Topic 5 Nucleic Acids as Drug

Targets
Nucleic Acids-Chapter 7 Patrick
and Corey 187, 188, 193-194,
198-199
1. DEOXYRIBONUCLEIC ACID (DNA)
1.2 Secondary Structure - Double Helix

Thymine Adenine
o
10A
O P
Me O H2N N O
G C O O
AT 3'
O P N
TA
T A O NH N
G C O
Major G C N N 5'
groove O O
TA 5' O
T A O
T A
NH2 O O P
Minor AT N O
groove 3'
AT
T A
o
34A
O
C G O P N O
G C
O N HN 3'
TA O N N
T A
G C
O 5'
5' O H2N O
GC
GC O
T A O
A T 3' Cytosine Guanine P
C G O O
TA O P O
T A O

DNA DOUBLE HELIX Base Pairing

G-C base pairing involves 3 H-bonds
A-T base pairing involves 2 H-bonds
1. DEOXYRIBONUCLEIC ACID (DNA)
1.3 Tertiary Structure

• Double helix coils into a 3D shape - supercoiling

• Double helix has to unravel during replication

• Unravelling leads to strain

• Relieved by enzyme catalysed cutting and repair of DNA

chain

• Important to the activity of the quinolone and fluoroquinolone

antibacterial agents which act as enzyme inhibitors
2. RIBONUCLEIC ACID (RNA)
2.1 Primary structure

• Similar to DNA with the following exceptions

• Ribose is used instead of deoxyribose
• Uracil is used rather than thymine
O
HOCH2 O OH

H H HN
H H

OH OH O N
H
Ribose Uracil
2. RIBONUCLEIC ACID (RNA)
2.2 Secondary structure

• Single stranded

• Some regions of helical secondary structure exist due to base

pairing within the same strand (see t-RNA)

• Adenine pairs to uracil; guanine pairs to cytosine

2. RIBONUCLEIC ACID (RNA)
2.3 Tertiary structure

• Three types of RNA are involved in protein synthesis:

• Messenger RNA (mRNA)

Relays the code for a protein from DNA to the protein
production site

• Transfer RNA (tRNA)

The adapter unit linking the triplet code on mRNA to specific
amino acids

• Ribosomal RNA (rRNA)

Present in ribosomes (the production site for protein synthesis).
Important both structurally and catalytically
2. RIBONUCLEIC ACID (RNA)
3'p
2.3 Tertiary structure end

A AMINO
5'p
ACID
C
end
C
Base Pairing
A
G C
mI Methylinosine G C
G U
I Inosine C G
UH2 Dihydrouridine G C
T Ribothymidine U U
G
A U G C U UA
Ps Pseudouridine G
C G C G mGU
UH A G G C C
mG Methylguanosine C 2 G Amino
U C C G G acid
m2G Dimethylguanosine G A G C G C m2G C T PsC
G UH2 C G A UH2
G
U A t-RNA
C G
C G
C G Yeast alanine-tRNA AC G
U Ps
Anticodon
U mI binding region
I C for m-RNA
G ANTICODON

Anticodon - the 3 bases are specific for the attached amino acid
- base pair to the complementary triplet code on m-
RNA (the codon)
 2. RIBONUCLEIC ACID (RNA)
2.5 Translation - protein synthesis
PEPTIDE
NH NH2

R C H R' C H
O C O C
HO O HO O
H
H
H H H OH H H H OH

O O O P O PEPTIDE
Adenine O P O Adenine
O O NH
t RNA t RNA R C H
O C
Transfer of NH
growing peptide
chain to next R' C H
amino acid HO OH O C
H
H H H HO O
OH H
O O P O H H H
Adenine OH
O O O P O
Adenine
t RNA O
t RNA
2. RIBONUCLEIC ACID (RNA)
2.5 Translation - protein synthesis mRNA
Overview
Ribosome

Amino acid
DNA
tRNA

mRNA

Translation

Transcription

Nucleus

Protein
Contents

Part 2: Section 7.3 (Drugs acting on DNA)

