Antibiotics
Step 1: How to Kill a Bacterium.
• What are the bacterial weak points?
• Specifically, which commercial antibiotics
target each of these points?
Target 1: The Bacterial Cell
Envelope
Two types of bacteria
• Gram-positive: Stained dark blue by
Gram-staining procedure
• Gram-negative: Don’t take up the crystal
violet stain, and take up counterstain
(safranin) instead, staining pink in the
Gram procedure.
Structure of the bacterial cell envelope. Gram-positive. Gram-negative.
Gram staining animation
http://student.ccbcmd.edu/courses/bio141/labmanua/lab6/imag
es/gram_stain_11.swf
Structure of peptidoglycan. Peptidoglycan synthesis requires cross-linking of
disaccharide polymers by penicillin-binding proteins (PBPs). NAMA, N-acetylmuramic acid; NAGA, N-acetyl-glucosamine.
Antibiotics that Target the Bacterial
Cell Envelope Include:
• The b-Lactam Antibiotics
• Vancomycin
• Daptomycin
Target 2: The Bacterial Process of
Protein Production
An overview of the process by which proteins are produced within bacteria.
Structure of the bacterial ribosome.
Antibiotics that Block Bacterial
Protein Production Include:
•
•
•
•
•
•
•
•
Rifamycins
Aminoglycosides
Macrolides and Ketolides
Tetracyclines and Glycylcyclines
Chloramphenicol
Clindamycin
Streptogramins
Linezolid (member of Oxazolidinone Class)
Target 3: DNA and Bacterial
Replication
Bacterial synthesis of tetrahydrofolate.
Supercoiling of the double helical structure of DNA. Twisting of DNA results in
formation of supercoils. During transcription, the movement of RNA polymerase
along the chromosome results in the accumulation of positive supercoils ahead
of the enzyme and negative supercoils behind it. (Adapted with permission from
Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. New York:
Garland Science, 2002:314.)
Replication of the bacterial chromosome. A consequence of the circular nature of
the bacterial chromosome is that replicated chromosomes are interlinked,
requiring topoisomerase for appropriate segregation.
Antibiotics that Target DNA and
Replication Include:
• Sulfa Drugs
• Quinolones
• Metronidazole
Which Bacteria are Clinically
Important?
General Classes of Clinically
Important Bacteria Include:
•
•
•
•
•
•
Gram-positive aerobic bacteria
Gram-negative aerobic bacteria
Anaerobic bacteria (both Gram + and -)
Atypical bacteria
Spirochetes
Mycobacteria
Gram-positive Bacteria of
Clinical Importance
• Staphylococci
– Staphylococcus aureus
– Staphylococcus epidermidis
Staphylococcus
aureus
• Streptococci
–
–
–
–
Streptococcus pneumoniae
Streptococcus pyogenes
Streptococcus agalactiae
Streptococcus viridans
• Enterococci
– Enterococcus faecalis
– Enterococcus faecium
• Listeria monocytogenes
• Bacillus anthracis
Streptococcus
viridans
Gram-negative Bacteria of
Clinical Importance
• Enterobacteriaceae
– Escherichia coli, Enterobacter, Klebsiella, Proteus, Salmonella,
Shigella, Yersinia, etc.
• Pseudomonas aeruginosa
• Neisseria
– Neisseria meningitidis and Neisseria gonorrhoeae
• Curved Gram-negative Bacilli
– Campylobacter jejuni, Helicobacter pylori, and Vibrio cholerae
•
•
•
•
Haemophilus Influenzae
Bordetella Pertussis
Moraxella Catarrhalis
Acinetobacter baumannii
Anaerobic Bacteria of Clinical
Importance
• Gram-positive anaerobic bacilli
– Clostridium difficile
– Clostridium tetani
– Clostridium botulinum
• Gram-negative anaerobic bacilli
– Bacteroides fragilis
Atypical Bacteria of Clinical
Importance Include:
•
•
•
•
•
•
Chlamydia
Mycoplasma
Legionella
Brucella
Francisella tularensis
Rickettsia
Spirochetes of Clinical
Importance Include:
• Treponema pallidum
• Borrelia burgdorferi
• Leptospira interrogans
Mycobacteria of Clinical
Importance Include:
• Mycobacterium tuberculosis
• Mycobacterium avium
• Mycobacterium leprae
Antibiotics that Target the Bacterial
Cell Envelope
• The b-Lactam Antibiotics
Mechanism of action of β-lactam antibiotics. Normally, a new subunit of Nacetylmuramic acid (NAMA) and N-acetylglucosamine (NAGA) disaccharide with an
attached peptide side chain is linked to an existing peptidoglycan polymer. This may
occur by covalent attachment of a glycine () bridge from one peptide side chain to
another through the enzymatic action of a penicillin-binding protein (PBP). In the
presence of a β-lactam antibiotic, this process is disrupted. The β-lactam antibiotic
binds the PBP and prevents it from cross-linking the glycine bridge to the peptide
side chain, thus blocking incorporation of the disaccharide subunit into the existing
peptidoglycan polymer.
Mechanism of penicillin-binding protein (PBP) inhibition by β-lactam antibiotics.
PBPs recognize and catalyze the peptide bond between two alanine subunits of
the peptidoglycan peptide side chain. The β-lactam ring mimics this peptide
bond. Thus, the PBPs attempt to catalyze the β-lactam ring, resulting in
inactivation of the PBPs.
Six P's by which the
action of βlactams may be
blocked:
(1) penetration,
(2) porins,
(3) pumps,
(4) penicillinases (βlactamases),
(5) penicillin-binding
proteins (PBPs),
and
(6) peptidoglycan.
The Penicillins
Category
Parenteral Agents
Oral Agents
Natural Penicillins
Penicillin G
Penicillin V
Antistaphylococcal
penicillins
Nafcillin, oxacillin
Dicloxacillin
Aminopenicillins
Ampicillin
Amoxicillin and Ampicillin
Aminopenicillin + blactamase inhibitor
Ampicillin-sulbactam
Amoxicillin-clavulanate
Extended-spectrum
penicillin
Piperacillin, ticaricillin
Carbenicillin
Extended-spectrum
penicillin + b-lactamase
inhibitor
Piperacillin-tazobactam,
ticaricillin-clavulanate
INTRODUCTION
•
•
•
•
•
•
•
•
•
•
Antibacterial agents which inhibit bacterial cell wall synthesis
Discovered by Fleming from a fungal colony (1928)
Shown to be non toxic and antibacterial
Isolated and purified by Florey and Chain (1938)
First successful clinical trial (1941)
Produced by large scale fermentation (1944)
Structure established by X-Ray crystallography (1945)
Full synthesis developed by Sheehan (1957)
Isolation of 6-APA by Beecham (1958-60)
- development of semi-synthetic penicillins
Discovery of clavulanic acid and b-lactamase inhibitors
http://www.microbelibrary.org/microbelibrary/files/ccImages/Articl
eimages/Spencer/spencer_cellwall.html
STRUCTURE
R=
O
CH2
C
Benzyl penicillin (Pen G)
H
S
Me
6-Aminopenicillanic acid
(6-APA)
R
R=
O
H H
N
Acyl side
chain
CH2
N
Me
O
CO2H
b-Lactam
ring
Phenoxymethyl penicillin (Pen V)
Thiazolidine
ring
Side chain varies depending on carboxylic acid present in fermentation medium
CH2
CO2H
Penicillin G
present in corn steep liquor
OCH2
CO2H
Penicillin V
(first orally active penicillin)
Shape of Penicillin G
O
C
R
Me
H
NH
S
Me
O
H
N
H
CO2H
..
