Within organic chemistry, there are a number of different functional groups. A functional group is a characteristic chemical structure that gives a molecule its properties. It can be difficult to remember the difference between all these groups, as some of the names can be very similar to each other. The functional groups are very important in relation to how well a drug binds in its target, and thus how well the drug works.

Simple groups

Alcohol
One of the simplest functional groups that exist is the alcohols. Alcoholsare substances on which there is an OH group. Alcohols are important in the development of new medicines, as they are good at making hydrogen bonds with targets, as alcohols can act as a hydrogen bond donor (HBD) via the hydrogen atom and act as a hydrogen bond acceptor (HBA) via the oxygen atom’s two free electron pairs. The alcohols also help to make the molecule more polar, so that it can be more easily dissolved in water. An alcohol group that sits directly on an aromatic ring is called a phenol.

Halid
A group as simple as the alcohols are the Halids. Halides are molecules to which a halogen atom is attached, e.g. F, Cl, Br or I. The halide shown is called an alkyl halide because the group is made up of an alkane, on which a hydrogen atom is replaced with a halogen.

Figure 27. Alcohol, here is ethanol.

 

Figure 28. Alkyl Halide

 

 

Figure 29. Substitution reaction between nucleophil and alkyl halide. The movement of electrons is indicated by blue. A nucleophile’s electrons react to the carbon atom, on which a halogen is attached. The electrons move further out onto the halogen, so the halogen is released. The nucleophile is now bound to the carbon atom.

 

A medicine containing bromine and iodine may therefore become bound to a nucleophile, which may adversely affect the effect of the medicine. The reaction shown in Figure 29 can also take place with chlorine as a halide. Chlorine is relatively often used in pharmaceuticals, but often it is an arylhalide. An aryl halide is a molecule in which the halogen sits on an aromatic ring. The reason why an SN2 reaction does not occur with an aryl halide is because the nucleophile in an SN2 reaction has to attack the molecule from the “back”, and this cannot be done in an aromatic ring.

The bond between fluorine and carbon is relatively strong, and an SN2 reaction can therefore not take place, regardless of whether it is an alkyl or aryl halide. Fluorine is often used to replace a hydrogen atom, as fluorine and hydrogen are about the same size and therefore take up the same space in the target. The replacement of hydrogen with fluorine changes the appearance of the molecule in relation to metabolic enzymes so that it does not break down. The replacement therefore makes it possible for functional groups that are normally broken down in the body to survive the encounter with different metabolic enzymes. This aspect is discussed in more depth in the article “Identification of the target and its structure”.

Carbonyls

Ketone
Ketones are hydrocarbons that contain a double-bonded oxygen atom. This functional group can function as HBA via the two free pairs of electrons of the double-bonded oxygen atom.

Aldehyde
Aldehydes are a form of terminal ketones, as they are only found at the end of hydrocarbon chains. The aldehydes can make the same bonds and interactions in the target as the ketones can, but they are rarely used in pharmaceuticals because they are easily oxidized into carboxylic acids. This is because aldehydes are more reactive than ketones because the aldehydes have a hydrogen atom, -CHO, which can be temporarily removed, and ketones do not.

Figure 30. Ketone

 

Figure 31. Aldehyd

 

Carboxylic Acid

Carboxylic acids contain two oxygen atoms. One of the two oxygen atoms is bound in an OH group, while the other oxygen atom is double-bonded to the carbon atom to which the OH group is bonded. The double-bonded oxygen atom is called the carbonyl part of the carboxylic acid. A carboxylic acid can give off a hydron (H+), also called a proton, which is why it is an acid. This property allows the group to become negatively charged, and in this state, the group is called a carboxylation. This ability can help make a drug more effective. If the target contains a positive charge, an ionic bond can form between the target and the drug if it has a negative charge. In addition to ionic bonds, a carboxylic acid will also be able to function both as an HBD and an HBA. At the pH value of the blood (approx. 7.4), the carboxylic acid will be ionized, i.e. a carboxylation, and here the carboxylic acid is a particularly strong HBA.

Figure 32. Carboxylic Acid

 

Ester
In addition to a carbonyl group, an ester contains another oxygen atom, which is bound by a single bond to a carbon atom and to the carbonyl group. An ester can act as an HBA via both oxygen atoms. The double-bonded oxygen atom is the one that is best because it “sticks out” from the molecule. Esters are often used to temporarily hide other functional groups such as carboxylic acids when a drug is to be absorbed into the body. Once the substance has been absorbed into the body, the body will split the ester into a carboxylic acid and an alcohol, so that the right functional group is present in the drug. This will be elaborated on in the article “The drug’s path through the body” and in the article “Optimization of the drug”.

Figure 33. Ester

 

Ether

An ether, contains an oxygen atom that is the bottom of two carbon atoms in the middle of a hydrocarbon chain. This group can function as an HBA.

Functional groups containing nitrogen

Amine
The simplest and most widely used functional group with nitrogen is the amine. The structure of amines can be compared to the structure of ammonia. Amines can be located inside the hydrocarbon chain, but can also be terminal. The terminated amines consist of a nitrogen atom bonded to a carbon atom and to two hydrogen atoms. These are called primary amines, as they are only bound to one carbon atom. Amines located inside the chain can be both secondaryand tertiary. The secondary amine is bonded to two carbon atoms, while the tertiary amine is bonded to three. Amines can act as HBD if the nitrogen atom is bound to a hydrogen, and as HBA via the nitrogen atom’s free electron pair.

Amid
Amides have an oxygen atom that is double-bonded to a carbon atom. To this carbon atom is also attached a nitrogen atom. Amides are the groups that form peptide bonds that put amino acids together into proteins. Amides can act both as HBA and HBD (but are not really good at it).

Heterocyclic rings

As described in the article “Organic chemistry and pharmaceuticals”, there are ring systems called aromatic rings when there are three double bonds in a six-membered ring. These aromatic rings, if present in a drug, can make Van der Waals interactions with the target. Nitrogen can also be an integral part of various ring systems. These are called heterocyclic molecules. As a whole, the ring system can be part of a hydrophobic interaction, where the nitrogen can sometimes act as HBA. In addition to nitrogen, oxygen and sulfur can also be part of a heterocyclic molecule.

 

Figure 34. Ether

 

Figure 35. Amines

 

Figure 36. Amid

 

Figure 37. Heterocyclic rings

 

  • Theory

    Introduction to Pharmaceuticals

    We have probably all used some form of medicine at some point in our lives. It can be a headache pill from time to time, antibiotics to fight an infection, an antihistamine for allergies, or asthma medication. You can probably think of a number of other types of medication that you have used at some point in your life, and it should be obvious that drugs have many different functions. A general definition of what a medicinal product is: “A medicinal product is a product which is intended to be administered to humans or animals in order to prevent, alleviate, treat or cure disease, disease symptoms and pain, or to affect bodily functions”. While this definition is easy to understand, the development of drugs is far from simple. The broad definition of a medicinal product also allows a large group of very different chemical substances to be used.


    It requires interdisciplinary understanding and creativity to develop new drugs, and problems will undoubtedly arise during the process. These problems can be of various kinds. There may be complications in the absorption of the drug into the body, there may be toxic, i.e. toxic, side effects, and it may occur that the active substance in the drug does not bind sufficiently to its     At the end of the day, Due to these possible problems, this material will give you insight into what things you need to take into account when designing your own medicine.

    A cure for psoriasis

    Before the actual development of a new drug can begin, it is necessary to decide which disease you want to treat. In the following, we will take as our starting point how a drug was developed for the disease psoriasis. Psoriasis is a skin disease in which the cells in the skin begin to divide more than normal. This forms a thicker skin that peels heavily.

    Once you have decided which disease you want to treat, you need to find a target. A target is the place in the body where a drug must bind to in order to produce the desired effect. A target can be many things, but virtually all targets are proteins in the body. These can be, for example, transport proteins, enzymes or receptors. How a drug binds to its target and thereby exerts a function in the body is described by the drug’s pharmacodynamics. Pharmacodynamics is the part of drug development that describes what a drug does to the body. You can read more about this in the article “Identification of Target and its Structure”. (Conversely, pharmacokinetics is the description of what the body does to the drug.)

    When developing new drugs, a wide range of different substances are systematically examined for their binding to the target found. In the 1980s, it was discovered that vitamin D had a positive effect on a special type of cancer cells. By giving vitamin D to the cells, it was seen that they did not grow as quickly. The theory was developed that cancer patients who had the special cancer cells in their bodies could be treated by vitamin D. However, this did not prove possible due to a serious side effect. Vitamin D also regulates the amount of calcium in the blood, and when the substance is dosed in the relatively large amount necessary for effective treatment, the concentration of calcium increases so much in the blood that calcium precipitates in the kidneys, among other things. This is called a calcemic effect. It was therefore necessary to develop new substances that had the good growth-inhibiting effect on the cancer cells, but had no calcemic effect – more on this later.

    In order for vitamin D to act on a cell, the vitamin D receptor (target for Vitamin D) must be present, as it was in the given cancer cells. Figure 1 shows the vitamin D receptor bound to a ligand.

