DNA As Drug Targets Flashcards
(53 cards)
1
Q
Oswald Avery
Franklin
Watson Crick
A
DNA is main constituent of genes
First Xray picture of DNA
DNA Structure
2
Q
RNA
A
- Phospho linked polymer of phosphoribose glycosides
- Has the second -OH group
3
Q
Purine:
Adenine
A
Has 1 HB acceptor / 1 HB donor
small Arrow shows RIBOSE or DEoxyribose Attachment
4
Q
Guanine
(purine)
A
2 HB Donor’s /1 HB Acceptor
small Arrow shows RIBOSE or DEoxyribose Attachment
5
Q
Pyrimidine:
Cytosine
A
2 HB Acceptors / 1 HB Donor
Small arrow shows only DEOXYRIBOSE Attachment
6
Q
Thymine / Uracil
Pyrimadine
A
1 HB acceptor / 1 HB Donor
Small arrow shows only DEOXYRIBOSE Attachment
7
Q
DNA
Details
A
- NONREDUCING polyglycoside
- DOES NOT exist in equiibruim with an OPEN chain sugar
- Depurination process (from drugs / diseases)
- –> result in equilibrium
- –> DNA STRAND SCISSION
- –> result in equilibrium
8
Q
Why is RNA not a reliable storage medium?
A
- Typically for DNA, Phosphodiester bond is EXTERMELY resistant to Hydroysis
- half life ~12million years
-
RNA is 1000x faster
- due to the presence of the 2’-OH group in RNA
- poised for attack on the phosphorus of 3’ phosphodiester
- due to the presence of the 2’-OH group in RNA
9
Q
Structure of Nucleotides
A
- Nucleotides have B-configuration of the Glycosidic Bond
-
PUCKERED
- determined by what is bound to the ring
- destablizing eclipsing steric interactions of substituents on adjacent carbon atom
- = TORSION STRAIN
*
- = TORSION STRAIN
10
Q
Canonical B-Dna
A
- C2-endo sugar puckers
- HIGH anti-glycosidic angles
- 3.4Angstrom helical rise per residue
- Right Handed (10 base pairs per turn)
- <15 degree bending
11
Q
A Form DNA
A
- C3’s endo puckers
- Anti glycosidic angle
- Base pairs TWISTED
- small helix rise
- 11 bp per repeat
- Distinction between MINOR & MAJOR
- Major groove = DEEP & Narrow
- Minor grove = WIDE & SHALLOW
- Larger diameter
12
Q
Z-Form DNA
A
- LEFT HANDED HELIX
- GC-Rich sequences
- Narrower / most elongated
- Grooves are NOT well defined
-
Favored by HIGH SALT conc
- some base subs
- Needs alternating purine/pyrimidine sequence
13
Q
Classes of DNA Interactive Drugs
A
-
Reversible Binders
- reversible DNA interactions
-
Alkylators
- react COVALENTLY w/ DNA bases
-
Strand Breakers
- generate REACTIVE RADICALS that CLEAVE polynucelotide strands
14
Q
Cancer Cells
A
- Constantly need DNA & precursers
-
Selective Toxicity
- Rapid uptake of drug molecules
- repair mechanisms are too slow
- activation of proteins such as P53 in normal cells
- –> response to DNA damage
- ^dna repair enzymes
- Cell cycle arrest (time to repair)
- apoptosis
- –> response to DNA damage
15
Q
Combination Chemotherapy
A
- Compared to a SINGLE drug
- Able to fight AQUIRED resistance
- Different MOA’s –> increased effectiveness
- Covalent modifcations can be REVERSED by repair enzymes
- Inhibitors of DNA repair can be added
16
Q
Major Groove
A
Deep & Wide (24Angs)
rich in Basic Atoms
36A x 20A
- DNA ligands have high specificity to WHICH GROOVE they bind
- typically poor sequence speficity
- more specific on which groove
17
Q
Minor Groove
A
Deep and NARROW (20Angs)
lined w/ HYDROPHOBIC H-atoms of ribose
- 4A x 20A
* Small Molecules (<1000D) bind in minor groove
18
Q
3 Ways to Reversibly Bind to Duplex DNA
A
-
External Electrostatic
- Backbone = Negatively charged (due to phosphodiester groups)
- –> Charge Interactions w/ charged groups
- EX. NH3+ ——- (-)phosphodiester groups
- Groove Binder
-
Intercalation
-
