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Al bustanji D, Alnabulsi S, Al-Hurani EA. Hit-to-lead optimization of amino-carboxamide benzothiazoles as LSD1 inhibitors. Med Chem Res 2023. [DOI: 10.1007/s00044-023-03046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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2
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Mills CM, Turner J, Piña IC, Garrabrant KA, Geerts D, Bachmann AS, Peterson YK, Woster PM. Synthesis and evaluation of small molecule inhibitors of LSD1 for use against MYCN-expressing neuroblastoma. Eur J Med Chem 2022; 244:114818. [DOI: 10.1016/j.ejmech.2022.114818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
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3
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Zhang X, Sun Y, Huang H, Wang X, Wu T, Yin W, Li X, Wang L, Gu Y, Zhao D, Cheng M. Identification of novel indole derivatives as highly potent and efficacious LSD1 inhibitors. Eur J Med Chem 2022; 239:114523. [PMID: 35732082 DOI: 10.1016/j.ejmech.2022.114523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 11/04/2022]
Abstract
Lysine-specific demethylase 1 (LSD1) is a FAD-dependent histone demethylase to catalyze the demethylation of H3K4 and H3K9 and thus is an attractive target for therapeutic cancer. Starting with a high micromolar compound 17i, structure-based optimization of novel indole derivatives is described by a bioelectronic isosteric strategy. Grounded by molecular modeling, medicinal chemistry has efficiently yielded low nanomolar LSD1 inhibitors. One of the compounds, B35, exhibited excellent LSD1 inhibition (IC50 = 0.050 ± 0.005 μM) and anti-proliferation against A549 cells (IC50 = 0.74 ± 0.14 μM). The further PK studies indicated compound B35 possessed favorable metabolic stability, in which the plasma t1/2 of p.o. and i.v. were 6.27 ± 0.72 h and 8.78 ± 1.31 h, respectively. Additionally, inhibitor B35 shows a strong antitumor effect and good safety in vivo. Meanwhile, compound B35 regulated genes are closely associated with transcriptional dislocation in cancer and PI3K/AKT pathway involving IGFBP3. Taken together, B35 could be a potent LSD1 inhibitor for further drug development.
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Affiliation(s)
- Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Hailan Huang
- Department of Physiology, Life Science and Biopharmaceutical Institution, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinran Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Chaoyang District, Beijing, 102488, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Xiaojia Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Lin Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Yanting Gu
- Department of Physiology, Life Science and Biopharmaceutical Institution, Shenyang Pharmaceutical University, Shenyang, China.
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
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Moghadam ES, Mireskandari K, Abdel-Jalil R, Amini M. An approach to pharmacological targets of pyrrole family from a medicinal chemistry viewpoint. Mini Rev Med Chem 2022; 22:2486-2561. [PMID: 35339175 DOI: 10.2174/1389557522666220325150531] [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: 11/27/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Pyrrole is one of the most widely used heterocycles in the pharmaceutical industry. Due to the importance of pyrrole structure in drug design and development, herein, we tried to conduct an extensive review of the bioactive pyrrole based compounds reported recently. The bioactivity of pyrrole derivatives varies, so in the review, we categorized them based on their direct pharmacologic targets. Therefore, readers are able to find the variety of biologic targets for pyrrole containing compounds easily. This review explains around seventy different biologic targets for pyrrole based derivatives, so, it is helpful for medicinal chemists in design and development novel bioactive compounds for different diseases. This review presents an extensive meaningful structure activity relationship for each reported structure as much as possible. The review focuses on papers published between 2018 and 2020.
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Affiliation(s)
- Ebrahim Saeedian Moghadam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Katayoon Mireskandari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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5
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The Synthesis and Evaluation of Amidoximes as Cytotoxic Agents on Model Bacterial E. coli Strains. MATERIALS 2021; 14:ma14247577. [PMID: 34947169 PMCID: PMC8708467 DOI: 10.3390/ma14247577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022]
Abstract
The biological research on newly synthesized amidoximes, Boc-protected amidoximes and Boc-derived amidines, obtained by a reduction of the parent amidoximes is reported, herein. Due to the presence of a free amino group in both amidines and amidoximes, these compounds can undergo various chemical reactions such as N-alkylation and N-acylation. One such reaction is Boc-protection, often used in organic synthesis to protect the amino and imino groups. Until now, Boc-protected amidoximes have not been tested for biological activity. Amidoxime derivatives were tested on bacterial E. coli strains. Initial cellular studies tests and digestion with Fpg after the modification of bacterial DNA, suggest that these compounds may have greater potential as antibacterial agents compared to antibiotics such as ciprofloxacin (ci), bleomycin (b) and cloxacillin (cl). The described compounds are highly specific for pathogenic E. coli strains on the basis of the model strains used and may be used in the future as new substitutes for commonly used antibiotics in clinical and hospital infections in the pandemic era.
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6
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Intermolecular insights into allosteric inhibition of histone lysine-specific demethylase 1. Biochim Biophys Acta Gen Subj 2021; 1865:129990. [PMID: 34390793 DOI: 10.1016/j.bbagen.2021.129990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Histone lysine-specific demethylase 1 (LSD1) has become a potential anticancer target for the novel drug discovery. Recent reports have shown that SP2509 and its derivatives strongly inhibit LSD1 as allosteric inhibitors. However, the binding mechanism of these allosteric inhibitors in the allosteric site of LSD1 is not known yet. METHODS The stability and binding mechanism of allosteric inhibitors in the binding site of LSD1 were evaluated by molecular docking, ligand-based pharmacophore, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM/GBSA) analysis, quantum mechanics/molecular mechanics (QM/MM) calculation and Hirshfeld surface analysis. RESULTS The conformational geometry and the intermolecular interactions of allosteric inhibitors showed high binding affinity towards allosteric site of LSD1 with the neighboring amino acids (Gly358, Cys360, Leu362, Asp375 and Glu379). Meanwhile, MD simulations and MM/GBSA analysis were performed on selected allosteric inhibitors in complex with LSD1 protein, which confirmed the high stability and binding affinity of these inhibitors in the allosteric site of LSD1. CONCLUSION The simulation results revealed the crucial factors accounting for allosteric inhibitors of LSD1, including different protein-ligand interactions, the positions and conformations of key residues, and the ligands flexibilities. Meanwhile, a halogen bond interaction between chlorine atom of ligand and key residues Trp531 and His532 was recurrent in our analysis confirming its importance. GENERAL SIGNIFICANCE Overall, our research analyzed in depth the binding modes of allosteric inhibitors with LSD1 and could provide useful information for the design of novel allosteric inhibitors.
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Yan J, Gu Y, Sun Y, Zhang Z, Zhang X, Wang X, Wu T, Zhao D, Cheng M. Design, synthesis, and biological evaluation of 5-aminotetrahydroquinoline-based LSD1 inhibitors acting on Asp375. Arch Pharm (Weinheim) 2021; 354:e2100102. [PMID: 33987875 DOI: 10.1002/ardp.202100102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 11/12/2022]
Abstract
The abnormal expression of lysine-specific histone demethylase 1 (LSD1) is associated with different cancer types, and LSD1 inhibitory activity seems to have high therapeutic potential in cancer treatment. Here, we report the design, synthesis, and biochemical evaluation of novel 5-aminotetrahydroquinoline-based LSD1 inhibitors. Among them, compounds A6, A8, B1-B5, and C4 showed preferable inhibitory effects on LSD1, with IC50 = 0.19-0.82 µM. Several potent compounds were selected to evaluate their antiproliferative activity on A549 cells and MCF-7 cells with a high expression of LSD1. The potential binding modes of the compounds were revealed through molecular docking to rationalize the potency of compounds toward LSD1. Our data recognized that the 5-aminotetrahydroquinoline scaffold may serve as a starting point for developing potent LSD1 inhibitors for cancer therapy.
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Affiliation(s)
- Jiangkun Yan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanting Gu
- The School of Life Science and Biopharmaceutical, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ziheng Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinran Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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8
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Design, synthesis and biological evaluation of novel benzofuran derivatives as potent LSD1 inhibitors. Eur J Med Chem 2021; 220:113501. [PMID: 33945992 DOI: 10.1016/j.ejmech.2021.113501] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a FAD-dependent enzyme, which has been proposed as a promising target for therapeutic cancer. Herein, a series of benzofuran derivatives were designed, synthesized and biochemical evaluated as novel LSD1 inhibitors based on scaffold hopping and conformational restriction strategy. Most of the compounds potently suppressed the enzymatic activities of LSD1 and potently inhibited tumor cells proliferation. In particular, the representative compound 17i exhibited excellent LSD1 inhibition at the molecular levels with IC50 = 0.065 μM, as well as anti-proliferation against MCF-7, MGC-803, H460, A549 and THP-1 tumor cells with IC50 values of 2.90 ± 0.32, 5.85 ± 0.35, 2.06 ± 0.27, 5.74 ± 1.03 and 6.15 ± 0.49 μM, respectively. The binding modes of these compounds were rationalized by molecular docking. Meanwhile, a preliminary druggability evaluation showed that compound 17i displayed favorable liver microsomal stability and weak inhibitory activity against CYPs at 10 μM. Remarkably, H460 xenograft tumors studies revealed that 17i demonstrated robust in vivo antitumor efficacy without significant side effects. All the results demonstrated that compound 17i could represent a promising lead for further development.
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. QSAR Modeling, Molecular Docking and Molecular Dynamics Simulations Studies of Lysine-Specific Demethylase 1 (LSD1) Inhibitors as Anticancer Agents. Anticancer Agents Med Chem 2021; 21:987-1018. [PMID: 32698753 DOI: 10.2174/1871520620666200721134010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/07/2020] [Accepted: 05/17/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone Lysine Demetylases1 (LSD1) is a promising medication to treat cancer, which plays a crucial role in epigenetic modulation of gene expression. Inhibition of LSD1with small molecules has emerged as a vital mechanism to treat cancer. OBJECTIVE In the present research, molecular modeling investigations, such as CoMFA, CoMFA-RF, CoMSIA and HQSAR, molecular docking and Molecular Dynamics (MD) simulations were carried out on some tranylcypromine derivatives as LSD1 inhibitors. METHODS The QSAR models were carried out on a series of Tranylcypromine derivatives as data set via the SYBYL-X2.1.1 program. Molecular docking and MD simulations were carried out by the MOE software and the SYBYL program, respectively. The internal and external predictability performances related to the generated models for these LSD1 inhibitors were justified by evaluating cross-validated correlation coefficient (q2), noncross- validated correlation coefficient (r2ncv) and predicted correlation coefficient (r2pred) of the training and test set molecules, respectively. RESULTS The CoMFA (q2, 0.670; r2ncv, 0.930; r2pred, 0.968), CoMFA-RF (q2, 0.694; r2ncr, 0.926; r2pred, 0.927), CoMSIA (q2, 0.834; r2ncv, 0.956; r2pred, 0.958) and HQSAR models (q2, 0.854; r2ncv, 0.900; r2pred, 0.728) for training as well as the test set of LSD1 inhibition resulted in significant findings. CONCLUSION These QSAR models were found to be perfect and strong with better predictability. Contour maps of all models were generated and it was proven by molecular docking studies and molecular dynamics simulation that the hydrophobic, electrostatic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determining the structure-activity relationship. These theoretical results are possibly beneficial to design new strong LSD1 inhibitors with enhanced activity to treat cancer.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Esfandiar Heidarian
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
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10
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Dai XJ, Liu Y, Xue LP, Xiong XP, Zhou Y, Zheng YC, Liu HM. Reversible Lysine Specific Demethylase 1 (LSD1) Inhibitors: A Promising Wrench to Impair LSD1. J Med Chem 2021; 64:2466-2488. [PMID: 33619958 DOI: 10.1021/acs.jmedchem.0c02176] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a flavin adenine dinucleotide (FAD)-dependent monoamine oxidase, lysine specific demethylase 1 (LSD1/KDM1A) functions as a transcription coactivator or corepressor to regulate the methylation of histone 3 lysine 4 and 9 (H3K4/9), and it has emerged as a promising epigenetic target for anticancer treatment. To date, numerous inhibitors targeting LSD1 have been developed, some of which are undergoing clinical trials for cancer therapy. Although only two reversible LSD1 inhibitors CC-90011 and SP-2577 are in the clinical stage, the past decade has seen remarkable advances in the development of reversible LSD1 inhibitors. Herein, we provide a comprehensive review about structures, biological evaluation, and structure-activity relationship (SAR) of reversible LSD1 inhibitors.
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Affiliation(s)
- Xing-Jie Dai
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Lei-Peng Xue
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiao-Peng Xiong
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Zhou
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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Endo S, Oguri H, Segawa J, Kawai M, Hu D, Xia S, Okada T, Irie K, Fujii S, Gouda H, Iguchi K, Matsukawa T, Fujimoto N, Nakayama T, Toyooka N, Matsunaga T, Ikari A. Development of Novel AKR1C3 Inhibitors as New Potential Treatment for Castration-Resistant Prostate Cancer. J Med Chem 2020; 63:10396-10411. [PMID: 32847363 DOI: 10.1021/acs.jmedchem.0c00939] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aldo-keto reductase (AKR) 1C3 catalyzes the synthesis of active androgens that promote the progression of prostate cancer. AKR1C3 also contributes to androgen-independent cell proliferation and survival through the metabolism of prostaglandins and reactive aldehydes. Because of its elevation in castration-resistant prostate cancer (CRPC) tissues, AKR1C3 is a promising therapeutic target for CRPC. In this study, we found a novel potent AKR1C3 inhibitor, N-(4-fluorophenyl)-8-hydroxy-2-imino-2H-chromene-3-carboxamide (2d), and synthesized its derivatives with IC50 values of 25-56 nM and >220-fold selectivity over other AKRs (1C1, 1C2, and 1C4). The structural factors for the inhibitory potency were elucidated by crystallographic study of AKR1C3 complexes with 2j and 2l. The inhibitors suppressed proliferation of prostate cancer 22Rv1 and PC3 cells through both androgen-dependent and androgen-independent mechanisms. Additionally, 2j and 2l prevented prostate tumor growth in a xenograft mouse model. Furthermore, the inhibitors significantly augmented apoptotic cell death induced by anti-CRPC drugs (abiraterone or enzalutamide).
