Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Tuning the phase behavior of semicrystalline hydrogenated polynorbornene via epimerization

Hydrogenated polynorbornene (hPN) synthesized by ring‐opening metathesis polymerization (ROMP) exhibits a thermoreversible change in crystal polymorph at a temperature T _cc below its melting point, T _m. The polymorphic transition corresponds to a sharp increase in rotational disorder around the chain axis as the temperature is increased above T _cc. Saturation of ROMP polynorbornene (PN) to hPN can be achieved through both catalytic and noncatalytic approaches. Here, three different hydrogenation routes were employed on the same precursor polymer: catalytic routes over either supported Pd⁰ or a Ni/Al complex, and noncatalytic saturation with diimide. The different hydrogenation routes result in hPNs with varying degrees of epimerization of the cyclopentylene ring (from cis to trans); these epimerized units are included in the hPN crystals. The crystal structure of the rotationally ordered hPN polymorph, observed below T _cc, changes sharply at low levels of epimerization and then is weakly influenced by further increases in trans content. The stability of the rotationally ordered hPN polymorph decreases with increasing epimerization, as reflected in a reduction of T _cc from 134 °C to 92 °C at 22% epimerization. T _cc is less affected by epimerization than by the inclusion of a similar content of 5‐methylnorbornene units, reflecting the smaller size of the trans defect. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1188–1195     

Controlling thermomechanical behavior of semicrystalline hydrogenated polynorbornene through the cis- to trans-cyclopentylene ratio

Though polynorbornene synthesized by ring-opening metathesis polymerization has an intrinsically all-cis configuration of the cyclopentylene backbone rings, a fraction of these rings can be epimerized to the trans configuration during hydrogenation over suitable catalysts. By varying the method of hydrogenation, semicrystalline hydrogenated polynorbornenes (hPNs) with trans levels between 0 and 36% were obtained. With increasing trans content, the glass transition temperature, melting point, and enthalpy of melting decrease modestly. By contrast, the temperature at which the hPN crystal transitions into a rotationally disordered polymorph varies strongly with trans content, ranging from 126 °C (all-cis) to 71 °C at 27% trans; at trans contents of 34% and above, no rotationally-ordered phase is observed at any temperature. The room-temperature Young's modulus shows no dependence on trans content, while the yield stress drops by 20% at 1% trans content and slowly decreases further with additional epimerization. The temperature dependence of the Young's modulus differs for trans-containing versus all-cis polymers, while the temperature dependence of the yield stress is set by the polymorph type (rotationally ordered vs. disordered).     

A Lock-and-Kill Anticancer Photoactivated Chemotherapy Agent†

Photosubstitutionally active ruthenium complexes show high potential as prodrugs for the photoactivated chemotherapy (PACT) treatment of tumors. One of the problems in PACT is that the localization of the ruthenium compound is hard to trace. Here, a ruthenium PACT prodrug, [Ru(3)(biq)(STF-31)](PF₆)₂ (where 3 = 3-(([2,2′:6′,2″-ter- pyridin]-4′-yloxy)propyl-4-(pyren-1-yl)butanoate) and biq = 2,2′-biquinoline), has been prepared, in which a pyrene tracker is attached via an ester bond. The proximity between the fluorophore and the ruthenium center leads to fluorescence quenching. Upon intracellular hydrolysis of the ester linkage, however, the fluorescence of the pyrene moiety is recovered, thus demonstrating prodrug cellular uptake. Further light irradiation of this molecule liberates by photosubstitution STF-31, a known cytotoxic nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, as well as singlet oxygen via excitation of the free pyrene chromophore. The dark and light cytotoxicity of the prodrug, embedded in liposomes, as well as the appearance of blue emission upon uptake, were evaluated in A375 human skin melanoma cells. The cytotoxicity of the liposome-embedded prodrug was indeed increased by light irradiation. This work realizes an in vitro proof-of-concept of the lock-and-kill principle, which may ultimately be used to design strategies aimed at knowing where and when light irradiation should be realized in vivo.     

Coronaviruses Use ACE2 Monomers as Entry-Receptors

The angiotensin-converting enzyme 2 (ACE2) has been identified as entry receptor on cells enabling binding and infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via trimeric spike (S) proteins protruding from the viral surface. It has been suggested that trimeric S proteins preferably bind to plasma membrane areas with high concentrations of possibly multimeric ACE2 receptors to achieve a higher binding and infection efficiency. Here we used direct stochastic optical reconstruction microscopy (dSTORM) in combination with different labeling approaches to visualize the distribution and quantify the expression of ACE2 on different cells. Our results reveal that endogenous ACE2 receptors are present as monomers in the plasma membrane with densities of only 1–2 receptors μm⁻². In addition, binding of trimeric S proteins does not induce the formation of ACE2 oligomers in the plasma membrane. Supported by infection studies using vesicular stomatitis virus (VSV) particles bearing S proteins our data demonstrate that a single S protein interaction per virus particle with a monomeric ACE2 receptor is sufficient for infection, which provides SARS-CoV-2 a high infectivity.     

Structure of Framework Aluminum Lewis Sites and Perturbed Aluminum Atoms in Zeolites as Determined by 27Al{1H} REDOR (3Q) MAS NMR Spectroscopy and DFT/Molecular Mechanics

Zeolites are highly important heterogeneous catalysts. Besides Brønsted SiOHAl acid sites, also framework Al_FR Lewis acid sites are often found in their H‐forms. The formation of Al_FR Lewis sites in zeolites is a key issue regarding their selectivity in acid‐catalyzed reactions. The local structures of Al_FR Lewis sites in dehydrated zeolites and their precursors—“perturbed” Al_FR atoms in hydrated zeolites—were studied by high‐resolution MAS NMR and FTIR spectroscopy and DFT/MM calculations. Perturbed framework Al atoms correspond to (SiO)₃AlOH groups and are characterized by a broad ²⁷Al NMR resonance (δ_i=59–62 ppm, C_Q=5 MHz, and η=0.3–0.4) with a shoulder at 40 ppm in the ²⁷Al MAS NMR spectrum. Dehydroxylation of (SiO)₃AlOH occurs at mild temperatures and leads to the formation of Al_FR Lewis sites tricoordinated to the zeolite framework. Al atoms of these (SiO)₃Al Lewis sites exhibit an extremely broad ²⁷Al NMR resonance (δ_i≈67 ppm, C_Q≈20 MHz, and η≈0.1).