1
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Sarhan MO, Haffez H, Elsayed NA, El-Haggar RS, Zaghary WA. New phenothiazine conjugates as apoptosis inducing agents: Design, synthesis, In-vitro anti-cancer screening and 131I-radiolabeling for in-vivo evaluation. Bioorg Chem 2023; 141:106924. [PMID: 37871390 DOI: 10.1016/j.bioorg.2023.106924] [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: 08/22/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Phenothiazines (PTZs) are a group of compounds characterized by the presence of the 10H-dibenzo-[b,e]-1,4-thiazine system. PTZs used in clinics as antipsychotic drugs with other diverse biological activities. The current aim of the study is to investigate and understand the effect of potent PTZs compounds using a group of In-vitro and In-vivo assays. A total of seventeen novel phenothiazine derivatives have been designed, synthesized, and evaluated primarily in-vitro for their ability to inhibit proliferation activity against NCI-60 cancer cell lines, including several multi-drug resistant (MDR) tumor cell lines. Almost all compounds were active and displayed promising cellular activities with GI50 values in the sub-micromolar range. Four of the most promising derivatives (4b, 4h, 4g and 6e) have been further tested against two selected sensitive cancer cell lines (colon cancer; HCT-116 and breast cancer; MDA-MB231). The apoptosis assay showed that all the selected compounds were able to induce early apoptosis and compound 6e was able to induce additional cellular necrosis. Cell cycle assay showed all selected compounds were able to induce cell cycle arrest at sub-molecular phase of G0-G1 with compound 6e induced cell cycle arrest at G2M in HCT-116 cells. Accordingly, the apoptotic effect of the selected compounds was extensively investigated on genetic level and Casp-3, Casp-9 and Bax gene were up-regulated with down-regulation of Bcl-2 gene suggesting the activation of both intrinsic and extrinsic pathways. In-vivo evaluation of the antitumor activity of compound 4b in solid tumor bearing mice showed promising therapeutic effect with manifestation of dose and time dependent toxic effects at higher doses. For better evaluation of the degree of localization of 4b, its 131I-congener (131I-4b) was injected intravenously in Ehrlich solid tumor bearing mice that showed good localization at tumor site with rapid distribution and clearance from the blood. In-silico study suggested NADPH oxidases (NOXs) as potential molecular target. The compounds introduced in the current study work provided a cutting-edge phenothiazine hybrid scaffold with promising anti-proliferation action that may suggest their anti-cancer activity.
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Affiliation(s)
- Mona O Sarhan
- Labelled Compounds Department, Hot Lab Centre, Egyptian Atomic Energy Authority, Egypt
| | - Hesham Haffez
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt; Center of Scientific Excellence "Helwan Structural Biology Research, (HSBR)", Helwan University, 11795 Cairo, Egypt.
| | - Nosaiba A Elsayed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt
| | - Radwan S El-Haggar
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt
| | - Wafaa A Zaghary
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt.
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2
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Li Q, Ma Z, Qin S, Zhao WJ. Virtual Screening-Based Drug Development for the Treatment of Nervous System Diseases. Curr Neuropharmacol 2023; 21:2447-2464. [PMID: 36043797 PMCID: PMC10616913 DOI: 10.2174/1570159x20666220830105350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022] Open
Abstract
The incidence rate of nervous system diseases has increased in recent years. Nerve injury or neurodegenerative diseases usually cause neuronal loss and neuronal circuit damage, which seriously affect motor nerve and autonomic nervous function. Therefore, safe and effective treatment is needed. As traditional drug research becomes slower and more expensive, it is vital to enlist the help of cutting- edge technology. Virtual screening (VS) is an attractive option for the identification and development of promising new compounds with high efficiency and low cost. With the assistance of computer- aided drug design (CADD), VS is becoming more and more popular in new drug development and research. In recent years, it has become a reality to transform non-neuronal cells into functional neurons through small molecular compounds, which provides a broader application prospect than transcription factor-mediated neuronal reprogramming. This review mainly summarizes related theory and technology of VS and the drug research and development using VS technology in nervous system diseases in recent years, and focuses more on the potential application of VS technology in neuronal reprogramming, thus facilitating new drug design for both prevention and treatment of nervous system diseases.
