1
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Wang W, Chen X, Chen J, Xu M, Liu Y, Yang S, Zhao W, Tan S. Engineering lentivirus envelope VSV-G for liver targeted delivery of IDOL-shRNA to ameliorate hypercholesterolemia and atherosclerosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102115. [PMID: 38314097 PMCID: PMC10835450 DOI: 10.1016/j.omtn.2024.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024]
Abstract
Lentiviral vectors (LVs) have been widely used as a tool for gene therapies. However, tissue-selective transduction after systemic delivery remains a challenge. Inducible degrader of low-density lipoprotein receptor is an attractive target for treating hypercholesterolemia. Here, a liver-targeted LV, CS8-LV-shIDOL, is developed by incorporating a hepatocyte-targeted peptide derived from circumsporozoite protein (CSP) into the lentivirus envelope for liver-targeted delivery of IDOL-shRNA (short hairpin RNA) to alleviate hypercholesterolemia. Tail-vein injection of CS8-LV-shIDOL results in extremely high accumulation in liver and nearly undetectable levels in other organs in mice. In addition, it shows superior therapeutic efficacy in lowering serum low-density lipoprotein cholesterol (LDL-C) and reducing atherosclerotic lesions over unmodified LV-shIDOL in hyperlipidemic mice. Mechanically, the envelope-engineered CS8-LV-shIDOL can enter liver cells via low-density lipoprotein receptor-related protein (LRP). Thus, this study provides a novel approach for liver-targeted delivery of IDOL-shRNA to treat hypercholesterolemia by using an envelope-engineered LV, and this delivery system has great potential for liver-targeted transgene therapy.
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Affiliation(s)
- Wei Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Xuemei Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Jiali Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Liu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shijie Yang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
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2
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Pel P, Kim YM, Kim HJ, Nhoek P, An CY, Son MG, Won H, Lee SE, Lee J, Kim HW, Choi YH, Lee CH, Chin YW. Isocoumarins and Benzoquinones with Their Proprotein Convertase Subtilisin/Kexin Type 9 Expression Inhibitory Activities from Dried Roots of Lysimachia vulgaris. ACS OMEGA 2022; 7:47296-47305. [PMID: 36570277 PMCID: PMC9774376 DOI: 10.1021/acsomega.2c06660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
A phytochemical investigation of the n-hexane-soluble chemical constituents of Lysimachia vulgaris roots allowed for selection using a proprotein convertase subtilisin-kexin type 9 (PCSK9) mRNA expression monitoring assay in HepG2 cells. This led to the isolation of two previously undescribed isocoumarins of natural origin, 8'Z,11'Z-octadecadienyl-6,8-dihydroxyisocoumarin (1) and 3-pentadecyl-6,8-dihydroxyisocoumarin (2), along with 20 previously reported compounds (3-22). All of the structures were established using NMR spectroscopic data and MS analysis. Of the isolates, 1 and 3 were found to inhibit PCSK9, inducible degrader of the low-density lipoprotein receptor (IDOL), and SREBP2 mRNA expression. Further computational dockings of both 1 and 3 to C-ring of IDOL E3 ubiquitin ligase predicted the mechanism behind the inhibitory effect of these compounds on the enzyme.
