Patrick: An Introduction

to Medicinal Chemistry 6e
Chapter 9

DRUGS TARGETING
NUCLEIC ACIDS
DNA & RNA

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1. DRUGS ACTING ON DNA
Intercalating agents

Topoisomerase poisons

Alkylating agents

Metallating agents

Chain cutters

Chain terminators

Control of gene transcription

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1. DRUGS ACTING ON DNA
1.1 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

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1. DRUGS ACTING ON DNA
1.1 Intercalating agents

H2N N NH2

Proflavine

• 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

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1. DRUGS ACTING ON DNA
1.1 Intercalating agents
Example - Proflavine

Proflavine
G C
AT
H3N N NH3
TA
T A
G C
G C Sugar phosphate
TA backbone R
T A
T A
AT T A
AT
T A
C G
G C Proflavine
TA H3N NH3
T A
G C
GC
O O
GC
T A
A T G C
C G
TA
T A R R

DNA DOUBLE HELIX

van der Waals interactions

Ionic interactions
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1. DRUGS ACTING ON DNA
1.1 Intercalating agents
Examples - anticancer agents
Planar rings

N-Me-Gly N-Me-Gly O
O OH
N-Me-L-Val L-Pro N-Me-L-Val L-Pro CH2OH
D-Val D-Val
O O OH
C C
C O C O
H C H C
H H
Me Me OMe O OH H O
NH NH
C O O C H
H O
N NH2
Me
H H
Planar rings HO
H
O O
H
CH3 CH3 NH3

Dactinomycin Doxorubicin (Adriamycin)

Extra binding to sugar phosphate Extra binding to sugar phosphate

backbone by cyclic peptides backbone by NH3

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1. DRUGS ACTING ON DNA
1.1 Intercalating agents

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

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1. DRUGS ACTING ON DNA
1.1 Intercalating agents
Examples - Bleomycins
Primary amine
CONH2 NH2
H H NH O
N 2
H Primary amide
R
O N
Pyrimidine N N Me O
ring S
H H H H
O HO N
H2N O NH N Bithiazole
H intercalating
Primary amine Me HN O region
N Me HO Me S
H H H
HO N
O Imidazole
OH H ring
O NH
O +
OH Bleomycin A2 R = NHCH2CH2CH2SMe2
Bleomycin B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH
OH

O OH
OH
O
NH2

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1. DRUGS ACTING ON DNA
1.1 Intercalating agents

Notes on bleomycins

• Used as anticancer agents

• Intercalate DNA 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

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1. DRUGS ACTING ON DNA
1.2 Topoisomerase poisons - non-intercalating
Examples
H H
O O
Me O O
O O
HO HO
HO O S HO O

O 4 O 4
O O
O O
Etoposide Teniposide
O O

MeO 4' OMe MeO 4' OMe

OH OH

Notes on etoposide and teniposide

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

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1. DRUGS ACTING ON DNA
1.2 Topoisomerase poisons - non-intercalating
Examples - Camptothecin

O
A B C N
N D
Lactone ring
E O

Me HO O

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

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1. DRUGS ACTING ON DNA
1.2 Topoisomerase poisons - non-intercalating
Examples - Quinolones and fluoroquinilones

O O

CO2H F CO2H

Me N N N N

CH2CH3 HN

Nalidixic acid Ciprofloxacin

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

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1. DRUGS ACTING ON DNA
1.2 Topoisomerase poisons - non-intercalating
Examples - Quinolones and fluoroquinilones

Topoisomerase
enzyme
Region binding to DNA
R5 O O
Region Region
R6 binding
binding O
to enzyme to enzyme

R7 X8 N
R1
Stacking domain

Fluoroquinolones

• Four drug molecules are stacked in the bound complex

• Bound to DNA and enzyme by hydrogen and ionic bonds
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1. DRUGS ACTING ON DNA
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

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Crosslinking

X X
X X

Nu Nu
Nu
Nu Nu Nu
Nu
Nu

Intrastrand crosslinking Interstrand crosslinking

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Nucleophilic groups on nucleic acid bases

Nucleophilic
groups

NH2 O NH2
7

N N 3
1
N HN N
Nucleophilic
groups 3
N H2N N N
N O N
R R
R
Adenine Guanine Cytosine

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents

Normal base pairing Miscoding resulting from

alkylated nucleic acid bases

Thymine Alkylated guanine

Cytosine Guanine
DRUG
NH2 O N Me O HO N

N HN N N
R NH N
N N N N R
R O H2N R O H2N

Guanine prefers Abnormal base pairing.