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Affiliation(s)
- Qian Li
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Zhaobin Ma
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, Yunnan, P.R. China
| | - Shuhua Qin
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, Yunnan, P.R. China
| | - Wei-Jiang Zhao
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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3
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Xu L, Ru X, Song R. Application of Machine Learning for Drug-Target Interaction Prediction. Front Genet 2021; 12:680117. [PMID: 34234813 PMCID: PMC8255962 DOI: 10.3389/fgene.2021.680117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Exploring drug–target interactions by biomedical experiments requires a lot of human, financial, and material resources. To save time and cost to meet the needs of the present generation, machine learning methods have been introduced into the prediction of drug–target interactions. The large amount of available drug and target data in existing databases, the evolving and innovative computer technologies, and the inherent characteristics of various types of machine learning have made machine learning techniques the mainstream method for drug–target interaction prediction research. In this review, details of the specific applications of machine learning in drug–target interaction prediction are summarized, the characteristics of each algorithm are analyzed, and the issues that need to be further addressed and explored for future research are discussed. The aim of this review is to provide a sound basis for the construction of high-performance models.
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Affiliation(s)
- Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Xiaoqing Ru
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Rong Song
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
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4
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Matsumoto K, Miyao T, Funatsu K. Ranking-Oriented Quantitative Structure-Activity Relationship Modeling Combined with Assay-Wise Data Integration. ACS OMEGA 2021; 6:11964-11973. [PMID: 34056351 PMCID: PMC8154010 DOI: 10.1021/acsomega.1c00463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 05/15/2023]
Abstract
In ligand-based drug design, quantitative structure-activity relationship (QSAR) models play an important role in activity prediction. One of the major end points of QSAR models is half-maximal inhibitory concentration (IC50). Experimental IC50 data from various research groups have been accumulated in publicly accessible databases, providing an opportunity for us to use such data in predictive QSAR models. In this study, we focused on using a ranking-oriented QSAR model as a predictive model because relative potency strength within the same assay is solid information that is not based on any mechanical assumptions. We conducted rigorous validation using the ChEMBL database and previously reported data sets. Ranking support vector machine (ranking-SVM) models trained on compounds from similar assays were as good as support vector regression (SVR) with the Tanimoto kernel trained on compounds from all the assays. As effective ways of data integration, for ranking-SVM, integrated compounds should be selected from only similar assays in terms of compounds. For SVR with the Tanimoto kernel, entire compounds from different assays can be incorporated.
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Affiliation(s)
- Katsuhisa Matsumoto
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data
Science Center, Nara Institute of Science
and Technology, 8916-5
Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Kimito Funatsu
- Data
Science Center, Nara Institute of Science
and Technology, 8916-5
Takayama-cho, Ikoma, Nara, 630-0192, Japan
- Department
of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- E-mail: . Phone: +81-3-5841-7751. Fax: +81-3-5841-7771
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5
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Drug-Target Interaction Prediction Based on Adversarial Bayesian Personalized Ranking. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6690154. [PMID: 33628808 PMCID: PMC7889346 DOI: 10.1155/2021/6690154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/17/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022]
Abstract
The prediction of drug-target interaction (DTI) is a key step in drug repositioning. In recent years, many studies have tried to use matrix factorization to predict DTI, but they only use known DTIs and ignore the features of drug and target expression profiles, resulting in limited prediction performance. In this study, we propose a new DTI prediction model named AdvB-DTI. Within this model, the features of drug and target expression profiles are associated with Adversarial Bayesian Personalized Ranking through matrix factorization. Firstly, according to the known drug-target relationships, a set of ternary partial order relationships is generated. Next, these partial order relationships are used to train the latent factor matrix of drugs and targets using the Adversarial Bayesian Personalized Ranking method, and the matrix factorization is improved by the features of drug and target expression profiles. Finally, the scores of drug-target pairs are achieved by the inner product of latent factors, and the DTI prediction is performed based on the score ranking. The proposed model effectively takes advantage of the idea of learning to rank to overcome the problem of data sparsity, and perturbation factors are introduced to make the model more robust. Experimental results show that our model could achieve a better DTI prediction performance.
