Combinatorial Strategies for the Discovery of Novel Protease Specificities. Pp. 73-90.
S. Lien, G.L. Francis and L.D. Graham
[Abstract]
Computational Ligand Design. Pp. 91-104.
J. Apostolakis and A. Caflisch
[Abstract]
Combinatorial Libraries by Portioning and Mixing. Pp. 105-122.
A. Furka and W. D. Bennett
[Abstract]
[Back to top] Combinatorial Strategies for the Discovery of Novel Protease Specificities. S. Lien, G.L. Francis and L.D. Graham.
This article discusses proven and possible ways to generate novel cleavage specificities in serine proteases using combinatorial mutagenesis, compares the different ways of screening or selecting for desirable mutants, and examines the ways in which combinatorial substrate libraries can be used to gain a more comprehensive insight into protease cleavage preferences The use of bacteriophage to display both combinatorial protease libraries and combinatorial substrate libraries will be discussed.
[Back to top] Computational Ligand Design. J. Apostolakis and A. Caflisch.
A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug-like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative structure-activity relationships (QSAR) are presented. These have gained significantly from recent developments of experimental techniques for combinatorial synthesis and high-throughput screening as well as the use of powerful computational procedures like genetic algorithms and neural networks for the derivation of models. Secondly, empirical energy functions are shown to lead to more general models than standard QSAR, since they are fitted to a variety of complexes. They have been used recently with considerable success. Thirdly, we briefly outline free energy calculations based on molecular dynamics simulations, the method with the most sound theoretical foundation. Recent developments are reestablishing the interest in this approach. In the last part of this review structure-based ligand design programs are described. These are closely related to docking, with the difference that in design, unlike in most docking procedures, ligands are built on a fragment-by-fragment basis. Finally, a short description of our approach to computational combinatorial ligand design is given.
[Back to top] Combinatorial Libraries by Portioning and Mixing. A. Furka and W. D. Bennett.
Combinatorial chemistry - due to its radically new synthetic methods - can be considered a forerunner of chemistry in the next century. One of the most important methods is the portioning-mixing (split-mix) synthesis which embodies the combinatorial principle. It is easily realized. Both manual and automatic devices have been described. Some features that contribute to its popularity include: it produces all possible structural combinations of the monomers, it has outstanding productivity, it leads to the formation of individual compounds in nearly equimolar quantities (affected by statistics and incomplete reactions), and it can be applied to all classes of organic compounds. Since an enormously large number of compounds can be produced in principle in a relatively short time, some practical considerations are discussed that can be useful in library design. Encoding organic libraries by peptide or nucleotide sequences or with binary tags are also described together with methods for tagging macroscopic support units with electronic chips, two dimensional bar codes or colored resin and capsule caps. Among the deconvolution strategies, the iteration method, positional scanning, omission libraries, the Selectide and the Pharmacopela methods are mentioned. A collection of libraries prepared by portioning-mixing is also included in graphical format.