Appunti corso: Medicinal Chemistry

Medicinal chemistry

It’s a chemistry based discipline, involving aspects of biological, medical and pharmaceutical sciences. It is concerned with the invention, discovery and identification of biologically active compounds, the study of their metabolism and the construction of structure-activity relationship (SAR).

There are three phases involved in drug action. The first one is pharmaceutical phase: for an orally administered drug, this includes the disintegration of a pill or capsule in the gastrointestinal tract (GI), the release of the drug and its dissolution.

Pharmaceutically availability is reached and the drug is available for absorption.

The second phase is the pharmacokinetic (PK) one which starts with absorption from the GI tract into the blood supply and continue with distribution, metabolism and excretion. At this point the drug is biologically available and can proceed with its action entering the third phase: pharmacodynamics one which involves the mechanism by which a drug interacts with its molecular target and produce the pharmacological effect, which can be therapeutic or toxic.

Pharmaceutics

Science of dosage form, it’s the study of formulation factors on therapeutic effect.

Dosage forms are a mixture of active drug component and non-drug component which help the release of the drug in solution. Depending on the method of administration they come in several types such as solution, suspension, capsules or pills.

Depending on the dosage form are requested different routes of administration (ROA) such as oral, inhalational, topical or parenteral injection. These are classified by application location.

This classification distinguishes whether the effect is local (near the application site, for topical administration) or systemic (far from the administration site, for enteral and parenteral administration).

The ROA that is chosen may have profound effect upon the speed and efficiency with which the drug acts.

Three main ROA

• Topical.
• Enteral: Drug is placed directly in the GI tract.
• Parenteral.

Enteral

• Sublingual Placed under the tongue. Rapid absorption and avoid the first-pass effect, but à must be in small doses and can have an unpleasant taste.
• Oral Can be self-administered and it’s easy to take, it’s quite cheap, but It can be inefficient à because of the first pass effect because it is transported to the liver via portal vein; it can irritate the gastric mucosa and its effects are too slow for emergencies.
• Rectum Absorption through rectum à

First pass effect

First pass effect: Drugs that are taken orally pass directly to the liver once they enter the blood supply. Here, they are exposed to drug metabolism before they are distributed around the rest of the body, and so a certain percentage of the drug is transformed before it has the chance to reach its target. it is known as the first pass effect. Drugs that are administered in a different fashion (e.g. injection or inhalation) avoid the first pass effect and are distributed around the body before reaching the liver.

Parenteral

• Intravascular (IV) into the blood stream; in this way, the absorption phase is à Directly bypassed and there is the 100% of bioavailability.
• Intramuscular (IM) into skeletal muscle à Injected.
• Subcutaneous Absorption from the subcutaneous tissues à
• Inhalation Absorption through the lungs à

Depending on the ROA the time until effect can be different: IV (30-60 sec), Sublingual (3-5 min), Ingestion (30-90 min). - 1 -

Pharmacokinetics

Pharmacokinetics: Includes the study of the mechanism of absorption and distribution of the administered drug, the rate at which a drug action begins and the duration of the effect, the chemical changes of the substance (metabolism) and the effects and also the route of excretion of the metabolites of the drug. It involves also studies on the relationship between these processes and the intensity of the pharmacological effects.

It is divided in 4 areas commonly known as ADME scheme:

• Absorption: Process of a substance entering the blood circulation.
• Distribution: Dispersion of substances throughout the fluids and tissues of the body.
• Metabolism: Irreversible transformation of parent compound into metabolites.
• Excretion: Elimination of the substance from the body.

PK parameters

Half-life (t½): Time required for the concentration of the drug to reach half of its original value.

Clearance (CL): Volume of plasma cleared of the drug per unit time to produce the observed rate of elimination, measured in mL/min.

C: Maximum observed concentration, reached at the tmax max!

AUC: Area under the curve = ∫"

Bioavailability: Fraction of extravascularly administered dose that reaches systemic circulation. It’s the fraction of dose that reaches blood circulation.

#$% ' = #$% ()

f=1 for IV administration. F if expressed in %

f = f + fa fp

f = oral availability, fraction of the applied dose that reaches the portal vein.

f = fraction of the adsorbed dose that reaches blood circulation.

For certain compounds the passage through the liver is the end of their lives: they show good adsorption but are metabolized in the liver and excreted via the bile.

Absolute bioavailability is the dose corrected AUC divided by AUC non-iv iv = It compares the bioavailability of the active drug in the systemic circulation following non-intravenous administration with the bioavailability of the same drug following iv administration; this comparison must be dose normalized.

Relative bioavailability measures the bioavailability of a formulation A of a certain drug when compared with another formulation B of the same drug.

Absorption

Absorption: Process by which a drug enters the blood stream without being chemically altered.

Absorption is influenced by different factors, such as: type of transport, phys-chem properties of drugs, ROA, dosage form and concentration.

Absorption and distribution to the tissues determine the rate at which a drug reaches its site of action.

A drug has to overcome physical barriers (membranes), phys-chem barriers (solubility, pH) and biochemical barriers (metabolizing enzymes).

So the drug must cross lipid barriers/cell walls (gut wall, capillary wall, cell wall & BBB) and the mechanism of transport can be passive diffusion, filtration, endocytosis, ion pairing or active transport.

Capillaries in most of the body are made up of cells with gaps in between the cells which allows some substances to move in and out of the capillaries. - 2 -

In BBB cell are more tightly packed so molecules have to move through the cells themselves. This barrier is important because the brain has no immune system and is a highly selective barrier. It’s formed by capillary endothelia cells which are connected by tight junction. The passage through the cell membrane can be: Diffusion trough lipid (diffusion gradient), Carrier mediated or endocytosis.

Efficient crossing of the membranes means an efficient absorption and distribution into the body.

Mechanism of transport

Mechanism of transport: Diffusion or passive diffusion consists of the diffusion of substances through the membrane without expending metabolic energy and without the aid of transport proteins just by the existing concentration gradient.

As few molecules are able to diffuse through a lipid the majority of the transport processes involve transport proteins, in this case the transport may be passive by using channels of facilitative transporters or active, driven by ATP using metabolic energy and may involve also secondary transporters.

• Small non-polar molecules (O2, N2, CO2) Passive diffusion à
• Weak electrolytes (most drug) Passive diffusion of the non-ionized form à
• Small polar molecules (water) Filtration through pores à
• Large polar molecules (glucose) Facilitated diffusion à
• Ions/charged molecules Active transport à
• Proteins and large molecules Vesicular transport (endocytosis) à

Passive diffusion: First order process, absorption rate directly proportional to the concentration.

Active transport: Saturable (number of carrier molecules).

Endocytosis: Vesicular transport in which molecules move into the cell enclosed as vesicles. Vesicles are bubble-like structures surrounded by a membrane.

Phys-chem properties of the drug influence the passage through lipid membranes (phys-chem barriers) such as molecular dimension, solubility in water/lipid (ionized/unionized form) and acid/base properties.

Just remember that cell membranes are made of lipids, and so lipid solubility favors the passage. Ionized drugs are less lipid soluble, in this case it’s required a transport protein. Only small water-soluble molecule (< 4A) can cross the membrane by using hydrophilic pores. - 3 -

Acid base properties and pH-dependent absorption

Acid base properties and pH-dependent absorption in the GI tract:

• Acid pKa > 8 always non-ionized.
• Strong acid pKa < 2 prevalence of ionized fraction.

The extent of ionization at a particular pH can be determined by the Henderson-Hasselback equation:

Amine is a very important functional group, having a pKa in the range 6-8 and a correct balance of the dual requirement: water and lipid solubility. In their ionized form can interact with receptor, while in the neutral form is able to cross membrane.

Note that compounds with pKa 6-8 are approximately 50 % ionized at blood pH of 7.4

Lipophilicity: Describes the affinity of a molecule for a lipophilic environment and it’s measured in a biphasic system (organic solvent representing the membrane and the aqueous buffer representing the plasma). It is expressed by the partition coefficient P or logP. The higher the lipid/water p.c the greater the rate of transfer across the membrane. Increasing polarity of drug will decrease the p.c.

% %!"#$%!& !"#$%!& P > 1, log P > 0 lipophilic= = log à% %'$#() '$#()

There’s also the distribution coefficient D, which is the ratio of all forms of a ionizable compound dissolved in two not miscible solvents. It’s pH dependent, while P is constant.

*+,-.*/= (*.(0123.*.(.(*.(012 (. 4-,15

The condition for gastric absorption are adverse (small abs area, pH variation, poorly vascularized). Its acidic pH allows the absorption of weak acids; non-ionized compounds are adsorbed by passive diffusion depending on their p.c 2

Intestinal absorption presents favourable conditions (large abs area 200 m², slow passage, highly vascularized, pH suitable for passive diffusion of many non-ionized drugs and presence of many active transport systems).

The absorption is affected also by the disintegration and dissolution of the drug, the chemical stability of the drug and its stability to enzymes.

Distribution

Distribution: Process that brings drug from the bloodstream to target tissue and affects concentration at site of action. There are pores between cells in capillaries which are large enough to allow most drug to pass through but not large enough to allow the plasma proteins present in the blood to escape. So, drugs do not have to cross cell membrane in order to leave the blood system and can be freely and rapidly distributed into the aqueous fluid surrounding the various tissues and organs.

In the blood, a certain percentage of drug will bind to plasma proteins reducing the amount of free molecules able to leave. If it is added later another substance capable of binding with these proteins, the amount of the free drug number 1 will increase.

Once a drug has reached the tissues, it can immediately be effective if its target site is a receptor situated in a cell membrane. However, there are many drugs that have to enter the individual cells of tissues in order - 4 - to reach their target. Just remember that in case of oral absorption the compound will pass through the liver before distribution to the rest of body and a certain percentage will be metabolized (first pass effect).

Metabolism

Metabolism: When drugs enter the body, they are subject to attack from a range of metabolic enzymes. The role of these enzymes is to degrade or modify the foreign structure, such that it can be more easily excreted. As a result, most drugs undergo some form of metabolic reaction, resulting in structures known as metabolites. Very often, these metabolites lose the activity of the original drug, but, in some cases, they may retain a certain level of activity. In exceptional cases, the metabolite may even be more active than the parent drug. Some metabolites can possess a different activity from the parent drugs, resulting in side effects or toxicity.