Folded ‘envelope’ shape
Properties of Penicillin G
•
•
•
•
•
•
•
Active vs. Gram +ve bacilli and some Gram -ve cocci
Non toxic
Limited range of activity
Not orally active - must be injected
Sensitive to b-lactamases
(enzymes which hydrolyse the b-lactam ring)
Some patients are allergic
Inactive vs. Staphylococci
Drug Development
Aims
• To increase chemical stability for oral administration
• To increase resistance to b-lactamases
• To increase the range of activity
SAR
Amide essential
O
C
H
N
Cis Stereochemistry essential
H
H
S
R
Me
N
O
b Lactam essential CO2H
Conclusions
•
•
•
•
•
•
•
Me
Carboxylic acid essential
Bicyclic system ess ential
Amide and carboxylic acid are involved in binding
Carboxylic acid binds as the carboxylate ion
Mechanism of action involves the b-lactam ring
Activity related to b-lactam ring strain
(subject to stability factors)
Bicyclic system increases b-lactam ring strain
Not much variation in structure is possible
Variations are limited to the side chain (R)
Mechanism of action
•
Penicillins inhibit a bacterial enzyme called the transpeptidase
enzyme which is involved in the synthesis of the bacterial cell
wall
The b-lactam ring is involved in the mechanism of inhibition
Penicillin becomes covalently linked to the enzyme’s active site
leading to irreversible inhibition
•
•
O
C
H H
N
S
R
N
Nu
O
H
Me
Me
O
Enz
C
CO2H
H H
N
R
Enz-Nu
-H
O
H
S
N
Me
Me
O
H
CO2H
C
H H
N
H
R
O C HN
Nu-Enz
S
Me
Me
CO2H
Covalent bond formed
to transpeptidase enzyme
Irreversible inhibition
Mechanism of action - bacterial cell wall synthesis
NAM
L-Ala
D-Glu
L-Lys
NAG
NAM
L-Ala
D-Glu
L-Lys
Bond formation
inhibited by
penicillin
NAM
L-Ala
NAG
D-Glu
NAM
L-Lys
L-Ala
NAG
NAM
L-Ala
NAG
D-Glu
L-Lys
NAM
L-Ala
NAG
NAM
D-Glu
L-Ala
NAM
NAG
L-Lys
NAM
D-Glu
L-Ala
L-Lys
L-Ala
D-Glu
D-Glu
D-Glu
L-Lys
L-Lys
L-Lys
Mechanism of action - bacterial cell wall synthesis
NAM
NAG
NAM
L-Ala
L-Ala
D-Glu
D-Glu
L-Lys
Gly Gly Gly Gly Gly
NAG
L-Lys
D-Ala
D-Ala
D-Ala
D-Ala
SUGAR
BACKBONE
Gly Gly Gly Gly Gly
PENICILLIN
D-Alanine
NAM
NAG
TRANSPEPTIDASE
NAM
L-Ala
L-Ala
D-Glu
D-Glu
L-Lys
D-Ala
Gly Gly Gly Gly Gly
Cross linking
L-Lys
D-Ala
NAG
Gly Gly Gly Gly Gly
SUGAR
BACKBONE
Mechanism of action - bacterial cell wall synthesis
•
Penicillin inhibits final crosslinking stage of cell wall synthesis
•
It reacts with the transpeptidase enzyme to form an
irreversible covalent bond
•
Inhibition of transpeptidase leads to a weakened cell wall
•
Cells swell due to water entering the cell, then burst (lysis)
•
Penicillin possibly acts as an analogue of the L-Ala-g-D-Glu
portion of the pentapeptide chain. However, the carboxylate
group that is essential to penicillin activity is not present in
this portion
Mechanism of action - bacterial cell wall synthesis
Alternative theory- Pencillin mimics D-Ala-D-Ala.
Normal Mechanism
Pe ptide
Chain
D-Ala
OH
Pe ptide
Chain
Pe ptide
Chain
D-Ala
CO 2H
Pe ptide
Chain
D-Ala
Gly
D-Ala
O
H
OH
Pe ptide
Chain
Gly
Mechanism of action - bacterial cell wall synthesis
Alternative theory- Penicillin mimics D-Ala-D-Ala.
