1
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Kawaf RR, Ramadan WS, El-Awady R. Deciphering the interplay of histone post-translational modifications in cancer: Co-targeting histone modulators for precision therapy. Life Sci 2024; 346:122639. [PMID: 38615747 DOI: 10.1016/j.lfs.2024.122639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
Chromatin undergoes dynamic regulation through reversible histone post-translational modifications (PTMs), orchestrated by "writers," "erasers," and "readers" enzymes. Dysregulation of these histone modulators is well implicated in shaping the cancer epigenome and providing avenues for precision therapies. The approval of six drugs for cancer therapy targeting histone modulators, along with the ongoing clinical trials of numerous candidates, represents a significant advancement in the field of precision medicine. Recently, it became apparent that histone PTMs act together in a coordinated manner to control gene expression. The intricate crosstalk of histone PTMs has been reported to be dysregulated in cancer, thus emerging as a critical factor in the complex landscape of cancer development. This formed the foundation of the swift emergence of co-targeting different histone modulators as a new strategy in cancer therapy. This review dissects how histone PTMs, encompassing acetylation, phosphorylation, methylation, SUMOylation and ubiquitination, collaboratively influence the chromatin states and impact cellular processes. Furthermore, we explore the significance of histone modification crosstalk in cancer and discuss the potential of targeting histone modification crosstalk in cancer management. Moreover, we underscore the significant strides made in developing dual epigenetic inhibitors, which hold promise as emerging candidates for effective cancer therapy.
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Affiliation(s)
- Rawan R Kawaf
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
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2
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Koijam AS, Singh KD, Nameirakpam BS, Haobam R, Rajashekar Y. Drug addiction and treatment: An epigenetic perspective. Biomed Pharmacother 2024; 170:115951. [PMID: 38043446 DOI: 10.1016/j.biopha.2023.115951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Drug addiction is a complex disease affected by numerous genetic and environmental factors. Brain regions in reward pathway, neuronal adaptations, genetic and epigenetic interactions causing transcriptional enhancement or repression of multiple genes induce different addiction phenotypes for varying duration. Addictive drug use causes epigenetic alterations and similarly epigenetic changes induced by environment can promote addiction. Epigenetic mechanisms include DNA methylation and post-translational modifications like methylation, acetylation, phosphorylation, ubiquitylation, sumoylation, dopaminylation and crotonylation of histones, and ADP-ribosylation. Non-coding RNAs also induce epigenetic changes. This review discusses these above areas and stresses the need for exploring epidrugs as a treatment alternative and adjunct, considering the limited success of current addiction treatment strategies. Epigenome editing complexes have lately been effective in eukaryotic systems. Targeted DNA cleavage techniques such as CRISPR-Cas9 system, CRISPR-dCas9 complexes, transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs) have been exploited as targeted DNA recognition or anchoring platforms, fused with epigenetic writer or eraser proteins and delivered by transfection or transduction methods. Efficacy of epidrugs is seen in various neuropsychiatric conditions and initial results in addiction treatment involving model organisms are remarkable. Epidrugs present a promising alternative treatment for addiction.
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Affiliation(s)
- Arunkumar Singh Koijam
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Kabrambam Dasanta Singh
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Bunindro Singh Nameirakpam
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Reena Haobam
- Department of Biotechnology, Manipur University, Canchipur, Imphal 795003, Manipur, India
| | - Yallappa Rajashekar
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India.
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3
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Ru J, Wang Y, Li Z, Wang J, Ren C, Zhang J. Technologies of targeting histone deacetylase in drug discovery: Current progress and emerging prospects. Eur J Med Chem 2023; 261:115800. [PMID: 37708798 DOI: 10.1016/j.ejmech.2023.115800] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Histone deacetylases (HDACs) catalyze the hydrolysis of acetyl-l-lysine side chains in histones and non-histones, which are key to epigenetic regulation in humans. Targeting HDACs has emerged as a promising strategy for treating various types of cancer, including myeloma and hematologic malignancies. At present, numerous small molecule inhibitors targeting HDACs are actively being investigated in clinical trials. Despite their potential efficacy in cancer treatment, HDAC inhibitors suffer from multi-directional selectivity and preclinical resistance issues. Hence, developing novel inhibitors based on cutting-edge medicinal chemistry techniques is essential to overcome these limitations and improve clinical outcomes. This manuscript presents an extensive overview of the properties and biological functions of HDACs in cancer, provides an overview of the current state of development and limitations of clinical HDAC inhibitors, and analyzes a range of innovative medicinal chemistry techniques that are applied. These techniques include selective inhibitors, dual-target inhibitors, proteolysis targeting chimeras, and protein-protein interaction inhibitors.
