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Chunarkar-Patil P, Kaleem M, Mishra R, Ray S, Ahmad A, Verma D, Bhayye S, Dubey R, Singh HN, Kumar S. Anticancer Drug Discovery Based on Natural Products: From Computational Approaches to Clinical Studies. Biomedicines 2024; 12:201. [PMID: 38255306 PMCID: PMC10813144 DOI: 10.3390/biomedicines12010201] [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: 12/02/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Globally, malignancies cause one out of six mortalities, which is a serious health problem. Cancer therapy has always been challenging, apart from major advances in immunotherapies, stem cell transplantation, targeted therapies, hormonal therapies, precision medicine, and palliative care, and traditional therapies such as surgery, radiation therapy, and chemotherapy. Natural products are integral to the development of innovative anticancer drugs in cancer research, offering the scientific community the possibility of exploring novel natural compounds against cancers. The role of natural products like Vincristine and Vinblastine has been thoroughly implicated in the management of leukemia and Hodgkin's disease. The computational method is the initial key approach in drug discovery, among various approaches. This review investigates the synergy between natural products and computational techniques, and highlights their significance in the drug discovery process. The transition from computational to experimental validation has been highlighted through in vitro and in vivo studies, with examples such as betulinic acid and withaferin A. The path toward therapeutic applications have been demonstrated through clinical studies of compounds such as silvestrol and artemisinin, from preclinical investigations to clinical trials. This article also addresses the challenges and limitations in the development of natural products as potential anti-cancer drugs. Moreover, the integration of deep learning and artificial intelligence with traditional computational drug discovery methods may be useful for enhancing the anticancer potential of natural products.
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Affiliation(s)
- Pritee Chunarkar-Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune 411046, Maharashtra, India
| | - Mohammed Kaleem
- Department of Pharmacology, Dadasaheb Balpande, College of Pharmacy, Nagpur 440037, Maharashtra, India;
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Ta. Waghodia, Vadodara 391760, Gujarat, India;
| | - Subhasree Ray
- Department of Life Science, Sharda School of Basic Sciences and Research, Greater Noida 201310, Uttar Pradesh, India
| | - Aftab Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Pharmacovigilance and Medication Safety Unit, Center of Research Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun 248002, Uttarkhand, India;
| | - Sagar Bhayye
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune 411046, Maharashtra, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Himanshu Narayan Singh
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida 201310, Uttar Pradesh, India
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Yadav V, Banerjee S, Baidya SK, Adhikari N, Jha T. Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:1-22. [PMID: 34979835 DOI: 10.1080/1062936x.2021.2013317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Histone deacetylase 2 (HDAC2) has been implicated in a variety of cardiovascular and neurodegenerative disorders as well as in cancers. Thus, HDAC2 has become an exclusive target for anticancer drug development. Therefore, the development of newer HDAC2 inhibitors in disease conditions is a prime goal to restrain such a scenario. Although a handful of HDAC inhibitors was accepted for the treatment of HDAC-related disease conditions, the non-selective nature of these entities is one of the major setbacks in the treatment of specific HDAC isoform-related pathophysiology. In this framework, the analyses of pre-existing molecules are essential to identify the important structural features that can fulfil the requirements for the cap and linker moieties to obtain potent and effective HDAC2 inhibition. Thus, in this study, the implementation of a combined comparative 2D and 3D molecular modelling techniques was done on a group of 92 diverse hydroxamate derivatives having a wide range of HDAC2 inhibitory potency. Besides other crucial features, this study upheld the importance of groups like triazole and benzyl moieties along with the molecular fields that are crucial for regulating HDAC2 inhibition. The outcomes of this study may be employed for the designing of HDAC2 inhibitors in future.
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Affiliation(s)
- V Yadav
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Tong J, Wang T, Feng Y. Drug design and molecular docking simulations of Polo-like kinase 1 inhibitors based on QSAR study. NEW J CHEM 2020. [DOI: 10.1039/d0nj04367b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Computationally exploring novel potential Polo-like kinase 1 inhibitors using a systematic modeling study.
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Affiliation(s)
- Jianbo Tong
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
| | - Tianhao Wang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
| | - Yi Feng
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
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Development of classification models for identification of important structural features of isoform-selective histone deacetylase inhibitors (class I). Mol Divers 2019; 24:1077-1094. [DOI: 10.1007/s11030-019-10013-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
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5
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Kamsri P, Punkvang A, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:775-800. [PMID: 31607177 DOI: 10.1080/1062936x.2019.1658218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC50 and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R2 substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.
