1
|
Ramakrishnan J, Magudeeswaran S, Suresh S, Poomani K. Investigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis. J Biomol Struct Dyn 2023; 41:1351-1365. [PMID: 34974819 DOI: 10.1080/07391102.2021.2020164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The p300 histone acetyltransferase (HAT) enzyme acetylates the lysine residue of histone promotes the transcription reaction. The abnormal function of p300 HAT enzyme causes various diseases such as Cancer, Asthma, Alzheimer, Diabetics, and AIDS. In the recent years, several studies have been conducted to design potential drug to inhibit this enzyme. Recently, an in vitro study has been performed on the synthetic molecules PU139 and PU141 to inhibit the p300 HAT enzyme. The present study aims to understand the binding affinity, intermolecular interactions, conformational stability and binding energy of PU139 and PU141 molecules in the active site of p300 HAT enzyme from the in silico studies. The molecular docking and molecular dynamics (MD) simulations were carried out for both ligands with the p300 HAT enzyme. The molecular docking and MD simulations reveals that both molecules forms expected interactions with the catalytic site key residues of p300 enzyme. The MD simulation shows the maximum RMSD value for the PU141 is 2.3 Å, whereas for PU139 is 3.3 Å; these low RMSD values indicate that both molecules are highly stable in the active site of p300. The calculated binding free energy of PU141 (-20.62 kcal/mol) is higher than the molecule PU139 (-17.67 kcal/mol). Among the results, PU141 shows the high binding affinity with p300 while comparing with PU139. The results of this in-silico study coupled with the findings reported in the in vitro study confirm that PU141 may be suitable for clinical study.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Sivanandam Magudeeswaran
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| |
Collapse
|
2
|
Feng J, Meng X. Histone modification and histone modification-targeted anti-cancer drugs in breast cancer: Fundamentals and beyond. Front Pharmacol 2022; 13:946811. [PMID: 36188615 PMCID: PMC9522521 DOI: 10.3389/fphar.2022.946811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/15/2022] [Indexed: 12/21/2022] Open
Abstract
Dysregulated epigenetic enzymes and resultant abnormal epigenetic modifications (EMs) have been suggested to be closely related to tumor occurrence and progression. Histone modifications (HMs) can assist in maintaining genome stability, DNA repair, transcription, and chromatin modulation within breast cancer (BC) cells. In addition, HMs are reversible, dynamic processes involving the associations of different enzymes with molecular compounds. Abnormal HMs (e.g. histone methylation and histone acetylation) have been identified to be tightly related to BC occurrence and development, even though their underlying mechanisms remain largely unclear. EMs are reversible, and as a result, epigenetic enzymes have aroused wide attention as anti-tumor therapeutic targets. At present, treatments to restore aberrant EMs within BC cells have entered preclinical or clinical trials. In addition, no existing studies have comprehensively analyzed aberrant HMs within BC cells; in addition, HM-targeting BC treatments remain to be further investigated. Histone and non-histone protein methylation is becoming an attractive anti-tumor epigenetic therapeutic target; such methylation-related enzyme inhibitors are under development at present. Consequently, the present work focuses on summarizing relevant studies on HMs related to BC and the possible mechanisms associated with abnormal HMs. Additionally, we also aim to analyze existing therapeutic agents together with those drugs approved and tested through pre-clinical and clinical trials, to assess their roles in HMs. Moreover, epi-drugs that target HMT inhibitors and HDAC inhibitors should be tested in preclinical and clinical studies for the treatment of BC. Epi-drugs that target histone methylation (HMT inhibitors) and histone acetylation (HDAC inhibitors) have now entered clinical trials or are approved by the US Food and Drug Administration (FDA). Therefore, the review covers the difficulties in applying HM-targeting treatments in clinics and proposes feasible approaches for overcoming such difficulties and promoting their use in treating BC cases.