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Hiroaki Oguri
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Jin Segawa
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Mina Kawai
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Dawei Hu
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Shuang Xia
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Takuya Okada
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Katsumasa Irie
- Cellular and Structural Physiology Institute, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Shinya Fujii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo 101-0062, Japan
| | - Hiroaki Gouda
- School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Kazuhiro Iguchi
- Laboratory of Community Pharmacy, Department of Pharmacy, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Takuo Matsukawa
- Department of Urology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Naohiro Fujimoto
- Department of Urology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Toshiyuki Nakayama
- Department of Pathology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Naoki Toyooka
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Toshiyuki Matsunaga
- Education Center of Green Pharmaceutical Sciences, Gifu Pharmaceutical University, Gifu 502-8585, Japan
| | - Akira Ikari
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
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12
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Holshouser S, Cafiero R, Robinson M, Kirkpatrick J, Casero RA, Hyacinth HI, Woster PM. Epigenetic Reexpression of Hemoglobin F Using Reversible LSD1 Inhibitors: Potential Therapies for Sickle Cell Disease. ACS OMEGA 2020; 5:14750-14758. [PMID: 32596612 PMCID: PMC7315572 DOI: 10.1021/acsomega.0c01585] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Sickle cell disease (SCD) is caused by a single nucleotide polymorphism on chromosome 11 in the β-globin gene. The resulting mutant hemoglobin S (HbS) is a poor oxygen transporter and causes a variety of vascular symptoms and organ failures. At birth, the DRED epigenetic complex forms and silences the γ-globin gene, and fetal hemoglobin (HbF, 2 α-, and 2 γ-subunits) is replaced by adult HbA (α2β2) or HbS (α2βs 2) in SCD patients. HbF is a potent inhibitor of HbS polymerization, thus alleviating the symptoms of SCD. The current therapy, hydroxyurea (HU), increases γ-globin and the HbF content in sickle cells but is highly underutilized due to concern for adverse effects and other complications. The DRED complex contains the epigenetic eraser lysine-specific demethylase 1 (LSD1), which appears to serve as a scaffolding protein. Our recently discovered 1,2,4-triazole derivatives and cyclic peptide LSD1 inhibitors promote the upregulation of γ-globin production in vitro without significant toxicity. Herein, we demonstrate that these LSD1 inhibitors can be used to disrupt the DRED complex and increase the cellular HbF content in vitro and in vivo. This approach could lead to an innovative and effective treatment for SCD.
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Affiliation(s)
- Steven Holshouser
- Department
of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, South Carolina 29414, United States
| | - Rebecca Cafiero
- Department
of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, South Carolina 29414, United States
| | - Mayra Robinson
- Department
of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, South Carolina 29414, United States
| | - Joy Kirkpatrick
- Department
of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, South Carolina 29414, United States
| | - Robert A. Casero
- Sidney
Kimmel Comprehensive Cancer Center, Johns
Hopkins School of Medicine, 1650 Orleans St. Room 551, Baltimore, Maryland 21287, United States
| | - Hyacinth I. Hyacinth
- Department
of Pediatrics, School of Medicine, Emory
University, 2015 Uppergate Dr., Atlanta, Georgia 30322, United
States
| | - Patrick M. Woster
- Department
of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, South Carolina 29414, United States
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Amino-carboxamide benzothiazoles as potential LSD1 hit inhibitors. Part I: Computational fragment-based drug design. J Mol Graph Model 2019; 93:107440. [DOI: 10.1016/j.jmgm.2019.107440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 01/08/2023]
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14
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In silico evaluation of 5-hydroxypyrazoles as LSD1 inhibitors based on molecular docking derived descriptors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Lee A, Borrello MT, Ganesan A. LSD
(Lysine‐Specific Demethylase): A Decade‐Long Trip from Discovery to Clinical Trials. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527809257.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sun X, Ding L, Liu HM. Probing the binding mode and unbinding mechanism of LSD1 inhibitors by combined computational methods. Phys Chem Chem Phys 2018; 20:29833-29846. [PMID: 30468219 DOI: 10.1039/c8cp03090a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine specific demethylase 1 (LSD1) has emerged as a potential drug target in cancer therapy and a variety of inhibitors have been reported. We have recently reported the discovery of a series of triazole-dithiocarbamate based compounds, which were basically confirmed as cofactor flavin adenine dinucleotide (FAD)-competing inhibitors by experiments. However, the binding modes of the inhibitors to the binding site were undetermined. Here, we employed computational methods including molecular docking, classical molecular dynamics (MD) and steered molecular dynamics (SMD) simulations to investigate the potential binding modes of these inhibitors to LSD1. Based on the high correlation between the mean non-equilibrium pulling work W and experimental binding affinity, we identified the optimal binding modes of this class of compounds with LSD1. Using the optimal inhibitor binding conformation, we then performed SMD to study the ligand unbinding mechanism with a lower pulling velocity at 0.0005 nm ps-1. We found that residue Arg316 plays a crucial role in the binding/unbinding process. Furthermore, a gatekeeper residue Trp756 influences the ligand unbinding process by acting like a switch via steric hindrance but can enhance the hydrophobic interaction with the inhibitor. Hydrophobic interaction also dominated the interaction between LSD1 and the inhibitors. The pivotal residues and interactions between LSD1 and inhibitors determined from this study can be used to improve the inhibition activity of this series of inhibitors in development and to discover new scaffolds as FAD-competing inhibitors in compound screening.
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Affiliation(s)
- Xudong Sun
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.
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17
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Sun XD, Zheng YC, Ma CY, Yang J, Gao QB, Yan Y, Wang ZZ, Li W, Zhao W, Liu HM, Ding L. Identifying the novel inhibitors of lysine-specific demethylase 1 (LSD1) combining pharmacophore-based and structure-based virtual screening. J Biomol Struct Dyn 2018; 37:4200-4214. [PMID: 30366512 DOI: 10.1080/07391102.2018.1538903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) has been reported to connect with a range of solid tumors. Thus, the exploration of LSD1 inhibitors has emerged as an effective strategy for cancer treatment. In this study, we constructed a pharmacophore model based on a series of flavin adenine dinucleotide (FAD)-competing inhibitors bearing triazole - dithiocarbamate scaffold combining docking, structure-activity relationship (SAR) study, and molecular dynamic (MD) simulation. Meanwhile, another pharmacophore model was also constructed manually, relying on several speculated substrate-competing inhibitors and reported putative vital interactions with LSD1. On the basis of the two pharmacophore models, multi-step virtual screenings (VSs) were performed against substrate-binding pocket and FAD-binding pocket, respectively, combining pharmacophore-based and structure-based strategy to exploit novel LSD1 inhibitors. After bioassay evaluation, four compounds among 21 hits with diverse and novel scaffolds exhibited inhibition activity at the range of 3.63-101.43 μM. Furthermore, substructure-based enrichment was performed, and four compounds with a more potent activity were identified. After that, the time-dependent assay proved that the most potent compound with IC50 2.21 μM inhibits LSD1 activity in a manner of time-independent. In addition, the compound exhibited a cellular inhibitory effect against LSD1 in MGC-803 cells and may inhibit cell migration and invasion by reversing EMT in cultured gastric cancer cells. Considering the binding mode and SAR of the series of compounds, we could roughly deem that these compounds containing 3-methylxanthine scaffold act through occupying substrate-binding pocket competitively. This study presented a new starting point to develop novel LSD1 inhibitors.
