SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in evading the hosts innate immune responses. We established a high-throughput X-ray screening to identify inhibitors by elucidating the native PLpro structure refined to 1.42 Angstroms and performing co-crystallization utilizing a diverse library of selected natural compounds. We identified three phenolic compounds as potential inhibitors. Crystal structures of PLpro inhibitor complexes, obtained to resolutions between 1.7-1.9 Angstroms, show that all three compounds bind at the ISG15/Ub-S2 allosteric binding site, preventing the essential ISG15-PLpro molecular interactions. All compounds demonstrate clear inhibition in a deISGylation assay, two exhibit distinct antiviral activity and one inhibited a cytopathic effect in a non-cytotoxic concentration range. These results highlight the druggability of the rarely explored ISG15/Ub-S2 PLpro allosteric binding site to identify new and effective antiviral compounds. Importantly, in the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

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Sequence analysis, structure prediction of receptor proteins and In silico study of potential inhibitors for management of life threatening COVID-19

Letters in Drug Design & Discovery ◽

10.2174/1570180818666210804141613 ◽

2021 ◽

Vol 18 ◽

Author(s):

Hriday K. Basak ◽

Soumen Saha ◽

Joydeep Ghosh ◽

Uttam Paswan ◽

Sujoy Karmakar ◽

...

Keyword(s):

Binding Site ◽

Ursolic Acid ◽

Density Functional ◽

Actinomycin D ◽

3D Structure ◽

Natural Compounds ◽

Surface Glycoprotein ◽

Basis Set ◽

3D Structures ◽

Potential Inhibitors

Background: Treatment of the Covid-19 pandemic caused by the highly contagious and pathogenic SARS-CoV-2 is a global menace. Day by day this pandemic is getting worse. Doctors, Scientists and Researchers across the world are urgently scrambling for a cure for novel corona virus and continuously working at break neck speed to develop vaccine or drugs. But to date, there are no specific drugs or vaccine available in the market to cope up the virus. Objective: The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also to identify best natural compounds as potential inhibitors against COVID-19. Methods: The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool. Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study a small library of natural compounds (fifty compounds) was docked to the ACE2 binding site of the modelled surface glycoprotein of SARS-CoV-2 using Auto Dock Vina to repurpose these inhibitors for SARS-CoV-2. Conceptual density functional theory calculations of best eight compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and drug likeliness of the compounds were analyzed in the swissADME website. Results: In this study we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein and envelope protein obtained from different parts of the globe. We have modelled all the different sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular target which is essential for the development of therapeutics. Different electronic properties of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARS-CoV-2 showed that all the eight inhibitors (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here many folds better compared to hydroxychloroquine which has been found to be effective to treat patients suffering fromCOVID-19 pandemic. All the inhibitors meet most of criteria of drug likeness assessment. Conclusion: We will expect that eight compounds (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors against SARS-CoV-2.

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In silicoidentification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1886174 ◽

2021 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Anshuman Chandra ◽

Meenakshi Chaudhary ◽

Imteyaz Qamar ◽

Nagendra Singh ◽

Vikrant Nain

Keyword(s):

Antiviral Compounds ◽

Potential Inhibitors

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Antiviral Natural Products for Arbovirus Infections

Molecules ◽

10.3390/molecules25122796 ◽

2020 ◽

Vol 25 (12) ◽

pp. 2796 ◽

Cited By ~ 4

Author(s):

Vanessa Shi Li Goh ◽

Chee-Keng Mok ◽

Justin Jang Hann Chu

Keyword(s):

Natural Products ◽

Side Effects ◽

Plant Extracts ◽

Antiviral Drug ◽

Good Tolerability ◽

Antiviral Compounds ◽

Potential Source ◽

Herbal Plants ◽

Antiviral Activities ◽

Arboviral Diseases

Over the course of the last 50 years, the emergence of several arboviruses have resulted in countless outbreaks globally. With a high proportion of infections occurring in tropical and subtropical regions where arthropods tend to be abundant, Asia in particular is a region that is heavily affected by arboviral diseases caused by dengue, Japanese encephalitis, West Nile, Zika, and chikungunya viruses. Major gaps in protection against the most significant emerging arboviruses remains as there are currently no antivirals available, and vaccines are only available for some. A potential source of antiviral compounds could be discovered in natural products—such as vegetables, fruits, flowers, herbal plants, marine organisms and microorganisms—from which various compounds have been documented to exhibit antiviral activities and are expected to have good tolerability and minimal side effects. Polyphenols and plant extracts have been extensively studied for their antiviral properties against arboviruses and have demonstrated promising results. With an abundance of natural products to screen for new antiviral compounds, it is highly optimistic that natural products will continue to play an important role in contributing to antiviral drug development and in reducing the global infection burden of arboviruses.