Collapse
|
3
|
Shanmugam MK, Dharmarajan A, Warrier S, Bishayee A, Kumar AP, Sethi G, Ahn KS. Role of histone acetyltransferase inhibitors in cancer therapy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 125:149-191. [PMID: 33931138 DOI: 10.1016/bs.apcsb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of cancer is a complex phenomenon driven by various extrinsic as well as intrinsic risk factors including epigenetic modifications. These post-translational modifications are encountered in diverse cancer cells and appear for a relatively short span of time. These changes can significantly affect various oncogenic genes and proteins involved in cancer initiation and progression. Histone lysine acetylation and deacetylation processes are controlled by two opposing classes of enzymes that modulate gene regulation either by adding an acetyl moiety on a histone lysine residue by histone lysine acetyltransferases (KATs) or via removing it by histone deacetylases (KDACs). Deregulated KAT activity has been implicated in the development of several diseases including cancer and can be targeted for the development of anti-neoplastic drugs. Here, we describe the predominant epigenetic changes that can affect key KAT superfamily members during carcinogenesis and briefly highlight the pharmacological potential of employing lysine acetyltransferase inhibitors (KATi) for cancer therapy.
Collapse
Affiliation(s)
- Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Arunasalam Dharmarajan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences Technology and Research, Sri Ramachandra Institute of Higher Education & Research, Chennai, India
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, India
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL, United States
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Kwang Seok Ahn
- Department of Science in Korean Medicine, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea.
| |
Collapse
|
4
|
Stacy AJ, Zhang J, Craig MP, Hira A, Dole N, Kadakia MP. TIP60 up-regulates ΔNp63α to promote cellular proliferation. J Biol Chem 2019; 294:17007-17016. [PMID: 31601649 DOI: 10.1074/jbc.ra119.010388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/03/2019] [Indexed: 01/08/2023] Open
Abstract
An estimated 5.4 million cases of nonmelanoma skin cancer are reported in the United States at an associated cost of $4.8 billion. ΔNp63α, a proto-oncogene in the p53 family of transcription factors, is overexpressed in squamous cell carcinoma (SCC) and associated with poor prognosis and survival. ΔNp63α elicits its tumorigenic effects in part by promoting cellular proliferation and cell survival. Despite its importance in SCC, the upstream regulation of ΔNp63α is poorly understood. In this study, we identify TIP60 as a novel upstream regulator of ΔNp63α. Using a combination of overexpression, silencing, stable expression, and pharmacological approaches in multiple cell lines, we showed that TIP60 up-regulates ΔNp63α expression. Utilizing cycloheximide treatment, we showed that TIP60 catalytic activity is required for stabilization of ΔNp63α protein levels. We further showed that TIP60 coexpression inhibits ΔNp63α ubiquitination and proteasomal degradation. Stabilization of ΔNp63α protein was further associated with TIP60-mediated acetylation. Finally, we demonstrated that TIP60-mediated regulation of ΔNp63α increases cellular proliferation by promoting G2/M progression through MTS assays and flow cytometry. Taken together, our findings provide evidence that TIP60 may contribute to SCC progression by increasing ΔNp63α protein levels, thereby promoting cellular proliferation.
Collapse
Affiliation(s)
- Andrew J Stacy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Jin Zhang
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Michael P Craig
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Akshay Hira
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Nikhil Dole
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Madhavi P Kadakia
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| |
Collapse
|
5
|
Huang M, Huang J, Zheng Y, Sun Q. Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. Eur J Med Chem 2019; 178:259-286. [PMID: 31195169 DOI: 10.1016/j.ejmech.2019.05.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 02/05/2023]
Abstract
Acetylation, a key component in post-translational modification regulated by HATs and HDACs, is relevant to many crucial cellular contexts in organisms. Based on crucial pharmacophore patterns and the structure of targeted proteins, HAT inhibitors are designed and modified for higher affinity and better bioactivity. However, there are still some challenges, such as cell permeability, selectivity, toxicity and synthetic availability, which limit the improvement of HAT inhibitors. So far, only few HAT inhibitors have been approved for commercialization, indicating the urgent need for more successful and effective structure-based drug design and synthetic strategies. Here, we summarized three classes of HAT inhibitors based on their sources and structural scaffolds, emphasizing on their synthetic methods and structure-activity relationships and molecular mechanisms, hoping to facilitate the development and further application of HAT inhibitors.
