3: DNA-targeted pharmacology

Question 1

Is DNA a drug target? If so, what type?

Answer 1

Yes, some drugs function by binding directly to DNA through covalent or non-covalent binding

Question 2

Effect of covalent binding on DNA

Answer 2

compounds can alkylate DNA bases and then change the make up of DNA to mess with DNA synthesis
-good for cancer cells

Question 3

effect of non-covalent binding to DNA

Answer 3

• some drugs bind to DNA grooves or intercalate between bases
• they insert themselves into the grooves between base pairs and mess up DNA synthesis
• good for targeting cancer cells

Question 4

covalent binding to DNA: how/where do compounds alkylate the DNA?

Answer 4

• alkylating agents covalently attach to DNA at the alkylation site
• alkylation site is whatever site is most assessable and available
• interrupt normal functions of enzymes involved in DNA replication (DNA polymerase)
• alkylation can cause mutuations

Question 5

What happens when DNA is alkylated?

Answer 5

cross-link is formed after 2 monoalkylations

DNA containing alkyl adducts cannot be replicated and this leads to cell death and cell cycle arrest bc they are cross-linked and cannot be unzipped

Question 6

What are some forces that contribute to non-covalent binding?

Answer 6

• van der waals
• hydrogen bonds
• electrostatic interactions
• hydration/dehydration of the binding site

Question 7

How do non-covalent drugs bind to DNA?

Answer 7

they can bind to the grooves or intercalate between bases

Question 8

Describe how distamycin works

Answer 8

• distamycin binds to the minor groove of DNA through hydrogen bonds and hydrophobic interactions
• because of the neg. charge on the sugar backbone, terminal amidine is positively charged and creates an attractive force
• distamycin binds to regions with high attractive force
• 2-amino group of guanine prevents binding to GC region

Question 9

How does doxorubicin work?

Answer 9

doxorubicin is an anthracycline antibiotic that intercalates between base pairs
- van der waals interactions are critical because of the stacking interactions between base pairs

Question 10

Describe how dynemicin A works

Answer 10

Dynemicin A intercalates and binds to the minor groove as well.
- combines an anthracycline and enediyne
- activated by light, thiols, or NAPDH
- when it binds to DNA, it cleaves one or both strands

Question 11

What are nucleotide analog drugs (nucleic acid analogs)?

Answer 11

Analogs resemble nucleotides but are chemically different (mimics nucleotides)
- substrates or inhibitors of enzymes that metabolize normal nucleic acids (they act on enzymes that do normal functions)
- affects DNA and RNA synthesis and replication accuracy
- must be converted to their active triphosphate form in order to work

Question 12

true or false: chemical modifications only occur at the base of nucleotides

Answer 12

False: chemical modifications can occur to functional groups at various parts of the nucleotide
- the effect of the drug depends on where on the nucleotide it modified

Question 13

How do viruses replicate in the body?

Answer 13

• retroviruses use reverse transcriptase to make DNA from RNA
• the DNA of the virus enters the nucleus and inserts itself into the cell’s own DNA
• the cell continues to make copies of the modified DNA
• protease helps the new virus mature
• normal human cells do not contain reverse transcriptase, which is what leads to drug selectivity of RT inhibitors

Question 14

How does zidovudine work as an antiviral?

Answer 14

Zidovudine is a reverse transcriptase INHIBITOR
- dehydroxylated version of thymidine
- azido group prevent DNA chain elongation bc 3’-hydroxyl group is substituted and replication is not possible since theres no -OH
- azido group DOESN’T block phosphorylation f the 5’-carbon to the triphosphate (allows for bioactivation)

Question 15

How does Adefovir work as an antiviral?

Answer 15

Adefovir is a reverse transcriptase INHIBITOR (chain terminator)
- the sugar ring has been opened/eliminated, preventing DNA elongation during replication bc of the missing OH group
- phosphate is replaced with phosphonate, increasing stability

Question 16

How does Remdesivir act as an antiviral?

Answer 16

Remdesivir is a prodrug (it needs to be converted from its inactive to active form)
- ring is present, phosphate present (but phosphate modified)
- 1’ cyano group

Question 17

What happens when we use anticancer agents to block DNA synthesis?

Answer 17

Blocking DNA synthesis leads to S (synthesis) phase cell cycle arrest.
Cells aren’t able to complete S phase and instead pile up in G1 phase.

Question 18

What are the four key stages of the cell cycle?

Answer 18

1. Gap 1 (G1) - duplicates organelles and cytosolic components, starts replicating centrosome.
2. synthesis (S) - DNA chromosome is replicated
3. Gap 2 (G2) - cell growth continues, enzymes and proteins are synthesized and replication of centrosomes is completed.
4. mitosis - cell division

Question 19

How does fluorouracil work as an anticancer agent?

Answer 19

Fluorouracil is a pyrimidine analog (looks just like uracil)
- uracil has undergone halogenation to add a fluorine group
- this can mess up DNA synthesis and RNA synthesis

Question 20

Match the conversion of fluorouracil to the outcome:
a) conversion to FdUMP 1) causes RNA damage
b) conversion to FdUTP 2) causes DNA damage
c) conversion to FUTP 3) inhibits thymidylate synthase

Answer 20

a - 3
b - 2
c - 1

Question 20

How does Cytarabine work as an anticancer agent?

Answer 20

Cytarabine is an isomer of cytidine from hydroxylation/dehydroxylation
- converted to the triphosphate, incorporated into DNA, and causes DNA damage

Question 21

How does Gemcitabine work as an anticancer agent?

Answer 21

Gemcitabine is an analog of cytidine formed by halogenation (replacement of OH with fluorine)
- converted to the triphosphate, incorporated into DNA, causes DNA damage
- the population of cells increase in G1 bc they cannot go into S phase bc gemcitabine causes S-phase arrest