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Gaffar S, Tayara H, Chong KT. Stack-AAgP: Computational prediction and interpretation of anti-angiogenic peptides using a meta-learning framework. Comput Biol Med 2024; 174:108438. [PMID: 38613893 DOI: 10.1016/j.compbiomed.2024.108438] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Angiogenesis plays a vital role in the pathogenesis of several human diseases, particularly in the case of solid tumors. In the realm of cancer treatment, recent investigations into peptides with anti-angiogenic properties have yielded encouraging outcomes, thereby creating a hopeful therapeutic avenue for the treatment of cancer. Therefore, correctly identifying the anti-angiogenic peptides is extremely important in comprehending their biophysical and biochemical traits, laying the groundwork for uncovering novel drugs to combat cancer. METHODS In this work, we present a novel ensemble-learning-based model, Stack-AAgP, specifically designed for the accurate identification and interpretation of anti-angiogenic peptides (AAPs). Initially, a feature representation approach is employed, generating 24 baseline models through six machine learning algorithms (random forest [RF], extra tree classifier [ETC], extreme gradient boosting [XGB], light gradient boosting machine [LGBM], CatBoost, and SVM) and four feature encodings (pseudo-amino acid composition [PAAC], amphiphilic pseudo-amino acid composition [APAAC], composition of k-spaced amino acid pairs [CKSAAP], and quasi-sequence-order [QSOrder]). Subsequently, the output (predicted probabilities) from 24 baseline models was inputted into the same six machine-learning classifiers to generate their respective meta-classifiers. Finally, the meta-classifiers were stacked together using the ensemble-learning framework to construct the final predictive model. RESULTS Findings from the independent test demonstrate that Stack-AAgP outperforms the state-of-the-art methods by a considerable margin. Systematic experiments were conducted to assess the influence of hyperparameters on the proposed model. Our model, Stack-AAgP, was evaluated on the independent NT15 dataset, revealing superiority over existing predictors with an accuracy improvement ranging from 5% to 7.5% and an increase in Matthews Correlation Coefficient (MCC) from 7.2% to 12.2%.
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Affiliation(s)
- Saima Gaffar
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea; Advances Electronics and Information Research Centre, Jeonbuk National University, Jeonju, 54896, South Korea.
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2
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Zhang Y, Wu M, Wang S, Chen W. EFMSDTI: Drug-target interaction prediction based on an efficient fusion of multi-source data. Front Pharmacol 2022; 13:1009996. [PMID: 36210804 PMCID: PMC9538487 DOI: 10.3389/fphar.2022.1009996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Accurate identification of Drug Target Interactions (DTIs) is of great significance for understanding the mechanism of drug treatment and discovering new drugs for disease treatment. Currently, computational methods of DTIs prediction that combine drug and target multi-source data can effectively reduce the cost and time of drug development. However, in multi-source data processing, the contribution of different source data to DTIs is often not considered. Therefore, how to make full use of the contribution of different source data to predict DTIs for efficient fusion is the key to improving the prediction accuracy of DTIs. In this paper, considering the contribution of different source data to DTIs prediction, a DTIs prediction approach based on an effective fusion of drug and target multi-source data is proposed, named EFMSDTI. EFMSDTI first builds 15 similarity networks based on multi-source information networks classified as topological and semantic graphs of drugs and targets according to their biological characteristics. Then, the multi-networks are fused by selective and entropy weighting based on similarity network fusion (SNF) according to their contribution to DTIs prediction. The deep neural networks model learns the embedding of low-dimensional vectors of drugs and targets. Finally, the LightGBM algorithm based on Gradient Boosting Decision Tree (GBDT) is used to complete DTIs prediction. Experimental results show that EFMSDTI has better performance (AUROC and AUPR are 0.982) than several state-of-the-art algorithms. Also, it has a good effect on analyzing the top 1000 prediction results, while 990 of the first 1000DTIs were confirmed. Code and data are available at https://github.com/meng-jie/EFMSDTI.
