Chemical Physics Letters

This paper presents identification of potential inhibitors of SARS-CoV-2 papain-like protease from tropane alkaloids from Schizanthus porrigens, using molecular docking method. Binding affinities were compared with those obtained with Lopinavir as a SARS-CoV-2 papain-like protease inhibitor. Overall, our findings indicate that Schizanthine Z binds to the SARS-CoV-2 papain-like protease with relatively high affinity and favorable ADME properties. Therefore, Schizanthine Z may represent an appropriate compound for further evaluation in antiviral assays...

Prenatal COVID infection is one of the worst affected and least attended aspects of the COVID-19 disease. Like other coronaviruses, CoV2 infection is anticipated to affect fetal development by maternal inflammatory response on the fetus and placenta. Studies showed that higher prenatal choline level in mother's body can safeguard the developing brain of the fetus from the adverse effects of CoV2 infection. Choline is commonly used as food supplement. By virtual screening, molecular docking and molecular dynamics techniques, we have established a strong inhibitory possibility of choline for SARS 3CLpro protease which may provide a lead for prenatal COVID-19 treatment...

In this paper, the electronic properties of a carbon allotrope, graphene with a kagome lattice structure, are investigated. Spin-polarized density functional theory (DFT) calculations with Grimme dispersion corrections were done. Bond lengths, electronic band structure, and projected density of states were calculated. Electronic band structure calculations show kagome flat-band formation with higher d-orbital contributed bonding behavior than the pristine graphene structure. The structural parameters and electronic band results of this 2D carbon allotrope show wider possible usage in many applications from desalination membranes to possible high-temperature superconductors...

The emerging paradigm shift from 'one molecule, one target, for one disease' towards 'multi-targeted small molecules' has paved an ingenious pathway in drug discovery in recent years. We extracted this idea for the investigation of drugs for COVID-19. Perceiving the importance of organosulfur compounds, seventy-six known organosulfur compounds were screened and studied for the interaction with multiple SARS-CoV-2 target proteins by molecular dynamics simulation. Lurasidone and its derivatives displayed substantial binding affinity against five proteins (Mpro, PLpro, Spro, helicase and RdRp)...

Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models...

Chloroquine (CQ) has been reported as an effective drug in the control of COVID-19 infection. Since C60 fullerene has been considered as a drug delivery system, the interaction between pristine fullerene and chloroquine drug and also the interaction between B, Al, Si doped fullerene and chloroquine drug have been investigated based on the density functional theory calculations. The results of this study show that the doped fullerene, especially Al and Si doped fullerene could be the better drug delivery vehicles for chloroquine drug because of their relatively better energetic and electronic properties with chloroquine...

SARS-CoV-2 is the pathogen agent of the new corona virus disease that appeared at the end of 2019 in China. There is, currently, no effective treatment against COVID-19. We report in this study a molecular docking study of ten Aloe vera molecules with the main protease (3CLpro) responsible for the replication of coronaviruses. The outcome of their molecular simulation and ADMET properties reveal three potential inhibitors of the enzyme (ligands 6 , 1 and 8 ) with a clear preference of ligand 6 that has the highest binding energy (-7...

We have applied a computational strategy, using a combination of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease 3CLpro of the SARS-CoV2 Coronavirus. Based on the X-ray structure (PDB code: 6LU7), ligands were generated using a multimodal structure-based design and then docked to the monomer in the active state. Docking calculations show that ligand-binding is strikingly similar in SARS-CoV and SARS-CoV2 main proteases...

Metal-enhanced fluorescence (MEF) is a promising technology with impact in diagnostics, electronics, and sensing. Despite investigation into MEF fundamentals, some properties remain unresearched, notably spectral distortion. To date, publications have described its underpinnings, yet comprehensive analysis is needed, as presented recently for silver films. Herein we expand this description using zinc substrates (ZnNPs). Significant red-edge and blue-edge distortions are reported using Rose Bengal. Radiative decay rate modification is identified as key in amplifying fast/slow electronic transitions by the enhanced emission mechanism...

We report suppression of multiphoton ionization (MPI) of aniline doped large superfluid helium droplets containing over 5 × 106 atoms. In contrast, surface-bound sodium atoms and dimers are readily desorbed and ionized. Adequacy of the experimental conditions is also confirmed from ejection of embedded aniline cations from smaller droplets containing multiple cations, and MPI of gaseous aniline. The photoelectrons have a mean-free-path of less than 1 nm and a thermalization distance of 10 nm. In a droplet with a diameter of over 70 nm, effective charge recombination within the droplet is expected...

The metabolic cofactor and energy carrier NADH (nicotinamide adenine dinucleotide, reduced) has fluorescence yield and lifetime that depends strongly on conformation, a fact that has enabled metabolic monitoring of cells via FLIM (Fluorescence Lifetime Microscopy). Using femtosecond fluorescence upconversion, we show that this molecule in solution participates in ultrafast self-quenching along with both bulk solvent relaxation and spectral relaxation on 1.4 and 26 ps timescales. This, in effect, means up to a third of NADH is effectively "dark" for FLIM in the 400-500 nm observation window commonly employed...

The use of nanometer-sized semiconductor crystals, known as quantum dots, allows us to directly observe individual biomolecular transactions through a fluorescence microscope. Here, we review the evolution of single quantum dot tracking over the past two decades, highlight key biophysical discoveries facilitated by quantum dots, briefly discuss biochemical and optical implementation strategies for a single quantum dot tracking experiment, and report recent accomplishments of our group at the interface of molecular neuroscience and nanoscience...

The fragment of the 1-methylpyrene cation, <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mtext>C</mml:mtext> <mml:mrow> <mml:mn>17</mml:mn> </mml:mrow> </mml:msub> <mml:msubsup> <mml:mtext>H</mml:mtext> <mml:mrow> <mml:mn>11</mml:mn> </mml:mrow> <mml:mo>+</mml:mo> </mml:msubsup> <mml:mo>,</mml:mo> </mml:mrow> </mml:math> is expected to exist in two isomeric forms, 1-pyrenemethylium <mml:math xmlns:mml="https://www...

The Li+ -ligand binding energies are computed for seven ligands and their perfluoro analogs using Density Functional Theory. The bonding is mostly electrostatic in origin. Thus the size of the binding energy tends to correlate with the ligand dipole moment, however, the charge-induced dipole contribution can be sufficiently large to affect the dipolebinding energy correlation. The perfluoro species are significantly less strongly bound than their parents, because the electron withdrawing power of the fluorine reduces the ligand dipole moment...

Several cyanotryptophans have been shown to be useful biological fluorophores. However, how their fluorescence lifetimes vary with solvent has not been examined. In this regard, herein we measure the fluorescence decay kinetics as well as the absorption and emission spectra of six cyanoindoles in different solvents. In particular, we find, among other results, that only 4-cyanoindole affords a long fluorescence lifetime and hence high quantum yield in H2 O. Therefore, our measurements provide not only a guide for choosing which cyanotryptophan to use in practice but also data for computational modeling of the substitution effect on the electronic transitions of indole...

The low-lying singlet and triplet states of MgO have been studied using a SA-CASCF/IC-MRCI approach using the aug-cc-pV5Z basis set. The spectroscopic constants ( r e , w e , and T e ) are in good agreement with the available experimental data. The computed lifetime for the B state is in excellent agreement with two of the three experimental results. The d state lifetime is in good agreement with experiment, while the computed D state lifetime is about twice as long as experiment.

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions...

Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13 C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum...

We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields...

We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition...