Patrick An Introduction to Medicinal Chemistry 3/e Chapter 19 ANTIBACTERIAL AGENTS
Mar 17, 2018
Patrick
An Introduction to Medicinal Chemistry 3/e
Chapter 19
ANTIBACTERIAL AGENTS
Valinomycin and Gramicidin A
(Ionophores)
Act as ion carrier The peptides valinomycin and gramicidin A both act as ion-
conducting antibiotics (ionophores) and allow the uncontrolled
movement of ions across the cell membrane.
Valinomycin is a cyclic structure obtained from Streptomyces
fermentation
It contains three molecules of l-valine, three molecules of d-
valine, three molecules of l-lactic acid, and three molecules of
d-hydroxyisovalerate.
These four components are linked in an ordered fashion such
that there is an alternating sequence of ester and amide
linking bonds around the cyclic structure.
This is achieved by the presence of a lactic or
hydroxyisovaleric acid unit between each of the six valine
units.
Further ordering can be observed by noting that the l and d
portions of valine alternate around the cycle, as do the
lactate and hydroxyisovalerate units.
Valinomycin acts as an ion carrier and could be
looked upon as an inverted detergent.
As it is cyclic, it forms a doughnut-type structure
where the polar carbonyl oxygens of the ester and
amide groups face inwards, while the
hydrophobic side chains of the valine and
hydroxyisovalerate units point outwards.
This is clearly favoured because the hydrophobic
side chains can interact via van der Waals
interactions with the fatty lipid interior of the cell
membrane, while the polar hydrophilic groups
are clustered together in the centre of the
doughnut to produce a hydrophilic environment
This hydrophilic centre is large enough to
accommodate an ion and it is found that a
‘naked’ potassium ion (i.e. one with no
surrounding water molecules) fits the space and
is complexed by the amide carboxyl groups
• Valinomycin can, therefore, collect a potassium ion from the inner
surface of the membrane, carry it across the membrane and deposit it
outside the cell, thus disrupting the ionic equilibrium of the cell.
• Normally, cells contain a high concentration of potassium ions and a low
concentration of sodium ions.
• The fatty cell membrane prevents passage of ions between the cell and its
environment, and ions can only pass through the cell membrane aided by
specialized and controlled ion transport systems
• Valinomycin introduces an uncontrolled ion transport system which
proves fatal.
• Valinomycin is specific for potassium ions over sodium ions
• The real reason is that sodium ions do not lose their surrounding water
molecules very easily and would have to be transported as the hydrated
ion. As such, they are too big for the central cavity of valinomycin.
Ionophore Mechanism of action
Valinomycin disrupts the ionic equilibrium of a cell
Ionophores act on the plasma membrane and result in the uncontrolled
movement of ions across the cell membrane, leading to cell death.
Gramicidin
• 15 Amino Acids: coil in helix: Hydrophobic-out and hydrophilic-in
• Gramicidin is a heterogeneous mixture of six antibiotic compounds, Gramicidins A, B and C, making up 80%, 6%, and 14% respectively
More Ionophores:
used in veterinary
medicine
The ionophores nigericin ,
monensin A , and lasalocid
Function in much the same way as
valinomycin and are used in
veterinary medicine to control the
levels of bacteria
Polymixin B
1. Can differentiate between different cellular plasma membranes Selectivity
• It causes the leakage of SMALL
MOLECULES (nucleoside) from the
cell rather than ions (valinomycin)
1. Injected intramuscular
2. Active against Pseudomonas strains that are resistant to antibacterial agents
3. Can be used topically
4. Has good activity against G –Ve
5. Less effective against G +Ve due to penetration problem (large MW)
Polypeptide
From soil bacteria
(Bacillus polymyxa) DAB: α,γ-diaminobutyric acid
primarily used for resistant
gram negative infections
Polymyxin B Mechanism of Action
1. Positively charged amino groups in the cyclic peptide
portion binds to a negatively charged site in the
lipopolysaccharide layer (an electrostatic attraction)
Alters cytoplasmic membrane permeability
1. Fatty acid portion dissolves in hydrophobic region of
membrane and disrupts membrane integrity
2. Leakage of cellular molecules, inhibition of cellular
respiration.
