drugs targeting nucleic acids dna & rna · 2oconh 2 nh ome 1.3 alkylating agents 1. drugs...

© Oxford University Press, 2013

DRUGS TARGETING NUCLEIC ACIDS

DNA & RNA

Patrick: An Introduction to Medicinal Chemistry 5e

Chapter 9


1. DRUGS ACTING ON DNAIntercalating agentsTopoisomerase poisonsAlkylating agentsMetallating agentsChain cuttersChain terminatorsControl of gene transcription


1. DRUGS ACTING ON DNA1.1 Intercalating agents

Mechanism of action•  Contain planar aromatic or heteroaromatic ring systems•  Planar systems slip between the layers of nucleic acid pairs and disrupt the shape of the helix•  Preference is often shown for the minor or major groove•  Intercalation prevents replication and transcription •  Intercalation can inhibit topoisomerases


1. DRUGS ACTING ON DNA1.1 Intercalating agentsExample - Proflavine

Proflavine NH2N NH2

•  Planar tricyclic system•  The amino substituents are protonated and charged•  Used as a topical antibacterial agent in the second world war•  Targets bacterial DNA•  Too toxic for systemic use


T A

G C

H3N NH3

O O

proflavine

sugar phosphatebackbone

NH3N NH3

Proflavine

Ionic interactions

T

DNA DOUBLE HELIX

TAG

C

ATC

GCTA

ATCG

AT A

T ATA

TAT A

G CC

T ATA

AG CT

CGCG

ATAT

G

G

1. DRUGS ACTING ON DNA1.1 Intercalating agentsExample - Proflavine

van der Waals interactions


Extra binding to sugar phosphate backbone by NH3

Doxorubicin (Adriamycin)

OMe

O

O

OH

OH H O

OH

OCH2OH

O

NH3

H

H

H

H

MeH

HOH

O

N

O

NH2

CH3CH3

C C

NH

ONH

CC

D-Val

C

D-Val

L-Pro

N-Me-Gly

L-ProN-Me-Gly

C

O

N-Me-L-ValN-Me-L-Val

C

O

Me MeH H

CO O

H H

O

DactinomycinExtra binding to sugar phosphate

backbone by cyclic peptides


Examples - anticancer agents

Planar rings


OMe

O

O

OH

OH H O

OH

OCH2OH

O

NH3

H

H

H

H

MeH

HOH

O

N

O

NH2

CH3CH3

C C

NH

ONH

CC

D-Val

C

D-Val

L-Pro

N-Me-Gly

L-ProN-Me-Gly

C

O


C

O

Me MeH H

CO O

H H

O

Dactinomycin

Planar rings

Planar rings


OMe

O

O

OH

OH H O

OH

OCH2OH

O

NH3

H

H

H

H

MeH

HOH

O

N

O

NH2

CH3CH3

C C

NH

ONH

CC

D-Val

C

D-Val

L-Pro

N-Me-Gly

L-ProN-Me-Gly

C

O


C

O

Me MeH H

CO O

H H

O

Dactinomycin

Planar rings

Planar rings


OMe

O

O

OH

OH H O

OH

OCH2OH

O

NH3

H

H

H

H

MeH

HOH

O

N

O

NH2

CH3CH3

C C

NH

ONH

CC

D-Val

C

D-Val

L-Pro

N-Me-Gly

L-ProN-Me-Gly

C

O


C

O

Me MeH H

CO O

H H

O

Dactinomycin



Notes on dactinomycin•  Intercalates via minor groove of DNA double helix•  Prevents unwinding of DNA double helix•  Blocks transcription by blocking DNA-dependent RNA polymerase

Notes on doxorubicin•  Intercalates via the major groove of DNA double helix•  Blocks the action of topoisomerase II by stabilising the DNA-enzyme complex •  Acts as a topoisomerase poison


1. DRUGS ACTING ON DNA1.1 Intercalating agentsExamples - Bleomycins

N N

CONH2HN

NH2NH2

O

H2N

Me

O

HNNH

O

Me

HO

MeHN

OHO Me

NH

O

S

N

SN R

O

O

NH

N

O

HO

OH

OH

O

OH

OHO

NH2

O

H

H

H

H

H

H H

H H

OH

Bleomycin A2 R = NHCH2CH2CH2SMe2Bleomycin B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH

imidazolering

pyrimidinering

primary amine

primary amine

primary amide

Bithiazoleintercalatingregion

N N

CONH2HN

NH2NH2

O

H2N

Me

O

HNNH

O

Me

HO

MeHN

OHO Me

NH

O

S

N

SN R

O

O

NH

N

O

HO

OH

OH

O

OH

OHO

NH2

O

H

H

H

H

H

H H

H H

OH

Bleomycin A2 R = NHCH2CH2CH2SMe2Bleomycin B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH

imidazolering

pyrimidinering

primary amine

primary amine

primary amide


1. DRUGS ACTING ON DNA1.1 Intercalating agentsNotes on bleomycins•  Used as anticancer agents

•  Intercalated by means of bithiazole ring system

•  Ferrous ion then chelated by nitrogens of the primary amines, amide and pyrimidine ring

