Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods.

Autoxidation of drugs and drug-like molecules is a major concern in the development of safe and effective therapeutics. Because active pharmaceutical ingredients (APIs) that contain sulfur atoms can form sulfoxides under oxidative stress, predicting oxidative susceptibilities within an organic molecule can have a major impact in accelerating the compound's stability assessment. For investigation of a sulfur atom's oxidative stability, density functional theory (DFT) methods were applied to accurately predict S-O estimated bond dissociation enthalpies (BDEs) of sulfoxides. Our process employed B3LYP/6-31+G(d) for geometry optimization and frequency calculation, and we employed B3P86/6-311++G(2df,2p) to obtain electronic energies from single-point energy calculations. A total of 84 drug-like molecules containing 50 different sulfide scaffolds were used to develop a risk scale. Our results showed that when S-O BDE is less than 69 kcal/mol, the sulfur atom has low oxidative susceptibility. High oxidation risk occurs when the S-O BDE is greater than 75 kcal/mol. The risk scale was successful in predicting the relative propensities of sulfide oxidation among the small organic molecules and commercial drugs examined.

Practical Synthesis of Terminal Vinyl Fluorides.

The synthesis of di- and trisubstituted vinyl fluorides with high isomeric purity remains a challenge for organic synthesis. While many methods exist to access these compounds, the separation of the desired isomer from the minor isomer and/or starting materials often is difficult. Herein, we report a practical method to access di- and trisubstituted vinyl fluorides via a selective Horner-Wadsworth-Emmons olefination/hydrolysis, which provides crystalline 2-fluoroacrylic acids in high (>98%) E-isomeric purity. A subsequent silver-catalyzed stereoretentive decarboxylation provides the title substances with high isomeric purity and without the need for tedious chromatography to remove the minor isomer. The process was amenable to a variety of aldehydes and ketones and provided a diverse array of di- and trisubstituted vinyl fluorides. The sequence was applied to the synthesis of antibacterial and anti-inflammatory compounds.

N-oxidation Regioselectivity and Risk Prediction Using DFT-ALIE Calculations.

INTRODUCTION: The formation of N-oxide degradants is a major concern in development of new drugs due to potential effects on a compound's pharmacological activity. Such effects include but are not limited to solubility, stability, toxicity, and efficacy. In addition, these chemical transformations can impact physicochemical properties that affect drug manufacturability. Hence identification and control of N-oxide transformations is of critical importance in the development of new therapeutics. OBJECTIVE: This study describes the development of an in-silico approach to identify N-oxide formation in APIs with respect to autoxidation. METHODS: Average Local Ionization Energy (ALIE) calculations were carried out using molecular modeling techniques and application of Density Functional Theory (DFT) at the B3LYP/6-31G(d,p) level of theory. A total of 257 nitrogen atoms and 15 different oxidizable nitrogen types were used in developing this method. RESULTS: The results show that ALIE could be reliably used to predict the most susceptible nitrogen for N-oxide formation. A risk scale was developed that rapidly categorizes nitrogen's oxidative vulnerabilities as small, medium, or high. CONCLUSIONS: The developed process presents a powerful tool to identify structural susceptibilities for N-oxidation as well as enabling rapid structure elucidation in resolving potential experimental ambiguities.

Deconvolution of fast exchange equilibrium states in NMR spectroscopy using virtual reference standards and probability theory.

A methodology for deconvolution of fast exchange equilibrium states in NMR spectroscopy (DFEQNMR) was developed based on DFT-GIAO NMR chemical shift prediction and a probability theory algorithm. Proof-of-concept studies were performed to estimate the protonation state of N-containing organic molecules involving fast proton exchange equilibrium and evaluate the solution tautomerism of a purine derivative. DFT-GIAO calculations were optimized to achieve good accuracy in 13C, 1H and 15N chemical shift prediction for protonated species. The probability theory algorithm enabled the determination of solution species ratios and yielded 95% confidence regions by comparing experimental and simulated chemical shift data sets. The calculation showed good accuracy for model partial salts with various functionalities and application in structure elucidation of complex natural product partial salts was also demonstrated. This method showed promising potential in acquisition of important insight into fast exchange equilibrium systems with only one experimental NMR chemical shift data set.

D iCE: Diastereomeric in Silico Chiral Elucidation, Expanded DP4 Probability Theory Method for Diastereomer and Structural Assignment.

NMR chemical shift prediction at the B3LYP/cc-pVDZ level of theory was used to develop a highly accurate probability theory algorithm for the determination of the stereochemistry of diastereomers as well as the regiochemistry. DFT-GIAO calculations were performed for each conformer using geometry optimization and a CPCM solvent model. Boltzmann averaged shielding constants were converted to chemical shifts for 1H and 13C, using the generalized linear scaling terms determined in four different solvents for 1H and 13C and extended to 15N in DMSO. The probability theory algorithm, D iCE, was based on the DP4 method and developed for 1H, 13C, and 15N NMR using individual and combined probability data. The chemical shift calculation errors were fitted to a Student's t-distribution for 1H and 13C and a normal distribution for 15N. The application yielded a high accuracy for structural assignment with a low computational cost.

