D-EXP021

Docking Imines and Amines Against Tubulin Using Autodock Vina

 * Researchers: ** Andrew SID Lang, Lori Fielding, Jesse Patsolic, and Matthew Wilson

Objective
To dock library 10 (570 imines and 570 amines) [|UClib010output] against tubulin using vina (version 1.1.1) autodock vina on ORU's cluster.

Procedure
The SMILES of the imine and the reduced imine columns from the UClib010output spreadsheet were saved as plaintext and saved as a .smi file. This file was used as input to the molconvert program which is part of the JChem and Marvin suites by [|ChemAxon]. The output of the molconvert program yields one .pdb file per SMILE. [**Describe the code used for molconvert. JP]**

The .pbd files were then converted into .pdbqt files which are required for autodock vina. **[What program did you use to convert the files? -JP]**

The 1140 .pdbqt files were then run through autodock vina on the ORU cluster computer in about 9 hours. The output from autodock vina was processed into a table giving the best energies for each ligand. **[Add vina code. JP]**

The top ten energies for the Imines are given in the following table. The full table is given here:.


 * Ligand || Energy || SMILES ||
 * Imine46 || -8.7 || C(c2cc3c(c1c2cccc1)cccc3)=Nc1cc(Cl)ccc1 ||
 * Imine8 || -8.7 || C(c2cc3c(c1c2cccc1)cccc3)=Nc1ccccc1Cl ||
 * Imine236 || -8.5 || C(c2cc3c(c1c2cccc1)cccc3)=NC1CCCCC1 ||
 * Imine122 || -8.4 || C(c2cc3c(c1c2cccc1)cccc3)=Nc1ccccc1 ||
 * Imine160 || -8.3 || C(c2cc3c(c1c2cccc1)cccc3)=NCc1ccccc1 ||
 * Imine21 || -8.2 || C(c1cc(C(F)(F)(F))cc(C(F)(F)(F))c1)=Nc1ccccc1Cl ||
 * Imine84 || -8.1 || C(c2cc3c(c1c2cccc1)cccc3)=NCc1oc(cc1)C ||
 * Imine59 || -8 || C(c1cc(C(F)(F)(F))cc(C(F)(F)(F))c1)=Nc1cc(Cl)ccc1 ||
 * Imine63 || -8 || C(C2=CC=C(OC)C1=CC=C(OC)C=C12)=Nc1cc(Cl)ccc1 ||
 * Imine274 || -7.9 || C(c2cc3c(c1c2cccc1)cccc3)=NCc1ccco1 ||

The top Imine is depicted below.



The top ten energies for the ReducedImines are given in the following table. The full table is given here:.


 * Ligand || Energy || SMILES ||
 * ReducedImine8 || -8.5 || C(c2cc3c(c1c2cccc1)cccc3)Nc1ccccc1Cl ||
 * ReducedImine46 || -8.3 || C(c2cc3c(c1c2cccc1)cccc3)Nc1cc(Cl)ccc1 ||
 * ReducedImine122 || -8.2 || C(c2cc3c(c1c2cccc1)cccc3)Nc1ccccc1 ||
 * ReducedImine236 || -8 || C(c2cc3c(c1c2cccc1)cccc3)NC1CCCCC1 ||
 * ReducedImine45 || -8 || C(C(c1ccccc1)c2ccccc2)Nc1cc(Cl)ccc1 ||
 * ReducedImine7 || -7.9 || C(C(c1ccccc1)c2ccccc2)Nc1ccccc1Cl ||
 * ReducedImine59 || -7.8 || C(c1cc(C(F)(F)(F))cc(C(F)(F)(F))c1)Nc1cc(Cl)ccc1 ||
 * ReducedImine63 || -7.8 || C(C2=CC=C(OC)C1=CC=C(OC)C=C12)Nc1cc(Cl)ccc1 ||
 * ReducedImine121 || -7.7 || C(C(c1ccccc1)c2ccccc2)Nc1ccccc1 ||
 * ReducedImine56 || -7.7 || C(c1ccc2ccccc2(c1))Nc1cc(Cl)ccc1 ||

The top Reduced Imine is depicted below.