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Affiliation(s)
- Xu-Dong Sun
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Yi-Chao Zheng
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Chao-Ya Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Jing Yang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Qi-Bing Gao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Ying Yan
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Zhi-Zheng Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Wen Li
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Wen Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University , Zhengzhou , PR China
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18
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Yang GJ, Lei PM, Wong SY, Ma DL, Leung CH. Pharmacological Inhibition of LSD1 for Cancer Treatment. Molecules 2018; 23:E3194. [PMID: 30518104 PMCID: PMC6320820 DOI: 10.3390/molecules23123194] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Lysine-specific demethylase 1A (LSD1, also named KDM1A) is a demethylase that can remove methyl groups from histones H3K4me1/2 and H3K9me1/2. It is aberrantly expressed in many cancers, where it impedes differentiation and contributes to cancer cell proliferation, cell metastasis and invasiveness, and is associated with inferior prognosis. Pharmacological inhibition of LSD1 has been reported to significantly attenuate tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. This review will present the structural aspects of LSD1, its role in carcinogenesis, a comparison of currently available approaches for screening LSD1 inhibitors, a classification of LSD1 inhibitors, and its potential as a drug target in cancer therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Pui-Man Lei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Suk-Yu Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
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19
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Duan Y, Qin W, Suo F, Zhai X, Guan Y, Wang X, Zheng Y, Liu H. Design, synthesis and in vitro evaluation of stilbene derivatives as novel LSD1 inhibitors for AML therapy. Bioorg Med Chem 2018; 26:6000-6014. [PMID: 30448189 DOI: 10.1016/j.bmc.2018.10.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022]
Abstract
LSD1 is implicated in a number of malignancies and has emerged as an exciting target. As part of our sustained efforts to develop novel reversible LSD1 inhibitors for epigenetic therapy of cancers, in this study, we reported a series of stilbene derivatives and evaluated their LSD1 inhibitory activities, obtaining several compounds as potent LSD1 inhibitors with IC50 values in submicromolar range. Enzyme kinetics studies and SPR assay suggested that compound 8c, the most active LSD1 inhibitor (IC50 = 283 nM), potently inhibited LSD1 in a reversible and FAD competitive manner. Consistent with the kinetics data, molecular docking showed that compound 8c can be well docked into the FAD binding site of LSD1. Flow cytometry analysis showed that compound 8c was capable of up-regulating the expression of the surrogate cellular biomarker CD86 in THP-1 human leukemia cells, suggesting the ability to block LSD1 activity in cells. Compound 8c showed good inhibition against THP-1 and MOLM-13 cells with IC50 values of 5.76 and 8.34 μM, respectively. Moreover, compound 8c significantly inhibited colony formation of THP-1 cells dose dependently.
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Affiliation(s)
- Yingchao Duan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Wenping Qin
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Fengzhi Suo
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiaoyu Zhai
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Yuanyuan Guan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Xiaojuan Wang
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China
| | - Yichao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Hongmin Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
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20
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Xu S, Zhou C, Liu R, Zhu Q, Xu Y, Lan F, Zha X. Optimization of 5-arylidene barbiturates as potent, selective, reversible LSD1 inhibitors for the treatment of acute promyelocytic leukemia. Bioorg Med Chem 2018; 26:4871-4880. [PMID: 30153955 DOI: 10.1016/j.bmc.2018.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 02/08/2023]
Abstract
Histone lysine specific demethylase 1 (LSD1) is overexpressed in diverse hematologic disorders and recognized as a promising target for blood medicines. In this study, molecular docking-based virtual screening united with bioevaluation was utilized to identify novel skeleton of 5-arylidene barbiturate as small-molecule inhibitors of LSD1. Among the synthesized derivatives, 12a exhibited reversible and potent inhibition (IC50 = 0.41 μM) and high selectivity over the MAO-A and MAO-B. Notably, 12a strongly induced differentiation effect on acute promyelocytic leukemia NB4 cell line and distinctly escalated the methylation level on histone 3 lysine 4 (H3K4). Our findings indicate that 5-arylidene barbiturate may represent a new skeleton of LSD1 inhibitors and 12a deserve as a promising agent for the further research.
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Affiliation(s)
- Siyuan Xu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Chen Zhou
- Department of Pharmaceutical Engineering, Department of Biomedical Engineering, Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China
| | - Rongfeng Liu
- Shanghai ChemPartner Co. Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Qihua Zhu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Department of Pharmaceutical Engineering, Department of Biomedical Engineering, Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China.
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21
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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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Abstract
Lung cancer is the leading cause of cancer-related deaths in the world. Despite significant advances in the early detection and treatment of the disease, the prognosis remains poor, with an overall 5-year survival rate ranging from 15% to 20%. This poor prognosis results largely from early micrometastatic spread of cancer cells to nearby lymph nodes or tissues and partially from early recurrence after curative surgical resection. Recently, precision medicines that target potential oncogenic driver mutations have been approved to treat lung cancer. However, some lung cancer patients do not have targetable mutations, and many patients develop resistance to targeted therapy. Tumor heterogeneity and mutational density are also challenges in treating lung cancer, which underscores the need for developing alternative therapeutic strategies for treating lung cancer. Epigenetic therapy may circumvent the problems of tumor heterogeneity and drug resistance by affecting the expression of several hundred target genes. This review highlights precision medicine using an innovative approach of epigenetic priming prior to conventional standard therapy or targeted cancer therapy in lung cancer.
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Affiliation(s)
- Dongho Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea. .,Samsung Medical Center, Research Institute for Future Medicine, Seoul, South Korea.
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Abstract
This chapter provides an overview of how the polyamine pathway has been exploited as a target for the treatment and prevention of multiple forms of cancer, since this pathway is disrupted in all cancers. It is divided into three main sections. The first explores how the polyamine pathway has been targeted for chemotherapy, starting from the first drug to target it, difluoromethylornithine (DFMO) to the large variety of polyamine analogues that have been synthesised and tested throughout the years with all their potentials and pitfalls. The second section focuses on the use of polyamines as vectors for drug delivery. Knowing that the polyamine transport system is upregulated in cancers and that polyamines naturally bind to DNA, a range of polyamine analogues and polyamine-like structures have been synthesised to target epigenetic regulators, with encouraging results. Furthermore, the use of polyamines as transport vectors to introduce toxic/bioactive/fluorescent agents more selectively to the intended target in cancer cells is discussed. The last section concentrates on chemoprevention, where the different strategies that have been undertaken to interfere with polyamine metabolism and function for antiproliferative intervention are outlined and discussed.
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Affiliation(s)
- Elisabetta Damiani
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Heather M Wallace
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK.
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Zalloum WA, Zalloum HM. Exploring the Active Center of the LSD1/CoREST Complex by Molecular Dynamics Simulation Utilizing Its Co-crystallized Co-factor Tetrahydrofolate as a Probe. J Chem Inf Model 2017; 57:3022-3031. [PMID: 29161028 DOI: 10.1021/acs.jcim.7b00256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic targeting of cancer is a recent effort to manipulate the gene without destroying the genetic material. Lysine-specific demethylase 1 (LSD1) is one of the enzymes associated with the chromatin for post-translational modifications, where it demethylates lysine amino acid in the chromatin H3 tail. Many studies showed that inhibiting LSD1 could potentially be used to treat cancer epigenetically. LSD1 is associated with its corepressor protein CoREST, and it uses tetrahydrofolate as a co-factor to accept CH2 from the demethylation process. In this study, the co-crystallized co-factor tetrahydrofolate was utilized to determine possible binding regions in the active center of the LSD1/CoREST complex. Also, the flexibility of the complex has been investigated by molecular dynamics simulation and subsequent analysis by clustering and principal component analysis. This research supported other studies and showed that LSD1/CoREST complex exists in two main conformational structures: open and closed. Furthermore, this study showed that tetrahydrofolate stably binds to the LSD1/CoREST complex, in its open conformation, at its entrance. It then binds to the core of the complex, inducing the closed conformation. Furthermore, the interactions of tetrahydrofolate to these two binding regions and the corresponding binding mode of tetrahydrofolate were investigated to be used in structure-based drug design.
