Improving API Synthesis

August 2, 2011
Patricia Van Arnum
Pharmaceutical Technology

Volume 35, Issue 8

O-arylation and O-alkylation, a one-pot protein synthesis, a combined approach in continued and chemocatalysis, and green-chemistry applications are the target of some recent advances in API synthesis.

Organic chemists face the ongoing challenge of developing and optimizing a synthesis for active pharmaceutical ingredients (APIs). These challenges involve a multitude of issues designed to improve yield, purity, stereoselectivity, process conditions (i.e., temperature and pressure), scalability, and production economics. A recent literature review reveals insight into some of these challenges as they relate to organic chemical production overall and pharmaceutical chemical development in particular.


O-arylation and O-alkylation

Researchers at Merck & Co. recently reported on a large-scale synthesis of a potent glucokinase inhibitor, MK-0941, through selective O-arylation and O-alkylation. Glucokinase inhibitors are under clinical development for treating Type II diabetes. MK-0941 is a glucokinase inhibitor that has a differentially substituted 3,5-dihydroxybenzamide structure, and an efficient synthesis that would be suitable for large-scale preparation was required. The researchers reported on several drawbacks of the early-stage synthesis, including multiple recrystallizations to improve enantomeric purity, yield variability, and batch-to-batch variability in the impurity profile of the desired compound. Several factors were key to improving the synthesis: a highly selective mono-O-arylation of methyl 3,5-dihydroxybenzoate with 2-ethanesulfonyl-5-chloropyridine and the selection of a proper protective group for the SN2 O-alkylation (1).

Patricia Van Arnum

One-pot protein synthesis

Researchers at the University of Chicago recently developed a one-pot protein synthesis involving a 204-residue covalent-dimer vascular endothelial growth factor (VEGF). VEGF is a protein involved in vasculogenesis and angiogenesis and is studied in reference to pharmaceutical compounds, particularly anticancer compounds. The researchers reported that they prepared a 204-residue covalent dimmer VEGF with full mitogenic activity from three unprotected peptide segments by one-pot native chemical ligations. The covalent structure of the synthetic VEGF was confirmed through mass measurements, and the three-dimensional structure of the synthetic protein was determined by high-resolution X-ray crystallography (2, 3).

Chemical protein synthesis is one research area of University of Chicago professor Stephen B.H. Kent, a co-author of the recently published research on the VEGF synthesis. One area of focus is the preparation of long polypeptide chains of protein molecules by the chemoselective reaction (i.e. chemical ligation) of unprotected protein segments containing mutually reactive functional groups. An example of these ligation chemistries is thioester-mediated, amide-forming ligation or native ligation. The resulting polypeptide chains are folded with good efficiency to produce high-purity synthetic proteins. The covalent structure of the molecule is confirmed by mass spectrometry, and the three-dimensional fold structure of the synthetic protein is determined by X-ray crystallography. Another area of research focus is kinetically controlled ligation, a chemistry used for the full convergent synthesis of large protein molecules. The research group is examining insertion reactions for creating molecular diversity in preformed molecular scaffolds and the use of polymer-supported ligation.

Suzuki-Miyaura cross couplings in a continuous flow system

Researchers at the Massachusetts Institute of Technology (MIT) reported on the development of a Suzuki–Miyaura cross-coupling reaction in a continuous-flow microreactor system. Specifically, the researchers reported on a continuous-flow Suzuki–Miyaura cross-coupling reaction that started from phenols and produced various biaryls in good yield using a microfluidic-extraction operation and a packed-bed reactor. The project used a multidisciplinary approach with the research on microreactor technology developed by a team led by Klaus F. Jensen, department head, Warren K. Lewis professor of chemical engineering, and professor of materials science and engineering at MIT. The organic synthesis portion of the project was developed by a group led by Stephen Buchwald, Camille Dreyfus professor of chemistry at MIT (4, 5).

Suzuki coupling is a palladium-catalyzed coupling between organoboron compounds and organohalides and is an important reaction in organic chemistry in general and in the development of pharmaceutical compounds specifically. Akira Suzuki, distinguished professor emeritus at Hokkaido University in Sapporo, Japan, was a corecipient of the 2010 Nobel Prize in Chemistry for the development of palladium-catalyzed cross coupling (6).