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Affiliation(s)
- Yuanyuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, Shandong, China
- College of Computer science and Technology, China University of Petroleum (East China), Qingdao, Shandong, China
- *Correspondence: Yuanyuan Zhang,
| | - Mengjie Wu
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, Shandong, China
| | - Shudong Wang
- College of Computer science and Technology, China University of Petroleum (East China), Qingdao, Shandong, China
| | - Wei Chen
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, Shandong, China
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3
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Noor F, Tahir ul Qamar M, Ashfaq UA, Albutti A, Alwashmi ASS, Aljasir MA. Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals (Basel) 2022; 15:572. [PMID: 35631398 PMCID: PMC9143318 DOI: 10.3390/ph15050572] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
| | - Mohammad Abdullah Aljasir
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
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4
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Xue W, Fu T, Deng S, Yang F, Yang J, Zhu F. Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram. ACS Chem Neurosci 2022; 13:340-351. [PMID: 35041375 DOI: 10.1021/acschemneuro.1c00694] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human serotine transporter (hSERT) is one of the most influential drug targets, and its allosteric modulators (e.g., escitalopram) have emerged to be the next-generation medication for psychiatric disorders. However, the molecular mechanism underlying the allosteric modulation of hSERT is still elusive. Here, the simulation strategies of conventional (cMD) and steered (SMD) molecular dynamics were applied to investigate this molecular mechanism from distinct perspectives. First, cMD simulations revealed that escitalopram's binding to hSERT's allosteric site simultaneously enhanced its binding to the orthosteric site. Then, SMD simulation identified that the occupation of hSERT's allosteric site by escitalopram could also block its dissociation from the orthosteric site. Finally, by comparing the simulated structures of two hSERT-escitalopram complexes with and without allosteric modulation, a new conformational coupling between an extracellular (Arg104-Glu494) and an intracellular (Lys490-Glu494) salt bridge was identified. In summary, this study explored the mechanism underlying the allosteric modulation of hSERT by collectively applying two MD simulation strategies, which could facilitate our understanding of the allosteric modulations of not only hSERT but also other clinically important therapeutic targets.
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Affiliation(s)
- Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Central Nervous System Drug Key Laboratory of Sichuan Province, Luzhou 646000, China
| | - Tingting Fu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Shengzhe Deng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jingyi Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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5
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Zhai Y, Zhang J, Zhang T, Gong Y, Zhang Z, Zhang D, Zhao Y. AOPM: Application of Antioxidant Protein Classification Model in Predicting the Composition of Antioxidant Drugs. Front Pharmacol 2022; 12:818115. [PMID: 35115948 PMCID: PMC8803896 DOI: 10.3389/fphar.2021.818115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022] Open
Abstract
Antioxidant proteins can not only balance the oxidative stress in the body, but are also an important component of antioxidant drugs. Accurate identification of antioxidant proteins is essential to help humans fight diseases and develop new drugs. In this paper, we developed a friendly method AOPM to identify antioxidant proteins. 188D and the Composition of k-spaced Amino Acid Pairs were adopted as the feature extraction method. In addition, the Max-Relevance-Max-Distance algorithm (MRMD) and random forest were the feature selection and classifier, respectively. We used 5-folds cross-validation and independent test dataset to evaluate our model. On the test dataset, AOPM presented a higher performance compared with the state-of-the-art methods. The sensitivity, specificity, accuracy, Matthew’s Correlation Coefficient and an Area Under the Curve reached 87.3, 94.2, 92.0%, 0.815 and 0.972, respectively. In addition, AOPM still has excellent performance in predicting the catalytic enzymes of antioxidant drugs. This work proved the feasibility of virtual drug screening based on sequence information and provided new ideas and solutions for drug development.
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Affiliation(s)
- Yixiao Zhai
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Jingyu Zhang
- Department of Neurology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yue Gong
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Zixiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Dandan Zhang, ; Yuming Zhao,
| | - Yuming Zhao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Dandan Zhang, ; Yuming Zhao,
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6
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Lin C, Wang L, Shi L. AAPred-CNN: accurate predictor based on deep convolution neural network for identification of anti-angiogenic peptides. Methods 2022; 204:442-448. [PMID: 35031486 DOI: 10.1016/j.ymeth.2022.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022] Open
Abstract
Recently, deep learning techniques have been developed for various bioactive peptide prediction tasks. However, there are only conventional machine learning-based methods for the prediction of anti-angiogenic peptides (AAP), which play an important role in cancer treatment. The main reason why no deep learning method has been involved in this field is that there are too few experimentally validated AAPs to support the training of deep models but researchers have believed that deep learning seriously depends on the amounts of labeled data. In this paper, as a tentative work, we try to predict AAP by constructing different classical deep learning models and propose the first deep convolution neural network-based predictor (AAPred-CNN) for AAP. Contrary to intuition, the experimental results show that deep learning models can achieve superior or comparable performance to the state-of-the-art model, although they are given a few labeled sequences to train. We also decipher the influence of hyper-parameters and training samples on the performance of deep learning models to help understand how the model work. Furthermore, we also visualize the learned embeddings by dimension reduction to increase the model interpretability and reveal the residue propensity of AAP through the statistics of convolutional features for different residues. In summary, this work demonstrates the powerful representation ability of AAPred-CNNfor AAP prediction, further improving the prediction accuracy of AAP.
