Covalent Docking

To model the tethering experiments in silico the ligands should covalently dock to the flexible side chain of cysteines (e.g., Cys195 of the active site of hTS 1hvy). A covalent docking is possible in GOLD but it requires a linking atom existing in both, the protein and the ligand. The linking atom should have an open valence electron (a hydrogen atom bound to the linking atom of the ligand will be displayed but not considered in the scoring function). The flexibility of a protein residue can be specified in GOLD by adding manually a rotamer_lib block to the gold.conf.

Linking atom

file:///sw/mcm/app/gold/gold_v3.1.1/gold/doc/portable_html/gold_portable-3-049.html
/sw/mcm/app/gold/gold_v3.1.1/gold/rotamer_library.txt

Side chain flexibility

file:///sw/mcm/app/gold/gold_v3.1.1/gold/doc/portable_html/gold_portable-3-023.html

Problems

  1. How to combine the flexibility of a protein residue with covalent docking?
  2. How to remove parts of the ligand?
    R1-S-S-R2 -- R1-S-S*- and R2-S-S*- -- R1-S*-Cys and R2-S*-Cys
  3. How to replace parts of the ligand?
    R1-S*-H -- R1-S*- and -S*-Cys -- R1-S*-Cys
Problem 1. In GOLD it is not possible to use the flexibility of a side chain (not shown) to move the linking atom. The linking atom of the ligand is everytime at the same position.
(question to the GOLD support)
A possibility to solve this problem is to use the Cys side chain as a part of the ligand and attach it to the backbone CA atom of the protein.

fixed-linking-atom.png

Problem 2 and 3. So far unsolved!
May be possible with ChemAxon's Reactor

gold.conf
GOLD CONFIGURATION FILE

generated by gold front end (GOLD v3.1.1)

POPULATION
popsiz = 100
select_pressure = 1.1
n_islands = 5
maxops = 100000
niche_siz = 2

GENETIC OPERATORS
pt_crosswt = 95
allele_mutatewt = 95
migratewt = 10

FLOOD FILL
radius = 15
origin = 0 0 0
do_cavity = 1
floodfill_atom_no = 2703
cavity_file = bmode.mol2
floodfill_center = atom

DATA FILES
protein_datafile = protein.pdb
ligand_data_file tioles.sdf 10
param_file = DEFAULT
set_ligand_atom_types = 1
set_protein_atom_types = 1
directory = .
tordist_file = DEFAULT
make_subdirs = 1
save_lone_pairs = 1
fit_points_file = fit_pts.mol2
read_fitpts = 0

FLAGS
display = 0
internal_ligand_h_bonds = 0
n_ligand_bumps = 0
flip_free_corners = 0
flip_amide_bonds = 0
flip_planar_n = 1 flip_ring_NRR flip_ring_NHR
flip_pyramidal_n = 0
rotate_carboxylic_oh = flip
use_tordist = 1

TERMINATION
early_termination = 0
n_top_solutions = 3
rms_tolerance = 1.5

CONSTRAINTS
force_constraints = 0

COVALENT BONDING
covalent = 1
covalent_protein_atom_no = 2704
covalent_substructure = 1
covalent_substructure_filename =substructure.mol2
covalent_substructure_atom_no = 2
covalent_topology = 1

SAVE OPTIONS
save_score_in_file = 1
save_protein_torsions = 1
output_file_format = MACCS

FITNESS FUNCTION SETTINGS
initial_virtual_pt_match_max = 2.5
relative_ligand_energy = 0
score_param_file = DEFAULT
start_vdw_linear_cutoff = 4

rotamer_lib
name cys195
chi1 2699 2698 2700 2699
chi2 2698 2699 2702 2703
chi3 2699 2702 2703 2704
rotamer 0 (30) 62 (11) 180 (17)
rotamer 0 (30) -177 (10) 65 (15)
rotamer 0 (30) -177 (10) 180 (11)
rotamer 0 (30) -67 (10) 180 (12)
rotamer 0 (30) -65 (9) -65 (10)
end_rotamer_lib

substructure.mol2
# Creating user name: henricsn
# Creation time: 11. 03. 2007 11:58

