Organic Medicinal and Pharmaceutical Chemistry Textbook PDF

 ‫مفردات منهج االمتحان التنافسي‬ ‫ماجستير علوم صيدلة‬ ‫جامعة الكوفة‬ ‫‪2023-2022‬‬ ‫علَ ْي ِه ت َ َو َك ْلت َو ِإلَ ْي ِه أنِيب (‪))88‬‬ ‫(و َما ت َ ْوفِي ِقي ِإ َال بِ َ‬ ‫اّللِ...

 ‫مفردات منهج االمتحان التنافسي‬ ‫ماجستير علوم صيدلة‬ ‫جامعة الكوفة‬ ‫‪2023-2022‬‬ ‫علَ ْي ِه ت َ َو َك ْلت َو ِإلَ ْي ِه أنِيب (‪))88‬‬ ‫(و َما ت َ ْوفِي ِقي ِإ َال بِ َ‬ ‫اّللِ ۚ َ‬ ‫َ‬ ‫‪TKH‬‬ C H A P T E R 2 Drug Design Strategies JOHN H. BLOCK to the right. At the same time, the drug will be expected to C H A P T E R O V E R V I E W dissociate from the receptor and reenter the systemic circu- lation to be excreted. Major exceptions include the alkylat- Modern drug design as compared with the classical ing agents used in cancer chemotherapy (see Chapter 10), approach—let’s make a change on an existing compound or a few inhibitors of the enzyme acetylcholinesterase (see synthesize a new structure and see what happens— Chapter 17), suicide inhibitors of monoamine oxidase continues to evolve rapidly as an approach to solving a drug (see Chapter 16), and the aromatase inhibitors 4-hydrox- design problem. The combination of increasing power and yandrostenedione and exemestane (see Chapter 25). These decreasing cost of desktop computing has had a major im- pharmacological agents form covalent bonds with the re- pact on solving drug design problems. Although drug design ceptor, usually an enzyme’s active site. In these cases, the increasingly is based on modern computational chemical cell must destroy the receptor or enzyme, or, in the case of techniques, it also uses sophisticated knowledge of disease the alkylating agents, the cell would be replaced, ideally mechanisms and receptor properties. A good understanding with a normal cell. In other words, the usual use of drugs of how the drug is transported into the body, distributed in medical treatment calls for the drug’s effect to last for a throughout the body compartments, metabolically altered by finite period of time. Then, if it is to be repeated, the drug the liver and other organs, and excreted from the patient is will be administered again. If the patient does not tolerate required, along with the structural characteristics of the the drug well, it is even more important that the agent dis- receptor. Acid–base chemistry is used to aid in formulation sociate from the receptor and be excreted from the body. and biodistribution. Structural attributes and substituent pat- terns responsible for optimum pharmacological activity can often be predicted by statistical techniques such as re- Oral Administration gression analysis. Computerized conformational analysis An examination of the obstacle course (Fig. 2.1) faced by permits the medicinal chemist to predict the drug’s three- the drug will give a better understanding of what is involved dimensional (3D) shape that is seen by the receptor. With in developing a commercially feasible product. Assume that the isolation and structural determination of specific recep- the drug is administered orally. The drug must go into solu- tors and the availability of computer software that can esti- tion to pass through the gastrointestinal mucosa. Even drugs mate the 3D shape of the receptor, it is possible to design administered as true solutions may not remain in solution as molecules that will show an optimum fit to the receptor. they enter the acidic stomach and then pass into the alkaline intestinal tract. (This is explained further in the discussion on acid–base chemistry.) The ability of the drug to dissolve is governed by several factors, including its chemical struc- DRUG DISTRIBUTION ture, variation in particle size and particle surface area, na- ture of the crystal form, type of tablet coating, and type of A drug is a chemical molecule. Following introduction into tablet matrix. By varying the dosage form and physical char- the body, a drug must pass through many barriers, survive al- acteristics of the drug, it is possible to have a drug dissolve ternate sites of attachment and storage, and avoid significant quickly or slowly, with the latter being the situation for metabolic destruction before it reaches the site of action, many of the sustained-action products. An example is orally usually a receptor on or in a cell (Fig. 2.1). At the receptor, administered sodium phenytoin, with which variation of the following equilibrium (Rx. 2.1) usually holds: both the crystal form and tablet adjuvants can significantly alter the bioavailability of this drug widely used in the treat- ment of epilepsy. Chemical modification is also used to a limited extent to facilitate a drug reaching its desired target (see Chapter 3). An example is olsalazine, used in the treatment of ulcera- (Rx. 2.1) tive colitis. This drug is a dimer of the pharmacologically active mesalamine (5-aminosalicylic acid). The latter is The ideal drug molecule will show favorable binding not effective orally because it is metabolized to inactive characteristics to the receptor, and the equilibrium will lie forms before reaching the colon. The dimeric form passes 3 0003-0042_17865_Ch02.qxd 12/4/09 2:51 AM Page 4 4 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry Figure 2.1 Summary of drug distribution. through a significant portion of the intestinal tract before (2.5 mg/mL) to come in contact with the taste receptors on being cleaved by the intestinal bacteria to two equivalents the tongue, producing an unpalatable bitterness. To mask of mesalamine. this intense bitter taste, the palmitic acid moiety is added as an ester of chloramphenicol’s primary alcohol. This reduces the parent drug’s water solubility (1.05 mg/mL), enough so that it can be formulated as a suspension that passes over the bitter taste receptors on the tongue. Once in the intestinal tract, the ester linkage is hydrolyzed by the digestive es- terases to the active antibiotic chloramphenicol and the very common dietary fatty acid palmitic acid. As illustrated by olsalazine, any compound passing through the gastrointestinal tract will encounter a large num- ber and variety of digestive and bacterial enzymes, which, in theory, can degrade the drug molecule. In practice, a new drug entity under investigation will likely be dropped from Olsalazine and chloramphenicol palmitate are examples further consideration if it cannot survive in the intestinal of prodrugs. Most prodrugs are compounds that are inactive tract or its oral bioavailability is low, necessitating par- in their native form but are easily metabolized to the active enteral dosage forms only. An exception would be a drug for agent. Olsalazine and chloramphenicol palmitate are exam- which there is no effective alternative or which is more ef- ples of prodrugs that are cleaved to smaller compounds, one fective than existing products and can be administered by an of which is the active drug. Others are metabolic precursors alternate route, including parenteral, buccal, or transdermal. to the active form. An example of this type of prodrug is In contrast, these same digestive enzymes can be used menadione, a simple naphthoquinone that is converted in the to advantage. Chloramphenicol is water soluble enough liver to phytonadione (vitamin K2(20)).  Chapter 2 Drug Design Strategies 5 molecules are too large to enter the cell by an active transport mechanism through the passages. The latter, many times, pass into the patient’s circulatory system by passive diffusion. Parenteral Administration Many times, there will be therapeutic advantages in bypass- ing the intestinal barrier by using parenteral (injectable) dosage forms. This is common in patients who, because of illness, cannot tolerate or are incapable of accepting drugs orally. Some drugs are so rapidly and completely metabo- lized to inactive products in the liver (first-pass effect) that oral administration is precluded. But that does not mean that the drug administered by injection is not confronted by obstacles (Fig. 2.1). Intravenous administration places the drug directly into the circulatory system, where it will be rapidly distributed throughout the body, including tissue Occasionally, the prodrug approach is used to enhance depots and the liver, where most biotransformations occur the absorption of a drug that is poorly absorbed from the (see later in this chapter), in addition to the receptors. gastrointestinal tract. Enalapril is the ethyl ester of Subcutaneous and intramuscular injections slow distribu- enalaprilic acid, an active inhibitor of angiotensin- tion of the drug, because it must diffuse from the site of in- converting enzyme (ACE). The ester prodrug is much jection into systemic circulation. more readily absorbed orally than the pharmacologically It is possible to inject the drug directly into specific or- active carboxylic acid. gans or areas of the body. Intraspinal and intracerebral routes will place the drug directly into the spinal fluid or brain, respectively. This bypasses a specialized epithelial tissue, the blood-brain barrier, which protects the brain from exposure to a large number of metabolites and chemicals. The blood-brain barrier is composed of membranes of tightly joined epithelial cells lining the cerebral capillaries. The net result is that the brain is not exposed to the same va- riety of compounds that other organs are. Local anesthetics are examples of administration of a drug directly onto the desired nerve. A spinal block is a form of anesthesia per- formed by injecting a local anesthetic directly into the spinal cord at a specific location to block transmission along spe- Unless the drug is intended to act locally in the gas- cific neurons. trointestinal tract, it will have to pass through the gastroin- Most of the injections a patient will experience in a life- testinal mucosal barrier into venous circulation to reach time will be subcutaneous or intramuscular. These par- the site of the receptor. The drug’s route involves distribu- enteral routes produce a depot in the tissues (Fig. 2.1), from tion or partitioning between the aqueous environment of which the drug must reach the blood or lymph. Once in sys- the gastrointestinal tract, the lipid bilayer cell membrane of temic circulation, the drug will undergo the same distribu- the mucosal cells, possibly the aqueous interior of the mu- tive phenomena as orally and intravenously administered cosal cells, the lipid bilayer membranes on the venous side agents before reaching the target receptor. In general, the of the gastrointestinal tract, and the aqueous environment same factors that control the drug’s passage through the gas- of venous circulation. Some very lipid-soluble drugs may trointestinal mucosa will also determine the rate of move- follow the route of dietary lipids by becoming part of the ment out of the tissue depot. mixed micelles, incorporating into the chylomicrons in the The prodrug approach described previously can also be mucosal cells into the lymph ducts, servicing the intes- used to alter the solubility characteristics, which, in turn, tines, and finally entering venous circulation via the tho- can increase the flexibility in formulating dosage forms. racic duct. The solubility of methylprednisolone can be altered from The drug’s passage through the mucosal cells can be essentially water-insoluble methylprednisolone acetate to passive or active. As is discussed later in this chapter, slightly water-insoluble methylprednisolone to water-soluble the lipid membranes are very complex with a highly or- methylprednisolone sodium succinate. The water-soluble dered structure. Part of this membrane is a series of chan- sodium hemisuccinate salt is used in oral, intravenous, and nels or tunnels that form, disappear, and reform. There intramuscular dosage forms. Methylprednisolone itself is are receptors that move compounds into the cell by a normally found in tablets. The acetate ester is found in topi- process called pinocytosis. Drugs that resemble a normal cal ointments and sterile aqueous suspensions for intramus- metabolic precursor or intermediate may be actively trans- cular injection. Both the succinate and acetate esters are ported into the cell by the same system that transports the hydrolyzed to the active methylprednisolone by the patient’s endogenous compound. On the other hand, most drug own systemic hydrolytic enzymes (esterases). 6 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry Protein Binding Once the drug enters the systemic circulation (Fig. 2.1), it can undergo several events. It may stay in solution, but many drugs will be bound to the serum proteins, usually al- bumin (Rx. 2.2). Thus, a new equilibrium must be consid- ered. Depending on the equilibrium constant, the drug can remain in systemic circulation bound to albumin for a con- siderable period and not be available to the sites of biotrans- formation, the pharmacological receptors, and excretion. (Rx. 2.2) Protein binding can have a profound effect on the drug’s effective solubility, biodistribution, half-life in the body, and interaction with other drugs. A drug with such poor water solubility that therapeutic concentrations of the un- bound (active) drug normally cannot be maintained still can be a very effective agent. The albumin–drug complex acts as Another example of how prodrug design can significantly a reservoir by providing large enough concentrations of free alter biodistribution and biological half-life is illustrated by drug to cause a pharmacological response at the receptor. two drugs based on the retinoic acid structure used systemi- Protein binding may also limit access to certain body cally to treat psoriasis, a nonmalignant hyperplasia. Etretinate compartments. The placenta is able to block passage of pro- has a 120-day terminal half-life after 6 months of therapy. In teins from maternal to fetal circulation. Thus, drugs that nor- contrast, the active metabolite, acitretin, has a 33- to 96-hour mally would be expected to cross the placental barrier and terminal half-life. Both drugs are potentially teratogenic. possibly harm the fetus are retained in the maternal circula- Women of childbearing age must sign statements that they tion, bound to the mother’s serum proteins. are aware of the risks and usually are administered a preg- Protein binding also can prolong the drug’s duration of ac- nancy test before a prescription is issued. Acitretin, with its tion. The drug–protein complex is too large to pass through shorter half-life, is recommended for a woman who would the renal glomerular membranes, preventing rapid excretion like to become pregnant, because it can clear her body within of the drug. Protein binding limits the amount of drug avail- a reasonable time frame. When effective, etretinate can keep able for biotransformation (see later in this chapter and a patient clear of psoriasis lesions for several months. Chapter 3) and for interaction with specific receptor sites. For  Chapter 2 Drug Design Strategies 7 example, the large, polar trypanocide suramin remains in the transported into the hepatocyte, where it may be metabo- body in the protein-bound form for as long as 3 months (t1/2 lized by hepatic enzymes to inactive chemicals during the ! 50 days). The maintenance dose for this drug is based on initial trip through the liver, by what is known as the first- weekly administration. At first, this might seem to be an ad- pass effect (see Chapter 3). vantage to the patient. It can be, but it also means that, should Lidocaine is a classic example of the significance of the the patient have serious adverse reactions, a significant length first-pass effect. Over 60% of this local anesthetic antiar- of time will be required before the concentration of drug falls rhythmic agent is metabolized during its initial passage below toxic levels. through the liver, resulting in it being impractical to admin- The drug–protein binding phenomenon can lead to some ister orally. When used for cardiac arrhythmias, it is admin- clinically significant drug–drug interactions that result when istered intravenously. This rapid metabolism of lidocaine is one drug displaces another from the binding site on albumin. used to advantage when stabilizing a patient with cardiac A large number of drugs can displace the anticoagulant war- arrhythmias. Should too much lidocaine be administered farin from its albumin-binding sites. This increases the ef- intravenously, toxic responses will tend to decrease be- fective concentration of warfarin at the receptor, leading to cause of rapid biotransformation to inactive metabolites. an increased prothrombin time (increased time for clot for- An understanding of the metabolic labile site on lidocaine mation) and potential hemorrhage. led to the development of the primary amine analog tocainide. In contrast to lidocaine’s half-life of less than Tissue Depots 2 hours, tocainide’s half-life is approximately 15 hours, The drug can also be stored in tissue depots. Neutral fat con- with 40% of the drug excreted unchanged. The develop- stitutes some 20% to 50% of body weight and constitutes a ment of orally active antiarrhythmic agents is discussed in depot of considerable importance. The more lipophilic the more detail in Chapter 19. drug, the more likely it will concentrate in these pharmaco- logically inert depots. The ultra–short-acting, lipophilic bar- biturate thiopental’s concentration rapidly decreases below its effective concentration following administration. It dis- appears into tissue protein, redistributes into body fat, and then slowly diffuses back out of the tissue depots but in con- centrations too low for a pharmacological response. Thus, only the initially administered thiopental is present in high enough concentrations to combine with its receptors. The re- maining thiopental diffuses out of the tissue depots into sys- temic circulation in concentrations too small to be effective (Fig. 2.1), is metabolized in the liver, and is excreted. In general, structural changes in the barbiturate series (see Chapter 12) that favor partitioning into the lipid tissue stores decrease duration of action but increase central ner- vous system (CNS) depression. Conversely, the barbiturates with the slowest onset of action and longest duration of ac- A study of the metabolic fate of a drug is required for all tion contain the more polar side chains. This latter group of new drug products. Often it is found that the metabolites are barbiturates both enters and leaves the CNS more slowly also active. Sometimes the metabolite is the pharmaco- than the more lipophilic thiopental. logically active molecule. These drug metabolites can pro- vide leads for additional investigations of potentially new Drug Metabolism products. Examples of an inactive parent drug that is con- All substances in the circulatory system, including drugs, verted to an active metabolite include the nonsteroidal anti- metabolites, and nutrients, will pass through the liver. inflammatory agent sulindac being reduced to the active Most molecules absorbed from the gastrointestinal tract sulfide metabolite, the immunosuppressant azathioprine enter the portal vein and are initially transported to the being cleaved to the purine antimetabolite 6-mercaptopurine, liver. A significant proportion of a drug will partition or be and purine and pyrimidine antimetabolites and antiviral 8 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry agents being conjugated to their nucleotide form (acyclovir Although a drug’s metabolism can be a source of frustra- phosphorylated to acyclovir triphosphate). Often both the tion for the medicinal chemist, pharmacist, and physician parent drug and its metabolite are active, which has led to ad- and lead to inconvenience and compliance problems with ditional commercial products, instead of just one being mar- the patient, it is fortunate that the body has the ability to me- keted. About 75% to 80% of phenacetin (now withdrawn tabolize foreign molecules (xenobiotics). Otherwise, many from the U.S. market) is converted to acetaminophen. In the of these substances could remain in the body for years. This tricyclic antidepressant series (see Chapter 12), imipramine has been the complaint against certain lipophilic chemical and amitriptyline are N-demethylated to desipramine and pollutants, including the once very popular insecticide nortriptyline, respectively. All four compounds have been dichlorodiphenyltrichloroethane (DDT). After entering the marketed in the United States. Drug metabolism is discussed body, these chemicals reside in body tissues, slowly diffus- more fully in Chapter 3. ing out of the depots and potentially harming the individual on a chronic basis for several years. They can also reside in tissues of commercial food animals that have been slaugh- tered before the drug has washed out of the body. Excretion The main route of excretion of a drug and its metabolites is through the kidney. For some drugs, enterohepatic circula- tion (Fig. 2.1), in which the drug reenters the intestinal tract from the liver through the bile duct, can be an important part of the agent’s distribution in the body and route of excretion. Either the drug or drug metabolite can reenter systemic cir- culation by passing once again through the intestinal mu- cosa. A portion of either also may be excreted in the feces. Nursing mothers must be concerned, because drugs and their metabolites can be excreted in human milk and be in- gested by the nursing infant. One should keep a sense of perspective when learning about drug metabolism. As explained in Chapter 3, drug me- tabolism can be conceptualized as occurring in two stages or phases. Intermediate metabolites that are pharmacologically active usually are produced by phase I reactions. The prod- ucts from the phase I chemistry are converted into inactive, usually water-soluble end products by phase II reactions. The latter, commonly called conjugation reactions, can be thought of as synthetic reactions that involve addition of water-soluble substituents. In human drug metabolism, the main conjugation reactions add glucuronic acid, sulfate, or glutathione. Obviously, drugs that are bound to serum pro- tein or show favorable partitioning into tissue depots are going to be metabolized and excreted more slowly for the reasons discussed previously. This does not mean that drugs that remain in the body for longer periods of time can be administered in lower doses or be taken fewer times per day by the patient. Several vari- ables determine dosing regimens, of which the affinity of the drug for the receptor is crucial. Reexamine Reaction 2.1 and Figure 2.1. If the equilibrium does not favor formation of the drug–receptor complex, higher and usually more fre- quent doses must be administered. Further, if partitioning into tissue stores or metabolic degradation and/or excretion is favored, it will take more of the drug and usually more frequent administration to maintain therapeutic concentra- tions at the receptor. The Receptor With the possible exception of general anesthetics (see Chapter 22), the working model for a pharmacological re- sponse consists of a drug binding to a specific receptor. Many drug receptors are the same as those used by endoge- nously produced ligands. Cholinergic agents interact with the same receptors as the neurotransmitter acetylcholine.  Chapter 2 Drug Design Strategies 9 Synthetic corticosteroids bind to the same receptors as cor- early that molecules with certain structural features would tisone and hydrocortisone. Often, receptors for the same li- elucidate a specific biological response. Very slight changes gand are found in various tissues throughout the body. The in structure could cause significant changes in biological ac- nonsteroidal anti-inflammatory agents (see Chapter 26) in- tivity. These structural variations could increase or decrease hibit the prostaglandin-forming enzyme cyclooxygenase, activity or change an agonist into an antagonist. This early which is found in nearly every tissue. This class of drugs has and fundamentally correct interpretation called for the drug a long list of side effects with many patient complaints. Note (ligand) to fit onto some surface (the receptor) that had fairly in Figure 2.1 that, depending on which receptors contain strict structural requirements for proper binding of the drug. bound drug, there may be desired or undesired effects. This The initial receptor model was based on a rigid lock-and-key is because various receptors with similar structural require- concept, with the drug (key) fitting into a receptor (lock). It ments are found in several organs and tissues. Thus, the has been used to explain why certain structural attributes pro- nonsteroidal anti-inflammatory drugs combine with the duce a predictable pharmacological action. This model still is desired cyclooxygenase receptors at the site of the inflam- useful, although one must realize that both the drug and the mation and the undesired cyclooxygenase receptors in the receptor can have considerable flexibility. Molecular graph- gastrointestinal mucosa, causing severe discomfort and ics, using programs that calculate the preferred conformations sometimes ulceration. One of the second-generation antihis- of drug and receptor, show that the receptor can undergo an tamines, fexofenadine, is claimed to cause less sedation be- adjustment in 3D structure when the drug makes contact. cause it does not readily penetrate the blood-brain barrier. Using space-age language, the drug docks with the receptor. The rationale is that less of this antihistamine is available for More complex receptors now are being isolated, char- the receptors in the CNS, which are responsible for the se- acterized, and cloned. The first receptors to be isolated and dation response characteristic of antihistamines. In contrast, characterized were the reactive and regulatory sites on some antihistamines are used for their CNS depressant ac- enzymes. Acetylcholinesterase, dihydrofolate reductase, an- tivity because a significant proportion of the administered giotensin, and human immunodeficiency virus (HIV) dose is crossing the blood-brain barrier relative to binding to protease-converting enzyme are examples of enzymes whose the histamine H1 receptors in the periphery. active sites (the receptors) have been modeled. Most drug re- Although it is normal to think of side effects as undesir- ceptors probably are receptors for natural ligands used to reg- able, they sometimes can be beneficial and lead to new ulate cellular biochemistry and function and to communicate products. The successful development of oral hypoglycemic between cells. Receptors include a relatively small region of agents used in the treatment of diabetes began when it was a macromolecule, which may be an isolatable enzyme, a found that certain sulfonamides had a hypoglycemic effect. structural and functional component of a cell membrane, or a Nevertheless, a real problem in drug therapy is patient com- specific intracellular substance such as a protein or nucleic pliance in taking the drug as directed. Drugs that cause seri- acid. Specific regions of these macromolecules are visual- ous problems and discomfort tend to be avoided by patients. ized as being oriented in space in a manner that permits their At this point, let us assume that the drug has entered the functional groups to interact with the complementary func- systemic circulation (Fig. 2.1), passed through the lipid bar- tional groups of the drug. This interaction initiates changes in riers, and is now going to make contact with the receptor. As structure and function of the macromolecule, which lead ul- illustrated in Reaction 2.1, this is an equilibrium process. A timately to the observable biological response. The concept good ability to fit the receptor favors binding and the desired of spatially oriented functional areas forming a receptor leads pharmacological response. In contrast, a poor fit favors the directly to specific structural requirements for functional reverse reaction. With only a small amount of drug bound to groups of a drug, which must complement the receptor. the receptor, there will be a much smaller pharmacological It now is possible to isolate membrane-bound receptors, effect. If the amount of drug bound to the receptor is too although it still is difficult to elucidate their structural chem- small, there may be no discernible response. Many variables istry, because once separated from the cell membranes, contribute to a drug’s binding to the receptor. These include these receptors may lose their native shape. This is because the structural class, the 3D shape of the molecule, and the the membrane is required to hold the receptor in its correct types of chemical bonding involved in the binding of the tertiary structure. One method of receptor isolation is affin- drug to the receptor. ity chromatography. In this technique, a ligand, often an al- Most drugs that belong to the same pharmacological tered drug molecule known to combine with the receptor, is class have certain structural features in common. The bar- attached to a chromatographic support phase. A solution biturates act on specific CNS receptors, causing depressant containing the desired receptor is passed over this column. effects; hydantoins act on CNS receptors, producing an The receptor will combine with the ligand. It is common to anticonvulsant response; benzodiazepines combine with the add a chemically reactive grouping to the drug, resulting in !-aminobutyric acid (GABA) receptors, with resulting the receptor and drug covalently binding with each other. anxiolytic activity; steroids can be divided into such classes The drug–receptor complex is washed from the column and as corticosteroids, anabolic steroids, progestogens, and es- then characterized further. trogens, each acting on specific receptors; nonsteroidal anti- A more recent technique uses recombinant DNA. The inflammatory agents inhibit enzymes required for the gene for the receptor is located and cloned. It is transferred prostaglandin cascade; penicillins and cephalosporins in- into a bacterium, yeast, or animal, which then produces the hibit enzymes required to construct the bacterial cell wall; receptor in large enough quantities to permit further study. and tetracyclines act on bacterial ribosomes. Sometimes it is possible to determine the DNA sequence of With the isolation and characterization of receptors be- the cloned gene. By using the genetic code for amino acids, coming a common occurrence, it is hard to realize that the the amino acid sequence of the protein component of the concept of receptors began as a postulate. It had been realized receptor can be determined, and the receptor then modeled, 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 10 10 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry producing an estimated 3D shape. The model for the recep- process as pictured by the earlier lock-and-key concept of a tor becomes the template for designing new ligands. receptor. Rather, the binding or partial insertion of groups of Genome mapping has greatly increased the information on moderate size onto or into a macromolecular pouch appears receptors. Besides the human genome, the genetic composi- to be a continuous process, at least over a limited range, as tion of viruses, bacteria, fungi, and parasites has increased indicated by the frequently occurring regular increase and the possible sites for drugs to act. The new field of pro- decrease in biological activity as one ascends a homologous teomics studies the proteins produced by structural genes. series of drugs. A range of productive associations between The earlier discussion in this chapter emphasizes that the drug and receptor may be pictured, which leads to agonist cell membrane is a highly organized, dynamic structure that responses, such as those produced by cholinergic and adren- interacts with small molecules in specific ways; its focus is ergic drugs. Similarly, strong associations may lead to on the lipid bilayer component of this complex structure. unproductive changes in the configuration of the macromol- The receptor components of the membranes appear to be ecule, leading to an antagonistic or blocking response, such mainly protein. They constitute a highly organized, inter- as that produced by anticholinergic agents and HIV protease twined region of the cell membrane. The same type of mo- inhibitors. Although the fundamental structural unit of the lecular specificity seen in such proteins as enzymes and drug receptor is generally considered to be protein, it may be antibodies is also a property of drug receptors. The nature of supplemented by its associations with other units, such as the amide link in proteins provides a unique opportunity for mucopolysaccharides and nucleic acids. the formation of multiple internal hydrogen bonds, as well Humans (and mammals in general) are very complex or- as internal formation of hydrophobic, van der Waals, and ganisms that have developed specialized organ systems. It is ionic bonds by side chain groups, leading to such organized not surprising that receptors are not distributed equally structures as the "-helix, which contains about four amino throughout the body. It now is realized that, depending on the acid residues for each turn of the helix. An organized pro- organ in which it is located, the same receptor class may be- tein structure would hold the amino acid side chains at rel- have differently. This can be advantageous by focusing drug atively fixed positions in space and available for specific therapy on a specific organ system, but it can also cause interactions with a small molecule. adverse drug responses because the drug is exerting two dif- Proteins can potentially adopt many different conforma- ferent responses based on the location of the receptors. An ex- tions in space without breaking their covalent amide ample is the selective estrogen receptor modulators (SERMs). linkages. They may shift from highly coiled structures to par- They cannot be classified simply as agonists or antagonists. tially disorganized structures, with parts of the molecule ex- Rather, they can be considered variable agonists and antago- isting in random chain or folded sheet structures, contingent nists. Their selectivity is very complex because it depends on on the environment. In the monolayer of a cell membrane, the organ in which the receptor is located. the interaction of a small foreign molecule with an organized This complexity can be illustrated with tamoxifen and protein may lead to a significant change in the structural and raloxifene (Fig. 2.2). Tamoxifen is used for estrogen-sensitive physical properties of the membrane. Such changes could breast cancer and for reducing bone loss from osteoporosis. well be the initiating events in the tissue or organ response to Unfortunately, prolonged treatment increases the risk of en- a drug, such as the ion-translocation effects produced by in- dometrial cancer because of the response from the uterine es- teraction of acetylcholine and the cholinergic receptor. trogen receptors. Thus, tamoxifen is an estrogen antagonist in The large body of information now available on relation- the mammary gland and an agonist in the uterus and bone. In ships between chemical structure and biological activity contrast, raloxifene does not appear to have much agonist strongly supports the concept of flexible receptors. The fit of property in the uterus but, like tamoxifen, is an antagonist in drugs onto or into macromolecules is rarely an all-or-none the breast and agonist in the bone. Figure 2.2 Selective SERMs. 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 11 Chapter 2 Drug Design Strategies 11 Figure 2.3 Examples of phosphodiesterase type 5 inhibitors. There are a wide variety of phosphodiesterases through- creased specificity for the target receptor that will produce the out the body. These enzymes hydrolyze the cyclic phosphate desired pharmacological response while decreasing the affin- esters of adenosine monophosphate (cAMP) and guanosine ity for undesired receptors that produce adverse responses; monophosphate (cGMP). Although the substrates for this and (c) the still experimental approach of attaching the drug family of enzymes are cAMP and cGMP, there are differ- to a monoclonal antibody (see Chapter 5) that will bind to a ences in the active sites. Figure 2.3 illustrates three drugs specific tissue antigenic for the antibody. Biodistribution can used to treat erectile dysfunction (sildenafil, tadalafil, and be altered by changing the drug’s solubility, enhancing its vardenafil). These three take advantage of the differences in ability to resist being metabolized (usually in the liver), alter- active site structural requirements between phosphodi- ing the formulation or physical characteristics of the drug, and esterase type 5 and the other phosphodiesterases. They have changing the route of administration. If a drug molecule can an important role in maintaining a desired lifestyle: treatment be designed so that its binding to the desired receptor is en- of erectile dysfunction caused by various medical conditions. hanced relative to the undesired receptor and biodistribution The drugs approved for this indication were discovered by remains favorable, smaller doses of the drug can be adminis- accident. The goal was to develop a newer treatment of tered. This, in turn, reduces the amount of drug available for angina. The approach was to develop phosphodiesterase in- binding to those receptors responsible for its adverse effects. hibitors that would prolong the activity of cGMP. The end The medicinal chemist is confronted with several chal- result was drugs that were not effective inhibitors of the lenges in designing a bioactive molecule. A good fit to a phosphodiesterase that would treat angina, but were effective specific receptor is desirable, but the drug would normally inhibitors of the one found in the corpus cavernosum. The be expected to dissociate from the receptor eventually. The vasodilation in this organ results in penile erection. specificity for the receptor would minimize side effects. The drug would be expected to clear the body within a reason- able time. Its rate of metabolic degradation should allow Summary reasonable dosing schedules and, ideally, oral administra- One of the goals is to design drugs that will interact with re- tion. Many times, the drug chosen for commercial sales has ceptors at specific tissues. There are several ways to do this, been selected from hundreds of compounds that have been including (a) altering the molecule, which, in turn, can change screened. It usually is a compromise product that meets a the biodistribution; (b) searching for structures that show in- medical need while demonstrating good patient acceptance. 12 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry Acid Strength ACID–BASE PROPERTIES While any acid–base reaction can be written as an equilib- Most drugs used today can be classified as acids or bases. rium reaction, an attempt has been made in Table 2.1 to As is noted shortly, a large number of drugs can behave indicate which sequences are unidirectional or show only a as either acids or bases as they begin their journey into small reversal. For hydrochloric acid (reaction a), the conju- the patient in different dosage forms and end up in systemic gate base, Cl#, is such a weak base that it essentially does circulation. A drug’s acid–base properties can greatly influ- not function as a proton acceptor. In a similar manner, water ence its biodistribution and partitioning characteristics. is such a weak conjugate acid that there is little reverse re- Over the years, at least four major definitions of acids action involving water donating a proton to the hydroxide and bases have been developed. The model commonly used anion of sodium hydroxide (reaction b). in pharmacy and biochemistry was developed independently Two logical questions to ask at this point are how one by Lowry and Brønsted. In their definition, an acid is predicts in which direction an acid–base reaction lies and to defined as a proton donor and a base is defined as a proton what extent the reaction goes to completion. The common acceptor. Notice that for a base, there is no mention of the physical chemical measurement that contains this informa- hydroxide ion. In the Brønsted-Lowry model, the acid plus tion is known as the pKa. The pKa is the negative logarithm base reaction can be expressed as: of the modified equilibrium constant, Ka (Eq. 2.1), for an acid–base reaction written so that water is the base or proton acceptor (reactions a, c, e, g, i, k, m, Table 2.1). (Rx. 2.3) [conj. acid][conj. base] Ka ! (Eq. 2.1) acid Acid/Base–Conjugate Acid/Conjugate Base Pairs Equation 2.1 is based on Rx. 2.3. The square brackets indicate molar concentrations. Because the molar concentra- Representative pairings of acids with their conjugate tion of water (the base in these acid–base reactions) is consid- bases and bases with their conjugate acids are shown in ered constant in the dilute solutions used in pharmacy and Table 2.1. Careful study of this table shows water func- medicine, it is incorporated into the Ka. Rewriting Equation tioning as a proton acceptor (base) in reactions a, c, e, g, 2.1 by taking the negative logarithm of the Ka, results in the i, k, and m and a proton donor (base) in reactions b, d, f, familiar Henderson-Hasselbalch equation (Eq. 2.2). h, j, l, and n. Hence, water is known as an amphoteric substance. Water can be either a weak base accepting a [conj. base] proton to form the strongly acidic hydrated proton or hy- pH ! pKa " log (Eq. 2.2) [acid] dronium ion H3O" (reactions a, c, e, g, i, k, and m), or a weak acid donating a proton to form the strongly basic Warning! It is important to recognize that a pKa for a (proton accepting) hydroxide anion OH# (reactions b, d, base is in reality the pKa of the conjugate acid (acid donor f, h, j, l, and n). or protonated form, BH") of the base. The pKa is listed in Also note the shift between un-ionized and ionized forms the Appendix as 9.6 for ephedrine and as 9.3 for ammonia. in Table 2.1. Examples of un-ionized acids donating their In reality, this is the pKa of the protonated form, such as protons forming ionized conjugate bases are acetic acid- ephedrine hydrochloride (reaction m in Table 2.1) and am- acetate (reaction g), phenobarbital-phenobarbiturate (reac- monium chloride (reaction e in Table 2.1), respectively. tion i), and saccharin-saccharate (reaction k). In contrast, This is confusing to students, pharmacists, clinicians, and examples of ionized acids yielding un-ionized conjugate experienced scientists. It is crucial that the chemistry of the bases are ammonium chloride-ammonia (reaction e) and drug be understood when interpreting a pKa value. When ephedrine hydrochloride (reaction m). A similar shift be- reading tables of pKa values, such as those found in the tween un-ionized and ionized forms is seen with bases and Appendix, one must realize that the listed value is for the their conjugate acids. Examples of un-ionized bases yield- proton donor form of the molecule, no matter what form is ing their ionized conjugate acids include ammonia and indicated by the name. See Table 2.2 for several worked ex- ammonium (reaction f ) and ephedrine and protonated amples of how the pKa is used to calculate pHs of solutions, ephedrine (reaction n). Whereas examples of ionized bases required ratios of [conjugate base]/[acid], and percent ion- yielding un-ionized conjugate acids are acetate forming ization (discussed later) at specific pHs. acetic acid (reaction h), phenobarbiturate yielding pheno- Just how strong or weak are the acids whose reactions in barbital (reaction j), and saccharate yielding saccharin (reac- water are illustrated in Table 2.1? Remember that the Kas or tion l). Complicated as it may seem at first, conjugate acids pKa’s are modified equilibrium constants that indicate the and conjugate bases are nothing more than the products of extent to which the acid (proton donor) reacts with water to an acid–base reaction. In other words, they appear to the form conjugate acid and conjugate base. The equilibrium for right of the reaction arrows. a strong acid (low pKa) in water lies to the right, favoring Representative examples of pharmaceutically important the formation of products (conjugate acid and conjugate acidic drugs are listed in Table 2.1. Each acid, or proton base). The equilibrium for a weak acid (high pKa) in water donor, yields a conjugate base. The latter is the product after lies to the left, meaning that the conjugate acid is a better the proton is lost from the acid. Conjugate bases range from proton donor than the parent acid is or that the conjugate the chloride ion (reaction a), which does not accept a proton base is a good proton acceptor. in aqueous media, to ephedrine (reaction h), which is an ex- Refer back to Equation 2.1 and, using the Ka values in cellent proton acceptor. Table 2.3, substitute the Ka term for each of the acids. For 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 13 Chapter 2 Drug Design Strategies 13 TABLE 2.1 Examples of Acid–Base Reactions (with the Exception of Hydrochloric Acid, Whose Conjugate Base [Cl! ] Has No Basic Properties in Water, and Sodium Hydroxide, which Generates Hydroxide, the Reaction of the Conjugate Base in Water Is Shown for Each Acid) Acid " Base Conjugate Acid " Conjugate Base Hydrochloric acid (a) HCl " H2O H3O" " Cl# Sodium hydroxide (b) H2O " NaOH H2O " OH#(Na")a Sodium dihydrogen phosphate and its conjugate base, sodium monohydrogen phosphate (c) H2PO4#(Na")a " H2O H3O" " HPO42#(Na")a 2# (d) H2O " HPO4 (2Na )" a H2PO42#(Na")a " OH#(Na")a Ammonium chloride and its conjugate base, ammonia (e) NH4"(Cl#)a " H2O H3O"(Cl#)a " NH3 (f) H2O " NH3 NH4" " OH# Acetic acid and its conjugate base, sodium acetate (g) CH3COOH " H2O H3O" " CH3COO# " a (h) H2O " CH3COO (Na ) # CH3COOH " OH#(Na")a Indomethacin and its conjugate base, indomethacin sodium, show the identical acid–base chemistry as acetic acid and sodium acetate, respectively. Phenobarbital and its conjugate base, phenobarbital sodium (i) " H2O H3O" " (j) H2O " " OH#(Na")a Saccharin and its conjugate base, saccharin sodium (k) " H2O H3O" " (l) H2O " " OH#(Na")a Ephedrine HCl and its conjugate base, ephedrine (m) " H2O H3O"(Cl#)a " (n) H2O " " OH# a The chloride anion and sodium cation are present only to maintain charge balance. These anions play no other acid–base role. 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 14 14 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry TABLE 2.2 Examples of Calculations Requiring the pKa TABLE 2.3 Representative Ka and pKa Values from the Reactions Listed in Table 2.1 (See the Appendix) 1. What is the ratio of ephedrine to ephedrine HCl (pKa 9.6) in the intestinal tract at pH 8.0? Use Equation 2.2. Hydrochloric acid 1.26 $ 106 #6.1 Dihydrogen phosphate 6.31 $ 10#8 7.2 [ephedrine] Ammonia (ammonium) 5.01 $ 10#10 9.3 8.0 ! 9.6 " log ! #1.6 Acetic acid 1.58 $ 10#5 4.8 [ephedrine HCl] Phenobarbital 3.16 $ 10#8 7.5 [ephedrine] Saccharin 2.51 $ 10#2 1.6 lndomethacin 3.16 10#5 4.5 [ephedrine HCl] ! 0.025 $ Ephedrine (as the HCI salt) 2.51 $ 10#10 9.6 The number whose log is #1.6 is 0.025, meaning that there are 25 parts ephedrine for every 1,000 parts ephedrine HCl in the intestinal tract whose environment is pH 8.0. hydrochloric acid, a Ka of 1.26 $ 106 means that the product 2. What is the pH of a buffer containing 0.1-M acetic acid of the molar concentrations of the conjugate acid, [H3O"], (pKa 4.8) and 0.08-M sodium acetate? Use Equation 2.2. and the conjugate base, [Cl#], is huge relative to the denomi- nator term, [HCl]. In other words, there essentially is no un- 0.08 pH ! 4.8 " log 0.1 ! 4.7 reacted HCl left in an aqueous solution of hydrochloric acid. At the other extreme is ephedrine HCl with a pKa of 9.6 or a 3. What is the pH of a 0.1-M acetic acid solution? Use the Ka of 2.51 $ 10#10. Here, the denominator representing the following equation for calculating the pH of a solution concentration of ephedrine HCl greatly predominates over containing either an HA or BH" acid. that of the products, which, in this example, is ephedrine (conjugate base) and H3O" (conjugate acid). In other words, pKa # log[acid] the protonated form of ephedrine is a very poor proton donor. pH ! ! 2.9 2 It holds onto the proton. Free ephedrine (the conjugate base in 4. What is the pH of a 0.08-M sodium acetate solution? this reaction) is an excellent proton acceptor. Remember, even though this is the conjugate base of A general rule for determining whether a chemical is acetic acid, the pKa is still used. The pKw term in the strong or weak acid or base is following equation corrects for the fact that a proton acceptor (acetate anion) is present in the solution. The pKa %2: strong acid; conjugate base has no meaningful equation for calculating the pH of a solution containing basic properties in water either an A# or B base is pKa 4 to 6: weak acid; weak conjugate base pKa 8 to 10: very weak acid; conjugate base getting stronger pKw " pKa " log[base] pKa &12: essentially no acidic properties in water; strong pH ! ! 8.9 2 conjugate base 5. What is the pH of an ammonium acetate solution? The This delineation is only approximate. Other properties pKa of the ammonium (NH4") cation is 9.3. Always bear also become important when considering cautions in in mind that the pKa refers to the ability of the proton donor form to release the proton into water to form handling acids and bases. Phenol has a pKa of 9.9, slightly H3O". Since this is the salt of a weak acid (NH4") and less than that of ephedrine HCl. Why is phenol considered the conjugate base of a weak acid (acetate anion), the corrosive to the skin, whereas ephedrine HCl or free following equation is used. Note that molar ephedrine is considered innocuous when applied to the skin? concentration is not a variable in this calculation. Phenol has the ability to partition through the normally pro- pKa1 " pKa2 tective lipid layers of the skin. Because of this property, this pH ! 2 ! 7.1 extremely weak acid has carried the name carbolic acid. Thus, the pKa simply tells a person the acid properties of the 6. What is the percentage ionization of ephedrine HCl (pKa protonated form of the chemical. It does not represent any- 9.6) in an intestinal tract buffered at pH 8.0 (see example thing else concerning other potential toxicities. 1)? Use Equation 2.4 because this is a BH" acid. Percent Ionization 100 % ionization ! ! 97.6% 1 " 10(8.0#9.6) Using the drug’s pKa, the formulation or compounding pharmacist can adjust the pH to ensure maximum water Only 2.4% of ephedrine is present as the un-ionized solubility (ionic form of the drug) or maximum solubility in conjugate base. nonpolar media (un-ionic form). This is where understand- 7. What is the percentage ionization of indomethacin (pKa 4.5) in an intestinal tract buffered at pH 8.0? Use ing the drug’s acid–base chemistry becomes important. Equation 2.3 because this is an HA acid. Note Reactions 2.4 and 2.5: 100 Conj. Conj. % ionization ! ! 99.97% Acid Base Acid Base 1 " 10(4.5#8.0) HA(un-ionized) " H2O D H3O" " A#(ionized) (Rx. 2.4) For all practical purposes, indomethacin is present only as the anionic conjugate base in that region of the intestine Conj. Conj. buffered at pH 8.0. Acid Base Acid Base BH"(ionized) " H2O D H3O" " B(un-ionized) (Rx. 2.5) 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 15 Chapter 2 Drug Design Strategies 15 Acids can be divided into two types, HA and BH", on the basis of the ionic form of the acid (or conjugate base). HA acids go from un-ionized acids to ionized conjugate bases (Rx. 2.4). In contrast, BH" acids go from ionized (polar) acids to un-ionized (nonpolar) conjugate bases (Rx. 2.5). In general, pharmaceutically important HA acids include the inorganic acids (e.g., HCl, H2SO4), enols (e.g., barbiturates, hydantoins), carboxylic acids (e.g., low–molecular-weight organic acids, arylacetic acids, N-aryl anthranilic acids, salicylic acids), and amides and imides (e.g., sulfonamides and saccharin, respectively). The chemistry is simpler for the pharmaceutically important BH" acids: They are all pro- tonated amines. A polyfunctional drug can have several pKa’s (e.g., amoxicillin). The latter’s ionic state is based on amoxicillin’s ionic state at physiological pH 7.4. Figure 2.4 Percent ionized versus pH for indomethacin (pKa 4.5) and ephedrine (pKa 9.6). ionized conjugate base form but results in a BH" acid (ephedrine HCl) decreasing its percent ionization to only 9.1%. An increase of 2 pH units essentially shifts an HA acid to complete ionization (99%) and a BH" acid to the nonionic conjugate base form (0.99%). Just the opposite is seen when the medium is made more acidic relative to the drug’s pKa value. Increasing the hydro- The percent ionization of a drug is calculated by using gen ion concentration (decreasing the pH) will shift the Equation 2.3 for HA acids and Equation 2.4 for BH" acids. equilibrium to the left, thereby increasing the concentration of the acid and decreasing the concentration of conjugate % ionization ! 100 (Eq. 2.3) base. In the case of indomethacin, a decrease of 1 pH unit 1 " 10(pKa#pH) below the pKa will increase the concentration of un-ionized 100 (protonated) indomethacin to 9.1%. Similarly, a decrease of % ionization ! (Eq. 2.4) 2 pH units results in only 0.99% of the indomethacin being 1 " 10(pH#pKa) present in the ionized conjugate base form. The opposite is A plot of percent ionization versus pH illustrates how the seen for the BH" acids. The percentage of ephedrine pres- degree of ionization can be shifted significantly with small ent as the ionized (protonated) acid is 90.9% at 1 pH unit changes in pH. The curves for an HA acid (indomethacin) below the pKa and is 99.0% at 2 pH units below the pKa. and BH" (protonated ephedrine, Table 2.1, reaction m) are These results are summarized in Table 2.4. shown in Figure 2.4. First, note that when pH ! pKa, the With this knowledge in mind, return to the drawing of compound is 50% ionized (or 50% un-ionized). In other amoxicillin. At physiological pH, the carboxylic acid (HA words, when the pKa is equal to the pH, the molar concen- acid; pKa1 2.4) will be in the ionized carboxylate form, the tration of the acid equals the molar concentration of its primary amine (BH" acid; pKa2 7.4) will be 50% protonated conjugate base. In the Henderson-Hasselbalch equation, and 50% in the free amine form, and the phenol (HA acid; pKa ! pH when log [conjugate base]/[acid] ! 1. An in- pKa3 9.6) will be in the un-ionized protonated form. crease of 1 pH unit from the pKa (increase in alkalinity) Knowledge of percent ionization makes it easier to explain causes an HA acid (indomethacin) to become 90.9% in the and predict why the use of some preparations can cause 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 16 16 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry near the drug’s pKa, only 50% will be in the water-soluble TABLE 2.4 Percentage Ionization Relative to the pKa form. There is a medical indication requiring intravenous Ionization (%) administration of indomethacin to premature infants. The intravenous dosage form is the lyophilized (freeze-dried) HA Acids BH Acids sodium salt, which is reconstituted just prior to use. pKa # 2 pH units 0.99 99.0 pKa # 1 pH unit 9.1 90.9 Drug Distribution and pKa pKa ! pH 50.0 50.0 pKa " 1 pH unit 90.9 9.1 The pKa can have a pronounced effect on the pharmacoki- pKa " 2 pH units 99.0 0.99 netics of the drug. As discussed previously, drugs are trans- ported in the aqueous environment of the blood. Those drugs in an ionized form will tend to distribute throughout problems and discomfort as a result of pH extremes. the body more rapidly than will un-ionized (nonpolar) mol- Phenytoin (HA acid; pKa 8.3) injection must be adjusted to ecules. With few exceptions, the drug must leave the polar pH 12 with sodium hydroxide to ensure complete ionization environment of the plasma to reach the site of action. In gen- and maximize water solubility. In theory, a pH of 10.3 will eral, drugs pass through the nonpolar membranes of capil- result in 99.0% of the drug being an anionic water-soluble lary walls, cell membranes, and the blood-brain barrier in conjugate base. To lower the concentration of phenytoin in the un-ionized (nonpolar) form. For HA acids, it is the par- the insoluble acid form even further and maintain excess al- ent acid that will readily cross these membranes (Fig. 2.5). kalinity, the pH is raised to 12 to obtain 99.98% of the drug The situation is just the opposite for the BH" acids. The un- in the ionized form. Even then, a cosolvent system of 40% ionized conjugate base (free amine) is the species most read- propylene glycol, 10% ethyl alcohol, and 50% water for ily crossing the nonpolar membranes (Fig. 2.6). injection is used to ensure complete solution. This highly al- Consider the changing pH environment experienced by kaline solution is irritating to the patient and generally can- the drug molecule orally administered. The drug first en- not be administered as an admixture with other intravenous counters the acidic stomach, where the pH can range from 2 fluids that are buffered more closely at physiological pH to 6 depending on the presence of food. HA acids with pKa’s 7.4. This decrease in pH would result in the parent un- of 4 to 5 will tend to be nonionic and be absorbed partially ionized phenytoin precipitating out of solution. through the gastric mucosa. (The main reason most acidic drugs are absorbed from the intestinal tract rather than the stomach is that the microvilli of the intestinal mucosa pro- vide a large surface area relative to that found in the gastric mucosa of the stomach.) In contrast, amines (pKa 9–10) will be protonated (BH" acids) in the acidic stomach and usually will not be absorbed until reaching the mildly alkaline intes- tinal tract (pH 8). Even here, only a portion of the amine- containing drugs will be in their nonpolar conjugate base form (Fig. 2.4). Remember that the reactions shown in Figures 2.3 and 2.4 are equilibrium reactions with Ka values. Tropicamide is an anticholinergic drug administered as Therefore, whenever the nonpolar form of either an HA acid eye drops for its mydriatic response during eye examina- (as the acid) or a B base (the conjugate base of the BH" tions. With a pKa of 5.2, the drug has to be buffered near acid) passes the lipid barrier, the ratio of conjugate base to pH 4 to obtain more than 90% ionization. The acidic eye acid (percent ionization) will be maintained. Based on drops can sting. Some optometrists and ophthalmologists Equations 2.3 and 2.4, this ratio depends on the pKa (a con- use local anesthetic eye drops to minimize the patient’s stant) and the pH of the medium. discomfort. The only atom with a meaningful pKa is the For example, once in systemic circulation, the plasma pyridine nitrogen. The amide nitrogen has no acid–base pH of 7.4 will be one of the determinants of whether the properties in aqueous media. drug will tend to remain in the aqueous environment of the blood or partition across lipid membranes into hepatic tissue to be metabolized, into the kidney for excretion, into tissue depots, or to the receptor tissue. A useful exercise is to calculate either the [conjugate base]/[acid] ratio using the Henderson-Hasselbalch equation (Eq. 2.2) or percent Adjustments in pH to maintain water solubility can sometimes lead to chemical stability problems. An example is indomethacin (HA acid; pKa 4.5), which is unstable in al- kaline media. Therefore, the preferred oral liquid dosage form is a suspension buffered at pH 4 to 5. Because this is Figure 2.5 Passage of HA acids through lipid barriers.  Chapter 2 Drug Design Strategies 17 (c) to design a test set of compounds to maximize the amount of information concerning structural requirements for activity from a minimum number of compounds tested. This aspect of medicinal chemistry is commonly referred to as quantitative structure–activity relationships (QSAR). The goals of QSAR studies were first proposed about 1865 to 1870 by Crum-Brown and Fraser, who showed that the gradual chemical modification in the molecular structure of a series of poisons produced some important differences Figure 2.6 Passage of BH" acids through lipid barriers. in their action.1 They postulated that the physiological ac- tion, #, of a molecule is a function of its chemical constitu- tion, C. This can be expressed in Equation 2.5: ionization for ephedrine (pKa 9.6; Eq. 2.4) and in- # ! f(C) (Eq. 2.5) domethacin (pKa 4.5; Eq. 2.3) at pH 3.5 (stomach), pH 8.0 (intestine), and pH 7.4 (plasma) (see examples 1, 6, and 7 in Equation 2.5 states that a defined change in chemical Table 2.2). Of course, the effect of protein binding, dis- structure results in a predictable change in physiological ac- cussed previously, can greatly alter any prediction of biodis- tion. The problem now becomes one of numerically defining tribution based solely on pKa. chemical structure. It still is a fertile area of research. What has been found is that biological response can be predicted from physical chemical properties such as vapor pressure, water solubility, electronic parameters, steric descriptors, COMPUTER-AIDED DRUG DESIGN: and partition coefficients (Eq. 2.6). Today, the partition coef- EARLY METHODS ficient has become the single most important physical chem- Initially, the design of new drugs was based on starting with ical measurement for QSAR studies. Note that Equation 2.6 a prototypical molecule, usually a natural product and mak- is the equation for a straight line (Y ! mx " b). ing structural modifications. Examples include steroidal log BR ! a(physical chemical property) " c (Eq. 2.6) hormones based on naturally occurring cortisone, testos- terone, progesterone and estrogen; adrenergic drugs based where on epinephrine; local anesthetics based on cocaine; opiate BR ! a defined pharmacological response usually ex- analgesics based on morphine; antibiotics based on peni- pressed in millimoles such as the inhibitory constant cillin, cephalosporin and tetracycline. Examples of proto- Ki, the effective dose in 50% of the subjects (ED50), typical molecules that were not natural in origin include the the lethal dose in 50% of the subjects (LD50), or the antipsychotic phenothiazines, bisphosphonates for osteo- minimum inhibitory concentration (MIC). It is com- porosis, benzodiazepines indicated for various CNS treat- mon to express the biological response as a recipro- ments. Although prototypical molecules have produced cal, 1/BR or 1/C significant advancements in treating diseases, this approach a ! the regression coefficient or slope of the straight line to drug development is limited to the initial discovery of the c ! the intercept term on the y axis (when the physical prototypical molecule. Today, it is more common to take a chemical property equals zero) holistic approach that, where possible, involves understand- ing the etiology of the disease and the structure of the recep- To understand the concepts in the next few paragraphs, it tor where the ligand (drug) will bind. Increasing computer is necessary to know how to interpret defined pharmacolog- power coupled with applicable software, both at reasonable ical concepts such as the ED50, which is the amount of the cost, has lead to more focused approaches for the develop- drug needed to obtain the defined pharmacological response ment of new drugs. Computational methodologies include in 50% of the test subjects. Let us assume that drug A’s mathematical equations correlating structure with biological ED50 is 1 mmol and drug B’s ED50 is 2 mmol. Drug A is activity, searching chemical databases for leads and rapid twice as potent as drug B. In other words, the smaller the docking of ligand to the receptor. The latter requires 3D ED50 (or ED90, LD50, MIC, etc.), the more potent is the sub- structure information of the receptor. Originally crystallized stance being tested. enzymes were the common receptors, and their spatial The logarithmic value of the dependent variable (concen- arrangements determined by x-ray crystallography. Today’s tration necessary to obtain a defined biological response) is software can calculate possible 3D structures of protein used to linearize the data. As shown later in this chapter, starting with the amino acid sequence. QSARs are not always linear. Nevertheless, using logarithms is an acceptable statistical technique (taking reciprocals ob- Statistical Prediction of tained from a Michaelis-Menton study produces the linear Pharmacological Activity Lineweaver-Burke plots found in any biochemistry textbook). Now, why is the biological response usually expressed as Just as mathematical modeling is used to explain and model a reciprocal? Sometimes, one obtains a statistically more many chemical processes, it has been the goal of medicinal valid relationship. More importantly, expressing the biolog- chemists to quantify the effect of a structural change on a de- ical response as a reciprocal usually produces a positive fined pharmacological response. This would meet three goals slope (Fig. 2.7). Let us examine the following published in drug design: (a) to predict biological activity in untested example (Table 2.5). The BR is the LD100 (lethal dose in compounds, (b) to define the structural requirements required 100% of the subjects). The mechanism of death is general for a good fit between the drug molecule and the receptor, and depression of the CNS. 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 18 18 Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry Figure 2.7 Plot of (BR $ 1,000) versus (PC $ 0.01). Figure 2.8 Plot of log BR versus log PC. The most lethal compound in this assay was chlorprom- logarithmic units. Similarly, the difference between chlor- azine, with a BR (LD100) of only 0.00000631 mmol; and the promazine’s partition coefficient and that of ethanol is 4.53 least active was ethanol, with a BR of 0.087096 mmol. In logarithmic units. Figure 2.8 shows the plot and regression other words, it takes about 13,800 times as many millimoles line for log BR versus log PC. It is an inverse relationship of ethanol than of chlorpromazine to kill 100% of the test (Eq. 2.8) between physicochemical property and biological subjects in this particular assay. response. Otherwise, the regression equation is excellent Plotting BR versus PC (partition coefficient) produces with a correlation coefficient of 0.9191. the nonlinear scatter shown in Figure 2.7. Note that com- log BR ! #1.1517 log PC # 1.4888 (Eq. 2.8) pounds 1 and 11 lie at a considerable distance from the re- maining nine compounds. In addition to the 13,800 times Although there is no statistical advantage to using the log difference in activity, there is a 33,900 times difference in of the reciprocal of the biological response, the positive rela- the octanol/water partition coefficient. An attempt at obtain- tionship is consistent with common observation that the bio- ing a linear regression equation produces the meaningless logical activity increases as the partition coefficient (or other Equation. 2.7 whose equation is: physicochemical parameter) increases. In interpreting plots such as that in Figure 2.9, remember that biological activity is BR ! #0.0000 PC " 0.0117 (Eq. 2.7) increasing as the amount of compound required to obtain the It is meaningless statistically. The slope is 0, meaning defined biological response is decreasing. The equation for that the partition coefficient has no effect on biological ac- the line in Figure 2.9 is identical to Equation 2.8, except for tivity, and yet from the plot and Table 2.5, it is obvious that the change to positive slope and sign of the intercept. The cor- the higher the octanol/water partition coefficient, the more relation coefficient also remains the same at 0.9191. toxic the compound. The correlation coefficient (r2) is 0.05, log 1/BR ! 1.517 log PC " 1.4888 (Eq. 2.9) meaning that there is no significant statistical relationship between activity and partition coefficient. Now, let us see if the data can be linearized by using the Partition Coefficient logarithms of the biological activity and partition coef- ficient. Notice the logarithmic terms. The difference be- The most common physicochemical descriptor is the mole- tween the LD100 of chlorpromazine and ethanol is only 4.14 cule’s partition coefficient in an octanol/water system. As TABLE 2.5 Data Used for a Quantitative Structure–Activity Relationship Study Compound Log 1/BR 1/BR BR BR $ 1,000 Log BR Log PC PC ! 0.01 1. Chlorpromazine 5.20 158,489.32 0.000006 0.006310 #5.2000 4.22 165.95869 2. Propoxyphene 5.08 120,226.44 0.000008 0.008318 #5.0800 2.36 2.2908677 3. Amitriptyline 4.92 83,176.38 0.000012 0.012023 #4.9200 2.50 3.1622777 4. Dothiepin 4.75 56,234.13 0.000018 0.017783 #4.7500 2.76 5.7543994 5. Secobarbital 4.19 15,488.17 0.000065 0.064565 #4.1900 1.97 0.9332543 6. Phenobarbital 3.71 5,128.61 0.000195 0.194984 #3.7100 1.14 0.1380384 7. Chloroform 3.60 3,981.07 0.000251 0.251189 #3.6000 1.97 0.9332543 8. Chlormethiazole 3.51 3,235.94 0.000309 0.309030 #3.5100 2.12 1.3182567 9. Paraldehyde 2.88 758.58 0.001318 1.318257 #2.8800 0.67 0.0467735 10. Ether 2.17 147.91 0.006761 6.760830 #2.1700 0.89 0.0776247 11. Ethanol 1.06 11.48 0.087096 87.096359 #1.0600 #0.31 0.0048978 Source: Hansch, C., Björkroth, J. P., and Leo, A.: J. Pharm. Sci. 76:663, 1987. BR is defined as the LD100, and PC is the octanol/water partition coefficient. 0003-0042_17865_Ch02.qxd 12/4/09 2:52 AM Page 19 Chapter 2 Drug Design Strategies