Collapse
Affiliation(s)
- Mengyuan Huang
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yongcheng Zheng
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Qiu Sun
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| |
Collapse
|
6
|
Ngo L, Brown T, Zheng YG. Bisubstrate inhibitors to target histone acetyltransferase 1. Chem Biol Drug Des 2019; 93:865-873. [PMID: 30637990 DOI: 10.1111/cbdd.13476] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/24/2022]
Abstract
Developing selective enzyme inhibitors allows for the expansion of molecular toolboxes to investigate functions and activities of target enzymes. The histone acetyltransferase 1 (HAT1) is among the first histone acetyltransferase (HAT) enzymes that were discovered in the mid-1990s; however, it remains one of the poorly studied enzymes in comparison with the other HATs. Although HAT1 has been linked to various disease states, no inhibitors have been reported to target HAT1. Here, we designed a set of peptide-CoA conjugates as bisubstrate inhibitors of HAT1 with submicromolar potency. In particular, the bisubstrate inhibitor H4K12CoA exhibited a low Ki value of 1.1 nM for HAT1. In addition, H4K12CoA was shown to be a competitive inhibitor with respect to both AcCoA and H4 peptide, suggesting a unique kinetic mechanism of HAT1 catalysis. Creating these submicromolar inhibitors offers mechanistic tools to better understand how HAT1 recognizes substrates and cofactors, as well as provides chemical leads to further develop therapeutic agents to target this important enzyme for disease therapy.
Collapse
Affiliation(s)
- Liza Ngo
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Yujun G Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| |
Collapse
|
7
|
Sadoogh Abbasian S, Soufian S, Ghaznavi-Rad E, Abtahi H. High Level Activity of Recombinant Lysostaphin After Computer Simulation and Additive-Based Refolding. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9769-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
8
|
Lysine acetyltransferase inhibitors: structure-activity relationships and potential therapeutic implications. Future Med Chem 2018; 10:1067-1091. [PMID: 29676588 DOI: 10.4155/fmc-2017-0244] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Lysine acetylation is a post-translational modification of both histone and nonhistone proteins that is catalyzed by lysine acetyltransferases and plays a key role in numerous biological contexts. The dysregulation of this enzyme activity is implicated in many human pathologies such as cancer, neurological and inflammatory disorders. Many lysine acetyltransferase inhibitors (KATi) have been developed so far, but there is still the need for new, more potent, metabolically stable and selective KATi as chemical tools for studying KAT biology and/or as potential therapeutic agents. This review will examine the features of KAT enzymes and related diseases, with particular emphasis on KATi (bisubstrate analogs, natural compounds and synthetic derivatives), analyzing their mechanism of action, structure-activity relationships, pharmacokinetic/pharmacodynamic properties and potential future applications.
Collapse
|
9
|
Di Martile M, Del Bufalo D, Trisciuoglio D. The multifaceted role of lysine acetylation in cancer: prognostic biomarker and therapeutic target. Oncotarget 2018; 7:55789-55810. [PMID: 27322556 PMCID: PMC5342454 DOI: 10.18632/oncotarget.10048] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022] Open
Abstract
Lysine acetylation is a post-translational modification that regulates gene transcription by targeting histones as well as a variety of transcription factors in the nucleus. Recently, several reports have demonstrated that numerous cytosolic proteins are also acetylated and that this modification, affecting protein activity, localization and stability has profound consequences on their cellular functions. Interestingly, most non-histone proteins targeted by acetylation are relevant for tumorigenesis. In this review, we will analyze the functional implications of lysine acetylation in different cellular compartments, and will examine our current understanding of lysine acetyltransferases family, highlighting the biological role and prognostic value of these enzymes and their substrates in cancer. The latter part of the article will address challenges and current status of molecules targeting lysine acetyltransferase enzymes in cancer therapy.
