![Page 1: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/1.jpg)
![Page 2: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/2.jpg)
PROTEIN STRUCTURE AS A TARGET FOR
LIGAND DESIGN
![Page 3: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/3.jpg)
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
![Page 4: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/4.jpg)
Biological problem
Target
Structure of target(MMP9, Cellulase, Chymotrypsin)
Proteins as a target
![Page 5: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/5.jpg)
Matrix Metalloproteinase-9
- Zinc-dependent metalloproteinase
- Degrades Extracellular matrix components
Signal domain Fibronectin-like domain
Propeptide Hinge region
Hemopexin-like domainZn2+
Catalytic domain
92 kD
![Page 6: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/6.jpg)
- Physiological Conditions :
- Tissue remodelling, wound healing, angiogenesis
- Pathological Conditions :
- Cancer metastasis, cardiovascular aneurysms and rupture
MMP9 IMPORTANCE
![Page 7: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/7.jpg)
MMP9 IN METASTASIS
![Page 8: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/8.jpg)
Peter Carmeliet, (2000) J Clin Invest 105(11) 1519-1520
MMPs in cardiovascular aneurysms and rupture
![Page 9: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/9.jpg)
Purification of truncated form of MMP-9
Expression in E. Coli
Inclusion body
Expression using Baculovirus system
Zn2+
S P C
F
![Page 10: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/10.jpg)
Load Wash 0.1-2.0M NaCl
Heparin-Sepharose column
![Page 11: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/11.jpg)
55kD
Gelatin-Sepharose column
Load 2% DMSO
![Page 12: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/12.jpg)
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.
![Page 13: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/13.jpg)
The STRUCTURE OF CELLULASES FROM THE
FUNGUS ASPERGILLUS NIGER
![Page 14: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/14.jpg)
Problem : Cellulase producing fungi destroying cellulose-based materials.
Target : Cellulase from Fungus Aspergillus niger.
Cellulase as a Target
![Page 15: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/15.jpg)
Ribbon Stereo Diagram of EglA
![Page 16: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/16.jpg)
The Binding Cleft of EglA
![Page 17: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/17.jpg)
![Page 18: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/18.jpg)
Pd2+
Glu 116Glu 204
Met 118
![Page 19: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/19.jpg)
The STRUCTURE OF CELLULASES FROM A
WOOD- EATING TERMITE
![Page 20: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/20.jpg)
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.
![Page 21: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/21.jpg)
NtEgl Crystals
Initial crystals
Final crystal
![Page 22: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/22.jpg)
Ribbon Representation of NtEgl
![Page 23: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/23.jpg)
Surface potential of NtEgl
![Page 24: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/24.jpg)
W253
F205
D57D54
W301
E412Y408
W127R361
H124
H359
Y417
Ca2+
W516
N-RE RE
The Binding Cleft of NtEgl
![Page 25: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/25.jpg)
D210
D213 E214
D254
N252
Water Water
Ca2+
The Ca2+ Binding Site of NtEgl at pH 5.6
![Page 26: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/26.jpg)
D213 E214
D210
D254
N252
The Ca2+ Binding Site of NtEgl at pH 2.5
![Page 27: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/27.jpg)
H359
A55
Y417
Y408
Catalytic Acid/Base Glu 412 at pH 5.6 and 6.5
![Page 28: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/28.jpg)
The STRUCTURE OF A SERINE PROTEASE FROM
FIRE ANT
![Page 29: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/29.jpg)
The Problem: fire ant
![Page 30: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/30.jpg)
Crystallization of C3
![Page 31: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/31.jpg)
Asp 102His 57
Ser 195
PMS
![Page 32: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/32.jpg)
- C3- Cymotrypsine- Trypsine- Elastase- Collagenase
![Page 33: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/33.jpg)
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
![Page 34: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/34.jpg)
Asp 102
His 57
Ser 195
PMS
IPS
![Page 35: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/35.jpg)
![Page 36: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/36.jpg)
Structure-Based Drug Design
Protein structure
Small molecule database
Docking
Protein structure
Crystallography
Molecular MechanicsDynamics calculations
Protein structure
![Page 37: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/37.jpg)
Touching Molecules: force feedback as an aid to docking
![Page 38: 066 protein structure as a target for ligand design](https://reader035.vdocuments.us/reader035/viewer/2022070509/589f489f1a28abec418b46bf/html5/thumbnails/38.jpg)
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