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Preset3

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SHAPE Society

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Preset3

  1. 1. PROTEIN STRUCTURE AS A TARGET FOR LIGAND DESIGN
  2. 2. 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
  3. 3. Biological problem Target Structure of target (MMP9, Cellulase, Chymotrypsin) Proteins as a target
  4. 4. 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
  5. 5. - Physiological Conditions : - Tissue remodelling, wound healing, angiogenesis - Pathological Conditions : - Cancer metastasis, cardiovascular aneurysms and rupture MMP9 IMPORTANCE
  6. 6. MMP9 IN METASTASIS
  7. 7. Peter Carmeliet, (2000) J Clin Invest 105(11) 1519-1520 MMPs in cardiovascular aneurysms and rupture
  8. 8. Purification of truncated form of MMP-9 Expression in E. Coli Inclusion body Expression using Baculovirus system Zn2+ S P C F
  9. 9. Load Wash 0.1-2.0M NaCl Heparin-Sepharose column
  10. 10. 55kD Gelatin-Sepharose column Load 2% DMSO
  11. 11. 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.
  12. 12. The STRUCTURE OF CELLULASES FROM THE FUNGUS ASPERGILLUS NIGER
  13. 13. Problem : Cellulase producing fungi destroying cellulose-based materials. Target : Cellulase from Fungus Aspergillus niger. Cellulase as a Target
  14. 14. Ribbon Stereo Diagram of EglA
  15. 15. The Binding Cleft of EglA
  16. 16. Pd2+ Glu 116 Glu 204 Met 118
  17. 17. The STRUCTURE OF CELLULASES FROM A WOOD- EATING TERMITE
  18. 18. 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.
  19. 19. NtEgl Crystals Initial crystals Final crystal
  20. 20. Ribbon Representation of NtEgl
  21. 21. Surface potential of NtEgl
  22. 22. W253 F205 D57 D54 W301 E412 Y408 W127 R361 H124 H359 Y417 Ca2+ W516 N-RE RE The Binding Cleft of NtEgl
  23. 23. D210 D213 E214 D254 N252 Water Water Ca2+ The Ca2+ Binding Site of NtEgl at pH 5.6
  24. 24. D213 E214 D210 D254 N252 The Ca2+ Binding Site of NtEgl at pH 2.5
  25. 25. H359 A55 Y417 Y408 Catalytic Acid/Base Glu 412 at pH 5.6 and 6.5
  26. 26. The STRUCTURE OF A SERINE PROTEASE FROM FIRE ANT
  27. 27. The Problem: fire ant
  28. 28. Crystallization of C3
  29. 29. Asp 102 His 57 Ser 195 PMS
  30. 30. - C3 - Cymotrypsine - Trypsine - Elastase - Collagenase
  31. 31. 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
  32. 32. Asp 102 His 57 Ser 195 PMS IPS
  33. 33. Structure-Based Drug Design Protein structure Small molecule database Docking Protein structure Crystallography Molecular Mechanics Dynamics calculations Protein structure
  34. 34. Touching Molecules: force feedback as an aid to docking
  35. 35. 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

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