Download 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
Thymine
o
10A
Me
G C
AT
Major
groove
O
O
H2N
N
O
O P
O
TA
T A
G C
G C
NH
O
O
5'
TA
T A
AT
AT
T A
C G
G C
TA
T A
G C
GC
GC
T A
A T
C G
TA
T A
DNA DOUBLE HELIX
o
34A
O
P
O
O
O
P
N
O
O
5'
NH2
3'
3'
O
O
P
O
O
5'
N
O
O
O
3'
N
N
N
T A
Minor
groove
Adenine
O
N
N
HN
3'
O
P
O
O
N
N
O
Cytosine
H2N
Guanine
5'
O
O
O
P
O
O
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
H
H
OH
HN
H
H
OH
OH
Ribose
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)
•
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)
2.3 Tertiary structure
3'p
end
A
AMINO
ACID
5'p
C
end
C
Base Pairing
A
G
C
G
C
mI Methylinosine
G
U
I
Inosine
C
G
UH2 Dihydrouridine
G
C
T
Ribothymidine
U
U
A
U
U UA
G
G
C
G
Ps Pseudouridine
A G G C C
UH
C G C G mGU
G
mG Methylguanosine C 2
U C C G G
m2G Dimethylguanosine G
C
T PsC
A G C G C m2G
G UH2
C
G A UH2
G
U
A
C
G
C
G
C
G
Ps
U
U
mI
I
C
ANTICODON
G
Yeast alanine-tRNA
Anticodon
- the 3 bases are specific for the attached amino acid
- base pair to the complementary triplet code on mRNA (the codon)
Amino
acid
t-RNA
AC G
Anticodon
binding region
for m-RNA
2. RIBONUCLEIC ACID (RNA)
2.5 Translation - protein synthesis
PEPTIDE
NH2
NH
R' C H
O C
R C H
O C
HO
H
H
Adenine
HO
H
H
O
H H OH
O
O
P O
O
Adenine
O
H H OH
O
O
PEPTIDE
P O
O
NH
t RNA
t RNA
Transfer of
growing peptide
chain to next
amino acid
R C H
O C
NH
HO
H
H
Adenine
R' C H
O C
OH
H H
O
OH
O P O
O
t RNA
HO
H
H
Adenine
O
H H
O
OH
O P O
O
t RNA
2. RIBONUCLEIC ACID (RNA)
2.5 Translation - protein synthesis
Overview
mRNA
Ribosome
Amino acid
tRNA
DNA
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'
Tyr
DNA
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
Tyr
DNA
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
3
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
4
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
5'
O
H
H
Base
TopoII
H
H
H
HO
O P
O O
Base
O
H
Tyr
H
O
3'
H
H
TopoII
Tyr
O
O P
O O
Base
O
H
H
H
H
HO
H
O
H
H
H
H
H
O
3'
H
3. DRUGS ACTING ON DNA
3.1 Intercalating agents
Examples
Planar rings
N-Me-Gly
N-Me-Gly
L-Pro
N-Me-L-Val
D-Val
O
H
N-Me-L-Val
C
Me
C
C
H
H
NH
C
L-Pro
O
O
C
Me
C
C
CH2OH
OH
O
H
OMe
NH
O
OH H
C
N
O
H
O
O
H
NH2
O
CH3
O
OH
D-Val
O
O
O
Planar rings
CH3
Dactinomycin
Extra binding to sugar phosphate
backbone by cyclic peptide
HO
Me
H
NH3
H
H
H
Doxorubicin (Adriamycin)
Extra binding to sugar
phosphate backbone by NH3
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
