On Antibiotics and the Fight Against Drug-Resistant Pathogens

Imagine a world in which antibiotics didn’t exist.  Imagine if instead of requiring a week-long prescription and bed rest, a bout of pneumonia was fatal.  Or if a staph infection couldn’t be cleared up by a simple cephalexin regiment.

You only have to think back about 90 years to realize this hypothetical scenario.  Prior to the discovery of penicillin by Alexander Fleming in 1928, such common bacterial infections were debilitating and potentially lethal.  And we as a species are slowly (some would argue rapidly) regressing to this scenario.

Thanks to bacterial drug resistance, our line of antibiotic defense is becoming obsolete.  Antibiotic research is a tricky area.  It’s an evolutionary arms race of sorts — humans come up with new antibiotics, then microbes acquire selective resistance to them.  Repeat ad infinitum.  Except we can’t repeat forever.  Not at our current pace.

See, there are about a dozen classes of antibiotics.  They are generally classified by structure and by mechanism of action.  Medicinal chemists can make minor tweaks to existing structures, which generate new antibiotics that are very similar to the old ones.  This can stave off bacterial resistance for a little while.  But in order to really put the pressure on microbes, you need a whole new class of antibiotics.  And it’s been over 30 years since we discovered a new class.  Until this week.

Enter last week’s article in Nature.  A team of researchers spanning industry and academia published a very interesting paper in which they describe the discovery of a new antibiotic, termed “teixobactin.”  It’s large, has lot’s of chiral centers, and has some strange looking amino acid residues.

Structure of teixobactin

Structure of teixobactin

Teixobactin scores respectably well against a host of pathogens, as shown in “table 1” in the paper (reproduced below).  In some cases, it even surpasses the efficacy of current generation antibiotics.  In mouse models infected with methicillin-resistant S. aureus (MRSA), all animals treated with teixobactin survived down to doses as low as 1 mg/kg body mass (single dose, i.v., 1 hour post-infection).

MIC table

Interestingly, the authors report that the compound does not induce drug-resistance in staphylococcus aureus or mycobacterium tuberculosis, two common disease-causing organisms.  To quote the article (emphasis my own):

Serial passage of S. aureus in the presence of sub-MIC levels of teixobactin over a period of 27 days failed to produce resistant mutants as well.  This usually points to a non-specific mode of action, with accompanying toxicity. However, teixobactin had no toxicity against mammalian NIH/3T3 and HepG2 cells at 100 µg/ml (the highest dose tested). The compound showed no haemolytic activity and did not bind DNA.

This is pretty important, since it indicates that teixobactin seems to act with selectivity; there are lot’s of compounds that kill bacteria very effectively, but will kill your body’s cells as well.  The team went on to investigate the mechanism of action of the new compound.  They found that it acts as a peptidoglycan synthesis inhibitor; the peptidoglycan layer forms the cell wall for bacteria, and is essential to their growth and survival.  Teixobactin appears to consume precursors to peptidoglycan synthesis, and does not appear to act directly on any known protein targets.  This distinction is likely the reason bacterial cells do not develop resistance to the compound.

But, what’s even more important than the discovery of this new antibacterial compound is the method used to discover it.  All of the antibiotics that have so far been discovered have been through isolation of chemical compounds made by other organisms.  Interestingly, bacteria themselves often generate antibacterial compounds.  Perhaps somewhat counter intuitive, but it makes a good deal of sense from an evolutionary perspective; if an organism can produce a compound toxic to other species, it gains a powerful tool for survival.  A major challenge for scientists is growing bacterial cultures in the laboratory.  Some, such as E. coli and S. aureus, grow quite nicely on Petri dishes.  The other 99% of bacterial species cannot be cultured in the laboratory.

Since this bulk of the bacterial biosphere cannot be easily cultured, it has never been screened for antibacterial properties.  The researchers in this paper came up with a piece of technology they dubbed the “iChip” (Steve would be proud).  The iChip allows a single bacterial cell to be isolated from a soil sample, while being kept separate from the rest of the soil microbes.  The cell, affixed to the chip, is then placed back in the soil from which it came, where it can multiply into a colony.  The large colonies produced can then be grown in vitro as is typical for “well-behaved” microbes.

The optimists out there are hopeful that new-found access to “unculturable” bacteria will allow scientists to rapidly screen for natural product-based antibiotics.  Of course, like with so many other discoveries, only time will tell if this method proves to be of practical use for drug discovery.


