SlideShare a Scribd company logo
melinamottin@gmail.com
Dr. Melina Mottin
Carolina Horta Andrade Alexander L. Perryman Sean Ekins
13th Jul 2017
http://openzika.ufg.br
Opening the Discovery of New
Antiviral Candidates Against
Zika Virus and Insights into
Dynamic Behavior of NS3
Helicase
Rodolpho Braga
Roosevelt A. da Silva
João H. Martins
Transmission:
• mosquito
• sperm
• blood
• breast milk
OpenZika Project: Antivirals
• IBM philanthropic initiative
• idle processing power of computer/mobile phone
• massive supercomputing data
• Free of charge!
Transmission:
• mosquito
• sperm
• blood
• breast milk
OpenZika Project: Antivirals
• IBM philanthropic initiative
• idle processing power of computer/mobile phone
• massive supercomputing data
• Free of charge!
OpenZika = # crunching for a cure
Ekins, S.; Perryman, A. L.; Horta Andrade, C. PLoS Negl. Trop. Dis. 2016, 10, e0005023.
Zika proteins
Virtual screening
Molecular docking
> 30 millions of
compounds
Zika virus proteins
NS3 helicase structure
and binding sites
• unwinds viral RNA strand
• facilitates replication of the viral genome
-> attractive target for antivirals
www.ftmap.bu.edu
Mottin, M, Braga, R C, da Silva R A, da Silva J H M, Perryman, A L, Ekins, S, Andrade C H; Biochem
Biophysical Res Comm; 2017, in press.
Dynamic behavior of
ZIKV NS3 helicase
Mottin, M, Braga, R C, da Silva R A, da Silva J H M, Perryman, A L, Ekins, S, Andrade C H; Biochem
Biophysical Res Comm; 2017, in press.
MD Program: Gromacs 5.1.2
Amber Force Field99SB-ILDN
MD trajectories: 100 ns
NS3 helicase selected candidates
Target specific
ZIKV NS3
Helicase (5JMT)
ZIKV NS3 Helicase
with RNA (5GJB)
150 cpds
22 cpds
2 cpds
232 cpds
74 cpds
4 cpds
free energy filter
Molecular Docking (AutoDock Vina)
Selected hits
QSAR phenotypic model
MedChem
based
inspection
ZINC subsets: FDA approved
+ NIH clinical collection+
Prestwick Chemicals
7600 compounds
Dr. Jair Siqueira-Neto
ZIKV Selected candidates
Full data sets
ZINC subsets: FDA approved + NIH
clinical collection+ Prestwick
Chemicals
3600 cpds
QSAR phenotypic model
51 cpds
consensus model
prediction, visual
inspection, $$$
9 virtual hits
Zika proteins
Dataset for modeling
Zika bioassay (AID1224857)
~ 5,700 compounds
Balanced dataset: 90 compounds
Active<10µM
NS1
NS2B-NS3 protease
NS3 helicase
NS5 RNA polymerase
20.000 volunteers donating CPU time
Approximate total # of results now
~ 3,5 billion docking jobs submitted*
~ 1,9 billion results received*
Updated Outcomes
OpenZika Project
*84 target sites: ZIKV, Dengue Virus, Hepatitis C Virus, Yellow Fever
Virus, Japanese Encephalitis Virus
Compounds database
Future Steps
Protein - hit
MD simulations
NS3
Helicase
NS5
Methiltransferase
other Zika proteins
Virtual Screening
Enzymatic assays
OpenZika Team
Alexander Perryman
Wim Degrave
Ana Carolina Ramos
João H. Martins
Joel Freundlich
Pedro Torres
Carolina Andrade Sean Ekins
Rodolpho Braga
Melina Mottin
Roosevelt Silva
Jair Siqueira-Neto
Bruno Neves
Joyce Borba Cleber Melo-Filho
Be a WCG volunteer and help us!
http://openzika.ufg.br
Acknowledgments
melinamottin@gmail.com

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Opening the Discovery of New Antiviral Candidates Against Zika Virus and Insights into Dynamic Behavior of NS3 Helicase

  • 1. melinamottin@gmail.com Dr. Melina Mottin Carolina Horta Andrade Alexander L. Perryman Sean Ekins 13th Jul 2017 http://openzika.ufg.br Opening the Discovery of New Antiviral Candidates Against Zika Virus and Insights into Dynamic Behavior of NS3 Helicase Rodolpho Braga Roosevelt A. da Silva João H. Martins
  • 2. Transmission: • mosquito • sperm • blood • breast milk OpenZika Project: Antivirals • IBM philanthropic initiative • idle processing power of computer/mobile phone • massive supercomputing data • Free of charge!
  • 3. Transmission: • mosquito • sperm • blood • breast milk OpenZika Project: Antivirals • IBM philanthropic initiative • idle processing power of computer/mobile phone • massive supercomputing data • Free of charge!
  • 4. OpenZika = # crunching for a cure Ekins, S.; Perryman, A. L.; Horta Andrade, C. PLoS Negl. Trop. Dis. 2016, 10, e0005023. Zika proteins Virtual screening Molecular docking > 30 millions of compounds Zika virus proteins
  • 5. NS3 helicase structure and binding sites • unwinds viral RNA strand • facilitates replication of the viral genome -> attractive target for antivirals www.ftmap.bu.edu Mottin, M, Braga, R C, da Silva R A, da Silva J H M, Perryman, A L, Ekins, S, Andrade C H; Biochem Biophysical Res Comm; 2017, in press.
  • 6. Dynamic behavior of ZIKV NS3 helicase Mottin, M, Braga, R C, da Silva R A, da Silva J H M, Perryman, A L, Ekins, S, Andrade C H; Biochem Biophysical Res Comm; 2017, in press. MD Program: Gromacs 5.1.2 Amber Force Field99SB-ILDN MD trajectories: 100 ns
  • 7. NS3 helicase selected candidates Target specific ZIKV NS3 Helicase (5JMT) ZIKV NS3 Helicase with RNA (5GJB) 150 cpds 22 cpds 2 cpds 232 cpds 74 cpds 4 cpds free energy filter Molecular Docking (AutoDock Vina) Selected hits QSAR phenotypic model MedChem based inspection ZINC subsets: FDA approved + NIH clinical collection+ Prestwick Chemicals 7600 compounds Dr. Jair Siqueira-Neto
  • 8. ZIKV Selected candidates Full data sets ZINC subsets: FDA approved + NIH clinical collection+ Prestwick Chemicals 3600 cpds QSAR phenotypic model 51 cpds consensus model prediction, visual inspection, $$$ 9 virtual hits Zika proteins Dataset for modeling Zika bioassay (AID1224857) ~ 5,700 compounds Balanced dataset: 90 compounds Active<10µM
  • 9. NS1 NS2B-NS3 protease NS3 helicase NS5 RNA polymerase 20.000 volunteers donating CPU time Approximate total # of results now ~ 3,5 billion docking jobs submitted* ~ 1,9 billion results received* Updated Outcomes OpenZika Project *84 target sites: ZIKV, Dengue Virus, Hepatitis C Virus, Yellow Fever Virus, Japanese Encephalitis Virus Compounds database
  • 10. Future Steps Protein - hit MD simulations NS3 Helicase NS5 Methiltransferase other Zika proteins Virtual Screening Enzymatic assays
  • 11. OpenZika Team Alexander Perryman Wim Degrave Ana Carolina Ramos João H. Martins Joel Freundlich Pedro Torres Carolina Andrade Sean Ekins Rodolpho Braga Melina Mottin Roosevelt Silva Jair Siqueira-Neto Bruno Neves Joyce Borba Cleber Melo-Filho Be a WCG volunteer and help us! http://openzika.ufg.br