SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions.

The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also cleaves peptide bonds between host cell proteins and ubiquitin (or ubiquitin-like proteins), which is associated with a violation of immune processes. Nine structures of the most effective inhibitors of the PLpro active center were prioritized according to the parameters of biochemical (IC 50) and cellular tests to assess the suppression of viral replication (EC 50) and cytotoxicity (CC 50). A literature search has shown that PLpro can interact with at least 60 potential protein partners in cells, 23 of which are targets for other viral proteins (human papillomavirus and Epstein-Barr virus). The analysis of protein-protein interactions showed that the proteins USP3, UBE2J1, RCHY1, and FAF2 involved in deubiquitinylation and ubiquitinylation processes contain the largest number of bonds with other proteins; the interaction of viral proteins with them can affect the architecture of the entire network of protein-protein interactions. Using the example of a spatial model of the PLpro/ubiquitin complex and a set of 154 naturally occurring compounds with known antiviral activity, 13 compounds (molecular masses in the range of 454-954 Da) were predicted as potential PLpro inhibitors. These compounds bind to the "hot" amino acid residues of the protease at the positions Gly163, Asp164, Arg166, Glu167, and Tyr264 involved in the interaction with ubiquitin. Thus, pharmacological effects on peripheral PLpro sites, which play important roles in binding protein substrates, may be an additional target-oriented antiviral strategy.

NWChem: Past, present, and future.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

The local phase transitions of the solvent in the neighborhood of a solvophobic polymer at high pressures.

We investigate local phase transitions of the solvent in the neighborhood of a solvophobic polymer chain which is induced by a change of the polymer-solvent repulsion and the solvent pressure in the bulk solution. We describe the polymer in solution by the Edwards model, where the conditional partition function of the polymer chain at a fixed radius of gyration is described by a mean-field theory. The contributions of the polymer-solvent and the solvent-solvent interactions to the total free energy are described within the mean-field approximation. We obtain the total free energy of the solution as a function of the radius of gyration and the average solvent number density within the gyration volume. The resulting system of coupled equations is solved varying the polymer-solvent repulsion strength at high solvent pressure in the bulk. We show that the coil-globule (globule-coil) transition occurs accompanied by a local solvent evaporation (condensation) within the gyration volume.

[Advanced models based on the integral equation theory of molecular liquids for calculating the hydration of ions].

An advanced model based on the integral equation theory of molecular liquids has been developed. The model is a modification of the RISM/HNC method in which the solvent electrostatic potential is approximated by a linear dependence on the solute charge, while the solvent response of the solute is calculated by introducing the empirical repulsive bridge function accounting steric constrains. The hydration energies for a series of atomic and molecular ions have been calculated. The results of the calculations deviate only by a few percent from the experimental data.

Hydration of hydrophobic solutes treated by the fundamental measure approach.

We have developed a method to calculate the hydration of hydrophobic solutes by the fundamental measure theory. This method allows us to carry out calculations of the density profile and the hydration energy for hydrophobic molecules. An additional benefit of the method is the possibility to calculate interaction forces between solvated nanoparticles. Based on the designed method, we calculate hydration of spherical solutes of various sizes from one angstrom up to several nanometers. We have applied methods to evaluate the free energies, the enthalpies, and the entropies of hydrated rare gases and hydrocarbons. The obtained results are in agreement with available experimental data and simulations.

[Estimation of the hydrophobic effect based on the density functional theory].

Using the fundamental measure treatment of the density functional theory, we have developed a method to calculate the solvation of hydrophobic solutes. The method allows one to calculate the density profile and the solvation energy for hydrophobic molecules. An additional benefit of the method is the possibility to calculate interaction forces and the mean force potential between hydrophobic nanoparticles. On the basis of the method, the solvation energies for spherical solutes of different sizes from one angstrom up to several nanometers were calculated.

[A probabilistic method for the calculation of energy of hydrophobic interactions].

A theoretical approach to the quantitative estimation of the energy of hydrophobic interactions on the molecular level has been developed. The model is based on the fundamental relationship between the probability of shaping of a cavity of the excluded volume in liquid water that results from fluctuations of density and free energy of prime hydrophobic solvates, hard spheres. This probability was estimated with the use of the probabilistic method in combination with experimentally observed data on density and radial distribution function of allocation. Free energy of hydrophobic interactions for a complex consisting of several hard spheres was determined. The critical value of the particles included in the complex was estimated.

Wavelet treatment of the intrachain correlation functions of homopolymers in dilute solutions.

Discrete wavelets are applied to the parametrization of the intrachain two-point correlation functions of homopolymers in dilute solutions obtained from Monte Carlo simulations. Several orthogonal and biorthogonal basis sets have been investigated for use in the truncated wavelet approximation. The quality of the approximation has been assessed by calculation of the scaling exponents obtained from the des Cloizeaux ansatz for the correlation functions of homopolymers with different connectivities in a good solvent. The resulting exponents are in better agreement with those from recent renormalization group calculations as compared to the data without the wavelet denoising. We also discuss how the wavelet treatment improves the quality of data for correlation functions from simulations of homopolymers at varied solvent conditions and of heteropolymers.

Wavelet treatment of structure and thermodynamics of simple liquids.

