Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.     

The solute-solvent system: solvent constraints on the conformational dynamics of acetylcholine

The objective of this study was to determine if and how a solvent influences internal motions in a solute molecule. Acetylcholine was chosen as the object of study given its interesting molecular structure and major biological significance. Molecular dynamics simulations were carried out in the vacuum (10 ns), water (5 ns), methanol (5 ns), and octanol (1.5 ns). Seven clusters of conformers were identified, namely, +g+g, -g-g, +gt, -gt, t+g, t-g, and tt, where the gauche and trans labels refer to the dihedral angles tau(2) and tau(3), respectively. As expected, the relative proportion of these conformational clusters was highly solvent-dependent and corresponded to a progressive loss of conformational freedom with increasing molecular weight of the solvent. More importantly, the conformational clusters were used to calculate instantaneous and median angular velocity (omega and omega(M), respectively) and instantaneous and median angular acceleration (alpha and alpha(M), respectively). Angular velocity and angular acceleration were both found to decrease markedly with increasing molecular weight of the solvent, i.e., vacuum (epsilon = 1) > water > methanol > octanol. The decrease from the vacuum to octanol was approximately 40% for tau(2) and approximately 60% for tau(3). Such solvent-dependent constraints on a solute's internal motions may be biologically and pharmacologically relevant.     

On caps with weighted points in PG(t, q)

In this note the study of caps with weighted points inPG(t,q), t?2, is investigated. Some relations between parameters of a(k>,nf)-cap and its characters are found. Monoidal caps are also considered and some examples are given. Finally, the(k,n;f)-caps of type (0,n>) are characterized.     

Characterization of bacterial lipid profiles by using rapid sample preparation and fast comprehensive two‐dimensional gas chromatography in combination with mass spectrometry

The bacteria fatty acid profile has been extensively studied for taxonomic classification purposes, since bacteria, in general, contain particular and rare fatty acids, compared with animal and plant tissues. As for any real‐world sample type, the development of rapid and reliable methods for (i) sample identification (in this case, bacterium type), and (ii) constituent identification (in this instance, the fatty acid profile) is desirable. In this research, a half‐an‐hour procedure, to analyze bacteria, was developed: a 2‐min one‐step sample preparation step was followed by a relatively fast comprehensive 2D GC‐MS separation (25 min). Furthermore, dedicated MS libraries were constructed for the identification of bacteria and fatty acids. Finally, data processing, only qualitative at this stage, was carried out with the support of a novel comprehensive 2D GC software.     

A cryogenic underground observatory for rare events: CUORE, an update

CUORE is a proposed tightly packed array of 1000 TeO₂ bolometers, each being a cube 5 cm on a side with a mass of 750 g. The array consists of 25 vertical towers, arranged in a square of 5 towers by 5 towers, each containing ten layers of four crystals. The design of the detector is optimized for ultralow-background searches for neutrinoless double beta decay of ¹³⁰Te (33.8% abundance), cold dark matter, solar axions, and rare nuclear decays. A preliminary experiment involving 20 crystals of various sizes (MIBETA) has been completed, and a single CUORE tower is being constructed as a smaller scale experiment called CUORICINO. The expected performance and sensitivity, based on Monte Carlo simulations and extrapolations of present results, are reported.     

Measurement of the p to s wave branching ratio of 187Re beta decay from beta environmental fine structure

The mixed occurrence of s-wave and p-wave contributions in a first forbidden unique Gamow-Teller beta decay has been investigated for the first time by measuring the beta environmental fine structure (BEFS) in a 187Re crystalline compound. The experiment has been carried out with an array of eight AgReO4 thermal detectors operating at a temperature of approximately 100 mK. A fit of the observed BEFS spectrum indicates the p-wave electron emission as the dominant channel. The complete understanding of the BEFS distortion of the 187Re beta decay spectrum is crucial for future experiments aiming at the precise calorimetric measurement of the antineutrino mass.     

Evidence for the intermediacy of Wheland-Meisenheimer complexes in SEAr reactions of aminothiazoles with 4,6-dinitrobenzofuroxan

Reactions of DNBF with a series of 2-aminothiazoles (1 a-f) to afford thermodynamically stable C-bonded sigma-adducts have been investigated in acetonitrile. A most significant finding emerged on recording NMR spectra immediately after mixing of equimolar amounts of DNBF and the unsubstituted 2-aminothiazole (1 a) in Me2SO: namely, that the formation of 9 a is preceded by that of a short-lived intermediate species X. From the 1H NMR parameters characterizing this intermediate, as well as the dependence of its lifetime on the experimental conditions-the presence of excess DNBF over 1 a increases the lifetime of X while an excess of base (1 a) accelerates its conversion into 9 a--it is convincingly demonstrated that the structure of X combines the presence of a positively charged Wheland complex moiety (with regard to the thiazole ring) with that of a negatively charged Meisenheimer complex moiety (with regard to the benzofuroxan system). So far, only one intermediate of this type (noted WM) has been successfully characterized, in the reactions of DNBF with 1,3,5-tris(N,N-dialkylamino)benzenes. Among the key features supporting the intermediacy of X along the reaction coordinate leading to 9 a is the fact that the reactions of DNBF with 1 a in the presence of an alcohol (MeOH, EtOH, nPrOH) produce new adducts arising from the addition of an alcohol molecule to the thiazole moiety of WM-1 a. Reflecting the presence of three chiral centres, these species are formed as mixtures of several diastereomers that could all be characterized in their racemic forms in ethanol. These findings generalize the previous report on the formation of Wheland-Meisenheimer carbon-carbon complexes in homocyclic series.     

Multiphonon Raman scattering and gap states in cis-polyacetylene

The different features of the Raman scattering in resonance with electronic absorption band in cis and trans-polyacetylene are discussed. The strong multiphonon scattering observed in cis-polyacetylene is accounted for in terms of a localized gap state, which dominates the scattering process near the absorption edge.     

Organic Stereochemistry. Part 1. Symmetry Elements and Operations,Classification of Stereoisomers

This review initiates a general presentation of the principles of stereochemistry with special reference to medicinal compounds. The format is essentially identical with that of a previous Series of seven reviews on the Metabolism of Drugs and Other Xenobiotics published between October 2006 and October 2009 by B. T. and Stefanie Krämer in Chemistry & Biodiversity. Here, there will be eight reviews published in Helvetica Chimica Acta, to be grouped and published in book form together with some additional material. Part 1 introduces this new series by presenting and illustrating basic concepts on which the edifice of stereochemistry is built. At the most basic level of such foundations, we find symmetry as presented here in terms of its elements, operations, and point groups. This is followed by a classification of isomeric molecular structures, as well as a classification of steric relationships between molecular fragments.     

A molecular modelling approach to rationalize the stereochemical outcome of the Burkholderia cepacia lipase-catalyzed transesterification of aromatic primary alcohols with vinyl esters with different chain lengths in chloroform

The Burkholderia cepacia lipase-catalyzed transesterification of 2-methyl-3-phenyl-1-propanol with vinyl esters proceeds with high enantioselectivity independently of the acyl chain length and the low enantioselectivity of the same reaction with 2-phenyl-1-propanol is not affected by chain length of the vinyl esters. A molecular modelling approach has been developed in order to rationalize the enzymatic results.