A Supramolecular Approach to Medicinal Chemistry: Medicine Beyond

Chemistry for Everyone edited by

Products of Chemistry

George B. Kauffman California State University Fresno, CA 93740

A Supramolecular Approach to Medicinal Chemistry: Medicine Beyond the Molecule

David K. Smith Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom; [email protected]

Over the past 150 years, life expectancy has increased dramatically. This is a consequence of a number of factors, including improved public hygiene, enhanced safety awareness, better medical care, and more effective medicines and, as such, is one of the most compelling arguments in support of modern chemical science. Medicine provides an exciting arena for exploring the applications of chemistry, but the general public do not necessarily associate advances in medicine with “chemistry”, being seduced instead by the primary role of the health care professional as portrayed through popular television shows such as ER. Exploring the connections between chemistry and medicine can therefore be a key motivating factor in demonstrating the importance of studying chemistry at higher levels. This is particularly true as students often have a strong ambition to seek employment that they feel benefits society. For this reason, many students choose to study courses associated with the “caring professions”, but fewer realize that chemistry can provide an excellent vehicle for being directly involved in life-changing discoveries (1). As a consequence of this perception gap, I have developed an interactive demonstration lecture that explores themes of medicinal chemistry. This lecture (2) has now been delivered to well over 10,000 advanced high school students in the United Kingdom (age 16–18 years) over the last three years, and has provided a loose framework for some of the concepts developed further in this article. This article focuses on the essential roles played by intermolecular forces in mediating the interactions between chemical molecules and biological systems. Intermolecular forces constitute a key topic in chemistry programs followed by students at high school, college, and university, yet can sometimes seem disconnected from real-life applications. However, by taking a supramolecular (3) view of medicinal chemistry and focusing on interactions between molecules, it is possible to look at medicinal chemistry beyond the limitations of an individual drug molecule and, as such, we can come to a deeper understanding of recent developments in medicine beyond the molecule. This allows us to gain a real insight into the interface between biology and chemistry— an interdisciplinary area that is crucial for the development of modern medicinal therapies. This article, taken as a whole, emphasizes a conceptual view of medicinal chemistry that has important implications for the future, as the supramolecular approach to medicinal-chemistry products outlined here is rapidly allowing nanotechnology to converge with modern biology and medicine (4). Discovering Drug Molecules Traditionally, drug molecules have been discovered largely by accident, with many active pharmaceuticals being natural products. For example, it was known in ancient Greece www.JCE.DivCHED.org

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that the bark of the willow tree was able to act as an analgesic against headaches. This observation became the basis for the development of aspirin in the late 19th century (5). Even today, many drugs are still discovered as a consequence of natural-product isolation (6). However, given the limited rate at which varied natural products can be discovered, chemists have recently also turned to high-throughput (or combinatorial) synthesis, to generate large numbers of compounds with potential pharmaceutical activity (7). These large libraries of compounds are screened for their activity and promising candidates can be developed further. The aim of this essentially random approach is to increase the odds of finding an active lead compound. However, chemists are not completely reliant on chance to discover new pharmaceuticals, and over recent years methods have developed that have enabled the ab initio design of drug molecules from first principles. To achieve this goal, it is essential to have a good understanding of the ways in which a chemical species (i.e., the potential drug, shown in dark lines throughout this article) actually interacts with a biological target (i.e., the target bacterium or virus or indeed the patient themselves, shown in gray lines throughout this article). How Do Chemistry and Biology Interact? In 1894, Emil Fischer published his seminal article that described a mechanism for the interaction between chemical molecules and biological systems, specifically enzymes. He proposed that the two come together “wie Schloss und Schlüssel: (like lock and key; Figure 1) (8). In other words, the substrate for an enzyme is complementary to the shape of the enzyme’s active site. Furthermore, the intermolecular interactions between enzyme and substrate will also be arranged in a complementary fashion with matching electrostatic interactions, hydrogen bonds, coordinate bonds, hydrophobic

electrostatic attraction

ligand–metal interaction M

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hydrophobic hydrogen interaction bonds Figure 1. The “Lock and Key Hypothesis” developed by Fischer. Dark lines indicate the drug and the gray lines indicate the bacterium or virus.

