In Silico study of methyltransferase inhibitor’s effects on dengue virus

Gustavo A MartinezJuan E MaldonadoStudent Mentor: Dr. Hector Maldonado

Prologue: Dengue Fever• Life threatening disease caused by Dengue Virus

– Dengue Fever– Dengue hemorrhagic fever– Dengue Shock Syndrome

• Many People are affected:– 2.5 billion are at risk – Locally, 12,580 cases reported (CDC 2010)

• Transmitted by the bite of an Aedes mosquito infected with any one of the four dengue viruses

• No approved treatment or prevention

Prologue: Dengue virus• The dengue viruses are single-stranded RNA viruses• Four serotypes:

– DENV-1– DENV-2– DENV-3– DENV-4

• They belong to the family Flaviviridae and the genus Flavivirus– Other members of the family include:

• West Nile virus• Yellow Fever virus• Japanese Encephalitis virus• St. Louis Encephalitis virus

Prologue: Methyltransferase• A family of enzymes that catalyze the transfer of

a methyl group from a donator to an acceptor• These methyl groups are important for

controlling genes in different types of cells• This methyl group is usually obtained from SAM

(S-Adenosyl methionine)• The energy necessary for these processes comes

from GTP

Introduction• What would happen if GTP does not reach the

methyltransfarase?– The protein will not have any source of energy to

complete the transfers.– If there are no more transfers of methyl groups, then

the DNA will not be properly sequenced.

Hypothesis

“Utilizing a high affinity compound to block the GTP from reacting, In Sillico research will reveal

how to disable the methyltransfare’s capabilities, ceasing viral production.”

Hypothesis (2)

Through In Sillico study, the GTP can be inhibited by a higher affinity compound, resulting in the

cease of production of the Dengue virus

Methodology Software Used:• PyMOL Molecular Graphics System v1.3 http://www.pymol.org• AutoDock (protein-protein docking software) http://autodock.scripps.edu/• Auto Dock Tools: Graphical Interfase for AutoDock

http://mgltools.scripps.edu/downloads• LigandScout: Advanced Pharmacophore Modeling and Screening of Drug

Databases. http://www.inteligand.com/ligandscout/

Databases Used:• National Center for Biotechnology Information (NCBI), Basic Local Alignment

Search Tool (BLAST) http://www.ncbi.nlm.nih.gov/blast/Blast.cgi• Research Collaboratory for Structural Bioinformatics (RCSB) www.pdb.org• ZINC: A free database for virtual screening: http://zinc.docking.org/

DENV2: 2P1D Protein - Clean

Protein clean

GIF Protein with colors

GTP

SAH

GTP

RNAbinding site

SAH

F25

D146

K61

K180

E216

2P1D.pdb DENV2 Methyltransferase

Three Benzenes were determined to be in the hotspots

Ben 230

Ben 01

Ben 267

01

230 267

Rank Compound Affinity1 DENV-M2_1 -10.42 DENV-M2_2 -10.33 DENV-M2_3 -10.24 DENV-M2_4 -10.25 DENV-M2_5 -10.26 DENV-M2_6 -10.27 DENV-M2_7 -10.18 DENV-M2_8 -10.19 DENV-M2_9 -10.1

10 DENV-M2_10 -1011 DENV-M2_11 -1012 DENV-M2_12 -1013 DENV-M2_13 -1014 DENV-M2_14 -1015 DENV-M2_15 -1016 DENV-M2_16 -9.917 DENV-M2_17 -9.918 DENV-M2_18 -9.919 DENV-M2_19 -9.920 DENV-M2_20 -9.921 DENV-M2_21 -9.922 DENV-M2_22 -9.923 DENV-M2_23 -9.924 DENV-M2_24 -9.825 DENV-M2_25 -9.8

-10.4 1-10.3 1-10.2 4-10.1 3

-10 6-9.9 8-9.8 20-9.7 29-9.6 41-9.5 49

162

Results

• For the three benzene rings, many compounds were found that could fit in the pocket.

• The top three with the most affinity were chosen:– ZINC00946278– ZINC04112974– ZINC04994141

DENV-M2_1 DENV-M2_2 DENV-M2_310.05

10.1

10.15

10.2

10.25

10.3

10.35

10.4

Binding Energy

GTP

SAH

GTP

RNAbinding site

SAH

F25

D146

K61

K180

E216

2P1D.pdb DENV2 Methyltransferase

Conclusion

• Of the compounds with the most affinity, DENV-M2_1 was chosen because of its affinity of -10.4

• This compound showed to occupy the best within the methyltransferase.

• Also, this compound was the one that positioned itself within the protein in a manner similar to the benzene circles.

Acknowledgements