Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays

SARS-CoV-2 main protease (Mpro) is one of the most extensive exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based Flip-GFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.

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Validation and invalidation of SARS-CoV-2 papain-like protease inhibitors

10.1101/2021.11.04.467342 ◽

2021 ◽

Author(s):

Chunlong Ma ◽

Jun Wang

Keyword(s):

High Throughput Screening ◽

Drug Targets ◽

Immune Modulation ◽

Binding Assay ◽

Antiviral Drug ◽

Cysteine Proteases ◽

Tanshinone Iia ◽

Host Proteins ◽

Main Protease ◽

Thermal Shift

SARS-CoV-2 encodes two viral cysteine proteases, the main protease (Mpro) and the papain-like protease (PLpro), both of which are validated antiviral drug targets. The PLpro is involved in the cleavage of viral polyproteins as well as immune modulation through removing ubiquitin and interferon-stimulated gene product 15 (ISG15) from host proteins. Therefore, targeting PLpro might be a two-pronged approach. Several compounds including YM155, cryptotanshinone, tanshinone I, dihydrotanshinone I, tanshinone IIA, SJB2-043, 6-thioguanine, and 6-mercaptopurine were recently identified as SARS-CoV-2 PLpro inhibitors through high-throughput screening. In this study, we aim to validate/invalidate the reported PLpro inhibitors using a combination of PLpro target specific assays including enzymatic FRET assay, thermal shift binding assay (TSA), and the cell based FlipGFP assay. Collectively, our results showed that all compounds tested either did not show binding or led to denaturation of the PLpro in the TSA binding assay, which might explain their weak enzymatic inhibition in the FRET assay. In addition, none of the compounds showed cellular inhibition of PLpro as revealed by the FlipGFP assay. Therefore, more efforts are needed to search for specific and potent SARS-CoV-2 PLpro inhibitors.

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Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are non-specific promiscuous SARS-CoV-2 main protease inhibitors

10.1101/2020.09.15.299164 ◽

2020 ◽

Author(s):

Chunlong Ma ◽

Yanmei Hu ◽

Julia Alma Townsend ◽

Panagiotis I. Lagarias ◽

Michael Thomas Marty ◽

...

Keyword(s):

Antiviral Activity ◽

Drug Targets ◽

Cysteine Proteases ◽

Native Mass Spectrometry ◽

Main Protease ◽

Enterovirus A71 ◽

Dynamics Simulations ◽

Hit Validation ◽

Viral Polyprotein ◽

Inhibition Potency

AbstractThere is an urgent need for vaccines and antiviral drugs to combat the COVID-19 pandemic. Encouraging progress has been made in developing antivirals targeting SARS-CoV-2, the etiological agent of COVID-19. Among the drug targets being investigated, the viral main protease (Mpro) is one of the most extensively studied drug targets. Mpro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites and it is highly conserved among coronaviruses. In addition, Mpro has a unique substrate preference for glutamine in the P1 position. Taken together, it appears that Mpro inhibitors can achieve both broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compounds have been reported as Mpro inhibitors, with several of which also showed antiviral activity in cell culture. In this study, we investigated the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of Mpro by these six compounds is non-specific and the inhibition is abolished or greatly reduced with the addition of reducing reagent DTT. In the absence of DTT, these six compounds not only inhibit Mpro, but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease, the 2Apro and 3Cpro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 are non-specific SARS-CoV-2 Mpro inhibitors, and urge the scientific community to be stringent with hit validation.

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Discovery of Anti-2019-nCoV Agents from 38 Chinese Patent Drugs toward Respiratory Diseases via Docking Screening

10.20944/preprints202002.0254.v2 ◽

2020 ◽

Cited By ~ 1

Author(s):

Yong-Ming Yan ◽

Xin Shen ◽

Yong-Kai Cao ◽

Jiao-Jiao Zhang ◽

Yan Wang ◽

...

Keyword(s):

