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High-Throughput Chemistry-Alleviating Bottlenecks in Drug Lead Generation
(source: Drug & Market Development Publications Feb 1999)


  • Combinatorial chemistry methodology can produce massive libraries of compounds, but may do little to alleviate major bottlenecks in drug discovery programs requiring more focused and rationally driven chemical synthesis for lead optimization. Alternative approaches that enhance the throughput of compound library generation, but provide more control over compound synthesis, are becoming increasingly competitive and cost effective.
  • A successful development candidate must have suitable pharmacokinetics and an acceptable safety profile and, traditionally, these properties are defined by low through-put in vivo testing far downstream of the initial in vitro drug lead identification process. Novel approaches are now being implemented to alleviate this bottleneck by high-throug-hput in vitro compound analysis.
  • This article focuses on selected new approaches to com-pound synthesis and analysis (termed here "high-through-put chemistry"), with the goal of anticipating the role such approaches may play in the near future and pre-dicting their long-term impact in the drug dis-covery process.
  • ArQule (Medford, MA), whose technology hybridizes combinatorial chemistry with high-throughput parallel synthesis, analysis and purification, is one of the firms reviewed in this article. Such "first tier" combinatorial chemistry companies are encountering competition from the internal combichem efforts within large pharma-ceutical companies, contract research organi-zations (CROs), and purveyors of instrumentation and devices for high-speed parallel synthesis (e.g. Argonaut and IRORI, also reviewed here).
  • This article was written by Stan M. Goldin, Ph.D., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and President, Goldin R&D Group. Phone: 617-861-9431. Email:

Introduction and Overview

Even with modern advances in combinatorial chemistry and pharmacogenomics in the 1990s, the drug discovery process resembles—in its basic format—the traditional approach developed and refined in earlier decades. Drug discovery strategies still typically involve the following sequence of steps: (a) identification and validation of a drug target; (b) generation or acquisition of compound libraries; (c) development of screening assays; (d) the compound screening process; (e) drug lead identification; and (f) drug lead optimization. Step (a) has been enhanced by advances in genomics and new information on the molecular mechanisms responsible for disease, which together have generated a proliferation of new drug targets (cf D&MD 9:37; D&MD 9:64; D&MD 9:338). Step (b) has been impacted, if not revolutionized, by combinatorial chemistry technologies, which are now capable of gener-ating libraries of millions of compounds (cf D&MD 9:155). Novel high-throughput screening (HTS) strategies are greatly accelerating the primary stages of the drug screening process [steps (c) & (d), cf D&MD 9:89; D&MD 9:119]. Steps (e) and (f) commonly comprise the biggest bottlenecks in the drug discovery process. In addition to its primary biological activity (potency and specificity for its drug target), a suitable drug development candidate must have appropriate physical properties (e.g. solubility and cell membrane permeability), pharmacokinetics and toxi-cology. In most cases, these downstream steps still entail the use of conventional "low-throughput" medicinal chemistry to synthesize compounds with the desired properties. This is typically coupled with low-throughput in vivo char-acterization of the development candidate’s pharmacology and toxicology.

Labor-intensive in vivo pharmacology is, arguably, unavoidable in the final stages of development candidate selection. But, even in the face of convincing animal data, projects not uncommonly fail because the efficacy, pharma-cokinetics or toxicity of a compound in humans funda-mentally differs from that predicted by animal models (such frustrations are exemplified by recent failures in stroke drug development, to be discussed in a D&MD article next month). A recent survey found that about 33% of failures of drugs during clinical development are due to inappropriate pharmacokinetics (Monro, A.M., 1997 in "Use of Human In Vitro Systems to Support Preclinical and Clinical Safety Assessment", Tyckgruppen Press, Sweden). Many would agree that there is no substitute, at present, for the skill and intuition of medicinal chemists, but there is nonetheless a great need for more efficient methodology and tools to translate a medicinal chemist’s expertise into new compounds for lead optimization.

A case can also be made for application of high-through-put medicinal chemistry at an earlier stage of the drug discovery process [step (b)]. It is increasingly appre-ciated that in certain cases, the subtleties of drug-target inter-actions necessitate detailed mechanistic studies of such interactions as soon as possible in the screening process. Salient examples are drug leads which are ion channel modulators and/or ligands for G protein-coupled receptors. What is needed in such cases is a "movie" of the pharma-codynamics of drug-target interactions (such as now affor-ded by conventional labor-intensive electro-physiology), rather than a "snapshot" provided by conventional HTS ligand-receptor binding assays. To appreciate the current status and future prospects of "high-throughput chemistry", this article presents both an overview of recent develop-ments and a more intensive discussion of the three follow-ing firms:

• ArQule, a combinatorial chemistry-focused firm which is broadening its technology platform to include high- throughput parallel synthesis and chemical analysis.

• Argonaut (San Carlos, CA ), a leading designer and vendor of "turnkey" systems for automated parallel synthesis.

• IRORI (La Jolla, CA), which has developed flexible technology that incorporates features of both parallel synthesis and conventional "split-and-pool" combina-torial chemistry.

Table 14 highlights selected novel approaches to high- throughput compound synthesis. As shown, significant technological innovations are arising within large pharma-ceutical firms, as well as within smaller technology plat-form companies. Table 15 highlights selected novel ap-proaches to high-throughput compound analysis and/or purification. Again, a trend towards internal technology development within big pharma is apparent, and this com-petition has implications for the future of smaller tech-nology and instrumentation companies, the more visible source of such innovations.

Combinatorial Chemistry Firms in Transition: Focus on Arqule

Founded in 1993 by Joseph C. Hogan, Jr., Ph.D., and partners, ArQule rapidly rose over the next several years to the front ranks of combinatorial chemistry firms, achieving a valuation of over ~$300 million by 1997 (stock price approaching $30/share). ArQule’s pharma-ceutical and bio-technology collaborators number about 30, and include Roche Biosciences (Palo Alto, CA), Abbott Laboratories (Abbot Park, IL) and American Home Products (Madison, NJ). ArQule also has joint programs for lead generation and optimization with a number of biotechnology companies including Aurora Biosciences (San Diego, CA; mammalian cell-based assays), Cadus Pharmaceuticals (Tarrytown, NY; signal transduction), Cubist Pharmaceuticals (Cambridge, MA; infectious dis-eases), ICAgen (Durham, NC; ion chan-nel targets), Scriptgen (Medford, MA; RNA/protein inter-actions), Signal Pharmaceuticals (San Diego, CA; gene tran-scrip-tion/transcription factors), SUGEN (South San Francisco, CA; signal transduction), T Cell Sciences [Need-ham, MA (now Avant Immunotherapeutics); T cell acti-vation/inhibition] and, most recently (October ‘98), Ge-nome Therapeutics (Waltham, MA) in the area of infec-tious disease. ArQule provides its collaborative part-ners with two types of synthetic compound libraries:

• Mapping Array libraries, which are diverse arrays of novel, discrete small molecule compounds used for screening against biological targets. Participation in ArQule’s Mapping Array Program generally entails a multi-year subscription to a group of compound libraries which are designed around certain core structures or themes selected by ArQule. ArQule has typically pro-vided 15 to 20 Mapping Array compound sets, which in aggregate total at least 100,000 compounds. Subscribers to this program are not restricted to the targets the compounds may be screened against.

• Directed Array libraries, which are arrays of analogs of a particular lead compound synthesized for lead optimi-zation, typically with exclusivity to the colla-borator. Beginning either with a collaborator’s own lead com-pound or with active compounds from the afore-mentioned Mapping Array Program, the Directed Array Program’s objective is to optimize desired compound properties, by an iterative process. It is this program in particular that heavily draws on ArQule’s capability in parallel synthesis.

ArQule’s technology platform comprises modular building block strategies for combinatorial synthesis, structure-guided design, information technology and, not-ably, an Automated Molecular Assembly Plant parallel synthesis system ("AMAP"), using modular robotic work-stations, linked via a computer network. According to company sources, AMAP is capable of synthesizing, purify-ing and analyzing thousands of novel compounds in milli-gram quantities using either solution or solid phase chemi-stries (cf 1998 US Patents #5,736,412 & 5,712,171). AMAP also verifies structural data throughout the synthesis process. Compound structures are analyzed by flow injection mass spectrometry and purity is determined by HPLC coupled with UV and light scattering measurements (cf Goetzinger, W.K., and Kyranos, J.N., American Laboratory, April 1998:42). AMAP’s compound management system is designed to facilitate both the introduction of the resulting compound arrays into collaborators’ own screening assays and the identification of biologically active compounds. A computer tracking system identifies the compound in each microtiter well and characterizes its composition, structure and synthesis.

ArQule’s technology platform has not yet resulted in the commercialization of a product. This, arguably, is not sur-prising for a firm this young, considering the time frame required for drug development. Nonetheless, the sub-stantial deterioration in ArQule’s stock price in the past year (from a high of 25.5 early in 1998 to a December price of 5.0) appa-rently reflects unfulfilled investor expectations (see Table 16 for stock price history of selected combi-chem firms).

