Inkjet dispensing technology: applications in drug discovery

The past year has seen significant advances in the reduction to practice of inkjet dispensing technology in drug discovery applications. Although much of the work in this area has been done by relatively few ‘early innovators’, broader acceptance of the feasibility of the use of inkjet dispensing is on the rise. Of the three main areas of drug discovery — genomics, high-throughput screening, and combinatorial chemistry — high-throughput screening has had the most applications to date. The burgeoning field of genomics has seen rapid incorporation of technologies that enable miniaturization of gene expression experiments. Inkjet dispensing has a clear role in this effort. Finally, as the miniaturization needs of combinatorial chemistry become more clear, inkjet dispensing technology will potentially play a role.     

Microfluidic combinatorial chemistry

Microreactors are finding increasing application in the field of combinatorial chemistry. In the past few years, microreactor chemistry has shown great promise as a novel method on which to build new chemical technology and processes. It has been conclusively demonstrated that reactions performed within microreactors invariably generate relatively pure products in high yield. One of the immediate and obvious applications is therefore in combinatorial chemistry and drug discovery.     

Discovery of an Aurora kinase inhibitor through site-specific dynamic combinatorial chemistry

We demonstrate a fragment-based lead discovery method that combines site-directed ligand discovery with dynamic combinatorial chemistry. Our technique targets dynamic combinatorial screening to a specified region of a protein by using reversible disulfide chemistry. We have used this technology to rapidly identify inhibitors of the drug target Aurora A that span the purine-binding site and the adaptive pocket of the kinase. The binding mode of a noncovalent inhibitor has been further characterized through crystallography.     

Using NMR for ligand discovery and optimization

Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment-based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas.     

High-throughput protein crystallization

The combinatorial chemistry industry has made major advances in the handling and mixing of small volumes, and in the development of robust liquid-handling systems. In addition, developments have been made in the area of material handling for the high-throughput drug screening and combinatorial chemistry fields. Lastly, improvements in beamline optics at synchrotron sources have enabled the use of flash-frozen micron-sized (10-50 microm) crystals. The combination of these and other recent advances will make high-throughput protein crystallography possible. Further advances in high-throughput methods of protein crystallography will require application of the above developments and the accumulation of success/failure data in a more systematic manner. Major changes in crystallography technology will emerge based on the data collected by first-generation high-throughput systems.     

The chemical-biological interface: developments in automated and miniaturised screening technology

The rapidly changing developments in genomics and combinatorial chemistry, generating new drug targets and large numbers of compounds, have caused a revolution in high-throughput screening technologies. Key to this revolution has been the introduction of robotics and automation, together with new biological assay technologies (e.g., homogeneous time resolved fluorescence). With ever increasing workloads, together with economic and logistical constraints, miniaturisation is rapidly becoming essential for the future of high-throughput screening and combinatorial chemistry. This is evident from the introduction of high-density microtitre plates, small volume liquid handling robots and associated detection technology.     

Pharmacogenomics - it''s not just pharmacogenetics

New technologies in both combinatorial chemistry and combinatorial biology promise to unlock new opportunities for drug discovery and lead optimisation. Using such genome-based technologies to measure the dynamic properties of pharmacological systems, pharmacogenomics can now provide an objective measure of a drug's biological efficacy, including its potential adverse effects.     

Small molecule microarrays: recent advances and applications

Directed or exploratory drug development programs constantly seek robust screening platforms for the high fidelity identification and validation of potential targets. Small-molecule microarrays (SMMs) have risen to this call by elegantly forging the capability of combinatorial chemistry in producing myriad compounds with the powerful throughput afforded by microarrays. This synergism offers scientists a versatile tool for rapid compound analysis and discovery. Microarrays of small molecules have already been successfully applied in important areas ranging from protein profiling to the discovery of therapeutic leads. Recent interesting developments towards improved immobilization strategies and library creation methods, together with novel advances herein described, have set the stage for SMMs to take on wider and more routine applications in academia and industry. As a rapidly maturing technology, SMMs pave the way forward in high-throughput exploration, both in the identification of biologically significant natural and synthetic small molecules and in harnessing their vast potential towards medicinal and diagnostic applications.     

Structure-directed combinatorial library design

In recent years pharmaceutical companies have utilized structure-based drug design and combinatorial library design techniques to speed up their drug discovery efforts. Both approaches are routinely used in the lead discovery and lead optimization stages of the drug discovery process. Fragment-based drug design, a new power tool in the drug design toolbox, is also gaining acceptance across the pharmaceutical industry. This review will focus on the interplay between these three design techniques and recent developments in computational methodologies that enhance their integration. Examples of successful synergistic applications of these three techniques will be highlighted. Opinion regarding possible future directions of the field will be given.     

'One bead two compound libraries' for detecting chemical and biochemical conversions

When combinatorial chemistry was introduced 13 years ago, the expectations were high for the delivery of results, particularly in the pharmaceutical industry. However, combinatorial chemistry was implemented independently of the application for which the products were going to be used. Resins developed only for efficient solid-phase synthesis were used and products were employed in existing assays developed for traditional solution studies. There was almost no assay or technology development and the use of real combinatorial methods soon had to give way to high-throughput synthesis and traditional screening. However, during recent years more sophisticated resins and assay techniques have been developed that may result in a second and more successful implementation of real integrated combinatorial chemistry. The first in this line of new developments is the 'one bead two compound' assay, in which the resin bead in addition to a combinatorial library member contains a reporter compound that can act as a beacon to monitor the activity of the library member. This powerful concept can be generally applied in all fields of combinatorial chemistry including drug, catalysts and material development.     

Natural products: A continuing source of novel drug leads

Background

Nature has been a source of medicinal products for millennia, with many useful drugs developed from plant sources. Following discovery of the penicillins, drug discovery from microbial sources occurred and diving techniques in the 1970s opened the seas. Combinatorial chemistry (late 1980s), shifted the focus of drug discovery efforts from Nature to the laboratory bench.

Scope of Review

This review traces natural products drug discovery, outlining important drugs from natural sources that revolutionized treatment of serious diseases. It is clear Nature will continue to be a major source of new structural leads, and effective drug development depends on multidisciplinary collaborations.

Major Conclusions

The explosion of genetic information led not only to novel screens, but the genetic techniques permitted the implementation of combinatorial biosynthetic technology and genome mining. The knowledge gained has allowed unknown molecules to be identified. These novel bioactive structures can be optimized by using combinatorial chemistry generating new drug candidates for many diseases.

General Significance

The advent of genetic techniques that permitted the isolation / expression of biosynthetic cassettes from microbes may well be the new frontier for natural products lead discovery. It is now apparent that biodiversity may be much greater in those organisms. The numbers of potential species involved in the microbial world are many orders of magnitude greater than those of plants and multi-celled animals. Coupling these numbers to the number of currently unexpressed biosynthetic clusters now identified (> 10 per species) the potential of microbial diversity remains essentially untapped.     

Combinatorial biocatalysis: taking the lead from nature

Combinatorial biocatalysis is an emerging technology in the field of drug discovery. The biocatalytic approach to combinatorial chemistry uses enzymatic, chemoenzymatic, and microbial transformations to generate libraries from lead compounds. Important recent advances in combinatorial biocatalysis include iterative derivatization of small molecules and complex natural products, regioselectively controlled libraries, novel one-pot library syntheses, process automation, and biocatalyst enhancements.     

A solid-phase synthesis for beta-turn mimetics of sialyl Lewis X

A solid-phase synthesis of heterocyclic beta-turn mimetics of sialyl Lewis X, which is a natural carbohydrate ligand of selectins, was established. This synthetic method could be very useful for drug discovery of selectin antagonists using combinatorial chemistry techniques.     

The inverse problems for some topological indices in combinatorial chemistry.

In the original paper, Goldman et al. (2000) launched the study of the inverse problems in combinatorial chemistry, which is closely related to the design of combinatorial libraries for drug discovery. Following their ideas, we investigate four other topological indices, i.e., the sigma-index, the c-index, the Z-index, and the M(1)-index, with a special emphasis on the sigma-index. Like the Wiener index, these four indices are very popular in combinatorial chemistry and reflect many chemical and physical properties. We give algorithmic and analytical solutions for the inverse problems of the four indices. We also show that the SUBTREEVALUE reconstruction problem for the sigma-index is NP-hard.     

