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Kubatzky KF, Gao Y, Yu D. Post-translational modulation of cell signalling through protein succinylation. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1260-1285. [PMID: 38213532 PMCID: PMC10776603 DOI: 10.37349/etat.2023.00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cells need to adapt their activities to extra- and intracellular signalling cues. To translate a received extracellular signal, cells have specific receptors that transmit the signal to downstream proteins so that it can reach the nucleus to initiate or repress gene transcription. Post-translational modifications (PTMs) of proteins are reversible or irreversible chemical modifications that help to further modulate protein activity. The most commonly observed PTMs are the phosphorylation of serine, threonine, and tyrosine residues, followed by acetylation, glycosylation, and amidation. In addition to PTMs that involve the modification of a certain amino acid (phosphorylation, hydrophobic groups for membrane localisation, or chemical groups like acylation), or the conjugation of peptides (SUMOylation, NEDDylation), structural changes such as the formation of disulphide bridge, protein cleavage or splicing can also be classified as PTMs. Recently, it was discovered that metabolites from the tricarboxylic acid (TCA) cycle are not only intermediates that support cellular metabolism but can also modify lysine residues. This has been shown for acetate, succinate, and lactate, among others. Due to the importance of mitochondria for the overall fitness of organisms, the regulatory function of such PTMs is critical for protection from aging, neurodegeneration, or cardiovascular disease. Cancer cells and activated immune cells display a phenotype of accelerated metabolic activity known as the Warburg effect. This metabolic state is characterised by enhanced glycolysis, the use of the pentose phosphate pathway as well as a disruption of the TCA cycle, ultimately causing the accumulation of metabolites like citrate, succinate, and malate. Succinate can then serve as a signalling molecule by directly interacting with proteins, by binding to its G protein-coupled receptor 91 (GPR91) and by post-translationally modifying proteins through succinylation of lysine residues, respectively. This review is focus on the process of protein succinylation and its importance in health and disease.
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Affiliation(s)
- Katharina F. Kubatzky
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yue Gao
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Dayoung Yu
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
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2
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Pichlak M, Sobierajski T, Błażewska KM, Gendaszewska-Darmach E. Targeting reversible post-translational modifications with PROTACs: a focus on enzymes modifying protein lysine and arginine residues. J Enzyme Inhib Med Chem 2023; 38:2254012. [PMID: 37667522 PMCID: PMC10481767 DOI: 10.1080/14756366.2023.2254012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
PROTACs represent an emerging field in medicinal chemistry, which has already led to the development of compounds that reached clinical studies. Posttranslational modifications contribute to the complexity of proteomes, with 2846 disease-associated sites. PROTAC field is very advanced in targeting kinases, while its use for enzymes mediating posttranslational modifications of the basic amino acid residues, started to be developed recently. Therefore, we bring together this less popular class of PROTACs, targeting lysine acetyltransferases/deacetylases, lysine and arginine methyltransferases, ADP-ribosyltransferases, E3 ligases, and ubiquitin-specific proteases. We put special emphasis on structural aspects of PROTAC elements to facilitate the lengthy experimental endeavours directed towards developing PROTACs. We will cover the period from the inception of the field, 2017, to April 2023.
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Affiliation(s)
- Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
| | - Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
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3
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Zhang Q, Yan P, Zhao P, Zhao D, Cao H, Lu J, Mao B. Design, Synthesis, and Biological Evaluation of mTOR-Targeting PROTACs Based on MLN0128 and Pomalidomide. Chem Pharm Bull (Tokyo) 2023; 71:120-128. [PMID: 36436947 DOI: 10.1248/cpb.c22-00576] [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: 11/27/2022]
Abstract
Mechanistic target of rapamycin (mTOR) is an effective anti-tumor drug target. Several mTOR kinase inhibitors have entered clinical research, but there are still challenges of potential toxicity. As a new type of targeted drug, proteolysis targeting chimeras (PROTACs) have features of low dosage and low toxicity. However, this approach has been rarely reported to involve mTOR degradation. In this study, the mTOR kinase inhibitor MLN0128 was used as the ligand to the protein of interest and conjugated with pomalidomide by diverse intermediate linkage chains. Several potential small molecule PROTACs for the degradation of mTOR were designed and synthesized. PROTAC compounds exhibited mTOR inhibitory activity and suppressed MCF-7 cell proliferation. The representative compound P1 could inhibit the expression of mTOR downstream proteins and the growth of cancer cells by inducing autophagy but not affecting the cell cycle and not inducing apoptosis.