     

    Figure 1. Shows the vitamin D receptor with calcipotriol bound to it [Source: www.pdb.org; H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242].

    Vitamin D binds to the vitamin D receptor via a series of chemical bonds in the right positions. This activates the receptor and acts as an agonist on the receptor. In order to develop new candidates for testing, it is fundamental to know something about the bonds between target and drug. This can be read about in the article “Organic Chemistry and Pharmaceuticals”. When vitamin D binds to its receptor, hydrogen bonds are formed, as can be seen in Figure 2, and some hydrophobic interactions, as can be seen in Figure 3.

    The desire to develop new substances with a good effect on cell growth and minimal calcemic effect was coupled with knowledge of the vitamin D receptor. They began to optimize the structure of vitamin D, i.e. produce analogues that affected the target as an agonist, but which did not have a calcemic effect. First of all, it was necessary to find out which functional groups on the vitamin D molecule are individually necessary for the “agonistic” activity. This can be done via a SAR study (Structure Activity Relationship study), where the different functional groups are removed individually from the molecule, and tested for activity against the target – in this case, the growth of the cancer cells. In this way, it is possible to either rule out or confirm in stages whether the group in question is necessary to maintain the effectiveness of the medicine. You can read more about this in the article “Optimisation of the medicine”. For vitamin D, it was found that the inhibitory effect on cell growth was preserved when the basic structure of vitamin D was preserved. If you instead changed a side group, it resulted in a reduced calcemic effect (Fig. 4). A special analogue was found that was a good agonist and had no calcemic effect. This analogue was called calcipotriol.

    It turned out that calcipotriol did not show a calcemic effect because the substance is very quickly broken down/metabolized in the liver. Therefore, the drug was only available in the blood for a limited period of time. Unfortunately, the time period was so short that it did not have a sufficient effect on the cancer cells. It was decided that calcipotriol was not suitable as an oral drug. (At LEO Pharma, work continued to find a good vitamin D analogue, and the substance seocalcitol was developed. This substance was tested in cancer patients and had a positive effect, but unfortunately, the calcemic effect appeared after treatment for a long time, and the development of seocalcitol had to be stopped. )

    Figure 2. Shows calcipotriol and the amino acids from the vitamin D receptor that form hydrogen bonds together [Source: www.pdb.org; H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242].

    Figure 3. Shows calcipotriol and the amino acids from the vitamin D receptor that form hydrophobic interactions [Source: www.pdb.org; H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242].

    Shortly after calcipotriol was discarded as an oral drug, it was observed that a Japanese patient with osteoporosis who was treated with vitamin D as a “positive side effect” had his psoriasis significantly reduced. Independently of this, it was also found that the vitamin D receptor is found in the cells of the skin. These two findings were linked by LEO Pharma and they therefore tried to use calcipotriol instead for topical treatment of psoriasis. In vitro experiments were conducted with calcipotriol on skin cells containing the vitamin D receptor. Calcipotriol was found to have the same positive effects as vitamin D on skin cells. There was therefore a basis for continuing to work with calcipotriol. They began to investigate how calcipotriol was metabolized. The metabolism of calcipotriol is part of pharmacokinetics, and you can read more about this in the article “The drug’s path through the body”. In vitro, they tested how calcipotriol was metabolized by adding an extract extracted from a liver. Figure 5 shows the metabolites of calcipotriol that were identified.

    Figure 4. Shows vitamin D3 and the side chain that has been altered to form the drug Calcipotriol.

    LEO Pharma’s showed that calcipotriol’s metabolites are not toxic. However, this is not always the case, and you therefore have to take a step back in the development and change the structure of the drug again. In this way, you will many times in the development of a drug. Whether it is to change the toxic metabolites, or because the drug does not have the desired effect, you have to go back and change the structure of the drug again and again until the right analogue is produced. This is one of the reasons why the development of a drug takes many years from the start of research until you can put a drug on the market.

    When it has been shown through various in vitro experiments that the drug binds well to the target and how it is metabolized, it is necessary to conduct experiments with animals (in vivo experiments). The vast majority of substances are discarded after in vitro tests and only a fraction are tested in vivo. The in vivo experiments are carried out to confirm that the results obtained in the in vitro experiments also apply to a living organism. After LEO Pharma had done in vitro metabolism experiments (with the liver extract), they switched to in vivo metabolism experiments. Rats and mini-pigs were given radioactive calcipotriol, which could be followed in the body. It turned out that exactly the same metabolites were formed in the animals as were found in the in vitro experiments. It is also important to test for metabolites in animals because some of the metabolites formed can have an undesirable side effect. Metabolism tests are not the only in vivo tests that are being done. It is also tested to see if the drug has the right pharmacodynamic effect in a living organism.

    Once it has been shown that the drug has the right effect in animals, and it has no unwanted side effects, you will start testing the drug on humans. There are three different phases of what are called clinical studies: phase I, II and III. In phase I studies, the drug is tested on healthy volunteers to see if there are any side effects in humans that were not seen in the test animals. When calcipotriol was tested on the skin of healthy people, it was found that there were no serious side effects of the drug – in particular, no calcemic effect was observed. In phase II, the trials are expanded to include patients, to be able to prove that the drug relieves the disease, and to test which dose should be used. Finally, you go to phase III, where you use a large group of patients.

    Calcipotriol was also tested on a large group of psoriasis patients. A great improvement in the skin was seen and it was now possible to market calcipotriol.

    Figure 5. Calcipotriol is metabolized in the body by first turning an alcohol into a ketone, and then removing a double bond.

    Figure 6. Before and after picture when treating psoriasis with calcipotriol [Source: LEO Pharma].

    Identification of the target and its structure

    Before we can make a drug, it is necessary to know something about the disease to be treated and the target to be targeted. A target is in the vast majority of cases a protein and knowledge about proteins and their composition is of course important.

    There are many different proteins, transport proteins, structure proteins, enzymes, receptors and more. The most important are enzymes and receptors, which also constitute the vast majority of targets for the drugs we know today.

    Enzymes

    A chemical equilibrium can set itself quickly or slowly, depending on how reactive the reactants are. If a reaction is very slow and you want to increase the speed, you need to use a catalyst. Enzymes are catalysts in that they increase the speed of reaction without even being consumed during the process. Enzymes cannot cause reactions that would not normally take place to happen, but they can increase the speed of reactions in both directions for reactions that would normally occur. Therefore, an equilibrium will adjust faster. The way enzymes increase the reaction rate is by lowering the activation energy, but enzymes do not change where the equilibrium lies.

    An enzyme is a protein, and proteins consist of amino acids linked together by peptide bonds. There are twenty different amino acids in the human body, each of which has a variable group, called the R group. Since enzymes are proteins, enzymes are also folded into a certain three-dimensional structure. Due to the three-dimensional structure, there will be different clefts/holes in the protein and in some of them, the reactant(s) (which for enzymes are called the substrate(s)) fit perfectly in, and in such a cleft, the reaction is catalyzed. The gap where the substrate fits in is called the active site. The active site is very specific. This means that only a few substrates with a very similar structure will fit in. This is because in the active site there are a number of R-groups from the amino acids that can make certain bonds with the substrate. These can be both intermolecular and intramolecular bonds. The intramolecular bonds can be temporary, but can also be permanent (which is often the case for inhibitors, see later). If these bonds are not created, the substrate will naturally not bind to the enzyme.

    • In a solution where a reaction is to take place between two molecules, the two molecules must bump into each other correctly in order to react. Here, the enzyme helps by collecting the two right molecules and placing them correctly in relation to each other. The reaction process is therefore made easier.
    • When a reaction is to take place, some covalent bonds often have to be broken. The enzyme makes the covalent bonds in the substrate weaker as the enzymes pull on the bonds. This makes splitting the substrate into two easier.
    • A reaction sometimes takes place by converting the reactant/substrate into an intermediate product. For this intermediate, some functional groups must sometimes be used that do not come from the reactant/substrate itself. Enzymes can add temporary functional groups to the substrate. This is done by means of. The R groups in the enzyme that can “transfer” their functional group or parts of them to the substrate. A number of reactions then take place so that the enzyme’s functional groups are restored.

    In addition, some enzymes may require a different molecule in the active site to function. This can either be a coenzyme (molecule containing carbon), a cofactor (metal ion e.g. copper, zinc or iron) or a prosthetic group (molecule that is constantly bound to the enzyme).

     

    Figure 7. Activation energy for a reaction without the use of enzyme and with the use of enzyme. When using enzymes, a lower activation energy is seen and the reaction therefore takes place more easily.

     

    Induced fit

    In the past, it was thought that a substrate’s binding to the active site worked in the same way as when a key fits into a lock. The way in which a substrate binds to the enzyme was therefore described using the “lock and key” model. However, there was one problem with this model. It could not explain how several similar substrates could fit into the enzyme. According to the model, there would only be one substrate that would be specific enough to fit in, just like a lock can only be opened by one particular key.

    Figure 8. The enzyme adapts to the substrate by a conformational change.

     

    A slightly different model has now been proposed, which is based on the fact that a substrate does not have the perfect structure in relation to the active site. Instead, the active site adapts to the substrate, and thus several substrates that are similar to each other can fit into the active site. This is called induced fit. When a substrate approaches an empty active site, bonds will form between enzyme and substrate. This causes a conformational change in the enzyme, so that the enzyme closes around the substrate. This means that the enzyme will be more tightly packed around the substrate, so that more of the necessary bonds can be formed. A conformation change thus simply means that the enzyme changes its three-dimensional structure in an area.

    Induced fit also has another very important function, namely the exclusion of water. When the enzyme closes together, water will automatically be squeezed out of the active site. This is convenient, as some reactions are not favorable when water is present. This may be due to the fact that water forms hydrogen bonds with the target molecule, so that the target molecule will not be able to form the necessary bonds with the drug.

    Inhibitors

    It was mentioned in the case story that there are two types of drugs, agonists and antagonists. Inhibitors can be said to be the enzymes’ antagonists. Inhibitors bind to the enzyme’s active site, just like the substrate does, but instead of activating the enzyme, the enzyme’s activity is inhibited when an inhibitor binds. The reaction rate of the enzyme is slowed down because the inhibitors interfere with the binding of substrate to the active site.

    There are different types of inhibitors. An inhibitor can bind covalently to the enzyme, so that the enzyme is constantly inhibited. These substances are called irreversible inhibitors. Many harmful substances are irreversible inhibitors, for example nerve gases are irreversible inhibitors. However, there are also many non-harmful substances that are irreversible inhibitors such as Antabuse. This is a drug that inhibits the enzyme alcohol dehydrogenase, which breaks down the alcohol we consume. An inhibitor can also bind in the active site for a short time with non-covalent bonds. These substances are therefore called reversible inhibitors.

    Receptors

    Receptors are very similar to enzymes in their structure, but are usually located on a cell membrane. Receptors, like enzymes, also contain a cleft to which a molecule binds. The cleft is called the binding site, where in the enzymes it is called the active site. The reason why it cannot be called an active site in the receptors is that there is usually no conversion of a precursor in this area. When a ligand (which is the same for a receptor as a substrate is for an enzyme) binds in the binding site, a conformational change occurs, i.e. an induced fit. This happens in all receptors. What this change of conformation entails, however, is different.

     

     

    Figure 9. Illustration of the general mechanism of a G-protein-coupled receptor. When a ligand binds to the receptor, a conformational change occurs in the receptor, so that an active site appears inside the cell so that a G protein (bound to GDP) can bind. When the G-protein is bound to the active site, the G-protein will be split into three parts, where the part bound to GDP will have GDP replaced with GTP. This part of the G protein can now move to another place in the cell, where it will bind to another enzyme, thereby activating this.

     

    G-protein coupled receptors

    As can be seen from Figure 9, the conformational change from the binding to a ligand from the outside can cause the part of the receptor inside the cell to also change its structure. This creates a new binding site, which is somewhat similar to an active site, as it is able to function as an enzyme. A new ligand (G-protein, bound to GDP) from the cell’s interior can now bind to the active site, thereby splitting the G-protein inside the cell. A part of the G protein can then send a signal on to a membrane-bound enzyme inside the cell, which is then activated. The functions of this enzyme vary greatly depending on the type of enzyme to which the G protein binds. These receptors are called G-protein coupled receptors.

     

    Ion channels

    Another kind of receptor is the ion channels. These consist of five protein subunits that go all the way through the cell membrane, thereby forming a channel through the membrane. This allows ions to enter and exit the cell. The five subunits are not exactly the same, as in one of them there is a binding site. When a ligand binds to the binding site, the ion channel is activated so that the channel opens. The conformational change in an ion channel takes place by the five subunits pulling away from the center, so that a channel is formed.

    A drug that works on an ion channel can also work in two different ways. Either as a blocker or as an opener of the channel. A blocker will make sure that the channel is constantly closed and is therefore an antagonist. An opener will keep the ion channel open all the time and is an agonist.

     

    Figure 10. Figuren illustrerer hvordan en iokanal er placeret i en cellemembran og hvordan ionkanalen åbner sig når en ligand bindes til ionkanalen

     

    Transport proteins

    Transport proteins are the body’s “smugglers”, as they smuggle molecules across cell membranes, as the molecule itself is too polar to cross. A transport protein is therefore hydrophobic/nonpolar on the outside, so that it can sit inside the membrane, but is hydrophilic/polar on the inside, so that polar molecules can be transported into the protein. The transport protein closes around the molecule to be transported. It is then transported through the cell membrane and released on the other side.

     

    Figure 11. Illustrates how a drug can be transported across a cell membrane via a transport protein.

     

    A drug that acts on a transporter protein can work in different ways. The medicine can work by being transported itself across the cell membrane by mimicking the molecules that are normally transported across the membrane. The medicine can also work by blocking the transport protein, thereby inhibiting the absorption of the substance that the protein transports. For example, cocaine works in the central nervous system by inhibiting the reuptake of serotonin and dopamine through a transport protein. This inhibition will cause there to be more serotonin and dopamine in the synaptic cleft between the two nerve endings, and there will therefore be a prolonged and increased signal through the nerves.

    Table 1

    Drug Target Mechanism of Action
    Receptors Agonist / Antagonist
    Enzymes Reversible / Irreversible
    Ion Channel Blocker / Opens

     

    To sum up, there are a number of different types of proteins that can act as a drug target. These are specifically receptors, enzymes and transport proteins. The way in which these drug targets work has been described above and can be summarised in Table 1. In addition to proteins, there are a number of other types of drug targets. These can be DNA and RNA, for example.

    Tolerance and dependence

    If a cell is exposed to an antagonist for a long time, the cell will receive no signal from the receptor. To compensate for this, the cell will upregulate the formation of new receptors (Figure 12b). The cell can now again detect signals from the natural ligand (Figure 12d). Therefore, in order to get the desired medical effect using the antagonist, a higher dose of the drug must be given (Figure 12c). This cycle, in which the cell makes more receptors and a higher dose is given, can keep repeating. The state the cell gets into, and thus also the state the body gets into, is called tolerance, as the body needs more of the drug to achieve the “normal” effect.

    When the intake of the drug stops, all the receptors are released. This means that all the new receptors as well as the original ones will be activated by the natural ligand (Figure 12e). This is very uncomfortable, and one will feel an urge to take the drug again because it will feel like a normal response. This is called addiction because you have to take the drug to feel good. Over a longer period of time, the number of receptors will fall back to a normal level (Figure 12f), but until then the patient is in weaning.

    Figure 12. The illustration shows how tolerance and dependence on a drug can occur.

     

    Organic chemistry and pharmaceuticals

    If you know your target and the amino acids involved in binding to a drug, it is possible to design a drug based on chemical knowledge. The functional groups of the medicinal product must be adapted so that the right interactions can take place between the target and the medicinal product.

    Pharmacophore and scaffold

    The pharmacophore is an expression of the functional groups that are in a drug, and thus which bonds are essential for the activity of a drug. A scaffold , on the other hand, is a basic structure that provides a good starting point for the development of the drug.

    When developing a new drug, you must first and foremost have a good basic structure, i.e. a good scaffold. To a scaffold, you can bind different functional groups (R-groups) that must make interactions to the target, so that the best possible binding is achieved. A good scaffold is a small molecule where it is possible to attach functional groups throughout the molecule. The scaffold and its functional groups can be compared to a spider because a spider has a body with legs distributed evenly around the entire body, just like a scaffold should preferably have.

    Do you think that indole as seen in figure 14 is a good scaffold? What about β-lactam, hydantoin, and a steroid?

    Once a scaffold is selected, the page groups are primarily selected based on what binding interactions they can make. The bonds that exist in the medicine itself are different from the bonds that exist between a medicine and a target. The bonds that take place in the drug itself are called intramolecular bonds, or colloquially known as covalent bonds. The bonds that exist between the drug and the target are called the intermolecular bond types, as these bond types exist between molecules. There are several different intermolecular bonds and will be discussed in this text.

    But why do atoms bind together at all? The answer is that they bond to each other because they want to look like one of the noble gases. A noble gas is an atom that is in the 8th main group of the Periodic Table. Atoms would very much like to have the character of a noble gas, because a noble gas is very stable, as it fulfills the octet rule of having 8 valence electrons. This is also why carbon makes exactly four bonds to other atoms. Carbon has four valence electrons and by taking up four more electrons from other atoms, who are willing to donate or share an electron, the octet rule will be met. This can be fulfilled by four atoms or by fewer atoms, because some atoms donate more than one electron, so that a double or triple bond is formed between the donor and carbon atom.

    Figure 13. The spider model with a body, also called a scaffold, in the middle, with legs distributed all around with functional groups attached.

     

    Figure 14. Different scaffolds with R-groups that can be varied so that the molecule fits into the target.

     

    Figure 15. Bond-forming electrons in methane, ammonia and water, respectively, as well as available electron pairs for ammonia and water.

     

    The same is true for all other atoms; The number of bonds an atom can form depends on how many valence electrons the atom has. If the atom has five valence electrons (e.g. nitrogen), it lacks three electrons to reach a total of eight electrons in its outermost shell. Therefore, it can form three bonds to other atoms. An atom with six valence electrons (e.g. oxygen) can therefore form two bonds, etc.

    An atom with six valence electrons, e.g. the oxygen atom inH2O, has two pairs of electrons, which are made up of the atom’s own electrons. These pairs of electrons are called free pairs of electrons (or lone pairs) and appear as two dots in conjunction with the atom.

    Intermolecular bonds

    Electronegativity and ionic bonds
    The different atoms in the Periodic Table have different electronegativity (EN). Electronegativity is a measure of an atom’s ability to draw electrons to itself through a bond to another atom. If two atoms that are bound to each other have an electronegativity that is close to each other, e.g. a hydrogen atom bound to a carbon atom, there will not be any of the atoms that will be electronegative enough to be able to pull the electrons in the bond to themselves. Therefore, there will not be a large displacement of charges through the bond. It is therefore said that the electrons are equally distributed through the bond, and the bond is therefore covalent. A covalent bond between a carbon atom and a hydrogen atom is nonpolar, as there is only a small difference in the electronegativity of the atoms. If, on the other hand, there is a very large difference in electronegativity between two bonded atoms, a difference of more than two units, there will no longer be a covalent bond. This is because in such a situation, the electrons will be drawn completely onto one of the atoms in the bond. An example is NaCl, which has a difference in electronegativity of 2.1 units. A bond between Na and Cl is called an ionic bond. An ionic bond is not a covalent bond formed by two electrons, but instead consists of two oppositely charged ions. Ionic bonds are the strongest of the intermolecular bond types, but they become weaker the further away the two charged molecules get from each other. Since the ionic bonds are the strongest bonds, they are often also the first to be formed when a drug is to bind to its target. This can help to pull the medicine into the correct position.

     

    Figure 16. Illustration of an ionic bond between a negatively charged carboxylic acid and a positively charged amine.

     

    Figure 17. Illustration of how Van der Waal’s powers arise.

     

    Van der Waals interaction
    Van der Waals interactions, also called London bonds, occur in the hydrophobic parts of molecules. This is because the regions of a molecule that are considered neutral and nonpolar are never really neutral. There will always be a charge shift in the molecule due to the electronegativity of the different atoms. Therefore, a very slight temporary displacement of charges occurs in the molecule. A drug and a target can therefore be attracted to each other when they have opposing charge shifts and form a Van der Waals interaction.

    Hydrogen bonds
    Hydrogen bonds occur between two molecules, one of which is an electron-rich atom, such as oxygen or nitrogen, that has an excess free electron pair, which can donate the electrons to an electron-poor hydrogen. An electron-poor hydrogen is a hydrogen atom that is bonded to a more electronegative atom than itself, and therefore this atom will pull the electrons from the intramolecular bond with the hydrogen atom towards itself. The hydrogen atom will now be slightly positively charged and a bond will occur between a slightly positively charged and a slightly negatively charged atom. A molecule with such a hydrogen atom is called a hydrogen bond donor (HBD) because it can donate its hydrogen atom. The electron-rich atom is called a hydrogen bond acceptor (HBA) because it can accept a hydrogen atom from another molecule. These two abbreviations will be used in the rest of the material.

    Figure 18. The figure shows a hydrogen bond between an alcohol in a drug and an amine in the target.

     

    There are functional groups that possess both functions because they contain both an electron-poor hydrogen atom and an electron-rich oxygen or nitrogen atom. The most important in this group of both donors and acceptors are alcohols (-OH) and amines (-NH2).

    Hydrophobic interactions
    A drug that has a hydrophobic area, for example an aromatic ring, is water repellent in this particular area. Since the hydrophobic areas are water-repellent, these areas would very much like to be close to other water-repellent areas in the target. When an interaction occurs between two water-repellent molecules, a hydrophobic interaction is formed between the molecules.

    Molecules that mainly contain carbon and hydrogen are highly hydrophobic/non-polar and cannot be mixed with water, just as oil and water cannot be mixed with each other. These molecules are much more soluble in hydrophobic solutions, and they are said to be fat-soluble. Functional groups that contain oxygen or nitrogen can make hydrogen bonds. Since these groups can make hydrogen bonds, water molecules can wrap themselves around the groups via a lot of hydrogen bonds. Molecules containing functional groups with nitrogen and oxygen will therefore be polar/hydrophilic in the area where the group is located, and water can therefore wrap around the functional groups.

     

    Figure 19. The figure shows how water can interact with both the drug’s and target’s binding groups. When water is removed, a bond can now occur between the medicine and the target.

     

    Table 2: Types of intra- and intermolecular bonds, and their bond strength.

      Type Strength
    Intramolecular Covalent Bond 200 – 450 kJ/mol
    Intermolecular Ionic Bonding 20 – 40 kJ/mol
    Hydrogen bonding 10-30 kJ/mol
    Hydrophobic interaction 4-8 kJ/mol
    Van der Waals interaction 2-4 kJ/mol

     

    Organic chemistry

    As mentioned earlier, carbon atoms can form covalent bonds to each other, thus forming long chains. If you imagine two, three, four or more carbon atoms put together in a straight chain, you have what is called an alkane, see Figure 20. If you replace two bonds of two hydrogen atoms with another bond between two carbon atoms, you get a double bond somewhere in the chain, and the molecule is now called an alkene. If you replace two more hydrogen atoms with an extra bond in the same place as the previous bond, so that there is now a triple bond between two carbon atoms in the chain, what is called an alkyne is obtained. These molecules are called hydrocarbons or hydrocarbons. When there is neither a double nor a triple bond present in the chain, the hydrocarbon is said to be saturated. Alkanes are therefore saturated, while both alkenes and alkynes are unsaturated. Figure 20 also shows a line formula for both the alkane, the alkene and the alkyne. Line formulas are read so that each bend indicates a carbon atom and one line leading between each bend indicates one bond. For each carbon atom there must be four bonds, and if there are no four lines from a kink, the rest of the bonds must be for hydrogen atoms. For example, the kinks in the alkane are equal to CH2.

     

    Isomerism (branches and ring systems)

    Hydrocarbons don’t just have to be perfectly straight chains. They can also be branched, which is called isomeri. This means that a chain consisting of four carbon atoms, for example, does not have to be a chain that is four carbon atoms long. This means that the two molecules have the same number of carbon and hydrogen atoms, but that they are arranged differently, so that it gives different structures of the molecules.

    In addition to the fact that hydrocarbons can be branched, they can also form rings. Rings with many different numbers of carbon atoms can be formed. The most common sizes of rings consist of either five or six carbon atoms, because they are most stable in their structure. In these rings, double and triple bindings can also be made, where double bonds are by far the most seen. If there are three double bonds in a six-membered ring, this is called an aromatic. The name originates from the 1800s, when aromatics were found when extracts from plants that smelled (had aroma). To an aromatic ring, different groups can be attached, which are called side groups. An aromatic ring can have these side groups tied in different positions. An aromatic can be substituted in the ortho, meta, and para positions in relation to a side group. The ortho position is the position that sits right next to the side group, the meta-position is the position that is two carbon atoms away, and the para position is the position that sits three carbon atoms away or just opposite the side group, see Figure 22.

    Stereochemistry

    In addition to binding interactions between the drug and the target, it is important to keep in mind that the three-dimensional structure of the drug can cause problems in connection with binding. A famous example is the development of the active ingredient in the antidepressant, Citalopram, which will be described later.

    Stereochemistry is the part of chemistry that deals with the three-dimensional structure of a molecule. There are several forms of stereochemistry, e.g. cis-trans isomerism and mirror-image isomerism. Here, mirror image isomerism will be briefly described, as this is extremely important for the effect of drugs.

    As mentioned earlier, a carbon atom always makes four bonds. If there are no double or triple bonds present, a carbon atom will form a tetrahedral structure.

     

    Figure 20. Adding extra bonds to a hydrocarbon.

     

    Figure 21. Unbranched butane shown on the left and branched isobutane/2-methylpropane shown on the right. These molecules are two different isomers with the same molecular formula: C4H10.

     

    Figure 22. Different sizes of rings, as well as an aromatic ring containing three double bonds. The substitution pattern of aromatics with ortho(o)-, meta(m)-, and Para(P) substitution is indicated. In addition, the fragrance in vanilla is illustrated, which contains an aromatic ring.

     

    In 1989, the Danish company Lundbeck developed an antidepressant drug called Citalopram. Citalopram has a single stereocentre, which is indicated by an asterisk in Figure 26, and citalopram is therefore a chiral molecule with two enantiomers. Citalopram was initially marketed as a mixture consisting of 50% of one enantiomer and 50% of the other enantiomer, a racemic mixture. Later, Lundbeck found out that it was actually only one enantiomer that was responsible for binding to the target and thus the biological effect, namely (S)-(+)-citalopram. Lundbeck started selling this one enantiomer in its pure form instead, and now called the drug escitalopram. The result of the change from a racemic mixture, where half of the content was not active, to a drug where all the ingredients are active, is a drug that is far more potent and therefore a lower dose is needed to give the desired effect. Having a more potent compound is an important aspect of drug development, as it helps to reduce the number and magnitude of unwanted side effects.

     

    Figure 23. This figure illustrates how two seemingly identical structures do not fit into the same shape (the enzyme). No matter how you try to turn the structure to the left, it will never fit into the mold.

     

    If four different atoms are bound to the carbon atom, the carbon atom is called a stereocenter (marked with an *), and the molecule is typically chiral. This means that a mirror image of the molecule will be as little identical as your two hands are identical. No matter how many times you twist and turn your hands, they will never be exactly the same, as they are mirrored in relation to each other. Your hands are therefore stereoisomers of each other. It’s exactly the same with chiral molecules. They will never be identical. You can determine whether a molecule is chiral by drawing a plane of symmetry through the center of the molecule. The symmetry plane is drawn so that two halves of a molecule that can be identical come on opposite sides of the plane. If the two sides are different, the molecule is chiral, but if a plane of symmetry cannot be drawn, the molecule is achiral. If you draw a plane of symmetry all the way through a spoon, you will see that both sides are the same. If you draw a plane of symmetry through your hand, no matter which way the plane is facing, you will never be able to get the two sides to be the same, and the hand is therefore chiral.

    Figure 24. Tetrahedral structure of a carbon atom with four different groups attached to it.

     

    All enzymes and receptors in the body have adapted according to which isomers of their substrates existed in nature. For example, all amino acids are the same isomer (except for glycine, which has no stereocenter), and all the enzymes that are supposed to break down proteins into amino acids can only recognize this one isomeric form. It is therefore important in the development of new drugs to think about the stereochemistry of the molecule. You have to be aware that if the molecule you design resembles an amino acid, for example, then it must have the right stereochemistry.

    If it turns out that a potential drug has no effect in the body, it does not have to be because the general structure of the drug is wrong. It may just be that the molecule does not fit into the target because the stereochemistry does not match the binding areas in the target.

    Figure 26. Shows the two enantiomeric forms of the drug cialopram. The stereo centre is indicated by an asterisk.

     

    Figure 25. The figure shows a hand and a spoon through which a mirror is illustrated. It can be seen that the spoon is the same on both sides of the mirror and the hand is not the same on both sides of the mirror, and therefore the spoon is not chiral and the hand is chiral. This theory can be applied to chemical molecules, as illustrated to the right in the figure for two simple molecules.

     

    The drug's path through the body

    In addition to the fact that a drug must be designed to bind to the target, it is important to take into account that the drug must be able to cope with a lot of challenges on its way through the body. The drug must resist stomach acid and digestive enzymes, be absorbed across the intestine, resist metabolic enzymes in the liver, and avoid accumulation in fat tissue. It must have a suitable lifespan that is not too long and is not too short. All of this is called ADME in the pharmaceutical industry, which stands for Absorption, Distrubution, Metabolization and Excretion.

    Anatomy

    When designing a drug, you must first and foremost know something about the challenges a drug encounters on its way through the body. When a drug is taken orally, it comes through the entire digestive tract. The digestive tract can be divided into mouth, oesophagus, stomach and intestines. In the mouth, the drug is exposed to the various enzymes found in our saliva. However, these are relatively small amounts of enzymes compared to the amount of enzymes to which the medicine is exposed later.

    The medicine then moves on to the stomach. In the stomach, the medicine will be exposed to the very acidic stomach acid (pH = 1 – 3), which can very quickly break down the medicine. If the drug survives this, it is sent on to the intestines, where it is exposed to a large amount of digestive enzymes. These digestive enzymes usually break down the food we consume. If the drug has survived these “attacks,” now is the time to cross the epithelial cell layer in the intestine to enter the bloodstream. In order to be absorbed into the bloodstream, the drug must have the right polarity. This includes that the drug must be able to cross cell membranes, which are hydrophobic, but it must also be able to be in the blood, which is hydrophilic.

    After the drug is absorbed into the bloodstream, it will be transported to the liver. In the liver there are a number of enzymes that have the task of changing the chemical structure of substances that are foreign to the body. This is called metabolization of the substances. When the substances are changed, they are more easily excreted in the urine. The fact that the drug passes the liver before it reaches the tissue is called the first pass effect. If the drug is easily metabolized and the metabolism occurs quickly, none of the drug will be distributed to the tissue. The drug must therefore have a slower metabolism so that it can be active.

     

    Absorption

    Once a drug has been taken orally and has been through the entire digestive tract, it must be absorbed across the intestine. This is called absorption of the medicine and a number of different problems can arise during the absorption phase.

     

    Acid/base chemistry

    If a drug is ionized, it cannot be absorbed into the body through the intestine because ionized molecules cannotdiffuse passively across a cell membrane. It is therefore important to know when a molecule is ionized and when it is not, and this is where acid/base chemistry becomes important.

    There are several different definitions of acids and bases; e.g. the Brønsted-Lowry and Lewis definitions. The Brønsted-Lowry definition is the one that is used the most and is the general perception of what acids and bases are. A Brønsted-Lowry acid is a molecule that can give off a hydron (ionized hydrogen, H+), and a Brønsted-Lowry base is a molecule that can absorb a hydron. A molecule can also be both at the same time. Water, for example, is both an acid and a base. Water can give off a hydron, whereby it acts as an acid:

    H_2O\rightarrow H^+ + OH^-

    Reaction 1. Water’s reaction as an acid.

    Water can also absorb a hydron, thereby acting as a base:

    H_2O+H^+\rightarrowH_3O^+

    Reaction 2. The reaction of water as a base.

    When a chemical reaction takes place, an equilibrium will be established. This also applies to water’s reaction with itself. When an equilibrium has occurred, it means that the reaction has reached a certain point where there is as much conversion from reactant to product as there is conversion from product to reactant. The reaction speed is therefore equally fast back and forth, but there is not necessarily the same amount of product and reactant.

    As described above, water is not only made up ofH2O molecules, but also of H+ and OH–. An equilibrium for H2O can therefore be written up as follows:

    H_2O\rightleftharpoons H^++OH^-

    Reaction 3. Equilibrium forH2O

    From this equilibrium, pH can be calculated. pH is an expression of how many hydrons there are in the mixture, and thus how acidic the mixture is. Quite simply, you take the negative logarithm to the concentration of the hydrons:

    pH=-\log_{10}(H_3O^+)

    Equation 1. Formula for calculating pH

    If water is mixed together with, for example, an acid, an equilibrium will also be established in the mixture. This equilibrium depends on how strong or weak the acid is. If it is a strong acid, the equilibrium will be shifted all the way to the right in the reaction chart shown in Figure 38 and all the original acid is converted to the conjugating base.

    Figure 38. Shows the equilibrium of the reaction between an acid andH2O, whereH2Oreacts as a base. The formula for the associated acid strength is also constantly indicated.

    The strength of an acid can be determined via the acid strength constant, Ks. This can be calculated via the formula shown in Figure 38. You take the concentration of the products that are on the right side of the equilibrium arrows and divide them by the concentration of the reactants that are on the left side of the equilibrium arrows. Water is not included, as it is considered a solvent, and is therefore neither a reactant nor a product. However, the strength of the acid is mostly given as pKs, which is equivalent to taking the negative logarithm to Ks:

    pK_s = -\log_{10}(K_s)

    Equation 2. Formula for calculating pKS.

    When the acid strength is calculated from the above formula, strong acids will have a low pKs value, and weak acids will have a high pKs value.

    The same constant exists for bases as well. However, the base strength is rarely stated, and it is usually the acid strength of the corresponding acid to the base that can be looked up. Fortunately, however, you can easily calculate the base strength from the acid strength constant via the following formula:

    pK_b =14-pK_s

    Equation 3. Formula for calculating pKb

    As mentioned earlier, acid/base chemistry is important for the absorption of drugs in the gut. When weak bases dissolve in a mixture that has a pH higher than pK >value, the base is unionized. The weak base can therefore cross over the cells of the intestine, as only unionized molecules can diffuse over cells. In the areas of the intestine where substances are absorbed into the body, there is a pH value of between 6 and 9. A drug that has apKS value of about 8 is a weak base. So if the drug has a pKS value of 8, the drug will most likely be able to be absorbed through the intestine. Acids, like bases, must also be unionized in order to be absorbed in the intestine. This is possible for weak acids when the pH of the gut is below the pH of the drug. It is therefore important to have a medicine with apKS value between 6 and 8. Today, there are a number of drugs on the market that contain amines. There are two good reasons for this. Firstly, amines bind well to many targets, but most importantly, the amines are good at being absorbed into the body, as they have a pKS value that fluctuates between 6 and 8.

     

    Partitionkoefficienten P

    Some drugs are so hydrophobic that they will get trapped in cell membranes and accumulate in adipose tissue. Other drugs are so hydrophilic that they will not be able to cross cell membranes and therefore will not be able to be absorbed orally. One way to assess how hydrophobic or hydrophilic a drug is, i.e. how soluble the drug is in either fat or water, is based on the partition coefficient P. The partition coefficient is determined by putting its molecule into a mixture of 50% octanol and 50% water. In such a system, hydrophobic molecules will be in the octazero layer, while the molecules that are not hydrophobic, but rather hydrophilic, will be in the water layer:

    P=\frac{[Molekyle]_{octanol}}{[Molekyle]_{vand}}

    Equation 4. Formula for calculating the partition coefficient P. Square brackets are used to indicate concentrations in the two phases, octanol and water.

