Combinatorial Chemistry & High Throughput Screening - Volume 8, Issue 2, 2005

High throughput screening approaches have found their way into many if not all pharmaceutical companies and have made important contributions to basic science as well as to drug development. An important aspect is that the combinatorial principle has not only been applied in molecular biology techniques, where randomized oligonucleotides have been incorporated into genes coding for phage and bacteria surface proteins. In the last ten years we have also seen fundamental progress in glycobiology, chemical protease inhibitor development and synthetic peptide library development. A further important point, which can be seen in nearly all reviews in this special issue, is the fundamental influence of structural biology. Most if not all biotechnological and therapeutic interventions at one point or the other rely on the interaction of drugs with proteins. Therefore, the availability of protein structural data is often pivotal to the understanding of the mechanism of action of a drug. Furthermore, many inhibitors of enzymes have been refined using structural data of their respective target proteins. The idea of this special issue was to assemble reviews of research fields which are strongly influenced by combinatorial approaches, although they would prima vista be judged to be scientifically unrelated. There are, however, many points where similar techniques were used or similar problems arose. The aim of this special issue has been to demonstrate the interdisciplinary aspect of combinatorial approaches. This special issue of Combinatorial Chemistry & High Throughput Screening on the screening for proteins and inhibitors brings together leading scientists from diverse fields involved in protein and inhibitor research such as biochemistry, structural biology, signal transduction, combinatorial chemistry and recombinant antibody technology. This issue provides the reader with important breakthroughs of the last years and demonstrates that combinatorial approaches in chemistry and molecular biology are possible, necessary and successful.

For almost 15 years phage display is being used for the selection of specific antigen-binders from artificial libraries of single chain antibodies. Filamentous phages have been developed in a way to express foreign proteins on the surface and at the same time carrying the genetic information of the surface expressed molecule within the phage capsid. This property guarantees the coupling of phenotype and genotype during phage amplification and affinity selection. The possibility to generate large antibody libraries and the simplified antibody-backbone of a single chain antibody has made antibody-phage display to a powerful tool for the development of new therapeutics against various human diseases. In this review we discuss the general principles and latest developments and applications in antibody phage display technology.

A multitude of systems for the presentation of foreign peptides or proteins on the surface of microorganisms has been developed within the past two decades. However, the majority of the bacterial surface display systems are devoted to the presentation of heterologous antigens to the immune system (vaccine generation). Bacteria are the preferable hosts for the generation of vast genetic repertoires, and their genetic manipulation and cultivation is easy. As a consequence, they provide promising systems for large-scale functional screenings, e.g. for enzyme activity or protein-protein interactions. This review will focus on examples of microbial surface display used for the screening of combinatorial repertoires. Further, we discuss future opportunities and promising candidate proteins not yet employed for that task.

Synthetic peptides have a long tradition as molecular tools in biomedical research and drug discovery. The introduction of high-throughput synthesis and screening technologies for synthetic peptides, such as arrays and combinatorial libraries, enabled the large-scale and detailed exploration of protein-ligand interactions, as well as the discovery of novel biologically active peptides. This review summarizes currently available synthetic peptide array and library technologies, in particular mixture-based peptide libraries, which are illustrated by numerous applications in various fields of biomedical research.

With the success of the human genome project, the focus of life science research has shifted to the functional and structural analyses of proteins, such as disease proteomics and structural genomics. These novel approaches to the analyses of proteins, including newly identified ones, are expected to help in the identification and development of protein therapies for various diseases. Thus, disease proteomic-based drug discovery has a very high profile. Nevertheless, the use of bioactive proteins in the clinical setting is not straightforward because, in vivo, these proteins have a low stability and a pleiotropic action. To promote disease proteomic-based drug discovery and development, we have attempted to establish a system for creating functional mutant proteins (muteins) with the desired properties, and also to develop a site-specific polymerconjugation system for further improving their therapeutic potency. These innovative protein-drug systems are discussed in this review.

The application of combinatorial chemistry to glycobiology historically has proven challenging due to numerous synthetic hurdles. The advent of novel methodologies has enabled the production of natural as well as mimetic analogues for proof-of-concept experiments and SAR. This review highlights some of the recent synthetic advances in combinatorial carbohydrate synthesis. The application of carbohydrate libraries in glycobiology is also discussed.