3. Binds and inactivates endotoxin
4. Relative absence of selective toxicity: nonspecific for cell
membranes of any type highly toxic
• Polymyxin B operates selectively on the plasma membrane of bacteria and
causes the uncontrolled movement of small molecules across the
membrane.
Neosporin: Bacitracin, Neomycin, and
Polymyxin B
Antibiotic ointment used in the prevention of
infection and speeding the healing of wounds
Killer Nanotubes • Cyclic peptides with an even number of alternating D,L-
α-amino acid residues are known to self-assemble into
organic nanotubes
• Cyclic peptides with self-assemble properties
Killer Nanotubes
Self assembly of ‘killer nanotubes
• Killer Nanotubes increase membrane permeability,
collapse transmembrane ion potentials, and cause rapid
cell death
• The nanotubes would allow molecules to leach out from
the cell and cause cell death.
Killer Nanotubes
1. Stacking via hydrogen bonds (HB)
2. Hydrophobic R-groups in exterior
3. R-group modified for selectivity
(mammalian vs. bacterial)
4. Polar NH/CO in core
5. Work in progress
Cyclic Lipopeptides New class of antibiotics
1. Daptomycin: derived from Streptomyces roseosporus
2. Disturbs cellular membrane functions
3. Used in treating skin infection
4. Active against MRSA
Decanoic chain
Daptomycin
Asp-X-Asp-Gly motif
The lipid portion of the molecule is derived from decanoic acid and the yield of product
obtained is increased if decanoic acid is added to the fermentation medium
• Cyclic peptides are being designed which will self-assemble to form
nanotubes in the cell membranes of bacteria
• Cyclic lipopeptides are a new class of antibiotic
More Cyclic
Lipopeptides
Antibacterial Agents that Impair
Protein Synthesis (Translation)
Stages at which antibacterial agents inhibit translation
Aminoglycosides: Streptomycin & Gentamycin C1a
Streptomycin (1944):
From Soil bacteria
(Streptomyces griseus)
first of a class of drugs
called aminoglycosides
and was the first
antibiotic remedy for
tuberculosis.
1. Basic Amine: At pH 7.4 the amine is +ve charge
2. The +ve charge help them to penetrate the outer cell wall of
Gram -ve.
They bind the 30S subunit and prevent the movement of
the Ribosome along the mRNA
2-deoxystreptamine (2-DOS)
Inhibition of protein biosynthesis by
Aminoglycosides
• Fast acting BUT might cause some ear and
kidney problems.
• Effective in treating infections caused by
aerobic Gram –Ve bacteria.
• The only compounds active against P.
aeruginosa
• Because of high polarity they have to be
injected.
• Not able to cross the BBB
Properties of Aminoglycosides
Streptomycin
Structure-activity Relationship
• Reduction of the aldehyde to the alcohol results in a compound,
dihydrostreptomycin, which has activity similar to STM but with
a greater potential for producing delayed severe deafness
(major side effect).
• Oxidation of the aldehyde to a carboxyl group or conversion to
Schiff’s base derivatives (oxime, semicarbazone, or
phenylhydrazone) results in inactive analogs.
• Oxidation of the methyl group in α-streptose to a methylene
hydroxy gives an active analog but with no advantage over
STM.
Streptomycin
Structure-activity Relationship
• Modification of the aminomethyl group in the glucosamine
portion of the molecule by demethylation or by replacement
with larger alkyl groups reduces activity.
• Removal or modification of either guanidine in the streptidine
nucleus results in decreased activity.
Streptomycin
• Metabolism
More Aminoglycosides
1949
General structures of Kanamycins and ring I
substituents
Glucopyranosyl
SAR of Gentamicin
Tetracyclines and Chloramphinicol
Tetracyclines:
Inhibit protein synthesis by
binding to 30S subunit and
preventing aminoacyl-tRNA
from binding
Chloramphenicol:
Binds to the 50S subunit and inhibit
the movement of the ribosome along
the mRNA, probably by inhibiting the
peptidyl transferase reaction by which
the peptide chain is extended.
Tetracyclines are bacteriostatic antibiotics which have a
broad spectrum of activity and are the most widely
prescribed form of antibiotic after penicillins. They are also
capable of attacking the malarial parasite
Tetracyclines cross the outer membrane of gram –ve bacteria
by passive diffusion through the porins
Commonly used tetracyclines in the clinic are tetracycline,
demeclocycline , doxycycline , lymecycline , minocycline , and
Oxytetracycline
The use of chlortetracycline has decreased over the years
because it kills the intestinal flora that produce vitamin K
R5 R4 R3 R2 R1.
Chlortetracycline H H OH CH3 Cl
Oxytetracycline H OH OH CH3 H
Tetracycline H H OH CH3 H
Demethylchlortetracycline H H OR H CI
Rolitetracycline + H OH CH3 H
Metacycline H OH CH2 H
Doxycycline H OH H CH3 H
Minocycline H H H N(CH3)2 32
• Retention of the configuration of the asymmetric centres C-4, C-
4a and C-12a is essential, whereas the configurations at C-5, C-
5a and C-6 may be altered:
• The amide hydrogen may be replaced with a methyl group, but
larger groups have a deleterious effect except for those which
are eliIminated spontaneously in water
• The dimethyl amino group may be replaced by a primary amino
group without loss of in vitro activity but all other changes so far
lead to decreased bacteriostatic action
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• The hydrophobic part of the molecule from C-5 to C-9 may be
altered in various ways:
• modifications at C-6 and C-7 in particular afford products having
greater chemical stability.
• increased antibiotic activity and more favourable
pharmacokinetics
• Dehydrogenation to form a double bond between C-5a and C-11a
markedly decreases activity
• Polar substituents at C-5 and C-6 contribute decreased lipid
versus water solubility to the tetracycline
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Side effect:
Dermatological:-Skin reactions, photosensitivity
GIT:-nausea, vomiting, and diarrhea.
CNS:-Dizziness,visual disturbances .
Immune System:-allergic reactions.
Other:-yellowish-grayish-brown discoloration of the
teeth.
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Drug interaction of tetracyclines
Antacids containing aluminum,
calcium, or magnesium, and
iron-containing preparations
Impaire the Absorption of tetracyclines
anticoagulant therapy
Because tetracyclines have been shown to
depress plasma prothrombin activity,
patients who are on anticoagulant therapy
may require downward adjustment of their
anticoagulant dosage.
bacteriostatic drugs
interfere with the bactericidal action of
penicillin, it is advisable to avoid giving
tetracycline-class drugs in conjunction
with penicillin
.
Oral contraceptives Concurrent use of tetracyclines with oral
contraceptives may render oral
contraceptives less effective.
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Bile acid sequestrants
May decrease tetracycline
absorption
Iron preparations
May decrease absorption of
tetracyclines
Methoxyflurane when concurrent with tetracycline)
may cause fatal nephrotoxicity;
concurrent use is contraindicated.
Methotrexate: Clearance of methotrexate (high-
dose therapy) may be decreased by
tetracyclines.
Ergot alkaloids or their
derivatives are given with
tetracyclines.
Increased risk of ergotism
Drug interaction of tetracyclines
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Chloramphenicol is now prepared synthetically and has two
asymmetric centres. Only the R,R -isomer is active.
Chloramphenicol binds to the 50S subunit of ribosomes and appears
to act by inhibiting the movement of ribosomes along mRNA,
probably by inhibiting the peptidyl transferase reaction by which
the peptide chain is extended
The nitro group and both alcohol groups are involved in binding
interactions.
The dichloroacetamide group is also important, but can be replaced
by other electronegative groups. Chloramphenicol is quite toxic and
the nitro substituent is thought to be responsible for this
Macrolides
Erythromycins
• 14-membered macrocyclic lactone
• Sugars and amino-sugars attached
• Bind to 50S subunit of the bacterial ribosome
• Inhibiting translocation!!
