admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties

Yang, Hong-Chang; Lou, Chaofeng; Sun, Lixia; Li, Jie; Cai, Yingchun; Wang, Zhuang; Li, Weihua; Liu, Guixia

doi:10.1093/bioinformatics/bty707

Cited by 962 publications

(525 citation statements)

References 13 publications

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“…A potential solution is to predict candidate pharmacogenes according to the chemical structure of a new drug by the artificial intelligence and machine learning algorithm [21,22] . Then related molecular biological studies can be conducted to validate these candidate pharmacogenes rapidly.…”

Section: Discussionmentioning

confidence: 99%

Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19

Wang

Cui

Ouyang

et al. 2020

Preprint

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Background:The coronavirus disease 2019 has become a global pandemic currently. Many drugs showed potential for COVID-19 therapy. However, genetic factors which can lead to different drug efficiency and toxicity among populations are still undisclosed in COVID-19 therapy. Methods:We selected 67 potential drugs for COVID-19 therapy (DCTs) from clinical guideline and clinical trials databases. 313 pharmaco-genes related to these therapeutic drugs were included. Variation information in 125,748 exomes were collected for racial differences analyses. The expression level of pharmaco-genes in single cell resolution was evaluated from single-cell RNA sequencing (scRNA-seq) data of 17 healthy adults.Results: Pharmacogenes, including CYP3A4, ABCB1, SLCO1B1, ALB, CYP3A5, were involved in the process of more than multi DCTs. 224 potential drug-drug interactions (DDIs) of DCTs were predicted, while 112 of them have been reported.Racial discrepancy of common nonsynonymous mutations was found in pharmacogenes including: VDR, ITPA, G6PD, CYP3A4 and ABCB1 which related to DCTs including ribavirin, α -interferon, chloroquine and lopinavir. Moreover, ACE2, the target of 2019-nCoV, was only found in parts of lung cells, which makes drugs like chloroquine that prevent virus binding to ACE2 more specific than other targeted drugs such as camostat mesylate.

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Section: Discussionmentioning

confidence: 99%

Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19

Wang

Cui

Ouyang

et al. 2020

Preprint

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“…Although actein differs in the structure of these mental‐treated drugs, it is found that they are similar in expression by the method of biclustering, which indicates that there is a similar activity between actein and these drugs. And the ADMET‐associated (Absorption, distribution, metabolism, excretion, and toxicity) properties of actein are predicted by admetSAR, a web platform developed as a comprehensive source and free tool for the prediction of chemical ADMET properties . According to the predicted values, most of the properties of actein basically meet Lipinski's principle, which indicates that it is suitable as a candidate drug.…”

Section: Resultsmentioning

confidence: 99%

“…And the ADMETassociated (Absorption, distribution, metabolism, excretion, and toxicity) properties of actein are predicted by admetSAR, a web platform developed as a comprehensive source and free tool for the prediction of chemical ADMET properties. [13] According to the predicted values, most of the properties of actein basically meet Lipinski's principle, which indicates that it is suitable as a candidate drug. (As shown in Table 3).…”

Section: Similarity Analysis Of Module Regulationmentioning

confidence: 95%

Potential Targets of Actein Identified by Systems Chemical Biology Methods

Liao

Zhang

et al. 2019

ChemMedChem

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Actein is the main active ingredient of medicinal plant Cimicifuga racemosa (L.) Nutt, which has been reported to have various pharmacological effects, but the mechanism of actein remains undetermined. In this study, systems chemical biology methods were used to predict the targets and elucidate the pharmacological mechanisms of actein. First, 54 gene co‐expression modules were obtained by biclustering. Then, the top 1 % agents with the highest regulatory similarity were screened out to be highly functionally similar to actein. Finally, the results of molecular docking and molecular dynamics simulation showed that actein has a stronger interaction with eight targets than original ligands. It suggests that the antipsychotic effect of actein probably occurs by targeting the key residues of the eight receptors, which are compatible with previously reported information. This study not only provides predicted targets of actein, but also a new method for exploring the mechanisms of other natural products in drug discovery.

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“…Absorption, distribution, metabolism, excretion, and toxicity (ADMET) screening of ligands helps to determine their absorption properties, toxicity, and drug-likeness. Ligand molecules saved in .smiles format and selected drugs [29,30].…”

Section: Admet and Toxicity Predictionmentioning

confidence: 99%

Docking studies in targeting proteins involved in cardiovascular disorders using phytocompounds fromTerminalia arjuna

Kumar

Sharma²,

Sourirajan

et al. 2020

Preprint

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Terminalia arjuna (Roxb.) Wight and Arnot (T. arjuna) commonly known as Arjuna has been known for its cardiotonic nature in heart failure, ischemic, cardiomyopathy, atherosclerosis, myocardium necrosis and also has been used in the treatment of different human disorders such as blood diseases, anaemia and viral diseases. Our focus has been on phytochemicals which do not exhibit any cytotoxicity and have significant cardioprotective activity. Since Protein-Ligand interactions play a key role in structure-based drug design, therefore with the help of molecular docking, we screened 19 phytochemicals present in T. arjuna and investigated their binding affinity against different cardiovascular target proteins. The three-dimensional (3D) structure of target cardiovascular proteins were retrieved from Protein Data Bank, and docked with 3D Pubchem structures of 19 phytochemicals using Autodock vina. Molecular docking and drug-likeness studies were made using ADMET properties while Lipinski's rule of five was performed for the phytochemicals to evaluate their cardio protective activity. Among all selected phytocompounds, arjunic acid, arjungenin, and terminic acid were found to fulfill all ADMET rules, drug likeness, and are less toxic in nature. Our studies, therefore revealed that these three phytochemicals from T. arjuna can be used as promising candidates for developing broad spectrum drugs against cardiovascular diseases.

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admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 962 publications

References 13 publications

Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19

Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19

Potential Targets of Actein Identified by Systems Chemical Biology Methods

Docking studies in targeting proteins involved in cardiovascular disorders using phytocompounds fromTerminalia arjuna

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