DOCKovalent linker design tutoral

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This was written on April 4, 2018.

This tutorial is for designing linkers for a covalent inhibitor and is supplement the work in preparation (Wan et al 2018).

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial

Step 1. Custom Ligand and Library Generation

1/Custom Ligand / Library Generation

cd 1-Custom-Ligand-Library-Generation

For meta-SF library building

reaction1: scaffod.smi is the smile of the scaffold for reaction 817.zinc.list.smi is the smile of collect 817 different diamine linkers

python scaffod.smi 817.zinc.list.smi


python scaffold.ism
                       inputfile: scaffold.ism is the primary products without the SF
                       outputfile: final_scaffold1.smi

reaction3: remove the doubles

python final_scaffold1.smi
                       outputfile: no_doubles_out.ism

The no_double_out.ism was used to generate db2 file for covalent docking log into gimel

setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-beta9-min
setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
/nfs/soft/tools/utils/qsub-slice/qsub-mr-meta -tc 50 --map-instance-script "/nfs/soft/tools/utils/qsub-slice/" -s $BUILD_ENVIRONMENT -l 1 no_doubles_out.ism $DOCKBASE/ligand/generate/ --no-db --no-solv --no-mol2 --single --covalent

Step 2 Protein preparation (different lysine rotamers)

2/Protein preparation (different lysine rotamers)

cd 2-Protein-preparation-different-lysine-rotamers

find the modification lys number in the PDB

echo "5K9I-B-X44      B       295">>lys.list
bash  5K9I-B-X44

In the window of chimera, select all of the 27 lysine rotamers and click the button of OK. Reselect all the lysine rotamers in the PDB structure, and the save to PDB format LYS-5K9I-B-X44.pdb Then, to generate all 28 structure folds, and then automatically calculate the steric clash with nearby residues, and select the rotamer with no steric clashes. This scripts will also calculate the nearest atom of in the compound to the lysine NZ atom

bash 5K9I-B-X44 
5K9E-B-X44      SBH     2.038
5K9B-B-X44      SBH     2.321
5K9I-B-X44      OBI     2.949
5K9L-B-X44      SBH     4.683
5K9R-B-X44      OBI     4.925

Each folder contains rec.pdb and xtal-lig.pdb

For each folder

bash 5K9I-B-X44 box_margin(10) 1(covalent docking)

box_margin is defined from the center of the xtal-lig.pdb file

Step 3 modify the INDOCK parameters for saving multiple poses

cd 3-modify-the-INDOCK-parameters change the default parameters for covalent docking

 bump_maximum                  100
 bump_rigid                    100
 number_save                   1000
 number_write                  1000
 molecules_maximum             100000
 bond_len                      1.61
 bond_ang1                     121.02
 bond_ang2                     107.36
 len_range                     0.0
 len_step                      0.1
 ang1_range                    20.0
 ang2_range                    20.0
 ang1_step                     5
 ang2_step                     5
 check_clashes                 no
 per_atom_scores               yes

Step 4 run the covalent docking in gimel

cd 4-run-the-covalent-docking

contain a pharmacophore filter ( exclusion criteria that ligands should form hydrogen bonds with the kinase hinge region, and the shared pyrimidine 3-aminopyrazole scaffold should be within 2 Å compared to the crystal conformation)

Prepare 1)the modified INDOCK file INDOCK.bump1000000000000.pose1000.20.5.5

       2)the gate residue file (define the two redicue in the SRC kinase domain LYS295  MET341  VAL399)

Inputfile :

       1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
       2) the ligand library folder name (lib1)
       3)the linker name list (lib1.list)
 bash /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_cys_wiki-tutorial/4-run-the-covalent-docking/qsub_multipe_jobs structure-list lib1  lib1.list