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Table 4 Results from searching the ZINC Database using structure based pharmacophores

From: In silico work flow for scaffold hopping in Leishmania

Inhibitor no.

No. of pharmaco-phoric features

No. of Omitted features

Area Under the ROC Curve (AUC)

SMILES of topmost hit

ZINCID

i1

9

2

0.97

C/C2 = N/C = 1/N = C(/N)N = C(N)C = 1/N = C2/C = 3C = CC([Cl]) = C([Cl])C = 3

ZINC34515729

    

C#CC[C@@](CC = 2C = NC1 = NC(N) = NC(N) = C1N = 2)(C = 3C = CC(=CC = 3)C([O-]) = O)C([O-]) = O

ZINC22012802

    

C#CC[C@](CC = 2C = NC1 = NC(N) = NC(N) = C1N = 2)(C = 3C = CC(=CC = 3)C([O-]) = O)C([O-]) = O

ZINC22012807

    

CC = 1C = CC = C(C = 1)C2 = NC = 3C(/N = C2/N) = NC(N) = NC = 3 N

ZINC01566881

    

C#CC[C@]([H])(CC = 2C = NC1 = NC(N) = NC(N) = C1N = 2)C = 3C = CC(=CC = 3)C([O-]) = O

ZINC22012811

    

C#CC[C@@]([H])(CC = 2C = NC1 = NC(N) = NC(N) = C1N = 2)C = 3C = CC(=CC = 3)C([O-]) = O

ZINC22012815

i3

8

3

0.88

CC = 1C = CC = CC = 1NC(=O)C = 3[S]C = 2/N = C(/N)C(C#N) = CC = 2C = 3 N

ZINC18240380

    

C#CC[C@@]([H])(CC = 2C = NC1 = NC(N) = NC(N) = C1N = 2)C = 3C = CC(=CC = 3)C([O-]) = O

ZINC22012815

i4

6

1

0.97

CN(C)C = [N+]C(=[S])NC = 1C = CC([F]) = CC = 1

ZINC03028809

i5

7

2

0.97

CC = 1/C = C(/C)N = C(N = 1)N/C(=N\C(=[S])NC = 2/C = C(/OC)C([Cl]) = CC = 2OC)N3CCC[C@@](C)([H])C3

ZINC14160212

i6

6

1

0.97

CN(C)C = 1[N+] = CC = CC = 1CNC(N[C@@]2([H])CC[C@@]([H])(C2)[S]C) = [N+]C

ZINC72776752

i7

5

1

0.9

COC = 1C = CC(=CC = 1NC(=[S])NC = 2C = CC([F]) = CC = 2)[N+]([O-]) = O

ZINC00493353

    

C/C1 = C/C = NC = 2C1 = CC(=CC = 2 N[C@@](C)([H])CCC[N+]CCC)OC

ZINC01600860

i9

6

1

0.97

CN(C)C = [N+]C(=[S])NC = 1C = CC([F]) = CC = 1

ZINC03028809

iTb4

6

1

0.97

CN(C)C = [N+]C(=[S])NC = 1C = CC([F]) = CC = 1

ZINC03028809

iTb5

7

2

0.99

CC = 1/C = C(/C)N = C(N = 1)N/C(=N\C(=[S])NC = 2/C = C(/OC)C([Cl]) = CC = 2OC)N3CCC[C@@](C)([H])C3

ZINC14160212

iTb6

7

2

0.98

CC = 1/C = C(/C)N = C(N = 1)N/C(=N/C(=[S])NC = 2C = CC([F]) = CC = 2)NCC = 3C = CC([F]) = CC = 3

ZINC14156881

iTb7

5

1

0.9

C/C1 = C(/C(=NN1C[C@@]2([H])CCC[N+]2C)C([F])([F])[F])C(=O)NCCC[N+](C)C

ZINC49362845

    

C/C1 = C/C = NC = 2C1 = CC(=CC = 2 N[C@@](C)([H])CCC[N+]CCC)OC

ZINC01600860

iTb8

8

3

0.99

CC = 1/C = C(/C)N = C(N = 1)N/C(=N\C(=[S])NC = 2/C = C(/OC)C([Cl]) = CC = 2OC)N3CCC[C@](C)([H])C3

ZINC14160209

i10

7

2

0.91

C/C2 = C/C1 = N/N = C(/[S]CCCCCO)N1C(C) = N2

ZINC72058109

i12

7

3

0.97

CC(=O)NC = 4C = 1/C = C(/[F])C = CC = 1N3C[C@](C)(C(=O)N[C@@]2([H])CCCC2)N(CC[N+](CC)CC)C(=O)C3 = 4

ZINC21866480

i13

4

1

0.99

CC = 1C = CC(=CC = 1)C[N+]2CCC([H])(CC2)CC(N) = O

ZINC40540751

i15

5

2

0.78

C[C@@]1([H])CN(C[C@@](C)([H])O1)[C@]([H])(C(=O)NC = 2C = CC(=CC = 2)NC(=O)COC)C(C)(C)[H]

ZINC58203407

i18

4

1

0.76

C[C@@]1([H])C[C@]([H])(CC)N(C1)C(=O)CC[C@@]2([H])NC(=O)NC2 = O

ZINC73336547

    

CC = 1C = C/C = C(/C)C = 1NC(=O)CNC = 2C = CC = C(C = 2)NC(C) = O

ZINC29396021

i19

6

2

0.93

C[C@@]34CC[C@@]1([H])[C@@]([H])(CC[C@@]2(O)C[C@](O)([H])CC[C@]12/C = [N+]/[C@@]([H])(CC)CO)[C@@]3(O)CC[C@]4([H])C5 = CC(=O)OC5

ZINC09167567

    

C[C@]3([H])O[C@]([H])(O[C@@]1([H])[C@@](O)([H])[C@@](O)([H])[C@]([H])(O[C@]1([H])CO)O[C@@]2([H])[C@@](O)([H])[C@@](O)([H])[C@@](O)([H])O[C@]2([H])CO)[C@](O)([H])[C@](O)([H])[C@]3([H])[N+](C)[C@]4([H])C = C(CO)[C@@](O)([H])[C@@](O)([H])[C@@]4(O)[H]

ZINC77302460

i21

6

1

0.88

O[C@@]1([H])CO[C@@]([H])([C@]1(O)[H])[C@@](O)([H])CO

ZINC05157080

    

C[C@](O)([H])[C@](O)([H])[C@@](O)([H])[C@@](O)([H])CO

ZINC03872643

    

CC(=O)C(=O)[C@@](O)([H])[C@](O)([H])[C@@](O)([H])[C@@](O)([H])CO

ZINC64219378

    

CN/C2 = N/C1 = C(/N = C(/N)NC1 = O)N2[C@]3([H])O[C@]([H])(CO)[C@](O)([H])[C@]3(O)[H]

ZINC13361972

i22

6

2

0.75

OCC(CO)(CO)[N+]C[C@@](O)([H])CN2C1 = C/C = C(/[Br])C = C1C = 3/C = C(/[Br])C = CC2 = 3

ZINC10384387

    

[N+][C@]2([H])C[C@@]([N+])([H])[C@]([H])(O[C@@]1([H])O[C@]([H])(C[N+])[C@](O)([H])[C@@](O)([H])[C@]1(O)[H])[C@@](O)([H])[C@@]2([H])O[C@@]3([H])O[C@]([H])(CO)[C@](O)([H])[C@@]([N+])([H])[C@]3(O)[H]

ZINC08214767

    

C[C@]3(O)CO[C@@]([H])(O[C@]2([H])[C@@]([N+])([H])C[C@]([N+])([H])[C@]([H])(O[C@@]1([H])CC(=CC[C@]1([N+])[H])C[N+])[C@]2(O)[H])[C@@](O)([H])[C@@]3([H])[N+]C

ZINC70672630

    

[N+][C@@]2([H])[C@](O)([H])[C@]([H])(O[C@]1([H])O[C@@]([H])(CO)[C@](O)([H])[C@](O)([H])[C@]1([N+])[H])[C@@]([H])(CO)O[C@]2(O)[H]

ZINC43758958

i23

7

2

0.87

OC = 1C = C/C(=C(/O)C = 1)C2 = NN/C(=C2/C4 = N/C = 3C = CC = CC = 3[S]4)C([F])([F])[F]

ZINC04126006

    

[O-]C(=O)C[C@](O)([H])C[C@](O)([H])C = CC = 2C(=C1C = CC = CC1 = NC = 2[C@]3([H])CC3)C = 4C = CC([F]) = CC = 4

ZINC11616582

i24

7

2

0.87

CC = 1C(O) = CC = C(C = 1O)C2 = NN = C[C@@]2([H])C4 = NC = 3C = CC = CC = 3[S]4

ZINC18188334

    

CN2C = 1/N = C(/NCCO)N(CCO)C = 1C(=O)NC2 = O

ZINC01876281

i25

6

2

0.8

CC = 1C = CC(=CC = 1)CN2C(=O)C(=CNC2 = O)CC([O-]) = O

ZINC20156415

  1. The topmost hits from the ZINC database utilizing the pharmacophores from the protein – inhibitor complexes. For each pharmacophore the area under the ROC curve and the number of omitted pharmacophoric features while validation have been given in columns 3,4. Also included are hits (given in bold) which have features very similar to approved drugs. The ZINC Id of the hit is given in the last column.