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Affiliation(s)
- Jinxiao Ru
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Zijia Li
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, USA
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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4
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Chen S, Zheng Y, Liang B, Yin Y, Yao J, Wang Q, Liu Y, Neamati N. The application of PROTAC in HDAC. Eur J Med Chem 2023; 260:115746. [PMID: 37607440 DOI: 10.1016/j.ejmech.2023.115746] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
Inducing protein degradation by proteolysis targeting chimera (PROTAC) has provided great opportunities for scientific research and industrial applications. Histone deacetylase (HDAC)-PROTAC has been widely developed since the first report of its ability to induce the degradation of SIRT2 in 2017. To date, ten of the eighteen HDACs (HDACs 1-8, HDAC10, and SIRT2) have been successfully targeted and degraded by HDAC-PROTACs. HDAC-PROTACs surpass traditional HDAC inhibitors in many aspects, such as higher selectivity, more potent antiproliferative activity, and the ability to disrupt the enzyme-independent functions of a multifunctional protein and overcome drug resistance. Rationally designing HDAC-PROTACs is a main challenge in development because slight variations in chemical structure can lead to drastic effects on the efficiency and selectivity of the degradation. In the future, HDAC-PROTACs can potentially be involved in clinical research with the support of the increased amount of in vivo data, pharmacokinetic evaluation, and pharmacological studies.
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Affiliation(s)
- Shaoting Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yuxiang Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Benji Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yudong Yin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Jian Yao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Quande Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Yanghan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States.
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5
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König B, Watson PR, Reßing N, Cragin AD, Schäker-Hübner L, Christianson DW, Hansen FK. Difluoromethyl-1,3,4-oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6. J Med Chem 2023; 66:13821-13837. [PMID: 37782298 PMCID: PMC10591924 DOI: 10.1021/acs.jmedchem.3c01345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an important drug target in oncological and non-oncological diseases. Most available HDAC6 inhibitors (HDAC6i) utilize hydroxamic acids as a zinc-binding group, which limits therapeutic opportunities due to its genotoxic potential. Recently, difluoromethyl-1,3,4-oxadiazoles (DFMOs) were reported as potent and selective HDAC6i but their mode of inhibition remained enigmatic. Herein, we report that DFMOs act as mechanism-based and essentially irreversible HDAC6i. Biochemical data confirm that DFMO 6 is a tight-binding HDAC6i capable of inhibiting HDAC6 via a two-step slow-binding mechanism. Crystallographic and mechanistic experiments suggest that the attack of 6 by the zinc-bound water at the sp2 carbon closest to the difluoromethyl moiety followed by a subsequent ring opening of the oxadiazole yields deprotonated difluoroacetylhydrazide 13 as active species. The strong anionic zinc coordination of 13 and the binding of the difluoromethyl moiety in the P571 pocket finally result in an essentially irreversible inhibition of HDAC6.
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Affiliation(s)
- Beate König
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Nina Reßing
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Abigail D Cragin
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Linda Schäker-Hübner
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
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6
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Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells. Cancers (Basel) 2022; 14:cancers14236014. [PMID: 36497494 PMCID: PMC9737972 DOI: 10.3390/cancers14236014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022] Open
Abstract
Defects in epigenetic pathways are key drivers of oncogenic cell proliferation. We developed a LSD1/HDAC6 multitargeting inhibitor (iDual), a hydroxamic acid analogue of the clinical candidate LSD1 inhibitor GSK2879552. iDual inhibits both targets with IC50 values of 540, 110, and 290 nM, respectively, against LSD1, HDAC6, and HDAC8. We compared its activity to structurally similar control probes that act by HDAC or LSD1 inhibition alone, as well as an inactive null compound. iDual inhibited the growth of leukemia cell lines at a higher level than GSK2879552 with micromolar IC50 values. Dual engagement with LSD1 and HDAC6 was supported by dose dependent increases in substrate levels, biomarkers, and cellular thermal shift assay. Both histone methylation and acetylation of tubulin were increased, while acetylated histone levels were only mildly affected, indicating selectivity for HDAC6. Downstream gene expression (CD11b, CD86, p21) was also elevated in response to iDual treatment. Remarkably, iDual synergized with doxorubicin, triggering significant levels of apoptosis with a sublethal concentration of the drug. While mechanistic studies did not reveal changes in DNA repair or drug efflux pathways, the expression of AGPAT9, ALOX5, BTG1, HIPK2, IFI44L, and LRP1, previously implicated in doxorubicin sensitivity, was significantly elevated.