Planar groups slide INBETWEEN
- VDW interactions + Pi Pi stacking
-
Planar groups slide INBETWEEN
19
Q
Cis-Platinum
(anti-neoplastic)
A
Covalent = IRREVERSIBLE
Anti-cancer
- Way that SMALL molecule can bind to DNA
- Very Stable
20
Q
3 Ways small molecules can bind to DNA
A
Covalent - Irreversible
cis-plat
Minor Groove Bider
netropsin
Intercalator
dynemyci
21
Q
Netropsin
A
Minor Groove Binder
Peptide analog Antibiotic (+/- Bacteria)
- Small molecule that binds to DNA
- 4 consecutive bases = H-bonding
- Displaces WATER
22
Q
Dynemycin
A
DNA Intercalator
Enediyne Anticancer Drug
- small molecule that binds to DNA duplex
- Planar Pi Pi Binding
23
Q
Major Groove Dna BInders
A
- Some might just BIND, –> small or NO EFFECT on structure
- C2-Repressor
- Some may cause Major Distortions
- TATA Binding Protein
- Spermine
- binds to DNA by electrostatic forces
24
Q
Methylproamine
A
Minor Groove Binder
Radioprotector / DNA STAIN
- planar but CURVED to fit in minor groove
25
***Minor*** **groove binders**
* long / planar / **crescent(bent) shaped molecules**
* **hydroPHOBIC**
* ****but w/ HB capability to form HB's w' DNA bases
* Most bind to **AT-Rich sequences (are where minor groove is NARROWER)**
* **AntiMicrobial / AntiTumor activities**
* BOTH **Reversible & Irreversable**
* ****Reversible --\> prevent access of cell proteins to DNA
* ****irreversable dmg -- \> alkylation of bases
26
**Platinum Based Anti-neoplastics**
**Structures & Types**
**Cis-platin / Carboplatin / Oxaliplatin / Phenatriplatin**
27
**Platinum Anti-neoplastics**
**MOA**
* **Covalent Binding --\> dGpG-N7 NITROGENS**
* ****form **intra-strand crosslink**
* bond to platimum **_cannot be too LABILE = Toxic_**
* nor **too strong = low activity**
* Bridges the two bases --\> DISTORTION in DNA
* inhibition of **Transcription**
* **RNA Polymerase STALLS --\> Apoptosis**
* typically carbon --\> TETRAHYDRAL
*
28
**Phenanthriplatin**
**7-40 Times MORE POTANT** than Cis-Platin
* result of better Transport & possible intercalation of drug
* Steven Lippard still develiping the drug for human cancer
29
**DNA Alkylators**
**Examples & Structures**
**Carmustine (BCNU) / Cyclophosphamide / Melphalan**
**2x -Chlorine**
30
**DNA Alkylators**
* Target DNA by **ALKYLATING the DNA Bases**
* Common: Alkylation of **GUANINE N-7** (most preferred \>N-3 of adenine)
* generates POSITIVE charge @ nitrogen
* --\> **profound hydrolytic instability of glycosidic bond**
* **--\> DEPURINation & DNA strand SCISSION**
* **Bifunctional Alkylators --\> DNA-crosslinking**
* ****Two bonds on sense / anti-sense
* Makes them _unable to be transcribed_
* _due to the COVALENT bond_
* **NONSELECTIVE = TOXIC**
31
**Order of NUCLEOPHILICITY**
of DNA sites in ALKYLATION RXNS
**N-7 of guanine \> N-3 of adenine**
\> N-7 of adenine \> N-3 of guanine \> N-1 of adenine \> N-1 of cytosine
\**N-3 of cytosine / O-6 of guanine & phosphate groups can also be alkylated*
32
**MOA of Alkylating Drugs**
* Nitrogen Nucleophilicity **CRITICAL**
* _Unsubstituated mustards = too reactive / toxic_
* **EWG** substituants (linked to the nitrogen, R group)
* --\> *LOWER nucleophlicity/reactivity*
33
**Negatives of DNA Alkalators**
* Can result in **MUTATIONS**
* **--\> lead to _secondary cancer_**
* after the remission
* **Modification** can lead to **DNA DEPURINation (abasic sites)**
* and/or **Strand scission**
* --\> trigger DNA repair
* if attack is too massive, DNA repair can not cope with it.
34
All DNA modifying agents are...
