1
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Petrovicz VL, Pasztuhov I, Martinek TA, Hegedüs Z. Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α. RSC Chem Biol 2024; 5:711-720. [PMID: 39092442 PMCID: PMC11289882 DOI: 10.1039/d4cb00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/27/2024] [Indexed: 08/04/2024] Open
Abstract
The interaction between the intrinsically disordered transcription factor HIF-1α and the coactivator proteins p300/CBP is essential in the fast response to low oxygenation. The negative feedback regulator, CITED2, switches off the hypoxic response through a very efficient irreversible mechanism. The negative cooperativity with HIF-1α relies on the formation of a ternary intermediate that leads to allosteric structural changes in p300/CBP, in which the cooperative folding/binding of the CITED2 sequence motifs plays a key role. Understanding the contribution of a binding motif to the structural changes in relation to competition efficiency provides invaluable insights into the molecular mechanism. Our strategy is to site-directedly perturb the p300-CITED2 complex's structure without significantly affecting binding thermodynamics. In this way, the contribution of a sequence motif to the negative cooperativity with HIF-1α would mainly depend on the induced structural changes, and to a lesser extent on binding affinity. Using biophysical assays and NMR measurements, we show here that the interplay between the N-terminal tail and the rest of the binding motifs of CITED2 is crucial for the unidirectional displacement of HIF-1α. We introduce an advantageous approach for evaluating the roles of the different sequence parts with the help of motif-by-motif backbone perturbations.
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Affiliation(s)
- Vencel L Petrovicz
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - István Pasztuhov
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - Tamás A Martinek
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
- HUN-REN SZTE Biomimetic Systems Research Group 8 Dóm tér Szeged 6720 Hungary
| | - Zsófia Hegedüs
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
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2
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Britton D, Katsara O, Mishkit O, Wang A, Pandya N, Liu C, Mao H, Legocki J, Jia S, Xiao Y, Aristizabal O, Paul D, Deng Y, Schneider R, Wadghiri YZ, Montclare JK. Engineered coiled-coil HIF1α protein domain mimic. Biomater Sci 2024; 12:2951-2959. [PMID: 38656316 PMCID: PMC11191652 DOI: 10.1039/d4bm00354c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Andrew Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
| | - Neelam Pandya
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Heather Mao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jakub Legocki
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yingxin Xiao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Orlando Aristizabal
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Deven Paul
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yan Deng
- Microscopy Laboratory, New York University Langone Health, New York, NY, 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, 10016, USA
| | - Youssef Z Wadghiri
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
- Department of Biomedical Engineering, New York University, New York, NY, 11201, USA
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3
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Splandesci M, Wróbel MZ, Madura ID, Dawidowski M. Ugi 5-center-4-component reaction of α-amino aldehydes and its application in synthesis of 2-oxopiperazines. Mol Divers 2024; 28:229-248. [PMID: 38104301 PMCID: PMC10876754 DOI: 10.1007/s11030-023-10760-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023]
Abstract
A synthetic route leading to densely functionalized 2-oxopiperazines is presented. The strategy employs a 5-center-4-component variant of Ugi multicomponent reaction followed by a deprotection/cyclization sequence. N-Boc-α-amino aldehydes were used for the first time as carbonyl components in a key Ugi 5-center-4-component reaction (U-5C-4CR). It is shown that the presented synthetic route can lead to rigid, heterocyclic scaffolds, as demonstrated by the synthesis of tetrahydro-2H-pyrazino[1,2-a]pyrazine-3,6,9(4H)-trione β-turn mimetic and derivatives of 1,6-dioxooctahydropyrrolo[1,2-a]pyrazine and 3,8-dioxohexahydro-3H-oxazolo[3,4-a]pyrazine.
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Affiliation(s)
- Marta Splandesci
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Martyna Z Wróbel
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Izabela D Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland.
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4
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Zhao Y, Xiong W, Li C, Zhao R, Lu H, Song S, Zhou Y, Hu Y, Shi B, Ge J. Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets. Signal Transduct Target Ther 2023; 8:431. [PMID: 37981648 PMCID: PMC10658171 DOI: 10.1038/s41392-023-01652-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 11/21/2023] Open
Abstract
Hypoxia, characterized by reduced oxygen concentration, is a significant stressor that affects the survival of aerobic species and plays a prominent role in cardiovascular diseases. From the research history and milestone events related to hypoxia in cardiovascular development and diseases, The "hypoxia-inducible factors (HIFs) switch" can be observed from both temporal and spatial perspectives, encompassing the occurrence and progression of hypoxia (gradual decline in oxygen concentration), the acute and chronic manifestations of hypoxia, and the geographical characteristics of hypoxia (natural selection at high altitudes). Furthermore, hypoxia signaling pathways are associated with natural rhythms, such as diurnal and hibernation processes. In addition to innate factors and natural selection, it has been found that epigenetics, as a postnatal factor, profoundly influences the hypoxic response and progression within the cardiovascular system. Within this intricate process, interactions between different tissues and organs within the cardiovascular system and other systems in the context of hypoxia signaling pathways have been established. Thus, it is the time to summarize and to construct a multi-level regulatory framework of hypoxia signaling and mechanisms in cardiovascular diseases for developing more therapeutic targets and make reasonable advancements in clinical research, including FDA-approved drugs and ongoing clinical trials, to guide future clinical practice in the field of hypoxia signaling in cardiovascular diseases.
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Affiliation(s)
- Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Ranzun Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - You Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
| | - Bei Shi
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Junbo Ge
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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5
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Jiang W, Abdulkadir S, Zhao X, Sang P, Tomatsidou A, Zhang X, Chen Y, Calcul L, Sun X, Cheng F, Hu Y, Cai J. Inhibition of Hypoxia-Inducible Transcription Factor (HIF-1α) Signaling with Sulfonyl-γ-AApeptide Helices. J Am Chem Soc 2023; 145:20009-20020. [PMID: 37665648 PMCID: PMC10637359 DOI: 10.1021/jacs.3c06694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The development of inhibitors that selectively block protein-protein interactions (PPIs) is crucial for chemical biology, medicinal chemistry, and biomedical sciences. Herein, we reported the design, synthesis, and investigation of sulfonyl-γ-AApeptide as an alternative strategy of canonical peptide-based inhibitors to disrupt hypoxia-inducible factor 1α (HIF-1α) and p300 PPI by mimicking the helical domain of HIF-1α involved in the binding to p300. The designed molecules recognized the p300 protein with high affinity and potently inhibited the hypoxia-inducible signaling pathway. Gene expression profiling supported the idea that the lead molecules selectively inhibited hypoxia-inducible genes involved in the signaling cascade. Our studies also demonstrated that both helical faces consisting of either chiral side chains or achiral sulfonyl side chains of sulfonyl-γ-AApeptides could be adopted for mimicry of the α-helix engaging in PPIs. Furthermore, these sulfonyl-γ-AApeptides were cell-permeable and exhibited favorable stability and pharmacokinetic profiles. Our results could inspire the design of helical sulfonyl-γ-AApeptides as a general strategy to mimic the protein helical domain and modulate many other PPIs.
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Affiliation(s)
- Wei Jiang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
- Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Sami Abdulkadir
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
| | - Xue Zhao
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
| | - Anastasia Tomatsidou
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Laurent Calcul
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Feng Cheng
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida 33612, United States
| | - Yong Hu
- Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, Florida 33620, United States
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6
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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7
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Marciniak M, Mróz P, Napolitano V, Kalel VC, Fino R, Pykacz E, Schliebs W, Plettenburg O, Erdmann R, Sattler M, Popowicz GM, Dawidowski M. Development of novel PEX5-PEX14 protein-protein interaction (PPI) inhibitors based on an oxopiperazine template. Eur J Med Chem 2023; 258:115587. [PMID: 37406382 DOI: 10.1016/j.ejmech.2023.115587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Protein-protein interactions (PPIs) constitute an important but challenging class of molecular targets for small molecules. The PEX5-PEX14 PPI has been shown to play a critical role in glycosome biogenesis and its disruption impairs the metabolism in Trpanosoma parasites, eventually leading to their death. Therefore, this PPI is a potential molecular target for new drugs against diseases caused by Trypanosoma infections. Here, we report a new class of peptidomimetic scaffolds to target the PEX5-PEX14 PPI. The molecular design was based on an oxopiperazine template for the α-helical mimetics. A structural simplification along with modifications of the central oxopiperazine scaffold and addressing the lipophilic interactions led to the development of peptidomimetics that inhibit PEX5-TbPEX14 PPI and display cellular activity against T. b. brucei. This approach provides an alternative approach towards the development of trypanocidal agents and may be generally useful for the design of helical mimetics as PPI inhibitors.
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Affiliation(s)
- Monika Marciniak
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Piotr Mróz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Valeria Napolitano
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Roberto Fino
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Emilia Pykacz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany; Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1b, Hannover, 30167, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland.
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8
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Muthamil S, Kim HY, Jang HJ, Lyu JH, Shin UC, Go Y, Park SH, Lee HG, Park JH. Understanding the relationship between cancer associated cachexia and hypoxia-inducible factor-1. Biomed Pharmacother 2023; 163:114802. [PMID: 37146421 DOI: 10.1016/j.biopha.2023.114802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
Cancer-associated cachexia (CAC) is a multifactorial disorder characterized by an unrestricted loss of body weight as a result of muscle and adipose tissue atrophy. Cachexia is influenced by several factors, including decreased metabolic activity and food intake, an imbalance between energy uptake and expenditure, excessive catabolism, and inflammation. Cachexia is highly associated with all types of cancers responsible for more than half of cancer-related mortalities worldwide. In healthy individuals, adipose tissue significantly regulates energy balance and glucose homeostasis. However, in metastatic cancer patients, CAC occurs mainly because of an imbalance between muscle protein synthesis and degradation which are organized by certain extracellular ligands and associated signaling pathways. Under hypoxic conditions, hypoxia-inducible factor-1 (HIF-1α) accumulated and translocated to the nucleus and activate numerous genes involved in cell survival, invasion, angiogenesis, metastasis, metabolic reprogramming, and cancer stemness. On the other hand, the ubiquitination proteasome pathway is inhibited during low O2 levels which promote muscle wasting in cancer patients. Therefore, understanding the mechanism of the HIF-1 pathway and its metabolic adaptation to biomolecules is important for developing a novel therapeutic method for cancer and cachexia therapy. Even though many HIF inhibitors are already in a clinical trial, their mechanism of action remains unknown. With this background, this review summarizes the basic concepts of cachexia, the role of inflammatory cytokines, pathways connected with cachexia with special reference to the HIF-1 pathway and its regulation, metabolic changes, and inhibitors of HIFs.
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Affiliation(s)
- Subramanian Muthamil
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Hyun Yong Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Hyun-Jun Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Ji-Hyo Lyu
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Ung Cheol Shin
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Younghoon Go
- Korean Medicine (KM)-application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| | - Seong-Hoon Park
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon 34141, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jun Hong Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea; University of Science & Technology (UST), KIOM campus, Korean Convergence Medicine Major, Daejeon 34054, Republic of Korea.
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9
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Maity D. Inhibition of Amyloid Protein Aggregation Using Selected Peptidomimetics. ChemMedChem 2023; 18:e202200499. [PMID: 36317359 DOI: 10.1002/cmdc.202200499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Aberrant protein aggregation leads to the formation of amyloid fibrils. This phenomenon is linked to the development of more than 40 irremediable diseases such as Alzheimer's disease, Parkinson's disease, type 2 diabetes, and cancer. Plenty of research efforts have been given to understanding the underlying mechanism of protein aggregation, associated toxicity, and the development of amyloid inhibitors. Recently, the peptidomimetic approach has emerged as a potential tool to modulate several protein-protein interactions (PPIs). In this review, we discussed selected peptidomimetic-based approaches for the modulation of important amyloid proteins (Islet Amyloid Polypeptide, Amyloid Beta, α-synuclein, mutant p53, and insulin) aggregation. This approach holds a powerful platform for creating an essential stepping stone for the vital development of anti-amyloid therapeutic agents.
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Affiliation(s)
- Debabrata Maity
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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10
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Xie R, Zhou H, Lu H, Mu Y, Xu G, Chang M. Transition-Metal-Catalyzed Asymmetric Reductive Amination and Amidation Cascade Reaction for the Synthesis of Piperazinones. Org Lett 2022; 24:9033-9037. [DOI: 10.1021/acs.orglett.2c03664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rongrong Xie
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huan Zhou
- College of Plant Protection, Shaanxi Research Center of Biopesticide Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hui Lu
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yawei Mu
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gong Xu
- College of Plant Protection, Shaanxi Research Center of Biopesticide Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxin Chang
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Shaanxi Research Center of Biopesticide Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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11
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Merritt HI, Sawyer N, Watkins AM, Arora PS. Anchor Residues Govern Binding and Folding of an Intrinsically Disordered Domain. ACS Chem Biol 2022; 17:2723-2727. [PMID: 36153968 PMCID: PMC9773862 DOI: 10.1021/acschembio.2c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Minimal protein mimics have yielded novel classes of protein-protein interaction inhibitors; however, this success has not been extended to targeting intrinsically disordered proteins, which represent a significant proportion of important therapeutic targets. We sought to determine the requirements for binding an intrinsically disordered region (IDR) by its native binding partner as a prelude to developing minimal protein mimics that regulate IDR interactions. Our analysis reinforces the hypothesis that IDRs reside on a fulcrum between unfolded and folded states and that a handful of key binding residues on partner protein surfaces dictate their folding. Our studies also suggest that minimal mimics of protein surfaces may not offer specific ligands for IDRs and that it would be more judicious to target the globular protein partners of IDRs.