Although batch manufacturing is the predominant form of manufacturing in the pharmaceutical industry, there is growing interest in microreactor technology. In general, microstructured devices with small internal volumes and high surface-to-volume ratios offer transport capabilities for rapid mixing, enhanced heat transfer for good temperature control, and intensified mass transfer. Microstructured devices operate in continuous-flow environment, which can offer certain advantages, such as controlled process conditions, high flow rates, and high mass throughput. Continuous operations also may allow bulk-chemistry processes to have high production capacities. Fluid dynamics determine the characteristics of continuous-flow equipment such as pressure loss, residence time, heat-transfer characteristics, and mixing time (7).

Buchwald is engaged in various research projects involving catalysis, including the creation and study of new ligands, the design of new methods to form carbon–nitrogen bonds through the use of metal catalysts, such as palladium or copper, new methods for the formation of carbon–carbon bonds, including asymmetric transformations, as well as continuous flow chemistry using microreactors and capillary tubing. Buchwald recently reported on the continuous-flow synthesis of 3,3-disubstituted oxindoles by a palladium-catalyzed a-arylation/alkylation sequence. Specifically, he reported on the pallidum-catalyzed a-arylation of oxindoles in continuous flow involving a biphasic system, a precatalyst, and a packed-bed microreactor. The reaction was integrated into a two-step continuous-flow sequence for rapid, modular, and efficient syntheses of 3,3-disubstituted oxindoles (8).

Jensen's research is focused on understanding and controlling the interaction of reaction and transport processes in realizing and testing functional microstructured and nanostructured materials and devices for chemical, biological, optical, electronic, and energy applications, including the use of microfabricated systems. He recently reported on research using an automated microfluidic system for online optimization in chemical synthesis. He reported that the time and material required for an optimization trial were minimized by performing reactions in an integrated silicon microreactor and incorporating high-performance liquid chromatography for in-line monitoring of the reaction performance. The system was used to optimize two different reactions to understand the potential impact of the system for reaction development. The two reactions studied were a Knoevenagel condensation reaction and a mulitparameter optimization to maximize the yield of benzaldehyde in the oxidation pathway of benzyl alcohol to benzaldehyde to benzoic acid (9).

In other work, Jensen's team reported on the design and use of a high-pressure and high-temperature microsystem. Key parameters for the fabrication of the microreactors and modular fluidic packaging were to withstand high pressure and temperature conditions (i.e., 30MPa and 400 °C). The researchers reported on various applications of the high-pressure/high-temperature plug and play microsystems. These applications included multiphase follow visualization through the transition of liquid–liquid immiscible hexane–water segmented flow to homogeneous supercritical flow, on-chip supercritical water oxidation, and synthesis of iron oxide nanoparticles (10).

Green-chemistry applications

Green chemistry is an important tool in improving reactions, which may for example, improve production economics through reduced energy requirements, lower solvent use, fewer byproducts, and less waste generation. Bruce H. Lipshutz, professor in the chemistry and biochemistry department at the University of California at Santa Barbara, was recognized in June with a Presidential Green Chemistry Challenge Award, an annual recognition by the US Environmental Protection Agency for advances in green chemistry (11).

Nanodispersed surfactant. Lipshutz was recognized for designing a second-generation surfactant, TPGS-750-M, which can be used in industrial processes to replace large amounts of organic solvents with small amounts of the surfactant nanodispersed in water only. TPGS-750-M is composed of tocopherol (i.e., vitamin E), succinic acid, and methoxy polyethylene glycol. TPGS-750-M forms nanomicelles in water that are lipophilic on the interior and hydrophilic on the exterior. A small amount of TPGS-750-M may be used to spontaneously form 50–100-nm diameter micelles in water to serve as nanoreactors. The particle size of TPGS-750-M is engineered to facilitate organic reactions, such as cross-couplings. Reactants and catalysts dissolve in the micelles, resulting in high concentrations that lead to increased reaction rates at ambient temperature (11).

Several common organic reactions that are catalyzed by transition metals can take place within TPGS-750-M micelles in water at room temperature and in high isolated yields. These reactions include ruthenium-catalyzed olefin metatheses (Grubbs), palladium-catalyzed cross-couplings (Suzuki, Heck, and Sonogashira), unsymmetrical aminations, allylic aminations and silylations, and aryl borylations. The technology also offers the potential for palladium-catalyzed aromatic carbon–hydrogen bond activation for carbon–carbon bond formation at room temperature. In its awards recognition, EPA cited other advantages to the technology: straightforward product isolation; elimination of frothing and foaming commonly associated with other surfactants; efficient recycling of the surfactant after use; recovery of the insoluble product by extraction; and reuse of the aqueous surfactant with negligible loss of activity. Future generations of surfactants may include a catalyst tethered to a surfactant to provide both the reaction vessel (i.e., the inside of the micelle) and the catalyst to enable the reaction (11).