Intrastrand cross linking
Nu
Nu
Nu
Interstrand cross linking
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Mechanism of action
DNA
DNA
O
G = Guanine
H
N
NH 2
Cl
N
CH3
N
CH3
H
N
O
N
+
N
N
N
CH3
G
Cl
NH 2
N
N
N
Cl
Cl
Aziridine ion
Mechlorethamine
N
N
NH
N
NH 2
N
G
N
DNA
O
CH3
+
N
NH
DNA
H
N
O
NH 2
NH 2
N
Crosslinked DNA
N
N
N
NH 2
O
O
H
N
N
N
N
N
N
NH 2
NH
N
O
N
N
CH3
N
N
NH 2
NH
O
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Mechlorethamine analogues
Cl
Cl
O
N
N
HN
Cl
Aromatic ring - e withdrawing effect
N is less nucleophilic
Less reactive alkylating agent
Selective for stronger nucleophiles
(e.g. guanine)
O
N
H
Cl
Uracil mustard
Used vs leukemia
Attached to a nucleic acid building
block
Concentrated in fast growing cells
(tumours)
Some selectivity
3. DRUGS ACTING ON DNA
3.2 Alkylating agents
Cisplatin
Mitomycin C
Cl
NH3
Pt
Cl
NH3
O
CH2OCONH2
H2N
OMe
N
Me
NH
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
CH2OCONH2
H2N
H2N
OMe
N
Me
NH
Reduction
H2N
OMe
N
Me
NH
N
Me
O
H
C
NH2
O
OH
CH2OCONH 2
H2N
CH2
H2 N-DNA
H2N
NH-DNA
H2 N-DNA
N
Me
NH2
OH
NH
OH
OH
H
O
CH2OCONH 2
-MeOH
O
-H +
Ring
opening
O
CH2OCONH2
N
Me
NH2
OH
Alkylating agent
O Guanine
N
HN
NH
NH-DNA
OH
CH2
CH2
H 2N
H2N
-CO2
-NH3
OH
NH
NH-DNA
OH
NH2
OH
O Guanine
N
HN
N
N
Me
N
Me
N
N
NH2
Crosslinked DNA
N
H
3. DRUGS ACTING ON DNA
3.3 Chain cutters
CONH2
NH2
NH2
N
H
N
O
N
O
H2N
O
CH3 HN
CH3
HO
H
N
O
CH3 HO
N
H
R
N
O
NH
CH3
Bleomycin
Used vs skin cancer
S
N
S
N
O
HO
O
OH
O
N
H
O
OH
OH
BLEOMYCIN A2
BLEOMYCIN B2
R = NHCH2CH2CH2SMe2
R = NHCH2CH2CH2CH2NHC(NH2)=NH
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
H2N
OH
HO H
OH
C
Me
H
O
CH2OH
O
R
O
O
Me
Chloramphenicol
(vs typhoid)
H
Me
HO
H
H
H
H
OMe
O
H
C
Me H OH
Streptomycin
O
CH2OH
H MeHN
H
Me
H
NMe2
CH3
HO
O
Rifamycins
O
OH
O
H3C
CH3
HO
OH
NH2
OH
Cl
HO
Me
H3C
CH3
O
O
CH3
O
CH3
OH
O
Me
Chlortetracycline
(Aureomycin)
O
CH3
H
NMe2
O
HO
O
O
H
OH
O
OH
OH
OH
H
OH
Me
H
H
Me
O
CHCl2
NH2
H
O
O
C
CHO
H
OH
Me
HN
H
H
H
N
Me
HN H
NH
OH H
HO
H
O2N
C
NH
NH
Erythromycin
OMe
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
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
O
Azidothymidine (AZT)
(Zidovudine;Retrovir)
O
CH3
HN
O
N
O
O
O
HO P O P O P O
HO
O
CH3
HN
OH
OH
O
N
O
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
HN
H2 N
Acyclovir
(Zovirax)
AcO
N
N
O
HO
N
N
Chain
terminating
group
N
OAc
Famciclovir
(Famvir)
Notes:
Same mechanisms of action as AZT
Used vs herpes simplex and shingles
N
N
NH2
Chain
terminating
group