1. Anti-Microbial Agents Anti-bacterial (antibiotics)
Basic Bacteriology
Part-11
Anti-Microbial Agents
Anti-bacterial (antibiotics)
Anti-Fungal
Anti-Viral

3. General Characteristics of Antimicrobial Drugs
For chemical to be used an antimicrobial agent (a drug), it has to have the following characteristics
Has a selective toxicity: which means that the chemical agent has the ability to kill or inhibit the growth of the infecting pathogen without affecting the host
Has good pharmacokinetics and pharmacodynamics  properties
To be chemically stable
To be financially affordable (inexpensive)
Spectrum of action of antibacterial agents (antibiotics):
1- Narrow-spectrum drugs: are those drugs that affect Gram-positive or Gram-negative bacteria
2- Broad-spectrum drugs: are those drugs that affect both Gram-positive and Gram-negative bacteria
3- Limited spectrum drugs: are those drugs that affect only particular bacterial pathogens such as anti-Mycobacterial antibiotics

4. Bactericidal antibiotics: are those antibiotics that have the ability to kill bacteria.
Note: the suffix cidal means lethal
Bacteriostatic antibiotics: are those antibiotics that inhibit growth of bacteria.
Note: the suffix static means to stop (inhibit), which means here, to stop or inhibit bacterial replication.
Effectiveness of an antibiotic can expressed in two ways:
1- Minimal Inhibitory Concentration (MIC): is the lowest concentration of an antibiotic that inhibits bacterial growth.
2- Minimal Bactericidal Concentration (MBC): is the lowest concentration of an antibiotic that kill bacteria.
Mechanisms of action of antibiotics:
Inhibition of peptidoglycan synthesis
Inhibition of protein synthesis
Inhibition of nucleotides synthesis
Inhibition of nucleic acid synthesis (DNA or RNA)
Disruption of microbial cell membrane

5. I-Antibiotics that inhibit peptidoglycan synthesis:
A- Beta-lactam antibiotics:
These antibiotics were given this name because they share the presence of the β-lactam ring in their chemical structures.
β-lactam ring is essential for their antibacterial activities
β-lactam antibiotics can be classified into four subfamilies:
Penicillins (core structure: 6-aminopenicillanic acid)
Cephalosporins (core structure: 7-aminocephalosporanic acid)
Carbapenems
Monobactam

6. Mechanism of action of β-lactam antibiotics:
β-lactam antibiotics bind to the transpeptidase enzyme which mediates cross-linking of peptidoglycan.
Binding of β-lactam antibiotics to this enzyme will inhibit its activity.
This will results in the formation of structurally-weak peptidoglycan.
In case that the bacterial cell is present in an environment with an osmotic pressure less than the osmotic pressure of the bacterial cell, water moves into the bacterial cell, the bacterial cell swells and eventually burses.
Accordingly, β-lactam antibiotics are bactericidal.
Note: β-lactam antibiotics are only effective while the bacteria is replicating. Why?

7. B- Glycopeptides:
Glycopeptides antibiotics inhibit peptidoglycan synthesis by a mechanism that is different from that of β-lactam antibiotics.
Glycopeptides antibiotics bind to and cover the last two amino acids of the peptide side chains peptidoglycan.
This will interfere with the cross-linking process that is mediated by the transpeptidase enzyme resulting the formation of structurally-weak peptidoglycan.
In case that the bacterial cell is present in an environment with an osmotic pressure less than the osmotic pressure of the bacterial cell, water moves into the bacterial cell, the bacterial cell swells and eventually burses.
Accordingly, Glycopeptides , are bactericidal.
Note: Because of their bulky structure, Glycopeptides antibiotics are unable to go through the outer membrane of Gram-negative bacteria. Accordingly, all Gram-negative are not affected by Glycopeptides

9. II-Antibiotics That Inhibit Bacterial Ribosome:
These antibiotics bind specifically to the bacterial ribosome to inhibit translation and thus inhibition of protein synthesis. These antibiotics can be classified into those that
Bind to 30S (small subunit of the ribosome), while others
Bind to or 50S (large subunit of the ribosome)
Binding of these antibiotics to the ribosome will interfere with the translation process by one of the following mechanisms.
1-Inhibiting the association of the small subunit of the ribosome with the large subunit
2- Inhibiting binding of aminoacyl-tRNA to the A site or releasing of tRNA form the E site
3-Inhibiting peptide bond formation
4- Interfering with mRNA reading

10. Examples of Antibiotics That Inhibit The Small Subunit of Bacterial Ribosome: (Please, memorize the underlined)
1- Aminoglycosides: ( Examples: Gentamicin, streptomycin)
2- Tetracyclines:
Examples of Antibiotics That Inhibit The Large Subunit of Bacterial Ribosome:
1- Macrolides: Example: erythromycin
2- Chloramphenicol

11. III-Antibiotics that inhibit nucleotide biosynthesis:
(Please, memorize the underlined)
These antibiotics are structural analogs that compete with the nucleotide intermediates in binding of the enzymes of the nucleotides biosynthetic pathways in bacteria.
Examples: Sulfonamides (sulfa drugs) and Trimethoprim

13. IV-Antibiotics that inhibit nucleic acid synthesis:
(Please, memorize the underlined)
These antibiotics inhibit nucleic acid synthesis (DNA and RNA). Examples:
A- Inhibition of bacterial DNA Gyrase (Helicase/Topoisomerase). This can be mediated by Nalidixic acid, Quinolones and Fluoroquinolones
B- Inhibition of bacterial RNA polymerase (inhibition of RNA synthesis)
Examples: Rifampin and Rifampicin

14. V- Inhibition of Bacterial Cell Membrane Function:
Some antibiotics kill bacterial cells by making pores in the bacterial cell membrane.
However, because the structural and biochemical similarities between bacterial and human cell membranes, these antibiotics do not exhibit selective toxicity. These antibiotics must not be given systematically and are used only as ointments .
Example:
Polymyxins, which are cyclic polypeptides that have positively charged free amino groups.
The positively charged free amino groups that act as cationic detergents to disrupt the phospholipid structure of the cell membrane.
(Please, memorize the underlined)

15. Drug Resistance in Bacteria:
1- Natural Resistance:
Natural resistance means that a bacterium is naturally not affected by an antibiotic by virtue of its natural structure.
A- Absence of the antibiotic target: (Mycoplasma are naturally resistance to all antibiotics that affect the cell wall because this bacterium has no cell wall)

16. B- Inability of the drug to get into the bacterial cell:
Modified cell wall (Mycobacteria have very hydrophobic cell wall that is impermeable to most antibiotics )
Porins with narrow diameter (pseudomonas)
Presence of outer membrane in Gram-negative bacteria (Glycopeptides antibiotics have a bulky structure that does not allow them to go through the outer membrane of Gram-negative bacteria

17. 2- Acquired Resistance (Genetically-Based Resistance):
In this case, a microbe, which was originally sensitive to a drug became resistant to that drug by virtue of a genitally-based event that altered the ability of the drug to affect this microbe.
Thee the genetically-based events that mediate antibiotic resistance include:
I-Mutations
II- Gaining of an antibiotic resistant gene from another bacterium by horizontal gene transfer

18. I-Mutation- based acquired resistant
1- Mutations that affect drug entry into the bacterial cell: (mutations in porins or transporters), so that the drug can not reach an effective cytoplasmic concentration in the bacterial cell
2- Mutations that alter the antibiotic binding site on its target .

19. B- Acquirement of drug resistance genes from another microbes by one of the horizontal gene transfer mechanisms ( conjugation, transduction or transformation)
Antibiotic resistance genes may encode for:
1- Efflux pumps: these are transporters that move the drug that has reach the cytoplasm out of the bacterial cell so that the drug can not reach an effective concentration within the cytoplasm of the bacterial cell..
2- Enzymes that inactivate antibiotics:
These enzymes inactivate antibiotics either by modifying their chemical structure either by
A- cleavage of a chemical bond in its structure or
B- addition of a chemical group to the antibiotic
This will make the antibiotic unable to bind to its target.
Examples: Beta lactamases cleave a covalent bond in the beta-lactam ring of beta-lactam antibiotics thus inactivating the antibiotic
3- Enzymes that chemically modify the antibiotic binding site on its target.

