1
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Fujimura A, Ishida H, Nozaki T, Terada S, Azumaya Y, Ishiguro T, Kamimura YR, Kujirai T, Kurumizaka H, Kono H, Yamatsugu K, Kawashima SA, Kanai M. Designer Adaptor Proteins for Functional Conversion of Peptides to Small-Molecule Ligands toward In-Cell Catalytic Protein Modification. ACS CENTRAL SCIENCE 2023; 9:2115-2128. [PMID: 38033808 PMCID: PMC10683481 DOI: 10.1021/acscentsci.3c00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Peptides are privileged ligands for diverse biomacromolecules, including proteins; however, their utility is often limited due to low membrane permeability and in-cell instability. Here, we report peptide ligand-inserted eDHFR (PLIED) fusion protein as a universal adaptor for targeting proteins of interest (POI) with cell-permeable and stable synthetic functional small molecules (SFSM). PLIED binds to POI through the peptide moiety, properly orienting its eDHFR moiety, which then recruits trimethoprim (TMP)-conjugated SFSM to POI. Using a lysine-acylating BAHA catalyst as SFSM, we demonstrate that POI (MDM2 and chromatin histone) are post-translationally and synthetically acetylated at specific lysine residues. The residue-selectivity is predictable in an atomic resolution from molecular dynamics simulations of the POI/PLIED/TMP-BAHA (MTX was used as a TMP model) ternary complex. This designer adaptor approach universally enables functional conversion of impermeable peptide ligands to permeable small-molecule ligands, thus expanding the in-cell toolbox of chemical biology.
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Affiliation(s)
- Akiko Fujimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Hisashi Ishida
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Tamiko Nozaki
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shuhei Terada
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yuto Azumaya
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tadashi Ishiguro
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yugo R. Kamimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tomoya Kujirai
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hidetoshi Kono
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kenzo Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shigehiro A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
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2
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Kawashima SA, Kanai M. Live Cell Synthetic Histone Acetylation by Chemical Catalyst. Methods Mol Biol 2023; 2519:155-161. [PMID: 36066720 DOI: 10.1007/978-1-0716-2433-3_17] [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] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) of histones, such as lysine acetylation and ubiquitination, regulate chromatin structure and gene expression. In living organisms, histone PTMs are catalyzed by histone-modifying enzymes. Here, we describe an entirely chemical method to introduce histone modifications in living cells without genetic manipulation. The chemical catalyst PEG-LANA-DSSMe activates a thioester acetyl donor, N,S-diacetylcysteamine (NAC-Ac), and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells.
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Affiliation(s)
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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3
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Catalysis medicine: Participating in the chemical networks of living organisms through catalysts. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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4
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022; 61:e202205570. [DOI: 10.1002/anie.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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5
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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6
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Adamson C, Kajino H, Kawashima SA, Yamatsugu K, Kanai M. Live-Cell Protein Modification by Boronate-Assisted Hydroxamic Acid Catalysis. J Am Chem Soc 2021; 143:14976-14980. [PMID: 34506708 DOI: 10.1021/jacs.1c07060] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Selective methods for introducing protein post-translational modifications (PTMs) within living cells have proven valuable for interrogating their biological function. In contrast to enzymatic methods, abiotic catalysis should offer access to diverse and new-to-nature PTMs. Herein, we report the boronate-assisted hydroxamic acid (BAHA) catalyst system, which comprises a protein ligand, a hydroxamic acid Lewis base, and a diol moiety. In concert with a boronic acid-bearing acyl donor, our catalyst leverages a local molarity effect to promote acyl transfer to a target lysine residue. Our catalyst system employs micromolar reagent concentrations and affords minimal off-target protein reactivity. Critically, BAHA is resistant to glutathione, a metabolite which has hampered many efforts toward abiotic chemistry within living cells. To showcase this methodology, we installed a variety of acyl groups in E. coli dihydrofolate reductase expressed within human cells. Our results further establish the well-known boronic acid-diol complexation as a bona fide bio-orthogonal reaction with applications in chemical biology and in-cell catalysis.
