the medicine Flashcards
(210 cards)
1
Q
what is attrition
A
clinical trial
10-20 marketed drugs only roughly 2 will make a profit
2
Q
what is Ligand-based Drug Design (LBDD)
A
uses
knowledge of ligand structure with or without
knowledge of the receptor to create models
based on structural properties able to
discriminate good compounds from bad.
3
Q
what is Structure-based Drug Design (SBDD)
A
uses
knowledge of the receptor structure to guide
the design of new compounds able to exploit
unfulfilled interactions and shape
complementarity.
4
Q
what is Drug Design
(optimising affinity)
A
From the way a compound sits in the enzyme
active site, potentially we can suggest
modifications to the compound that will increase
its affinity.
5
Q
how can we measure how a set of
compounds sit in the active site of an enzyme then
we can make judgements on the relative affinities
of the compounds (scoring and ranking)
A
X-ray crystallography
Neutron diffraction
Solution NMR
6
Q
how can we how a set of
compounds sit in the active site of an enzyme then
we can make judgements on the relative affinities
of the compounds (scoring and ranking).
A
Protein-ligand docking
7
Q
what is Steric
Complementarity
A
We can do this if we have a plausible set of 3D
coordinates for the protein-ligand complex.
look to pick up favourable intercations
8
Q
why dont you want really attractive groups in your drug molecule
A
they will reacy with everything
9
Q
what is docking
A
computational methods for finding the best matching between two molecules,
a receptor and a ligand.
10
Q
what two methods does the docking process require
A
posing and scoring method
11
Q
what is the scoring method
A
to give each
individual pose a score in order to
determine the best pose (and later
to rank a compound set)
12
Q
what is the poising method
A
placing the
ligand into the active site
13
Q
what do you need for Protein-Ligand Docking (Virtual ligand screening)
A
the receptor structure - from homology or experiment
The location of the active site (binding cavity)
The structures of the compounds to be docked
14
Q
what are the complications with posing
A
The protein and the ligand are both flexible:
→ Hundreds of degrees of freedom
→ Impossibly large number of possible
conformations
Compromise: fully flexible ligand; rigid protein with
flexible binding site residues.
Dock ligand into binding pocket → generate a large
number of possible orientations, score each one by an
energy function and select the best set.
15
Q
Posing Methods
Random searching: Genetic algorithms
A
A class of computational problem-
solving approaches that adapt the principles of biological competition and
population dynamics.
model perameters
16
Q
Posing Methods
Random searching: Monte Carlo simulations (simplified)
A
- Generate an initial configuration of a ligand in an active site consisting of a
random conformation, translation and rotation. - Score the initial configuration.
- Generate a new random configuration and score it.
- If the new solution scores better than the previous one, it is accepted.
- Repeat previous steps until the desired number of configurations is obtained.
17
Q
Posing Methods
Fast shape matching:
A
Match triangles of interaction sites onto complementary ligand atoms
18
Q
Posing Methods
Incremental construction
A
The receptor interaction surface is derived from
crystallographic information and approximated by a finite
set of interaction centers.
* The ligand is fragmented into base fragments.
* The ligand fragments are placed into the active site by
matching the interaction centers.
* The number of solutions is reduced by clash testing.
* The base fragments are linked in compliance with a
torsional database or a force field.
19
Q
complications with scoring
A
Ligand-binding events are driven by a combination of enthalpic
and entropic effects, either of which can dominate specific
interactions.
* Problem: most scoring functions are much more focused on
capturing energetic (energetic & van der Waals interactions)
than entropic effects. (-TdeltaS)
enthalpy delta H
20
Q
Other complications in predicting binding conformations and
compound activity!!!
v important
A
limited resolution of crystallographic targets
* inherent flexibility of the protein
* induced fit or other conformational changes upon binding
* the participation of water molecules in protein–ligand
interactions.
21
Q
x-ray and NMR crystal structures
A
x-ray: It may be that the X-ray crystal structure of the particular
protein has been determined many times with a range of
different ligands. The protein conformation will be slightly
different in each case.
NMR: may contain 10-20
conformations – use each of these to
dock into.
22
Q
Three major classes of scoring functions are currently applied
A
Force-field-based
Empirical
Knowledge-based scoring functions
23
Q
what is computational stability
A
permits efficient screening of
large compound databases.
24
Q
benefits of protein ligand docking
A
quantification of conformational changes
can handle solvent and ionic effects
mod to high level of ligand effects
Allows for receptor and ligand rearrangements to obtain lower
energy conformations of the docked complex.
25
potential problems for PLD
high computational cost
analysis of huge output
26
QSAR – the principle
Quantitative Structure Activity
Relationships
1. Draw the structures of the compounds and optimise
their 3D geometries.
2. Calculate molecular properties (descriptors)
3. Use the descriptors together with the biological data to
derive equations that predict the biological activity.
4. Calculate the descriptors for new compounds and use
the equation to predict their biological activities.
27
The QSAR Equation
The QSAR equation relates the experimentally-
observed biological activity to the calculated molecular
properties.
This allows one to predict the activity of a new
compound.
28
what does QSAR not require ny knowledge of
QSAR does not require any knowledge of the
receptor, active site or the mechanism of action.
Only the structures of a set of compounds of
known biological activity are required.
It is necessary, however, that the compounds all
act in the same way at the same receptor or
active site.
29
describe the general process of QSAR
Select a set of molecules
interacting with the same receptor
with known activities.
Calculate features (e.g.
physicochemical
properties, etc., 2D, 3D)
Divide the set to two
subgroups: one for training
and one for testing.
30
what is the training set
Build a model: find the
mathematical relationship
between the activities and
properties
31
what is the testing set
Test the model on
the test dataset
32
what is geometry optimisation
Change the geometry to
minimise the energy of the molecule.
33
Molecular Mechanics Geometry Optimisation (4)
Considers atoms as balls and bond as springs
Does not consider the electrons
Fast
Low quality but OK for a quick clean up of a drawn
structure.
34
Preparation of the structures (structures of known
biological activity)
(4)
1. Draw the compounds.
2. Clean up the structure by performing a molecular
mechanics geometry optimisation.*** [Change the geometry to
minimise the energy of the molecule.]
3. Identify key rotatable bonds and perform a conformation
search.****
4. Perform a semi-empirical quantum mechanical geometry
optimisation on the lowest energy conformation identified in
step 3.
35
Semi-Empirical Quantum Mechanical Geometry
Optimisation
The valence electrons are used to construct molecular
orbitals.
The inner electrons are approximated via a parameter
set.
Slower than MM but much better quality (molecular mechanics)
36
what happens at room temp
At room temperature, the lowest energy conformer prevails.
37
what is confirmation searching
Each rotatable in turn bond is stepped round in small
increments and the energies of the resulting
conformations are calculated.
This is used to find the approximate position of the
GLOBAL MINIMUM ENERGY POTENTIAL WELL.
After that a high quality energy-minimisation technique
can be used to refine the structure down to the global
minimum energy conformation. (EG Semi-empirical
quantum mechanical geometry optimisation)
37
what is energy minimisation not capable of finding
the global energy minimum
All energy minimisation techniques concentrate on searching
downhill - they therefore tend to find the nearest local
minimum on the energy surface. If a much deeper (i.e. better)
energy minimum is nearby, but separated from the starting
point by a high energy barrier, it will not be found.
conformation
searching is used
38
Molecular Descriptors
Some descriptors can be calculated rapidly
e.g. molecular weight, dimensions
Other descriptors may be time-consuming to calculate
such as those derived from quantum mechanics.
HOMO-LUMO energy gap
polarisability
partial atomic charge
Some descriptors have an obvious experimental
counterpart with which the calculation can be
compared e.g partition coefficient.
Other descriptors are purely computational e.g. a
binary fingerprint.
Some descriptors refer to properties of the whole
molecule; others refer to the properties of individual
atoms
39
Molecular Descriptors 2D and 3D
If a 3D structure is required then which molecular
conformation should be adopted?
usually the
global minimum energy conformation.
Some descriptors such as lipole, dipole, moments of
inertia have components along the orthogonal x,y,z axes
(i.e., they are vectors.)
Thus to compare the values from one molecule to another,
each molecule in the set must be orientated in the same
way.
40
what is the Ellipsoid Volume.
A measure of the distribution of mass within a molecule.
The moments of inertia and principal axes of inertia for a
molecule are calculated using the inertia tensor. These
results are reported in TSAR as Moment 1 Size, Moment 1
Length, etc.
The volume defined by these values is calculated and
reported as the Ellipsoid Volume.
41
Moments of Inertia and Ellipsoid Volume
You can view the molecule and an ellipsoid of inertia.
The ellipsoid’s principal axes are aligned with the axes of
the inertia tensor. The length of each axis is inversely
proportional to the moment of inertia around that axis. The
resulting ellipsoid is then scaled so that the atom furthest
from the centre of gravity of the molecule appears on the
ellipsoid surface.
42
LogP
Lipophilicity
43
What is Lipophilicity
Lipophilicity is a measure of the ability of molecules to
move between fat and water. It is often used to indicate
how easily a molecule may be transported across
membranes.
44
how to estimate LogP/Lipophilicity
Most people use the partition coefficient for
water/octanol (log P) as an estimate of lipophilicity.
Atomic values or substituent values are available
from a database of experimentally determined values.
The values for the appropriate atomic or substituent
fragments are simply added together to derive the
molecular LogP value
45
Molar Refractivity:
This is compiled by reference to a
database of experimentally determined values: Substituent
contributions and atomic contributions to molecular molar
refractivity values
46
what increases with alkyl chain length
Both log P and MR increase with alkyl chain length, so
log P and MR show a strong correlation.
47
what do polar functional groups do to MR
Polar functional groups increase MR, but decrease log
P. Perhaps MR is a measure of nonlipophillic
interactions, while log P is a measure of lipophillic
interactions.
MR has a strong correlation with the molecular
polarisability.
48
Molecular Descriptors 2D and 3D
Polarizability
A measure of the ease with which the electron cloud
of the molecule can be distorted by an applied
electric field.
The attractive part of the Van der Waals interaction
is a good measure of the polarisability.
Highly polarisable molecules can be expected to
have strong attractions with other molecules.
The polarisability of a molecule can also enhance
aqueous solubility.
49
Molecular Descriptors 2D and 3D
Dipole moment
Dipole moment calculations use partial charge
information.
Total dipole moments for whole molecules and
substituents are calculated using the centre of charge
as an origin, and are in Debye units.