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Affiliation(s)
- Changhang Lin
- School of Big Data and Artificial Intelligence, Fujian Polytechnic Normal University, Fuzhou, China
| | - Lei Wang
- Beidahuang Industry Group General Hospital, Harbin, China.
| | - Lei Shi
- Department of Spine Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
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7
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Yu L, Zheng Y, Gao L. MiRNA-disease association prediction based on meta-paths. Brief Bioinform 2022; 23:6501422. [PMID: 35018405 DOI: 10.1093/bib/bbab571] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 01/09/2023] Open
Abstract
Since miRNAs can participate in the posttranscriptional regulation of gene expression, they may provide ideas for the development of new drugs or become new biomarkers for drug targets or disease diagnosis. In this work, we propose an miRNA-disease association prediction method based on meta-paths (MDPBMP). First, an miRNA-disease-gene heterogeneous information network was constructed, and seven symmetrical meta-paths were defined according to different semantics. After constructing the initial feature vector for the node, the vector information carried by all nodes on the meta-path instance is extracted and aggregated to update the feature vector of the starting node. Then, the vector information obtained by the nodes on different meta-paths is aggregated. Finally, miRNA and disease embedding feature vectors are used to calculate their associated scores. Compared with the other methods, MDPBMP obtained the highest AUC value of 0.9214. Among the top 50 predicted miRNAs for lung neoplasms, esophageal neoplasms, colon neoplasms and breast neoplasms, 49, 48, 49 and 50 have been verified. Furthermore, for breast neoplasms, we deleted all the known associations between breast neoplasms and miRNAs from the training set. These results also show that for new diseases without known related miRNA information, our model can predict their potential miRNAs. Code and data are available at https://github.com/LiangYu-Xidian/MDPBMP.
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Affiliation(s)
- Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an 710071, P.R. China
| | - Yujia Zheng
- School of Computer Science and Technology, Xidian University, Xi'an 710071, P.R. China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an 710071, P.R. China
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8
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Jia Y, Huang S, Zhang T. KK-DBP: A Multi-Feature Fusion Method for DNA-Binding Protein Identification Based on Random Forest. Front Genet 2021; 12:811158. [PMID: 34912382 PMCID: PMC8667860 DOI: 10.3389/fgene.2021.811158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/15/2021] [Indexed: 02/04/2023] Open
Abstract
DNA-binding protein (DBP) is a protein with a special DNA binding domain that is associated with many important molecular biological mechanisms. Rapid development of computational methods has made it possible to predict DBP on a large scale; however, existing methods do not fully integrate DBP-related features, resulting in rough prediction results. In this article, we develop a DNA-binding protein identification method called KK-DBP. To improve prediction accuracy, we propose a feature extraction method that fuses multiple PSSM features. The experimental results show a prediction accuracy on the independent test dataset PDB186 of 81.22%, which is the highest of all existing methods.
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Affiliation(s)
- Yuran Jia
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Shan Huang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
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9
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Chen J, Zhang Q, Liu T, Tang H. Roles of M6A Regulators in Hepatocellular Carcinoma: Promotion or Suppression. Curr Gene Ther 2021; 22:40-50. [PMID: 34825870 DOI: 10.2174/1566523221666211126105940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/15/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is the sixth globally diagnosed cancer with a poor prognosis. Although the pathological factors of hepatocellular carcinoma are well elucidated, the underlying molecular mechanisms remain unclear. N6-methyladenosine (m6A) is an adenosine methylation occurring at the N6 site, which is the most prevalent modification of eukaryotic mRNA. Recent studies have shown that m6A can regulate gene expression, thus modulating the processes of cell self-renewal, differentiation, and apoptosis. The methyls in m6A are installed by methyltransferases ("writers"), removed by demethylases ("erasers") and recognized by m6A-binding proteins ("readers"). In this review, we discuss the roles of above regulators in the progression and prognosis of HCC, and summarize the clinical association between m6A modification and hepatocellular carcinoma, so as to provide more valuable information for clinical treatment.