Development of a 13C NMR Chemical Shift Prediction Procedure Using B3LYP/cc-pVDZ and Empirically Derived Systematic Error Correction Terms: A Computational Small Molecule Structure Elucidation Method.

An accurate and efficient procedure was developed for performing 13C NMR chemical shift calculations employing density functional theory with the gauge invariant atomic orbitals (DFT-GIAO). Benchmarking analysis was carried out, incorporating several density functionals and basis sets commonly used for prediction of 13C NMR chemical shifts, from which the B3LYP/cc-pVDZ level of theory was found to provide accurate results at low computational cost. Statistical analyses from a large data set of 13C NMR chemical shifts in DMSO are presented with TMS as the calculated reference and with empirical scaling parameters obtained from a linear regression analysis. Systematic errors were observed locally for key functional groups and carbon types, and correction factors were determined. The application of this process and associated correction factors enabled assignment of the correct structures of therapeutically relevant compounds in cases where experimental data yielded inconclusive or ambiguous results. Overall, the use of B3LYP/cc-pVDZ with linear scaling and correction terms affords a powerful and efficient tool for structure elucidation.

Systematic investigation of DFT-GIAO 15N NMR chemical shift prediction using B3LYP/cc-pVDZ: application to studies of regioisomers, tautomers, protonation states and N-oxides.

The calculation of 15N NMR chemical shifts has been systematically investigated using density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/cc-pVDZ level of theory. General linear regression terms for 15N chemical shift predictions were calculated for nitromethane and liquid ammonia references in DMSO. Both aliphatic and aromatic nitrogens were studied using a diverse set of molecular scaffolds. Statistical error analysis between experiment and prediction revealed that, with the exception of primary amines, 95% of linear scaled N-15 chemical shifts are within a ±9.56 ppm range. Comparison of the 15N calculated isotropic chemical shifts with the experimentally determined chemical shifts provided accurate assignment of the correct structure in cases where experimental data was ambiguous or inconclusive. Application of 15N prediction proved to be highly effective in identifying the correct regio-isomer, oxidation state, protonation state and preferred tautomer in solution.

Rhodium-Catalyzed Addition of Aryl Boronic Acids to 2,2-Disubstituted Malononitriles.

ß-Ketonitriles bearing a quaternary carbon at the 2-position were prepared through Rh-catalyzed addition of aryl boronic acids to 2,2-disubstituted malononitriles. In contrast to the previously described transnitrilative cyanation of aryl boronic acids with dialkylmalononitriles, the present reaction avoids retro-Thorpe collapse of the intermediate addition product through the use of a milder base. The reaction was amenable to a variety of aryl boronic acids and disubstituted malononitriles, providing a diverse array of ß-ketonitriles. The products could be further derivatized to valuable chiral α,α-disubstituted-ß-aminonitriles through addition reactions to the corresponding N-tert-butanesulfinyl imines.

Three-dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model.

The three-dimensional solution conformation of teicoplanin aglycone was determined using NMR spectroscopy. A combination of NOE and dihedral angle restraints in a DMSO solvation model was used to calculate an ensemble of structures having a root mean square deviation of 0.17 Å. The structures were generated using systematic searches of conformational space for optimal satisfaction of distance and dihedral angle restraints. Comparison of the NMR-derived structure of teicoplanin aglycone with the X-ray structure of a teicoplanin aglycone analog revealed a common backbone conformation with deviation of two aromatic side chain substituents. Experimentally determined backbone (13)C chemical shifts showed good agreement with those computed at the density functional level of theory, providing a cross validation of the backbone conformation. The flexible portion of the molecule was consistent with the region that changes conformation to accommodate protein binding. The results showed that a hydrogen-bonded DMSO molecule in combination with NMR-derived restraints together enabled calculation of structures that satisfied experimental data.

A mild dihydrobenzooxaphosphole oxazoline/iridium catalytic system for asymmetric hydrogenation of unfunctionalized dialins.

Air-stable P-chiral dihydrobenzooxaphosphole oxazoline ligands were designed and synthesized. When they were used in the iridium-catalyzed asymmetric hydrogenation of unfunctionalized 1-aryl-3,4-dihydronaphthalenes under one atmosphere pressure of H2 , up to 99:1 e.r. was obtained. High enantioselectivities were also observed in the reduction of the exocyclic imine derivatives of 1-tetralones.

