Structural Biochemistry/Antibiotics

History
Antibiotics were first produced with Penicillin in 1928 and was very effective. Many pharmaceutical companies looked at Penicillin as an example, and later generated other antibiotics products of their own. Antibiotics quickly had a large impact on human, animals, and the living bacteria. According to an article, "Multidrug Resistance in Bacteria", by Hiroshi NIkaido, an estimate of 100,000 tons of antibiotics were produced each year; and due to its ability to cure diseases and popularity, we took advantage and over used the antibiotics; in which resulted in a multi-drug resistance.

Key Characteristics of Antibiotics
The use of antibiotics in a clinical setting has been directed by several key characteristics of antibiotics:
 * 1) Antibiotics have selective toxicity: This allows for detection of bacterial targets rather than eukaryotic cells that the body needs.
 * 2) Antibiotics have a limited spectrum of activity: Therefore each antibiotic only affect a few bacterial species, so there is a need for many different antibiotics. An example is penicillin, which mainly kills gram-positive bacteria. On the other hand, ampicillin has an additional amino group that allows for the penetration of a gram-negative outer membrane. Ampicillin therefore has a wider spectrum of activity than penicillin.
 * 3) Antibiotics may be either bactericidal or bacteriostatic.
 * 4) Bactericidal antibiotics kill the bacterial microbe.
 * 5) Bacteriostatic antibiotics prevent bacterial growth.

Why are human cells not affected?
Many antibiotics block protein synthesis. All cellular organisms, including bacteria, have ribosomes. And all ribosomes are composed of proteins and ribosomal RNA. But the precise shapes of these proteins differ in several very specific ways between humans and bacteria. That’s a good thing for researchers trying to develop bacteria-killing medicines called antibiotics because it means that scientists may be able to devise therapies that knock out bacterial ribosomes (and the bacteria along with them) without affecting the human hosts.

Multidrug Resistance
Bacteria resistance to drugs can emerge in one of two ways:

1. By storing up and collecting numerous genes, and classifying them to fight in a individual drug within that cell, or

2. When more and more genes are organized under the "multi-drug efflux pumps", (Hiroshi, 2009, p. 119), and are forcing out large groups of drugs.

Types of Antibiotics


Although there are well over 100 antibiotics, the majority comes from only a few types of drugs. These are the main classes of antibiotics:

1. Aminoglycoside They are mainly used to battle infections that were formed through gram-negative bacteria. Bacteria is said to be capable to improve a resistance to this; however, bacteria is able to improve resistance to just about anything. The bad side effects that can be caused from aminoglycoside are injury to your kidneys or ears. The main result of aminoglycoside is that it halts the bacteria from producing proteins in your body.

2. Cephalosporin There are 3 different creation types of cephalosporin. The higher the generation, the larger gram-negative antimicrobial property it has. The particular late generation cephalosporin also has a greater chance of bacteria not becoming resistant to it. This is clearly an advantage because it means that the medicine will be efficient for a longer period of time.

3. Fluoroquinolone This type of antibiotic is active against several different types of bacteria, but it is mostly used to treat UTI's (urinary tract infections), respiratory infections, and skin infections. It causes nausea, diarrhea, sickness, or minimal pain in the stomach while using fluoroquinolones. This works because it inhibits with bacteria’s ability to create DNA, so it is harder for the bacteria to be able to multiply.

4. Penicillin This was essentially the first type of antibiotic exposed in 1929 by Alexander Fleming. Penicillin is largely used to treat dental infections, respiratory infections, gonorrhea, UTI’s (urinary tract infections), and skin infections. Penicillin operates by hindering the growth of bacteria cell walls. Ultimately, the walls decline, and the bacteria is killed over a period of time due to this. Although, you can get an allergic reaction to this antibiotic, Doctors believe penicillin to be extremely safe.

5. Tetracycline These were the most general antibiotics whenever they were initially recognized back in the 1940s. The most common use for tetracycline is for upper respiratory infections, STD’s, Lyme disease, mild acne, and typhus. They are used to fight a wide amount of different bacterial infections for most of the time. Doxycycline and minocycline are kinds of tetracycline.

