Identification of natural compounds targeting SARS-CoV-2 Mpro by virtual screening and molecular dynamics simulations

The SARS-CoV-2 main protease (Mpro) has been chosen as a conserved molecular target to develop broad-spectrum antiviral drugs. Using molecular docking and molecular dynamics (MD) simulations, a total of 5600 natural compounds available for virtual screening were tested to identify potential inhibitors of SARS-CoV-2 Mpro. As a result, three natural compounds (pentagalloylglucose, malonylawobanin and gnetin E dihydride) were found to be potential inhibitors of SARS-CoV-2, which confirms the theoretical and practical significance of this approach for the design of SARS-CoV-2 inhibitors.     

Impact of TMPRSS2 Expression,Mutation Prognostics,and Small Molecule (CD,AD, TQ,and TQFL12) Inhibition on Pan-Cancer Tumors and Susceptibility to SARS-CoV-2

As a cellular protease, transmembrane serine protease 2 (TMPRSS2) plays roles in various physiological and pathological processes, including cancer and viral entry, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we conducted expression, mutation, and prognostic analyses for the TMPRSS2 gene in pan-cancers as well as in COVID-19-infected lung tissues. The results indicate that TMPRSS2 expression was highest in prostate cancer. A high expression of TMPRSS2 was significantly associated with a short overall survival in breast invasive carcinoma (BRCA), sarcoma (SARC), and uveal melanoma (UVM), while a low expression of TMPRSS2 was significantly associated with a short overall survival in lung adenocarcinoma (LUAD), demonstrating TMPRSS2 roles in cancer patient susceptibility and severity. Additionally, TMPRSS2 expression in COVID-19-infected lung tissues was significantly reduced compared to healthy lung tissues, indicating that a low TMPRSS2 expression may result in COVID-19 severity and death. Importantly, TMPRSS2 mutation frequency was significantly higher in prostate adenocarcinoma (PRAD), and the mutant TMPRSS2 pan-cancer group was significantly associated with long overall, progression-free, disease-specific, and disease-free survival rates compared to the wild-type (WT) TMPRSS2 pan-cancer group, demonstrating loss of functional roles due to mutation. Cancer cell lines were treated with small molecules, including cordycepin (CD), adenosine (AD), thymoquinone (TQ), and TQFL12, to mediate TMPRSS2 expression. Notably, CD, AD, TQ, and TQFL12 inhibited TMPRSS2 expression in cancer cell lines, including the PC3 prostate cancer cell line, implying a therapeutic role for preventing COVID-19 in cancer patients. Together, these findings are the first to demonstrate that small molecules, such as CD, AD, TQ, and TQFL12, inhibit TMPRSS2 expression, providing novel therapeutic strategies for preventing COVID-19 and cancers.     

Significant Inactivation of SARS-CoV-2 In Vitro by a Green Tea Catechin,a Catechin-Derivative,and Black Tea Galloylated Theaflavins

Potential effects of tea and its constituents on SARS-CoV-2 infection were assessed in vitro. Infectivity of SARS-CoV-2 was decreased to 1/100 to undetectable levels after a treatment with black tea, green tea, roasted green tea, or oolong tea for 1 min. An addition of (−) epigallocatechin gallate (EGCG) significantly inactivated SARS-CoV-2, while the same concentration of theasinensin A (TSA) and galloylated theaflavins including theaflavin 3,3′-di-O-gallate (TFDG) had more remarkable anti-viral activities. EGCG, TSA, and TFDG at 1 mM, 40 µM, and 60 µM, respectively, which are comparable to the concentrations of these compounds in tea beverages, significantly reduced infectivity of the virus, viral RNA replication in cells, and secondary virus production from the cells. EGCG, TSA, and TFDG significantly inhibited interaction between recombinant ACE2 and RBD of S protein. These results suggest potential usefulness of tea in prevention of person-to-person transmission of the novel coronavirus.     