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subunits, π–π interactions, and so forth. In other words, intermolecular forces provide the vocabulary by which a (chemical) molecule is able to express itself on its surrounding (biological) environment. Fischer’s well-known pictorial concept has proven extraordinarily useful in understanding the function of biological systems throughout the 20th century. More importantly, given recent advances in the determination of protein structures, Fischer’s hypothesis has allowed chemists with an understanding of intermolecular forces to develop novel drugs ab initio (9, 10). Some of the first drugs to be developed using this rational approach have recently been released as products to the market. Interactions Beyond the Molecule: Ab Initio Drug Design Active Site Pathogens, for example viruses, are reliant on key enzymes for their survival. A fundamental approach to drug design argues that to “knockout” or inhibit a key viral enzyme will prevent the virus from functioning efficiently. This in turn can lead to death of the virus and hence a cure for the patient. For this reason, the crystal structures of enzymes associated with key disease pathways and pathogens are particularly prized, as they provide a molecular-scale insight that offers the medicinal chemist methods of attack. In addition to the enzyme structure, it is also important to have some idea which parts of the enzyme are essential for its activity. This allows the active site of the enzyme to be located. The medicinal chemist can then begin to design molecules that should interact with the active site. The goal is to develop molecules that will bind to the active site so avidly that the normal function of the enzyme will become impossible. Such molecules act as inhibitors, effectively switching the enzyme off, and hence preventing the disease pathway from being expressed. In this way, the patient is cured, or at least has relief of symptoms. Relenza (Zanamivir), Glaxo Smith Kline’s recently released anti-influenza drug, was developed using this type of rational approach (11, 12). Influenza is a key medicinal target, particularly given that it affects so many people. For example, more people worldwide were killed by the Spanish flu pandemic of 1918–1919 than died in World War I. In particular, influenza has high mortality rates among the very young, the very old, and the immuno-compromised. Relenza was designed to target the sialidase enzyme, which is a key enzyme on the surface of the influenza virus. This enzyme enables the release of the influenza virus from infected cells, by hydrolyzing glycosidic bonds to remove the sialic acid receptors from the host cell. Consequently, inhibiting this enzyme prevents the virus spreading through the body. There are nine different subtypes of sialidase identified for influenza A and only one subtype for influenza B, and importantly 30% of the overall amino acid sequence is conserved between all known sialidases. The conserved residues are those in the active site, so it was argued that an effective inhibitor for this enzyme should inhibit most types of flu, making it an attractive site for therapeutic intervention. Once a sialidase enzyme had been crystallized in 1978 by Laver, and the structure determined in 1983 by Colman and Varghese (13, 14), rational methods could be used to 394


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Arg 371 NH

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Figure 2. Docking of Relenza (dark lines) into the active site of the sialidase enzyme (gray lines) located on the surface of the influenza virus.

