The process of scaling up is always very challenging. While sometimes products can be easily purified through methods like extraction or recrystallization, in certain cases, intermediates present a unique set of obstacles. Such was the scenario in this case where most of the intermediates were rich oily mixtures for which all the attempts of recrystallization failed.

Identifying the issue

SigutLabs undertook the scale-up synthesis of a highly active clindamycin derivative for the Institute of Microbiology of the Czech Academy of Science (Figure 1).

The given synthetic procedure was only designed for a small scale (100 mg) and contained several hidden issues. An illustrative example was the selective oxidation of -SMe moiety to sulfoxide with m-chloroperoxybenzoic acid (mCPBA). According to the given procedure, only 1 eq. of mCPBA was used even though the oxidation of amine nitrogen in the proline part of the lincomycin was also possible. This expected oxidation might significantly decrease the overall yield of the whole synthesis during scale-up.

Methodology insight

To address this challenge, we devised an alternative approach consisting of mild overoxidation to sulfoxide-N-oxide followed by the selective reduction of N‑oxide with sulfoxide moiety preservation. This action reduced the significant mass losses. Analyzing the intermediates posed another challenge, as the given procedure only utilized TLC for analysis, leaving a lack of information regarding the mixture composition. Moreover, HPLC and a similar method based on light absorption could not be used due to the very low absorption of the intermediates. However, we successfully overcame this challenge by the use of LC/MS as a convenient method for characterizing the crude reaction mixtures (Figure 2).

The last step of the synthesis, the selective chlorination of the secondary hydroxyl group, proved to be even more challenging. The lincomycin derivative molecule contains four secondary hydroxyl moieties which can be subsequently replaced by chlorine atoms. The frequently used chlorination agents (SOCl2, POCl3, PPh3 + NCS, PPh3 + CCl4,…) lead ultimately to overchlorination or undesired elimination of HCl from the molecule. Finally, we identified a mixture of DMF and (COCl)2 to serve our purpose as a very mild chlorination reagent.

Positive outcome

Using these reaction conditions, only traces of overchlorination were observed and ubiquitous elimination was negligible. The final purification process, conducted via reverse column chromatography on multigram scales, yielded the target product with purity exceeding 90 % (Figure 3).