Penicillin

Antimicrobial and Antiviral Agents

Group 3
Aurelia Jeanita Sumarli 21010003
Calvianus Gery Pangestu 20010068
Griselia Suryani 20010133
Preish Kishore Raisinghani 20010220
Queen Saint Monica Vannessa Liu 20010222
Table of contents
01 02 03
Introduction Development Receptor
Pharmacological & PK Process & timeline Structure & function

04 05
Physicochemical SAR
Properties Drug-receptor interaction, drug design
Lipinski’s Rule of Five strategies, QSAR & CADD study
 01
Introduction
Drug name, classification, indication, MoA, ADME
Penicillin G
Generic Name :
Penicillin G / Benzylpenicillin /

Medical usage
benzylpenicillinc acid

IUPAC :
(2S,5R,6R)-3,3-dimethyl-7-oxo-6-[(2-phenyl
acetyl)amino]-4-thia-1-azabicyclo[3.2.0]hep
tane-2-carboxylic acid
Brand and Company :
Procaine Penicllin G - PT. Meiji Indonesia
Drug Classification → Beta lactam antimicrobial
● Used for treat several types of microbial
infection from both gram positive and gram
negative, as well as, most anaerobes
bacteria
● Resistance → Enterococci
● Administration →IV and IM injection in 4-6
doses apart

(Yip & Gerriets, 2022)

Mechanism of Action

Inhibiting the cell wall synthesis

Bacteria peptidoglycan has ability to prevent osmotic lysis
→ Penicillin inhibit the cross linking with catalyst used is
DD-transpeptidase enzyme

4-membered beta lactam ring

These beta lactam ring could bind to enzyme to inactive it
→ bacteria won’t be able to build the cell wall →
weakening of cell wall lead to death of cell

(Yip & Gerriets, 2022)

Adverse eect

Hypersensitivity Hematologic
Immediate onset and High dose may lead
delayed onset (rare) to coombs positive
hemolytic anemia
and neutropenia
Metabolic Nervous Urogenital
Salt from penicillin G Hyperreflexia, Urological
may cause electrolyte myoclonic twitches, manifestations with
imbalance seizure, and coma large IV dose include
after IV doses renal tubular damage
Indication
Pneumonia Streptococcal
infection
dose 600,000 - dose 600,000 -
1,000.000 units/day 1,000.000 units/day

Staphylococcal Bacterial
infection endocarditis Rat bite fever
dose 600,000 - dose 600,000 - dose 600,000 -
1,000.000 units/day 1,000.000 units/day 1,000.000 units/day

(Yip & Gerriets, 2022)

ADME
Absorption Distribution
Rapidly absorbed by VD 0.53 - 0.67 L/kg
IV and IM Injection and bind to serum
protein 45 - 68%

Metabolism Elimination
16-30% → penicilloic acid Eliminated by kidney
Small amount → hydoxylated Non renal clearance include
into 1 or more active hepatic metabolism
metabolite

(Yip & Gerriets, 2022)

 02
Drug Discovery and
Development
involves two steps
 The Discovery Stage of Antibacterial of Penicillin

1928 1939 1943 1945

Alexander Florey & Edward & Hodgkin &
Fleming Heatly Chain Low
Penicillin has an antibiotic Extraction, isolation, and Core of the chemical Confirmed the core of the
impact on Staphylococci production of penicillin structure of penicillin penicillin chemical
were discovered. was able to identified structure (𝛽- lactam)
(Cunha et al., 2019) (Bynum, 2019) (Lobanovska, 2019)
(Sahoo & Banik, 2020)

The Development Stage of Antibacterial of Penicillin

Synthesis of Pre-clinical and Post Marketing

Penicillin Clinical trial Surveillance
The synthesis of penicillin In 1941, Florey first Antimicrobial resistance
G is carried out by performed pre-clinical and surveillance is caused by
Penicillium chrysogenum clinical trials of penicillin 𝛽-lactamase
 How penicillin G is synthesized?
To synthesize Penicillin G, Penicillium chrysogenum required amino
acids (such as valine, and cysteine) (Sahoo & Banik, 2020).

Semi-synthetic preparation of
penicillin analogues starts from
6-APA.
(Sahoo & Banik, 2020)

Penicillin analogs are prepared

semi-synthetic

The biosynthesis of Penicillin G

 03
Receptor Structure
and Function
Structural of Penicillin Binding Protein (PBPs)
 Penicillin Binding Proteins
Protein binding proteins (PBPs) → the biosynthesis of peptidoglycan
(Sobhanifar et al., 2013).

TRANSGLYCOSYLASE TRANSPEPTIDASE
(TGase) (TPase)
in charge of lengthening create cross-links
the glycan strands between glycan strands
(Cho et al., 2016). (Cho et al., 2016).

Structure of PBP1b-beta lactam

complexes
(King et al., 2016)
 04
Physicochemical
Properties
Physical & chemical properties
Lipinski’s Rule of Five
Physical Properties
- Appearance: amorphous white powder

- Melting point: 214-217°C

- Solubility: slightly soluble in water (210 mg/L);

soluble in ethanol, ethyl acetate, benzene;
insoluble in petroleum ether

- Stability: inactivate in the presence of acids &

alkali hydroxides

(National Center for Biotechnology Information, 2023)

Chemical Properties
Properties Values Lipinski’s Rule of Five:
● MW less than 500
Molecular weight 334.4 g/mol ● No more than 5 HBD groups
Hydrogen bond donor 2 ● No more than 10 HBA groups
● Log P value less than +5
Hydrogen bond acceptor 5
Log P 1.83 Penicillin G: poor absorption
5 °C= 2.74
pKa
25 °C= 2.76
Heavy atom 23
Rotatable bond 4
Covalently-bonded unit 1

(National Center for Biotechnology Information, 2023)

 05
SAR Study
Drug-receptor interaction, QSAR, CADD
Drug Receptor Interaction

● Target Protein: PBP

○ PDB Code : 5OJ1 (PBP 2X from
S.pneumoniae in complex with
oxacillin & a tetrasaccharide)

● Drug used: Penicillin G

○ Belongs to β-lactam antibiotics
 Drug Receptor Interaction Cont’d

1) Recognition & Binding : Penicillin G → interact with active

site of PBP

2) Covalent Bond formation : β-lactam ring of penicillin-G →

covalent bond with a serine residue in active site of PBP
● covalent acylation inhibits the transpeptidase activity of
PBPs → preventing the cross-linking of peptidoglycan

3) Cell Lysis & death : Cell wall is disrupted → cells become

prone to osmotic pressure → cell lysis & death

(Montserrat Mora-Ochomogo & Lohans, 2021)

Drug design strategy

Modification of β-Lactam Ring

Computational
Approaches
Side Chain Optimization

Overcoming β-Lactamase
Resistance
Modification of ß-Lactamase Ring

● β-lactam ring → crucial for penicillin

○ Modifying this ring → improve PBP
binding ainity & antimicrobial
activity

● Examples of modification
○ variations in the side chain, ring
size, or ring substitutions →
enhance stability with PBPs

NOTE: Incorporating dierent heterocyclic rings, such as

thiazolidine or oxazolidine, in place of the β-lactam ring.
Side Chain Optimizations

● Rational modifications to the side chain:

○ Altering its length, introducing
dierent functional groups, or
optimizing the stereochemistry

● Examples of modification
○ incorporating a hydrophobic group,
such as an ethyl or isopropyl group →
strengthen hydrophobic interactions
& ↑lipophilicity of molecule
Overcoming ß-Lactamase Resistance

● Β-lactamase enzymes → degrade

penicillin G
○ Design strategy → introduce
steric hindrance and optimize the
electrostatic properties of drug

● Examples of modification
○ Adding large groups, such as
tert-butyl or phenyl, to the
β-lactam ring to increase steric
hindrance.
Computational Approaches
Ligand based drug design
● Used in absence of the receptor 3D information
● Relies on knowledge of molecules that bind to the biological target of interest
● Examples: 3D QSAR and ligand based pharmacophore mapping

Structure based drug design

● Used when there is available 3D structure of the receptor in PDB (Protein Data
Bank)
● Relies on clear relationship/ homology between sequence of target protein and at
least one known structure
● Examples: molecular docking and structure based pharmacophore modeling
Side Chains Variations

