L1 + L2: Drug discovery and development pipeline part 2 Flashcards
lead optimisation?
Making manipulations in structure e.g: to make higher affinity, bind more effectively, change physical properties to help be absorbed from the gut for example, solubility, ionisation etc.
what makes a good medicinal drug: physical properties, pharmacokinetic properties, pharmacodynamic properties
physical properties?
Physical properties
The passive properties of a molecule
Molecular Weight
Lipophilicity (Log P) - how lipid soluble does a drug have to be? Drugs have to be aqueous e.g: if oral then has to dissolve in gut. Intravenously has to dissolve in plasma. These are aqueous environments. Particularly orally- has to cross membranes of cells that line the gut wall and into the bloodstream. Difficult to balance aqueous and lipid solubility.
Ionisation properties (pKa)
Aqueous Solubility
“In the discovery setting (for drugs with oral therapeutic efficacy) ‘the rule of 5’ predicts that poor absorption or permeation is more likely when there are more than 5 H-bond donors, 10 H-bond acceptors, the molecular weight is greater than 500 and the calculated Log P is greater than 5”. Lipinski et al (2001) Adv. Drug Delivery Rev. Vol 46: 3-26.
Whilst Lipinski’s rule is a guide it is not absolute. For example, a recent review of 48 approved, orally active small molecule protein kinase inhibitors showed that 20 failed to conform to the “rule of five”. (Roskoskijr, (2019) Pharmacological Research , Vol 144: 19-50 (https://doi.org/10.1016/j.phrs.2019.03.006 )
So rule of five is a guide not absolute.
a note on log p and d?
P = the Partition Coefficient, and tells us something about the lipid solubility of the drug
Usually compare the water solubility with solubility in octanol (a organic solvent)
P = [drug]octanol/[drug]water
Log P = Log {[drug]octanol/[drug]water}
NB; because it is a log scale, a log P of 3 means there is 1000 times more of the drug in the octanol than the aqueous phase
In general, the more lipophilic a drug, the more likely it is to bind to unwanted targets i.e. to be non-selective
Conical flash half with octanol and water. Shake it up. See conc in of drug in octanol and in water. More lipid soluble = in octanol phase and vise versa
In lapinksis rules- log p should be 5. Log scale, evertime log p foes up by 1 , 10 fold difference in ratio of octanol to ratio. If lof p 3 = 1000 more times of drug in octanol than water. If log p 4 then 10,000 more drug in octanol than water. Log p =5 the
A note of log D
P assumes that the drug only exists in a non-ionised form
But many drugs are ionisable for example and the ratio of ionised to non-ionised forms will vary with pH
In this case we measure what is called the Distribution Coefficient (D), or more typically Log D.
This measures the relative concentration of all forms of the drug (ionised and non-ionised) in octanol vs an aqueous phase of stated pH (typically pH 7.4)
{[ionised drug] + [non-ionised drug]}octanol Log D = Log c
{[ionised drug] + [non-ionised drug]}aqueous
What is conc of ionised vs non ionised drug? In octanol and in aqueous. For drug that ionisases = PH dependet. Particularly for oral - ph changes from gut stomach and along intestine. Degree of ionisation changes as ph changes so log d valuechanges depending on where the drug is in gastric system?
pharmacodynamic properties?
Pharmacodynmaic properties (effect of drug on body/organisms)
What do we need to know?
Mechanism of Action: is the drug an enzyme inhibitor, receptor antagonist or receptor agonist?
Affinity: over what concentration range will the drug have its effect? higher affinity = lower conc of drug needed to prod desired effect
Efficacy: What is the drug’s maximum effect? How big of a response, whats the maximum?
Kinetics: does the drug bind reversibly or irreversibly to its target receptor (is it competitive)? Generally look at reversible drugs.
Selectivity: what effects will the drug have on other targets, and over what concentration range?
If act at others is conc range same as conc range effecting cells elsewhere? Will be problem f conc needed to effect chosen is the same as other targets. Hopefully if conc kept low enough beneficial with less side effects? Need low enough conc for validated target before it starts to interact with other targets.
So tweak these.
pharmacokinetic properties?
VERY IMPORTANT GRAPH!
Absorption, distribution, metbaolism ad excretion. So tell us how quickly drug acts, how long its action is and plasma conc of drug with time.
Time along x axis. Plot on the left= single dose of the drug. Drug given orally. Plasma conc on y. Plasma conc builds up reaches a max and then starts to fall. Shades area = area under the curve. Totle exposure of body tissues to the drug. For all drugs there is a minimum conc to reach before it starts having an effect (minimum effective conc). There is a max conc above which the drug starts to produce side effects. Therapeutic window- do not want above that line or drug = toxicity. Time vs plasma conc profiles hope to get situation where drug stays in therapeutic window and does not reach conc to prod toxicity.
Time that it is above the minimum conc = time it is having an effect (time of action). If drug for hypertension- want drug to constantly stay above the minimum effective conc. So with that have to give dose several times so conc of drug fluctuates. Always goes up and down as body gets rid of it and you take it again. One of the things these pharmacokinetic data show How often to take drug, how long to wait before conc slips below minimum effective conc to take again, how much to take etc.
