Boron is special

My lab and I have been heavily entrenched in the design of boron-containing covalent inhibitors of proteases. In my view, synthetic students optimally relate to the challenges of chemical biology when they think about the fundamentals of polar bimolecular reactivity. This is exactly what I like to teach in my classes when I describe enzymes as giant nucleophiles. If you then take a look at the electrophilic options out there, you might first consider epoxides, aziridines, and acrylates. These molecules are useful, but are somewhat boring because they offer a singular outcome upon interaction with the enzyme target. This is not the case with boron, which is something my PhD student Diego Diaz and I realized and presented in a recent Nature Chemistry paper. We have analyzed well-known covalent inhibitors containing boron and concluded that this element is unique in its ‘chameleonic’ ability to display a range of coordination modes upon interaction with protein targets. It turns out that organoboron inhibitors leverage boron’s capacity to switch between an uncharged trigonal-planar structure to an anionic tetrahedral one. It is here where boron deviates from common electrophiles that display a singular type of interaction with active site nucleophiles. As a corollary, boron is well suited to act as a flexible anchoring element that is adaptive to structural changes upon binding. Where do you think we are taking this? If you have guessed that we are using these properties to adjust the residence time of boron-containing inhibitors, you are on the right track.


Not just another way to remove Boc

I typically do not comment on deprotection conditions, but there is something special in the two papers below. When I read the one by Lattanzi and colleagues, I thought that their nice asymmetric chemistry had been somewhat overshadowed by a single carbamate cleavage condition using TBAF. I am not sure how many of you are experienced with aziridines, but they do not easily withstand typical Boc removal with TFA. When I saw the yield of 98%, I was literally floored. In the interest of full disclosure, I learned about this deprotection from a paper I recently refereed. I dug a bit deeper and found that the TBAF condition goes back to the 2004 Tetrahedron report by Coudert and colleagues. In it, the authors considered a number of substrates and even carried out mechanistic studies that seem to suggest that the reaction proceeds through the formation of carbamoyl fluoride. Really strange, I know, but there is some very clever evidence in the Coudert paper. That 2004 study centered on the use of common amines and there was nothing as exotic as aziridines. Unless you are familiar with the pain of dealing with these three-membered rings, you might not think that a new way to remove Boc is worthy of note. This simple TBAF trick might be consequential to a lot of people interested in the chemistry of aziridines.





Between my desk and recycling bin

I am a fan of small amine-containing compounds with relatively short history in synthetic organic chemistry. Such molecules are admittedly hard to come by, but when I see them, I marvel at what might be done with them and why people have not considered them more broadly.

The other day I was flipping through the 2017 Strem catalog for no logical reason other than I got this shiny new booklet in the mail and felt guilty to toss it straight into the blue recycling bin, the destination of all catalogs I receive on a weekly basis. My attention got piqued by 2-aminoethane-1,1-disulfonic acid (let’s call it ADSA), which is offered by Strem for some unknown reason (metal catalysts is their main focus). Unaware of ADSA’s existence, I looked through standard search engines and found very little prior to 2010. There was some work done by Wagner and co-workers in the 60’s, but not much since. The synthesis of this compound is simple, yet interesting as it involves a modified Ritter reaction with oleum, decarboxylation, and sulfonation of the enamide. ADSA offers as an outstanding way to improve aqueous solubility of fairly hydrophobic molecules such as Alexa Fluor dyes. I find the geminal bis(sulfonate) functionality rather interesting because it reminds me of bis(phosphonates), which are of course miles ahead in terms of demonstrated use and significance as components of drugs that prevent the loss of bone mass.


Residence time

It would be a good idea for me to get back to blogging. I have been busy with a couple of conferences and grant writing, which explains my lack of attention to what’s cooking in the science universe.

