1
|
Bare A, Thomas J, Etoroma D, Lee SG. Functional analysis of phosphoethanolamine N-methyltransferase in plants and parasites: Essential S-adenosylmethionine-dependent methyltransferase in choline and phospholipid metabolism. Methods Enzymol 2023; 680:101-137. [PMID: 36710008 DOI: 10.1016/bs.mie.2022.08.028] [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: 02/01/2023]
Abstract
Phospholipids play an essential role as a barrier between cell content and the extracellular environment and regulate various cell signaling processes. Phosphatidylcholine (PtdCho) is one of the most abundant phospholipids in plant, animal, and some prokaryote cell membranes. In plants and some parasites, the biosynthesis of PtdCho begins with the amino acid serine, followed mainly through a phosphoethanolamine N-methyltransferase (PMT)-mediated biosynthetic pathway to phosphocholine (pCho). Because the PMT-mediated pathway, referred to as the phosphobase methylation pathway, produces a series of important primary and specialized metabolites for plant development and stress response, understanding the PMT enzyme is a key aspect of engineering plants with improved stress tolerance and fortified nutrients. Importantly, given the very limited phylogenetic distribution of PMTs, functional analysis and the identification of inhibitors targeting PMTs have potential and positive impacts in humans and in veterinary and agricultural fields. Here, we describe detailed basic knowledge and practical research methods to enable the systematic study of the biochemical and biophysical functions of PMT. The research methods described in this chapter are also applicable to the studies of other ubiquitous S-adenosyl-l-methionine (SAM)-dependent methyltransferases in all kingdoms.
Collapse
Affiliation(s)
- Alex Bare
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Jaime Thomas
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Etoroma
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Soon Goo Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States.
| |
Collapse
|
3
|
Song Y, Li L, Chen Y, Liu J, Xiao S, Lian F, Zhang N, Ding H, Zhang Y, Chen K, Jiang H, Zhang C, Liu YC, Chen S, Luo C. Discovery of potent DOT1L inhibitors by AlphaLISA based High Throughput Screening assay. Bioorg Med Chem 2018. [PMID: 29534934 DOI: 10.1016/j.bmc.2018.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DOT1L (the disruptor of telomeric silencing 1-like), through its methyltransferase activity of H3K79, plays essential roles in transcriptional regulation, cell cycle regulation, and DNA damage response. In addition, DOT1L is believed to be involved in the development of MLL-rearranged leukemia driven by the MLL (mixed-lineage leukemia) fusion proteins, which thus to be a crucial target for leukemia therapy. Hence, discovering of novel DOT1L inhibitors has been in a great demand. In this study, we initiated the discovering process from setting up the AlphaLISA based High Throughput Screening (HTS) assay of DOT1L. Combining with radioactive inhibition assay and Surface Plasmon Resonance (SPR) binding assay, we identified compound 3 and its active analogues as novel DOT1L inhibitors with IC50 values range from 7 μM to 20 μM in vitro. Together with the analysis of structure activity relationships (SAR) and binding modes of these compounds, we provided clues to assist in the future development of more potent DOT1L inhibitors. Moreover, compounds 3 and 9 effectively inhibited the proliferation of MLL-rearranged leukemia cells MV4-11, which could induce cell cycle arrest and apoptosis. In conclusion, we developed a HTS platform based on AlphaLISA method for screening and discovery of DOT1L novel inhibitor, through which we discovered compound 3 and its analogues as potent DOT1L inhibitors with promising MLL-rearranged leukemia therapeutic application.
Collapse
Affiliation(s)
- Yakai Song
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Linjuan Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Yantao Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jingqiu Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Senhao Xiao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Fulin Lian
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Naixia Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hong Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yuanyuan Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Chenhua Zhang
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Shijie Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| |
Collapse
|
4
|
Guitot K, Drujon T, Burlina F, Sagan S, Beaupierre S, Pamlard O, Dodd RH, Guillou C, Bolbach G, Sachon E, Guianvarc'h D. A direct label-free MALDI-TOF mass spectrometry based assay for the characterization of inhibitors of protein lysine methyltransferases. Anal Bioanal Chem 2017; 409:3767-3777. [PMID: 28389916 DOI: 10.1007/s00216-017-0319-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/06/2017] [Accepted: 03/14/2017] [Indexed: 12/27/2022]
Abstract
Histone lysine methylation is associated with essential biological functions like transcription activation or repression, depending on the position and the degree of methylation. This post-translational modification is introduced by protein lysine methyltransferases (KMTs) which catalyze the transfer of one to three methyl groups from the methyl donor S-adenosyl-L-methionine (AdoMet) to the amino group on the side chain of lysines. The regulation of protein lysine methylation plays a primary role not only in the basic functioning of normal cells but also in various pathologies and KMT deregulation is associated with diseases including cancer. These enzymes are therefore attractive targets for the development of new antitumor agents, and there is still a need for direct methodology to screen, identify, and characterize KMT inhibitors. We report here a simple and robust in vitro assay to quantify the enzymatic methylation of KMT by MALDI-TOF mass spectrometry. Following this protocol, we can monitor the methylation events over time on a peptide substrate. We detect in the same spectrum the modified and unmodified substrates, and the ratios of both signals are used to quantify the amount of methylated substrate. We first demonstrated the validity of the assay by determining inhibition parameters of two known inhibitors of the KMT SET7/9 ((R)-PFI-2 and sinefungin). Next, based on structural comparison with these inhibitors, we selected 42 compounds from a chemical library. We applied the MALDI-TOF assay to screen their activity as inhibitors of the KMT SET7/9. This study allowed us to determine inhibition constants as well as kinetic parameters of a series of SET7/9 inhibitors and to initiate a structure activity discussion with this family of compounds. This assay is versatile and can be easily adapted to other KMT substrates and enzymes as well as automatized.
Collapse
Affiliation(s)
- Karine Guitot
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Thierry Drujon
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Fabienne Burlina
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Sandrine Sagan
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Sandra Beaupierre
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Olivier Pamlard
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Robert H Dodd
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Catherine Guillou
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Gérard Bolbach
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France.,UPMC Univ Paris 06, IBPS/FR3631, Plateforme de Spectrométrie de Masse et Protéomique, 7-9 Quai Saint Bernard, 75005, Paris, France
| | - Emmanuelle Sachon
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France.,UPMC Univ Paris 06, IBPS/FR3631, Plateforme de Spectrométrie de Masse et Protéomique, 7-9 Quai Saint Bernard, 75005, Paris, France
| | - Dominique Guianvarc'h
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005, Paris, France. .,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France.
| |
Collapse
|