The Enantiomers’ Swimming Competition

Image Source.

The spatial arrangement of some large molecules can exist in two different versions which are mirror images of each other, yet their chemical composition is entirely identical. These mirror versions of molecules are said to have a different “chirality” and are called “enantiomers.” The image to the right shows the two chiralities of alanine, known as L-alanine and D-alanine.

Many chemical reactions depend not only on the atomic composition of molecules but also on their spatial arrangement, and thus enantiomers can have very different chemical behaviors. Since organisms are not chirally neutral, medical properties of drugs made from enantiomers depend on which chirality of the active ingredient is present. One enantiomer might have a beneficial effect, while the other one is harmful. This is the case for example for Ethambutol (one enantiomer treats tuberculosis, the other causes blindness), or Naproxen (one enantiomer treats arthritis pain, the other causes liver poisoning).

The chemical synthesis of molecules however typically produces molecules of both chiralities in approximately equal amounts, which creates the need to separate them. One way to do this is to use chemical reactions that are sensitive to the molecules’ chirality. Such a procedure has the disadvantage though that it is specific to one particular molecule and cannot be used for any other.

Now three physicists have shown, by experimental and numerical analysis, that there may be a universal way to separate enantiomers

Separation of chiral colloidal particles in a helical flow field
Maria Aristov, Ralf Eichhorn, and Clemens Bechinger
Soft Matter, 2013,9, 2525-2530 

It’s strikingly simple: chiral particles swim differently in a stream of water that has a swirl to it. How fast they travel with the stream depends on whether their chirality is the same or the opposite of the water swirl’s orientation. Wait far enough downstream, and the particles that arrive first will almost exclusively be the ones whose chirality matches that of the water swirl.

They have shown this as follows.

Molecules are typically of the size of some nanometers or so, and the swimming performance for molecules of different chirality is difficult to observe. Instead, the authors used micrometer-sized three-dimensional particles made of a type of polymer (called SU-8) by a process called photolithography. The particles created this way are the simplest example of configurations of different chirality. They labeled the right-handed particles with a blue fluorescent dye, and the left-handed particles with a green fluorescent dye. This allows taking images of them by a fluorescent microscope. Below you see a microscope image of the particles

Next you need a narrow channel through which water flows under some pressure. The swirl is created by gratings in the wall of the channel. The length of this channel is about a meter, but its height and width is only of the order 150 μm. Then you let bunches of the mixed chiral particles flow through the channel and photograph them on a handful of locations. From the amount of blue and green that you see in the image, you can tell how many of each type were present at a given time. Here’s what they see (click to enlarge)

This figure is an overlay of measurements at 5 different locations as a function of time (in seconds). The green shade is for molecules with the chirality that matches the water swirl orientation, the blue shade is for those with the opposite chirality. They start out, at x=32.5mm, in almost identical concentration. Then they begin to run apart. Look at the left tail of the x=942.5 mm measurement. The green distribution is almost 200 seconds ahead of the blue one.

If you aren’t impressed by this experiment, let me show you the numerical results. They modeled the particles as rigidly coupled spheres in a flow field with friction and torque, added some Gaussian white noise, and integrated the equations. Below is the result of the numerical computation for 1000 realizations (click to enlarge)

I am seriously amazed how well the numerical results agree with the experiment! I’d have expected hydrodynamics to be much messier.

The merit of the numerical analysis is that it provides us with understanding of why this separation is happening. Due to the interaction of the fluid with the channel walls, the flow is slower towards the walls than in the middle. The particles are trying to minimize their frictional losses with the fluid, and how to best achieve this depends on their chirality relative to the swirl of the fluid. The particles whose chirality is aligned with the swirl preferably move towards the middle where the flow is faster, while the particles of the opposite chirality move towards the channel walls where the flow is slower. This is what causes them to travel at different average velocities.

