Virtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A.

Single stranded DNA (ssDNA)/RNA aptamers, are screened through the labor intensive, iterative Systematic Evolution of Ligand by Exponential Enrichment process (SELEX) method. Complete sequence of screened aptamers never interacts with target or participates in final structure. Hence, tools can be used to redesign a short length aptamer from previously reported aptamers which can have high affinity and specificity to the target.

Effectivity of repurposed drugs against SARS-CoV-2 infections, A hope for COVID 19: inhibitor modelling studies by docking and molecular dynamics.

In the present study, we have done a comparative study on the efficacy of some currently used repurposed drugs: Oseltamivir (O), Favipiravir (F) and Hydroxychloroquine (H) in individual and in their combinational mode against CoV-2 infections. The ADME analysis has helped us to identify the inhibitory possibility of the tested drugs towards receptor 3CL protein of SARS-CoV-2. Various thermodynamical parameters obtained from Molecular Docking, Molecular dynamics (MD) and MMPBSA simulations like binding affinity, potential energy (E), RMSD, RMSF, SASA energy, interaction energies, Gibbs free energy (ΔG) etc.

Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations.

Abstract: The unavailability of a proper drug against SARS-CoV-2 infections and the emergence of various variants created a global crisis. In the present work, we have studied the antiviral behavior of feverfew plant in treating COVID-19. We have reported a systematic in silico study with the antiviral effects of various phytoconstituents Borneol (CHO), Camphene (CH), Camphor (CHO), Alpha-thujene (CH), Eugenol (CHO), Carvacrol (CHO) and Parthenolide (CHO) of feverfew on the viral protein of SARS-CoV-2.

DFT and MD simulation investigation of favipiravir as an emerging antiviral option against viral protease (3CL) of SARS-CoV-2.

As per date, around 20 million COVID-19 cases reported from across the globe due to a tiny 125 nm sized virus: SARS-CoV-2 which has created a pandemic and left an unforgettable impact on our world. Besides vaccine, medical community is in a race to identify an effective drug, which can fight against this disease effectively. Favipiravir () has recently attracted too much attention as an effective repurposed drug against COVID-19.

Neuroprotective immunity by essential nutrient "Choline" for the prevention of SARS CoV2 infections: An in silico study by molecular dynamics approach.

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.

Computational study of the intermolecular interactions and their effect on the UV-visible spectra of the ternary liquid mixture of benzene, ethanol and propylene glycol.

Quantum chemical calculations are well-equipped to provide answers to the questions regarding the different aspects of intermolecular interactions. We investigate the benzene, ethanol and 1,2 propanediol ternary mixture with theoretical as well as experimental UV-Vis spectroscopy. An extensive theoretical study on the molecular structure and UV-Vis spectral analysis was undertaken using density functional theory (DFT) method.

In silico investigation of phytoconstituents from Indian medicinal herb ' (giloy)' against SARS-CoV-2 (COVID-19) by molecular dynamics approach.

The recent appearance of COVID-19 virus has created a global crisis due to unavailability of any vaccine or drug that can effectively and deterministically work against it. Naturally, different possibilities (including herbal medicines having known therapeutic significance) have been explored by the scientists. The systematic scientific study (beginning with in silico study) of herbal medicines in particular and any drug in general is now possible as the structural components (proteins) of COVID-19 are already characterized.

Perturbation of hydrogen bonding in hydrated pyrrole-2-carboxaldehyde complexes.

The interaction of external water molecules with hydrated pyrrole-2-carboxaldehyde PCL/(HO) complexes was investigated. The work was supported by both theoretical [DFT/TD-DFT methods using 6-311G++(d,p) basis set in the ground (S) and excited (S, S, S)states] and experimental [UV-Vis, FTIR and Raman] verification. The focus of the present work was on the weak intermolecular O-H⋯O, N-H⋯O-H hydrogen bonded interaction (IHB) between PCL and external water molecules, and the influence of increasing the number of water molecules to form hydrated PCL/(HO) complexes.

Effects of hydrogen bonding between pyrrole-2-carboxaldehyde and nearest polar and nonpolar environment.

The present paper represents dominant effects of hydrogen bonding on the existence of different molecular aggregates in one of the heterocyclic pyrrole system: pyrrole-2-carboxaldehyde (PCL). Theoretical and experimental Raman spectral evidence verifies the existence of different molecular aggregates like dimeric, monomeric, hydrated complex states in PCL. Atoms in molecules (AIMs) analysis and fluorescence decay profile provide a strong signature of intermolecular hydrogen bonding (IHB) as the possible reason for the existence of cis form of dimeric (X) molecular aggregates.

Excited state behavior of pyrrole 2-carboxyldehyde: theoretical and experimental study.

Photophysical and photochemical dynamics of excited state proton transfer reaction have been reported for Pyrrole 2-carboxyldehyde (PCL). Experimental and theoretical observations yield all possible signatures of intramolecular and intermolecular proton transfer in an excited state. Dual emission (~325 nm, ~375 nm) on photo excitation indicates the existence of more than one species in an excited state.

White light generation by carbonyl based indole derivatives due to proton transfer: an efficient fluorescence sensor.

The motivation of the present work is to understand the optical, chemical, and electrical aspects of the proton transfer mechanism of indole (I) and some carbonyl based indole derivatives: indole-3-carboxaldehyde (I3C) and indole-7-carboxaldehyde (I7C) for both powder form and their liquid solution. Structural information for indole derivatives (isolated molecule and in solution) is obtained with density functional theory (DFT) and time dependent DFT (TD-DFT) methods. Calculated transition energies are used to generate UV-vis, FTIR, Raman, and NMR spectra which are later verified with the experimental spectra.

Raman and X-ray investigations of ferroelectric phase transition in NH4HSO4.

Temperature-dependent Raman spectroscopy and X-ray diffraction studies have been carried out on NH(4)HSO(4) single crystals in the temperature range 77-298 K. Two structural transitions driven by the molecular ordering and change in crystal symmetries are observed below 263 and 143 K. These phase transitions are marked by the anomalies in the temperature dependence of wavenumber and fwhm of several internal vibrational modes.

Photophysical behaviour of 4-(imidazole-1-yl) phenol and its complexation with beta-cyclodextrin in ground and excited states.

This paper mainly dwells on photophysics of 4-(imidazole-1-yl) phenol (IDP) in different solvents and temperatures from the investigations of absorption, emission and laser flash photolysis and also on the nature of complexation with beta-cyclodextrin (CD) in ground and excited states. IDP makes 1:1 inclusion complex with beta-CD in ground, excited singlet and also in triplet states. The orientation of complex could be ascertained as imidazole moiety stays inside the cavity with phenol moiety stays in the bulk.