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Affiliation(s)
- Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba , P.O. Box 2882, Amman 11821, Jordan
| | - Hiba M Zalloum
- Hamdi Mango Research Center for Scientific Research, The University of Jordan , Amman 11942, Jordan
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Sun K, Peng JD, Suo FZ, Zhang T, Fu YD, Zheng YC, Liu HM. Discovery of tranylcypromine analogs with an acylhydrazone substituent as LSD1 inactivators: Design, synthesis and their biological evaluation. Bioorg Med Chem Lett 2017; 27:5036-5039. [PMID: 29037950 DOI: 10.1016/j.bmcl.2017.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/29/2017] [Accepted: 10/01/2017] [Indexed: 02/07/2023]
Abstract
Lysine specific demethylase 1 (LSD1), the first identified histone demethylase, plays an important role in epigenetic regulation of gene activation and repression, has been reported to be up-regulated and involved in numbers of solid malignant tumors. In this study, we identified a series of phenylalanyl hydrazones based LSD1 inhibitors, and the most potent one, compound 4q, can inactivate LSD1 with IC50 = 91.83 nM. In cellular level, compound 4q can induce the accumulation of CD86 as well as H3K4me2, and inhibit gastric cancer cell proliferation by inactivating LSD1. Our findings indicated that compound 4q may serve as a potential leading compound to target LSD1 overexpressed gastric cancer.
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Affiliation(s)
- Kai Sun
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jia-Di Peng
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Feng-Zhi Suo
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Ting Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yun-Dong Fu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yi-Chao Zheng
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; National Center for International Research of Micro-nano Molding Technology & Key Laboratory for Micro Molding Technology of Henan Province, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.
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Duan YC, Ma YC, Qin WP, Ding LN, Zheng YC, Zhu YL, Zhai XY, Yang J, Ma CY, Guan YY. Design and synthesis of tranylcypromine derivatives as novel LSD1/HDACs dual inhibitors for cancer treatment. Eur J Med Chem 2017; 140:392-402. [PMID: 28987602 DOI: 10.1016/j.ejmech.2017.09.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022]
Abstract
Lysine specific demethylase 1 (LSD1) and Histone deacetylases (HDACs) are promising drug targets for cancers. Recent studies reveal an important functional interplay between LSD1 and HDACs, and there is evidence for the synergistic effect of combined LSD1 and HDAC inhibitors on cancers. Therefore, development of inhibitors targeting both LSD1 and HDACs might be a promising strategy for epigenetic therapy of cancers. We report herein the synthesis of a series of tranylcypromine derivatives as LSD1/HDACs dual inhibitors. Most compounds showed potent LSD1 and HDACs inhibitory activity, especially compound 7 displayed the most potent inhibitory activity against HDAC1 and HDAC2 with IC50 of 15 nM and 23 nM, as well as potent inhibition against LSD1 with IC50 of 1.20 μM. Compound 7 demonstrated stronger anti-proliferative activities than SAHA with IC50 values ranging from 0.81 to 4.28 μM against MGC-803, MCF-7, SW-620 and A-549 human cancer cell lines. Further mechanistic studies showed that compound 7 treatment in MGC-803 cells dose-dependently increased cellular H3K4 and H3K9 methylation, as well as H3 acetylation, decreased the mitochondrial membrane potential and induced remarkable apoptosis. Docking studies showed that compound 7 can be well docked into the active binding sites of LSD1 and HDAC2. This finding highlights the potential for the development of LSD1/HDACs dual inhibitors as novel anticancer drugs.
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Affiliation(s)
- Ying-Chao Duan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China.
| | - Yong-Cheng Ma
- Department of Pharmacy, Zhengzhou University People's Hospital, No. 7, Wei Wu Road, Zhengzhou, Henan, China
| | - Wen-Ping Qin
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Li-Na Ding
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying-Li Zhu
- Department of Pharmacy, Zhengzhou University People's Hospital, No. 7, Wei Wu Road, Zhengzhou, Henan, China
| | - Xiao-Yu Zhai
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Jing Yang
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Chao-Ya Ma
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yuan-Yuan Guan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China.
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27
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Christoff RM, Murray GL, Kostoulias XP, Peleg AY, Abbott BM. Synthesis of novel 1,2,5-oxadiazoles and evaluation of action against Acinetobacter baumannii. Bioorg Med Chem 2017; 25:6267-6272. [PMID: 29032931 DOI: 10.1016/j.bmc.2017.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/31/2017] [Accepted: 08/08/2017] [Indexed: 11/27/2022]
Abstract
With multidrug resistant bacteria on the rise, novel antibiotics are becoming highly sought after. In 2008, eleven compounds were identified by high throughput screening as inhibitors of BasE, a key enzyme of the non-ribosomal peptide synthetase pathway found in Acinetobacter baumannii. Herein, we describe the preparation of four structurally similar heterocyclic lead compounds from that study, including one 1,2,5-oxadiazole. A further library of 30 analogues containing the oxadiazole moiety was then generated. All compounds were screened against Acinetobacter baumannii and their minimum inhibitory concentration data is reported, with (E)-3-(2-hydroxyphenyl)-N-(4-methyl-1,2,5-oxadiazol-3-yl)acrylamide 32 found to have an MIC of 0.5mM. This work provides the foundation for further investigation of 1,2,5-oxadizoles as novel inhibitors of A. baumannii.
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Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Gerald L Murray
- Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia; Royal Women's Hospital, Melbourne, Victoria 3052, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Xenia P Kostoulias
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Anton Y Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia; Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, Victoria 3004, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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Abstract
LSD1 has become an important biologically validated epigenetic target for cancer therapy since its identification in 2004. LSD1 mediates many cellular signaling pathways and is involved in the initiation and development of cancers. Aberrant overexpression of LSD1 has been observed in different types of cancers, and inactivation by small molecules suppresses cancer cell differentiation, proliferation, invasion and migration. To date, a large number of LSD1 inhibitors have been reported, RG6016, GSK-2879552, INCB059872, IMG-7289 and CC-90011 are currently undergoing clinical assessment for the treatment of acute myeloid leukemia, small-cell lung cancer, etc. In this review, we briefly highlight recent advances of LSD1 inhibitors mainly covering the literatures from 2015 to 2017 and tentatively propose our perspectives on the design of new LSD1 inhibitors for cancer therapy.
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29
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Xi J, Xu S, Wu L, Ma T, Liu R, Liu YC, Deng D, Gu Y, Zhou J, Lan F, Zha X. Design, synthesis and biological activity of 3-oxoamino-benzenesulfonamides as selective and reversible LSD1 inhibitors. Bioorg Chem 2017; 72:182-189. [PMID: 28460360 DOI: 10.1016/j.bioorg.2017.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/30/2017] [Accepted: 04/13/2017] [Indexed: 12/09/2022]
Abstract
Lysine specific demethylase 1 (LSD1) is a flavin-dependent amine oxidase that selectively removes one or two methyl groups from H3 at Lys4 and is recognized as a promising therapeutic target for cancer and other diseases. Here, a series of 3-oxoamino-benzenesulfonamides were synthesized and evaluated for their inhibitory activity against LSD1. Compounds 7b and 7h showed the most potent inhibition with the IC50 values of 9.5 and 6.9μM, respectively. Furthermore, the LSD1 inhibition of 7b and 7h were reversible and selective. Docking study presented the possible binding mode between 7b, 7h and the LSD1 active site. Taken together, 3-oxoamino-benzenesulfonamides may represent a new class of reversible LSD1 inhibitors and 7b and 7h were two hit compounds deserved further structural optimization.
