1. Peptidomimetic Inhibitors : An Integrated Synthetic and Theoretical Approach to their Design
Everardo Macias, Patrick Tomboc Eamonn F. Healy,
Chemistry Department,
St. Edward’s University,
Austin TX 78704

2. Abstract
Peptidomimetics represent a powerful approach to pharmaceutical treatments based on enzymatically controlled reactions. Peptidomimetics are simply small organic molecules that serve to mimic the transition state of the natural substrate and thus serve to competitively inhibit the enzyme process. We are focusing on the design and synthesis of inhibitors for the serine protease thrombin. Thrombin plays a critical role in the formation of insoluble fibrin that can lead to life threatening medical conditions. Our synthetic scheme utilizes hydroxy-aldehydes in the synthesis of polypeptide isoteres for active site inhibition. QSAR studies aid in the understanding of the steric and hydrophobic requirements of the enzymaticbinding sites.

3. Enzyme
Thrombin, a sub-class of the hydrolyases is a serine protease that promotes blood clotting
Thrombin has an active site consisting of the catalytic triad: Ser 195, His 57 and Asp 102

4. Enzyme BindingSite
In addition thrombin has three binding sites, labelled as S1, S2 and S3, that determine the strength and specificity of binding
The lipophilicity of S3 has been well determined S3 S2 S1

5. Peptidomimetics Saquinavir
Small peptide-like molecules that mimic transition state of substrate and work by competitive inhibiting binding of the natural substrate
Peptide analog must be stable
Drug must be a reversible inhibitor of the enzyme but can be irreversible if the enzyme is unique to the disease
Saquinavir

6. Project Design
Design a polypeptide isotere based on a natural thrombin substrate (Phe-Pro-Arg tripeptide), shown on the right
Optimize a generalized scheme for isotere synthesis
Model the S2 and S3 steric and hydrophobic requirements

7. Project
Use Quantitative Structure-Activity Relationships (QSAR) to identify optimum R2 and R3 binding fragments
Synthesize the isotere, shown in red on the right, designed to mimic the serine-195 mediated transition state

8. Retrosynthesis &
Synthesis

9. Results >70% 3100 cm-1, sharp; 2950 cm-1 ; 1610 cm -1, weak
d , multiplet, 2H ; d 0.4, singlet, 9H
d , multiplet, 2H ;d 3.6,multiplet,1H
d , multiplet, 4H

11. Structure-Activity Results from Ref 2
R3 R2 Ki (nm)
CH3 benzyl (S) 17
CH3 phenethyl (R) 550
CH3 phenethyl (S) 235
CH3 phenylpropyl (R) 100
CH3 phenylpropyl (S) 4
H benzyl (R) 1112
H benzyl (S) 8

12. QSAR
Quantitative structure-activity relationships (QSAR) represent an attempt to correlate structural or property descriptors of compounds with their activities. These physicochemical descriptors, including parameters describing hydrophobicity, topology, electronic effects and steric effects, can be determined empirically or by computational methods. Once a correlation between structure and activity/property is found, new compounds can be screened to select those with the desired properties. Activities in which QSAR has found wide application include biological assays, chemical measurements, environmental risk assessment and de novo drug design.

13. QSAR Methodology
Linear regression analysis of the predicted versus observed activity/property is most commonly used to develop the QSAR relationship. The higher the r2 value the better the fit. The technique of leave-one-out cross-validation, quantified as rCV, is used to assess the predictive power of the QSAR model.
Two parameters, molecular connectivity and valence connectivity, developed by Kier and Hall were used extensively in this study. While these are fundamentally topological parameters they have been shown to contain electronic as well as structural information.

14. Connectivity Indices

15. Results
Preliminary results, summarized by the plot of the predicted (y-axis) versus experimental (x-axis) binding constants, clearly show that a functional predictive model of the steric and electronic requirements of the S2 and S3 binding sites can be constructed. Initial results seem to indicate the energetic descriptors are more useful as predictors than simple topological properties. This work continues.

16. Results

17. Results

18. References Acknowledgements
Alessandro Dondoni, et al.; Synthesis of TSTs and Reactions with Carbonyl Compounds; J. Org. Chem. 1988, 53,
Benoit Bachand , et al.; Synthesis and Structure-Reactivity of Potent Bicyclic Lactam Thrombin Inhibitors; Bioinorg. & Med. Chem. 1999, 9,
Acknowledgements
We gratefully acknowledge the support of the Welch Foundation in the form of a Departmental Research Grant