This year is finally coming to an end, and as we've done for the past four years, Practical Fragments will highlight some of the reviews that we didn't cover previously.
In terms of what we did cover, there were several excellent events, including the eleventh annual CHI FBDD Conference in San Diego, an inaugural meeting in Houston, and of course the first-ever major fragment event in Boston, FBLD 2016.
The twentieth anniversary of SAR by NMR was also commemorated by the eighth book devoted to FBLD, as well as a massive two volume work on lead generation. We also covered a special issue of Molecules and reviews on clinical candidates and library design.
Another review on library design was published recently in Drug Disc. Today by Ian Gilbert, Paul Wyatt, and colleagues at the University of Dundee. The researchers have built a set of 356 diverse compounds consisting of “capped” scaffolds, such that any hits could be rapidly expanded. Undergraduates did much of the actual library assembly, learning skills such as parallel chemistry and how to work with polar compounds. There is lots of nice detail in this paper, including on library storage conditions.
Practical Fragments often highlights successful fragment to lead programs, and these were the focus of a Perspective in J. Med. Chem. by Christopher Johnson (Astex) and collaborators: all 27 cases published in 2015 in which the affinity of a fragment was improved at least 100-fold to a 2 µM or better lead. Many of these were covered in Practical Fragments, including BTK, DDR1/2, ERK2, MELK, Mtb TMK, PKCθ, RET, FactorXIa, MMP-13, BCATm, PDE10A, soluble epoxide hydrolase, tankyrase, ATAD2, MCL-1, RAD51, XIAP/cIAP, and mGluR5. The paper also draws general conclusions about target types, molecular weights, cLogP values, and LE.
Targeting tuberculosis (TB) is the subject of two reviews from University of Cambridge researchers, one in Drug Discov. Today by Vitor Mendes and Tom Blundell and one in Parasitology by Anthony Coyne, Chris Abell, and colleagues. Fragment-based approaches have been more or less successful against several TB proteins, including pantothenate synthetase, CYP121, BioA, EthR, and thymidylate kinase, while other targets – such as shikimate kinase and CYP144 – have proven more difficult.
July was bromodomain month at Practical Fragments, and this target class is the subject of a review in Drug Discov. Today: Technol. by Dimitrios Spiliotopoulos and Amedeo Caflisch at the University of Zurich. The focus is on computational fragment screening methods, with examples for BRD4 and CREBBP. And while we’re on the topic of computational methods, Olgun Guvench of SilcsBio has a brief review in Drug Discov. Today on computational functional group mapping.
Rounding out target-focused reviews, Paramjit Arora and colleagues at New York University focus on protein-protein interactions (PPIs) in a Trends Pharm. Sci. paper. This covers multiple approaches to finding PPI inhibitors, including fragment-based, and also touches on hotspots and structure-based design.
It is impossible to imagine FBLD without biophysics, and this is the topic of an authoritative review in Nat. Rev. Drug Disc. by Jean-Paul Renaud (NovAliX), Chun-wa Chung (GlaxoSmithKline), U. Helena Danielson (Uppsala University), Ursula Egner (Bayer), Michael Hennig (leadXpro), Rod Hubbard (University of York) and Herbert Nar (Boehringer Ingelheim). In addition to covering all the major techniques, the paper does a great job of delving into some of the more obscure and emerging methods, providing an excellent discussion of the throughput and requirements for each technique as well as the kinds of information obtained. Although the review is broader than FBLD, the application of biophysical techniques to fragments is a major theme. The researchers also remind us that, “contrary to the belief that all drug discovery challenges are best solved through the introduction of new technologies, substantial advances can also be driven by innovative application.”
Individual biophysical techniques also received plenty of attention over the year, including three on NMR. The first, by Alvar Gossert and Wolfgang Jahnke (Novartis) in Prog. Nucl. Magn. Reson. Spectrosc., is a 44-page practical guide to identifying and validating protein ligands. This contains a wealth of information on most of the NMR methods you will ever likely encounter; it includes a handy chart summarizing the molecular weight and concentration limits for each technique, suggested workflows, and thorough discussions of potential pitfalls. The review may appear daunting to the novitiate – it is replete with equations and pulse sequences – but the writing is clear. In the end, much comes down to the concept of the “validation cross”, a rubric for assessing the integrity of both ligand and protein, and evaluating binding effects on both ligand and protein.
Two additional reviews, both from William Pomerantz and colleauges at the University of Minnesota, focus specifically on protein-observed 19F NMR. The first, a Perspective in J. Med. Chem., is a good general introduction. Despite being the 13th most abundant element on our planet, only five natural products are confirmed to contain fluorine. Introducing this element into proteins – as has been done in more than 70 cases – can be a useful approach for discovering new ligands. And if you want to start doing this yourself, a paper in Nature Protocols provides practical details.
Turning to other biophysical techniques, surface plasmon resonance (SPR) continues to be very popular, and is reviewed by Alain Chavanieu and Partine Pugnière in Expert Opin. Drug Discov. The paper provides a good general overview on using SPR for FBLD, covering the theory, history, various screening strategies, comparison to other methods, recent applications to a variety of different targets, and a suggested workflow.
Calorimetry is less commonly used for fragment screening, even though it can provide thermodynamic data. Michael Recht and collaborators at the Palo Alto Research Center and Zenobia discuss both enthalpy arrays as well as more conventional isothermal titration calorimetry (ITC) in a Methods Enzymol. chapter.
But while biophysics is important, FBLD would be nowhere without chemistry. In MedChemComm, Stefan Kathman and Alexander Statsyuk (then Northwestern, now University of Houston) review one chemical approach, covalent tethering. This touches on the original reversible (thermodynamically-controlled) disulfide tethering approach developed back at Sunesis but is primarily focused on irreversible (kinetically-controlled) methods. The paper does an excellent job summarizing challenges, potential pitfalls, design rules, and recent successes. As of early this year the Statsyuk lab had sent their 100-member covalent fragment library to nine different research groups, three of which had already identified hits. The review ends with some provocative questions, and it will be fun for practitioners to answer them as covalent approaches garner increasing attention.
Another chemical technique we’ve touched on is substrate activity screening (SAS), and this is reviewed in ChemMedChem by Pieter Van der Veken and collaborators at the University of Antwerp. All published examples are summarized, including the modified approach developed by the Van der Veken lab; some unpublished data are also discussed. The paper also includes a good general section on the subtleties and complexities of transforming substrates into inhibitors.
Finally, if all this is a bit too much, a good general review on FBLD was published in Pharmacol. Ther. by Martin Scanlon and colleagues at Monash University. This concise but thorough paper covers theory, history, library design, hit finding and characterization, and select clinical success stories. The longest section is devoted to chemical strategies for elaborating fragments, and includes some of the less commonly used methods such as target-guided synthesis, Tethering, and off-rate screening.