Investigation of a failed DNA assay leads to identification of an unexpected contaminant in a commonly used chromatography buffer.

For mammalian cell-derived recombinant biotherapeutics, controlling host cell DNA levels below a threshold is a regulatory requirement to ensure patient safety. DNA removal during drug substance manufacture is accomplished by a series of chromatography-based purification steps and a qPCR-based analytical method is most used to measure DNA content in the purified drug substance to enable material disposition. While the qPCR approach is mature and its application to DNA measurement is widespread in the industry, it is susceptible to trace levels of process-related contaminants that are carried forward. In this study, we observed failures in spike recovery studies that are an integral component of the qPCR-based DNA testing, suggesting the presence of an inhibitory compound in the sample matrix. We generated hypotheses around the origin of the inhibitory compound and generated multiple sample matrices and deployed a suite of analytical techniques including Raman and NMR spectroscopy to determine the origin and identity of the inhibitory compound. The caustic wash step and depth filter extractables were ruled out as root causes after extensive experimentation and DNA testing. Subsequently, 2-(N-morpholino)ethanesulfonic acid (MES), a buffer used in the chromatography unit operations, was identified as the source of the contaminant. A 500-fold concentration followed by Raman and NMR spectroscopy analysis revealed the identity of the inhibitory compound as polyvinyl sulfone (PVS), an impurity that originates in the MES manufacturing process. We have implemented PVS concentration controls for incoming MES raw material, and our work highlights the need for rigor in raw material qualification and control.

Application of 1D 15 N and band-selective 2D 1 H-15 N CLIP-HSQMBC to detect 35/37 Cl isotope effect on nitrogen for unequivocal structure elucidation of the N-Cl moiety in molecules.

An impurity, designated MS204, was isolated from a scale-up production of an intermediate toward the synthesis of an active pharmaceutical ingredient. Structural elucidation of this chloro-containing impurity was performed based on the analysis of the MS and NMR data. Band-selective 2D 1 H-15 N CLIP-HSQMBC experiment was developed to unequivocally identify the ionic N-Cl moiety in the molecule by discovering the two isotope-shifted nitrogen peaks as 3 to 1 ratio separated by about 1 Δ15 N(37/35 Cl) = 19.6 ppb (1.19 Hz) due to the Cl isotope effect. 1D 15 N and 2D 1 H-15 N CLIP-HSQMBC experiments were applied to commercially available compounds to further confirm the techniques by detecting the isotope shift of nitrogen peaks for the N-Cl moiety in molecules.

Use of the 2D 1H-13C HSQC NMR Methyl Region to Evaluate the Higher Order Structural Integrity of Biopharmaceuticals.

The higher-order structure (HOS) of protein therapeutics is directly related to the function and represents a critical quality attribute. Currently, the HOS of protein therapeutics is characterized by methods with low to medium structural resolution, such as Fourier transform infrared (FTIR), circular dichroism (CD), intrinsic fluorescence spectroscopy (FLD), and differential scanning calorimetry (DSC). High-resolution nuclear magnetic resonance (NMR) methods have now been introduced, representing powerful approaches for HOS characterization (HOS by NMR). NMR is a multi-attribute method with unique abilities to give information on all structural levels of proteins in solution. In this study, we have compared 2D 1H-13C HSQC NMR with two established biophysical methods, i.e., near-ultraviolet circular dichroism (NUV-CD) and intrinsic fluorescence spectroscopy, for the HOS assessments for the folded and unfolded states of two monoclonal antibodies belonging to the subclasses IgG1 and IgG2. The study shows that the methyl region of the 1H-13C HSQC NMR spectrum is sensitive to both the secondary and tertiary structure of proteins and therefore represents a powerful tool in assessing the overall higher-order structural integrity of biopharmaceutical molecules.

Telescoped Process to Manufacture 6,6,6-Trifluorofucose via Diastereoselective Transfer Hydrogenation: Scalable Access to an Inhibitor of Fucosylation Utilized in Monoclonal Antibody Production.

IgG1 monoclonal antibodies with reduced glycan fucosylation have been shown to improve antibody-dependent cellular cytotoxicity (ADCC) by allowing more effective binding of the Fc region of these proteins to T cells receptors. Increased in vivo efficacy in animal models and oncology clinical trials has been associated with the enhanced ADCC provided by these engineered mAbs. 6,6,6-Trifluorofucose (1) is a new inhibitor of fucosylation that has been demonstrated to allow the preparation of IgG1 monoclonal antibodies with lower fucosylation levels and thus improve the ADCC of these proteins. A new process has been developed to support the preparation of 1 on large-scale for wide mAb manufacture applications. The target fucosylation inhibitor (1) was synthesized from readily available d-arabinose in 11% overall yield and >99.5/0.5 dr (diastereomeric ratio). The heavily telescoped process includes seven steps, two crystallizations as purification handles, and no chromatography. The key transformation of the sequence involves the diastereoselective preparation of the desired trifluoromethyl-bearing alcohol in >9/1 dr from a trimethylsilylketal intermediate via a ruthenium-catalyzed tandem ketal hydrolysis-transfer hydrogenation process.

