Drugs targeting DNA and RNA

Objectives: A number of drugs target DNA and RNA. At the end of the lecture, the student will be aware of the classes of low-molecular weight drugs that target DNA and RNA, including specific examples. In addition, knowledge of the forces important for the binding strength and specificity of those drugs will be presented.

Small molecules vs. oligonucleotides as drugs

Targeting DNA or RNA

i) Alter regulation of replication, transcription or translation ii) Kill cells, not alter regulation General problems i) Poor tissue specificity, leading to side effects and high toxicity ii) Mutagenic, teratogenic and carcinogenic properties

Important aspects of DNA and RNA structure

Watson-Crick base pairs Minor and Major Grooves Phosphodiester backbone

Conformational flexibility

Watson-Crick base pairs

DNA conformational flexibility

Structure of the GCTATAAAAGGCA 13-mer from the TATA-box binding protein crystal structure

DNA intercalators
CH3O NHSO2CH3

NH

NH2

NH2

Proflavin

Amsacrine

DNA minor groove binders

O C NH H N CH3 C NH O O

Distamycin A
NH2

N CH3

C NH O N O CH3

C NH NH

C NH NH N CH3 NH O

C
NH CH2 CH2 NH2+ NH2

Netropsin

C
N CH3 NH CH2 CH2 NH2+ NH2

Structure of Distamycin A bound to DNA

Combine intercalation with minor groove binding

Sar Pro D-Val Thr O C N Me-Val O Pro D-Val Thr C Sar Me-Val O

O NH2

O CH3 CH3

Actinomycin D (Dactinomycin)

Alkylating Agents
i) Wide variety of alkylations of DNA/RNA possible N7 of Gua or Ade (also N2 and N3 atoms) Both SN1 and SN2 mechanisms ii) Many alkylating agents are mutagenic and/or carcinogenic iii) Also react with other biomolecules iv) Generally block synthesis of DNA v) Both monofunctional and bifunctional alkylating agents are known. Some bifunctional agents can crosslink DNA strands.

SN1 and SN2 mechanisms

R+ + X[X...R...Y] YRY + XRY + XSN1 SN2

RX RX + Y

Metabolic activation of Benzo(a)pyrene leading the alkylation of DNA

cyt P450 NADPH O2

O Benzo(a)pyrene Epoxide Hydroxylase H2O cyt P450 NADPH O2 OH OH Carcinogen DNA O N N DNA HN N OH NH OH

OH

and other adducts

OH OH

Nitrogen Mustards
Cl CH2CH2 S Cl CH2CH2 Cl CH2CH2 Cl CH2CH2 N R

Bischloroethylsulfide (sulfur mustard)

Bischloroethylamine (nitrogen mustards) R = -CH3 R = -CH2CH2Cl

3' Gua
CH3

5' Cyt N Cyt CH3 PO4Interstrand covalent linkage

Cl

CH2CH2

.. N

CH3

Cl

CH2CH2

N (+)

Cl

CH2CH2 .. R-NH2 (Guanine base) CH3 Cl CH2CH2 N CH2CH2 NH R(Gbase)

PO4

Gua 3'

5'

.. R2-NH2 (Guanine base 2) CH3 R2(Gbase) NH CH2CH2 N CH2CH2 NH R(Gbase)

Platinum containing agents

NH3 Pt NH3

G PO4G

C PO4C

NH3 Pt NH3

G PO4A

C PO4T

Intrastrand covalent linkages NH3 Pt NH3

G PO4N PO4G

C PO4N PO4C

Nucleotide analogs incorporated into DNA

NH2 N N HOCH2 O N O OH NH2 N O HOCH2 N O F NH2 N O

O HOCH2

OH

OH

OH

deoxycytidine

Cytabine Arabinose cytosine AraC

Gemcitibine 2'-2'-difluorodeoxycytidine

Possible mechanisms i) termination of DNA strand synthesis ii) incorporation into genome

RNA directed agents

16

G-G-C-C-A-G-A C-C-G-G-U-C-U

46

G-A-G-C C-U G C-U-C-G A-G G

CH2NH2 O HO HO HOCH2 HO HO O NH2 CH2NH2 O NH2 OH O O OH NH2 NH2

NH2 NH2

NH2

IC50 = 0.9 uM
OH

NH2

IC50 = 1.3 uM
N N N NH

IC50 = 10 uM

NH

O2 N

NH

Ribosome
http://www.molgen.mpg.de/~ag_ribo/ag_franceschi/

Protein/RNA complex that synthesizes proteins (translation) Some antibiotics target the ribosome
erythromycins tetracyclines aminoglycosides