Patrick An Introduction to Medicinal Chemistry 3/e Chapter 16

ANTIBACTERIAL AGENTS
Part 1: Penicillins

PENICILLINS
O C R N O CO2H H N H H S Me

Me

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 Beechams (1958-60) - development of semi-synthetic penicillins Discovery of clavulanic acid and b-lactamase inhibitors

STRUCTURE
R=

O
CH2

C R
Acyl side chain

H H N

H S N Me Me CO2H
6-Aminopenicillanic acid (6-APA)

Benzyl penicillin (Pen G) R=

O CH2

O
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 R C NH H Me S Me O H N H CO2H

..

Folded envelope shape

Biosynthesis of Penicillins

O C R N O CO2H H N S Me

Me

CYS

VAL

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 1

SAR

Amide essential

Cis Stereochemistry essential

O C R

H N

Me

N O
bLactam essential CO2H

Me
Carboxylic acid essential

Conclusions

Bicyclic system essential

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 enzymes active site leading to irreversible inhibition
H H N H S N O Enz CO2H Me Me

O C R

O C

H H N

H S N H Me Me CO2H

O C R

H H N

H S Me Me CO2H

Nu

R Enz-Nu

-H

O C HN Nu-Enz

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

NAM
L-Ala NAG D-Glu

NAG NAM NAG

L-Ala D-Glu L-Lys

NAM
L-Ala NAG D-Glu L-Lys

NAM NAG
L-Ala D-Glu L-Ala D-Glu L-Lys L-Lys L-Ala D-Glu L-Lys

NAM
L-Lys L-Ala D-Glu

NAM

NAM

Bond formation inhibited by penicillin

L-Lys

Mechanism of action - bacterial cell wall synthesis

NAM L-Ala D-Glu L-Lys D-Ala D-Ala Gly Gly Gly Gly Gly NAG NAM L-Ala D-Glu L-Lys D-Ala D-Ala Gly Gly Gly Gly Gly NAG

SUGAR BACKBONE

PENICI LLI N

D-Alanin e

TRANSPEPTIDASE

NAM L-Ala D-Glu L-Lys D-Ala

NAG

NAM L-Ala D-Glu

NAG

SUGAR BACKBONE

Gly Gly Gly Gly Gly

L-Lys D-Ala

Gly Gly Gly Gly Gly

Cross linking

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

Peptide Chain
D-Ala
OH

Peptid e Chain
D-Ala CO 2H
D-Ala O

Peptide Ch ain

Peptid e Chain
D-Ala

Peptid e Chain

Gly

Gly

OH

Mechanism of action - bacterial cell wall synthesis

Alternative theory- Pencillin mimics D-Ala-D-Ala.
Mechanism inhibited by penicillin

Blocked
O R C NH H S N O
H

Peptide Ch ain

Blocked H2 O
O R C O NH H S Me Me CO2H

O
Me Me CO2H

Gly
NH O O H S Me

HN

HN O

Me CO2H

OH

Blocked

Irreve rsibly blocke d

Mechanism of action - bacterial cell wall synthesis

Penicillin can be seen to mimic acyl-D-Ala-D-Ala
R C O N O Me H N H H S Me

R C O O
CO2H

H N

Me H H N H CH3 CO2H

Penicillin

Acyl-D-Ala-D-Ala

R C H N Me H S N O Me Me CO2H

But 6-methylpenicillin is inactive despite being a closer analogue

Mechanism of action - bacterial cell wall synthesis

Penicillin may act as an umbrella inhibitor

R C O

H N

D- A l a - D - A l a

H S N Me Me CO2H R C H N H S HN O

Blocked

O
HO

Me Me

Acylation

Active Site
OH

CO2H
OH

Resistance to Penicillins
Penicillins have to cross the bacterial cell wall in order to reach their target enzyme But cell walls are porous and are not a barrier The cell walls of Gram +ve bacteria are thicker than Gram ve cell walls, but the former are more susceptible to penicillins

Resistance to Penicillins
Gram +ve bacteria Thick cell wall No outer membrane More susceptible to penicillins

Thick porous cell wall

Cell membrane Cell

Resistance to Penicillins
Gram -ve bacteria Thin cell wall Hydrophobic outer membrane More resistant to penicillins

Outer membrane L Periplasmic space

Hydrophobic barrier Porin Lactamase enzymes

L L

Thin cell wall L

Cell membrane

Cell

Resistance to Penicillins
Factors Gram -ve bacteria have a lipopolysaccharide outer membrane preventing access to the cell wall Penicillins can only cross via porins in the outer membrane Porins only allow small hydrophilic molecules that can exist as zwitterions to cross High levels of transpeptidase enzyme may be present The transpeptidase enzyme may have a low affinity for penicillins (e.g. PBP 2a for S. aureus) Presence of b-lactamases Concentration of b-lactamases in periplasmic space Mutations Transfer of b-lactamases between strains Efflux mechanisms pumping penicillin out of periplasmic space 1

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 C CH2 N O H N H S Me Penicillin G Me CO2H

Penicillin acylase or chemical hydrolysis

Fermentation

H2N

H S N Me Me CO2H
Cl

O
6-APA
O R C

O C R N O CO2H Me H H N H S Me

Semi-synthetic penicillins

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 N O CO2H Cl PhCH2 C N OR
ROH

PCl5

PhCH2 C N

H2O

PEN

PEN

6-APA

Note - Reaction with PCl5 requires involvement of nitrogens lone pair of electrons. Not possible for the b-lactam nitrogen.
1

Problems with Penicillin G

It is sensitive to stomach acids It is sensitive to b-lactamases - enzymes which hydrolyse the b-lactam ring it has a limited range of activity

Problem 1 - Acid Sensitivity

Reasons for sensitivity 1) Ring Strain

O C R
H2O

H N

H S N Me

Acid or enzyme

O C R HO N H N H H S Me

O C R HO2C HN H N H H S Me

Me CO2H

Me CO2H

Me CO2H

O
H

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 C O NR2
O R C N R R

Unreactive

b-Lactam
S

Me
S Me

Me O N H CO2H

N O CO2H

Me

Folded ring system

Impossibly strained

Interaction of nitrogens 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 C O N

H H S N O

S N O
H

S HN O

-H
O
O

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
E.W.G. C O N O H N H S

Decreases nucleophilicity

Problem 1 - Acid Sensitivity

Examples
PhO CH2 C H N H S

X HC R
N O

a
C O

H N

H S N O

electronegative oxygen

Penicillin V (orally active)

X = NH2, Cl, PhOCONH, Heterocycles, CO 2H

Better acid stability and orally active But sensitive to b-lactamases Slightly less active than Penicillin G Allergy problems with some patients

Very successful semisynthetic penicillins e.g. ampicillin, oxacillin

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 C R N O CO2H H N H S Me
R O C H N H S HO2C HN Me

Me

b-Lactamase

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
R

H N

H S Me

Me CO2H

Enzyme

Problem 2 - Sensitivity to b-Lactamases

Examples - Methicillin (Beechams - 1960)
ortho groups important
O MeO C H N H H S N O CO2H Me

OMe

Me

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 -ve bacteria

Problem 2 - Sensitivity to b-Lactamases

Examples - Oxacillin
R' O C R H N H H S N O CO2H Me

N O Me

Oxacillin R = R' = H Cloxacillin R = Cl, R' = H Flucloxacillin R = Cl, R' = F

Me

Bulk y and e- withdrawing

Orally active and acid resistant Resistant to b-lactamases Active vs. Staphylococcus aureus Less active than other penicillins Inactive vs. Gram -ve 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

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. 1

Problem 3 - Range of Activity

Results of varying R in Pen G 1. R= hydrophobic results in high activity vs. Gram +ve bacteria and poor activity vs. Gram -ve bacteria 2. Increasing hydrophobicity has little effect on Gram +ve activity but lowers Gram -ve activity 3. Increasing hydrophilic character has little effect on Gram +ve activity but increases Gram -ve activity 4. Hydrophilic groups at the a-position (e.g. NH2, OH, CO2H) increase activity vs Gram -ve bacteria

Problem 3 - Range of Activity

Examples of Broad Spectrum Penicillins Class 1 - NH2 at the a-position Ampicillin and Amoxycillin (Beechams, 1964)
H C C O H N H
O

NH2
HO

H C

NH2 H N

Ampicillin (Penbritin) 2nd most used penicillin

Amoxycillin (Amoxil)

Problem 3 - Range of Activity

Examples of Broad Spectrum Penicillins Properties Active vs Gram +ve bacteria and Gram -ve 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 diarrhoea Inactive vs. Pseudomonas aeruginosa

Problem 3 - Range of Activity

Prodrugs of Ampicillin (Leo Pharmaceuticals - 1969)
O

H C

NH2 H N

R=

C CH2O CMe3

PIVAMPICILLIN

C O

H S N Me Me
O

R=

TALAMPICILLIN

O CO2R

R=

CH Me

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 1

Problem 3 - Range of Activity

Mechanism

PEN

O C

PEN
CMe3 O

PEN
H O O

C O CH2 O O

C O CH2

C OH

ENZYME

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 1

Problem 3 - Range of Activity

Examples of Broad Spectrum Penicillins Class 2 - CO2H at the a-position (carboxypenicillins) Examples
CO2R CH C O N O CO2H H N H H S Me Me

R=H R = Ph

CARBENICILLIN CARFECILLIN

Carfecillin = prodrug for carbenicillin Active over a wider range of Gram -ve bacteria than ampicillin Active vs. Pseudomonas aeruginosa Resistant to most b-lactamases Less active vs Gram +ve bacteria (note the hydrophilic group) Acid sensitive and must be injected Stereochemistry at the a-position is important CO2H at the a-position is ionised at blood pH

Problem 3 - Range of Activity

Examples of Broad Spectrum Penicillins Class 2 - CO2H at a-position (carboxypenicillins) Examples
CO2H H H N H S Me Me CO2H

O O

TICARCILLIN

Administered by injection Identical antibacterial spectrum to carbenicillin Smaller doses required compared to carbenicillin More effective against P. aeruginosa Fewer side effects Can be administered with clavulanic acid

Problem 3 - Range of Activity

Examples of Broad Spectrum Penicillins Class 3 - Urea group at the a-position (ureidopenicillins) Examples
O

Azlocillin
Mezlocillin
MeO2S

HN

O R2N NH H H N H

N O

Me Me

Piperacillin

Et N O

N O

N O

CO2H

Administered by injection Generally more active than carboxypenicillins vs. streptococci and Haemophilus species Generally have similar activity vs Gram -ve aerobic rods Generally more active vs other Gram -ve bacteria Azlocillin is effective vs P. aeruginosa Piperacillin can be administered alongside tazobactam