SHAPE Society

2. PROTEIN STRUCTURE AS A TARGET FOR LIGAND
DESIGN

3. Finding the target
Crystallography
Pre-clinical trials,
Clinical trials
Protein
structure
Drug Development Diagram
Synthesis and testing
Available compound or
lead compounds, substrates
Protein
structure
Lead
Improvement

4. Biological problem
Target
Structure of target
(MMP9, Cellulase, Chymotrypsin)
Proteins as a target

5. Matrix Metalloproteinase-9
- Zinc-dependent metalloproteinase
- Degrades Extracellular matrix components
Signal domain Fibronectin-like domain
Propeptide Hinge region
Hemopexin-like domain
Zn2+
Catalytic domain
92 kD

6. - Physiological Conditions :
- Tissue remodelling, wound healing, angiogenesis
- Pathological Conditions :
- Cancer metastasis, cardiovascular aneurysms
and rupture
MMP9 IMPORTANCE

7. MMP9 IN METASTASIS

8. Peter Carmeliet, (2000) J Clin Invest 105(11) 1519-1520
MMPs in cardiovascular aneurysms and rupture

9. Purification of truncated form of MMP-9
Expression in E. Coli
Inclusion body
Expression using Baculovirus system
Zn2+
S P C
F

10. Load Wash 0.1-2.0M NaCl
Heparin-Sepharose column

11. 55kD
Gelatin-Sepharose column
Load 2% DMSO

12. Characterization of truncated form of MMP-9
- TIMP-1 binds and inhibits the catalytic domain
- Fibronectin-like domain is not sufficient for
heparin binding
Zn2+
C
F
~38kD
Sadatmansoori, S (2001) protein expression and purification 23(3) 447-452.

13. The STRUCTURE OF CELLULASES FROM THE
FUNGUS ASPERGILLUS NIGER

14. Problem : Cellulase producing fungi destroying
cellulose-based materials.
Target : Cellulase from Fungus Aspergillus
niger.
Cellulase as a Target

15. Ribbon Stereo Diagram of EglA

16. The Binding Cleft of EglA

18. Pd2+
Glu 116
Glu 204
Met 118

19. The STRUCTURE OF CELLULASES FROM A
WOOD- EATING TERMITE

20. The problem: Termite
- $1 billion damage a year!
- 1000 lbs wood a year!
- $15 million effort a year
- Inhibition of digestive enzymes
- The best choice is Cellulase.

21. NtEgl Crystals
Initial crystals Final crystal

22. Ribbon Representation of NtEgl

23. Surface potential of NtEgl

24. W253
F205
D57
D54
W301
E412
Y408
W127
R361
H124
H359
Y417
Ca2+
W516
N-RE RE
The Binding Cleft of NtEgl

25. D210
D213 E214
D254
N252
Water
Water
Ca2+
The Ca2+
Binding Site of NtEgl at pH 5.6

26. D213 E214
D210
D254
N252
The Ca2+
Binding Site of NtEgl at pH 2.5

27. H359
A55
Y417
Y408
Catalytic Acid/Base Glu 412 at pH 5.6 and 6.5

28. The STRUCTURE OF A SERINE PROTEASE FROM
FIRE ANT

29. The Problem: fire ant

30. Crystallization of C3

31. Asp 102
His 57
Ser 195
PMS

32. - C3
- Cymotrypsine
- Trypsine
- Elastase
- Collagenase

33. 182 195 214 228
- Chymotrypsin CAG-ASGV-SSCMGDS … SWGSST-CS-TSTPGVY
- Trypsin CVGFLEGGKDSCQGDS … SWGYG--CALPDNPGVY
- Elastase CAGGDG-VRSGCQGDS … SFVSRLGCNVTRKPTVE
- Collagenase CID-STGGKGTCDGDS … SFGAAAGCEA-GYPDAE
- C3 CANDPSAQKGACKGDS … SW--SLDCALTTHPTVY
Asp 102
His 57
Ser 195PMS
Ser 217

34. Asp 102
His 57
Ser 195
PMS
IPS

36. Structure-Based Drug Design
Protein
structure
Small molecule database
Docking
Protein
structure
Crystallography
Molecular Mechanics
Dynamics calculations
Protein
structure

37. Touching Molecules: force feedback as an
aid to docking

38. Acknowledgement
-Dr. Edgar Meyer - Dr. Linda A. Guarino
- Dr. Hirofumi Watanabe - Dr. Arnold Wartenberg
- Dr. Sepideh Sadatmansoori - Dr. Reza Forough
- Dr. Erik Meyer
- Dr. Stanley and Rosemarie Swanson
- Robert A. Welch Foundation
- Texas Advanced Technology Program