Topoisomerases – The Obvious Targets

If minute differences in FQ molecular structure can make such a difference between drug-protein interactions, then minute differences in our DNA/protein structure could equally do the same.


The entire success, extreme popularity, and profitability of the FQ class of antibiotics rests on the sole argument that “in general”, and in “therapeutic concentrations”, the FQ’s only target the bacterial Topoisomerase enzymes, not the human Topoisomerase enzymes or any other human enzymes or proteins.

However, bacterial and human Topoisomerases have quite a bit in common, in terms of both structure and function.   Here, in this page, I explore the possibility of why “crossover” reactions might occur in those of us with FQT/FQAD, in particular, if unique polymorphisms might exist in our human nuclear or mitochondrial Topoisomerases which might increase our susceptibility.   As usual, I make a plea for research in this area, because human Topoisomerases are an obvious target to consider.

If a mutation in a prokaryotic TOPO can result in sensitivity of that TOPO to a eukaryotic TOPO inhibitor, then isn’t it entirely possible that a mutation in a eukaryotic TOPO could result in sensitivity of that TOPO to a prokaryotic inhibitor, ie, an FQ?    This is why the TOPO’s of the FQT/FQAD population need to be studied genomically, and enzymatically if possible. 


What FQ Binding Site Properties Might Susceptible Bacteria, Chloroplasts, and Mitochondria Have in Common?

The big question is, for those of us affected, where are these drugs binding?   Because it’s obvious they are binding to more than “only the bacterial TOPOs” in us.  They are no doubt promiscuously binding to any number of unintentional targets, as most drugs do.   However, it’s also known that even in “clinically relevant therapeutic concentrations” they do bind to mammalian TOPOs in vitro, and of course in higher doses can function as anti-neoplastic agents in human cells.   FQ’s are also suspected of causing “mitochondrial toxicity”, and mitochondria utilize their own specific topoisomerases.   If one considers that mitochondria, bacteria, and chloroplasts may be evolutionarily related, it makes sense that FQ’s might perhaps target enzymes common to all three, in this case, I’m focusing on the topoisomerases.   FQ’s do target and inhibit both bacterial and chloroplast gyrases (it seems the world may soon be blessed with Cipro or FQ derivatives as herbicides too).   It seems to me, that if this is the case, then those adversely affected by FQ’s *might* have mitochondrial topoisomerases with something in common to bacterial and chloroplast topoisomerases.   It could easily be a one amino acid substitution, most likely located close to the active-site tyrosine, that enhances FQ binding to human mitochondrial TOPO’s despite being exposed to the lower “clinically relevant therapeutic concentrations”.   It could easily be a one nucleotide substitution, which would make no difference in function for us under normal circumstances – until an FQ comes along and binding is enhanced.   The same is true of other DNA replication and repair enzymes which also may be unintentional targets of the FQ’s.

I think studying comparisons of human “susceptible” mitochondrial topoisomerases against “susceptible” bacterial/chloroplast topoisomerases, might help to elucidate who in the human population might be “susceptible” to these drugs.   Conversely, the question of what do the “resistant” human mitochondrial topoisomerases have in common with the “resistant” bacterial and chloroplast topoisomerases in that QRDR or somewhere near the active-site tyrosine?   Maybe even just do a bioinformatics search and comparison in that region of the various topoisomerases looking for commonalities?   There are always ongoing studies on what creates bacterial resistance to FQ’s in an attempt to stay ahead of the resistance issue, so there’s actually quite a bit of information out there by the folks who study this as to which amino acid substitutions make all the differences in resistance, and possibly, binding.   If “drugs targeting TOPOII likely bind to regions of the proteins that are highly conserved between prokaryotic and eukaryotic enzymes”, then it seems to me to be possible that the FQ antibiotics targeting bacterial TOPO’s could bind to human TOPO’s as well in some cases.

