Transcript Lecture 07, pharmaco - Cal State LA

Recap:
Intermolecular forces and binding
Overview of classes of targets for drugs
Quantitation of
•Drug activity (functional assay) EC50, ED50, IC50
•Drug binding (binding titration) KD, KI
Most common lab techniques (many)
•Receptors - we covered radioligand binding assay
•Enzymes - kinetics used (later in quarter)
Back to drug discovery:
Choose a disease/condition
Choose a drug target
• Inferred from action of drug, poison, natural product,
chemical signal found in humans; revealed through
genomics
• Unique to a species or tissue
• May require multiple targets for effective treatment
Choose a bioassay
In vivo, in vitro; high throughput screening
Two idealized approaches:
Start with a known “lead compound” (isolate, purify,
identify)…Pharmacophore-based approach
Start with a known target structure (isolate, purify,
identify)…Target-based approach
Hopefully, information about both lead and target are determined.
Pharmacophore-based drug design
0. Determine identity of a “lead compound”:
•Screen natural and synthetic banks of compounds for activity
•Folk medicine
•Natural ligand
•Drug already known
•Computer-aided drug design
•Computerized search of structural databases
1. Data collection: Publications; patents; biological activity;
NMR and X-ray data; physiochemical properties
Determine the effects of structural changes on activity of drug:
structure-activity relationships (SARs)
Pharmacophore-based drug design
2. Analysis: integrate information about drug (and target) to generate
hypothesis about activity
This information will result in the identification of a
pharmacophore…
Pharmacophore: A specific 3D arrangement of chemical groups
common to active molecules and essential to their biological
activities
Pharmacophore-based drug design
3. Design new structures.
If you know the pharmacophore for your target, you can create
new lead compounds based on the pharmacophore!
Why make new lead compounds?
•Increase activity (make binding stronger)
•Decrease side effects (increase selectivity)
•Improve ease and efficiency of administration to patient
•Potentially find a better synthetic route
Approach: Molecular mimicry.
Pharmacophore-Based Drug Design
Simple example 1: 3D structures are known
1. Data collection: biological activity of lead compound (and other
compounds)
2. Analysis: biologically active molecules share the same
pharmacophoric features (superimpose 3D structures&find common
features)
Pharmacophore-Based Drug Design
Simple example 1: 3D structures are known
3. Design new structures. New molecular mimic will be
tested.
Pharmacophore-Based Drug Design
Example 2: (A more typical example) Biologically active
conformations are not known.
1. Data collection: biological activity. Two molecules below
show good activity.
Data collection: Determination of biologically active conformation
Pharmacophore-Based Drug Design
Example 2 (cont):
Data collection: Determination of biologically active conformation
If no 3D data are available, use computers!
•Bioactive conformations are not always the most stable
conformations, but are within about 12kJ/mole or 3kcal/mole)
Pharmacophore-Based Drug Design
Example 2 (cont):
Data collection: Determination of biologically active conformation
•Generate low energy conformations for each active molecule:
A:
B:
Etc…
Etc…
2. Data analysis. Hypothesis: bioactive conformations share 3D
features required for activity…Superimpose the generated
conformations to define a pharmacophore
Pharmacophore-Based Drug Design
Example 2 (cont):
3. Design: Use this pharmacophore to design new molecules to test
Notes:
•More rigid molecules have fewer conformations – easier to analyze
•Flexible molecules have many conformations – often must examine
conformationally restricted analogs to determine bioactive
conformation. (Move from computer to lab: Chemical synthesis of
analogs!) (Ex. GABA MC C2.5.2)
•Superimposing molecules: don’t look at sterics only – think of
physical properties of molecule.
Pharmacophore-Based Drug Design
Superimposition of properties: Example
Dihydrofolate and methotrexate bind to the catalytic site of
dihydrofolate reductase.
However, X-ray structures of
these complexes shows that
they don’t overlap as
expected by sterics:
Pharmacophore-Based Drug Design
Superimposition of properties: Example, cont.
Examine electron density distribution of the molecules:
Pharmacophore-Based Drug Design
Design: use analyzed data to design new compounds - hopefully
with better properties
Four Methods used to design better drugs:
1. Chemical modification
2. Database searching
3. De novo
4. Manual
These approaches generate more data, which yet again can be
used to generate new hypotheses and structures, etc.
Pharmacophore-based drug design
Design method 1: Chemical modification
Goal: Determine Structure- activity relationships:
What functional groups are important to biological activity?
Pharmacophore-based drug design
Design method 1: Chemical modification
Procedure: Alter or remove groups using chemical
synthesis and test the activity of the altered molecule
(analog). Infer role of those groups in binding.
Consequences of chemical modification to drug activity in
addition to altering binding interactions:
metabolism of drug
pharmacokinetics
Pharmacophore-based drug design
Design method 1: Chemical modification
Initial chemical modification: simplification
Once a biologically active compound is found, a common first
tactic is to simplify it to determine the essential parts for activity.
•For complex molecules, this often leads to easier synthesis.
•Will not be successful if all parts of the molecule are needed for
activity
Example: ergot alkaloids like bromocriptine were starting points
for simplified synthetic analogs shown below
Pharmacophore-based drug design
Design method 1: Chemical modification
Common alterations of compounds: replacement of groups with
isosteres. Isosteres: atoms or groups of atoms which have the
same valency
Examples:
O
N
N
OH isosteres: SH, NH2, CH3
H
H
O isosteres: S, NH, CH2
pyrrole
amide
H isostere: F
If you change an O to CH2 - sterics same, but no dipole or lone pair
If you change an OH To SH - sterics different, but still a lone pair
example
OH
O
OH
N
H
S
OH
N
H
Propranolol (beta blocker)
N
H
no activity
?
no activity
N
H
OH
no activity
HN
OH
N
H
active
(but less than
Propranolol)
Pharmacophore-based drug design
Design method 1: Chemical modification
Pharmacophore-based drug design
Design method 1: Chemical modification
Common alterations of compounds: replacement of groups with
bioisosteres. Bioisosteres - different chemical groups with the same
biological activity. No restriction on sterics and electronics, unlike
classical isosteres.
O
OH
N
H
Propranolol (beta blocker)
potent
O
OH
N
H
Pindolol
very potent
N
H
Pharmacophore-based drug design
Design method 1: Chemical modification
Pharmacophore-based drug design
Design method 1: Chemical modification
Ring expansion/contractions - changes geometry
Ring variations - may add a binding interaction with heteroatom;
Pharmacophore-based drug design
Design method 1: Chemical modification
Extend structure by adding a functional group to lead compound
Extend or contract linking chain length between groups
Pharmacophore-based drug design
Design method 1: Chemical modification
Rigidification - limit number of possible conformations
Can help identify bioactive conformation
Locks molecule in most active conformation - more effective
Add a ring
Add rigid groups
Pharmacophore-based drug design
Design method 1: Chemical modification
Rigidification (continued)
Add a bulky groups (but recall it may not just affect conformaion; it
may affect sterics
Alter Stereochemistry: usually different stereoisomers have different
activity
Pharmacophore-based drug design
Design method 1: Chemical modification
Probing specific functional groups in a molecule
Binding role of hydroxy groups: H-bond donor or acceptor
Convert to:
•methyl ether (no H-bond donor now; maybe steric problem)
•an ester (no H-bond donor now; poor H-bond acceptor; maybe steric
problem)
Probing specific functional groups in a molecule
Binding role of hydroxy groups (continued):
methyl ether (no H-bond donor now; still H-bond acceptor; maybe
steric problem)
an ester (no H-bond donor now; poor H-bond acceptor; maybe steric
problem)
Probing specific functional groups in a molecule
Binding role of amino groups: H-bond donor (if N-H is present) or
acceptor; ionic (protonation of N to form a salt; recall pKa)
Convert to:
•amide (no protonation; no H-bond acceptor now; steric problem?)
•Tertiary amine (no H-bond donor now; still H-bond acceptor; sterics?)
