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Luo L, Tan H, Liao Y. In silico analysis of marine natural product for protein arginine methyltransferase 5(PRMT5) inhibitors based on pharmacophore and molecular docking. J Biomol Struct Dyn 2023; 41:13180-13197. [PMID: 36856049 DOI: 10.1080/07391102.2023.2184172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/15/2023] [Indexed: 03/02/2023]
Abstract
Over the past few decades, various inhibitors of PRMT5 have been developed because of its involvement in a variety of tumor development processes. As of now, no drugs targeting PRMT5 have been approved, and multiple drugs entering clinical trials have proven to have side effects. In this study, PRMT5 was used to perform virtual screening of 52119 marine natural compounds by combining various methods. We constructed 20 pharmacophore models based on multiple ligands. The best pharmacophore model AARR_2 was selected by analyzing the statistical parameters of the pharmacophore model and the binding characteristics of the ligand active site, and then 3552 compounds were screened out. Compared with the positive compound, 46 compounds were selected based on the molecular docking fraction and docking mode analysis. Then, 3D-QSAR was used to analyze the relationship between structure and activity of the compounds. Then, in addition to marine compounds 36404, 36405 and 14436, we selected compound 46 (the positive control compound) and used the CLC-Pred online Web server to predict their cytotoxicity to human cell lines, making cell experiments possible. Finally, we conducted the prediction of ADMET in order to better promote clinical trials. After comprehensive judgment, we screened out the marine natural compounds 36404 and 36405 as candidates for PRMT5 substrate competitive inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, Guangdong, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, Guangdong, China
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang, Guangdong, China
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Computer-aided prediction of biological activity spectra for organic compounds: the possibilities and limitations. Russ Chem Bull 2020. [DOI: 10.1007/s11172-019-2683-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Druzhilovskiy DS, Rudik AV, Filimonov DA, Gloriozova TA, Lagunin AA, Dmitriev AV, Pogodin PV, Dubovskaya VI, Ivanov SM, Tarasova OA, Bezhentsev VM, Murtazalieva KA, Semin MI, Maiorov IS, Gaur AS, Sastry GN, Poroikov VV. Computational platform Way2Drug: from the prediction of biological activity to drug repurposing. Russ Chem Bull 2018. [DOI: 10.1007/s11172-017-1954-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lagunin AA, Dubovskaja VI, Rudik AV, Pogodin PV, Druzhilovskiy DS, Gloriozova TA, Filimonov DA, Sastry NG, Poroikov VV. CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds. PLoS One 2018; 13:e0191838. [PMID: 29370280 PMCID: PMC5784992 DOI: 10.1371/journal.pone.0191838] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 01/11/2018] [Indexed: 11/19/2022] Open
Abstract
In silico methods of phenotypic screening are necessary to reduce the time and cost of the experimental in vivo screening of anticancer agents through dozens of millions of natural and synthetic chemical compounds. We used the previously developed PASS (Prediction of Activity Spectra for Substances) algorithm to create and validate the classification SAR models for predicting the cytotoxicity of chemicals against different types of human cell lines using ChEMBL experimental data. A training set from 59,882 structures of compounds was created based on the experimental data (IG50, IC50, and % inhibition values) from ChEMBL. The average accuracy of prediction (AUC) calculated by leave-one-out and a 20-fold cross-validation procedure during the training was 0.930 and 0.927 for 278 cancer cell lines, respectively, and 0.948 and 0.947 for cytotoxicity prediction for 27 normal cell lines, respectively. Using the given SAR models, we developed a freely available web-service for cell-line cytotoxicity profile prediction (CLC-Pred: Cell-Line Cytotoxicity Predictor) based on the following structural formula: http://way2drug.com/Cell-line/.
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Affiliation(s)
- Alexey A. Lagunin
- Department for Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department for Bioinformatics, Medico-Biologic Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
- * E-mail:
| | | | - Anastasia V. Rudik
- Department for Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Pavel V. Pogodin
- Department for Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - Dmitry A. Filimonov
- Department for Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Narahari G. Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Vladimir V. Poroikov
- Department for Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Filimonov D, Druzhilovskiy D, Lagunin A, Gloriozova T, Rudik A, Dmitriev A, Pogodin P, Poroikov V. Computer-aided prediction of biological activity spectra for chemical compounds: opportunities and limitation. ACTA ACUST UNITED AC 2018. [DOI: 10.18097/bmcrm00004] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An essential characteristic of chemical compounds is their biological activity since its presence can become the basis for the use of the substance for therapeutic purposes, or, on the contrary, limit the possibilities of its practical application due to the manifestation of side action and toxic effects. Computer assessment of the biological activity spectra makes it possible to determine the most promising directions for the study of the pharmacological action of particular substances, and to filter out potentially dangerous molecules at the early stages of research. For more than 25 years, we have been developing and improving the computer program PASS (Prediction of Activity Spectra for Substances), designed to predict the biological activity spectrum of substance based on the structural formula of its molecules. The prediction is carried out by the analysis of structure-activity relationships for the training set, which currently contains information on structures and known biological activities for more than one million molecules. The structure of the organic compound is represented in PASS using Multilevel Neighborhoods of Atoms descriptors; the activity prediction for new compounds is performed by the naive Bayes classifier and the structure-activity relationships determined by the analysis of the training set. We have created and improved both local versions of the PASS program and freely available web resources based on PASS (http://www.way2drug.com). They predict several thousand biological activities (pharmacological effects, molecular mechanisms of action, specific toxicity and adverse effects, interaction with the unwanted targets, metabolism and action on molecular transport), cytotoxicity for tumor and non-tumor cell lines, carcinogenicity, induced changes of gene expression profiles, metabolic sites of the major enzymes of the first and second phases of xenobiotics biotransformation, and belonging to substrates and/or metabolites of metabolic enzymes. The web resource Way2Drug is used by over 18,000 researchers from more than 90 countries around the world, which allowed them to obtain over 600,000 predictions and publish about 500 papers describing the obtained results. The analysis of the published works shows that in some cases the interpretation of the prediction results presented by the authors of these publications requires an adjustment. In this work, we provide the theoretical basis and consider, on particular examples, the opportunities and limitations of computer-aided prediction of biological activity spectra.
