scholarly journals Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases - PLpro and Mpro in in vitro studies

2020 ◽  
Author(s):  
Mikolaj Zmudzinski ◽  
Wioletta Rut ◽  
Kamila Olech ◽  
Jarosław Granda ◽  
Mirosław Giurg ◽  
...  
Keyword(s):  
Small Molecule ◽  
Antiviral Agents ◽  
Small Molecule Drug ◽  
Main Protease ◽  
Promising Target ◽  
Viral Survival ◽  
Dual Inhibitors ◽  
Viral Polyprotein ◽  
Covalent Inhibitor

AbstractProteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage - a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 23 ebselen derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Our work shows that ebselen constitutes a promising platform for development of new antiviral agents targeting both SARS-CoV-2 PLpro and Mpro.

scholarly journals A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shin-ichiro Hattori ◽  
Nobuyo Higashi-Kuwata ◽  
Hironori Hayashi ◽  
Srinivasa Rao Allu ◽  
Jakka Raghavaiah ◽  
...  
Keyword(s):  
Small Molecule ◽  
Covalent Bond ◽  
Amino Acid Residues ◽  
X Ray ◽  
Viral Breakthrough ◽  
Main Protease ◽  
Small Molecule Compound ◽  
Polar Interactions ◽  
High Concentrations

AbstractExcept remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (Mpro). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC50 values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with Mpro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead Mpro inhibitor for the development of therapeutics for SARS-CoV-2 infection.

scholarly journals Development of a simple and miniaturized sandwich-like fluorescence polarization assay for rapid screening of SARS-CoV-2 main protease inhibitors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gangan Yan ◽  
Dongsheng Li ◽  
Yuan Lin ◽  
Zhenghao Fu ◽  
Haiyan Qi ◽  
...  
Keyword(s):  
Fluorescence Polarization ◽  
High Throughput Screening ◽  
Antiviral Agents ◽  
Competitive Inhibitor ◽  
Rapid Screening ◽  
Screening Assay ◽  
Hydrogen Bond Interactions ◽  
Main Protease ◽  
Fluorescence Polarization Assay

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible and has caused a pandemic named coronavirus disease 2019 (COVID-19), which has quickly spread worldwide. Although several therapeutic agents have been evaluated or approved for the treatment of COVID-19 patients, efficacious antiviral agents are still lacking. An attractive therapeutic target for SARS-CoV-2 is the main protease (Mpro), as this highly conserved enzyme plays a key role in viral polyprotein processing and genomic RNA replication. Therefore, the identification of efficacious antiviral agents against SARS-CoV-2 Mpro using a rapid, miniaturized and economical high-throughput screening (HTS) assay is of the highest importance at the present. Results In this study, we first combined the fluorescence polarization (FP) technique with biotin-avidin system (BAS) to develop a novel and step-by-step sandwich-like FP screening assay to quickly identify SARS-CoV-2 Mpro inhibitors from a natural product library. Using this screening assay, dieckol, a natural phlorotannin component extracted from a Chinese traditional medicine Ecklonia cava, was identified as a novel competitive inhibitor against SARS-CoV-2 Mpro in vitro with an IC50 value of 4.5 ± 0.4 µM. Additionally, dieckol exhibited a high affinity with SARS-CoV-2 Mpro using surface plasmon resonance (SPR) analysis and could bind to the catalytic sites of Mpro through hydrogen-bond interactions in the predicted docking model. Conclusions This innovative sandwich-like FP screening assay enables the rapid discovery of antiviral agents targeting viral proteases, and dieckol will be an excellent lead compound for generating more potent and selective antiviral agents targeting SARS-CoV-2 Mpro.

scholarly journals Structure and inhibition of the SARS-CoV-2 main protease reveals strategy for developing dual inhibitors against Mpro and cathepsin L

2020 ◽  
Author(s):  
Michael Dominic Sacco ◽  
Chunlong Ma ◽  
Panagiotis Lagarias ◽  
Ang Gao ◽  
Julia Alma Townsend ◽  
...  
Keyword(s):  
Viral Entry ◽  
Cathepsin L ◽  
Antiviral Drug ◽  
Binding Mode ◽  
Calpain Inhibitor ◽  
Catalytic Core ◽  
Main Protease ◽  
Dual Inhibitors ◽  
Calpain Inhibitors

