The 'wonder drug'
Prior to World War II, having a bacterial infection would have a significant risk of death. The accidental discovery of modern day penicillin in 1928 from a fungus, by Alexander Fleming, not only helped in combating bacterial infections in wartime, but also saved millions of lives around the world to date.
Dorothy Hodgkin first crystallized and determined the structure of penicillin in the early 1940’s, allowing it to be easily synthesized. It is still the most frequently prescribed antibiotic in general practice to treat common bacterial infections. Penicillin acts by binding penicillin-binding protein (PBP) (1pwc) using its beta-lactam ring.This causes inhibition of PBP cross-linking activity in synthesizing new bacterial cell wall, thereby killing the bacteria.
A visualisation of the active site for a PBP (D-alanyl-D-alanine carboxypeptidase) bound to various beta-lactam ligands which have been superposed using the ‘View all ligands� option on the PDBe-KB page for PBP.
A key difference
Today, over 100 different antibiotics are available to cure both minor and life-threatening infections. Although antibiotics are useful in a variety of infections, it is important to understand that they only treat bacterial infections and do not have any effect on viral infections, like the common cold, sore throats and flu, or in fungal infections, such as ringworm.
Antibiotics are powerful drugs that either kill the bacteria (bactericidal) or slow their growth (bacteriostatic) to inhibit them from spreading. The success of penicillin and other antibiotics is because they precisely target bacterial proteins while having no effect on any human proteins. This specificity, along with easy availability of effective antibiotics, has completely changed modern medicine.
Antibiotics can be classified into groups based on their chemical structure (as shown above) or according to their mode of action:
1. Inhibition of cell wall biosynthesis - while human and animal cells lack cell wall, this structure is critical for the survival of bacterial species. Antibiotics like penicillins, amoxicillin, cephalosporins, bacitracin and vancomycin selectively target proteins involved in cell wall synthesis, thereby killing or inhibiting the bacterial organisms.
2. Inhibition of protein synthesis - ribosomes are the cell’s protein making machines and are highly complex and crucial structures required for protein synthesis to function properly. Antibiotics that target bacterial protein synthesis inhibit ribosomes causing disruption to normal bacterial processes, leading to their death. Bacteriostatic antibiotics include macrolides (erythromycin, clarithromycin, azithromycin) and tetracyclines , while bactericidal antibiotics include the aminoglycosides, such as streptomycin, paromomycin, gentamicin, neomycin, and kanamycin.
3. Inhibition of nucleic acid synthesis - DNA and RNA play an essential role in the process of replication for all living forms, including bacteria. Fluoroquinolones such as ciprofloxacin, levofloxacin are a group of antibiotics that interfere with DNA synthesis by inhibiting topoisomerase, an enzyme involved in DNA replication. On the other hand, rifampicin blocks RNA synthesis by specifically inhibiting bacterial RNA polymerase. These antibiotics interfere with bacterial replication causing bactericidal activities.
4. Inhibitors of other metabolic processes - Other antibiotics act on selected cellular processes essential for the survival of bacterial pathogens. For example, both sulfonamides and trimethoprim disrupt the folic acid pathway, required for the bacteria to produce precursors important for DNA synthesis. Sulfonamides target and bind to dihydropteroate synthase, while trimethophrim inhibits dihydrofolate reductase; both these enzymes are essential for the production of folic acid, a vitamin synthesized by bacteria, but not humans.
5. Alteration of cell membrane - cell membranes are important barriers that segregate and regulate the intra- and extracellular flow of substances. Daptomycin alters membrane curvature, creating holes that leak ions. This causes rapid depolarization, resulting in a loss of membrane potential leading to inhibition of protein, DNA, and RNA synthesis, which results in bacterial cell death.
Schematic representation of site of action and potential mechanisms of bacterial resistance agents. Mulvey MR, Simor AE. CMAJ. 2009 Feb 17;180(4):408-15.
