DNA-drug interactions

Nucleic Acid Chemistry

Third term 2022-2023

Randy Bryant

Department of Biochemistry and Molecular Biology

Johns Hopkins Bloomberg School of Public Health

Minor groove binding drugs
 Major and minor grooves

minor groove outer edges

5.7 Å

major groove
11.7 Å

inner edges

B-form DNA has a major groove and a minor groove

 Minor groove binding drugs

distamycin netropsin

berenil lexitropsin
 Distamycin

Pyrrole-amidine antibiotic isolated

from Streptomyces distallicus

Flexible crescent shaped molecule

pyrrole-amidine Binds to the minor groove of DNA

group

Has antibacterial and antiviral activity

Distamycin-DNA complex

Binds to the minor groove of DNA

Requires 5-6 contiguous A-T base

pairs for optimum binding

Stabilized by electrostatic, hydrogen

bonding, and hydrophobic interactions

Inhibits DNA and RNA synthesis

DNA intercalating drugs
 DNA intercalation

Planar aromatic ring systems can intercalate between adjacent

base pairs in DNA
Results in a separation of the base pairs and a partial unwinding
of the DNA
 Intercalation by ethidium bromide

ethidium bromide ethidium bromide-dsDNA complex

Intercalation of ethidium bromide results in a partial unwinding

of the DNA
 Anthracycline antibiotics

doxorubicin daunorubicin

epirubicin idarubicin
 Doxorubicin

Also known as adriamycin

Anthracycline antibiotic isolated from

Streptomyces peucetius
anthracycline ring

Used to treat leukemia and a wide

daunosamine range of solid tumors

WHO List of Essential Medicines

for basic health care systems
 Doxorubicin-DNA complex

Planar anthracycline ring intercalates

between adjacent base pairs in DNA

Daunosamine group binds in DNA

minor groove

Inhibits DNA and RNA synthesis

Also creates strand breaks by inhibiting

topoisomerase reactions
Yang et. al. Biochem. Biophys. Acta 1845, 84 (2013)
 Dactinomycin

Also known as actinomycin D

pentapeptides

Polypeptide antibiotic isolated

from Streptomyces antibioticus

Used to treat several types of

cancer

phenoxazone ring
WHO List of Essential Medicines
for basic health care systems
 Dactinomycin-DNA complex

Planar phenoxazone ring intercalates

between base pairs in DNA

Pentapeptide side chains interact with

the DNA minor groove

Inhibits DNA and RNA synthesis

Wang et. al. Plos One 7. e47101 (2012)

Monofunctional alkylating drugs
 Chloroethylating nitrosoureas

carmustine lomustine

nimustine semustine
 Carmustine

Also known as bis-chloroethylnitrosurea

(BCNU)

Synthetic N-nitroso compound

N-nitroso group Breaks down in aqueous solution to

form chloroethyl cations which can
alkylate DNA

Used to treat several types of brain

cancer
 Carmustine reaction mechanism

carmustine

N7

+ 2-chloroethyl
cation
lysine

guanine

protein
carbamylation
7-chloroethylguanine
 Carmustine-mediated DNA crosslinking reaction

7 7 +

guanine 7-chloroethylguanine

- Cl-

+ 7 7
+

carmustine DNA crosslink

(inter-strand)

1,2-bis-[7-guanyl]ethane
 Temozolomide

Synthetic triazene compound

Breaks down in aqueous solution

to form methyldiazonium ions
which can methylate DNA
triazene group

Used to treat malignant and intractable

brain tumors
 Temozolomide reaction mechanism

temozolomide

methyldiazonium
ion

mispair with thymine ← O6-methylguanine N7-methylguanine → deglycosylation /strand breakage

or FAPy formation

Babu et. al. Cryst. Eng. Comm. 15, 666 (2013)

Bifunctional alkylating drugs
 Busulfan

methylsulfonate
Synthetic alkyl sulfonate compound
group

Bifunctional DNA crosslinking agent

Used to treat various types of leukemia

and other blood disorders
methylsulfonate
group
 Busulfan reaction mechanism

DNA-Nu -
DNA-Nu
Nu-DNA methyl
sulfonate
busulfan mono-adduct

Nu-DNA
-
DNA-Nu

DNA crosslink methyl

sulfonate
 Nitrogen mustards

CH3

mechlorethamine chlorambucil

melphalan cyclophosphamide
 Nitrogen mustard reaction mechanism

- Cl-

aziridine ring mono-adduct

nitrogen mustard
- Cl-

aziridine ring

..
DNA crosslink

Intramolecular displacement of chloride ion yields three-membered

aziridine rings
Subsequent reaction with N7-guanine yields DNA crosslinks
 Nitrogen mustard-mediated DNA crosslinks

