Antibiotics - Penicillins

Medicinal Chemistry 3

PCH 423

Lecture 3

Number of slides: 37

Apr 17, 2024 1

 Intended Learning Outcomes (ILOs)

• At the end of the lecture the students will be able to:

 Define and classify antibiotics

 Write the nomenclature of penicillins

 Describe the mechanism of action of penicillins

 Explain the Structure Activity Relationship (SAR)

 Mention the pharmacological activity

 Tell the assay methods of β-lactam antibiotics

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 Antibiotics - Introduction
Definition:
Antibiotics are microbial metabolites or synthetic analogs of microbial
metabolites, are capable of inhibiting the growth and/or survival of one
or more species of microorganisms in low concentrations.
Any substance to be classified as an antibiotic should meet the
following conditions:
1.Product of metabolism.
2.Synthetic product produced as a structural analogue of a naturally
occurring antibiotic.
3.Antagonizes the growth or survival of one or more species of
microorganisms.
4.Effective in low concentrations.

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 Antibiotics – Chemical Classification
Name of the Structural features Examples
group
β-lactam antibiotics
1. Penicillins Four membered β-lactam ring 1. Ampicillin
2. Cephalosporins 2. Cephalexin
3. Monobactams 3. Aztreonam
Non-β-lactam antibiotics
1. Tetracyclines Four annulated six-membered Chlortetracycline
rings (derivatives of Doxycycline
octahydronaphthacene) Minocycline
2. Amphenicols Class of compounds with Chloramphenicol
phenylpropanoid structure Thiamphenicol
3. Macrolides A large lactone ring with a Erythromycin
ketone group (macrolide) Clarithromycin
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 Antibiotics – Chemical Classification Cont.
Name of the group Structural features Examples
4. Lincomycins Contain an unusal 8-carbon Lincomycin
(Lincosaminides) sugar, a thiomethyl Clindamycin
aminooctoside
5. Polypeptides Possess a polypeptide structure Bacitracin
Polymyxin B
6. Ansamycins Contain a macrocyclic ring Rifampin
bridged across two nonadjacent Rifabutin
positions of an aromatic
nucleus
7. Aminoglycosides Amino sugars linked Streptomycin
glycosidically to rest of the Neomycin
structure Paromomycin

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 β-Lactam Antibiotics
Antibiotics that possess the β-lactam (a four-membered cyclic amide)
ring structure are the dominant class of agents currently used for the
chemotherapy of bacterial infections.

Three major groups of β-lactam antibiotics are: Penicillins,

cephalosporins and monobactams.

Penicillin contains a highly unstable bicyclic system consisting of a

four-membered ß-lactam ring fused to a five-membered thiazolidine
ring. The skeleton of the molecule suggests that it is derived from the
amino acids cysteine and valine.

The overall shape of the molecule is like a half-open book

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 Nomenclature of Penicillins
Two numbering systems for the fused bicyclic heterocyclic system
exist.
1. The Chemical Abstracts system initiates the numbering with the
sulfur atom and assigns the ring nitrogen the 4 position. Thus penicillins
are named as 1-thia-4-azabicyclo[3.2.0]heptanes, according to this
system.
2. The USP numbering system is the reverse of the Chemical Abstracts
procedure, assigning number 1 to the nitrogen and number 4 to the
sulfur atom.

1-Thia-4-azabicyclo 4-Thia-1-azabicyclo
[3.2.0]heptane [3.2.0]heptane

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 Nomenclature of Penicillins Cont.
Three simplified forms of penicillin nomenclatures:
1. Based on the name “penam” (β-lactam + thiazolidine)
4
5 S
6
6-Acylamino-3,3-
3
N dimethyl-penam-2-
7 1
2 carboxylic acid
O

Penam
(4-Thia-1-azabicyclo-
[3.2.0]heptane)-7-one)

2. Based on the name “penicillanic acid”

6-Acylamino
penicillanic acid

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 Nomenclature of Penicillins Cont.
3. Trivial nomenclature:
The entire 6-carbonylaminopenicillanic acid portion of the molecule is
named as “penicillin” and distinguishes the compounds on the basis of
the R group of the acyl portion of the molecule.
Thus, penicillin G is names benzylpenicillin and penicillin V is
phenoxymethylpenicillin.
H 4
N
6 5 S CH3
3
O
N
7 1 2 CH3
O
O
R = Benzyl HO
Penicillin G
Penicillin (Benzylpenicillin)

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 Structural features of Penicillins
Penicillin contains a highly unstable bicyclic system consisting of a
four-membered β-lactam ring fused to a five-membered thiazolidine
ring.
The skeleton of the molecule suggests that it is derived from the
amino acids cysteine and valine. The overall shape of the molecule is
like a half-open book.

