1. Uttamchandani, M., Walsh, D. P., Yao, S. Q., Chang, Y. T. “Small Molecule Microarrays – Recent Advances and Applications” Curr. Opin. Chem. Biol. 2005, 9, 4-13.
2. Uttamchandani, M., Huang, X., Chen, G. Y. J., Yao, S. Q. “Nanodroplet Profiling of Enzymatic Activity on Microarrays” Bioorg. Med. Chem. Lett. 2005, 15, 2135-2139.
3. Wang, J., Uttamchandani, M., Sun, L.P., Yao, S.Q. “Activity-Based High-Throughput Profiling of Metalloprotease Inhibitors Using Small Molecule Microarrays” Chem. Comm. 2005, 7, 717-719.
4. Uttamchandani, M., Wang, J., Yao, S.Q. “Protein and Small Molecule Microarrays: Powerful Tools for High-Throughput Proteomics” Mol. BioSyst.2006, 2, 58-68.
5. Srinivasen, R., Uttamchandani, M., Yao, S. Q. “Rapid Assembly and In Situ Screening of Bidentate Inhibitors of Protein Tyrosine Phosphatases (PTPs), Org. Lett. 2006, 8, 713-716.
6. Hu, Y., Uttamchandani, M., Yao, S. Q. “Microarray: A Versatile Platform for High-Throughput Functional Proteomics”, Comb. Chem. High Throughput Screening. 2006, 9, 203-212.
7. Wang, J., Uttamchandani, M., Hong, Y., Yao, S. Q. “Applications of Microarrays with Special Tagged Libraries” QSAR Comb. Sc. 2006, 11, 1009-1019.
8. Wang, J., Uttamchandani, M., Li, J., Hu, M., Yao, S. Q. “Rapid Assembly of Matrix Metalloproteases (MMP) Inhibitors Using Click Chemistry” Org. Lett. 2006, 8, 3821-3824.
9. Wang, J., Uttamchandani, M., Li, J., Hu, M., Yao, S. Q. ““Click” Synthesis of Small Molecule Probes for Activity-Based Fingerprinting of Matrix Metalloproteases” Chem. Comm. 2006, 36, 3783-3785.
10. Uttamchandani, M., K, Liu., Panicker, R. C., Yao, S. Q., “Activity-Based Fingerprinting and Inhibitor Discovery of Cysteine Proteases in a Microarray” Chem. Comm. 2007, 15, 1518-1520.
11. Uttamchandani, M., Wang, J., Li, J., Hu, M., Sun, H., Chen, K. Y. -T., Liu, K., Yao, S. Q. “Inhibitor Fingerprinting of Matrix Metalloproteases using a Combinatorial Peptide Hydroxamate Library” J. Am. Chem. Soc. 2007, 129, 7848-7858.
12. Lee, W. L., Li, J., Uttamchandani, M., Sun, H., Yao, S. Q. “Inhibitor Fingerprinting of Metalloproteases Using Microplate and Microarray Platforms – An Enabling Technology in Catalomics” Nat. Protocols. 2007, 2, 2126-2138.
13. Uttamchandani, M., Lee, W. L., Wang, J., Yao, S. Q. “Quantitative Inhibitor Fingerprinting of Metalloproteases using a Peptide Hydroxamate Microarray” 2007, 129, 13110-13117.
List of Figures
Figure Page
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Various strategies developed for fabricating protein microarrays.
Various strategies developed for fabricating SMM
Novel strategies in applying SMM
Heat-map of 1,400 inhibitors profiled against panel of 7 MMPs
Averaged inhibition contributions across permuted P1’, P2’ and P3’ positions.
Cladograms of MMPs.
Hierarchical clustering across the P1’ position.
Distribution of top 100 inhibitors.
Docking configurations of selected inhibitors with MMPs.
A three-fold dilution series of trypsin printed on bodipy casein coated slides scanned after one hour of incubation.
Profiles obtained using the 39 proteins in microtitre plate and on microarray.
Microarray images taken at different time points.
Phosphatase sensitive slides screened against three representative alkaline phosphatases.
Structure of 400-member hydroxamate inhibitors.
