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Table 2 TNF-α, TNFR1, TNF-α -TNFR1 complex inhibitors and their molecular properties and drug-likeness predicted by Molsoft and FAF-Drugs4

From: Identification of novel inhibitors for TNFα, TNFR1 and TNFα-TNFR1 complex using pharmacophore-based approaches

TNF-α inhibitors
Molecular Properties and drug-likeness ZINC09609430 ZINC13113075 ZINC25251930 ZINC39907639 ZINC49467549 307 (default ligand)
Molecular formula C28 H29 F N4 O3 C22 H20 F N3 O3 S C25 H22 N6 O C28 H26 N2 O3 C28 H24 N4 O3 S
Molecular weight 488.22 425.12 422.19 438.19 496.16
Number of HBA 5 6 4 4 6
Number of HBD 1 1 1 0 1
MolLogP 4.21 4.10 4.08 6.19 (> 5) 4.83
MolLogS − 7.68 (in Log(moles/L)) 0.01 (in mg/L) − 6.63 (in Log(moles/L)) 0.10 (in mg/L) − 5.18 (in Log(moles/L)) 2.78 (in mg/L) − 6.59 (in Log(moles/L)) 0.11 (in mg/L) − 5.50 (in Log(moles/L)) 1.59 (in mg/L)
MolPSA 60.03 A2 60.52 A2 54.90 A2 33.34 A2 70.46 A2
MolVol 490.82 A3 401.38 A3 420.54 A3 435.86 A3 495.76 A3
Number of stereo centers 1 2 1 0 0
Drug-likeness model score 1.06 0.30 0.56 0.81 0.74
TNFR1 inhibitors
Molecular Properties and drug-likeness ZINC02968981 ZINC08704414 ZINC09544246 ZINC58047088 ZINC72021182 ZINC33832439 (query)
Molecular formula C24 H18 N6 O3 S C21 H21 N5 O S C18 H15 N5 O4 S2 C20 H17 F N5 O2 S C23 H19 Cl N2 O4 C22 H22 O10
Molecular weight 470.12 391.15 429.06 410.11 422.10 446.12
Number of HBA 7 5 8 5 4 10
Number of HBD 1 1 4 2 3 5
MolLogP 4.10 3.50 1.94 3.31 3.44 0.23
MolLogS − 6.69 (in Log(moles/L)) 0.10 (in mg/L) − 4.42 (in Log(moles/L)) 14.86 (in mg/L) − 6.71 (in Log(moles/L)) 0.08 (in mg/L) − 4.98 (in Log(moles/L)) 4.30 (in mg/L) − 5.25 (in Log(moles/L)) 2.36 (in mg/L) − 5.78 (in Log(moles/L)) 0.74 (in mg/L)
MolPSA 92.53 A2 54.37 A2 113.69 A2 67.36 A2 79.03 A2 130.22 A2
MolVol 417.94 A3 371.69 A3 367.90 A3 387.22 A3 397.84 A3 411.01 A3
Number of stereo centers 0 1 0 0 0 5
Drug-likeness model score 0.34 0.59 0.78 1.05 1.91 0.77
TNF-α–TNFR1 complex inhibitors
Molecular Properties and drug-likeness ZINC05328058 ZINC23553920 ZINC17206695 ZINC05462670 ZINC35681945 ZINC08214556 (query)
Molecular formula C28 H22 O10 C24 H26 N8 O S C19 H26 N6 O4 C30 H26 O10 C23 H30 N7 O4 C20 H8 I4 O5
Molecular weight 518.12 (> 500) 474.20 402.20 546.15 (> 500) 468.24 835.66 (> 500)
Number of HBA 10 7 6 10 6 5
Number of HBD 6 (> 5) 3 3 6 (> 5) 5 2
MolLogP 4.07 5.02 (> 5) 3.47 5.12 (> 5) 2.53 7.86 (> 5)
MolLogS − 5.82 (in Log(moles/L)) 0.79 (in mg/L) − 7.02 (in Log(moles/L)) 0.05 (in mg/L) − 5.61 (in Log(moles/L)) 0.99 (in mg/L) − 6.81 (in Log(moles/L)) 0.08 (in mg/L) − 6.48 (in Log(moles/L)) 0.15 (in mg/L) − 6.87 (in Log(moles/L)) 0.11 (in mg/L)
MolPSA 137.14 A2 92.52 A2 104.94 A2 138.17 A2 115.18 A2 58.97 A2
MolVol 489.42 A3 451.02 A3 377.73 A3 528.68 A3 444.44 A3 430.17 A3
Number of stereo centers 2 0 2 4 1 0
Drug-likeness model score − 0.35 0.14 0.54 − 0.69 1.12 0.20