Presentation on theme: "Peptidomimetic Inhibitors : An Integrated Synthetic and Theoretical Approach to their Design Everardo Macias, Patrick Tomboc Eamonn F. Healy, Chemistry."— Presentation transcript:
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
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.
Enzyme l Thrombin, a sub-class of the hydrolyases is a serine protease that promotes blood clotting l Thrombin has an active site consisting of the catalytic triad: Ser 195, His 57 and Asp 102
Enzyme BindingSite l In addition thrombin has three binding sites, labelled as S1, S2 and S3, that determine the strength and specificity of binding l The lipophilicity of S3 has been well determined
Peptidomimetics l Small peptide-like molecules that mimic transition state of substrate and work by competitive inhibiting binding of the natural substrate l Peptide analog must be stable l Drug must be a reversible inhibitor of the enzyme but can be irreversible if the enzyme is unique to the disease Saquinavir
Project Design l Design a polypeptide isotere based on a natural thrombin substrate (Phe-Pro- Arg tripeptide), shown on the right l Optimize a generalized scheme for isotere synthesis l Model the S2 and S3 steric and hydrophobic requirements
Project l Use Quantitative Structure-Activity Relationships (QSAR) to identify optimum R2 and R3 binding fragments l Synthesize the isotere, shown in red on the right, designed to mimic the serine-195 mediated transition state
Structure-Activity Results from Ref 2 R 3 R 2 Ki (nm) CH3benzyl (S)17 CH3phenethyl (R)550 CH3phenethyl (S)235 CH3phenylpropyl (R)100 CH3phenylpropyl (S)4 Hbenzyl (R)1112 Hbenzyl (S)8
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.
QSAR Methodology Linear regression analysis of the predicted versus observed activity/property is most commonly used to develop the QSAR relationship. The higher the r 2 value the better the fit. The technique of leave-one-out cross-validation, quantified as r CV, 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.
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.
References l Alessandro Dondoni, et al.; Synthesis of TSTs and Reactions with Carbonyl Compounds; J. Org. Chem. 1988, 53, l Benoit Bachand, et al.; Synthesis and Structure- Reactivity of Potent Bicyclic Lactam Thrombin Inhibitors; Bioinorg. & Med. Chem. 1999, 9, Acknowledgements l We gratefully acknowledge the support of the Welch Foundation in the form of a Departmental Research Grant