One of the most memorable talks I heard at a recent CSC meeting held here in Toronto (I was in charge of the organic program, by the way) was that by Professor David Fairlie of The University of Queensland in Australia, an expert in drug design and a long time aficionado of cyclic peptides. As you might recall, cyclic peptides are often erroneously associated with pretty dreadful drug-like properties. Their oral bioavailability can be particularly dismal. The Fairlie paper says: “Who cares?”. Residence time is the main theme of the article. This parameter relates to the duration that a ligand is bound to its target. Fairlie considers his 3D53 molecule, which is a C5A antagonist, and reminds us that it is easy to fall prey to the assumption that IC50 (the concentration of an inhibitor where the binding is reduced by half) is the one and only “holy grail” when it comes to bioactive molecules. The reality is that IC50 is concentration dependent, which propels residence time to the foreground of Fairlie’s arguments. The paper nicely demonstrates that one might have a compound that is way inferior to its competitor when judged through in vitro biochemical binding assays, but jumps way ahead when evaluated in cellulo. In other words, a “lousy” molecule that is not too orally bioavailable and is not particularly potent, can stick to its receptor when it really matters and override potential shortcomings. Incidentally, this is one of the main reasons why there has been a lot of interest in reversible covalent inhibitors: they can drastically improve residence time. Another interesting fact about 3D53 is its synthesis, which I mentioned it in the past. It is a perfect reminder that there are remarkably well-behaved cyclizations that proceed on 100g-scale without the need for dilution.


In defence of grease

I feel like I should dedicate several blog posts to hydrophobic effect. Many of us have developed an instinctive disdain for purely alkyl side chains in bioactive molecules. Seeing excessively greasy portions of natural products rarely elicits mainstream enthusiasm to prepare analogs whose structures contain primarily hydrophobic variations. Marvelous examples of truncated versions of natural products, in which excessively hydrophobic portions have been cut off, prove the point. But are there teachable nuances out there? I will turn to Klebe’s paper published in the J. Med. Chem. last year. The point of this study is that insufficiently protected water molecules covering protein surface should not be underestimated. You might recall me writing about the “underdehydrated” concept proposed by Fernandez in effort to explain Cyclosporine A’s capacity to protect hydrogen bonds from solvation. A somewhat similar situation takes place on the surface of a protein, where dynamic water networks respond differently to slight perturbations of hydrophobic groups that belong to an inhibitor. The structure below was found to be the best binder to thermolysin. If you look at the whole series, you will note that the heteroatom positions do not change and the only parameter that ensures variability is the subtle adjustment of the hydrophobic substituent. I think this is a marvelous case in defense of much maligned grease.222.jpg

Don’t overlook tautomerism

If you ever worked with both computer modelers and synthetic chemists on a given project, you know that these two breeds have little in common. My personal perspective is that of an organic chemist, so I will allow myself to make some chemistry-centric comments. Let’s face it: modelers rarely provide insights that are synthetically meaningful. But I don’t want to accuse them of not knowing what can or cannot be made. Instead, tonight is about subtleties that are intuitively clear to practitioners of synthesis and might be critical to understanding and predicting the biological activity of small molecules. Take tautomerism: there is little more foundational to organic chemistry than this concept. The question is whether or not tautomerism can be relevant to docking of small molecules into receptor sites. I have dealt with many modelers and have yet to hear their appreciation of this concept, but a fairly recent paper describing a series of DNA gyrase inhibitors by Chan and Gwynn of GlaxoSmithKline provides an insight. The authors described a range of tautomeric forms of the barbituric acid portion of their inhibitor (QPT-1) and determined the corresponding co-crystal structures. In docking experiments they evaluated eight tautomers of QPT-1 and assigned them to subtly different binding sites. A tantalizing possibility is for compounds such as QPT-1 to adopt nuanced tautomeric shapes that facilitate productive interactions with the ligand-binding pocket. I think we need to pay way more attention to tautomers, especially when it comes to omnipresent amides.


Aggregation is not always bad

An interesting paper by Lumb and colleagues recently appeared in J. Med. Chem. By way of background, approximately 15 years ago, Brian Shoichet published a provocative article, in which he presented evidence that promiscuous inhibitors often work by forming aggregates:

This was a landmark paper because it unveiled a plausible cause of false positives in high throughput screening. The formation of such false positives had nothing to do with any special protein/small molecule interaction but was, instead, a non-specific effect. The community took this to heart and went a bit overboard, as we always do, seeing potential aggregators in all sorts of settings. Lumb and colleagues present evidence that aggregate formation and specific molecular level interaction may not be mutually exclusive. This work provides an example of aggregation-based inhibition of a protein–protein interaction involving tumor necrosis factor α. The reported capacity of small molecule ensembles to mimic protein surfaces is super cool. Unfortunately, the pdb file has not been released yet, so forgive me for not providing my usual pretty picture to accompany a structural biology post. You do have an option to see some nice views of the crystallographically characterized complex in the paper. There are 5 (!) inhibitor molecules that clump together into an aggregate in this crystal, replacing an entire protein subunit. I am not sure that there is a general lesson here, but I love seeing exceptions from the rules.