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Guo Z, Sun Y, Liang L, Lu W, Luo B, Wu Z, Huo B, Hu Y, Huang P, Wu Q, Wen S. Design and Synthesis of Dual EZH2/BRD4 Inhibitors to Target Solid Tumors. J Med Chem 2022; 65:6573-6592. [PMID: 35500243 DOI: 10.1021/acs.jmedchem.1c01876] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
EZH2 inhibitors that prevent trimethylation of histone lysine 27 (H3K27) are often limited to the treatment of a subset of hematological malignancies. In most solid tumors, EZH2 inhibitors induce reciprocal H3K27 acetylation that subsequently results in acquired drug resistance. The combination of EZH2 and BRD4 inhibitors to resensitize solid cancer cells to EZH2 inhibitors has proven to be effective, underlying the significance of developing dual inhibitors. Herein, we present the design, synthesis, and biological evaluation of first-in-class dual EZH2/BRD4 inhibitors. Our most promising compound, YM458, displays potent inhibitory activity against EZH2 and BRD4 and remarkable antiproliferative capacity against 11 solid cancer cell lines. Its in vivo therapeutic potential is validated in both lung cancer and pancreatic cancer xenograft tumor mice models, highlighting the potential of EZH2/BRD4 dual inhibitors to target a broad scope of EZH2 inhibitor-resistant solid tumors.
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Affiliation(s)
- Zhirong Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Yameng Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Liyun Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Wenhua Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Bingling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Zhouming Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Bitao Huo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Yumin Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Qiang Wu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau 999078
| | - Shijun Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
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8
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7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1. Molecules 2022; 27:molecules27092892. [PMID: 35566242 PMCID: PMC9102847 DOI: 10.3390/molecules27092892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. To advance epigenetic probes and drug discovery, chemical companies are developing focused libraries for epigenetic targets. Based on a knowledge-based approach, herein we report the identification of two quinazoline-based derivatives identified in focused libraries with sub-micromolar inhibition of DNMT1 (30 and 81 nM), more potent than S-adenosylhomocysteine. Also, both compounds had a low micromolar affinity of DNMT3A and did not inhibit DNMT3B. The enzymatic inhibitory activity of DNMT1 and DNMT3A was rationalized with molecular modeling. The quinazolines reported in this work are known to have low cell toxicity and be potent inhibitors of the epigenetic target G9a. Therefore, the quinazoline-based compounds presented are attractive not only as novel potent inhibitors of DNMTs but also as dual and selective epigenetic agents targeting two families of epigenetic writers.
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9
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Crouch J, Shvedova M, Thanapaul RJRS, Botchkarev V, Roh D. Epigenetic Regulation of Cellular Senescence. Cells 2022; 11:672. [PMID: 35203320 PMCID: PMC8870565 DOI: 10.3390/cells11040672] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Senescence is a complex cellular stress response that abolishes proliferative capacity and generates a unique secretory pattern that is implicated in organismal aging and age-related disease. How a cell transitions to a senescent state is multifactorial and often requires transcriptional regulation of multiple genes. Epigenetic alterations to DNA and chromatin are powerful regulators of genome architecture and gene expression, and they play a crucial role in mediating the induction and maintenance of senescence. This review will highlight the changes in chromatin, DNA methylation, and histone alterations that establish and maintain cellular senescence, alongside the specific epigenetic regulation of the senescence-associated secretory phenotype (SASP).
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Affiliation(s)
- Jack Crouch
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Maria Shvedova
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Vladimir Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Daniel Roh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
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10
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Zhai S, Zhang H, Chen R, Wu J, Ai D, Tao S, Cai Y, Zhang JQ, Wang L. Design, synthesis and biological evaluation of novel hybrids targeting mTOR and HDACs for potential treatment of hepatocellular carcinoma. Eur J Med Chem 2021; 225:113824. [PMID: 34509167 DOI: 10.1016/j.ejmech.2021.113824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/19/2021] [Accepted: 08/28/2021] [Indexed: 01/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is a major contributor to global cancer incidence and mortality. Many pathways are involved in the development of HCC and various proteins including mTOR and HDACs have been identified as potential drug targets for HCC treatment. In the present study, two series of novel hybrid molecules targeting mTOR and HDACs were designed and synthesized based on parent inhibitors (MLN0128 and PP121 for mTOR, SAHA for HDACs) by using a fusion-type molecular hybridization strategy. In vitro antiproliferative assays demonstrated that these novel hybrids with suitable linker lengths exhibited broad cytotoxicity against various cancer cell lines, with significant activity against HepG2 cells. Notably, DI06, an MLN0128-based hybrid, exhibited antiproliferative activity against HepG2 cells with an IC50 value of 1.61 μM, which was comparable to those of both parent drugs (MLN0128, IC50 = 2.13 μM and SAHA, IC50 = 2.26 μM). In vitro enzyme inhibition assays indicated that DI06, DI07 and DI17 (PP121-based hybrid) exhibited nanomolar inhibitory activity against mTOR kinase and HDACs (e.g., HDAC1, HDAC2, HDAC3, HADC6 and HADC8). Cellular studies and western blot analyses uncovered that in HepG2 cells, DI06 and DI17 induced cell apoptosis by targeting mTOR and HDACs, blocked the cell cycle at the G0/G1 phase and suppressed cell migration. The potential binding modes of the hybrids (DI06 and DI17) with mTOR and HDACs were investigated by molecular docking. DI06 displayed better stability in rat liver microsomes than DI07 and DI17. Collectively, DI06 as a novel mTOR and HDACs inhibitor presented here warrants further investigation as a potential treatment of HCC.
