Binding modes identification through molecular dynamic simulations: A case study with carnosine enantiomers and the Teicoplanin A2‐2‐based chiral stationary phase

In the present study, an in silico methodology able to define the binding modes adopted by carnosine enantiomers in the setting of the chiral recognition process is described. The inter‐ and intramolecular forces involved in the enantioseparation process with the Teicoplanin A2‐2 chiral selector and carnosine as model compound are successfully identified. This approach fully rationalizes, at a molecular level, the (S) < (R) enantiomeric elution order obtained under reversed‐phase conditions. Consistent explanations were achieved by managing molecular dynamics results with advanced techniques of data analysis. As a result, the time‐dependent identification of all the interactions simultaneously occurring in the chiral selector‐enantiomeric analyte binding process was obtained. Accordingly, it was found that only (R)‐carnosine is able to engage a stabilizing charge–charge interaction through its ionized imidazole ring with the carboxylate counter‐part on the chiral selector. Instead, (S)‐carnosine establishes intramolecular contacts between its ionized functional groups, that limit its conformational freedom and impair the association with the chiral selector unit.     

Monitoring the Interaction of α-Synuclein with Calcium Ions through Exclusively Heteronuclear Nuclear Magnetic Resonance Experiments

Many properties of intrinsically disordered proteins (IDPs), or protein regions (IDRs), are modulated by the nature of amino acid side chains as well as by local solvent exposure. We propose a set of exclusively heteronuclear NMR experiments to investigate these features in different experimental conditions that are relevant for physiological function. The proposed approach is generally applicable to many IDPs/IDRs whose assignment is available in the Biological Magnetic Resonance Bank (BMRB) to investigate how their properties are modulated by different, physiologically relevant conditions. The experiments, tested on α-synuclein, are then used to investigate how α-synuclein senses Ca²⁺ concentration jumps associated with the transmission of nerve signals. Novel modules in the primary sequence of α-synuclein optimized for calcium sensing in highly flexible, disordered protein segments are identified.     

Selective bond breaking in beta-D-ribose by gas-phase electron attachment around 8 eV

Electron attachment experiments are carried out on the beta-d-ribose molecule in the gas phase for the energy region around 8 eV, and clear fragmentation products are observed for different mass values. A computational analysis of the relevant dynamics is also carried out for the beta-d-ribose in both the furanosic and pyranosic form as gaseous targets around that energy range. The quantum scattering attributes obtained from the calculations reveal in both systems the presence of transient negative ions (TNIs). An analysis of the spatial features of the excess resonant electron, together with the computation and characterization of the target molecular normal modes, suggests possible break-up pathways of the initial, metastable molecular species.     

Precision measurement of the (7)Be solar neutrino interaction rate in Borexino

The rate of neutrino-electron elastic scattering interactions from 862 keV (7)Be solar neutrinos in Borexino is determined to be 46.0±1.5(stat)(-1.6)(+1.5)(syst)?counts/(day·100 ton). This corresponds to a ν(e)-equivalent (7)Be solar neutrino flux of (3.10±0.15)×10(9) cm(-2)?s(-1) and, under the assumption of ν(e) transition to other active neutrino flavours, yields an electron neutrino survival probability of 0.51±0.07 at 862 keV. The no flavor change hypothesis is ruled out at 5.0?σ. A global solar neutrino analysis with free fluxes determines Φ(pp)=6.06(-0.06)(+0.02)×10(10) cm(-2)?s(-1) and Φ(CNO)<1.3×10(9) cm(-2)?s(-1) (95% C.L.). These results significantly improve the precision with which the Mikheyev-Smirnov-Wolfenstein large mixing angle neutrino oscillation model is experimentally tested at low energy.     

Pyrroloquinoxaline hydrazones as fluorescent probes for amyloid fibrils

Here we describe the identification and preliminary characterization of a new class of pyrrolo(imidazo)quinoxaline hydrazones as florescent probes for Aβ(1-42) fibrils. All the newly developed compounds were able to bind amyloid fibrils formed in vitro and some of them displayed an increase of their fluorescence upon binding. When tested on brain tissue preparations presenting Aβ deposits, the described hydrazones selectively stained amyloid structures and did not display aspecific binding. The hydrazones did not show antifibrillogenic activity and electron microscopy analysis revealed that they do not interfere with fibrils structure. The described pyrrolo(imidazo)quinoxalines could be useful for studying amyloid structures in vitro. Moreover, their experimentally proven ability to cross the blood-brain barrier in mouse opens the possibility of developing these compounds as potential amyloid imaging agents for in vivo applications.     

Oxidative coupling as a biomimetic approach to the synthesis of scytonemin

The first total synthesis of the dimeric alkaloid pigment scytonemin is described. The key transformations in its synthesis from 3-indole acetic acid are a Heck carbocyclization and a Suzuki-Miyaura cross-coupling, orchestrated in a stereospecific tandem fashion, followed by a biosynthetically inspired oxidative dimerization. The tandem sequence generates a tetracyclic (E)-3-(arylidene)-3,4-dihydrocyclopenta[b]indol-2(1H)-one that is subsequently dimerized into the unique homodimeric core structure of scytonemin.     

Evaluation of N719 amount in TiO2 films for DSSC by thermogravimetric analysis

The aim of this work is to evaluate the amount of N719 dye in TiO₂ films for DSSCs by thermogravimetric analysis coupled with mass spectrometry (TG-MS) in comparison with the traditional method based on the dye extraction in NaOH solutions. The characterization was carried out on TiO₂ films applied on FTO glasses by automatic screen printing method. For all the samples, TG-MS showed three well defined steps. The first, below 100 °C and coupled to an endothermic signal was due to water release. From 200 to about 300 °C, there was the release of CO₂ coming from decarboxylation reaction of N719. The last exothermic step was due to the combustion of organic residues. As the decarboxylation reaction occurs with release of 4 moles of CO₂ per mole of N719, it was used to determine the dye loading of the samples that resulted in the range 7?15 wt% well agreeing the relevant content of dye obtained by desorption with NaOH.     

Direct measurement of the 7Be solar neutrino flux with 192 days of borexino data

We report the direct measurement of the 7Be solar neutrino signal rate performed with the Borexino detector at the Laboratori Nazionali del Gran Sasso. The interaction rate of the 0.862 MeV 7Be neutrinos is 49+/-3stat+/-4syst counts/(day.100 ton). The hypothesis of no oscillation for 7Be solar neutrinos is inconsistent with our measurement at the 4sigma C.L. Our result is the first direct measurement of the survival probability for solar nu(e) in the transition region between matter-enhanced and vacuum-driven oscillations. The measurement improves the experimental determination of the flux of 7Be, pp, and CNO solar nu(e), and the limit on the effective neutrino magnetic moment using solar neutrinos.     

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M^pro, a cysteine protease, have been determined, facilitating structure-based drug design. M^pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, M^pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV M^pro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M^pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M^pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N_δ (HD) and N_ϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M^pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.     

Quality assessment of localization technique performance in small volume in vivo H MR spectroscopy

A new phantom and evaluation method for experimental evaluation of ¹H-magnetic resonance spectroscopy single volume localization techniques regarding signal contamination (C), defined as the part of the signal originating outside the volume of interest, is presented. The quality assessment method is based on a spherical phantom with an oil/water interface in order to reduce susceptibility effects, and applied for stimulated-echo acquisition method (STEAM) and spin-echo (SE) sequences, echo times of 270, 135, and 10 ms, and cubic volumes of interest (VOI) of 1³, 1.5³, 2³, 2.5³, and 3³ cm³. To be able to mimic measurements of the contamination in three dimensions the physical gradients representing the three orthogonal directions for slice selection were shifted in the pulse sequences. Contamination values in one dimension differed between 6.5% and 8.4% in SE sequences, and between 0.7% and 13.8% in STEAM sequences. In STEAM sequences a decrease of C with increasing VOI size was observed while SE sequences showed comparable C values for the different VOI sizes tested. The total contamination in three dimensions were 19% and 18% in SE and STEAM sequences with a TE of 270 ms, and 7% in a STEAM sequence with a TE of 10 ms, respectively. The presented evaluation method is easily applied to the new phantom and showed high reproducibility.