Mechanism inhibited by penicillin
Blocked
Pe ptide
Chain
Blocked
H2O
O
R
C
O
H
NH
S
N
O
H
OH
Me
Me
R
O
Gly
C
NH
H
O
R
S
NH
H
O
HN
HN
Me
CO2H
O
C
Me
CO2H
Blocked
O
S
Me
Me
CO2H
Irreversibly blocked
Mechanism of action - bacterial cell wall synthesis
Penicillin can be seen to mimic acyl-D-Ala-D-Ala
R
R
C
H
N
H
H
S
C
Me
O
H
N
H
H
N
O
N
O
Me
O
CO2H
Penicillin
Me
H
CH3
CO2H
Acyl-D-Ala-D-Ala
Penicillin Analogues - Preparation
1) By fermentation
• vary the carboxylic acid in the fermentation medium
• limited to unbranched acids at the a-position i.e. RCH2CO2H
• tedious and slow
2) By total synthesis
• only 1% overall yield (impractical)
3) By semi-synthetic procedures
• Use a naturally occurring structure as the starting material for
analogue synthesis
Penicillin Analogues - Preparation
O
H
N
C
H
S
CH2
Me
Penicillin G
N
Me
O
CO2H
Penicillin acylase
or chemical hydrolysis
H2N
Fermentation
H
H
S
N
Me
Me
O
6-APA
CO2H
O
R
C
Cl
O
C
H H
N
H
S
Me
R
N
Semi-synthetic penicillins
Me
O
CO2H
Penicillin Analogues - Preparation
Problem - How does one hydrolyse the side chain by chemical
means in presence of a labile b-lactam ring?
Answer - Activate the side chain first to make it more reactive
PhCH2
O
C NH
S
ROH
PhCH2 C N
PEN
N
O
PCl5
OR
Cl
H2O
PhCH2 C N
PEN
6-APA
CO2H
Note - Reaction with PCl5 requires involvement of nitrogen’s
lone pair of electrons. Not possible for the b-lactam nitrogen.
Problems with Penicillin G
•
It is sensitive to stomach acids
•
It is sensitive to b-lactamases enzymes which hydrolyse the blactam ring
•
it has a limited range of activity
Problem 1 - Acid Sensitivity
Reasons for sensitivity
1) Ring Strain
O
C
H
N
H
H
S
R
Me
Acid or
enzyme
O
O
C
H
N
N
Me
O
CO2H
H
S
R
HO
H2O
H
N
Me
Me
C
H
N
H
H
S
R
HO2C
HN
Me
Me
O
H
CO2H
CO2H
Relieves ring strain
Problem 1 - Acid Sensitivity
Reasons for sensitivity
2) Reactive b-lactam carbonyl group
Does not behave like a tertiary amide
Tertiary amide
R
R
C
R
C
NR2
O
O
b-Lactam
Unreactive
N
R
Me
S
S
Me
Me
O
N
CO2H
H
Folded ring
system
•
•
X
N
Me
O
CO2H
Impossibly
strained
Interaction of nitrogen’s lone pair with the carbonyl group is not possible
Results in a reactive carbonyl group
Problem 1 - Acid Sensitivity
Reasons for sensitivity
3) Acyl Side Chain
- neighbouring group participation in the hydrolysis mechanism
R
H
C
N
H
S
O
N
O
N
R
S
N
R
S
-H
O
N
O
O
HN
O
H
Further
reactions
Problem 1 - Acid Sensitivity
Conclusions
•
•
•
The b-lactam ring is essential for activity and must be
retained
Therefore, cannot tackle factors 1 and 2
Can only tackle factor 3
Strategy
Vary the acyl side group (R) to make it electron withdrawing to
decrease the nucleophilicity of the carbonyl oxygen
H
N
E.W.G.