Binding role of aromatic rings, alkenes: hydrophobic; cation-pi
Convert to:
•Saturated compound (not effective overlap; no pi system; more flexible)
Probing specific functional groups in a molecule
Binding role of ketones: H-bond acceptor; dipole-dipole
Convert to:
•Alcohol (geometry change can weaken H-bond or dipole-dipole)
Probing specific functional groups in a molecule
Binding role of alkyl substituents: hydrophobics/sterics
Convert to:
•Longer (homologation) or differently-branched groups
Alkyl groups most easily modified are
O
O
DRUG
OR
DRUG
DRUG
R
OR
CH3
DRUG
N
R
DRUG
O
H
N
O
O
DRUG
R
NR2
Probing specific functional groups in a molecule
Binding role of alkyl substituents (continued)
Notes:
•Recall impact of lipophilicity on drug transport through body
•Changing alkyl groups may also affect the preferred
conformation of the molecule!
Probing specific functional groups in a molecule
Binding role of alkyl substituents (continued)
Example: Nifedipine analogs
O2N
H3CO2C
H3C
CO2CH3
N
H
CH3
Nifedipene
Treats hypertension
CH3
O2N
H3CO2C
H3C
CO2CH3
N
H
CH3
Inactive
steric "bump"
O2N
H3CO2C
H3C
CH3
CO2CH3
N
H
CH3
Inactive
Different conformation
Chemical synthesis of analogs help validate or refute hypotheses
regarding mechanism of action/mode of binding - part of design
Probing specific functional groups in a molecule
Binding role of aryl substituents: various/ sterics
Convert to:
•Same substituents at different locations
•Different substituents: Recall substituent effects in organic chem!
•Substituents may affect each others’ properties (pKa)
MeSO2NH
O
6
7
O
NR
8
Anti-arhythmic benzopyran
Best when substituent was at position 7
Probing specific functional groups in a molecule
Binding role of aryl substituents: (continued)
Example: beta-adrenergic drugs, chemically related to
adrenaline and noradrenaline.
Probing specific functional groups in a molecule
Binding role of amides: H-bond acceptor; dipole-dipole
Convert to:
•Hydrolysis products (but will lose a piece); reduce (no more H-bond
acceptor
Pharmacophore-based drug design
Design method 1: Chemical modification
Activity data for modified drugs leads to a better pharmacophore
As computer analysis becomes more widespread, a
pharmacophore will be less “visual” and more numerical, with
numerical scoring of properties
Pharmacophore-based drug design
Design method 2: Database searching
•Use databases of known compounds – no new synthesis!
•Be careful of multiple conformations
•Content of database is crucial
a. 3D Search for a 3D pharmacophore
Example. Protein kinase C enzymes are targets for
chemotherapeutic intervention against cancer. The pharmacophore
was deduced from active phorbol esters like PD BU
Pharmacophore-based drug design
Design method 2: Database searching
The 3D database search led to the discovery of a new potent
protein kinase C inhibitor that is chemically very different from
the original reference phorbol esters. Alignment of the two:
Start over with this
“hit” as a new lead;
chemical
modification, etc…
Pharmacophore-based drug design
Design method 2: Database searching
b. 3D Shape searching on Databases - also finds chemically
different compounds, but is successful only if the pharmacophore
is also incorporated
Pharmacophore-based drug design
Design methods 3&4: De novo design and Manual design
Assemble disconnected functional groups (pharmacophoric groups)
with spacers with or without computer algorithms; using models or
computer modeling software
Example. 5-alpha reductase inhibitors inhibit the metabolism of
testosterone, and are used to treat prostate hyperplasia. The steroid
structure has side effects. Replacement with other structures should
help...
Pharmacophore-based drug design
Design methods 3&4: De novo design and Manual design
Computer algorithm was used to obtain the following compounds:
Overlay of one “hit”:
Other “hits”
References
Patrick, G. L. An Introduction to Medicinal Chemistry; Oxford University Press: New York, NY, 2001
Silverman, R. B. The Organic Chemistry of Drug Design and Drug Action ; Academic Press: San Diego,
CA, 1992.
Thomas, G. Medicinal Chemistry An Introduction; John Wiley and Sons, Ltd.: New York, NY, 2000.
Williams, D. A.; Lemke, T. L. Foye’s Principles of Medicinal Chemistry; Lippincott Williams and Wilkins,
New York, NY, 2002.
Molecular Conceptor, Synergix:
C1 “Rational Drug Design”
C2 “Structure Activity Relationships”
E1-3 “Pharmacophore-Based Drug Design”