Have similar antibacterial properties to macrolides
Lincosamides
Macrolides are bacteriostatic agents
Mechanisms of
Resistance
1. Methylation of the ribosomal
target of the antibiotics.
2. Antibiotic Efflux.
3. Drug Modification.
One way to stabilize would be by:
1. Methylation (protection of OH groups e.g. clarithromycin)
2. Increasing the size to 16 –membered ring
Acid Instability of Erythromycin
Intra-molecular ketal formation in Erythromycin
Erythromycin is unstable to stomach acids, but can be taken orally
in a tablet form. The formulation of the tablet involves a coating
The acid sensitivity is due to the presence of a ketone and two alcohol groups
which are set up for the acid catalysed intramolecular formation of a ketal
Erythromycin
1. Erythromycin and Chloramphenicol bind to
the same region of the ribosome they
should not be administered together (in
effective).
2. Erythromycin is used against penicillin-
resistant staphylococci.
3. Best described against the legionaries’
disease, diphtheria, acne.
4. The acid instability of Erythromycin is solved
by coated tablet.
Clarithromycin
1. More stable analogue of Erythromycin.
2. Improved oral absorption
3. Used in treatment of ulcers caused by H. Pylori
Resistance to Macrolides may be due to:
1) Efficient Efflux (pump the drug back out the cell)
2) Change in the binding site at the ribosome. Methylation
of the ribosomal target of the antibiotics (binding is
weakened)
3) Modification on the Macrolides by various enzymes
Increased stability acidic mediaNo intramolec. hemikatalisation
O
N
O
HOO
O
N
HO
HO
HO
O
O
O
OH
Azithromycin
Increased stability acidic mediaNo intramolec. hemikatalisationImproved ribosome binding, less resistansIncreased ribosome affinity
O
O
N
O
O
N
NN
O
MeOO
O
O
N
HO
Telithromycin
No intramolecular hemiketalizaion
Improved ribosome binding
Less Resistance
Increased ribosome affinity
contains a 15-membered macrocycle
where an N -methyl group has been
incorporated into the macrocycle. It is
one of the world’s best-selling drugs.
Telithromycin is a semi-synthetic derivative of erythromycin and
reached the European market in 2001.
The cladinose sugar in erythromycin has been replaced with a
keto-group and a carbamate ring has been fused to the
macrocyclic ring.
The two hydroxyl groups that cause the intramolecular ketal
formation in erythromycin have been masked, one as a methoxy
group and the other as part of the carbamate ring.
Streptogramins
1. Bind to different regions of 50S
2. The binding of Dalfopristin
increases the affinity for
Quinopristin.
3. Quinopristin inhibits the
peptide chain elongation.
4. Dalfopristin interferes with the
transfer of the peptide chain
from tRNA to the other.
Parenteral
Gram-positive bacteria: Streptococcus pyogenes, Viridans group streptococci, Streptococcus pneumoniae, Staphylococcus aureus, Some enterococci and especially
MRSA
Quinopristin
Dalfopristin
Streptogramins
Pritinamycin is a mixture of macrolactone structures obtained from
Streptomyces pristinaespiralis .
Two of the components ( quinupristin and dalfopristin ) have been isolated.
These agents bind to different regions of the bacterial ribosome’s 50S
subunit form a complex.
It is found that binding of dalfopristin increases the binding affinity for
quinupristin, and so the two agents actin synergy with each other.
Quinupristin inhibits peptide chain elongation, while dalfopristin
interferes with the transfer of the peptide chain from one tRNA to the next.
Quinupristin and dalfopristin are protein synthesis inhibitors in a
synergistic manner. While each of the two is only a bacteriostatic agent, the
combination shows bactericidal activity.
Quinupristin Dalfopristin
Morpholine
NO
O
Oxazolidin-2-one
NH
HO
F
NO
Oxazolidinones
1. Broad Spectrum
2. Active against
strains that acquired
resistance to other
antibacterial agents.
3. They bind at much
earlier stage in the
protein synthesis.
