Safety first

I am on my way to Europe for a week, which means that I will have less of a chance to update my blog. I will be on vacation with my wife, attending a wedding in Serbia, which will be followed by a couple of lectures in Germany – at Sanofi-Aventis and at the University of Mainz. There are many things one needs to do before going on vacation. There is always a ton of emails to write and several loose ends to tie up (crap, I just remembered about another one…). Lab safety is the item of substance that never leaves one’s mind before leaving town. Of particular concern is anything that is remotely dangerous and, in this regard, I have to admit that there are chemicals I admire much less than others. One of them is sodium azide and I just want to remind everyone not to use dichloromethane when dealing with this reagent. You would be surprised how many times I have encountered students in my lab who accidentally forgot this and turned to dichloromethane in conjunction with sodium azide. We all know how bad this combo is, yet somehow we forget. Why? Because we are the creatures of habit and dichloromethane is one of our trusted old friends in reaction work-up. Below is what might happen, though. I am also providing you a link to a paper that describes the explosion caused by diazidomethane. I am providing this link so that you do not think that my warning is purely anecdotal…


Need I say more?

This will be a short post. Some time ago, with a blessing from Professor de Meijere of the University of Göttingen, I agreed to serve as the guest editor for a special issue of Chemical Reviews dedicated to the impact of small ring heterocycles in synthesis. My sincere thanks go out to the following contributors, without whom none of this would be possible:

Prof. Hiroaki Ohno (Osaka, Japan)

Prof. Eric Rivard (Alberta, Canada)

Prof. Renzo Luisi (Bari, Italy)

Prof. Tom Lectka (Baltimore, USA)

Prof. Sven Mangelinckx (Belgium)

Prof. Tehshik Yoon (Madison, USA)

Prof. Pauline Chiu (Hong Kong, China)

Prof. Bob Coates (Cornell, USA)

Prof. Aby Doyle (Princeton, USA)

Prof. Yian Shi (Colorado, USA)

Prof. Erick Carreira (Zurich, Switzerland)

And, of course, I want to thank my students Ben Rotstein, Serge Zaretsky, and Vishal Rai, who contributed to writing our own contribution to this issue.

I am also really grateful to Prof. Guy Bertrand who made it all go very smoothly. I hope that you will have fun reading all of the papers in this collection. I know I will!

Avoiding some treacherous pockets

A week or so ago, Dr. David Price of Pfizer visited our department and gave a great talk on Maraviroc, an HIV antiretroviral drug. While the story David shared with us was unique in many ways, it did have a number of elements in common with other tour-de-force kinds of studies in medicinal chemistry. Invariably, these cases show that good chemistry is only a part of a journey to a successful drug. Chemistry is, nonetheless, a critical component of any drug discovery undertaking. We had some good fun with David, and we do look forward to seeing him again in the near future. While a lot of interesting stories can be mentioned about Maraviroc, I was particularly intrigued by David’s reference to one of the main killers of promising compounds in drug design. I refer to the infamous HERG potassium ion channel. The architecture of this channel offers a cemetery (of sorts) for aromatic compounds. The HERG liability is serious as molecules that plug this channel lead to cardiovascular side effects. David shared with me one of the papers from Pfizer that speaks to this problem:

I started digging into this area and, after doing a bit of further research, found another great article that is foundational when it comes to HERG and liabilities associated with it. This 2002 paper by Recanatini describes the HERG pharmacophore, which is similar in its topology to a Bermuda-like triangle, wherein many promising small molecules lie. The term “pharmacophore” is often synonymous with “we do not have a crystal structure, so here is the best model we could get that is based on analysis of a series of molecules”. While it may take some time to finally see a crystal structure for this channel, it seems that if you have the right constellation of three aromatic rings in your molecule coupled with a basic nitrogen, you might be in trouble. I wonder if macrocycles have a free pass here by virtue of their geometry… I doubt it, but who knows? By the way, the Pfizer team did a great job of steering away from this dreadful triangle in their Maraviroc campaign.


Best supporting actors

I will dedicate tonight’s post to the silent heroes of organic synthesis, namely some of the excipients we have grown to love. While the term “excipient” is most commonly associated with drug formulation, there is something to be said about an analogy to some key additives that serve their supporting, yet critical, roles in organic synthesis. Without these molecules, you would not see the light of day in many instances where a particularly reactive species needs to be formulated and delivered to a flask near you. In my personal experience (we are going back 15 years for that), urea-hydrogen peroxide was the first combination that taught me to appreciate the supporting role of certain chemicals. In this case – urea, when mixed with hydrogen peroxide, turns into a nice solid material that is commercially available in the form of pellets. I used to buy this stuff from Acros and employed it in reactions where excess water, that comes through the use of aquous hydrogen peroxide solutions, was detrimental to catalysis. Now – how about the iodonium-collidine perchlorate? This is a widely used electrophilic iodinating reagent that benefits from the presence of collidine…

DABSO is a notable recent addition to the list of molecules that deliver valuable and highly reactive species in synthesis. In this compound, developed by Mike Willis of Oxford, the molecule of DABCO is complexed with two molecules of sulfur dioxide. This association enables handling a nasty gas (SO2) in a very straightforward fashion. I am showing just two examples from Mike’s OrgLett paper. The diene case is especially notable as it represents a great way to employ the reversibility of Diels-Alder reaction to protect (and later release) dienes. I have to say: there is something quite special about DABCO in terms of its “supporting” role in many other reagents (Selectfluor comes to mind).