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Affiliation(s)
- Jiayue Xi
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Siyuan Xu
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China
| | - Liming Wu
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Tianfang Ma
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Rongfeng Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Dawei Deng
- Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yueqing Gu
- Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Fei Lan
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
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30
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Li ZH, Liu XQ, Geng PF, Suo FZ, Ma JL, Yu B, Zhao TQ, Zhou ZQ, Huang CX, Zheng YC, Liu HM. Discovery of [1,2,3]Triazolo[4,5- d]pyrimidine Derivatives as Novel LSD1 Inhibitors. ACS Med Chem Lett 2017; 8:384-389. [PMID: 28435523 DOI: 10.1021/acsmedchemlett.6b00423] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/06/2017] [Indexed: 11/29/2022] Open
Abstract
Lysine specific demethylase 1 (LSD1) plays a pivotal role in regulating the lysine methylation. The aberrant overexpression of LSD1 has been reported to be involved in the progression of certain human malignant tumors. Abrogation of LSD1 with RNAi or small molecule inhibitors may lead to the inhibition of cancer proliferation and migration. Herein, a series of [1,2,3]triazolo[4,5-d]pyrimidine derivatives were synthesized and evaluated for their LSD1 inhibitory effects. The structure-activity relationship studies (SARs) were conducted by exploring three regions of this scaffold, leading to the discovery of compound 27 as potent LSD1 inhibitor (IC50 = 0.564 μM). Compound 27 was identified as a reversible LSD1 inhibitor and showed certain selectivity to LSD1 over monoamine oxidase A/B (MAO-A/B). When MGC-803 cells were treated with compound 27, the activity of LSD1 can be significantly inhibited, and the cell migration ability was also suppressed. Docking studies indicated that the hydrogen interaction between the nitrogen atom in the pyridine ring and Met332 could be responsible for the improved activity of 2-thiopyridine series. The [1,2,3]triazolo[4,5-d]pyrimidine scaffold can be used as the template for designing new LSD1 inhibitors.
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Affiliation(s)
- Zhong-Hua Li
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xue-Qi Liu
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Peng-Fei Geng
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Feng-Zhi Suo
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jin-Lian Ma
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bin Yu
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Tao-Qian Zhao
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Zhao-Qing Zhou
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Chen-Xi Huang
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Laboratory of Technology of Drug Preparation
(Zhengzhou University), Ministry of Education; Key Laboratory of Henan
Province for Drug Quality and Evaluation; Collaborative Innovation
Center of New Drug Research and Safety Evaluation, Henan Province;
Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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32
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Niwa H, Umehara T. Structural insight into inhibitors of flavin adenine dinucleotide-dependent lysine demethylases. Epigenetics 2017; 12:340-352. [PMID: 28277979 PMCID: PMC5453194 DOI: 10.1080/15592294.2017.1290032] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Until 2004, many researchers believed that protein methylation in eukaryotic cells was an irreversible reaction. However, the discovery of lysine-specific demethylase 1 in 2004 drastically changed this view and the concept of chromatin regulation. Since then, the enzymes responsible for lysine demethylation and their cellular substrates, biological significance, and selective regulation have become major research topics in epigenetics and chromatin biology. Many cell-permeable inhibitors for lysine demethylases have been developed, including both target-specific and nonspecific inhibitors. Structural understanding of how these inhibitors bind to lysine demethylases is crucial both for validation of the inhibitors as chemical probes and for the rational design of more potent, target-specific inhibitors. This review focuses on published small-molecule inhibitors targeted at the two flavin adenine dinucleotide-dependent lysine demethylases, lysine-specific demethylases 1 and 2, and how the inhibitors interact with the tertiary structures of the enzymes.
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Affiliation(s)
- Hideaki Niwa
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan
| | - Takashi Umehara
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan.,b PRESTO, Japan Science and Technology Agency (JST) , Honcho, Kawaguchi , Saitama , Japan
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33
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Discovery of resveratrol derivatives as novel LSD1 inhibitors: Design, synthesis and their biological evaluation. Eur J Med Chem 2017; 126:246-258. [DOI: 10.1016/j.ejmech.2016.11.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/06/2023]
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34
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35
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Design, synthesis and biological activity of N-(3-substituted-phenyl)benzenesulfonamides as selective and reversible LSD1 inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1706-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Jiao P, Jin P, Li C, Cui L, Dong L, Pan B, Song W, Ma L, Dong J, Song L, Jin X, Li F, Wan M, Lv Z, Geng Q. Design, synthesis and in vitro evaluation of amidoximes as histone deacetylase inhibitors for cancer therapy. Bioorg Med Chem Lett 2016; 26:4679-4683. [PMID: 27597246 DOI: 10.1016/j.bmcl.2016.08.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/28/2016] [Accepted: 08/18/2016] [Indexed: 01/02/2023]
Abstract
Amindoximes are geometric isomers of N-hydroxyamidines which are bioisosteres of hydroxamates. Since amindoxime group is capable of chelating transition metal ions including zinc ion, amindoximes should possess histone deacetylases (HDACs) inhibitory activity. In this work, we designed and synthesized a series of amindoximes, examined their inhibitory activities against HDACs, and investigated their cytotoxicity to human cancer cells. Preliminary results demonstrated that amindoximes possessed submicromolar HDACs inhibitory activity, with noteworthy enhancement compared with hydroxamates. Furthermore, the amindoximes arrested HCT116 and A549 cells in G2/M phase and showed good efficacy in inducing cells death. We provided a proof-of-concept that amindoximes could be used as HDACs inhibitors and hold great promise as epigenetic drugs.
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Affiliation(s)
- Peifu Jiao
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Peng Jin
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Chencan Li
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Lechao Cui
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Lihua Dong
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Bin Pan
- Shandong Chengchuang Pharmaceutical R&D Co., Ltd, Jinan, Shandong 250101, China
| | - Wentong Song
- Shandong Chengchuang Pharmaceutical R&D Co., Ltd, Jinan, Shandong 250101, China
| | - Liang Ma
- Shandong Chengchuang Pharmaceutical R&D Co., Ltd, Jinan, Shandong 250101, China
| | - Jinlong Dong
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Lei Song
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Xinjie Jin
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Faming Li
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China
| | - Maosheng Wan
- School of Chemistry and Biological Engineering, Hezhou University, Hezhou, Guangxi 542899, China.
| | - Zhitao Lv
- Shandong Chengchuang Pharmaceutical R&D Co., Ltd, Jinan, Shandong 250101, China.
| | - Qiaohong Geng
- Department of Chemistry, Qilu Normal University, Jinan, Shandong 250200, China.
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37
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Maiques-Diaz A, Somervaille TCP. LSD1: biologic roles and therapeutic targeting. Epigenomics 2016; 8:1103-16. [PMID: 27479862 PMCID: PMC5066116 DOI: 10.2217/epi-2016-0009] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022] Open
Abstract
LSD1 (KDM1A; BHC110; AOF2) was the first protein reported to exhibit histone demethylase activity and has since been shown to have multiple essential roles in mammalian biology. Given its enzymatic activity and its high-level expression in many human malignancies, a significant recent focus has been the development of pharmacologic inhibitors. Here we summarize structural and biochemical knowledge of this important epigenetic regulator, with a particular emphasis on the functional and preclinical studies in oncology that have provided justification for the evaluation of tranylcypromine derivative LSD1 inhibitors in early phase clinical trials.