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Affiliation(s)
- Haley I Merritt
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nicholas Sawyer
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Andrew M Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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12
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Wang Z, Ji H. Characterization of Hydrophilic α-Helical Hot Spots on the Protein-Protein Interaction Interfaces for the Design of α-Helix Mimetics. J Chem Inf Model 2022; 62:1873-1890. [PMID: 35385659 DOI: 10.1021/acs.jcim.1c01556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cooperativity index, Kc, was developed to examine the binding synergy between hot spots of the ligand-protein. For the first time, the convergence of the side-chain spatial arrangements of hydrophilic α-helical hot spots Thr, Tyr, Asp, Asn, Ser, Cys, and His in protein-protein interaction (PPI) complex structures was disclosed and quantified by developing novel clustering models. In-depth analyses revealed the driving force for the protein-protein binding conformation convergence of hydrophilic α-helical hot spots. This observation allows deriving pharmacophore models to design new mimetics for hydrophilic α-helical hot spots. A computational protocol was developed to search amino acid analogues and small-molecule mimetics for each hydrophilic α-helical hot spot. As a pilot study, diverse building blocks of commercially available nonstandard L-type α-amino acids and the phenyl ring-containing small-molecule fragments were obtained, which serve as a fragment collection to mimic hydrophilic α-helical hot spots for the improvement of binding affinity, selectivity, physicochemical properties, and synthesis accessibility of α-helix mimetics.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
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13
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Singh MK, Lakshman MK. Recent developments in the utility of saturated azaheterocycles in peptidomimetics. Org Biomol Chem 2022; 20:963-979. [PMID: 35018952 DOI: 10.1039/d1ob01329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To a large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules to modulate conformational flexibility, improve bioavailability, and fine-tune electronics, and in order to achieve potency similar to or better than that of the natural peptide ligand. This mini-review delineates recent developments, limited to the past five years, in the utility of selected saturated 3- to 6-membered heterocyclic moieties in peptidomimetic design. Also discussed is the chemistry involved in the synthesis of the azaheterocyclic scaffolds and the structural implications of the introduction of these azaheterocycles in peptide backbones as well as side chains of the peptide mimics.
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Affiliation(s)
- Manish K Singh
- Department of Science, Technology, and Mathematics, Lincoln University, 820 Chestnut Street, Jefferson City, Missouri 65101, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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14
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Modell AE, Marrone F, Panigrahi NR, Zhang Y, Arora PS. Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery. J Am Chem Soc 2022; 144:1198-1204. [PMID: 35029987 PMCID: PMC8959088 DOI: 10.1021/jacs.1c09666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Constrained peptides have proven to be a rich source of ligands for protein surfaces, but are often limited in their binding potency. Deployment of nonnatural side chains that access unoccupied crevices on the receptor surface offers a potential avenue to enhance binding affinity. We recently described a computational approach to create topographic maps of protein surfaces to guide the design of nonnatural side chains [J. Am. Chem. Soc. 2017, 139, 15560]. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator. KIX has been the subject of numerous ligand discovery strategies, but potent inhibitors of its interaction with transcription factors remain difficult to access. Although the computational approach provided a significant enhancement in the binding affinity of the peptide, fine-tuning of nonnatural side chains required an experimental screening method. Here we implement a peptide-tethering strategy to screen fragments as nonnatural side chains on conformationally defined peptides. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nihar R Panigrahi
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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15
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Su BG, Henley MJ. Drugging Fuzzy Complexes in Transcription. Front Mol Biosci 2022; 8:795743. [PMID: 34993233 PMCID: PMC8724552 DOI: 10.3389/fmolb.2021.795743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) are one of the most promising but underutilized classes of drug targets. The high degree of intrinsic disorder in both the structure and the interactions (i.e., “fuzziness”) of TFs is one of the most important challenges to be addressed in this context. Here, we discuss the impacts of fuzziness on transcription factor drug discovery, describing how disorder poses fundamental problems to the typical drug design, and screening approaches used for other classes of proteins such as receptors or enzymes. We then speculate on ways modern biophysical and chemical biology approaches could synergize to overcome many of these challenges by directly addressing the challenges imposed by TF disorder and fuzziness.
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Affiliation(s)
- Bonnie G Su
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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16
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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17
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Qin X, Chen H, Tu L, Ma Y, Liu N, Zhang H, Li D, Riedl B, Bierer D, Yin F, Li Z. Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2. J Med Chem 2021; 64:13693-13703. [PMID: 34472840 DOI: 10.1021/acs.jmedchem.1c01043] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Disrupting the interaction between HIF1α and p300 is a promising strategy to modulate the hypoxia response of tumor cells. Herein, we designed a constrained peptide inhibitor derived from the CITED2/p300 complex to disturb the HIF1α/p300 interaction. Through truncation/mutation screening and a terminal aspartic acid-stabilized strategy, a constrained peptide was constructed with outstanding biochemical/biophysical properties, especially in binding affinity, cell penetration, and serum stability. To date, our study was the first one to showcase that stabilized peptides derived from CITED2 using helix-stabilizing methods acted as a promising candidate for modulating hypoxia-inducible signaling.
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Affiliation(s)
- Xuan Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hailing Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Licheng Tu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yue Ma
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Na Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Haowei Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Shenzhen Graduate School of Tsinghua University, Shenzhen 518055, China
| | - Di Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bernd Riedl
- Department of Medicinal Chemistry, Bayer AG, Aprather Weg 18A, Wuppertal 42096, Germany
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG, Aprather Weg 18A, Wuppertal 42096, Germany
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
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18
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Umedera K, Morita T, Yoshimori A, Yamada K, Katoh A, Kouji H, Nakamura H. Synthesis of Three-Dimensional (Di)Azatricyclododecene Scaffold and Its Application to Peptidomimetics. Chemistry 2021; 27:11888-11894. [PMID: 34060167 DOI: 10.1002/chem.202101440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 11/07/2022]
Abstract
A novel sp3 carbon-rich tricyclic 3D scaffold-based peptide mimetic compound library was constructed to target protein-protein interactions. Tricyclic framework 7 was synthesized from 9-azabicyclo[3,3,1]nonan-3-one (11) via a gold(I)-catalyzed Conia-ene reaction. The electron-donating group on the pendant alkyne of cyclization precursor 12 b-e was the key to forming 6-endo-dig cyclized product 7 with complete regioselectivity. Using the synthetic strategy for regioselective construction of bridged tricyclic framework 7, a diazatricyclododecene 3D-scaffold 8 a, which enables the introduction of substituents into the scaffold to mimic amino acid side chains, was designed and synthesized. The peptide mimetics 21 a-u were synthesized via step-by-step installation of three substituents on diazatricyclododecene scaffold 8 a. Compounds 21 a-h were synthesized as α-helix peptide mimics of hydrophobic ZZxxZ and ZxxZZ sequences (Z=Leu or Phe) and subjected to cell-based assays: antiproliferative activity, HIF-1 transcriptional activity which is considered to affect cancer malignancy, and antiviral activity against rabies virus. Compound 21 a showed the strongest inhibitory activity of HIF-1 transcriptional activity (IC50 =4.1±0.8 μM), whereas compounds 21 a-g showed antiviral activity with IC50 values of 4.2-12.4 μM, suggesting that the 3D-scaffold 8 a has potential as a versatile peptide mimic skeleton.
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Affiliation(s)
- Kohei Umedera
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Taiki Morita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, 251-0012, Japan
| | - Kentaro Yamada
- Faculty of Agriculture Department of Veterinary Sciences, University of Miyazaki, Miyazaki, 889-2192, Japan.,Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan
| | - Akira Katoh
- Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan.,Institute of Advanced Medcine, Inc., Oita University, 17-20, Higashi kasuga-machi, Oita-city, Oita, 870-0037, Japan
| | - Hiroyuki Kouji
- Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan.,Institute of Advanced Medcine, Inc., Oita University, 17-20, Higashi kasuga-machi, Oita-city, Oita, 870-0037, Japan
| | - Hiroyuki Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
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19
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A. Front Mol Biosci 2021; 8:650881. [PMID: 33842550 PMCID: PMC8032985 DOI: 10.3389/fmolb.2021.650881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 12/01/2022] Open
Abstract
Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.
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Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
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21
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Mylonis I, Chachami G, Simos G. Specific Inhibition of HIF Activity: Can Peptides Lead the Way? Cancers (Basel) 2021; 13:cancers13030410. [PMID: 33499237 PMCID: PMC7865418 DOI: 10.3390/cancers13030410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Cancer cells in solid tumors often experience lack of oxygen (hypoxia), which they overcome with the help of hypoxia inducible transcription factors (HIFs). When HIFs are activated, they stimulate the expression of many genes and cause the production of proteins that help cancer cells grow and migrate even in the presence of very little oxygen. Many experiments have shown that agents that block the activity of HIFs (HIF inhibitors) can prevent growth of cancer cells under hypoxia and, subsequently, hinder formation of malignant tumors or metastases. Most small chemical HIF inhibitors lack the selectivity required for development of safe anticancer drugs. On the other hand, peptides derived from HIFs themselves can be very selective HIF inhibitors by disrupting specific associations of HIFs with cellular components that are essential for HIF activation. This review discusses the nature of available peptide HIF inhibitors and their prospects as effective pharmaceuticals against cancer. Abstract Reduced oxygen availability (hypoxia) is a characteristic of many disorders including cancer. Central components of the systemic and cellular response to hypoxia are the Hypoxia Inducible Factors (HIFs), a small family of heterodimeric transcription factors that directly or indirectly regulate the expression of hundreds of genes, the products of which mediate adaptive changes in processes that include metabolism, erythropoiesis, and angiogenesis. The overexpression of HIFs has been linked to the pathogenesis and progression of cancer. Moreover, evidence from cellular and animal models have convincingly shown that targeting HIFs represents a valid approach to treat hypoxia-related disorders. However, targeting transcription factors with small molecules is a very demanding task and development of HIF inhibitors with specificity and therapeutic potential has largely remained an unattainable challenge. Another promising approach to inhibit HIFs is to use peptides modelled after HIF subunit domains known to be involved in protein–protein interactions that are critical for HIF function. Introduction of these peptides into cells can inhibit, through competition, the activity of endogenous HIFs in a sequence and, therefore also isoform, specific manner. This review summarizes the involvement of HIFs in cancer and the approaches for targeting them, with a special focus on the development of peptide HIF inhibitors and their prospects as highly-specific pharmacological agents.
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Affiliation(s)
- Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece;
- Correspondence: (I.M.); (G.S.)
| | - Georgia Chachami
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece;
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece;
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC H4A 3T2, Canada
- Correspondence: (I.M.); (G.S.)
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22
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Shimizu T, Takahashi N, Huber VJ, Asawa Y, Ueda H, Yoshimori A, Muramatsu Y, Seimiya H, Kouji H, Nakamura H, Oguri H. Design and synthesis of 14 and 15-membered macrocyclic scaffolds exhibiting inhibitory activities of hypoxia-inducible factor 1α. Bioorg Med Chem 2020; 30:115949. [PMID: 33360196 DOI: 10.1016/j.bmc.2020.115949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022]
Abstract
Inspired by the privileged molecular skeletons of 14- and 15-membered antibiotics, we adopted a relatively unexplored synthetic approach that exploits alkaloidal macrocyclic scaffolds to generate modulators of protein-protein interactions (PPIs). As mimetics of hot-spot residues in the α-helices responsible for the transcriptional regulation, three hydrophobic sidechains were displayed on each of the four distinct macrocyclic scaffolds generating diversity of their spatial arrangements. Modular assembly of the building blocks followed by ring-closing olefin metathesis reaction and subsequent hydrogenation allowed concise and divergent synthesis of scaffolds 1-4. The 14-membered alkaloidal macrocycles 2-4 demonstrated similar inhibition of hypoxia-inducible factor (HIF)-1α transcriptional activities (IC50 between 8.7 and 10 µM), and 4 demonstrated the most potent inhibition of cell proliferation in vitro (IC50 = 12 µM against HTC116 colon cancer cell line). A docking model suggested that 4 could mimic the LLxxL motif in HIF-1α, in which the three sidechains are capable of matching the spatial arrangements of the protein hot-spot residues. Unlike most of the stapled peptides, the 14-membered alkaloidal scaffold has a similar size to the α-helix backbone and does not require additional atoms to induce α-helix mimetic structure. These experimental results underscore the potential of alkaloidal macrocyclic scaffolds featuring flexibly customizable skeletal, stereochemical, substitutional, and conformational properties for the development of non-peptidyl PPI modulators targeting α-helix-forming consensus sequences responsible for the transcriptional regulation.
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Affiliation(s)
- Takahiro Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Norihito Takahashi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Vincent J Huber
- Oita University Institute of Advanced Medicine, Inc., 17-20 Higashi kasuga-machi, Oita-shi, Oita 870-0037, Japan
| | - Yasunobu Asawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroki Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yukiko Muramatsu
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Hiroyuki Kouji
- Oita University Institute of Advanced Medicine, Inc., 17-20 Higashi kasuga-machi, Oita-shi, Oita 870-0037, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroki Oguri
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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23
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Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020; 211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
Abstract
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
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Affiliation(s)
- Sergio Algar
- Instituto de Química Médica, IQM-CSIC, Juan de La Cierva 3, 28006, Madrid, Spain
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24
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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25
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Zhang Y, Cheng Y, Zhang Z, Bai Z, Jin H, Guo X, Huang X, Li M, Wang M, Shu XS, Yuan Y, Ying Y. CDCA2 Inhibits Apoptosis and Promotes Cell Proliferation in Prostate Cancer and Is Directly Regulated by HIF-1α Pathway. Front Oncol 2020; 10:725. [PMID: 32509575 PMCID: PMC7248370 DOI: 10.3389/fonc.2020.00725] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Prostate cancer (PCa) is a major serious malignant tumor and is commonly diagnosed in older men. Identification of novel cancer-related genes in PCa is important for understanding its tumorigenesis mechanism and developing new therapies against PCa. Here, we used RNA sequencing to identify the specific genes, which are upregulated in PCa cell lines and tissues. The cell division cycle associated protein (CDCA) family, which plays a critical role in cell division and proliferation, is upregulated in the PCa cell lines of our RNA-Sequencing data. Moreover, we found that CDCA2 is overexpressed, and its protein level positively correlates with its histological grade, clinical stage, and Gleason Score. CDCA2 was further found to be upregulated and correlated with poor prognosis and patient survival in multiple cancer types in The Cancer Genome Atlas (TCGA) dataset. The functional study suggests that inhibition of CDCA2 will lead to apoptosis and lower proliferation in vitro. Silencing of CDCA2 also repressed tumor growth in vivo. Loss of CDCA2 affects several oncogenic pathways, including MAPK signaling. In addition, we further demonstrated that CDCA2 was induced in hypoxia and directly regulated by the HIF-1α/Smad3 complex. Thus, our data indicate that CDCA2 could act as an oncogene and is regulated by hypoxia and the HIF-1αpathway. CDCA2 may be a useful prognostic biomarker and potential therapeutic target for PCa.