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Analysis of Ribonucleotide 5′-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01967-16 ◽

2016 ◽

Vol 61 (3) ◽

Cited By ~ 24

Author(s):

Gaofei Lu ◽

Gregory R. Bluemling ◽

Paul Collop ◽

Michael Hager ◽

Damien Kuiper ◽

...

Keyword(s):

Rna Polymerase ◽

Zika Virus ◽

Nonstructural Protein ◽

Rna Dependent Rna Polymerase ◽

Antiviral Compounds ◽

Double Stranded Dna ◽

Virus Rna ◽

Potential Inhibitors

ABSTRACT Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn2+ is required for enzymatic activity, while Mg2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5′-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2′-C-methyl- and 2′-C-ethynyl-substituted analog 5′-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.

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Binding-Site Identification and Genotypic Profiling of Hepatitis C Virus Polymerase Inhibitors

Journal of Virology ◽

10.1128/jvi.01543-06 ◽

2007 ◽

Vol 81 (13) ◽

pp. 6909-6919 ◽

Cited By ~ 53

Author(s):

Frederik Pauwels ◽

Wendy Mostmans ◽

Ludo M. M. Quirynen ◽

Liesbet van der Helm ◽

Carlo W. Boutton ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Binding Site ◽

Antiviral Drug ◽

Variable Binding ◽

Polymerase Inhibitors ◽

Binding Site Identification ◽

Virus Genotypes ◽

Binding Pockets ◽

Virus Mutant

ABSTRACT The search for hepatitis C virus polymerase inhibitors has resulted in the identification of several nonnucleoside binding pockets. The shape and nature of these binding sites differ across and even within diverse hepatitis C virus genotypes. These differences confront antiviral drug discovery with the challenge of finding compounds that are capable of inhibition in variable binding pockets. To address this, we have established a hepatitis C virus mutant and genotypic recombinant polymerase panel as a means of guiding medicinal chemistry through the elucidation of the site of action of novel inhibitors and profiling against genotypes. Using a genotype 1b backbone, we demonstrate that the recombinant P495L, M423T, M414T, and S282T mutant enzymes can be used to identify the binding site of an acyl pyrrolidine analog. We assess the inhibitory activity of this analog and other nonnucleoside inhibitors with our panel of enzyme isolates generated from clinical sera representing genotypes 1a, 1b, 2a, 2b, 3a, 4a, 5a, and 6a.

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Cyclophilin A as a target in the treatment of cytomegalovirus infections

Antiviral Chemistry and Chemotherapy ◽

10.1177/2040206618811413 ◽

2018 ◽

Vol 26 ◽

pp. 204020661881141 ◽

Cited By ~ 1

Author(s):

Ashwaq A Abdullah ◽

Rasedee Abdullah ◽

Zeenathul A Nazariah ◽

Krishnan N Balakrishnan ◽

Faez Firdaus J Abdullah ◽

...

Keyword(s):

Viral Replication ◽

Cyclosporin A ◽

Cell Function ◽

Antiviral Drug ◽

Cyclophilin A ◽

Dual Function ◽

Host Cell Proteins ◽

Early Protein ◽

Cellular Machinery ◽

Cytomegalovirus Infections

Background Viruses are obligate parasites that depend on the cellular machinery of the host to regenerate and manufacture their proteins. Most antiviral drugs on the market today target viral proteins. However, the more recent strategies involve targeting the host cell proteins or pathways that mediate viral replication. This new approach would be effective for most viruses while minimizing drug resistance and toxicity. Methods Cytomegalovirus replication, latency, and immune response are mediated by the intermediate early protein 2, the main protein that determines the effectiveness of drugs in cytomegalovirus inhibition. This review explains how intermediate early protein 2 can modify the action of cyclosporin A, an immunosuppressive, and antiviral drug. It also links all the pathways mediated by cyclosporin A, cytomegalovirus replication, and its encoded proteins. Results Intermediate early protein 2 can influence the cellular cyclophilin A pathway, affecting cyclosporin A as a mediator of viral replication or anti-cytomegalovirus drug. Conclusion Cyclosporin A has a dual function in cytomegalovirus pathogenesis. It has the immunosuppressive effect that establishes virus replication through the inhibition of T-cell function. It also has an anti-cytomegalovirus effect mediated by intermediate early protein 2. Both of these functions involve cyclophilin A pathway.

