ScienceWeek

PHARMACOLOGY: SMALL MOLECULES AND NEW DRUG DESIGN

The following points are made by C. Lipinski and A. Hopkins (Nature 2004 432:855):

1) The relationship between chemistry, biology, and medicine has been remarkably productive over the past century, since Paul Ehrlich (1854-1915) pioneered the idea of systematically searching for drugs. By screening just over 600 synthetic compounds, Ehrlich discovered arsphenamine (Salvarsan)[1], which greatly improved the treatment of syphilis. Researchers now routinely screen millions of compounds in the search for some that are biologically active. Yet even the compound files of the largest pharmaceutical companies (which typically contain approximately 10^(6) compounds) offer only a cursory examination of all the possible organic compounds that comprise "chemical space". Chemical space is for all practical purposes infinite and limited only by the chemist's imagination.

2) Not all biologically active compounds have the desired physicochemical properties to be a drug. A biologically active compound may be too lipophilic (greasy) to be orally absorbed, too polar to cross the gastrointestinal wall, or may have too much vulnerable chemical functionality that can be attacked by metabolizing systems in the liver, and therefore not remain intact long enough to have a useful in vivo effect. Recently, toxicity has replaced poor drug metabolism properties as a major cause of failure in the early clinical phase of drug discovery.

3) The determination of the characteristics of compounds that are more likely to yield safe, orally bioavailable medicines has led to the concept of "drug-likeness". Compounds that are drug-like have the potential to be developed into orally administered drugs[2], which are generally favored owing to their ease of use by patients. But biologically active compounds that do not have the exacting properties required of a drug can nevertheless be extremely useful to science as "tools" for dissecting biological mechanisms and testing hypotheses in model systems. In recent years, it has been argued that it would be useful to discover a chemical tool to modulate every known protein[3]. Indeed, the Molecular Libraries Screening Center Network that is being established as part of the recent National Institutes of Health (NIH) Roadmap is aiming to facilitate the discovery of new chemical tools to understand biology, some of which may aid future drug development[4]. This Roadmap will allow the public sector to obtain data from high-throughput screens of a large collection of compounds (initially about 500,000 compounds) in various biological assays.

4) Before the molecular biology revolution, the tools of the pharmacologist were usually the only ones available for probing the behavior of biological systems. The pharmacologist's tools were mostly chemicals, derived from natural sources or from chemical synthesis. Perturbations of biological systems using such tools, some of which led to the development of drugs, taught us much about biology. For example, the natural product staurosporine -- used as an early tool to probe the effects of tyrosine kinase inhibition -- was important in the discovery of the anticancer drug imatinib (Gleevec), an inhibitor of the BCR-ABL tyrosine kinase.

5) However, the discovery of a new pharmacological tool was, and still is, a relatively rare and somewhat serendipitous event. At the core of efforts to discover small molecules of biological interest is typically some form of biological screen, in which a collection of compounds (known as a library) is assayed for a particular biological activity. In the early era of pharmacology, the compounds were often derived from natural sources, and the assays were for effects such as anti-bacterial activity or anti-inflammatory activity, usually using in vivo primary screens. More recently, with the molecular biology revolution, screening against isolated macromolecular targets has become widespread, and the compounds screened are often purely synthetic products from combinatorial chemistry (an approach for creating molecules en masse) as opposed to natural products[5]. Indeed, since the publication of the first paper to describe the synthesis of a single combinatorial library in 1992, there has been a considerable increase in the numbers of combinatorial-chemistry compounds being developed for high-throughput screening experiments.

References (abridged):

1. Sneader, W. Drug Prototypes and their Exploitation (Wiley, London, 1996)

2. Lipinski, C. A., Lombardo, F., Dominy, B. W. & Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23, 3-25 (1997)

3. Schreiber, S. L. Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem. 6, 1127-1152 (1998)

4. Austin, C. P., Brady, L. S., Insel, T. R. & Collins, F. S.NIH molecular libraries initiative Science 306, 1138-1139 (2004)

5. Bleicher, K. H., Bohm, H. J., Muller, K. & Alanine, A. I. Hit and lead generation: beyond high-throughput screening. Nature Rev. Drug Discov. 2, 369-378 (2003)

Nature http://www.nature.com/nature

--------------------------------

Related Material:

BIOCHEMISTRY: PROTEIN KINASE IHHIBITORS AND DRUG DESIGN

The term "protein kinases" refers to a group of enzymes that phosphorylate one or more hydroxyl or phenolic groups in proteins, with ATP as the phosphoryl group donor.

The following points are made by M.E. Noble et al (Science 2004 303:1800):

1) A number of diseases, including cancer, diabetes, and inflammation, are linked to perturbation of protein kinase mediated cell signaling pathways. The human genome encodes some 518 protein kinases (1) that share a catalytic domain conserved in sequence and structure but which are notably different in how their catalysis is regulated. The ATP-binding pocket is between the two lobes of the kinase. This site, together with less conserved surrounding pockets, has been the focus of inhibitor design that has exploited differences in kinase structure and pliability in order to achieve selectivity. Drugs are in clinical trials that target all stages of signal transduction: from the receptor tyrosine kinases that initiate intracellular signaling, through second-messenger generators and kinases involved in signaling cascades, to the kinases that regulate the cell cycle that governs cellular fate (2 5).