Application of 1,1-ADEQUATE, HMBC, and Density Functional Theory To Determine Regioselectivity in the Halogenation of Pyridine N-Oxides.

The 1,1-ADEQUATE spectrum clearly shows specific two-bond proton to carbon correlations to unequivocally distinguish the major and minor regioisomers of ortho-halogenated pyridines and to aid in assignment of the corresponding proton and carbon chemical shifts. M06-2X/6-31+G(d,p) free energies of the regioisomeric intermediates arising from deprotonation correctly predict the experimentally observed preference and thus can be used to tune the substituent pattern to yield a desired regiochemical outcome.

Highly Regioselective Halogenation of Pyridine N-Oxide: Practical Access to 2-Halo-Substituted Pyridines.

A highly efficient and regioselective halogenation reaction of unsymmetrical pyridine N-oxide under mild conditions is described. The methodology provides a practical access to various 2-halo-substituted pyridines, which are pharmaceutically important intermediates.

Rh(III)-catalyzed C-H activation and double directing group strategy for the regioselective synthesis of naphthyridinones.

A general Rh(III)-catalyzed synthesis of naphthyridinone derivatives is described. It relies on a double-activation and directing approach leveraging nicotinamide N-oxides as substrates. In general, high yields and selectivities can be achieved using low catalyst loadings and mild conditions (room temperature) in the couplings with alkynes, while alkenes require slightly more elevated temperatures.

Application of two-dimensional selective-TOCSY HMBC for structure elucidation of impurities in mixture without separation.

In the pharmaceutical industry, regulatory expectations driven by patient safety considerations make structure elucidation of impurities at levels greater than 0.1% in the active pharmaceutical ingredient (API) of primary interest. Impurities can be generated from isomers in starting materials, or produced from different process steps toward the final API. Proton peaks belonging to different impurities could be potentially identified in the one-dimensional (1)H NMR spectrum, when evaluated in combination with two-dimensional (2-D) COSY and HSQC data. However, in 2-D HMBC data, correlation responses from different impurities may overlap with those from the major component, causing uncertainty of long-range proton to carbon correlations and quaternary carbon assignments. This observation prompts us to design the 2-D selective-TOCSY HMBC experiment to distinguish responses from different impurities in mixtures to obtain 2-D NMR data for each impurity, thus eliminating the use of a chromatographic isolation step to obtain material for NMR analysis. This methodology is demonstrated for structure elucidation of impurities ranging from 8.2% in the raw material to 0.4% in the API in this study, and would be particularly useful for industrial samples in which the solubility and availability of material are not an issue.

Two asymmetric syntheses of AMG 221, an inhibitor of 11beta-hydroxysteroid dehydrogenase type 1.

Two asymmetric syntheses of AMG 221 (2), an inhibitor of 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) discovered in our laboratories, are reported. One of the syntheses utilizes chiral trimethylsilyl cyanohydrin 12 as starting material and the other utilizes its enantiomer ent-12. The displacement approach involves the conversion of 12 to 2 via a six-step sequence, occurs with net inversion of configuration, and employs amine 6 as starting material. This route features a novel approach toward chiral dialkylsubstituted alpha-mercaptoacids. The cyclization approach entails the synthesis of 2 from ent-12 in 2 steps, takes place with net retention of configuration, and uses thiourea 8 as starting material. The final step of this route exemplifies a novel synthesis of chiral C-5 dialkylsubstituted 2-aminothiazolones from chiral alpha-hydroxyacids and thioureas. Insights into the mechanism of this transformation and study of the effect of the medium on the stereochemical outcome of the reaction are presented.

Photosensitized degradation of losartan potassium in an extemporaneous suspension formulation.

During development of an extemporaneous suspension formulation for losartan potassium, previously unknown degradation products were observed in experimental suspensions prepared in a commercial cherry syrup vehicle. These degradates increased rapidly when analytical solutions prepared from that suspension were exposed to ambient light. The structures of the degradates were determined using a combination of preparative HPLC, LC/MS, (13)C and (1)H NMR (1D and 2D), and mechanistic chemistry. Each degradate results from destruction of the imidazole ring of losartan. Formation of the two major degradates required exposure to light (UV or visible) and the presence of oxygen. Experiments using Rose Bengal (a singlet oxygen photosensitizer) and 1,4-diazabicyclooctane (DABCO; a singlet oxygen quencher) established that the major photodegradates are formed via the intermediacy of singlet oxygen. The identity of the photosensitizer in the formulation was not unequivocally determined; however, the experiments implicated the artificial flavoring in fulfilling this role.