    As with most other distribution coefficients, P is often given as the logP value. Hydrophobic molecules will have a high logP value, and hydrophilic molecules will have a low logP value.

    You can also get a computer program to calculate an estimated value, called ClogP (calculated logP). Just as individual functional groups, such as amines, can be ionised and non-ionised, the whole medicine including its functional groups can also be partially ionised or unionised. The LogP value indicates only the hydrophobicity of the non-ionized molecules. If you want to measure the ionized molecules, you should use logD instead. In this project, however, only logP we need.

     

    Lipinski’s Rule of 5

    In order to assess whether a drug can be absorbed orally and can be absorbed across the intestinal epithelial cell layer, and thus give the drug a good bioavailability, an important rule of thumb has been developed. This rule of thumb is called Lipinski’s rule of 5, because all the points add up to 5.

    The medicine must:

    • Have a molecular weight below 500 Da
    • Not have more than 5 hydrogen bond donors (HBD)
    • Not have more than 10 hydrogen bond acceptors (HBAs)
    • Have a logP below +5

    It should be mentioned that even if there are two free pairs of electrons on the same atom, such as on a double-bonded oxygen atom, these available pairs of electrons are only counted as one HBA according to Lipinski’s rule.

    If a molecule has logP > 5, the molecule will be too hydrophobic to dissolve in water. The molecule is therefore not soluble in the blood, which means that the molecule is retained in the cell membranes. If, on the other hand, the logP is very low for a molecule <1, the molecule will be too hydrophilic to be able to cross cell membranes. The molecule will therefore not be absorbed into the body, and it will be excreted by the body without having performed its effect.

    Drugs that have many groups that act like HBA or HBD are good at making hydrogen bonds with water. In order for a molecule to cross a cell membrane, it does not have to be bound to water and therefore a lot of hydrogen bonds must be broken between water and the molecule. Breaking these hydrogen bonds between the molecule and water requires energy, and therefore the number of HBAs and HBDs in the drug must be low in order for the least amount of energy to be used in transporting the molecule across the cell membrane.

    It is not a requirement that a good drug meets all of Lipinski’s rules. The rules have been developed by comparing the medicines available on the market to find some similarities between them. Therefore, there are also drugs that fall outside Lipinski’s rules. For example, cyclosporine, which is a drug that lowers the activity of the immune system, has a molecular weight of 1203 Da, which is far above the 500 Da specified by Lipinski’s rule. The molecule also has an extremely high number of hydrogen bond acceptors (HBA).

    Figure 39. Shows the drug ciclosporin, where HBA is shown in red and HBD in blue.

    The fact that a medicine has a high molecular weight does not mean that it has a low oral bioavailability. However, the larger a molecule, the more functional groups there will also be that may be able to form hydrogen bonds, which is precisely the case with cyclosporine. Therefore, a high molecular weight will most often result in low oral bioavailability.

    Distribution

    After the medicine has been absorbed into the body, it should be distributed around the body and in particular transported to the area where the medicine is to take effect. First of all, the drug is distributed around the body’s bloodstream (after first having been in the liver, see under metabolism section). From the blood, the drug will be absorbed by various cells in the body. This can have different consequences for the distribution of a drug, depending on the chemical structure of the molecule. For example, if the drug binds well to the red blood cells in the blood, it will not be absorbed into the body’s tissues, which was the intention.

    To be sure that a drug is properly distributed, it is important to balance how hydrophobic the drug is versus how hydrophilic it is. Too high a hydrophobicity can have undesirable side effects, as the drug can accumulate in fatty tissue. For example, overweight patients who are to undergo surgery must have a larger amount of some anaesthetics than people of normal weight, because the anesthetic accumulates in the fatty tissue of the obese patients. When the operation is over and the patient wakes up, there will still be a lot of anesthetic left in the fatty tissue. The anesthetic is released from the fatty tissue and can result in the patient becoming unconscious again, which is a very unfortunate side effect.

    Metabolism

    After oral ingestion of a drug and then absorption into the bloodstream, the liver is the first place to which a drug is directed (first pass effect). This is due to the fact that from the intestines there is a vein that leads directly to the liver. This vein is called the portal vein. A drug that is taken orally is therefore carried to the portal circulation, which is blood transport from the intestines and directly to the liver. If the drug is instead given by IV injection, it will enter the systemic circulation. In this case, the drug will circulate once through the bloodstream throughout the body before reaching the liver. With IV injection, a large percentage of the given dose of a drug will reach its target before it is taken to the liver and broken down. When the drug is taken orally, on the other hand, there is a large percentage of the drug that will not reach its target until it has been broken down in the liver.

    As mentioned, there are a number of enzymes in the liver. These enzymes have the task of changing the structure of the drug so that the drug is excreted from the body. Drugs that are highly polar will be immediately excreted from the blood through the kidneys and passed into the urine. Nonpolar molecules, on the other hand, are more difficult for the body to excrete through the kidneys, but through metabolic processes, the molecule can be made more polar so that it can be excreted. A metabolized molecule is called a metabolite. When a drug is metabolized, it will often lose its original effect. In some cases, however, the metabolite may still have some activity left. In addition, the change in the molecule can lead to the formation of toxic by-products, which can cause unwanted side effects. It is therefore important to know which metabolites can be formed in order to reduce toxic side effects.

    Any new medicine must have undergone an in vivo metabolite test to determine which metabolites are formed when the medicine is absorbed into a complex system. However, it is not certain that the metabolites formed in laboratory animals are the same as those that will be formed in humans. Therefore, it is never possible to be 100% sure which metabolites are formed in humans until a metabolite test in humans has been performed.

    In the article “Organic chemistry and drugs” it has been described how the type of isomer of a drug is important in relation to how the molecule affects its target. However, it is not only in relation to the impact on the target that the type of isomer is important. Stereochemistry is also important in the breakdown or modification of the drug. The enzymes that metabolize the drug also recognize only one particular isomer. If a drug consists of two different isomers of the same substance, two different metabolites catalyzed by two different enzymes may also be formed. One isomer can be relatively harmless, while the other can be highly toxic. Therefore, both isomers must be tested in vitro separately to determine which metabolites are formed from them. There will be more work to determine which metabolites are formed in vitro and what toxic side effects there may be from the other isomer, and it is therefore best to only have a single isomer in your drug. It is therefore important to design a method for the preparation of the drug in which only one isomer (stereospecific synthesis) is formed.

    There are two different types of metabolism, phase I and phase II metabolism, which can take place in the liver. Phase I metabolism is oxidation reactions that are catalyzed by cytochrome P450 enzymes (CYP). CYP enzymes have the task of making the molecule in question more polar. Phase II metabolism is conjugation reactions, where an extra molecule is bound to a polar group on the molecule, so that the entire molecule becomes more polar than it already was. Both types of metabolism will help the substance to be excreted from the body even faster.

    Phase I
    CYP enzymes are heme proteins, which means that they contain a heme group as well as iron. They belong to the group of monooxygenases and splitO2 present in the liver, so that one oxygen atom is transferred to the drug, which is thereby oxidized, while the other oxygen atom binds to two hydrogen atoms to form water. In order for the drug to be oxidized, there are substances that must necessarily be reduced. Therefore, the CYP enzymes require the presence of the coenzyme NADPH. When the drug becomes oxidized, NADPH is reduced to NADP.

    Figure 40. Shows a drug that is oxidized by cytochrome P450, at the same time as NADPH is reduced to NADP.

    There are at least 33 different CYP enzymes, which can be divided into different subgroups, each of which is responsible for a particular reaction. The first step in most Phase I metabolization reactions is the administration of an alcohol group. This can be introduced at different positions in a drug molecule, as illustrated in Figure 43. Depending on where the alcohol group is added, the OH group is often oxidized. This oxidation can either be to a ketone or an aldehyde. If the OH group has been converted to an aldehyde, the aldehyde will be oxidized further to a carboxylic acid. One of the functional groups to pay special attention to is methyl groups (CH3), as these are very easily oxidized to carboxylic acids via secondary alcohols. It can be seen in Figure 6 that nitrogenous functional groups are also oxidized.

    Figure 41. Shows a selection of different functional groups that are oxidized by CYP enzymes in phase I metabolism and what the different groups are oxidized to.

    Phase II
    Most enzymes responsible for phase II metabolism belong to the enzyme group transferases. Transferases are enzymes that transfer a functional group from one molecule to another. A functional group is conjugated to the drug, and phase II metabolism is therefore called conjugation reactions. The functional groups that are transferred can be many different. An example of a functional group that can be transferred in a phase II metabolism is the formation of O-glucuronides, from functional groups containing OH groups. Often, a phase II metabolization occurs after a phase I metabolization, so that in phase I an OH group is formed, on which in phase II a functional group is attached.

