Topic 5 Nucleic Acids as Drug Targets

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
Major
groove
Minor
groove
G C
A T
GA
TA
T
o
10A
TA
T A
T A
A T
A T
T A
C G
G C
TA
T A
G C
G C
G C
AA
TC
G
C T
C
G
TA
T A
DNA DOUBLE HELIX
o
34A
O
O
5'
O
O
5'
O
O
P
O
P
O
P
O
3'
O
O
3'
O
O
Me
Thymine Adenine
N
N
O
NH
O
NH 2
N
O
H 2N
N
O
HN
H 2N
N
N
N
N
Cytosine Guanine
Base Pairing
G-C base pairing involves 3 H-bonds
A-T base pairing involves 2 H-bonds
N
N
O
O
O
3'
O
3'
O
P
O
P
O
P
O
O
5'
O
5'
O
O
O

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
HOCH 2
H
H
OH
O OH
H
H
OH
Ribose
O
HN
O
N
H
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) t-RNA
• Adenine pairs to uracil; 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 ( tRNA)
The adapter unit linking the triplet code on mRNA to specific
amino acids
• Ribosomal RNA (rRNA ( rRNA)
Present in ribosomes (the production site for protein synthesis).
Important both structurally and catalytically

2. RIBONUCLEIC ACID (RNA)
2.3 Tertiary structure
Base Pairing
mI Methylinosine
I Inosine
UH2 Dihydrouridine
T Ribothymidine
Ps Pseudouridine
mG Methylguanosine
m2G Dimethylguanosine
G
UH 2
A
C
G
G
U
G
C
UH 2
G
A
G
C
C
G
G
C
G C
G
G U
C G
G
G C
mG U
A
C
C
A
C
C
U U
m2G C
U
C
C
C
U
U
I
G
G
G
Ps
mI
C
AMINO
ACID
Yeast alanine-tRNA
Anticodon - the 3 bases are specific for the attached amino acid
- base pair to the complementary triplet code on m-
RNA (the codon)
G
A
G
5'p
end
A
G
U C
C
UH2 A G
3'p
end
G
ANTICODON
C
C
U
C
U
A
G
G G
T
C
Ps
t-RNA
AC G
Anticodon
binding region
for m-RNA
Amino
acid

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

2. RIBONUCLEIC ACID (RNA)
2.5 Translation - protein synthesis
Overview
DNA
Transcription
Nucleus
mRNA
Protein
mRNA
Ribosome
tRNA
Amino acid
Translation

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.
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
5'
Topo II
Tyr
3' 5'
DNA
• Tyrosine residues in the enzyme are involved in the chain breaking
process
• The residues form covalent bonds to DNA
3'

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

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

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
5'
Topo II
Tyr
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
4
3'

3. DRUGS ACTING ON DNA
Topoisomerase II
Mechanism of chain cutting
O
O
5'
H
H
P
O
O
O
H
H
H
H
H
O
3'
Base
O
H
H
H
HO
Base
Tyr
TopoII
5'
O
O
H
H
HO
P
O
O
O
H
H
H
H
H
O
3'
Base
Tyr
O
H
H
H
Base
TopoII

3. DRUGS ACTING ON DNA
3.1 Intercalating agents
Examples
N-Me-L-Val
N-Me-Gly
L-Pro
O
D-Val
O
D-Val
H
C
Me
C
C
H
NH
O
H
C
Me
C
H
NH
C
O
C O O C
CH 3
N-Me-L-Val
N
O
N-Me-Gly
CH 3
Dactinomycin
NH 2
O
L-Pro
Planar rings
Extra binding to sugar phosphate
backbone by cyclic peptide
Planar rings
OMe
O
O
OH
OH
H
H
Me
HO H
NH 3
H O
OH
Doxorubicin (Adriamycin)
Doxorubicin
Extra binding to sugar
phosphate backbone by NH 3
O
H
H
O
H
CH 2OH

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)
CH 3
N
Cl
Cl

3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Cross linking
Nu
X X
Nu
Nu
Intrastrand cross linking
Nu Nu
Nu
X X
Nu
Interstrand cross linking
Nu

3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Mechanism of action
CH 3
N
Cl
Cl
Mechlorethamine
CH 3
N
+
CH 3
+
N
Aziridine ion
H
N
O NH 2
N
N
N
DNA
N
N
Cl
N
O
NH
O
N
NH 2
H
N
N
G
N
NH 2
DNA
G = Guanine
N
N
N
O
NH
NH 2
G
CH 3
O
H
N NH2 N
N
N
CH 3
N
N
DNA
O
H
N NH2 N
Cl
N
N
N
N
N
O
NH
DNA
NH 2
N
N
N
O
NH
Crosslinked DNA
NH 2

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

3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Cisplatin
Cl
Cl
Pt
NH 3
NH 3
Binds to DNA in regions rich in guanine
units
Intrastrand links rather than interstrand
Inhibits transcription
Mitomycin C
H 2N
Me
O
O
N
CH 2OCONH 2
OMe
NH
Converted to alkylating agent in the
body

H 2N
Me
Ring
opening
-CO 2
-NH 3
-H +
O
O
H 2 N
Me
H 2 N
Me
N
CH 2OCONH 2
H
O
OH
OH
OH
OMe
NH
N
CH 2OCONH 2
NH 2
Alkylating agent
N
CH 2
Reduction
NH 2
H 2N
NH-DNA
NH-DNA
Me
OH
OH
H 2N-DNA
N
CH 2OCONH 2
H 2N
Me
OMe
NH
H 2N
Me
OH
OH
-MeOH
N
OH
OH
O
O
C
CH 2
N
H 2 N
Me
H
NH 2
CH 2
NH 2
H
NH-DNA
NH
O
NH
OH
NH 2
Crosslinked DNA
HN
N
CH 2OCONH 2
H 2N-DNA
HN
N
N
NH
O Guanine
N
N
N
O Guanine
N
H

3. DRUGS ACTING ON DNA
3.3 Chain cutters
HO
H 2N
OH
CONH 2
N N
N
H
CH 3 HN
OH
O
O
O
NH 2
NH 2
O HO
O
OH
O
O
N
H
N
H
O
N
NH 2
CH 3
CH 3
OH
OH
H
N
O
HO
O
CH 3
NH N
Bleomycin
Used vs skin cancer
BLEOMYCIN A2 R = NHCH 2 CH 2 CH 2 SMe 2
BLEOMYCIN B2 R = NHCH 2 CH 2 CH 2 CH 2 NHC(NH 2 )=NH
• Abstracts H from DNA to generate radicals
• Radicals react with oxygen resulting in chain cutting
• Bleomycin also inhibits repair enzymes
S
N
S
O
R

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
O 2N
HO
O
HN
C
H
H
Chloramphenicol
(vs typhoid)
OH
Cl
HO
O
Me
CH 2OH
CHCl 2
OH
OH
H
Chlortetracycline
(Aureomycin)
O
NMe 2
O
OH
Me
Me
NH 2
O
O
OH
H
O
OH
OH
H
N
R
O
O
Me Me
H H
H
OMe O
C
Me H
Rifamycins
Me
OH
H
Me
HO
H 3C
Me
H
H
OH
O
H 3C
O
H 2N C
H
NH
O
CHO
Me
OH
H
HO O
CH2OH H MeHN
H
CH 3
HO
O
OH
H
CH 3
O
CH 3
Erythromycin
H
NH
H
O
H
HO
O
CH 3
O
HN C
OH H
H HO
H
H
Me
H
NH
OH
NH 2
Streptomycin
NMe 2
O
O
OMe
CH 3
CH 3
OH

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 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
Targets specific RNA
sequences for destruction
si RNAds,
~21BP, 2
base overhang +
phosphate
“Dicer” enzyme

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
Azidothymidine (AZT)
(Zidovudine;Retrovir) HN
HO
O
N 3
O
O
N
CH 3
HO
Chain terminating
group
•Enzyme Enzyme inhibitor
•AZT AZT is phosphorylated to a triphosphate in the body
•Triphosphate Triphosphate has two mechanisms of action
- inhibits a viral enzyme (reverse transcriptase)
- added to growing DNA chain and acts as chain terminator
O
P
OH
O
O
P
OH
O
O
P
OH
O
O
HN
N 3
O
O
N
CH 3

6. Drugs related to nucleic acid building blocks
Examples: Antiviral agents
H 2N
HO
HN
Acyclovir
(Zovirax)
O
N
O
N
N
Chain
terminating
group
Notes: Notes
Same mechanisms of action as AZT
Used vs herpes simplex and shingles
AcO
OAc
N
Famciclovir
(Famvir)
N
N N NH2 Chain
terminating
group