AbstractThe main protease (Mpro) of SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, is a key antiviral drug target. While most SARS-CoV-2 Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II/XII, which are also active against human cathepsin L, a host-protease that is important for viral entry. To determine the binding mode of these calpain inhibitors and establish a structure-activity relationship, we solved X-ray crystal structures of Mpro in complex with calpain inhibitors II and XII, and three analogues of GC-376, one of the most potent Mpro inhibitors in vitro. The structure of Mpro with calpain inhibitor II confirmed the S1 pocket of Mpro can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. Interestingly, the structure of calpain inhibitor XII revealed an unexpected, inverted binding pose where the P1’ pyridine inserts in the S1 pocket and the P1 norvaline is positioned in the S1’ pocket. The overall conformation is semi-helical, wrapping around the catalytic core, in contrast to the extended conformation of other peptidomimetic inhibitors. Additionally, the structures of three GC-376 analogues UAWJ246, UAWJ247, and UAWJ248 provide insight to the sidechain preference of the S1’, S2, S3 and S4 pockets, and the superior cell-based activity of the aldehyde warhead compared with the α-ketoamide. Taken together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of Mpro inhibitors as SARS-CoV-2 antivirals.

scholarly journals In silico Repositioning for Dual Inhibitor Discovery of SARS-CoV-2 (COVID-19) 3C-like Protease and Papain-like Peptidase

2020 ◽  
Author(s):  
Kowsar Bagherzadeh ◽  
Kourosh Daneshvarnejad ◽  
Mohammad Abbasinazari ◽  
homa azizian
Keyword(s):  
Active Sites ◽  
Reproduction Number ◽  
Antiviral Agents ◽  
Binding Energies ◽  
Dual Inhibitor ◽  
Main Protease ◽  
Inhibitor Discovery ◽  
Dual Inhibitors ◽  
Dual Inhibition ◽  
Novel Coronavirus

Aims: In late December 2019, early reports predicted the onset of a potential Coronavirus outbreak in china, given the estimate of a reproduction number for the 2019 Novel Coronavirus (COVID-19). Because of high ability of transmission and widespread prevalence, the mortality of COVID-19 infection is growing fast worldwide. Absent of an anti-COVID-19 has put scientists on the urge to repurpose already approved therapeutics or to find new active compounds against coronavirus. Here in this study, a set of computational approaches were performed in order to repurpose antivirals for dual inhibition of the frontier proteases involved in virus replication, papain-like protease (PLpro; corresponding to nsp3) and a main protease (Mpro), 3C‑like protease (3CLpro; corresponding to nsp5). Materials and Methods: In this regard, a rational virtual screening procedure including exhaustive docking techniques was performed for a database of 160 antiviral agents over 3CLpro and PLpro active sites of SARS-CoV-2. The compounds binding energies and interaction modes over 3CLpro and PLpro active sites were analyzed and ranked with the aid of free Gibbs binding energy. The most potent compounds, based on our filtering process, are then proposed as dual inhibitors of SARSC-CoV-2 proteases. Key findings: Accordingly, seven antiviral agents including two FDA approved (Nelfinavir, Valaganciclovir) and five investigational compounds (Merimepodib, Inarigivir, Remdesivir, Taribavirine and TAS106-106) are proposed as potential dual inhibitors of the enzymes necessary for RNA replication in which Remdesivir as well as Inagrivir have the highest binding affinity for both of the active sites. Significance: The mentioned drug proposed to inhibit both PLpro and 3CLpro enzymes with the aim of finding dual inhibitors of SARSC-CoV-2 proteases.

scholarly journals Peptide Derivatives of the Zonulin Inhibitor Larazotide (AT1001) as Potential Anti SARS CoV-2: Molecular Modelling, Synthesis and Bioactivity Evaluation

2021 ◽  
Vol 22 (17) ◽  
pp. 9427
Author(s):  
Simone Di Micco ◽  
Simona Musella ◽  
Marina Sala ◽  
Maria C. Scala ◽  
Graciela Andrei ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Antiviral Agents ◽  
Antiviral Drug ◽  
Drug Repurposing ◽  
Fast Response ◽  
Main Protease ◽  
Promising Target ◽  
Peptide Derivatives ◽  
Novel Coronavirus ◽  
Derivatives Of