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The Sp1-Responsive microRNA-15b Negatively Regulates Rhabdovirus-Triggered Innate Immune Responses in Lower Vertebrates by Targeting TBK1

Frontiers in Immunology ◽

10.3389/fimmu.2020.625828 ◽

2021 ◽

Vol 11 ◽

Author(s):

Renjie Chang ◽

Qing Chu ◽

Weiwei Zheng ◽

Lei Zhang ◽

Tianjun Xu

Keyword(s):

Immune Response ◽

Immune Responses ◽

Innate Immune ◽

Infection Model ◽

Regulation Mechanism ◽

Type I ◽

Innate Immune Responses ◽

Positive Role ◽

Siniperca Chuatsi ◽

Antiviral Immune Response

As is known to all, the production of type I interferon (IFN) plays pivotal roles in host innate antiviral immunity, and its moderate production play a positive role in promoting the activation of host innate antiviral immune response. However, the virus will establish a persistent infection model by interfering with the production of IFN, thereby evading the organism inherent antiviral immune response. Therefore, it is of great necessity to research the underlying regulatory mechanisms of type I IFN appropriate production under viral invasion. In this study, we report that a Sp1–responsive miR-15b plays a negative role in siniperca chuatsi rhabdovirus (SCRV)-triggered antiviral response in teleost fish. We found that SCRV could dramatically upregulate miiuy croaker miR-15b expression. Enhanced miR-15b could negatively regulate SCRV-triggered antiviral genes and inflammatory cytokines production by targeting TANK-binding kinase 1 (TBK1), thereby accelerating viral replication. Importantly, we found that miR-15b feedback regulates antiviral innate immune response through NF-κB and IRF3 signaling pathways. These findings highlight that miR-15b plays a crucial role in regulating virus–host interactions, which outlines a new regulation mechanism of fish’s innate immune responses.

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Identification of potential inhibitors for Sterol C-24 reductase of Leishmania donovani through virtual screening of natural compounds

BIOCELL ◽

10.32604/biocell.2021.016682 ◽

2021 ◽

Vol 45 (6) ◽

pp. 1601-1610

Author(s):

FAZLUR RAHMAN ◽

SHAMS TABREZ ◽

RAHAT ALI ◽

SAJJADUL KADIR AKAND ◽

MOHAMMED A. ALAIDAROUS ◽

...

Keyword(s):

Virtual Screening ◽

Leishmania Donovani ◽

Natural Compounds ◽

Potential Inhibitors

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Inhibitory Activity of Quercetin 3-O-Arabinofuranoside and 2-Oxopomolic Acid Derived from Malus domestica on Soluble Epoxide Hydrolase

Molecules ◽

10.3390/molecules25184352 ◽

2020 ◽

Vol 25 (18) ◽

pp. 4352

Author(s):

In Sook Cho ◽

Jang Hoon Kim ◽

Yunjia Lin ◽

Xiang Dong Su ◽

Jong Seong Kang ◽

...

Keyword(s):

Malus Domestica ◽

Epoxide Hydrolase ◽

Soluble Epoxide Hydrolase ◽

Corosolic Acid ◽

Allosteric Sites ◽

Ic50 Values ◽

Cardiovascular Tests ◽

Potential Inhibitors ◽

Molecular Docking And Dynamics

Flavonoids and triterpenoids were revealed to be the potential inhibitors on soluble epoxide hydrolase (sEH). The aim of this study is to reveal sEH inhibitors from Fuji apples. A flavonoid and three triterpenoids derived from the fruit of Malus domestica were identified as quercetin-3-O-arabinoside (1), ursolic acid (2), corosolic acid (3), and 2-oxopomolic acid (4). They had half-maximal inhibitory concentration of the inhibitors (IC50) values of 39.3 ± 3.4, 84.5 ± 9.5, 51.3 ± 4.9, and 11.4 ± 2.7 μM, respectively, on sEH. The inhibitors bound to allosteric sites of enzymes in mixed (1) and noncompetitive modes (2–4). Molecular simulations were carried out for inhibitors 1 and 4 to calculate the binding force of ligands to receptors. The inhibitors bound to the left (1) and right (4) pockets next to the enzyme’s active site. Based on analyses of their molecular docking and dynamics, it was shown that inhibitors 1 and 4 can stably bind sEH at 1 bar and 300 K. Finally, inhibitors 1 and 4 are promising candidates for further studies using cell-based assays and in vivo cardiovascular tests.

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