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COMPUTER-AIDED DESIGN, MOLECULAR MODELLING AND COMPUTER-ASSISTED COMBINATORIAL CHEMISTRY IN THE DEVELOPMENT OF NEW INHIBITORS OF THE ASPARTIC PROTEASE OF HIV-1
Domenico Romeo, Dipartimento di Biochimica Biofisica e Chimica delle Macromolecole, Trieste;
Stanislav Miertus, International Centre for Science and High Technology, Unido, Trieste
This project, aimed at the design, synthesis and testing of new inhibitors of the aspartic protease (AP) of HIV-1, is carried out by three laboratories (International Centre for Science and High Technology, Department of Biochemistry and Department of Chemical Sciences of the University of Trieste), which possess the know-how for molecular design, stereoselective organic synthesis, peptide chemistry and routine enzyme assays. The methodology of inhibitor design is based on a computer-aided approach as well as on computer-assisted combinatorial chemistry, which permit the generation of a great number of individual inhibitors as well as virtual combinatorial libraries. Designed inhibitors, based on dihydroxyethylene and monohydroxyethylene isosteres, are synthesised by a methodology that allows the production of differentially protected, stereodefined diaminodiols and diaminoalcohols from simple aminoacids and aldehydes. The availability of different, selectively protected central modules allows the assembly of peptidomimetic inhibitors, ranging from four to six residues, by adding the appropriate
flanking residues chosen from proteinogenic and non proteinogenic aminoacids as well as from aromatic carboxylic acids, suggested by the computational studies.
Figure 1. Aspartic protease of HIV-1 with Ritonavir - pseudopetide transition state mimetic inhibitor from Abbott Laboratories bound at the enzyme's catalytic site. The protease is shown in Kabsch and Sanders secondary structure rendering while the inhibitor is depicted using space filling CPK model.
The full virtual library, built from all available fragments, consists of more than 109 model compounds, which could be reduced to approximately 104 compounds using various filters, dictated by structural properties as well as by the cost of reagents. Such a restricted library can be further focussed so that only the 100 compounds with most favourable physicochemical molecular properties are retained. These are then scored against known HIV AP inhibitors with experimentally determined inhibition constant and compounds with predicted nanomolar Ki.are thus indicated. The final subset of approximately 20-30 leads is then synthesised and tested in vitro for inhibitory activity of AP.
A. Tossi, I. Bonin, N. Antcheva, S. Norbedo, F. Benedetti, S. Miertus, A.C. Nair, T. Maliar, F. Del Bello, G. Palù, and D. Romeo (2000) Aspartic protease inhibitors. An integrated approach for the design and synthesis of diaminodiol-based peptidomimetics. Eur. J. Biochem. 267, 1715-1722
V. Frecer, S. Miertus, A. Tossi, and D. Romeo (1998) Rational design of inhibitors for drug-resistant HIV-1 aspartic protease mutants. Drug Design Discov. 15, 211-231
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