design an appropriate inhibitor that would show high affinity for the active site. Initially, an inhibitor was designed that had an analogous structure to the transition state of the reaction normally catalyzed by the enzyme (15). Unfortunately, this compound also inhibited mammalian sialidases. However, the crystal structure of the sialidase soaked with this initial inhibitor allowed structure-based rational design to be applied, with the fit of the inhibitor within the active site being modified to generate enhanced binding (16, 17). This rational-design process was supported by computational methods that allow three-dimensional visualization of the enzyme and enabled different potential inhibitors to be docked into the active site. The supramolecular interactions between biological enzyme and chemical inhibitor could be optimized in each case—just like trying out a set of different keys in a lock to find the one that opens the door. It should be pointed out that a computer is not able to develop an effective drug on its own; chemists must apply their understanding of supramolecular interactions and molecular structure to develop the most effective inhibitors. The binding mode of Relenza within the active site of a sialidase enzyme is illustrated in Figure 2. The supramolecular interactions responsible for the strong binding of the drug to the target are shown. Each of the four substituents on the cyclic framework forms hydrogen-bond interactions with the active site of the enzyme. Two sets of these hydrogen-bonding interactions are reinforced by electrostatic interactions, making them significantly stronger. The negatively-charged carboxylate group on Relenza interacts with Arg 118, Arg 371, and Arg 292, all of which are positively charged. Furthermore, the positively-charged guanidinium group on Relenza interacts with anionic Glu 119, Glu 227, and Asp 151. Relenza, the product of a rational-design process, binds to the enzyme three times more strongly than the natural substrate, sialic acid, and, in addition, inhibits all standard influenza viruses. Relenza is now on the market worldwide as a treatment for influenza. It is delivered directly to the major source of infection (the lungs) by an inhaler (two inhalations, twice daily). Since the release of Relenza, Roche has also released a rationally-designed anti-influenza drug, Tamiflu (Oseltamivir) (18). This drug operates in an analogous way to Relenza and


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the two molecules have significant similarity in terms of their supramolecular vocabulary and the way this can be expressed on the enzyme active site. A comparison of the two structures focusing on the equivalence of the supramolecular interactions formed with the enzyme by the two inhibitors is provided in Figure 3. Both have carboxylate and acetamido substituents, while Tamiflu has a simple protonated amine instead of the positively charged guanidinium group of Relenza. The major difference between the structures is the existence of an additional hydrophobic unit on Tamiflu instead of the glycerol substituent of Relenza. This hydrophobic chain actually causes a minor rearrangement of the active site to generate a more hydrophobic pocket. Tamiflu is bioavailable via the oral route in the form of an ethyl ester prodrug and can hence be prescribed in capsule form.

Protein–Protein Interactions Interestingly, attention in the field of protein inhibition is beginning to turn away from focusing only on the active site and, in addition, is considering binding to protein surfaces (19). Protein–protein interactions are of vital importance in biological systems, and protein surface binding offers a mechanism for preventing proteins from communicating with one another—a new method for intervening in disease pathways. Clearly, binding a large, highly solvated protein surface is more challenging than binding in a directional, solvent shielded, well-organized active site, but significant progress is being made in developing an understanding of how to bind synthetic systems to solvent-exposed protein-surface sites. A good illustration of this approach has been published by Hamilton and co-workers who have used a synthetic helix mimic to disrupt assembly of the viral gp 41 protein complex, hence inhibiting viral fusion into host cells and having potential in treating HIV infection (20). It is anticipated that over the coming decades, protein surface binding will be a significant source of pharmaceutically-active molecules. Supramolecular Antibiotics The fight against bacterial infection is one of the most important ongoing battles in medicinal chemistry. Since Fleming’s discovery of penicillin, there has been an escalating battle between antibacterial chemotherapeutics and the evolutionary power of bacteria to evade them. Most antibiotics target the process of bacterial cell-wall synthesis, which is an ideal target for intervention because bacteria have a different type of cell wall from animals. A key step in bacterial cell-wall synthesis is the crosslinking of peptidoglycan units. In this reaction, a L-Lys-D-Ala-D-Ala segment of the amino acid chain is taken up by the transpeptidase enzyme. It is well established that penicillin operates by covalent modification of the transpeptidase enzyme (21). The betalactam ring in penicillin is relatively reactive and is therefore attacked by a nucleophilic group on the enzyme. This covalent bond-forming reaction is an irreversible process and blocks the transpeptidase enzyme, preventing it from operating. Hence the bacterial cell wall can no longer be crosslinked, and the cells become “leaky” and die. However, there are also antibiotics that operate via a purely noncovalent, or supramolecular, mechanism. One of the most advanced antibiotics is vancomycin (22)—the current antibiotic of last resort in many hospitals. Vancomycin www.JCE.DivCHED.org

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O H H

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Figure 3. Comparison of the structures of anti-influenza drugs Relenza and Tamiflu highlighting the similarity of the supramolecular strategies employed by these two inhibitors in binding to the sialidase enzyme. The dashed lines show the noncovalent interactions with the enzyme. Note that the active form of Tamiflu is illustrated, in which the carboxylic acid has been unmasked after in vivo hydrolysis of an ethyl ester.