keto tautomer Alkylated guanine prefers
enol tautomer

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents

Example
Chlormethine (nitrogen mustard)

Cl

Me N

Cl
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
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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Chlormethine - mechanism of action
DNA
G = Guanine DNA
H
O N NH2 H
O N NH2
Cl
N
N N
G N
H3C N H3C N N
H3C N N

Cl Cl
Chlormethine Aziridine ion N N NH2 Cl
N N NH2
NH
N NH
N
O G
O

DNA

DNA H
O N NH2
H N
O N NH2
N
N N
N Crosslinked DNA
H3C N N

N N NH2

N NH2 N NH
N N

NH O
N CH3
O © Oxford University Press, 2013
1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Example - Nitrosoureas

O O
Cl Cl Cl
N N N N
H H
N N
O O
Lomustine Carmustine

Mechanism of action
Decompose in body to form an alkylating agent and a carbamoylating
agent

O C N R
Isocyanate
O
(carbamoyating
Cl R agent
N N +
N2 + HO
N H Cl
N Cl
O
H O
N
OH Alkylating
agent
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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Example - Nitrosoureas Cl

X Y X Y
Cl DNA

Alkylating Akylation Cross linking

agent

DNA DNA

O
Protein-Lys-NH2
O C N R Protein-Lys-NH
Carbamoylation
Isocyanate HN R

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

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
O
O
S O Me Busulfan
Me O S
O
O
Synthetic agent used as anticancer agent
Causes interstrand crosslinking

Mechanism
O
O OSO2Me
S O Me
Me O S
O
O
O
N N N N
HN
N -MeSO3- -MeSO3-
Guanine
Guanine
N N N N
H2N N N
DNA DNA DNA DNA
DNA

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents

Dacarbazine HN N • Prodrug activated by demethylation in liver

• Decomposes to form a methyldiazonium ion
N N CONH2 • Alkylates guanine groups
H3C N
CH3

Mechanism
AIC
HN N HN N HN N HN N
Cyt P-450 -CH2O

Liver
N N CONH2 N N CONH2 N NH CONH2 H2N CONH2
H3C N N N
H H
CH3 H O CH3 CH3 N N CH3
Methyldiazonium ion

N2 + +CH3

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1. DRUGS ACTING ON DNA
1.3 Alkylating agents
Example - Mitomycin C
O
NH2

O O
H2N OMe

Me N NH

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

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 H
O OH O CH2OCONH2
CH2OCONH2 CH2OCONH2
H2N H2N H2N
OMe OMe

Reduction -MeOH
N NH N NH Me N NH
Me Me
H
O OH OH
Mitomycin C
O H

NH2
H O
O CH2OCONH2 OH CH2 ..
H2N H2N-DNA
-H + .. H2N
Ring H2N-DNA NH DNA
opening N
Me Me N

OH NH2 NH2
OH
Alkylating agent
O
HN N

N N
Guanine
OH H2C NH O
OH NH-DNA
H2C
H2N H HN N
H2N
N
-CO2 NH DNA N N
-NH3 Me N Guanine
Me N
OH NH2
OH NH2
Crosslinked DNA
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1. DRUGS ACTING ON DNA
1.4 Metallating agents Cl NH3
Pt Cisplatin
Cl NH3

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

+ 2+
Cl NH3 H2O NH3 H2O NH3 DNA NH3
H2O DNA
Pt Pt + Pt Pt
Cl NH3 Cl NH3 H2O NH3 DNA NH3
Cisplatin

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1. DRUGS ACTING ON DNA
1.4 Metallating agents Cl NH3
Pt Cisplatin
Cl NH3

• Binds to DNA in regions rich in guanine units

• Intrastrand links rather than interstrand
• Localised unwinding of DNA double helix
• Inhibits transcription

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1. DRUGS ACTING ON DNA
1.5 Chain cutters
CONH2 NH2 R
O
H
N
H
NH2 Bleomycin
H Used vs skin cancer
O N
N N CH3 O S
H H H
O HO N
H2N O NH N
H
CH3 HN O
N CH3 HO CH3 S
H H H
HO N
OH O
H
O NH
O
OH
OH BLEOMYCIN A2 R = NHCH2CH2CH2SMe2
BLEOMYCIN B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH
OH
OH O

O NH2

• Intercalating agent
• Abstracts H from DNA to generate radicals
• Radicals react with oxygen resulting in chain cutting
• Bleomycin also inhibits repair enzymes
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1. DRUGS ACTING ON DNA
1.5 Chain cutters