Fixing problems

I want to ruminate on a subject that has been of great interest to me for a number of years. To begin with, I will remind my readers about the difference between causation and association. I talked about this in the past. While this subject might not help you have an engaging conversation at your neighbor’s barbeque, it is absolutely central that we get this distinction right when analyzing data of any type – in chemistry, astronomy, medicine, etc.

Now let’s say we all got this distinction under our belts. In other words, we are really interested in causation more than anything else. Here comes the conundrum. The science of logic warns us of the following scenario:


In it, B is only an intermediate cause of the final outcome C, whereas A is the ultimate, all-important cause. A causes B and B causes C. I would bet that close to 99% of our failings in science must come from wild goose chases, in which we try to fix a given system by concentrating on the wrong variable. Here is a simple life example I read in a great book “Being Logical “ by D. Q. McInerny ( Let’s say you notice that your kitchen stinks and the smell emanates from water accumulating underneath your sink. You are desperately trying to fix it by frequently emptying buckets of water, the problem seems to temporarily go away, but it always comes back… The reason? The flaw in your logic: the ultimate cause is the leaky pipe and you have not thought about it. Once you replace it, life goes back to normal.

Here is a chemistry example: you run a solution phase reaction on some peptide. Let’s say that your goal is to modify its N-terminus. Nothing works… You change a ton of coupling reagents and you get nowhere. This is frustrating, because you think that the issue lies in the low nucleophilicity of the N-terminus. But then, after some time, you find out that the real trouble is that that particular sequence is prone to aggregation, which of course affects reactivity. There is nothing that you can fix with a different coupling reagent, but a simple change of solvent miraculously solves the problem.

This is a simple example and, as you might imagine, there are substantially more complex cases out there. However, I think that the mistake in focusing on an intermediate cause is a clear and present danger in our research endeavors.


A lot has been said about azide/alkyne cycloaddition reaction in recent years. This process (click chemistry) has been applied in a wide range of research fields and the spectrum of use keeps expanding. One particularly widely quoted tenet of this chemistry states that azides and alkynes are orthogonal to polar functionalities, but react with high selectivity with each other under copper catalysis. This is especially useful in the so-called bioorthogonal applications. While this principle is mostly true, it is certainly not universal, which is why it is instructive to see cases that disprove the basic assumption of alkynes’ “innocence”. Today I want to mention just one example. I have always been intrigued by the mechanism of covalent inhibition of Erb kinases that was elucidated by David Uehling and coworkers form GSK some years ago. This paper was published in PNAS and you can check it out below. Granted, the core of this particular line of inhibitors might be described as a fairly special alkyne unit that is perhaps more prone to nucleophilic addition than some others. Nonetheless, one should keep in mind that alkynes are not always orthogonal to nucleophilic species in biological systems.





Just to be clear

I want to comment on something many of you might consider self-explanatory. Yet, I have observed certain confusion in my discussions with students over the years, which is why it is best to just put it out there in the open. Here it is: there is a big difference between amide bonds and peptide bonds…


All peptides are amides, but not all amides are peptides. The reason this is significant is that I often hear comments that suggest that amides are to be avoided in drug design. I think those who say this really mean peptide bonds, and not amides in general. There is absolutely nothing wrong with amides that are very commonly used tools in medicinal chemistry. However, when the said amide is seen in an environment that contains flanking amino acid side chains, all sorts of red flags can be raised. The reason is that peptidases are uniquely suited to chop peptides. Peptidases recognize certain amino acid sequences and go after amide linkages in those particular contexts with a vengeance. This is the main reason why peptides are poorly bioavailable. Below you can see a view I made that corresponds to a peptide-based inhibitor bound to its cognate endopeptidase (pdb code 1a94). This crystal structure was obtained by replacing the scissile amide bond by its aminomethylene isostere. Without this trick, we would not have a chance to see the relevant pose because the substrate would have been cleaved in a hurry. But with the aminomethylene group in place of the key amide, one can observe how the rest of the molecule binds. You cannot expect a peptidase to easily cleave a non-peptide amide. Thus, amides and peptides are to be differentiated. It is too bad that we do not have a simple name for amides that are not peptides. Maybe we should come up with one.


