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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Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II

ABSTRACT

QM(UB3LYP)/MM(AMBER) calculations were performed for the locations of the transition structure (TS) of the oxygen–oxygen (O–O) bond formation in the S₄ state of the oxygen-evolving complex (OEC) of photosystem II (PSII). The natural orbital (NO) analysis of the broken-symmetry (BS) solutions was also performed to elucidate the nature of the chemical bonds at TS on the basis of several chemical indices defined by the occupation numbers of NO. The computational results revealed a concerted bond switching (CBS) mechanism for the oxygen–oxygen bond formation coupled with the one-electron transfer (OET) for water oxidation in OEC of PSII. The orbital interaction between the σ-HOMO of the Mn(IV)₄–O₍₅₎ bond and the π*-LUMO of the Mn(V)₁=O₍₆₎ bond plays an important role for the concerted O–O bond formation for water oxidation in the CaMn₄O₆ cluster of OEC of PSII. One electron transfer (OET) from the π-HOMO of the Mn(V)₁=O₍₆₎ bond to the σ*-LUMO of the Mn(IV)₄–O₍₅₎ bond occurs for the formation of electron transfer diradical, where the generated anion radical [Mn(IV)₄–O₍₅₎]^-? part is relaxed to the ?Mn(III)₄?…?O₍₅₎^- structure and the cation radical [O₍₆₎=Mn(V)₁]⁺ ? part is relaxed to the ⁺O₍₆₎–Mn(IV)₁? structure because of the charge-spin separation for the electron-and hole-doped Mn–oxo bonds. Therefore, the local spins are responsible for the one-electron reductions of Mn(IV)₄->Mn(III)₄ and Mn(V)₁->Mn(IV)₁. On the other hand, the O₍₅₎^- and O₍₆₎⁺ sites generated undergo the O–O bond formation in the CaMn₄O₆ cluster. The Ca(II) ion in the cubane- skeleton of the CaMn₄O₆ cluster assists the above orbital interactions by the lowering of the orbital energy levels of π*-LUMO of Mn(V)₁=O₍₆₎ and σ*-LUMO of Mn(IV)₄–O₍₅₎, indicating an important role of its Lewis acidity. Present CBS mechanism for the O–O bond formation coupled with one electron reductions of the high-valent Mn ions is different from the conventional radical coupling (RC) and acid-base (AB) mechanisms for water oxidation in artificial and native photosynthesis systems. The proton-coupled electron transfer (PC-OET) mechanism for the O–O bond formation is also touched in relation to the CBS-OET mechanism.     

Stability of O3 + N2, O3 + O2 and O3 + CO2 double hydrates: DFT study

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1,3-dihalo-5,5-dimethylhydantoin/NaNO2 as an efficient heterogeneous system for the N-nitrosation of N,N-dialkylamines under mild conditions

A combination of 1,3-dihalo-5,5-dimethylhydantoin (X = Br, Cl) and sodium nitrite in the presence of wet SiO₂ was used as an effective nitrosating agent for the nitrosation of N,N-dialkyl amines to their corresponding nitroso derivatives under mild and heterogeneous conditions in good to excellent yields.     

Character of the thermal motion of water molecules according to the data on quasielastic incoherent scattering of slow neutrons

The paper discusses the applicability of quasi-crystalline approximation to describing the thermal motion of water molecules in their normal and supercooled states. The problem is subjected to the critical analysis of experimental data on incoherent scattering of slow neutrons based on theories developed by Singwi-Sjolander [1] and Oskotsky [2] modified to duly take into account the limited applicability range of diffusion approximation. The applicability conditions of quasi-crystalline approximation are shown to be consistently satisfied only when water is in supercooled state and within a narrow temperature range above the melting temperature.     

Effect of phonon scattering from neutral and charged impurity centers on the lattice heat conductivity of PbTe:(Tl, Na)

Experimental data on the effect of thallium and sodium impurities on the lattice heat conductivity of PbTe at room temperature are reported. Because the lattice of lead chalcogenides is strongly polarized near charged impurities, the effect of impurities on the lattice heat conductivity depends substantially on their charge state. This property of the material has been used to determine the charge state of the thallium impurity in PbTe. The results obtained argue for a model of quasi-local thallium-impurity states which assumes low electron-correlation energy at an impurity center. Fiz. Tverd. Tela (St. Petersburg) 40, 1206–1208 (July 1998)     

Mössbauer study of Martian regolith analogues

Terrestrial basalt rocks considered to be a good analogues of the Martian regolith were studied by using the Mössbauer spectroscopy and X-ray diffraction. The weathering of basalts was followed by the changes of the Fe²⁺/Fe³⁺ ratio. The basalt rock undergoes alteration from primary mineral composition (olivine+pyroxene+plagioclase) through smectite to kaolinite clay with oxides and hydroxides with the increase of the Fe²⁺/Fe³⁺ ratio.     

Normalization and averaging on compact lie groups in nonlinear mechanics

We consider the method of normal forms, the Bogolyubov averaging method, and the method of asymptotic decomposition proposed by Yu. A. Mitropol’skii and the author of this paper. Under certain assumptions about group-theoretic properties of a system of zero approximation, the results obtained by the method of asymptotic decomposition coincide with the results obtained by the method of normal forms or the Bogolyubov averaging method. We develop a new algorithm of asymptotic decomposition by a part of the variables and its partial case — the algorithm of averaging on a compact Lie group. For the first time, it became possible to consider asymptotic expansions of solutions of differential equations on noncommutative compact groups.     

Temperature and field dependences of photo-induced changes in the magnetization in yttrium iron garnet

The changes in the magnetization of yttrium iron garnet (YIG) when irradiated by a pulsed neodymium laser beam with wavelength λ=1.06 μm are investigated. Measurements are performed in the temperature range from 100 K to 600 K in various external magnetic fields. YIG single crystals grown along the crystallographic (100), (110), and (111) directions are chosen so that the external anisotropy of the indicated processes can be determined. Characteristic temperature intervals dominated by different mechanisms of variation of the magnetization under the influence of a laser pulse are discussed. Fiz. Tverd. Tela (St. Petersburg) 39, 1263–1266 (July 1997)     

Temperature and frequency dependence of the spin-lattice relaxation times of E′1 centers in neutron-irradiated quartz glass

Results are reported for measurements of the spin-lattice relaxation times of E′₁ centers in quartz glass, produced by neutron irradiation, with the measurements made at two frequencies 9.25 and 24.0 GHz over a wide temperature interval 1.5–300 K. The experimental data are interpreted on the basis of interaction mechanisms of the spins with two-level systems with excitation energies ∼6, ∼26, and ∼420 cm⁻¹. A small modification of the existing theory allows us to explain a number of features of the observed temperature and frequency dependence of the relaxation rate. The results are compared with the data available in the literature on spin-lattice relaxation of irradiation centers in crystalline quartz and quartz glass. Fiz. Tverd. Tela (St. Petersburg) 39, 1335–1337 (August 1997)