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Affiliation(s)
- Pisey Pel
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Young-Mi Kim
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyun Ji Kim
- College
of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, 32 Dongguk-lo, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea
| | - Piseth Nhoek
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Chae-Yeong An
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Min-Gyung Son
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hongic Won
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seung Eun Lee
- Department
of Herbal Crop Research, National Institute
of Horticultural and Herbal Science (NIHHS) of Rural Development Administration, Eumseong 27709, Republic of Korea
| | - Jeonghoon Lee
- Department
of Herbal Crop Research, National Institute
of Horticultural and Herbal Science (NIHHS) of Rural Development Administration, Eumseong 27709, Republic of Korea
| | - Hyun Woo Kim
- College
of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, 32 Dongguk-lo, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea
| | - Young Hee Choi
- College
of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, 32 Dongguk-lo, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea
| | - Chang Hoon Lee
- College
of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, 32 Dongguk-lo, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea
| | - Young-Won Chin
- College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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3
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Chen Y, Duan C, Chen K, Sun S, Zhang D, Meng X. Screening technology of cyclic peptide library based on gene encoding. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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4
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Bouayad‐Gervais S, St‐Cyr DJ, Courcelles M, Bonneil É, Gohard FH, Thibault P, Earnshaw WC, Tyers M. Head‐to‐tail cyclization of side chain‐protected linear peptides to recapitulate genetically‐encoded cyclized peptides. Pept Sci (Hoboken) 2022; 114:e24254. [PMID: 35864841 PMCID: PMC9286623 DOI: 10.1002/pep2.24254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 12/13/2021] [Indexed: 11/08/2022]
Abstract
Genetically‐encoded cyclic peptide libraries allow rapid in vivo screens for inhibitors of any target protein of interest. In particular, the Split Intein Circular Ligation of Protein and Peptides (SICLOPPS) system exploits spontaneous protein splicing of inteins to produce intracellular cyclic peptides. A previous SICLOPPS screen against Aurora B kinase, which plays a critical role during chromosome segregation, identified several candidate inhibitors that we sought to recapitulate by chemical synthesis. We describe the syntheses of cyclic peptide hits and analogs via solution‐phase macrocyclization of side chain‐protected linear peptides obtained from standard solid‐phase peptide synthesis. Cyclic peptide targets, including cyclo‐[CTWAR], were designed to match both the variable portions and conserved cysteine residue of their genetically‐encoded counterparts. Synthetic products were characterized by tandem high‐resolution mass spectrometry to analyze a combination of exact mass, isotopic pattern, and collisional dissociation‐induced fragmentation pattern. The latter analyses facilitated the distinction between targets and oligomeric side products, and served to confirm peptidic sequences in a manner that can be readily extended to analyses of complex biological samples. This alternative chemical synthesis approach for cyclic peptides allows cost‐effective validation and facile chemical elaboration of hit candidates from SICLOPPS screens.
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Affiliation(s)
- Samir Bouayad‐Gervais
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
| | - Daniel J. St‐Cyr
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
| | - Mathieu Courcelles
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
| | - Éric Bonneil
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
| | - Florence H. Gohard
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology University of Edinburgh Edinburgh UK
| | - Pierre Thibault
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
| | - William C. Earnshaw
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology University of Edinburgh Edinburgh UK
| | - Mike Tyers
- Department of Medicine, Institute for Research in Immunology and Cancer Université de Montréal Montréal Canada
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5
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Choi YJ, Lee SJ, Kim HI, Lee HJ, Kang SJ, Kim TY, Cheon C, Ko SG. Platycodin D enhances LDLR expression and LDL uptake via down-regulation of IDOL mRNA in hepatic cells. Sci Rep 2020; 10:19834. [PMID: 33199761 PMCID: PMC7670405 DOI: 10.1038/s41598-020-76224-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
The root of Platycodon grandiflorum (PG) has long been used as a traditional herbal medicine in Asian country. Platycondin D (PD), triterpenoid saponin that is a main constituent of PG, exhibits various biological activities such as anti-inflammatory, anti-oxidant, anti-diabetic, and anti-cancer effects. A previous study showed that PD had cholesterol-lowering effects in mice that develop hypercholesterolemia, but the underlying molecular mechanisms have not been elucidated during the last decade. Here, we demonstrated that both PG and PD markedly increased levels of cell surface low-density lipoprotein receptor (LDLR) by down-regulation of the E3 ubiquitin ligase named inducible degrader of the LDLR (IDOL) mRNA, leading to the enhanced uptake of LDL-derived cholesterol (LDL-C) in hepatic cells. Furthermore, cycloheximide chase analysis and in vivo ubiquitination assay revealed that PD increased the half-life of LDLR protein by reducing IDOL-mediated LDLR ubiquitination. Finally, we demonstrated that treatment of HepG2 cells with simvastatin in combination with PG and PD had synergistic effects on the improvement of LDLR expression and LDL-C uptake. Together, these results provide the first molecular evidence for anti-hypercholesterolemic activity of PD and suggest that PD alone or together with statin could be a potential therapeutic option in the treatment of atherosclerotic cardiovascular disease.