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 Structural features of Penicillins cont.

• Consist of highly strained fused bicyclic rings [ β-lactam +

Thiazolidine]
• A free carboxylic function at C-2 with pKa value from 2.6 -2.7.
• One or more properly substituted amino function at C-6.
• Three chiral C-atoms (asymmentric centers) at C-2, C-5 and C-6
O
R NH
H S CH3

CH3
O H N H
COOH

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 Electrophilicity of carbonyl carbon
The ß-lactam nitrogen is unable to feed its lone pair of electrons into
the carbonyl group since this would require the bicyclic rings to
adopt an impossibly strained flat system.

As a result, the lone pair is localized on the nitrogen atom and the
carbonyl group is far more electrophilic than one would expect for a
tertiary amide. A normal tertiary amide is far less susceptible to
nucleophiles since the resonance structures above reduce the
electrophilic character of the carbonyl group.

In penicillin, the non-coplanarity of fused bicyclic rings along the

C-5, N-1 axis suppress the normal amide resonance

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 Electrophilicity of carbonyl carbon cont.

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 Mechanism of action
Penicillin kills susceptible bacteria by specifically inhibiting the
transpeptidase that catalyzes the final step in cell wall biosynthesis,
the cross-linking of peptidoglycan.
Penicillin is a structural analog of the acyl-D-alanyl-D-alanine
terminus of the pentapeptide side chains of nascent peptidoglycan, and
penicillin by virtue of its highly reactive beta-lactam structure,
irreversibly acylates the active site of the cell wall transpeptidase.

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 Mechanism of action Cont.

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 Instability of penicillins
1. Acid-catalysed degradation
Acid-catalyzed degradation of penicillins in the stomach leads to poor
oral bioavailability.

Substitution of an electron-withdrawing group in the 6-acyamino side

chain would minimize sensitivity of the β-lactam ring to acid hydrolysis.
2. Side arm aided ring opening (acid-catalyzed)

Azalactonization

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 Instability of penicillins cont.
The acylamino side chain can act as an internal nucleophile. EWGs
decrease the reactivity (nucleophilicity) of the side chain amide
carbonyl oxygen atom toward participation in β-lactam ring opening.
3. Enzymatic inactivation
Some bacteria (e.g. Staphylococcus aureus) resist the action of
penicillins by producing β-lactamases, they catalyze the hydrolytic
opening of the β-lactam ring of penicillins to produce inactive
penicilloic acids.

Introduction of bulky group (steric hindrance) into the 6-acyl amino

side chain will protect the penicillins from β-lactamases .
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 Structure Activity Relationship (SAR)
Acylamino side Four membered β-lactam Sulfur at position 4 is not
chain is essential ring is essential for activity essential for activity e.g.
carbapenems
Electron
Five membered thiazolidine
withdrawing groups
ring is preferable but not
(e.g. Cl, F, etc) and
essential for activity
EW heteroaromatic
e.g. Monobactams
ring (e.g.isoxazole)
– increases acid
stability Bicyclic system (penam)
confers further strain to β-
lactam ring and results in
Bulky group provides β-
↑ reactivity and ↓ stability
lactamase resistance
The ionized form of carboxylic group at C-2
Polar & ionizable groups is essential for binding to Lys-NH3+ of
yields broad-spectrum transpeptidase. Reduction to alcohol or
penicillins esterification will reduce the activity
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 Penicillins Classes
NH 4

1) Natural penicilins 6 5 S
3
CH3

O
N
• Penicillin G (Benzyl penicillin) and O
7 1 2 CH3

its derivatives O
• Penicillin V (Phenoxymethyl penicillin) HO
Penicillin G
• Produced naturally from culture media (Benzylpenicillin)

• Acid labile NH 4
O 6 5 S CH3
• Active only against G +ve bacteria 3
O
N
2 CH3
• β-lactamase labile O
7 1

O
Derivatives: HO
Penicillin V
Sod. salt, water soluble for IV injection (Phenoxmethylpenicillin)

