I thought I saw it…

Aromatic heterocycles form the backbone of drug discovery. It is difficult to deny this statement for two simple reasons: a. the relative resistance of aromatic heterocycles to oxidation and b. their capacity to partake in a gamut of interactions with protein targets (hydrogen bonds, hydrophobic interactions, etc). While linking heterocycles into oligomeric chains is best done by way of cross-coupling reactions, there is no better alternative to condensations when it comes to making heterocycles themselves. Copper-catalyzed azide/alkyne cycloaddition is an exception to this rule. If you are thinking about a pyrrole, a pyridine, or a pyrimidine (the list can go on and on), nothing comes close to gaining aromaticity by kicking out water molecule(s) from a carbonyl precursor. Aromatic heterocycles that contain N-N or N-O bonds belong to a particularly vast class of useful molecules. Some time ago, I wondered about reactions that provide access to pyrazoles or isoxazoles by building a heteroatom-heteroatom bond as part of the process. For the life of me, I could not think of an example. You might say: why bother? As a matter of fact, I would agree because hydrazines and hydroxylamines are some of the most versatile and readily accessible nucleophiles. However, if I put my basic scientist hat on, I want to see reactions of this kind. Until we get there, my claim stays put: there are no examples where heteroatom-heteroatom bonds are made in the course of aromatic heterocycle synthesis.



I was reading a cool paper by the Swedish group led by F. Almquist and, upon a cursory look at one of the schemes, I said to myself:  “Darn, this must be it! The N-N bond construction…”. Take a look above. On a sober glance, however, the reaction amounts to a Sandmeyer process gone “haywire”. In this reaction, the targeted diazonium intermediate activates the proximal methyl group. The reaction is rather unusual, which is why I like it. Still, this does not affect my assertion that there are no useful ways of making aromatic heterocycles by building heteroatom-heteroatom bonds. There might be something I am missing, of course. But I do not mean an obscure example, ladies and gentlemen. Please give me something synthetically useful.

Apart from the interesting pyrazole-forming reaction, this paper provides a neat example of peptidomimetic design. The tricyclic pyrazole-2-pyridone-thiazoline structures accessible with the Almquist method incorporate a dipeptide sequence within a rigid framework. Importantly, the two substituents that correspond to amino acid side chains may be varied, enabling construction of compounds libraries.

Squeezing fragments into cycles

Today is dedicated to the efforts of Chris White, my PhD student who is soon leaving us for Zurich, where he will work as a postdoctoral associate at the ETH in the laboratory of Professor Jeff Bode. Over the past 3 years, Chris has been painstakingly perfecting a reaction that amounts to insertion of amino acid fragments into cyclic peptides. While there is no precedent for integrative operations in the realm of synthetic chemistry, nature is known to do it. One particularly well-known process in biology involves integration of DNA fragments into host chromosomes. This function-driven insertion of “foreign” fragments into existing biological entities has far-reaching consequences. When we think about synthetic challenges in our lab, we often draw inspiration from nature. Several years ago we asked a question: if the retroviral enzyme integrase can do it by binding both termini of viral DNA, can we think of a reductionist approach to this process? How about instead of DNA and enzymes we teach some new tricks to lithium hydroxide and simple coupling reagents? Chris has capitalized on the susceptibility of N-acyl aziridines to amide hydrolysis –  their “Achilles’ heel” – and developed a tool to site-selectively incorporate molecular fragments into cyclic peptides. We think that this method should be readily adaptable to solid phase synthesis, be extended to split and pool protocols using molecular fragments of varying diversity, and help create non-amide bond forming approaches to fragment integration. Our lab will now actively work in these directions. Thanks Chris for your trailblazing efforts!

ccc 7.46.16 PM


Small amounts of alcohol

I flew into Boston last night and had a great time at the Chemistry Department (Boston University) earlier today. A special thanks goes to Professor Aaron Beeler, my main host, who is running an innovative program in flow synthesis, bioactive molecule synthesis, and reaction discovery at BU (http://www.bu.edu/chemistry/faculty/beeler/). I met Aaron last Summer at the Gordon Conference on High-Throughput Chemistry and Biology, where he invited me to visit his storied department. I just came back from our dinner at the Eastern Standard (awesome oysters there, ladies and gentlemen) with Aaron and Professor Scott Schaus. While we were having our drinks at this fine establishment, I kept thinking about the significance of much smaller amounts of alcohol. Sounds like an oxymoron, I know… What I mean is this: while talking to Scott earlier in the day, I was reminded about the significance of achiral additives in asymmetric catalysis. Below is a link to the Angewandte paper by Scott, who discovered a superb ketone allylation process and spent several years perfecting this catalysis.



The pre-2009 mechanistic work by the Schaus lab showed step A to be rate-limiting. The rate order in alcohol was not established at that time. One could logically assume this additive to have an inhibiting effect on the reaction. An important insight offered by the 2009 study is that the rate-determining ligand exchange process is in fact not the initial formation of the active boronate species (step A), but the liberation of the catalyst from allylation product (step B). Check out the role of the tert-butanol additive (Figure 2) on the reaction! This nice work also reminded me of the old review by Shibasaki pointing to the significance of ACHIRAL additives in ASYMMETRIC catalysis. I think we should spend way more attention to the effect of such species. Here is a link to the Shibasaki review:


Ok, I am off to bed – catching a 6am flight back to Toronto, where I am giving two lectures in my graduate class and second year organic class tomorrow… Thankfully my student Adam filled in for my CHM 249 class today!