OH NH3 H3C

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Figure 4. Vancomycin (dark lines) bound to cell-wall precursor L -Lys- D -Ala- D -Ala (gray lines). Hydrogen bonds are indicated by dashed lines. Hydrophobic interactions are not illustrated.

is particularly useful in combating infections arising from Staphylococcus aureus, the majority of which are resistant to penicillin-type drugs. Vancomycin was discovered by serendipity as a natural product isolated from a soil sample, but as an antibiotic, it clearly has a supramolecular mode of action. Unlike penicillin, which becomes covalently bonded to the transpeptidase enzyme, vancomycin forms noncovalent interactions with its target. In particular, vancomycin binds to a cell-wall precursor that has an L-Lys-D-Ala-D-Ala terminus (23). By binding this cell-wall precursor, vancomycin prevents the bacteria from using L-Lys-D-Ala-D-Ala in cell-wall synthesis, hence leading to the eventual death of the bacteria. The mode by which vancomycin binds to L-Lys-D-AlaD-Ala was first elucidated by Williams and co-workers using 1 H NMR methods, including the first use of intermolecular through-space nuclear Overhauser effect (NOE) to determine the structure of a host–guest complex (24, 25). The binding mode has recently been confirmed by X-ray crystallography (26–28) and is illustrated in Figure 4. Given the complexity of the structure of vancomycin (dark lines), the spatial ar-


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rangement of the docked complex cannot be accurately depicted, however, the key interactions can be illustrated. (i) The carboxylate anion at the terminus of the cell-wall precursor binds within a pocket of three amide N⫺H groups, which form hydrogen bonds with the anion. This is the primary source of binding (20–30 kJ mol᎑1), (29), with the pre-organized amide groups able to compete effectively with solvent (water) molecules. The defined stereochemistry of vancomycin causes these groups to point convergently into an appropriate pre-organized binding pocket (30). The concept of pre-organization was first outlined by Donald Cram with respect to his spherand receptors for alkali metal cations (31). (ii) Amide–amide hydrogen bonds form between vancomycin and the backbone of the cell-wall precursor. These interactions, although not as energetically favorable as carboxylate binding, appear to play a key role in orienting the peptide so that the carboxylate group can bind more effectively, and the hydrophobic interactions (see below) can occur. (iii) Hydrophobic interactions (not illustrated in Figure 4) exist between the alanine methyl groups and the aromatic rings of vancomycin. These interactions promote binding by a factor of about 103.

Vancomycin provides an excellent example of cooperativity in binding, with interactions (ii) and (iii) promoting binding by limiting the dynamic motion of the guest and hence strengthening interaction (i) still further. It is also worth mentioning, that in aqueous solution glycopeptide antibiotics such as vancomycin generally exist as hydrogen-bonded dimers (32) with dimerization being cooperative with cell-wall precursor binding (another supramolecular effect) (33). A full discussion of this dimerization process is beyond the scope of this article. Unfortunately, because bacteria are living organisms they are able to evolve. This is a particular problem in hospitals, where bacteria have had exposure to a wide range of antibiotics and has led to the development of highly resistant bacterial strains, sometimes referred to in the media as superbugs. In particular, some enterococci have become vancomycin resistant (34) (and some bacteria are, in fact, unable to be treated effectively using any antibiotics). The mechanism by which bacteria become vancomycin resistant is of particular interest. Effectively the bacteria learn to make their cell walls using L-Lys-D-Ala-D-Lac precursors, instead of L-Lys-D-AlaD-Ala (Figure 5). The only structural change on the molecular level is the conversion of one amide group to an ester, yet this has a dramatic effect on the ability of vancomycin to bind. Replacing an N⫺H group with an oxygen atom removes one hydrogen-bond interaction and replaces it with a repulsive interaction between two oxygens (35). This weakens the ability of vancomycin to bind to the bacterial cellwall precursor by a factor of around 1000. This means vancomycin would have to be dosed at much higher levels (100–1000 times) for the treatment of such resistant bacteria, and this is not viable (36). Consequently, knocking out just one hydrogen bond is sufficient to allow the bacteria to survive the antibiotic onslaught. It seems remarkable that a single intermolecular bond can have such a dramatic effect but this example indicates the importance of considering the way that medicines operate “beyond the molecule”. 396