50
what does lipole measure
The lipole of a molecule is a measure of the lipophilic
distribution.
51
how do you calculate lipole
It is calculated from the summed atomic log P values, as
dipole is calculated from the summed partial charges of a
molecule.
The total lipole for whole molecules and substituents is
calculated using the center of log P as an origin.
52
Molecular Descriptors 2D and 3D
Verloop Substituent Parameters
Verloop proposed a set of multi-dimensional steric
parameters to help explain the steric influence of
substituents in the interaction of organic compounds
with macromolecules or drug receptors
53
Verloop Substituent Parameters calculation
Verloop parameter calculations assume that all atoms
have Van der Waals radii and use these to define the
substituent’s space requirements.
The five Verloop parameters define a box that can be
used to characterize the shape and volume of the
substituent.
54
Verloop Substituent Parameters continued...... L
L, the length parameter: the maximum length of the
substituent along the axis of the bond between the first atom
of the substituent and the parent molecule.
55
Verloop Substituent Parameters continued...... B...
B1, the width parameter: the smallest width of the
substituent in any direction perpendicular to L.
B2, B3 & B4 are determined by measuring the width of the
substituent, as follows:
in the direction opposite to the axis defined by B1
in the two directions perpendicular to this axis and
the original bond axis.
56
what do the 5 verloop parameters define
The five Verloop parameters define a box that can be used
to characterize the shape and volume of the substituent.
57
Constructing the QSAR (relating the biological
activity to the calculated properties)
Use multiple regression* (an extension of linear
regression)
This calculates an equation describing the relationship
between a single dependent y variable and several
explanatory x variables.
It is very important to choose variables (calculated
properties) that are not correlated.
58
Techniques employed in quantitative structure–property
relationship (QSPR) studies
Multiple linear regression analysis (MLRA)
Free–Wilson analysis
Cluster analysis
Pattern recognition
Factor analysis
Discriminant analysis
Principal component analysis (PCA)
Partial least square (PLS) analysis
Comparative molecular field analysis (CoMFA)
Artificial neural networks (ANN)
Evolutionary algorithms, such as genetic function
approximation (GFA)
59
Constructing the QSAR
Simple multiple regression:
all the input x variables
(calculated properties) are used in the equation to
predict y (the bio-activity).
x to y
60
Constructing the QSAR
Stepwise multiple regression:
a selection algorithm is
used to choose a subset of input x variables.
61
Constructing the QSAR: is it reliable?
Having derived an equation for predicting y from a
series of independent variables, one needs to know
how reliable predictions made with this equation are
likely to be.
The multiple correlation coefficient r2 describes how
closely the equation fits the data. If the regression
equation describes the data perfectly then r2 will be 1.0.
62
Constructing the QSAR: overfitting
implications
The major drawback of regression analysis is the
danger of overfitting.
This is the risk that an apparently good regression
equation will be found, based on a chance numerical
relationship between the y variable and one or more of
the x variables, rather than a genuine predictive
relationship.
The QSAR equation will fit the training data very well
but be useless in predicting the activity of a compound
not in the training set.
63
Constructing the QSAR: overfitting
Dangers of overfitting
When an overfitted model is used predictively, the
predicted values for untested compounds will not be an
accurate prediction of the true values (when these are
eventually determined). Thus the regression equation
has no predictive power.
Use a of cross-validation technique to estimate the true
predictive power of every regression model. (See next slide).
The best way to avoid an overfitted regression equation
is to use just a few carefully selected (non-correlated) x
variables, and use as many data points as possible (at
least 5 per term in the equation).
64
Cross Validation of Results
Cross validation provides a rigorous internal check on the
models derived using regression, discriminant, or partial
least squares analysis.
Leave out one row: Each row is left out in turn, so that the
value of each row is predicted from all others.
Leave out groups of rows: Groups of rows are left out,
excluding a third of the data from each model in a fixed
pattern.
65
what leaves out groups of rows in a fixed
pattern, using three cross validation groups of rows.
TSAR
A third of the data is deleted and the values for these
rows predicted using the rest of the data.
This is repeated for the second and then the third
groups.
The model is judged based on these predictions.
66
Constructing the QSAR: r2(CV)
This is a key measure of the predictive power of
the model.
The closer the value is to 1.0, the better the
predictive power.
For a good model r2(CV) should be only slightly
lower than r2.
If r2(CV) << r2 then there is probably overfitting.
67
You have your QSAR valid equation
– now what?
Your QSAR equation is derived from a set of existing
compounds that have been tested.
You can now consider a new (non-existing, untested)
compound, calculate its properties, put these values
into the QSAR equation and calculate a prediction of
the compound’s activity.
68
Particle size distribution
Size > 250 µm
usually free flowing
69
Size < 100 µm
poor flow quality
70
Size < 10 µm
extreamly poor flow
71
Adjustable properties
Particle size
Particle shape
Surface characteristics e.g. energetics, roughness etc.
cohesion (single components) and adhesion (mixtures)
72
what is an aerosol
a suspension or dispersion of solid or liquid particles (<50µm) in a gaseous medium
73
Particle dispersion determined by a combination of factors:
size and density of the particles
density of the suspending medium
other physicochemical particle characteristics e.g. charge, energetics etc.
interactions (& number of interactions) between the particles in dispersion
74
what is sedimentation
when particle density is greater than the density of the suspending medium.