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Affiliation(s)
- Shiyang Zhai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Huimin Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Rui Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Jiangxia Wu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Daiqiao Ai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shunming Tao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yike Cai
- Center for Certification and Evaluation, Guangdong Drug Administration, Guangzhou, 510080, China
| | - Ji-Quan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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11
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An in silico pipeline for the discovery of multitarget ligands: A case study for epi-polypharmacology based on DNMT1/HDAC2 inhibition. ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES 2021; 1. [PMID: 35475037 PMCID: PMC9038114 DOI: 10.1016/j.ailsci.2021.100008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The search for novel therapeutic compounds remains an overwhelming task owing to the time-consuming and expensive nature of the drug development process and low success rates. Traditional methodologies that rely on the one drug-one target paradigm have proven insufficient for the treatment of multifactorial diseases, leading to a shift to multitarget approaches. In this emerging paradigm, molecules with off-target and promiscuous interactions may result in preferred therapies. In this study, we developed a general pipeline combining machine learning algorithms and a deep generator network to train a dual inhibitor classifier capable of identifying putative pharmacophoric traits. As a case study, we focused on dual inhibitors targeting DNA methyltransferase 1 (DNMT) and histone deacetylase 2 (HDAC2), two enzymes that play a central role in epigenetic regulation. We used this approach to identify dual inhibitors from a novel large natural product database in the public domain. We used docking and atomistic simulations as complementary approaches to establish the ligand-interaction profiles between the best hits and DNMT1/HDAC2. By using the combined ligand- and structure-based approaches, we discovered two promising novel scaffolds that can be used to simultaneously target both DNMT1 and HDAC2. We conclude that the flexibility and adaptability of the proposed pipeline has predictive capabilities of similar or derivative methods and is readily applicable to the discovery of small molecules targeting many other therapeutically relevant proteins.
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12
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Neganova M, Aleksandrova Y, Suslov E, Mozhaitsev E, Munkuev A, Tsypyshev D, Chicheva M, Rogachev A, Sukocheva O, Volcho K, Klochkov S. Novel Multitarget Hydroxamic Acids with a Natural Origin CAP Group against Alzheimer's Disease: Synthesis, Docking and Biological Evaluation. Pharmaceutics 2021; 13:pharmaceutics13111893. [PMID: 34834312 PMCID: PMC8623418 DOI: 10.3390/pharmaceutics13111893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 02/05/2023] Open
Abstract
Hydroxamic acids are one of the most promising and actively studied classes of chemical compounds in medicinal chemistry. In this study, we describe the directed synthesis and effects of HDAC6 inhibitors. Fragments of adamantane and natural terpenes camphane and fenchane, combined with linkers of various nature with an amide group, were used as the CAP groups. Accordingly, 11 original target compounds were developed, synthesized, and exposed to in vitro and in vivo biological evaluations, including in silico methods. In silico studies showed that all synthesized compounds were drug-like and could penetrate through the blood-brain barrier. According to the in vitro testing, hydroxamic acids 15 and 25, which effectively inhibited HDAC6 and exhibited anti-aggregation properties against β-amyloid peptides, were chosen as the most promising substances to study their neuroprotective activities in vivo. All in vivo studies were performed using 5xFAD transgenic mice simulating Alzheimer's disease. In these animals, the Novel Object Recognition and Morris Water Maze Test showed that the formation of hippocampus-dependent long-term episodic and spatial memory was deteriorated. Hydroxamic acid 15 restored normal memory functions to the level observed in control wild-type animals. Notably, this effect was precisely associated with the ability to restore lost cognitive functions, but not with the effect on motor and exploratory activities or on the level of anxiety in animals. Conclusively, hydroxamic acid 15 containing an adamantane fragment linked by an amide bond to a hydrocarbon linker is a possible potential multitarget agent against Alzheimer's disease.
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Affiliation(s)
- Margarita Neganova
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432 Moscow, Russia; (M.N.); (Y.A.); (M.C.)
| | - Yulia Aleksandrova
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432 Moscow, Russia; (M.N.); (Y.A.); (M.C.)
| | - Evgenii Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Evgenii Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Aldar Munkuev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Dmitry Tsypyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Maria Chicheva
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432 Moscow, Russia; (M.N.); (Y.A.); (M.C.)
| | - Artem Rogachev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Olga Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, SA 5042, Australia;
| | - Konstantin Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.S.); (E.M.); (A.M.); (D.T.); (A.R.); (K.V.)
| | - Sergey Klochkov
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432 Moscow, Russia; (M.N.); (Y.A.); (M.C.)