Identification of impurities in ivermectin bulk material by mass spectrometry and NMR.

The identification and characterization of four process impurities in bulk ivermectin and four process impurities in bulk avermectin, using a combination of MS and NMR, are discussed herein. These process impurities were shown to be 24-demethyl H2B1a, 3'-demethyl H2B1a, 3''-demethyl H2B1a and 24a-hydroxy B2a isomer. The impurities were shown to be process impurities and are present in avermectin bulk also.

Application of liquid chromatography/mass spectrometry and nuclear magnetic resonance to the identification of degradates of a novel insulin sensitizer in aqueous solutions.

Degradation of a novel insulin sensitizer in aqueous solutions was studied using high pressure liquid chromatography/mass spectrometry (LC/MS). The insulin sensitizer, containing a thiazolidine-2,4-dione (TZD), was a new class of antidiabetic agent for the treatment of type II diabetes. Chemical stability of the insulin sensitizer was evaluated by stressing its aqueous solutions at 40 degrees C for 24 h. Oxygen was removed from one of the solutions by bubbling pure nitrogen through to identify non-oxidative pathways. LC/MS analyses of the stressed solutions revealed that hydrolysis and oxidation are the primary degradation pathways for the studied compound. A alpha-thiol acetic acid, acyl amide, and two dimeric diastereomers were the main degradates of the insulin sensitizer. The alpha-thiol acetic acid served as an intermediate-like species, and oxidized to two dimeric degradates upon exposing to air. All of them were identified as ring-opening products of the TZD. The entities of the acyl amide and dimeric degradates were respectively verified by a synthetic standard or NMR following isolation of a diastereomeric degradate. Characterization using MS in both positive and negative ion scans were discussed for an isolated diastereomeric degradate. Mechanisms of fragmentation and formation for those degradates are presented based on the MS result.

Identification of oxidative degradates of the TRIS salt of a 5,6,7,8-tetrahydro-1,8-naphthyridine derivative by LC/MS/MS and NMR spectroscopy--interactions between the active pharmaceutical ingredient and its counterion.

The Tris(hydroxymethyl)aminomethane (TRIS) salt of a substituted 5,6,7,8-tetrahydro-1,8-naphthyridine compound (I) in a mannitol-based formulation was stressed at various conditions. Liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses of the stressed samples revealed that oxidation and dimerization were the primary degradation pathways for this compound. 1H- and 13C-nuclear magnetic resonance (NMR) spectroscopy were used to characterize the isolated dimers. The aromatized degradate, N-oxide, amide, and three dimeric products were all confirmed by either LC/MS using authentic standards or NMR spectroscopy. In general, the aromatized product was always the primary degradate produced under all stress conditions. When stressed at 80 degrees C, the TRIS counterion also underwent thermal degradation to yield formaldehyde in situ which reacted with the parent compound to form a unique methylene-bridged dimeric product and an N-formyl degradate. A minor condensation product between the compound I and the TRIS counterion was also detected in the 80 degrees C stressed samples. Under 40 degrees C/75% RH stress conditions, TRIS derived degradates were insignificant, while dimers formed by compound I became predominant. In addition, two hydroxylated products (7-OH and 5-OH) were also detected. Mechanisms for the formation of the oxidative and dimeric degradates were proposed.

The importance of chromatographic separation in LC/MS/MS quantitation of drugs in biological fluids: detection, characterization, and synthesis of a previously unknown low-level nitrone metabolite of a substance P antagonist.

The observation of an interference peak in plasma samples from dogs dosed with compound I led to the discovery of an unidentified metabolite. The unknown metabolite had the same molecular weight as the parent drug, and their fragmentation profiles were also quite similar. LC/MS/ MS analysis of the plasma extracts of dogs and rats dosed with I and its deuterium-labeled analogue suggested a nitrone structure for the unknown metabolite. Synthesized nitrone matched the unknown metabolite with identical retention time and nearly identical fragmentation profile. The nitrone slowly decomposed in acidic aqueous solution at ambient temperature and also underwent in-source, thermal-induced hydrolysis during electrospray ionization mass spectrometric analysis. The reaction of the nitrone with diethyl acetylenedicarboxylate readily generated a [2 + 3] cycloaddition product. The example shown here clearly demonstrates that precautions must be taken when LC/MS/MS quantitation is conducted in the selected reaction monitoring mode.