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Affiliation(s)
- Jiamao Chen
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Qian Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Ting Liu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Hua Tang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
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10
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Cinobufagin Exerts Anticancer Activity in Oral Squamous Cell Carcinoma Cells through Downregulation of ANO1. Int J Mol Sci 2021; 22:ijms222112037. [PMID: 34769467 PMCID: PMC8584692 DOI: 10.3390/ijms222112037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022] Open
Abstract
Anoctamin1 (ANO1), a calcium-activated chloride channel, is frequently overexpressed in several cancers, including oral squamous cell carcinoma (OSCC). OSCC is a highly aggressive cancer and the most common oral malignancy. ANO1 has been proposed as a potential candidate for targeted anticancer therapy. In this study, we performed a cell-based screening to identify novel regulators leading to the downregulation of ANO1, and discovered cinobufagin, which downregulated ANO1 expression in oral squamous cell carcinoma CAL-27 cells. ANO1 protein levels were significantly reduced by cinobufagin in a dose-dependent manner with an IC50 value of ~26 nM. Unlike previous ANO1 inhibitors, short-term (≤10 min) exposure to cinobufagin did not alter ANO1 chloride channel activity and ANO1-dependent intestinal smooth muscle contraction, whereas long-term (24 h) exposure to cinobufagin significantly reduced phosphorylation of STAT3 and mRNA expression of ANO1 in CAL-27 cells. Notably, cinobufagin inhibited cell proliferation of CAL-27 cells expressing high levels of ANO1 more potently than that of ANO1 knockout CAL-27 cells. In addition, cinobufagin significantly reduced cell migration and induced caspase-3 activation and PARP cleavage in CAL-27 cells. These results suggest that downregulation of ANO1 by cinobufagin is a potential mechanism for the anticancer effect of cinobufagin in OSCC.
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11
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Lv H, Shi L, Berkenpas JW, Dao FY, Zulfiqar H, Ding H, Zhang Y, Yang L, Cao R. Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design. Brief Bioinform 2021; 22:bbab320. [PMID: 34410360 PMCID: PMC8511807 DOI: 10.1093/bib/bbab320] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has led to a dramatic loss of human life worldwide. Despite many efforts, the development of effective drugs and vaccines for this novel virus will take considerable time. Artificial intelligence (AI) and machine learning (ML) offer promising solutions that could accelerate the discovery and optimization of new antivirals. Motivated by this, in this paper, we present an extensive survey on the application of AI and ML for combating COVID-19 based on the rapidly emerging literature. Particularly, we point out the challenges and future directions associated with state-of-the-art solutions to effectively control the COVID-19 pandemic. We hope that this review provides researchers with new insights into the ways AI and ML fight and have fought the COVID-19 outbreak.
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Affiliation(s)
- Hao Lv
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lei Shi
- Department of Spine Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200433, China
| | | | - Fu-Ying Dao
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hasan Zulfiqar
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Liming Yang
- Department of Pathophysiology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma 98447, USA
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12
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An Q, Yu L. A heterogeneous network embedding framework for predicting similarity-based drug-target interactions. Brief Bioinform 2021; 22:6346805. [PMID: 34373895 DOI: 10.1093/bib/bbab275] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 01/09/2023] Open
Abstract
Accurate prediction of drug-target interactions (DTIs) through biological data can reduce the time and economic cost of drug development. The prediction method of DTIs based on a similarity network is attracting increasing attention. Currently, many studies have focused on predicting DTIs. However, such approaches do not consider the features of drugs and targets in multiple networks or how to extract and merge them. In this study, we proposed a Network EmbeDding framework in mulTiPlex networks (NEDTP) to predict DTIs. NEDTP builds a similarity network of nodes based on 15 heterogeneous information networks. Next, we applied a random walk to extract the topology information of each node in the network and learn it as a low-dimensional vector. Finally, the Gradient Boosting Decision Tree model was constructed to complete the classification task. NEDTP achieved accurate results in DTI prediction, showing clear advantages over several state-of-the-art algorithms. The prediction of new DTIs was also verified from multiple perspectives. In addition, this study also proposes a reasonable model for the widespread negative sampling problem of DTI prediction, contributing new ideas to future research. Code and data are available at https://github.com/LiangYu-Xidian/NEDTP.
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Affiliation(s)
- Qi An
- College of Computer Science and Technology at Xidian University, Xi'an 710071, P.R. China
| | - Liang Yu
- College of Computer Science and Technology at Xidian University, Xi'an 710071, P.R. China
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Ru X, Ye X, Sakurai T, Zou Q, Xu L, Lin C. Current status and future prospects of drug-target interaction prediction. Brief Funct Genomics 2021; 20:312-322. [PMID: 34189559 DOI: 10.1093/bfgp/elab031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/09/2023] Open
Abstract
Drug-target interaction prediction is important for drug development and drug repurposing. Many computational methods have been proposed for drug-target interaction prediction due to their potential to the time and cost reduction. In this review, we introduce the molecular docking and machine learning-based methods, which have been widely applied to drug-target interaction prediction. Particularly, machine learning-based methods are divided into different types according to the data processing form and task type. For each type of method, we provide a specific description and propose some solutions to improve its capability. The knowledge of heterogeneous network and learning to rank are also summarized in this review. As far as we know, this is the first comprehensive review that summarizes the knowledge of heterogeneous network and learning to rank in the drug-target interaction prediction. Moreover, we propose three aspects that can be explored in depth for future research.