- Correspondence: ; Tel.: +7-(496)-5242525
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13
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Cao F, Xiao Z, Chen S, Zhao C, Chen D, Haisma HJ, Dekker FJ. HDAC/MIF dual inhibitor inhibits NSCLC cell survival and proliferation by blocking the AKT pathway. Bioorg Chem 2021; 117:105396. [PMID: 34649152 DOI: 10.1016/j.bioorg.2021.105396] [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: 03/05/2021] [Revised: 08/30/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
Non-small-cell lung carcinoma (NSCLC) is one of the most common forms of lung cancer, and a leading cause of cancer death among human beings. There is an urgent demand for novel therapeutics for the treatment of NSCLC to enhance the efficacy of the currently applied Tyrosine kinase inhibitors (TKIs) therapy and to overcome therapy-resistance. Here, we report a novel small-molecule inhibitor that simultaneously targets histone deacetylase (HDAC) and macrophage migration inhibitory factor (MIF). The HDAC/MIF dual inhibitor proved to be toxic for EGFR mutated (H1650, TKI-resistant) or knock out (A549 EGFR-/-) NSCLC cell lines. Further experiments showed that HDAC inhibition inhibits cell survival and proliferation, while MIF inhibition downregulates pAKT or AKT expression level, which both interfere with cell survival. Furthermore, the combination treatment of TKI and HDAC/MIF dual inhibitor showed that the dual inhibitor enhanced TKI inhibitory efficacy, highlighting the advantages of HDAC/MIF dual inhibitor for more effective treatment of NSCLC.
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Affiliation(s)
- Fangyuan Cao
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Zhangping Xiao
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Siwei Chen
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Chunlong Zhao
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Deng Chen
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Hidde J Haisma
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Frank J Dekker
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
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14
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Rodrigues DA, Roe A, Griffith D, Chonghaile TN. Advances in the Design and Development of PROTAC-mediated HDAC degradation. Curr Top Med Chem 2021; 22:408-424. [PMID: 34649488 DOI: 10.2174/1568026621666211015092047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023]
Abstract
Due to developments in modern chemistry, previously undruggable targets are becoming druggable thanks to selective degradation using the ubiquitin-proteasomal degradation system. PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules designed specifically to degrade target proteins (protein of interest, POI). They are of significant interest to industry and academia as they are highly specific and can target previously undruggable target proteins from transcription factors to enzymes. More than 15 degraders are expected to be evaluated in clinical trials by the end of 2021. Herein, we describe recent advances in the design and development of PROTAC-mediated degradation of histone deacetylases (HDACs). PROTAC-mediated degradation of HDACs can offer some significant advantages over direct inhibition, such as the use of substoichiometric doses and the potential to disrupt enzyme-independent HDAC function. Herein, we discuss the potential implications of the degradation of HDACs with HDAC knockout studies and the selection of HDAC inhibitors and E3 ligase ligands for the design of the PROTACs. The potential utility of HDAC PROTACs in various disease pathologies from cancer to inflammation to neurodegeneration is driving the interest in this field.
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Affiliation(s)
- Daniel Alencar Rodrigues
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Andrew Roe
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Darren Griffith
- Department of Chemistry, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Tríona Ní Chonghaile
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
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15
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Duan YC, Zhang SJ, Shi XJ, Jin LF, Yu T, Song Y, Guan YY. Research progress of dual inhibitors targeting crosstalk between histone epigenetic modulators for cancer therapy. Eur J Med Chem 2021; 222:113588. [PMID: 34107385 DOI: 10.1016/j.ejmech.2021.113588] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Abnormal epigenetics is a critical hallmark of human cancers. Anticancer drug discovery directed at histone epigenetic modulators has gained impressive advances with six drugs available for cancer therapy and numerous other candidates undergoing clinical trials. However, limited therapeutic profile, drug resistance, narrow safety margin, and dose-limiting toxicities pose intractable challenges for their clinical utility. Because histone epigenetic modulators undergo intricate crosstalk and act cooperatively to shape an aberrant epigenetic profile, co-targeting histone epigenetic modulators with a different mechanism of action has rapidly emerged as an attractive strategy to overcome the limitations faced by the single-target epigenetic inhibitors. In this review, we summarize in detail the crosstalk of histone epigenetic modulators in regulating gene transcription and the progress of dual epigenetic inhibitors targeting this crosstalk.
