This Lecture....
Is born from the ever growing
realisation that the drug discovery
turn-over rate must be rendered
more efficient...
Both
from
the
perspective
of
innovator companies & from that of
the ultimate beneficiary of the
process i.e. the patient
Chronologically…..
Chris Lipinski:
Drug-like is defined as those compounds that have
acceptable ADME/tox properties to survive through
the completion of human Phase 1 trials
And…
Ronald T. Borchardt:
Drug-like
responses
are
intrinsic
properties of the molecules, and it is the
responsibility of medicinal chemists to
optimise not only the pharmacological
properties, but also the drug-like
properties of the molecules
From the Previous Quotations it is
Possible to Infer…..
The term drug-like with respect to a
drug molecule implies that certain
properties of a particular compound
confer on that molecule a greater
propensity to become a successful
drug product
The Major Pioneer in This Field..
Is Chris Lipinski.
Examined the structural properties that
affect the physico-chemical properties of
solubility and permeability, and their effect
on drug absorption
Puts forward notion that many properties
are of interest in drug discovery….
The Structural Properties of the
Molecule
Hydrogen Bond Forming Moieties
Lipophilicity
Molecular Weight
Polar Surface Area
Shape
Reactivity
pKa
The Physico-Chemical
Properties
Solubility
Permeability
Chemical Stability
The Biochemical Properties
Metabolism (Phases 1 & 2)
Protein and Tissue Binding
Transport Modality
Pharmacokinetics & Toxicity
Clearance
Half-Life
Bioavailability
Drug-Drug Interactions
Structure Determines a Compound’s
Properties
Pharmacokinetics & Toxicity
Clearance, Halflife, Bioavailability,
LD50
Physicochemical Properties:
Solubility, Permeability &
Chemical Stability
Biochemical Properties:
Metabolism, Transporter
Affinity, Binding Target
Affinity
Physical
Environment
Structural Properties:
Molecular Weight, Hydrogen Bonds,
Lipophilicity, PSA, pKa, Shape,
Reactivity
Proteins
Therefore it May Be Inferred That…
Interaction between structural properties
and the physical environment characterises
the physicochemical properties of a
molecule eg solubility
Interaction between structural properties
and proteins characterises the biochemical
properties of a molecule eg metabolism
At the highest level, the interaction
between physicochemical & biochemical
properties & living systems characterises
the pK & toxicity of a molecule
The Corollary Therefore is ….
That it is possible for medicinal
chemists to control the pK and
toxicity properties of a molecule
through the modification of its
structure
The Drug Discovery & Development
Process:
DISCOVERY
•Biological Target
•ID & Characteristics
•Activity & Selectivity
•Chemical Synthesis
•Property Profiling
DEVELOPMENT
•Batch synthesis
•Analytical Release
•Formulation & stability
•Human Efficacy
•Safety & pK
CLINICAL
APPLICATION
•Manufacturing
•Patient Therapy
•Side Effect Monitoring
•Formulation Enhancement
•Phase 1- Human Safety & pK
•Phase 11- Human Efficacy
•Phase 111- Pivotal Large Scale Efficacy Studies
This Means That…
New candidates are found during the drug discovery
phase
They enter clinical development, and if approved by
EMEA or FDA they become drug products suitable for
use in patient therapy
The later stages i.e. development & clinical application
impose stringent drug-like requirements on the
properties of candidates
Thus it is necessary to anticipate these requirements
during drug discovery & promote exclusively those
molecules that have the highest chances of success to
the development phase
This Unit Focuses On Discovery. This
Stage May be Further Sub-Divided:
EXPLORATION
Understand target
& screen for hits
LEAD SELECTION
Pick diverse leads
• Biological Target
• In vitro enzyme &
(ID Validation &
Characterisation)
•Chemical Libraries
•HTP Screening
•Hit Selection
Receptor Assay
• Initial in vitro SAR
• Property Screens
• Initial Synthetic
Enhancement
LEAD OPTIMISATION
Best SAR; SPR
Least Side Effects
• In vivo SAR
• Selectivity Assays
• X Ray & NMR
Binding Studies
• Computational Modelling
• Custom Property
Studies for SPR
• In vitro pK &
Metabolism
• Analog Synthesis
DEVELOPMENT SELECTION
Meet Advancement
Criteria
• Synthetic Batch Scale-up
• In vitro & In vivo toxicity
•Formulation
•In-Depth Property Characterisation
•Clinical Candidate Advancement
Pick Diverse Leads.....
If the consensus is that leads are
ligands that typically exhibit suboptimal target binding affinity..
In this scenario acceptable leads
must
possess
very
specific
characteristics if they are to be
considered for further development:
Lead Molecules Must:
Have relatively simple chemical
features
Subscribe to a well established SAR
series
Enjoy a favourable patent situation
Possess good SPR characteristics i.e.
good ADME/tox properties
Identification
of
Molecules Involves:
Such
Casting a broad net that
pharmacophoric structural space
Narrowing possibilities such
selected
explores
Lead
diverse
that only a few are
Carrying out lead optimisation. This is the structural
modification of lead molecules to explore SAR.
Candidates selected for development subjected to indepth studies which qualify/disqualify them for further
development
THIS
REPRESENTS
A
CHANGE
IN
STRATEGY FROM OLDER DRUG DESIGN
METHODS….
Early drug design protocols focused on the
isolation of active compounds
Issues such as pK, toxicity & solubility were
addressed much later in the development
phase
A landmark paper published in the British
Journal of Clinical Pharmacology by Prentis
et al. in 1988 showed that drugs failed in
the development phase for precisely this
reason…
Prentis et al. SHOWED THAT…
∼39%
of
drugs
failed
during
the
development
phase
due
to
poor
biopharmaceutical properties
This represented a major economic loss for
pharmaceutical companies
Thus biopharmaceutical properties are
more correctly addressed during the
discovery phase
This would ensure that outright failures are
eliminated early in the discovery phase
Prentis, R.A., Lis, Y., & Walker, S.R. (1988). Pharmaceutical Innovation by the Seven UK-owned
Pharmaceutical Companies (1964-1985). British Journal of Clinical Pharmacology, 25, 387-396
Medicinal Chemistry Space Related to Drug
Discovery
Chemical Space
Druglike
Leadlike
THE REALITY IS…
That drugs with marginal properties
(poor solubility & stability) still make
it to the development phase
This still contributes to the general
inefficiency of the drug discovery
process
MORE ALARMINGLY the burden of
mediocre drug properties is sometimes
shifted to patients:
Poor drug absorption requires dose
increases in order to attain therapeutic
levels
Dosage regimens may require increased
frequency of administration or worse
change in route from oral to parenteral
(considered unacceptable for dosing among
wide patient populations)
Short t1/2 due to metabolic instability may
also require increased frequency of
administration at the expense of patient
compliance)
IN SUMMARY…..
It is better to improve the drug-like
properties of a molecule during the
discovery phase
This is best accomplished by changing the
chemical structure
Modifications are generally made at sites
shown by SAR studies as non-critical to
therapeutic binding
When this is not possible, drug molecules
though clinically promising, should be
discarded
STRESS ON CHANGE IN FOCUS IN
CONTEMPORARY DRUG DESIGN STRATEGY
PAST
CONTEMPORARY
Focus on binding
affinity to active site
Followed by
exploration of SAR
and..
Optimisation through
analog synthesis
around core structural
scaffold
PRESERVATION OF
DRUG-LIKE
PROPERTIES OF
PARAMOUNT
IMPORTANCE
REALISATION
THAT
DRUG
DESIGN
STUDIES BASED ON AFFINITY & POTENCY
ALONE INHERENTLY FLAWED………..
Candidates may be too polar to
penetrate BBB and reach CNS targets
Candidates may be unstable & rapidly
cleared through first pass metabolism
Candidates may be too soluble to be
absorbed from the intestine
COMPARING GRAPHICALLY………………
Properties
GOOD DRUG
GOOD LIGAND
Activity
THUS…
If the focus of a drug design study is
solely activity then this may yield
compounds that are effective ligands
for the target site but which have
inadequate properties that would
make them successful drugs
FOR EXAMPLE…
Increasing lipophilicity may increase
target protein binding at the expense
of aqueous solubility & metabolic
stability
THUS…
A holistic approach that balances
attention
between
activity
and
physicochemical properties is more
likely to yield candidates that can
become good drugs
AND…
The
most
active
or
compound may not make
drug product because of
limitations such as poor pK
profile
selective
the best
property
or safety
AND CONVERSELY…..
A less potent compound with better
properties may produce better in vivo
therapeutic response and prove to be
a better product for patients
MORE SIMPLY:
There are a number of hurdles which
a drug molecule must overcome
Juggling or simultaneously monitoring
and balancing an ensemble of crucial
elements is vital to ultimate success
Neglecting even one element may
cause the entire ensemble to crash
ADVANTAGES OF PROPERTY OPTIMISATION
INCLUDE...
Better planning, execution & interpreting of
discovery experiments
Reduced discovery time lag from not having
to fix property-based problems at a later
time
Faster & more economical pharmaceutical
development
Candidates with lower risk and higher
future value
Longer patent life
Higher patient acceptance and compliance
BARRIERS TO DRUG EXPOSURE
IN LIVING SYSTEMS
Physiological barriers reduce the amount of
dosed compound that reaches the target
Physiological barriers include membranes,
pH, metabolic enzymes, & transporters
Good properties facilitate good absorption,
distribution, low metabolism, reasonable
elimination & low toxicity
IN VIVO..