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19). The virus enzyme, called 3CLpro or main protease (Mpro), is essential for viral replication, making it a most promising target for antiviral drug development. Recently, we adopted the drug repurposing as appropriate strategy to give fast response to global COVID-19 epidemic, by demonstrating that the zonulin octapeptide inhibitor AT1001 (Larazotide acetate) binds Mpro catalytic domain. Thus, in the present study we tried to investigate the antiviral activity of AT1001, along with five derivatives, by cell-based assays. Our results provide with the identification of AT1001 peptide molecular framework for lead optimization step to develop new generations of antiviral agents of SARS-CoV-2 with an improved biological activity, expanding the chance for success in clinical trials.

scholarly journals Bepridil is potent against SARS-CoV-2 In Vitro

2020 ◽  
Author(s):  
Erol C. Vatansever ◽  
Kai Yang ◽  
Kaci C. Kratch ◽  
Aleksandra Drelich ◽  
Chia-Chuan Cho ◽  
...  
Keyword(s):  
Small Molecule ◽  
A549 Cells ◽  
Live Virus ◽  
Docking Analysis ◽  
Computational Docking ◽  
Main Protease ◽  
Infected Cells ◽  
Endosomal Ph ◽  
Cytopathogenic Effect

ABSTRACTGuided by a computational docking analysis, about 30 FDA/EMA-approved small molecule medicines were characterized on their inhibition of the SARS-CoV-2 main protease (MPro). Of these tested small molecule medicines, six displayed an IC50 value in inhibiting MPro below 100 μM. Three medicines pimozide, ebastine, and bepridil are basic small molecules. Their uses in COVID-19 patients potentiate dual functions by both raising endosomal pH to slow SARS-CoV-2 entry into the human cell host and inhibiting MPro in infected cells. A live virus-based microneutralization assay showed that bepridil inhibited cytopathogenic effect induced by SARS-CoV-2 in Vero E6 cells completely at and dose-dependently below 5 μM and in A549 cells completely at and dose-dependently below 6.25 μM. Therefore, the current study urges serious considerations of using bepridil in COVID-19 clinical tests.

scholarly journals Main protease mutants of SARS-CoV-2 variants remain susceptible to PF-07321332

2021 ◽  
Author(s):  
Sven Ullrich ◽  
Kasuni B Ekanayake ◽  
Gottfried Otting ◽  
Christoph Nitsche
Keyword(s):  
Public Health ◽  
Clinical Relevance ◽  
Drug Targets ◽  
Antiviral Agents ◽  
Spike Protein ◽  
Main Protease ◽  
Public Health Threat ◽  
Vitro Data ◽  
In Vitro Data

The COVID-19 pandemic continues to be a public health threat. Multiple mutations in the spike protein of emerging variants of SARS-CoV-2 appear to impact on the effectiveness of available vaccines. Specific antiviral agents are keenly anticipated but their efficacy may also be compromised in emerging variants. One of the most attractive coronaviral drug targets is the main protease (Mpro). A promising Mpro inhibitor of clinical relevance is the peptidomimetic PF-07321332. We expressed Mpro of five SARS-CoV-2 lineages (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, P.2 Zeta), each of which carries a strongly prevalent missense mutation (G15S, T21I, L89F, K90R, L205V). Enzyme kinetics showed that these Mpro variants are similarly catalytically competent as the wildtype. We show that PF-07321332 has similar potency against the variants as against the wildtype. Our in vitro data suggest that the efficacy of specific Mpro inhibitors such as PF-07321332 is not compromised in current COVID-19 variants.

scholarly journals Development of a NanoBRET assay to validate dual inhibitors of Sirt2-mediated lysine deacetylation and defatty-acylation that block prostate cancer cell migration

2021 ◽  
Author(s):  
Anja Vogelmann ◽  
Matthias Schiedel ◽  
Nathalie Wössner ◽  
Annika Merz ◽  
Daniel Herp ◽  
...  
Keyword(s):  
Cell Migration ◽  
Cancer Cell ◽  
Cancer Cell Migration ◽  
Target Engagement ◽  
Cellular Functions ◽  
Anticancer Effects ◽  
Promising Target ◽  
Cellular Target ◽  
Dual Inhibitors

