On good and bad privileges in chemistry

The notion of privileged scaffolds originated in the pharmaceutical industry. The term relates to disproportionately high occurrence of a given scaffold among drugs and other bioactive molecules. One excellent review dealing with this subject comes from Snyder and Stockwell:


Piperazine is a well-known example of a privileged structure. The are two troubles with this presumably worthwhile status: a. it is tough to carve out a good intellectual property niche because there are just too many molecules that contain a privileged scaffold (by definition) and b. many privileged scaffolds are associated with promiscuous binding to their biological targets. Thus, you might not only have trouble obtaining good claims in your patent, but you might also have to deal with molecules that lack target selectivity. The piperazine case is actually not that bad, but a mere mention of a urea to someone in drug discovery might make him/her cringe.


Personally, I get annoyed when those who do synthetic methodology talk about a new method of making a certain sub-structure and tout the method’s significance because there is a lot of molecules out there that contain that structural element. If you are interested in discovering new bioactive molecules, this prevalence should be a good reason for NOT making the darn thing, but I let go of this argument when I talk to students who get excited about producing a sub-structure that is present in 3 thousand other molecules. Why spoil the party? After all, we are in the business of education and there is a sense of synthetic accomplishment if you make a molecule that contains some omnipresent core, particularly if there is an interesting mechanism involved. We even mention this in our own papers…

There are other kinds of privileged structures that extend beyond drug discovery. I think Eric Jacobsen was the first to bring this term to asymmetric catalysis (see the link below). Here, there are some wonderful molecules that indeed possess seemingly magical properties in terms of enabling better control of chiral space around a given catalytic centre. BINOL is a good example. You might argue that some researchers used to over-interpret the significance of C2 symmetry in relation to its catalytic prowess, but, without a doubt, in the case of BINOL we have a really good reason to call it a privileged core.


I suppose there is some irony in all of this. The term “privileged” came from drug discovery, yet I think there are major negative connotations to the “privileged” status of many bioactive structures, which is certainly not the case for catalysis, where we do not judge molecules on the basis of their interaction with proteins and DNA. As a result, there are some highly desirable attributes in a select few cores.

Melting proteins in cells

I had a busy Friday, but it was a good day. I attended three different lectures, including one by Rebecca Courtemanche, my MSc student who presented her thesis work. Rebecca has been working on an ongoing project with SGC (Structural Genomics Consortium), in which we are using chemical synthesis in order to develop probes for epigenetic reader proteins. We use a range of methods to tackle this problem (a paper describing some of our advances is now being written in collaboration with the folks at SGC). From my lab’s perspective, this has been an exhilarating experience because my students see first-hand how physicochemical methods such as X-ray crystallography enable them to gain a molecular-level glimpse of how small molecules interact with complex protein targets. There are many methods we use and, while I was listening to Rebecca’s talk, I kept thinking about a paper that really amazed me not too long ago. Dr. Raymond Hui of SGC made me aware of this work. Here is a link to this work:


A short background is in order: when proteins in their native conformation are denatured, they quickly lose higher-order structures, transitioning to the unfolded states. A thermal shift assay allows you to measure how the melting temperature (Tm, or the temperature at which 50% of the protein is denatured) changes when small molecules interact with proteins. The stronger the binding, the larger is the value of Tm shift (it makes sense, because binding typically stabilizes the folded conformation). This thermal melt assay is one of the central experiments in understanding small molecule/protein binding, especially if your protein has no enzymatic function. The corresponding measurements are typically performed using isolated proteins that are well-behaved and characterized. In the 2013 Science report by Nordlund and colleagues (above), the thermal melt experiment was performed in within cells. This methodology is label free, which is to say there is no need to interfere with the chemical composition of the molecule being investigated, introduce any kinds of linkers, and do anything special for that matter. The method is called cellular thermal shift assay (CETSA). In brief, the authors took aliquots of lysates of mammalian cells, treated them with a drug versus control and heated cells to various temperatures. As the temperature increased, cells were lysed, and denatured protein aggregates (they are insoluble) were separated from their soluble counterparts by centrifugation. Now comes the best part: it was possible to assess the levels of target protein remaining in solution at each temperature by means of Western blotting. If you plot the relative band intensity of the soluble target protein against temperature, the melting temperature of the protein is derived for the free versus the drug-bound. The difference corresponds to the affinity of the interaction. The authors showed that the thermal stability of the target protein was increased when the drug was added in a dose-dependent manner. This is what I call a powerful method.

