Investigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations.

Eventhough the development of vaccine against COVID-19 pandemic is progressing in different part of the world a well-defined treatment plan is not yet developed. Therefore, we investigate the inhibitory activity of a group of dietary bioactive flavonoids against SARS-CoV-2 main protease (Mpro), which are identified as one of the potential targets in the drug discovery process of COVID-19. After the initial virtual screening of a number of bioactive flavonoids, the binding affinity of three compounds - Naringin, Naringenin and Amentoflavone - at the active site of Mpro was investigated through MD Simulations, MM-PBSA and DFT Binding Energy calculations. From the MD trajectory analysis, Amentoflavone and Naringin showed consistent protein-ligand interactions with the aminoacid residues of the active site domains of Mpro. The excellent inhibitory activity of Amentoflavone and Naringin was established from its MM-PBSA binding energy values of -190.50 and -129.87 kJ/mol respectively. The MET165 residue of Mpro is identified as one of the key residue which contributed significantly to MM-PBSA binding energy through hydrophobic interactions. Furthermore, the DFT binding energy values of Amentoflavone (-182.92 kJ/mol) and Naringin (-160.67 kJ/mol) in active site molecular clusters with hydrogen bonds confirmed their potential inhibitory activity. These compounds are of high interest because of their wide availability, low cost, no side effects, and long history of use. We can prevent the severity of this disease for home care patients using these effective dietary supplements. We are hopeful that our results have implications for the development of prophylaxis of COVID-19.Communicated by Ramaswamy H. Sarma.

Structure and dynamics of water inside endohedrally functionalized carbon nanotubes.

We have carried out classical molecular dynamics simulations on the formation of extended water chains inside single-walled carbon nanotubes (SWCNTs) in water in the presence of selected functional groups covalently attached to the inner wall of the tube. Analogues of polar amino acid sidechains have been chosen to carry out the endohedral functionalization of SWCNTs. Our results show a spontaneous and asymmetric filling of the nanotube with dynamical water chains in all the cases studied. The presence of Asp- and Glu-like sidechains is found to result in the formation of well-ordered water chains across the tube having the maximum number of water molecules being retained within the core with the largest residence times. The presence of methyl or methylene groups along the suspended chain is observed to disrupt the formation of water chains with higher length and/or longer residence times. The importance of hydrogen bonding in forming these water chains is assessed in terms of the relaxations of different hydrogen bond correlation functions. For a given dimension of the hydrophobic nanopore, we thus obtain a scale comparing the ability of carboxylic, alcohol, and imidazole groups in controlling the structure and dynamics of water in it. Our results also suggest that SWCNTs of varying lengths, endohedrally functionalized with Asp- and Glu-like sidechains, may be used as design templates in CNT-based water storage devices.

Proton affinities of some amino acid side chains in a restricted environment.

We investigate the dependence of proton affinity values of the side chains of amino acids such as Asp, Glu, His, Ser, and Thr on confinement in a single-walled carbon nanotube. The proton affinity values, estimated using the density functional theories (PW91/dnp and BLYP/dnp), are found to be highly sensitive toward confinement. We find that for both Asp and Glu, the proton affinity, while suspended inside the carbon nanotube, becomes much less in comparison to their respective gas phase values. In the case of His, Ser, and Thr side chains, on the other hand, the proton affinity inside the carbon nanotube becomes negative. Hydrogen bonding with neighboring polar groups is found to result in a marked increase in proton affinity inside the tube in all of the cases reported in this article. The increase is most remarkable in the case of His, Ser, and Thr side chains where the presence of polar neighboring groups within a hydrogen-bonding distance is found to augment the proton affinity value by more than 100 kcal mol(-1).