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Today we see an alarming trend where bacteria are becoming harder to kill as they quickly adapt and find ways of evading antibiotic treatment. Some bacteria can naturally resist certain kinds of antibiotics, while others can become resistant if their genes change or they acquire drug-resistant genes from other bacteria. This gives rise to antibiotic resistant bacteria or ‘superbugs�, making antibiotics less effective.
The antibiotic resistance of ‘superbugs� is one of the world's most pressing and emerging public health problems. This is compounded by the fact that the discovery of new classes of antibiotics is at an all-time low and many commonly used antibiotics are losing their effects. has recognised this as a serious global issue and issued a list of ‘superbugs�. Some of these ‘superbugs� include MRSA (methicillin-resistant Staphylococcus aureus), Carbapenem-Resistant Enterobacteriaceae (CRE), Vancomycin-Resistant Enterococcus (VRE), Multi-Drug-Resistant tuberculosis (MDR-TB) and many more drug-resistant bacteria and other microorganisms.
How does bacteria become resistant?
There are several methods that bacteria have developed over the years to exhibit resistance against antibiotics. They can take several approaches to evade antibiotics, such as attacking the antibiotics directly to make them inactive, altering the binding target such that antibiotics no longer recognise it, and pumping the antibiotics out of their cells.
Among the most common forms of resistance is beta-lactam antibiotic resistance and it occurs through three general mechanisms:
1. Hydrolysis of beta-lactam antibiotics by beta-lactamase enzymes
The mechanism of beta-lactamase-mediated degradation of beta-lactam antibiotics is seen in CRE ‘superbugs� that are resistant to beta-lactams like penicillin, cephalosporin and carbapenem. Infections caused by CRE strains have recently been associated with an increase in in-hospital mortality.
Beta-lactamases bind to the beta-lactam ring and break the reactive beta-lactam ring, by opening up the ring, thereby destroying the antibiotic. This in turn protects the bacterial penicillin-binding protein. An example is the enzyme metallo-beta-lactamase type 2. It is the presence of this beta-lactamase-degrading protein in CRE multidrug resistant bacteria that makes the beta-lactam antibiotics ineffective.
A superposition of all the available 270 structures of metallo-beta-lactamase type 2 structures available in the PDB left (putty representation), with their superimposed ligands on the right (pink ball and stick representation). The ligands superimposed include inactivated penicillin and other small molecules with beta-lactam rings, giving a clear indication of the binding/active site. This was created using the superposition tool in PDBe-KB for structures and ligands for metallo-beta-lactamase type 2.
A lot of emphasis has been made in an effort to combat the CRE strains by developing more effective beta-lactamase inhibitors or drug combinations. The latest antibiotics approved against CRE infections and already in clinical use are ceftazidime/avibactam (6q5b), meropenem/vaborbactam, plazomicin and eravacycline.
2. Target modification
Vancomycin, a glycopeptide antibiotic that inhibits cell wall biosynthesis, and remains the drug of choice for the treatment of severe MRSA infections. This acts similarly to beta-lactam antibiotics because it inhibits cell wall biosynthesis, but it targets a different protein.
Resistance to vancomycin by MRSA resistant bacteria has given rise to VRSA (Vancomycin-resistant Staphylococcus aureus) ‘superbugs�, which have become a major issue. Resistance is mediated through acquisition of van genes that cause changes in the structure of peptidoglycan precursors, and decrease in the binding ability of vancomycin 38nd. Three recently approved semi-synthetic glycopeptide derivatives, oritavancin, dalbavancin and telavancin (3run, 3rul, 3rum), are being treated as reserve antibiotics to be used sparingly to preserve their efficacy.
3. Presence of efflux pumps that expel beta-lactam drugs
Efflux pumps allow microorganisms to regulate their internal environment by removing toxic substances, including antimicrobial agents and metabolites. Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics out of the cell before they are able to do any damage.
The MexAB-OprM efflux pump plays a central role in multidrug resistance by ejecting various drug compounds, often leading to serious nosocomial infections. Atomic structures of the fully assembled pumps in 6iol and 6iok have revealed mechanisms for complex formation and drug efflux shown on the right.
Research concerning another bacterial multidrug efflux pump AcrAB-TolC, in resting and drug transport states has also revealed a structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. This work shed light on how the pump works to expel antibiotics from bacterial cells in 5o66 along with puromycin bound form in 5nc5, shown above.
The atomic structures freely available in the PDB help researchers to understand the details of such drug resistance mechanisms and also provide new ways to combat it.
Future goals
The mid-20th century was called the Golden Age for antibiotics, a time when scientists were discovering dozens of new molecules for many diseases. Modern medicine relies on the availability of effective antibiotics; without them it would be too risky to perform organ transplants, cancer chemotherapy or even common surgical procedures such as hip replacements. The smart use of antibiotics is the key to controlling the spread of resistance.
As the world fights the COVID-19 pandemic, another group of dangerous pathogens looms in the background. The threat of antibiotic resistance is here and getting worse. If COVID-19 has taught us one thing, it is that governments should be prepared for more global public health crises, and that includes finding new ways to combat ‘superbugs� that are becoming resistant to commonly used drugs.
Deepti Gupta
About the artwork
Abdi Abdiqani, a 16 year old student from Viewbank College Australia, researched the topic of ‘antibiotic and antibiotic resistance�.
He describes, with his artwork ‘The concept of the artwork was to depict the way in which the antibiotics (that are created to kill harmful bacteria) can also cause bacteria to actually become resistant to it. This immunity transforms bacteria into what is known as a “superbug�. I expressed this concept in a highly dramatized manner, showing the superbug to be sucking in arcs of energy and power from the antibiotic, turning a menacing warm colour in a haze of red, orange and yellow smoke and clouds, like that of a nuclear explosion. The contrasting blues of the antibiotic compared to the reds and yellows of the superbug establish an idea of evil vs good.�
PDB id: 2x1c
View the artwork in the .
Structures mentioned in this article
- Link to the PDB ID for the entries 1pwc, 6q5b, 38nd, 3run, 3rul, 3rum, 6iol, 6iok, 5o66, 5nc5
- Link to protein structure with antibiotics - penicillins, amoxicillin, bacitracin, vancomycin, erythromycin, clarithromycin, azithromycin, tetracyclines, streptomycin, paromomycin, gentamicin, neomycin, kanamycin, ciprofloxacin, levofloxacin, rifampicintrimethoprim, Daptomycin
- Link to PDBe-KB page for more information on PBP - D-alanyl-D-alanine carboxypeptidase, metallo-beta-lactamase type 2.
Sources
Mulvey MR, Simor AE. Antimicrobial resistance in hospitals: how concerned should we be? CMAJ. 2009 Feb 17;180(4):408-15. doi: 10.1503/cmaj.080239. PMID: 19221354; PMCID: PMC2638041.
Ventola CL. The antibiotic resistance crisis: part 1: causes and threats. P T. 2015 Apr;40(4):277-83. PMID: 25859123; PMCID: PMC4378521.
Ventola CL. The antibiotic resistance crisis: part 2: management strategies and new agents. P T. 2015 May;40(5):344-52. PMID: 25987823; PMCID: PMC4422635.
Reygaert WC. An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiol. 2018 Jun 26;4(3):482-501. doi: 10.3934/microbiol.2018.3.482. PMID: 31294229; PMCID: PMC6604941.
Lima LM, Silva BNMD, Barbosa G, Barreiro EJ. β-lactam antibiotics: An overview from a medicinal chemistry perspective. Eur J Med Chem. 2020 Dec 15;208:112829. doi: 10.1016/j.ejmech.2020.112829. Epub 2020 Sep 16. PMID: 33002736.