75
what is creaming
when particle density is less than the density of the suspending medium.
76
Particles < 1um...
will remain suspended within a system (= colloidal system)
Suspensions with particles > 1 m (most aerosols) only kinetically stable
i.e. relatively unstable
77
what is an agglomerated system
easily re dispersed
78
what is an aggregated system
difficult to re disperse
79
what is COPD
Chronic Obstructive Pulmonary Disease (COPD) is a chronic inflammatory lung disease that causes obstructed airflow from the lungs. It encompasses several conditions, including chronic bronchitis and emphysema. The primary characteristic of COPD is difficulty breathing due to airflow limitation, which is not fully reversible.
80
COPD
Risk Factors
smoking
pollutants
sex
race
economic status
genetic
occupational factors
81
WHY Deliver drugs to the lung? Local action
Target organ most affected by Chronic Respiratory Disease
Rapid onset of action
Avoid first pass metabolism
Targeted hence lower dose required
Multiple receptor targets for relief of reversible bronchospasm
82
WHY Deliver drugs to the lung? Systemic action
non invasive to systemic circulation
83
Formulations containing two or more components
complications
Difficult to mix
Difficult to control content uniformity
Difficult to dispense
mix well
84
what are computational approaches
Generate an ensemble of receptor conformations (eg from
NMR, X-ray, molecular dynamics) and dock to those.
X-Ray crystal structures
It may be that the X-ray crystal structure of the particular
protein has been determined many times with a range of
different ligands. The protein conformation will be slightly
different in each case
A NMR protein structure (obtained in
solution) may contain 10-20
conformations – use each of these to
dock into
85
Receptor flexibility: X-ray crystal structures of the same protein but with different ligands
Consider a set of crystal structures of the same protein but with different ligands .
The structural changes observed in such a collection of receptor structures include
regions capable of accommodating differently shaped ligands as well as areas of an
induced fit of the ligand.
* An ensemble or a subset of conformers may provide a more accurate representation of
the protein structure than a single energy-minimized average structure.
* Truly flexible regions within a binding site may be relevant to the plasticity of the fit
between receptor and ligand.
* Parts of the receptor structure will be ill-defined and therefore cannot be represented
accurately by a single structure.
86
Receptor flexibility: Computational approaches; Molecular dynamics (MD)
what does MD solve?
MD solves Newton’s equations of motion for an atomic system. The force on each atom is
calculated from a change in potential energy between current and new positions.
Atomic forces and masses are then used to determine atomic positions over series of very
small time steps. This provides a trajectory of changes in atomic positions over time.
Sample the protein’s
conformations at
various points in a
molecular dynamics
trajectory and dock
into these
87
affinity equation
and some of its limitations
Affinity: G = H –TS
enthalpy entropy
Scoring functions only really tackle H.
Calculating S is the unsolved problem
88
Upon complex formation:
water molecules are
* water molecules are released
* receptor and ligand lose degrees of freedom
* new interactions between ligand and receptor
89
what are degrees of freedom in receptor and ligand binding
In the context of receptor-ligand binding, "degrees of freedom" refer to the number of independent parameters or variables that can vary without violating the constraints of the system. In simpler terms, it's the number of ways a molecule or system can move or interact.
90
Three major classes of scoring functions / methods are currently applied, what are they?
Force-field-based
▪ Empirical
▪ Knowledge-based scoring functions
91
scoring methods
Potential of Mean Force or knowledge based methods
Description of observed interatomic distances and/or frequencies
implying that these describe favorable/unfavorable interactions
92
scoring methods
Potential of Mean Force or knowledge based methods
advantages
Computational simplicity → permits efficient screening of
large compound databases.
93
scoring methods
Potential of Mean Force or knowledge based methods
disadvantages
Disadvantage → their derivation is essentially based on
information implicitly encoded in limited sets of protein–
ligand complexes
94
what is PMF
PMF" can stand for various things depending on the context, but in the realm of molecular dynamics simulations and computational chemistry, "PMF" often refers to "Potential of Mean Force."
The Potential of Mean Force (PMF) is a concept used to describe the free energy landscape of a molecular system, particularly in the context of chemical reactions or molecular interactions. It represents the free energy change experienced by a system as a function of a chosen reaction coordinate or a set of collective variables.
In the context of receptor-ligand binding, for instance, PMF can be used to describe the energetic landscape of the binding process. By calculating the PMF, researchers can understand the thermodynamics of binding and gain insights into the stability and strength of the interaction between the receptor and ligand.
95
PMF calculation benefits
EG, ligand and protein)
approximate the free energy of each pair-wise
interaction as a function of inter-atomic
distance.
For fast calculations the interaction energies for
given pairs of atoms can be stored in a data
table and retrieved quickly for calculating the
PMF scores
96
Scoring Methods – general limitations
Scores scale poorly with ligand molecular mass and the
number of rotatable bonds.
* Large molecules can form many hypothetical interactions in
binding sites and therefore have the tendency to generate
better scores than smaller compounds.
* The entropy penalty for immobilisation of rotatable bonds,
which is frequently not taken into account, scales with the
number of such bonds. Thus, if entropy penalties are
included, flexible molecules tend to score lower than more
rigid ones
97
It is wise to conduct
molecular dynamics simulations after docking.
