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Xu L, Xia L, Pan S, Li Z. Triple Generative Self-Supervised Learning Method for Molecular Property Prediction. Int J Mol Sci 2024; 25:3794. [PMID: 38612602 PMCID: PMC11012122 DOI: 10.3390/ijms25073794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Molecular property prediction is an important task in drug discovery, and with help of self-supervised learning methods, the performance of molecular property prediction could be improved by utilizing large-scale unlabeled dataset. In this paper, we propose a triple generative self-supervised learning method for molecular property prediction, called TGSS. Three encoders including a bi-directional long short-term memory recurrent neural network (BiLSTM), a Transformer, and a graph attention network (GAT) are used in pre-training the model using molecular sequence and graph structure data to extract molecular features. The variational auto encoder (VAE) is used for reconstructing features from the three models. In the downstream task, in order to balance the information between different molecular features, a feature fusion module is added to assign different weights to each feature. In addition, to improve the interpretability of the model, atomic similarity heat maps were introduced to demonstrate the effectiveness and rationality of molecular feature extraction. We demonstrate the accuracy of the proposed method on chemical and biological benchmark datasets by comparative experiments.
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Affiliation(s)
| | | | | | - Zhen Li
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China; (L.X.); (L.X.); (S.P.)
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Ge Q, Zhang Z, Cao Z, Wu D, Xu C, Yao J, Gao J, Feng Y. Exploration of the in vitro Antiviral Effects and the Active Components of Changyanning Tablets Against Enterovirus 71. Drug Des Devel Ther 2024; 18:651-665. [PMID: 38450095 PMCID: PMC10916518 DOI: 10.2147/dddt.s444625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Purpose This study aims to investigate the in vitro antiviral effects of the aqueous solution of Changyanning (CYN) tablets on Enterovirus 71 (EV71), and to analyze its active components. Methods The in vitro anti-EV71 effects of CYN solution and its herbal ingredients were assessed by testing the relative viral RNA (vRNA) expression level and the cell viability rates. Material basis analysis was performed using HPLC-Q-TOF-MS/MS detection. Potential targets and active components were identified by network pharmacology and molecular docking. The screened components were verified by in vitro antiviral experiments. Results CYN solution exerted anti-EV71 activities as the vRNA is markedly reduced after treatment, with a half maximal inhibitory concentration (IC50) of 996.85 μg/mL. Of its five herbal ingredients, aqueous extract of Mosla chinensis (AEMC) and leaves of Liquidambar formosana Hance (AELLF) significantly inhibited the intracellular replication of EV71, and the IC50 was tested as 202.57 μg/mL and 174.77 μg/mL, respectively. Based on HPLC-Q-TOF-MS/MS results, as well as the comparison with the material basis of CYN solution, a total of 44 components were identified from AEMC and AELLF. Through network pharmacology, AKT1, ALB, and SRC were identified as core targets. Molecular docking performed between core targets and the components indicated that 21 components may have anti-EV71 effects. Of these, nine were selected for in vitro pharmacodynamic verification, and only rosmarinic acid manifested in vitro anti-EV71 activity, with an IC50 of 11.90 μg/mL. Moreover, rosmarinic acid can stably bind with three core targets by forming hydrogen bonds. Conclusion CYN solution has inhibitory effects on EV71 replication in vitro, and its active component was identified as rosmarinic acid. Our study provides a new approach for screening and confirmation of the effective components in Chinese herbal preparation.
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Affiliation(s)
- Qiong Ge
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Zhewen Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, People’s Republic of China
| | - Zhiming Cao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, People’s Republic of China
| | - Dan Wu
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine Pharmaceutical Technology, Zhejiang Conba Pharmaceutical Co., Ltd, Hangzhou, Zhejiang, 310057, People’s Republic of China
| | - Changping Xu
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Jianbiao Yao
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine Pharmaceutical Technology, Zhejiang Conba Pharmaceutical Co., Ltd, Hangzhou, Zhejiang, 310057, People’s Republic of China
| | - Jian Gao
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Yan Feng
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
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Georgiou N, Kakava MG, Routsi EA, Petsas E, Stavridis N, Freris C, Zoupanou N, Moschovou K, Kiriakidi S, Mavromoustakos T. Quercetin: A Potential Polydynamic Drug. Molecules 2023; 28:8141. [PMID: 38138630 PMCID: PMC10745404 DOI: 10.3390/molecules28248141] [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: 11/27/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
The study of natural products as potential drug leads has gained tremendous research interest. Quercetin is one of those natural products. It belongs to the family of flavonoids and, more specifically, flavonols. This review summarizes the beneficial pharmaceutical effects of quercetin, such as its anti-cancer, anti-inflammatory, and antimicrobial properties, which are some of the quercetin effects described in this review. Nevertheless, quercetin shows poor bioavailability and low solubility. For this reason, its encapsulation in macromolecules increases its bioavailability and therefore pharmaceutical efficiency. In this review, a brief description of the different forms of encapsulation of quercetin are described, and new ones are proposed. The beneficial effects of applying new pharmaceutical forms of nanotechnology are outlined.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Margarita Georgia Kakava
- Laboratory of Organic Chemistry and Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece;
| | - Efthymios Alexandros Routsi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Errikos Petsas
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Nikolaos Stavridis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Christoforos Freris
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Nikoletta Zoupanou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Kalliopi Moschovou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Sofia Kiriakidi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Departamento de Quimica Orgánica, Facultade de Quimica, Universidade de Vigo, 36310 Vigo, Spain
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
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