Cbz piperazine protection imparts differential reactivity between the carbamates of MR84907; however an additional step is required to reveal the piperazine's free amine. Trimethylsilyl iodide (TMSI) is a traditional deprotection reagent for this transformation. A number of batches were made using this methodology; however, benzyl iodide (BnI), a potentially mutagenic impurity (PMI) is coproduced. Though it purges well, elimination of this hazard is desired. Additionally, BnI can be trapped by the basic site (tertiary amine) of the prolinol generating a quaternary ammonium species. The removal of this species is not trivial and required the use of silica plug at the API stage in order to be fully rejected. A new Cbz-deprotection was developed which avoids BnI production. Reaction of MR84915 Tosylate with 2mercaptoethanol cleanly released the benzyl group and carbon dioxide. The coproduct of reaction (thioether) is a benign liquid which easily purges, and the thiol precursor is surprisingly minimally odiferous. By running the reaction in N,N-dimethylacetamide (DMAc) with K3PO4, there was no need to first isolate the free base of the acid complex, and MR84916 could be crystallized directly from the reaction mixture using water thus minimizing consumption of organic solvents (Figure ). Epimerization of the cyanomethyl was an unexpected consequence of the reaction under basic conditions. Conducting Step 5 without 2-mercaptoethanol illustrates this concept, and the epimer content increases over time (Figure ). The protons alpha to the nitrile can be deprotonated prior to deprotection of the carbamate. This species is then prone to piperazine ring opening via formation of an acrylonitrile. Subsequent Michael addition leads to the epimerization as the carbamate can attack either face of the olefin. Analogous experiments show that the deprotected MR84916 is not prone to epimerization since the amine is a poor leaving group. Characterization of the reaction via design-of-experiments (DoE) helped determine factors which impacted the reaction and define a robust operational space. Epimerization depends primarily upon temperature and water content, where higher values of these factors increased formation of the diastereomer. The reaction was well controlled by setting appropriate limits on these variables, and the diastereomer could be tolerated at levels up to 4% since ~50% purges in each of the two crystallization steps of MRTX849.