Revision as of 17:42, 25 February 2025

Introduction

This tutorial describes de novo method to refine ligand structure(s) using DOCK6. Rather than screening existing compounds, de novo refinement adds fragments based on known bioactive compounds, aiming to produce new ligands that bind more tightly to protein receptors than current options. This strategy is particularly valuable for:

• Improving suboptimal ligand binding profiles
• Overcoming resistance mechanisms
• Exploring novel scaffolds while maintaining critical pharmacophore features

In this tutorial, we will utilize PDB structure 1XMU - Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Roflumilast.

System Preparation

We first prepare a folder to contain all the input and output files for de novo refinement for 1XMU. This is the current directory structure under the upper directory dock6-1xmu.

Input File

Modify Ligand with Dummy Atom

Below shows the original ligand with hydrogen (mol2 file).

Select the atoms to delete and save the mol2 file as 1xmu_lig_wDu.mol2. Hover the cursor over the atom that you intend to change to a dummy atom. Here we are changing the C21 to a dummy atom.

Open the 1xmu_lig_wDu.mol2 file and edit the C21 atom type to Du as shown below.

Next reopen the 1xmu_lig_wDu.mol2 file to observe if the corresponding atom is now represented as Du in magenta.

DOCK6 input

The directory 008_dn_refine1 contains the following files:

The 01dnv.in contains the DOCK6 input parameters. Please note that the bolded lines represent customized items for this tutorial, including the input and output file names. Additionally, we intend to modify the ligand with only one layer while keeping the original pose. DOCK6 parameter files and fragment library have been previously prepared. Please refer to the virtual screening and genetic algorithm tutorials for further instructions if needed.

 conformer_search_type                                        denovo
 dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
 dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_linker.mol2
 dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
 dn_user_specified_anchor                                     yes
 dn_fraglib_anchor_file                                       1xmu_lig_wDu.mol2
 dn_torenv_table                                              ../006_ga_lib/unique_full_sorted_fraglib.dat
 dn_name_identifier                                           denovo
 dn_sampling_method                                           graph
 dn_graph_max_picks                                           30
 dn_graph_breadth                                             3
 dn_graph_depth                                               2
 dn_graph_temperature                                         100.0
 dn_pruning_conformer_score_cutoff                            100.0
 dn_pruning_conformer_score_scaling_factor                    2.0
 dn_pruning_clustering_cutoff                                 100.0
 dn_remove_duplicates                                         yes
 dn_max_duplicates_per_mol                                    0
 dn_write_pruned_duplicates                                   no
 dn_advanced_pruning                                          yes
 dn_prune_initial_sample                                      yes
 dn_sample_torsions                                           yes
 dn_prune_individual_torsions                                 yes
 dn_prune_combined_torsions                                   yes
 dn_random_root_selection                                     no
 dn_mol_wt_cutoff_type                                        soft
 dn_upper_constraint_mol_wt                                   1000
 dn_lower_constraint_mol_wt                                   0.0
 dn_mol_wt_std_dev                                            35.0
 dn_constraint_rot_bon                                        15
 dn_constraint_formal_charge                                  2.0
 dn_heur_unmatched_num                                        1
 dn_heur_matched_rmsd                                         2.0
 dn_unique_anchors                                            1
 dn_max_grow_layers                                           1
 dn_max_root_size                                             25
 dn_max_layer_size                                            25
 dn_max_current_aps                                           5
 dn_max_scaffolds_per_layer                                   1
 dn_max_successful_att_per_root                               50000
 dn_write_checkpoints                                         yes
 dn_write_prune_dump                                          yes
 dn_write_orients                                             no
 dn_write_growth_trees                                        no
 dn_output_prefix                                             1xmu_out
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 use_database_filter                                          no
 orient_ligand                                                no
 bump_filter                                                  no
 score_molecules                                              yes
 contact_score_primary                                        no
 grid_score_primary                                           yes
 grid_score_rep_rad_scale                                     1
 grid_score_vdw_scale                                         1
 grid_score_es_scale                                          1
 grid_lig_efficiency                                          no
 grid_score_grid_prefix                                       ../003_grid/grid
 minimize_ligand                                              yes
 minimize_anchor                                              yes
 minimize_flexible_growth                                     yes
 use_advanced_simplex_parameters                              no
 simplex_max_cycles                                           1
 simplex_score_converge                                       0.1
 simplex_cycle_converge                                       1.0
 simplex_trans_step                                           1.0
 simplex_rot_step                                             0.1
 simplex_tors_step                                            10.0
 simplex_anchor_max_iterations                                500
 simplex_grow_max_iterations                                  500
 simplex_grow_tors_premin_iterations                          0
 simplex_final_min                                            no
 simplex_random_seed                                          0
 simplex_restraint_min                                        no
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl