In this article we describe a novel Particle Swarm Optimization (PSO) approach to multi-objective optimization (MOO), called Time Variant Multi-Objective Particle Swarm Optimization (TV-MOPSO). TV-MOPSO is made adaptive in nature by allowing its vital parameters (viz., inertia weight and acceleration coefficients) to change with iterations. This adaptiveness helps the algorithm to explore the search space more efficiently. A new diversity parameter has been used to ensure sufficient diversity amongst the solutions of the non-dominated fronts, while retaining at the same time the convergence to the Pareto-optimal front. TV-MOPSO has been compared with some recently developed multi-objective PSO techniques and evolutionary algorithms for 11 function optimization problems, using different performance measures.
We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.
The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a global catastrophe. The virus requires main protease for processing the viral polyproteins PP1A and PP1AB translated from the viral RNA. In search of a quick, safe and successful therapeutic agent; we screened various clinically approved drugs for the in-vitro inhibitory effect on 3CL
Pro
which may be able to halt virus replication. The methods used includes protease activity assay, fluorescence quenching, surface plasmon resonance (SPR), Thermofluor® Assay, Size exclusion chromatography and in-silico docking studies. We found that Teicoplanin as most effective drug with IC
50
~ 1.5 μM. Additionally, through fluorescence quenching Stern–Volmer quenching constant (K
SV
) for Teicoplanin was estimated as 2.5 × 10
5
L·mol
−1
, which suggests a relatively high affinity between Teicoplanin and 3CL
Pro
protease. The SPR shows good interaction between Teicoplanin and 3CL
Pro
with K
D
~ 1.6 μM. Our results provide critical insights into the mechanism of action of Teicoplanin as a potential therapeutic against COVID-19. We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL
Pro
of SARS-CoV-2.
The COVID‐19 disease caused by the SARS‐CoV‐2 has emerged as a worldwide pandemic and caused huge damage to the lives and economy of more than hundred countries. As on May 10, 2020, more than 4,153,300 people stand infected from the virus due to an unprecedented rate of transmission and 282,700 have lost their lives because of the disease. In this context, medicinal plants may provide a way to treat the disease by targeting specific essential proteins of the virus. We screened about 51 medicinal plants and found that Tea (
Camellia sinensis)
and Haritaki (
Terminalia chebula
) has potential against SARS‐COV‐2 3CL
pro
, with an IC
50
for Green Tea as 8.9 ± 0.5 μg/ml and Haritaki 8.8 ± 0.5 μg/ml. The in‐silico studies suggested that Tea component Thearubigins binds to the cysteine 145 of protease active site and could be a pharmacoactive molecule. We predict that the inhibition in protease activity may be able to halt the SARS‐CoV‐2 replication cycle and therefore, we propose Green Tea, Black Tea, and Haritaki plant extracts as potential therapeutic candidates for SARS‐CoV‐2 infection. Further investigation on role of bioactive constituents of extracts is needed to establish the molecular basis of inhibition and towards expedited drug discovery.
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