Conformational Studies and Atropisomerism Kinetics of the ALK Clinical Candidate Lorlatinib (PF‐06463922) and Desmethyl Congeners

Lorlatinib (PF‐06463922) is an ALK/ROS1 inhibitor and is in clinical trials for the treatment of ALK positive or ROS1 positive NSCLC (i.e. specific subsets of NSCLC). One of the laboratory objectives for this molecule indicated that it would be desirable to advance a molecule which was CNS penetrant in order to treat brain metastases. From this perspective, a macrocyclic template was attractive for a number of reasons. In particular, this template reduces the number of rotatable bonds, provides the potential to shield polar surface area and reinforces binding through a restricted conformation. All of these features led to better permeability for the molecules of interest and thus increased the chance for better blood brain barrier penetration. With a CNS penetrant molecule, kinase selectivity is a key consideration particularly with regard to proteins such as TrkB, which are believed to influence cognitive function. Removal of the chiral benzylic methyl substituent from lorlatinib was perceived as not only a means to simplify synthetic complexity, but also as a strategy to further truncate the molecule of interest. Examination of the NMR of the desmethyl analogues revealed that the compound existed as a mixture of atropisomers, which proved separable by chiral SFC. The individual atropisomers were evaluated through a series of in vitro assays, and shown to have a favorable selectivity profile when compared to lorlatinib. The challenge to develop such a molecule lies in the rate at which the atropisomers interchange dictated by the energy barrier required to do this. Here, we describe the synthesis of the desmethyl macrocycles, conformational studies on the atropisomers, and the kinetics of the interconversion. In addition, the corresponding conformational studies on lorlatinib are reported providing a hypothesis for why a single diastereomer is observed when the chiral benzylic methyl group is introduced.     

A D3R prospective evaluation of machine learning for protein-ligand scoring

We assess the performance of several machine learning-based scoring methods at protein-ligand pose prediction, virtual screening, and binding affinity prediction. The methods and the manner in which they were trained make them sufficiently diverse to evaluate the utility of various strategies for training set curation and binding pose generation, but they share a novel approach to classification in the context of protein-ligand scoring. Rather than explicitly using structural data such as affinity values or information extracted from crystal binding poses for training, we instead exploit the abundance of data available from high-throughput screening to approach the problem as one of discriminating binders from non-binders. We evaluate the performance of our various scoring methods in the 2015 D3R Grand Challenge and find that although the merits of some features of our approach remain inconclusive, our scoring methods performed comparably to a state-of-the-art scoring function that was fit to binding affinity data.     

Quadrupole transitions revealed by Borrmann spectroscopy

The Borrmann effect-a dramatic increase in transparency to X-ray beams-is observed when X-rays satisfying Bragg's law diffract through a perfect crystal. The minimization of absorption seen in the Borrmann effect has been explained by noting that the electric field of the X-ray beam approaches zero amplitude at the crystal planes, thus avoiding the atoms. Here we show experimentally that under conditions of absorption suppression, the weaker electric quadrupole absorption transitions are effectively enhanced to such a degree that they can dominate the absorption spectrum. This effect can be exploited as an atomic spectroscopy technique; we show that quadrupole transitions give rise to additional structure at the L(1), L(2) and L(3) absorption edges of gadolinium in gadolinium gallium garnet, which mark the onset of excitations from 2s, 2p(1/2) and 2p(3/2) atomic core levels, respectively. Although the Borrmann effect served to underpin the development of the theory of X-ray diffraction, this is potentially the most important experimental application of the phenomenon since its first observation seven decades ago. Identifying quadrupole features in X-ray absorption spectroscopy is central to the interpretation of 'pre-edge' spectra, which are often taken to be indicators of local symmetry, valence and atomic environment. Quadrupolar absorption isolates states of different symmetries to that of the dominant dipole spectrum, and typically reveals orbitals that dominate the electronic ground-state properties of lanthanides and 3d transition metals, including magnetism. Results from our Borrmann spectroscopy technique feed into contemporary discussions regarding resonant X-ray diffraction and the nature of pre-edge lines identified by inelastic X-ray scattering. Furthermore, because the Borrmann effect has been observed in photonic materials, it seems likely that the quadrupole enhancement reported here will play an important role in modern optics.     

Mass spectrometric studies of the path of carbon in photosynthesis: positional isotopic analysis of (13)C-labelled C(4) to C(7) sugar phosphates

The (EIMS) electron ionization mass spectrometric fragmentation patterns of the methoxime- and ethoxime-trimethylsilyl (TMS) derivatives of C(4) to C(7) sugars involved as phosphates in the Calvin pathway of photosynthesis in plants were analysed by gas chromatography/EIMS using specifically labelled (13)C analogs. In general, most but not all of the major ions in the mass spectra arise from single carbon-carbon bond cleavages of the straight-chain derivatives. The results confirm that GC/MS of the alkoxime-TMS derivatives is a viable method for measuring (13)C incorporations at individual carbon atoms in each of the sugar phosphates during photosynthetic experiments with (13)CO(2).     

Towards tetrasilabicyclo[1.1.0]butane: reductive coupling of 1-t-butyl-2,2-dimesityl-1,1,2-trichlorodisilane

Reductive coupling of 1-$\text{t}$-butyl-2,2-dimesityl-1,1,2-trichlorodisilane employing Li-naphthalenide furnishes, on oxygenation or hydrolysis of the reaction mixture, products ($\text{8}$-$\text{11}$) that may arise from insertion of oxygen into or the addition of water across the Si-Si bonds of 1,3-di-$\text{t}$-butyl-2,2,4,4-tetramesityltetrasilabicyclo-[1.1.0]butane ($\text{3}$).     

