Muraglitazar was being developed by Bristol-Myers Squibb for the treatment for type 2 diabetes and dislipidemia. Process optimization included the minimization of the by-products. This endeavor was greatly facilitated by a clear understanding of by-product identity. By-products were isolated by preparative chromatography and identified using NMR and MS. The identified structures of the by-products provided useful information about the undesired side reactions, which were then minimized or eliminated by altering the reaction conditions appropriately. Copyright © 2016 John Wiley & Sons, Ltd.

Impurity A, observed during the process research and development of muraglitazar, was isolated via preparative HPLC for structural identification using one-dimensional and two-dimensional NMR techniques. The origin of impurity A was identified as arising three steps earlier as a minor contaminant present in one of the starting materials: 4-hydroxylbenzaldehyde. As a result, a series of corresponding impurities were formed in each synthetic step leading up to impurity A. These findings permitted the addition of a new specification for this starting material to eliminate the problem.

The use of protected amino acid chlorides for peptide coupling reactions has long been avoided due to the extensive racemization that commonly occurs during either the acid chloride formation or the coupling reaction itself. Conditions are described which allow N-trifluoroacetyl-protected amino acid chlorides to be generated in high purity and with high retention of stereochemical integrity. Control of temperature is the predominant factor in controlling racemization, and rapid formation of acid chlorides under low temperature can be conveniently achieved using Vilsmeier reagent. Stereochemical integrity is further maintained when coupling of N-trifluoroacetyl acid chlorides is carried out with amino acid esters under Schotten–Baumann conditions using specific controls on pH, temperature, and agitation. Second order rate constants for coupling and the azlactone formation associated with racemization were measured to be 4260 and 3.6L/mols, respectively. This high rate differential allows for the reaction to be run with a minimum excess of amine ester, and makes it suitable for continuous processing. The applicability of the preferred coupling conditions to a range of amino acid couplings is described.

Allysine ethylene acetal [(S)-2-amino-5-(1,3-dioxolan-2-yl)-pentanoic acid (2)] was prepared from the corresponding keto acid by reductive amination using phenylalanine dehydrogenase (PDH) from Thermoactinomyces intermedius ATCC 33205. Glutamate, alanine, and leucine dehydrogenases, and PDH from Sporosarcina species (listed in order of increasing effectiveness) also gave the desired amino acid but were less effective. The reaction requires ammonia and NADH. NAD produced during the reaction was recyled to NADH by the oxidation of formate to CO(2) using formate dehydrogenase (FDH). PDH was produced by growth of T. intermedius ATCC 33205 or by growth of recombinant Escherichia coli or Pichia pastoris expressing the Thermoactinomyces enzyme. Using heat-dried T. intermedius as a source of PDH and heat-dried Candida boidinii SC13822 as a source of FDH,98%, but production of T. intermedius could not be scaled up. Using heat-dried recombinant E. coli as a source of PDH and heat-dried Candida boidinii 98%. In a third generation process, heat-dried methanol-grown P. pastoris expressing endogenous FDH and recombinant Thermoactinomyces98% ee.

In an effort to remove residual palladium from a drug candidate prepared by palladium-catalyzed indolization, many treatments were examined. The most effective treatment was to precipitate palladium from solution using 2,4,6-trimercapto-s-triazine (TMT), which reduced palladium levels from 600-650 ppm to 20-60 ppm in an isolated indole intermediate. Subsequent crystallizations routinely afforded active pharmaceutical ingredient with <1 ppm of palladium. TMT treatment should prove useful to reduce the concentration of residual palladium in other reactions.