    Figure 42. Shows the formation of a O-glucoronide from a medicinal product containing an OH group that has been attached during a phase I metabolism.

    Figure 44 shows that when an O-glucoronide is formed, a large group binds to the drug, and the binding of this group makes the drug much more polar.

    If the medicine contains a carboxylic acid or if a carboxylic acid has been formed during phase I metabolisation, an amino acid may be conjugated to the medicine. In humans, it is often glutamine that is applied.

    Figure 43. Shows how amino acids (in this example, glutamine) are attached via three steps in a phase II metabolism.

    There are also a number of other forms of metabolism of the drug that do not take place in the liver. Among other things, there are a number of oxidative enzymes (like the CYP enzymes) distributed around the body’s tissues, which are also part of the phase I metabolism of various drugs. In addition, the blood is non-enzymatic, but rather chemically broken down by various functional groups. One of the most prominent chemical degradations is the conversion of esters into carboxylic acids and alcohols. This function is widely used in relation to the breakdown of prodrugs into the active drug, which is described in the article “Optimization of the drug”. It can therefore be difficult to achieve a long life in the body for a drug that contains an ester group, as it is quickly broken down in the blood.

    Excretion

    Most medicines will be excreted via the kidneys through the urine. However, up to 15% of the amount of a drug can be excreted through sweat. Some medicines can also be excreted via the lungs if the substance is a gas.

    The explanation for why polar substances are excreted better than non-polar substances in the urine lies in the way the kidneys work:

    The blood that comes from the liver is collected in the kidneys. Here it is filtered so that blood cells and platelets are not excreted, while all the “waste products” are separated. However, it is only a filtration, so both polar and nonpolar substances can pass into the kidneys, and thereby be retained in the body. After this, the urine is concentrated because there are some small pores, aquaporins, in the kidneys that can reabsorb the water from the urine back to the body. In addition to water being absorbed by aquaporins, a number of substances are reabsorbed through the cells in the kidneys. Because the substances are reabsorbed through the membranes of the cells, they must be quite non-polar/hydrophobic to be able to penetrate. The polar substances can therefore not get through, and they will be excreted quickly. The non-polar substances will be reabsorbed, and they can circulate around the body once more.

    Forms of admission

    A medicine can be taken in several different ways. The main forms of ingestion are orally, by injection, inhalation, or through the intestine and skin. Oral intake in pill form is by far the most commonly used form of ingestion, as it is the easiest way for the patient to take his or her medication. There is a greater chance that the patient will complete his or her course of treatment compared to a course where, for example, the patient has to have the drug injected under the skin several times a day.

    If the patient suffers from a serious illness and an oral form of absorption is not possible, another way of administering the drug needs to be found. Some patients have problems swallowing pills, either because they are unconscious or vomit a lot, and other forms of absorption than the oral one are therefore preferable. In addition, there are many children who have problems swallowing pills, and therefore absorption through the intestine, via a suppository, is widely used for children.

    When injected, the drug is injected into the body, and there is therefore a much faster response to the drug than with oral administration. This form of intake can therefore be smart for acute treatment of diseases. Injections can be done by injecting into the veins, into the muscles, under the skin or directly into the spine, depending on where the medicine is to work and how quickly it is to work. The fastest response comes by intravenous injection (IV) or injection into the spine. Injections into the spine are used, for example, in caesarean sections, where anaesthesia is injected into the spinal cord of the woman giving birth. To achieve a longer absorption time than with IV injection and a shorter absorption time than oral administration, the medicine can be injected under the skin or into the muscles. In order for the drug’s effect to occur, the drug must first diffuse across different cell membranes to get to the bloodstream.

    Ingestion of medicines can also be done by inhalation and is mainly used for asthma. In asthma patients, the medicine must have its effect locally in the lungs, and the medicine is therefore dosed directly to the lungs.

    Finally, the absorption of the drug through the skin. The most well-known form is nicotine patches, which are used in connection with smoking cessation, but various creams with, among other things, anaesthetics or substances against eczema are also absorbed through the skin. Absorption through the skin is a form of absorption where the substance must diffuse over all the skin layers, and the effect of the substance will therefore occur slowly, and last for a long time.

    Figure 44. The figure shows the different routes a drug can be administered.

     

    Optimisation of the medicine

    They have now found out both which target to hit with their newly developed drug, but they have also found out how the drug is affected by the body. But in the real world, the first drug made for a disease never works. Therefore, optimization strategies and ways to test these optimizations are needed. Optimisation of a medicine may also be necessary to lower the number of side effects or increase the activity of the medicine.

    SAR (Structure Activity Relationship)

    In the case of psoriasis, they had found out what the target looked like before they started designing a drug. But often you don’t actually know exactly what the target looks like when you design a drug. In this case, based on a basic structure of a drug, a number of different analogues are made, which can be compared and tested against each other via a SAR study. In the psoriasis case, where the target was known, it is also possible to do a SAR study, where you try to maintain the right interactions between target and drug and at the same time fill in the “pockets” that are in the target with different groups in the drug.

    Figure 45 shows a suggestion for a drug. The groups that have the opportunity to create different interactions with the target are indicated in the drawing. Below the molecule are shown four possible analogues, i.e. the same molecule only with different modifications.

    Figure 45. Illustrates the principle behind a SAR study. The functional groups in the drug that may be important for binding to target are given and four different analogues for testing whether the given functional group is important for binding to target.

     

    In the first analogue, the alcohol groups have been changed to methyl ethers. This removes the possibility that the hydrogen atom could be an HBD. The first analogue will be tested for activity in the target in an in vitro test, as it is not ethically justifiable to conduct an animal study yet. If the first analogue has a lower activity (higher IC50) than the original molecule, the alcohol groups have been important for binding in the target. If the activity of the first analogue is the same as or higher (lower IC50) than the original structure, the alcohol groups are not important for binding to the target.

    In the second analogue, which is shown, an aromatic ring is replaced with a cyclohexane ring. An aromatic ring will normally be involved in Van der Waals interactions with targets or other molecules, while a cyclohexane will have a harder time forming Van der Waals interactions because the cyclohexane ring does not have a flat structure like an aromatic ring does, as seen. The analogue is tested again for activity and the effect of the aromatic ring vs. cyclohexane ring is evaluated.

    Figure 46. The figure shows the three-dimensional difference between a cyclohexane ring and an aromatic ring. Where the aromatic ring has a flat structure, the cyclohexane ring is uneven.

     

    In the third analogue is a carboxylic acid, replaced with a methyl ether. Carboxylic acids that have given off a hydron can make ionic bonds, but can also make hydrogen bonds via their double-bonded oxygen atom. By removing the possibility of making an ionic bond, it is tested whether it is necessary for the drug’s activity to make an ionic bond to the target. Hydrogen bonds can still be made, so by using an ester as a test group, you ensure that it is one type of bond you test at a time.

    The last analogue shown is a test to determine whether the NH group makes a hydrogen bond to the target.

    In addition to the changes shown in the molecule in Figure 45, a number of other changes can also be made where other functional groups are inserted into the molecule. For alkenes, as with aromatics, it is a good idea to test an alkane (saturated hydrocarbon) with the same length as the alkene, as there is a difference in how much rotation there is in alkenes and alkanes, respectively.

     

    Optimization strategies

    Target binding
    Relocation, extension and expansion
    If a drug does not have the right interactions in the target, you have to optimize the structure so that the drug fits perfectly into the target. Optimisation of a medicine can be done in several different ways, depending on what the problem with the binding is. For example, it may be a case of a functional group on the drug being staggered in relation to a group in the target, so that the necessary binding cannot take place.

    The length of the hydrocarbon, as shown in Figure 49, can be varied to get the functional group in the right position.

    The functional group can also be located in a specific place in the molecule/scaffold, so that an interaction cannot take place. Therefore, you may have to move the position of the group.

    Figure 47. Illustration of how a drug’s hydrocarbon can be lengthened or shortened to get the optimal binding to the target.

     

    Figure 48. Shows how a functional group sitting on an aromatic ring can be moved so that the group binds to the right area in the target.

     

    Figure 49. By inserting an additional hydrophobic group into the drug, a hydrophobic pocket is filled, resulting in a better drug.

     

    You can also make ring expansions if a part of the molecule does not precisely hit its binding site. You can thus rearrange, lengthen and expand your molecule so that it will fit perfectly into the pockets found in the target.

    Functional groups and their modification

    Another way in which a drug can be improved is by changing the functional groups the molecule already possesses. For example, it may be a case of an HBD being used in the pharmacophore to make a hydrogen bond because there is an HBA in an area in the target, but the drug can only make ionic bonds. The functional group must thus be changed so that it can donate a hydrogen atom and thereby make a hydrogen bond.

    Figure 50. Extensions of ring systems can also be made so that the ring system binds to the right areas in the target.