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Affiliation(s)
- Yu-Jeong Choi
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Sol Ji Lee
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea.,Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Hyo In Kim
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hee Jung Lee
- Department Global Public Health and Korean Medicine Management, College of Korean Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - So Jung Kang
- Department of Clinical Koeran Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Tai Young Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34126, Republic of Korea. .,Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 1 Hoegi, Seoul, 130-701, Korea.
| | - Chunhoo Cheon
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 1 Hoegi, Seoul, 130-701, Korea
| | - Seong-Gyu Ko
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 1 Hoegi, Seoul, 130-701, Korea.
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6
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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7
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Adi D, Abuzhalihan J, Wang YH, Baituola G, Wu Y, Xie X, Fu ZY, Yang YN, Ma X, Li XM, Chen BD, Liu F, Ma YT. IDOL gene variant is associated with hyperlipidemia in Han population in Xinjiang, China. Sci Rep 2020; 10:14280. [PMID: 32868861 PMCID: PMC7459279 DOI: 10.1038/s41598-020-71241-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
Hyperlipidemia is one of the main risk factors that contributed to atherosclerosis and coronary artery disease (CAD). In the present study, our objective was to explore whether some genetic variants of human IDOL gene were associated with hyperlipidemia among Han population in Xinjiang, China. We designed a case–control study. A total of 1,172 subjects (588 diagnosed hyperlipidemia cases and 584 healthy controls) of Chinese Han were recruited. We genotyped three SNPs (rs9370867, rs909562, and rs2072783) of IDOL gene in all subjects by using the improved multiplex ligation detection reaction (iMLDR) method. Our study demonstrated that the distribution of the genotypes, the dominant model (AA vs GG + GA), and the overdominant model (AA + GG vs GA) of the rs9370867 SNP had significant differences between the case group and controls (all P < 0.001). For rs909562 and rs2072783, the distribution of the genotypes, the recessive model (AA + GA vs GG) showed significant differences between the case subjects and controls (P = 0.002, P = 0.007 and P = 0.045, P = 0.02, respectively). After multivariate adjustment for several confounders, the rs9370867 SNP is still an independent risk factor for hyperlipidemia [odds ratio (OR) = 1.380, 95% confidence interval (CI) = 1.201–1.586, P < 0.001]. The rs9370867 of human IDOL gene was associated with hyperlipidemia in Han population.
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Affiliation(s)
- Dilare Adi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Jialin Abuzhalihan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Ying-Hong Wang
- Health Checkup Department of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China
| | - Gulinaer Baituola
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Yun Wu
- Department of General Practice, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Xiang Xie
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Zhen-Yan Fu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Yi-Ning Yang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Xiang Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Xiao-Mei Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Bang-Dang Chen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China
| | - Fen Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China
| | - Yi-Tong Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, People's Republic of China. .,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, People's Republic of China.
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8
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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9
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Foster AD, Chung C, Hann MM, Simpson GL, Tavassoli A. Development of a fluorescent three‐hybrid system for the identification of protein‐protein associators. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | - Ali Tavassoli
- School of Chemistry University of Southampton Southampton UK
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10
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Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
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11
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van Loon NM, Rensen PCN, Zelcer N. IDOL in metabolic, neurodegenerative and cardiovascular disease. Aging (Albany NY) 2019; 10:3042-3043. [PMID: 30317226 PMCID: PMC6286838 DOI: 10.18632/aging.101597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/13/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Nienke M van Loon
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology and Einthoven Laboratory for Experimental Vascular and Regenerative Medicine, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Noam Zelcer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
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12
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Lennard KR, Gardner RM, Doigneaux C, Castillo F, Tavassoli A. Development of a Cyclic Peptide Inhibitor of the p6/UEV Protein-Protein Interaction. ACS Chem Biol 2019; 14:1874-1878. [PMID: 31411851 DOI: 10.1021/acschembio.9b00627] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The budding of HIV from infected cells is driven by the protein-protein interaction between the p6 domain of the HIV Gag protein and the UEV domain of the human TSG101 protein. We report the development of a cyclic peptide inhibitor of the p6/UEV interaction, from a non cell-permeable parent that was identified in a SICLOPPS screen. Amino acids critical for the activity of the parent cyclic peptide were uncovered using alanine-scanning, and a series of non-natural analogues synthesized and assessed. The most potent molecule disrupts the p6/UEV interaction with an IC50 of 6.17 ± 0.24 μM by binding to UEV with a Kd of 11.9 ± 2.8 μM. This compound is cell permeable and active in a cellular virus-like particle budding assay with an IC50 of ∼2 μM. This work further demonstrates the relative simplicity with which the potency and activity of cyclic peptides identified from SICLOPPS libraries can be optimized.