An Open Letter To The New York Times

To the editorial staff at The New York Times:

I am writing in regard to a November 10 opinion piece titled “The Word ‘Natural,’ Like Our Food, Has Become Polluted,” featuring the self-proclaimed advocate and educator Vani Hari, known colloquially as “The Food Babe.”

It is, quite frankly, appalling that pseudoscientific quackery like The Food Babe be given a soapbox from which to quack in any reputable publication.  I cannot imagine a scenario in which it would be anything other than uncouth to have someone as thoroughly discredited as Vani Hari weigh in about a topic she knows fundamentally nothing about.  At best, Ms. Hari’s ranting is ill-informed and uneducated.  At worst, it is willfully ignorant, intentionally deceitful, and unethical.

The title of the opinion column in which Hari is featured is titled “Room for Debate.”  The existence of a dissenting opinion is not, in and of itself, grounds for giving it weight commensurate with that of the breadth of knowledge on the subject.  Frequently, news outlets will allow “room for debate” regardless of whether such room exists.  But that is the subject of another discussion entirely.

Ms. Hari has been unequivocally ostracized from the scientific community, and for good reason; her opinions flagrantly defy the basic tenants of science first taught to us in middle school.  As such, it is irresponsible journalism to give a voice to such opinions.

There simply is not a place for her type of argument in educated debate.  Should Ms. Hari step back into the realm of reality, and away from the tin-foil hat clad members of the Church of Our Lizard Overlords, we will gladly welcome her to discuss facts with us.  Until such time, we will continue to regard her opinions with bemused frustration.


Mitchell T. Antalek

On Irresponsible, “Click-Bait” Science Journalism

You’ve all seen these articles.  They circulate Facebook, and are propagated by television personalities (Oprah, Dr. Oz, I’m looking at you), blogs, and aggregator sites such as Elite Daily (and others).  The headline will usually be something flashy ending in a question mark.  “Can eating a bar of chocolate every day prevent diabetes?”  Or “Is this new compound discovered at University X the cure for cancer/HIV/obesity/other?”  You get the gist of it.

The latest offender claims something along the lines of red wine being a substitute for physical exercise.  Wouldn’t that be nice?  If you could down a bottle of cabernet sauvignon instead of hitting the treadmill?  The headline, in its various forms claims a generalized version of the following “Scientists determine red wine better than exercise,” brazenly implying that we all got together and agreed.

Faux-science journalism keeps popping up.  It’s misleading at best, and unethical, deceptive, and manipulative at worst.  It’s a disservice to the actual scientific discoveries being pursued; not every study needs to cure cancer, nor does every new compound need to be a miracle weight-loss drug.  I’m going to take you through how real research turns into the abomination that is click-bait journalism in this post.

To the Source!

First thing’s first.  We need to go to the source of the reported claim.  I’m going forward with the red wine/exercise claim here.

Interestingly (but perhaps not surprisingly), you need to click through several links that claim to be the source until you get to the actual peer reviewed scientific paper from which this crazy claim is derived.

I started at an Elite Daily article titled “OMFG: Science Says A Glass Of Red Wine May Be Equivalent To An Hour At The Gym” [1] (protip: real scientific articles rarely have “OMFG” in the title).  Clicking the link to their source, I was taken to another article, this time at Science Daily.  Clicking the source link on SD led me to the actual paper, a full-length article published in the Journal of Physiology, a peer-reviewed academic journal.

Let’s examine how the claims evolved from science to complete bullshit over three iterations.

The Peer-Reviewed Paper

The actual paper is published in the Journal of Physiologyand is available to read for free on the publisher’s site.

Let’s examine the claims and methods of the paper.  I’ll keep this concise.

  • Resveratrol is a natural product found in red wine, many fruits, and some other plant matter
  • Supplementing rat’s diet with resveratrol resulted in a statistically significant increase in exercise performance
  • Skeletal muscle force, cardiovascular performance, and metabolism were all boosted in rats whose diets were supplemented with resveratrol

So, some scientists added this compound, resveratrol, to the diet of test rats, and maintained a group of rats without resveratrol as a control group.

The natural product resveratrol

Important to note is the dose of the compound given: 146 milligrams per kilogram of body mass per day.  Speaking from a pharmacokinetics perspective, this is a HUGE dose.  Most drug-like compounds are given in doses 10-1000x lower than that.  To put that in perspective, the dose of Tylenol for an adult male is about 10 milligrams per kilogram of body mass.  146 milligrams per kilogram of Tylenol corresponds to 20 extra-strength capsules, and would most likely destroy your liver.