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6
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Ru X, Ye X, Sakurai T, Zou Q. Application of learning to rank in bioinformatics tasks. Brief Bioinform 2021; 22:6102666. [PMID: 33454758 DOI: 10.1093/bib/bbaa394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decades, learning to rank (LTR) algorithms have been gradually applied to bioinformatics. Such methods have shown significant advantages in multiple research tasks in this field. Therefore, it is necessary to summarize and discuss the application of these algorithms so that these algorithms are convenient and contribute to bioinformatics. In this paper, the characteristics of LTR algorithms and their strengths over other types of algorithms are analyzed based on the application of multiple perspectives in bioinformatics. Finally, the paper further discusses the shortcomings of the LTR algorithms, the methods and means to better use the algorithms and some open problems that currently exist.
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Affiliation(s)
| | - Xiucai Ye
- Department of Computer Science and Center for Artificial Intelligence Research (C-AIR), University of Tsukuba
| | | | - Quan Zou
- University of Electronic Science and Technology of China
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7
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Zarei O, Faham N, Vankayalapati H, Raeppel SL, Welm AL, Hamzeh-Mivehroud M. Ligand-based Discovery of Novel Small Molecule Inhibitors of RON Receptor Tyrosine Kinase. Mol Inform 2020; 41:e2000181. [PMID: 33274845 DOI: 10.1002/minf.202000181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/18/2020] [Indexed: 11/05/2022]
Abstract
BACKGROUND RON (Recepteur d'Origine Nantais) receptor tyrosine kinase is a promising target for anti-cancer therapeutics. The aim of this study was to identify new RON inhibitors using virtual screening methods. METHODS To this end, a ligand-based virtual screening approach was employed for screening of ZINC database on the homology model of RON receptor. All the selected hits were inspected in terms of drug-likeness, ADME properties, and toxicity profiles. Ligand-based similarity searches along with further filtering criteria led to the identification of two compounds, TKI1 and TKI2 that were evaluated using in vitro cell-based RON inhibition assays. RESULTS The results showed that TKI1 and TKI2 could reduce phosphorylation of RON. Both compounds showed inhibitory activity of the downstream mTOR pathway with no apparent effects on other signaling mediators in a dose-dependent manner. CONCLUSION These compounds can provide a basis for developing novel anti-RON inhibitors applicable to cancer therapy using medicinal chemistry-oriented optimization strategies.
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Affiliation(s)
- Omid Zarei
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Najme Faham
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Hariprasad Vankayalapati
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Stéphane L Raeppel
- ChemRF Laboratories, 3194, rue Claude-Jodoin, Montréal, QC, H1Y 3M2, Canada
| | - Alana L Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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8
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Peng B, Yao X, Risacher SL, Saykin AJ, Shen L, Ning X. Cognitive biomarker prioritization in Alzheimer's Disease using brain morphometric data. BMC Med Inform Decis Mak 2020; 20:319. [PMID: 33267852 PMCID: PMC7709267 DOI: 10.1186/s12911-020-01339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Cognitive assessments represent the most common clinical routine for the diagnosis of Alzheimer's Disease (AD). Given a large number of cognitive assessment tools and time-limited office visits, it is important to determine a proper set of cognitive tests for different subjects. Most current studies create guidelines of cognitive test selection for a targeted population, but they are not customized for each individual subject. In this manuscript, we develop a machine learning paradigm enabling personalized cognitive assessments prioritization. METHOD We adapt a newly developed learning-to-rank approach [Formula: see text] to implement our paradigm. This method learns the latent scoring function that pushes the most effective cognitive assessments onto the top of the prioritization list. We also extend [Formula: see text] to better separate the most effective cognitive assessments and the less effective ones. RESULTS Our empirical study on the ADNI data shows that the proposed paradigm outperforms the state-of-the-art baselines on identifying and prioritizing individual-specific cognitive biomarkers. We conduct experiments in cross validation and level-out validation settings. In the two settings, our paradigm significantly outperforms the best baselines with improvement as much as 22.1% and 19.7%, respectively, on prioritizing cognitive features. CONCLUSIONS The proposed paradigm achieves superior performance on prioritizing cognitive biomarkers. The cognitive biomarkers prioritized on top have great potentials to facilitate personalized diagnosis, disease subtyping, and ultimately precision medicine in AD.