Carbamoyl anion addition to N-sulfinyl imines: highly diastereoselective synthesis of α-amino amides.

Carbamoyl anions, generated from N,N-disubstituted formamides and lithium diisopropylamide, add with high diastereoselectivity to chiral N-sulfinyl aldimines and ketimines to provide α-amino amides. The methodology enables the direct introduction of a carbonyl group without the requirement of unmasking steps as with other nucleophiles. The products may be converted to α-amino esters or 1,2-diamines. Iterative application of the reaction enabled the stereoselective synthesis of a dipeptide. Spectroscopic and computational studies support an anion structure with η(2) coordination of lithium by the carbonyl group.

Development of a large scale asymmetric synthesis of the glucocorticoid agonist BI 653048 BS H3PO4.

The development of a large scale synthesis of the glucocorticoid agonist BI 653048 BS H3PO4 (1·H3PO4) is presented. A key trifluoromethyl ketone intermediate 22 containing an N-(4-methoxyphenyl)ethyl amide was prepared by an enolization/bromine-magnesium exchange/electrophile trapping reaction. A nonselective propargylation of trifluoromethyl ketone 22 gave the desired diastereomer in 32% yield and with dr = 98:2 from a 1:1 diastereomeric mixture after crystallization. Subsequently, an asymmetric propargylation was developed which provided the desired diastereomer in 4:1 diastereoselectivity and 75% yield with dr = 99:1 after crystallization. The azaindole moiety was efficiently installed by a one-pot cross coupling/indolization reaction. An efficient deprotection of the 4-methoxyphenethyl group was developed using H3PO4/anisole to produce the anisole solvate of the API in high yield and purity. The final form, a phosphoric acid cocrystal, was produced in high yield and purity and with consistent control of particle size.

Chromatographic Separation and NMR An Integrated Approach in Pharmaceutical Development.

Over the past 10 years, major improvements in the performance of LC-NMR have been realized. The addition of postcolumn SPE, advances in probe technology including cryogenic probes and microcoil probes, improved solvent suppression pulse sequences, and shielded magnets with better homogeneity have all contributed to rapid advancements in this technology. Application of LC-NMR to problems in pharmaceutical development has had a major impact on structure elucidation studies. LC-NMR has been successfully applied to determine the structures of degradation products, impurities, mixtures of compounds, and metabolites. Use of stop flow techniques with LC-NMR experiments has been a critical means of identifying unstable compounds and studying conformational kinetics. The integration of SPE as an intermediate step between the LC unit and the NMR spectrometer has vastly improved the power of the hyphenated technique in trace analysis applications. Online postcolumn enrichment of chromatographic peaks by SPE dramatically reduces the NMR acquisition times by allowing repeated injections to be trapped onto the same cartridge or different cartridges. Because protonated solvents can be easily removed with a drying procedure, solvents and buffers may be freely chosen for maximizing chromatographic separation without compromising NMR spectral quality. The compound of interest may then be eluted from an SPE cartridge using deuterated organic solvent, which helps to reduce dynamic range issues. When combined with cryogenically cooled microcapillary probes, the sensitivity of the NMR signal increases about 10-fold over conventional room temperature probes, enabling full structure characterization at the microgram level. Heteronuclear experiments with concentrations previously only possible in a limited number of cases have now become standard experiments. The availability of HSQC and HMBC experiments and microcoil/cryogenic technology opens the possibility of using LC-(SPE) NMR for the structural elucidation of complete unknowns on a microgram scale. To enable significant future downscaling beyond the current capabilities, improved performance of the LC-NMR interface and improved SPE cartridge retention need to be addressed. In addition, the active volume of the NMR flow cell or capillary tube will have to shrink along with the corresponding detection coils in order not to lose filling factor. As the size of the NMR probes become more efficient with respect to mass sensitivity, techniques such as CE or capillary electrochromatography (CEC) may be interfaced more successfully with NMR spectroscopy. Overall, the current state of the art in LC-NMR has demonstrated proven utility in a variety of applications. When combined with SPE and cryotechnology, LC-NMR has become an extremely valuable tool for mass limited samples, enabling structure elucidation without the need for laborious serial isolation and purification procedures.

1H and 13C NMR assignments of all three isomeric o-fluoronaphthaldehydes and three o-fluorophenanthrene aldehydes.

Three isomeric o-fluoronaphthaldehydes, 9-fluorophenanthrene, and three previously unreported o-fluorophenanthrene aldehydes were analyzed in detail by multiple NMR techniques to provide unambiguous assignment of structures and resonances. The six aldehydes serve as the key starting materials for novel chiral ligands used in highly enantioselective rhodium-catalyzed asymmetric hydrogenation reactions.

(31)P solid state NMR study of structure and chemical stability of dichlorotriphenylphosphorane.

Solid state (31)P NMR spectroscopy was used to examine, monitor and quantify the compound integrity of the chemical reagent dichlorotriphenylphosphorane. Comparison was also made with solution (31)P NMR spectra which showed that this highly reactive species could be observed in dry benzene prior to conversion to the hydrolyzed product. This is the first reported solid state NMR study of the stability and reactivity of dichlorotriphenylphosphorane and the first account of its observation and comparison in the solution state. In the solid state, the ionic and covalent forms for dichlorotriphenylphosphorane were observed along with hydrolyzed products, however, the degree of hydrolysis was dependent upon the rotor packing conditions. Calculation of the relative percent composition of dichlorotriphenylphosphorane with hydrolyzed product was made for samples prepared in air versus under nitrogen atmosphere. This information was critical in adjusting the amount of reagent used in chemical development syntheses and scale up laboratories. All hydrolyzed products were identified, based upon chemical comparisons with spectra of pure materials.

Structure Elucidation of Poly-Faldaprevir: Polymer Backbone Solved Using Solid-State and Solution Nuclear Magnetic Resonance Spectroscopy.

A large-scale synthesis of the hepatitis C virus drug Faldaprevir revealed precipitation of an unknown insoluble solid from methanol solutions of the drug substance. The unknown impurity was determined to be a polymer of Faldaprevir based on analytical methods that included size exclusion chromatography in combination with electrospray ionization mass spectrometry, solution nuclear magnetic resonance (NMR), matrix-assisted laser desorption ionization-time of flight, ultracentrifugation, elemental analysis, and sodium quantitation by atom absorption spectroscopy. Structure elucidation of the polymeric backbone was achieved using solid-state NMR cross-polarization/magic angle spinning (CP/MAS), cross polarization-polarization inversion, and heteronuclear correlation (HETCOR) experiments. The polymerization was found to occur at the vinyl cyclopropane via a likely free radical initiation mechanism. Full proton and carbon chemical shift assignments of the polymer were obtained using solution NMR spectroscopy. The polymer structure was corroborated with chemical synthesis of the polymer and solution NMR analysis.

Diastereoselective Synthesis of α-Quaternary Aziridine-2-carboxylates via Aza-Corey-Chaykovsky Aziridination of N-tert-Butanesulfinyl Ketimino Esters.

A general, scalable, and highly diastereoselective aziridination of N-tert-butanesulfinyl ketimino esters is described. The methodology has been utilized to provide straightforward access to previously unobtainable, biologically relevant α-quaternary amino esters and derivatives starting from readily available precursors.

The design, structure, and clinical update of small molecular weight matrix metalloproteinase inhibitors.

Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes involved in the degradation and remodeling of extracellular matrix proteins. Under normal physiological conditions, the activities of these enzymes are well-regulated by endogenous tissue inhibitors of metalloproteinases (TIMPs). Chronic stimulation of MMP activities due to an imbalance in the levels of MMPs and TIMPs has been implicated in the pathogenesis of a variety of diseases such as cancer, osteoarthritis, and rheumatoid arthritis. Thus, MMP inhibitors are expected to be useful for the treatment of these disorders. Because of their importance in a variety of pathological conditions, a number of small molecular weight MMP inhibitors have entered clinical trials in humans. However, the results of these trials have been extremely disappointing and have led many investigators to conclude that MMP inhibitors have no therapeutic benefit in human cancer. To date, the first generation MMP inhibitors exhibited poor bioavailability while second-generation compounds revealed that prolonged treatment caused musculoskeletal pain and inflammation or had a lack of efficacy. This article describes the design of small molecular weight MMP inhibitors, a brief description of available three-dimensional MMP structures, a review of the proposed therapeutic utility of MMP inhibitors, and a clinical update of compounds that have entered clinical trials in humans. The experimentally determined structures used in the structure-based design of MMP inhibitors are thoroughly covered. Major emphasis is on recently published and/or patented potent MMP inhibitors, from approximately January 2000 to April 2003, and their pharmacological properties. Protein inhibitors of these proteolytic enzymes, i.e. TIMPs, will not be discussed.

Facile entry to an efficient and practical enantioselective synthesis of a polycyclic cholesteryl ester transfer protein inhibitor.

An efficient enantioselective synthesis of the chiral polycyclic cholesteryl ester transfer protein (CETP) inhibitor 1 has been developed. The synthesis was rendered practical for large scale via the development of a modified Hantzsch-type reaction to prepare the sterically hindered pyridine ring, enantioselective hydrogenation of hindered ketone 6 utilizing novel BIBOP-amino-pyridine derived Ru complex, efficient ICl promoted lactone formation, and a BF3 mediated hydrogenation process for diastereoselective lactol reduction. This efficient route was successfully scaled to produce multikilogram quantities of challenging CETP drug candidate 1.