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Affiliation(s)
- Christopher Adamson
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan, 113-0033
| | - Hidetoshi Kajino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan, 113-0033
| | - Shigehiro A Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan, 113-0033
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan, 113-0033
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan, 113-0033
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7
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Abstract
Life emerges from complicated and sophisticated chemical networks comprising numerous biomolecules (e.g., nucleic acids, proteins, sugars, and lipids) and chemical reactions catalyzed by enzymes. Dysregulation of these chemical networks is linked to the emergence of diseases. Our research goal is to develop abiotic chemical catalysts that can intervene into life's chemical networks by complementing, surrogating, or exceeding enzymes in living cells or multicellular organisms such as animals or plants. Mending dysregulated networks in pathological states by the chemical catalysts will lead to a new medicinal strategy, catalysis medicine. This research direction will also advance catalysis science, because highly active and selective chemical catalysts must be developed to promote the intended reactions in a complex mixture of life in aqueous solution at body temperature.Epigenetics exists at the crossroads of chemistry, biology, and medicine and is a suitable field to pursue this idea. Post-translational modifications (PTMs) of histones epigenetically regulate chromatin functions and gene transcription and are intimately related to various diseases. Investigating the functions and cross-talk of histone PTMs is crucial for mechanistic elucidation of diseases and their treatments. We launched a program to develop chemical catalysts enabling endogenous histone modifications in living cells without relying on enzymes. We reported two types of chemical catalyst systems so far for synthetic histone acylation. The first system comprised a DNA-binding oligo-4-dimethylaminopyridine (DMAP) catalyst and a phenyl ester acyl donor, PAc-gly. This system promoted histone hyperacetylation in Xenopus laevis sperm chromatin. Using the thus-synthesized hyperacetylated sperm chromatin, we found a novel relationship between histone acetylation and DNA replication. The second system involved a histone-binding catalyst, LANA-DSH, composed of a catalytic motif (DSH) and a histone-binding peptide ligand (LANA), and thioester acyl donors, including endogenous acyl-CoA. This system regioselectively (i.e., selectively to a lysine residue at a specific position) acylated lysine 120 of histone H2B (H2BK120), a lysine residue proximal to the DSH motif defined by binding of the LANA ligand to a nucleosome substrate. This catalyst system was optimized to achieve H2BK120-selective acetylation in living cells without genetic manipulation. The synthetically introduced H2BK120Ac inhibited enzyme-catalyzed ubiquitination at the same lysine residue, acting as a protecting group. H2BK120Ub is a mark recognized by methyltransferase that plays an essential role in mixed-lineage leukemia (MLL)-rearranged leukemia, suggesting the potential of the catalyst system as an epigenetic tool and a cancer therapy. We also discuss the prospects of chemical catalyst-promoted synthetic epigenetics for future PTM studies and therapeutic uses.
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Affiliation(s)
- Tamiko Nozaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Fujiwara Y, Yamanashi Y, Fujimura A, Sato Y, Kujirai T, Kurumizaka H, Kimura H, Yamatsugu K, Kawashima SA, Kanai M. Live-cell epigenome manipulation by synthetic histone acetylation catalyst system. Proc Natl Acad Sci U S A 2021; 118:e2019554118. [PMID: 33468653 PMCID: PMC7848698 DOI: 10.1073/pnas.2019554118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chemical modifications of histones, such as lysine acetylation and ubiquitination, play pivotal roles in epigenetic regulation of gene expression. Methods to alter the epigenome thus hold promise as tools for elucidating epigenetic mechanisms and as therapeutics. However, an entirely chemical method to introduce histone modifications in living cells without genetic manipulation is unprecedented. Here, we developed a chemical catalyst, PEG-LANA-DSSMe 11, that binds with nucleosome's acidic patch and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells. The size of polyethylene glycol in the catalyst was a critical determinant for its in-cell metabolic stability, binding affinity to histones, and high activity. The synthetic acetylation promoted by 11 without genetic manipulation competed with and suppressed physiological H2B ubiquitination, a mark regulating chromatin functions, such as transcription and DNA damage response. Thus, the chemical catalyst will be a useful tool to manipulate epigenome for unraveling epigenetic mechanisms in living cells.
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Affiliation(s)
- Yusuke Fujiwara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Yamanashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akiko Fujimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Shigehiro A Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
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9
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Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
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10
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Mizumoto S, Xi S, Fujiwara Y, Kawashima SA, Yamatsugu K, Kanai M. Hydroxamic Acid‐Piperidine Conjugate is an Activated Catalyst for Lysine Acetylation under Physiological Conditions. Chem Asian J 2020; 15:833-839. [DOI: 10.1002/asia.201901737] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/21/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Shinsuke Mizumoto
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Siqi Xi
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Fujiwara
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Shigehiro A. Kawashima
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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11
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Affiliation(s)
- Katsuya Maruyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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12
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Moos WH, Faller DV, Glavas IP, Harpp DN, Kanara I, Pinkert CA, Powers WR, Sampani K, Steliou K, Vavvas DG, Kodukula K, Zamboni RJ. Epigenetic treatment of dermatologic disorders. Drug Dev Res 2019. [DOI: 10.1002/ddr.21562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Walter H. Moos
- Department of Pharmaceutical Chemistry, School of PharmacyUniversity of California, San Francisco San Francisco California
- ShangPharma Innovation Inc. South San Francisco California
| | - Douglas V. Faller
- Department of MedicineBoston University School of Medicine Boston Massachusetts
- Cancer Research CenterBoston University School of Medicine Boston Massachusetts
| | - Ioannis P. Glavas
- Department of OphthalmologyNew York University School of Medicine New York City New York
| | - David N. Harpp
- Department of ChemistryMcGill University Montreal Quebec Canada
| | | | - Carl A. Pinkert
- Department of Pathobiology, College of Veterinary MedicineAuburn University Auburn Alabama
| | - Whitney R. Powers
- Department of Health SciencesBoston University Boston Massachusetts
- Department of AnatomyBoston University School of Medicine Boston Massachusetts
| | - Konstantina Sampani
- Beetham Eye InstituteJoslin Diabetes Center Boston Massachusetts
- Department of MedicineHarvard Medical School Boston Massachusetts
| | - Kosta Steliou
- Cancer Research CenterBoston University School of Medicine Boston Massachusetts
- PhenoMatriX, Inc. Natick Massachusetts
| | - Demetrios G. Vavvas
- Retina Service, Angiogenesis LaboratoryMassachusetts Eye and Ear Infirmary Boston Massachusetts
- Department of OphthalmologyHarvard Medical School Boston Massachusetts
| | - Krishna Kodukula
- ShangPharma Innovation Inc. South San Francisco California
- PhenoMatriX, Inc. Natick Massachusetts
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13
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Olivenza DR, Nicoloff H, Sánchez-Romero MA, Cota I, Andersson DI, Casadesús J. A portable epigenetic switch for bistable gene expression in bacteria. Sci Rep 2019; 9:11261. [PMID: 31375711 PMCID: PMC6677893 DOI: 10.1038/s41598-019-47650-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/22/2019] [Indexed: 02/04/2023] Open
Abstract
We describe a portable epigenetic switch based on opvAB, a Salmonella enterica operon that undergoes bistable expression under DNA methylation control. A DNA fragment containing the opvAB promoter and the opvAB upstream regulatory region confers bistability to heterologous genes, yielding OFF and ON subpopulations. Bistable expression under opvAB control is reproducible in Escherichia coli, showing that the opvAB switch can be functional in a heterologous host. Subpopulations of different sizes can be produced at will using engineered opvAB variants. Controlled formation of antibiotic-resistant and antibiotic-susceptible subpopulations may allow use of the opvAB switch in the study of bacterial heteroresistance to antibiotics.
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Affiliation(s)
- David R Olivenza
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
| | - Hervé Nicoloff
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden
| | | | - Ignacio Cota
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain.,Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain.
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14
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Hamajima W, Fujimura A, Fujiwara Y, Yamatsugu K, Kawashima SA, Kanai M. Site-Selective Synthetic Acylation of a Target Protein in Living Cells Promoted by a Chemical Catalyst/Donor System. ACS Chem Biol 2019; 14:1102-1109. [PMID: 31117394 DOI: 10.1021/acschembio.9b00102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell biology is tightly regulated by post-translational modifications of proteins. Methods to modulate post-translational modifications in living cells without relying on enzymes or genetic manipulation are, however, largely underexplored. We previously reported that a chemical catalyst (DSH) conjugated with a nucleosome-binding ligand can activate an acyl-CoA and promote site-selective lysine acylation of histones in test tubes. In-cell acylation by this catalyst system is challenging, however, mainly due to the low cell permeability of acyl-CoA and the propensity of DSH to form inactive disulfide. Here, we report a new catalyst system effective for in-cell acylation, comprising a cell-permeable acyl donor and pro-drugged DSH. Using E. coli dihydrofolate reductase and trimethoprim as a model protein and ligand pair, the catalyst system enabled site-selective acylation of the target protein in living cells. The findings will lead to the development of useful chemical biology tools and new therapeutic strategies capable of synthetically modulating post-translational modifications.
