Synthetic Antibacterial Agents

PHRM 412
 Antibacterial Agents
• Antibiotics– natural substances produced by
microorganisms: penicillins, tetracyclines.
• Semi-synthetic antibiotics– chemically
modified natural products: amoxicillin,
doxycycline.
• Synthetic antibacterial agents– chemically
synthesized, unrelated to natural substances:
sulfisoxazole, ciprofloxacin.
 Synthetic Antibacterial Agents
• Synthetic antibacterial compounds are divided
into two major classes: topical agents and
systemic agents.
• The topical agents are termed disinfectants,
antiseptics, and preservatives, depending on
how they are used.
 Systemic agents
Some chemical classes of synthetic
antibacterial agents include-
• Sulfonamides
• Quinolones
• Certain nitro-heterocyclic compounds,
(e.g. the nitrofurans and metronidazole)
 UT antiinfectives
• Nitrofurantoin (a nitrofuran), nalidixic acid (a
quinolone) and methenamine
• Failed to achieve plasma or tissue
concentration for treating systemic infections
• Concentrated in the urine where they can
eradicate urinary tract infections (UTI)
Synthetic Antibacterial Agents

QUINOLONES
 Quinolones
• The first quinolone to be marketed (in 1965)
was nalidixic acid.
• The quinolone antimicrobials possess
common an N-1-alkylated 3-carboxypyrid-4-
one ring fused to another aromatic ring, which
itself carries other substituents.

Nalidixic acid
 Quinolones
• Nalidixic acid and cinoxacin are classified as
first -generation quinolones
• They are considered to be minor urinary tract
disinfectants
• Thus, the quinolones were of little clinical
significance

Cinoxacin
 Quinolones
• Addition of a fluoro group to the 6-position of
the basic nucleus greatly increased the
biological activity.
• Brought to the market in 1986, norfloxacin,
the first of the second-generation quinolone.

Norfloxacin- R: ethyl X: CH
 Quinolones
• Following its introduction, intense
competition ensued, more than a thousand
second-, third-, and fourth generation
analogues have now been made.
• More recent quinolones also are referred to
as the fluoroquinolones
• Ciprofloxacin and levofloxacin dominate the
worldwide fluoroquinolone market
 Mechanism of action*
• The quinolones are rapidly bactericidal, largely
as a consequence of inhibit ion of DNA gyrase
and topoisomerase IV, key bacterial enzymes
that dictate the conformation of DNA.
• Topoisomerase IV seems to be more
important to some Gram-positive organisms
and DNA gyrase to some Gram-negative
organisms.
 Mechanism of action
• Humans shape their DNA with a
topoisomerase II, an analogous enzyme that
does not bind quinolones at normally
achievable doses, so the quinolones of
commerce do not kill host cells.
 Mechanism of action
• The Escherichia coli chromosome is a single,
circular molecule of approximately 1 mm in
length, whereas the cell is only 1 to 3 m long.
• Thus, the DNA molecule must be dramatically
compacted in a conformationally stable way
so that it can fit.
 Mechanism of action
• Using the energy generated by adenosine
triphosphate (ATP) hydrolysis, the molecule is
progressively wound about itself in a positive
super coil.
• It also must be partially unwound so that the
cell has access to the genetic information that
it contains.
 Mechanism of action
• DNA gyrase (topoisomerase II) is an enzyme
responsible for introducing negative super
coils into circular duplex DNA.
• Negative super coiling relieve the torsional
stress of helical DNA, facilitates unwinding,
and thereby, allows transcription and
replication to occur.
 Mechanism of action
• DNA topoisomerase IV decatenates (unties)
enchained daughter DNA molecules produced
through replication of circular DNA.
• Topoisomerase IV's second function in the cell
is to relax positive super coils. It shares this
role with DNA gyrase, which is also able to
relax positive super coils.
 Structure–activity relationship

4
1

• The essential pharmacophore for the activity

of quinolones is the carboxy-4-pyridone
nucleus
 Structure–activity relationship
• Apparently, the carboxylic acid and the ketone
are involved in binding to the DNA/DNA-
gyrase enzyme system.
• Reduction of the 2,3-double bond or the 4-
keto group inactivates the molecule, and
substitution at C-2 interferes with enzyme–
substrate complexation.
 Structure–activity relationship
• Fluoro substitution at the C-6 position greatly
improves antimicrobial activity by increasing
the lipophilicity of the molecule, which in turn
improves the drugs penetration through the
bacterial cell wall.
• Additionally, C-6 fluoro increases the DNA
gyrase inhibitory action.
 Structure–activity relationship
• An additional fluoro group at C-8 further
improves drug absorption and half- life but
also may increase drug-induced
photosensitivity.
 Structure–activity relationship
• Heterocyclic substitution at C-7 improves the
spectrum of activity especially against Gram-
negative organisms.
• The piperazinyl (as in ciprofloxacin) and
pyrrolidinyl (as in moxifloxacin) represent the
most significant antimicrobial improvement .

