1
|
Tong XY, Quan Y, Zhang HY. NUDT5 as a novel drug target and prognostic biomarker for ER-positive breast cancer. Drug Discov Today 2020; 26:620-625. [PMID: 33276127 DOI: 10.1016/j.drudis.2020.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/15/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022]
Abstract
Breast cancer (BRCA) is the most common malignant tumor in women. The estrogen receptor-positive (ER+) subtype accounts for ∼70% of BRCA cases. Estrogen is a crucial hormone that directly stimulates the growth and development of mammary glands. Recent studies revealed that, as an estrogen cofactor, ATP has an important role in determining the action of estrogen by mediating phase separation. NUDT5 has been recognized as a key factor for ATP production in the nucleus of BRCA cells and, therefore, could represent a novel drug target for ER+ BRCA. Based on a survival analysis of patients with BRCA documented in The Cancer Genome Atlas (TGCA) database, we show that NUDT5 is also a potential prognostic biomarker for ER+ BRCA.
Collapse
Affiliation(s)
- Xin-Yu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
| |
Collapse
|
2
|
Tong XY, Liao X, Gao M, Lv BM, Chen XH, Chu XY, Zhang QY, Zhang HY. Identification of NUDT5 Inhibitors From Approved Drugs. Front Mol Biosci 2020; 7:44. [PMID: 32300600 PMCID: PMC7145388 DOI: 10.3389/fmolb.2020.00044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent studies have revealed the important role of NUDT5 in estrogen signaling and breast cancer, but research on the corresponding targeted therapy has just started. Drug repositioning strategy can effectively reduce the time and economic resources spent on drug discovery. To find novel inhibitors of NUDT5, we investigated the previously identified connectivity map-based drug association models and found eighteen FDA approved drugs as candidates. The molecular docking and molecular dynamic simulation were performed and revealed that fourteen organic drugs have the potential to bind the NUDT5 target. Eight representative drugs were selected to perform the cell line viability inhibition analysis, and the results showed that seven of them were able to suppress MCF7 breast cancer cells. Two drugs, nomifensine and isoconazole, showed lower IC50 than the known antiestrogens raloxifene and tamoxifen, and they deserve further pharmacodynamic investigations to test their feasibility for use as NUDT5 inhibitors.
Collapse
Affiliation(s)
- Xin-Yu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xuan Liao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Min Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Bo-Min Lv
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Hui Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
3
|
Liao X, Zhang Q, Xu L, Zhang H. Potential Targets of Actein Identified by Systems Chemical Biology Methods. ChemMedChem 2020; 15:473-480. [DOI: 10.1002/cmdc.201900499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/03/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Xuan Liao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of InformaticsHuazhong Agricultural University Wuhan 430070 China
| | - Qing‐Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of InformaticsHuazhong Agricultural University Wuhan 430070 China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering School of Electrical and Information EngineeringJiangsu University of Technology Changzhou 213001 China
| | - Hong‐Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of InformaticsHuazhong Agricultural University Wuhan 430070 China
| |
Collapse
|
4
|
Gao M, Tang GY. Structural Basis for Great Protein-Binding Potential of Flavonoids: A Case Study of Quercetin. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701201142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Flavonoids exhibit a wide variety of biological effects and hold great protein-binding potential. In this study, we take quercetin, an extensively studied flavonoid, as an example to investigate the structural basis underlying their excellent protein-binding ability. Through calculating the pocket similarity of quercetin-binding proteins and comparing the binding modes between quercetins bound with different proteins, it was found that the great protein-binding capacity of quercetin not only arises from the structural conservation of target proteins, but also stems from its unique structure, in which molecular rigidity and flexibility is well-balanced and various chemical interactions could be formed between the small molecule and protein targets.