Functional
length branching
group

● Shorten/ lengthen side ● Introduce branching if ● Add or modify functional

chain → can impact the side chain → alter groups in the side chain
spatial arrangement and steric properties and → make new possible
interactions within PBP conformational flexibility interactions
active site
Ring Size Variation
Expansion or
Contractions
● Modify ring size of the
𝛽-lactam ring → impact
conformational flexibility and
shape complementary
Ring Substitution
Electrophilic
substitution
● Modify substituents on the
𝛽-lactam ring → influence
reactivity and stability

Heterocyclic Steric
Substitution hindrance
● Introduce hetero-atoms or ● Incorporate bulky
dierent heterocyclic rings substituent on the
in the 𝛽-lactam structure 𝛽-lactam ring → hinder
𝛽-lactamase access
 1. Substitute the S

Examples: a. By oxidation to SO2 or SO → improves acid

stability but decrease activity of agent

2. Introduce an EWG or electron donating group

a. Substitute with EWG at the 𝛼-position of penicillin G
→ further increase the stability of penicillin G

3. Replacement of acyl side chain

a. Replace with hydroxymethyl groups → improved
antimicrobial activity
b. Incorporate C-6 𝛼-methoxy group → have greater
stability against 𝛽-lactamase, increase duration
of action

4. Substitution of bulky group on 𝛼-carbon of side chain

a. Change the benzyl ring position (o or m position)
→ increase steric hindrance and protect drug
from lactamase resistance, gives more active
compound
CADD Study
● Receptor used: PBP 5OJ1
● Ligand used: penicillin G
● Molecular docking is done on
Chimera and Swiss Dock
● Data was used from SwissDock
● Free energy = -7.76
○ Had low binding energy
○ Had high binding ainity
● Penicillin G fits the pocket of
PBP
Limitations
1) Experimental Validation
● All modifications & strategy are based on theoretical considerations & in silico
modelling → need to validate the strategies via clinical trials & in vitro assay

2) Structural Variability of 5OJ1

● PBPs → very diverse and 5OJ1 may not be directly applicable to all PBPs

3) Pharmacokinetic considerations
● Factors such as oral bioavailability, distribution to target tissues, metabolism,
and elimination →impact the overall eicacy and therapeutic potential of the
drugs

4) Safety & Toxicity

● All modifications & strategy → need safety & toxicity profiles of modified
penicillin analogues
Conclusion
Penicillin G is a type of antimicrobial that is used to
treat several bacterial infection.
This drug is known to be less stable in acid and
interact with PBP.
In order to improve the penicillin G, several
modification could be done, such as ring
modification, ring substitution and etc.
References
Bynum, B. (2018). Rediscovering penicillin. The Lancet 392(10153), 1102-1109.
hps://doi.org/10.1016/S01406736(18)32295-5.
Cho, H., Wivagg, C. N., Kapoor, M., Barry, Z., Rohs, P. D. A., Suh, H., Marto, J. A., Garner, E.C., Bernhardt, T. G.(2016).
Bacterial cell wall biogenesis is mediated by SEDS and PBP polymerase families functioning
semi-autonomously. Nature Microbiology 1:16172. hps://doi.org/10.1038/nmicrobiol.2016.172.
Cunha, B. R., Fonseca, L. P., & Calado, C. R. C. (2019).
King, D. T., Wasney, G. A., Nosella, M., Fong, A., Strynadka, N. C. J. (2017). Structural Insights into Inhibition of
Escherichia coli Penicillin-binding Protein 1B. Journal of Biological CHemistry, 292(3), 979-993.
hps://doi.org/10.3390/antibiotics8020045.
Montserrat Mora-Ochomogo, & Lohans, C. T. (2021). β-Lactam antibiotic targets and resistance mechanisms: from
covalent inhibitors to substrates. 12(10), 1623–1639. hps://doi.org/10.1039/d1md00200g
National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 5904, Penicillin G.
Retrieved June 11, 2023 from hps://pubchem.ncbi.nlm.nih.gov/compound/Penicillin-G.
Sobhanifar, S., King, D. T., and Strynadka, N. C. (2013). Fortifying the wall: synthesis, regulation and degradation of
bacterial peptidoglycan. Current opinion in structural biology, 23(5),695-703.
hps://doi.org/10.1016/j.sbi.2013.07.008.
Yip, D. W., & Gerriets, V. (2022, May 19). Penicillin. PubMed; StatPearls Publishing.
hps://www.ncbi.nlm.nih.gov/books/NBK554560/
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