L3: Drug Targets, identification, and validation Flashcards
what are drug targets
a protein that drugs act upon – the drug changes the shape and thus function of the protein.
why are other macromolecules not good drug targets
- DNA and RNA – hard to find potent compounds
- Lipids (fats) – low specificity
- Carbohydrates (sugars/starches) – toxicity
what are the main types of drug targets for current drugs ( 2 types)
- Enzymes (protein machines that do work)
- Receptors (proteins involved in communicating a signal)
what do drugs look like when they interact with receptors and enzymes. use two respective examples
ex.
receptors
- the opioid receptor makes a pocket for the opioid drug on the plasma membrane
enzyme (ends with -ase)
- weight loss drug and its protein target is pancreatic lipase which is also in a pocket of the enzyme
explain enzyme and substrate mechanism (lock and key/induced fit)
substrates approach an enzyme’s active or catalytic site.
the substrates bind (enzyme changes shape to fit) and undergo a chemical reaction creating the products which are released from the enzyme-substrate/product complex as they dont fit as well.
explain how receptors works and its ligand
- Type of protein
- Involved in cell communication – relays information
- Found on surface or inside of cell
- Bind to chemical messengers called ligands (can be hormones)
- Relay the message to the cell
- Cell reacts by functioning differently
- Many hormone effects are mediated by receptors
what are the 5 types of recpeptors
- ligand/drug enters fully into the cell and binds to the receptor inside
- ligand/drug binds to the receptor outside the cell, and the product is created inside the cell as a reaction
- ligand approaches receptor on the membrane and an enzyme fits the inside of the receptor thus creating a product
- ion channel – ligand approaches the membrane and receptor and changes shape to pass through inside the cell, sending a signal inside the cell
- ligand approaches the receptor and causes the receptor to shift along the membrane binding to another receptor, creating a product
explain cell signaling
a chain of molecular events producing a communication inside the cell
hormone or environmental stimulus binds with receptor (reception) -> reaction is produced with secondary messengers (signal transduction)
-> an activation of cellular processes (response)
what is a drug-receptor complex
drug + receptor = DR complex –> produces an effect
what are pharmacodynamics?
what are normal and altered physiological responses?
pharmacodynamics: interaction with cellular targets
normal:
ligand approaches receptor and forms a normal physiological response (active)
altered:
drug covers the active site of the receptor so the ligand cannot bind. the bindment of the drug creates an altered physiological response –> this is the point of drugs
what is target identification and its premise
target identification: determining possible drug targets for drugs of the future.
premise to target identification:
*A macromolecule (usually a protein) exists that is central to the disease mechanism - drug target exists
* If we modulate this protein with a drug we will improve the health status of the patient
what is the difference between genomics and genetics
- Genomics: study of all the genes in the genome
and the interactions among them and their environment
*Genetics: study of single genes in isolation
why do we use genomes instead of protiens to identify targets
While drug targets are usually proteins, we use genomes to identify targets, due to the lower complexity of the genome
one way to finding targets – how do we find which genes/proteins are different between healthy people and those with disease?
Genome-wide association studies
- evaluate chromosomes of controls and patients, and identify which proteins/genes differ
explain the example of target identification by correlations study of the cancer genome
what is a con of this method
what is target validation
Cancer Genome Changes reveal possible drug targets (pathways): target identification
- con: there are too many possible targets identified. Cannot make a drug for each
- target validation:
which is the actual protein target that affects the mechanism of the disease – because not all that were found actually effect the disease to a large effect. how do we find if its worth developing a drug against all, lets say, 200 of these changes.
how do we find which proteins matter in synthesizing a drug for? (instead of making a drug for a change that doesn’t matter)
we can test drug possibilities on simple organisms that have very similar genomes to humans. by conducting tests, we can see which proteins are effected and how the drug reacts.
ex. budding yeast, zebrafish, roundworm, fruit flies, mice.
what are the 4 advantages of zebrafish for drug discovery?
- conserved targets
- conserved drug metabolism
- conserved physiology
- conserved pharmacology
what are SNPs
and what do they account for?
SNPs= sites of variations in our genomes
- Single nucleotide polymorphism (SNP): Substitution of one base for another at a single site
- > 10 million sites where SNPs occur (sites of variations) in the human genome
SNPs can account for differences in…
- Appearance
- Risk for certain diseases
- Response to drugs
Many SNPs have no apparent effect
what are some single gene and multiple genes diseases. how does this complexity effect drug creation
Single Gene
-Cystic Fibrosis
-TaySaks
- Sickle Cell Anemia
Mutation in a single gene causes the disease
Multiple genes
-Diabetes
-Schizophrenia
- Autism
-Obesity
variation in multiple genes is associated with disease
More genes = harder to get a specified and targeted drug
explain SNP association with Type II diabetes? what does this mean for the genetic and environmental risk correlations?
- Genetics and environmental factors play a role in the development of Type 2 Diabetes (T2D)
- not a single mutation that causes the disease
- Numerous SNPs = (slightly) increased risk for T2D
Determine the genetic risk for T2D by surveying one’s genome for disease associated SNPs.
Individuals at with high genetic risk should manage environmental risks
How are diseases and associated SNPs identified?
Genome Wide Association studies (GWAS) can be done
1. Compare DNA from individuals who suffer from a specific medical condition to healthy individuals
2. Search for differences between the 2 genomes
3. Identify SNPs that occur more often in the disease group than in the healthy group
what can you figure out when you know the SNPs correlated with a disease?
when you know the SNP correlated with a disease then you can:
- Determine risk for the disease
- Identifying drug target
canada personal genome project: what is it and what can it help us explain?
- sequence the genomes of many people and correlate sequence to health status
- “we need to decode 100,000 genomes worldwide to begin to make sense of those genetic variants that are involved in disease and those which protect us from it”
how do companies help us sequence our genes
- order kit online
- spit in a tube and send to the lab
- analyze dna in 6-8 weeks
- log in and start exploring genome
- with this we can see if we have any disease associated mutations and SNPs in our genome
- some risk and marketing strategies
- companies can offer lifestyle advice with data
what is the difference between target identification and target validation
identification: find the possible drug target and genes
validation: see if the genes protein plays an important role in disease
how can we test target validation - use example of zebrafish
ask whether removing the target matters to the organism
context: genes 1, 2, 3 might be involved in epilepsy. The genes 1, 2 or 3 code for protein 1, 2 and 3. Which protein should we create a drug against?
- strategy 1: use genetic engineering to remove gene 1, 2, 3
if lets say gene 2 is removed and protein 2 is missing and the fish seizures, we know we have to make a drug against protein 2.
- strategy 2: test the swimming and seizure patterns in the fish
if we genetically alter gene 2 again and we see, when compared to the control, that experimental condition has many seziures and a random chaotic swimming pattern, we can see protein 2 is the effected protein.
how can we test target validation - human cell cultures?
- instead of model organisms use human cell cultures
- same idea as zebrafish - genetically modify culture by removing gene 1, 2, or 3
- measure the behaviours that can be measured in cells (cell growth and cell death)
- whichever dies, thats the effected gene/protein
explain another way to culture cells: 3D organoids to model human organs
2D vs 3D cultures
what is an advantage of 3D
- closer to the actual physiology of humans
2D cultures:
- cells
- culture media, dishes, plates, wells
- extracellular adhesive proteins
3D organoids:
- multiple cell types
- cell-cell interactions
- extracellular proteins
- cell-induced extracellular remodelling
- pro: more relevant to human bio
