Personal Foreword

When approached to initiate this book project the initial thoughts were to remember a review published in 1997 [1]. The first memories of that endeavor were quite painful, so the first instinct was to politely turn down the kind offer to initiate this project. On second reflection, researching and preparing the 1997 review was an educational and rewarding experience. Therefore, with the help of a co-editor, the invitation to initiate and complete this endeavor was accepted.

The objective of this book is to provide a forward looking overview of the use of protein crystallography in drug discovery. It has been organized so that the early chapters review and describe some mature and emerging topics that would fall under the 'traditional structure-based design' umbrella, the middle chapters provide focused accounts of specific works, and the final chapters delve into new and fertile areas of research. This book does not attempt to be comprehensive; thus the final lineup of chapters was a compromise between the interests of the editors and the willingness of the authors to contribute a chapter.

The first two chapters review nuclear hormone receptors and protein kinases. Both of these chapters provide an overview of the topic and shed some insight into how small molecule ligands can achieve selectivity between related protein targets. The next two chapters review topics that begin to 'push the limit' on the size of the complexes that can be used in drug design. Both the proteosome and the ribosome are very large biological macromolecules that are the targets for drug discovery. In the ribosome chapter, an important point is made regarding what conclusions are warranted, or not warranted, based upon the resolution of the x-ray diffraction data. The ribosome chapter also introduces the topic and challenges of antibiotic resistance in drug discovery. The next two chapters provide accounts of detailed structure-based design studies aimed at obtaining inhibitors of both cathepsin K and Cdk4. The cathepsin K chapter provides a nice account of the iterative structure-based design process. This work is especially notable for the use of an unexpected crystallographic result to move a project in a novel direction. The Cdk4 chapter also does an excellent job of introducing many computational methods that are used in drug discovery. For those readers interested in protein-based virtual screening of chemical databases, we also recommend the work by Bissantz et al. [2] in which they evaluate different docking/scoring combinations. Chapter 7 describes applications of the protease inhibitor ecotin, particularly its use as a tool to obtain crystals of serine proteases and to study the interactions between serine proteases and their substrates. Chapter 8 reviews work on 'orthogonal ligand-receptor pairs' and the impact of crystallography on this area of research. While 'traditional structure-based design' uses the structure of a protein-li-gand complex as a tool to design modified ligands, the work on 'orthogonal li-gand-receptor pairs' uses the structure of the complex as a tool to design both modified proteins and modified ligands. This work has applications for deconvo-luting some cellular processes and also provides useful tools in the area of chemical genetics. Protein/ligand pairs may also have future applications in gene therapy. Chapters 7 and 8 present examples that use crystallography to design mutant proteins for additional structural studies. Chapter 9 discusses the use of mutant proteins as an entry into obtaining high-resolution crystal structures. In numerous past examples, when a human protein proved difficult to crystallize, a protein from another species such as mouse, rat, or chicken was often used as a surrogate protein. A potential problem with this approach is that the active sites of the human and the surrogate enzyme might be different. The chapter on "Engineering Proteins to Promote Crystallization" reviews examples where the surface of a human protein is modified in a location remote from the active site to produce a mutant human protein that can give useful crystals. The next chapter discusses "High-throughput crystallography"' which is an area of intense interest [3, 4]. This chapter provides a clear overview of the field, and has an informative section on crystallography in lead discovery. The final chapter describes miniaturization of crystallization utilizing the emergent technologies of microfluidics. This technology allows crystallization experiments to be performed on the nanoliter scale, thus conserving a very valuable resource in crystallography, the protein. Many of the technologies described in the final three chapters should impact crystallization and structure determination of the many new proteins identified in the human and other genomes.

We expect that this book will be a useful reference to practitioners of structure-based design. In addition, we hope that the technologies discussed in the later chapters will help researchers solve new problems in the next generation of structure-based design problems.

Cambridge, MA, April 2003 Robert E. Babine

Sherin S. Abdel-Meguid

1 Babine, R. E. and S.L. Bendeb, Molecular Recognition of Protein-Ligand Complexes: Applications to Drug Design.

3 Mountain, V., Innovation - Astex, Structural Genomix, and Syrrx. Chem. Biol. 2003, 10, 95-98.

ferent docking/scoring combinations. J. Med. Chem. 2000, 43(25), 4759-4767.

2 Bissantz, C., G. Folkees, and D. Rog-nan, Protein-based virtual screening of chemical databases. 1. Evaluation of dif

4 Bertini, I., Structural genomics. Acc. Chem. Res. 2003, 36(3), 155.

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