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Affiliation(s)
- Qi Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Peizheng Yan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Pan Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Dongsheng Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Heran Cao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Jing Lu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
| | - Beibei Mao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine
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Zhang C, Li X, Xing Z, Zhong H, Yu D, Yu R, Deng X. Plasma metabolites-based design of long-acting peptides and their anticancer evaluation. Int J Pharm 2023; 631:122483. [PMID: 36509220 DOI: 10.1016/j.ijpharm.2022.122483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/26/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Antimicrobial peptides (AMPs) are generally small cationic amphipathic peptides, which are thought to be ideal antineoplastic agents, owing to their favorable selectivity to cancer cells and the ability to overcome drug-resistance. In this study, an anticancer AMP (Mastoparan (INLKALAALAKKIL-NH2)) was selected as the lead compound and a series of Mastoparan derivatives were designed. Preliminary studies verified that an analogue of Mastoparan, KM8 (KLLKINLKALAALAKKIL-NH2), exhibited prominent selective antitumor effects. Instead, it presents a significant defect of metabolic instability, with a half-life in plasma of only about 0.5 h. Metabolite profiling of KM8 was performed and indicated the structure 9AL10 in peptide sequence could be the fragile site for KM8. Thus, the Aib (unnatural amnio acid) was employed to substitute the 9Ala residue in KM8, and generating a long-acting KM8 derivative, namely KM8-Aib. Further investigations revealed KM8-Aib possessed higher metabolic stability, more potent anticancer activity in vitro & in vivo, and lower toxicity. Therefore, KM8-Aib is suggested be a potential antimalignant agent that worthy of more in-depth study.
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Affiliation(s)
- Chenyu Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Xiang Li
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Zhenjian Xing
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Honglan Zhong
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Dianbao Yu
- Analytical Applications Center, Shimadzu (China) Co., Ltd., Guangzhou Branch, 230 Gaotang Road, Guangzhou 510656, China
| | - Rui Yu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
| | - Xin Deng
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
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Duarte IF, Caio J, Moedas MF, Rodrigues LA, Leandro AP, Rivera IA, Silva MFB. Dihydrolipoamide dehydrogenase, pyruvate oxidation, and acetylation-dependent mechanisms intersecting drug iatrogenesis. Cell Mol Life Sci 2021; 78:7451-7468. [PMID: 34718827 PMCID: PMC11072406 DOI: 10.1007/s00018-021-03996-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 10/19/2022]
Abstract
In human metabolism, pyruvate dehydrogenase complex (PDC) is one of the most intricate and large multimeric protein systems representing a central hub for cellular homeostasis. The worldwide used antiepileptic drug valproic acid (VPA) may potentially induce teratogenicity or a mild to severe hepatic toxicity, where the underlying mechanisms are not completely understood. This work aims to clarify the mechanisms that intersect VPA-related iatrogenic effects to PDC-associated dihydrolipoamide dehydrogenase (DLD; E3) activity. DLD is also a key enzyme of α-ketoglutarate dehydrogenase, branched-chain α-keto acid dehydrogenase, α-ketoadipate dehydrogenase, and the glycine decarboxylase complexes. The molecular effects of VPA will be reviewed underlining the data that sustain a potential interaction with DLD. The drug-associated effects on lipoic acid-related complexes activity may induce alterations on the flux of metabolites through tricarboxylic acid cycle, branched-chain amino acid oxidation, glycine metabolism and other cellular acetyl-CoA-connected reactions. The biotransformation of VPA involves its complete β-oxidation in mitochondria causing an imbalance on energy homeostasis. The drug consequences as histone deacetylase inhibitor and thus gene expression modulator have also been recognized. The mitochondrial localization of PDC is unequivocal, but its presence and function in the nucleus were also demonstrated, generating acetyl-CoA, crucial for histone acetylation. Bridging metabolism and epigenetics, this review gathers the evidence of VPA-induced interference with DLD or PDC functions, mainly in animal and cellular models, and highlights the uncharted in human. The consequences of this interaction may have significant impact either in mitochondrial or in nuclear acetyl-CoA-dependent processes.
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Affiliation(s)
- I F Duarte
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - J Caio
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - M F Moedas
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - L A Rodrigues
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - A P Leandro
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - I A Rivera
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - M F B Silva
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
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Iida T, Itoh Y, Takahashi Y, Yamashita Y, Kurohara T, Miyake Y, Oba M, Suzuki T. Design, Synthesis, and Biological Evaluation of Lysine Demethylase 5 C Degraders. ChemMedChem 2021; 16:1609-1618. [PMID: 33470543 DOI: 10.1002/cmdc.202000933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/18/2022]
Abstract
Lysine demethylase 5 C (KDM5C) controls epigenetic gene expression and is attracting great interest in the field of chemical epigenetics. KDM5C has emerged as a therapeutic target for anti-prostate cancer agents, and recently we identified triazole 1 as an inhibitor of KDM5C. Compound 1 exhibited highly potent KDM5C-inhibitory activity in in vitro enzyme assays, but did not show strong anticancer effects. Therefore, a different approach is needed for the development of anticancer agents targeting KDM5C. Here, we attempted to identify KDM5C degraders by focusing on a protein-knockdown strategy. Compound 3 b, which was designed based on compound 1, degraded KDM5C and inhibited the growth of prostate cancer PC-3 cells more strongly than compound 1. These findings suggest that KDM5C degraders are more effective as anticancer agents than compounds that only inhibit the catalytic activity of KDM5C.
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Affiliation(s)
- Tetsuya Iida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukari Takahashi
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yuka Miyake
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Makoto Oba
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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Ji Y, Ren C, Miao H, Pang Z, Xiao R, Yang X, Xuan W. Genetically encoding ε-N-benzoyllysine in proteins. Chem Commun (Camb) 2021; 57:1798-1801. [DOI: 10.1039/d0cc07954e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoding BzK can facilitate the biological investigation of the recently discovered protein PTM lysine ε-N-benzoylation.
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Affiliation(s)
- Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Conghui Ren
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Zhili Pang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Ruotong Xiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
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Cui W, Aouidate A, Wang S, Yu Q, Li Y, Yuan S. Discovering Anti-Cancer Drugs via Computational Methods. Front Pharmacol 2020; 11:733. [PMID: 32508653 PMCID: PMC7251168 DOI: 10.3389/fphar.2020.00733] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022] Open
Abstract
New drug discovery has been acknowledged as a complicated, expensive, time-consuming, and challenging project. It has been estimated that around 12 years and 2.7 billion USD, on average, are demanded for a new drug discovery via traditional drug development pipeline. How to reduce the research cost and speed up the development process of new drug discovery has become a challenging, urgent question for the pharmaceutical industry. Computer-aided drug discovery (CADD) has emerged as a powerful, and promising technology for faster, cheaper, and more effective drug design. Recently, the rapid growth of computational tools for drug discovery, including anticancer therapies, has exhibited a significant and outstanding impact on anticancer drug design, and has also provided fruitful insights into the area of cancer therapy. In this work, we discussed the different subareas of the computer-aided drug discovery process with a focus on anticancer drugs.
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Affiliation(s)
- Wenqiang Cui
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Adnane Aouidate
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shouguo Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiuliyang Yu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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