7 7

N7-alkylguanine residues at the DNA crosslink can undergo

deglycosylation to form abasic sites

Can lead to DNA strand breaks

 Chlorambucil

Synthetic nitrogen mustard compound

Bifunctional DNA crosslinking agent

nitrogen mustard
group Used to treat various types of
leukemia and lymphomas

WHO List of Essential Medicines

for basic health care systems
 Thiotepa

aziridine ring
Synthetic aziridine compound

Bifunctional DNA crosslinking agent

aziridine ring Used to treat several types of cancer

(breast, ovarian, and bladder)
aziridine ring
 Thiotepa reaction mechanism

Pathway 1

thiotepa mono-adduct DNA crosslink

Pathway 2

aziridine mono-adduct
thiotepa

Torabifard and Fattahi, Struct. Chem. 24, 1 (2013)

 Mitomycin C

Aziridine antibiotic from Streptomyces

caespitonis

aziridine ring
Bifunctional DNA crosslinking agent

Enzymatic reduction initiates alkylation

activity

Broad spectrum activity against solid

tumors
 Mitomycin C – DNA complex

Mitomycin C binds in the minor

groove of DNA

Reacts with the N2-amino groups

of guanine residues

Results in the formation of DNA

crosslinks

PDB 199D
 Mitomycin C reaction mechanism

H-
H H

H+

- CO2NH2

NQO1 = NADH quinone oxidoreductase

DNA crosslink
Colucci et. al. Org. Biomol. Chem. 6, 637 (2008)
 Mitomycin C-mediated DNA crosslinks

multiple 2
steps
2

mitomycin C DNA crosslink

Crosslinks are formed between guanine residues in

opposing DNA strands (inter-strand crosslink)
 Platinum drugs

cisplatin carboplatin

oxaliplatin satraplatin
 Cisplatin

Synthetic platinum compound

Bifunctional DNA crosslinking agent

Is used to treat different types of

cis-diamminedichloroplatinum cancer (testicular, ovarian)
(Pt+2 square planar complex)

WHO List of Essential Medicines

for basic health care systems
 Cisplatin reaction mechanism

cisplatin

Johnstone et. al. Phil. Trans. R. Soc. A 373 (2015)

Cisplatin-mediated DNA crosslinks

7 7
crosslink

cisplatin intra-strand crosslink

Johnstone et. al. Phil. Trans. R. Soc. A 373 (2015)

DNA cleaving drugs
 Enediyne antibiotics

calicheamicin esperamicin

neocarzinostatin dynemicin A
 Enediyne antibiotics

Most contain a ring with a 1,5-diyne-3-ene arrangement

of bonds

-C≡C-C=C-C≡C-
1 3 5

Structure of the enediyne antibiotic sterically stabilizes

the ring system

But chemical triggers that relax the ring can allow a

cyclization reaction to occur
 Bergmann cyclization of enediynes

2RH

radical
product
enediyne 1,4-arene diradical
arene

Bergman cyclization of enediynes results in the formation of

a 1,4-arene diradical

The diradical can then abstract hydrogens from DNA

Blackburn and Gait, Nucleic Acids in Chemistry and Biology (2006)

 Calicheamicin

Enediyne antibiotic isolated from

Micromonospora echinospora
enediyne

Binds to the minor groove of

DNA

Mediates DNA strand breakage

by abstracting a hydrogen from
C1´ deoxyribose

Has potent antitumor activity

 Calicheamicin reaction mechanism

calicheamicin
trigger brings alkynes
closer together

Bergman
thiol cyclization

hydrogen abstraction
from DNA
diradical

C1´ deoxyribose
radical

DNA strand break

Bleomycin

Glycopeptide antibiotic isolated from

Streptomyces verticillus

Generates hydroxyl radicals (·OH)

which react with DNA

Is used to treat testicular cancer,

ovarian cancer, and Hodgkins
disease

WHO List of Essential Medicines

for basic health care systems
 Bleomycin-Fe(II) complex

Goodwin et al. PNAS 105:5052-5056 (2008)

Bleomycin forms a complex with a Fe(II) ion

Bleomycin-Fe(II) complex binds to the minor groove of DNA

Bleomycin reaction mechanism

abstraction of
C4´-deoxyribose
hydrogens

DNA
strand breaks

Chen and Stubbe, Nature Reviews Cancer 5, 102 (2005)

 Psoralens

psoralen 8-methoxypsoralen

angelicin trixosalen
 8-methoxypsoralen

Also known as methoxsalen

Furocoumarin isolated from Ammi

majus

Forms photoadducts with DNA when

8-methoxypsoralen irradiated with UV-A light

Used to treat psoriasis, eczema, and

vitiligo
 8-methoxypsoralen intercalation

pyrone ring furan ring

Binds to DNA by intercalation

Forms both mono- and di-adducts with DNA when irradiated
at 320-360 nm
 8-methoxypsoralen reaction mechanism

pyrone
mono-adduct

OCH3

furan
OCH3
R mono-adduct

OCH3

thymine 8-methoxypsoralen

di-adduct
inter-strand crosslink
OCH3
8-methoxypsoralen-mediated DNA crosslinks

pyrone
mono-adduct

furan
mono-adduct

di-adduct
inter-strand
crosslink

8-methoxypsoralen
DNA crosslink 8-methoxypsoralen
DNA mono-adducts and crosslink