Again, I’m sure the drug is promiscuously binding to any number of other unintended targets, as most drugs do, and additional in vitro FQ studies have already revealed as such (scroll down to “Research”, here).   Despite this, toxic effects such as what I have experienced remain rare.   But for those of us affected, I can’t help but wonder what is different about us.  And one of my questions is if perhaps that difference is in reality a similarity, perhaps in only one amino acid or nucleotide, of one of my particular enzymes or receptors to the bacterial homologues, in this case, my mitochondrial (or nuclear) topoisomerases to bacterial gyrase, especially near the known binding sites.

Given that “mitochondrial toxicity” is a suspected mechanism for these adverse reactions, my hope is that researchers will consider doing comparison studies and reviews among the mitochondrial enzymes of the affected patient population with bacterial and chloroplast enzymes.   It seems to me the TOPO’s of these are a logical place to look for similarities or differences.   A further advantage to looking at maternally transmitted mtDNA, is that if a common mitochondrial mutation was found in the FQ-affected population, a next step would be to compare this mutation with unaffected and unexposed mothers or siblings.  This could help determine if the FQ was “unmasking” an existing mutation (in other words, finding a predisposition), or “creating” a new one somewhere.   Mitochondrial studies are challenging all around (tissue specific genotypes, heteroplasmy), but those barriers are slowly being dealt with as the field continues to grow.   Despite the current limitations, I think a lot could be learned from such studies overall, and perhaps prevent future tragedies such as my own.

My point here, is that one amino acid can make the difference in FQ resistance versus susceptibility – in bacteria, in plants . . . maybe in people too?   As an example, in regards to the paper below:    If a mutation in a prokaryotic TOPO can result in sensitivity of that TOPO to a eukaryotic TOPO inhibitor, then isn’t it entirely possible that a mutation in a eukaryotic TOPO could result in sensitivity of that TOPO to a prokaryotic inhibitor, ie, an FQ?   This is why the TOPO’s of the FQT/FQAD population need to be studied genomically and enzymatically if possible.

A mutation in Escherichia coli DNA gyrase conferring quinolone resistance results in sensitivity to drugs targeting eukaryotic topoisomerase II.    “There are several important implications for the conservation of most determinants of drug sensitivity between prokaryotic and eukaryotic enzymes.   First, drugs targeting topoisomerase II likely bind to regions of the proteins that are very highly conserved between prokaryotic and eukaryotic enzymes.   This is not a surprising conclusion, given the high degree of homology found throughout many of the type II topoisomerases (56).   However, the previous assumption that drugs such as etoposide acted against the eukaryotic enzyme but not the prokaryotic enzyme allowed for the possibility that such drugs interact with residues that are not highly conserved between the two kingdoms.   Our results argue against this possibility.   Second, our results support the hypothesis that many topoisomerase II-targeting drugs that lead to elevated levels of covalent complexes act near the same site.”

Although on this page I focus on the topoisomerases, I suspect that any number of other enzymes involved in DNA/RNA replication and repair are unintentional targets as well:

Ciprofloxacin is an inhibitor of the Mcm2-7 replicative helicase    

Fluoroquinolone Derivatives as Inhibitors of Human Tyrosyl-DNA Phosphodiesterase (Tdp1)  


Neural Crest Derivatives and Their Secretory Products: More at Risk?