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Affiliation(s)
- Ying-Chao Duan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
| | - Shao-Jie Zhang
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Xiao-Jing Shi
- Laboratory Animal Center, Academy of Medical Science, Zhengzhou University, 450052, Zhengzhou, Henan Province, PR China
| | - Lin-Feng Jin
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Tong Yu
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yu Song
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yuan-Yuan Guan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
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16
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Design, synthesis, and biological evaluation of novel dual inhibitors targeting lysine specific demethylase 1 (LSD1) and histone deacetylases (HDAC) for treatment of gastric cancer. Eur J Med Chem 2021; 220:113453. [PMID: 33957387 DOI: 10.1016/j.ejmech.2021.113453] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022]
Abstract
LSD1 and HDAC are physical and functional related to each other in various human cancers and simultaneous pharmacological inhibition of LSD1 and HDAC exerts synergistic anti-cancer effects. In this work, a series of novel LSD1/HDAC bifunctional inhibitors with a styrylpyridine skeleton were designed and synthesized based on our previously reported LSD1 inhibitors. The representative compounds 5d and 5m showed potent activity against LSD1 and HDAC at both molecular and cellular level and displayed high selectivity against MAO-A/B. Moreover, compounds 5d and 5m demonstrated potent antiproliferative activities against MGC-803 and HCT-116 cancer cell lines. Notably, compound 5m showed superior in vitro anticancer potency against a panel of gastric cancer cell lines than ORY-1001 and SP-2509 with IC50 values ranging from 0.23 to 1.56 μM. Compounds 5d and 5m significantly modulated the expression of Bcl-2, Bax, Vimentin, ZO-1 and E-cadherin, induced apoptosis, reduced colony formation and suppressed migration in MGC-803 cancer cells. In addition, preliminary absorption, distribution, metabolism, excretion (ADME) studies revealed that compounds 5d and 5m showed acceptable metabolic stability in human liver microsomes with minimal inhibition of cytochrome P450s (CYPs). Those results indicated that compound 5m could be a promising lead compound for further development as a therapeutic agent in gastric cancers via LSD1 and HDAC dual inhibition.
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17
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Sánchez-Cruz N, Medina-Franco JL. Epigenetic Target Fishing with Accurate Machine Learning Models. J Med Chem 2021; 64:8208-8220. [PMID: 33770434 DOI: 10.1021/acs.jmedchem.1c00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic targets are of significant importance in drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents many structure-activity relationships that have not been exploited thus far to develop predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26 318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. We built predictive models with high accuracy for small molecules' epigenetic target profiling through a systematic comparison of the machine learning models trained on different molecular fingerprints. The models were thoroughly validated, showing mean precisions of up to 0.952 for the epigenetic target prediction task. Our results indicate that the models reported herein have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as a freely accessible web application.
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Affiliation(s)
- Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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18
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He F, Chou CJ, Scheiner M, Poeta E, Yuan Chen N, Gunesch S, Hoffmann M, Sotriffer C, Monti B, Maurice T, Decker M. Melatonin- and Ferulic Acid-Based HDAC6 Selective Inhibitors Exhibit Pronounced Immunomodulatory Effects In Vitro and Neuroprotective Effects in a Pharmacological Alzheimer's Disease Mouse Model. J Med Chem 2021; 64:3794-3812. [PMID: 33769811 DOI: 10.1021/acs.jmedchem.0c01940] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structures of melatonin and ferulic acid were merged into tertiary amide-based histone deacetylase 6 (HDAC6) inhibitors to develop multi-target-directed inhibitors for neurodegenerative diseases to incorporate antioxidant effects without losing affinity and selectivity at HDAC6. Structure-activity relationships led to compound 10b as a hybrid molecule showing pronounced and selective inhibition of HDAC6 (IC50 = 30.7 nM, > 25-fold selectivity over other subtypes). This compound shows comparable DPPH radical scavenging ability to ferulic acid, comparable ORAC value to melatonin and comparable Cu2+ chelating ability to EDTA. It also lacks neurotoxicity on HT-22 cells, exhibits a pronounced immunomodulatory effect, and is active in vivo showing significantly higher efficacy in an AD mouse model to prevent both Aβ25-35-induced spatial working and long-term memory dysfunction at lower dose (0.3 mg/kg) compared to positive control HDAC6 inhibitor ACY1215 and an equimolar mixture of the three entities ACY1215, melatonin and ferulic acid, suggesting potentially disease-modifying properties.