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Affiliation(s)
| | | | - A.A. Lagunin
- Institute of Biomedical Chemistry; Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - A.V. Rudik
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.V. Pogodin
- Institute of Biomedical Chemistry, Moscow, Russia
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Rudik AV, Dmitriev AV, Bezhentsev VM, Lagunin AA, Filimonov DA, Poroikov VV. Prediction of metabolites of epoxidation reaction in MetaTox. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:833-842. [PMID: 29157013 DOI: 10.1080/1062936x.2017.1399165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Biotransformation is a process of the chemical modifications which may lead to the reactive metabolites, in particular the epoxides. Epoxide reactive metabolites may cause the toxic effects. The prediction of such metabolites is important for drug development and ecotoxicology studies. Epoxides are formed by some oxidation reactions, usually catalysed by cytochromes P450, and represent a large class of three-membered cyclic ethers. Identification of molecules, which may be epoxidized, and indication of the specific location of epoxide functional group (which is called SOE - site of epoxidation) are important for prediction of epoxide metabolites. Datasets from 355 molecules and 615 reactions were created for training and validation. The prediction of SOE is based on a combination of LMNA (Labelled Multilevel Neighbourhood of Atom) descriptors and Bayesian-like algorithm implemented in PASS software and MetaTox web-service. The average invariant accuracy of prediction (AUC) calculated in leave-one-out and 20-fold cross-validation procedures is 0.9. Prediction of epoxide formation based on the created SAR model is included as the component of MetaTox web-service ( http://www.way2drug.com/mg ).
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Affiliation(s)
- A V Rudik
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - A V Dmitriev
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - V M Bezhentsev
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - A A Lagunin
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
- b Medico-biological Faculty , Pirogov Russian National Research Medical University , Moscow , Russia
| | - D A Filimonov
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
| | - V V Poroikov
- a Institute of Biomedical Chemistry (IBMC) , Moscow , Russia
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Stasevych M, Zvarych V, Lunin V, Deniz NG, Gokmen Z, Akgun O, Ulukaya E, Poroikov V, Gloriozova T, Novikov V. Computer-aided prediction and cytotoxicity evaluation of dithiocarbamates of 9,10-anthracenedione as new anticancer agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:355-366. [PMID: 28524703 DOI: 10.1080/1062936x.2017.1323796] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Anticancer activity as an associated action for a series of dithiocarbamates of 9,10-anthracenedione was predicted using the PASS computer program and analysed with PharmaExpert software. The predicted cytotoxic activity of the dithiocarbamate derivatives of 9,10-anthracenedione was evaluated in vitro on cancer cells of the human lung (A549), prostate (PC3), colon (HT29) and human breast (MCF7) using the sulforhodamine B (SRB) cell viability assay. Among these compounds, 9,10-dioxo-9,10-dihydroanthracen-1-yl pyrrolidin-1-carbodithioate and 9,10-dioxo-9,10-dihydroanthracen-2-yl pyrrolidin-1-carbodithioate were identified as the most potent anticancer agents with cytotoxic activity against the MCF-7 human breast cell line with GI50 values of 1.40 μM and 1.52 μM, whereas the GI50 value for the reference anticancer drug mitoxantrone was 3.93 μM. Thus, anticancer activity predicted by PASS with a probability Pa > 30% was confirmed by the experiment. Relatively small Pa values estimated by PASS indicated the novelty of the considered derivatives comparing to the compounds from the PASS training set.
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Affiliation(s)
- M Stasevych
- a Department of Technology of Biologically Active Substances, Pharmacy and Biotechnology , Lviv Polytechnic National University , Lviv , Ukraine
| | - V Zvarych
- a Department of Technology of Biologically Active Substances, Pharmacy and Biotechnology , Lviv Polytechnic National University , Lviv , Ukraine
| | - V Lunin
- a Department of Technology of Biologically Active Substances, Pharmacy and Biotechnology , Lviv Polytechnic National University , Lviv , Ukraine
| | - N G Deniz
- b Department of Chemistry , Istanbul University , Istanbul , Turkey
| | - Z Gokmen
- b Department of Chemistry , Istanbul University , Istanbul , Turkey
| | - O Akgun
- c Department of Biology , Uludag University , Bursa , Turkey
| | - E Ulukaya
- d Department of Medical Biochemistry , Istinye University , Istanbul , Turkey
| | - V Poroikov
- e Department for Bioinformatics , Institute of Biomedical Chemistry , Moscow , Russia
| | - T Gloriozova
- e Department for Bioinformatics , Institute of Biomedical Chemistry , Moscow , Russia
| | - V Novikov
- a Department of Technology of Biologically Active Substances, Pharmacy and Biotechnology , Lviv Polytechnic National University , Lviv , Ukraine
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