<p></p><p></p><p>A novel coronavirus
(SARS-CoV-2) has caused a major outbreak in human all over the world. There are
several proteins interplay during the entry and replication of this virus in
human. Here, we have used text mining and named entity recognition method to identify
co-occurrence of the important COVID 19 genes/proteins in the interaction
network based on the frequency of the interaction. Network analysis revealed a
set of genes/proteins, highly dense genes/protein clusters and sub-networks of
Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric),
membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein.
The isolated proteins are screened against procyanidin-a flavonoid from plants
using molecular docking. Further, molecular dynamics simulation of critical
proteins such as ACE2, Mpro and spike proteins are performed to elucidate the
inhibition mechanism. The strong network of hydrogen bonds and hydrophobic
interactions along with van der Waals interactions inhibit receptors, which are
essential to the entry and replication of the SARS-CoV-2. The binding energy
which largely arises from van der Waals interactions is calculated (ACE2=-50.21
± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics
Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards
the critical receptors.</p><p></p><p></p>
Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions