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Affiliation(s)
- Feng He
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - C James Chou
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Matthias Scheiner
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Eleonora Poeta
- Department of Pharmacy and Biotechnologies, University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Natalia Yuan Chen
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Sandra Gunesch
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Matthias Hoffmann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Christoph Sotriffer
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Barbara Monti
- Department of Pharmacy and Biotechnologies, University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Tangui Maurice
- MMDN, Univ Montpellier, EPHE, INSERM, Montpellier 34095, France
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Am Hubland, Würzburg 97074, Germany
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19
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Santibáñez-Morán MG, Medina-Franco JL. The Acid/Base Characterization of Molecules with Epigenetic Activity. ChemMedChem 2021; 16:1744-1753. [PMID: 33594823 DOI: 10.1002/cmdc.202001009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Indexed: 12/12/2022]
Abstract
The acidic and basic functional groups in a molecule strongly influence its physicochemical properties, affinity for a macromolecule, pharmacokinetics, and toxicity. For instance, basicity has been correlated with molecular promiscuity, hERG blockade, and phospholipidosis. Nonetheless, no systematic characterization of the acid/base profile of epigenomic databases has been reported. This study describes an analysis of the acidic ionization constant distribution of a library of 7820 compounds with reported activity against epigenetic targets. Furthermore, the epigenomics database's acid/base profile was compared to the reference libraries of food chemicals, natural products, and approved drugs. It was found that the acid/base profile of histone lysine demethylase ligands is more similar to previously approved drugs, and histone acetyltransferase ligands have acidic and basic functional groups largely found in food chemicals and natural products; this support the potential of these libraries for finding new epigenetic inhibitors.
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Affiliation(s)
- Marisa G Santibáñez-Morán
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - José L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico
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20
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Jenke R, Reßing N, Hansen FK, Aigner A, Büch T. Anticancer Therapy with HDAC Inhibitors: Mechanism-Based Combination Strategies and Future Perspectives. Cancers (Basel) 2021; 13:cancers13040634. [PMID: 33562653 PMCID: PMC7915831 DOI: 10.3390/cancers13040634] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 12/26/2022] Open
Abstract
The increasing knowledge of molecular drivers of tumorigenesis has fueled targeted cancer therapies based on specific inhibitors. Beyond "classic" oncogene inhibitors, epigenetic therapy is an emerging field. Epigenetic alterations can occur at any time during cancer progression, altering the structure of the chromatin, the accessibility for transcription factors and thus the transcription of genes. They rely on post-translational histone modifications, particularly the acetylation of histone lysine residues, and are determined by the inverse action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Importantly, HDACs are often aberrantly overexpressed, predominantly leading to the transcriptional repression of tumor suppressor genes. Thus, histone deacetylase inhibitors (HDACis) are powerful drugs, with some already approved for certain hematological cancers. Albeit HDACis show activity in solid tumors as well, further refinement and the development of novel drugs are needed. This review describes the capability of HDACis to influence various pathways and, based on this knowledge, gives a comprehensive overview of various preclinical and clinical studies on solid tumors. A particular focus is placed on strategies for achieving higher efficacy by combination therapies, including phosphoinositide 3-kinase (PI3K)-EGFR inhibitors and hormone- or immunotherapy. This also includes new bifunctional inhibitors as well as novel approaches for HDAC degradation via PROteolysis-TArgeting Chimeras (PROTACs).
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Affiliation(s)
- Robert Jenke
- University Cancer Center Leipzig (UCCL), University Hospital Leipzig, D-04103 Leipzig, Germany
- Clinical Pharmacology, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Medical Faculty, University of Leipzig, D-04107 Leipzig, Germany;
- Correspondence: (R.J.); (A.A.); Tel.: +49-(0)341-97-24661 (A.A.)
| | - Nina Reßing
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, Rheinische Fried-rich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany; (N.R.); (F.K.H.)
| | - Finn K. Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, Rheinische Fried-rich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany; (N.R.); (F.K.H.)
| | - Achim Aigner
- Clinical Pharmacology, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Medical Faculty, University of Leipzig, D-04107 Leipzig, Germany;
- Correspondence: (R.J.); (A.A.); Tel.: +49-(0)341-97-24661 (A.A.)
| | - Thomas Büch
- Clinical Pharmacology, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Medical Faculty, University of Leipzig, D-04107 Leipzig, Germany;
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21
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Novel Approaches to Epigenetic Therapies: From Drug Combinations to Epigenetic Editing. Genes (Basel) 2021; 12:genes12020208. [PMID: 33572577 PMCID: PMC7911730 DOI: 10.3390/genes12020208] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer development involves both genetic and epigenetic alterations. Aberrant epigenetic modifications are reversible, allowing excellent opportunities for therapeutic intervention. Nowadays, several epigenetic drugs are used worldwide to treat, e.g., myelodysplastic syndromes and leukemias. However, overcoming resistance and widening the therapeutic profiles are the most important challenges faced by traditional epigenetic drugs. Recently, novel approaches to epigenetic therapies have been proposed. Next-generation epigenetic drugs, with longer half-life and better bioavailability, are being developed and tested. Since epigenetic phenomena are interdependent, treatment modalities include co-administration of two different epigenetic drugs. In order to sensitize cancer cells to chemotherapy, epigenetic drugs are administered prior to chemotherapy, or both epigenetic drug and chemotherapy are used together to achieve synergistic effects and maximize treatment efficacy. The combinations of epigenetic drug with immunotherapy are being tested, because they have proved to enhance antitumor immune responses. The next approach involves targeting the metabolic causes of epigenetic changes, i.e., enzymes which, when mutated, produce oncometabolites. Finally, epigenome editing makes it possible to modify individual chromatin marks at a defined region with unprecedented specificity and efficiency. This review summarizes the above attempts in fulfilling the promise of epigenetic drugs in the effective cancer treatment.