Drugs encounter many barriers from
the point of administration up to the
time it reaches its therapeutic target
Thus, besides the inherent affinity
that a drug has for a therapeutic
target, its ability to overcome these
barriers determines the in vivo
efficacy of the drug
PHYSIOLOGICAL BARRIERS:
When a drug molecule encounters a
barrier, the amount of drug reaching
the other side is diminished:
BARRIER
DRUG
TARGET
THUS….
The penetration of drugs to the
therapeutic target is slowed and
attenuated by the barrier
AND…
How molecules behave at each barrier
determines
the
rate
at
which
molecules progress to the target site
Optimisation of the behaviour of the
molecule at the barrier sites results in
the molecule arriving at the target at
higher concentrations which may lead
to the desirable sustainable efficacy
A DIVERSE ensemble of physicochemical &
biochemical processes is encountered by
drug molecules..
Cell Membranes
Metabolic Enzymes
Solution
pH
Efflux Transporters
Binding Proteins
Efficacy….
Is a function of the molecule’s
inherent affinity for the target site
Is a function of the exposureconcentration & duration of the
molecule to the target site
Thus the process of drug discovery is
representative of a search for molecules
possessing structural features that produce:
Strong target binding using Structure
Based Drug Design (SBDD) and
Structure Activity Relationship (SAR)
High performance at in vivo barriers
using property based design and the
Structure
Property
Relationship
(SPR)*
*
Van de Waterbeemd, H., Smith, D.A., Beaumont, K. & Walker, D.K., (2001) Property Based Design:
Optimisation of Drug Absorption & Pharmacokinetics. Journal of Medicinal Chemistry, 44, 13131333
SPR STUDIES:
PROPERTY
IMPLICATION
A molecule’s physicochemical
properties
The behaviour of a drug molecule in
solution & at membrane barriers
A molecule’s binding to and reaction
with, specific enzymes
How the molecule behaves at
metabolic barriers
A molecule’s binding to various
transporters & plasma proteins
The absorption, distribution &
excretion of the drug
A molecule’s reactivity & binding
Toxicity
DRUG DOSING
A
common
goal
of
pharmaceutical
researchers is the development of a drug
dosage form that:
Is a low dose tablet
Has an oral once daily dosage
regimen
IDEALLY SUCH A DRUG PRODUCT:
Has reasonable manufacturing &
storage costs
Attracts high patient compliance
COMPOUNDS with limited performance at
one or more in vivo barriers:
May have poor pK performance
Require adjustment from the ideal strategy previously
outlined
May require more frequent dosing (if t1/2 is short)
May require higher dosage (if bioavailability is low)
May require administration through an alternative route
(e.g. i.v.) (if absorption is low)
May require a different vehicle or formulation (if solubility is
low)
A TRADEOFF CONSEQUENTLY
EXISTS…
Between structural features that
enhance therapeutic drug binding
AND….
Structural features that enhance
delivery through optimal performance
at in vivo barriers
CONSEQUENTLY…
If a drug discovery program focuses
exclusively on activity optimisation
Poor drug properties may arise
POOR DRUG PROPERTIES MAY
INCLUDE…
Low absorption- low solubility or permeability
High clearance- owing to metabolism
High clearance by hydrolysis- in GIT or blood
Efflux- opposes uptake in many membranes which
enhances extraction in liver & kidney
High protein binding- limits free drug at target
Poor penetration of a blood-organ barrier at the target
organ
High volume of distribution due to lipophilicity
ALL MAY BE
CHEMISTS
MODIFICATION
IMPROVED
THROUGH
BY
MEDICINAL
STRUCTURAL
RULES GOVERNING RAPID PROPERTY
PROFILING FROM STRUCTURE
The application of rules provide a rapid
method through which the drug-like
properties of a compound may be
evaluated
These rules are a set of guidelines for the
structural properties of compounds that
have a higher probability of being well
absorbed after drug dosing
These rules are widely embedded in drug
modeling software packages
IMPORTANT CAVEATS
These guidelines are not absolute
They do not intend to form strict cutoff values to categorise between
drug-like and non-drug-like molecules
Nonetheless, they have been found to
be quite effective and efficient to
apply
LIPINSKI RULES
Medicinal chemists and pharmaceutical scientists have
used structural properties in various ways for many
years
Rules became more prominent and defined in the field
with the report by Lipinski et al.* of the Rule of 5, or
as they are better known the Lipinski Rules
These rules are a set of property values that were
derived from classifying the key physicochemical
properties of drug-like compounds
These rules were used at Pfizer for a few years prior
to their publication
Since then they have become very widely used
*Lipinski, C.A., Lombardo, F., Donimy, B.W., & Feeny, P.J. (1997). Experimental and Computational
Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings.
Advanced Drug Delivery Reviews, 23, 3-25
THE IMPACT OF THESE RULES IN
THE FIELD HAS BEEN HIGH…
Fast, easy & no cost to implement
5 mnemonic makes them easy to
remember
Intuitively
evident
to
medicinal
chemists
Widely used standard benchmark
Based
on
solid
research,
documentation and rationale
Work effectively
LIPINSKI’S ARTICLE STATES..
Poor absorption or permeation is more likely when:
1.
2.
3.
4.
5.
There are more than 5 hydrogen bond
donors (expressed as the sum of all OH
and NH groups)
MWt greater than 500
logP greater than 5
There are more than 10 hydrogen bond
acceptors (expressed as the sum of all
Ns and Os)
Substrates for biological transporters are
exceptions to this rule
EXPERIENCE SHOWS THAT…
Violation of one rule may not
necessarily result in poor absorption
However,
likelihood
of
poor
absorption increases with the number
of rules broken and the extent to
which they are exceeded
HOW WERE THE LIPINSKI RULES
DERIVED?
Examination of the structural properties of compounds
which had survived Phase 1 clinical trials and had moved on
to Phase 11 studies
Phase 1 studies involve human dosing to determine toxicity
and pharmacokinetics
The fact that they had moved on to Phase 11 studies
implied that these compounds were sufficiently well
absorbed in humans for pharmaceutical companies to
continue investing in their development
A set of 2200 compounds was examined, and the clear
trends that were observed became the basis for these rules
THE RULES WERE SET AT THE 90th
PERCENTILE OF THE COMPOUND SET
This means that 90% of the
compounds
that
had
sufficient
absorption after oral dosing had
molecular property values within the
Lipinski Rules
Compounds that approach or exceed
these values have a higher risk of
poor absorption after oral dosing
THE RULES ARE BASED ON A STRONG
PHYSICOCHEMICAL RATIONALE….1
Hydrogen bonds increase solubility in
water and must be broken in order
for a compound to permeate the lipid
bilayer membrane
Thus increasing the number of
hydrogen bonds reduces partitioning
from the aqueous phase into the lipid
bilayer membrane for permeation by
passive diffusion
THE RULES ARE BASED ON A STRONG
PHYSICOCHEMICAL RATIONALE….2
Molecular Weight is related to the size of
the molecule
As molecular size increases, a larger cavity
must be formed in water to solubilise the
compound thus decreasing solubility
Increasing size also impedes passive
diffusion through the tightly packed
aliphatic side chains of the lipid bilayer
membrane
THE RULES ARE BASED ON A STRONG
PHYSICOCHEMICAL RATIONALE….3
Increasing logP decreases aqueous
solubility which reduces absorption
Membrane transporters can either
enhance
or
reduce
compound
absorption by either active uptake
transport or efflux respectively
This means that transporters can
have a strong impact on increasing or
decreasing absorption
LIPINSKI et al. ….
In their paper discuss the important
implications of these rules in the light of
current drug discovery strategies:
The discovery lead optimisation stage often
increases
target
binding
by
adding
hydrogen bonds and increasing lipophilicity
This means that activity optimisation may
reduce the drug-like properties of a
compound series
THE LIPINSKI RULES
are widely used as a filter and
measurement of the drug-likeness of
a series of molecules.
They are used to such an extent that
they almost ‘copyright’ the field of
drug- likeness compound scoring.
However, other experiments have
also been carried out in this area…..
VEBER RULES
The results of an experiment performed by
Veber
et
al.*
examining
the
oral
bioavailability of potential drug candidates
in the rat let to the conclusion that other
parameters existed for the description of
drug likeness than the Lipinski rules.
The main parameter taken into account
during this experiment was the number of
rotatable bonds – as an indication of
molecular flexibility.
*Veber, D.F., Johnson, S.R., Cheng, H., Smith, B.R., Ward, K.W., & Kopple, K.D. (2002). Molecular
Properties that Influence the Oral Bioavailability of Drug Candidates. Journal of Medicinal Chemistry, 45,
2615-2623
VEBER RULES
Veber’s experiments indicated that the main factor
influencing the possibility of uptake by the lumen is not
molecular weight but, in fact the number of rotatable
bonds.
This could be explained by the entropic cost of presenting
an acceptable drug surface area to hydrophobic surface of
the membrane in the sense that a compact molecule is
easier to absorb than extended one.
In addition to the number of rotatable bonds Veber et al.
found that the polar surface area can be used as a good
indication of permeation.
Crossing the lumen requires for a molecule that it is rather
non-polar, and therefore having a large polar area as part
of the surface makes the interaction and uptake over a lipid
bilayer difficult.