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Affiliation(s)
- Wataru Hamajima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiko Fujimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Fujiwara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigehiro A. Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Rezhdo A, Islam M, Huang M, Van Deventer JA. Future prospects for noncanonical amino acids in biological therapeutics. Curr Opin Biotechnol 2019; 60:168-178. [PMID: 30974337 DOI: 10.1016/j.copbio.2019.02.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/22/2019] [Indexed: 12/12/2022]
Abstract
There is growing evidence that noncanonical amino acids (ncAAs) can be utilized in the creation of biological therapeutics ranging from protein conjugates to cell-based therapies. However, when does genetically encoding ncAAs yield biologics with unique properties compared to other approaches? In this review, we attempt to answer this question in the broader context of therapeutic development, emphasizing advances within the past two years. In several areas, ncAAs add valuable routes to therapeutically relevant entities, but application-specific needs ultimately determine whether ncAA-mediated or alternative solutions are preferred. Looking forward, using ncAAs to perform 'protein medicinal chemistry,' in which atomic-level changes to proteins dramatically enhance therapeutic properties, is a promising emerging area. Further upgrades to the performance of ncAA incorporation technologies will be essential to realizing the full potential of ncAAs in biological therapeutics.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States; Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States.
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16
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Vafadar A, Mokaram P, Erfani M, Yousefi Z, Farhadi A, Elham Shirazi T, Tamaddon G. The effect of decitabine on the expression and methylation of the PPP1CA, BTG2, and PTEN in association with changes in miR-125b, miR-17, and miR-181b in NALM6 cell line. J Cell Biochem 2019; 120:13156-13167. [PMID: 30912184 DOI: 10.1002/jcb.28590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 02/01/2023]
Abstract
Precursor B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent pediatric cancer. DNA methylation and changes in the microRNAs (miRNAs) expression are known to be important causes of B-ALL. Decitabine as a DNA methyltransferase inhibitor agent is able to induce hypomethylation in several tumor suppressor genes. Much evidence has proven BTG2, PPP1CA, and PTEN act as tumor suppressor genes in many malignancies. In this case control study, the messenger RNA (mRNA) expression of PPP1CA, BTG2, and PTEN genes using quantitative real-time polymerase chain reaction (rRT-PCR) in Nalm6 cell line and five patients suffer from ALL with mean age 5.6 years were determined in compare with seven normal healthy donors age and sex matched. qRT-PCR analysis revealed that the expression levels of PPP1CA, BTG2, and PTEN genes were significantly decreased in Nalm6 ([FC] = 0.46, [FC] = 0.046, [FC] = 0.54) and according to the Methylation-specific PCR (MSP) analysis, these genes were hypermethylated in Nalm6. In next step, the effects of decitabine treatment on the methylation and expression of these genes in association with changes in miR-125b, miR-17, and miR-181b expression levels were evaluated in optimal concentration 2.5 µM of decitabine. Our data showed that decitabine is able to restore the expression levels of aforementioned genes and downregulate expression levels of oncomiRs; including miR-125b, miR-17, and miR-181b in Nalm6 cell line. Therefore, it seems that decitabine can be used as a potential drug for the first line treatment of patients with B-ALL, but further in vivo investigation is necessary.