Results of the nanodroplet inhibitor profiling strategy with thermolysin.
Normalized microarray data across all 400 samples were plotted against data obtained using the microplate method.
Results of the nanodroplet inhibitors profiling strategy with collagenase.
Gel-based fingerprints of 12 probes against 7 metalloenzymes.
Heat-map fingerprints of 12 probes against 7 metalloenzymes
Gel-based labelling in the presence and absence of the UV-irradiation step
An increasing concentration of thermolysin was incubated with the Leu probe.
An increasing concentration of probes were incubated with thermolysin.
Labelling of thermolysin in the presence of cellular extract.
Protein microarray of various metalloenzymes sceened by the Leu probe.
Structure of general hydroxamate inhibitors and “click chemistry inhibitors reported herein against metalloproteases.
Building blocks for rapid assembly of metalloproteases inhibitors.
Inhibitor fingerprints of 96-member click library screened against MMP-7, thermolysin and collagenase.
Inhibitor fingerprints of 3 metallopteases tested with the inhibitor library.
Quantitative evaluation of selected inhibitors.
In silico docking displays the possible binding mode of G6/MMP-7 complex.
Reciprocal labelling and application strategy for activity dependent high-throughput microarray screening.
Dual-colour reciprocal labelling/ screening strategy.
Graph displaying equivalent concentrations of Cy3 and Cy5 dye that were spotted and scanned.
The 400 member P1’ L sub-library was screened using microplate and compared with the fingerprint obtained using SMM.
Activity-dependent fingerprints of thermolysin, collagenase, carboxypeptidase and Anthrax LF with the 1,400 molecule hydroxamate inhibitor library.
Distribution of top 100 inhibitors.
Cladograms of metalloproteases based on SMM inhibitor fingerprints.
Large-scale KD determination for thermolysin using SMM.
Docking configurations of lF-F-L with anthrax LF.
Inhibition potencies with the complete 1,400 inhibitor library against 7 MMPs.
Docking configurations of selected inhibitors with MMPs.
IC50 determination for selected inhibitors with MMP panel.
Graphs for determining IC50 values of selected inhibitors against thermolysin.
Graphs for determining Ki values of 2 representative inhibitors and GM6001 against thermolysin.
Graphs for determining IC50 values of selected samples for collagenase inhibitors.
The data combined from both reciprocal experiments were presented in a 3D cube plot for enzymes in the panel.
Averaged inhibition contributions permuted across P1’, P2’ and P3’ positions.
Protein sequence alignment of the selected metalloproteases.
IC50 and KD curves for selected inhibitors with Anthrax LF.
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Table Page
2.1
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7.1
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11.6
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11.8
IC50 of selected inhibitors against panel of enzymes.
A set of 39 protein printed on bodipy casein coated slides.
Ki/IC50 values of 6 selected inhibitors from the library together with commercial inhibitor GM6001.
IC50 values of 3 inhibitors selected from large-scale microarray screens.
IC50 and Ki evaluation of selected inhibitors against panel of enzymes
SPR was used to confirm the KD values obtained against thermolysin on the SMM for 3 selected inhibitors.
KD and IC50 results of selected inhibitors against anthrax LF.
Names and classification of MMPs.
Library design for 1,400-member hydroxamate peptides.
A. Selective inhibitors uncovered from the top 100 inhibitor lists.
B. Broad-range inhibitors uncovered from the top 100 inhibitor lists.
Motif selectivity comparisons.
The classification of the panel of 4 metalloproteases used in the study.
Motif selectivity comparisons.
A. Selective inhibitors uncovered from the top 100 inhibitor lists.
B. Broad-range inhibitors uncovered from the top 100 inhibitor lists.
KD analysis for thermolysin and anthrax LF.
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Scheme Page
2.1
3.1
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7.1
Design of combinatorial peptide hydroxamate library.
A strategy for rapid screening of enzymes using microarrays.
Nanodroplet SMM strategy for high-throughput profiling of potential MMP inhibitors.
General structures of the 1st and 2nd generation MMP probes.
General structures of the 12 MMP probes used in this work.
Design of 1,400 member hydroxamate peptide inhibitor library.
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MT1-MMP 30ng/ lane