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.


In Memory of George A. Olah

I have not been able to write my posts for a while, which is partly due to travelling and partly to my attempts to finish up some papers while carrying on with teaching duties. I visited UC Davis and UC Merced two weeks ago. Dean Tantillo (Davis) and Ben Stokes (Merced) made this visit into a memorable stay. In the middle of that week came a dreadfully sad moment when I found out about the passing of George A. Olah, one of my PhD mentors. A lot has been said about George, particularly in recent weeks. His science has had transcending impact on organic chemistry and not a week goes by without me mentioning some of his insights in my 2nd year organic chemistry class. In particular, I refer to the concept of stable ion conditions. I cannot think of a more lucid idea that explains how an electron-poor intermediate such as carbocation can be made to persist in the liquid phase. I fondly recall our group meetings, where George’s lightning fast mind was on display. He was a towering figure and a true gentleman, who always came to lab impeccably dressed with a suite and tie, which is not something we do these days. Apart from this air of elegance, George was always eager to share his wisdom with students, who benefited tremendously from his wit. I could use many superlatives in describing George, but, upon reflection, one thing stands out: he was one of those people whom you do not want to disappoint. I will miss Professor Olah dearly.


George A. Olah (1927 – 2017)

Random byproducts revisited

Deciphering the structures of random reaction by-products is rarely on top of our “to do” list. This avoidance is understandable because constant pressure to move toward the stated goal makes us focused, which is both good and bad. Noticing reaction by-products is how one makes important breakthroughs, yet the chances of finding something truly spectacular in the “noise” are not in one’s favor.

As a research advisor, I love learning about crude NMRs. But I am also aware that our resources and bandwidth to pay attention to what comes our way are not limitless. This inevitably leads to (un)healthy skepticism. A recent paper in Organic Process Research and Development stopped in my tracks the other day because I clearly recall hearing about allene formation (by NMR) in one of our peptide coupling reactions. This observation was made while analyzing the reaction by-products and I dismissed it as “OK, the NMR might suggest there is something like an allene but it is unlikely, so let’s move on”. In the case of Knapp and colleagues, the acid used in the coupling process did lead to an allene. There is even a crystal structure of the product reported (it is a complex structure, so I am avoiding it here). The mechanism of allene formation is cool and involves ketene formation. I am not saying that definitive identification of a similar structure in our reaction several years ago would have affected the line of research we had been pursuing at that time, but I just wish we all had more time to dwell on what’s brewing in our flasks. Incidentally, I think it was BASF that has been pushing T3P as a fairly inexpensive reagent for amino acid coupling. It is a nice little molecule.


The power of weak interactions

Here is a question for tonight: how many cases are out there where a single hydrogen bond dominates the regiochemical outcome of a chemical transformation? Let’s say we are comparing the protio version to its methylated congener, which is arguably the smallest steric perturbation that does not produce a confounding effect. Here is a case from Paul Carlier’s lab published some time ago in Organic Letters. If you look at the two epoxide-containing anilines depicted below, you will note that they differ by a methyl group. Their behavior is strikingly dissimilar, demonstrating how a single hydrogen bond can affect the reactive conformation. The reactions were run neat, by the way. Both outcomes are driven by the logic of trans-diaxial epoxide ring opening, yet the NH-to-O interaction flips the reactive conformation in the first case compared to the second one. If you are looking for a powerful demonstration of the Fürst-Plattner rule, there is probably no better way to show how a relatively weak interaction can control the reaction outcome.