Phar2011 - Week 1
Lecture 1- Intro to Pharmacology
What is pharmacology?
Study of how drugs work and how they affect our bodies
The word pharmacology comes from the ancient Greek words ‘pharmakon’ meaning of both drug and poison and ‘logia’ meaning knowledge of or the study of something
Pharmacology incorporates knowledge and skills from other science disciplines
There are many sub-disciplines:
Molecular pharmacology
Toxicology
Pharmaco-kinetics
Clinical pharmacology
Systems and Integrative Pharmacology
Chemo-therapy
Drug Metabolism and Disposition
Drug Discovery and Development
Pharmaco-genomics
Drugs, Medicines and Ligands
Drugs are substances that have a physiological effect when introduced into the body
Medicines are types of drugs that have been approved as therapeutic goods and are used to treat or prevent specific health conditions
All medicines = drugs, not all drugs = medicines
Ligands are molecules that bind to a receptor; can be endogenous to the body or introduced into the body (i.e., a drug)
What is a therapeutic good?
A medicine or device approved by the TGA (in USA, that is the FDA)
Uses:
Preventing, diagnosis, curing or alleviating a disease, ailment, defect or injury
Influencing, inhibiting or modifying a physiological process
Testing the susceptibility of persons to a disease or ailment
Influencing, controlling or preventing conception
Testing for pregnancy
Used as an ingredient or component in the manufacture of therapeutic goods
Drugs come in a diversity of size
Small molecules; peptides; biological
Peptides and Proteins
Peptides and proteins are made of chains of amino acids joined together by peptide bonds
Peptides (<50 amino acids) such as insulin, glucagon-like peptide agonists (semaglutide), oxytocin
Larger molecules (>50 amino acids) such as monoclonal antibodies, growth factors, etc.
Large size and potential enzymatic digestion make them not suitable for oral administration, most are administered by injection
Small Molecule drugs vs Biologics
Small Molecules Drugs
Low molecular weight (majority <500 Da)
Small size may allow easier absorption into the body and crossing cell membranes
Natural or synthetic
E.g., Aspirin (analgesic; ~180 Daltons)
Biologicals
Derived from living organisms - yeast, bacteria, insect and mammalian cell lines, animals. e.g., proteins
Large and complex (>1 kDa)
Include vaccines, blood/blood components, somatic cells, growth factors, recombinant peptides and proteins, immune modulators, monoclonal antibodies
E.g., infliximab (rheumatoid arthritis; ~150 kDa)
Nucleic Acid-Based therapies (DNA or RNA)
Target components inside the cell to either correct or compensate for disease caused by genetic mutations or altered gene expression
Gene therapy:
Antisense oligonucleotides
Small interfering RNA
mRNA therapies
CRISPR/Cas9 editing
MicroRNA
e.g., inclisiran targets the mRNA encoding PCSK9 a protein involves in regulating LDL levels, used in the treatment of homozygous familial hypercholesterolemia
Drug Names
IUPAC names
International Non-proprietary Name (INN)
Is approved by WHO - each INN is a unique name that is globally recognised
A non-proprietary name is also known as a generic name
INN must end in an approved ‘stem’ - the same stem is used for pharmacologically related substances
-olol - for B-adrenergic receptor antagonists
-pril for ACE inhibitors
-siran small interfering RNA
-mab monoclonal antobodies
-glutide e.g., GLP drugs like semaglutide
Brand or trademark name
Trade names are proper nouns, if they used in the middle of a sentence, they should start with a capital letter
Examples
IUPAC
(RS)-4-[2-tert-Butylamino)-1-hydroxyethy]-2-(hydroxymethyl)phenol
INN
Salbutamol
Brand name
In Australia = Ventolin, Airomir, Asmol, Zempreon
Pharmacodynamics
What the drug does to the body → how does the drug change physiology of body
The study of the molecular, biochemical, and physiological effects of drugs on cellular systems and their mechanisms of action
Enzyme: A type of protein that acts as a biological catalyst, speeding up specifical chemical reactions in living organisms without being consumed in the process
Active site: the site on the enzyme where the substrate molecules bind and the chemical reactions occur
Inhibitor: A substance that reduces catalytic activity of an eynzyme
Receptor: A macromolecule (e.g., protein) that mediates the actions of endogenous and exogenous ligands. The formulation of the drug-receptor complex leads to a biological response
Binding site: the region on the receptor where a ligand binds. The site where the endogenous ligand binds is the orthosteric site. Binding sites outside of orthosteric site are called allosteric sites
