The Potential of P1 Site Alterations in Peptidomimetic Protease Inhibitors as Suggested by Virtual Screening and Explored by the Use of CC-Coupling Reagents

Leibniz Institute for Molecular Pharmacology (FMP), and Free University Berlin, Takustrasse 3, 14195 Berlin, Germany.
ChemMedChem (Impact Factor: 2.97). 05/2006; 1(4):445-57. DOI: 10.1002/cmdc.200500027
Source: PubMed


A synthetic concept is presented that allows the construction of peptide isostere libraries through polymer-supported C-acylation reactions. A phosphorane linker reagent is used as a carbanion equivalent; by employing MSNT as a coupling reagent, the C-acylation can be conducted without racemization. Diastereoselective reduction was effected with L-selectride. The reagent linker allows the preparation of a norstatine library with full variation of the isosteric positions including the P1 side chain that addresses the protease S1 pocket. Therefore, the concept was employed to investigate the P1 site specificity of peptide isostere inhibitors systematically. The S1 pocket of several aspartic proteases including plasmepsin II and cathepsin D was modeled and docked with approximately 500 amino acid side chains. Inspired by this virtual screen, a P1 site mutation library was designed, synthesized, and screened against three aspartic proteases (plasmepsin II, HIV protease, and cathepsin D). The potency of norstatine inhibitors was found to depend strongly on the P1 substituent. Large, hydrophobic residues such as biphenyl, 4-bromophenyl, and 4-nitrophenyl enhanced the inhibitory activity (IC50) by up to 70-fold against plasmepsin II. In addition, P1 variation introduced significant selectivity, as up to 9-fold greater activity was found against plasmepsin II relative to human cathepsin D. The active P1 site residues did not fit into the crystal structure; however, molecular dynamics simulation suggested a possible alternative binding mode.

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    • "Drug development efforts targeting the plasmepsins have been facilitated by previous studies on other aspartic proteases, particularly renin and cathepsin, which have provided most of the inhibitors used in the crystallographic studies. There have been many works that applied to the plasmepsins case some of the above-mentioned docking software; among the most used are AutoDock [29, 93–96], Gold [55–58], and FlexX [29, 64, 67]. These programs have been employed principally to obtain complexes structures that helped to the interpretation of the experimental results; for the screening of different combinatorial libraries of ligands and to generate plasmepsin-substrate conformations used to establish the enzyme reaction mechanism [97]. "
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