Penicillin G procaine, water insoluble,

for IM injection (Depot effect)
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2) Semisynthetic penicilins
• Prepared by adding precursors to the fermentation media ,
e.g. carboxylic acid.
• The added precursor will be incorporated into the side chain
of the new penicillin. (Limited results)
• Isolation of 6-Aminopenicillanic acid (6-APA) and then
acylation chemically

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2.1) Acid-stable penicilins

• Powerful electron withdrawing group in the acylamino side chain

prevents the acidic rearrangement
• The inductive pulling effect should draw electrons away from the
carbonyl oxygen and reduce its tendency to act as a nucleophile.
CH3

4 NH 4
NH
O 6 5 S CH3 O 6 5 S CH3
3 3
O O
N N
7 1 2 CH3 7 1 2 CH3
O O
O O
HO HO
Penicillin V Phenethicillin
(Phenoxmethylpenicillin)

• Acid stable and orally active

• Active against G +ve bacteria only
• β-lactamase labile.
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 2.2) -Lactamase-resistant penicillins
OCH3
In general increasing the steric hindrance
NH 4
(introducing bulkier group) at the α-carbon
6 5 S CH3 of the acyl group increased resistance to β-
3
OCH3 O
7
N
2 CH3
lactamase-producing bacteria. The α-acyl
1
O
carbon could be a part of an aromatic (e.g.,
O
HO phenyl or naphthyl) or heteroaromatic (e.g.,
Methicillin
(2,6-Dimethoxyphenylpenicillin) 4-isoxazolyl) system
Substitutions at the ortho positions of a
phenyl ring (e.g., 2,6-dimethoxyl
H
[methicillin] or the 2 position of the naphthyl
4
N
6 5 S CH3 system (e.g., 2-ethoxy [nafcillin]) increase
OC2H5 O N
3
the steric hindrance of the acyl group and
CH3
confer more β-lactamase resistance than
7 1 2
O

HO
O
shown by unsubstituted compounds.
Nafcillin
(2-Ethoxy-1-naphthylpenicillin)

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-Lactamase Resistant penicillins cont.
For bulkier substituents the members of
the 4-isoxazolyl penicillin family (e.g.,
R' R
oxacillin, cloxacillin, and dicloxacillin)
N H
N
S
4 require both the 3-aryl and 5-methyl
6 5 CH3
O

CH3
O N
3

CH3
substituents for effectiveness against β-
7 1 2
O
O lactamase-producing bacteria.
HO

R, R'= H Oxacillin (5-Methyl-3-phenyl-4-isoxazolylpenicillin)

R = Cl, R' = H Cloxacillin (5-Methyl-3-(2-chlorophenyl)-4-isoxazolylpenicillin)

R, R'= Cl Dicloxacillin (5-Methyl-3-(2,6-dichlorophenyl)-4-isoxazolylpenicillin)

R = Cl, R' = F Flucloxacillin (5-Methyl-3-(2-chloro-6-fluorophenyl)-4-isoxazolylpenicillin)

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 Why do penicillins show poor activity against G –ve
bacteria?
1. G-ve bacteria have a coating on the outside of their cell wall
consists of a mixture of fats, sugars and proteins. The outer
surface may have an overall –ve or +ve charge depending on its
constituents. Penicillin has a free carboxylic acid which if
ionized would be repelled by the -ve charge.
Alternatively, the fatty portion of the coating may act as a
barrier to the polar hydrophilic penicillin molecule.
The only way penicillin can pass such a barrier is through
protein channels in the outer coating.
2. High levels of transpeptidase enzyme in some G-ve bacteria.
3. Modification of the transpeptidase by mutation.
4. Presence of ß-lactamase.
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 2.3 Broad-spectrum penicillins
a) α-Amino group
NH2
Introduction of an ionized or polar
H
N 4
6 5 S CH3 groups (-NH2, -OH) into the α-position
3
O N
O
7 1 2 CH3
of the acylamino side chain confers
O
HO activity against Gram-negative bacilli
Ampicillin
α-Aminobenzyl penicillin
(e.g., ampicillin and amoxicillin). The
NH2
H
introduction of α-amino group creates
N 4
S
6 5