Collapse
Affiliation(s)
- Marta Di Martile
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
| | - Donatella Del Bufalo
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Trisciuoglio
- Preclinical Models and New Therapeutic Agents Unit, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Rome, Italy
| |
Collapse
|
10
|
Brown JAL. In Vitro Histone Acetylation Assay. ACTA ACUST UNITED AC 2017; 79:3.14.1-3.14.16. [PMID: 29261229 DOI: 10.1002/cpph.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Acetylation is a core cellular process involved in maintaining genomic integrity, gene regulation, and metabolism. Histone acetyltransferases (HATs) are an enzyme family that regulates these processes by catalyzing the transfer of an acetyl moiety onto target proteins. Perturbations of cellular acetylation profiles have been associated with a variety of disease states, including cancer. Changes in acetylation profiles can be achieved by mechanisms associated with acetyltransferases, such as gene down-regulation or alterations in the activity of key acetyltransferase enzymes. An important set of tools for quantifying enzyme activity are in vitro histone acetylation assays, using either endogenous or tagged overexpressed proteins. Detailed in this unit is an in vitro acetylation assay used to quantify HAT activity. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- James A L Brown
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland, Galway, Ireland
| |
Collapse
|
11
|
Abstract
Two opposing enzyme classes regulate fundamental elements of genome maintenance, gene regulation and metabolism, either through addition of an acetyl moiety by histone acetyltransferases (HATs) or its removal by histone de-acetyltransferases (HDAC), and are exciting targets for drug development. Importantly, dysfunctional acetylation has been implicated in numerous diseases, including cancer. Within the HAT superfamily the MYST family holds particular interest, as its members are directly involved in the DNA damage response and repair pathways and crucially, several members have been shown to be down-regulated in common cancers (such as breast and prostate). In the present study we focus on the development of lysine (K) acetyltransferase inhibitors (KATi) targeting the MYST family member Tip60 (Kat5), an essential protein, designed or discovered through screening libraries. Importantly, Tip60 has been demonstrated to be significantly down-regulated in many cancers which urgently require new treatment options. We highlight current and future efforts employing these KATi as cancer treatments and their ability to synergize and enhance current cancer treatments. We investigate the different methods of KATi production or discovery, their mechanisms and their validation models. Importantly, the utility of KATi is based on a key concept: using KATi to abrogate the activity of an already down-regulated essential protein (effectively creating a lethal knockout) provides another innovative mechanism for targeting cancer cells, while significantly minimizing any off-target effects to normal cells. This approach, combined with the rapidly developing interest in KATi, suggests that KATi have a bright future for providing truly personalized therapies.
Collapse
|
12
|
Lillico R, Stesco N, Khorshid Amhad T, Cortes C, Namaka MP, Lakowski TM. Inhibitors of enzymes catalyzing modifications to histone lysine residues: structure, function and activity. Future Med Chem 2016; 8:879-97. [PMID: 27173004 DOI: 10.4155/fmc-2016-0021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Gene expression is partly controlled by epigenetic mechanisms including histone-modifying enzymes. Some diseases are caused by changes in gene expression that can be mitigated by inhibiting histone-modifying enzymes. This review covers the enzyme inhibitors targeting histone lysine modifications. We summarize the enzymatic mechanisms of histone lysine acetylation, deacetylation, methylation and demethylation and discuss the biochemical roles of these modifications in gene expression and in disease. We discuss inhibitors of lysine acetylation, deacetylation, methylation and demethylation defining their structure-activity relationships and their potential mechanisms. We show that there are potentially indiscriminant off-target effects on gene expression even with the use of selective epigenetic enzyme inhibitors.
Collapse
Affiliation(s)
- Ryan Lillico
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicholas Stesco
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tina Khorshid Amhad
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Claudia Cortes
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Mike P Namaka
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Ted M Lakowski
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
13
|
Yuan H, Marmorstein R. Histone acetyltransferases: Rising ancient counterparts to protein kinases. Biopolymers 2016; 99:98-111. [PMID: 23175385 DOI: 10.1002/bip.22128] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 07/01/2012] [Accepted: 07/06/2012] [Indexed: 01/19/2023]
Abstract
Protein kinases catalyze phosphorylation, a posttranslational modification widely utilized in cell signaling. Histone acetyltransferases (HATs) catalyze a counterpart posttranslational modification of acetylation which marks histones for epigenetic signaling but in some cases modifies non-histone proteins to mediate other cellular activities. In addition, recent proteomic studies have revealed that thousands of proteins are acetylated throughout the cell to regulate diverse biological processes, thus placing acetyltransferases on the same playing field as kinases. Emerging biochemical and structural data further supports mechanistic and biological links between the two enzyme families. In this article, we will review what is known to date about the structure, catalysis and mode of regulation of HAT enzymes and draw analogies, where relevant, to protein kinases. This comparison reveals that HATs may be rising ancient counterparts to protein kinases.
Collapse
Affiliation(s)
- Hua Yuan
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104
| | | |
Collapse
|
14
|
McCullough CE, Marmorstein R. In Vitro Activity Assays for MYST Histone Acetyltransferases and Adaptation for High-Throughput Inhibitor Screening. Methods Enzymol 2016; 573:139-60. [PMID: 27372752 DOI: 10.1016/bs.mie.2016.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Lysine acetylation is a posttranslational modification that is carried out by acetyltransferases. The MYST proteins form the largest and most diverse family of acetyltransferases, which regulate gene expression, DNA repair, and cell cycle homeostasis, among other activities, by acetylating both histone and nonhistone proteins. This chapter will describe methods for the preparation and biochemical characterization of MYST family acetyltransferases, including protocols for the preparation of recombinant protein, enzyme assays for measuring steady-state parameters, and binding assays to measure cofactor and inhibitor binding. We also provide details on adapting these assays for high-throughput screening for small molecule MYST inhibitors. This chapter seeks to prepare researchers for some hurdles that they may encounter when studying the MYST proteins so that there may be better opportunity to plan appropriate controls and obtain high-quality data.