3. Drugs acting on DNA

3.1. Intercalating agents
- Topoisomerase II
- Example – Proflavine
3.2. Alkylating agents
3.3. Chain cutters
3. DRUGS ACTING ON DNA
3.1 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 inhibits topoisomerase II- see Doxorubicin, p.198
Corey.
3. DRUGS ACTING ON DNA
Topoisomerase II
• Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr

5' 3'
3' 5'
DNA

• Tyrosine residues in the enzyme are involved in the chain breaking

process
• The residues form covalent bonds to DNA
3. DRUGS ACTING ON DNA
Topoisomerase II
• Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr
5' 3'
3' 5'
DNA
Tyr
Topo II

• Tyrosine residues in the enzyme are involved in the chain breaking

process
• The residues form covalent bonds to DNA
• The enzyme pulls the chains apart to create a gap
3. DRUGS ACTING ON DNA
Topoisomerase II
• Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr

DNA
Tyr
Topo II

• Tyrosine residues in the enzyme are involved in the chain breaking

process
• The residues form covalent bonds to DNA
• The enzyme pulls the chains apart to create a gap
• The intact strand of DNA is passed through the gap
3. DRUGS ACTING ON DNA
Topoisomerase II
• Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr
5' 3'
3' 5'

Tyr
Topo II

• Tyrosine residues in the enzyme are involved in the chain breaking

process
• The residues form covalent bonds to DNA
• The enzyme pulls the chains apart to create a gap
• The intact strand of DNA is passed through the gap
• The break is resealed
3. DRUGS ACTING ON DNA
Topoisomerase II
• Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr
5' 3'
3' 5'

• Tyrosine residues in the enzyme are involved in the chain breaking

process
• The residues form covalent bonds to DNA
• The enzyme pulls the chains apart to create a gap
• The intact strand of DNA is passed through the gap
• The break is resealed
3. DRUGS ACTING ON DNA
Topoisomerase II
Mechanism of chain cutting

5' Base
O
H H
5' Base
O H H
H H TopoII HO H
H H TopoII
HO Tyr
O Tyr
O H
O P O P
O O Base O O Base
O O
H H H H
H H H H
O H O H

3' 3'
3. DRUGS ACTING ON DNA
3.1 Intercalating agents
Examples
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
O
N NH2 H
Me
H H
H
O O
Planar rings HO
H
CH3 CH3 NH3

Dactinomycin Doxorubicin (Adriamycin)

Extra binding to sugar
Extra binding to sugar phosphate phosphate backbone by NH3
backbone by cyclic peptide
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
• Contain highly electrophilic groups
• Form covalent bonds to nucleophilic groups in DNA
(e.g. 7-N of guanine)
• Prevent replication and transcription
• Useful anti-tumour agents
• Toxic side effects (e.g. alkylation of proteins)

Example
Mechlorethamine (nitrogen mustard)
Cl

CH3 N

Cl
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Cross linking

X X
X X

Nu Nu
Nu
Nu Nu Nu
Nu
Nu

Intrastrand cross linking Interstrand cross linking

 3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Mechanism of action
DNA DNA

H G = Guanine
O N NH 2
H
Cl O N NH 2
N
N
+ N
CH3 N CH3 N N N
CH3 N N
G
Cl Cl
Aziridine ion Cl
Mechlorethamine N
N NH 2 N NH 2
N
NH
NH N
N G
O O

DNA DNA

H
O N NH 2
H
O N NH 2
N

N
N N
N
Crosslinked DNA
CH3 N N
+

N N N NH 2
N N NH 2
NH
NH CH3 N
N
O
O
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Mechlorethamine analogues

Cl
Cl O
N
N HN

O N Cl
Cl
H
Aromatic ring - e withdrawing effect Uracil mustard
N is less nucleophilic Used vs leukemia
Less reactive alkylating agent Attached to a nucleic acid building
Selective for stronger nucleophiles block
(e.g. guanine) Concentrated in fast growing cells
(tumours)
Some selectivity
3. DRUGS ACTING ON DNA
3.2 Alkylating agents