# Modifying user name: henricsn
# Modification time: 11. 03. 2007 11:58

# Program: corina_permanent_Linux2 3.20 0003 11.05.2005

@TRIPOSMOLECULE
ZINC00029124.mol
2 1 0 0 0
SMALL
NO_CHARGES

@TRIPOSATOM
1 C1 -0.0225 1.8097 0.0120 C.3
2 S2 0.0021 -0.0041 0.0020 S.3
@TRIPOSBOND
1 1 2 1

# End of record

(selected75_tioles.sdf)
tioles.sdf
ZINC00029124
3D
Structure written by MMmdl.
32 35 0 0 1 0 999 V2000
-0.1727 1.2404 0.0779 C 0 0 0 0 0 0
0.9414 1.9464 0.5731 C 0 0 0 0 0 0
2.2175 1.3506 0.5566 C 0 0 0 0 0 0
2.3766 0.0464 0.0443 C 0 0 0 0 0 0
1.2623 -0.6605 -0.4530 C 0 0 0 0 0 0
-0.0125 -0.0620 -0.4351 C 0 0 0 0 0 0
3.6521 -0.5544 0.0342 N 0 0 0 0 0 0
4.5504 -0.4824 -0.9579 C 0 0 0 0 0 0
5.6602 -1.1593 -0.6603 N 0 0 0 0 0 0
5.4488 -1.6948 0.6047 N 0 0 0 0 0 0
4.2248 -1.3090 0.9940 C 0 0 0 0 0 0
3.6643 -1.6947 2.2910 C 0 0 0 0 0 0
2.4045 -1.2630 2.6245 O 0 0 0 0 0 0
2.1257 -1.7613 3.8788 C 0 0 0 0 0 0
0.9515 -1.5794 4.6279 C 0 0 0 0 0 0
0.8652 -2.1779 5.8993 C 0 0 0 0 0 0
1.9457 -2.9398 6.3920 C 0 0 0 0 0 0
3.1163 -3.1087 5.6203 C 0 0 0 0 0 0
3.2306 -2.5189 4.3397 C 0 0 0 0 0 0
4.2123 -2.4607 3.2953 C 0 0 0 0 0 0
4.2821 0.4237 -2.5068 S 0 0 0 0 0 0
-1.1509 1.6982 0.0914 H 0 0 0 0 0 0
0.8170 2.9446 0.9662 H 0 0 0 0 0 0
3.0700 1.8930 0.9388 H 0 0 0 0 0 0
1.3823 -1.6601 -0.8448 H 0 0 0 0 0 0
-0.8676 -0.6020 -0.8142 H 0 0 0 0 0 0
0.1343 -0.9928 4.2350 H 0 0 0 0 0 0
-0.0264 -2.0540 6.4966 H 0 0 0 0 0 0
1.8766 -3.3979 7.3679 H 0 0 0 0 0 0
3.9345 -3.6949 6.0117 H 0 0 0 0 0 0
5.1859 -2.9279 3.3032 H 0 0 0 0 0 0
5.4700 0.1284 -3.0421 H 0 0 0 0 0 0
1 6 2 0 0 0
1 2 1 0 0 0
1 22 1 0 0 0
2 3 2 0 0 0
2 23 1 0 0 0
3 4 1 0 0 0
3 24 1 0 0 0
4 5 2 0 0 0
4 7 1 0 0 0
5 6 1 0 0 0
5 25 1 0 0 0
6 26 1 0 0 0
7 11 1 0 0 0
7 8 1 0 0 0
8 9 2 0 0 0
8 21 1 0 0 0
9 10 1 0 0 0
10 11 2 0 0 0
11 12 1 0 0 0
12 20 2 0 0 0
12 13 1 0 0 0
13 14 1 0 0 0
14 19 2 0 0 0
14 15 1 0 0 0
15 16 2 0 0 0
15 27 1 0 0 0
16 17 1 0 0 0
16 28 1 0 0 0
17 18 2 0 0 0
17 29 1 0 0 0
18 19 1 0 0 0
18 30 1 0 0 0
19 20 1 0 0 0
20 31 1 0 0 0
21 32 1 0 0 0
M END
$$$$


mono1hvy_4tethering_3.pdb
...
ATOM 2698 N CYS 195 7.739 -7.833 8.777 1.00 20.64 N
ATOM 2699 CA CYS 195 7.659 -6.656 7.922 1.00 20.35 C
ATOM 2700 C CYS 195 8.864 -5.802 8.312 1.00 19.16 C
ATOM 2701 O CYS 195 9.350 -4.994 7.521 1.00 20.76 O
ATOM 2702 CB CYS 195 6.347 -5.895 8.163 1.00 19.79 C
ATOM 2703 SG CYS 195 4.869 -6.842 7.681 1.00 20.42 S
ATOM 2704 SG2 CYS 195 4.264 -8.012 9.251 1.00 20.42 S
ATOM 2705 H02 CYS 195 7.106 -7.925 9.558 1.00 20.64 H
ATOM 2706 H03 CYS 195 7.670 -6.917 6.864 1.00 20.35 H
ATOM 2707 H04 CYS 195 6.371 -4.971 7.586 1.00 19.79 H
ATOM 2708 H06 CYS 195 6.275 -5.706 9.234 1.00 19.79 H
...