23. Resistance that attributed to other reasons:
1- The presence of the bacterial pathogen (infection) in a tissue with an osmotic pressure that equals the osmotic pressure of the bacterial cell.
In this case, antibiotics that affect cell wall synthesis will not be effective. Initially, these antibiotic may inhibit replication of the bacterial pathogen as they interfere with peptidoglycan synthesis, however, they will not be killed. Once antibiotic treatment is stopped, they will resume synthesis of peptidoglycan and thus consequently resume replication resulting in re-stating the infection process.
2- The presence of an abscess: the abscess regions has no blood supply due to destruction of the tissue and blood vessels within the abscess region. Accordingly, systemically or even locally administered antibiotics will not be able to reach the infection site. That why it is so important to drain the abscess before antibiotic treatment.
3- The presence of a foreign object that interferes with the ability of an antibiotic to reach the infection site.
4- The presence of a calculi (a stone) that may provide the bacterial pathogen that can survive deep within its pores. Thus these calculi may provide the bacterial pathogen with a shelter that protects it from antibiotics (Example: kidney stones can be a source of re-current UTI).
5- The presence of the bacterial pathogens within a Biofilm: in this case, it is important either to remove the Biofilm or remove the object on which the Biofilm was formed on (such as prosthetic joins and heart valves).

24. Anti-Fungal and Anti-Viral Drugs

25. Anti-Fungal Drugs:
Because of similarity of fungal cells and human cells (both are eukaryotic cells) , the number of the drugs available for treatment of fungal infections there are less than those available for the treatment of bacterial infections.
In addition, antifungal drugs have a higher level of side effects once compared to anti-bacterial drugs. So, it is always easier to treat superficial mycoses than systemic infections.
Most of the approved anti-fungal dugs targets cellular components or biosynthetic pathways that are not present in human cells or at least have some differences to those found in our cells.

26. The most effective anti-fungal drugs are Amphotericin B and the various azoles drugs that exploit the presence of Ergosterol in fungal cell membranes (Ergosterol is not found in human cell membranes).
Examples:
Amphotericin B disrupts fungal cell membranes by binding to Ergosterol in the cell membrane of fungal cells.
Azoles: which are a group of antifungal drugs that inhibit the biosynthetic pathway of Ergosterol, which is an essential component of fungal cell membranes.
Caspofungin: it inhibits the biosynthetic pathways Glucan, which is found in fungal cell walls but ((human cells do not have a cell wall))

28. Anti-viral Drugs:
Viruses are obligate intracellular pathogens. Unlike other infectious agents, viruses are not cells, that is to say, they do not have organelles, ribosomes, ATP generation systems biosynthetic pathways. Accordingly, it has been always difficult to interfere with viral replication.
Accordingly, that main strategy for the development of is to try to find any specific vial enzyme (s) that is important for viral replication (If available) so that can be targeted by an inhibitor or to target any vial component (such as viral surface proteins such as the spikes that could interfere with viral attachment to host cells ).
Based o the above mentioned points, Anti-viral drug development has been slow and the number of the available antiviral dugs is limited, not to mention that many of them have important side effects

29. Examples of anti-viral drugs:
Anti-influenza virus drug:
1- Amantidine: is used to prevent influenza infections. It blocks viral entry into host cells and also interfere with viral uncoating of influenza virus in host cells.
2- Tamiflu: Anti-influenza virus drug. It inhibits the a neuraminidase enzyme (of the spikes) that is involved in the release of the virus from infected cells.
Anti-Herpes Virus drugs
1- Acyclovir: inhibits only Herpes Simplex Virus DNA polymerase
2- Foscarnet: inhibits both Herpes Simplex Virus and Cytomegalovirus DNA polymerase
Broad Spectrum Anti-viral drugs:
Cidofovir (HPMPC): it is conspired as a broad spectrum antiviral drug because it can inhibit the viral DNA polymerase of several viruses (such as papovaviruses, adenoviruses, herpes viruses and poxviruses.

30. Anti-HIV Drugs:
Anti-HIV dugs target and inhibit HIV specific enzymes that are important for HIV virus replication
A- Reverse transcriptase (RT) inhibitors: inhibit HIV reverse transcriptase enzyme
B-Integrase inhibitors: inhibit HIV integrase enzyme
C- Protease inhibitors: Inhibit HIV protease enzyme
D- Fusion inhibitors: Interfere with entry of HIV virus into host cells
In HIV infection, most successful treatment is to use several types of anti-HIV drugs at the same time (Drug cocktails) so as to lower the possibility of the mergence of resistant HIV variants (See Part 18).