Protein-ligand docking, despite the hype from the software
providers, is an imperfect science
Run a molecular dynamics simulation after docking to examine the
stability of the docked conformation and the strength of binding
* Allows for receptor and ligand rearrangements to obtain lower
energy conformations of the docked complex.
* Computationally expensive (can take days for a single calculation)
98
molecular dynamics MD advantages
you an find the midel conformation to limit
99
MD dynamics adv
you can find model conformation to limited extent
know quantification of kimited steos
can ahndle solvent, ionic effects and membrane bound protein
100
MD dis
conventional cost£££
may fail due to short times. and therefore you may miss the next best for the pt
101
It is wise to conduct
molecular dynamics simulations after docking. why
Run a molecular dynamics simulation after docking to examine the
stability of the docked conformation and the strength of binding
* Allows for receptor and ligand rearrangements to obtain lower
energy conformations of the docked complex.
* Computationally expensive (can take days for a single calculation)
Protein-ligand docking is an imperfect science
102
what are ome examples of reactional functional groups
acid chloride
sulfonyl chloride
isocyanate
isothiocyanate
epoxide
aziridine
thiirane
all are very reactive with NH2 amine
103
what is the difference between iv infusion and iv bolus dose
bolus - quick injection into blood
IV - push into blood over time certain dose
104
Iv bolus dose and IV infusion dose differences in pharmacokinetics
IV bolus dose
When repeated doses are required
or when you need to maintain drug
concentrations in the patient, its
not a very convenient approach
IV infusion
Used within hospitals to provide a constant level of
therapy to an individual
Allows control and maintenance of plasma concentrations
and is a precise and controlled system.
Drug infusion can be stopped if there are adverse
problems
105
what is steady state accumulation, IV infusion dose
IV infusions balance the INFUSION RATE (going in) with the CLEARANCE of the drug (going out).
When this is balance you reach steady plasma concentrations, and this is called steady-state
𝐶𝑠𝑠 = 𝑅𝑖𝑛𝑓/𝐶𝐿 = 𝑅𝑖𝑛𝑓/𝑘𝑒𝑙. 𝑉𝑑
106
how many half lives to reach steady state for every drug?
4-5 half-lives to reach STEADY STATE for every drug
107
3 phases of IV infusion dose
drug in (infusion)
steady state
elimination
108
what happens after 4-5 half lives
all of the drug is eliminated
also takes 4-5 half lives to reach steady state
have to keep infusing up to the 4-5 half life point
109
what is the steady state equation to give you the conc of drug at any point during the infusion
Ct-inf = Css (1 - e–kt)
Ct-inf = (conc at any time during infusion)
Css = steady state conc
e-k = elimination rate constant
t = time
110
What two factors control the Css?
How could you reach the TW?
increase rate of difusion
(ss conc increases)
elimination / Cl
111
what does a faster rate of infusion not change
does not change the time needed to reach steady state, only the steady state concentration.
112
what happens when concentration of steady state increases
it takes a little longer to reach steady state after Css has increased. This suggests a change in the half-life and clearance. If Css
goes up CL must have gone down (based on eq) Therefore the half-life gets longer and drug
stays for longer hence increase concentrations
113
how do you calculate half life when given the time to reach steady state? eg
2 hours to reach steady state
to remove all the drug from the body takes 4/5 half lives
to reach steady state = 4-5 half lives
2 hours
2/5 and 2/4
0.4-0.5 hours is the half life
to calculate how long it takes to eliminate to drug from the body
0.4 X 5 and 0.5 X 5
2-2.5 hours to eliminate the drug from the body
overall, relates back to the 4-5
114
what is a loading dose
In many clinical situations, we
require rapid clinical onset. In
these cases we often LOAD
the patient with a high dose
of drug to being with. This is
called a LOADING DOSE.
This approach pre-loads the
patients with the clinically
active dose
works in some scenarios
give an IV bolus dose, some therapy, then srart an infusion
115
when do we use a loading dose
when drugs have a long half life eg 24 hours
then it takes 4 - 5 days to reach steady state. not ideal.
so we preload with bolus then you can start infusion
116
If you know the target CSS is 6-10 ng/mL, how would you
work out an appropriate loading dose?
𝐶𝑠𝑠 = 𝐿𝐷/𝑉𝑑
𝐿𝐷 = 𝑅𝑖𝑛𝑓/𝑘𝑒𝑙
The choice depends on which type of information you have availability in the
clinical situation
117
IV infusion what graphs do we get in clinical practice vs excel
clinical = 3 dots = eg 3 blood samples
excel = line graph
118
tell me about the point you stop giving the infusion
When we STOP the infusion it is the same
as when we give a patient and IV-bolus
dose at that EXACT moment
The infusion is giving drug into the
venous circulation and when we stop the
infusion the only thing controlling the
drug is its loss from the body
At the end of the infusion, you can use the same type of analysis to
determine drug levels at any time when you stop the infusion along with
things like the half-life and clearance of your drug.
119
how can you work out half life with 1/2 data points
We can use the FIRST-ORDER equation:
𝐶𝑡 = 𝐶0𝑒−𝑘𝑡
and assume C0 is actually CSS.
you can log the scale to get a straight line for visual or
You can then treat calculate the slope of
a LN vs time or Semi-Log vs time graph to
determine t1/2 or this can be done
visually. Treat as an IV bolus dose
example
120
how does an oral dose differ from an IV dose
Oral - GI tract affected by pH, food, Bioavailability varies due to first-pass metabolism and incomplete absorption, Slower onset but can produce prolonged effects, Easy self-administration, suitable for chronic treatments.