Cytotoxic and insecticidal activities of derivatives of harmine, a natural insecticidal component isolated from Peganum harmala

In a continuing effort to develop novel β-carbolines endowed with better insecticidal activity, a simple high-yielding method for the synthesis of harmine compounds starting from L-tryptophan has been developed and a series of 1,3-substituted β-carboline derivatives have been synthesized and evaluated for their cytotoxicity against insect cultured Sf9 cell line in vitro and insecticidal activities against 4th instar larvae of mosquitos, Culex pipiens quinquefasciatus and mustard aphid, Lipaphis erysimi. The results demonstrated that 1-phenyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (compound 2) and methyl 1-phenyl-β-carboline-3-carboxylate (compound 13) represented the best potential compounds, with Sf9 cells inhibition rates of 71.55% and 60.21% after 24 h treatment at concentrations of 50-200 mg/L, respectively. Both compounds 2 and 13 also showed strong insecticidal activity towards 4th instar larvae of mosquitos with LC(50) values of 20.82 mg/L and 23.98 mg/L, and their LC(90) values were 88.29 mg/L and 295.13 mg/L, respectively. Furthermore, the LC(50) values of compounds 2 and 13 against mustard aphids were 53.16 mg/L and 68.05 mg/L, and their LC(90) values were 240.10 mg/L and 418.63 mg/L after 48 h treatment. The in vitro cytotoxicity of these compounds was consistent with the insecticidal activity in vivo. The results indicated that the 1- and 3-positions of the β-carboline ring deserve further investigation to develop biorational insecticides based on the natural compound harmine as a lead compound.     

Neuropeptides,New Ligands of SARS-CoV-2 Nucleoprotein,a Potential Link between Replication,Inflammation and Neurotransmission

This work identifies new ligands of the nucleoprotein N of SARS-CoV-2 by in silico screening, which used a new model of N, built from an Alphafold model refined by molecular dynamic simulations. The ligands were neuropeptides, such as substance P (1-7) and enkephalin, bound at a large site of the C-terminal or associated with the N-terminal β−sheet. The BA4 and BA5 Omicron variants of N also exhibited a large site as in wt N, and an increased flexibility of the BA5 variant, enabling substance P binding. The binding sites of some ligands deduced from modeling in wt N were assessed by mutation studies in surface plasmon resonance experiments. Dynamic light scattering showed that the ligands impeded RNA binding to N, which likely inhibited replication. We suggest that the physiological role of these neuropeptides in neurotransmission, pain and vasodilation for cholecystokinin and substance P could be altered by binding to N. We speculate that N may link between viral replication and multiple pathways leading to long COVID-19 symptoms. Therefore, N may constitute a “danger hub” that needs to be inhibited, even at high cost for the host. Antivirals targeted to N may therefore reduce the risk of brain fog and stroke, and improve patients’ health.     

Deciphering composition and connectivity of a natural product with the assistance of MS and 2D NMR

A complementary application of three analytical techniques, viz. multidimensional nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), and single‐crystal X‐ray diffractometry was required to identify and refine two natural products isolated from Millettia versicolor and solvent of crystallization. The two compounds, namely 3‐(2H‐1,3‐benzodioxol‐5‐yl)‐6‐methoxy‐8,8‐dimethyl‐4H ,8H‐pyrano[2,3‐h ]chromen‐4‐one, or durmillone, (I), and (2E )‐1‐(4‐{[(2E )‐3,7‐dimethylocta‐2,6‐dien‐1‐yl]oxy}‐2‐hydroxyphenyl)‐3‐(4‐hydroxyphenyl)prop‐2‐en‐1‐one, (II), could not be separated by routine column chromatography and cocrystallized in a 2:1 ratio with 0.13 molecules of ethanol solvent. Compound (II) and ethanol could not be initially identified by single‐crystal X‐ray analysis due to complex disorder in the aliphatic chain region of (II). Mass spectrometry ensured that (II) represented only one species disordered over several positions in the solid state, rather than several species cohabitating on the same crystallographic site. The atomic identification and connectivity in (II) were established by several 2D (two‐dimensional) NMR techniques, which in turn relied on a knowledge of its exact mass. The derived connectivity was then used in the single‐crystal analysis to model the disorder of the aliphatic chain in (II) over three positions and allowed identification of a partially occupied ethanol solvent molecule that was disordered over an inversion center. The disordered moieties were refined with restraints and constraints.     