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22
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Juárez-Mercado KE, Prieto-Martínez FD, Sánchez-Cruz N, Peña-Castillo A, Prada-Gracia D, Medina-Franco JL. Expanding the Structural Diversity of DNA Methyltransferase Inhibitors. Pharmaceuticals (Basel) 2020; 14:ph14010017. [PMID: 33375520 PMCID: PMC7824300 DOI: 10.3390/ph14010017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug discovery. They are also chemical tools to understand the biochemistry of epigenetic processes. Herein, we report five distinct inhibitors of DNMT1 characterized in enzymatic inhibition assays that did not show activity with DNMT3B. It was concluded that the dietary component theaflavin is an inhibitor of DNMT1. Two additional novel inhibitors of DNMT1 are the approved drugs glyburide and panobinostat. The DNMT1 enzymatic inhibitory activity of panobinostat, a known pan inhibitor of histone deacetylases, agrees with experimental reports of its ability to reduce DNMT1 activity in liver cancer cell lines. Molecular docking of the active compounds with DNMT1, and re-scoring with the recently developed extended connectivity interaction features approach, led to an excellent agreement between the experimental IC50 values and docking scores.
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Affiliation(s)
- K. Eurídice Juárez-Mercado
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Fernando D. Prieto-Martínez
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Andrea Peña-Castillo
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Diego Prada-Gracia
- Research Unit on Computational Biology and Drug Design, Children’s Hospital of Mexico Federico Gomez, Mexico City 06720, Mexico;
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
- Correspondence:
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23
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Rodrigues DA, Pinheiro PSM, Fraga CAM. Multitarget Inhibition of Histone Deacetylase (HDAC) and Phosphatidylinositol-3-kinase (PI3K): Current and Future Prospects. ChemMedChem 2020; 16:448-457. [PMID: 33049098 DOI: 10.1002/cmdc.202000643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/06/2020] [Indexed: 12/11/2022]
Abstract
The discovery of histone deacetylase (HDAC) inhibitors is a hot topic in the medicinal chemistry community regarding cancer research. This is related primarily to two factors: success in the clinic, e. g., the four FDA-approved HDAC inhibitors, and strong versatility to combine their pharmacophoric features to design new hybrid compounds with multitarget profiles. Thus, the selection of adequate pharmacophores to combine, i. e., combining targets that can result in a synergistic effect, is desirable, as it increases the probability of discovering a new useful therapeutic strategy. In this work, we highlight the design of multitarget HDAC/PI3K inhibitors. Although this approach is still in its early stages, many significant works have described the design and pharmacological evaluation of this new promising class of multitarget inhibitors, where compound CUDC-907, which is already in clinical trials, stands out. Therefore, the question emerges of whether there still space for the design and evaluation of new multitarget HDAC/PI3K inhibitors. When considering the selectivity profile of the described multitarget compounds, the answer appears to be in the affirmative, especially since the first examples of compounds with a certain selectivity profile only recently appeared in 2020.
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Affiliation(s)
- Daniel A Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Pedro S M Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Carlos A M Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
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Recent progress on cheminformatics approaches to epigenetic drug discovery. Drug Discov Today 2020; 25:2268-2276. [PMID: 33010481 DOI: 10.1016/j.drudis.2020.09.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/31/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022]
Abstract
The ability of epigenetic markers to affect genome function has enabled transformative changes in drug discovery, especially in cancer and other emerging therapeutic areas. Concordant with the introduction of the term 'epi-informatics', the size of the epigenetically relevant chemical space has grown substantially and so did the number of applications of cheminformatic methods to epigenetics. Recent progress in epi-informatics has improved our understanding of the structure-epigenetic activity relationships and boosted the development of models predicting novel epigenetic agents. Herein, we review the advances in computational approaches to drug discovery of small molecules with epigenetic modulation profiles, summarize the current chemogenomics data available for epigenetic targets, and provide a perspective on the greater utility of biomedical knowledge mining as a means to advance the epigenetic drug discovery.
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25
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Abstract
It is now 30 years since the first report of a potent zinc-dependent histone deacetylase (HDAC) inhibitor appeared. Since then, five HDAC inhibitors have received regulatory approval for cancer chemotherapy while many others are in clinical development for oncology as well as other therapeutic indications. This Perspective reviews the biological and medicinal chemistry advances over the past 3 decades with an emphasis on the design of selective inhibitors that discriminate between the 11 human HDAC isoforms.
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Affiliation(s)
- Terence C S Ho
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Alex H Y Chan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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