S
The structure of Linezolide
Both oral and parenteral
Peptidyl transferase center (PTC)
They bind to 50S subunit and prevent the formation of
ribosome complex
Oxazolidinones
• The oxazolidinones are a new class of synthetic antibacterial agents.
They inhibit protein synthesis at a much earlier stage than previous
agents, and, consequently, do not suffer the same resistance problems
• Before protein synthesis can start, a 70S ribosome has to be formed by
the combination of a 30S ribosome with a 50S ribosome. The
oxazolidinones bind to the 50S ribosome and prevent this from
happening. As a result, translation cannot even start.
• Other agents that inhibit protein synthesis do so during the translation
process itself
• Linezolid was the first of this class of compounds to reach the market in
2000, and by 2010, it was netting sales of £716 million per year
• The oxazolidinones have a broad spectrum of activity and are active
against bacterial strains which have acquired resistance to other
antibacterial agents acting against protein synthesis
• Linezolid has good activity against most clinically important Gram-
positive bacteria, including MRSA. It can also be taken orally with
100% uptake from the gastrointestinal tract
• Unfortunately, there is a high level of side effects related to its use
and, as it is a bacteriostatic agent, there is a greater risk of bacterial
resistance developing
• Radezolid is one such structure which binds 10,000 times more strongly as a
result of extra binding interactions (extension the structure)
Thiopeptide Antibiotics: Thiostrepton
• Thiopeptides are sulfur-rich macrocyclic peptides containing highly-modified amino
acids
• They have antibiotic activity against Gram-positive bacteria, but little or no activity
against Gram-negative bacteria
• They are characterized by a nitrogen-containing six-membered ring (such as
piperidine, dehydropiperidine, or pyridine) substituted with multiple thiazole rings
and dehydroamino acids
Agents Acting on Nucleic
Acid Transcription Quinolones and Fluoroquinolones
1. They inhibit the replication and transcription of bacterial
DNA by stabilizing the complex formed between DNA and
topoisomerases
2. By forming a ternary complex (Drug-Enzyme-DNA)
Nalidixic Acid
• First to be discovered-1962
• Active against G –ve
• Short-term UTI
• Bacteria can develop quickly resistance.
N N
O
OH
O
Enoxacin
1. Wider spectrum of activity (G+ve and G-ve)
2. Active against highly resistant P. aeruginosa
3. 6-Flourine:
– Increased the activity
– Increased the cellular Uptake
N N
O
OH
O
N
F
HN
6
1 2
3
7 8
7-Piperazyl Improvements :
1. Oral absorption
2. Tissue distribution
3. Metabolic stability
4. Level of activity
5. Spectrum of activity (G-ve and P.
aeruginosa) 1980s
form a zwitterion with the
carboxylic acid group at position 3
Ciprofloxacin
Cyclopropy substituent:
– Increase the spectrum
of activity (S. Aureus)
N
O
OH
O
N
F
HN
6
1 2
3
7 8
Replacement Nitrogen at position 8
with carbon Reduced side effects
1. Highly potent against G-ve
2. Used in treatment of wide range of infections: urinary,
respiratory, GI tract, skin, joints.
3. MOST ACTIVE BRAOD SPECTRUM ANTIBIOTIC
IN THE MARKET
Bacterial Topoisomerase IV is
inhibited
Topoisomerase IV is predominantly responsible for separation of daughter DNA strands during cell
1ST and 2nd generation
Fluoroquinolone limitations
1. The moderate activity against S. aureus.
2. The quick development of resistance
3. Only marginal activity against anaerobic
Streptococcus pneumoniae.
Third- and fourth-generation fluoroquinolones, such as ofloxacin,
levofloxacin , moxifloxacin, and besifloxacin began to be developed in
the early 1990s to tackle these issues
• Ofloxacin has an asymmetric centre and is sold as a racemic mixture
of both enantiomers, one of which is active and one of which is not.
• Levofloxacin is the active enantiomer of oflaxacin and is twice as
active as the racemate.
3rd Generation: Trovafloxacin and
others
3-azabicyclo[3.1.0]hexyl substituent at the C-7 position,
Developed by the 1990s
All of them are with improved activity against Streptococcus
pneumoniae
Fluoroquinolone
Rifamycin Antibiotics
• The rifamycins are natural products produced by Streptomyces mediterranei.
• This chemical class is an aliphatic chain forming a bridge
between two nonadjacent positions of an aromatic moiety.
• Semisynthetic derivatives are prepared via conversion of the
natural rifamycins to 3-formylrifamycin which is derivatized with
various hydrazines to give products such as rifampin and
rifapentine.
• Rifampin and rifapentine have significant benefit over previously
investigated rifamycins in that they are orally active, highly
effective against a variety of gram-positive and gram-negative
organisms, and have high clinical efficacy in the oral treatment
of tuberculosis.
Rifamycin Antibiotics
Rifamycin Antibiotics
Mechanism of Action:
• The rifamycins inhibit bacterial DNA-dependent RNA polymerase
(DDRP) by binding to the β-subunit of the enzyme leads to a
blocking of the initiation of chain formation in RNA synthesis.
• Rifamycins are highly active against rapidly dividing intracellular
and extracellular bacilli.
•
• Rifampin is active against DDRP from both gram-positive and
gram-negative bacteria but due to poor penetration of the cell
wall of gram-negative organisms by rifampin, the drug has less
value in infections caused by such organisms.
Structure-activity Relationship:
o Free OH groups are required at C-l,8,21 and 23 as they are
important binding groups for attachment to DDRP.
o Acetylation of C-21 and C-23 produces inactive compounds.
o Reduction of the double bonds in the macro ring results in a
progressive decrease in activity.
Structure-activity Relationship:
o Opening of the macro ring gives inactive compounds. These
latter two changes greatly affect the conformational structure of
the rifamycins which in turn decreases binding to DDRP.
o Substitution at C-3 or C-4 results in compounds with varying
degrees of antibacterial activity.
Metabolism:
• Rifampin and rifapentine are readily absorbed from the intestine
although food in the tract may affect absorption.
• The major metabolism of rifampin and rifapentine is
deacetylation which occurs at the C-25 acetate to give
desacetylrifampin and desacetylrifapentine, which are still active
antibacterial agents.
Therapeutic Application:
• Rifampin (Rifadin, Rimactane) is always used in combination with
one or more other antitubercular agents. The drug is potentially
hepatotoxic and may produce gastrointestinal disturbances, rash
and thrombocytopenic purpura (low levels of platelets that
prevents bleeding).
• Rifampin is known to induce CYP3A4 and CYP2C isoforms and may
decrease the effectiveness of oral contraceptives, corticosteroids,
Warfarin, quinidine, methadone, zidovudine, clarithromycin, and
the azole antifungal agents.
• Rifapentine is introduced for the treatment of pulmonary
tuberculosis and has major advantage over rifampin is the fact that
when used in combination therapy rifapentine can be orally
administered twice weekly during the "intense" phase of therapy
followed by once a week during the "continuous" phase of therapy.
• In contrast, rifampin is normally administered daily during the
"intense" phase of therapy followed by twice a week dosing during
the "continuous" phase of therapy.
Summary
Aminoglycosides, tetracyclines, chloramphenicol, streptogramins,
lincosamides, and macrolides inhibit protein synthesis by binding to the
bacterial ribosomes involved in the translation process.
• Resistance can arise from a variety of mechanisms, such as drug efflux,
altered binding affinity of the ribosome, altered membrane permeability,
and metabolic reactions.
• Oxazolidinones prevent the formation of the 70S ribosome by binding to
the 50S subunit.
• Quinolones and fluoroquinolones inhibit topoisomerase enzymes, resulting
in inhibition of replication and transcription.
Rifamycins inhibit the enzyme RNA polymerase and prevent RNA
synthesis. In turn, this prevents protein synthesis. Rifampicin is used to treat
tuberculosis and staphylococcus infections. Fidaxomicin is a macrocycle
which also targets RNA polymerase.
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