The Royal Society of Chemistry puts out RSC Med. Chem., and last year they asked David Rees (Astex), Anna Hirsch (Helmholtz Institute for Pharmaceutical Research Saarland), and me whether a special themed issue on FBDD would be useful for the community. Naturally we said yes, and the results have now been published. You can read our introduction here.
Unlike olden days, when special issues were bound between covers, this is a virtual special issue, with papers published over a period of several months. Indeed, we already wrote about two of them last year: one on combining DNA-encoded libraries (DEL) with FBLD and one on inhibitors of PRMT5/MTA. (Both of these were also topics at the CHI FBDD meeting earlier this month.) In the next few paragraphs we highlight the rest.
AstraZeneca has been doing FBDD since 2002, and has gained hard-won wisdom, some of which was shared in a 2016 review we wrote about here. After years of screening, their fragment library had started to deteriorate, so they rebuilt it entirely, as described by Simon Lucas and colleagues. Some of the starting fragments came from their previous library, but they also considered molecules from their larger collection. Rather than focusing on the rule of three, they developed their own multiparameter optimization function, “FragScore,” which incorporates logD7.4, heavy atom count, number of rotatable bonds, and number of hydrogen bond donors. All compounds were inspected to make sure they would be synthetically tractable, and quality was assessed by SPR, NMR, redox activity, and solubility. The final set consists of 2741 fragments, with a subset of 1152 maximally diverse and attractive fragments for ligandability assessments or screening hard-to-make proteins. They also gathered 16,806 near neighbors for hit follow-up. So far the effort has paid off, with all four of the targets screened thus far yielding progressible hits. If you’re building or renovating a fragment library, you should read this paper.
Continuing on the theme of libraries, Bradley Doak, Martin Scanlon, and colleagues at Monash University describe their “MicroFrag” library, a set of 91 tiny (5-8 non-hydrogen atom) compounds similar to MiniFrags and FragLites. A crystallographic screen (at 1 M concentration!) of the MicroFrag library against the difficult E. coli target DsbA yielded a 52% hit rate, compared with a 2% hit rate with a conventional fragment library. Importantly, the MicroFrag screen identified the two main hot spots previously discovered from the conventional fragment library, along with ten others that may be less actionable. Interestingly, a crystallographic screen of 15 organic solvents at even higher concentrations (50-80%) was less informative: the primary hot spot did not distinguish itself from others. In the case of MicroFrags, not only did this hotspot bind the largest number of fragments, but all the molecular interactions seen for larger fragments were observed.
Fluorine NMR takes advantage of its own specialized library, the subject of a paper by Chojiro Kojima (Osaka University), Midori Takimoto-Kamimura (CBI Research Institute) and collaborators from several institutions. The researchers describe the construction of a 220-member library divided into pools of 10-21 compounds. This library was screened against four diverse proteins, yielding between 3 and 16 hits. The three hits against FKBP were characterized in more detail, including two-dimensional NMR and isothermal titration calorimetry. The researchers also discuss using 19F STD experiments to determine the binding mode of bound fragments.
Fluorine is not the only halogen of interest for library design. We’ve previously described the halogen-enriched fragment library (HEFLib, here and here), which consists of chlorine, bromine, and iodine-containing molecules. Frank Boeckler and collaborators at Eberhard Karls Universität Tübingen and the Max Planck Institute describe screening this library against the Y220C mutant of p53 in an expansion of work they first described back in 2012. Of 14 hits identified by thermal shift or STD NMR, ten confirmed by two-dimensional 1H-15N-HSQC NMR. Four of these bound in the cleft created by the Y220C oncogenic mutation. Two other fragments turned out to be covalent binders, though they reacted with more than one cysteine residue. Although all the fragments have low affinities, they could potentially serve as starting points for optimization.
An ongoing debate is whether there is an advantage to screening more “three dimensional” fragments as opposed to planar aromatic fragments. If your taste tends towards the former, the synthetic chemistry can get tricky. According to an analysis we highlighted last year, the piperidine ring is the third most common scaffold found in drugs. Now, Peter O’Brien (University of York) and an international group of collaborators report efficient synthetic routes to all 20 cis- and trans-piperidines substituted with a methyl group and a methyl ester. A virtual library of 80 compounds in which the secondary amine is capped with simple substituents such as methyl or acetyl groups was found to be quite shapely, particularly compared with the disubstituted pyridyl starting materials. Moreover, the fragments are still reasonably sized, with no more than 15 non-hydrogen atoms and ClogP values < 2.
Machine learning is gaining prominence everywhere, not least in drug discovery. In 2021 we highlighted an “autoencoder” designed for constructing fragment libraries biased towards “privileged” fragments more likely to generate hits. However, the method required considerable programming savvy. Now Angelo Pugliese (BioAscent) and collaborators at the Beatson Institute have implemented their model in the open-source KNIME platform, making it accessible to a wider range of researchers. As an example they use the method to construct a GPCR-focused fragment library, with the structures of all the members provided in the supporting information.
On the subject of fragment libraries, please make sure to vote in our 6-question poll on library design (right side of page; you may need to scroll up).
Not all the papers in this special issue involve library design. Marko Hyvönen, David Spring, and collaborators at University of Cambridge and National University of Singapore describe allosteric inhibitors of the kinase CK2α, which has been implicated in cancer cell survival. We highlighted some of their work against this target in 2017, in which they used fragment linking to find high nanomolar inhibitors of the enzyme. In the new paper, the researchers describe additional fragment binders at the so-called αD pocket, distant from the ATP-binding site. Virtual screening for analogs led to a fragment with mid-micromolar activity in biochemical and cell assays, and fragment merging led to low micromolar inhibitors.
This is a nice collection of papers, and for those of you without easy literature access make sure to check them out soon: for the next six months all of them are free to read after free RSC registration. Enjoy!