So pharmacokinetics important for can we keep drug in body long enough for it to have the effects that we need? These things are all altered by chemical nature of drug. Lipid solubility - absorption. How quickly from gastroitestinal tract. Aqueous solubility can get rid of frugs by filtered through urine???
metabolism?
Particularly enzymes in liver metabolising drugs.
chlorampjenicol antibiotic - innactive with sugar attached?
Cytochrome p450 enzymes. Particularly important for several reasons. Genetics of enzymes are differnt. Some are fast metabolisers or slow metabolisers. Time drug lasts vary from person to person depending on liver enzyme. Some drugs can induce or inhibit liver enzymes so some drugs dampen or speed up enzyme activity. Okay if taking 1 drug, if starting to take 2 one of which inhibits then second drug will be more effective - drug-drug interactions. Understanding how drugs are metabolised is important.
propanolol
beta blocker ——-> 4-hydroxypropanolol (phase 1 oxidation)
chloeramphenicol antibiotic—-> chloramphenicol-O-glucurinoside (phase 2 conjugation)
parallel screening cascade?
The parallel screening cascade is a method used in drug discovery to identify the best compound for development by evaluating multiple properties in parallel. The process involves testing various drug-like properties of different compounds, balancing them to select the most promising candidate. Here’s how the cascade works and how it connects to your example:
- Synthesis and Initial Screening
Synthesis: This is the first step, where compounds are synthesized or created in the lab.
Affinity: The compound’s binding affinity to the target is assessed. In this case, they’re measuring how well the compound binds to the target in vitro (outside the body, like in a test tube or petri dish).
Example: The compound might show an IC50 of 10 nM, meaning it needs 10 nanomolar concentration to inhibit 50% of the target’s activity. This is a measure of how potent the compound is.
Cell IC50: The compound’s potency in a living cell (in a biological environment) is measured. In this case, it’s 100 nM, which is a bit higher, indicating it’s less potent in the cells than in the test tube.
- Physical Properties
Next, the compound is evaluated for physical properties, which impact how it behaves in the body:
LogD < 5: LogD is a measure of how the compound dissolves in fat vs. water. A value below 5 suggests the compound is not too fat-soluble, meaning it will likely be able to pass through cell membranes easily.
Molecular Weight (MW) < 500: Drugs with smaller molecular weight are generally better absorbed and metabolized. A compound with a molecular weight below 500 is ideal for drug development.
- Metabolism Testing
This step assesses how the compound will be broken down and processed by the body:
Rat Hepatocytes: Testing in cultured rat liver cells (hepatocytes) helps assess how the compound is metabolized, as the liver is a key organ for metabolizing drugs.
Clearance: This measures how quickly the drug is removed from the body. The ideal clearance rate is <3 microliters/mg/min, which indicates that the compound is cleared at a reasonable rate, not too fast (which could reduce its effectiveness) or too slow (which could lead to toxicity).
- In Vivo Testing
At this stage, compounds are tested in live animals (in vivo) to assess how they perform in a whole organism:
Efficacy Testing: This step evaluates whether the compound works as expected in a living system. For example, does it reduce the symptoms of the disease it’s targeting (e.g., reducing pain, inhibiting tumor growth)?
- The Best Compound Is a Balance of Drug-Like Properties
The goal is to find the best compound that has:
Good affinity to the target (meaning it can interact effectively with the biological target).
Desirable physical properties (like solubility and molecular weight) that make it easily absorbed and distributed in the body.
Appropriate metabolism and clearance rates that ensure the compound stays in the body long enough to be effective but doesn’t cause toxicity.
Parallel Testing in Different Groups:
Different groups within a pharmaceutical company or collaborating companies often work in parallel to evaluate these different properties:
One group might focus on affinity, testing how much of the compound is needed to produce the desired biological effect.
Another group could focus on physical properties, making sure the compound is drug-like (e.g., soluble and small enough to be absorbed by the body).
A third group could focus on how the compound is metabolized in cells or animals to ensure it is processed safely by the liver.
Final Outcome:
After testing these properties in parallel, the most promising compound is selected. The goal is to find a compound that balances all these factors:
It should be able to stay in the body long enough to have a therapeutic effect.
It should be well-absorbed by the gastrointestinal tract when taken orally.
It should be safe, with a manageable metabolism and clearance rate.
Once a balance of these factors is achieved, the compound can move forward in the drug development process and eventually be tested in human clinical trials.
preclinical development?
physical properties—> focus on scaling up pharmaceutics for production
pharmacodynamic properties–> focus on safety pharmacology, toxicology
pharmacokinetics–> metabolite id, dose linearity, toxicokinetics
In pre clinical- 1. Physical Properties – Scaling Up Manufacturing
Problem: Paracetamol in its raw form is a powder, and to create a tablet (e.g., 500 mg of paracetamol), other substances are required to hold the tablet together, such as binding agents.
