An automated synthesis programme for drug discovery Automation has revolutionised the way that organic synthesis is performed in the research laboratory. Dr James Harness, Bohdan Automation Inc Combinatorial chemistry has rapidly become the method of choice for new compound discovery activities in a variety of industries. Companies in the pharmaceutical, chemical and - most recently - the materials science industries have now accepted combinatorial chemistry as their fundamental approach to new compound discovery. The change to a new discovery philosophy in these industries has also included considerable change in the way that organic synthesis is performed in the research laboratory. Today, these companies are employing high-throughput organic synthesis as their primary mechanism for preparing new compounds. This has made them rely heavily on automation for their synthesis efforts, and also incorporate automation as a major support requirement for their synthesis activities. This demand for automated equipment has spurred growth of the automation industry in the area of compound synthesis and marked the development of numerous automated synthesisers and synthesis-related devices. The automation of organic or medicinal chemistry in the pharmaceutical laboratory has evolved considerably over the past five years. Most of the early automated synthesisers were designed to support the performance of high-throughput, solid-phase synthesis. Solid-phase synthesis was deemed to be the method of choice because the chemistry could be controlled more exactly and the products of the synthesis were much more readily recoverable in a pure form. Unfortunately, the science of solid-phase chemistry was not sufficiently developed to handle the spectrum of chemistries required to support a complete medicinal chemistry programme. Therefore, after an initial peak in interest in solid-phase synthesisers, the industry returned to the fundamentals of solutionphase synthesis. At this point, the chemistry laboratory began to incorporate more solutionphase synthesisers into the discovery process, and also to restructure the laboratory in a more automation-based configuration. This change helped to stabilise the chemistry performed on the automated equipment, but it did little to address the needs of the many bench chemists in medicinal Figure 1. Automated high-throughput drug discovery groups. Today... companies are employing high-throughput organic synthesis as their primary mechanism for preparing new compounds Innovations in Pharmaceutical Technology 37
... solutionphase synthesis continues to be the primary synthetic activity adopted throughout the pharmaceutical industry chemistry laboratories. In order to expand the utilisation of automated devices by the bench chemist, smaller less complicated devices had to be developed. This led to the incorporation of personal synthesisers into the chemistry laboratory, resulting in the general structure of the chemistry laboratory as it exists today. Details of the automation developments that have occurred over the last several years, and the logic surrounding the implementation of this automation in the chemistry laboratory, will be discussed in this article. High-throughput drug discovery High-throughput drug discovery has evolved into three primary automated discovery groups (Figure 1): automated organic synthesis, biological screening and chemical analysis. Automation of these three groups individually, and automation of the interaction between these groups, has evolved into the high-throughput discovery capability known today. This evolution began with advances in biological testing that permitted the development of high-throughput in vitro testing scenarios. As high-throughput screening advanced in the drug discovery area, the need to synthesise compounds at a faster rate became a limiting factor. This led to automation of the organic synthesis process, and ultimately to the automation of chemical analysis to support the synthesis effort. The automation of organic synthesis and the implementation of this automation in the medicinal chemistry laboratory have proven to be a very difficult venture. Changes in the organic or medicinal chemistry laboratory in recent years have included not only automation but also advances in the area of solid-phase synthesis. Solid-phase synthesis techniques have become very popular for generating libraries, in that the chemistry can be driven to completion and product can be recovered more easily in pure form. Despite the advantages of solid-phase synthesis, solution-phase synthesis continues to be the primary synthetic activity adopted throughout the pharmaceutical industry. Figure 2 shows the synthesis groups that have developed recently in the medicinal chemistry field. As already mentioned, solution-phase synthesis continues to be the primary technique utilised to develop new chemistry methods and also to generate specific library types. Solutionphase chemistry techniques are then adapted to solid phase and used in a higher throughput mode to generate larger libraries of compounds. Both solution-phase and solid-phase chemistries are adapted to automated devices in order to prepare large numbers of compounds in a higher throughput synthesis mode. This has led to the inclusion of an automated chemistry development group in the medicinal chemistry area. Figure 2. Figure 3. Automated organic chemistry. Synthesis capability requirements. The types of chemistries to be performed, the reaction conditions for these chemistries and the throughput requirements for these activities are all considerations that must be addressed by the automated chemistry development group (Figure 3). These considerations will determine the type of automated device that can be used for synthesising the desired compounds. As shown in the figure, solution-phase chemistry techniques generally require an automated device with full synthesis capabilities. This means an automated synthesiser with a broad spectrum of capabilities for temperature, pressure, material-handling, mixing and chemical resistance. These synthesis capabilities are necessary because a full spectrum of chemical reactions will typically be run on the solution-phase synthesiser. In general, however, solution-phase techniques are not often used for generating large libraries of compounds, and so high-throughput or high capacity is not a major consideration. For developmental, diversity or parallel synthesis activities, solution-phase synthesis is typically performed on a limited number of reactions per run. By contrast, solid-phase synthesis is most commonly used to generate a large number of molecules in a very pure form. The automated equipment used for solid-phase synthesisers thus needs to be directed more at high throughput than full synthesis capability. 38 Innovations in Pharmaceutical Technology