Although this comes at a time when the technology-rich NASDAQ is reaching record high levels, other esta-blished combinatorial chemistry firms [e.g. Pharmacopeia (Prince-ton, NJ) and CombiChem (San Diego, CA)] have shared the same fate, as Table 16 illustrates. The erosion in stock price is not as extreme as for certain "fully integrated drug discovery" companies whose flagship drugs have recently failed in clinical trials (the two cases shown in Table 16 are Cambridge NeuroScience and CoCensys, each of whom had NMDA antagonists for stroke that fell out of the clinic—the ion channel blocker Cerestat and the gly-cine site antagonist ACEA 1021, respectively). On the other hand, despite the skittishness of biotech investors this year, such bad news is not characteristic of all technology platform-focused bio-tech firms that came of age in the 1990s. For example, InCyte Pharmaceuticals (Palo Alto, CA), a genomics/bio-inform-atics leader, and Sepracor (Marlborough, MA), whose tech-nology centers around developing biologically active isomers of previously successful drugs (such as Pfizer’s Pro-zac®, soon to go off patent), have enjoyed considerable finan--cial success.

Several factors may account for the lackluster perfor-mance of most combichem firms of late, including:

• Commoditization of combinatorial chemistry. Several CROs, among them MDS Panlabs (Bothell, WA) and Medi-Chem Research (Lemont, IL), offer combichem on a fee-for-service basis, with little or no expectation of down-stream royalties.

• Development by big pharmaceutical companies of internal expertise in combichem and other areas of high throughput chemistry, e.g. Glaxo-Wellcome (London, UK), Merck & Co. (Whitehouse, NJ) and Bristol-Myers Squibb (Prince-ton, NJ).

• Failure of combinatorial chemistry firms to deliver pro-mising development candidates as rapidly as investors had expected. How many combinatorially designed com-pounds have made it into advanced clinical develop-ment so far? Very few.

In the specific case of ArQule, its ongoing transition from a supplier of molecules for drug discovery to a drug discovery company with a more fully integrated internal technology platform may also have fed investor uncer-tainty, as have the recent resignations of two key exe-cutives. The founding CEO Eric Gordon resigned in July 1998; according to company sources, its Board of Direct-ors (including Mr. Gordon), voted to look for a new CEO with "...extensive experience in leading large-scale drug discovery activities." Recently (November 1998), Dr. David L. Coffen, Senior Vice President of Chemistry, also announced his resignation. However, it is reasonable to suggest that ArQule’s short-term financial difficulties and personnel changes may result from strategic decisions that will pay off in the long run. Last summer, the company began construction of a new 130,000-square-foot head-quarters and R&D facility in Woburn, MA which will double ArQule’s current space, affording room for an additional 100 employees. In addition, ArQule’s revenues from its expanding base of collaborators have increased substantially. For the nine months ending September 30, 1998, revenues were $16,283,000, up 45% from revenues of $11,227,000 in the first nine months of 1997. ArQule’s larger capital loss of $3,850,000, or ($0.32) per share, compared to a net loss of $427,000, or ($0.04) per share, for the same period last year; the increased losses resulted primarily from increased expenditure for its expansion into new chemistry-based drug discovery technologies. Vital qualities for a new CEO include a strong scientific background along with substantial experience in drug discovery, as is what characterizes ArQule’s most recently appointed directors, Patrick Gage (Wyeth-Ayerst Research’s President) and Dr. Michael Rosenblatt (formerly of Merck & Co; Rahway, NJ).

Argonaut Technologies’ Parallel Synthesis Machinery

In addition to CROs offering combichem on a contract basis, firms such as ArQule are facing another dimension of competition from companies offering off-the-shelf instru-mentation and technical support services for high- throughput compound library generation. This business strategy, implemented by firms such as privately held Argonaut (San Carlos, CA), is more analogous to the way in which a provider would interact with the purchaser of a large piece of analytical instrumentation, such as a high-end NMR machine. Argonaut’s first product, the Nautilus (current embodiment, the Nautilus 2400) enables totally automated organic synthesis of up to 24 compounds in parallel, in either solution- or solid-phase. Argonaut claims that, "...the Nautilus offers the flexibility to synthesize small molecules using a broad range of chem-istries. The only limit is your imagination." How-ever, the major current concern of users of the machine is that its design, while affording efficiency increases for some synthetic strategies, may have more limited applicability for certain other classes of chemical synthesis. Argonaut has been receptive to feedback from its current con-sortium of customers, and its products are continually evol-ving to obviate these concerns. For example, Argo-naut recently introduced five new reaction vessels for the Nautilus, designed to enhance the machine’s versatility for lead optimization.