Hydrogen chemisorption on gallium oxide polymorphs

The chemisorption of H(2) over a set of gallia polymorphs (alpha-, beta-, and gamma-Ga(2)O(3)) has been studied by temperature-programmed adsorption equilibrium and desorption (TPA and TPD, respectively) experiments, using in situ transmission infrared spectroscopy. Upon heating the gallium oxides above 500 K in 101.3 kPa of H(2), two overlapped infrared signals developed. The 2003- and 1980-cm(-1) bands were assigned to the stretching frequencies of H bonded to coordinatively unsaturated (cus) gallium cations in tetrahedral and octahedral positions [nu(Ga(t)-H) and nu(Ga(o)-H), respectively]. Irrespective to the gallium cation geometrical environment, (i) a linear relationship between the integrated intensity of the whole nu(Ga-H) infrared band versus the Brunauer-Emmett-Teller surface area of the gallia was found and (ii) TPA and TPD results revealed that molecular hydrogen is dissociatively chemisorbed on any bulk gallium oxide polymorph following two reaction pathways. An endothermal, homolytic dissociation occurs over surface cus-gallium sites at T > 450 K, giving rise to Ga-H(I) bonds. The heat and entropy of this type I hydrogen adsorption were determined by the Langmuir's adsorption model as Deltah(I) = 155 +/- 25 kJ mol(-1) and Deltas(I) = 0.27 +/- 0.11 kJ mol(-1) K(-1). In addition, another exothermic, heterolytic adsorption sets in already in the low-temperature region. This type of hydrogen chemisorption involves surface Ga-O-Ga species, originating GaO-H and Ga-H(II) bonds which can only be removed from the gallia surface after heating under evacuation at T > 650 K. The measured desorption energy of this last, second-order process was equal to 77 +/- 10 kJ mol(-1). The potential of the H(2) chemisorption as a tool to measure or estimate the specific surface area of gallia and to discern the nature and proportion of gallium cation coordination sites on the surface of bulk gallium oxides is also analyzed.     

Characterization of zirconized silica supports for HPLC

The preparation and characterization of zirconized silica has been investigated. The material was prepared via the reaction of silica with zirconium tetrabutoxide, optimized by a central composite design and response surface methodology. The new material was characterized by nitrogen adsorption-desorption investigations (BET/BJH) showing specific surface areas adequate for use as a chromatographic support. DRUVS, FTIR, XPS, XAS, XRF and SEM methods also were used to characterize the new material. It was shown that silica networks were not significantly modified with the introduction of zirconium. Surface analyses show that there is appreciable element enrichment at the surface, while significant changes in binding energies of Zr 3d, Si 2p, and O 1s have been detected. The above observations indicate that SiOZr bonds were formed, with zirconium grafted onto the silica surface, yielding a support suitable for HPLC.     

The unambiguous synthesis of lignans of the 2,6-diaryl-3,7-dioxabicyclo-[3.3.0]octane series. The synthesis of eudesmin and 4,8-dihydroxysesamin.

The syntheses of two lignans are described. The syntheses are based on dilactones of unambiguous structure and proceed in such a way that ring opened intermediates are not involved and structures can be unequivocally assigned.     

Nonaqueous based microchip separation of toxic metal ions using 2-(5-bromo-2-pyridylazo)-5-(N-propyl-N-sulfopropylamino)phenol

The colorimetric metal chelating agent, 2-(5-bromo-2-pyridylazo)-5-(N-propyl-N-sulfopropylamino)phenol (5-Br-PAPS), was demonstrated on a capillary electrophoresis microchip in the separation and detection of six metal ions of environmental concern, Cd2+, Pb2+, Cu2+, Co2+, Ni2+, and Hg2+. The inclusion of methanol in the buffer was found to improve both the separation efficiency and sensitivity, in addition to making the technique directly amenable to the application of solid-phase extraction. The combination of metal chelation with solid-phase extraction on a C18 silica gel microcolumn gave several hundred fold improvements in detection limits for the CE microchip measurements of toxic metal ions in water and extracted from a solid Plexiglas surface.     

A chip-based capillary electrophoresis-contactless conductivity microsystem for fast measurements of low-explosive ionic components

A miniaturized analytical system for separating and detecting inorganic explosive residues, based on the coupling of a micromachined capillary electrophoresis (CE) chip with a contactless conductivity detector is described. The low electroosmotic flow (EOF) of the poly(methylmethacrylate) (PMMA) chip material facilitates the rapid switching between analyses of cations and anions using the same microchannel and run buffer (and without an EOF modifier), and hence offers rapid (< 1 min) measurement of seven explosive-related cations and anions. Experimental parameters relevant to the separation and detection processes have been optimized. Addition of a 18-crown-6 ether modifier has been used for separating the peaks of co-migrating potassium and ammonium ions. The ionic-explosive microchip system combines the distinct advantages of contactless conductivity detection with the attractive features of plastic CE microchips. The new microsystem offers great promise for monitoring explosive-related ions at the sample source, with significant advantages of speed/warning, efficiency, cost, or sample size.