•  Reaction with oxygen results in a ferric ion and reactive oxygen species

•  Results in radical formation and chain cutting

•  Bleomycin prevents DNA ligase from repairing damage


1. DRUGS ACTING ON DNA1.2 Topoisomerase poisons - non-intercalating

Examples

OO

O

O

MeO

OH

OMe

O

OOOHO

Me

H

HO

4'

4

EtoposideO

O

O

O

MeO

OH

OMe

O

OOOHO

H

HO

4'

4

S

Teniposide

Notes on etoposide and teniposide•  Stabilise the complex between DNA and topoisomerase enzymes•  Used as anticancer agents•  Also cause chain cutting



Examples - Camptothecin

Notes•  Stabilises complex between DNA and topoisomerase I•  Single-strand breaks accumulate in the chain•  Irreversible double-strand breaks occur during transcription•  Semi-synthetic analogues used as anticancer agents

N

N

O

O

OHO

A B CD

E Lactone ring

Me



Examples - Quinolones and fluoroquinilones

Notes•  Synthetic agents used as antibacterial agents•  Stabilise complex between bacterial DNA and topoisomerases•  Binding site for agents revealed once DNA strands are ‘nicked’

N N

O

CH2CH3

CO2H

Me

Nalidixic acid

N

CO2H

N

O

HN

F

Ciprofloxacin



Examples - Quinolones and fluoroquinilones

Fluoroquinolones

Topoisomeraseenzyme

•  Four drug molecules are stacked in the bound complex•  Bound to DNA and enzyme by hydrogen and ionic bonds

X8 N

R6

R7

R5 O

O

O

R1

Region binding to DNA

Stacking domain

X8 N

R6

R7

R5 O

O

O

R1

Region binding to enzymeRegion

binding to enzyme

X8 N

R6

R7

R5 O

O

O

R1X8 N

R6

R7

R5 O

O

O

R1

Region binding to enzymeRegion

binding to enzyme

X8 N

R6

R7

R5 O

O

O

R1


1.3 Alkylating agents

Notes•  Contain highly electrophilic groups•  Form covalent bonds to nucleophilic groups in DNA

(e.g. 7-N of guanine)•  Prevent replication and transcription•  Useful anticancer agents•  Toxic side effects (e.g. alkylation of proteins)•  Can cause interstrand and intrastrand crosslinking if two electrophilic groups present•  Alkylation of nucleic acid bases can result in miscoding

1. DRUGS ACTING ON DNA


Interstrand crosslinkingIntrastrand crosslinking

Crosslinking

NuNu Nu

Nu

1.3 Alkylating agents1. DRUGS ACTING ON DNA

X X

NuNu

X X

Nu

Nu



Nucleophilic groups on nucleic acid bases


nucleophilicgroups

nucleophilicgroups

NH2

N

N

N

N

1

3

R

H2N

HN

N N

N

O7

R

NH2

N

NR

O

3

CytosineGuanineAdenine


Cytosine Guanine

NN

NH2

OR

HNN

N

NO

H2N

R

Normal base pairing


Thymine Alkylated guanine

NNH

O

O

Me

R

NN

N

NHO

R

H2N

DRUG

Miscoding resulting from alkylated nucleic acid bases


Guanine prefers keto tautomer!

Abnormal base pairing.!Alkylated guanine prefers

enol tautomer!



ExampleChlormethine (nitrogen mustard)


Notes•  Used medicinally in 1942•  Causes intrastrand and interstrand cross-linking•  Prevents replication•  Mono-alkylation of guanine also possible•  Analogues with better properties have been prepared

Me N

Cl

Cl


Mechlorethamine

H3C N

Cl

Cl Cl

NH3C

Aziridine ion

G = Guanine

DNA

G

N

HN

NN

N

N NH

N

O

O

NH2

NH2

G

DNA

N

N

N

NN

HN

NH

N

O

NH2

O NH2

H3C N

Cl

DNA

NN

N

N NH

N

O

NH2

N

HNO NH2

NH3C

DNA

CH3

N

N

N

N

N

N

HN

NH

N

O NH2

O

NH2

Crosslinked DNA

Mechanism of action

Alkylating agentsChlormethine


Cl

N2 + HO

Alkylatingagent

ClN N

N

O

O

R

H

1.3 Alkylating agentsExample - Nitrosoureas


MechanismDecompose in body to form an alkylating agent and a carbamoylating agent

O

N NH

NO

Cl Cl

Carmustine

O

N NH

NO

Cl

Lomustine

O C N R

ClN

NOH

+

Isocyanate(carbamoylating agent)