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Figure 5. Vancomycin-resistant enterococci use L-Lys-D-Ala-D-Lac for the synthesis of their cell walls rather than L-Lys-D-Ala-D-Ala. This replaces an attractive hydrogen bond with a repulsive interaction, denoted with the double arrow.

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Figure 6. (A) Structure of β-cyclodextrin and (B) schematic illustration of the torus-shape and mode of complexation.

Using this supramolecular understanding of the way vancomycin operates “beyond the molecule”, improved versions of the drug are being developed that will hopefully overcome problems of resistance. Later in the article, we will also see how more complex supramolecular architectures, which can express themselves on the nanoscale, have the potential to be applied as new weapons against bacterial infection. Special Delivery: Supramolecular Complexes as Special Delivery Vehicles Supramolecular chemistry does not only offer a means for understanding the way in which a drug can interact with a biological target. It also offers a method for the more effective delivery of pharmaceuticals. Many drugs with useful activity profiles can exhibit very poor biodistribution properties. One method that has been developed to assist drug formulation is the synthesis of active complexes of the drug molecule, in which the complex has a significantly improved biodistribution when compared to the free drug. Cyclodextrin (37) has been one of the most widely employed complexing agents in pharmaceutical products (38– 40). It is composed of a cyclic ring of glucose units linked in a head-to-tail manner. There are three common forms of cyclodextrin, the α, β, and γ isomers, which have 6, 7, and 8 glucose units in the ring, respectively. The most commonly used is the 7-membered β form (Figure 6A). Cyclodextrins are naturally occurring products generated from the degradation of starch and are consequently available in commercially viable quantities at reasonably low cost, in spite of their apparent structural complexity. Cyclodextrins are ideal complexing agents in aqueous solution as they possess a hydrophobic inner cavity, yet have alcohol groups on the top and bottom of the cylindrical structure that provide aqueous-phase solubility (Figure 6B). Bind-


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Chemistry for Everyone NH2

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Figure 7. (A) Structure of a small polyamidoamine (PAMAM) dendrimer and (B) schematic diagram of the complex formed between PAMAM and genetic material as a consequence of interactions between protonated amine and anionic phosphate groups, followed by transfection of the complex into a cell.

ing within the cyclodextrin is reversible and the dominant driving force is hydrophobicity—the release of water molecules from the constraints of the receptor cavity. Sometimes, hydrogen bonds between the OH groups on the top and bottom rims of the cyclodextrin and functional groups on the guest molecule are also proposed. It is likely that such interactions, although not providing significant quantities of energetic stabilization to the complex, may help orient the guest within the cyclodextrin cavity. Cyclodextrins have been widely employed for the formulation of hydrophobic drugs, which usually have poor oral bioavailability as a consequence of their low solubility. Cyclodextrins therefore act as effective solubilizing agents for oral-route administration. In addition, however, cyclodextrins have proved themselves useful for rectal (41), nasal (42), ocular (43), and transdermal (41) delivery processes—indicating the high degree of compatibility between cyclodextrin–drug complexes and the human body. In addition to enhancing solubility, cyclodextrins also offer enhanced drug stability, which can enable the administration of pharmaceuticals at lower doses. Many different drugs benefit from formulation with cyclodextrins. In addition to enhancing drug solubility, stability, and hence bioavailability, cyclodextrins also offer minor beneficial effects such as flavor masking and volatility control, which can be important in www.JCE.DivCHED.org

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increasing patient compliance or the shelf life of pharmaceutical formulations. Although cyclodextrins can increase the biocompatibility of many important drug molecules as described above, perhaps the most widely available drugs formulated with cyclodextrins are the steroids. These hydrophobic drugs are widely used or abused as muscle-building agents by professional (and amateur) sportspeople. Indeed, a simple Internet search for “cyclodextrin” reveals many hits for Web sites offering formulations such as “Cycloroid” or “Cyclonordiol”. Cyclodextrins are effective chaperone molecules for steroid drugs and enable lower dosing and more rapid uptake of the active ingredient. In addition to cyclodextrins, supramolecular chemistry offers other delivery vehicles. For example, there is currently an active search for nonviral vectors that are capable of transporting genetic material into cells. Such delivery agents are potentially useful in gene therapy, a method by which it is proposed that patients with genetic disorders can be treated using a “correct” copy of their faulty gene (44). Previous attempts at gene therapy have used viruses as the delivery vehicles for the genetic material. However, there have been a number of unexplained side effects—including death (45)— that may be a consequence of the viral delivery system. Non viral, synthetic delivery systems are therefore of considerable interest for such applications. There are many kinds of supramolecular delivery systems that operate in vitro for gene delivery. The majority of these bind the polyanionic phosphate-based DNA backbone using ammonium cations, with binding taking place through a combination of electrostatic interaction reinforced by hydrogen bonding (Figure 7) (46). The complex formed between a protonated amine (R⫺NH 3+) and an anionic phosphate is charge neutral and can hence migrate through cell membranes. An example of this class of delivery vehicles is provided by the polyamidoamine (PAMAM) dendrimers (branched polymers—Figure 7) (47–49) that bind DNA in this manner and transport it effectively into cells. Transfection agents based on this supramolecular approach can be purchased in commercially available kit form for in vitro applications. Extensive work is in progress to develop effective nontoxic synthetic delivery vehicles that operate in vivo for gene therapy applications. Supramolecular Disease Pathways: Alzheimers and Creutzfeldt–Jakob Diseases In recent years, there has been increasing focus on a number of severe diseases that actually arise via a supramolecular pathway. Of particular interest are Alzheimer’s disease and Creutzfeldt–Jakob Disease (CJD) (50, 51). Both of these diseases are caused by the aggregation of proteins in the extracellular spaces of the brain. These aggregated proteins cause dramatic and distressing loss of mental function. These diseases occur when the protein involved picks up a mutation that causes the protein to fold in a different manner. The protein, instead of performing its normal role, then undergoes aggregation mediated by supramolecular forces. This eventually leads to fibrils or plaques of protein aggregate that damage the brain. In amyloidosis, it is known that point mutation of the protein has the effect of uncovering β-sheet regions of the protein


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partly unfolded protein denatured protein

native protein

amyloid fibril beta sheet core structure

Towards Complexity: Emerging Nanoscale Medicinal Materials

unidirectional fibril growth Figure 8. Schematic illustration of the aggregation pathway by which amyloid fibrils are formed in Alzheimer’s disease.

