In silico and in vitro assays reveal potential inhibitors against 3CLpro main protease of SARS-CoV-2.

The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not showing any sign of slowing down even after the ongoing efforts of vaccination. The threats of new strains are concerning, as some of them are more infectious than the original one. A therapeutic against the disease is, therefore, of urgent need. Here, we use the DrugBank database to screen for potential inhibitors against the 3CLpro main protease of SARS-CoV-2. Instead of using the traditional approach of computational screening by docking, we developed a kernel ridge regressor (using a part of the docking data) to predict the binding energy of ligands. We used this model to screen the DrugBank database and shortlist two lead candidates (bromocriptine and avoralstat) for in vitro enzymatic study. Our results show that the 3CLpro enzyme activity in presence of 100 µM concentration of bromocriptine and avoralstat is 9.9% and 15.9%, respectively. Remarkably, bromocriptine exhibited submicromolar IC50 of 130 nM (0.13 µM). Avoralstat showed an IC50 of 2.16 µM. Further, the interactions of both drugs with 3CLpro were analyzed using molecular dynamics simulations of 100 ns. Results indicate that both ligands are stable in the binding pocket of the 3CLpro receptor. In addition, the MM-PBSA analysis revealed that bromocriptine (-29.37 kcal/mol) has a lower binding free energy compared to avoralstat (-6.91 kcal/mol). Further, hydrogen bond analysis also showed that bromocriptine interacts with the two catalytic residues, His41 and Cys145, more frequently than avoralstat.Communicated by Ramaswamy H. Sarma.

Reactive Grand-Canonical Monte Carlo Simulations for Modeling Hydration of MgCl2.

Thermochemical heat-storage applications, based on the reversible endo-/exothermic hydration reaction of salts, are intensively investigated to search for compact heat-storage devices. To achieve a truly valuable storage system, progressively complex salts are investigated. For these salts, the equilibrium temperature and pressure conditions are not always easy to predict. However, these conditions are crucial for the design of thermochemical heat-storage systems. A biased grand-canonical Monte Carlo (GCMC) tool is developed, enabling the study of equilibrium conditions at the molecular level. The GCMC algorithm is combined with reactive force field molecular dynamics (ReaxFF), which allows bond formation within the simulation. The Weeks-Chandler-Andersen (WCA) potential is used to scan multiple trial positions for the GCMC algorithm at a small cost. The most promising trial positions can be selected for recomputation with the more expensive ReaxFF. The developed WCA-ReaxFF-GCMC tool was used to study the hydration of MgCl2·nH2O. The simulation results show a good agreement with experimental and thermodynamic equilibriums for multiple hydration levels. The hydration shows that water, present at the surface of crystalline salt, deforms the surface layers and promotes further hydration of these deformed layers. Additionally, the WCA-ReaxFF-GCMC algorithm can be used to study other, non-TCM-related, reactive sorption processes.

Gibbs Ensemble Monte Carlo for Reactive Force Fields to Determine the Vapor-Liquid Equilibrium of CO2 and H2O.

Absorption and reactive properties of fluids in porous media are key to the design and improvement of numerous energy related applications. Molecular simulations of these systems require accurate force fields that capture the involved chemical reactions and have the ability to describe the vapor-liquid equilibrium (VLE). Two new reactive force fields (ReaxFF) for CO2 and H2O are developed, which are capable of not only modeling bond breaking and formation in reactive environments but also predicting their VLEs at saturation conditions. These new force fields include extra terms (ReaxFF-lg) to improve the long-range interactions between the molecules. For validation, we have developed a new Gibbs ensemble Monte Carlo (GEMC-ReaxFF) approach to predict the VLE. Computed VLE data show good agreement with National Institute of Standards and Technology reference data as well as existing nonreactive force fields. This validation proves the applicability of the GEMC-ReaxFF method to test new reactive force fields, and simultaneously it proves the applicability to extend newly developed ReaxFF force fields to other more complex reactive systems.

Water nucleation in helium, methane, and argon: A molecular dynamics study.

Nucleation of highly supersaturated water vapor in helium, methane, and argon carrier gases at 350 K was investigated using molecular dynamics simulations. Nucleation rates obtained from the mean first passage time (MFPT) method are typically one order of magnitude lower than those from the Yasuoka and Matsumoto method, which can be attributed to the overestimation of the critical cluster size in the MFPT method. It was found that faster nucleation will occur in carrier gases that have better thermalization properties such that latent heat is removed more efficiently. These thermalization properties are shown to be strongly dependent on the molecular mass and Lennard-Jones (LJ) parameters. By varying the molecular mass, for unaltered LJ parameters, it was found that a heavier carrier gas removes less heat although it has a higher collision rate with water than a lighter carrier. Thus, it was shown that a clear distinction between water vapor-carrier gas collisions and water cluster-carrier gas collisions is indispensable for understanding the effect of collision rates on thermalization. It was also found that higher concentration of carrier gas leads to higher nucleation rate. The nucleation rates increased by a factor of 1.3 for a doubled concentration and by almost a factor of two for a tripled concentration.