So, after eating this resveratrol-rich diet, the rats were examined for exercise capacity.  How was this done?  With tiny treadmills, of course.  No, I am not joking.


Rat treadmills, a real thing

And what exactly was concluded from this effort?

  • The performance of rats on the resveratrol diet was 21% better than the rats without resveratrol (at 99.9% confidence interval)
  • Rapid (twitch) muscle forces increased 1.8x, and endurance (tetanic) increased 1.2x over the control group (at 95% confidence)
  • A measure of cardiovascular efficiency (ventricular ejection) increased 10% (95% confidence)
  • Fatty acid oxidation (a measure of metabolism) increased by a factor of 1.2x (95% confidence)

Looking good so far!  I think this paper reaches some interesting (though not exactly earth-shattering) conclusions.  Apparently they are moving onto limited clinical trials to see if resveratrol helps patients with impaired heart function.  However, I would not be at all surprised if resveratrol is cytotoxic or even carcinogenic at the doses given to rats in the study.  My own skepticism aside, the paper has valid methodology, reaches real, statistically significant conclusions, and demonstrates potential for further study.

You may notice, however, that nowhere does anyone related to the study claim that red wine somehow equals exercise.  Nor do they suggest a diet including red wine is a viable way to ingest resveratrol in biologically relevant concentrations.

So where did we go wrong?

Iteration Two: Science Daily

Science Daily is a scientific news aggregator site.  They compile recent scientific articles, and summarize them for a non-technical audience.  Generally speaking, they do a pretty decent job of maintaining the conclusions drawn in the original paper without sensationalizing the results.  Their articles are short, generally include no data, and tend to over-emphasize the results.  That’s not necessarily a bad thing.  At least they cite the original paper.

The first line of the article states “A natural compound found in some fruits, nuts, and red wine may enhance exercise training and performance, demonstrates newly published medical research from the University of Alberta.” [3]  That claim is not at all false.  However, you can probably see how without the underlying context, this claim could be blown out of proportion.

Iteration Three: Elite Daily

Here we go.

The title of the ED article claims that a glass of red wine is equivalent to an hour at the gym.  First off, no one ever mentioned anything about equivalence.  Who came up with the “one glass equals one hour” thing?  Certainly not the authors of the paper.  The article goes on to say that “the benefits only come from one single glass,” citing another (even more sensationalized) article at the Latin Times [4].

Let’s first examine the resveratrol content of red wine.  Red wine contains between 1 and 13 milligrams of resveratrol per liter [5].  Let’s be generous and assume the upper end.  To reach the same dosage of resveratrol given to the rats, an adult male would need to consume about 11 grams of pure resveratrol.  This corresponds to 730 liters of wine.  For those of you metrically challenged, that’s just shy of 200 gallons.  Of wine.  Per day.  Do not try to drink 200 gallons of wine per day.

Or do.  Whatever, I'm not a doctor.

Or do. Whatever, I’m not a doctor.

The claim that exercise could be substituted, in part or in whole, by drinking red wine is clearly complete fabrication; there is simply no way a human could consume enough red wine to intake a comparatively useful dose of resveratrol.

 In Conclusion

  1. Be wary of scientific news coming out of aggregator sites.  The best place to get the real deal behind a paper is, unsurprisingly, to read the paper itself.  That’s not always and option for a large number of reasons.  However, the abstract is always free to read, and any major conclusions are always (at least in well-written articles) stated upfront in the abstract.  If it was discovered that exercise could be substituted for red wine, you better believe the first of second sentence of the paper’s abstract would say as such.
  2. Check the sources!  If a news release links to another news release as its source, you’ve most likely entered the realm of unverified speculation, or complete fabrication.
  3. Even the more reputable news sites (like Science Daily) generally sacrifice scientific rigor for the sake of clarity.  While fabrications are rare, conclusions can be exaggerated, or key details omitted in the name of brevity.


[1] http://elitedaily.com/news/world/glass-wine-equivalent-going-gym/770635/

[2] http://jp.physoc.org/content/590/11/2783

[3] http://www.sciencedaily.com/releases/2012/06/120619225941.htm

[4] http://www.latintimes.com/drinking-wine-better-going-gym-according-scientists-yes-261496

[5] http://etd.lsu.edu/docs/available/etd-01202006-082858/

On Research and Public Awareness (Re: #IceBucketChallenge)

In the last week or so, I’ve seen dozens of posts on various social media outlets promoting awareness for amyotrophic lateral sclerosis (ALS, Lou Gehrig’s Disease) using #IceBucketChallenge.  This is awesome, and spreading public awareness about this disease is certainly an important step in the right direction.