Separation of CO2 and CH4 by a DDR membrane

The permeation of CO₂ and CH₄ and their binary mixtures through a DDR membrane has been investigated over a wide range of temperatures and pressures. The synthesized DDR membrane exhibits a high permeance and maintains a very high selectivity for CO₂. At a total pressure of 101 kPa, the highest selectivity for CO₂ in a 50∶50 feed mixture was found to be over 4000 at 225 K. This is ascribed to the higher adsorption affinity, as well as to the higher mobility for the smaller CO₂ molecules in the zeolite, preventing the bypassing of the CH₄ through the membrane. An engineering model, based on the generalized Maxwell-Stefan equations, has been used to interpret the transport phenomena in the membrane. The feasibility of DDR membranes as applied to CO₂ removal from natural gas or biogas is anticipated.     

The preparation and analysis of fluoro-polyphosphates by F, P, 2D F-P HETCOR and 2D P-P COSY NMR

A complex mixture of fluoro-polyphosphates (FPPs) and polyphosphates was prepared by heating a mixture of NaF and sodium tripolyphosphate (STPP) at 600 °C in nitrogen atmosphere. Two-dimensional ³¹P-¹⁹F heteronuclear correlation spectroscopy (HETCOR) NMR was developed in identifying the atomic connection between F and P in the mixed FPPs. ¹⁹F, ³¹P and ³¹P-³¹P correlation spectroscopy (COSY) NMR methods were employed to identify the components of the mixture and measure the chain length of each FPP ingredient. NMR results clearly demonstrated that the mixture contains four kinds of fluoro-phosphates with different chain length of polyphosphate, which are monofluoro-phosphate (MFP), monofluoro-dipolyphosphate (MFDPP), monofluoro-tripolyphosphate (MFTPP) and difluoro-tripolyphosphate (DFTPP). Other phosphates and polyphosphates also were found in the mixture.     

2D relayed15N,1H correlated NMR spectroscopy of a pentadecapeptide at natural abundance of15N

Summary Proton-detected H-relayed N,H correlation NMR spectroscopy at natural abundance of¹⁵N has been used to demonstrate the enormous value of heteronuclear NMR spectroscopy for the proton assignment of medium-sized oligopeptides.

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Zweidimensionalerelayed ¹⁵N,¹H-korrelierte NMR-Spektroskopie an einem Pentadecapeptid bei natürlicher Häufigkeit von¹⁵N

Zusammenfassung Anhand¹H-detektierterrelayed-N,H-korrelierter NMR-Spektroskopie bei natürlicher Häufigkeit von¹⁵N wird die große Bedeutung der heteronuklearen Kernresonanzspektroskopie für die Protonenzuordnung mittlerer Oligopeptide demonstriert.

     

Pertraction of methylene blue using a mixture of D2EHPA/M2EHPA and sesame oil as a liquid membrane

An experimental study on the pertraction of methylene blue (MB) through a supported liquid membrane (SLM) using a mixture of mono-(2-etylhexyl) ester of phosphoric acid (M2EHPA) and bis-(2-etylhexyl) ester of phosphoric acid (D2EHPA) and sesame oil as the liquid membrane (LM) was performed. Parameters affecting the pertraction of MB such as initial MB concentration, carrier concentration, feed phase pH, and stripping phase concentration were analyzed. Optimal experimental conditions for MB pertraction (permeability of 5.63 × 10^?6) were obtained after a 7 h separation with the MB concentration in the feed phase of 80 mg L^?1, D2EHPA/M2EHPA concentration in membrane phase of 40 vol. %, feed pH of 6, and acetic acid concentration in the stripping phase of 0.4 mol L^?1. Kinetics of transport and stability of the SLM system were also studied and the mass transfer coefficient for this system was evaluated. Scanning electron microscopy (SEM) was used to morphologically characterize the membrane surface.     