that are unstable, as well as exposing hydrophobic surfaces (52). The proteins then begin to stack together in order to minimize their exposed hydrophobic surface and also to pack together the β-sheet regions to maximize hydrogen-bonding interactions. This eventually gives rise to a extended fibrillar structure as shown in Figure 8. NMR studies of prion proteins, which are implicated in CJD, have shown that the mutated amino acids are located in the part of the protein responsible for maintaining the hydrophobic core, and it is argued that this gives rise to protein unfolding, which in turn leads to protein aggregation (53). Initially, small soluble aggregates are generated, which can exhibit negative effects on health. These later assemble into larger insoluble aggregates (54). It is interesting to note that numerous synthetic molecules developed by supramolecular chemists also illustrate the ability to assemble into fibrillar structures (55). Interestingly, minor chemical modifications to the molecular building blocks used to assemble these fibers can dramatically transform fiber formation, either inhibiting molecular aggregation or changing the structure of the resultant aggregate altogether (56). In analogy with the previous discussion of Alzheimer’s disease, small soluble supramolecular polymers form first, and these then go on to assemble to form insoluble tangled fibrous aggregates (57). In this way, supramolecular chemistry acts as a useful model system for important biological processes. In addition to modeling the disease pathway itself, however, it is also possible to utilize a supramolecular understanding of protein unfolding and aggregation to develop novel therapeutics. There are various possible approaches to preventing protein aggregation that could be imagined. For example, it may be possible to employ an approach to prevent the mutation that leads to aggregation. However, of particu398


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lar interest to us is the search for small molecule pharmaceuticals that can interfere with the protein aggregation pathway. This can occur if the pharmaceutical is able to express itself on the supramolecular level, interacting with the defective protein, and hence inhibiting its aggregation by blocking key protein–protein contacts (58). Achieving this is a question of programming a small molecule with the correct supramolecular vocabulary. A number of peptidomimetics have been developed that block amyloid fibril formation (59), but unfortunately the pharmacological profile of these compounds is often far from ideal. Many pharmaceutical companies are developing nonpeptidic, aromatic-rich aggrgegation inhibitors; however, a key challenge that lies ahead is engineering these inhibitors to be specific for the undesirable amyloid associated with Alzheimer’s disease, as some mammalian cells actually generate amyloid for functional purposes. Achieving effective pharmaceutical transport across the blood–brain barrier is also a challenge associated with treating this type of disease, and one in which supramolecular approaches to drug delivery may be useful.

Self-assembly (60–62) is an extremely powerful concept that chemists have borrowed from biological systems such as the tobacco mosaic virus. Molecules will self-assemble to form new nanoscale architectures if they have been carefully programmed with molecular-scale information. This information expresses itself through supramolecular interactions which specifically, spontaneously, and reversibly cause a novel architecture to assemble. Interestingly, attention is increasingly turning to the potential of self-assembled supramolecular architectures with medicinal applications (4). Such nanoscale supramolecular systems have the potential to act as novel therapeutics, assist with targeted delivery, and act as biomaterials (63). Using supramolecular chemistry to construct potential new therapeutic agents held together not by covalent bonds, but by noncovalent interactions has significant advantages. For example, such therapeutics, because they are constructed using reversible intermolecular forces, have the potential to exhibit dynamic behavior and may, to some extent, be able to evolve their own structures to counteract the evolution of a biological target. An excellent example of this supramolecular approach to nanomedicine has been provided in the area of antibiotic development by the group of Ghadiri in the United States (64). Ghadiri and co-workers have developed a range of cyclic peptides constructed using amino acids with alternating D and L stereochemistries (Figure 9) (65). Alternating the stereochemistry in this way gives rise to a cyclic peptide with a relatively flat, rigid conformation, that is, the shape of a hoop. Furthermore, the repeating CONH groups in the peptide ring mean that the cyclic peptides are able to hydrogen bond to one another and form a stacked structure, particularly in nonpolar environments where water molecules cannot compete for the hydrogen-bonding sites (Figure 9). The stacked structures that are formed are referred to as supramolecular nanotubes. Ghadiri and co-workers argued that their nanotubes would have a tendency to assemble in the nonpolar bacterial cell wall, disrupting the cell wall around the bacterium, caus-


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Chemistry for Everyone R O HN R

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Figure 9. Cyclic peptides based on D and L amino acid building bocks self-assemble into a nanotube through the formation of an array of hydrogen bonds. The side chain R groups on the nanotube are not all shown for clarity.