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Affiliation(s)
- P Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - A Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - S Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University , Bangkok , Thailand
| | - K Suttisintong
- National Nanotechnology Center, NSTDA , Pathum Thani , Thailand
| | - P Kittakoop
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy , Bangkok , Thailand
- Chulabhorn Research Institute , Bangkok , Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education , Bangkok , Thailand
| | - J Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Bristol , UK
| | - A J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol , UK
| | - P Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University , Ubon Ratchathani , Thailand
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6
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Zheng J, Wörl B, Breit B. Rhodium-Catalyzed Chemo-, Regio-, and Enantioselective Allylation of 2-Aminothiazoles with Terminal Allenes. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jun Zheng
- Institut für Organische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Benjamin Wörl
- Institut für Organische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Bernhard Breit
- Institut für Organische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
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Li X, Zhou H, Mo X, Zhang L, Li J. In silico study of febuxostat analogs as inhibitors of xanthine oxidoreductase: A combined 3D-QSAR and molecular docking study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Shi J, Zhao G, Wei Y. Computational QSAR model combined molecular descriptors and fingerprints to predict HDAC1 inhibitors. Med Sci (Paris) 2018; 34 Focus issue F1:52-58. [PMID: 30403176 DOI: 10.1051/medsci/201834f110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dynamic balance between acetylation and deacetylation of histones plays a crucial role in the epigenetic regulation of gene expression. It is equilibrated by two families of enzymes: histone acetyltransferases and histone deacetylases (HDACs). HDACs repress transcription by regulating the conformation of the higher-order chromatin structure. HDAC inhibitors have recently become a class of chemical agents for potential treatment of the abnormal chromatin remodeling process involved in certain cancers. In this study, we constructed a large dataset to predict the activity value of HDAC1 inhibitors. Each compound was represented with seven fingerprints, and computational models were subsequently developed to predict HDAC1 inhibitors via five machine learning methods. These methods include naïve Bayes, κ-nearest neighbor, C4.5 decision tree, random forest, and support vector machine (SVM) algorithms. The best predicting model was CDK fingerprint with SVM, which exhibited an accuracy of 0.89. This model also performed best in five-fold cross-validation. Some representative substructure alerts responsible for HDAC1 inhibitors were identified by using MoSS in KNIME, which could facilitate the identification of HDAC1 inhibitors.
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Affiliation(s)
- Jingsheng Shi
- Division of Orthopaedic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Guanglei Zhao
- Division of Orthopaedic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yibing Wei
- Division of Orthopaedic Surgery, Huashan Hospital, Fudan University, Shanghai, China
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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Uba Aİ, Yelekçi K. Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors. Turk J Biol 2017; 41:901-918. [PMID: 30814855 DOI: 10.3906/biy-1701-26] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. "Classical" HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivity.
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Affiliation(s)
- Abdullahi İbrahim Uba
- Center for Biotechnology Research, Bayero University Kano , Nigeria.,Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University , İstanbul , Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University , İstanbul , Turkey
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Pham-The H, Casañola-Martin G, Diéguez-Santana K, Nguyen-Hai N, Ngoc NT, Vu-Duc L, Le-Thi-Thu H. Quantitative structure-activity relationship analysis and virtual screening studies for identifying HDAC2 inhibitors from known HDAC bioactive chemical libraries. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:199-220. [PMID: 28332438 DOI: 10.1080/1062936x.2017.1294198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/08/2017] [Indexed: 05/22/2023]
Abstract
Histone deacetylases (HDAC) are emerging as promising targets in cancer, neuronal diseases and immune disorders. Computational modelling approaches have been widely applied for the virtual screening and rational design of novel HDAC inhibitors. In this study, different machine learning (ML) techniques were applied for the development of models that accurately discriminate HDAC2 inhibitors form non-inhibitors. The obtained models showed encouraging results, with the global accuracy in the external set ranging from 0.83 to 0.90. Various aspects related to the comparison of modelling techniques, applicability domain and descriptor interpretations were discussed. Finally, consensus predictions of these models were used for screening HDAC2 inhibitors from four chemical libraries whose bioactivities against HDAC1, HDAC3, HDAC6 and HDAC8 have been known. According to the results of virtual screening assays, structures of some hits with pair-isoform-selective activity (between HDAC2 and other HDACs) were revealed. This study illustrates the power of ML-based QSAR approaches for the screening and discovery of potent, isoform-selective HDACIs.
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Affiliation(s)
- H Pham-The
- a Hanoi University of Pharmacy , Hanoi , Vietnam
| | - G Casañola-Martin
- b Department of Systems and Computer Engineering , Carleton University , Ottawa , ON , Canada
| | - K Diéguez-Santana
- c Faculty of Life Sciences , Amazonian State University , Puyo , Pastaza , Ecuador
| | - N Nguyen-Hai
- a Hanoi University of Pharmacy , Hanoi , Vietnam
| | - N T Ngoc
- a Hanoi University of Pharmacy , Hanoi , Vietnam
| | - L Vu-Duc
- d School of Medicine and Pharmacy, Vietnam National University , Hanoi , Vietnam
| | - H Le-Thi-Thu
- d School of Medicine and Pharmacy, Vietnam National University , Hanoi , Vietnam
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12
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Huang YX, Zhao J, Song QH, Zheng LH, Fan C, Liu TT, Bao YL, Sun LG, Zhang LB, Li YX. Virtual screening and experimental validation of novel histone deacetylase inhibitors. BMC Pharmacol Toxicol 2016; 17:32. [PMID: 27443303 PMCID: PMC4955146 DOI: 10.1186/s40360-016-0075-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/12/2016] [Indexed: 12/11/2022] Open
Abstract
Background Histone deacetylases (HDACs) are promising therapeutic targets for the treatment of cancer, diabetes and other human diseases. HDAC inhibitors, as a new class of potential therapeutic agents, have attracted a great deal of interest for both research and clinical applications. Increasing efforts have been focused on the discovery of HDAC inhibitors and some HDAC inhibitors have been approved for use in cancer therapy. However, most HDAC inhibitors, including the clinically approved agents, do not selectively inhibit the deacetylase activity of class I and II HDAC isforms, and many suffer from metabolic instability. This study aims to identify new HDAC inhibitors by using a high-throughput virtual screening approach. Methods An integration of in silico virtual screening and in vitro experimental validation was used to identify novel HDAC inhibitors from a chemical database. Results A virtual screening workflow for HDAC inhibitors were created by integrating ligand- and receptor- based virtual screening methods. Using the virtual screening workflow, 22 hit compounds were selected and further tested via in vitro assays. Enzyme inhibition assays showed that three of the 22 compounds had HDAC inhibitory properties. Among these three compounds, ZINC12555961 significantly inhibited HDAC activity. Further in vitro experiments indicated that ZINC12555961 can selectively inhibit proliferation and promote apoptosis of cancer cells. Conclusions In summary, our study presents three new and potent HDAC inhibitors and one of these HDAC inhibitors shows anti-proliferative and apoptosis-inducing activity against various cancer cell lines. These results suggest that the developed virtual screening workflow can provide a useful source of information for the screening and validation of new HDAC inhibitors. The new-found HDAC inhibitors are worthy to further and more comprehensive investigations. Electronic supplementary material The online version of this article (doi:10.1186/s40360-016-0075-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan-Xin Huang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China.
| | - Jian Zhao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Qiu-Hang Song
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Li-Hua Zheng
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Cong Fan
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Ting-Ting Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Yong-Li Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Lu-Guo Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Li-Biao Zhang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China.
| | - Yu-Xin Li
- Research Center of Agriculture and Medicine Gene Engineering of Ministry of Education, Northeast Normal University, ChangChun, 130117, China.
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Yu R, Wang J, Wang R, Lin Y, Hu Y, Wang Y, Shu M, Lin Z. Combined pharmacophore modeling, 3D-QSAR, homology modeling and docking studies on CYP11B1 inhibitors. Molecules 2015; 20:1014-30. [PMID: 25584832 PMCID: PMC6272247 DOI: 10.3390/molecules20011014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 11/29/2014] [Indexed: 11/16/2022] Open
Abstract
The mitochondrial cytochrome P450 enzymes inhibitor steroid 11β-hydroxylase (CYP11B1) can decrease the production of cortisol. Therefore, these inhibitors have an effect in the treatment of Cushing’s syndrome. A pharmacophore model generated by Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD) was used to align the compounds and perform comparative molecular field analysis (CoMFA) with Q2 = 0.658, R2 = 0.959. The pharmacophore model contained six hydrophobic regions and one acceptor atom, and electropositive and bulky substituents would be tolerated at the A and B sites, respectively. A three-dimensional quantitative structure-activity relationship (3D-QSAR) study based on the alignment with the atom root mean square (RMS) was applied using comparative molecular field analysis (CoMFA) with Q2 = 0.666, R2 = 0.978, and comparative molecular similarity indices analysis (CoMSIA) with Q2 = 0.721, R2 = 0.972. These results proved that all the models have good predictability of the bioactivities of inhibitors. Furthermore, the QSAR models indicated that a hydrogen bond acceptor substituent would be disfavored at the A and B groups, while hydrophobic groups would be favored at the B site. The three-dimensional (3D) model of the CYP11B1 was generated based on the crystal structure of the CYP11B2 (PDB code 4DVQ). In order to probe the ligand-binding modes, Surflex-dock was employed to dock CYP11B1 inhibitory compounds into the active site of the receptor. The docking result showed that the imidazolidine ring of CYP11B1 inhibitors form H bonds with the amino group of residue Arg155 and Arg519, which suggested that an electronegative substituent at these positions could enhance the activities of compounds. All the models generated by GALAHAD QSAR and Docking methods provide guidance about how to design novel and potential drugs for Cushing’s syndrome treatment.
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Affiliation(s)
- Rui Yu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Juan Wang
- College of Bioengineering, Chongqing University, Chongqing 400044, China.
| | - Rui Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yong Lin
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yong Hu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Zhihua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
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Li GB, Yang LL, Yuan Y, Zou J, Cao Y, Yang SY, Xiang R, Xiang M. Virtual screening in small molecule discovery for epigenetic targets. Methods 2015; 71:158-66. [DOI: 10.1016/j.ymeth.2014.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/27/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022] Open
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15
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Xu K, Thieme N, Breit B. Atom-Economic, Regiodivergent, and Stereoselective Coupling of Imidazole Derivatives with Terminal Allenes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309126] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Xu K, Thieme N, Breit B. Atom-Economic, Regiodivergent, and Stereoselective Coupling of Imidazole Derivatives with Terminal Allenes. Angew Chem Int Ed Engl 2014; 53:2162-5. [DOI: 10.1002/anie.201309126] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Indexed: 11/08/2022]
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