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what is portal circulation
Portal circulation refers to a specialized circulatory system found in the body that involves the transport of blood from one organ (or group of organs) directly to another organ before returning to the heart. The most well-known example of portal circulation is the hepatic portal system.
The hepatic portal system carries blood from the gastrointestinal (GI) tract, spleen, and pancreas to the liver before it returns to the heart
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describe oral absorption
Absorption is into portal circulation
NOT into the body, the latter being defined as the Bioavailability
123
oral - Changes in the rate of
absorption
Impacts on the time required to elicit a clinical
response and hence the onset. The rate affects
the peak (Cmax) and the time it takes to reach
the peak (tmax)
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what does changes in the rate of absorption do to elimination
elimination stays the same
125
What does the extent of
absorption mean?
The extent of absorption refers to the proportion of an administered dose of a drug that enters the systemic circulation after passing through the absorption barriers in the body. In simpler terms, it indicates how much of the drug actually gets absorbed into the bloodstream and becomes available for distribution to target tissues and organs.
The extent of absorption is typically expressed as a percentage and can vary widely depending on several factors, including the drug's physicochemical properties, formulation, route of administration, and the physiological conditions of the individual patient.
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What is bioavailability a measure of ?
Fraction of the dose administered that reaches the systemic circulation
It is a number between 0-1 (or 0 - 100%)
Its given the term F
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decsribe target window bioavailibility
If the TW is between 0.25-0.5 mg/mL, the ‘black’
drug shows poor bioavailability and does not even
reach the TW to elicit a clinical effect.
The red drug shows sufficient bioavailability to
give a good clinical response.
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Giving an oral dose of a drug to two different
patients. Assume the dose here is the same in
both. What do you think is physically different
between each patient?
Standard weight and Overweight patient
Higher dose for Overweight
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when does absorption not change
The absorption rate hasn’t changed as we are doing the same
drug in the same patient. The results show a slight change in
Cmax and tmax.
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what does an example where Cl has increased by 50% show
Clearly the elimination part has altered and appears to be
increased—the black profile shows faster elimination than the
red profile. This is confirmed in the reduction in half-life and
change in the AUC.
This example is an example where the clearance has increased
(by 50 %). This could be a result of a drug-drug interaction.
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give an example where drug-drug interactions increase when a certain drug is given
The classical example is carbamazepine (an antiepileptic) which
can induce (increase) the metabolism of co-administered drugs.
This patient was prescribed a drug, which was shown to be
involved in a DDI with newly prescribed carbamazepine leading
to a DDI and the enhanced clearance and hence poor clinical
activity (see TW) of the original drug.
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Physicochemical properties of your chemical (3)
1. Hydrophobic/Hydrophilic
2. Ionized/Nonionized/Weak acid/base
3. Molecular weight
133
lipophillic oral drugs absorption rate
Lipophilic (LogP)
Readily partition
Absorption rate is usually quick
134
ionised oral drugs absorption rate
Ionised (Charged)
Usually don’t partition well
Absorption rates slower
135
tell me about ionissation and pH of drugs with absorption
The pH and ionisation of drugs is key in their absorption
Ionised molecules cannot cross membranes
Only unionised molecules may be absorbed
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blood pH?
Blood pH = 7.4
137
stomach acid pH?
1.2
138
A weak acid drug, HA will exist as:
The unionised form within the stomach
The ionised form within the blood
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what does the henderson hasstle back equation show
tells you how much ionised / unionised drug there is
140
what is the henderson hasstle back equation for acids
pH - pKa = log (ionised/unionised)
141
what is the henderson hasstleback equation for bases
pH - pKa = log(unionised/ionised)
142
how does stomach fluid affect absorption
Excess HA (unionised) exists thus
the concentration gradient sends
it into the blood
absorption increased
143
how does blood affect absorption
Excess A- (ionised) exists thus it
cannot go back to the intestinal
fluid
absorption increased
144
Weak bases: ionisation can be a disadvantage
why?
There is a pH difference between stomach fluid and
blood
Intestinal fluid pH = 1.2
Blood pH = 7.4
A weak base drug, BH+ will exist as:
The ionised form within the stomach fluid [Limited absorption]
The unionised form within the blood [Diffusion back into stomach]
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how does stomach fluid affect absorption, weak base
Excess BH+ (ionised) exists
thus little crosses the
membrane
absorption decreased
146
how does blood affect absorption, weak base
Excess B (unionised) exists thus the
concentration gradient sends it back
to the intestinal fluid
absorption decreased
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Switching formulations
Palliative care
We will come back to this in more detail
later on.
When giving a drug orally, we have to
account for drug loss on its pathway
through the stomach, small-intestine and
liver.
The IV dose will deliver the drug directly
into the blood. The oral dose requires a
higher loading dose compared to the IV
route to accommodate the drug loss.
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larger the particle size relating to flow
larger the particle size usually more free flowing
149
adjustable particle properties
Particle size
Particle shape
Surface characteristics e.g. energetics, roughness etc.
cohesion (single components) and adhesion (mixtures)
150
what is an aerosol
Aerosol = a suspension or dispersion of solid or liquid particles (<50µm) in a gaseous medium
151
tell me about aerosol stability
Aerosol stability is not unlike suspension stability
152
Particle dispersion determined by a combination of factors including:
size and density of the particles
density of the suspending medium
other physicochemical particle characteristics e.g. charge, energetics etc.
interactions (& number of interactions) between the particles in dispersion
153
sedimentation definition
when particle density is greater than the density of the suspending medium.