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Affiliation(s)
- Bo Peng
- The Ohio State University, Columbus, USA
| | - Xiaohui Yao
- University of Pennsylvania, Philadelphia, USA
| | | | | | - Li Shen
- University of Pennsylvania, Philadelphia, USA
| | - Xia Ning
- The Ohio State University, Columbus, USA
| | - for the ADNI
- The Ohio State University, Columbus, USA
- University of Pennsylvania, Philadelphia, USA
- Indiana University, Indianapolis, USA
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9
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How Sure Can We Be about ML Methods-Based Evaluation of Compound Activity: Incorporation of Information about Prediction Uncertainty Using Deep Learning Techniques. Molecules 2020; 25:molecules25061452. [PMID: 32210186 PMCID: PMC7144469 DOI: 10.3390/molecules25061452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/22/2020] [Indexed: 11/17/2022] Open
Abstract
A great variety of computational approaches support drug design processes, helping in selection of new potentially active compounds, and optimization of their physicochemical and ADMET properties. Machine learning is a group of methods that are able to evaluate in relatively short time enormous amounts of data. However, the quality of machine-learning-based prediction depends on the data supplied for model training. In this study, we used deep neural networks for the task of compound activity prediction and developed dropout-based approaches for estimating prediction uncertainty. Several types of analyses were performed: the relationships between the prediction error, similarity to the training set, prediction uncertainty, number and standard deviation of activity values were examined. It was tested whether incorporation of information about prediction uncertainty influences compounds ranking based on predicted activity and prediction uncertainty was used to search for the potential errors in the ChEMBL database. The obtained outcome indicates that incorporation of information about uncertainty of compound activity prediction can be of great help during virtual screening experiments.
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10
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Ru X, Wang L, Li L, Ding H, Ye X, Zou Q. Exploration of the correlation between GPCRs and drugs based on a learning to rank algorithm. Comput Biol Med 2020; 119:103660. [PMID: 32090901 DOI: 10.1016/j.compbiomed.2020.103660] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/04/2020] [Accepted: 02/12/2020] [Indexed: 02/01/2023]
Abstract
Exploring the protein - drug correlation can not only solve the problem of selecting candidate compounds but also solve related problems such as drug redirection and finding potential drug targets. Therefore, many researchers have proposed different machine learning methods for prediction of protein-drug correlations. However, many existing models simply divide the protein-drug relationship into related or irrelevant categories and do not deeply explore the most relevant target (or drug) for a given drug (or target). In order to solve this problem, this paper applies the ranking concept to the prediction of the GPCR (G Protein-Coupled Receptors)-drug correlation. This study uses two different types of data sets to explore candidate compound and potential target problems, and both sets achieved good results. In addition, this study also found that the family to which a protein belongs is not an inherent factor that affects the ranking of GPCR-drug correlations; however, if the drug affects other family members of the protein, then the protein is likely to be a potential target of the drug. This study showed that the learning to rank algorithm is a good tool for exploring protein-drug correlations.
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Affiliation(s)
- Xiaoqing Ru
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China; School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Lida Wang
- Scientific Research Department, Heilongjiang Agricultural Recalmation General Hospital, Harbin, China.
| | - Lihong Li
- School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Hui Ding
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba Science City, Japan
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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11
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He Y, Liu J, Ning X. Drug Selection via Joint Push and Learning to Rank. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:110-123. [PMID: 29994481 DOI: 10.1109/tcbb.2018.2848908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Selecting the right drugs for the right patients is a primary goal of precision medicine. In this article, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1) the ranking positions of sensitive drugs and 2) the ranking orders among sensitive drugs in cancer cell lines based on their responses to cancer drugs. We have developed a new learning-to-rank method, denoted as pLETORg, that predicts drug ranking structures in each cell line via using drug latent vectors and cell line latent vectors. The pLETORg method learns such latent vectors through explicitly enforcing that, in the drug ranking list of each cell line, the sensitive drugs are pushed above insensitive drugs, and meanwhile the ranking orders among sensitive drugs are correct. Genomics information on cell lines is leveraged in learning the latent vectors. Our experimental results on a benchmark cell line-drug response dataset demonstrate that the new pLETORg significantly outperforms the state-of-the-art method in prioritizing new sensitive drugs.