H
S
C
N
O
Decreases
nucleophilicity
O
Problem 1 - Acid Sensitivity
Examples
PhO
X
H
N
CH2
H
S
C
electronegative
oxygen
•
•
•
•
HC
N
Better acid stability and orally active
But sensitive to b-lactamases
Slightly less active than Penicillin G
Allergy problems with some patients
H
S
N
O
O
Penicillin V
(orally active)
H
N
C
R
O
a
O
X = NH 2, Cl, PhOCONH,
Heterocycles, CO2H
•
Very successful semisynthetic penicillins
e.g. ampicillin, oxacillin
Natural penicillins include Penicillin
G (parenteral) and Penicillin V (oral)
Gram-positive
bacteria
Streptococcus pyogenes, Viridans group
streptococci, Some Streptococcus
pneumoniae, Some Enterococci, Listeria
monocytogenes
Gram-negative
bacterai
Neisseria meningitidis, Some Haemophilus
influenzae
Anaerobic
bacteria
Clostridia spp. (except C. difficile),
Antinomyces israelii
Spirochetes
Treponema pallidum Leptospira spp.
Problem 2 - Sensitivity to b-Lactamases
Notes on b-Lactamases
• Enzymes that inactivate penicillins by opening b-lactam rings
• Allow bacteria to be resistant to penicillin
• Transferable between bacterial strains (i.e. bacteria can
acquire resistance)
• Important w.r.t. Staphylococcus aureus infections in hospitals
• 80% Staph. infections in hospitals were resistant to penicillin
and other antibacterial agents by 1960
• Mechanism of action for lactamases is identical to the
mechanism of inhibition for the target enzyme
•
But product is removed efficiently from the lactamase active
site
O
O
C
H
N
H
C
S
R
N
O
CO2H
H
S
Me
Me
H
N
R
b-Lactamase
HO2C
HN
Me
Me
CO2H
Problem 2 - Sensitivity to b-Lactamases
Strategy
• Block access of penicillin to active site of enzyme by
introducing bulky groups to the side chain to act as steric
shields
• Size of shield is crucial to inhibit reaction of penicillins with blactamases but not with the target enzyme (transpeptidase)
O
Bulky
group
C
H
N
H
H
S
Me
R
N
Enzyme
Me
O
CO2H
Problem 2 - Sensitivity to b-Lactamases
Examples - Methicillin (Beecham - 1960)
ortho groups
important
O
MeO
C
H
N
H
H
S
N
OMe
Me
Me
O
CO2H
•
•
•
•
•
•
•
Methoxy groups block access to b-lactamases but not to transpeptidases
Active against some penicillin G resistant strains (e.g. Staphylococcus)
Acid sensitive (no e-withdrawing group) and must be injected
Lower activity w.r.t. Pen G vs. Pen G sensitive bacteria (reduced access
to transpeptidase)
Poorer range of activity
Poor activity vs. some streptococci
Inactive vs. Gram - bacteria
Problem 2 - Sensitivity to b-Lactamases
Examples - Oxacillin
R'
O
C
R
N
O
H
H
S
N
Me
Bulky and
e- withdrawing
•
•
•
•
•
•
•
•
H
N
Me
Oxacillin
R = R' = H
Cloxacillin R = Cl, R' = H
Flucloxacillin R = Cl, R' = F
Me
O
CO2H
Orally active and acid resistant
Resistant to b-lactamases
Active vs. Staphylococcus aureus
Less active than other penicillins
Inactive vs. Gram - bacteria
Nature of R & R’ influences absorption and plasma protein binding
Cloxacillin better absorbed than oxacillin
Flucloxacillin less bound to plasma protein, leading to higher
levels of free drug
Antistaphylococcal Penicillins include Nafcillin and Oxacillin (parenteral) as well as
Dicloxacillin (oral)
Gram-positive bacteria
Some Staphylococcus
aureus, Some
Staphylococcus
epidermidis
Problem 3 - Range of Activity
Factors
1. Cell wall may have a coat preventing access to the cell
2. Excess transpeptidase enzyme may be present
3. Resistant transpeptidase enzyme (modified structure)
4. Presence of b-lactamases
5. Transfer of b-lactamases between strains
6. Efflux mechanisms
Strategy
• The number of factors involved make a single strategy
impossible
• Use trial and error by varying R groups on the side chain
• Successful in producing broad spectrum antibiotics
• Results demonstrate general rules for broad spectrum
activity.