Ciprofloxacin R: Cylopropyl; X: CH Moxifloxacin

 Structure–activity relationship
• Unfortunately, the piperazinyl group at C-7
also increases binding to central nervous
system (CNS) γ-aminobutyric acid (GABA)
receptors, which accounts for CNS side
effects.
• Alkyl substitution on the piperazine
(lomefloxacin and ofloxacin) is reported to
decrease binding to GABA, as does the
addition of bulky groups at the N-1 position
(sparfloxacin).
 Structure–activity relationship

Lomefloxacin (phototoxicity) Ofloxacin

Sparfloxacin
 Structure–activity relationship
• The cyclopropyl substitution (Moxifloxacin,
Sparfloxacin, Gatifloxacin) at N-1 appears to
broaden activity of the quinolones to include
activity against atypical bacteria, including
Mycoplasma, Chlamydia, and Legionella
species.

Moxifloxacin Sparfloxacin
 Structure–activity relationship
• The introduction of a third ring to the nucleus
of the quinolones gives rise to ofloxacin.
• Additionally, ofloxaxin has an asymmetric
carbon at the C-3' position.

Ofloxacin
 Structure–activity relationship
• The S- (–) -isomer (levofloxacin) is twice as
active as ofloxacin and 8- to 128-fold more
potent than the R-(+)-isomer resulting from
increased binding to the DNA-gyrase.
 Structure–activity relationship
• Several of the quinolones produce mild to
severe photosensitivity. A C-8 halogen
appears to produce the highest incidence of
photosensitivity via singlet oxygen and radical
induction.
• Lomefloxacin has been reported to have the
highest potential for producing phototoxicity.
 Structure–activity relationship
• Substitution of a methoxy group at C-8 has
been reported to reduce the photosensitivi ty
(gatifloxacin).

Gatifloxacin
 Structure–activity relationship
• A chemical incompatibility common to all the
quinolones involves the ability of these drugs
to chelate polyvalent metal ions (Ca2+, Mg2+,
Zn2+, Fe2+, and Al3+), resulting in decreased
solubility and reduced drug absorption.
 Structure–activity relationship
• Chelation occurs between the metal and the
3-carboxylic acid and 4-keto groups. Agents
containing polyvalent metals should be
administered at least 4 hours before or 2
hours after the quinolones.

Chelation of quinolones
 Resistance
• Bacterial DNA gyrase is a tetrameric enzyme
consisting of two A and two B subunits,
encoded by the gyrA and gyrB genes.
• Bacterial strains resistant to the quinolones
have been identified with decreased binding
affinity to the enzyme because of amino acid
substitution in either A or B subunits resulting
from mutations in either gyrA and gyrB genes.
 Resistance
• The highly polar quinolones are believed to
enter the bacterial cell through densely
charged porin channels in the outer bacterial
membrane.
• Mutation leading to altered porin protein can
lead in decreased uptake of quinolones and
cause resistance.
 Resistance
• In contrast to nalidixic acid, resistance to the
fluoroquinolones is slow to appear but when it
does appear, it is mainly due to efflux
mechanisms which pump the drug back out of
the cell.
 Resistance
• Less common resistance mechanisms include
mutations to the topoisomerase enzymes,
which reduce their affinity to the agents, and
alteration of porins in the outer membrane of
Gram-negative organisms to limit access.
Synthetic Antibacterial Agents

NITROHETEROAROMATIC
COMPOUNDS
 Metronidazole
• Metronidazole was introduced in 1959 as an
anti-protozoal agent, but began to be used as
an antibacterial agent in the 1970s.