By the way, the extended conformation you see is typical of an endopeptidase. There is a great review by Fairlie on this topic:


Boron – some recent developments

In our fragment-based drug discovery projects, we constantly think about new ways of stitching together heterocycles. It is particularly satisfying if we find a way to make completely new, previously unexplored, chemistry matter. As you might imagine, herein lies a dilemma. On the one hand, we want high ligand efficiency, which goes implies relatively small size. On the other hand, try to plug something completely new (for instance, a 6-membered ring) that is composed of common heteroatoms into SciFinder. Good luck with that. Chances are, your composition of matter has been disclosed in a patent or, worse yet, published in peer-reviewed literature. Challenges notwithstanding, we recently bravely embarked on a journey that has sought the discovery and development of new kinds of small and medium rings. One of our favorite examples is the so-called boromorpholinone, which is obtained by plugging a boron atom into the framework of a well-familiar morpholinone scaffold. You see a model of a representative member of this class of compounds in the graphic below (boron is green). Earlier this year, Aleksandra Holownia (pictured below) joined our efforts as a Summer undergraduate student. Under the direction of my graduate student Adam Zajdlik, Aleksandra not only helped us understand the boromorpholinone area better, but earlier today won one of the AstraZeneca poster awards. I applaud her dedication to this project. As you might imagine, the boron atom in these sorts of rings is not going to be an innocent bystander. There are, in fact, many applications that await these compounds, which is something we are engaged in together with Ben Cravatt at Scripps. Speaking of Adam, he just came back from a one month internship at Anacor in California, where he further learned about the use of boron. Anacor is the pioneer in the deployment of boron-containing molecules in drug design. There are myriad reasons to like boron and I will give you just one: boric acid, the main metabolite of organoboron therapeutics, has LD50 of 2.7 g/kg. This toxicity is comparable to that of table salt. Once again, congratulations, Aleksandra!


Life unknown

In tonight’s post I will attempt to bridge hydrophobic interactions and life as we know it. It might get philosophical, so bear with me. As many of you probably know, not long ago, Romesberg and colleagues at Scripps created the first organism that can grow and replicate with a completely unnatural base pair in its DNA. The DNA of this organism can, in principle, code for up to 172 amino acids. On a molecular level, the “glue” that holds the novel base pair together is purely hydrophobic in nature (the pair comprises a substituted methylisoquinoline and a methoxynaphthalene). There are no hydrogen bonds there at all:


The most interesting part of this research is how the authors managed to get their cells to replicate. In order to pull this off, they needed to figure out a way to smuggle the new bases inside the E. coli bacteria. The team found a unique protein transporter that was able to specifically take up the aforementioned synthetic bases. As a result, the new base pair was incorporated into DNA and was later found in replicated plasmids.

While there are many hurdles that prevent this system from being truly efficient, there are as many ethical questions that can be posed here. Apparently, the Romesberg study has already resulted in renewed calls to halt research in synthetic biology (for instance, by the ETC group: I am not an expert in these kinds of debates and it is difficult to speculate on the dangers of this science at this point. But I do want to note something else that might be interesting. Without going into a theological discourse, I note that anti-religion zealots such as Richard Dawkins are (ironically) not that far from some of the key principles they try to attack at all costs. I refer to how Dawkins looks back in time to find our ancestors, assuming that evolution is progressive, culminating with us. He does it in his book The Ancestor’s Tale. The amusing feature of this logic is that he ends up with a chain of being that is very similar to what religion promotes, namely that man is the culmination of it all. There is an excellent piece published by Sean Nee in Nature close to 10 years ago (I urge you to read it) that discusses this central issue and presents an alternative view of evolution. This essay offers a conjecture. Nee reminds us that over the past 600 million years a great variety of Bacteria, Archaea and microbial Eukarya have been evolving. And (I quote): “One of the huge species, Homo sapiens, got remarkably self-important. But when, to his surprise, a virus wiped him out, most of life on Earth took no notice at all.”

The lesson here is that we tend to assume too much about our relative significance in the great chain of being. But how does this relate to synthetic biology? We have curious minds. What if we do indeed create a form of life that will prove Nee’s conjecture that we might have gotten somewhat self-important?


On monomethylation

I was looking at an old paper collection that I have, trying to find methods that enable clean monomethylation of amines (we rely on this reaction in our macrocycle work) and came across a brilliant old paper by Grieco. I have always been very fond of this reaction. As you might imagine, many studies in organocatalysis have this 1987 report as one of their cornerstones. The question of amine monomethylation may sound simple, but it is anything but trivial. Low chemoselectivity is usually quoted as the main obstacle towards high yields in this chemistry. The trouble is typical of amine transformations: the product is more reactive than the starting material. Even reductive amination cannot offer a decent monomethylation solution, which is due to the fact that the corresponding imine is not easy to isolate and that formaldehyde is quite reactive. The workaround developed by Grieco involved in situ Diels-Alder chemistry that rapidly generates the azanorbornene skeleton shown below. Once this is accomplished, the adduct can be carried through various steps and can then be cleanly reversed to the iminium ion through retro-Diels-Alder reaction. In the presence of triethylsilane as the hydride source, the desired methylated amine is generated. Temporary masking of reactive functional groups using reversible processes is a really useful trick. We need to use this process more often in our own peptide synthesis efforts.