Problem 3 - Range of Activity
Results of varying R in Pen G
1. R= hydrophobic results in high activity vs. Gram + bacteria
and poor activity vs. Gram - bacteria
2. Increasing hydrophobicity has little effect on Gram + activity
but lowers Gram - activity
3. Increasing hydrophilic character has little effect on Gram
+ activity but increases Gram - activity
4. Hydrophilic groups at the a-position (e.g. NH2, OH, CO2H)
increase activity vs Gram - bacteria
Problem 3 - Range of Activity
Examples of Aminopenicillins include:
Class 1 - NH2 at the a-position
Ampicillin and Amoxicillin (Beecham, 1964)
H
H
NH2
HO
C
C
H
N
NH2
C
H
C
H
N
H
O
O
O
Ampicillin (Penbritin)
2nd most used penicillin
O
Amoxicillin (Amoxil)
Problem 3 - Range of Activity
Examples of Aminopenicillins Include:
Properties
• Active vs Gram + bacteria and Gram - bacteria which do
not produce b-lactamases
• Acid resistant and orally active
• Non toxic
• Sensitive to b-lactamases
• Increased polarity due to extra amino group
• Poor absorption through the gut wall
• Disruption of gut flora leading to diarrhea
• Inactive vs. Pseudomonas aeruginosa
•Amoxicillin is sometimes used together with
clarithromycin (Biaxin) to treat stomach ulcers
caused by Helicobacter pylori, a Gram - bacteria
•Also, a stomach acid reducer (lansoprazole, or
Prevacid) is sometimes added.
Helicobacter pylori
Helicobacter pylori is linked to stomach inflammation,
which may also result in gastric ulcers and stomach
cancer
•In the early 20th century, ulcers were believed caused by
stress
•In 1982, Robin Warren and Barry Marshall, two Australian
physicians, suggested link between H. pylori and ulcers
•Medical community was slow to accept (first abstract
describing such results was rejected for a poster)
In 2005, the two researchers, Barry Marshall and J.
Robin Warren, received the Nobel Prize in medicine
for their discovery of the bacterium Helicobacter pylori
and its role in gastritis and peptic ulcer disease
Problem 3 - Range of Activity
Prodrugs of Ampicillin (Leo Pharmaceuticals - 1969)
O
H
R=
NH2
C
CH2O
CMe3
PIVAMPICILLIN
C
C
H
N
O
H
H
S
O
Me
R=
TALAMPICILLIN
O
Me
N
O
O
CO2R
R=
CH
Me
O
C
O
CH2Me
BACAMPICILLIN
Properties
• Increased cell membrane permeability
• Polar carboxylic acid group is masked by the ester
• Ester is metabolised in the body by esterases to give the free
drug
Problem 3 - Range of Activity
Mechanism
H
PEN
O
H
PEN
H
C
C O CH2 O
C O CH2
CMe3
ENZYME
C OH
O
O
O
O
•
•
•
PEN
Formaldehyde
Ester is less shielded by penicillin nucleus
Hydrolysed product is chemically unstable and degrades
Methyl ester of ampicillin is not hydrolysed in the
body - bulky penicillin nucleus acts as a steric shield
The aminopenicillins include Ampicillin (parenteral) as well as
Amoxicillin and Ampicillin (both oral)
Gram-positive bacteria
Streptococcus pyogenes,
Viridans streptococci,
Some Streptococcus
pneumoniae, Some
enterococci Listeria
monocytogenes
Gram-negative bacteria
Neisseria meningitidis,
Some Haemophilus
influenzae, Some
Enterobacteriaceae
Anaerobic bacteria
Clostridia spp. (except C.
difficile), Antinomyces
israelii
Spirochetes
Borrelia burgdorferi