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Grid enabled in silico drug discovery

Grid enabled in silico drug discovery. BUI The Quang Prof. Vincent Breton Prof. Doman Kim Prof. NGUYEN Hong Quang Prof. PHAM Quoc Long. Laboratories involved. CNU, Gwangju , Korea IFI, Hanoi, Vietnam INPC, Hanoi, Vietnam KISTI, Seoul, Korea LPC, Clermont-Ferrand, France.

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Grid enabled in silico drug discovery

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  1. Grid enabled in silico drug discovery BUI The Quang Prof. Vincent Breton Prof. Doman Kim Prof. NGUYEN Hong Quang Prof. PHAM Quoc Long

  2. Laboratories involved • CNU, Gwangju, Korea • IFI, Hanoi, Vietnam • INPC, Hanoi, Vietnam • KISTI, Seoul, Korea • LPC, Clermont-Ferrand, France

  3. Content • Activity in Korea • Activity in Vietnam • Activity in France

  4. Activity in Korea - Publication 1 • Human maltase: • A α-glucosidase, belongs to glycosides hydrolase family 31 (EC 3.2.1.20 and 3.2.1.3) and located on chromosome 7 with 868 amino acids and contains five distinct protein domains. • Important target in treatment of diabetes type 2. Credit: Doman Kim

  5. Filtration process 454,000 chemical compounds from Chembridge Scoring based on docking score ( 308,307) Statistics of data challenge deployment on WISDOM production environment 3016 compounds selected Interaction with key residues 2616 compounds selected Key interactions binding models clustering 42 compound selected In vitro test Credit: Doman Kim

  6. Inhibition on human maltase & pancreatic α-amylase • Unlike acarbose, compounds 17 and 18 were competitive inhibitors exclusively for HMA without any in vitro inhibition for human pancreatic alpha-amylase. Credit: Doman Kim

  7. Activity in Korea - Publication 2 A global outbreak of Severe Acute Respiratory Syndrome (SARS) between March 2003 and July 2003 caused over 8,000 cases and 774 deaths (9.6%) (World Health Organization). The 3C-like protease (3CLpro) is needed for SARS-CoV replication and is a promising drug target. World Health Organization. Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003 (based on data as of the 31. December 2003). http://www.who.int/csr/sars/country/table2004_04_21/en/. Credit: Doman Kim

  8. Virtual screening 3CL protease of SARS on WISDOM production environment Docking parameters: Ga_run=50, Ga_pop_size=250, Ga_num_generation=27000, Ga_num_evaluation= 2500000 Virtual screening on WISDOM production environment 308,307 compounds 54 compounds were selected for In vitro assay Credit: Doman Kim

  9. Activity in Vietnam • The WPE platform • Used in WISDOM projects(Wide In SilicoDocking On Malaria) for discovery of medicine for malaria • Developed by LPC Clermont-Ferrand laboratory • Reduce many time for finishing these challenges • The DIRAC platform • DIRAC: Distributed Infrastructure with Remote Agent Control • DIRAC forms a layer between a particular community and various compute resources to allow optimized, transparent and reliable usage • Comparison between the WPE & DIRAC platform • Performance • Stability • Capability of submission of pilot agent

  10. Comparison of performance WPE is faster than DIRAC WPE is faster than DIRAC DIRAC is faster than WPE DIRAC is faster than WPE • DIRAC submit faster pilot agent than WPE • one WPE’s agent execute many task while one DIRAC’s agent execute only one task

  11. Comparison of stability Percentage of DIRAC pilot agent is terminated by unknown cause is less than WPE platform  Pilot agent of DIRAC is more stable than pilot agent of WPE Rate of WPE’s & DIRAC’s pilot agents is terminated by unknown cause(test with Autodock)

  12. Comparison of capability of submission of pilot agent Rate of DIRAC pilot agent submission successful to grid is higher than WPE platform  DIRAC platform submits better pilot agent to grid than WPE platform Rate of pilot agent submission successful to grid

  13. Result from INPC laboratory • Database of natural products isolated from biodiversity in Vietnam (~1000 ligands) • Anti-malarialtestson 43 compounds with 2 biological targets: chloroquine-susceptible T96 and chloroquineresistant K1 • Ongoing research to look for compounds with anti-malarial bioactivity by virtual screening on the database of natural products (2011) • Key protein: protein plasmepsin II (1LEE) • Use ofAUTODOCK software for virtual screening

  14. Activity in France Design a virtual screening system for multi-user Scheduler Grid resource Problem of virtual screening on grid • Speed of machine are different • Task arrive in random process • Available duration of machine are random  Find out the policy for maximizing the throughput of all users Workflow of research • Find out the policy and prove by theory • Valid on the grid simulator SIMGRID • Programming scheduler on the DIRAC platform

  15. Thank you for your attention

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