Agonist: A ligand that binds to a receptor and stimulates it to function
Antagonist: A ligand that blocks binding of agonist ligands to a receptor preventing signalling by the receptor
Pharmacokinetics
What the body does to the drug → how the body takes the drug in
The study of the absorption, distribution, metabolism and excretion (ADME) of drugs by the body
Medicine is taken → absorbed into bloodstream → broken down by liver (metabolism) → distributed → excreted
Therapeutics
The uses of drugs and the methods of their administration in the treatment of disease
The information we need to know about a drug:
Drug target - what the drug binds to elicit an effect e.g, a receptor
Mechanisms of action - how the drug works, how it modulates the function of the target
Indications - what disease(s) or condition(s) the drug is used in the treatment of
Contraindications - what disease or condition or patient population the drug shuold not be used in
Route(s) of administration - how the drug can be given
Pharmacokinetic parameters - ADME factors that affect the clinical efficacy of the drug
Drug interactions - a change in a drug’s effect due to interactions with other drugs, food, or a medical condition
Adverse effects or side effects
Drug Interactions
Drug-Drug Interaction → change in a drug’s effect on the body (pharmacodynamics) and the body’s effect on the drug (pharmokinetics) when it is taken together with a second drug
The drugs can have additive effects or opposing effects due to their mechanisms of action
A drug-drug interaction can delay, decrease or enhance absorption of either drug, it may change the metabolism or excretion of one or both drugs
a Drug-drug interaction may increase or decrease the effects of one or both drugs
Adverse (Drug) Events, Adverse Effects and Side Effects: What’s the Difference?
Adverse Event: An unexpected medical event that is generally harmful to the participant that occurs during treatment with a pharmaceutical product, but which does not necessarily have a causal relationship with treatment
Adverse effect: unintended pharmacological effects that occur when a medication is administered correctly.
Adverse effects include any unexpected medical event that is generally harmful to the participant due to taking the treatment
Adverse effects are known to occur in a percentage of patients - determined from clinical trials
Side effects are unintended but predictable symptoms that can develop while taking a drug
They can happen at normal, recommended doses, and they are unrelated to the intended purpose of the medication
Side effects are often dose-related
Side effects may be desirable, adverse, or inconsequential. An adverse or negative side effect = adverse effect
Side effects can be due to actions at the unintended target (on-target) or an unintended target (off-target)
Dose-response and when do we use concentration-response to describe the action of a drug?
Dose-response → when observing the effect of a drug in a whole animal or human (in vivo)
Concentration-response: when observing the effect of a drug isolated cells or tissues (in vitro or ex vivo)
When testing drug in vitro, the drug is confined to a known volume (e.g., well of a plate or test tube) therefore the concentration of the drug is known and doesn’t change, equilibrium can be reached
An, in vivo system the concentration of drug available to interact to interact with its target is changing over time due to ADME factors
A precise concentration can not be determined, the only thing we know is the dose of the drug given
Drug Discovery and Development Process
Unmet medical need: condition or symptom whose treatment or diagnosis is not addressed adequately by available therapy
Target: a specific molecule, often a protein, in the body that is closely linked to a particular disease process and can be influenced by a drug to produce a desired therapeutic outcome
Lead: a chemical compound that shows promise as a treatment for a disease and may lead to the development of a new drug
Lecture 2 - Pharmacodynamics 1
Affinity
Agents cannot without binding
Drug affinity is the physical interaction between the drug and the receptor
Drug affinity measures how strongly a drug interacts with the receptor
Types of interactions between a receptor and a ligand
Receptor = ‘key’, ligand = ‘lock’
What determines the shape is the folding of the protein
Different types of bonds i.e., ionic, covalent, hydrogen
How does interaction between the ligand and receptor relate to the affinity and specificity of a drug?