H O

arrow

Cl

N2 + HO

Alkylatingagent


Cl DNA X Y

Cl

X YCross-linking

DNA DNA

AlkylationAlkylatingagent

1.3 Alkylating agentsExample - Nitrosoureas


Notes•  Alkylating agent causes interstrand crosslinking•  Crosslinking between G-G or G-C•  Carbamoylating agent reacts with lysine residues on proteins•  May inactivate DNA repair enzymes

O C N RIsocyanate

Protein-Lys-NH2Protein-Lys-NH

O

HN RCarbamoylation



Synthetic agent used as anticancer agentCauses interstrand crosslinking

Busulfan

OO

SMe

OO

SMe

OO

Mechanism

OO

SMe

OO

SMe

OO

HN

N N

N

O

H2N

Guanine

DNA

-MeSO3-

N

N

DNA

N

N

DNA

N

N

DNA

N

N

DNA

-MeSO3-

OSO2Me


Notes•  Neutral inactive molecule acting as a prodrug•  Platinum covalently linked to chloro substituents•  Ammonia molecules act as ligands•  Activated in cells with low chloride ion concentration•  Chloro substituents replaced with neutral water ligands•  Produces positively charged species

1.4 Metallating agents1. DRUGS ACTING ON DNA

PtNH3Cl

NH3ClCisplatin

PtNH3Cl

NH3Cl

H2OPt

NH3H2O

NH3ClPt

NH3H2O

NH3H2O

+ 2+

+DNA Pt

NH3DNA

NH3DNACisplatin


Notes

1.4 Metallating agents1. DRUGS ACTING ON DNA

PtNH3Cl

NH3ClCisplatin

•  Binds to DNA in regions rich in guanine units •  Intrastrand links rather than interstrand•  Localised unwinding of DNA double helix•  Inhibits transcription



Mechanism

•  Prodrug activated by demethylation in liver•  Decomposes to form a methyldiazonium ion•  Alkylates guanine groups

HN N

CONH2NNNH3CCH3

Cyt P-450

liver

HN N

CONH2NNN

CH3OHH

HN N

CONH2NHNNCH3

-CH2O

H

HN N

CONH2H2N

N N CH3

AIC

Methyldiazonium ion

N2 + CH3

HN N

CONH2NNNH3CCH3

Dacarbazine


O

O

N

H2N

Me

CH2OCONH2

NH

OMe


Example - Mitomycin C

Notes•  Prodrug activated in the body to form an alkylating agent•  One of the most toxic anticancer drugs in clinical use


OH

OH

N

H2N

Me

CH2

NH2

NH

NH

HN

N N

NO

HN

N N

NO Guanine

Guanine

H2N-DNA

O

O

N

H2N

Me

CH2OCONH2

NH

OMe

O

OH

N

H2N

Me

CH2OCONH2

NH

H

-MeOH

O

OH

N

H2N

Me

CH2OCONH2

NH2

Ring opening

-H +

Alkylating agent

OH

OH

N

H2N

Me

CH2

NH2

NH-DNA

NH-DNA

-CO2 -NH3

Crosslinked DNA

OH

OH

N

H2N

Me

CH2OCONH2

NH

OMe

Reduction

OH

OH

N

H2N

Me

CH2

NH2

NH-DNA

OC

O

NH2

H2N-DNA

H

H

H


•  Intercalating agent•  Abstracts H from DNA to generate radicals•  Radicals react with oxygen resulting in chain cutting•  Bleomycin also inhibits repair enzymes

BLEOMYCIN A2 R = NHCH2CH2CH2SMe2BLEOMYCIN B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH

BleomycinUsed vs skin cancer

N N

NH

NH2CONH2NH2

H2N

CH3 HN

O

NH

O HO

CH3

CH3

OCH3HO

HN

NH N

S

S

N

O

ONH

N

O

HO

OH

OH

OH

OH

OHO

O NH2

O

ROO

1.5 Chain cutters1. DRUGS ACTING ON DNA


•  Generates DNA diradical•  DNA diradical reacts with oxygen•  Results in chain cutting


OOMe

ICH3

O

OHMeOHOH3C

OMe

S

O

OH3C

OH

O NH

OH3C

HOO

O

MeO

HN

H3C

HS

SS

H3C

HOO

NHCO2Me

Calicheamicin γ1I

Antitumour agent Enediyne system


RS

HO O

NHCO2Me

SMeS

Nu

RS

HOO

NHCO2Me

Cycloaromatisation!

RS

HOO

NHCO2Me

O2!

Oxidative!cleavage!

DNA DNA(Diradical)

RS

HOO

H

HNHCO2Me

Michael!addition!