For those of us affected, there is a wide spectrum of symptoms, which at first look often appear unrelated.   Yet, these symptoms are actually very characteristic, creating a “bell shaped curve” in the affected group.   Many of these symptoms can be traced back to neural crest derivatives.   Furthermore, many symptoms seem to involve secretory epithelial cells, with well developed ER/Golgi or secretory vesicles, for example.   From a TOPO perspective, this may make sense, when you consider the anti-neoplastic mechanism of action for these drugs.   From Osheroff’s “Topoisomerase Poisons: Harnessing the Dark Side of Enzyme Mechanism”:   “Due to the mechanism of drug action, the higher the physiological concentration of topoisomerases, the more lethal these poisons become.   Levels of topoisomerases I and II are generally elevated in cells that are undergoing rapid proliferation.  This probably contributes to the increased response of aggressive cancers to topoisomerase-targeted agents”.   Cells that produce large amounts or rapid cellular products, ie, secretory products, would be more affected via higher rates of topoisomerase activity for those products.   This would include neurotransmitter, neuroendocrine, and endocrine and exocrine gland cells, for example, but would also include a wide variety of other proteins which need to continually and/or rapidly be replaced, such as some collagens and keratins.   This would also include proteins which are drastically depleted and need to be replaced due to the FQ promiscuously binding to them as well as to the TOPOs.    Since TOPO-DNA cleavage complexes are mutagenic in nature, this could certainly increase the chances of de novo mutations occurring for these protein products or the cells that make them.   This mechanism could also help explain why the symptoms of FQT/FQAD so often appear to be so similar to the “side effects” of some patients undergoing traditional chemotherapy for cancer.

My symptoms, which are pretty classic for these reactions all around, do seem to read very much like a road map of neural crest derivative cells.   What underlying factors (enzymes, growth factors, etc.) do these NCC’s continue to have in common in the adult despite being differentiated?


“The Overdose Approach”: Look at P450’s and Relevant Drug Transporters

For another approach, I think looking at the P450 enzyme genes might be useful (the “overdose” approach).   The FQ research on FQ’s and mammalian/human mitochondrial binding suggests it might be concentration dependent (ie, in vitro, FQ’s in “therapeutic amounts” bind to only bacterial gyrase, but above that binding to human TOPOs may be increased).   Given the huge variations in drug metabolism via the P450 route and concentrations of drugs in plasma, that could play a role in potential human TOPO binding as well.   “Drug Metabolism Panels”, looking at some of the P450 genes are popping up for clinical use, but none that I know of are looking directly at FQ-related.    And most, if not all, FQ patients experience moderate to severe caffeine, theobromine, theophylline, etc hypersensitivities/intolerances post FQ, suggesting P450 issues.   So this would be another good place to look, in terms of why FQ’s might have enhanced binding to human TOPOs in some patients.   The same is true with relevant drug transporters which may be involved with renal clearance, for example, polymorphisms of organic ion, organic cation, and undetermined transporter families.

Organic Anion Transporter 3 (Oat3/Slc22a8) Interacts with Carboxyfluoroquinolones and Deletion Increases Systemic Exposure to Ciprofloxacin



Identify Epigenetic Methylation Patterns Between FQAD Population versus FQ-Unaffected and FQ-Unexposed:

Recently, the first study to show global epigenetic changes induced by FQ antibiotics was published:

Non-antibiotic effects of fluoroquinolones in mammalian cells.  (July 2015).   This is the first study to show global epigenetic changes induced by FQ antibiotics.   Iron chelation by fluoroquinolone antibiotics results in DNA and histone hypermethylation, suppression of collagen prolylhydroxylation, and inhibition of HIF mRNA translation.

I contacted an epigenetics researcher with questions about studying these reactions in twins.   My question was the following:  would there be any way to make comparisons of the epigenetic tags between identical twins, one of whom took an FQ and has been affected?    Could this be used to help narrow down the search for where these FQ’s may be acting or causing problems?    Her reply was yes, this could be a valid approach to try and identify the methylation changes caused by the different exposures.    However, ideally, 30-50 twin pairs would be needed to reach sufficient study power, which simply doesn’t exist in the current FQ-affected population.

I explained there exists probably about 5,000 FQ-Affected patients available for study where there appears a strong correlation between taking the drug and onset of symptoms (ie, previously healthy, many athletic, both genders, all ages, reactions occurred within hours to weeks of taking the drugs).   She replied this would be more than sufficient for certain types of studies.

I am hoping that someone will consider studying the FQ-Affected population for epigenetic changes, in an effort to explore this possibility further.