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Affiliation(s)
| | - Xiucai Ye
- Department of Computer Science, and Center for Artificial Intelligence Research (C-AIR), University of Tsukuba
| | - Tetsuya Sakurai
- Department of Computer Science and is the director of the C-AIR, University of Tsukuba
| | - Quan Zou
- University of Electronic Science and Technology of China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic
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14
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Yin J, Li X, Li F, Lu Y, Zeng S, Zhu F. Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. Comput Struct Biotechnol J 2021; 19:2318-2328. [PMID: 33995923 PMCID: PMC8105181 DOI: 10.1016/j.csbj.2021.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
An appropriate therapeutic index is crucial for drug discovery and development since narrow therapeutic index (NTI) drugs with slight dosage variation may induce severe adverse drug reactions or potential treatment failure. To date, the shared characteristics underlying the targets of NTI drugs have been explored by several studies, which have been applied to identify potential drug targets. However, the association between the drug therapeutic index and the related disease has not been dissected, which is important for revealing the NTI drug mechanism and optimizing drug design. Therefore, in this study, two classes of disease (cancers and cardiovascular disorders) with the largest number of NTI drugs were selected, and the target property of the corresponding NTI drugs was analyzed. By calculating the biological system profiles and human protein–protein interaction (PPI) network properties of drug targets and adopting an AI-based algorithm, differentiated features between two diseases were discovered to reveal the distinct underlying mechanisms of NTI drugs in different diseases. Consequently, ten shared features and four unique features were identified for both diseases to distinguish NTI from NNTI drug targets. These computational discoveries, as well as the newly found features, suggest that in the clinical study of avoiding narrow therapeutic index in those diseases, the ability of target to be a hub and the efficiency of target signaling in the human PPI network should be considered, and it could thus provide novel guidance in the drug discovery and clinical research process and help to estimate the drug safety of cancer and cardiovascular disease.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoxu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China.,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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15
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Yang J, Li H, Wang F, Xiao F, Yan W, Hu G. Network-Based Target Prioritization and Drug Candidate Identification for Multiple Sclerosis: From Analyzing "Omics Data" to Druggability Simulations. ACS Chem Neurosci 2021; 12:917-929. [PMID: 33565875 DOI: 10.1021/acschemneuro.1c00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is the most common chronic inflammatory demyelinating disease of the central nervous system. While the drugs currently available for MS provide symptomatic benefit, there is no curative treatment. The emergence of large-scale multiomics data and network theory provide new opportunities for drug discovery in MS, as these are promising strategies for developing novel drugs. In this study, we proposed a computational framework that combined biomolecular network modeling and structural dynamics analysis to facilitate the discovery of new drugs with potential activity in MS. First, we developed a new shortest path-based algorithm that prioritized differentially expressed genes using a newly topological and functional exploration of protein-protein interaction network. Then, pathway enrichment analysis and an assessment of target druggability suggested that TNF-α-induced protein 3 (TNFAIP3), which is involved in NF-κ B signaling, could be a potential therapeutic target for MS. Finally, druggability simulations and mutation enrichment analysis of the TNFAIP3 dimer presented two druggable sites. Follow-up pharmacophore model-based virtual screening of the two sites yielded 30 hit compounds with low energy scores. In summary, this novel method based on analyzing "omics data" and performing druggability simulations, is a systematic approach that unravels disease mechanisms and links them to the chemical space to develop treatments and can be applied to other complex diseases.
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Affiliation(s)
- Ji Yang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Hongchun Li
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fan Wang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Fei Xiao
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Wenying Yan
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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16
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Recent Advances in Predicting Protein S-Nitrosylation Sites. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5542224. [PMID: 33628788 PMCID: PMC7892234 DOI: 10.1155/2021/5542224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023]
Abstract
Protein S-nitrosylation (SNO) is a process of covalent modification of nitric oxide (NO) and its derivatives and cysteine residues. SNO plays an essential role in reversible posttranslational modifications of proteins. The accurate prediction of SNO sites is crucial in revealing a certain biological mechanism of NO regulation and related drug development. Identification of the sites of SNO in proteins is currently a very hot topic. In this review, we briefly summarize recent advances in computationally identifying SNO sites. The challenges and future perspectives for identifying SNO sites are also discussed. We anticipate that this review will provide insights into research on SNO site prediction.
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