6. Macrolide These are used largely to cure gastrointestinal tract and other tract infections. They bind with ribosomes from susceptible bacteria which will help avoid any protein production. This helps kill off all the bad bacteria over time. The only actual side effect for macrolides is that they can make the stomach to be upset, but there are no sides of any serious nature.

Bacitracin
Bacitracin is an antibiotic made by bacterial microorganisms. The bacitracin antibiotic is isolated from Bacillus subtilis. Bacitracin is a narrow-spectrum peptide antibiotic that inhibits cell-wall synthesis in gram-positive bacteria. Bacitracin is a major ingredient in the ointment Neosporin that is used to fight skin infection caused by Staphylococcus and Streptococcus species. This antibiotic was first isolated in 1945. It is meant to be used topically, on the skin, for disinfecting minor cuts, and not to be used orally. Bacitracin is usually not taken orally because it is more effective as a topical antibiotic.

Overview
Bacitracin works best on gram-positive bacteria because gram-negative bacteria have an outer membrane in their cell wall. Bacitracin kills bacteria by targeting bactoprenol, a lipid in the cytoplasmic membrane that is normally used to transport a disaccharide unit of peptidoglycan across the cell membrane to add to a growing peptidoglycan chain.

How It Works
In the bacterial formation of peptidoglycan, the sugars NAM and NAG are linked together within the cell at a newly phosphorylated bactoprenol. The NAM-NAG disaccharide unit is then transported to the outside cell membrane via the bactoprenol. After the disaccharide unit is added to the growing peptidoglycan chain, bactoprenol is removed from the NAM-NAG unit. This bactoprenol then releases a phosphate, and then the desphosphorylated bactoprenol moves back towards the cytoplasmic part of the cell membrane to repeat the cycle.

Bacitracin works by binding to bactoprenol, just after a disaccharide unit is added to the growing peptidoglycan. This inhibits the dephosphorylation of the bactoprenol, thereby preventing bactoprenol from accepting UDP-NAM within the cell. In this way bacitracin leads to a stop in the synthesis of bacterial peptidoglycan cell wall. A growing bacterium will then lyse due to increasing pressure from within the cell.

Side effects
Side effects are close to none, but in rare cases of allergic reactions, rashes, itching, dizziness, or trouble breathing may occur.

Rifamycin B
Rifamycin B was first discovered in 1957, along with six other rifamycins: A, C, D, E, S, and SV. Rifamycin B was the first to be used commercially. It was praised as being the solution to antibiotic-resistance tuberculosis in the 1960s.

Mechanism
Rifamycin B selectively binds to bacterial RNA polymerase to inhibit translation of mRNA. It binds to the beta subunit of the polymerase, which is near the Mg2+ activation site. When this happens the developing peptide chain cannot exit the RNA polymerase and it is stuck. However, it is important to note that Rifamycin B only works when it binds to a RNA polymerase that has just started translation, otherwise it cannot block the already growing peptide chain.

Uses
Rifamycin B is very effective in treatment of bacterial infections caused by mycobacteria, bacteria with a very thick and waxy cell wall, which makes antibiotics that target cell walls ineffective (penicillin, and vancomycin). Some of these diseases are tuberculosis and leprosy.

Actinomycin D
Actinomycin D was the first antibiotic discovered to have anti-cancer properties. It was first used in 1964. It is used a chemotherapy drug.

Mechanism
Actinomycin D 's structure allows it to mimic a nucleic base and insert itself in between guanine and cytosine. This blocks RNA polymerase from continuing the elongation process in transcription. However, the problem is that Actinomycin D binds non-selectively into any DNA, not just bacterial.

Uses
Actinomycin D is used as a chemotherapy drug to inihibit DNA synthesis and thus cell division. This makes it particularly effective against tumor cells that divide uncontrollably.

Side Effects
Since Actinomycin D is not meant to treat infections and it does not specifically target pathogenic DNA, it can inhibit DNA synthesis in normal cells. Other side effects are bone marrow suppression, hair loss, fatigue, mouth ulcers, loss of appetite, and diarrhea.

Streptomycin
Streptomycin is a type of aminoglycoside that affects bacterial translation.

The aminoglycoside antibiotic, streptomycin, is made by some bacteria to protect themselves from competing bacteria. They are particularly effective because they are specific: they attack bacterial ribosomes, corrupting protein synthesis in the bacterium, but they don’t attack the ribosomes of many other organisms including ribosomes in human body. Therefore, it makes the perfect antibiotic drug that controls a bacterial infection with few side effects on our own cells.

Mechanism
Streptomycin binds to the 16S rRNA of the 30S ribosomal subunit and to the protein S12, thereby inhibiting the formation of the 70S bacterial ribosome. In low concentrations of streptomycin, translation can occur but the A site of the ribosome allows the matching of inaccurate codon and anticodon, leading to a faulty translation of protein.

Bacterial Resistance
Bacteria can become resistant to streptomycin by initiating a mutation in S12 so that streptomycin can’t bind. Bacteria can also modify the streptomycin so that it won’t be able to bind to a certain molecule.

Effects
Streptomycin affects the bacterial protein synthesis. It effects the way that messenger RNA is read, causing errors in translation and inhibiting the orderly stepping of the ribosome along the mRNA strand. It also blocks the recycling of ribosomes after they are finished making a protein.

Tetracycline
Tetracycline is an antibiotic that affects bacterial translation. An advantage of using tetracyclines or doxycycline as an antibiotic treatment is that it is broad-spectrum which indicates that the antibiotic can fight against a wide-variety of bacterial strains, such as Mycoplasma species, Rickettsia rickettsia, which causes Rocky Mountain spotted fever, and Chlamydia trachomatis.

Mechanism
Tetracycline prevents tRNA from binding to the A site, thereby stopping the synthesis of proteins. It does this by binding to the 16S rRNA site so that new tRNA can’t be added to that site.

Bacterial Resistance
Resistance to tetracycline occurs when a bacterial transport system moves the antibiotic to the outside of the bacterial cell so that tetracycline can no longer affect the cell.

Chloramphenicol
Chloramphenicol is an antibiotic that affects bacterial translation.

Mechanism
Chloramphenicol stops translation by attacking the 50S ribosomal subunit. In attacking the 50S subunit, chloramphenicol will then bind to a peptidyltransferase site on a 23S rRNA. This peptidyltransferase is used to bind new amino acids to an existing translated protein chain. Therefore, the binding of chloramphenicol will stop the formation of peptide bonds.

Bacterial Resistance
Bacteria become resistant to chloramphenicol when they create chloramphenicol acetyltransferase, an enzyme that stops any activity by chloramphenicol by changing the identity of the antibiotic.

Erythromycin
Erythromycin is an antibiotic under the macrolides and is characteristic of having a lactone ring of 12-22 carbons. Erythromycin or azithromycin can treat gram-positive strains of bacteria, such as Corynebacterium diphtheriae that causes diphtheria, as well as gram-negative bacteria, such Bordetella pertussis that causes pertussis, or whooping cough.

Mechanism
Erythromycin will attach to the 50S ribosomal subunit by attaching in the peptidyltrasnsferase cavity protein L15 and 23S rRNA. This binding will lead to the ejection of peptidyl-tRNA from the P site.

Bacterial Resistance
Some bacteria grow resistant to erythromycin by having mutations in the L15, so that it isn’t binding. Bacteria can also reduce the erythromycin binding by methylating the area 23S rRNA using an enzyme, thereby inhibiting the binding of L15.

Vancomycin
Vancomycin was isolated in 1952 from Streptomyces orientalis in a soil sample from Borneo; it was found to be active against most gram-positive organisms. It was especially valued at the time of its discovery because it worked against many organisms that were resistant to other antibiotics of the time. It was approved by the US FDA in 1958 and rose to popularity in that decade. Vancomycin fell out of popularity due to concerns of toxicity in the years following. It resurged in the 1980s, and reports of resistance began coming in from Europe and the US by 1987.

Mechanism
This antibiotic works by targeting the terminal D-alanyl-D-alanine of the peptidoglycan chain on the cell walls of growing bacteria; it latches to this alanine dimer and prevents the protective cell wall from forming.

Resistance
Resistant bacteria have modified this double alanine chain to be either D-alanyl-D-lactate or D-alanyl-D-serine (depending on the classification of the drug-resistant species); against these, vancomycin is ineffective. Experiments have shown that for certain vancomycin-resistant strains of bacteria, a combination of the antibiotics teicoplanin and gentamicin are more effective that vancomycin or teicoplanin monotherapy alone. Another vancomycin-resistant strain of bacteria responded to high doses of glycopeptides. Ultimately, one study recommended combination drug therapy involving gentamicin.

Clinical Dosage and Usage
No standard clinical dosage is reported, but nomograms have been popularly used in the past. One problem that persists with clinical vancomycin usage is that serum levels are not monitored consistently or studied extensively. Some physicians never monitor the serum, monitor it occasionally, or insist on monitoring frequently when a patient is prescribed vancomycin. This is something that needs to be addressed in the future in order for vancomycin to be used effectively.

Penicillin G
Penicillin G is an antibiotic made by fungal microorganisms. This antibiotic, isolated from Penicillium species, inhibits cell-wall synthesis in fungi by preventing enzymes from producing amino acid cross-bridges in peptidoglycan. Therefore, this antibiotic is used on gram-positive bacteria, which contain thick peptidoglycan layers.

Structural components
1. Thiazolidine ring

2. β-lactam ring

3. R-group (differs in side-chains)

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Cephalosporin C
Cephalosporin C is an antibiotic made from fungal microorganisms. This antibiotic is used on gram-positive bacteria and isolated from Cephalosporium acremonium, which is a mold. Cephalosporin C can contribute to the inhibition of fungal cell-wall synthesis and contains a β-lactam group and R-groups for modification.

Advantages
1. Broader-spectrum than penicillin

2. Fewer allergies than penicillin

3. Resistant to penicillinase (an enzyme made by bacteria to destroy penicillin)

Disadvantages
1. Poorly absorbed from the intestines

2. Medication given parenterally (non-orally) via injection into veins (intravenous) or into muscles (intramuscular)

Silver
Silver has been known and used an antimicrobial agent since the 19th century, and in 1998 one study examined and tried to optimize such a treatment. Although bacteria do develop resistance to other forms of antibiotics, there have been no reports of bacteria developing resistance to antimicrobial silver (though genes for heavy metal-resistance do exist and are linked to antibiotic-resistance genes).

Mechanism
Silver ions are toxic to bacteria because they blocks several processes essential to bacterial function: silver ions prevent respiratory enzymes from working properly, block some parts of the electron transport system, and impair some DNA functions.

In Vitro Trials
In the past, silver ions in cream forms had been tested and found to be less than ideal due to the nature of creams (they tend to dry out, and patients find changing dressings uncomfortable). Very strong ionic solution proved to be irritating to skin. In a study conducted by Wright et al., three different silver compounds delivered in dressings were tested: silver nitrate in dressing, silver sulfadiazine in dressing, and nanocrystalline silver in dressing. These were inoculated with bacteria strains that were resistant to several antibiotics each; the bacteria was strained and regrown, and bacteria regrowth was measured. The nanocrystalline silver dressing reduced the regrowth most noticeably. It does not irritate skin as much as the other two treatments do. Additionally, serum proteins (tested in this study by a calf serum solution) did not reduce the efficacy of the nanocrystalline silver treatment. It appears that such a treatment could be very valuable in a clinical setting.

Outcome
Many bacteria have become resistant to the antibiotics available. In addition, some diseases such as Staphylococcus Aureus (MRSA) will not respond to most drugs because they have aquired resistance to most of the antibiotic. These can only be treated with "reserve antibiotics" ,usually reserved for life threatening systemic infections, like vancomycin.

Protein Synthesis
Antibiotic is a medicine that inhibits the growth or destroys of a microorganism. Compared to eukaryotes’ 80S ribosomes, bacteria have 70S ribosomes that use antibiotics to block the synthesis of protein. An antibiotic is lucrative when it is able to bind and interfere with the formation of a “protein synthesis initiation complex” in bacteria. We need antibiotics to fight against bacteria. So antibiotics are there to interrupt the development of bacteria. The difference between the ribosomes that are in the mitochondria and the ribosomes in bacteria is that antibiotics affect the function.