Robust fragment-based method of calculating hydrogen atom transfer activation barrier in complex molecules.

Dynamic processes driven by non-covalent interactions (NCI), such as conformational exchange, molecular binding, and solvation, can strongly influence the rate constants of reactions with low activation barriers, especially at low temperatures. Examples of this may include hydrogen-atom-transfer (HAT) reactions involved in the oxidative stress of an active pharmaceutical ingredient (API). Here, we develop an automated workflow to generate HAT transition-state (TS) geometries for complex and flexible APIs and then systematically evaluate the influences of NCI on the free activation energies, based on the multi-conformational transition-state theory (MC-TST) within the framework of a multi-step reaction path. The two APIs studied: fesoterodine and imipramine, display considerable conformational complexity and have multiple ways of forming hydrogen bonds with the abstracting radical-a hydroxymethyl peroxyl radical. Our results underscore the significance of considering conformational exchange and multiple activation pathways in activation calculations. We also show that structural elements and NCIs outside the reaction site minimally influence TS core geometry and covalent activation barrier, although they more strongly affect reactant binding and consequently the overall activation barrier. We further propose a robust and economical fragment-based method to obtain overall activation barriers, by combining the covalent activation barrier calculated for a small molecular fragment with the binding free energy calculated for the whole molecule.

Kinetic Modeling of API Oxidation: (2) Imipramine Stress Testing.

Gauging the chemical stability of active pharmaceutical ingredients (APIs) is critical at various stages of pharmaceutical development to identify potential risks from drug degradation and ensure the quality and safety of the drug product. Stress testing has been the major experimental method to study API stability, but this analytical approach is time-consuming, resource-intensive, and limited by API availability, especially during the early stages of drug development. Novel computational chemistry methods may assist in screening for API chemical stability prior to synthesis and augment contemporary API stress testing studies, with the potential to significantly accelerate drug development and reduce costs. In this work, we leverage quantum chemical calculations and automated reaction mechanism generation to provide new insights into API degradation studies. In the continuation of part one in this series of studies [Grinberg Dana et al., Mol. Pharm. 2021 18 (8), 3037-3049], we have generated the first ab initio predictive chemical kinetic model of free-radical oxidative degradation for API stress testing. We focused on imipramine oxidation in an azobis(isobutyronitrile) (AIBN)/H2O/CH3OH solution and compared the model's predictions with concurrent experimental observations. We analytically determined iminodibenzyl and desimipramine as imipramine's two major degradation products under industry-standard AIBN stress testing conditions, and our ab initio kinetic model successfully identified both of them in its prediction for the top three degradation products. This work shows the potential and utility of predictive chemical kinetic modeling and quantum chemical computations to elucidate API chemical stability issues. Further, we envision an automated digital workflow that integrates first-principle models with data-driven methods that, when actively and iteratively combined with high-throughput experiments, can substantially accelerate and transform future API chemical stability studies.

Assessing the Relevance of Solution Phase Stress Testing of Solid Dosage Form Drug Products: A Cross-Industry Benchmarking Study.

Stress testing (also known as forced degradation) of pharmaceutical products has long been recognized as a critical part of the drug development process, providing foundational information related to intrinsic stability characteristics and to the development of stability-indicating analytical methods. A benchmarking study was undertaken by nine pharmaceutical companies and the Brazilian Health Regulatory Agency (Agência Nacional de Vigilância Sanitária, or ANVISA) with a goal of understanding the utility of various stress testing conditions for producing pharmaceutically-relevant chemical degradation of drugs. Special consideration was given to determining whether solution phase stress testing of solid drug products produced degradation products that were both unique when compared to other stress conditions and relevant to the formal drug product stability data. The results from studies of 62 solid dosage form drug products were compiled.  A total of 387 degradation products were reported as being observed in stress testing studies, along with 173 degradation products observed in accelerated and/or long-term stability studies for the 62 drug products.  Among these, 25 of the stress testing degradation products were unique to the solution phase stress testing of the drug products; however, none of these unique degradation products were relevant to the formal stability data. The relevant degradation products were sufficiently accounted for by stress testing studies that included only drug substance stressing (in solution and in the solid state) and drug product stressing (in the solid state). Based on these results, it is the opinion of the authors that for solid dosage form drug products, well-designed stress testing studies need not include solution phase stress testing of the drug product in order to be comprehensive.

Kinetic Modeling of API Oxidation: (1) The AIBN/H2O/CH3OH Radical "Soup".

Stress testing of active pharmaceutical ingredients (API) is an important tool used to gauge chemical stability and identify potential degradation products. While different flavors of API stress testing systems have been used in experimental investigations for decades, the detailed kinetics of such systems as well as the chemical composition of prominent reactive species, specifically reactive oxygen species, are unknown. As a first step toward understanding and modeling API oxidation in stress testing, we investigated a typical radical "soup" solution an API is subject to during stress testing. Here we applied ab initio electronic structure calculations to automatically generate and refine a detailed chemical kinetics model, taking a fresh look at API oxidation. We generated a detailed kinetic model for a representative azobis(isobutyronitrile) (AIBN)/H2O/CH3OH stress-testing system with a varied cosolvent ratio (50%/50%-99.5%/0.5% vol water/methanol) for 5.0 mM AIBN and representative pH values of 4-10 at 40 °C that was stirred and open to the atmosphere. At acidic conditions, hydroxymethyl alkoxyl is the dominant alkoxyl radical, and at basic conditions, for most studied initial methanol concentrations, cyanoisopropyl alkoxyl becomes the dominant alkoxyl radical, albeit at an overall lower concentration. At acidic conditions, the levels of cyanoisopropyl peroxyl, hydroxymethyl peroxyl, and hydroperoxyl radicals are relatively high and comparable, while, at both neutral and basic pH conditions, superoxide becomes the prominent radical in the system. The present work reveals the prominent species in a common model API stress testing system at various cosolvent and pH conditions, sets the stage for an in-depth quantitative API kinetic study, and demonstrates the usage of novel software tools for automated chemical kinetic model generation and ab initio refinement.

Artifactual degradation of secondary amine-containing drugs during accelerated stability testing when saturated sodium nitrite solutions are used for humidity control.

Accelerated stability studies of pharmaceutical products are commonly conducted at various combinations of temperature and relative humidity (RH). The RH of the sample environment can be controlled to set points using humidity-controlled stability chambers or via storage of the sample in a closed container in the presence of a saturated aqueous salt solution. Herein we report an unexpected N-nitrosation reaction that occurs upon storage of carvedilol- or propranolol-excipient blends in a stability chamber in the presence of saturated sodium nitrite (NaNO2) solution to control relative humidity (∼60% RH). In both cases, the major products were identified as the corresponding N-nitroso derivatives of the secondary amine drugs based on mass spectrometry, UV-vis and retention time. These degradation products were not observed upon storage of the samples at the same temperature and humidity but in the presence of saturated potassium iodide (KI) solution (∼60% RH) for humidity control. The levels of the N-nitrosamine derivatives varied with the pH of various NaNO2 batches. The presence of volatile NOx species in the headspace of a container containing saturated NaNO2 solution was confirmed via the Griess assay. The process for formation of the N-nitrosamine derivatives is proposed to involve volatilization of nitric oxide (NO) from aqueous nitrite solution into the headspace of the container followed by diffusion into the solid drug-excipient blend and subsequent reaction of NOx with the secondary amine.

Drug-Excipient Interactions in the Solid State: The Role of Different Stress Factors.

Understanding properties and mechanisms that govern drug degradation in the solid state is of high importance to ensure drug stability and safety of solid dosage forms. In this study, we attempt to understand drug-excipient interactions in the solid state using both theoretical and experimental approaches. The model active pharmaceutical ingredients (APIs) under study are carvedilol (CAR) and codeine phosphate (COP), which are known to undergo esterification with citric acid (CA) in the solid state. Starting from the crystal structures of two different polymorphs of each compound, we calculated the exposure and accessibility of reactive hydroxyl groups for a number of relevant crystal surfaces, as well as descriptors that could be associated with surface stabilities using molecular simulations. Accelerated degradation experiments at elevated temperature and controlled humidity were conducted to assess the propensity of different solid forms of the model APIs to undergo chemical reactions with anhydrous CA or CA monohydrate. In addition, for CAR, we studied the solid state degradation at varying humidity levels and also under mechano-activation. Regarding the relative degradation propensities, we found that variations in the exposure and accessibility of molecules on the crystal surface play a minor role compared to the impact of molecular mobility due to different levels of moisture. We further studied drug-excipient interactions under mechano-activation (comilling of API and CA) and found that the reaction proceeded even faster than in physical powder mixtures kept at accelerated storage conditions.

Artifacts Generated During Azoalkane Peroxy Radical Oxidative Stress Testing of Pharmaceuticals Containing Primary and Secondary Amines.

We report artifactual degradation of pharmaceutical compounds containing primary and secondary amines during peroxy radical-mediated oxidative stress carried out using azoalkane initiators. Two degradation products were detected when model drug compounds dissolved in methanol/water were heated to 40°C with radical initiators such as 2,2'-azobis(2-methylpropionitrile) (AIBN). The primary artifact was identified as an α-aminonitrile generated from the reaction of the amine group of the model drug with formaldehyde and hydrogen cyanide, generated as byproducts of the stress reaction. A minor artifact was generated from the reaction between the amine group and isocyanic acid, also a byproduct of the stress reaction. We report the effects of pH, initiator/drug molar ratio, and type of azoalkane initiator on the formation of these artifacts. Mass spectrometry and nuclear magnetic resonance were used for structure elucidation, whereas mechanistic studies, including stable isotope labeling experiments, cyanide analysis, and experiments exploring the effects of butylated hydroxyanisole addition, were employed to support the degradation pathways.

A practical application of two in silico systems for identification of potentially mutagenic impurities.

The International Conference on Harmonization (ICH) M7 guidance for the assessment and control of DNA reactive impurities in pharmaceutical products includes the use of in silico prediction systems as part of the hazard identification and risk assessment strategy. This is the first internationally agreed guidance document to include the use of these types of approaches. The guideline requires the use of two complementary approaches, an expert rule-based method and a statistical algorithm. In addition, the guidance states that the output from these computer-based assessments can be reviewed using expert knowledge to provide additional support or resolve conflicting predictions. This approach is designed to maximize the sensitivity for correctly identifying DNA reactive compounds while providing a framework to reduce the number of compounds that need to be synthesized, purified and subsequently tested in an Ames assay. Using a data set of 801 chemicals and pharmaceutical intermediates, we have examined the relative predictive performances of some popular commercial in silico systems that are in common use across the pharmaceutical industry. The overall accuracy of each of these systems was fairly comparable ranging from 68% to 73%; however, the sensitivity of each system (i.e. how many Ames positive compounds are correctly identified) varied much more dramatically from 48% to 68%. We have explored how these systems can be combined under the ICH M7 guidance to enhance the detection of DNA reactive molecules. Finally, using four smaller sets of molecules, we have explored the value of expert knowledge in the review process, especially in cases where the two systems disagreed on their predictions, and the need for care when evaluating the predictions for large data sets.

Determination and control of TEMPO, a potentially genotoxic free radical reagent used in the synthesis of filibuvir.

The synthesis of filibuvir, a hepatitis C virus polymerase inhibitor candidate, involves use of 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO), a potentially genotoxic free radical reagent. A headspace gas chromatographic method utilizing selected-ion monitoring (SIM) mode mass spectrometric detection was developed, validated and applied to the determination of low levels of TEMPO in filibuvir. The GC-MS method was validated in terms of specificity, linearity, precision, accuracy/recovery, limit of quantitation (LOQ) and limit of detection (LOD). The method was shown to be specific for detection of TEMPO in the presence of filibuvir and exhibited acceptable linearity (r ≥ 0.997) over the range of 4-60 ppm vs. filibuvir (0.4-6.0 µg/mL). The system precision was 14% and 8% relative standard deviation (RSD) at the 4 ppm and 8 ppm levels, respectively. Method repeatability was 15% and 13% RSD at the 4 ppm and 8 ppm levels, respectively. Recovery was approximately 50-80% across the method range. Accuracy was 135% and 91% vs. nominal at the 4 and 8 ppm levels, respectively. The LOQ and LOD are 4 ppm and 2 ppm, respectively. Thirteen batches of filibuvir drug substance had no detectable TEMPO (≤ 2 ppm). Purge studies demonstrated that the synthetic process has an extremely high capability to remove TEMPO and consistently delivers filibuvir drug substance with TEMPO levels well below the staged threshold of toxicological concern.