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Affiliation(s)
- Alba Maiques-Diaz
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
| | - Tim CP Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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38
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Wang X, Huang B, Suzuki T, Liu X, Zhan P. Medicinal chemistry insights in the discovery of novel LSD1 inhibitors. Epigenomics 2015; 7:1379-96. [PMID: 26646727 DOI: 10.2217/epi.15.86] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
LSD1 is an epigenetic modulator associated with transcriptional regulation of genes involved in a broad spectrum of key cellular processes, and its activity is often altered under pathological conditions. LSD1 inhibitors are considered to be candidates for therapy of cancer, viral diseases and neurodegeneration. Many LSD1 inhibitors with various scaffolds have been disclosed, and a few potent molecules are in different stages of clinical development. In this review, we summarize recent biological findings on the roles of LSD1 and the current understanding of the clinical significance of LSD1, and focus on the medicinal chemistry strategies used in the design and development of LSD1 inhibitors as drug-like epigenetic modulators since 2012, including a brief consideration of structure–activity relationships.
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Affiliation(s)
- Xueshun Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
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39
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Zhang X, Li M, Wang Y, Zhao Y. Insight into the binding mode of a novel LSD1 inhibitor by molecular docking and molecular dynamics simulations. J Recept Signal Transduct Res 2015; 35:363-9. [PMID: 26364657 DOI: 10.3109/10799893.2015.1049360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lysine-specific demethylase (LSD1) is an important enzyme for histone lysine methylation. Downregulated LSD1 expression has been linked to cancer proliferation, migration and invasion, indicating that it is an important target for anti-cancer medication. In the present study, the binding modes of a recent reported new series of LSD1 inhibitor were analyzed by using molecular docking and molecular dynamics simulations. A binding mode of these inhibitors was proposed based on the results. According to this binding mode, Thr628 can form two important hydrogen bonds with these inhibitors. Moreover, if the inhibitors can form an additional hydrogen bond with hydroxyl group of Ser289, the potency of the inhibitor can be greatly improved, such as the best inhibitor (compound 12d) in this series. Hydrophobic interactions between the inhibitors and LSD1 are also key contributor here, such as the interaction between the hydrophobic groups (benzene rings) of the inhibitors and the hydrophobic residues of LSD1 (including Val288, Val317, Val811, Ala814, Leu659, Trp751 and Tyr761). Based on the results and analysis, it may provide some useful information for future novel LSD1 inhibitor design.
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Affiliation(s)
- Xu Zhang
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Mo Li
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Yu Wang
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Yi Zhao
- b Department of Oncology , The First Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China
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40
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Targeting Chromatin-Mediated Transcriptional Control of Gene Expression in Non-Small Cell Lung Cancer Therapy: Preclinical Rationale and Clinical Results. Drugs 2015; 75:1757-71. [DOI: 10.1007/s40265-015-0461-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Zheng YC, Ma J, Wang Z, Li J, Jiang B, Zhou W, Shi X, Wang X, Zhao W, Liu HM. A Systematic Review of Histone Lysine-Specific Demethylase 1 and Its Inhibitors. Med Res Rev 2015; 35:1032-71. [PMID: 25990136 DOI: 10.1002/med.21350] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/02/2015] [Accepted: 04/19/2015] [Indexed: 12/11/2022]
Abstract
Histone lysine-specific demethylase 1 (LSD1) is the first discovered and reported histone demethylase by Dr. Shi Yang's group in 2004. It is classified as a member of amine oxidase superfamily, the common feature of which is using the flavin adenine dinucleotide (FAD) as its cofactor. Since it is located in cell nucleus and acts as a histone methylation eraser, LSD1 specifically removes mono- or dimethylated histone H3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) through formaldehyde-generating oxidation. It has been indicated that LSD1 and its downstream targets are involved in a wide range of biological courses, including embryonic development and tumor-cell growth and metastasis. LSD1 has been reported to be overexpressed in variety of tumors. Inactivating LSD1 or downregulating its expression inhibits cancer-cell development. LSD1 targeting inhibitors may represent a new insight in anticancer drug discovery. This review summarizes recent studies about LSD1 and mainly focuses on the basic physiological function of LSD1 and its involved mechanisms in pathophysiologic conditions, as well as the development of LSD1 inhibitors as potential anticancer therapeutic agents.
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Affiliation(s)
- Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinlian Ma
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Zhiru Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinfeng Li
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Bailing Jiang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wenjuan Zhou
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xiaojing Shi
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xixin Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wen Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
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42
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Mould DP, McGonagle AE, Wiseman DH, Williams EL, Jordan AM. Reversible inhibitors of LSD1 as therapeutic agents in acute myeloid leukemia: clinical significance and progress to date. Med Res Rev 2015; 35:586-618. [PMID: 25418875 DOI: 10.1002/med.21334] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the 10 years since the discovery of lysine-specific demethylase 1 (LSD1), this epigenetic eraser has emerged as an important target of interest in oncology. More specifically, research has demonstrated that it plays an essential role in the self-renewal of leukemic stem cells in acute myeloid leukemia (AML). This review will cover clinical aspects of AML, the role of epigenetics in the disease, and discuss the research that led to the first irreversible inhibitors of LSD1 entering clinical trials for the treatment of AML in 2014. We also review recent achievements and progress in the development of potent and selective reversible inhibitors of LSD1. These compounds differ in their mode of action from tranylcypromine derivatives and could facilitate novel biochemical studies to probe the pathways mediated by LSD1. In this review, we will critically evaluate the strengths and weaknesses of published series of reversible LSD1 inhibitors. Overall, while the development of reversible inhibitors to date has been less fruitful than that of irreversible inhibitors, there is still the possibility for their use to facilitate further research into the roles and functions of LSD1 and to expand the therapeutic applications of LSD1 inhibitors in the clinic.
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Affiliation(s)
- Daniel P Mould
- Department of Drug Discovery, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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43
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Nowotarski SL, Pachaiyappan B, Holshouser SL, Kutz CJ, Li Y, Huang Y, Sharma SK, Casero RA, Woster PM. Structure-activity study for (bis)ureidopropyl- and (bis)thioureidopropyldiamine LSD1 inhibitors with 3-5-3 and 3-6-3 carbon backbone architectures. Bioorg Med Chem 2015; 23:1601-12. [PMID: 25725609 PMCID: PMC4396983 DOI: 10.1016/j.bmc.2015.01.049] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/16/2022]
Abstract
Methylation at specific histone lysine residues is a critical post-translational modification that alters chromatin architecture, and dysregulated lysine methylation/demethylation is associated with the silencing of tumor suppressor genes. The enzyme lysine-specific demethylase 1 (LSD1) complexed to specific transcription factors catalyzes the oxidative demethylation of mono- and dimethyllysine 4 of histone H3 (H3K4me and H3K4me2, respectively). We have previously reported potent (bis)urea and (bis)thiourea LSD1 inhibitors that increase cellular levels of H3K4me and H3K4me2, promote the re-expression of silenced tumor suppressor genes and suppress tumor growth in vitro. Here we report the design additional (bis)urea and (bis)thiourea LSD1 inhibitors that feature 3-5-3 or 3-6-3 carbon backbone architectures. Three of these compounds displayed single-digit IC50 values in a recombinant LSD1 assay. In addition, compound 6d exhibited an IC50 of 4.2μM against the Calu-6 human lung adenocarcinoma line, and 4.8μM against the MCF7 breast tumor cell line, in an MTS cell viability assay. Following treatment with 6b-6d, Calu-6 cells exhibited a significant increase in the mRNA expression for the silenced tumor suppressor genes SFRP2, HCAD and p16, and modest increases in GATA4 message. The compounds described in this paper represent the most potent epigenetic modulators in this series, and have potential for use as antitumor agents.
