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Journal of Biomolecular Structure and Dynamics Volume 38, 2020 - Issue 2
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Research Articles

Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing

Jian LiuSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; ;Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China; ;Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, ChinaView further author information
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Yehua ZhuSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
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Yufang HeSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
,
Haohao ZhuSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
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Yi GaoSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
,
Zhi LiSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
,
Junru ZhuSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
,
Xinjie SunSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
,
Fang FangSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; View further author information
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Hongmei WenSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; ;Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China; ;Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, ChinaView further author information
&
Wei LiSchool of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; ;Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China; ;Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, ChinaCorrespondence[email protected]
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Pages 533-547 | Received 21 Dec 2018, Accepted 09 Feb 2019, Published online: 02 Apr 2019

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Jingyu Zhu, Xintong Li, Huiqin Meng, Lei Jia, Lei Xu, Yanfei Cai, Yun Chen, Jian Jin, Li Yu & Mingzhu Gao. (2023) Molecular modeling strategy for detailing the primary mechanism of action of copanlisib to PI3K: combined ligand-based and target-based approach. Journal of Biomolecular Structure and Dynamics 0:0, pages 1-12.
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Lili Sun, Zixiao Wang, Zhigang Yang, XiuJuan Liu & Haiyan Dong. (2023) Virtual screening and structure–activity relationship study of novel BTK inhibitors in Traditional Chinese Medicine for the treatment of rheumatoid arthritis. Journal of Biomolecular Structure and Dynamics 0:0, pages 1-15.
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Anu Manhas, Sujeet Kumar & Prakash C. Jha. (2022) Identification of the natural compound inhibitors against Plasmodium falciparum plasmepsin-II via common feature based screening and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 40:1, pages 31-43.
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Kartik Mitra, Prasanth Ghanta, Sushank Acharya, Gayathri Chakrapani, Basavaraju Ramaiah & Mukesh Doble. (2021) Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads. Journal of Biomolecular Structure and Dynamics 39:16, pages 6324-6337.
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Guoyi Yan, Dongxiao Li, Xinxin Zhong, Ge Liu, Xueqin Wang, Yuanxiang Lu, Fangyuan Qin, Yuqi Guo, Shaofeng Duan & Deyu Li. (2021) Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics 39:6, pages 1928-1939.
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Yanyun Zhu, Jiangbo Zhan, Yi Zhang, Ying Lin & Xiaorong Yang. (2021) The K428 residue from Thermus thermophilus SG0.5JP17-16 laccase plays the substantial role in substrate binding and oxidation. Journal of Biomolecular Structure and Dynamics 39:4, pages 1312-1320.
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Kodidasu Satish Kumar, Ravichandiran Velayutham & Kuldeep K. Roy. (2020) A systematic computational analysis of human matrix metalloproteinase 13 (MMP-13) crystal structures and structure-based identification of prospective drug candidates as MMP-13 inhibitors repurposable for osteoarthritis. Journal of Biomolecular Structure and Dynamics 38:10, pages 3074-3086.
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Anu Manhas, Saikat Dubey & Prakash C. Jha. (2020) A profound computational study to prioritize the natural compound inhibitors against the P. falciparum orotidine-5-monophosphate decarboxylase enzyme. Journal of Biomolecular Structure and Dynamics 38:9, pages 2704-2716.
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Articles from other publishers (7)

Saedeh Khadempar, Marzieh Lotfi, Fatemeh Haghiralsadat, Massoud Saidijam, Nasrin Ghasemi & Saeid Afshar. (2023) Lansoprazole as a potent HDAC2 inhibitor for treatment of colorectal cancer: An in-silico analysis and experimental validation. Computers in Biology and Medicine 166, pages 107518.
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ShaoJun Chen & LiHua Zhang. (2023) Unraveling the Potential Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Mechanisms of Ginger by Computational Target Fishing. Journal of Medicinal Food 26:10, pages 721-731.
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Ekta SHIRBHATE, Jaiprakash PANDEY, Vijay Kumar PATEL, Ravichandran VEERASAMY & Harish RAJAK. (2023) Exploration of Structure-Activity Relationship Using Integrated Structure and Ligand Based Approach: Hydroxamic Acid-Based HDAC Inhibitors and Cytotoxic Agents. Turkish Journal of Pharmaceutical Sciences 20:4, pages 270-284.
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Priya Poonia, Monika Sharma, Prakash Jha & Madhu Chopra. (2022) Pharmacophore-based virtual screening of ZINC database, molecular modeling and designing new derivatives as potential HDAC6 inhibitors. Molecular Diversity.
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Speranta Avram, Miruna Silvia Stan, Ana Maria Udrea, Cătălin Buiu, Anca Andreea Boboc & Maria Mernea. (2021) 3D-ALMOND-QSAR Models to Predict the Antidepressant Effect of Some Natural Compounds. Pharmaceutics 13:9, pages 1449.
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Rahman Abdizadeh, Keihan Ghatreh-Samani, Farzin Hadizadeh & Tooba Abdizadeh. (2021) Structural investigation of isatin-based benzenesulfonamides as carbonic anhydrase isoform IX inhibitors endowed with anticancer activity using molecular modeling approaches. Journal of Molecular Structure 1229, pages 129735.
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Tingting Liu, Shubin Song, Xu Wang & Jifu Hao. (2021) Small-molecule inhibitors of breast cancer-related targets: Potential therapeutic agents for breast cancer. European Journal of Medicinal Chemistry 210, pages 112954.
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