TOP-LEAD IDENTIFICATION USING ENSEMBLE BASED VIRTUAL SCREENING AND

PHARMACOPHORE DRUG DESIGN FOR BREAST CANCER METASTATIC BETA ARRESTIN 2

Student: ÔNG ĐĂNG QUANG – BTBTIU10003

Supervisor: Dr. LÊ THỊ LÝ

International University National University – HCMC

OUTLINE

1

2

3

4

5

INTRODUCTION

MATERIALS & METHODS

RESULTS

DISCUSION & CONCLUSION

REFERENCES

INTRODUCTION

!

INTRODUCTIONCANCER DISEASE

VIETNAM

125,000 new cases per year

2012

76%

Cancer mortality of VN 201294,743 cancer deaths per year

www.cancerresearchuk.orgwww.cancerindex.org/Vietnam

2012

INTRODUCTIONCase study: TYROSINE KINASE (TK) INHIBITOR

ACTIVATE TK TUMOR CELL

increaseTKI

Arora, Amit, and Eric M. Scholar. (2005)

INTRODUCTIONβ - ARRESTIN 2 (ARRB2)

ARRB2

Cytoplasmic proteinDesensitization

Internalization Signaling/Scaffolding

INTRODUCTIONβ - ARRESTIN 2 INHIBITOR

ARRB2

progression of breast cancer invasiveness

CXCR4-mediated chemotaxis

breast cancer metastasis, migration.

extracellular-signal-regulated kinase (ERK1/2)

Lysophosphatidic Acid (LPA)

protease-activated receptor-2 (PAR-2)

ARRB2 INHIBITOR

Li TT, et al. (2009), Michal AM, et al. (2011), Sun, Yue, et al.(2002), Ge, Lan, et al.(2004), Pampillo, et al.(2009), Alemayehu M, et al. (2013), Mills GB, Moolenaar WH (2003).

MATERIALS&

METHODS

PROJECT FLOWCHART

TOPDRUG

CANDIDATES

EnsembleDocking

PharmacophoreGeneration

3D-ARRB2Conformations

Novel DrugLibrary

Potential DrugMolecules

VirtualScreening/

Docking

DrugbankDatabase

Human3D

ARRB2

MolecularDynamicsSimulation

HomologyModeling

ARRB2Protein

Sequence

(AutoDock Vina)

(LigandScout)

(AutoDock Vina)

(SWISS-MODEL)

(GROMACS)

RESULT

6

RESULTSβ - ARRESTIN 2 SEQUENCE ANALYSIS

>95% identity among 15 species.

Glaser, Fabian, et al. "ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information." Bioinformatics 19.1 (2003): 163-164.

RESULTS3D STRUCTURE OF β – ARRESTIN 2

A B

blue is modeled structure red is crystal structure of Bovin

Singh, Salam Pradeep, et al. "Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling." Bioinformation 8.5 (2012): 212.

3D STRUCTURE OF β – ARRESTIN 2Z-SCORE

z-score value of the modeled structure is -7.17

Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35: W407–410.

3D STRUCTURE OF β – ARRESTIN 2RAMACHARAN PLOT

- No. of residues in favoured region: 333 (84.3%)

- No. of residues in allowed region: 39 (9.9%)

- No. of residues in outlier region: 23 (5.8%)

Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35: W407–410.

TOP 15 POTENTIAL DRUGS MOLECULESRESULTS

Trott, O.; Olson, A.J., Autodock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010, 31, 455-461.

TOP 15 POTENTIAL DRUGS MOLECULES

Wishart, David S., et al. "DrugBank: a comprehensive resource for in silicodrug discovery and exploration." Nucleic acids research 34.suppl 1 (2006): D668-D672.

PHARMACOPHORE GENERATION

Hydrogen Bond Donor as green vectored spheres

Hydrogen Bond Acceptor as red vectored spheres

Hydrophobic as yellow spheres

β-Arrestin2 active site is shown as green.

(for column 1 & 2)

(for column 3)

COMMON PHARMACOPHORE FEATURES

Hydrogen Bond Donor as green vectored spheres

Hydrogen Bond Acceptor as red vectored spheres

Wolber, Gerhard, and Thierry Langer. "LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters." Journal of chemical information and modeling 45.1 (2005): 160-169.

RESULTSMOLECULAR SIMULATION

Total energy profile of human β-Arrestin 2

Kresse, Georg, and Jürgen Hafner. "Ab initio molecular dynamics for liquid metals." Physical Review B 47.1 (1993): 558.

MOLECULAR SIMULATIONROOT MEAN SQUARE DEVIATION & FLUCTUATION ANALYSIS

≈ 0.1 nm or 1 Å

17000 (ps)

Brunger, Axel T., J. Kuriyan, and Martin Karplus. "Crystallographic R factor refinement by molecular dynamics." Science 235.4787 (1987): 458-460.

MOLECULAR SIMULATIONRADIUS OF GYRATION CALCULATION

≈ 0.05 nm or 0.5 Å

Lindahl, Erik, Berk Hess, and David Van Der Spoel. "GROMACS 3.0: a package for molecular simulation and trajectory analysis." Molecular modeling annual 7.8 (2001): 306-317.

RESULTSTOP NOVAL DRUG CANDIDATES

AM: arithmetic meansHM: harmonic mean

Beigel, J. H.; Farrar, J.; Han, A. M.; Hayden, F. G.; Hyer, R.; de Jong, M. D.; Lochindarat, S.; Nguyen, T. K.; Nguyen, T. H.; Tran, T. H.; Nicoll, A.; Touch, S.; Yuen, K. Y. Avian influenza A (H5N1) infection in humans. N. Engl. J. Med. 2005, 353 (13), 1374–1385.

THE BEST 2 DRUG CANDIDATES

Rank ID Min.HM

(kcal/mol)

Predicted Ki

(µM)

AM

(kcal/mol)

SD

(kcal/mol)

1 26 -8.4 -7.682 2.669 -7.604 0.3

2 1 -8 -7.169 6.555 -7.071 0.33

Compound 26 Compound 01

DISCUSSION&

CONCLUSION

- Examining 3D structure of human ARRB2 model.- Screening Drugbank database entirely for ARRB2 potential inhibitors.- Suggesting pharmacophore features for ARRB2 inhibitors.- Suggesting 2 best potential drug molecules as ARRB2 inhibitors.

- Time- Computational resources- Practical results

- Running molecular simulation for ARRB2-inhibitor complex.- Building more good drug molecules as ARRB2 inhibitors.- Cooperate computational methods with practical results.- Try different drug database such as NCI (National Cancer Institute).

ACHIEVEMENTS

LIMITATIONS

FUTURE PLANS

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The mean square fluctuation (MSF) is a measure of the deviation between the

position of particle i and some reference position.

where T is the time over which one wants to average, and is the reference

position of particle i. Typically this reference position will be the time-averaged

position of the same particle i, i.e.

Note that the difference between RMSD and RMSF is that with the latter the average is taken over time, giving a value for each particle i. With RMSD the average is

taken over the particles, giving time resolved values.

When a dynamical system fluctuates about some well-defined average position, the RMSD from the average over time can be referred to as the RMSF or root mean square fluctuation.