Drug development and design Flashcards
LO
1.Conventional therapeutics
2.Biopharmaceuticals
3.Gene therapy
4.Cell-based therapies
5.Tissue and organ transplantation
Convnetional therapeutics can use small molecule drugs. What are the two forms of these drugs?
- Natural compounds
- (semi) synthetic chemistry
Tell me about natural compound drugs and some examples
- Normally produced by organisms.
- penicillin’s: bacterial cell wall
- rapamycin: mTORC1 inhibitor: discovered on Easter island: isolated from Streptomyces hygroscopicus
- morphine: found in a number of plants
Tell me about drugs made via (semi) synthetic chemistry
- modified natural compounds (semisynthetic)
- libraries of chemically synthesised compounds
Tell me about the history of morphine usage
Tell me about its initial use, some side effects and the risks associated with the drug
Morphine
- Use dates back to 3400 BC, when the Sumerians of Mesopotamia were already cultivating the opium poppy, which they named the ‘joy plant.
- First isolated by Friedrich Wilhelm Sertürner between 1803 and 1805 and marketed by Merck
- used initially for pain relief and to reduce coughs
- Side effects: decreased respiratory effort, low blood pressure, Vomiting, constipation, drowsiness.
- Morphine has a high potential for addiction and abuse
What was Heroin initially developed for?
How is it produced?
- Initially developed and marketed by Beyer as a non-addictive version of morphine.
- Obviously not! Produced by boiling morphine with acetic acid
Tell me about Codeine
How is it converted to morphine?
Codeine
- weak agonist at the opioid receptor; converted to morphine by the cytP450 system
- People who express high levels of this system convert substantial amounts leading to high morphine levels and respiratory deficiency.
Name 2 morphine derivatives?
codeine and heroin (diamorphine hydrochloride)
Tell me about some general ways that drug development can occur
- Natural isolate: serendipitous
- Semi synthetic: Structural modifications on a natural background. Change’s activity of the natural compound
- Synthetic: Rational design based on the natural compound but structurally different Mimic
- A look alike that acts as an inhibitor: rational combined with suck it and see.
Small molecule modulators do not have to look like their endogenous counterparts
Give some examples of some endogenous opioid agonists?
1. Enkephalins: penta peptide
Met-enkephalin is Tyr-Gly-Gly-Phe-Met.
Leu-enkephalin is Tyr-Gly-Gly-Phe-Leu.
2. B-Endorphins
Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-Leu-Phe-Lys-Asn-Ala-Ile-Ile-Lys-Asn-Ala-Tyr-Lys-Lys-Gly-Glu
3. Dynorphins
Why do we need new drugs?
- Emerging diseases or previously untreatable ones
- Improved action (lower toxicity)
- Altered pharmacokinetics (A.D.M.E.)
- Cheaper synthesis
- Competition
- Resistance
Cellular constituents that have been developed as drug targets
What must an oral drug be able to do?
- dissolve
- survive a range of pHs (1.5 to 8.0)
- survive intestinal bacteria
- cross membranes
- survive liver metabolism
- avoid active transport to bile
- avoid excretion by kidneys
- partition into target organ
- avoid partition into undesired places (e.g., brain, foetus)
- Bind to and modulate its target
A drug needs to be able to do many things other than bind to the active site of the receptor! This diagram illustrates a model for an oral drug to treat a problem with the foot. It is a very complicated model of a human, and it’s hard, if not impossible, to measure all these processes directly. In addition, it is much better to have an in vitro model than have to carry out these tests in living animals or whole organs.
Drug distribution in the body
A typical pharmaceutical drug pipeline
During pre-clinical testing, what do you need to do to test the efficacy (ability to produce a desired or intended result) of a drug?
- determine potency and selectivity
- Off target effects
How do you determine the potency and selectivity of a drug?
dose response curves against targets and non-targets. For example, molecules targeting a specific kinase could be tested against many other different kinases to determine a selectivity profile.
Tell me about the off target effects of pre-clinical drug tests
determine potency for known off targets that would preclude use in human. For example, the HERG channel (potassium channel in the heart).
Tell me about cell based studies
Cell based studies. Does the drug do what you expect it to do in a straightforward cell-based assay. If it’s an anti-oncogenic target, does it stop growth of cells that express the selective oncogene. What happens in cells that do not express that particular oncogene? Studies can be confirmed using RNAi or CRISPR CAS9. In oncology we now have banks of tumour cell lines that can be used to determine cancer target possibilities if not known (see later slides) .
Tell me about studies in vivo during pre-clinical testing
Studies in vivo: normally mouse models. Gives information about efficacy in vivo (should be taken with some caution). Also gives information about possible toxicities
What tests are done during pre-clinical toxicity testing?
- Genetic
- Acute
- Short-term
- Sub-chronic
- Chronic
- Reproductive
Tell me about genetic pre-clinical toxicity testing
Various genetic endpoints in bacteria (Ames-test) and mammalian cells (chromosome aberrations); used as a screen for potential carcinogens
Tell me about acute pre-clinical toxicity testing
Usually, single dose study; various limit tests have replaced the notorious LD50 test
Tell me about short-term pre-clinical toxicity testing
Repeated daily doses for 14-28 days in two animal species (rodent and dog); identifies the target organ
Tell me about the sub-chronic pre-clinical toxicity testing
Repeated daily doses for 90 days in two animal species (rodent and dog); gives dose-response, and used for dose selection in chronic studies
Tell me about chronic pre-clinical toxicity testing
Repeated daily doses for two years in rodents and one year in dogs; used to investigate carcinogenicity
Tell me about reproductive pre-clinical toxicity testing
Dosing occurs before during and after reproduction to investigate effects on foetal and neonatal development
Pharmacokinetics ADME: Absorption, distribution, metabolism and elimination
How many phases of clinical studies are there with volunteers or patients?
4
Tell me about phase 1 of clinical studies
Phase 1 studies
- To define the pharmacology, route and metabolic fate in humans
- Initial dose is usually 1/20 or 1/50 of the effective dose in animals
- Side-effects monitored by clinical biochemistry etc
- Small numbers studied - typically 36 or less
Tell me about phase 2 of clinical studies
Phase 2 studies
- To define therapeutic profile and dose regimen
- Dose-ranging means that a lot of data are at sub-optimal doses
- Patients usually studied and larger numbers cf. Phase 1
- Limited number of clinical centers involved
Tell me about phase 3 of clinical studies
Phase 3 studies
- To determine clinical efficacy compared to placebo / comparator
- Greater duration of treatment and larger numbers studied
- Multi-center and often multiple indications investigated
- Close monitoring of compliance, other drugs and side effects
Tell me about phase 4 of clinical studies
Phase 4 studies- post marketing surveillance
- Clinical practice is less controlled than Phase 3 studies
- Larger numbers and more diverse patients treated
- Adverse drug reactions (ADRs) are reported by practitioners
- Black triangle drugs - all ADRs and events should be reported
Why do drugs fail to get to market?
- Lack of efficacy at the target
- Lack of target linkage
- No testable model
- Lack of suitable biomarker
Data from ASTRA Zeneca over the past few years on targets that fail
Tell me the types of targets for small molecular weight molecules
- Active sites of enzymes: kinases, metabolic enzymes, neuronal enzymes (acetylcholine esterase’s)
- Receptors: GPCR, RTK
- Ion channels:
- Protein/ Protein interaction sites:
Where do the molecules come from?
- Large scale library screening: often in the range of 1 million compounds
- targeted library screens: for example, a specific type of kinase: range 100000
- Small libraries: can be naturally occurring compounds or libraries of drugs that are have already been used in the clinic. For example, NCI oncology set
- In silico derived drugs. Often screen 3-4 million compounds to start
Tell me about the robust assay system for drug screening and validation
- Adequate frequency of positive and negative control values
- Adequate data variability band of both positive and negative controls in which the standard deviation is reasonably small
- Adequate assay signal, that is the separation band where the standard deviations of the negative and positive controls do not overlap
Tell me about the automation of screening system
- Robust biophysical methods - detection
- Miniaturization (96- or 384-well plates etc.)
- High-throughput - Robotics
- Automated data analysis and management
Whats Alzheimers disease and how many people did it effect?
Alzheimer’s disease (AD) is a neurodegenerative disease and 1 in 10 people would be affected by AD world-wide
- Actual cause of the disease –> yet to be identified
- Aggregation and accumulation of neurofibrillary tangles and β-amyloid (Aβ) plaques
- A dramatic decrease in cholinergic innervation in cortex
What are the functions of the drugs for Alzheimers disease?
Symptomatic treatments
- Increase Ach levels
- Inhibiting AChE
- Preventing Aβ plaque accumulation
Tell me about the etiologically based treatments of alzheimers disease
etiologically based treatments – slowing or halting the rate of progression
Cell-based assay system
AChE inhibitor assay system
High-throughout assay system
Reiterative rounds of chemistry and biology drive the development of a lead compound.
Why do we need to modify a lead target drug?
- Generate new specificities
- Increase target selectivity
- Increase bioactivity
- Increase efficacy and potency
- Change ADME profiles: membrane permeability, elimination, toxicity profile
Tell me about the characteristics of small molecular weight drug like molecules
- Simple diffusion: depends largely on lipid solubility or the partition coefficient and the molecular size. Most orally available drugs.
- Facilitated diffusion: aquaporins, glucose transporters
- Active transport: ABC transporters (often important in pumping drugs out) , SLC family
- Endocytosis
Ionisation: the importace of pH and pKa
Weak acid such as aspirin
Ionisation: the importance of pH and pKa
Weak base such as codeine
And here is the corresponding diagram for a basic compound. Below about pH 7, the molecule will be completely protonated. Do you know why the ring nitrogen protonates rather than the NH2?
The importance of compartment pH in adsorption and elimination of drugs
Drug traversal across membranes: the importance of ionisation
Whats the Lipinsky role of 5 for orally available drugs (not really five rules)?
- molecular weight < 500
- octanol-water partition coefficient logP < 5
- < 5 H-bond donors (sum of NH and OH)
- < 10 H-bond acceptors (sum of N and O)
Name a nicotinic receptor inhibitor
Name muscarinic receptor inhibitor
What is atropine isolated from?
Tell me about oestradiol i.e., what it binds to an activates?
What is it required during?
What does it control?
Tell me about Diethylstilbesterol
What subtle changes are required to maintain beneficial characterisitcs of drugs?
What are Isosteres?
Isosteres: concept developed by Langmuir (1919): isosteres are those atoms or groups of atoms or molecules or compounds (organic or inorganic) that have the same arrangement and/or number of electrons (isoelectronic) or similar shape (isosteric). These isosteres share many similar chemical properties.
e.g.
-H=, -F
-N=, -CH-
-O-, -NH-, -CH2-
-F, -OH, -NH2, -CH3
What are Bioisosteres?
- novel inhibitory activities
- Molecules which possess broadly similar biological activities and identified by identical physical or chemical properties
- Both of these drugs are on the World Health Organisation list of essential medicines
- 5-FU first line treatment for many cancers: colorectal, pancreatic, oesophageal, stomach
- 6-TG AML
Tell me about Bioisosteres generating novel specificity
Tell me about Bioisosteres novel ADME properties
- SC-58125 good selectivity and potency for COX2 over COX1. however, it has poor ADME properties. Long half-life, low metabolism by the p450 system
- Isosteric replacement of the CH3 group and replacement of the fluorine group
- Lack of inhibition of COX1 should in theory enable anti-inflammatory effects without aggravating gastrointestinal issues (which occur with non-specific NSAIDS such as aspirin, naproxen)
- However long term they have an association with an increase in cardiovascular problems
Give an example of a novel ADME property
Tell me about the structure guided generation of a novel m-opioid receptor (m-OR) agonist
- Used the structure of the m-opioid receptor bound to b-FNA (funaltrexamide: antagonist) to dock with 3 million compounds in silico.
- Narrowed down to 2500 manually visualised for interaction with important residues (asp147).
- Led to 23 compounds with Ki ranging between 2.3-14uM
Analogue docking identifies a high affinity active agonist of the opioid receptor
The following show the three methods to enhance low affinity biding of compound 7 (2.5uM)…
- Docked 500 analogues of compounds 4, 5 and 7 that retained the key recognition groups but added packing substituents or extended further towards
the extracellular side of the receptor, where the opioid receptors are more variable. Generated analogues with Ki values between 42 nM and 4.7 μM
- These were tested and found to be specific for the μOR over κOR
- Investigated potency and efficacy (note that the initial protein structure is an inactive structure) for receptor activation. Compound, 12 strongly activated Gi/o with low levels of β -arrestin-2 recruitment
Resolving the stereochemistry together with structure guided modification identifies a high affinity specific agonist
- Phenolic hydroxyl of bFNA creates water-based interactions with Histidine 297. missing in compound 12
- Introduction of a phenolic hydroxyl to compound 12 to generate PZM21 enhances the affinity for binding the mOR 5-fold.
- Gi/o activation. PZM21 is more potent than morphine
PZM21 a new pharmacophore for m-OR agonism
- PZM21 had no detectable κ OR nociception receptor agonist
- activity—it a selective μ OR agonist.
- To investigate specificity more broadly, PZM21 was counter-screened for agonism against 316 other GPCRs30. Activity at 10 μ M was observed at several peptide and
- protein receptors: however, no potent activity was confirmed with a
- full dose–response experiment at these receptors. PZM21 therefore has high agonist
- specificity among GPCRs
- PZM21 showed very low activity at the hERG ion channel and the dopamine, norepinephrine and serotonin neurotransmitter.
- Thus, PZM21 is a potent, selective, and efficacious μ opioid agonist.
Thalidomide
- Thalidomide consists of a racemic mixture of S(-) and R(+) enantiomers
- The R(+) enantiomer- responsible for sedation
- The S(-) enantiomer for the teratogenic effects of thalidomide, which cause the abnormalities that occur during embryonic development
- Rapid interconversion takes place between the two enantiomers under physiological conditions
- Teratogenic effects observed in rodent models
- This effect was not observed in the New Zealand rabbit
Receptor mapping studies
base on structure-activity- relationships
Nicotinic receptor
Some fill in gap examples in lecture 22 notes