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Affiliation(s)
- Yixiang Zhang
- Department of Urology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Yingduan Cheng
- Department of Translational Molecular Medicine, Saint John's Health Center, John Wayne Cancer Institute, PHS, Santa Monica, CA, United States
| | - Zhaoxia Zhang
- Department of Pediatrics, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Zhongyuan Bai
- Department of Urology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Hongtao Jin
- Department of Pathology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Xiaojing Guo
- Department of Pathology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Xiaoyan Huang
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen University, Shenzhen, China
| | - Meiqi Li
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen University, Shenzhen, China
| | - Maolin Wang
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen University, Shenzhen, China
| | - Xing-Sheng Shu
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen University, Shenzhen, China
| | - Yeqing Yuan
- Department of Urology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Ying Ying
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen University, Shenzhen, China
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26
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Wang Z, Ji H. Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7. J Med Chem 2019; 62:9906-9917. [PMID: 31593458 DOI: 10.1021/acs.jmedchem.9b01324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated protein-protein interaction (PPI) complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. These provide the foundation for designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivities between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 1 was disclosed. The close positioning of this small molecule to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule inhibitors for α-helix-mediated PPIs.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
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27
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Lam GC, Sefton MV. Hypoxia-Inducible Factor Drives Vascularization of Modularly Assembled Engineered Tissue. Tissue Eng Part A 2019; 25:1127-1136. [PMID: 30585759 DOI: 10.1089/ten.tea.2018.0294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
IMPACT STATEMENT Using two inhibitory methods, we demonstrated that hypoxia-inducible factor (HIF) plays an important role in vascularizing and oxygenating modularly-assembled engineered tissues. Each inhibitory technique elucidated a different mechanism by which this occurred. Whereas systemic inhibition negatively impacted early recruitment of host-derived cells, genetic inhibition in grafted endothelial cells was detrimental to their survival. Taken together, our study suggests that methods of HIF-mediated mechanisms could be harnessed to tune the extent and rate of vascularization in engineered tissue constructs.
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Affiliation(s)
- Gabrielle C Lam
- 1Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Michael V Sefton
- 1Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,2Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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28
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Revuelto A, Ruiz-Santaquiteria M, de Lucio H, Gamo A, Carriles AA, Gutiérrez KJ, Sánchez-Murcia PA, Hermoso JA, Gago F, Camarasa MJ, Jiménez-Ruiz A, Velázquez S. Pyrrolopyrimidine vs Imidazole-Phenyl-Thiazole Scaffolds in Nonpeptidic Dimerization Inhibitors of Leishmania infantum Trypanothione Reductase. ACS Infect Dis 2019; 5:873-891. [PMID: 30983322 DOI: 10.1021/acsinfecdis.8b00355] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Disruption of protein-protein interactions of essential oligomeric enzymes by small molecules represents a significant challenge. We recently reported some linear and cyclic peptides derived from an α-helical region present in the homodimeric interface of Leishmania infantum trypanothione reductase ( Li-TryR) that showed potent effects on both dimerization and redox activity of this essential enzyme. Here, we describe our first steps toward the design of nonpeptidic small-molecule Li-TryR dimerization disruptors using a proteomimetic approach. The pyrrolopyrimidine and the 5-6-5 imidazole-phenyl-thiazole α-helix-mimetic scaffolds were suitably decorated with substituents that could mimic three key residues (K, Q, and I) of the linear peptide prototype (PKIIQSVGIS-Nle-K-Nle). Extensive optimization of previously described synthetic methodologies was required. A library of 15 compounds bearing different hydrophobic alkyl and aromatic substituents was synthesized. The imidazole-phenyl-thiazole-based analogues outperformed the pyrrolopyrimidine-based derivatives in both inhibiting the enzyme and killing extracellular and intracellular parasites in cell culture. The most active imidazole-phenyl-thiazole compounds 3e and 3f inhibit Li-TryR and prevent growth of the parasites at low micromolar concentrations similar to those required by the peptide prototype. The intrinsic fluorescence of these compounds inside the parasites visually demonstrates their good permeability in comparison with previous peptide-based Li-TryR dimerization disruptors.
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Affiliation(s)
| | | | - Héctor de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Ana Gamo
- Instituto de Química Médica (IQM-CSIC), Madrid E-28006, Spain
| | - Alejandra A. Carriles
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Kilian Jesús Gutiérrez
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Pedro A. Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | | | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
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29
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Iegre J, Brear P, Baker DJ, Tan YS, Atkinson EL, Sore HF, O' Donovan DH, Verma CS, Hyvönen M, Spring DR. Efficient development of stable and highly functionalised peptides targeting the CK2α/CK2β protein-protein interaction. Chem Sci 2019; 10:5056-5063. [PMID: 31183056 PMCID: PMC6530537 DOI: 10.1039/c9sc00798a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be applied to many PPI targets and has the potential to ease the study of PPIs by efficiently providing access to functionalised peptides.
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Paul Brear
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David J Baker
- Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
| | - Eleanor L Atkinson
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
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30
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Taechalertpaisarn J, Lyu RL, Arancillo M, Lin CM, Perez LM, Ioerger TR, Burgess K. Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis. Org Biomol Chem 2019; 17:3267-3274. [PMID: 30847453 PMCID: PMC6863600 DOI: 10.1039/c9ob00204a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An active segment of the research community designing small molecules ("minimalist mimics" of peptide fragments) to interfere with protein-protein interactions have based their studies on an implicit hypothesis. Here we refer to this as the Secondary Structure Hypothesis, that might be defined as, "If a small molecule can orient amino acid side-chains in directions that resemble side-chains of the parent secondary structure at the interface, then that small molecule is a candidate to perturb the protein-protein interaction". Rigorous tests of this hypothesis require co-crystallization of minimalist mimics with protein receptors, and comparison of the bound conformations with the interface secondary structures they were designed to resemble. Unfortunately, to the best of our knowledge, there is no such analysis in the literature, and it is unlikely that enough examples will emerge in the near future to test the hypothesis. Research described here was designed to challenge this hypothesis from a different perspective. In a previous study, preferred conformations of a series of novel minimalist mimics were simulated then systematically overlaid on >240 000 crystallographically characterized protein-protein interfaces. Select data from that overlay procedure revealed chemotypes that overlay side chains on various PPI interfaces with a relatively high frequency of occurrence. The first aim of this work was to determine if good secondary structure mimics overlay frequently on PPI interfaces. The second aim of this work was to determine if overlays of preferred conformers at interface regions involve secondary structures. Thus situations where these conformations overlaid extremely well on PPI interfaces were analyzed to determine if secondary structures featured the PPI regions where these molecules overlaid in the previous study. Combining conclusions from these two studies enabled us to formulate a hypothesis that is complementary to the Secondary Structure Hypothesis, but, unlike this, is supported by abundant data. We call this the Interface Mimicry Hypothesis.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
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31
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Wellhöfer I, Frydenvang K, Kotesova S, Christiansen AM, Laursen JS, Olsen CA. Functionalized Helical β-Peptoids. J Org Chem 2019; 84:3762-3779. [DOI: 10.1021/acs.joc.9b00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Isabelle Wellhöfer
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Simona Kotesova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Andreas M. Christiansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jonas S. Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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32
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Wang D, Li W, Zhao R, Chen L, Liu N, Tian Y, Zhao H, Xie M, Lu F, Fang Q, Liang W, Yin F, Li Z. Stabilized Peptide HDAC Inhibitors Derived from HDAC1 Substrate H3K56 for the Treatment of Cancer Stem-Like Cells In Vivo. Cancer Res 2019; 79:1769-1783. [PMID: 30842103 DOI: 10.1158/0008-5472.can-18-1421] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/25/2018] [Accepted: 02/28/2019] [Indexed: 11/16/2022]
Abstract
FDA-approved HDAC inhibitors exhibit dose-limiting adverse effects; thus, we sought to improve the therapeutic windows for this class of drugs. In this report, we describe a new class of peptide-based HDAC inhibitors derived from the HDAC1-specific substrate H3K56 with improved nonspecific toxicity compared with traditional small-molecular inhibitors. We showed that our designed peptides exerted superior antiproliferation effects on cancer stem-like cells with minimal toxicity to normal cells compared with the small-molecular inhibitor SAHA, which showed nonspecific toxicity to normal and cancer cells. These peptide inhibitors also inactivated cellular HDAC1 and HDAC6 and disrupted the formation of the HDAC1, LSD1, and CoREST complex. In ovarian teratocarcinoma (PA-1) and testicular embryonic carcinoma (NTERA-2) cell xenograft animal models (5 mice/group, 50 mg/kg, every other day, intraperitoneal injection), these peptides inhibited tumor growth by 80% to 90% with negligible organ (heart, liver, spleen, lung, kidney, brain) lesions. These results represent the first attempt to design chemically stabilized peptide inhibitors to investigate HDAC inhibition in cancer stem-like cells. These novel peptide inhibitors have significantly enhanced therapeutic window and offer promising opportunities for cancer therapy. SIGNIFICANCE: Selective antiproliferative effects of stabilized peptide HDAC inhibitors toward cancer stem-like cells provide a therapeutic alternative that avoids high nonspecific toxicity of current drugs.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/8/1769/F1.large.jpg.
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Affiliation(s)
- Dongyuan Wang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Rongtong Zhao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Longjian Chen
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Na Liu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yuan Tian
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Hui Zhao
- Division of Life Science, Clarivate Analytics, Beijing, China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Fei Lu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Qi Fang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Wei Liang
- Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Feng Yin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School; State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China.
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33
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Yu Z, Liu Y, Zhu J, Han J, Tian X, Han W, Zhao L. Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300. J Biomol Struct Dyn 2019; 38:1-12. [DOI: 10.1080/07391102.2019.1580616] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jiarui Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Xiaopian Tian
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Li Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
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34
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Berlow RB, Martinez-Yamout MA, Dyson HJ, Wright PE. Role of Backbone Dynamics in Modulating the Interactions of Disordered Ligands with the TAZ1 Domain of the CREB-Binding Protein. Biochemistry 2019; 58:1354-1362. [PMID: 30775911 DOI: 10.1021/acs.biochem.8b01290] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The intrinsically disordered transactivation domains of HIF-1α and CITED2 compete for binding of the TAZ1 domain of the CREB-binding protein by a unidirectional allosteric mechanism involving direct competition for shared binding sites, ternary complex formation, and TAZ1 conformational changes. To gain insight into the mechanism by which CITED2 displaces HIF-1α from TAZ1, we used nuclear magnetic resonance spin relaxation methods to obtain an atomic-level description of the picosecond to nanosecond backbone dynamics that contribute to TAZ1 binding and competition. We show that HIF-1α and CITED2 adopt different dynamics in their complexes with TAZ1, with flexibility observed for HIF-1α in regions that would maintain accessibility for CITED2 to bind to TAZ1 and facilitate subsequent HIF-1α dissociation. In contrast, critical regions of CITED2 adopt a rigid structure in its complex with TAZ1, minimizing the ability of HIF-1α to compete for binding. We also find that TAZ1, previously thought to be a rigid scaffold for binding of disordered protein ligands, displays altered backbone dynamics in its various bound states. TAZ1 is more rigid in its CITED2-bound state than in its free state or in complex with HIF-1α, with increased rigidity observed not only in the CITED2 binding site but also in regions of TAZ1 that undergo conformational changes between the HIF-1α- and CITED2-bound structures. Taken together, these data suggest that backbone dynamics in TAZ1, as well as in the HIF-1α and CITED2 ligands, play a role in modulating the occupancy of TAZ1 and highlight the importance of characterizing both binding partners in molecular interactions.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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36
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Hegedus Z, Grison CM, Miles JA, Rodriguez-Marin S, Warriner SL, Webb ME, Wilson AJ. A catalytic protein-proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S. Chem Sci 2019; 10:3956-3962. [PMID: 31015935 PMCID: PMC6461108 DOI: 10.1039/c9sc00374f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 12/27/2022] Open
Abstract
Foldamers are abiotic molecules that mimic the ability of bio-macromolecules to adopt well-defined and organised secondary, tertiary or quaternary structure. Such templates have enabled the generation of defined architectures which present structurally defined surfaces that can achieve molecular recognition of diverse and complex targets. Far less explored is whether this mimicry of nature can extend to more advanced functions of biological macromolecules such as the generation and activation of catalytic function. In this work, we adopt a novel replacement strategy whereby a segment of protein structure (the S-peptide from RNase S) is replaced by a foldamer that mimics an α-helix. The resultant prosthetic replacement forms a non-covalent complex with the S-protein leading to restoration of catalytic function, despite the absence of a key catalytic residue. Thus this functional protein-proteomimetic complex provides proof that significant segments of protein can be replaced with non-natural building blocks that may, in turn, confer advantageous properties.
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Affiliation(s)
- Zsofia Hegedus
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Claire M Grison
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Silvia Rodriguez-Marin
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Michael E Webb
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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37
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Li J, Xi W, Li X, Sun H, Li Y. Advances in inhibition of protein-protein interactions targeting hypoxia-inducible factor-1 for cancer therapy. Bioorg Med Chem 2019; 27:1145-1158. [PMID: 30819620 DOI: 10.1016/j.bmc.2019.01.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/23/2022]
Abstract
Hypoxia is a common characteristic of many types of solid tumors and is associated with tumor propagation, malignant progression, and resistance to anti-cancer therapy. HIF-1 pathway is one of the survival pathways activated in tumor in response to hypoxia. In hypoxic condition, hypoxia-inducible factor-1α (HIF-1α) is stabilized and translocated into nucleus where it forms heterodimer with HIF-1β and regulates the expression of a plethora of genes involved in different processes, such as cell proliferation, differentiation, apoptosis, vascularization/angiogenesis, tumor invasion and metastasis. Recruitment of co-activator p300 or CBP to HIF-1α is critical to the transactivation activity of HIF-1 dimer, therefore, small molecules which can block the dimerization of HIF-1α and HIF-1β or inhibit the interaction between HIF-1α and p300 can function as inhibitors of HIF-1 and have the potential to be developed as novel therapies for the treatment of human cancers. In this review, recent progress of small molecular inhibitors of protein-protein interactions targeting HIF-1 is summarized, the mechanism of functions of these compounds and their potential usage as anti-cancer agents have also been discussed.
