Introduction
In 1900, Baeyer established the nomenclature of spirocycles, a chemical moiety that features a quaternary carbon atom between two rings1. The first spirocyclic drug, Griseofulvin, an antifungal agent, was approved in 19592. Since then, spirocyclic moieties have often been seen in drug design, such as CRGP inhibitor Ubrogepant3, DNA gyrase inhibitor ETX09144 and newly discovered pan-CoV inhibitor ASAP-00174455 (Figure 1).
Recently, spirocycles have been increasingly investigated in drug design programs, as they can provide numerous benefits when designing molecules6. They can be used as bioisosteres of common heterocycles to modulate properties such as lipophilicity and pKa. Due to their three-dimensionality, they can increase solubility by reducing crystal packing. Metabolic stability issues can be alleviated by the inclusion of additional steric hindrance near the site of metabolic susceptibility7. As spirocycles feature numerous sp3 centers, they can provide new exit vectors to grow into hard-to-reach pockets. With all these qualities in mind, integrating spirocycles into compounds is a potentially lucrative design route.
Fraction of sp3 carbon atoms, Fsp3, is a common metric to measure the amount of 3D complexity a molecule possesses which, as outlined in the previous paragraph, can benefit drug discovery8. Whilst this can be done by introducing spirocycles to a molecule, sp3 rich bioisosteric replacements of phenyl groups are also a popular route of compound optimization. Replacing these flat rings with a more three dimensional substituent can introduce similar benefits as introducing a spirocyclic core9. Examples of the inclusion of sp3 rich moieties to generate new vectors for interactions and rigidification to increase activity can be seen in BCL-XL inhibitor A-133185210 and autotaxin inhibitor ONO-843050611 (Figure 2).
Cresset’s bioisostere replacement tool, Spark™, can suggest sp3 rich design elements to introduce these benefits. By focusing the search of libraries with the correct SMARTS filters, Spark will suggest moieties with high globularity that closely match the shape similarity and 3D similarity (represented by Cresset’s field points to model electrostatics, Van der Waal’s and hydrophobics12) of the input molecule.
Spirocycles from bicycles: an illustrative example
Ikeda et al. sought to find how spiro derivatives of Monoacylglycerol Lipase (MAGL) inhibitors might improve compound properties13. Hit molecule 6 (Figure 3) was identified as a starting point owing to the presence of key His121 and Arg57 interactions with the bicyclic moiety. With a view to retaining these interactions, alternative groups were substituted in iteratively and tested for activity and lipophilic ligand efficiency. This culminated in the inclusion of spiro scaffolds that are novel bioisosteres of the 3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl moiety.
Spirocycles and aliphatic rings from phenyl: an illustrative example
Levterov et al. investigated 2-oxabicyclo[2.2.2]octane as a bioisostere for a para-substituted phenyl ring14. Phenyl rings are ubiquitous throughout natural products and bioactive compounds but can lead to undesirable properties, such as poor solubility.
Crystallographic analysis of 2-oxabicyclo[2.2.2]octanes showed very similar cross-ring distances to the phenyl ring in Imatinib (Figure 4), which is an issue with phenyl bioisosteres such as bicyclo[1.1.1]pentane. 2-oxabicyclo[2.2.2]octanes also closely retain the collinearity of exit vectors, maintaining molecular shape. The inclusion of the oxygen atom into the bicyclo[2.2.2]octane ring improves the solubility of the group.
When substituted into Imatinib, the 2-oxabicyclo[2.2.2]octane containing compound showed much improved solubility, a prolonged metabolic half-life, and generally improved ADME profile.
Discovering spirocyclic candidates with Spark
We aimed to explore these bioisosteric substitutions by performing two separate Spark experiments. Through inputting the starting molecules into Spark and then running searches focused upon spirocyclic and sp3 rich moieties, we aimed to find the replacements that the authors chose along with alternative valid options (Figure 5).
Monoacylglycerol lipase Inhibitor replacing aromatic rings
For investigating Ikeda et al.’s study searches, where they aimed to find reversible MAGL inhibitors through the introduction of spirocyclic moieties, we kept the default Spark settings whilst introducing these SMARTS filters in the Advanced Filters tab:
Table 1. The SMARTS strings used to instruct Spark to only output replacement moieties that follow these patterns. These SMARTS used also allow searching of closely related compounds. As an example, the SMARTS shown for bicyclohexanes will also give structures for bicyclohexenes, bicyclohexones, diazabicyclohexanes, and so on.
| Component | SMARTS string |
|---|---|
| Spirocycles | [X4;R2;r](@[r])(@[r])@[r] |
| Adamantanes | A~1~A~2~A~A~3~A~A(~A~A~1~A~3)~A~2 |
| Cubanes | A~1~2~A~3~A~4~A~1~A~5~A~2~A~3~A~4~5 |
| Bicyclooctanes | A~1~2~A~A~A(~A~A~1)~A~A~2 |
| Bicyclohexanes | A~1~2~A~A(~A~A~1)~A~2 |
| Bicyclopentanes | A~1~2~A~A(~A~1)~A~2 |
Cresset’s Spark was able to identify bioisosteric replacements shown in this study and no custom libraries were needed for these searches; the sp3 rich fragments were available in the default ChEMBL and SureChEMBL databases distributed for use in Spark by Cresset (Figure 6).
Further treatment can help to optimize the results output from Spark. In the case of Ikeda et al., we performed Conf Hunt & Align on the results. For this, we selected the Quick Conf Hunt and MCS Alignment, using the input molecule as the reference.
Ikeda et al. note that hydrogen bonds to His121 and Arg 57 are essential for potent binding. Therefore, we used a script in the Python interpreter in Flare, to add a tag to results that make these essential contacts (please reach out to Cresset support if you would like this Python script). The tags could then be used to generate a list of compounds that maintained these essential interactions to focus on. This identified twelve results out of the five hundred generated, including the molecule the authors synthesized (Figure 7).
Replacing phenyl ring with 2-oxabicyclo[2.2.2]octane in known drugs
For the results generated from Levterov et al.’s study14, whereby the effect of substituting in a 2-oxabicyclo[2.2.2]octane core in place of the phenyl ring in Imatinib and Vorinostat was studied, we added some additional constraints to the Spark run, alongside including the aforementioned SMARTS patterns. A key component of this study was to maintain the distance across, and exit vectors of, the bioisosteric replacements compared to the phenyl ring of the input molecule, so we edited Sparks advanced settings to reduce the geometric tolerance of the search. This ensured that the exit vectors of the output molecules spatially resembled those of the input phenyl ring. This was done by modifying the “Allowed attachment point distance error” and “Allowed attachment point angle errors” in the Advanced options of the Spark wizard to the lowest recommended settings (Figure 8).
The output of this experiment gave us 59 scaffold replacement suggestions from the ChEMBL and SureChEMBL databases (Figure 9). This was filtered down to 51 suggestions by omitting those molecules that were flagged as possessing an unstable moiety. Both 2-oxabicyclo[2.2.2]octane and bicyclo[2.2.2]octane were present in these results, showing positive BIF% scores (bioisostere factor, a measure of how closely a bioisostere replacement reflects the input moiety).
Conclusion
By utilizing SMARTS filters available in Spark, chemists can focus searches on sp3 rich fragments for bioisosteric ideas, exploiting the properties of these types of sp3 rich rings to achieve compound designs with improved properties. Here, we showed how Spark reproduced results from two investigative studies which aimed to introduce sp3 rich moieties to improve the properties of known active molecules.
Through judicious use of filters, Spark can provide ideas not just for hit generation, but also for lead optimization to improve compound qualities such as solubility and metabolic stability.
References
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