Assessment of a Computational Approach to Predict Drug Resistance Mutations for HIV,HBV and SARS-CoV-2

Viral resistance is a worldwide problem mitigating the effectiveness of antiviral drugs. Mutations in the drug-targeting proteins are the primary mechanism for the emergence of drug resistance. It is essential to identify the drug resistance mutations to elucidate the mechanism of resistance and to suggest promising treatment strategies to counter the drug resistance. However, experimental identification of drug resistance mutations is challenging, laborious and time-consuming. Hence, effective and time-saving computational structure-based approaches for predicting drug resistance mutations are essential and are of high interest in drug discovery research. However, these approaches are dependent on accurate estimation of binding free energies which indirectly correlate to the computational cost. Towards this goal, we developed a computational workflow to predict drug resistance mutations for any viral proteins where the structure is known. This approach can qualitatively predict the change in binding free energies due to mutations through residue scanning and Prime MM-GBSA calculations. To test the approach, we predicted resistance mutations in HIV-RT selected by (-)-FTC and demonstrated accurate identification of the clinical mutations. Furthermore, we predicted resistance mutations in HBV core protein for GLP-26 and in SARS-CoV-2 3CLpro for nirmatrelvir. Mutagenesis experiments were performed on two predicted resistance and three predicted sensitivity mutations in HBV core protein for GLP-26, corroborating the accuracy of the predictions.     

Discovery of Potential SARS-CoV-2M Protease Inhibitors by Virtual Screening,Molecular Dynamics,and Binding Free Energy Analyses

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) gained tremendous attention due to its high infectivity and pathogenicity. The 3-chymotrypsin-like hydrolase protease(Mpro) of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity. To better identify the drugs with potential in treating coronavirus disease 2019(COVID-19) caused by SARS-CoV-2 and according to the crystal structure of Mpro, we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials. As a result, 9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2. Consequently, molecular dynamics(MD) simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro. The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes. Based on the binding free energy calculated by using MM/PBSA, Lopiravir, an inhibitor of human immunodeficiency virus(HIV) protease, is under investigation for the treatment of COVID-19 in combination with ritionavir, and it might inhibit Mpro effectively. Moreover, Ombitasvir, an inhibitor for non-structural protein 5 A of hepatitis C virus(HCV), has good inhibitory potency for Mpro. It is notable that the GS-6620 has a binding free energy, with respect to binding Mpro, comparable to that of ombitasvir. Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19, and that GS-6620 has good anti-SARS-CoV-2 activity.     

Conformation and Interaction of a D,L-alternating peptide with a bilayer membrane: x-ray reflectivity, CD, and FTIR spectroscopy.

Peptides with alternating amino acid configuration provide helical secondary structures that are especially known from the membrane channel and pore-forming gramicidin A. In analogy to this natural D,L-alternating pentadecapeptide, the potential of D,L-alternating peptides for membrane insertion is investigated using the model dodecamer peptide H-(Phe-Tyr)(5)-Trp-Trp-OH. This aromatic peptide is introduced as a novel pore-forming synthetic analogue of gramicidin A. It forms a well-organized homodimer similar to one of the gramicidin A transmembrane motifs. X-ray reflectivity measurements are performed on solid-supported peptide-lipid complexes to obtain information about the influence of the artificial dodecamer peptide on the bilayer parameters. In addition, Fourier-transform infrared (FTIR) and circular dichroism (CD) spectroscopic studies determine the conformational state of H-(Phe-Tyr)(5)-Trp-Trp-OH within the model membrane. Site-specific iodine labeling assists in determining the topology of the membrane-embedded peptide by pinpointing the position of the iodine label within the bilayers.     

Studies on the mechanism of action of prekinamycin, a member of the diazoparaquinone family of natural products: evidence for both sp2 radical and orthoquinonemethide intermediates

The putative reductive activation chemistry of the diazoparaquinone antibiotics was modeled with Bu(3)Sn-H and prekinamycin dimethyl ether along with prekinamycin itself. Reaction in various combinations of aromatic solvents, with and without the nucleophile benzylmercaptan present, led to isolation of both radical-trapping arene adducts and nucleophilic capture benzyl thioether products. On the basis of these product distribution studies, the intermediacies of, first, a cyclopentenyl radical and, next, an orthoquinonemethide electrophile are postulated.     

Separation and preconcentration of cadmium ions in natural water using a liquid membrane system with 2-acetylpyridine benzoylhydrazone as carrier by flame atomic absorption spectrometry

A method for the determination of Cd in natural water by flame atomic absorption spectrometry after separation and preconcentration with a bulk liquid membrane containing 2-acetylpyridine benzoylhydrazone as mobile carrier dissolved in toluene has been developed. Effects of carrier concentration, volume of organic phase and pH of feed and receiving solutions on the flux for Cd across the membrane have been studied, being optimized by the modified simplex method. Optimum values for these variables were: carrier concentration of 0.84 g l⁻¹, 74 ml of toluene, pH 7.8 in the feed solution and 0.06 mol l⁻¹ of HNO₃ in the receiving solution, allowing a preconcentration factor of 17.9. The preconcentration step required 7 h to be accomplished. The recovery of Cd at optimum conditions was 101.0±2.7%, even with saline matrix, with good relative standard deviation (2.5%) at 95% confidence level. The detection limit of blank sample was 6 ng l⁻¹ of Cd. The method was validated using a certified reference material (TMDA-62) and also applied successfully to the analysis of Cd in four samples of seawater collected from the coast of Huelva (Spain). The relative errors of determinations were −7.6% for certified reference material and ranging between +2.4 and +7.1%, for samples of seawater (obtained between the results of the proposed and differential pulse anodic stripping voltammetry methods).     

Fixation of both O2 and CO2 from air by a crystalline palladium complex bearing N-heterocyclic carbene ligands

Crystals of the two-coordinate palladium(0) complex 1 bearing the new N-heterocyclic carbene ligand, ITmt, directly and rapidly fixed both O2 and CO2 from air to produce the corresponding palladium(II) peroxocarbonate complex 2. The present reaction consists of dioxygenation of the palladium(0) complex 1 to the palladium(II) peroxo complex 3 and the subsequent CO2 insertion to produce the peroxocarbonate complex 2. Reaction of the crystals of 1 with air was monitored by microscopic IR spectroscopy to confirm the sequence of the two-step solid-state reaction. The unique reactivity of solid 1 toward air was explained in terms of the structural features of the carbene ligand, ITmt.     

Cardiolipin, a key component to mimic the E. coli bacterial membrane in model systems revealed by dynamic light scattering and steady-state fluorescence anisotropy

The phase transition temperatures of several lipidic systems were determined using two different techniques: dynamic light scattering (DLS) and steady-state fluorescence anisotropy, using two fluorescent probes that report different membrane regions (TMA-DPH and DPH). Atomic force microscopy (AFM) was used as a complementary technique to characterize different lipid model systems under study. The systems were chosen due to the increased interest in bacterial membrane studies due to the problem of antibiotic drug resistance. The simpler models studied comprised of mixtures of POPE and POPG lipids, which form a commonly used model system for Escherichia coli membranes. Given the important role of cardiolipin (CL) in natural membranes, a ternary model system, POPE/POPG/CL, was then considered. The results obtained in these mimetic systems were compared with those obtained for the natural systems E. coli polar and total lipid extract. DLS and fluorescence anisotropy are not commonly used to study lipid phase transitions, but it was shown that they can give useful information about the thermotropic behaviors of model systems for bacterial membranes. These two techniques provided very similar results, validating their use as methods to measure phase transitions in lipid model systems. The temperature transitions obtained from these two very different techniques and the AFM results clearly show that cardiolipin is a fundamental component to mimic bacteria membranes. The results suggest that the less commonly used ternary system is a considerably better mimic for natural E. coli membranes than binary lipid mixture.     

D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency,Geographical Distribution,and Structural Effect

The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.