VEBER RULES
They therefore suggest the following filter for drug-likeness:
Rotatable bonds < 12
Polar surface area < 140
Also, Veber et al. (2002) therefore raise the issue of
molecular weight being a proper descriptor for absorption
measurement as molecular weight might just be positively
correlated with more precise properties like the rotatable
bonds count, polar surface area and hydrogen bonds count.
The Veber et al. experiments referred to above underline
the difficulties met with when trying to make generalizing
rules for complex systems.
CORRESPONDENCE BETWEEN MOLECULAR
WEIGHT, THE NUMBER OF ROTATABLE BONDS
AND THE DEGREE
OF BIOAVAILABILITY IN THE RAT
APPLICATION OF RULES FOR
COMPOUND ASSESSMENT
TO ANTICIPATE THE DRUG LIKE PROPERTIES
OF COMPOUNDS WHEN PLANNING SYNTHESIS
TO ESTIMATE THE DRUG LIKE PROPERTIES OF
HITS FROM HIGH THROUGHPUT SCREENING
TO EVALUATE THE DRUG LIKE PROPERTIES OF
COMPOUNDS
BEING
CONSIDERED
AS
CANDIDATES FOR PURCHASE FROM A VENDOR
This Philosophy Recalls the
Adage:
The house built on a
foundation (LEAD
STRUCTURE) of sand
will fall, but the house
built on rock will prosper
In the Drug Discovery Process:
If the lead molecule (foundation) is
strong, the project team can build a
strong drug-like clinical candidate
If the lead molecule (foundation) is
weak, the team’s effort may never
advance a drug-like compound to
development
Hits That Serve as Starting
Points for Leads Come From..
High Throughput Screening
Virtual Screening
Natural Ligands
Natural Products
Scientific Literature
Hit-to-Lead Phase- Emerging
Concepts
Lead likeness
Template Conservation
Triage
Fragment-based Screening
Lead Likeness.......................1
Was initially based on Rule of 5
(invaluable as property guidelines in
lead selection)
Implication was that the leads
(foundation) would be free of major
liabilities that would later impede
viability as clinical candidates
Lead Likeness.......................2
With acquired experience it was
recognised
that
during
lead
optimisation often substructures were
added to lead templates to enhance
target affinity and selectivity:
Non-polar groups added to enhance
binding to lipophilic pockets
Polar groups added to increase
hydrogen bonding to binding site
Lead Likeness.......................3
This process often resulted in Rule of 5
violators with deleterious properties
Current philosophy advocates that screening
libraries select leads with:
1. Molecular weight between 100 & 350
2. ClogP between 1 & 3
This increases the odds that the optimisation
process results in molecules with acceptable
drug-like properties
Lead Likeness.......................4
Another caveat was that these
curtailed optimised lead molecules
would be more likely to bind to target
proteins owing to the fact that it is
easier for them to adopt bioactive
conformations
than
their
larger
counterparts which are commonly
included in screening libraries
Lead Likeness.......................5
Criteria for Inclusion to
Lead-Like Screening
Libraries
MW
≤460
Log P
-4≤Log P≤4.2
Log Sw
≤-5
Rotatable
Bonds
≤10
Rings
≤4
Hbond Donors
≤5
Hbond
Acceptors
≤9
Pharmacokinetic Criteria for
Inclusion to Lead-Like
Screening Libraries
Bioavailability
(%F)
≥30%
Clearance (Cl)
≤30ml/min/kg
in rat
Log D
0≤Log D7.4≤3
Cytochrome
P450 Binding
Low
Plasma Protein
Binding
≤99.5%
Acute &
Chronic
Toxicity
None (in
therapeutic
window)
Template Conservation..........1
Often a large portion of lead structure
is
conserved
throughout
lead
optimisation
Lead optimisation is synonymous with
structural additions
Properties associated with the core
continue to be a primary component
of the properties of analogs and of
the eventual clinical candidate
Template Conservation..........2
O
N
Screening Lead
S
O
N
O
Liranaftate
S
O
H
Natural Product
Lead
H
O
O
Exemestane
H
O
H
Many drugs retain
large portions of
lead core
structures
Implication is that
it is sensible to
lock in favourable
properties at the
lead selection
stage
Template Conservation..........3
Going back to the analogy with houses
and foundations, attempts to endow
non-drug-like
leads
with
drug-like
properties,
would
be
similar
to
attempting
to
reconstruct
the
foundations of a house that has already
been built.
Complexity,
time
and
financial
intensiveness would make such an
exercise unfeasible
Triage..................................1
Early screening in a drug design project
normally
yields
many
hits
for
consideration
Inclusion of property characteristics with
activity, selectivity & novelty represents
a sound strategy that ensures strong
leads i.e. Those with the greatest
chance of success at the expense of
those with high failure risk which are
consequently downgraded
Triage..................................2
Sets goals for each key criteria of the
lead
Disciplined process
Guides initial synthetic modifications
for improvement & selection of leads
for optimisation
LEAD
ANALOG
DESIRED PROFILE
MW
330
445
<450
clogP
1.9
5.19
<4.0
IC50 (µM)
4.2
>20
<1.0µM
Binding to Target
X-ray
Yes
MIC
B. subtilis
>200µM
50µM
<200µM
S. aureus MRSA
>200µM
25µM
<200µM
S. aureus ATTC
>200µM
200µM
<200µM
S. pneumo +
>200µM
25µM
<200µM
Selectivity: C. albicans (MIC µg/ml)
>200
>200
>10 fold
Aqueous Solubility (µg/ml @ pH 7.4
>100
26.5
>60
0
0.15
>1
CYP3A4 (%inhibition @ 3µM)
11
7
<15
CYP2D6 (%inhibition @ 3µM)
0
1
<15
CYP2C9 (%inhibition @ 3µM)
NT
23
<15
Microsome stability (% remaining
@30 mins)
NT
NT
>80
Definable series
Yes
Yes
Yes
Definable SAR
Yes
Yes
Yes
Permeability (10-6 m/s @ pH 7.4)
Example of goals used by Wyeth Research exploratory medicinal chemists for hit selection, initial structural
modification & lead selection in an acyl carrier protein synthase (AcpS) inhibitor project
Fragment-Based Screening.....1
Based on the theory that screening with
larger structures that fit (shape,
electrostatic interactions, & hydrophobic
contacts) the binding site of the target
does
not
constitute
Good
Drug
Discovery Practice
The use of smaller, less complex
compounds or fragments is more likely
to bind to a portion of the binding site
Fragment-Based Screening.....2
From a fragment core, functionality can be
added to enhance binding.
By selecting fragments that bind to different
portions of the site and joining them together
with a tether the likeliehood of finding a final
lead that binds appreciably to the site
increases.
Although fragments bind with low affinity,
tethered fragments forming a larger molecule
normally bind with a greater affinity.
Fragment-Based Screening.....3
When fragments bind they generally have a
lower affinity (IC50 50µM-1µM) but have a high
efficiency of binding for their size.
Fragment binding is difficult to detect using
biological assays, but X-ray crystallography
and NMR may be used to resolve such weakly
binding fragments
This is important in ligand binding pocket
orientation determination
Disadvantage: Expense
Excellent reviews published
Lesuisse, D., Lange, G., Deprez, P., Bernard, D., Schoot, B., Delettre, G., et al. (2002). SAR and X-Ray. A New Approach
Combining Fragment Based Screening and Rational Drug Design: Application to the Discovery of Nanomolar Inhibitors of
Src SH2. Journal of Medicinal Chemistry, 45, 2379-2387.
Fragment-Based Screening.....4
Complements the goal of selecting leads
with good properties.
When
screening
large
molecules
(common in conventional screening
libraries), often, considerable portions of
the structure are uninvolved in binding
interactions
All that is achieved is an increase in MW,
hbonds and lipophilicity that detract
from the lead-like properties.
Fragment-Based Screening.....5
Fragment use can minimise superfluous
structural moieties that would detract
from optimum absorption profiles.
Fragment libraries are in fact now being
constructed exclusively from these small
molecules, which already have good
lead-like properties.
Fragment-Based Screening.....6
This has lead to the
establishment of
guidelines for
properties which
molecules must
possess in order to
be included in
fragment libraries
Property
Value
MW
≤300
ClogP
≤3
Rotatable
Bonds
≤3
Hbond Donors
≤3
Hbond
Acceptors
≤3
PSA
≤60Å2
Lipophilicity
Tendency of compound to partition into a
nonpolar liquid matrix versus an aqueous one
Estimated using logP from octanol/water
partitioning
Lipophilicity is major determinant of many
ADME/Tox properties & of pharmacological
activity
It can be quickly measured or calculated
thanks to work of Hansch & Leo (advantage)
Its inclusion into the Rule of 5 indicates its
effectiveness in initial compound assessment
Hansch, C., Leo, A., & Hoekman, D., (1995). Exploring QSAR. Fundamentals and Applications in Chemistry &
Biology, Volume 1. Hydrophobic, Electronic & Steric Constants, Volume 2. New York: Oxford University Press
Traditionally Lipophilicity
Assessed:
By partitioning compound between
nonpolar (octanol) and polar (water)
phases
Partitioning values measured are
LogP and Log D
LogP
Log of partition coefficient of the
compound between an organic phase
and an aqueous phase at a pH when all
of the compound molecules are neutral:
Log P=log ([Compoundorganic]/[Compoundaqueous])
Depends on partitioning of molecules
between 2 matrices
Log D
Log of distribution coefficient of the compound
between an organic phase and an aqueous
phase at a specific pH(x). A portion of the
compound molecules may be in the ionic form
and a portion may be in the neutral form:
Log DpHx=log ([Compoundorganic]/[Compoundaqueous])
LogD
Depends on partitioning of the neutral portion
of the molecule population plus the partitioning
of the ionised portion of the molecule
population.
Ions have greater affinity for the polar aqueous
phase than for the nonpolar organic phase.
Fraction of ionised molecules is dependent on
pH of the aqueous solution, the pKa of the
compound, and on whether it is an acid or a
base.
LogD
For acids, the neutral/anion ratio of
molecules in solution decreases with
increasing pH.
Thus logD decreases with increasing pH.
For bases, the neutral/anion ratio of
molecules in solution in.creases with
increasing pH.
Thus logD increases with increasing pH.
LogP
Abraham et al. showed that logP is
affected by several fundamental
structural
properties
of
the
compound:
1. Molecular Volume
2. Dipolarity
3. Hydrogen Bond Acidity
4. Hydrogen Bond Basicity
Abraham, M.H., Chadha, H.S., Leitao, R.A.E., Mitchell, R.C., Lambert, W.J., Kaliszan, R., et al. (1997) Determination of
Solute Lipophilicity, as logP(octanol) and log P(alkane) Using Poly(styrene-divinylbenzene) and Immobilised Artificial
Membrane Stationary Phases in Reversed Phase High Performance Liquid Chromatography. Journal of Chromatography A,
766, 35-47
Log P
Molecular Volume: related to molecular weight
& affects the size of the cavity that must be
formed in the solvent to solubilise the molecule
Dipolarity: affects the polar alignment of the
molecule with the solvent
Hbond Acidity: related to hbond donation
Hbond basicity: related to hbond acceptance
Lipophilicity
Changes with the condition of the
phases:
1.
2.
3.
4.
5.
Partitioning solvents
pH
Ionic strength
Buffer
Co-solutes/Co-solvents
Lipophilicity
Partitioning between octanol and water different to that
between cyclohexane and water due to differences in the
molecular properties of the phases
pH affects degree of ionisation
Increasing ionic strength results in increasing polarity of
the aqueous phase
The buffer also affects polarity, molecular interactions
and formation of in situ salts as counterions with drug
molecules
Co-solvents such as DMSO can interact with solutes &
change their partitioning behaviour
Lipophilicity
Generally
optimal
GI
absorption
by
passive
diffusion after oral dosing is
to have a moderate LogPrange 0-3
In this range, a good
balance of permeability and
solubility exists
Compounds with a lower
LogP are more polar and
have poorer lipid bilayer
permeability
Compounds with a higher
LogP are more non-polar
and have poor aqueous
solubility
LogD7.4
Common
Impact on
Drug-like
Properties
Common Impact in
vivo
<1
High Solubility
Low
Permeability by
passive
diffusion
Paracellular
permeability
possible if MW
<200
Vd low
Oral absorption and
BBB penetration
unfavourable
Renal Clearance may
be high
Solubility
moderate
Permeability
moderate
Balanced Vd
Solubility Low
Permeability
high
Metabolism
moderate to
high
Oral bioavailability
moderate to low
Oral absorption
variable
Solubility low
High Vd especially
amines
Oral absorption
unfavourable &
variable
1-3
3-5
>5
Permeability
high
Metabolism
high
Oral absorption and
BBB penetration
unfavourable
LogD7.4 <1: good solubility but low
absorption or brain penetration owing to
low passive diffusion permeability .
1 < LogD7.4 <3: This is an ideal range.
These compounds generally have good
intestinal absorption owing to a good
balance of solubility and passive diffusion
permeability. Metabolism is minimised
owing to lower binding to metabolic
enzymes .
3 < LogD7.4 <5: These compounds have
good permeability but lower absorption
due to low solubility. Metabolism is
increased in this range, owing to
increased binding to metabolic enzymes.
LogD7.4 <5: Compounds in this range tend
to have low absorption and bioavailability,
owing
to
low
solubility.
Metabolic
clearance is high because of high affinity
for metabolic enzymes. Vd and half life
are high because compounds partition
into, and stay in tissues
∆logP
Is used to predict permeation of BBB
It is the logP from partitioning between octanol and
water, minus the logP from partitioning between
cyclohexane and water.
The difference is attributed to the contribution of
hbonding to log Pow (octanol/water) compared to log Pcw
(cyclohexane/water)
As ∆logP increases, BBB permeability generally
decreases.
Its correlation to BBB permeation has been interpreted
in terms of hbonding on BBB permeability
pKa
The ionisability of a compound is
indicated by its pKa
Ionisability is a major determinant of
solubility and permeability
When pH=pKa, the concentration of
ionised and neutral molecules in solution
are equal
Basicity of bases increases as pKa
increases; acidity of acids increases as
pKa decreases
pKa
The great majority of
drugs contain ionisable
groups
Most are basic
Some are acidic
Only
5%
are
not
ionisable
Medicinal chemists can
modify acidic or basic
substructures in order to
obtain the desired pKa
which affects solubility &
permeability
pKa Fundamentals
pKa: negative log
of the ionisation
constant Ka
It is common to
use pKa for both
acids and bases
For Acids:
HA=H++ApKa=-log([H+][A-]/[HA])
For Bases:
HB=H++BpKa=-log([H+][B]/[HB+])
Therefore:
For acids, as pH decreases there is a
greater concentration of neutral acid
molecules
(HA)
and
a
lower
concentration
of
anionic
acid
molecules (A-) in solution
Acids with a lower pKa are strongerwith a greater tendency to form A-
And Therefore:
For bases, as pH decreases there is a
lower concentration of neutral base
molecules
(B)
and
a
higher
concentration
of
cationic
base
molecules (HB+) in solution
Bases with a lower pKa are weakerwith a lower tendency to form HB+
The Henderson-Hasselbach
Equation:
Is a useful
relationship for
discovery:
For acids:
pH=pKa+log([A-]/[HA]) or [HA]/[A-]=10(pKa-pH)
For bases:
pH=pKa+log([B-]/[HB+]) or [BH+]/[B]=10(pKa-pH)
These relationships
provide a means of
calculating the
concentration of
ionic and neutral
species at any pH if
pKa is known.
Moreover:
Moreover, it is useful
to note that when
pH=pKa, then there
is an equal
concentration of
ionic and neutral
species in solution.
Pka Effects...
Ionised molecules are more soluble in
aqueous
media
than
neutral
molecules because they are more
polar
Solubility is determined both by the
intrinsic solubility of the neutral
molecule and that of the ionised
species which is much greater
Conversely:
Ionised
molecules
are
less
permeable than neutral molecules
The neutral molecules are more
lipophilic
than
their
ionised
counterparts and are considered to
be
the
dominant
form
that
permeates by passive diffusion
Pka Effects...
Since pKa determines the degree of ionisation,
it has a major effect on solubility and
permeability.
These in turn determine intestinal absorption
after oral dosing.
Thus, highly permeable compounds often have
low solubility and vice versa.
Thus there is a tradeoff between solubility and
permeability because of the opposite effects of
ionisation on these properties
For Example:
An acidic compound with
a pKa of 5 exhibits
decreasing permeability
as the pH of the solution
increases.
Conversely, the solubility
increases at increasing
solution pH.
pKa also affects the
activity of a structural
series. This is due to
changes in interactions
at the active site of the
target protein
pKa Case Studies
Bases
pKa
Guanidine
13.6
Acetamide
12.4
Pyrrolidine
11.3
Piperidine
11.1
Acids
pKa
Methylamine
10.6
CF3COOH
0.23
Piperazine
9.8;5.3
CCl3COOH
0.9
Trimethylamine
9.8
CCl2HCOOH
1.3
Glycine
9.8
CClH2COOH
2.9
Morpholine
8.4
HCOOH
3.8
Imidazole
6.8
C6H5COOH
4.2
Pyridine
5.2
Succinic Acid
4.2;5.6
Quinoline
4.9
H3COOH
4.8
Aniline
4.9
Thiophenol
6.5
Triazole
2.5
p-Nitrophenol
7.2
Purine
2.4
m-Nitrophenol
9.3
Pyrimidine
1.2
C6H5OH
10.0
Diphenylamine
0.8
Drugs & pKa
Acids
pKa
Penicillin V
2.7
Salicylic Acid
3.0;13.8
Acetylsalicylic
Acid
3.5
Diclofenac
4.1
Sulfathiazole
7.1
Phenobarbital
7.4;11.8
Phenytoin
8.3
Acetaminophen
9.9
Caffeine
14
Bases
pKa
Caffeine
0.6
Quinidine
4.1;8.0
Tolbutamide
5.3
Cocaine
8.4
Ephedrine
9.4
Imipramine
9.5
Atropine
9.7
In Summary:
When synthetic modifications are
planned for the purpose of improving
the water solubilty or permeability of
a structural series, a wide selection of
substructures can be used.
It is important to remember that
structural modifications that increase
solubility
will
also
decrease
permeability
In Summary:
By modifying the substructures of a
molecule to introduce groups with
differing
pKa
values,
medicinal
chemists can modify the solubility
and permeability of the compound