The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.     

Dielectric properties of selected laterally fluoro-substituted 4,4′′-dialkyl,dialkoxy and alkyl-alkoxy [1:1′;4′:1′′]terphenyls

Measurements of the complex permittivity, ε*?=?ε′ – iε″, within the frequency range 200 Hz to 10 MHz for 15 laterally fluoro-substituted terphenyls have been conducted. In most cases the substances exhibited the nematic phase over a broad temperature range. All substances were characterised by negative dielectric anisotropy, and are potentially useful for vertical alignment mode systems. The static permittivity tensor components have been analysed in relation to the dipole structure of the molecules. Dielectric relaxation processes observed in the liquid crystalline (LC) and solid rotator (R) phases (obtained by slow cooling of the samples) are characterised by calculation of the relaxation times and activation barriers. The rotation motions around the short axes are typical for LC phases, whereas rotations about the long axes, accompanied in some cases by internal motions, are present in the R phase.     

Phase diagram and dielectric relaxation studies of n-octyl-isothiocyanato-biphenyl (8BT) in the crystalline E phase under high pressure

The pressure-temperature phase diagram of n-octyl-isothiocyanato-biphenyl (8BT) in the pressure range up to 250 MPa (2.5 kbar) and the temperature range 250-400 K was established with the aid of DTA. At 1 atm the substance exhibits exclusively CrE polymorphism. At pressures above 190 MPa, the clearing line splits showing an additional phase which is not yet identified. Dielectric relaxation measurements on the CrE phase of 8BT were performed in the pressure range 0.1-120 MPa and the temperature range 304-345 K. A Debye-type relaxation process was observed in the frequency range 100 Hz-1 MHz. The longitudinal relaxation time τ, characterizing the molecular reorientations around the short axis, was analysed with respect to the pressure and temperature, yielding the activation volume, Δ^# V = RT(? ln τ/?p)_T, and activation enthalpy, Δ^# H = R(? ln τ/? T^-1)_p, respectively. The results are compared with analogous data obtained recently for similar compounds having other liquid crystalline phases (N, SmA).     

Structural Study of Membrane Glycoprotein-Precursor of β-Amyloid and Proteins Involved in Its Proteolysis

Crystallography Reports - Alzheimer’s disease is the most widespread form of neurodegenerative disease in the world. Its clinical manifestations are explained by selective degeneration of...     

Investigating Chain Dynamics in Highly Crosslinked Polymers using Solid‐State 1H NMR Spectroscopy

Solid state ¹H NMR line‐shape analysis and (double quantum) DQ ¹H NMR experiments have been used to investigate the segmental and polymer chain dynamics as a function of temperature for a series of thermosetting epoxy resins produced using different diamine curing agents. In these thermosets, chemical crosslinks introduce topological constraints leading to residual stresses during curing. Materials containing a unique ferrocene‐based diamine (FcDA) curing agent were evaluated to address the role of the ferrocene fluxional process on the atomic‐level polymer dynamics. At temperatures above the glass transition temperature (T_g), the DQ ¹H NMR experiments provided a measure of the relative effective crosslink and entanglement densities for these materials and revealed significant polymer chain dynamic heterogeneity in the FcDA‐cured thermosets. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1143–1156     

Synthesis of cyclic norspermidine derivative of protohemin IX

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Marinocyanins,cytotoxic bromo-phenazinone meroterpenoids from a marine bacterium from the streptomycete clade MAR4

Six cytotoxic and antimicrobial metabolites of a new bromo-phenazinone class, the marinocyanins A-F (1–6), were isolated together with the known bacterial metabolites 2-bromo-1-hydroxyphenazine (7), lavanducyanin (8, WS-9659A) and its chlorinated analog WS-9659B (9). These metabolites were purified by bioassay-guided fractionation of the extracts of our MAR4 marine actinomycete strains CNS-284 and CNY-960. The structures of the new compounds were determined by detailed spectroscopic methods and marinocyanin A (1) was confirmed by crystallographic methods. The marinocyanins represent the first bromo-phenazinones with an N-isoprenoid substituent in the skeleton. Marinocyanins A-F show strong to weak cytotoxicity against HCT-116 human colon carcinoma and possess modest antimicrobial activities against Staphylococcus aureus and amphotericin-resistant Candida albicans.     

Ion mobility-mass correlation trend line separation of glycoprotein digests without deglycosylation

A high-throughput ion mobility mass spectrometer (IMMS) was used to rapidly separate and analyze peptides and glycopeptides derived from glycoproteins. Two glycoproteins, human α-1-acid glycoprotein and antithrombin III were digested with trypsin and subjected to electro-spray traveling wave IMMS analysis. No deglycosylation steps were performed; samples were complex mixtures of peptides and glycopeptides. Peptides and glycosylated peptides with different charge states (up to 4 charges) were observed and fell on distinguishable trend lines in 2-D IMMS spectra in both positive and negative modes. The trend line separation patterns matched between both modes. Peptide sequence was identified based on the corresponding extracted mass spectra and collision induced dissociation (CID) experiments were performed for selected compounds to prove class identification. The signal-to-noise ratio of the glycopeptides was increased dramatically with ion mobility trend line separation compared to non-trend line separation, primarily due to selection of precursor ion subsets within specific mobility windows. In addition, isomeric mobility peaks were detected for specific glycopeptides. IMMS demonstrated unique capabilities and advantages for investigating and separating glycoprotein digests in this study and suggests a novel strategy for rapid glycoproteomics studies in the future.     

Spectral properties of coumarin derivatives in various environments

The structural and spectral properties of coumarin derivatives in complex environments were investigated within the time-dependent density functional theory (TD DFT). Absorption spectra calculations were obtained at TD PBE0/6-31+G(d,p) level of theory for coumarin47 in the gas-phase and in various polar and non-polar organic solvents. The geometries of coumarins 6, 30, 47 and 522 in the gas phase and in inclusion complexes with the β-cyclodextrin (βCD) were determined by PM3 and DFT (HCTH/6-31G) calculations. Encapsulation of coumarin in βCD and associated changes in electronic structure produced either a red or blue shift in the absorption spectra of coumarins. A proposed cavity model for βCD-coumarin complex in water solution allowed identification of various contributions to the overall shift in the absorption spectra of coumarin upon complex formation in a solvent environment