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Affiliation(s)
- Asma Vafadar
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokaram
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehran Erfani
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Yousefi
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Ali Farhadi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tehrani Elham Shirazi
- Department of Pharmacology & Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamhossein Tamaddon
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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17
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Yonamine CY, Alves-Wagner AB, Esteves JV, Okamoto MM, Correa-Giannella ML, Giannella-Neto D, Machado UF. Diabetes induces tri-methylation at lysine 9 of histone 3 at Slc2a4 gene in skeletal muscle: A new target to improve glycemic control. Mol Cell Endocrinol 2019; 481:26-34. [PMID: 30528377 DOI: 10.1016/j.mce.2018.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/05/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022]
Abstract
Expression of the glucose transporter GLUT4, encoded by Slc2a4 gene, is reduced in both type 1 and type 2 diabetes (T1D and T2D), contributing to glycemic impairment. The present study investigated epigenetic regulations at the Slc2a4 promoter in skeletal muscle of T1D- and T2D-like experimental models. Slc2a4/GLUT4 repression was observed in T1D and T2D and that was reversed by insulin and resveratrol treatments, respectively. In both T1D-like and T2D-like animals, tri-methylation at lysine 9 of histone 3 (H3K9me3) increased in the Slc2a4 enhancer segment, whereas MEF2A/D binding into this segment was reduced; all effects were reversed by respective treatments. This study reveals that increased H3K9me3 in the Slc2a4 promoter enhancer segment contributes to reduce GLUT4 expression in skeletal muscle and to worse glycemic control in diabetes, pointing to the H3K9me3 of Slc2a4 promoter as a potential target for development of new approaches for treating diabetes.
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Affiliation(s)
- Caio Y Yonamine
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil.
| | - Ana B Alves-Wagner
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - João V Esteves
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Maristela M Okamoto
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Maria L Correa-Giannella
- Laboratório de Carboidratos e Radioimunoensaio, LIM-18, Hospital das Clinicas HCFMUSP, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil; Programa de Pos-Graduaçao em Medicina, Universidade Nove de Julho (UNINOVE), Sao Paulo, Brazil
| | - Daniel Giannella-Neto
- Programa de Pos-Graduaçao em Medicina, Universidade Nove de Julho (UNINOVE), Sao Paulo, Brazil
| | - Ubiratan F Machado
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
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18
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Yamatsugu K. [How My Experiences in Asymmetric Catalysis and Glycobiology Led to My Current Research in Synthetic Post-translational Modifications by Chemical Catalysts]. YAKUGAKU ZASSHI 2019; 139:187-198. [PMID: 30713228 DOI: 10.1248/yakushi.18-00169-1] [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: 11/22/2022]
Abstract
Conducting research abroad can be an invaluable experience. I would like to share my own experiences as an example of how one's PhD course research (in the laboratory of Shibasaki Masakatsu) and research abroad (University of Wisconsin-Madison, laboratory of Laura Kiessling) can contribute to one's subsequent research. During my PhD course research in Japan, I investigated asymmetric catalysis in the efficient production of physiologically active substances. Then I moved to the U.S. and worked on the functional analysis of enzymes (biocatalysts), with a specific focus on glycosyltranspolymerase. Now I am working on the development of chemical catalysts that can introduce post-translational modifications into proteins, especially histones. Being based in catalysis, I have aimed at research that can contribute to the life sciences. In this account, I share my thought process on selecting such a career path, discuss how it affected my current research, and touch on the positive aspects as well as points for reflection when conducting research abroad.
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Affiliation(s)
- Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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19
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Yamatsugu K, Furuta M, Xi S, Amamoto Y, Liu J, Kawashima SA, Kanai M. Kinetic analyses and structure-activity relationship studies of synthetic lysine acetylation catalysts. Bioorg Med Chem 2018; 26:5359-5367. [PMID: 30006145 DOI: 10.1016/j.bmc.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/20/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022]
Abstract
Lysine acylation of proteins is a crucial chemical reaction, both as a post-translational modification and as a method for bioconjugation. We previously developed a chemical catalyst, DSH, which activates a chemically stable thioester including acyl-CoA, allowing the site-selective lysine acylation of histones under physiological conditions. However, a more active catalyst is required for efficient lysine acylation in more complex biological milieu, such as in living cells, but there are no rational guidelines for developing efficient lysine acylation catalysts for use under physiological conditions as opposed to in organic solvents. We, herein, conducted a kinetic analysis of the ability of DSH and several derivatives to mediate lysine acetylation to better understand the structural elements essential for high acetylation activity under physiological conditions. Interestingly, the obtained trend in reactivity was different from that observed in organic solvents, suggesting that a different principle is necessary for designing chemical catalysts specifically for use under physiological conditions compared to catalysts for use in organic solvents. Based on the obtained information, we identified a new catalyst scaffold with high activity and structural flexibility for further modification to improve this catalyst system.
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Affiliation(s)
- Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan.
| | - Masahiro Furuta
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Siqi Xi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshifumi Amamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan
| | - Jiaan Liu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigehiro A Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan.
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