Flow processing. Eli Lilly submitted two entries to EPA's Green Chemistry Presidential Challenge. The first involved the commercial production of LY2624803*H3PO4, an investigational new drug candidate in Phase II clinical trials and a drug acquired by Lilly with its acquisition of Hypnion. The original synthesis was not amenable to large-scale manufacture and had several environmental and safety issues with the original chemistry. Among them were: dimethylformamide/sodium hydride in step one of the synthesis; methylene in various steps; a molten step with observed self-heating; an aldehyde purification that would be unsafe at increased scale; phosphoryl chloride in large excess; and chromatographic purification (11).

The company made several improvements to the synthesis using flow processing. An efficient carbonylation replaced an inefficient oxidation catalyzed by tetramethyl pentahydropyridine oxide. Hydrogen replaced sodium triacetoxyborohydride in a reductive amination. Although both operations required high pressure (i.e., 1000 psi), which would be difficult to manage in a batch environment, both operations were amenable to flow processing (11).

Process mass intensity (PMI), a measure of the efficiency of a synthesis, was improved. PMI is the total mass of raw materials (including water) put into a process for every kilogram of product produced. The original route had a PMI of more than 1000 before chromatography. The new route has a net PMI of 59, representing a 94% reduction in PMI and a 96% percent reduction with chromatography. Lilly implemented its new route for LY2624803*H3PO4 on a pilot-plant scale in Indianapolis, Indiana, during 2009 and on a commercial scale in Kinsale, Ireland, during 2010, according to the EPA report (11).

Improved Grignard chemistry. Another entry from Eli Lilly involved the development of Grignard chemistry using a continuous stirred tank reactor. The Grignard reaction is applied to many industrial reactions, including producing intermediates for pharmaceutical compounds. Some commercial-scale problems with the reaction, however, are strongly exothermic activation and reaction steps, heterogeneous reactions with potential problems suspending and mixing the reaction mixture, and operational hazards posed by ethereal solvents, such as diethyl ether (11).

Eli Lilly developed inherently safer Grignard chemistry using a continuous stirred tank reactor that allowed continuous formation of Grignard reagents with continuous coupling and quenching. This approach minimized hazards by operating at a small reaction volume, performed metal activation only once during each campaign, and used 2-methyltetrahydrofuran (MeTHF). MeTHF offers certain advantages, such as that it may be derived from renewable resources and may provide improved chemoselectivity and stereoselectivity compared with Grignard products using other ethereal solvents. The continuous approach provided reductions of 43% in metal use, 10% in Grignard reagent stoichiometry, and 30% in PMI (11) According to the EPA report, Lilly is using the continuous stirred tank reactor Grignard approach to produce two key materials: the penultimate intermediate of LY2216684*HCl, a norepinephrine reuptake inhibitor currently under clinical investigation, and for an intermediate for another drug under clinical development. Commercial production on a 22-L scale is under consideration (11).

Patricia Van Arnum is a senior editor at Pharmaceutical Technology, 485 Route One South, Bldg F, First Floor, Iselin, NJ 08830 tel. 732.346.3072,


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3. L.K. Wolf, Chem. & Eng. News 89 (29), 27–28 (2011).

4. T. Noel et al., Suzuki–Miyaura Cross-Coupling Reactions in Flow: Multistep Synthesis Enabled by a Microfluidic Extraction, Agnew. Chem. Int. Ed. online, DOI: 10.1002/anie.201101480, May 17, 2011.

5. S.R. Ritter, Chem. & Eng. News 89 (23), 39 (2011).

6. P. Van Arnum, Pharm. Technol. 34 (12) 40–42 (2010).

7. N. Korman et al., API Synthesis, Formulation Development, and Manufacturing, asupplement to Pharm. Technol., s32–s36 (2010).

8. P. Li and S. L. Buchwald, Continuous-Flow Synthesis of 3,3-Disubstituted Oxindoles by a Palladium-Catalyzed a-Arylation/Alkylation Sequence, Agnew. Chem. Int. Ed. online, DOI: 10.1002/anie.201102401, June 7, 2011.

9. J.P. McMullen and K.F. Jensen, Org. Process Res. Dev. 14 (5), 1169–1176 (2010).

10. K.F. Jensen et al., Ind. Eng. Chem. Res. 49 (22), 11310–11320 (2010).

11. EPA, Presidential Green Chemistry Challenge Awards Program: Summary of 2011 Award Entries and Recipients (Washington, DC, June 2011).