If the drug is polar, it will be quickly excreted by the kidneys. However, non-polar drugs are not easily excreted and the purpose of drug metabolism is to convert such compounds into more polar molecules that can be easily excreted.

Non-specific enzymes (particularly cytochrome P450 enzymes in the liver) are able to add polar functional groups to a wide variety of drugs. Once the polar functional group has been added, the overall drug is more polar and water soluble, and is more likely to be excreted when it passes through the kidneys.

These reactions are classed as phase I reactions and generally involve oxidation, reduction, and hydrolysis and they take place in the smooth endoplasmic reticulum (microsomes).

A series of metabolic reactions classed as phase II reactions also occur and take place in the cytoplasma. Most of these reactions are conjugation reactions, whereby a polar molecule is attached to a suitable polar ‘handle’ that is already present on the drug or has been introduced by a phase I reaction. The resulting conjugate has greatly increased polarity, thus increasing its excretion rate in urine or bile.

Both sets of reactions can also be regioselective and stereoselective.

Phase I

Phase I: it’s catalyzed by cytochrome P450 enzymes (CYP) that belong to the class of the monooxygenase (insertion of one atom of oxygen into an organic substrate while the other one is reduced to water).

They contain an heme cofactor and so it’s a hemeprotein. His substrates can be xenobiotic substances such ad drugs but also endogenous metabolic intermediates.

The reaction of oxidation need a mixed function system: NADPH cytochrome P450 reductase and cytochrome P450 (P450 reductase is a membrane-bound enzyme required for electron transfer to P450)

2Examples: Oxidation of terminal methyl group, oxidation of activated carbon centres next to sp and sp carbons, dealkylation of amine, ethers and thioethers.

Reductive reactions are less common while hydrolysis of ester and amides is more frequent.

Phase II

Phase II: Most phase II reactions are conjugation reactions catalysed by transferase enzymes. The resulting conjugates are usually inactive.

• Glucuronic acid conjugation is the most common of these reactions. Phenols, alcohols, hydroxylamines, and carboxylic acids form O-glucuronides by reaction with UDFP-glucuronate such that a highly polar glucuronic acid molecule is attached to the drug. The resulting conjugate is excreted in the urine, but may also be excreted in the bile if the molecular weight is over 300. A variety of other functional groups, such as sulphonamides, amides, amines, and thiols can react to form N- or S-glucuronides. C-glucuronides are also possible in situations where there is an activated carbon centre next to carbonyl groups.
• Another form of conjugation is sulphate conjugation. It is less common than glucuronation and is restricted mainly to phenols, alcohols, arylamines, and N-hydroxy compounds. The reaction is catalysed by sulphotransferases using the cofactor 3ʹ-phosphoadenosine 5ʹ-phosphosulfate as the sulphate source.
• Drugs bearing a carboxylic acid group can become conjugated to amino acids by the formation of a peptide link.
• Electrophilic functional groups, such as epoxides, alkyl halides, sulphonates, disulphides, and radical species, can react with the nucleophilic thiol group of the tripeptide glutathione to give glutathione conjugates. The glutathione conjugation reaction is catalysed by glutathione transferase. This conjugation - 5 - reaction is important in detoxifying potentially dangerous environmental toxins or electrophilic alkylating agents formed by phase I reactions. Glutathione conjugates are often excreted in the bile, but are more usually converted to mercapturic acid conjugates before excretion.
• Not all phase II reactions result in increased polarity. Methylation and acetylation are important phase II reactions which usually decrease the polarity of the drug. The enzyme cofactors involved in contributing the methyl group or acetyl group are S-adenosyl methionine and acetyl SCoA respectively.

Metabolism is affected by different factors such as race, age and sex but also other drugs and food (drug-drug interaction and drug-food interaction).

Inhibitors, such as cimetidine and grapefruit juice, prolong action of drugs or inhibits action of those transformed to active agents causing a lower concentration of the active biocompound.

Inducers, such as barbiturates and carbamazepine and cigarette smoke shorten action of drugs or increase effects of of those transformed to active agents. For example, carbamazepines promote the activity of CYP450 enzymes and decrease the effectiveness of contraceptives.

Excretion

Excretion: Drugs and their metabolites can be excreted from the body by a number of routes.

• Via the kidney through urine.
• Via biliary excretion or fecal excretion (process start in the liver, pass through the gut until the product is excreted along with feces MW >350).
• Through the lungs (volatile agents).

Among them the most common site for excretion is the kidney, the process involves three sequences which occur in the nephron (microscopic functional unit of kidney):

• Glomerular filtration: Small drugs are allowed to filter from the blood through the pores in the capillary walls into the nephron while large drugs and those bound to plasma proteins cannot be filtered. Note that this is a filtration process, so it does not matter whether the drug is polar or hydrophobic: all drugs and drug metabolites will be passed equally efficiently into the nephron. However, this does not mean t