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12
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Learning-to-rank technique based on ignoring meaningless ranking orders between compounds. J Mol Graph Model 2019; 92:192-200. [DOI: 10.1016/j.jmgm.2019.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022]
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13
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Soekhai V, Whichello C, Levitan B, Veldwijk J, Pinto CA, Donkers B, Huys I, van Overbeeke E, Juhaeri J, de Bekker-Grob EW. Methods for exploring and eliciting patient preferences in the medical product lifecycle: a literature review. Drug Discov Today 2019; 24:1324-1331. [PMID: 31077814 DOI: 10.1016/j.drudis.2019.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/08/2019] [Accepted: 05/02/2019] [Indexed: 01/13/2023]
Abstract
Preference studies are becoming increasingly important within the medical product decision-making context. Currently, there is limited understanding of the range of methods to gain insights into patient preferences. We developed a compendium and taxonomy of preference exploration (qualitative) and elicitation (quantitative) methods by conducting a systematic literature review to identify these methods. This review was followed by analyzing prior preference method reviews, to cross-validate our results, and consulting intercontinental experts, to confirm our outcomes. This resulted in the identification of 32 unique preference methods. The developed compendium and taxonomy can serve as an important resource for assessing these methods and helping to determine which are most appropriate for different research questions at varying points in the medical product lifecycle.
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Affiliation(s)
- Vikas Soekhai
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Erasmus Choice Modelling Centre, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Department of Public Health, Erasmus MC - University Medical Centre, Dr. Molewaterplein 40, 3000 CA Rotterdam
| | - Chiara Whichello
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Erasmus Choice Modelling Centre, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands
| | - Bennett Levitan
- Janssen Research & Development, 1125 Trenton-Harbourton Road, PO Box 200, Titusville, NJ, 08560, USA
| | - Jorien Veldwijk
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Erasmus Choice Modelling Centre, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands
| | - Cathy Anne Pinto
- Merck, Sharpe & Dome, 2000 Galloping Hill Rd., Kenilworth, NJ, 07033, USA
| | - Bas Donkers
- Department of Business Economics, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Erasmus Choice Modelling Centre, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands
| | - Isabelle Huys
- Clinical Pharmacology and Pharmacotherapy, University of Leuven, Herestraat 49 Box 521, Leuven, 3000 Belgium
| | - Eline van Overbeeke
- Clinical Pharmacology and Pharmacotherapy, University of Leuven, Herestraat 49 Box 521, Leuven, 3000 Belgium
| | | | - Esther W de Bekker-Grob
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands; Erasmus Choice Modelling Centre, Erasmus University Rotterdam, P.O. Box 1738, Rotterdam, 3000 DR the Netherlands.
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14
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Yasuo N, Sekijima M. Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning. J Chem Inf Model 2019; 59:1050-1061. [PMID: 30808172 DOI: 10.1021/acs.jcim.8b00673] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Virtual screening is a promising method for obtaining novel hit compounds in drug discovery. It aims to enrich potentially active compounds from a large chemical library for further biological experiments. However, the accuracy of current virtual screening methods is insufficient. In this study, we develop a new virtual screening method named Similarity of Interaction Energy VEctor Score (SIEVE-Score), in which protein-ligand interaction energies are extracted to represent docking poses for machine learning. SIEVE-Score offers substantial improvements compared to other state-of-the-art virtual screening methods, namely, other machine-learning-based scoring functions, interaction fingerprints, and docking software, for the enrichment factor 1% results on the Directory of Useful Decoys, Enhanced (DUD-E). The screening results are also human-interpretable in the form of important interactions for distinguishing between active and inactive compounds. The source code is available at https://github.com/sekijima-lab/SIEVE-Score .