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Affiliation(s)
- Jia Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Wanlin Xi
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaofang Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
| | - Yuyan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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38
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Li Z, You Q, Zhang X. Small-Molecule Modulators of the Hypoxia-Inducible Factor Pathway: Development and Therapeutic Applications. J Med Chem 2019; 62:5725-5749. [DOI: 10.1021/acs.jmedchem.8b01596] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
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39
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40
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Breen ME, Mapp AK. Modulating the masters: chemical tools to dissect CBP and p300 function. Curr Opin Chem Biol 2018; 45:195-203. [PMID: 30025258 DOI: 10.1016/j.cbpa.2018.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 01/07/2023]
Abstract
Dysregulation of transcription is found in nearly every human disease, and as a result there has been intense interest in developing new therapeutics that target regulators of transcription. CREB binding protein (CBP) and its paralogue p300 are attractive targets due to their function as `master coactivators'. Although inhibitors of several CBP/p300 domains have been identified, the selectivity of many of these compounds has remained underexplored. Here, we review recent successes in the development of chemical tools targeting several CBP/p300 domains with selectivity acceptable for use as chemical probes. Additionally, we highlight recent studies which have used these probes to expand our understanding of interdomain interactions and differential coactivator usage.
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Affiliation(s)
- Meghan E Breen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA.
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41
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Rogers JM, Kwon S, Dawson SJ, Mandal PK, Suga H, Huc I. Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids. Nat Chem 2018; 10:405-412. [PMID: 29556052 DOI: 10.1038/s41557-018-0007-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/24/2017] [Indexed: 11/09/2022]
Abstract
Translation, the mRNA-templated synthesis of peptides by the ribosome, can be manipulated to incorporate variants of the 20 cognate amino acids. Such approaches for expanding the range of chemical entities that can be produced by the ribosome may accelerate the discovery of molecules that can perform functions for which poorly folded, short peptidic sequences are ill suited. Here, we show that the ribosome tolerates some artificial helical aromatic oligomers, so-called foldamers. Using a flexible tRNA-acylation ribozyme-flexizyme-foldamers were attached to tRNA, and the resulting acylated tRNAs were delivered to the ribosome to initiate the synthesis of non-cyclic and cyclic foldamer-peptide hybrid molecules. Passing through the ribosome exit tunnel requires the foldamers to unfold. Yet foldamers encode sufficient folding information to influence the peptide structure once translation is completed. We also show that in cyclic hybrids, the foldamer portion can fold into a helix and force the peptide segment to adopt a constrained and stretched conformation.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sunbum Kwon
- CBMN Laboratory, Univ. Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Simon J Dawson
- CBMN Laboratory, Univ. Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Pradeep K Mandal
- CBMN Laboratory, Univ. Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ivan Huc
- CBMN Laboratory, Univ. Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, Pessac, France. .,Department of Pharmacy, Ludwig-Maximilians-Universität, München, Germany.
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42
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Arrata I, Barnard A, Tomlinson DC, Wilson AJ. Interfacing native and non-native peptides: using Affimers to recognise α-helix mimicking foldamers. Chem Commun (Camb) 2018; 53:2834-2837. [PMID: 28217789 DOI: 10.1039/c6cc09395g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Selection methods are used to identify Affimers that recognise α-helix mimicking N-alkylated aromatic oligoamides thus demonstrating foldamer and natural α-amino acid codes are compatible.
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Affiliation(s)
- Irene Arrata
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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43
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Michaelides MR, Kluge A, Patane M, Van Drie JH, Wang C, Hansen TM, Risi RM, Mantei R, Hertel C, Karukurichi K, Nesterov A, McElligott D, de Vries P, Langston JW, Cole PA, Marmorstein R, Liu H, Lasko L, Bromberg KD, Lai A, Kesicki EA. Discovery of Spiro Oxazolidinediones as Selective, Orally Bioavailable Inhibitors of p300/CBP Histone Acetyltransferases. ACS Med Chem Lett 2018; 9:28-33. [PMID: 29348807 PMCID: PMC5767893 DOI: 10.1021/acsmedchemlett.7b00395] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022] Open
Abstract
![]()
p300
and its paralog CBP can acetylate histones and other proteins
and have been implicated in a number of diseases characterized by
aberrant gene activation, such as cancer. A novel, highly selective,
orally bioavailable histone acetyltransferase (HAT) domain inhibitor
has been identified through virtual ligand screening and subsequent
optimization of a unique hydantoin screening hit. Conformational restraint
in the form of a spirocyclization followed by substitution with a
urea led to a significant improvement in potency. Replacement of the
hydantoin moiety with an oxazolidinedione followed by fluoro substitution
led to A-485, which exhibits potent cell activity, low
clearance, and high oral bioavailability.
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Affiliation(s)
| | - Arthur Kluge
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Michael Patane
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - John H. Van Drie
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Ce Wang
- BioDuro, No. 29 Life
Science Park Road, Changping District, Beijing 102206, P. R. China
| | - T. Matthew Hansen
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Roberto M. Risi
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Robert Mantei
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Carmen Hertel
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Kannan Karukurichi
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Alexandre Nesterov
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - David McElligott
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Peter de Vries
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - J. William Langston
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Philip A. Cole
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Ronen Marmorstein
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
| | - Hong Liu
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Loren Lasko
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenneth D. Bromberg
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Albert Lai
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Edward A. Kesicki
- Acylin Therapeutics, Inc., 1616
Eastlake Avenue E, Suite 200, Seattle, Washington 98012, United States
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44
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Jiang J, Xia Y, Liang Y, Yang M, Zeng W, Zeng X. miR-190a-5p participates in the regulation of hypoxia-induced pulmonary hypertension by targeting KLF15 and can serve as a biomarker of diagnosis and prognosis in chronic obstructive pulmonary disease complicated with pulmonary hypertension. Int J Chron Obstruct Pulmon Dis 2018; 13:3777-3790. [PMID: 30538440 PMCID: PMC6251363 DOI: 10.2147/copd.s182504] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE miR-190a-5p expression alters dynamically in response to hypoxia. However, the role of miR-190a-5p expression in hypoxia-induced pulmonary hypertension (PH) remains unclear. We sought to correlate the miR-190a-5p expression levels with the severity, diagnosis, and prognosis of PH in relation to chronic obstructive pulmonary disease (COPD-PH). Additionally, we evaluated the effect of miR-190a-5p through in vitro experiments on human pulmonary endothelial cells (HPECs) that were exposed to hypoxia and in vivo experiments using an animal model of hypoxia-induced PH. METHODS Circulating miR-190a-5p levels were measured from 73 patients with PH and 32 healthy controls through quantitative real-time PCR. The levels of miR-190a-5p and the expression of Krüppel-like factor 15 (KLF15) were analyzed in HPECs that were exposed to hypoxia, and the effects of antagomir-190a-5p in mice with chronic hypoxia-induced PH were tested. Target gene analysis was performed by Western blot and luciferase assay. RESULTS The miR-190a-5p level was significantly higher in patients with COPD-PH than in the healthy controls. Higher miR-190a-5p levels were associated with a greater severity of COPD-PH. In vitro experiments on HPECs showed that exposure to hypoxia increased the miR-190a-5p levels significantly. KLF15 was validated as a target of miR-190a-5p. Transfection with miR-190a-5p mimicked inhibition of KLF15 expression in HPECs. In the mouse model of PH, antagomir-190a-5p reduced right ventricular systolic pressure and enhanced the KLF15 expression levels in lung tissue. CONCLUSION miR-190a-5p regulates hypoxia-induced PH by targeting KLF15. The circulating levels of miR-190a-5p correlate with the severity of COPD-PH, thereby confirming the diagnostic and prognostic value of this parameter in COPD-PH.