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Figure 10. Peptide nanotubes (dark lines) interfere with bacterial membrane assembly (gray lines) by inserting themselves vertically (or horizontally, not shown) into the membrane, making it permeable and hence killing the bacterium.

ing gross disruption and leading to bacterial death. They therefore tested these nanotubes for their antibiotic activity against different bacterial infections (66). Importantly, they found that some cyclic peptides were preferentially active against bacterial cells compared with mammalian cells. The effect of the cyclic peptides on bacteria was rapid and catastrophic, with bacteria dying in minutes. The peptides essentially kill bacteria on contact—they are bactericidal. Most antibiotics are bacteriostatic, and only slow the growth of bacteria. The nanotubes were found to interfere with membrane formation either by spanning the membrane vertically (Figure 10) or by inserting themselves horizontally into the membrane. In animal models, these cyclic peptides were effective against standard bacterial infections, but they were also able to prevent infection with methicillin resistant staphylococcus aureus (MRSA). Untreated mice infected with MRSA died within 48 hours, whereas those treated with the cyclic peptides survived for at least 7 days. Resistant bacteria, such as MRSA, are becoming an increasing problem as described earwww.JCE.DivCHED.org

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lier in the article. These results indicate that supramolecular systems may offer new approaches for fighting disease. Interestingly, the potential to vary the side chain of the amino acids provides these assemblies with a huge range of dynamic possibilities. Not only can any individual cyclic peptide contain hugely different combinations of amino acids, but the nanotubes can stack with these amino acids in an even greater number of different relative orientations. Ghadiri argues that even if bacteria could develop resistance to a specific nanotube, it is possible that the cyclic peptides could overcome this in their own right by stacking in a different manner. Hence the pharmaceutical has its own potential to evolve. This offers a new supramolecular paradigm for the future development of pharmaceuticals and illustrates the potential importance of dynamic systems that can assemble and respond to the conditions they discover in vivo. This example illustrates the ability of supramolecular chemistry to create complex architectures from simple molecular skeletons, yielding nanoscale structures with intriguing applications. This is a key current idea in medicinal chemistry. For example, assembled supramolecular architectures with nanoscale fibrous structures are being used as scaffolds for tissue engineering (67). These nanofibers can be generated by controlling hydrophobic and electrostatic interactions between peptide building blocks. Such an approach is particularly interesting for the directional growth of nerve cells, which may be important in the future treatment of patients with nerve damage and spinal injuries (68). Supramolecular assemblies are also being applied as templates for mineralization processes (69), with mineral growth being important in cases where bone damage has occurred. The use of a supramolecular approach to generate scaffolds for biomedical applications is particularly interesting because, in principle, the reversibility of the supramolecular interactions means that the scaffold can easily be broken apart and removed once it has performed its job. Conclusions This article has illustrated the power of considering medicinal chemistry at a level “beyond the molecule”. The examples in this article illustrate how high-tech medicinal products are wholly dependent on the simple intermolecular interactions taught to students at all levels of the education system. By taking a conceptual supramolecular view of the interactions between chemical therapeutics and biological systems, we are able to obtain clear insights into the mode of action of current pharmaceutical products. In addition, this article has illustrated how considerations of intermolecular forces enable the development of completely new approaches to fighting disease, which may well form the foundation of many future products created by the pharmaceutical industry. Literature Cited 1. In recent years, the number of students applying to study chemistry courses has dropped dramatically. For example, in the United Kingdom, 3910 students applied to study chemistry degrees in 1996, a number that by 2002 had fallen by 27% to just 2860 students; statistics from http://www.ucas.co.uk (accessed Dec 2004). This fall in chemistry student numbers should be set against a background of increasing general levels of university course participation in the United Kingdom. It is therefore of key importance to ensure that students see the specific


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A Supramolecular Approach to Medicinal Chemistry: Medicine Beyond

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