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Affiliation(s)
- Nobuaki Yasuo
- Department of Computer Science , Tokyo Institute of Technology , 4259-J3-23, Nagatsuta-cho , Midori-ku, Yokohama , Japan
| | - Masakazu Sekijima
- Department of Computer Science , Tokyo Institute of Technology , 4259-J3-23, Nagatsuta-cho , Midori-ku, Yokohama , Japan.,Advanced Computational Drug Discovery Unit , Tokyo Institute of Technology , 4259-J3-23, Nagatsuta-cho , Midori-ku, Yokohama , Japan
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15
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Prediction Methods of Herbal Compounds in Chinese Medicinal Herbs. Molecules 2018; 23:molecules23092303. [PMID: 30201875 PMCID: PMC6225236 DOI: 10.3390/molecules23092303] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
Chinese herbal medicine has recently gained worldwide attention. The curative mechanism of Chinese herbal medicine is compared with that of western medicine at the molecular level. The treatment mechanism of most Chinese herbal medicines is still not clear. How do we integrate Chinese herbal medicine compounds with modern medicine? Chinese herbal medicine drug-like prediction method is particularly important. A growing number of Chinese herbal source compounds are now widely used as drug-like compound candidates. An important way for pharmaceutical companies to develop drugs is to discover potentially active compounds from related herbs in Chinese herbs. The methods for predicting the drug-like properties of Chinese herbal compounds include the virtual screening method, pharmacophore model method and machine learning method. In this paper, we focus on the prediction methods for the medicinal properties of Chinese herbal medicines. We analyze the advantages and disadvantages of the above three methods, and then introduce the specific steps of the virtual screening method. Finally, we present the prospect of the joint application of various methods.
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QEX: target-specific druglikeness filter enhances ligand-based virtual screening. Mol Divers 2018; 23:11-18. [PMID: 29971617 PMCID: PMC6394530 DOI: 10.1007/s11030-018-9842-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/12/2018] [Indexed: 11/22/2022]
Abstract
Druglikeness is a useful concept for screening drug candidate compounds. We developed QEX, which is a new druglikeness index specific to individual targets. QEX is an improvement of the quantitative estimate of druglikeness (QED) method, which is a popular quantitative evaluation method of druglikeness proposed by Bickerton et al. QEX models the physicochemical properties of compounds that act on each target protein based on the concept of QED modeling physicochemical properties from information on US Food and Drug Administration-approved drugs. The result of the evaluation of PubChem assay data revealed that QEX showed better performance than the original QED did (the area under the curve value of the receiver operating characteristic curve improved by 0.069-0.236). We also present the c-Src inhibitor filtering results of the QEX constructed using Src family kinase inhibitors as a case study. QEX distinguished the inhibitors and non-inhibitors better than QED did. QEX works efficiently even when datasets of inactive compounds are unavailable. If both active and inactive compounds are present, QEX can be used as an initial filter to enhance the screening ability of conventional ligand-based virtual screenings.