The transmembrane metzinkin-proteases of the ADAM (a disintegrin and a metalloproteinase)-family ADAM10 and ADAM 17 are both implicated in the ectodomain shedding of various cell surface molecules including the IL6-receptor and the transmembrane chemokines CX3CL1 and CXCL16. These molecules are constitutively released from cultured cells, a process that can be rapidly enhanced by cell stimulation with phorbol esters such as PMA. Recent research supports the view that the constitutive cleavage predominantly involves ADAM10 while the inducible one is mediated to a large extent by ADAM17. We here describe the discovery of hydroxamate compounds with different potency against ADAM10 and ADAM17 and different ability to block constitutive and inducible cleavage of IL6R, CX3CL1 and CXCL16 by the two proteases. By screening a number of hydroxamate inhibitors for the inhibition of recombinant metalloproteinases, a compound was found inhibiting ADAM10 with more than 100-fold higher potency than ADAM17, which may be explained by an improved fit of the compound to the S1' specificity pocket of ADAM10 as compared to that of ADAM17. In cell-based cleavage experiments this compound (GI254023X) potently blocked the constitutive release of IL6R, CX3CL1 and CXCL16, which was in line with the reported involvement of ADAM10 but not ADAM17 in this process. By contrast, the compound did not affect the PMA-induced shedding, which was only blocked by GW280264X, a potent inhibitor of ADAM17. As expected, GI254023X did not further decrease the residual release of CX3CL1 and CXCL16 in ADAM10-deficient cells verifying that the compound's effect on the constitutive shedding of these molecules was exclusively due to the inhibition of ADAM10. Thus, GI254023X may by of use as a preferential inhibitor of constitutive shedding events without effecting the inducible shedding in response to agonists acting similar to PMA.

Cytokines are important mediators of many cellular functions including coordination of the immune system and regulation of regenerative processes. Therefore, cytokines can be exploited for therapeutic strategies. Cytokines can be altered in a way that their biologic activity is enhanced or antagonized. This can be accomplished by changing the interaction of cytokines with their cognate cytokine receptor complexes. Therefore, many research groups tried to design cytokines, which bind with higher affinity to their receptors. Alternatively, cytokine variants have been created which do bind to their receptors but do not elicit a signal. Such strategies have been followed using high throughput techniques like error-prone polymerase chain reaction and phage display. Designer cytokines can be used to specifically inhibit cytokine functions. Moreover, peptides have been generated with the help of phage display techniques, which exhibit cytokine activity. Surprisingly, such mimetic peptides do not show any sequence similarity to the parental cytokines. Such peptide mimetics can be used as lead structures for the generation of non-peptidic chemical compounds with cytokine activity.

The pivotal role of kinases in signal transduction and cellular regulation has lent them considerable appeal as pharmacological targets across a broad spectrum of pathologies. Since the discovery that the v-Src oncogene encoded a protein kinase in 1978, kinases have remained a focus of research for pharmaceutical laboratories and academic groups alike. Many have sought to develop orally available low molecular weight synthetic kinase modulators (predominantly inhibitors) and thus capitalize on the links between aberrant regulation and disease. This interest in kinases as drug targets was fueled in recent years by the success of several kinase inhibitors in the clinic, primarily Gleevec for the treatment of chronic myelogenous leukemia and Iressa for the treatment of advanced non-small cell lung cancer. This review focuses on the development of small molecule drugs, most of them binding in or close to the ATP binding pocket. After some general considerations regarding the selection of a particular kinase for drug discovery, we will discuss the encouraging lessons learned from some of the kinase inhibitors currently in various stages of development. The majority of this review is dedicated to a detailed description and discussion of the various assay formats currently being employed for high throughput screening.

Proteases are key regulators of many physiological and pathological processes [1,2], and are recognized as important and tractable drug candidates. Consequently, knowledge of protease substrate recognition and specificity promotes identification of biologically relevant substrates, helps elucidating a protease's biological function, and the design of specific inhibitors. Traditional methods for establishing substrate recognition profiles involve the identification of the scissile bond within a given protein substrate by proteomic methods such as Edman degradation. Then, synthetic peptide variants of this sequence can be screened in an iterative fashion to arrive at more optimized substrates. Even though it can be fruitful, this iterative strategy is biased toward the original substrate sequence and it is also tremendously cumbersome. Furthermore, it is not amenable to high throughput analysis. In 1993, Matthew & Wells presented a method for the use of monovalent “substrate phage” libraries for discovering peptide substrates for proteases, in which more than 107 potential substrates can be tested concurrently [3]. A library of fusion proteins was constructed containing randomized substrate sequences placed between a binding domain and the gene III coat protein of the filamentous phage, M13, which displays the fusion protein and packages the gene coding for it inside. Each fusion protein was displayed as a single copy on filamentous phagemid particles (substrate phage). This method allows one to rapidly survey the substrate recognition and specificity of individual or closely related members of proteases. Over the past decade, substrate phage screening has shown terrific utility in rapidly determining protease specificity and characterization of substrate recognition profile of proteases. In some cases, the structural insights of the catalytic domain were obtained from comparison of substrate specificity among closely related family of proteases [4-6]. The number of proteases (from various classes) characterized by this approach testifies to its power. Since the initial development of substrate phage library, different versions of the substrate phage cloning vectors have been constructed to further improve the utility of substrate phage display. This review will provide an overview of the construction of substrate phage display libraries, screening of substrate phage libraries, examples of application, summary and future directions.