Metronidazole R: -OH
Nitroimidazole structure
 Metronidazole
• After drug entering the bacterial cell the nitro
group is reduced. This lowers the
concentration of metronidazole within the
cell which create a concentration gradient. As
a result more drug can enter inside the cell.
 Metronidazole
• The reduction mechanism proves toxic to the
cell since free radicals (reactive oxygen
species) are formed which act on DNA.
• Thus it inhibiting bacterial nucleic acid
synthesis and resulting in bacterial cell death.
Ferrodoxin:
Electron transport
protein

Figure: Structure of metronidazole and its mechanism of action

 Metronidazole
• Metronidazole also is a component of a
multidrug cocktail used to treat Helicobacter
pylori infections associated with gastric ulcers.
 Tinidazole
• Tinidazole, another nitroimidazole, has been
introduced as a competitor of metronidazole
• Compared to metornidazole it has longer
duration of action

Tinidazole R: -SO2C2H5
 Nitrofurantoin
• Nitrofurantoin, a widely used oral
antibacterial nitrofuran, has been available
since World War II.
• It is used for prophylaxis or treatment of acute
urinary tract infections (UTI)
 Nitrofurantoin
• Nitrofurantoin inhibits DNA and RNA functions
through mechanisms that are not well
understood, although bioreductive activation
is suspected to be an important component of
this. (undergoes reduction within bacterial
cells to form radical species which act on DNA)
 Methenamine
• Methenamine is a stable, inactive compound
when the pH is more than 5.
• At a more acidic pH, the compound
spontaneously degrades to generate
formaldehyde, which has antibacterial
properties.
 Methenamine
• This is useful in the treatment of urinary tract
infections. The normal pH of blood is slightly
alkaline (7.4) and so methenamine passes
round the body unchanged.

Methenamine (hexamethylenetetramine)
 Methenamine
• However, once it is excreted into the infected
urinary tract, it encounters urine which is
acidic as a result of certain bacterial
infections. Consequently, methenamine
degrades to generate formaldehyde just
where it is needed.
 Methenamine
• Formaldehyde is an extremely reactive
chemical and its antimicrobial action appears
to be due to its ability to inactivate cell
constituents such as proteins and nucleic
acids.
• Vegetative cells are killed more quickly by
formaldehyde than are spores.
• Formalin: 37-40% (w/v) formaldehyde
 Methenamine
• Methenamine, a cyclic hydrocarbon, is
hydrolyzed in an acid medium into ammonia
and formaldehyde according to the following
reaction:
H +
N4(CH2)6 + 6H2O → 4 NH3 + 6HCHO
Methenamine Formaldehyde
Figure: Formation of formaldehyde from methenamine at acid pH
 Methenamine
• Several characteristics of methenamine make
it highly suitable for treating infections of the
lower urinary tract:
(i) Bacterial resistance to formaldehyde has not
been shown to develop
(ii) Significant levels of formaldehyde are not
generated in the gut or in body tissues
 Methenamine
(iii) Because of the first two, bacterial flora is not
likely to be altered by administration of
methenamine
(iv) Methenamine is relatively nontoxic and
(v) Even in the form of an enteric tablet which
may be necessary to bypass gastric acidity,
this drug is relatively inexpensive.
 Methenamine
• Methenamine in ordinarily used doses is not
likely to be effective in treating urinary
infections when the urine pH ≥ 5.85.
• Under these circumstances, two alternative
approaches could be considered:
(i) Increasing the dosage of methenamine; or
 Methenamine
(ii) Acidifying the urine by withholding fluids or
using pharmacologic doses of systemic urinary
acidifiers such as ammonium chloride and
ascorbic acid.

• Methenamine is frequently formulated with a

weak acid, such as mandelic acid or hippuric
acid.
 Methenamine
• Despite the popularity of combinations of
methenamine with mandelic or hippuric acid,
there is no convincing evidence that in the
doses used these organic acids significantly
lower urine pH.

Mandelic acid Hippuric acid

 Urinary analgesics
• Phenazopyridine, which is 2,6-diamino-3-
(phenylazo)pyridine, is a urinary tract
analgesic, commercially available as tablet.
 Urinary analgesics
• Phenazopyridine hydrochloride is an azo dye
with local analgesic and anaesthetic effects on
the urinary tract.
• Phenazopyridine is a chemical which, when
excreted into the urine (65% of an oral dose ),
has a local analgesic effect.
 Urinary analgesics
• It is typically used in conjunction with an
antibiotic when treating a urinary tract
infection.
• In this combination, phenazopyridine is taken
for only a short time, typically two days, while
the antibiotic is continued for longer.
• After two days, there is little evidence of any
benefit from continued administration of
phenazopyridine versus administration of an
antibiotic only.
Urinary analgesics