This leaves the question whether this study of particles of micrometer size can be scaled down to molecules of nanometer size. To address this question, the authors demonstrate with another numerical simulation that the efficiency of the separation (the amount of delay) depends on the product of the length of the channel and the velocity of the fluid, divided by the particle’s diffusion coefficient in the fluid. This allows one to estimate what is required for smaller particles. If this scaling holds, particles of about 120 nm size could be separated in a channel of about 3cm length and 3.2 μm diameter, at a pressure of about 10⁸ Pa, which is possible with presently existing technology.

Soft matter is not anywhere near by my area of research, so it is hard for me to tell whether there are effects at scales of some hundred nanometers that might become relevant and spoil this simple scaling, or whether more complicated molecule configurations alter the behavior in the fluid. But if not, this seems to me a tremendously useful result with important applications.

Book Review: "The Quest for the Cure" by B.R. Stockwell

The Quest for the Cure: The Science and Stories Behind the Next Generation of Medicines
By Brent R. Stockwell
Columbia University Press (June 1, 2011)

As a particle physicist, I am always amazed when I read about recent advances in biochemistry. For what I am concerned, the human body is made of ups and downs and electrons, kept together by photons and gluons - and that's pretty much it. But in biochemistry, they have all these educated sounding words. They have enzymes and aminoacids, they have proteases, peptides and kineases. They have a lot of proteins, and molecules with fancy names used to drug them. And these things do stuff. Like break up and fold and bind together. All these fancy sounding things and their interactions is what makes your body work; they decide over your health and your demise.

With all that foreign terminology however, I've found it difficult to impossible to read any paper on the topic. In most cases, I don't even understand the title. If I make an effort, I have to look up every second word. I do just fine with the popular science accounts, but these always leave me wondering just how do they know this molecule does this and how do they know this protein breaks there, fits there, and that causes cancer and that blocks some cell-function? What are the techniques they use and how do they work?

When I came across Stockwell's book "The Quest for the Cure" I thought it would help me solve some of these mysteries. Stockwell himself is a professor for biology and chemistry at Columbia university. He's a guy with many well-cited papers. He knows words like oligonucleotides and is happy to tell you how to pronounce them: oh-lig-oh-NOOK-lee-oh-tide. Phosphodiesterase: FOS-foh-dai-ESS-ter-ays. Nicotinonitrile: NIH-koh-tin-oh-NIH-trayl. Erythropoitin: eh-REETH-roh-POIY-oh-ten. As a non-native speaker I want to complain that this pronunciation help isn't of much use for a non-phonetic language; I can think of at least three ways to pronounce the syllable "lig." But then that's not what I bought the book for anyway.

The starting point of "The Quest for the Cure" is a graph showing the drop in drug approvals since 1995. Stockwell sets out to first explain what is the origin of this trend and then what can be done about it. In a nutshell, the issue is that many diseases are caused by proteins which are today considered "undruggable" which means they are folded in a way that small molecules, that are suitable for creating drugs, can't bind to the proteins' surfaces. Unfortunately, it's only a small number of proteins that can be targeted by presently known drugs:

"Here is the surprising fact: All of the 20,000 or so drug products that ever have been approved by the U.S. Food and Drug Administration interact with just 2% of the proteins found in human cells."

And fewer than 15% are considered druggable at all.

Stockwell covers a lot of ground in his book, from the early days of genetics and chemistry to today's frontier of research. The first part of the book, in which he lays out the problem of the undruggable proteins, is very accessible and well-written. Evidently, a lot of thought went into it. It comes with stories of researchers and patients who were treated with new drugs, and how our understanding of diseases has improved. In the first chapters, every word is meticulously explained or technical terms are avoided to the level that "taken orally" has been replaced by "taken by mouth."

Unfortunately, the style deteriorates somewhat thereafter. To give you an impression, it starts more reading like this

"Although sorafenib was discovered and developed as an inhibitor of RAF, because of the similarity of many kinases, it also inhibits several other kinases, including the patelet-derived growth factor, the vascular endothelia growth factor (VEGF) receptors 2 and 3, and the c-KIT receptor."