Figure 4. Table 1. Solution-phase synthesis equipment From an automation perspective, there are five fundamental steps involved in the process of solution-phase synthesis; these include reagent preparation, reagent mapping, the solution-phase reaction itself, quenching or stopping the reaction, and reaction clean-ups such as liquid/liquid or solid-phase extraction. Performing all of these synthesis-related steps on a single automated workstation offers the advantage of reducing equipment costs and saving on laboratory space, but means that the overall throughput of the equipment will be limited. The reason that Automated Neptune Synthesiser. Chemistry capabilities for Neptune and Ram. throughput is compromised in this way is because the workstation has many functions to undertake and must thus spend portions of its time performing these different operations. As a result, throughput can be no more than 150 to 250 compounds per week; fortunately, however, these levels of throughput are generally sufficient for most solution-phase synthesis programmes. An example of a solution-phase synthesis workstation that can support all the steps in solution-phase chemistry is shown in Figure 4. The Neptune Workstation consists of a robotic chassis that holds a balance, a vortex mixer, a variety of racks and the RAM Synthesiser reaction block (1). Grippers are provided on the robotic arm to permit pick-and-place movement of vials and other containers to the balance and vortex mixer. The arm also contains a liquid-handling system that consists of two septum-piercing, argon-purging, vented cannulas. The dual cannula system is designed to segregate reagent-handling for aqueous reagents and dry solvents, as well as to provide flexibility to support up to 12 different solution reservoirs. Reaction block capabilities include 48 reaction vessels that can be argon-purged, pressurised to two atmospheres, evacuated using vacuum and heated/cooled over a range from - 40 o C to 150 o C. Reaction mixtures can be stirred independently using magnetic stir bars on the workstation, or simultaneously in an orbital shaker off the workstation. Removing the reaction block from the workstation during the incubation permits simultaneous use of the workstation to perform other synthesis-related tasks. Table 1 shows some commonly performed reactions that are readily supported by the equipment on the Neptune Workstation. Solid-phase synthesis equipment The seven primary steps associated with solid-phase synthesis include reagent preparation, resin loading, resin swelling, reagent mapping, the solid-phase reaction itself, resin washing and compound cleavage. Automating solid-phase synthesis techniques in a workstation format usually involves using a series of workstations that are each dedicated to the performance of specific functions in the synthesis protocol. This is done to provide the high throughput that is usually required with solid-phase synthesis programmes. By having the individual workstations performing activities simultaneously, very high-throughput set-ups can be established. The primary consideration that must be addressed during the development phase for a series of workstations is the synthesis workstation itself. The capabilities and characteristics of the synthesis workstation will determine the required components needed for both the upstream and 40 Innovations in Pharmaceutical Technology
Figure 5. Solid phase reaction block and orbital shaker. Figure 6. Automated solid-phase synthesis workstation. downstream activities. This workstation will also determine the types of chemistries that can be performed and the overall flexibility of the entire set-up. For this reason, the selection of the synthesis workstation must be handled first and given the most consideration. Also, since a single-synthesis workstation cannot handle all activities - such as chemistry development, rehearsal chemistry and high-throughput library generation - consideration must be given to how all these components will fit together in the final equipment assembly. Along this line, there are several scenarios that can be considered. There are two fundamentally different automation approaches that can be taken to achieve the same objective - that objective being to use a single automated synthesis format and accommodate all synthesis considerations. In other words, with a single reaction vessel and reaction block format, the aim is to establish the capability to handle chemistry development, rehearsal chemistry, diversity synthesis and high-throughput parallel synthesis. The two approaches are: first, to utilise a portable reaction block design that can be manually transferred from workstation to workstation to accomplish all aspects of synthesis and synthesis support; and second, to utilise a reaction block design that can be automatically transferred from work area to work area. The first approach uses a reaction block design, as shown in Figure 5; this is capable of performing solid-phase synthesis at temperatures from the -40 o C to 150 o C at ambient pressure or pressures up to two atmospheres. The block incorporates glass reaction vessels and bottom filtration to support high-throughput washing and cleavage/collection of synthesised materials. The manually transportable block is simply moved from workstation to workstation to accomplish all required activities. The synthesis workstation for this particular block design is shown in Figure 6, and supports reaction mapping for virtually all reaction types and high-speed resin-washing for clean-up between reaction steps (2). The second, and more fully automated, approach has been designed to include two primary components. The first is a personal synthesiser that can be used for both chemistry development, small library synthesis and rehearsal chemistry for large library synthesis; the second is a fully automated synthesis/synthesis support 42 Innovations in Pharmaceutical Technology
Figure 7. By having the individual workstations performing activities simultaneously, very high-throughput set-ups can be established Myriad Personal Synthesiser. device that uses the same vessels and racks as the personal synthesiser, and performs all the required functions for continuous library preparation. The personal synthesiser, as shown in Figure 7, utilises a uniquely designed reaction vessel that not only supports solid-phase synthesis techniques but also supports solution-phase chemistry. The workstation has the unique feature of employing chemicallyresistant pipette tips to handle reagent transfers; these tips are positive displacement tips that can handle reagent slurries. Also, the reagent vials and reaction vessels have specially designed caps that allow these tips to access the containers and still maintain an inert environment. The core synthesis system (Figure 8) uses the same technological advances as the personal synthesiser but incorporates them in a fully automated synthesiser. Because both devices utilise the same basic technology and design components, use of the personal synthesiser as a chemistry development/rehearsal chemistry synthesiser is an ideal technique transfer situation. Solid-phase chemistry programmes that do not involve extremely brutal chemistries for compound generation have the option of incorporating a less complicated and less expensive approach to library generation. This approach utilises a more manual and less cumbersome reaction block. Figure 9 shows the MiniBlock a synthesiser that was designed specifically for this purpose (3,4). This reaction block design incorporates two 48-position reaction blocks that can be collected into a single 96-well microtitre plate. The reaction blocks include a valve body that closes all 96 vessels simultaneously and permits transport of the blocks from one support device to another. The reaction vessels are made of polypropylene and can be uniformly heated from -10 o C to 100 o C using an aluminium manifold. Mixing is accomplished on an orbital shaker, and a variety of other support devices are available to assist with resin washing, inert environment generation and solid-phase extraction. The blocks are also specifically designed to fit on a variety of different liquidhandling devices so that mapping can be performed with automation support. This permits the build-up of an automation capability in a more conservative and less expensive way. The simplicity of the blocks also helps chemists adapt more readily to this different style of synthetic chemistry. Conclusion The pharmaceutical industry is rapidly adopting the practice of automating synthetic activities in the medicinal chemistry laboratory to support high-throughput new compound development. This practice has become necessary as techniques such as high-throughput screening have evolved and created a need for more compounds at a faster rate. Incorporation of automation into the synthesis laboratory has caused substantial change in the structure and function of the chemistry group. These changes include the addition of groups such as the automated chemistry development group, along with a more focused use of solid-phase synthesis techniques. The automation technology that has been developed to support a high-throughput synthesis has also changed considerably over the past several years. Figure 8. Myriad Core Synthesis System. 44 Innovations in Pharmaceutical Technology
Figure 9. MiniBlock Synthesiser. Equipment is now available that can be used on a more manual basis, as well as equipment that can perform virtually all aspects of the synthesis process. Specific pieces of equipment have also been designed to support the unique activities that go on in the different medicinal chemistry laboratories. Combined, these permit the industry to automate as much of the organic synthesis process as desired. Dr James Harness has been Chief Scientist at Bohdan for over seven years. He has 23 years industrial experience in the life sciences area with ten years direct experience of automating a wide variety of laboratory processes. For the past five years, Dr Harness has focused primarily on the automation of organic synthesis for combinatorial chemistry and related activities in the US, Europe and Japan. Under his technical direction, Bohdan has patents issued for synthesisers to perform synthesis activities for solution- and solid-phase combinatorial chemistry, process research and development, and new materials discovery. Trademarks RAM Synthesizer is a registered trademark of PathoGenesis Corporation. MiniBlock is a registered trademark of Bohdan Automation Inc. Neptune is a registered trademark of Bohdan Automation Inc. References 1. Ahrweiler PM et al. (1997). American Laboratory, October Issue. 2. Goodman BA, Bjergarde K, Boymel JL (1997). Am Biotech Lab 15 (5), 60-62. 3. Weller H (1999). Proceedings Lab Automation 99. 4. Brase S, Dahmen D, Heuts J (1999). Tetrahedron Letters, 40, 6201-6203. Incorporation of automation into the synthesis laboratory has caused substantial change in the structure and function of the chemistry group Innovations in Pharmaceutical Technology 45