1. Application of High-Throughput Methodology to Human Drug Targets
Duncan E. McRee, Ph.D.
President, ActiveSight

2. ActiveSight Background
Founded in 2003 by Duncan McRee, Ron Swanson and Les Tari
Funded by Rigaku Americas Corp.
14 Personnel -10 Humans and 4 Robots
Mission:
Advance medicine by providing a portfolio of validated drug discovery target proteins for structure-based drug design and providing these as a service to biotech and pharma.

3. Structural Genomics Progress
PDB Fruit Stand

4. Chemical Genomics

5. Fragment Based Screening

6. Fragment Screening Small fragments are screened by X-ray
Small compounds ~200 MW at 10 mM or higher
Several compounds are soaked at once to increase efficiency
Hit rates are typically 3-4%

7. Small Fragments Have a higher hit rate Have higher ligand efficiency
Leave more chemical space
Need a smaller library

8. Chemical Space 50
100
150
200
500
Molecular Weight
H C N O S Cl Fl Br

9. = Free energy per heavy atom
Ligand Efficiency
Δg / #Heavy Atoms
= Free energy per heavy atom
Hopkins, Groom and Alex, Drug Disc. Today (2004) 19, 430-1
IC(50) = 1 mM, 8 heavy atoms
LE = 0.5
IC(50) = 10 nM, 38 heavy atoms
LE = .29 kcal/mol

10. Ligand Efficiency
From Wenlock et al (2003), J Med Chem 46,

11. Potency vs. Efficiency HTS Hit Kd = 10 uM LE = 0.1 Fragment Hit

12. Connecting Fragments
K(A) = 1 mM
K(B) = 1 mM
K(AB)=K(A)K(B)L
≤ 1 uM

13. ActiveSight Fragment Library
420 compounds expert selected, checked for solubility and validated at ActiveSight
- typical molecular weights Da
- rigid, low complexity, single core

14. Example: targeting hsp90
Target the “closed” conformation
Data collection
soaking 2-30 minutes, 2-10 mM concentrations
in house data sets ~2Å, 30min/dataset
Structure Solution
Python script

15. Hsp90 Screening Results
Compound RA1014

16. Inhibitor built from adenine core
PDB entry: 1UY6
JRNL AUTH L.WRIGHT,X.BARRIL,B.DYMOCK,L.SHERIDAN,A.SURGENOR,
JRNL AUTH 2 M.BESWICK,M.DRYSDALE,A.COLLIER,A.MASSEY,N.DAVIES,
JRNL AUTH 3 A.FINK,C.FROMONT,W.AHERNE,K.BOXALL,S.SHARP,
JRNL AUTH 4 P.WORKMAN,R.HUBBARD
JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIPS IN PURINE-BASED
JRNL TITL 2 INHIBITOR BINDING TO HSP90 ISOFORMS
JRNL REF CHEM.BIOL V
JRNL REFN ASTM CBOLE2 UK ISSN

17. Scripps Fragment Screening Collaborations
AIDS Protease with Holly Heaslet, Bruce Torbett, John Elder and Dave Stout
AIDS is an enormous epidemic – a global health crisis
AIDS protease inhibitors are highly successful at slowing disease but resistant strains of virus always arising so that new drugs must be continuously developed
We are developing an affinity grid of the active sight to facilitate drug design efforts

18. Scripps Fragment Screening Collaborations
SARS Structural Genomics with Peter Kuhn and Ray Stevens
A number of SARS proteins have been solved that have unknown function
With fragment screening we hope to identify binding sites and inhibitors for functional studies

19. Automated Structure Solution

20. MIAutoStructure Automated system Python script
MIFit GUI
CommandLine
Automated system or or
Keyworded parameter file
Python script
Launch, analyze intermediate results, log
External applications (CCP4, SHELX)

21. MIFit
Ligand Density

22. For more information go to
Acknowledgements
Robin Rosenfeld
Les Tari
Ron Swanson
Isaac Hoffman
Dan Bensen
John Badger
Paul Collins
Bradley Smith
For more information go to
and