RS

HO O

NHCO2Me


Mechanism

H


Notes:•  Azidothymidine is a prodrug used in the treatment of HIV•  AZT is phosphorylated to a triphosphate in the body•  Triphosphate has two mechanisms of action

- inhibits a viral enzyme (reverse transcriptase)- is added to growing DNA chain and acts as chain terminator

Azidothymidine (AZT) (Zidovudine;Retrovir) HN

N

OCH3

O

OHO

N3

HN

N

OCH3

O

OO

N3

PO

OHOP

O

OHOP

O

OHHO

1.6 Chain terminators1. DRUGS ACTING ON DNA

Chain terminating group

HN

N

OCH3

O

OO

N3

PO

OHOP

O

OHOP

O

OHHO


HN

N

O

H2N N

N

OHO

Aciclovir(Zovirax)

Notes:•  Prodrugs used as antiviral agents•  Same mechanisms of action as AZT•  Used vs herpes simplex and shingles

Famciclovir(Famvir)

N

NN

N NH2AcO

OAc


Chainterminating group

HN

N

O

H2N N

N

OHO

Chainterminating group

N

NN

N NH2AcO

OAc



a) Normal replication

PGP P

ATCGAACC

TAG OH3'

DNA template Growing

chain

A

T

C

G

A

A

C

C

T

A OH3'

DNA template

Growingchain


PDrug

P P


b) Chain termination

A

T

C

G

A

A

C

C

T

A OH3'

DNA template

Growingchain

ATCGAACC

TA

Drug H3'

DNA template Growing

chain

Chain termination


1.7 Control of gene transcription1. DRUGS ACTING ON DNA

Notes:•  Design of synthetic molecules capable of controlling gene transcription•  Molecules capable of recognising and binding to specific base pairs•  Hairpin polyamides containing heterocyclic rings are capable of binding to the minor groove•  Binding involves amide groups and heterocycles•  Particular patterns of heterocyclic rings allow recognition of perticular base pairs•  Capable of inhibiting transcription•  Designed to bind to regulatory element of a gene


A

C

A

T

G

T

T

G

T

A

C

A

5'3'


OO

NH

NN Me

NO

H

NMe

O

ONH

N

N

NH

O

Me

ONH

N

O

H

NMe

MeH

Me

NMe

N HO

N OMe

N H

O

NN

Me

H

N

NMe

O

N

H

H

H

Py

Im

Hp

Py

Py

Py

Hp

Im

Linker

ArmArm


2. DRUGS ACTING ON rRNAAntibiotics

O2NCH2OH

HO

HN

H

H

CO CHCl2

Chloramphenicol(vs typhoid)

R

Me

O

HNMe

MeOH

O

OHOH

OHO

MeO

O

C

Me Me

OMe O MeMe

OH

H

H

H

H

H

H

H

H

Rifamycins

Streptomycin

H2N C

NH

NH

O

HN C

NH

NH2

O

OO

H

OHH HO

HH

OHH

H

CHO

OH

H

Me

CH2OH

HHO

H

OH

H

H

MeHNH

H

OOHOOH

Cl

OH

NMe2

O

HO

NH2

Me H

OH

Chlortetracycline(Aureomycin)

HO

O

O

O

H3C

CH3

CH3

O

CH3

CH3

HO

H3C

OO

O

CH3

CH3

Me

NMe2

HO

OHOMe

Erythromycin


Antisense Therapy

Protein synthesis!

3. DRUGS ACTING ON mRNA

m-RNA

antisense molecule

U C A G A U G C A A

A G U C U A C G U U

AAUG A A G Um-RNA

antisensemolecule


Advantages•  Same effect as an enzyme inhibitor or receptor antagonist•  Highly specific where the oligonucleotide is 17 nucleotides or more•  Smaller dose levels required compared to inhibitors or antagonists•  Potentially less side effectsDisadvantages•  ‘Exposed’ sections of mRNA must be targeted•  Instability and polarity of oligonucleotides (pharmacokinetics)•  Short lifetime of oligonucleotides and poor absorption across cell membranes

Antisense Therapy



•  Short segments of double stranded RNA•  Recognised by enzyme complex RISC to produce single stranded RNA - small interfering or small inhibitory RNA (siRNA)•  Binds to complementary region of mRNA• mRNA is cleaved by enzyme complex

Micro-RNA (miRNA)


RISC

miRNA

RISC

miRNA

RI SC

siRNA

RISC

mRNA


Advantages•  siRNAs have potential to be used in gene therapy•  Greater efficiency in silencing mRNA than conventional antisense therapy•  One siRNA could lead to cleavage of several mRNA molecules

Micro-RNA (miRNA)


Problems•  siRNAs need to be metabolically stable •  Need to reach target cells•  Need to enter target cells

drugs targeting nucleic acids dna & rna · 2oconh 2 nh ome 1.3 alkylating agents 1. drugs...

Documents