When I was in grad school, I was faced with the choice of two NMR labs to join (after starting as a organic chemist and flirting with enzymology). Both used NMR, but with very different goals. One lab used NMR and found systems to study using NMR. The other studied interesting problems. The PI would say if NMR is most appropriate than using, but don't be a slave to it. I have taken that attitude my entire career. In industry, it also has to be the mantra: best tool for the problem. Academics tend to have the opposite mindset: let's make my tool work for anything.
The Krimm lab has been cited here, here, here, here, and here on the blog and I hold their approach to academic tool creation for drug discovery in good regard. In this paper, they present a combination computational/NMR method for determining if a fragment induces conformational changes in the target. In their own words:
The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding.
Sometimes good people do bad things.
I am not going to get into the details, but rest assured the science is sound. Their approach is to evaluate H-N (you could also use H-C, why not) chemicals shifts from titration data to simulated CSPs. When they did compare experimental with calculated CSPs they could not explain some of these shifts, even when they included ring current-induced shifts. To further investigate this phenomenon, they used Residual Dipolar Couplings (RDCs) to further explore these unexplained CSPs. It does.
What are my problems with this paper? Practicality, primarily. Is this another anti-compchem rant? Nope. The problem here is that everything they propose to do, and they do it well, relies upon a whole sh!tpile of a priori
knowledge: 1. the structure of the protein (typically from X-ray) and
2. the assignments of the protein (not trivial). Additionally, the RDCs require acquiring two sets of data, aligned and unaligned. RDCs are wholly impractical. All of this should red flag this paper as a "Impractical" approach. It also does not present a method for interrogating structural changes induced by ligands that is any better or more robust than the current standard of analysis.
So why did was the paper published?
ReplyDeleteI am sorry you had such a bad idea of this paper.
ReplyDeleteThe method we used indeed requires the NMR assignment (but of the backbone only) and the structure of the protein. Bcl-xL is a protein well studied by NMR.
The SAR by NMR method also requires an assigned spectrum and a protein structure.
I totally agree that RDC are "unpractical". Here we used RDC only to demonstrate that our conclusion from the CSP is good and correct.
The idea in the paper is to use experimental data that people typically use when they do titration by NMR. Here we tell them that they (in most of the cases) could also check if a subtle conformational change occurs upon binding to fragments.
To demonstrate the usefulness of an easy method, sometimes it is necessary to add (as a proof) the results of another unpractical method.
Again, I am sad the paper was not understood as it should have.