Argonaut’s newest product, introduced last Fall, is the "Trident" Automated Library Synthesizer. Trident is de-signed for the production of focused libraries, usually made after primary screening steps (analogous to the step for which ArQule’s Directed Array Program is applied). Tri-dent is capable of parallel synthesis of up to 192 com-pounds per run in an inert environment, preventing un-wanted side reactions. It affords automated control of the key synthetic parameters, including solvent and reagent delivery, temperature control, agitation, rinsing and wash-ing, product cleavage and compound collection. Tri-dent was conceived as the result of a consortium between Argo-naut and the following group of pharmaceutical com-panies, which designated their own scientists to work as a team with Argonaut:

  • Abbott Laboratories
  • Ariad Pharmaceuticals
  • Astra AB
  • DuPont
  • Genetics Institute
  • Merck & Co.
  • Merck KgAA
  • Rhône-Poulenc Rorer
  • Sumitomo

According to David Binkley, Argonaut’s president and CEO, "Input from the consortium was invaluable in designing a flexible system that supports the way chemists work." Mark A. Scialdone, Ph.D., principal investigator in the combinatorial chemistry group at DuPont Central Research & Development (Wilmington, DE), one of the consortium members, stated, "We often perform complex reactions and need the control over reagent delivery and reaction conditions that Trident delivers."

IRORI’s Proprietary Approach to Parallel Synthesis: RF Coding and Directed Sorting Of Individual Reactors

IRORI (La Jolla, CA), a privately held company of ~80 employees founded in 1995, exemplifies a promising new breed of high-throughput chemistry company. IRORI’s initial focus has been the application of proprietary memory devices [e.g., radio frequency (RF) tags and two-dimensional optical bar codes] in microreactor chambers to facilitate the design, creation and management of chemical libraries produced by parallel synthesis (see Figure 2). IRORI’s "Microreactors" are miniaturized devices that contain both a functionalized solid phase support and a unique tag identifier, and can accommodate the synthesis of discrete compounds in quantities of up to 100 mg. By splitting and pooling microreactors using a process known as "directed sorting," one discrete compound can be synthesized in each microreactor, giving the chemist the ability to generate and manage large compound libraries simultaneously. As an indication of the growing acceptance of IRORI’s tech-nology, one of Argonaut’s new parallel synthesis machines (the Quest 205) is designed expressly to provide compat-ibility with IRORI’s disposable microreactors.

In 1998, Irori introduced a family of supporting products, software and automation, including the following:

• Synthesis Manager. A software package that controls the "directed sorting" library synthesis approach. It also serves as a database for chemical building blocks, react-ion intermediates and reaction procedures.

• The AutoSort™-10K Microreactor Sorting System. Typical library sizes of discrete compounds practicable by the IRORI technique are under a thousand compounds, if sorted manually. The AutoSort-10K automates the reaction and cleavage sorting operations, accommodates up to 10,000 microreactors at a sorting rate of 1,000 reactors/hour, and thus enables a capability for generation of larger compound libraries (³10,000 compounds).

• AccuCleave-96 Cleavage Station for simultaneous cleaving of 96 compounds from the solid polymer supports within the microreactor, and transfer of the cleaved products to standard 96-well microplate format.

Concluding Remarks and Prognostications

An exciting development may evolve from early indications that an "industry standard" could be emerging for parallel chemical synthesis technology. A case in point: IRORI microreactors, containing the coding devices to manage and track nearly any type of chemical synthesis, may conceivably become the preferred vehicle for managing chemical synthesis (i.e. what the VHS format is to current video recording standards). Innovative firms such as IRORI—and firms with synergistic technology such as Argonaut—may work coopera-tively with big pharma-ceutical firms (and with one another) in future consortium arrangements to evolve increasingly sophisticated and "user friendly," "massively parallel" high-throughput chemical synthesis systems. The ultimate goal of such high-throughput chemistry systems is the synthesis of compounds free of the practical constraints now encountered when a first class medicinal chemist confronts current embodi-ments of combinatorial chemistry or parallel synthesis tech-nology. It is at that point that the early stages of high- throughput screening will increasingly benefit from the traditional expertise of the medicinal chemist, and the process of lead optimi-zation will be enhanced far beyond its current capabilities. Extrapolation of current developments and trends suggests that this might occur very early in the new millennium.

Other developments, summarized in Table 15, suggest that new technologies may soon profoundly impact other major bottlenecks in lead optimization; that is, creation of development candidates with the most desirable human pharmacokinetic and toxicological properties. A forthcoming D&MD article will focus on recent developments and future trends in this arena.

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