Xiaobo wan: Created page with " 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 ..."

2018-06-18T20:08:55Z

Created page with " 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 ..."

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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 step1-reaction-amines-Br.py scaffod.smi 817.zinc.list.smi

reaction2:
python step2-reaction-SF-meta.py scaffold.ism
input file: scaffold.ism is the primary product without the SF
output file: final_scaffold1.smi

reaction3: remove the doubles
python step3-remove_doubles.py final_scaffold1.smi
inputfile: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 /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
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/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT -l 1 no_doubles_out.ism $DOCKBASE/ligand/generate/build_database_ligand.sh --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 step0_prepare_build_system.sh 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 script will also calculate the nearest atom of in the compound to the lysine NZ atom
bash step1_run_build_system.sh 5K9I-B-X44
results
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 step1_DOCKINV.blastermaster.sh 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 residue in the SRC kinase domain MET341 VAL399)
Input file :
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

==Step 5 Analysis and combine the top1 pose from different structures==

cd 5-Analysis-and-combine-the-top1-poses-from-different-structures
after the covalent docking, analyze the docking results

bash step1_extract_the_best_score.sh structure-list lib1 lib1.list
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)

combine the docking results

bash step3_combine-best-energy.sh structure-list lib1

Input file :
1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
2) the ligand library folder name (lib1)
Output file:
1)sort.final.combine-new.aura-A-X63.list.dat rank all of the top1 pose for each linker
2)submit.new.aura-A-X63.list.dat the name of structure file and linker

==Step 6 Run the minimization and MM/GBSA rescoreing==

cd 6-Run-the-minimization-and-MMGBSA-rescoring
First, check the protonation state of each linker after when using the chimera to add hydrogen
second, the different H position of linkers will result in the different labelling number of the attached NH of lysine residue
prepare the list for each linker containing two informations in XO44.charge.list file (default:xabs 1 1)

bash step7_fix_prolem_resubmit_MMPBSA.minimization.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB
INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB is the folder for runing minimization

after minimization, then run the AMBER MMGBSA rescoring
bash step10_fix_prolem_resubmit_MMPBSA_score.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB

extract the scoring number for each linker
bash step6_resubmit.extract_GBscore.sh list
the list contains (INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB)

==Step 7 analyze the final pose by chimera==
cd 7-analyze-the-final-pose-by-chimera
first sort the linker according to the MMGBSA score
cat MMGBSA.list | sort -nk 2 >sort.MMGBSA.list

1-extract the pose without the protein
perl fix-step3_extract_best_score_combinepdb_after_minimize.pl sort.MMGBSA.list
2-extract the pose with the protein
perl fix-step4_extract_best_score_combinepdb_after_minimize_with_rec.pl sort.MMGBSA.list

using the chimera to visualize these poses and select the final linker (save to PDB file)
save the linker viewdock state: P
perl step0-filter_by_the_chimera.pl pdb to extract the final poses

DOCKovalent linker design tutorial - Revision history

Xiaobo wan: Created page with " 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 ..."