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 well studies mechanistically and structurally yielding 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 DNA gyrase
are gyrA and gyrB and these remove supercoils which involves breakage and resealing of
double-strand. 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). 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 gram
gram positive bacteria and the bacteria
absent of the original dye color were
labeled gram negative bacteria. This is
not the only distinction between these
classes: gram negative bacteria are harder
to kill because of an impenetrable cell
wall as shown in the diagram to the left.
Kibdelomycin is an antibiotic that has
shown activity against both gram positive
and gram negative bacteria, in other
words it kills a broad range of bacteria.
Kibdelomycin was isolated from the
forest soil in the Central African
Republic. Some other drugs similar to
Kibdelomycin are Aminocoumarins,
Novobiocin, Chlorobiocin and
Coumermycin A1. The reason why it is
known that Kibdelomycin and these forementioned drugs are similar is that all these 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 1)
known coumarin antibiotic, 2) new coumarin analog or 3) 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 parameter 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 inhibited DNA gyrase
ATPase at an IC50 value of 11nM and topoIV ATPase at 900nM. In other cases
Kibdelomycin showed superior activity: 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 an good attempt
shedding light on the increasingly urgent need for antibiotics.
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 Bacteria vs Gram-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