3
CH3
an additional chiral center.
O N
2 CH3
They are more labile than penicillin G to
7 1
HO O
O
HO

Amoxicillin
the action of β-lactamase.
α-Amino-p-hydroxybenzyl penicillin

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The expanded spectrum of activity is associated with the hydrophilic
property of the molecules which facilitates the selective penetration
through porin channels of the Gram-negative bacteria.
The α-aminobenzylpenicillins (ampicillin & amoxicillin) exists as the
protonated form in acidic (as well as neutral ) solutions, and the
ammonium group is known to be powerfully electron-withdrawing and
prevent acid rearrangement of β-lactam ring .

b) α-Carboxyl group

Incorporation of an acidic substituent (-COOH) at the α-benzyl

carbon atom of penicillin G results in α-caboxybenzyl penicillin
(carbenicillin). The high polarity of carbenicillin allows the molecule
to penetrate through the cell envelope of Gram-negative bacteria via
porin channels.

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 COOH
H
N 4
Ticarcillin is an isostere of carbenicillin
6 5 S CH3 in which the phenyl group is replaced
3
O
N
2 CH3
by a thienyl group.
7 1
O Advantages of ticarcillin:
O
HO 1.Better pharmacokinetic properties
Carbenicillin
(higher serum levels and longer
α-Caboxybenzyl penicillin duration of action)
COOH 2.Greater invitro potency against
H
N 4 several species of Gram-negative
S
6 5 S CH3
bacilli.
3
O
7
N
1 2 CH3 •Active against Pseudomonas
O
O aurogenosa
HO
•Acid labile
Ticarcillin

α-Caboxy-3-thienylpenicillin
•Active against Gram-negative bacteria

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 c) Acylureidopenicillins (e.g., Azlocillin, Mezlocillin and
O O Piperacillin
•These are acylated derivatives of
HN
N
NH ampicillin.
H
N
S CH
6
•Greater activity against some
5
4

O N
Gram-negative bacilli 3

CH
O
7
•Active against anaerobic bacteria
1 2 3

O
HO •Sensitive to β-lactamases
Azlocillin
•Unstable under acidic conditions
O O
O
Mezlocillin is a broad-spectrum
N N
NH Penicillin. It is active against both
H
N 4 Gram-negative and some Gram-
6 5 S CH3

O
3 positive bacteria.
N
O
7 1 2 CH3
It is excreted by the liver, therefore
HO
O
it is useful for biliary tract
Piperacillin infections, such as ascending
cholangitis
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 d) 6-α-methoxy penicillin e.g., Temocillin
COOH
H OCH3 4
N
5 S CH3
S 6
3
O
N
7 1 2 CH3
O
O
HO
Temocillin

Temocillin (6-α-methoxy-ticarcillin) is a semisynthetic, narrow-

spectrum, beta-lactamase-resistant penicillin with antibacterial
activity.
Temocillin is an alternative to treat urinary tract infections with
bacteria producing extended spectrum beta-lactamase (ESBL).
The methoxy group attached to the C6 position of the penam
nucleus confers stability against a wide variety of β-lactamases,
including most ESBLs, AmpCs and even some carbapenemases.
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2.4 Latent Penicillins
NH2 Pivampicillin is a
H
N 4 pivaloyloxymethyl ester of
S
6 5

3
CH3
ampicillin. It is a prodrug, which is
O
O 7
N
1 2 CH3 thought to enhance the oral
O
O
bioavailability of ampicillin because
H3C
O
O
of its greater lipophilicity
H3C
CH3 compared to that of ampicillin.
NH2
Pivampicillin
Bacampicillin is 1-ethoxycarbonyl-
H
N 4 oxyethyl ester of ampicillin. It is a
S CH3
prodrug of ampicillin with no anti-
6 5

3
O
7
N
1 2 CH3 bacterial activity. After oral
O
O absorption, bacampicillin is
H3C O O O
hydrolyzed by esterases in the
O CH3
plasma to form ampicillin.
Bacampicillin

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 β-lactamase resistant combinations
1) Clavulanic acid and Amoxicillin (Augmentin®) 4
5 O
6

• Clavulanic acid is an antibiotic isolated N 2

3 CH CH2OH

from Streptomyces clavuligeris O

7 1

COOH
• It is a 1-oxopenam derivative Clavulanic acid
• Lack of 6-acylamino side chain
but possessing a 2-hydroxyethylidene moiety at C-3, acid-stable.
• Weak antibacterial activity, but potent inhibitor of β–lactamases.
• Combination of amoxicillin and potassium clavulanate is used for the
treatment of skin, respiratory, ear, and urinary tract infections caused
by β-lactamase-producing bacterial strains.
• It is also used in combination with ticarcillin, for the treatment of
septicemia, lower respiratory tract infections, and urinary tract
infections caused by β-lactamase-producing bacteria.

