ProTox-II: a webserver for the prediction of toxicity of chemicals

Banerjee, Priyanka; Eckert, Andreas; Schrey, Anna K.; Preißner, Robert

doi:10.1093/nar/gky318

Cited by 1,925 publications

(1,166 citation statements)

References 38 publications

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“…Based on their calculated free energy of interaction, we have selected, and listed in Table 3, eight of the best candidates for further experimental investigations. [11] It is interesting to note that the eight best ligand candidates reported in Table 3 are all binding pocket #1. Fig 3 reports the sterical features of the interaction between ergoloid and pocket #1.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization

Bongini

Trezza

Bianchini

et al. 2020

Biochemical and Biophysical Research Communications

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The recent release of COVID-19 spike glycoprotein allows detailed analysis of the structural features that are required for stabilizing the infective form of its quaternary assembly. Trying to disassemble the trimeric structure of COVID-19 spike glycoprotein, we analyzed single protomer surfaces searching for concave moieties that are located at the three protomer-protomer interfaces. The presence of some druggable pockets at these interfaces suggested that some of the available drugs in Drug Bank could destabilize the quaternary spike glycoprotein formation by binding to these pockets, therefore interfering with COVID-19 life cycle. The approach we propose here can be an additional strategy to fight against the deadly virus. Ligands of COVID-19 spike glycoprotein that we have predicted in the present computational investigation, might be the basis for new experimental studies in vitro and in vivo.

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Section: Resultsmentioning

confidence: 99%

“…Autodock VinaXB [9] was used to calculate free energy of interaction between COVID-19 S glycoprotein at pocket #1 and #6 with ligands contained in the DrugBank database v.5.1.5 [10]. Ligad toxicity has been analyzed according to ProTox II [11]. Open source PyMOL v. 1.7.1.0 has been used for structural data analysis and presentation.…”

Section: Methodsmentioning

confidence: 99%

A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization

Bongini

Trezza

Bianchini

et al. 2020

Biochemical and Biophysical Research Communications

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“…In silico method of drug screening using PROTOX II, showed that Solanidine is cytotoxic and immunotoxic. Prototox II is a cost and time conservative approach of testing and determining the toxicity of a compound to be considered a drug of choice(13). It incorporates molecular similarity, pharmacophores, fragment propensities and machine-learning models for the prediction of various toxicity endpoints; such as acute toxicity, hepatotoxicity, cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity, adverse outcomes pathways (Tox21) and toxicity targets(13)…”

Section: Discussionmentioning

confidence: 99%

Molecular Docking Analysis Of Some Phytochemicals On Two SARS-CoV-2 Targets: Potential Lead Compounds Against Two Target Sites of SARS-CoV-2 Obtained from Plants

Ubani

Agwom

RuthMorenikeji

et al. 2020

Preprint

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COV spike (S) glycoprotein and Mpro are two key targets that have been identified for vaccines and drug development against the COVID-19 disease. Virtual screening of some compounds of plants origin that have shown antiviral activities were carried out on the two targets, 6lu7 and 6vsb by docking with the PyRx software. The binding affinities were compared with other compounds and drugs already identified as potential ligands for 6lu7 and 6vsb as well as Chloroquine and hydroxychloroquine. The docked compounds with best binding affinities were also filtered for drug likeness using the SwissADME and PROTOX platforms on the basis of Physicochemical properties and toxicity respectively. The docking results revealed that scopodulcic acid and dammarenolic acid had the best binding affinity on the s-glycoprotein and Mpro protein targets respectively. Silybinin also demonstrated a good binding affinity to both protein targets making it a potential candidate for further evaluation as repurposed candidate for SARS COV2 with likelihood of having a multitarget activity.

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“…This server gives protein structural model on the basis of protein flexibility, contact map and all residue fluctuation between the residues. Toxicity analysis: Toxicity analysis of selected natural compounds was done by the ProTox-II web server [21]. ProTox-II is a kind of virtual lab which integrates several parameters like molecular similarity, fragment propensities and most frequent features.…”

Section: Molecular Dynamics (Md) Simulation: Structural Conformationsmentioning

confidence: 99%

Natural compounds as potential inhibitors of novel coronavirus (COVID-19) main protease: An in silico study

Mishra¹,

Pathak²,

Choudhir³

et al. 2020

Preprint

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COVID-19 pandemic, a novel coronavirus disease is caused by severe acute respiratory syndrome corona virus, SARS-CoV-2. It was first reported in Wuhan, China and has now expanded to more than 190 countries across the world. Till date, there is no specific medication available to prevent or target SARS CoV-2 infection. Very recently, the crystal structure of COVID-19 main protease (M pro ) was revealed by Liu et al. (2020). SARS-CoV-2 main protease (M pro ) is a key enzyme that plays a crucial role in viral replication and transcription. Thus, M pro could be a promising target to inhibit SARS-CoV-2 infection. Natural compounds due to their structural diversity and safety are considered as an excellent source of antiviral drugs. In this study, we selected Herbacetin, Rhoifolin, Pectolinarin, Apigenin, Luteolin, Amentoflavone, Daidzein, Puerarin, Epigallocatechin, Gallocatechin gallate, Resveratrol, Maslinic acid, Piperine and Ganomycin B to target the SARS-CoV-2 main protease (M pro ) using in silico tools. These compounds were examined based on ADME, drug likeness, docking studies, MD simulations using CABS-flex 2.0, and prediction of major toxicity parameters (hepatotoxicity & cytotoxicity) to check the safety aspects of the selected compounds. We also investigated the similarity of these compounds, if any, with FDA approved drugs using Swiss similarity. The docking results were found in the order of Amentoflavone (-9.13 kcal/mol), Ritonavir (-8.52 kcal/mol), Lopinavir (-8.5 kcal/mol), Puerarin (-7.97 kcal/mol), Maslinic acid (-7.97 kcal/mol), Piperine (-7.65 kcal/mol), Gallocatechin gallate (-7.59 kcal/mol), Luteolin (-7.58 kcal/mol), Apigenin (-7.42 kcal/mol), Resveratrol (-7.41 kcal/mol), Herbacetin (-7.4 kcal/mol), Daidzein (-7.32 kcal/mol),Rhoifolin (-6.71 kcal/mol), Ganomycin B (-6.46 kcal/mol), Epigallocatechin (-6.13 kcal/mol), and Pectolinarin (-5.88 kcal/mol). Among these selected natural compounds, Amentoflavone and Puerarin were the two top leads which showed the lowest binding energies. Interestingly, Amentoflavone showed highest binding affinity among all the selected compounds. Our promising findings based on in-silico studies warrants further clinical trial in order to use these compounds as potential inhibitors of SARS-CoV-2 protease.

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ProTox-II: a webserver for the prediction of toxicity of chemicals

Cited by 1,925 publications

References 38 publications

A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization

A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization

Molecular Docking Analysis Of Some Phytochemicals On Two SARS-CoV-2 Targets: Potential Lead Compounds Against Two Target Sites of SARS-CoV-2 Obtained from Plants

Natural compounds as potential inhibitors of novel coronavirus (COVID-19) main protease: An in silico study

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