molecular docking

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MOLECULAR DOCKING OF

ANAPLASTIC LYMPHOMA KINASE

WITH LIGANDS USING AUTODOCK TOOLS

J. Janiba Jeslin

15/PCHA/508

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WHAT IS DOCKING?

Computational method that mimics the binding of a ligand to a

protein

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Docking depends on main two components

• Scoring function

• Genetic algorithm

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SCORING FUNCTIONIt predict the strength of interactions

between two molecules after they have docked

Emprical scoring function Force field scoring function Knowledge based scoring function

GENETIC ALGORITHM

• Genetic algorithm is one of the conformational search

• It give scoring function for each pose of ligand

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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

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Force field scoring function

Autodock uses force field to evaluate the conformations during docking .

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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

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RETRIEVING PROTEIN AND LIGAND FROM DATABASE

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Retrieve protein from protein data bankopen it in chimera Remove water from protein. save as .pdb

Structure of anaplastic lymphoma kinase

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Appearance of target with water molecule in chimera

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Retrieve ligand from pubchemOpen 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

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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.

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preparation of coordinate files

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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

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Appearance of target.pdbqt in autodock

Ligand torsion tree detect rootLigand torsion tree choose torsionsLigand output save as ligand.pdbqt

Appearance of ligand in screen

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Preparing grid parameter file

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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

Appearance of grid box

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To run AutoGrid Run Run autogrid

Run autogrid dialog box

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After the completion of autogrid running ,it will create different files namely

List of grid files created by autodock

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Preparation of docking parameter file

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• 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

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To run autodock

Run run auto dock

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ANALYSING THE RESULT OF PROTEIN-LIGAND INTERACTION

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Analyze docking open

docking log file dialog box will be appear

select target.dlg open

Analyse conformations play. Click on show conformation

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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..

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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.

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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 -8.47Loratinib-1_9 -8.05Loratinib-1_10 -8.58


Ceritinib-2_1 -7.41

Ceritinib-2_2 -7.04

Ceritinib-2_3 -8.6

Ceritinib-2_4 -7.28

Ceritinib-2_5 -6.09Ceritinib-2_6 -7.18Ceritinib-2_7 -7.28

Ceritinib-2_8 -8.22Ceritinib-2_9 -7.73Ceritinib-2_10 -8.65

Binding energies for Loratinib and Ceritinib

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Crizotinib-2_1 -6.8

Crizotinib -2_2 -5.94



Crizotinib -2_5 -6.84Crizotinib -2_6 -6.95Crizotinib -2_7 -5.6

Crizotinib -2_8 -5.93Crizotinib -2_9 -6.8Crizotinib -2_10 -5.57


Alectinib-2_1 -7.55

Alectinib-2_2 -7.5

Alectinib-2_3 -7.28

Alectinib-2_4 -7.53

Alectinib-2_5 -7.67Alectinib-2_6 -7.72Alectinib-2_7 -7.33

Alectinib-2_8 -7.49Alectinib-2_9 -7.5Alectinib-2_10 -7.54

Binding energies for Crizotinib and Alectinib

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VISUALIZING THE RESULTS

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Analyze Clustering Show

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CONCLUSION

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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REFERENCES

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1. Anderson A. Chem Biol 2003; 10:787–97.2. Gilbert D. Brief Bioinform 2004:300-4.3. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK et al. J Comput Chem 1998:1639–62.4. Kalyaanamoorthy S and Chen YP Drug Discovery Today 2011 :831–839.5. Blaney, J. A J. Computer. Aided Mol. Des. 2012, 13–14.6. Berman, H.M. Nucleic Acids Res. 2000, 235–242.7. Weigelt, J. Exp. Cell Res. 2010, 1332–13388. Mandal, S.; Moudgil, M.N.; Mandal, S.K. Eur. J. Pharmacol. 2009, 90–100.9. Urwyler, S. Pharmacology. Rev. 2011, 59–126.10. Wilson, G.L.; Lill, M.A. Future Med. Chem. 2011, , 735–750.11. Fang, Y. ExpertOpin. Drug Discov. 2012, , 969–988.12. Kahsai, A.W.; Xiao, K.; Rajagopal, S.; Ahn, S.; Shukla, A.K.; Sun, J.; Oas, T.G.; Lefkowitz, R.J. Nat. Chem. Biol. 2011, , 692–700. 13. Shoichet, B.K.; Kobilka, B.K. Sci. 2012, 33, 268–272.14. Chandrika, B.R.; Subramanian, J.; Sharma, S.D. Drug Discov. Today 2009, 14, 394–400.

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15. Durrant, J.D.; McCammon, J.A. Curr. Opin. Pharmacol. 2010, 10, 770– 774.16. Huang, S.Y.; Grinter, S.Z.; Zou, X. Phys. Chem. Chem. Phys. 2010, 12, 12899–12908.17. Englebienne, P.; Moitessier, N. J. Chem. Inf. Model. 2009, 2564–2571.18. Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J.. Nat. Rev. Drug Discov. 2004, , 935– 949.19.Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson,A. J. J. Comput. Chem., 2009: 2785-2791. 20. Morris, G.M.; Goodsell, D.S.; Huey, R.; Olson, A.J. J. Comput. Aided Mol. Des. 1996, 10,293–304.

molecular docking

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