Identification of phytocompounds from Houttuynia cordata Thunb. as potential inhibitors for SARS-CoV-2 replication proteins through GC–MS/LC–MS characterization,molecular docking and molecular dynamics simulation

The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a massive viral disease outbreak of international concerns. The present study is mainly intended to identify the bioactive phytocompounds from traditional antiviral herb Houttuynia cordata Thunb. as potential inhibitors for three main replication proteins of SARS-CoV-2, namely Main protease (Mpro), Papain-Like protease (PLpro) and ADP ribose phosphatase (ADRP) which control the replication process. A total of 177 phytocompounds were characterized from H. cordata using GC–MS/LC–MS and they were docked against three SARS-CoV-2 proteins (receptors), namely Mpro, PLpro and ADRP using Epic, LigPrep and Glide module of Schrödinger suite 2020-3. During docking studies, phytocompounds (ligand) 6-Hydroxyondansetron (A104) have demonstrated strong binding affinity toward receptors Mpro (PDB ID 6LU7) and PLpro (PDB ID 7JRN) with G-score of???7.274 and???5.672, respectively, while Quercitrin (A166) also showed strong binding affinity toward ADRP (PDB ID 6W02) with G-score -6.788. Molecular Dynamics Simulation (MDS) performed using Desmond module of Schrödinger suite 2020–3 has demonstrated better stability in the ligand–receptor complexes A104-6LU7 and A166-6W02 within 100 ns than the A104-7JRN complex. The ADME-Tox study performed using SwissADMEserver for pharmacokinetics of the selected phytocompounds 6-Hydroxyondansetron (A104) and Quercitrin (A166) demonstrated that 6-Hydroxyondansetron passes all the required drug discovery rules which can potentially inhibit Mpro and PLpro of SARS-CoV-2 without causing toxicity while Quercitrin demonstrated less drug-like properties but also demonstrated as potential inhibitor for ADRP. Present findings confer opportunities for 6-Hydroxyondansetron and Quercitrin to be developed as new therapeutic drug against COVID-19.

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Persistent Monitoring by Multiple Unmanned Aerial Vehicles Using Bernstein Polynomials

Journal of Optimization Theory and Applications - A framework for monitoring a target modeled as Dubins car using multiple UAVs is proposed. The UAVs are subject to minimum and maximum speed,...     

Modeling of Hysteretic Behavior of Soil–Water Retention Curves Using an Original Pore Network Model

Soil–water retention curve (SRWC), also called soil moisture characteristic, is used for simulation models of soil water storage or soil aggregate stability. The present study addresses the modeling of SRWC with particular attention paid to hysteresis effects of water filling and draining the pores attributed to ink-bottle effects. For that purpose, an idealized pore size distribution previously developed for predicting water sorption isotherms on cementitious materials, and which can consider the double porosity structure of soils, is used. The input data of the model are assessed only from mercury intrusion porosimetry tests (MIP) and from grain size distribution (GSD). The hysteretic behavior of SRWC is reproduced in a satisfactory way. The model can also predict the specific surface area.

     

Optimization of Transducer Location for Novel Non-Intrusive Methodologies of Diagnosis in Diesel Engines

The health monitoring has been studied to ensure integrity of design of engine structure by detection, quantification, and prediction of damages. Early detection of faults may allow the downtime of maintenance to be rescheduled, thus preventing sudden shutdown of machines. In cylinder pressure developed, vibrations and noise emissions data provide a rich source of information about condition of engines. Monitoring of vibrations and noise emissions are novel non-intrusive methodologies for which positioning of various transducers are important issue. The presented work shows applicability of these diagnosis methodologies adopted in case of diesel engines. The effects of changing various fuel injection parameters was analyzed. Scope of using non-intrusive technique has been analyzed by changing locations of microphone. Novelty of this worklies in exploring signal processing methods for various locations around the engine test set up. Various frequency ranges of contributing noise and vibration sources were identified. Time-Frequency analysis showed the onset of various cyclic. Based on the identification of various frequency bands, it is possible to device suitable filters in order to extract more information.     

Alkaline oxygen evolution: exploring synergy between fcc and hcp cobalt nanoparticles entrapped in N-doped graphene

Herein, we report a Mott-Schottky catalyst by entrapping cobalt nanoparticles inside the N-doped graphene shell (Co@NC). The Co@NC delivered excellent oxygen evolution activity with an overpotential of merely 248 mV at a current density of 10 mA cm^–2 with promising long-term stability. The importance of Co encapsulated in NC has further been demonstrated by synthesizing Co nanoparticles without NC shell. The synergy between the hexagonal close-packed (hcp) and face-centered cubic (fcc) Co plays a major role to improve the OER activity, whereas the NC shell optimizes the electronic structure, improves the electron conductivity, and offers a large number of active sites in Co@NC. The density functional theory calculations have revealed that the hcp Co has a dominant role in the surface reaction of electrocatalytic oxygen evolution, whereas the fcc phase induces the built-in electric field at the interfaces with N-doped graphene to accelerate the H⁺ ion transport.     

Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Experimental investigation for stability and surface properties of TiO2 and Al2O3 water-based nanofluids

Journal of Thermal Analysis and Calorimetry - Nanofluids have gained recent attention because of their potential applications in diverse engineering fields like enhancing thermal transport,...     

A short note on the entrainment and exit boundary conditions

An attempt is made to find out the suitable entrainment and exit boundary conditions in laminar flow situations. Streamfunction vorticity formulation of the Navier–Stokes equations are solved by ADI method. Two‐dimensional laminar plane wall jet flow is used to test different forms of the boundary conditions. Results are compared with the experimental and similarity solution and the proper boundary condition is suggested. The Kind 1 boundary condition is recommended. It consists of zero first derivative condition for velocity variable and for streamfunction equation, mixed derivative at the entrainment and exit boundaries. Copyright © 2005 John Wiley & Sons, Ltd.     

Analysis of anharmonic and thermoelastic properties of non-centrosymmetric crystals

In the present paper an analytical potential form is used for overlap repulsive energy, derived by Harrison from quantum mechanical considerations, along with the composite effect of three-body forces and intersublattice displacement. The short-range overlap parameters in Harrison's potential form have direct correlation with the valence state energies for outermost electrons. The potential model is applied to calculate the third and fourth order elastic constants, first and second pressure derivatives of second order elastic constants, Grüneisen parameter and its volume dependence, Anderson parameter, and thermal expansion coefficient for three non-centrosymmetric crystals, viz. CaF₂, SrF₂ and BaF₂. The calculated values of various physical quantities are found to be in good agreement with experimental data.The authors are grateful to Dr. Mansour Khalef, the Head of Physics Department, TNRC, Tajura (Tripoli) for the facilities and encouragements.