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1.
Viruses ; 13(9)2021 09 14.
Article in English | MEDLINE | ID: covidwho-1411090

ABSTRACT

The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3CLpro using different software and found hypericin bound to 3CLpro through two pockets. These binding pockets were further verified by another docking between hypericin and PEDV 3CLpro pocket mutants, and the fluorescence resonance energy transfer (FRET) assay confirmed that hypericin inhibits the PEDV 3CLpro activity. Moreover, the alignments of α-CoV 3CLpro sequences or crystal structure revealed that the pockets mediating hypericin and PEDV 3CLpro binding were highly conserved, especially in transmissible gastroenteritis virus (TGEV). We then validated the anti-TGEV effect of hypericin through viral replication and egression. Overall, our results push forward that hypericin was for the first time shown to have an inhibitory effect on PEDV and TGEV by targeting 3CLpro, and it deserves further attention as not only a pan-anti-α-CoV compound but potentially also as a compound of other coronaviral infections.


Subject(s)
Alphacoronavirus/drug effects , Alphacoronavirus/physiology , Anthracenes/pharmacology , Antiviral Agents/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus Infections/virology , Perylene/analogs & derivatives , Virus Replication/drug effects , Amino Acid Sequence , Animals , Antiviral Agents/chemistry , Chlorocebus aethiops , Coronavirus 3C Proteases/chemistry , Enzyme Activation/drug effects , Models, Molecular , Perylene/pharmacology , Porcine epidemic diarrhea virus/drug effects , Recombinant Proteins , Structure-Activity Relationship , Swine , Swine Diseases/virology , Vero Cells
3.
J Nat Prod ; 84(2): 436-443, 2021 02 26.
Article in English | MEDLINE | ID: covidwho-1072094

ABSTRACT

A new axial chiral binaphtoquinone, hypocrellone (1), and a new perylenequinone, hypomycin F (2), were isolated from the stromata of Hypocrella bambusae, together with five known compounds, 3-7. The structures of 1 and 2 were assigned by spectroscopic and HRESIMS data analyses. The axial chirality of 1 was determined by electronic circular dichroism data analysis, and the absolute configurations of 2 and 3 were determined by X-ray crystallography. The axial chirality of 7 was determined by UV-induced photooxidation from 4. Compounds 1, 4, and 5 showed inhibitory activity against pseudotyped SARS-CoV-2 infection in 293T-ACE2 cells with IC50 values of 0.17, 0.038, and 0.12 µM. Compounds 4 and 5 were also active against live SARS-CoV-2 infection with EC50 values of 0.22 and 0.21 µM, respectively. Further cell-cell fusion assays, surface plasmon resonance assays, and molecular docking studies revealed that 4 and 5 could bind with the receptor-binding domain of SARS-CoV-2 S protein to prevent its interaction with human angiotensin-converting enzyme II receptor. Our results revealed that 4 and 5 are potential SARS-CoV-2 entry inhibitors.


Subject(s)
Hypocreales/chemistry , Naphthoquinones/pharmacology , Perylene/analogs & derivatives , Quinones/pharmacology , SARS-CoV-2/drug effects , Virus Internalization/drug effects , Naphthoquinones/chemistry , Perylene/chemistry , Perylene/pharmacology , Quinones/chemistry , SARS-CoV-2/physiology
4.
J Mol Graph Model ; 104: 107851, 2021 05.
Article in English | MEDLINE | ID: covidwho-1053559

ABSTRACT

The SARS-CoV-2 virus is causing COVID-19, an ongoing pandemic, with extraordinary global health, social, and political implications. Currently, extensive research and development efforts are aimed at producing a safe and effective vaccine. In the interim, small molecules are being widely investigated for antiviral effects. With respect to viral replication, the papain-like (PLpro) and main proteases (Mpro), are critical for processing viral replicase polypeptides. Further, the PLpro possesses deubiquitinating activity affecting key signalling pathways, including inhibition of interferon and innate immune antagonism. Therefore, inhibition of PLpro activity with small molecules is an important research direction. Our aim was to focus on identification of potential inhibitors of the protease activity of SARS-CoV-2 PLpro. We investigated 300 small compounds derived predominantly from our OliveNet™ library (222 phenolics) and supplemented with synthetic and dietary compounds with reported antiviral activities. An initial docking screen, using the potent and selective noncovalent PLpro inhibitor, GRL-0617 as a control, enabled a selection of 30 compounds for further analyses. From further in silico analyses, including docking to scenes derived from a publicly available molecular dynamics simulation trajectory (100 µs PDB 6WX4; DESRES-ANTON-11441075), we identified lead compounds for further in vitro evaluation using an enzymatic inhibition assay measuring SARS-CoV-2 PLpro protease activity. Our findings indicate that hypericin possessed inhibition activity, and both rutin and cyanidin-3-O-glucoside resulted in a concentration-dependent inhibition of the PLpro, with activity in the micromolar range. Overall, hypericin, rutin, and cyanidin-3-O-glucoside can be considered lead compounds requiring further characterisation for potential antiviral effects in appropriate model systems.


Subject(s)
Anthocyanins/chemistry , Antiviral Agents/chemistry , Coronavirus 3C Proteases/chemistry , Perylene/analogs & derivatives , Rutin/chemistry , Small Molecule Libraries/chemistry , Anthocyanins/pharmacology , Anthracenes , Antiviral Agents/pharmacology , Binding Sites , COVID-19/drug therapy , COVID-19/virology , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/metabolism , Enzyme Assays , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Perylene/chemistry , Perylene/pharmacology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Quantum Theory , Rutin/pharmacology , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/metabolism , Small Molecule Libraries/pharmacology , Thermodynamics
5.
Virus Res ; 286: 198068, 2020 09.
Article in English | MEDLINE | ID: covidwho-603573

ABSTRACT

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a renewed interest in studying the role of the spike S glycoprotein in regulating coronavirus infections in the natural host. Taking advantage of the cryo-electron microscopy structure of SARS-CoV-2 S trimer in the prefusion conformation, we performed a virtual screening simulation with the aim to identify novel molecules that could be used as fusion inhibitors. The spike glycoprotein structure has been completed using modeling techniques and its inner cavity, needful for the postfusion transition of the trimer, has been scanned for the identification of strongly interacting available drugs. Finally, the stability of the protein-drug top complexes has been tested using classical molecular dynamics simulations. The free energy of interaction of the molecules to the spike protein has been evaluated through the MM/GBSA method and per-residue decomposition analysis. Results have been critically discussed considering previous scientific knowledge concerning the selected compounds and sequence alignments have been carried out to evaluate the spike glycoprotein similarity among the betacoronavirus family members. Finally, a cocktail of drugs that may be used as SARS-CoV-2 fusion inhibitors has been suggested.


Subject(s)
Antiviral Agents/chemistry , Betacoronavirus/chemistry , Heterocyclic Compounds, 4 or More Rings/chemistry , Indoles/chemistry , Perylene/analogs & derivatives , Spike Glycoprotein, Coronavirus/chemistry , Sulfonamides/chemistry , Anthracenes , Antiviral Agents/pharmacology , Betacoronavirus/pathogenicity , Binding Sites , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Gene Expression , Heterocyclic Compounds, 4 or More Rings/pharmacology , High-Throughput Screening Assays , Humans , Indoles/pharmacology , Isoindoles , Molecular Docking Simulation , Molecular Dynamics Simulation , Pandemics , Perylene/chemistry , Perylene/pharmacology , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , SARS-CoV-2 , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Sulfonamides/pharmacology , Thermodynamics , User-Computer Interface , Virus Internalization/drug effects
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