You probably sense a “but” coming.  You’d be right.

Admittedly, I don’t work in ALS research.  I am, however, a researcher whose work is funded primarily by federal grant money.  And let me tell you one thing: getting funded is unequivocally difficult.

An inordinately large number of researchers spend a disproportionately large amount of their time engaging in grant writing, not research.

A 2007 study found that upwards of 40% of university faculty member’s time was spent on the grant securing process.  Since you may not work in research, allow me to frame that in a more accessible way:

Imagine you work in a factory making widgets.  Now imagine that every time you want to make a widget, which let’s remember is your primary job function, you must walk to your CFO’s office, and give him a 30-minute presentation outlining, in perfect detail, exactly why you want to make a widget.  He will consider your request, and 15-20% of the time, he will allow you to make a widget.  The other 80-85% of the time, he will say to you “I’m sorry, but right now we can’t give you the resources to make a widget.  Come up with a better reason why we should, then come see me again.”

You can probably imagine in this hypothetical situation, widgets are not produced with particularly high efficiency.

Supporting ALS awareness is great.  But what’s even better is funding the research that will ultimately allow us to find better treatments.

I’d ask that you do one of two things if you care about the progress of research for ALS treatment:

  1. Donate.  Give to the ALS Association, or give to the ALS Therapy Development Institute (a non-profit biotechnology firm).  Nothing will expedite the research and development process faster than money.
  2. Don’t have money to spare?  That’s fine, you can still help.  Call your federal representative.  Call your senator.  Tell them you think federal funding for biomedical research and development should be a national priority.

You Are What You Eat

This one’s for all you foodies out there.  The average American consumes somewhere around 2700 calories every day [1].  To put that number in perspective, a human consumes enough food energy to power a 100 Watt light bulb.  A family of four could power a desktop computer.  Your body functions by taking the chemical energy stored in the bonds of saccharides, proteins, and lipids (fats) and converting it into mechanical energy through a process called metabolism.  Micronutrients, such as vitamins and metal ions (iron, cobalt, sodium) are also introduced to the body through metabolic processes.

But not only does the body get much needed nutrients through eating, harmful substances can also be introduced in this way.  Toxic heavy metals can be introduced through contaminated ground water, or even fish.  Carcinogens, such as polycyclic aromatic hydrocarbons and dicarbonyls, can be found in cooked meats and liquors, respectively [2].

With that in mind, let’s examine some of the hazardous chemical compounds you didn’t know where in many of the foods you consume daily.



Where it’s found: desserts, breads, baked goods, some perfumes, used as insecticide [7]

What it does: (2E)-3-phenylprop-2-enal is a skin and respiratory irritant.  In high enough doses, this compound is acutely toxic [3].

(9Z)-Octadec-9-enoic acid


Where it’s found: most meats, including chicken, turkey, and beef, peanuts, and olives

What it does: In the blood stream, (9Z)-Octadec-9-enoic acid has been shown to induce severe respiratory failure and subsequent death by pulmonary edema in sheep [4].  It has furthermore been associated with increased incidence of breast cancer [5].



Where it’s found: many over the counter pain relievers and decongestants (Excedrin, DayQuil, others), chocolate, soda, tea, and coffee

What it does: First and foremost, 1,3,7-Trimethyl-1H-purine-2,6(3H,7H)-dione is teratogenic and mutagenic [6].  It is addictive and frequent consumption causes rapid physical dependence.  Furthermore, it is acutely toxic at certain doses, causing death by cardiac arrest.



Where it’s found: fruits of plants belonging to the Capsicum genus, including bell peppers and jalapenos, paprika

What it does: In the laboratory, 8-Methyl-N-vanillyl-trans-6-nonenamide is classified as a hazardous material and requires the use of a respirator for safe handling.  Contact with skin or eyes results in severe irritation and burning, accompanied by local swelling.  Inhalation results in respiratory tract irritation.  It is acutely toxic in sufficient doses, and may have neurotoxic effects [8].

I Have a Confession to Make…

Up to this point, this entire article has been quite deceptive.  Intentionally so.  But I wrote it that way for a good reason, I promise.  Time for a quick poll: how many of you Google’d any of the compounds I just listed?  If you did, you would have found that I gave the systematic IUPAC names for quite common chemicals.

