Nucleotide Metabolism - Part 1 (Purine Biosynthesis)
Nucleotide Metabolism - Part 1 (Purine Biosynthesis)
Nucleotide Metabolism - Part 1 (Purine Biosynthesis)
(purine biosynthesis)
Biological significance of
nucleotide metabolism
• Nucleotides make up nucleic acids (DNA and
RNA)
• Nucleotide triphosphates are the “energy
carriers” in cells (primarily ATP)
• Many metabolic pathways are regulated by the
level of the individual nucleotides
– Example: cAMP regulation of glucose release
• Adenine nucleotides are components of many
of the coenzymes
– Examples: NAD+, NADP+, FAD, FMN, coenzyme A
Dietary nucleotides
• do not contribute energy as do carbs,
proteins and fats
• are not incorporated into RNA or DNA
unless given I.V.
• normally metabolized to individual
components (bases, sugar and phosphate)
• purines are converted to uric acid which
is then excreted
Medical significance of
nucleotide metabolism
• Anticancer agents:
• Rapidly dividing cells biosynthesize lots of
purines and pyrimidines, but other cells reuse
them. Cancer cells are rapidly dividing, so
inhibitor of nucleotide metabolism kill them
• Antiviral agents
– Zidovudine (Retrovir)
– Lamivudine (Epivir)
– Valacyclovir (Valtrex)
Structures of nucleotide
building blocks and nucleotides
6 7 4
5
N 5
1 N 3N
8
2 2 6
N 4 N N
9
3 H 1
PURINE PYRIMIDINE
Structures of nucleotide building
blocks and nucleotides
O O O
NH2 NH2
CH3
N N HN HN
N N N
N H2N N N O N O N O N
N
H H H H H
ADENINE GUANINE THYMINE URACIL CYTOSINE
RIBONUCLEOTIDE DEOXYRIBONUCLEOTIDE
N
HN
N N
Aspartate + GTP
Synthesis of adenine IMP
Ribose-P
IMP dehydrogenase
GDP NAD+
and guanine nucleotides A.S.
synthetase NADH
COO-
O
-OOC
NH N
HN
N
N N
O N
Ribose-P
N H
N
Ribose-P
xanthine monophosphate
Adenylosuccinate
XMP
glutamine + ATP
A.S.
lyase
fumarate Glutamate + AMP
+ PPi
NH2 O
N N
N HN
N H2N N N
N
Ribose-P Ribose-P
AMP GMP
Purine nucleoside diphosphates and triphosphates:
- to be incorporated into DNA and RNA, nucleoside
monophosphates (NMP’s) must be converted into
nucleoside triphosphates (NTP’s)
amidophosphoribosyl
ribose-P-pyrophosphokinase transferase
Ribose-5-P PRPP 5-P-ribosylamine
AMP + GMP
ADP + GDP
The purine salvage pathway
• Purine bases created by degradation of RNA or
DNA and intermediate of purine synthesis were
costly for the cell to make, so there are
pathways to recover these bases in the form of
nucleotides
• Two phosphoribosyl transferases are involved:
– APRT (adenine phosphoribosyl transferase) for
adenine
– HGPRT (hypoxanthine guanine phosphoribosyl
transferase) for guanine or hypoxanthine
Salvage of purines
OH
OH P O CH 2 H
O
O O
O H H adenine
H O P O P O-
OH OH PPi
O- O-
NH2
N
N
Adenine OH N N
phosphoribosyltransferase OH P O CH 2
O
(APRT) O H H
H H
OH OH
Salvage of purines
• Salvage is needed to maintain the purine pool (biosynthesis
is not completely adequate, especially in neural tissue)
• Hypoxanthine-guanine phosphoribosyltransferase
(HGPRT)
• Hypoxanthine + PRPP IMP + Ppi
• Guanine + PRPP GMP + Ppi
• Lack of HGPRT leads to Lesch-Nyhan syndrome. Lack of
enzyme leads to overproduction of purines which are
metabolized to uric acid, which damages cells
Lesch-Nyhan syndrome
• there is a defect or lack in the HGPRT
enzyme
• the rate of purine synthesis is increased
about 200X
• uric acid level rises and there is gout
• in addition there are mental aberrations
• patients will self-mutilate by biting lips
and fingers off
Lesch-Nyhan syndrome