What’s in a Ph.D.

There’s this question about what constitutes the optimal set of individual qualities that lead to a successful PhD in science. This is a loaded question as there are so many interrelated considerations. People are different and everyone has his/her preferences of how to work in the lab. If I were to comment on which individual quality I respect, the ability to stand one’s ground and be assertive in defending a viewpoint is probably on the very top of my list. This trait speaks to one’s intellectual maturity and capacity to take a stand when it matters. In every PhD there is a time when a student has to take control over a field he/she feels passionate about, circle the wagons, and have the guts to voice a strong view. In this regard, I found David Evans’ answer to the question “Which advice would you give to someone who is embarking on a career in science now?” both eloquent and instructive. This talk was recorded at the 2013 National Organic Symposium. Please take a look – the question/answer are at around 1:15:49 in the link below.


Hydrazines in electrochemistry

The challenge of oxidative nitrogen transfer is fascinating because nature does not know how to do it, at least not when it comes to oxidative C-N bond formation. I already commented on this feature of biosynthesis in the past and there is no need to belabor the point. The arsenal of synthetic tricks we have is astounding. The trouble is, of course, that generation of nitrogen oxidants can require rough conditions that might adversely affect other “spinach” that hangs off your molecule. We worked on this problem in the past and found electrosynthesis to be full of options. Here is an old pic of one of our reactions along with the reactor we used. I am only indicating the process taking place at the anodic compartment, in which we oxidized the hydrazine-containing starting material. The cathodic compartment separated by a frit you see, is colorless. It is actually possible to see hydrogen bubbles on this picture – they come as a result of proton reduction (protons are produced during oxidation). I am also attaching a link to the JACS paper where we demonstrated how anodic electrochemistry helped us solve some challenging problems of oxidative nitrogen transfer. Image


When I visited the Dallas ACS meeting a couple of weeks ago, I heard Phil Baran speak about his lab’s use of electrochemistry in natural product total synthesis. I saw his JACS communication earlier today and enjoyed reading this work because it brought back many fond memories of hydrazine chemistry. As was the case in our oxidative approach to aziridines, the beauty of electrochemistry in Phil’s case is in offering a glimpse of synthetic opportunity by judiciously choosing the right window of applied anodic potential at which the amine can be selectively oxidized. In this particular case, electrooxidation leads to the formation of a hydrazine-containing natural product dixiamycin B. Any chemical oxidants Phil’s lab tried, failed in this oxidation reaction. I was not surprised that carbon was the best electrode material in this case. It is almost certain that the “flat-ish” substrate you see interacts quite well with the anode surface. We could not use carbon in our aziridine chemistry, though. Platinum was the key to us as graphite led to strong background currents corresponding to alkene oxidation.



Really bad ideas

It’s tough to be a graduate student. If you are a Professor, you can sit in your ivory tower and think about all manner of nutty ideas and, as long as none of them violate any laws of thermodynamics, they will be eventually reduced to practice (and improved!) by our capable graduate students and postdocs. But the devil is in the detail and all those brave souls are left figuring out how to lower the kinetic barriers of reactions we contemplate. There are reactions (unfortunately, a lot), in which there are just too many energetically similar pathways, which is why we get in trouble with by-products… Apart from this insignificant detail (I am being sarcastic), chemistry is deceptively simple: any idea about an isolable endpoint of synthesis that is not uphill in energy, is worth the risk. Needless to say, you can design special conditions and isolate uphill intermediates (e.g. carbocations), but this would amount to imposing a kinetic barrier of some sort. Now, are there ridiculous (but seemingly plausible) ideas out there that can throw us for a loop unless we sit down and think about them for a second? Here’s one of the problems I like to discuss with my colleague, Professor Jik Chin. Consider the following generalized process:



Imagine that you want to develop a catalyst that would run this reaction. Can such catalyst exist? No, it can’t. The way this reaction is written is sheer nonsense. For this conversion to have a chance to work in the forward direction, the Gibbs free energy change must be less than zero. In the example above we clearly have no entropy change and enthalpy does not change either. In addition to the violation of the Second Law of thermodynamics, there is a problem with the principle of microscopic reversibility here as any catalyst that works in the forward direction should be capable of catalyzing the opposite process. Of course, stoichiometric reactions can be designed and there are many solutions for this “R into S” type of problem. Enzymes can do this too (and catalytically!), but those reactions are coupled processes, which means that there is something else that goes on with either your product or your starting material. Hence, the energy of the product is not the same as the energy of the starting material. You can break microscopic reversibility with photochemistry, but if you are interested in thermal activation, any catalyst that you think might promote the aforementioned process, will necessarily have to violate microscopic reversibility and the Second Law. Back to my starting point: unless we propose thermodynamically ludicrous ideas, being a Professor is the best job out there. The way George Olah would say, “Hey – I am doing my hobby and the University even pays me for it!”

Uphill battles in amide couplings

Earlier today, our Encycle team had a discussion regarding some of the issues pertaining to N-Me amino acid coupling reactions. Overall, we typically have no trouble introducing N-Me groups into peptides. All we need is an appropriately protected N-Me building block for the solid-phase Fmoc chemistry and off we go. The trouble is, sometimes this coupling fails miserably if hindered amino acids are brought together. There is an ingeneous solution to the problem and it offers a workaround. The reaction was developed by Professor Schafmeister of Temple University and it involves amino acid fluorides as electrophiles. A few words about them: in brief, acid fluorides are remarkably stable to aqueous hydrolysis. In contrast to their chloride congeners, fluorides also resist racemization. One of the classic ways to prepare them is through the use of DAST (there are better alternatives these days). Kaduk’s way cited below is as simple as it gets – just mix an Fmoc-protected amino acid with DAST in dichloromethane and get your acid fluoride product after aqueous work-up. The product can be crystallized from dichloromethane/hexanes, which makes for a rather practical method.



Back to the hindered amide workaround developed by Schafmeister. The mechanism involves mixed anhydride formation, which is the central trick here. Once this electrophilic intermediate has been formed, the rest is “downhill history” as nitrogen acylation becomes an intramolecular process. Even exceptionally hindered amides can be made using this procedure. Connoisseurs of multicomponent reaction might notice a similarity with Ugi’s mixed anhydride. We are attempting to run the Schafmeister process this week (wish us luck, we have a tough substrate that failed with everything else).



Some rare natural products

There are elements in the periodic table that, despite their abundance on earth, appear extremely infrequently in natural products. Fluorine is a good example: there are only a handful of natural products that contain monofluoroalkyl substituents and there are none with CF2 and CF3 groups. The rarity of the latter two tends to surprise students when they hear it for the first time. I suppose this has to do with the omnipresence of CF2 and CF3 substituents in therapeutic agents, which is why some people assume that the inspiration for their emergence must have come from some natural product. There is a tendency to forget that if we think about how C-F bonds are biosynthetically introduced into organic compounds, it is almost impossible to place more than one fluorine atom on the same carbon.



Boron is another enigma. There is a lot of it on our planet, yet we rarely see boron in natural products. A marine natural product borophycin is one of those rarities. Earlier today we had Professor Jon Clardy of Harvard Medical School give one of University of Toronto’s annual Gordon lectures (this is a set of three lectures given by one person and the topics vary from talk to talk). While the theme of today’s lecture was not related to boron, I caught myself reminiscing on some of the work Jon had done 20 years ago. He is responsible for a spectacular collection of isolated and characterized natural products, and one of them is borophycin (see above). I am showing the structure of this intriguing compound and a link to Jon’s 1994 paper together with Moore and their colleagues. Isolated from green-blue algae, borophycin is a potent cytotoxin which was characterized by both NMR and X-ray in the 1994 JOC report. I don’t think there is unequivocal evidence supporting or refuting the essential nature of boron to the biological activity of this molecule, but it is a really nice example of a rare boron-containing compound found in nature. By the way, this molecule might also provide a clue as to why boron is NOT (contrary to some popular belief) benign from the standpoint of toxicity. Boron-containing waste is a big problem and it is known that it causes blue algae to grow. Perhaps there is a link there with borophycin, but I am not sure.