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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