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Affiliation(s)
- Shannon L Nowotarski
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Boobalan Pachaiyappan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Steven L Holshouser
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Craig J Kutz
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Youxuan Li
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Yi Huang
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Shiv K Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy, Wayne State University, 259 Mack Avenue, Detroit, MI 48202, United States
| | - Robert A Casero
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States.
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44
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Monaldi D, Ruoppolo G, Tilset M, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts. Eur J Med Chem 2015; 94:163-74. [DOI: 10.1016/j.ejmech.2015.02.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 12/12/2022]
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45
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McGrath J, Trojer P. Targeting histone lysine methylation in cancer. Pharmacol Ther 2015; 150:1-22. [PMID: 25578037 DOI: 10.1016/j.pharmthera.2015.01.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 02/06/2023]
Abstract
Within the vast landscape of histone modifications lysine methylation has gained increasing attention because of its profound regulatory potential. The methylation of lysine residues on histone proteins modulates chromatin structure and thereby contributes to the regulation of DNA-based nuclear processes such as transcription, replication and repair. Protein families with opposing catalytic activities, lysine methyltransferases (KMTs) and demethylases (KDMs), dynamically control levels of histone lysine methylation and individual enzymes within these families have become candidate oncology targets in recent years. A number of high quality small molecule inhibitors of these enzymes have been identified. Several of these compounds elicit selective cancer cell killing in vitro and robust efficacy in vivo, suggesting that targeting 'histone lysine methylation pathways' may be a relevant, emerging cancer therapeutic strategy. Here, we discuss individual histone lysine methylation pathway targets, the properties of currently available small molecule inhibitors and their application in the context of cancer.
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Affiliation(s)
- John McGrath
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA.
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46
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Hu D, Miyagi N, Arai Y, Oguri H, Miura T, Nishinaka T, Terada T, Gouda H, El-Kabbani O, Xia S, Toyooka N, Hara A, Matsunaga T, Ikari A, Endo S. Synthesis of 8-hydroxy-2-iminochromene derivatives as selective and potent inhibitors of human carbonyl reductase 1. Org Biomol Chem 2015; 13:7487-99. [DOI: 10.1039/c5ob00847f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human carbonyl reductase 1 (CBR1), a member of the short-chain dehydrogenase/reductase superfamily, reduces anthracycline anticancer drugs to their less potent anticancer C-13 hydroxy metabolites, which are linked with pathogenesis of cardiotoxicity, a side effect of the drugs.
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47
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Zhou C, Kang D, Xu Y, Zhang L, Zha X. Identification of Novel Selective Lysine-Specific Demethylase 1 (LSD1) Inhibitors Using a Pharmacophore-Based Virtual Screening Combined with Docking. Chem Biol Drug Des 2014; 85:659-71. [DOI: 10.1111/cbdd.12461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Chen Zhou
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Di Kang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Luyong Zhang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
| | - Xiaoming Zha
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
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48
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Kutz CJ, Holshouser SL, Marrow EA, Woster PM. 3,5-Diamino-1,2,4-triazoles as a novel scaffold for potent, reversible LSD1 (KDM1A) inhibitors. MEDCHEMCOMM 2014; 5:1863-1870. [PMID: 25580204 PMCID: PMC4286191 DOI: 10.1039/c4md00283k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The chromatin remodeling amine oxidase lysine-specific demethylase 1 (LSD1) has become an attractive target for the design of specific inhibitors with therapeutic potential. We, and others, have described LSD1 inhibitors that have potential as antitumor agents. Many of the currently known LSD1 inhibitors are poor drug candidates, or are structurally based on the tranylcypromine backbone, thus increasing the potential for off-target effects mediated by other amine oxidases. We now describe a series of potent LSD1 inhibitors based on a novel 1,2,4-triazole scaffold; these inhibitors show a high degree of specificity for LSD1 in vitro, and cause increases in cellular histone 3 dimethyllysine 4 (H3K4me2), a gene transcription activating mark. Importantly, these inhibitors are not toxic to mammalian cells in vitro, and thus they may show utility in the treatment of epigenetically-based diseases where cell death is not a desired endpoint Figure 1. Structures of LSD1 inhibitors 1, verlindamycin 2, (bis)thioureas 3, amidoxime 4, cyclic peptide 5, N3-(2-chloro-6-phenoxybenzyl)-4H-1,2,4-triazole-3,5-diamine 6 and N3,N5-bis(2-methoxybenzyl)-1H-1,2,4-triazole-3,5-diamine 7.
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Affiliation(s)
- Craig J Kutz
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Steven L Holshouser
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Ethan A Marrow
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, 70 President St., Charleston, SC 29425
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Rani R, Granchi C. Bioactive heterocycles containing endocyclic N-hydroxy groups. Eur J Med Chem 2014; 97:505-24. [PMID: 25466924 DOI: 10.1016/j.ejmech.2014.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/13/2014] [Accepted: 11/15/2014] [Indexed: 10/24/2022]
Abstract
Drug-likeness rules consider N-O single bonds as "structural alerts" which should not be present in a perspective drug candidate. In most cases this concern is correct, since it is known that N-hydroxy metabolites of branded drugs produce reactive species that cause serious side effects. However, this dangerous reactivity of the N-OH species generally takes place when the nitrogen atom is not comprised in a cyclic moiety. In fact, the same type of metabolic behavior should not be expected when the nitrogen atom is included in the ring of an aromatic heterocyclic scaffold. Nevertheless, heterocycles bearing endocyclic N-hydroxy portions have so far been poorly studied as chemical classes that may provide new therapeutic agents. This review provides an overview of N-OH-containing heterocycles with reported bioactivities that may be considered as therapeutically relevant and, therefore, may extend the chemical space available for the future development of novel pharmaceuticals. A systematic treatment of the various chemical classes belonging to this particular family of molecules is described along with a discussion of the biological activities associated to the most important examples.
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Affiliation(s)
- Reshma Rani
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Carlotta Granchi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
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50
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Dhanak D, Jackson P. Development and classes of epigenetic drugs for cancer. Biochem Biophys Res Commun 2014; 455:58-69. [PMID: 25016182 DOI: 10.1016/j.bbrc.2014.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022]
Abstract
Emerging evidence supports an important, etiologic role for epigenetic modifications in cancer. Various post translational modifications of histone proteins together with DNA methylation constitute an 'epigenetic code' regulating the transcriptional status of the cell and aberrant writing and/or interpretation of the code can contribute to a dysregulated, hyperproliferative state. In some cases, epigenetic deregulation has also been reported to result in tumor initiation. The discovery of somatic mutations in some chromatin binding proteins associated with subtypes of lymphomas and the ability to regulate expression of proto oncogenes such as Myc has spurred the development of specific small molecule modulators of histone binding proteins. Several of these compounds have entered clinical development for the treatment of heme malignancies. This review summarizes progress in the discovery and advancement of epigenetic therapeutics for cancer and provides a perspective for future development.
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Affiliation(s)
- Dashyant Dhanak
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Paul Jackson
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA
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