This document describes molecular docking of ligands to the anaplastic lymphoma kinase protein using Autodock Tools. It discusses docking methodology including scoring functions, genetic algorithms, and the Autodock software. The document then outlines the steps taken to dock four ligands (loratinib, ceritinib, crizotinib, alectinib) to the protein, including preparing files and running Autodock. It analyzes and compares the binding energies of the different ligand-protein complexes and visualizes the results, finding that loratinib had the strongest binding to the protein.

1. MOLECULAR DOCKING OF
ANAPLASTIC LYMPHOMA KINASE
WITH LIGANDS USING AUTODOCK TOOLS
J. Janiba Jeslin
15/PCHA/508
1

2. WHAT IS DOCKING?
Computational method that
mimics the binding of a ligand to a
protein
2

3. Docking depends on main two
components
• Scoring function
• Genetic algorithm
3

4. SCORING FUNCTION
It predict the strength of interactions
between two molecules after they have
docked
 Emprical scoring function
 Force field scoring function
 Knowledge based scoring function
4

5. GENETIC ALGORITHM
• Genetic algorithm is one of the
conformational search
• It give scoring function for each
pose of ligand
5

6. AUTO DOCK
• Autodock is a software used to
predict the interaction of ligands
with bio macromolecular targets
• AutoDock, using the Lamarckian
Genetic Algorithm and force field
scoring function
6

7. Force field scoring function
Autodock uses force field to evaluate the
conformations during docking .
7

8. Autodock has several steps
 Retrieving the protein and ligand from
databases
 Preparation of coordinate files
 Preparation of grid parameter file
 Preparation of docking parameter file
 Analysis of results
8

9. RETRIEVING PROTEIN AND LIGAND
FROM DATABASE
9

10. Retrieve protein from protein data bank
open it in chimera
Remove water from protein.
save as .pdb
10
Structure of anaplastic lymphoma kinase

11. 11
Appearance of target with water molecule in chimera

12. 12
Retrieve ligand from pubchem
Open it in chimera
Save as .pdb format
Loratinib
Ceritinib
5-chloro-N2-[5-methyl-4-(piperidin-4-yl)-2-
(propan-2-yloxy)phenyl]-N4-[2-(propane-2-
sulfonyl)phenyl]pyrimidine-2,4-diamine.
7-amino-12-fluoro-2,10,16-trimethyl-
15-oxo-10,15,16,17-tetrahydro-2H-8,4-
(metheno)pyrazolo(4,3-
h)(2,5,11)benzoxadiazacyclotetradecine
-3-carbonitrile

13. 13
Crizotinib Alectinib
3-[(1R)-1-(2, 6-dichloro-3-fluorophenyl)
ethoxy]-5-[1-(piperidin-4-yl)-1H-pyrazol-
4-yl] pyridin-2-amine
9-ethyl-6,6-dimethyl-8-[4-(morpholin-4-
yl)piperidin-1-yl]-11-oxo-5H,6H,11H-
benzo[b]carbazole-3-carbonitrile.

14. preparation of coordinate files
14

15. Click edit Hydrogen add. Then select
polar only ok.
Then again click edit charge add
kollmann charge ok
Open grid macromolecule choose
target select molecule ok
Now save target.pdb as target.pdbqt
15

16. 16
Appearance of target.pdbqt in autodock

17. Ligand torsion tree detect root
Ligand torsion tree choose torsions
Ligand output save as ligand.pdbqt
Appearance of ligand in screen

18. Preparing grid parameter file
18

19. Grid set map type choose ligand select
ligand select ligand
Grid Grid box file close saving current
(set the dimensions according to grid box)
Grid output save gpf file
19
Appearance of grid box

20. To run AutoGrid
Run Run autogrid
20
Run autogrid dialog box

21. 21
After the completion of autogrid running ,it will create different files
namely
List of grid files created by autodock

22. Preparation of docking
parameter file
22

23. • Docking macromolecule set rigid file name
select target open
Docking ligand choose ligand select ligand
Docking search parameter genetic algorithm
accept
Docking docking parameters accept
Docking output lamarikan
23

24. To run autodock
Run run auto dock
24

25. ANALYSING THE RESULT OF
PROTEIN-LIGAND INTERACTION
25

26. Analyze docking open
docking log file dialog box will be appear
select target.dlg open
26
Analyse conformations play. Click on show
conformation

27. 27

28. Binding energy is the sum of the
intermolecular energy and the torsional free-
energy penalty.
Docking energy is the sum of the
intermolecular energy and the ligand’s
internal energy.
Inhib_constant is calculated in
autodock as follows:
Ki=exp ((deltaG*1000.)/ (Rcal*TK)
Where deltaG is docking energy, Rcal is
1.98719 and TK is 298.15
.
. 28

29. refRMS is rms difference between current
conformation coordinates and current reference
structure.
clRMS is rms difference between current
conformation and the lowest energy conformation in
its cluster.
Torsional_energy is the number of active
torsions .
rseed1 and rseed2 are the specific random
number used for Current conformation’s docking
run.
29

30. 30
conformations Binding energy
Loratinib-1_1 -8.96
Loratinib-1_2 -8.23
Loratinib-1_3 -8.71
Loratinib-1_4 -9.09
Loratinib-1_5 -8.62
Loratinib-1_6 -11.03
Loratinib-1_7 -8.82
Loratinib-1_8 -8.47
Loratinib-1_9 -8.05
Loratinib-1_10 -8.58
conformations Binding energy
Ceritinib-2_1 -7.41
Ceritinib-2_2 -7.04
Ceritinib-2_3 -8.6
Ceritinib-2_4 -7.28
Ceritinib-2_5 -6.09
Ceritinib-2_6 -7.18
Ceritinib-2_7 -7.28
Ceritinib-2_8 -8.22
Ceritinib-2_9 -7.73
Ceritinib-2_10 -8.65
Binding energies for Loratinib and Ceritinib

31. 31
conformations Binding energy
Crizotinib-2_1 -6.8
Crizotinib -2_2 -5.94
Crizotinib -2_3 -6.19
Crizotinib -2_4 -6.01
Crizotinib -2_5 -6.84
Crizotinib -2_6 -6.95
Crizotinib -2_7 -5.6
Crizotinib -2_8 -5.93
Crizotinib -2_9 -6.8
Crizotinib -2_10 -5.57
conformations Binding energy
Alectinib-2_1 -7.55
Alectinib-2_2 -7.5
Alectinib-2_3 -7.28
Alectinib-2_4 -7.53
Alectinib-2_5 -7.67
Alectinib-2_6 -7.72
Alectinib-2_7 -7.33
Alectinib-2_8 -7.49
Alectinib-2_9 -7.5
Alectinib-2_10 -7.54
Binding energies for Crizotinib and Alectinib

32. VISUALIZING THE RESULTS
32

33. Analyze Clustering Show
33

34. CONCLUSION
34
This molecular docking reveals that all
ligands(loratinib, centinib, Crizotinib,
Alectinib ) binding to anaplastic lymphoma
kinase. The most strongest docking will be
between the loratinib and anaplastic
lymphoma kinase which have binding energy
of -11.03. the least docking will be between
the Crizotinib and anaplastic lymphoma
kinase which have binding energy of -7.67.

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35

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