Challenge: Mixing these substances uniformly is crucial to ensure that each tablet contains exactly 500 mg of paracetamol. The goal is to ensure consistent quality in every tablet, so when a person takes a tablet, they get the exact dosage intended.
Scale-up: During preclinical development, one of the key focuses is to determine if you can scale up manufacturing. This involves ensuring that the process of mixing the powder and other ingredients can be done efficiently for large quantities. Technology (like specialized machinery) is used to ensure uniformity across every tablet during mass production.
Pharmacodynamic properties no. shift focus to safety pharmacology instead as next step is to take to humans.
n Preclinical Studies: The pharmacokinetic properties of a drug determine how it moves through the body (how it’s absorbed, how long it stays in the body, and how it’s eliminated).
testing will focus on:
Metabolite Identification: What does the body break the drug down into? Are any of these metabolites potentially active (meaning they contribute to the drug’s effects) or toxic (meaning they could cause harm)?
Dose Linearity: Does the drug’s effect increase proportionally with the dose? If someone takes two tablets (1,000 mg of paracetamol), will they experience twice the pain relief of one tablet, or is there a non-linear relationship?
Toxicokinetics: How does the drug break down in the body? Are there any toxic metabolites that accumulate at higher doses, and could this cause problems in the liver or kidneys?
These studies ensure that the drug will not accumulate in the body to dangerous levels and that dosage recommendations are safe.
formal safety testing?
Formal safety testing
Carried out to establish a Safety Window. i think this happens in the lead optimisation stage
Key Points:
Safety Window:
Safety Window refers to the range of drug concentrations that are effective but non-toxic. A drug is safe if the concentration required to produce toxicity is much higher than the concentration needed for therapeutic effectiveness. The larger the safety window, the safer the drug.
Cardiac Integrated Risk Assessment:
This includes tests to evaluate the drug’s potential impact on the heart, using methods such as:
hERG test (to check if the drug affects a type of potassium channel in the heart that could lead to arrhythmias).
Purkinje fibers and Langendorff (to assess how the drug might influence heart muscle activity and overall cardiac function).
Genotoxicity Testing:
Tests like the Ames test and micronucleus test are used to determine if the drug has the potential to damage genetic material or cause mutations, which could lead to cancer or other genetic disorders.
Selectivity Testing:
Broader tests to ensure that the drug only targets the desired molecules and not other unrelated proteins, reducing the risk of unintended effects in the body.
Safety Pharmacology Studies (ICH S7A):
ICH S7A guidelines refer to a set of safety pharmacology studies required to assess potential risks to:
Cardiovascular (CV) system
Central Nervous System (CNS)
Respiratory system
Toxicity Studies:
7-28 day toxicity studies are done in two species (typically animals) to determine the Maximum Tolerated Dose (MTD), the highest dose that does not cause unacceptable harm.
Also, the No Observable Adverse Effect Level (NOAEL) is determined, which is the highest dose at which no harmful effects are seen.
Safety Window Concept:
Hoping that drugs that produce toxicity require a much higher concentration than the therapeutic dose. This creates a “safety window” where the drug can be effective without causing harm.
If the effective concentration and the toxic concentration are too close, it’s easy to cause harm because small changes in dosage can be dangerous.
Summary:
The aim is to ensure that before a drug goes into clinical trials, it is proven to be effective at the molecular level and safe in terms of its ability to not cause harmful effects at therapeutic doses.
If the safety window is large, the drug is considered to have a good safety profile, which makes it more likely to proceed to trials with lower risk.
Convinced drug effective- acts on molecular targets and is safe so taken to clinical trials. Costs go up and involves humans so potential to do harm.
why carry out clinical trials?
Why carry out clinical trials?
Market Authorisation - authorsation to sell drugs in diff countries.
Regulatory Authorities (MHRA (UK), FDA (USA), EMEA (Europe), MHLW (Japan), CFDA (China), CDSCO (India)
Local Healthcare Recommendations (NIHCE)
Benefit - needs to be better than current compeition / added benefit. Doesnt mean drug prod bigger effect but maybe have to take only once a day (as mentioned before). Improve patient compliance etc.
Efficacy
Beneficial Clinical Effect
Standard of Care
Risk
Adverse events due to study medication
On-target/Off-target
Likelihood and power
On drugs: most common side effects lists first and so on (possible info needed for cv?)
Likelihood of detecting an event depends on Exposure x Frequency
Exposure = Number of patients observed & Duration of study
Frequency = Likelihood of an event & Threshold for event
For Adverse Drug Reactions (ADRs)
Very Common ~ 1/10 - 30 people
Common ~ 1/100 - 300 people
Uncommon ~ 1/1000 - 3000 people
Rare ~ 1/10,000
Very rare < 1/10,000
Need more people to test in for rarer side effects?
Rare and very rare side effects are not picked up in clinical trials as cannot have that many people. So still chance of causing rare and very rare side effects since havent picked up in drug development stage.
Power
95% likelihood of observing an ADR with 1/n frequency requires ~ 3n patients
n is multiplied for >1 ADRs