Homogeneous nucleation of water in argon. Nucleation rate computation from molecular simulations of TIP4P and TIP4P/2005 water model.

Molecular dynamics (MD) simulations were conducted to study nucleation of water at 350 K in argon using TIP4P and TIP4P/2005 water models. We found that the stability of any cluster, even if large, strongly depends on the energetic interactions with its vicinity, while the stable clusters change their composition almost entirely during nucleation. Using the threshold method, direct nucleation rates are obtained. Our nucleation rates are found to be 1.08×1027 cm-3 s-1 for TIP4P and 2.30×1027 cm-3 s-1 for TIP4P/2005. The latter model prescribes a faster dynamics than the former, with a nucleation rate two times larger due to its higher electrostatic charges. The non-equilibrium water densities derived from simulations and state-of-art equilibrium parameters from Vega and de Miguel [J. Chem. Phys. 126, 154707 (2007)] are used for the classical nucleation theory (CNT) prediction. The CNT overestimates our results for both water models, where TIP4P/2005 shows largest discrepancy. Our results complement earlier data at high nucleation rates and supersaturations in the Hale plot [Phys. Rev. A 33, 4156 (1986)], and are consistent with MD data on the SPC/E and the TIP4P/2005 model.

Cross-plane heat transfer through single-layer carbon structures.

Graphene-based nano-structures have been recently proposed to function as additives to improve the conductivity of thermally sluggish phase change materials (PCMs). Based on the existing research studies, the improvement is dependent not only on the matrix material, but also on the geometry of the carbon structure. To gain more insight into the nano-scale thermal transport problem, we launched the current pilot research using water as the matrix material, to represent the hydroxyl-group-rich sugar alcohols as PCMs. We have found that the heat conduction across a graphene layer to water is much faster than the heat conduction to the graphene layer itself. Also, the high graphene-water thermal contact resistance fails to acknowledge the fast thermal kinetics of the low frequency phonons. In the investigation of the geometry effect, the cross-plane heat transfer coefficient is found to decrease with decreasing CNT diameter except CNT(9,9).

Molecular simulation of water vapor outgassing from silica nanopores.

The outgassing problem is solved numerically by molecular dynamics. A slit-shaped nanopore consisting of cavity and channel is built with an implicit tabulated wall potential that describes the water-silicon/silica interaction. A flexible three-point water model is used for the simulation. The effects of varying the system temperature, outlet pressure, geometry, and materials of the nanopore on the outgassing rate are investigated. The results show that the temperature plays an important role in the outgassing rate, while the effect of the outlet pressure is negligible as long as it is in the high to medium vacuum range. The geometry of the channel also has an influence on the outgassing rate, but not as much as the surface material. Three different types of silica materials are tested: silicon, silica-cristobalite (hydrophilic material), and silica-quartz (super hydrophilic material). The fastest outgassing rate is found for a silicon nanopore. It is also found that a thin water film is formed on the surface of the silica-quartz nanopore. This material shows hardly any outgassing of water.

Computation of accommodation coefficients and the use of velocity correlation profiles in molecular dynamics simulations.

For understanding the behavior of a gas close to a channel wall it is important to model the gas-wall interactions as detailed as possible. When using molecular dynamics simulations these interactions can be modeled explicitly, but the computations are time consuming. Replacing the explicit wall with a wall model reduces the computational time but the same characteristics should still remain. Elaborate wall models, such as the Maxwell-Yamamoto model or the Cercignani-Lampis model need a phenomenological parameter (the accommodation coefficient) for the description of the gas-wall interaction as an input. Therefore, computing these accommodation coefficients in a reliable way is very important. In this paper, two systems (platinum walls with either argon or xenon gas confined between them) are investigated and are used for comparison of the accommodation coefficients for the wall models and the explicit molecular dynamics simulations. Velocity correlations between incoming and outgoing particles colliding with the wall have been used to compare explicit simulations and wall models even further. Furthermore, based on these velocity correlations, a method to compute the accommodation coefficients is presented, and these newly computed accommodation coefficients are used to show improved correlation behavior for the wall models.

Steady-state properties of single-file systems with conversion.

We have used Monte Carlo methods and analytical techniques to investigate the influence of the characteristic parameters, such as pipe length, diffusion, adsorption, desorption, and reaction rate constants on the steady-state properties of single-file systems with a reaction. We looked at cases when all the sites are reactive and when only some of them are reactive. Comparisons between mean-field predictions and Monte Carlo simulations for the occupancy profiles and reactivity are made. Substantial differences between mean-field and the simulations are found when rates of diffusion are high. Mean-field results only include single-file behavior by changing the diffusion rate constant, but it effectively allows passing of particles. Reactivity converges to a limit value if more reactive sites are added: sites in the middle of the system have little or no effect on the kinetics. Occupancy profiles show approximately exponential behavior from the ends to the middle of the system.