I have been fascinated with selenium-containing heterocycles, particularly after seeing the Science paper that described the co-crystal structures of a couple of selenazole-containing macrocycles with p-glycoprotein (I blogged about it on January 9th). A good way of making selenazoles would go a long way because you have to admit it – these are not your average, garden-variety heterocycles. They are exotic, yet endowed with very interesting and unusual hydrophobic properties in a dense area of space. Below is a simple method of preparing selenazoles using Ishihara’s reagent. This paper attracted my attention mainly due to the ease of converting LAH into a useful selenium transfer agent. In order to prepare Ishihara’s reagent, you need to mix LAH with elemental selenium in THF under inert atmosphere. The lithium hydrogen selenide (LiAlHSeH) is formed in situ as a gray solution that can be directly used in subsequent steps. The selenazole core was prepared by Mahler through straightforward cycloisomerization of
 propargyl selenoamides prepared in
 situ using LiAlHSeH. The method is concise and user-friendly.



An upper hand on biosynthesis

Some time ago I noticed that Mother Nature, despite its amazing virtues, does not know how to make C-N bonds by oxidation. Think about it: there are so many C-N bonds out there (in DNA, in alkaloids, you name it), yet none of them are made using oxidative enzyme machinery. If you are thinking about C-O bonds, then there are many examples of their construction using oxidative enzymes such as p450’s and others. However, all C-N bonds have reduction as their origin or are made using carbonyl condensation reactions. One might speculate as to why this might be the case. From Mother Nature’s standpoint, the most plausible reason would be “why bother?”. The metal-based nitrogen oxidants are inherently more difficult to produce compared to their oxygen counterparts (for example, metal nitrenes vs metal oxo species), so there is no evolutionary reason to go high in energy if the key bond-forming events can be accomplished using simpler means. The key factor is that molecular oxygen is our readily accessible terminal oxidant and there is just no nitrogen analog that is similarly abundant. We later wrote a short commentary in Nature Chemical Biology discussing this problem. This paper continues to be well cited (primarily by synthetic folks who need a believable justification for why synthetic nitrogen transfer systems are cool):


Now it turns out that chemists can teach Mother Nature some new tricks. Take a look at the paper by Bollinger and co-workers in Nature Chemical Biology:



The α-ketoglutarate/iron-dependent dioxygenases and halogenases are typically recruited to run a wide range of enzymatic reactions ranging from hydroxylation to halogenation. Despite this useful palette of reactions, no C-N coupling by this class of enzymes has previously been reported. Bollinger et al. discovered that an αKG/Fe-dependent halogenase, SyrB2, can catalyze aliphatic nitration and azidation reactions. I am showing the azidation process above, which takes place when excess sodium azide is fed to the enzyme (thus, azide anions outcompete chloride anions). Despite the fact that chemical yields in the present version of the process are still very low, this study opens up new possibilities for nitrogen transfer by selective enzymatic C-H activation. It is conceivable that engineering of substrate specificity through directed evolution might be achieved in the future iterations of this system.

How about doing it in fluo?

I already mentioned a sustained current interest in flow chemistry. I am a believer in this method. It is interesting to see reports where chemistry is run in thin capillaries where residence time rules. This parameter is unheard of in our typical “flask-based” reactions. Of particular significance to me is the paper by my former PhD student, Zhi He, who is now doing his postdoctoral work with Tim Jamison at MIT. Zhi’s manuscript, which just came out in Angewandte, documents a flow approach to phenols starting from Grignard reagents. This work serves as an example of an economical approach to phenol synthesis, whereby aryl Grignard reagents are directly oxidized using compressed air in “continuous gas-liquid segmented flow system”. Many functional groups are tolerated in this process. What’s interesting is that the determined reaction profile prescribes the optimal region of pressure/temperature around -25 oC and 200 psi. An opportunity to quickly scan the 2D pressure/temperature grid is powerful. The concept of residence time is critical to the success of flow approaches and, given the importance of kinetics in chemistry, there is potential to look at space/time control of REALLY exotic intermediates.



In vivo, in vitro, in silico… How about in fluo? After all, “fluo” is the Latin for flow. Have you heard anyone refer to flow synthesis this way? I just thought about this term now, but there are probably precedents of its use out there.

Great job, Zhi!

There’s an antidote for almost anything

Nerve agents are scary molecules. Thankfully, there is an antidote for pretty much anything, but only if taken at the right time (recall all those old Hollywood action movies…). There is a very interesting Swedish structural biology paper that describes molecular-level interactions between a series of nerve agents and their target – acetylcholinesterase (AChE). Nerve agents are fairly simple organophosphorous compounds that wreak havoc by covalent modification of Serine-203 in the active site of AChE. HI-6 is an oxime-containing antidote for several types of phosphorous-containing nerve agents. This oxime is remarkably efficient, acting as a competing nucleophile that reacts with the phosphorus center of the modified AChE, thereby restoring its normal enzyme activity. Is there a better way to demonstrate the marvels of chemistry? Everything here makes sense from the standpoint of simple polar interactions. Below I am showing a crystallographic view of Russian VX-modified AChE as well as the reaction of HI-6 that restores enzyme activity. The paper is remarkable because it also provides evidence why HI-6 fails with certain kinds of nerve agents such as tabun (tabun-modified Serine-203 is shown in the box). Apparently, the Phe338/His447 array close to Serine-203 reduces the conformational mobility in the tabun-AChE complex. The steric interactions interfere with the approach of oxime-pyridinium group of HI-6 to the phosphorus atom of the adduct. The kinetics of reactivation are thereby significantly slower and other (smaller) antidotes need to be designed.




Olympics and graduate research

I want to talk about an interesting parallel between Olympics and research in graduate school. You are probably thinking: “What on Earth is he talking about now?”…

I follow the updates from Sochi and, once in a while, tune in to see some of the events. The athletes do mind-boggling tricks and I constantly hear about medal counts. I respectfully disagree with the notion that getting a medal is the only way to evaluate a given athlete’s success. I think that the concept of personal best is equally important, especially in the events where execution over a defined period of time counts for success. When I look at athletes who do not end up reaching the podium, I catch myself thinking that they often demonstrate tenacity and hunger to improve over their past accomplishments. To me, this is what Olympics should be all about, but personal best metrics of success are not often mentioned.

I also think that in graduate research, each student should strive to achieve his or her personal best. This is naturally accomplished by improving on the number and quality of papers compared to what he or she had published the year before. Striving for a paper in NatureScience, or other type of high impact journal, is probably akin to getting some sort of a medal. These are great goals to have, but we all know that such papers are rare and are not entirely under student control due to a number of complicating factors (politics, etc). On the other hand, if a student publishes a couple of papers in a given year, the following year should be an improvement: how about three papers, or two papers in the same level of journal and one in a higher impact journal? This way one’s personal best is established and there is definite progress.

In trouble? Just add lithium…

Conformations of complex molecules such as cyclic peptides are tough to decipher. What a truism! I have mentioned this many times on this blog. Every now and then, I am forced to ask myself: how much effort do we really want to spend studying these complex systems? At times it feels as if we have a good grip on a given molecule, only to be disappointed by some capricious twist that throws all of our theories down the drain. The main reason things are difficult lies in the effects of media and additives, which can turn into the frustrating end of science. There are just so many geometrical variables a peptide of some complexity possesses that it is no surprise that things aren’t simple.

There are some monumental teachings from the past that suggest there is light at the end of the tunnel. Slowly but surely, I am compiling a list of additives with demonstrable ability to affect conformations as well as biological properties of cyclic peptides. One of these days I am going to publish a paper on this subject. For now, I just want to draw your attention to Dan Rich’s JACS paper from 1992 (the year I started graduate school, by the way). Cyclosporine A (shown below) is a known immunosuppressant that binds to cyclophilin (which is cyclosporine’s protein target). The trouble is, if the Leu-Leu amide bond in cyclosporine A is in its cis state, the molecule is biologically inactive. Dan Rich’s contribution demonstrates that the addition of LiCl to cyclosporine A in THF shifts the cis/trans equilibrium towards the bioactive trans form. What’s remarkable here is that the authors did not stop at evaluating the NMR spectra with and without LiCl, but convincingly demonstrated that the LiCl perturbation method works to alter the biological properties of cyclosporine A. According to the authors, a significantly more potent inhibition of cyclophilin is recorded in the presence of LiCl. Now – how about the effect of LiCl on the cellular permeability of cyclic peptides?



Keep it simple – from electrochemistry to flow synthesis

I remember Kevin Moeller’s instructive paper in Tetrahedron, where he showed that, in order to run complicated electroorganic experiments, all you need is a simple Lantern battery from Home Depot. While fancy set-ups with high precision capabilities are available, good experimentalists who lack access to complex set-ups always find a way around the problem:


These days, many of our students are attracted to flow synthesis. We recently had a nice departmental seminar on this subject by Thomas Johnson, one of Mark Lautens’ PhD students. I think chemists relate to the idea that new ways of improving mass transport can accelerate the rate of a given reaction, dramatically improving its efficiency. One of my former PhD students, Zhi He, is now heavily involved in flow synthesis in the lab of Prof. Tim Jamison at MIT. While I see the virtues of flow synthesis, I wonder: what can a lab with no access to microfluidics do in order to run reactions in flow? In short: be resourceful (just like Kevin Moeller). Here is a link to a great recent paper in J. Chem. Ed. by Prof. Thomas Wirth. Thomas was a visiting scholar at the University of Toronto several years ago and taught organic chemistry to our graduate students. The point of this work is to show that one can reap the benefits of flow set-ups and do it in an undergraduate lab using inexpensive syringes and glass tubes.


By the way, you can get glass reactors for these kinds of experiments from a cool German company by the name of “Little Things Factory”: