DOCKovalent lysine inhibitor design tutorial
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