**Electrophiles**
form covalent adducts w/ DNA nuceleophilic sites (bases/phosphodiester groups)
35
**DNA Strand Scission** by Alkylating Drugs
## Footnote
**MOA**
* Positive charge on N --\> Glycoside break up
* --\> **Ribose Hemiacetal** (in EQ w/ open chain)
* --\> **Open Chain Ribose**
* **Beta-Elimination**
* ****strand scission w/ the Phosphate group
36
**DNA Supercoiling**
**Topoisomerases**
**RELIEVES POSITIVE TWISTING**
* Topoisomerase catalyzes the transition of the topological forms of DNA
* **Critical Step =** formation of **covalent-cleavable complex**
* Attack of active site TYROSINE -OH group on P-group of DNA chain
* **P-O** bond Scission
* Dna has to be **RELIGATED** to liberate the tyrosine
* \*if this step does not occur
* topo is IRREVERSIBLY INACTIVATED
****
37
**Actinomycin**
**DNA Intercalator**
**Antitumor agent**
_rhabdomyosarcoma and trophoblastic neoplasia_
* Derived from _Streptomyces_
* **Stabalizes cleavable complex of topoisomerases**
* ****Cyclic **pentapeptide** --\> aromatic **Chromophore**
* via amide bonds (numerous H-bonds)
38
**Topotecan-Resistant Topoisomerase 1**
* Intercalator comes in and SPLITS the 2 bases
* **Topo Inhibitor prevents the intercalator from releasing**
* ****--\> keeps the Nucleic acid from re-joining together
* _Disruption of Topo Catalysis_ w/ **topotecan**
* **--\>** stabilization of **DNA-Topo adduct**
* & DNA lesion
39
**Topo Inhibitors as Drugs**
* Topo inhibitors = **DNA Intercalators**
* ****But intercalation is NOT sufficient for TOPO inhibitor
* **must also STABILIZE the cleavable topo-dna complex**
* where DNA is covalently linked to **TOP-TYR residue**
* Cleavable complex _cannot be religated_
* **__**due to conformational change imposed on TOPO by inhibitor
* --\> DNA strand breaks that *CANNOT* be repaired by DNA ligase
40
**Doxorubicin**
**Daunorubicin**
**Idarubicin**
**Anthracyclin Antibiotics** (contain CHROMATIN)
**Topoisomerase Inhibitors**
* Common anticancer drugs --\>
* _Leukemia / Hodkins Lymphoma / Bladder/breast/lung cancer_
* __Limiting factor --\> ***Adverse heart effects***
* ******related to formation of **ROS (**reactive oxygen species)
* Antracyclin residue undergoes **redox processes**
* --\> generation of **-OH radical**
* --\> can cleave DNA strand
41
**Camptothecin**
**Topotecan**
**DNA Intercalaters that are ALSO TOPO-Inhibitors**
*in principle MOST DNA intercalators are CARCINOGENS*
42
**Duocarmycins**
**Minor Groove Binder**
activated by conformational change after binding to minor groove
43
**Mitomycin**
**Target DNA**
Activated by **metabolic reduction**
44
**Dacarbazine**
**Target DNA**
activated by **P450 hydroxylation**
45
**Leinamycin**
**Drug that targets DNA**
Activated **metobolically by reactions with THIOLS**
46
**Anthracyclins:**
**Rubicins / Bleomycin / Enidyns antitumor AB's**
**Hydroxyl Radical** Forming drugs
Based from **DNA-based radicals**
cause **DNA Scission / Lesions**
47
**Thymidylate Synthase Inhibitors**
**RT inhibitors**
**Modulators of Epigenic control of DNA Replication**
**Target DNA**
**Affect DNA SYNTHESIS**
48
**Antisense Drugs**
* Synthetic nuclease-reisistant oligomers of DNA
* form **stable duplexes w/ RNA**
* --\> **_inhibit TRANSLATION of any specific gene_**
* **__**in principle can be made to treat any disease resulting from gene overexpression
* by using a proper sequence of nucleobases
* **__**4 drugs have been approved by FDA
* **Etlepirsen (2016)**
* --\> treatment of _Duchenne muscular dystrophy_
* __Challenges:
* **Drug delivery** (high neg charge / MW )
* very high cost
*
49
**Antisense Nucleotides**
* Requirements for an effective antisense oligonucleotide:
* Form **Stable Duplex** w/ native DNA/RNA
* **Resist Action of Nucleases**
* ****Modifications to DNA structure:
* phosphorothiorate analog
* protection of 2'-OH group of ribose
* replacement of ribose by **morpholino residue**
* removal of negative charge
50
How platin adducts affect DNA fxn?
DNA Adduct = segment of DNA bound to cancer causing chemical
**Covalently bind to N7 nitrogens --\> Intrastrand crosslink**
crosslink --\> **INHIBIT TRANSCRIPTION**
**--\> APOPTOSIS**
51
**Mono vs BI-functional**
DNA Alkylators
* **MONO-functional** = alkylation --\> **positive charge on nitrogen**
* **profound hydrolytic instability**
* --\>**depurination --\> _DNA Strand Scission_**
* * **Bi-Functiona**l = TWO bonds on sense and anti-sense
* **Cross-links the two bonds, _makes them unable to be trascribed_**
* Due to the covalant bond
52
**Cyclophosphamide**
**DNA Alkylating Drug**
* **Has a NON-NUCLEOPHILIC NITROGEN**
* needs to be metabolicly activated in order to render the Nitrogen nucleophilic
* = **PRODRUG**
53
**Topoisomerase**
* **RELIEVE** the supercoiling of **DNA** so that replication could occur
* **Inhibiting TOPO**
* stabilizes the cleavable complex between DNA / TOP
* --\> prevent **re-ligation of the excised DNA fragments**
* = anti-cancer drug
* TOPOs cut DNA strands as part of their catalytic mechanism of relaxation of DNA superhelical state.