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Affiliation(s)
- Katherine R. Lennard
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Reece M. Gardner
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Cyrielle Doigneaux
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Francisco Castillo
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
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13
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van Loon NM, Lindholm D, Zelcer N. The E3 ubiquitin ligase inducible degrader of the LDL receptor/myosin light chain interacting protein in health and disease. Curr Opin Lipidol 2019; 30:192-197. [PMID: 30896554 DOI: 10.1097/mol.0000000000000593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE OF REVIEW The RING E3 ubiquitin ligase inducible degrader of the LDL receptor (IDOL, also known as MYLIP) promotes ubiquitylation and subsequent lysosomal degradation of the LDL receptor (LDLR), thus acting to limit uptake of lipoprotein-derived cholesterol into cells. Next to the LDLR, IDOL also promotes degradation of two related receptors, the very LDL receptor (VLDLR) and apolipoprotein E receptor 2 (APOER2), which have important signaling functions in the brain. We review here the emerging role of IDOL in lipoprotein and energy metabolism, neurodegenerative diseases, and the potential for therapeutic targeting of IDOL. RECENT FINDINGS Genetic studies suggest an association between IDOL and lipoprotein metabolism in humans. Studies in rodents and nonhuman primates support an in-vivo role for IDOL in lipoprotein metabolism, and also uncovered an unexpected role in whole-body energy metabolism. Recent evaluation of IDOL function in the brain revealed a role in memory formation and progression of Alzheimer's disease. The report of the first IDOL inhibitor may facilitate further investigations on therapeutic strategies to target IDOL. SUMMARY IDOL is emerging as an important determinant of lipid and energy metabolism in metabolic disease as well as in Alzheimer's disease. IDOL targeting may be beneficial in treating these conditions.
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Affiliation(s)
- Nienke M van Loon
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Dan Lindholm
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki
- Minerva Foundation Institute for Medical Research, Biomedicum-2, Helsinki, Finland
| | - Noam Zelcer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
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14
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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15
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Castillo F, Tavassoli A. Genetic Selections with SICLOPPS Libraries: Toward the Identification of Novel Protein-Protein Interaction Inhibitors and Chemical Tools. Methods Mol Biol 2019; 2001:317-328. [PMID: 31134578 DOI: 10.1007/978-1-4939-9504-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyclic peptide libraries have successfully been employed for the identification of inhibitors of highly challenging targets. While several methodologies exist for the generation of cyclic peptide libraries, genetically encoded libraries hold several advantages over purely in vitro methods of library generation, including the ability to conduct cell-based functional screens and straightforward hit deconvolution. Here we detail the use of split-intein circular ligation of peptides and proteins (SICLOPPS) for the identification and optimization of several first-in-class and best-in-class inhibitors. We describe the current advances in the identification of SICLOPPS-derived inhibitors, as well as the optimization of library generation through the use of new inteins. Finally, we discuss the production of more diverse libraries as a way of enhancing the hit rate against difficult protein-protein interactions.
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Affiliation(s)
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, UK.
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16
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Abstract
With the increasing utilization of high-throughput screening for lead identification in drug discovery, the need for easily constructed and diverse libraries which cover significant chemical space is greater than ever. Cyclic peptides address this need; they combine the advantageous properties of peptides (ease of production, high diversity, high potential specificity) with increased resistance to proteolysis and often increased biological activity (due to conformational locking). There are a number of techniques for the generation and screening of cyclic peptide libraries. As drug discovery moves toward tackling challenging targets, such as protein-protein interactions, cyclic peptide libraries are expected to continue producing hits where small molecule libraries may be stymied. However, it is important to design robust systems for the generation and screening of these large libraries, and to be able to make sense of structure-activity relationships in these highly variable scaffolds. There are a plethora of possible modifications that can be made to cyclic peptides, which is both a weakness and a strength of these scaffolds; high variability will allow more precise tuning of leads to targets, but exploring the whole range of modifications may become an overwhelming challenge.
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