.42 17 ChemBridge39229227 -8.35 -21.83 -6.28 422.533 3.19 1 5 -2.66 18 ChemBridge46500603 -8.53 -18.75 -5.99 351.410 2.83 1 6 -2.85 19 ChemBridge58982400 -7.47 -18.30 -6.42 401.551 2.63 2 5 -2.52 20 ChemBridge78620441 -8.25 -19.03 -6.00 386.492 1.46 4 6 -2.41 21 ChemBridge80485459 -8.07 -17.54 -5.40 405.502 3.69 1 5 -2.84 22 ChemBridge83081330 -7.96 -21.91 -8.06 383.488 4.05 1 4 -3.69 - Table 2
- Structure and Simplified Molecular-Input Line-Entry System (SMILE) ID of compounds that successfully passes the pan assay interference compounds filter.
Ligand PAINS Filter Structure SMILE ID ChemBridge14695864 Passed 
c1(cccc(c1)NC1=C(C(CC(C1)(C)C)NC(=O)c1n[nH]c(=O)cc1)CN)F ChemBridge16586858 Passed c1ccc(cc1)CCCC1NC2C(O1)CC=C(C2)C(=O)NCCN1CCCC(C1)O ChemBridge16610636 Passed C1C(CC(=CC1)CNC(=O)CC1CCN(CC1)CC1C(C(=CCC1)[O-])O)C(P)(I)P ZINC06893293 Passed O=C(CCS(=O)(=O)c1ccc2c(c1)NC(=O)CO2)N1CCc2ccccc2C1
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