以生物合成为基础的代谢工程和组合生物合成

代谢工程和组合生物合成在筛选和发展新型药物方面日益成为生物、化学和医药界关注的重点。基于聚酮和聚肽类天然产物的独特化学结构和良好生物活性,研究它们的生物合成机制,将为合理化遗传修饰生物合成途径获得结构类似物提供遗传和生物化学的基础,实现利用现代生物学和化学的技术手段在微生物体内进行药物开发的目的。     

Fragment-based drug discovery of carbonic anhydrase II inhibitors by dynamic combinatorial chemistry utilizing alkene cross metathesis

A fragment-based drug discovery approach to the synthesis and identification of small molecule inhibitors of bovine carbonic anhydrase II (bCA II) is described. The classical bCA II recognition fragment is an aromatic sulfonamide (ArSO2NH2) moiety. This fragment was incorporated into a scaffold building block, which was subsequently derivatized by dynamic combinatorial chemistry utilizing alkene cross metathesis as the reversible reaction. Screening against bCA II was then carried out and the results allowed determination of the relative bCA II binding affinities of the cross metathesis products that contained the ArSO2NH2 fragment. A bCA II competitive binding assay validated these results with a representative number of pure compounds. The results for screening, without prior isolation of the active constituent, were in full agreement with those obtained for equilibrium dissociation constants (K(i)'s) of pure compounds. Some of these compounds exhibited K(i)'s in the low nanomolar range. Heterogeneous catalysis was shown to be very effective in this drug discovery application of dynamic combinatorial chemistry.     

Signaling protein networks as targets of new antineoplastic drugs

In-depth analysis of molecular regulatory networks in cancer holds the promise of improved knowledge of the pathophysiology of tumor cells so that it will become possible to design a detailed molecular tumor taxonomy. This knowledge will also offer new opportunities for the identification and validation of key molecular tumor targets to be exploited for novel therapeutic approaches. Some signaling proteins have already been identified as such, e.g. c-Myc, Cyclin D1, Bcl-XL, kinases and some nuclear receptors. This has led to the successful development of a few function-modulatory drugs (Glivec, SERM, Iressa), providing proof-of-principle of the validity of this approach. Further developments are likely to derive from "-omic" approaches, aimed at the understanding of signaling networks and of the mechanism of action of newfound lead molecules. High-throughput screening of small drug-like molecules from combinatorial chemical libraries or from microbial extracts will identify novel, "intelligent" drug candidates. An additional medicinal chemistry strategy (via 40-50 unit rosary-bead chains) has the potential to be much more effective than small molecules in interfering with protein-protein interactions. This may lead to considerably higher selectivity and effectiveness compared with historical approaches in drug discovery.     

Parallel solid-phase synthesis of nucleoside phosphoramidate libraries

Combinatorial chemistry is playing an increasingly prominent role in the process of drug discovery. A nucleic acid-based (NAB) scaffold can be engineered to create functional group and topological diversity in a library. Described herein is the parallel solid-phase synthesis of combinatorial libraries of nucleoside phosphoramidates, and the first evaluation of antiviral activity against hepatitis B virus (HBV).     

Fragonomics: fragment-based drug discovery

The use of smaller molecules (fragments) in the drug discovery process has led to success in delivering novel leads for many different targets. This process is a highly integrated process, starting from library design to screening and medicinal chemistry. An overview of this process is presented with particular emphasis placed on the NMR aspect of screening.     

Innovative approaches to novel antibacterial drug discovery

Increasing antibiotic resistance in microorganisms and new emerging pathogens have become a major problem in our society. Rising to satisfy this urgent medical need is a recent confluence of powerful new drug discovery technologies: combinatorial chemistry; sequence and functional genomic analysis; and novel methods of high-throughput screening. The combination of these technologies will bring to bear untapped power in the search for new antimicrobials.