C151C5 - Antibiotics and Kibdelomycin

C151C5 - Antibiotics and Kibdelomycin

The development of antibiotics over the years has not met the growing demand created by increased resistance and emergence of new pathogens. The first antibiotics were sulfa drugs in the year 1936, followed by Penicillin in 1941. Then came the golden era from 1940 to 1970 where Aminoglycosides, Chloramphenicol, Macrolides, Glycopeptides, Quinolones, Cephalosporins, Strptogramins, Spectinomycin, Rifampicin, Clindamycin. After a few decades Carbapenems were discovered in 1985, Streptogramins in 1999, Oxazolidinones in 2001 and Daptomycin in 2004. Since then there is a sort of drought and lack of funding in the field of antibiotics. New antibiotics are very important because of the resurgence of pathogens with resistance developed due to the evolutionary pressures posed by anti-bacterial agents. These resistant strains, the most famous of which is probably Methicillin-resistant Staphylococcus aureus (MRSA), are frightening and brilliant in their adaptively. Medicinal chemist have tried to circumvent the resistance issues by chemical modifications at the site of known resistance but the rate of bacterial resistance is exponentially faster than the rate at which antibiotics can be developed.

Antibiotics are categorized by; 1) Structure similarities, 2) Mechanism of action and 3) Target sight. There are various targets that are focus of different classes of antibiotics: cell wall synthesis inhibitors such as Bacitracin, Daptomycin and Glycopepetides, Metabolism Inhibitors like Sulfamethoxazole and Trimethoprin, RNA Synthesis inhibitors like Rifampin, Protein Synthesis inhibitors like Macrolides and Tetracylins and aminoglycosides such as streptomycin target the A-site of the bacterial ribosomal RNA or the protein making factory in cells. Aminoglycosides are thought to disrupt key steps during protein synthesis or translation. Much like the A-site of the ribosomal RNA, another key step in the life cycle of bacteria is DNA synthesis. Clearly This pertinent process has been thoroughly studied mechanistically and structurally, yielding to many potent drugs that target one or multiple steps. Lastly, DNA synthesis is also a drug target. DNA synthesis like other biological processes is heavily dependent on cofactors, enzymes and other components that direct, carry out, and terminate both essential and non-essential processes.

One such enzyme called type II isomerase is responsible for the topology of DNA. DNA replication occurs at 50,000 base pairs per minute and these strands have defects such as tangles, catenates and crossovers that must be removed. These enzymes catalyze catenation (linking) and decatenation (unlinking). Gene clusters comprising of DNA gyrase, gyrA and gyrB, remove supercoils by breaking and resealing double-strand DNA. Another DNA gyrase is topo IV which removes catenaes (Hermann, 2012). Two classes of antibiotics – Aminocoumarins and Quinolones target topoisomerases and disrupt this repair mechanism. These antibiotics inhibit bacterial type II isomerases, preferentially DNA gyrase and topoisomerase IV (Lodish et al., 2000; Lawson et al., 2012). However, Kibdelomycin is the only new novel type II isomerase inhibitor to be discovered in almost 60 yrs (Demain, 2011).

Apart from targets in bacterial, medicinal chemists also have to take into consideration the type of organism that is being targeted. There are two types of bacteria: gram negative like E.coli and gram positive like Staphylococcus aureus. The origins of the two classes stem from scientist Hans Christian Gram and his observations after staining bacterium with crystal violet dye. Some of the bacteria become blue whereas others showed up as red or pink. The retention of the color of the dye earned the blue batch the label

known that Kibdelomycin and these forementioned drugs are similar is that all these molecules generated similar profiles when subjected to the Antisense Induced Strain Sensitivity (AISS) test. The AISS test is used to determine the mechanism of action (MOA) and molecules with similar MOAs are generally clustered together. The test consists of 245 RNA antisense strains, including ones engineered to represent essential bacterial processes such as cell wall biosynthesis, transcription and translation. In other words, genetically modified strands that bear known sites targeted by this class of antibiotics are created, then reacted with different antibiotics and the reaction is monitored. The data provided elucidates MOAs. With regulation of gene expression by inducible antisense RNA, systematic elucidation of mechanism of action of small molecule antibiotics becomes feasible (Donald et al.).

Structural comparison of Kibdelomycin and classing type II topoisomerase inhibitors Novobiocin & Clorobiocin

In the case of Kibdelomycin, the fitness test predicted the mechanism of action of either known coumarin antibiotic, new coumarin analog, or a new structural class with a mechanism of action similar to novobiocin. Kibdelomycin fit the third profile and underwent further structural, mechanistic and concentration studies. Using various NMR techniques including ROESY and COSY, fragments of the molecule were used to compile a complete structural picture. Kibdelomycin is structurally very close to aminocoumarin’s which are also a class of DNA gyrase inhibitors. Mechanistic studies showed that Kibdelomycin, similar to aminocoumarins was specifically targeting ATPase activity of DNA gyrase (gyrA/B) and topoIV (parC/E). It is clear that Kibdelomycin targets DNA. It was also discovered that not only is Kibdelomycin potent against bacteria but it is also potent against strains that have developed resistance to known antibiotics.

The AISS profiling process is a tool that can be implemented to systematical organizes the search for new, desperately needed antibacterial candidates. Kibdelomycin itself can potentially become a much awaited solution to the growing problem of diseases caused by bacteria and bacterial resistance. The AISS profile test will accelerate the process of the search for new potential drugs.

Additional parameters of determining the potency of drugs is known as IC50 value or 50% of the inhibitory concentration and minimum inhibitory concentration or the least amount of drug needed to see activity. Kibdelomycin was just as potent as the existing aminocoumarins: In a catalytic ATPase assay, Kibdelomycin inhibites DNA gyrase ATPase at an IC50 value of 11nM and topoIV ATPase at 900nM. In other cases Kibdelomycin showed superior activity when a S. aureus strain, 125 fold resistant to coumermycin A1 (MB 5957/H7), was 4 times less resistant to Kibdelomycin (Philips et. al). The MIC values of Kibdelomycin when compared to other DNA gyrase inhibitors attest to its strong antibacterial activity. In conclusion, an incredibly intelligent screening process has led to the discovery of Kibdelomycin, a structurally new, mechanistically familiar, fascinating new DNA type II isomerase inhibitor.

It is very important to mention that these numbers for Kibdelomycin are from in-vitro assays; that is in buffers and test-tubes not inside biological systems under physiological conditions. Therefore, although the story of Kibdelomycin is exciting it remains incomplete. The structural exoticness of the molecule was perhaps one the main reasons it excited the scientific community. Arrays of molecules have shown promise in in-vitro testing so the numbers related to do not speak much to the actual potential of the molecule as a drug because there are numerous obstacles that a molecule has to encounter before reaching the target. Furthermore, being structurally so similar to existing antibiotics it is reasonable to expect that Kibdelomycin will most likely encounter similar resistance, toxicity and other known issues. Nevertheless, this is a good attempt shedding light on the increasingly urgent need for antibiotics.

Your paper is on Kibdelomycin, but you don’t do a good job introducing the drug in the beginning paragraphs. It also seemed to me that you mainly focused on once type of cell inhibiton, being the inhibition of isomerase. Rather than opening the reader to so many, why not just mention one in the beginning paragraphs.

Overall, the paper was somewhat hard to follow at times, with so many tests and drugs being thrown at me at once. This makes you lose track of what the paper is actually supposed to be about.

References:

C. et al. Biological Activities of Novel Gyrase Inhibitors of the Aminocoumarin Class. (2008). Anti. Ag. Chem. (2009). 52, 1982.

Donald, R. et al. A Staphylococcus aureus Fitness Test Platform for Mechanism-Based Profiling of Antibacterial Compounds. (2009). Chem. Bio. 16, 826-836.

Gram-negative BacteriavsGram-positive Bacteria.

http://www.diffen.com/difference/Gramnegative_Bacteria_vs_Gram-positive_Bacteria Anderle

Hermann, T. Antibiotics Classes & Targets Part III: Drugs Targeting DNA & RNA Biosynthesis. Chem 259. (2012). Department of Chemistry and Biochemistry, University of California, San Diego.

Lodish H., Berk A., Zipursky S.L., et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman. (2000). The Role of Topoisomerases in DNA Replication.

Philips, J.W. et al., Discovery of Kibdelomycin, A Potent New Class of Bacterial Type II Topoisomerase Inhibitor by Chemical-Genetic Profiling in Staphylococcus aureus. (2011). Chem. Bio. 18, 955–965.

Wright, G. D. Making Sense of Antisense in Antibiotic Drug Discovery. Cell Host & Microbe. 6, 197–198