Collapse
Affiliation(s)
- Min Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Guang-Yan Tang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| |
Collapse
|
5
|
Isgut M, Rao M, Yang C, Subrahmanyam V, Rida PCG, Aneja R. Application of Combination High-Throughput Phenotypic Screening and Target Identification Methods for the Discovery of Natural Product-Based Combination Drugs. Med Res Rev 2017; 38:504-524. [DOI: 10.1002/med.21444] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 02/06/2017] [Accepted: 03/01/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Monica Isgut
- Department of Biology; Georgia State University; Atlanta GA 30303
| | - Mukkavilli Rao
- Department of Biology; Georgia State University; Atlanta GA 30303
| | - Chunhua Yang
- Department of Biology; Georgia State University; Atlanta GA 30303
| | | | - Padmashree C. G. Rida
- Department of Biology; Georgia State University; Atlanta GA 30303
- Novazoi Theranostics; Rolling Hills Estates CA 90274
| | - Ritu Aneja
- Department of Biology; Georgia State University; Atlanta GA 30303
| |
Collapse
|
6
|
Quan Y, Xiong L, Chen J, Zhang HY. Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection. J Biomol Struct Dyn 2016; 35:616-621. [DOI: 10.1080/07391102.2016.1157037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Le Xiong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jing Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| |
Collapse
|
7
|
Tang GY. Why Polyphenols have Promiscuous Actions? An Investigation by Chemical Bioinformatics. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Despite their diverse pharmacological effects, polyphenols are poor for use as drugs, which have been traditionally ascribed to their low bioavailability. However, Baell and co-workers recently proposed that the redox potential of polyphenols also plays an important role in this, because redox reactions bring promiscuous actions on various protein targets and thus produce non-specific pharmacological effects. To investigate whether the redox reactivity behaves as a critical factor in polyphenol promiscuity, we performed a chemical bioinformatics analysis on the structure-activity relationships of twenty polyphenols. It was found that the gene expression profiles of human cell lines induced by polyphenols were not correlated with the presence or not of redox moieties in the polyphenols, but significantly correlated with their molecular structures. Therefore, it is concluded that the promiscuous actions of polyphenols are likely to result from their inherent structural features rather than their redox potential.
Collapse
Affiliation(s)
- Guang-Yan Tang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| |
Collapse
|
8
|
Quan Y, Li B, Sun YM, Zhang HY. Elucidating pharmacological mechanisms of natural medicines by biclustering analysis of the gene expression profile: a case study on curcumin and Si-Wu-Tang. Int J Mol Sci 2014; 16:510-20. [PMID: 25551600 PMCID: PMC4307259 DOI: 10.3390/ijms16010510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/19/2014] [Indexed: 12/16/2022] Open
Abstract
Natural medicines have attracted wide attention in recent years. It is of great significance to clarify the pharmacological mechanisms of natural medicines. In prior studies, we established a method for elucidating pharmacological mechanisms of natural products contained in connectivity map (cMap), in terms of module profiles of gene expression in chemical treatments. In this study, we explore whether this methodology is applicable to dissecting the pharmacological mechanisms of natural medicines beyond the agents contained in cMap. First, the gene expression profiles of curcumin (a typical isolated natural medicine) and Si-Wu-Tang (a classic traditional Chinese medicine formula) treatments were merged with those of cMap-derived 1309 agents, respectively. Then, a biclustering analysis was performed using FABIA method to identify gene modules. The biological functions of gene modules provide preliminary insights into pharmacological mechanisms of both natural medicines. The module profile can be characterized by a binary vector, which allowed us to compare the expression profiles of natural medicines with those of cMap-derived agents. Accordingly, we predicted a series of pharmacological effects for curcumin and Si-Wu-Tang by the indications of cMap-covered drugs. Most predictions were supported by experimental observations, suggesting the potential use of this method in natural medicine dissection.
Collapse
Affiliation(s)
- Yuan Quan
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Bin Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - You-Min Sun
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China.
| | - Hong-Yu Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
9
|
Zhong WZ, Zhou SF. Molecular science for drug development and biomedicine. Int J Mol Sci 2014; 15:20072-8. [PMID: 25375190 PMCID: PMC4264156 DOI: 10.3390/ijms151120072] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/24/2014] [Indexed: 01/21/2023] Open
Affiliation(s)
- Wei-Zhu Zhong
- Gordon Life Science Institute, Belmont, MA 02478, USA.
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|