  • (2E)-3-phenylprop-2-enal is more commonly referred to cinnamaldehyde, and is the chief favorant in cinnamon.  Pure cinnamaldehyde, isolated from the essential oil of cinnamon tree bark, is a skin irritant; however, the cinnamaldehyde content in ground cinnamon is low enough for this to be a non-issue.  Furthermore, while it is technically toxic, the amount you would need to eat for negative effects to occur is huge – about half a pound for a healthy adult.
  • (9Z)-Octadec-9-enoic acid might be more recognizable as oleic acid, and makes up about 60% by mass of olive and canola oils.  It’s a very common fatty acid, usually found as a triglyceride in animal fat and many seeds and nuts.  Consumption of such monounsaturated fatty acids has been shown by trial after trial to have health benefits such as lower “bad” cholesterol.  While one study did show a link between high consumption of these fats and breast cancer, others have shown quite the opposite [9].  As for respiratory failure and pulmonary edema?  The researches induced these conditions in sheep intentionally by injecting pure oleic acid directly into their bloodstream.  So as long as you’re not shooting up olive oil, you should be alright there.
  • 1,3,7-Trimethyl-1H-purine-2,6(3H,7H)-dione might wake you up every morning, you probably just call it caffeine.  It is in fact mutagenic, hence why expectant mothers are instructed to avoid it.  However, the study demonstrating these properties in rats used injections of caffeine equivalent to a human dose of 100 cups of coffee.  This amount is incidentally very close to the median lethal dose in humans, which would of course be impossible to achieve by drinking coffee alone [10].
  • 8-Methyl-N-vanillyl-trans-6-nonenamide is what gives your chili its kick, but you most likely know it as capsaicin.  It’s in every chili pepper you cook with, from serranos to jalapenos to those absurd Indian ghost peppers.  Of course it’s an irritant, ever rubbed your eyes after eating something spicy?  The pure stuff, extracted and isolated from the peppers, is just much, much more potent.

So What’s the Point Here?

There seems to be some sort of pervasive fear of chemistry in society.  To a degree, I understand it; the 1950’s, gung-ho blind devotion to “Better Living Through Chemistry” brought us thalidomide and agent orange.  Carelessness brought us the tragic Bhopal incident in 1984.  It seems as though in a number of ways, chemical research has changed from “this is useful” to “this is dangerous” in the mind of the public.  I seldom go two days without seeing a link to some blog touting the horrors of synthetic food additives, GMO foods, or fluoride in the water.  The repeated chanting of “synthetic is bad, natural is good” ignores the fact that chemistry itself is indifferent.  I could just as easily have written this article from the opposite perspective: “All-Natural Drugs Found in Food.”  Hydrogen cyanide in Yuca plants, coniine in the hemlock bush, and amanitin in Amanita mushrooms, all of which are natural but deadly.

All science, let alone chemistry, requires a certain level of skepticism, without which true objectivity would be impossible.  A double-dose of skepticism may be necessary when dealing with things you ultimately put in your body.  With that being said, I hope the take-home message from this article is simply “think critically.”  Remember, any Joe (myself included) with some free time and $20 can set up a website and say whatever they want.  There is a vast amount of wonderfully useful information out there.  Unfortunately, there is also a huge quantity of misinformation mixed in with it.  As the 16th century German physician Paracelsus said, “All things are poison, and nothing is without poison; only the dose permits something not to be poisonous.”



P.S. This post is a bit different from what I usually publish, so as always, I welcome feedback.  Leave me a comment or shoot me an email (mtantalek@gmail.com).  I’m also interested in hearing what you would like to read about in future posts.


  1. http://www.usda.gov/factbook/chapter2.pdf
  2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2379645/pdf/canfamphys00111-0173.pdf
  3. http://www.ncbi.nlm.nih.gov/pubmed/10866983
  4. http://jap.physiology.org/content/60/2/433.long
  5. http://jnci.oxfordjournals.org/content/93/14/1088
  6. http://onlinelibrary.wiley.com/doi/10.1002/tera.1420080109/abstract
  7. http://pubs.acs.org/doi/abs/10.1021/jf0497152
  8. http://www.sciencelab.com/msds.php?msdsId=9923296
  9. http://onlinelibrary.wiley.com/doi/10.1002/ijc.2910580604/abstract
  10. http://onlinelibrary.wiley.com/doi/10.1002/j.1552-4604.1967.tb00034.x/abstract