     

    Bioisosters
    A third way to change the medicine is by using what are called bioissters. Bioistables are functional groups that can replace other functional groups, but the biological activity and overall three-dimensional structure are preserved. In cases where bioissters are a solution to the problem with the drug, it is neither the location of the functional group nor the functionality of the group that has caused the problem. Sultoprid is a dopamine antagonist that was altered, the structure is seen in Figure 51. In sultoprid, there is an amide, which resembles a peptide bond that is easily broken down in the body. In sultoprid, you can change the amide to a pyrrole ring, so that the overall structure of the molecule is retained, and it is still possible to make a hydrogen bond to the target. The advantage of the bioisester of starvoprid is that there is now no group in the molecule that resembles a peptide bond, and the molecule will therefore be broken down more slowly in the body.

    Figure 52 shows various examples of bioissters for amides.

    Esters, as described earlier, are often broken down or altered in metabolic reactions. If this is a problem for the drug’s activity, it can be remedied by changing the methyl group on the ester to an amine.

    Absorption/Illuminance

    As mentioned earlier, it is very important that the newly developed drug has the right solubility and polarity for it to be absorbed. Also for the purpose of absorption, one can optimize the structure of the drug. If the molecule is too polar (i.e. hydrophilic/water-loving), it will be quickly excreted in the kidneys, and it is therefore a good idea to hide the polar groups. You can hide an alcohol by turning it into an ester or an ether.

    You can hide a carboxylic acid by turning it into an ester or amide, or you can turn primary and secondary amines into amides or tertiary amines. In addition to the polar group being hidden, an extra hydrophobic part is also added to the molecule, which makes the structure of it less polar overall.

    Figure 51. The drug Sultaprid and its bioisoester.

     

    Figure 52. Shows different bioissters for an amide.

    Figure 53. Ester bioisoester

    The opposite scenario, where the molecule is too non-polar, can also be changed to make it more polar. The easy solution to this problem is to add extra polar groups to the molecule. Of course, this is not always possible, for example because in this way functional groups may be added that can make unwanted bonds in the target, or because there is just no room for extra functional groups in the molecule. If it is not possible to introduce more functional groups, it may be possible to change the groups that are already present in the molecule. For example, it can be a methyl ether that can be changed to an alcohol, or it may be possible to remove groups that make parts of the molecule hydrophobic.

    It is important that there are hydrophobic groups around the entire molecule, otherwise only one side of the molecule will be hydrophobic enough to be absorbed across cell membranes. If the hydrophobic groups are not distributed evenly in the molecule, there is a risk that one part of the molecule sits in the membrane, while the other part of the molecule sticks out of the membrane. In this way, the molecule is trapped in the membrane. It may be a good idea to vary the size of the hydrophobic groups so that they are elongated on one side and shortened on the other side of the molecule, so that the hydrophobic groups are distributed evenly all the way around the molecule.

    When a drug’s pKs comes outside the optimal range, pKS = 6-9, there is a high probability that it will be too ionized and therefore will not be able to be absorbed over cell membranes. If pKs is outside the optimal range, either save functional groups that are very alkaline or very acidic, or remove these groups. For example, you can store a basic nitrogen atom inside a heteroaromatic ring.

     

    Craig plot
    In some cases, it can be difficult to know which functional groups need to be changed or what the groups need to be changed to in order to increase the activity of a drug. A drug has some physicochemical properties that can be related to its biological activity. There are two physicochemical properties that are particularly important in relation to biological activity. One property is the hydrophobicity of the molecule’s functional groups, and it is indicated by the Greek character pi, π. π > 0 indicates that the molecule is hydrophobic, while π < 0 indicates that the molecule is hydrophilic. The second property is how electron donating or attractive an aromatic substitute is in the drug. This characteristic is indicated by the Greek sign sigma, σ. If σ > 0, it means that the aromatic substitute is electron-attractive, while the aromatic substitute is electron-donating, if σ < 0. When π and σ are plotted in a diagram for different functional groups, what is called a craig plot in pharmacology emerges. From a craig plot, you can get an overview of which functional groups you can change the current substituents in a molecule to, for example to change the hydrophobicity of the molecule. Figure 55 is a craig plot for aromatic substitutes in the para position. The para-position of aromatic rings is described in more detail in the article “Organic chemistry and drugs”. A drug that has a t-butyl group (located in the 4th quadrant of the craig plot) will be highly hydrophobic due to this group. It may be that the molecule is so hydrophobic that the logP value is above 5. It is therefore necessary to change the functional groups of the medicine so that it becomes less hydrophobic. One can therefore use the craig plot to see which groups are less hydrophobic than t-butyl. The group Me (Methyl) has a lower π-value than t-butyl and a replacement will therefore make the molecule less hydrophobic, thereby lowering the logP value to below 5. It may now be possible to take the medicine orally.

    Figure 54. Craig plot with positive and negative values for σ and π in the para-position of an aromatic ring.

    Figure 55. Topliss scheme for aromatic substitutes. L = Lower activity, S = Same activity, H = Higher activity .

    Figure 56. TOPLISS table for aliphatic substitutes. L = Lower activity, S = Same activity, H = Higher activity .

    Figure 57. Shows fentanyl and remifentanil, both of which are drugs used for anesthesia. The duration of the anaesthetic for remifentanil is shorter than for fentanyl because remifentanil contains two ester groups that are easily broken down in the blood .

    Topliss Schedule
    In addition to orienting yourself in a craig plot, it can also be a good idea to use a Topliss scheme. A Topliss chart is a diagram where the next analogue to be tested for activity is indicated, so that it provides a logical sequence in relation to the substitutes’ π and σ values. For every analogue tested, there are three possible fates; The analogue can have higher, lower, or the same activity as the original molecule. Depending on the degree of activity of the analogue, the next analogue is chosen based on the branch in the chart. There are two different Topliss schemes. One scheme belongs to aromatic substitutes and is shown in Figure 55, while the other scheme belongs to hydrocarbon side chains and is shown in Figure 56.

     

    Figure 58. The self-destructive drug atracurium breaks down when it enters the bloodstream due to the pH value of the blood.

    Metabolism

    As described in a previous article, some functional groups are particularly vulnerable to metabolization (i.e. a transformation of the groups) in the body. This includes esters, amides and methyl groups. The metabolism causes the molecule to be rapidly excreted from the body through the kidneys, and the drug has a short half-life. An easy way to protect extra vulnerable groups from metabolism is by introducing a steric barrier/steric shield into the molecule. Steric obstruction is the insertion of a chemical group close to a certain functional group that must be protected so that the metabolizing enzymes cannot get to the group because the group you have inserted is in the way. The particularly vulnerable groups can also be completely removed or replaced with other groups, e.g. bioissters.

    The opposite scenario, where the drug has too long a half-life in the body, can also occur. Fentanyl, which is an anesthetic used during surgery, has been created from the substance remifentanil by, among other things, replacing two aromatic rings (abbreviated Ph) with two esters. This change caused the effect of the anaesthetic to be shorter, because the esters were broken down into carboxylic acids in the blood. In this way, a substance was obtained that could be used for more short-term operations.

    Another example of a substance used to anaesthetise patients is atracurium, which is referred to as a self-destructive drug. Atracurium is stable at low pH values, pH < 4, such as in gastric acid, but as soon as atracurium enters the bloodstream, where the pH value is neutral or slightly alkaline, the molecule breaks down and no longer has any effect. The drug is therefore best given with an intravenous drip, as it can be dosed continuously and the patient can wake up immediately after the operation.

    Prodrugs

    Prodrugs are drugs that do not have their active chemical structure when ingested. During its way through the body to the target, the structure is changed, and especially in the liver, the substance will be subjected to modification. It will then recirculate in the body if it is not excreted, and since the medicine has now been changed to the correct structure, it will have its proper effect. In the design of a prodrug, it is therefore important to take into account which metabolizations take place in the drug. One of the functional groups that are easily metabolized is esters. A drug containing a carboxylic acid is not very well absorbed across the intestine. A good way to make sure that a drug containing a carboxylic acid can be absorbed across the intestine is to convert it to an ester before it is consumed. The ester will quickly be converted into a carboxylic acid (or an alcohol, depending on the functionality desired) when the drug enters the bloodstream and liver. An example of the use of esters in prodrugs is salicylic acid, which is a painkiller. Salicylic acid cannot be taken directly, as it causes bleeding in the stomach due to the phenolic group of the substance. If the phenolic group is stored away via an ester, acetylsalicylic acid is formed. Acetylsalicylic acid does not cause bleeding in the stomach, but is also not a painkiller. When aspirin is absorbed across the intestines and is in the bloodstream, it will be hydrolyzed into salicylic acid, which is an analgesic. With this strategy, you therefore avoid having salicylic acid in the stomach while the active drug is present in the body. Acetylsalicylic acid is an example of a prodrug where the active molecule is a carboxylic acid that you want to form. In the painkiller Aspirin® , it is precisely this reaction from acetylsalicylic acid to salicylic acid that is exploited.

    An example where it is an alcohol that you must get out as the active substance is the drug valaciclovir, which is used against the herpes virus. Valaciclovir is converted to aciclovir after absorption. The reason why it is necessary to administer valaciclovir instead of aciclovir is due to the fact that aciclovir is absorbed very poorly across the intestine.

    Figure 59. The painkiller Aspirin®.

    Figure 60. The drugvalaciclovir is a prodrug that is converted into the active substance aciclovir and the amino acid valine.