A new algorithm is developed to solve integral equations for simple liquids. The algorithm is based on the discrete wavelet transform of radial distribution functions. The Coifman 2 basis set is employed for the wavelet treatment. To solve integral equations we have applied the combined scheme in which the coarse part of the solution is calculated by wavelets, while the fine part by the direct iterations. Tests on the PY and HNC approximations have indicated that the proposed procedure is more effective than the conventional method based on the hybrid algorithm. Possibilities for application of the method to molecular liquids and mixed quantum-classical systems are discussed.

Wavelet treatment of radial distribution functions of solutes.

Discrete wavelets are applied to parametrize the radial distribution functions of hydrated ions and hydrophobic solutes. The data on radial distribution functions are derived from the integral equation theory and neutron scattering experiment. The Coifman and the discrete Meyer basis sets are used for the wavelet approximation. The quality of the approximation is verified by calculations of the solvation energy, the coordination number, and the change in chemical potential of solutes.

Mean-field treatment of polarons in strong electrolytes.

Using variational estimates for the grand partition function, we have developed a microscopic theory of an excess electron in an ionic liquid at high ion concentrations. We have derived the free-energy functional for the electron and have calculated electron energies for the ground and the first excited states as well as electron-ion correlation functions versus thermodynamic parameters of liquid and parameters of electron-ion potentials. We have found that the energetic characteristics of solvated electron are mainly determined by the Coulomb interaction which gives birth to polaronlike states, while ion cores have a pronounced quantitative effect on these characteristics. The local solvent structure around the excess electron is determined by the mean field induced by ions. Using the method developed we have calculated polaron characteristics in molten salts, such as the maximum of the absorption spectrum and its variations caused by changes in temperature, density, and composition of the electrolyte. The data obtained are in agreement with experiments and computer simulations.

Superexchange coupling and electron transfer in globular proteins via polaron excitations.

The polaron approach is used to treat long-range electron transfersbetween globular proteins. A rate expression for the polaron transfer model is given along with a description of appropriate conditions forits use. Assuming that electrons transfer via a superexchange couplingdue to a polaron excitation, we have estimated the distance dependenceof the rate constant for the self-exchange reactions between globularproteins in solutions. The distance dependence of the polaron coupling andsolvent reorganization energy are provided as a basis forunderstanding and interpreting a long-range electron transfer experiment.The difficulties and problems of the polaron treatment of long-rangeelectron transfers are discussed, and suggestions for new experimentsare made.

Superexchange coupling and electron transfer in globular proteins via polaron excitations.

The polaron approach is used to treat long-range electron transfers between globular proteins. A rate expression for the polaron transfer model is given along with a description of appropriate conditions for its use. Assuming that electrons transfer via a superexchange coupling due to a polaron excitation, we have estimated the distance dependence of the rate constant for the self-exchange reactions between globular proteins in solutions. The distance dependence of the polaron coupling and solvent reorganization energy are provided as a basis for understanding and interpreting a long-range electron transfer experiment. The difficulties and problems of the polaron treatment of long-range electron transfers are discussed, and suggestions for new experiments are made.

[Electron transfer between globular proteins. Evaluation of a matrix element]. / Perenos élektrona mezhdu globuliarnymi belkami. Otsenka matrichnogo élementa.

The dependence of the matrix element of the probability of interprotein electron transfer on the mutual orientation of the donor and acceptor centers and the distance between them was calculated. The calculations were made under the assumption that electron transfer proceeds mainly by a collective excitation of polaron nature, like a solvated electron state. The results obtained are consistent with experimental data and indicate the nonexponential behavior of this dependence in the case when the distance transfer is less than 20 A.

[Electron transfer between globular proteins. Dependence of the rate of transfer on distance]. / Perenos élektrona mezhdu globuliarnymi belkami. Zavisimost' skorosti perenosa ot rasstoianiia.

Based on the assumption that electron transfer between globular proteins occurs by a collective excitation of polaron type, the dependence of the rate of this process on the distance between the donor and acceptor centers with regard to their detailed electron structure was calculated. The electron structure of the heme was calculated by the quantum-chemical MNDO-PM3 method. The results were compared with experimental data on interprotein and intraglobular electron transfer. It is shown that, in the framework of this model, the electron transfer is not exponential and does not require a particular transfer pathway since the whole protein macromolecule is involved in the formation of the electron excited state.

[Long-range electron transfer in globular proteins by polaron excitation]. / Perenos élektrona na bol'shie rasstoianiia v globuliarnykh belkakh posredstvom poliaronnykh vozbuzhdenii.

Considering polaron model, we have calculated an electron state localized in the protein heme. Using these calculations: the electron density and electron energy, we estimated the self-exchange rate constant for cyt c (horse heart), its reorganization energy, matrix element, and dependence of this rate on the distance between hemes. The results are compared with the experimental data and other theoretical estimations. We discuss the role of polaron excitations in the long-range electron transfer in globular proteins.

A polaron model for electron transfer in globular proteins.

Polaron models have been considered for the electron states in protein globules existing in a solvent. These models account for two fundamental effects, viz, polarization interaction of an electron with the conformational vibrations and the heterogeneity of the medium. Equations have been derived to determine the electron state in a protein globule. The parameters of this state show that it is an extended state with an energy of 2 eV. The electron transfer rate for cyt C self-exchange reaction has been calculated in the polaron model. Reorganization energy, tunneling matrix element and the rate constant have also been estimated. The results are compared with experimental data. The influence of model parameters on the significance of the data obtained has been studied. The potentialities of the model are discussed.