Cisplatin Mitomycin C
O CH2OCONH2
Cl NH3
H2N OMe
Pt
Cl NH3 N NH
Me
O

Binds to DNA in regions rich in guanine Converted to alkylating agent in the

units body
Intrastrand links rather than interstrand
Inhibits transcription
 H
O OH O CH2OCONH 2
CH2OCONH2 CH2OCONH2
H2N OMe H2N OMe H2N

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

O H
C NH2
H O
O CH2OCONH 2 OH CH2
-H + H2N H2N H2 N-DNA
Ring H2 N-DNA NH-DNA
opening N
Me Me N
NH2 NH2
OH OH
Alkylating agent
O Guanine

HN N

N N
NH
NH-DNA OH
OH CH2 O Guanine
CH2
H 2N N
H2N HN
NH
NH-DNA N
-CO2 N
Me N
-NH3 N
Me NH2
NH2 OH
OH
Crosslinked DNA
3. DRUGS ACTING ON DNA
3.3 Chain cutters

CONH2 NH2

N
NH2 O Bleomycin
H
O
N R
Used vs skin cancer
N N CH3 O
H
O HO N
H2N O NH N S

CH3 HN O
N CH3 HO CH3 S
H

HO O N
OH
O N
O H BLEOMYCIN A2 R = NHCH2CH2CH2SMe2
OH
BLEOMYCIN B2 R = NHCH2CH2CH2CH2NHC(NH2)=NH
OH

OH
O
OH

O NH2

• Abstracts H from DNA to generate radicals

• Radicals react with oxygen resulting in chain cutting
• Bleomycin also inhibits repair enzymes
Contents

Part 3: Section 7.3 (Drugs acting on RNA)

4. Drugs Acting On rRNA

- Antibiotics
5. Drugs Acting On mRNA
- Antisense Therapy
- siRNA
6. Drugs related to nucleic acid building blocks
- Examples: Antiviral agents
- Examples
4. DRUGS ACTING ON rRNA
Antibiotics NH
H HN
NH

C NH2
H2N C NH
H
OH H
H HO
OH OH Me
H H OH
HO H Me N
O H
O2N H O
CH2OH O CHO
O R H
HN H Me H

C
Me OH Me OH Streptomycin
O H O
O CHCl2 OH
HO O
O Me Me H CH2OH
H H
Chloramphenicol H MeHN
H
(vs typhoid) H
H H
H Me
OMe O Me H OH OH H
C
CH3 NMe2
O
O HO
Rifamycins H3C CH3
HO O
OH O OH O O O CH3
HO
OH

NH2 H3C CH3

O CH3
O
O
OH CH3
HO Me H
Cl NMe2 O OH
Me OMe
Chlortetracycline
Erythromycin
(Aureomycin)
5. DRUGS ACTING ON mRNA
Antisense RNA Therapy
5. 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
5. DRUGS ACTING ON or through RNA
Small Interfering RNA-siRNA “Dicer” enzyme

Targets specific RNA

sequences for destruction

si RNA-
ds, ~21BP, 2
base overhang +
phosphate
5. DRUGS ACTING ON or through RNA
Small Interfering RNA-siRNA

http://www.rnaiweb.com/RNAi/RNAi_Web_Resources/RNAi_Therapy___Clinical_Trials/
 6. Drugs related to nucleic acid building blocks
Examples: Antiviral agents
O
O CH3
Azidothymidine (AZT) HN
CH3
(Zidovudine;Retrovir) HN
O N
O N O O O
HO P O P O P O O
HO O OH OH OH

N3
N3
Chain terminating
group
•Enzyme inhibitor
•AZT is phosphorylated to a triphosphate in the body
•Triphosphate has two mechanisms of action
- inhibits a viral enzyme (reverse transcriptase)
- added to growing DNA chain and acts as chain terminator
6. Drugs related to nucleic acid building blocks
Examples: Antiviral agents
O
N N N
HN
AcO N
H2 N N N N NH2

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

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