Development and validation of a GC method for quantitative determination of enantiomeric purity of a proline derivative.

Enantioselective HPLC, SFC and GC methods were evaluated for separation and quantitative determination of chiral purity of (2R,4R)-1-(1-tert-butoxyvinyl)-4-methoxypyrrolidine-2-carboxylic acid [(2R,4R)-TBMPCA], a common building block in organic synthesis. All three separation methods can provide baseline resolution of (2R,4R)-TBMPCA and its enantiomer (2S,4S)-TBMPCA; however, both enantioselective HPLC and SFC are unsuitable for quantitation of low levels of the undesired enantiomer in (2R,4R)-TBMPCA. Comparatively, the enantioselective GC method not only separates the derivatized enantioselective pair with resolution as high as 4, but also was shown to be sufficiently linear, precise, and accurate to enable quantitation of derivatized (2S,4S)-TBMPCA down to 2.4 microg/ml (0.04% of nominal concentration). The sample derivatization procedure is simple, and no sample clean-up is needed before injecting samples for enantiomeric GC analysis. Compared to the enantioselective HPLC and SFC methods, the enantioselective GC method is advantageous because of its high efficiency and high sensitivity.

Development and validation of a sensitive GC-MS method for the determination of trace levels of an alkylating reagent in a beta-lactam active pharmaceutical ingredient.

A direct injection gas chromatographic method utilizing selected-ion monitoring (SIM) mode mass selective detection was developed and validated for the trace analysis of an impurity, carbonic acid chloromethyl tetrahydro-pyran-4-yl ester (CCMTHP), present in a beta-lactam active pharmaceutical ingredient (API). A variety of analytical techniques including LC-MS, GC-FID, GC-ECD and GC-MS were evaluated during the method development. GC-MS with SIM at m/z=49 demonstrated the best detection sensitivity. A 10 ppm (5 pg on column) limit of quantitation (LOQ) was attained and the linearity of the method was demonstrated in the range of 10-1000 ppm. Accurate and precise quantitation of the impurity in drug substance was achieved with external standardization. A 10:1 split injection was applied to limit the amount of non-volatile API loading onto the column. The effects of injection and detection parameters such as split ratio, liner type, injection temperature and number of mass ions monitored were studied. Full validation proved the accuracy, precision and specificity of the method, which was successfully employed to analyze many pilot lots of the API.

EXUBERA: pharmaceutical development of a novel product for pulmonary delivery of insulin.

Development of a product for pulmonary delivery of insulin presented significant technology challenges for this first-in-class pharmaceutical product. These included developing (a) a chemically stabilized protein, (b) a dry powder formulation exhibiting required aerosol physical characteristics, (c) low-dose powder filling and packaging technology, and (d) a mechanical device for powder dispersal and reliable dosing to the patient. The insulin drug is formulated using a novel excipient combination to create a powder with a high glass transition temperature (Tg). The high Tg minimizes insulin mobility (thus reactivity), enabling ambient storage conditions. The formulation composition results in minimal hygroscopicity, where customized packaging produced product ruggedness to humidity. The formulated insulin powder is manufactured by spray-drying. This technology was further engineered to produce the desired reproducible powder characteristics with tight control over particle size and moisture content. A solution step prior to drying assures homogeneity and minimizes dependence on the physical form of the components. Novel low-dose filling and packaging technology reproducibly meters milligram quantities of microfine powder to meet stringent quality requirements for dose control. The technology for accurate, uniform, high-throughput metering of drug powders allows for automation and is scaleable for commercial operations. Finally, the mechanical device design provides powder deagglomeration and dispersion processes in a reusable dry powder inhaler with unique characteristics. The device was designed to rely on patient-generated compressed air as the energy source. A sonic discharge of air through the novel TransJector reproducibly extracts, deagglomerates, and disperses the inhalation powder. A clear holding (spacer-type) chamber allows for patient feedback via dose visualization, and separates powder dispersal from the inspiratory effort. The EXUBERA [Pfizer (New York, NY) and sanofi-aventis (Paris, France)] product provides insulin into the bloodstream with similar reproducibly and effectiveness as subcutaneous injections.