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Suzuki SD, Ohue M, Akiyama Y. PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM. ARTIFICIAL LIFE AND ROBOTICS 2017. [DOI: 10.1007/s10015-017-0416-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yuan Q, Gao J, Wu D, Zhang S, Mamitsuka H, Zhu S. DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinformatics 2017; 32:i18-i27. [PMID: 27307615 PMCID: PMC4908328 DOI: 10.1093/bioinformatics/btw244] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Motivation: Identifying drug–target interactions is an important task in drug discovery. To reduce heavy time and financial cost in experimental way, many computational approaches have been proposed. Although these approaches have used many different principles, their performance is far from satisfactory, especially in predicting drug–target interactions of new candidate drugs or targets. Methods: Approaches based on machine learning for this problem can be divided into two types: feature-based and similarity-based methods. Learning to rank is the most powerful technique in the feature-based methods. Similarity-based methods are well accepted, due to their idea of connecting the chemical and genomic spaces, represented by drug and target similarities, respectively. We propose a new method, DrugE-Rank, to improve the prediction performance by nicely combining the advantages of the two different types of methods. That is, DrugE-Rank uses LTR, for which multiple well-known similarity-based methods can be used as components of ensemble learning. Results: The performance of DrugE-Rank is thoroughly examined by three main experiments using data from DrugBank: (i) cross-validation on FDA (US Food and Drug Administration) approved drugs before March 2014; (ii) independent test on FDA approved drugs after March 2014; and (iii) independent test on FDA experimental drugs. Experimental results show that DrugE-Rank outperforms competing methods significantly, especially achieving more than 30% improvement in Area under Prediction Recall curve for FDA approved new drugs and FDA experimental drugs. Availability:http://datamining-iip.fudan.edu.cn/service/DrugE-Rank Contact:zhusf@fudan.edu.cn Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qingjun Yuan
- School of Computer Science, Fudan University, Shanghai, China Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
| | - Junning Gao
- School of Computer Science, Fudan University, Shanghai, China Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
| | - Dongliang Wu
- School of Computer Science, Fudan University, Shanghai, China Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
| | - Shihua Zhang
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Hiroshi Mamitsuka
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan Department of Computer Science, Aalto University, Finland
| | - Shanfeng Zhu
- School of Computer Science, Fudan University, Shanghai, China Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China Centre for Computational System Biology, Fudan University, Shanghai, China
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Wang B, Zhao Z, Nguyen DD, Wei GW. Feature functional theory–binding predictor (FFT–BP) for the blind prediction of binding free energies. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2083-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Liu J, Ning X. Multi-Assay-Based Compound Prioritization via Assistance Utilization: A Machine Learning Framework. J Chem Inf Model 2017; 57:484-498. [PMID: 28234477 DOI: 10.1021/acs.jcim.6b00737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junfeng Liu
- Indiana University-Purdue University, Indianapolis, 723 West Michigan St., SL 280, Indianapolis, Indiana 46202, United States
| | - Xia Ning
- Indiana University-Purdue University, Indianapolis, 723 West Michigan St., SL 280, Indianapolis, Indiana 46202, United States
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th St., HITS 5000, Indianapolis, Indiana 46202, United States
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Wang K, Wan M, Wang RS, Weng Z. Opportunities for Web-based Drug Repositioning: Searching for Potential Antihypertensive Agents with Hypotension Adverse Events. J Med Internet Res 2016; 18:e76. [PMID: 27036325 PMCID: PMC4833875 DOI: 10.2196/jmir.4541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 12/02/2015] [Accepted: 01/04/2016] [Indexed: 12/21/2022] Open
Abstract
Background Drug repositioning refers to the process of developing new indications for existing drugs. As a phenotypic indicator of drug response in humans, clinical side effects may provide straightforward signals and unique opportunities for drug repositioning. Objective We aimed to identify drugs frequently associated with hypotension adverse reactions (ie, the opposite condition of hypertension), which could be potential candidates as antihypertensive agents. Methods We systematically searched the electronic records of the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) through the openFDA platform to assess the association between hypotension incidence and antihypertensive therapeutic effect regarding a list of 683 drugs. Results Statistical analysis of FAERS data demonstrated that those drugs frequently co-occurring with hypotension events were more likely to have antihypertensive activity. Ranked by the statistical significance of frequent hypotension reporting, the well-known antihypertensive drugs were effectively distinguished from others (with an area under the receiver operating characteristic curve > 0.80 and a normalized discounted cumulative gain of 0.77). In addition, we found a series of antihypertensive agents (particularly drugs originally developed for treating nervous system diseases) among the drugs with top significant reporting, suggesting the good potential of Web-based and data-driven drug repositioning. Conclusions We found several candidate agents among the hypotension-related drugs on our list that may be redirected for lowering blood pressure. More important, we showed that a pharmacovigilance system could alternatively be used to identify antihypertensive agents and sustainably create opportunities for drug repositioning.
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Affiliation(s)
- Kejian Wang
- CoMed Technology & Consulting Co., Ltd., Hong Kong, China
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