Collapse
Affiliation(s)
- C E McCullough
- University of Pennsylvania, Philadelphia, PA, United States
| | - R Marmorstein
- University of Pennsylvania, Philadelphia, PA, United States; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
15
|
Kaypee S, Sudarshan D, Shanmugam MK, Mukherjee D, Sethi G, Kundu TK. Aberrant lysine acetylation in tumorigenesis: Implications in the development of therapeutics. Pharmacol Ther 2016; 162:98-119. [PMID: 26808162 DOI: 10.1016/j.pharmthera.2016.01.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 'language' of covalent histone modifications translates environmental and cellular cues into gene expression. This vast array of post-translational modifications on histones are more than just covalent moieties added onto a protein, as they also form a platform on which crucial cellular signals are relayed. The reversible lysine acetylation has emerged as an important post-translational modification of both histone and non-histone proteins, dictating numerous epigenetic programs within a cell. Thus, understanding the complex biology of lysine acetylation and its regulators is essential for the development of epigenetic therapeutics. In this review, we will attempt to address the complexities of lysine acetylation in the context of tumorigenesis, their role in cancer progression and emphasize on the modalities developed to target lysine acetyltransferases towards cancer treatment.
Collapse
Affiliation(s)
- Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Deepthi Sudarshan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| | - Debanjan Mukherjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India.
| |
Collapse
|
16
|
Simon RP, Robaa D, Alhalabi Z, Sippl W, Jung M. KATching-Up on Small Molecule Modulators of Lysine Acetyltransferases. J Med Chem 2016; 59:1249-70. [PMID: 26701186 DOI: 10.1021/acs.jmedchem.5b01502] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reversible acetylation of lysines is one of the best characterized epigenetic modifications. Its involvement in many key physiological and pathological processes has been documented in numerous studies. Lysine deacetylases (KDACs) and acetyltransferases (KATs) maintain the acetylation equilibrium at histones but also many other proteins. Besides acetylation, also other acyl groups are reversibly installed at the side chain of lysines in proteins. Because of their involvement in disease, KDACs and KATs were proposed to be promising drug targets, and for KDACs, indeed, five inhibitors are now approved for human use. While there is a similar level of evidence for the potential of KATs as drug targets, no inhibitor is in clinical trials. Here, we review the evidence for the diverse roles of KATs in disease pathology, provide an overview of structural features and the available modulators, including those targeting the bromodomains of KATs, and present an outlook.
Collapse
Affiliation(s)
- Roman P Simon
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Zayan Alhalabi
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
| |
Collapse
|
17
|
Couderc T, Lecuit M. Chikungunya virus pathogenesis: From bedside to bench. Antiviral Res 2015; 121:120-31. [PMID: 26159730 DOI: 10.1016/j.antiviral.2015.07.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/04/2015] [Indexed: 11/28/2022]
Abstract
Chikungunya virus (CHIKV) is an arbovirus transmitted to humans by mosquito bite. A decade ago, the virus caused a major outbreak in the islands of the Indian Ocean, then reached India and Southeast Asia. More recently, CHIKV has emerged in the Americas, first reaching the Caribbean and now extending to Central, South and North America. It is therefore considered a major public health and economic threat. CHIKV causes febrile illness typically associated with debilitating joint pains. In rare cases, it may also cause central nervous system disease, notably in neonates. Joint symptoms may persist for months to years, and lead to arthritis. This review focuses on the spectrum of signs and symptoms associated with CHIKV infection in humans. It also illustrates how the analysis of clinical and biological data from human cohorts and the development of animal and cellular models of infection has helped to identify the tissue and cell tropisms of the virus and to decipher host responses in benign, severe or persistent disease. This article forms part of a symposium in Antiviral Research on "Chikungunya discovers the New World".
Collapse
Affiliation(s)
- Thérèse Couderc
- Institut Pasteur, Biology of Infection Unit, Paris, France; Inserm U1117, Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Paris, France; Inserm U1117, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Institut Imagine, Paris, France; Global Virus Network.
| |
Collapse
|
18
|
Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
| |
Collapse
|
19
|
Gajer JM, Furdas SD, Gründer A, Gothwal M, Heinicke U, Keller K, Colland F, Fulda S, Pahl HL, Fichtner I, Sippl W, Jung M. Histone acetyltransferase inhibitors block neuroblastoma cell growth in vivo. Oncogenesis 2015; 4:e137. [PMID: 25664930 PMCID: PMC4338425 DOI: 10.1038/oncsis.2014.51] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/09/2014] [Indexed: 12/25/2022] Open
Abstract
We have previously described novel histone acetyltransferase (HAT) inhibitors that block neuroblastoma cell growth in vitro. Here we show that two selected pyridoisothiazolone HAT inhibitors, PU139 and PU141, induce cellular histone hypoacetylation and inhibit growth of several neoplastic cell lines originating from different tissues. Broader in vitro selectivity profiling shows that PU139 blocks the HATs Gcn5, p300/CBP-associated factor (PCAF), CREB (cAMP response element-binding) protein (CBP) and p300, whereas PU141 is selective toward CBP and p300. The pan-inhibitor PU139 triggers caspase-independent cell death in cell culture. Both inhibitors block growth of SK-N-SH neuroblastoma xenografts in mice and the PU139 was shown to synergize with doxorubicin in vivo. The latter also reduces histone lysine acetylation in vivo at concentrations that block neoplastic xenograft growth. This is one of the very few reports on hypoacetylating agents with in vivo anticancer activity.
Collapse
Affiliation(s)
- J M Gajer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - S D Furdas
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - A Gründer
- Section of Molecular Hematology, Department of Hematology/Oncology, University Hospital Freiburg, Freiburg, Germany
| | - M Gothwal
- Section of Molecular Hematology, Department of Hematology/Oncology, University Hospital Freiburg, Freiburg, Germany
| | - U Heinicke
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - K Keller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - F Colland
- Hybrigenics, 3-5 impasse Reille, Paris, France
| | - S Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - H L Pahl
- Section of Molecular Hematology, Department of Hematology/Oncology, University Hospital Freiburg, Freiburg, Germany
| | - I Fichtner
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin-Buch, Germany
| | - W Sippl
- Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Department of Pharmaceutical Chemistry, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - M Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
| |
Collapse
|
20
|
Marmorstein R, Zhou MM. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol 2014; 6:a018762. [PMID: 24984779 DOI: 10.1101/cshperspect.a018762] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone acetylation marks are written by histone acetyltransferases (HATs) and read by bromodomains (BrDs), and less commonly by other protein modules. These proteins regulate many transcription-mediated biological processes, and their aberrant activities are correlated with several human diseases. Consequently, small molecule HAT and BrD inhibitors with therapeutic potential have been developed. Structural and biochemical studies of HATs and BrDs have revealed that HATs fall into distinct subfamilies containing a structurally related core for cofactor binding, but divergent flanking regions for substrate-specific binding, catalysis, and autoregulation. BrDs adopt a conserved left-handed four-helix bundle to recognize acetyllysine; divergent loop residues contribute to substrate-specific acetyllysine recognition.
Collapse
Affiliation(s)
- Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10065
| |
Collapse
|
21
|
Gao C, Bourke E, Scobie M, Famme MA, Koolmeister T, Helleday T, Eriksson LA, Lowndes NF, Brown JAL. Rational design and validation of a Tip60 histone acetyltransferase inhibitor. Sci Rep 2014; 4:5372. [PMID: 24947938 PMCID: PMC4064327 DOI: 10.1038/srep05372] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/02/2014] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is required for many aspects of gene regulation, genome maintenance and metabolism and dysfunctional acetylation is implicated in numerous diseases, including cancer. Acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases and currently, few general HAT inhibitors have been described. We identified the HAT Tip60 as an excellent candidate for targeted drug development, as Tip60 is a key mediator of the DNA damage response and transcriptional co-activator. Our modeling of Tip60 indicated that the active binding pocket possesses opposite charges at each end, with the positive charges attributed to two specific side chains. We used structure based drug design to develop a novel Tip60 inhibitor, TH1834, to fit this specific pocket. We demonstrate that TH1834 significantly inhibits Tip60 activity in vitro and treating cells with TH1834 results in apoptosis and increased unrepaired DNA damage (following ionizing radiation treatment) in breast cancer but not control cell lines. Furthermore, TH1834 did not affect the activity of related HAT MOF, as indicated by H4K16Ac, demonstrating specificity. The modeling and validation of the small molecule inhibitor TH1834 represents a first step towards developing additional specific, targeted inhibitors of Tip60 that may lead to further improvements in the treatment of breast cancer.
Collapse
Affiliation(s)
- Chunxia Gao
- 1] School of Chemistry, National University of Ireland Galway, Galway, Ireland [2] Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden [3]
| | - Emer Bourke
- 1] Discipline of Pathology, School of Medicine, Clinical Science Institute, Costello Road, National University of Ireland Galway, Galway, Ireland [2]
| | - Martin Scobie
- 1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden [2]
| | - Melina Arcos Famme
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Leif A Eriksson
- 1] School of Chemistry, National University of Ireland Galway, Galway, Ireland [2] Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden [3]
| | - Noel F Lowndes
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - James A L Brown
- 1] Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland [2] [3]
| |
Collapse
|
22
|
Zhu P, Peng H, Ni N, Wang B, Li M. Novel AI-2 quorum sensing inhibitors in Vibrio harveyi identified through structure-based virtual screening. Bioorg Med Chem Lett 2012; 22:6413-7. [PMID: 22963763 DOI: 10.1016/j.bmcl.2012.08.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 07/21/2012] [Accepted: 08/16/2012] [Indexed: 12/11/2022]
Abstract
In this letter, a high-throughput virtual screening was accomplished to identify potent inhibitors against AI-2 quorum sensing on the basis of Vibrio harveyi LuxPQ crystal structure. Seven compounds were found to inhibit AI-2 quorum sensing with IC(50) values in the micromolar range, and presented low cytotoxicity or no cytotoxicity in V. harveyi.
Collapse
Affiliation(s)
- Peng Zhu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, PR China
| | | | | | | | | |
Collapse
|
23
|
Abstract
This review focuses on the progress in the development of the second generation of epigenetic modifiers able to modulate histone marks, and restore normal gene transcription.
Collapse
Affiliation(s)
- Philip Jones
- Institute for Applied Cancer Sciences
- MD Anderson Cancer Center
- Houston
- USA
| |
Collapse
|
24
|
Liszczak G, Arnesen T, Marmorstein R. Structure of a ternary Naa50p (NAT5/SAN) N-terminal acetyltransferase complex reveals the molecular basis for substrate-specific acetylation. J Biol Chem 2011; 286:37002-10. [PMID: 21900231 PMCID: PMC3196119 DOI: 10.1074/jbc.m111.282863] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/26/2011] [Indexed: 01/28/2023] Open
Abstract
The co-translational modification of N-terminal acetylation is ubiquitous among eukaryotes and has been reported to have a wide range of biological effects. The human N-terminal acetyltransferase (NAT) Naa50p (NAT5/SAN) acetylates the α-amino group of proteins containing an N-terminal methionine residue and is essential for proper sister chromatid cohesion and chromosome condensation. The elevated activity of NATs has also been correlated with cancer, making these enzymes attractive therapeutic targets. We report the x-ray crystal structure of Naa50p bound to a native substrate peptide fragment and CoA. We found that the peptide backbone of the substrate is anchored to the protein through a series of backbone hydrogen bonds with the first methionine residue specified through multiple van der Waals contacts, together creating an α-amino methionine-specific pocket. We also employed structure-based mutagenesis; the results support the importance of the α-amino methionine-specific pocket of Naa50p and are consistent with the proposal that conserved histidine and tyrosine residues play important catalytic roles. Superposition of the ternary Naa50p complex with the peptide-bound Gcn5 histone acetyltransferase revealed that the two enzymes share a Gcn5-related N-acetyltransferase fold but differ in their respective substrate-binding grooves such that Naa50p can accommodate only an α-amino substrate and not a side chain lysine substrate that is acetylated by lysine acetyltransferase enzymes such as Gcn5. The structure of the ternary Naa50p complex also provides the first molecular scaffold for the design of NAT-specific small molecule inhibitors with possible therapeutic applications.
Collapse
Affiliation(s)
- Glen Liszczak
- From The Wistar Institute and
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Thomas Arnesen
- the Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway, and
- the Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ronen Marmorstein
- From The Wistar Institute and
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|