Salvage of purine bases
Nucleotide metabolism – Part 2
(pyrimidine biosynthesis)
Synthesis of pyrimidine
ribonucleotides
• shorter pathway than for purines
• base is made first, then attached to ribose-P
(unlike purine biosynthesis)
• only 2 precursors (aspartate and glutamine,
plus HCO3-) contribute to the 6-membered ring
• requires 6 steps (instead of 11 for purine)
• the product is UMP (uridine monophosphate)
Origin of atoms in pyrimidine ring
The big picture
Step 1: synthesis of carbamoyl
phosphate
• Condensation of glutamine, bicarbonate
in the presence of ATP
• Carbamoyl phosphate synthetase exists
in 2 types: CPS-I which is a
mitochondrial enzyme and is dedicated to
the urea cycle and arginine biosynthesis)
and CPS-II, a cytosolic enzyme used here
Step 1: pyrimidine synthesis
HO P O CH2 H
O
OH
O O
H H
O
H O P O P O-
HN O- O-
OH OH
O N COO-
orotate phosphoribosyl transferase PPi
H
O
O
HN
HN
O O
O N COO-
HO P O CH2 O N
O HO P O CH2
O
OH OH
CO2
H H H H
H H H
H
OMP decarboxylase
(uses no cofactors)
OH OH OH OH
O H
O H
C N CF3
NC C C N CF3
C
N HO CH3
CH3
O
O N
O N
Ribose 3 phosphate
Ribose 3 phosphate
UTP CTP
ribonucleotide reductase
OH
Base OH
Base
OH P O CH2
O OH P O CH2
O
O H H
O H H
H H
H H
OH OH
OH H
dADP, dGDP, dUDP and dCDP are all synthesized by the same enzyme
Synthesized from nucleoside diphosphate (not mono or triphosphate) by
ribonucleotide reductase
Synthesis of dTMP
• Methylation of d-UMP via N5,N10-
methylene THF
• Reaction inhibited by 5-fluorouracil
(Efudex)
O H
H N N H
H2 N
HN
H
HN
O N H N
O-
-O P O CH 2 O O N R
H
O H
H H
H H
OH H
d-UMP
CH3 H
HN
H2 N N N H
O- O N H
HN
-O P O CH 2 O N
O H O H N R
H
H H
OH H
H
H
H2N N N H
H2N N N H
H
H
HN
HN
N
N
O CH2 N R
O N R H
H
H
O O-
X X
HN HN
S cysteine attached to
protein
O N H O N H
R R
H H
H2N N N H H2N N N H
H H
HN HN
N N
O N R O N R
O CH2
O H
X -B
on enzyme
HN CH2 XB
S HN
S
O N
H O N
R H
R
H O
H2N N N H CH3
HN
+
+ XB
HN
N O N H
-S
O N R R
H
Activation of 5-fluorouracil
F
HN
O
O
O N H
HO P O CH2
F O
HN OH
H H
O N H H H
H
OH H
5-fluorouracil
H
Glycine
H2 N N N H
H Serine
HN
N
O N R
H
H
thymidylate synthase
H
H
NADPH NADP+ H2 N N N H
H2N N N H
H
dihydrofolate reductase HN
HN N
N
O H N
O H N
H
ANTIFOLATES
OCH 3
H2 N N N H2 N N OCH 3
HN N
N OCH 3
NH2 H3 C N R NH2
Methotrexate Trimethoprim
Dihydrofolate reductase
Nucleotide metabolism – Part 3
(nucleotide degradation)
Nucleotide degradation
nucleosidase
Base + 1-P-ribose
base + ribose
NH2 OH
Degradation H2 O NH3
N N
of AMP N N
AMP deaminase
N N N
N
Ribose-P Ribose-P
H2 O
H2 O
Nucleotidase
Nucleotidase Pi
Pi
O
NH2 NH3
H2O
N
N HN
N
Adenosine deaminase
N N
N N Pi
Ribose
Ribose Ribose-1-P
Purine nucleoside
phosphorylase
O
may be reused N
HN
through
salvage pathway
N N
H
hypoxanthine
NH2
H2N OH
N N
N HN
N N N
N
Ribose Ribose
transition state
H
OH
N
HN
N
N
Ribose O
Pentostatin N
(a transition state analog) HN
Ribose
MECHANISM OF ADENOSINE DEAMINASE
PENTOSTATIN
H N H N
N N
H2 N N N O N N
Ribose-P H Ribose-P
H2 O H2O
nucleotidase nucleotidase
Pi Pi
O
Degradation of O
H
GMP and XMP N
N H N
N
H2 N N N
O N N
Pi Ribose
Ribose
PNP H
Ribose-1P Pi
PNP
Ribose-1P
O
O
H N
N H N
N
H2 N N N
H2 O NH3 N
O N
H
H H
NH2 OH
N N
N N N
N
N N H2N N N
N N
H H
H
ADENINE GUANINE
(6-AMINOPURINE) 2-AMINO-6-OXYPURINE) PURINE
OH OH OH
N N N
N N N
OH
N HO N N N
N HO N
H H H
xanthine
HYPOXANTHINE + O 2 + H 2O oxidase XANTHINE + H 2O 2
xanthine
XANTHINE + O 2 + H 20 URIC ACID + H 2O 2