2) Dysregulation of growth factor signaling networks has been reported in multiple human cancers. Binding of growth factors to extracellular domains of receptor tyrosine kinases activates the intracellular kinase domain. The epidermal growth factor receptor (EGFR) is normally activated by oligomerization in response to ligand binding, but in cancer cells, family members [EGFR (ErbB1, HER1) and its homologs HER2, HER3, HER4] are frequently overactive. To block the EGFR signal, different therapeutic agents have been developed that target the extracellular ligand-binding and intracellular kinase domains.

3) The HER2/Neu gene product is upregulated in the tumor cells of about 30% of breast cancer patients. This finding provided the rationale for the development of Herceptin, a humanized monoclonal antibody that binds the HER2 receptor and induces receptor internalization. In clinical trials, Herceptin alone proved effective in treatment for 15% of patients with HER2-overexpressing metastatic breast cancer and was more effective when used in combination with chemotherapy agents such as paclitaxel.

4) Iressa and Tarceva are small-molecule inhibitors that bind to the EGFR tyrosine kinase domain. Iressa has been registered for treatment of metastatic non small cell lung cancer where other treatments have failed, and Tarceva is currently in phase III clinical trials for several tumor types such as non-small cell lung cancer and pancreatic cancer. Inhibitors that bind irreversibly to the EGFR through covalent bond formation with a cysteine residue in the ATP pocket are even more effective as kinase inhibitors. Their clinical efficacy is being evaluated.

5) In summary: Protein kinases are targets for treatment of a number of diseases. Structures have informed drug design and have illuminated the mechanism of inhibition. Advances have been made with cancer therapeutic agents such as Herceptin and Gleevec. Among the serine-threonine kinases, p38, Rho-kinase, cyclin-dependent kinases, and Chk1 have been targeted with productive results for inflammation and cancer. Structures have provided insights into targeting the inactive or active form of the kinase, for targeting the global constellation of residues at the ATP site or less conserved additional pockets or single residues, and into targeting noncatalytic domains.

References (abridged):

1. G. Manning, D. B. Whyte, R. Martinez, T. Hunter, S. Sudarsanam, Science 298, 1912 (2002)

2. P. Cohen, Nature Rev. Drug Discov. 1, 309 (2002)

3. D. Fabbro et al., Pharmacol. Ther. 93, 79 (2002)

4. A. Levitzki, Acc. Chem. Res. 36, 462 (2003)

5. D. J. Pratt, J. A. Endicott, M. E. Noble, Curr. Opin. Drug Discov. Dev., in press

Science http://www.sciencemag.org

--------------------------------

Related Material:

COMPUTATIONAL CHEMISTRY: ON COMPUTATION IN DRUG DISCOVERY

The following points are made by William L. Jorgensen (Science 2004 303:1813):

1) Is there really a case where a drug that's on the market was designed by a computer? When asked this, the author invokes the professorial mantra ("All questions are good questions."), while sensing that the desired answer is "no". Then, the inquisitor could go back to the lab with the reassurance that his or her choice to avoid learning about computational chemistry remains wise. The reality is that the use of computers and computational methods permeates all aspects of drug discovery today. Those who are most proficient with the computational tools have the advantage for delivering new drug candidates more quickly and at lower cost than their competitors.

2) However, the phrasing of the question suggests misunderstanding and oversimplification of the drug discovery process. First, it is the rare case today when an unmodified natural product like taxol becomes a drug. It is also inconceivable that a human with or without computational tools could propose a single chemical structure that ends up as a drug; there are far too many hurdles and subtleties along the way.

3) Most drugs now arise through discovery programs that begin with identification of a biomolecular target of potential therapeutic value through biological studies including, for example, analysis of mice with gene knockouts. A multidisciplinary project team is then assembled with the goal of finding clinical candidates, i.e., druglike compounds that are ready for human clinical trials, which typically selectively bind to the molecular target and interfere either with its activity as a receptor or enzyme.

4) Molecular libraries are screened, and the resulting leads are optimized in a cycle that features design, synthesis and assaying of numerous analogs, and animal studies. Crystal structure determination for complexes of some analogs with the biomolecular target is often possible, which enables "structure-based drug design" (SBDD) and the efficient optimization of leads. The success of SBDD is well documented (1,2); it has contributed to the introduction of 50 compounds into clinical trials and to numerous drug approvals. Minimally, the role of computation here is in the structure refinement using simulated annealing (3), development of the underlying molecular mechanics (MM) force fields, structure display, and building and MM evaluation of analogs. All top pharmaceutical companies have substantial structural biology and computational chemistry groups that are intertwined and participate on the project teams.

5) There is usually much "tweaking" toward the end of the preclinical period of drug discovery when a series of compounds with adequate potency has been identified and the remaining concerns focus on differences in pharmacological issues relating to bioavailabilty, duration of action, and toxicity. As an example, the methyl group in celecoxib (Celebrex) makes the compound a weaker COX-2 inhibitor than the unsubstituted parent or chloro analog; however, it also introduces a site for metabolic oxidation that then leads to acceptable clearance of the drug (4). In the more common case, too much metabolic activity reduces bioavailability, so, for example, a reactive hydrogen may be replaced by a halogen to block a metabolic process (5).

References (abridged):

1. L. W. Hardy, A. Malikayil, Curr. Drug. Discov. 15, (2003)

2. B. E. Maryanoff, J. Med. Chem. 47, 769 (2004)

3. A. T. Brunger et al., Acta Crystallogr. D 54, 905 (1998)

4. T. D. Penning et al., J. Med. Chem. 40, 1347 (1997)

5. J. B. Hester et al., J. Med. Chem. 44, 1099 (2001)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com