Sirtuin2 (Sirt2) with its NAD+-dependent deacetylase and defatty-acylase activities plays a central role in the regulation of specific cellular functions. Dysregulation of Sirt2 activity has been associated with the pathogenesis of many diseases, thus making Sirt2 a promising target for pharmaceutical intervention. Herein, we present new high affinity Sirt2 selective Sirtuin-Rearranging Ligands (SirReals) that inhibit both Sirt2-dependent deacetylation and defatty-acylation in vitro and in cells. We show that dual inhibition of Sirt2 results in strongly reduced levels of the oncogene c-Myc and an inhibition of cancer cell migration. Furthermore, we describe the development of a NanoBRET-based assay for Sirt2, thereby providing a method to study cellular target engagement for Sirt2 in a straightforward and accurately quantifiable manner. Applying this assay, we could confirm cellular Sirt2 binding of our new Sirt2 inhibitors and correlate their anticancer effects with their cellular target engagement.

scholarly journals Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro

2020 ◽  
Author(s):  
Hongbo Liu ◽  
Fei Ye ◽  
Qi Sun ◽  
Hao Liang ◽  
Chunmei Li ◽  
...  
Keyword(s):  
Ethanol Extract ◽  
Vero Cells ◽  
Scutellaria Baicalensis ◽  
Scutellariae Radix ◽  
Global Pandemic ◽  
Main Protease ◽  
Antiviral Activities ◽  
Viral Polyprotein ◽  
Effective Drugs

AbstractCOVID-19 has become a global pandemic that threatens millions of people worldwide. There is an urgent call for developing effective drugs against the virus (SARS-CoV-2) causing this disease. The main protease of SARS-CoV-2, 3C-like protease (3CLpro), is highly conserved across coronaviruses and is essential for the maturation process of viral polyprotein. Scutellariae radix (Huangqin in Chinese), the root of Scutellaria baicalensis has been widely used in traditional Chinese medicine to treat viral infection related symptoms. The extracts of S. baicalensis have exhibited broad spectrum antiviral activities. We studied the anti-SARS-CoV-2 activity of S. baicalensis and its ingredient compounds. We found that the ethanol extract of S. baicalensis inhibits SARS-CoV-2 3CLpro activity in vitro and the replication of SARS-CoV-2 in Vero cells with an EC50 of 0.74 μg/ml. Among the major components of S. baicalensis, baicalein strongly inhibits SARS-CoV-2 3CLpro activity with an IC50 of 0.39 μM. We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. Our study demonstrates that the extract of S. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors.

scholarly journals Structure-Based Screening of Novel Lichen Compounds for SARS Coronavirus Main protease (Mpro) and Angiotensin-Converting Enzyme 2 (ACE2) inhibitory potentials as multi-target inhibitors of COVID-19

2020 ◽  
Author(s):  
Tanuja Joshi ◽  
Priyanka Sharma ◽  
Tushar Joshi ◽  
Hemlata Pundir ◽  
Shalini Mathpal ◽  
...  
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Antiviral Agents ◽  
Converting Enzyme ◽  
Suitable Candidate ◽  
Angiotensin Converting Enzyme 2 ◽  
Drug Candidates ◽  
Main Protease ◽  
Toxicity Analysis ◽  
Dual Inhibitors ◽  
Lichen Compounds

Abstract Outbreak of SARS-CoV-2 and massing death caused by it all over world has imposed great concern on scientific community to develop potential drugs to combat with Coronaviruas disease 19 ( COVID-19 ). In this regard, lichen metabolites may offer a vast reservoir for discovery of anti-viral drug candidates. Therefore to find novel compounds against COVID-19, we created a library of 412 lichen compounds and subjected to virtual screening against two molecular targets; SARS-CoV-2 target- Main protease (Mpro) and host cell target- Angiotensin-converting enzyme 2 (ACE2). All the ligands were virtually screened, and 80 compounds were found to have better docking score with both the targets. These compounds were assessed for druglikeness analysis where 27 compounds were found to fit well for redocking studies. The results of redocking by X-Score showed that 7 out of 27 compounds were found to have high affinities with Mpro as well ACE2 which reflect that these compounds can function as dual inhibitors. Molecular docking, druglikeness, X-Score and toxicity analysis resulting seven novel lichen compounds (Orcinyllecanorate, Siphulin, Fremontol, Gyrophoric acid, Rhizocarpic acid, Ovoic acid, and Umbilicaric acid) with Mpro and ACE2 multi-target activities and they can be used as hit compounds to develop potential antiviral agents against SARS-CoV-2. These lichen compounds may be a suitable candidate for further experimental analysis.

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