oxidase
O O
H N H
N N
N
N N N
O N
O2 H202
H H
H
HYPOXANTHINE
XANTHINE
O2
H202
O O
H
H N H
N N
N
OH O
O N N N
O N
H H
H H
acidic proton
URIC ACID
GOUT
1. asymptomatic hyperuricemia
2. acute gouty arthritic attacks
3. asymptomatic intercritical period
4. tophaceous gout (characterized by the
formation of tophi in joints)
– podagra (big toe)
– cheiagra (wrist) according to Hippocrates
– gonadra (knee)
Diagnostic features
• usually affect joints in the lower extremities
( 95%)
• onset is fast and sudden
• pain is usually severe; joint may be swollen,
red and hot
• attack may be accompanied by fever,
leukocytosis and an elevated ESR
Drugs which may induce
hyperuricemia
• niacin
• thiazides and other diuretics
• low dose aspirin
• pyrazinamide
• ethambutol
• cyclosporine
• cytotoxic drugs
Non-pharmacological
approaches
• Avoid purine rich foods:
– red meat and organ meat (liver, kidneys)
– shellfish, anchovies, mackerel, herring
– meat extracts and gravies
– peas and beans, aspargus, lentils
– beer, lager, other alcoholic beverages
• Weight loss
• Control alcohol (binge drinking)
Pharmacological management of
gout
• based on the premise that the hyperuricemia is
due to both overproduction and
underexcretion of uric acid
• symptomatic relief of pain is also achieved
with analgesics (i.e. indomethacin)
• drugs used:
– analgesics (NSAIDs)
– uricosuric agents
– xanthine oxidase inhibitors
Therapy of acute gout
• treat with colchicine or NSAIDs
• avoid aspirin
• do not treat with allopurinol or
uricosuric drugs
• uric acid lowering agents should never be
started or stopped during acute attack
• pain resolution occurs within 48-72 hrs
Colchicine
CH 3O H
N
CH 3O C CH 3
O
OCH 3
O
OCH 3
COLCHICINE
O C3H7
HO2C S N
O C3H7
PROBENECID (BENEMID)
A uricosuric agent
Probenecid (Benemid)
N
N
N N
ALLOPURINOL (ZYLOPRIM)
O
allantoicase H2N COOH NH2
H2N C NH2
ALLANTOIC ACID
Rasburicase (Elitek)
A recombinant form of uric
acid oxidase. Used for initial
management of plasma uric
acid levels in pediatric
patients with leukemia,
lymphoma, and solid tumor
malignancies who are
receiving anticancer therapy
expected to result in tumor
lysis and subsequent elevation
of plasma uric acid.
Catabolism of a pyrimidine
Formation of deoxyribonucleotides
H H H
H H OH H H
O
OH OH OH OH
Base
R O CH 2
O
SH SH SH S-
H
H H
H2 O
OH OH 2+
Base Base
R O CH 2 R O CH 2
O O
S -S
H
H H
H H H
H
OH OH H
Base
R O CH 2
O
H H
H H
OH O
OH H
Reduction of the disulfide bond in
ribonucleotide reductase
• 2 proteins can perform this reductive
reaction:
– Thioredoxin (ubiquitous 12 kD monomer)
– Glutaredoxin which functions similarly to
thioredoxin. Oxidized glutredoxin is reduced
by glutathione (g-glutamylcysteinylglycine)
Regeneration of thioredoxin and ribonucleotide reductase
HYDROXYUREA (Hydrea)
• inhibits the enzyme ribonucleotide reductase
– this enzyme causes ribonucleotides to be converted to
deoxyribonucleotides
– DNA synthesis cannot occur
– cell are killed in the S phase
– drug holds other cells in the G1 phase
• primarily used to treat chronic myelogenous
leukemia H
• cancer cell develop resistance by: N OH
O N
HOCH 2
O
F
OH F
2',2'-DIFLUORODEOXYCYTIDINE
H2 N N N
N
N
OH NR
O O H B
F F
HN HN
O N O N S
S
dRP dRP
H2 N N N
Inactivation of thymidylate synthase
by 5-fluoro-2'-deoxyuridylate
N
N
OH NHR
O
HN B
F
O S
dRP
The purine nucleotide cycle for
anaplerotic replenishment of citric acid
cycle intermediates in skeletal muscle