Affinity is the strength of the interaction between a ligand and a receptor
It is governed by:
Shape complementarity e.g., if a molecule doesn’t fit into the binding pocket, less van der Waals interactions can occur leading to decreased affinity
The strength and number of non-covalent interactions between the ligand and the receptor. If more and/or stronger bonds form, then the affinity will be higher
Specificity describes the case when a ligand has increased affinity for one receptor over others
It is governed by:
Shape complementarity
Specific interactions between the ligand and receptor
Importance of affinity
When developing drugs, knowing if they have affinity for the target or other targets helps in development process
Establishing the affinity a compound has for the target allows us to compare it to other compounds so we can develop high affinity compounds
Ligand binding assays are easy to perform, can be automated to achieve high throughput. The data allows for the determination of drug affinity, but can detect allosteric interactions, the characterisation of receptor subtypes, and estimates of level of receptor expression in a tissue/cell
Quantifying the binding of a ligand to a receptor
Receptor theory → the interactions of drugs with targets and write them out as equations
What drives the reactants to create the product is kinetic rate
On-rate = time it takes to binds
Off-rate = time it takes to leave the receptor
If the ligand bound for longer = higher affinity for receptor
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Ligands only interact with receptor for a brief moment
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Affinity
The strength of the reversible interaction between a drug and its receptor, as measured by the binding dissociation constant ($K_D$)
$B_{max}$ is the total density (concentration) of receptors in a sample of tissue or per cell
The ‘binding maximum’
Used to work out how many binding receptors we have
$K_D$ is the ligand concentration at which half of the total number of receptors are bound to the ligand
Experimentally measuring Affinity: Saturation Assays
We need a method to measure amount of ligand bound to the receptor. Common approaches are to label the ligand with either a radioactive isotope or a fluorescent molecule
Saturation binding experiments use increasing concentrations of radioligand and require incubation until equilibrium is reached
Experimentally measuring Affinity: $K_D$ and $B_{max}$
Comparing the affinity of three different radioligands for same receptor
The higher the Kd value → the lower the affinity
Comparing the expression level of two different receptors
7.2 vs 5.7 fmol/mg → shows comparison of expression levels (use Bmax for this)
Enzyme kinetics vs saturation binding
Y-axis = amount of ligand bound vs rate of reaction on the right
X-axis = radioligand concentration vs substrate concentration
LEFT GRAPH:
Bmax = total density (concentration) of receptors in a sample of tissue or per cell
KD = ligand concentration at which half of the total number of receptors are bound to the ligand
RIGHT GRAPH:
Vmax is the maximum rate of an enzyme catalysed reaction
Km is the concentration of substrates when the reaction reaches half of Vmax
Experimentally measuring affinity: Competition binding assays
Labelling ligands is expensive, time consuming and sometimes impossible
Competition binding assays allow us to indirectly measure the affinity of an unlabelled ligand by determining the amount of the test ligand required to compete for receptor binding with the labelled ligand
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Competitive binding experiments use a single concentration of labelled ligand and increasing concentrations of unlabelled ligand and require incubation until equilibrium is reached
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Keep adding unlabelled drug until there is no more binding of the labelled drug
IC = inhibitory concentration → IC50 = concentration that inhibits labelled ligand at 50% of receptors
In this case, -8
Example 2: determining affinity of 3 different compounds
MC4 receptor binding assay; increasing concentrations of test compounds (1,2,3) were incubated with CHO cells expressing MC4 receptor in the presence of 10nM [3H]- SOMS for 1 hour at room temperature
Drug | IC_50 (nM) |
|---|---|
1 | 0.9 |
2 | 10 |
3 | 0.26 |
Drug 3 has highest affinity
Drug 2 has lowest affinity
Experimentally measuring affinity: $K_i$
The IC50 is a property of the experiment, as it is dependent on the concentration of labelled ligand
We can convert this to an absolute value for a ligand and receptor pair that is independent on the amount of labelled ligand added by using the Cheng-Prusoff equation
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Note: $K_i$ is a property of the receptor and unlabelled drug, while IC50 is a property of the experiment
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The IC50 values for compound-X are 20nm when 10nm of labelled-ligand was used and 500nM when 500 nM of labelled-ligand was used
Efficacy
The extent to which a drug can produce a response
Agonist: A compound that can bind to and cause activation of a receptor, thus mimicking the action of the endogenous ligand
Antagonist: a compound that can bind to but not activate a receptor, thus blocking the actions of the endogenous ligand
Experimentally measuring efficacy
Concentration (dose)-response curves
Increase concentration of drug → look at response of cell, tissue, organ etc and measure it
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Concentration-response relationships graphically describe the relationship between the concentration of a ligand applied to cells and the resulting response
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Hard to use linear scale because the reaction happens so quickly at the start → thus convert to log scale
Concentration response curves - Slope (hill slope)
Concentration response curves typically have a slope of 1 (Hill slope) - not all drugs though
Hill slope >1 indicates positive cooperativity (this means that when one ligand binds, it makes it easier for following ligands to bind to the same receptor)
Hill slope <1 indicates negative cooperativity
Drug 1 in the graph has a slope of 1; drug B slope = 4
Concentration response curves - efficacy
Efficacy = maximum response that can be achieved with a drug (maximum usually compared to reference ligand) Given by $E_{max}$
Since drug B has Emax = 100, it is a full agonist, as it has maximal efficacy compared to reference ligand (drug A)
Drug C has reduced efficacy because Emax only 50% → partial agonist