Chlorogenic Acid ◽

Drug Targets ◽

Respiratory Diseases ◽

Drug Repurposing ◽

Botanical Knowledge ◽

Main Protease ◽

Common Strategy ◽

Chinese Patent ◽

Novel Coronavirus ◽

Approved Drugs

The 2019 novel coronavirus (2019-nCoV) causes novel coronavirus pneumonia (NCP). Given that approved drug repurposing becomes a common strategy to quickly find antiviral treatments, a collection of FDA-approved drugs can be powerful resources for new anti-NCP indication discoveries. In addition to synthetic compounds, Chinese Patent Drugs (CPD), also play a key role in the treatment of virus related infections diseases in China. Here we compiled major components from 38 CPDs that are commonly used in the respiratory diseases and docked them against two drug targets, ACE2 receptor and viral main protease. According to our docking screening, 10 antiviral components, including hesperidin, saikosaponin A, rutin, corosolic acid, verbascoside, baicalin, glycyrrhizin, mulberroside A, cynaroside, and bilirubin, can directly bind to both host cell target ACE2 receptor and viral target main protease. In combination of the docking results, the natural abundance of the substances, and botanical knowledge, we proposed that artemisinin, rutin, glycyrrhizin, cholic acid, hyodeoxycholic acid, puerarin, oleanic acid, andrographolide, matrine, codeine, morphine, chlorogenic acid, and baicalin (or Yinhuang Injection containing chlorogenic acid and baicalin) might be of value for clinical trials during a 2019-nCov outbreak.

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Discovery of Anti-2019-nCoV Agents from Chinese Patent Drugs via Docking Screening

10.20944/preprints202002.0254.v1 ◽

2020 ◽

Cited By ~ 3

Author(s):

Yong-Ming Yan ◽

Xin Shen ◽

Yong-Kai Cao ◽

Jiao-Jiao Zhang ◽

Yan Wang ◽

...

Keyword(s):

Drug Targets ◽

Drug Repurposing ◽

Main Protease ◽

Common Strategy ◽

Mulberroside A ◽

Chinese Patent ◽

Novel Coronavirus ◽

Approved Drugs ◽

Viral Target ◽

Fda Approved Drugs

The 2019 novel coronavirus (2019-nCoV) causes novel coronavirus pneumonia (NCP). Given that approved drug repurposing becomes a common strategy to quickly find antiviral treatments, a collection of FDA-approved drugs can be powerful resources for new anti-NCP indication discoveries. In addition to synthetic compounds, Chinese Patent Drugs (CPD), also play a key role in the treatment of virus related infections diseases in China. Here we compiled major components from 38 CPDs that are commonly used in the respiratory diseases and docked them against two drug targets, ACE2 receptor and viral main protease. According to our docking screening, 10 antiviral components, including hesperidin, saikosaponin, rutin, baicalin, glycyrrhizin, mulberroside A, puerarin, orientin, amygdalin, and ilexgenin A, can directly bind to both host cell target ACE2 receptor and viral target main protease, indicating their potential for 2019-nCoV treatment.

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In-Silico Drug Repurposing for Targeting SARS-CoV-2 Mpro

10.26434/chemrxiv.12210845 ◽

2020 ◽

Author(s):

Shilpa Sharma ◽

Shashank Deep

Keyword(s):

In Silico ◽

Drug Targets ◽

Md Simulation ◽

Chemical Constituents ◽

Drug Repurposing ◽

Viral Disease ◽

Ayurvedic Drugs ◽

Main Protease ◽

Novel Coronavirus ◽

Potential Inhibitors

COVID-19, caused by novel coronavirus or SARS-CoV-2, is a viral disease which has infected millions worldwide. Considering the urgent need of the drug for fighting against this infectious disease, we performed in-silico drug repurposing. The main protease (Mpro) is one of the best characterized drug targets among coronaviruses, therefore, this was screened for already known drugs, including chemical constituents of Ayurvedic drugs, using docking and MD simulation. The results suggest EGCG, withaferin A and artesunate may act as potential inhibitors of the main protease (Mpro).

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In-Silico Drug Repurposing for Targeting SARS-CoV-2 Mpro

10.26434/chemrxiv.12210845.v1 ◽

2020 ◽

Author(s):

Shilpa Sharma ◽

Shashank Deep

Keyword(s):

In Silico ◽

Drug Targets ◽

Md Simulation ◽

Chemical Constituents ◽

Drug Repurposing ◽

Viral Disease ◽

Ayurvedic Drugs ◽

Main Protease ◽

Novel Coronavirus ◽

Potential Inhibitors

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Drug Repurposing Studies Targeting SARS-nCoV2: An Ensemble Docking Approach on Drug Target 3C-like Protease (3CLpro)

10.26434/chemrxiv.12228831 ◽

2020 ◽

Author(s):

Shruti Koulgi ◽

Vinod Jani ◽

Mallikarjunachari Uppuladinne ◽

Uddhavesh Sonavane ◽

Asheet Kumar Nath ◽

...

Keyword(s):

Drug Repurposing ◽

Drug Binding ◽

Ensemble Docking ◽

Drug Molecules ◽

Drug Binding Site ◽

Main Protease ◽

Docking Approach ◽

Novel Coronavirus ◽

Markov State Modeling ◽

Viral Polyprotein

The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome – novel Coronavirus 2 (SARS-nCoV2). SARS-nCoV2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-03. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-nCoV2. The high-resolution crystal structure of 3CLpro (main protease) of SARS-nCoV2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration (FDA) approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for main protease helped in exploring the conformational variation in the drug binding site of the main protease leading to efficient binding of more relevant drug molecules. The drugs obtained as best hits from the ensemble docking possessed anti-bacterial and anti-viral properties. Small molecules with these properties may prove to be useful to treat symptoms exhibited in COVID-19. This in-silico ensemble docking approach would support identification of potential candidates for repurposing against COVID-19.

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Systematic Design and Evaluation of Drug Repurposing-Oriented Alzheimer’s Disease Ontology (Preprint)

10.2196/preprints.17944 ◽

2020 ◽

Author(s):

Fang Li ◽

Muhammad "Tuan" Amith ◽

Grace Xiong ◽

Jingcheng Du ◽

Yang Xiang ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Drug Targets ◽

Drug Repurposing ◽

Essential Elements ◽

Genomic Research ◽

Core Knowledge ◽

Disease Ontology ◽

Hybrid Strategy ◽

Complementary Strategy

BACKGROUND Alzheimer’s Disease (AD) is a devastating neurodegenerative disease, of which the pathophysiology is insufficiently understood, and the curative drugs are long-awaited to be developed. Computational drug repurposing introduces a promising complementary strategy of drug discovery, which benefits from an accelerated development process and decreased failure rate. However, generating new hypotheses in AD drug repurposing requires multi-dimensional and multi-disciplinary data integration and connection, posing a great challenge in the era of big data. By integrating data with computable semantics, ontologies could infer unknown relationships through automated reasoning and fulfill an essential role in supporting computational drug repurposing. OBJECTIVE The study aimed to systematically design a robust Drug Repurposing-Oriented Alzheimer’s Disease Ontology (DROADO), which could model fundamental elements and their relationships involved in AD drug repurposing and integrate their up-to-date research advance comprehensively. METHODS We devised a core knowledge model of computational AD drug repurposing, based on both pre-genomic and post-genomic research paradigms. The model centered on the possible AD pathophysiology and abstracted the essential elements and their relationships. We adopted a hybrid strategy to populate the ontology (classes and properties), including importing from well-curated databases, extracting from high-quality papers and reusing the existing ontologies. We also leveraged n-ary relations and nanopublication graphs to enrich the object relations, making the knowledge stored in the ontology more powerful in supporting computational processing. The initially built ontology was evaluated by a semiotic-driven and web-based tool Ontokeeper. RESULTS The current version of DROADO was composed of 1,021 classes, 23 object properties and 3,207 axioms, depicting a fundamental network related to computational neuroscience concepts and relationships. Assessment using semiotic evaluation metrics by OntoKeeper indicated sufficient preliminary quality (semantics, usefulness and community-consensus) of the ontology. CONCLUSIONS As an in-depth knowledge base, DROADO would be promising in enabling computational algorithms to realize supervised mining from multi-source data, and ultimately, facilitating the discovery of novel AD drug targets and the realization of AD drug repurposing.

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Rapid Evaluation of Small Molecule Cellular Target Engagement with a Luminescent Thermal Shift Assay

ACS Medicinal Chemistry Letters ◽

10.1021/acsmedchemlett.1c00276 ◽

2021 ◽

Author(s):

Jonathan D. Mortison ◽

Ivan Cornella-Taracido ◽

Gireedhar Venkatchalam ◽

Anthony W. Partridge ◽

Nirodhini Siriwardana ◽

...

Keyword(s):

Small Molecule ◽

Rapid Evaluation ◽

Target Engagement ◽

Thermal Shift Assay ◽

Cellular Target ◽

Thermal Shift

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Genomics-driven drug discovery based on disease-susceptibility genes

Inflammation and Regeneration ◽

10.1186/s41232-021-00158-7 ◽

2021 ◽

Vol 41 (1) ◽

Author(s):

Kyuto Sonehara ◽

Yukinori Okada

Keyword(s):

Drug Discovery ◽

Drug Targets ◽

Disease Susceptibility ◽

Mendelian Randomization ◽

Association Studies ◽

Drug Repurposing ◽

Susceptibility Genes ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Disease Associations

AbstractGenome-wide association studies have identified numerous disease-susceptibility genes. As knowledge of gene–disease associations accumulates, it is becoming increasingly important to translate this knowledge into clinical practice. This challenge involves finding effective drug targets and estimating their potential side effects, which often results in failure of promising clinical trials. Here, we review recent advances and future perspectives in genetics-led drug discovery, with a focus on drug repurposing, Mendelian randomization, and the use of multifaceted omics data.

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