O
HO
CH3 O NHCO2Me
H3C S S
I H3C S
S O H
H3C
O N O Calicheamicin g1I
O OMe HHO Antitumour agent
OH O
OMe
Enediyne
H3C O
O system
HO H
MeO N
OH H3C MeO

• Generates DNA diradical

• DNA diradical reacts with oxygen
• Results in chain cutting

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1. DRUGS ACTING ON DNA
1.5 Chain cutters
Mechanism
O H O
HO
HO O
NHCO2Me Michael HO
NHCO2Me
addition NHCO2Me
S S
S R S
R
SMe R

Nu

O O
HO HO
NHCO2Me
Cycloaromatisation NHCO2Me
H

S DNA . DNA . S
(Diradical)
R R
O2 H

Oxidative
cleavage

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 1. DRUGS ACTING ON DNA
1.6 Chain terminators

O
O CH3
Azidothymidine (AZT) HN
CH3
(Zidovudine;Retrovir) HN
O N
O O O
O N
Enzymes HO P O P O P O O
HO O in vivo
OH OH OH

N3
N3
Chain terminating
group
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 a chain terminator
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1. DRUGS ACTING ON DNA
1.6 Chain terminators

O
N N
HN N
AcO
N N N NH2
H2N N

Chain Chain
O OAc terminating
HO terminating
group group
Aciclovir Famciclovir
(Zovirax) (Famvir)

•Prodrugs used as antiviral agents

• Same mechanisms of action as AZT
• Used vs herpes simplex and shingles

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1. DRUGS ACTING ON DNA
1.6 Chain terminators
a) Normal replication

C C
C C
A A
A A
G P P G
C G P C G OH
3'
T A OH T A
3'
A T A T

DNA Growing Growing

DNA
template chain chain
template

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1. DRUGS ACTING ON DNA
1.6 Chain terminators
b) Chain termination

C C
C C
A A
A A
P P
G G Chain termination
P
C Drug C Drug H
3'
T A OH T A
3'
A T A T

DNA Growing Growing

DNA
template chain chain
template

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1. DRUGS ACTING ON DNA
1.7 Control of gene transcription

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 particular base pairs
• Capable of inhibiting transcription
• Designed to bind to regulatory element of a gene

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1. DRUGS ACTING ON DNA
3' 5'

Me O

N O
N
Py A T
H N
O H
Im N Me
N
Me N
H C G
N
Py O
H N
A T
H
N
H Hp
O O N
Me
Me O T A H
N Hp N
H O

N H
G C Py
O N
N Me
H
Im T A N O
N
Me

Py
Me H H N
H
N N N Me
Me
O
O © Oxford University Press, 2013
2. DRUGS ACTING ON rRNA
Antibiotics HN
HO
NH2
HO N
H O H OH
Me Me O
CHO NH
HO H O HO
Me H2N
O2N Me H NH
CH2OH Me OH O OH O
O NHMe
OH OH Me
HN H
Me OH
Me NH OH
C O
O CHCl2 O

Me OH
Chloramphenicol Streptomycin
O
(vs typhoid)
O OH
O
O
Me Me Me

OH O OH O O OH OH
OH Rifamycins NMe2
Me OH Me
NH2 Me
Me Me HO O
O O
OH
Me H
HO O O OMe
Cl NMe2
Me
Me
Chlortetracycline O
OH
(Aureomycin) Me
Erythromycin

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3. DRUGS ACTING ON mRNA
Antisense Therapy

Antisense
molecule Protein synthesis
m-RNA

Antisense
molecule
A G U C U A C G U U

G U A A U C A G A U G C A A A A G U
m-RNA

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3. DRUGS ACTING ON mRNA
Antisense Therapy

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 effects

Disadvantages

• ‘Exposed’ sections of mRNA must be targeted

• Instability and polarity of oligonucleotides (pharmacokinetics)
• Short lifetime of oligonucleotides and poor absorption across cell
membranes

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3. DRUGS ACTING ON mRNA
Micro-RNA (miRNA)
• Short segments of double stranded RNA
• Recognised by enzyme complex RISC to produce single
stranded RNA (siRNA) in the form of a guide strand
• Guide strand remains bound to RISC and also binds to a
complementary region of mRNA
• mRNA is then cleaved by the enzyme complex

miRNA

Duplex Passenger strand Guide mRNA

miRNA strand

m-RNA RISC
RISC RISC RISC

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3. DRUGS ACTING ON mRNA
Micro-RNA (miRNA)
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

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

© Oxford University Press, 2013