Now the book contains a glossary, but it's incomplete (eg it neither contains VEGF nor c-KIT). With the large number of technical vocabulary, at some point it doesn't matter anymore if a word was introduced, because if it's not something you deal with every day it's difficult to keep in mind the names of all sorts of drugs and molecules. It gets worse if you put down the book for a day or two. This doesn't contribute to the readability of the book and is somewhat annoying if you realize that much of the terminology is never used again and one doesn't really know why it was necessary to use to begin with.

The second part of the book deals with the possibilities to overcome the problem of the undruggable molecules. In that part of the book, the stories of researchers curing patients are replaced with stories of the pharmaceutical industry, the start-up of companies and the ups and downs of their stock price.

Stockwell's explanations left me wanting in exactly the points that I would have been interested in. He writes for example a few pages about nuclear magnetic resonance and that it's routinely used to obtain high resolution 3-d pictures of small proteins. One does not however learn how this is actually done, other than that it requires "complicated magnetic manipulations" and "extremely sophisticated NMR methods." He spends a paragraph and an image on light-directed synthesis of peptides that is vague at best, and one learns that peptides can be "stapled" together, which improves their stability, yet one has no clue how this is done.

Now the book is extremely well referenced, and I could probably go and read the respective papers in Science. But then I would have hoped that Stockwell's book saves me exactly this effort.

On the upside, Stockwell does an amazingly good job communicating the relevance of basic research and the scientific method, and in my opinion this makes up for the above shortcomings. He tells stories of unexpected breakthroughs that came about by little more than coincidence, he writes about the relevance of negative results and control experiments, and how scientific research works:

"There is a popular notion about new ideas in science springing forth from a great mind fully formed in a dazzling eureka moment. In my experience this is not accurate. There are certainly sudden insights and ideas that apear to you from time to time. Many times, of course, a little further thought makes you realize it is really an absolutely terrible idea... But even when you have an exciting new idea, it begins as a raw, unprocessed idea. Some digging around in the literature will allow you to see what has been done before, and whether this idea is novel and likely to work. If the idea survives this stage, it is still full of problems and flaws, in both the content and the style of presenting it. However, the real processing comes from discussing the idea, informally at first... Then, as it is presented in seminars, each audience gives a series of comments, suggestions, and questions that help mold the idea into a better, sharper, and more robust proposal. Finally, there is the ultimate process of submission for publication, review and revision, and finally acceptance... The scientific process is a social process, where you refine your ideas through repeated discussions and presentations."

He also writes in a moderate dose about his own research and experience with the pharmaceutical industry.

The proposals that Stockwell has how to deal with the undruggable proteins have a solid basis in today's research. He isn't offering dreams or miracle cures, but points out hopeful recent developments, for example how it might be possible to use larger molecules. The problem with large molecules is that they tend to be less stable and don't enter cells readily, but he quotes research that shows possibilities to overcome this problem. He also explains the concept of a "privileged structure," structures that have been found with slight alterations to bind to several proteins. Using such privileged structures might allow one to sort through a vast parameter space of possible molecules with a higher success rate. He also talks about using naturally occurring structures and the difficulties with that. He ends his book by emphasizing the need for more research on this important problem of the undruggable proteins.

In summary: "The Quest for the Cure" is a well-written book, but it contains too many technical expressions, and in many places scientific explanations are vague or lacking. It comes with some figures which are very helpful, but there could have been more. You don't need to read the blurb to figure out that the author isn't a science writer but a researcher. I guess he's done his best, but I also think his editor should have dramatically sorted out the vocabulary or at least have insisted on a more complete glossary. Stockwell makes up for this overdose of biochemistry lingo with communicating very well the relevance of basic research and the power of the scientific method.

I'd give this book four out of five stars because I appreciate Stockwell has taken the time to write it to begin with.