Computational Approaches to Discover Novel Natural Compounds for SARS-CoV-2 Therapeutics

Scientists all over the world are facing a challenging task of finding effective therapeutics for the coronavirus disease (COVID-19). One of the fastest ways of finding putative drug candidates is the use of computational drug discovery approaches. The purpose of the current study is to retrieve natural compounds that have obeyed to drug-like properties as potential inhibitors. Computational molecular modelling techniques were employed to discover compounds with potential SARS-CoV-2 inhibition properties. Accordingly, the InterBioScreen (IBS) database was obtained and was prepared by minimizing the compounds. To the resultant compounds, the absorption, distribution, metabolism, excretion and toxicity (ADMET) and Lipinski's Rule of Five was applied to yield drug-like compounds. The obtained compounds were subjected to molecular dynamics simulation studies to evaluate their stabilities. In the current article, we have employed the docking based virtual screening method using InterBioScreen (IBS) natural compound database yielding two compounds has potential hits. These compounds have demonstrated higher binding affinity scores than the reference compound together with good pharmacokinetic properties. Additionally, the identified hits have displayed stable interaction results inferred by molecular dynamics simulation results. Taken together, we advocate the use of two natural compounds, STOCK1N-71493 and STOCK1N-45683 as SARS-CoV-2 treatment regime.     

Microwave digestion-ICP-MS for elemental analysis in ambient airborne fine particulate matter: rare earth elements and validation using a filter borne fine particle certified reference material

NIST standard reference material SRM 2783 was employed to validate a high temperature, high pressure, two-stage microwave assisted acid digestion procedure using HNO₃, HF and H₃BO₃ developed for the analysis of trace elements (including rare earths) in atmospheric fine particulate matter (PM_2.5) prior to inductively coupled plasma mass spectrometry (ICP-MS). This method quantitatively solubilized Na, Mg, Al, K, Ti, V, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sb, Cd, Cs, Ba, Pb, Th, U and several rare earth elements (REEs) (La, Ce, Pr, Nd, Gd, Dy, Er, Sm and Eu) from SRM 1648 and SRM 2783. A small amount of HF in the first stage was required to dissolve silicates necessitating the corresponding addition of H₃BO₃ in second stage to dissolve fluoride precipitates of Mg, La, Ce and Th. The optimized microwave dissolution—ICP-MS method detected Na, Mg, Al, K, Ti, V, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Cd, Mo, Sb, Cs, Ba, La, Ce, Pr, Nd, Sm, Gd, Pb, Th and U at trace to ultra-trace levels in ambient airborne fine particles from three sites in North Carolina. La to light lanthanide signature ratios suggested that soil and motor vehicles are the dominant REE sources in SRM 2783 and PM_2.5 samples collected during this study.     

X-ray and thermal studies on uranyl acetates of zinc,magnesium and nickel

Thermal decomposition of metal uranyl acetates is one of the best ways of preparation of uranates in crystalline form at low temperatures. Acetates of the type M(UO₂)₂(OAc)₆·7H₂O (M=Zn(II), Mg(II) and Ni(II) were prepared and characterised. Their X-ray powder diffraction analysis showed that they all belong to the orthorhombic crystal class.The thermal decomposition of acetates in air goes through the reduction of uranium(VI) to uranium(IV) during acetate decomposition followed by reoxidation by oxygen. Zinc uranylacetate gave on thermal decomposition ZnU₃O₁₀, the nickel salt gave NiU₃O₁₀ and the magnesium salt gave a mixture of MgUO₄ and MgU₃O₁₀. The thermal decomposition of acetates in helium led to reduction of uranium(VI) to uranium(IV) with the formation of UO₂. No lower valent uranates could be identified.

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Zusammenfassung Thermische Zersetzung von Metalluranylazetaten ist eine der geeignetsten Methoden zur Darstellung kristalliner Uranate bei niedrigen Temperaturen. Azetate des Types M(UO₂)₂(OAc)₆·7H₂O mitM=Zn(II), Mg(II) und Ni(II) wurden hergestellt und beschrieben. Eine Pulverdiffraktionsanalyse zeigte, daß alle der orthorhombischen Kristallklasse angehören. Der thermische Zerfall der Azetate in Luft vollzieht sich während des Azetatzerfalls über die Reduktion von Uran(VI) zu Uran(IV) bis zu einer anschließenden Reoxydation durch Sauerstoff. Bei der thermischen Zersetzung liefert Zinkuranylazetat ZnU₃O₁₀, das Nickelsalz liefert NiU₃O₁₀ und das Magnesiumsalz ein Gemisch aus MgUO₄ und MgU₃O₁₀. Der thermische Zerfall der Azetate in Helium führt zur Reduktion von Uran(VI) zu Uran(IV) unter Bildung von UO₃. Uranate mit niedrigerer Wertigkeit konnten nicht identifiziert werden.

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. M(UO₂)₂(OAc)₆ · 7H₂O, M = , . , . , . ZnU₃O₁₀, — NiU₃O₁₀, MgUO₄ MgU₃O₁₀. . .

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The authors thank Dr. D. D. Sood, Head, Fuel Chemistry Division, for his encouragement during the course of this work.     

Efficient synthesis of indolizines and new imidazo[1,2-a]pyridines via the expected cyclization of aromatic cycloimmonium ylides with electron deficient alkynes and ethyl cyanoformate

Aromatic cycloimmonium ylides underwent smooth cyclization with electron deficient alkynes in presence of anhydrous K₂CO₃ in DMF solvent at room temperature to afford substituted indolizines. Ylides have also undergone expected cyclization with ethyl cyanoformate to produce imidazo[1,2-a]pyridines. The structures of these newly synthesized compounds have been confirmed by spectroscopic techniques and X-ray diffraction studies.     

Analysis of refractometric fiber optic state-of-charge (SOC) monitoring sensor for lead acid battery

In situ monitoring of the state of charge (SOC) of lead acid battery is important to understand the residual electrical energy. Usage of battery reduces the charge content of the active electrolyte which in turn changes its refractive index. This paper reports refractometric fiber optic sensor developed for on-line monitoring of SOC. The SOC is monitored during discharging phases of the battery using the developed fiber optic sensor probe along with terminal voltage, temperature and depth of discharge using a LABVIEW based data acquisition system. The paper gives the working principle, design and construction details, results and calibration of the fiber optic sensor (FOS) probe. The in situ monitoring capability of the developed FOS is demonstrated in comparison with the contemporary off-line methods of specific gravity and terminal voltage measurements.     

Obtaining functional form for chaotic time series evolution using genetic algorithm

A genetic algorithm (GA) based strategy is presented for deducing an exact or near-exact functional form from a time series. The GA formalism proposed here utilizes (i) the "postfix" representation with a view to reduce the procedural complexities and (ii) the "elitist mating" scheme to produce fitter offspring strings. The GA procedure is exemplified by considering chaotic time series of the well-known logistic, Henon and universal maps. The GA correctly recovers the underlying functional forms for the respective time series. Measurements from a number of finite-dimensional physical, biological, and other systems often give rise to complex time series and the presented methodology should prove useful in obtaining functional forms describing accurately the evolution of the time series. (c) 1999 American Institute of Physics.     

A fluctuation theory for Markov chains

A fluctuation theory for Markov chains on an ordered countable state space is developed, using ladder processes. These are shown to be Markov renewal processes. Results are given for the joint distribution of the extremum (maximum or minimum) and the first time the extremum is achieved. Also a new classification of the states of a Markov chain is suggested. Two examples are given.     

Photoluminescence of SrS: Cu phosphors

Results of the investigation on the spectral characteristics of PL of SrS:Cu phosphors are presented. Probable emitters for the three observed bands, viz. 4710 Å, 5200 Å and 5480 Å, have been suggested.     

Integer programming formulations of vehicle routing problems

Various mathematical formulations are available for situations represented by vehicle routing problems. The assignment-based integer programming formulations of these problems are more common and easy to understand. Such formulations are discussed in this paper and a much simpler formulation for the vechicle routing problem is presented for the case, when all the vehicles have the same load capacity and maximum allowable cost per route.