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.     

Structurally Modelling the 2-His-1-Carboxylate Facial Triad with a Bulky N,N,O Phenolate Ligand

We present the synthesis and coordination chemistry of a bulky, tripodal N,N,O ligand, Im^Ph2NNO ^{t Bu} ( L ), designed to model the 2-His-1-carboxylate facial triad (2H1C) by means of two imidazole groups and an anionic 2,4-di-tert-butyl-subtituted phenolate. Reacting K-L with MCl₂ (M = Fe, Zn) affords the isostructural, tetrahedral non-heme complexes [Fe(L)(Cl)] ( 1 ) and [Zn(L)(Cl)] ( 2 ) in high yield. The tridentate N,N,O ligand coordination observed in their X-ray crystal structures remains intact and well-defined in MeCN and CH₂Cl₂ solution. Reacting 2 with NaSPh affords a tetrahedral zinc thiolate complex, [Zn(L)(SPh)] ( 4 ), that is relevant to isopenicillin N synthase (IPNS) biomimicry. Cyclic voltammetry studies demonstrate the ligand's redox non-innocence, where phenolate oxidation is the first electrochemical response observed in K-L , 2 and 4 . However, the first electrochemical oxidation in 1 is iron-centred, the assignment of which is supported by DFT calculations. Overall, Im^Ph2NNO ^{t Bu} provides access to well-defined mononuclear, monoligated, N,N,O-bound metal complexes, enabling more accurate structural modelling of the 2H1C to be achieved.     

Switch From Pauli-Lowering to LUMO-Lowering Catalysis in Brønsted Acid-Catalyzed Aza-Diels-Alder Reactions

Brønsted acid-catalyzed inverse-electron demand (IED) aza-Diels-Alder reactions between 2-aza-dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn-Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) “Pauli-lowering catalysis” for mono-protonated 2-aza-dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) “LUMO-lowering catalysis” for multi-protonated 2-aza-dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of “Pauli-lowering catalysis” can be overruled by the traditional concept of “LUMO-lowering catalysis” when the degree of LUMO stabilization is extreme as in the case of multi-protonated 2-aza-dienes.     

Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes

The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson–Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev–Bashford–Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson–Boltzmann model. © 2015 Wiley Periodicals, Inc.     

Moisture sorption in polyamide 6.6: Experimental investigation and comparison to four physical-based models

Water sorption in polyamide 6.6 has been characterized for a wide range of temperature (25°C to 80°C) and various water activities using a Dynamic Vapor Sorption testing machine. Complex sorption mechanisms govern the water uptake in the material. The competition between two main temperature dependant mechanisms has been observed: a Henry's sorption mechanism that mainly governs the sorption curve at low water activities, and a second mechanism at high water activities that could be related to the formation of water clusters. It is observed that the temperature dependency can mainly be attributed to the Henry's contribution. Four physically based models are then used and identified thanks to the extended experimental database. It is shown that a simple Flory-Huggins model is not able to capture the experimental observations at very high water activities for all the temperatures tested. The ENSIC model is a better choice, but good prediction for very high water activity cannot be obtained. Both modified Park and GAB models can accurately predict the volume fraction of water for the whole ranges of water activity and temperature, although the modified Park model should be preferred considering the number of parameters and the mathematical simplicity.     

Mechanism of Thyroxine Deiodination by Naphthyl‐Based Iodothyronine Deiodinase Mimics and the Halogen Bonding Role: A DFT Investigation

This paper deals with a systematic density functional theory (DFT) study aiming to unravel the mechanism of the thyroxine (T4) conversion into 3,3′,5‐triiodothyronine (rT3) by using different bio‐inspired naphthyl‐based models, which are able to reproduce the catalytic functions of the type‐3 deiodinase ID‐3. Such naphthalenes, having two selenols, two thiols, and a selenol–thiol pair in peri positions, which were previously synthesized and tested in their deiodinase activity, are able to remove iodine selectively from the inner ring of T4 to produce rT3. Calculations were performed including also an imidazole ring that, mimicking the role of the His residue, plays an essential role deprotonating the selenol/thiol moiety. For all the used complexes, the calculated potential energy surfaces show that the reaction proceeds via an intermediate, characterized by the presence of a X?I?C (X=Se, S) halogen bond, whose transformation into a subsequent intermediate in which the C?I bond is definitively cleaved and the incipient X?I bond is formed represents the rate‐determining step of the whole process. The calculated trend in the barrier heights of the corresponding transition states allows us to rationalize the experimentally observed superior deiodinase activity of the naphthyl‐based compound with two selenol groups. The role of the peri interactions between chalcogen atoms appears to be less prominent in determining the deiodination activity.     

Transition Metal Free Chemoselective Reduction of α,β‐Unsaturated Ketones to Saturated Ketones Using Tosyl Hydrazide as a Hydrogen Donor

An efficient, inexpensive and simple method for the reduction of various α,β‐unsaturated ketones to corresponding saturated ketones using tosyl hydrazide as a hydrogen donor in DMF using calcium oxide powder has been reported. A variety of enones underwent reduction without forming undesirable side products. High chemoselectivity, broad functional group tolerance and good yields are the noteworthy features of this protocol.     

Thermal Conductivity of Soils at Very Low Moisture Content and Moderate Temperatures

An analysis of soil thermal conductivity data shows that, at very low moisture content, this property first varies insignificantly and then begins to increase from a certain critical moisture content, whose value tends to depend on clay mass fraction. Two simple models evaluating the critical moisture content were developed; the first one is a fraction of the permanent wilting point; the second one is a simple linear function dependent on clay mass fraction. An insignificant variation of soil thermal conductivity is observed at 20°C, within a water pressure head ranging from 1×10³ to 1×10³m, while for higher temperatures (45–50°C) from 5000 to 100000m. Three extensions of the enhanced thermal conductivity model by Sundberg, namely SUN-1, SUN-2 and SUN-3, were proposed and tested. They produce an average root mean square error of 27%, 24% and 30%, respectively, with respect to experimental data. SUN-1and SUN-2 predictions could be further improved if better estimates of thermal conductivity at the dry state and the permanent wilting point were provided. SUN-3 is a simple model which does not require information about the PWP and critical moisture content. All SUN models have a potential for implementing the latent heat transfer component.     

The effect of velocity on rigid wheel performance

A simulation model to predict the effect of velocity on rigid-wheel performance for off-road terrain was examined. The soil–wheel simulation model is based on determining the forces acting on a wheel in steady state conditions. The stress distribution at the interface was analyzed from the instantaneous equilibrium between wheel and soil elements. The soil was presented by its reaction to penetration and shear. The simulation model describes the effect of wheel velocity on the soil–wheel interaction performances such as: wheel sinkage, wheel slip, net tractive ratio, gross traction ratio, tractive efficiency and motion resistance ratio. Simulation results from several soil-wheel configurations corroborate that the effect of velocity should be considered. It was found that wheel performance such as net tractive ratio and tractive efficiency, increases with increasing velocity. Both, relative wheel sinkage and relative free rolling wheel force ratio, decrease as velocity increases. The suggested model improves the performance prediction of off-road operating vehicles and can be used for applications such as controlling and improving off-road vehicle performance.