Study the FQT/FQAD Population

I took Cipro for a simple UTI, and went from a healthy athletic person with no known pre-existing conditions who could get on my bike and ride 50 miles, to being unable to walk or do anything else five days later.  This drug completely destroyed my life within a few days with a few pills.   Presumably, the opposite could just as easily occur – ie, a few pills and a few days could probably restore it, as long as the original insult(s) are found (Drugs for epigenetic silencing/enhancing, and targeted genome editing with CRISPR/Cas someday).   The *ONLY* difference between these two scenarios is that no one has any idea of why or how or where the first one occurred.   But if that’s found, that’s pretty powerful.    Here we have a drug that acts as an anti-bacterial, anti-viral, anti-neoplastic, and now, herbicidal agent.   It is directly involved with DNA replication and repair enzymes, and is known to target enzymes with metal cofactors.   The aromatic and zwitterionic nature may allow predictions for promiscuous binding of other enzymes, transporters, and receptors.   A lot is known already about at least one enzyme that is a common denominator in all this, ie, the topoisomerases being a major known target.   If you figure out the mechanisms of why they also sometimes bind to mammalian TOPOs or other enzymes or proteins in some of us and cause “Post-FQ syndrome”, answers will begin to be found for many millions of people suffering from similar syndromes, such as post-bacterial (ie, Lymes, sepsis), post-viral (ie, Ebola and a lot of other common viruses), and post-chemo syndromes (link), not to mention a host of other neuromuscular and neurological disorders.   I also think the “secretory cells with well developed ER/Golgi” approach opens up the door to the protein folding disorders down the line (which I suspect is a high possibility here) and potentially autoimmune issues as a result – which again, could be fundamentally related to the TOPOs initiating de novo mutations somewhere in that process.

I know it’s too late for me.   There is no help available, and there will be no positive outcome for me.   But with “Fluoroquinolone Associated Disability” (FQAD) increasingly recognized and now formally acknowledged by the FDA, and the push for “Personalized Medicine”, which is *supposed* to include increased safety for pharmaceutical use, perhaps funding might be more available for studies in this area.   This might not only help prevent this tragedy from occurring in potential future victims, but could also help provide more useful information about these enzymes in general.

To the researchers who study FQ’s and topoisomerase enzymes:    You, and your colleagues, are experts in the molecular mechanisms that are known about these enzymes so far.  You have the ability to sequence genes, and make comparisons, and possibly do some relevant in vitro experiments as well.   If anyone can help solve the problem of these severe, catastrophic, debilitating and permanent reactions which occur in some people who take FQ’s, it’s your group.   Please consider helping by incorporating the FQ-Affected population into some of your studies, genomically, epigenomically, and enzymatically if possible, and collaborating with other relevant researchers in this area.

Because of promiscuous binding, there are of course plenty of other areas and mechanisms to consider when it comes to FQT/FQAD.   I had my own long list of genes and enzymes which I think would be good candidates to explore, based on my own symptoms approach and the limited research I could do.   Just think how much more could be learned by collaboration of FQ/TOPO researchers with researchers in these and other areas.

I listened to one analogy by one TOPO researcher about how some of these drugs insert themselves into DNA, acting like a huge semi-truck stopped and blocking the “DNA Highway”.   When the DNA tries to replicate, it’s like all the traffic going 50 miles per hour slams into this truck at 50 miles per hour, killing all traffic — and killing the cell.    Well, that’s what it felt like in me.    Everything “stopped” on Day 5.    It feels like there are huge “semi-truck roadblocks” stuck on the major freeways of my body, shutting down these major speedy routes, and the only way anything works anymore is by using small neighborhood collateral routes of little dirt and gravel roads full of potholes.   Those “collateral routes” keep me alive, but that’s about it.   And even they are slowly closing off, one by one, as “traffic jams” continue to build up and close off these routes too.

These are devastating reactions for those of us who experience them.   Surely there must be a way to figure out who might be susceptible to these reactions other than finding out by taking the drug and becoming crippled, maimed, and permanently disabled, living a lifetime of suffering and misery.

To researchers, the FDA, and Pharma:    Do the right thing.   Do the research.




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