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 O 4 O
2) Sulbactam and Ampicillin 6
5 S CH3
3
N 2
7 1 CH3
• Sulbactam is a synthetic non-classical O
COONa

β–lactam derivative. Sulbactam

• It is penicillanic acid sulfone or Dioxopenicillanic acid.

• Weak antibacterial agent but potent inhibitor of β–lactamases.
• Sulbactam in combination with ampicillin is recommended for
the treatment of skin, tissue, intra-abdominal, and gynecological
infections caused by β-lactamase-producing strains of S.aureus,
E.coli, Klebsielle spp., P.mirabilis, B.fragilis, and Enterobacter
and Acinetobacter spp.

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3) Carbapenems 4
5 H H 4
6 HO
3
5
S
N 6 3 R
7 1 H3C
N 2
O 2 7 1
O
COOH
Carbapenem
(1-Azabicyclo-[3.2.0]- Carbapenems
hept-2-ene)-7-one)

• Two structural features of carbapenems are shared with penicillins

and cephalosporins: a fused bicyclic ring system containing a β-
lactam and an equivalently attached 2-carboxyl group.
• The bicyclic system consists of a carbapenem containing a double
bond between C-2 and C-3 (2-carbapenem or Δ2-carbapenem).
• 6α- 1-Hydroxyethyl group instead of the acylamino side chain
• Thioether function.
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3.1 Thienamycin 3.2 Imipenem
H H 4
H H 4
HO HO
S 5
S
6 5 6
3 NH2 3 NH NH
H3C H3C
2 N 2
N 7 1
7 1
O O
COOH COOH

Imipenem
Thienamycin

• Novel β-lactam antibiotic isolated from Streptomyces cattleya

•Resistant to inactivation by β-lactamases ( to be a function of the α-
1-hydroxyethyl side chain because this property is lost in 6-nor
derivative)
•Susceptible to hydrolysis in both acidic and alkaline solutions
(because of the strained nature its fused ring system containing an
endocyclic double bond), optimum stability at pH between 6 and 7
•Inactivation by intermolecular aminolysis
• Avoided by N-formimidoylation (c.f Imipenem)
• Broad spectrum (in vitro), mainly for urinary tract infections.
• Short t ½ (hydrolytic inactivation by renal dehydropeptidase-I).
overcame by combination with cilastatin (inhibitor of DHP-I)
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 H H
4) Monobactams H2N
• Monocyclic β-lactams. N
O SO3H
• Acidic function is sulfonic acid moiety.
3-Amino monobactamic acid
• 3-Amino function.
• 3-Amino monobactamic acid (3-AMA) derivatives.
S
• weak antibacterial activity. O H CH3
H2N N NH
4.1 Aztreonam Disodium O
N
N
O SO3Na
• Monobactam prepared synthetically.
COONa
• Effective against G –ve bacteria only
e.g: E.coli; K. pneumoniae; P. aeruogenosa. Aztreonam Disodium
• β-lactamase resistant
• Used for treatment of urinary and lower respiratory tract infections,
intra-abdominal infections, as well as septicemias.
• The disodium salt is very soluble in water and taken IV.

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 S CH3
4.2 Tigemonam O H
CH3
H2N N NH O
N
O N –
O O S O

O
O

OH
• Newer monobactam Tigemonam

• Orally active, oral absorption is excellent.

• Highly resistant to β-lactamase
• Very active against Enterobacteriaceae, including E.coli,
Klebsiella, Proteus, Citrobacter, serratia and Enterobacter spp.
• Exhibits good potency against H.influenzae and N.gonorrhoeae.
• Not effective against Gram-positive and anaerobic bacteria
• Inactive against P.aeruginosa.
Apr 17, 2024 36
 References:

1.Wilson and Gisvold's Textbook of Organic Medicinal and

Pharmaceutical Chemistry. 11th Edition. John H. Block and John
M. Beale, Jr., Lippincott, Williams & Wilkins Publishers 2004.

2.Foye’s “Principles of Medicinal Chemistry, Fifth Edition,” By

David A. Williams and Thomas L. Lemke, Lippincott Williams &
Wilkins Publishers, New York, 2002.

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