pharmacophore based drug design

Recap:

Intermolecular forces and bindingOverview of classes of targets for drugsQuantitation 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/conditionChoose 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 bioassayIn vivo, in vitro; high throughput screening

Two idealized approaches:Start with a known “lead compound” (isolate, purify, identify)

…Pharmacophore-based approachStart with a known target structure (isolate, purify, identify)…

Target-based approach

Hopefully, information about both lead and target are determined.

Pharmacophore-based drug design

Determine the effects of structural changes on activity of drug: structure-activity relationships (SARs)

1. Data collection: Publications; patents; biological activity; NMR and X-ray data; physiochemical properties

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

Pharmacophore: A specific 3D arrangement of chemical groups common to active molecules and essential to their biological activities


This information will result in the identification of a pharmacophore…

2. Analysis: integrate information about drug (and target) to generate hypothesis about activity

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.

If you know the pharmacophore for your target, you can create new lead compounds based on the pharmacophore!

3. Design new structures.

Pharmacophore-Based Drug Design

Simple example 1: 3D structures are known1. 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)


Simple example 1: 3D structures are known

3. Design new structures. New molecular mimic will be tested.


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


Example 2 (cont):

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)



•Generate low energy conformations for each active molecule:

A: Etc…

B: Etc…

2. Data analysis. Hypothesis: bioactive conformations share 3D features required for activity…Superimpose the generated conformations to define a pharmacophore

Example 2 (cont):


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.

3. Design: Use this pharmacophore to design new molecules to test

Example 2 (cont):


Superimposition of properties: Example

Dihydrofolate and methotrexate bind to the catalytic site of dihydrofolate reductase.

However, X-ray structures ofthese complexes shows that they don’t overlap as expected by sterics:


Examine electron density distribution of the molecules:


Superimposition of properties: Example, cont.

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?

Consequences of chemical modification to drug activity in addition to altering binding interactions:

metabolism of drugpharmacokinetics

Procedure: Alter or remove groups using chemical synthesis and test the activity of the altered molecule (analog). Infer role of those groups in binding.


Initial chemical modification: simplification

Example: ergot alkaloids like bromocriptine were starting points for simplified synthetic analogs shown below

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


Examples:OH isosteres: SH, NH2, CH3

O isosteres: S, NH, CH2

H isostere: FIf you change an O to CH2 - sterics same, but no dipole or lone pairIf you change an OH To SH - sterics different, but still a lone pair

O NH

amide

NH

pyrrole


Common alterations of compounds: replacement of groups with isosteres. Isosteres: atoms or groups of atoms which have the same valency

O NH

OH

Propranolol (beta blocker)

NH

OH

S NH

OH

NH

OH

HN NH

OH

no activity

no activity

no activity active(but less than Propranolol)

example

?

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 NH

OH

Propranolol (beta blocker)potent

O NH

OH

Pindolol very potent

NH


Ring expansion/contractions - changes geometry

Ring variations - may add a binding interaction with heteroatom;


Extend structure by adding a functional group to lead compound

Extend or contract linking chain length between groups


Rigidification - limit number of possible conformationsCan help identify bioactive conformationLocks molecule in most active conformation - more effective

Add a ring

Add rigid groups


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


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

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)

Binding role of hydroxy groups (continued):


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-piConvert to: •Saturated compound (not effective overlap; no pi system; more flexible)


Binding role of ketones: H-bond acceptor; dipole-dipoleConvert to: •Alcohol (geometry change can weaken H-bond or dipole-dipole)


Binding role of alkyl substituents: hydrophobics/stericsConvert to: •Longer (homologation) or differently-branched groups

Alkyl groups most easily modified are

DRUG OR DRUGO

OR

DRUGO

RO

DRUGO

R

HN DRUG

O

NR2

DRUG NCH3

R


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!


Example: Nifedipine analogs

Chemical synthesis of analogs help validate or refute hypotheses regarding mechanism of action/mode of binding - part of design

O2N

N CH3H3C

CO2CH3H3CO2C

H

NifedipeneTreats hypertension

O2N

N CH3H3C

CO2CH3H3CO2C

H

CH3

Inactivesteric "bump"

O2N

N CH3H3C

CO2CH3H3CO2C

H

InactiveDifferent conformation

CH3


Binding role of alkyl substituents (continued)

Binding role of aryl substituents: various/ stericsConvert to: •Same substituents at different locations•Different substituents: Recall substituent effects in organic chem!•Substituents may affect each others’ properties (pKa)

ONR

OMeSO2NH

6

8

7

Anti-arhythmic benzopyranBest when substituent was at position 7


Example: beta-adrenergic drugs, chemically related to adrenaline and noradrenaline.


Binding role of aryl substituents: (continued)

Binding role of amides: H-bond acceptor; dipole-dipoleConvert to: •Hydrolysis products (but will lose a piece); reduce (no more H-bond acceptor


As computer analysis becomes more widespread, a pharmacophore will be less “visual” and more numerical, with numerical scoring of properties


Activity data for modified drugs leads to a better pharmacophore

•Use databases of known compounds – no new synthesis!•Be careful of multiple conformations•Content of database is crucial

Example. Protein kinase C enzymes are targets for chemotherapeutic intervention against cancer. The pharmacophore was deduced from active phorbol esters like PDBU

Pharmacophore-based drug design Design method 2: Database searching

a. 3D Search for a 3D pharmacophore

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…

b. 3D Shape searching on Databases - also finds chemically different compounds, but is successful only if the pharmacophore is also incorporated


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”

Pharmacophore-based drug design Design methods 3&4: De novo design and Manual design

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”

References

pharmacophore based drug design

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