154
creaming definition
when particle density is less than the density of the suspending medium.
155
Aerosol stability theory (c.f. suspension stability theory)
Particles < 1m will remain suspended within a system (= colloidal system)
Suspensions with particles > 1 m (most aerosols) only kinetically stable
i.e. relatively unstable
156
what is an isolated system
no stirring or shaking
157
what is an agglomerated system
easily re dispersed particles
158
what is an aggregated system
difficult to redisperse
159
Inhalation medicines, the why, where, what, how and when
WHY target the lung
WHERE to target particles
WHAT are limitations to delivery
WHAT particles can be delivered
HOW to deliver beneficial powders to the lung
WHEN (some history) rather posology
160
Asthma
from Greek ‘aazein’ meaning to exhale with open mouth, to pant. Appeared for the first time in “The Iliad” by Homer (762BCE)
161
known suffers of asthma
william III
marcel proust
162
Chronic Obstructive Pulmonary Disease History
Characterised by airflow limitation that is not fully reversible. The airflow limitation is usually progressive and associated with an abnormal inflammatory response of the lungs to noxious particles or gases.
163
two examples of COPD
chronic bronchitis (80-85%)
emphysema (15-20%)
164
COPD
Risk Factors
Cigarette smoking – major risk factor (estimated 80 - 90% of risk)
Passive smoking is also a risk
Pollution - indoor (fuels used in cooking / heating) and outdoor (traffic)
Occupational factors - (exposure to dusts, chemicals etc.)
Genetic
Alpha1-antitrypsin deficiency (<1%)
Differences in susceptibility of smokers to get COPD
Sex, race and socioeconomic status
Men more sensitive than women
Mortality rates in whites are higher than BAME
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WHY Delivery to the lung? Chronic Respiratory Disease (CRD)
Target organ most affected by Chronic Respiratory Disease
Rapid onset of action
Avoid first pass metabolism
Targeted hence lower dose required
Multiple receptor targets for relief of reversible bronchospasm
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WHY Deliver drugs to the lung? Pharmacokinetics
Active pharmaceutical ingredient (API) treats the condition but inhaler delivers it, in the right form and concentration to the right place / site of action
example: Oral tablet 4.0 mg 20-30 minutes
Inhaler 0.2 mg 1-2 minutes
Inhaled Salbutamol / Albuterol ( bronchodilator)
20 times less API
20 times faster to act
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WHY Deliver drugs to the lung? Systemic action
Non-invasive access to systemic circulation
(peptides/proteins, vaccines, nicotine)
e.g. Exubera (Pfizer) inhaled powder insulin - rapid absorption pharmacokinetics similar to parenteral delivery
168
WHERE – limitations of delivery Relevant lung physiology and anatomy
trachea
lung
bronchioles
alveoli
capillary
O2 / CO2
169
HOW Lung deposition and particle size Deposition mechanisms
Particle deposition in the respiratory tract
governed by particle momentum (mass x velocity)
170
HOW (much) Formulation challenges Potency
Efficient delivery requires particles of API to be well dispersed and aerosolised
Good pharmaceutics with minimal use of excipients
171
HOW Delivery Dry Powder Inhaler (DPI) Formulation
Cohesion and adhesion
Inert carriers to disperse (lactose, mannitol, glucose)
Additional component(s) magnesium stearate, leucine (force control agents)
Manufacture and Dose Delivery
172
properties of fine powders
cohesive
poor flowing
heterogenous
polydisperse
173
what differences do spray dried APIs have
differing physico constraints eg - hydrophobic
differing sensitivity eg - temp and handling / environmental moisture
174
Formulations containing two or more components
Difficult to mix
Difficult to control content uniformity
Difficult to dispense
174
Dry powder dispersion
Powder mixing
Active Pharmaceutical Ingredient(s)
wide concentration ranges
0.1% - 50%w/w
Limited range of excipient(s)
Generally Recognised as Safe (GRAS)
175
DPI manufacturing process
controlled inputs to blending process
API1/2 synthesis
micronisation process
dispensing
blending (lactose sieving)
Each step adds new sources of potential variation into the medicine
176
DPI manufacturing process
Powders with right blend content uniformity and right flow characteristics deliver the right amount of API – right dose
177
Inhalation of powders - aerosolisation
inspiratiry force
flow and pressure
deaggregation
fine particle mass
178
Dry powder inhaler manufacturing process Conundrum
DPI formulation requires fine control of powder properties
(an interactive balance)
Flow
Uniform content
Structure resilient to processing
and
Particles un-agglomerated (or easily deagglomerated)
Effective detachment from carrier or from cohesive mixture
Efficient generation of individual aerosolised particles
179
Factory dispensed doses (dose set in manufacture)
Unit dose CAPSULES / BLISTERS
Multiple dose STRIP/ TAPE Dosing requires accurate device manipulation (Patient Information Leaflet)
180
Device dispensed doses (dose set in hands of patient)
Multiple dose RESERVOIR
with internal dosing mechanism
Dosing requires accurate device manipulation (Patient Information Leaflet)
181
Aerosolisation devices
2 weeks’ or 1 month’s therapy: single blister strip
Monotherapy and/or fixed-dose combination
eg, accuhaler, diskus
Poly-pharmacy single or multiple strip devices
eg, ellipta
Reservoir devices – 2 weeks or one month’s therapy:
Monotherapy or fixed-dose combination
eg, turbohaler, genuair, novoliser, nexthaler
182
Unit dose inhalation capsule
examples
Aerolizer, Rotacaps / Rotahaler, Breezhaler, Handyhaler, Spinhaler, etc,
183
Multiple unit dose inhalation blister
Rotadisk / Diskhaler
184
3 different dry powder inhaler choices
single unite dose
multiple unit dose
multi dose resevoir
185
Which medicine is best for the patient?
WWWWWH
WHY target the lung
WHERE to target particles
WHAT are limitations to delivery
WHAT particles can be delivered
HOW to deliver dry powders to the lung
WHEN (some history)
186
aerosol definition
= a suspension or dispersion of solid or liquid particles (<50µm) in a gaseous medium
187
DPIs - passive delivery systems (1 – 5 m particles)
Aerosol generated by patient’s inhalational energy
Patient lung dose may be restricted by ability to breath
Patient disease state, lung function, age – child, geriatric
Particles are delivered ‘dry’
188
Pressurised Metered-Dose Inhalers Inhaler formulation theory
pMDIs ‘Puffers’– delivery systems (1 – 5 m particles or droplets*)
Aerosol generated by internal energy (propelled by vaporisation)
Particles suspended or dissolved in propellant
Size determined
input API (or agglomerates of particles)
fine mist of liquid droplets
may contain particles of API or API in solution*
Patient ‘coordinates’ inhalation with generation of aerosol
189
characters of the propellant in a pMDI inhaler
Propellant (pressurisation agent)
inhaled by the patient
Liquefied compressed gas
Low boiling point
Non-toxic
No bad odour/taste
Optimum solvency
Density ideally same density as API
Non-flammable
Environmentally friendly
Cost effective
190
APIs in pMDI
Microfine Respirable particles
1 – 5 um diameter
191
pMDI excipients
Excipients (to stabilise dispersion / redispersion)
Surface Active Agents (Surfactants)
Chemical stabilisers
Engineered Particles
192
Pressurised Metered-Dose Inhalers Dispersion stability
Particle size control
Solubility characteristics
Particles likely to have finite solubility in propellant
Temperature fluctuations / trace water / non-polar contaminants
May result in the system becoming supersaturated
May result in particle ‘ripening’
May result in gross recrystallisation and destabilisation
193
tell me about particles in a pMDI canister
no stirring
no shaking
194
Pressurised Metered-Dose Inhalers Aerosol formation
The stability of suspension determined by:
The size and density of the particles,
Density of the suspending medium
Particle solubility characteristics
Interactions in suspension
Interactions with the pMDI components
Maintenance of suspension stability is KEY!
195
pMDIs canister made out of
aluminium
glass
thermoplastic eg PET
196
what is the metering valve in a pMDI
dose volume is critical to performance
measures dose vol
197
Aerosolisation Engine - Key components
actuator / dose counter
198
pMDIs The dose is determined by:
Concentration of suspension and volume of suspension in metering chamber
Leakage / closed or open system
May increase with age of inhaler
Suspension stability / Solution stability
Particle size
Particle solubility characteristics
Particle-particle interactions in suspension
Particle interactions with the components inside canister
how much dose the pt can access
HCP knowledge important and compliance is critical
199
which medicine is best for the pt, pMDIs, WWWWWH
WHY target the lung
WHERE to target particles
WHAT are limitations to delivery
WHAT particles can be delivered
HOW to deliver APIs to the lung
WHEN (some history)
200
what is in a nebule / composition
API (size reduced if suspension) Blow Fill
Water
Co-solvents (ethanol, propylene glycol)
pH adjustment (stability)
Sodium chloride (isotonicity)
201
what are the role of surfactants and stabilisers in pMDIs
stabilise the suspension
202
manufacture of nebules, solution and suspension
Dissolve water-soluble excipients
Disperse/dissolve API in excipient solution
Terminal sterilisation/aseptic filtration
blow, fill, seal
203
Nebulisers and Soft Mist Inhalers
A nebuliser converts liquid into liquid aerosol droplets suitable for inhalation
Aerosol generation is via pneumatic (jet) or mechanical (ultrasonic) means
204
tests undergpne for pMDIs
appearnace, identity tests, API content tests, mean fine particle mass, leak rate, microbial limits, drug related impurities,
205
How to assess performance in the hands of the patient?
To assess patient performance with inhalers:
Educate patients thoroughly.
Provide step-by-step checklists.
Offer hands-on training sessions.
Use demonstration devices.
Request return demonstrations.
Consider patient preferences for device selection.
Encourage pharmacist support.
Provide patient education materials.
206
In-vitro assessment of aerosol
Cascade Impaction
where drug is stimulated, stage 0-7 (8)
Quality control measure not lung dose prediction
207
In-vitro assessment
Cascade Impaction – operating principles
Progressively smaller orifices
increase the orifice velocity,
In eight successive stages.
Causing impaction of smaller
particles onto the collection
discs of each succeeding stage.
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