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MESH Headings
- Adult
- Aged
- Animals
- Biomarkers/metabolism
- Case-Control Studies
- Cell Hypoxia
- Cells, Cultured
- Disease Models, Animal
- Endothelial Cells/metabolism
- Female
- Gene Expression Regulation
- Humans
- Hypertension, Pulmonary/etiology
- Hypertension, Pulmonary/genetics
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/physiopathology
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- Lung/blood supply
- Male
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Middle Aged
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Predictive Value of Tests
- Prognosis
- Prospective Studies
- Pulmonary Disease, Chronic Obstructive/complications
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/physiopathology
- Severity of Illness Index
- Signal Transduction
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Affiliation(s)
- Jing Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yimeng Xia
- Department of Anesthesiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Yi Liang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Meiling Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Wen Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Xiaocong Zeng
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China,
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45
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Konkankit CC, Marker SC, Knopf KM, Wilson JJ. Anticancer activity of complexes of the third row transition metals, rhenium, osmium, and iridium. Dalton Trans 2018; 47:9934-9974. [DOI: 10.1039/c8dt01858h] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A summary of recent developments on the anticancer activity of complexes of rhenium, osmium, and iridium is described.
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Affiliation(s)
| | - Sierra C. Marker
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Kevin M. Knopf
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Justin J. Wilson
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
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46
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Cheloha RW, Chen B, Kumar NN, Watanabe T, Thorne RG, Li L, Gardella TJ, Gellman SH. Development of Potent, Protease-Resistant Agonists of the Parathyroid Hormone Receptor with Broad β Residue Distribution. J Med Chem 2017; 60:8816-8833. [PMID: 29064243 DOI: 10.1021/acs.jmedchem.7b00876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The parathyroid hormone receptor 1 (PTHR1) is a member of the B-family of GPCRs; these receptors are activated by long polypeptide hormones and constitute targets of drug development efforts. Parathyroid hormone (PTH, 84 residues) and PTH-related protein (PTHrP, 141 residues) are natural agonists of PTHR1, and an N-terminal fragment of PTH, PTH(1-34), is used clinically to treat osteoporosis. Conventional peptides in the 20-40-mer length range are rapidly degraded by proteases, which may limit their biomedical utility. We have used the PTHR1-ligand system to explore the impact of broadly distributed replacement of α-amino acid residues with β-amino acid residues on susceptibility to proteolysis and agonist activity. This effort led us to identify new PTHR1 agonists that contain α → β replacements throughout their sequences, manifest potent agonist activity in cellular assays, and display remarkable resistance to proteolysis, in cases remaining active after extended exposure to simulated gastric fluid. The strategy we have employed suggests a path toward identifying protease-resistant agonists of other B-family GPCRs.
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Affiliation(s)
- Ross W Cheloha
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Niyanta N Kumar
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Tomoyuki Watanabe
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Robert G Thorne
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States.,Clinical Neuroengineering Training Program, University of Wisconsin-Madison Biomedical Engineering , Engineering Centers Building, Room 2120, 1550 Engineering Drive, Madison Wisconsin 53706, United States.,Neuroscience Training Program & Center for Neuroscience, Wisconsin Institutes for Medical Research II , Rooms 9531 and 9533, 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Cellular and Molecular Pathology Graduate Training Program, UW Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison , 1685 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Thomas J Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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47
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Tsigelny IF, Mukthavaram R, Kouznetsova VL, Chao Y, Babic I, Nurmemmedov E, Pastorino S, Jiang P, Calligaris D, Agar N, Scadeng M, Pingle SC, Wrasidlo W, Makale MT, Kesari S. Multiple spatially related pharmacophores define small molecule inhibitors of OLIG2 in glioblastoma. Oncotarget 2017; 8:22370-22384. [PMID: 26517684 PMCID: PMC5410230 DOI: 10.18632/oncotarget.5633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/14/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factors (TFs) are a major class of protein signaling molecules that play key cellular roles in cancers such as the highly lethal brain cancer—glioblastoma (GBM). However, the development of specific TF inhibitors has proved difficult owing to expansive protein-protein interfaces and the absence of hydrophobic pockets. We uniquely defined the dimerization surface as an expansive parental pharmacophore comprised of several regional daughter pharmacophores. We targeted the OLIG2 TF which is essential for GBM survival and growth, we hypothesized that small molecules able to fit each subpharmacophore would inhibit OLIG2 activation. The most active compound was OLIG2 selective, it entered the brain, and it exhibited potent anti-GBM activity in cell-based assays and in pre-clinical mouse orthotopic models. These data suggest that (1) our multiple pharmacophore approach warrants further investigation, and (2) our most potent compounds merit detailed pharmacodynamic, biophysical, and mechanistic characterization for potential preclinical development as GBM therapeutics.
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Affiliation(s)
- Igor F Tsigelny
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Rajesh Mukthavaram
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ying Chao
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ivan Babic
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | | | - Sandra Pastorino
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Pengfei Jiang
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - David Calligaris
- Harvard Medical School, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathalie Agar
- Harvard Medical School, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Miriam Scadeng
- FMRI Research Center, Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Sandeep C Pingle
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Milan T Makale
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Santosh Kesari
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Current Address: John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
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48
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Ultsch M, Braisted A, Maun HR, Eigenbrot C. 3-2-1: Structural insights from stepwise shrinkage of a three-helix Fc-binding domain to a single helix. Protein Eng Des Sel 2017; 30:619-625. [PMID: 28475752 PMCID: PMC5914316 DOI: 10.1093/protein/gzx029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/07/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
The well-studied B-domain from Staphylococcal protein A is a 59 amino acid three-helix bundle that binds the Fc portion of IgG with a dissociation constant of ~35 nM. The B-domain variant bearing a Gly to Ala mutation (=Z-domain) has been the subject of efforts to minimize a domain's size while retaining its function. We report X-ray crystallographic characterization of three steps in such a process using complexes with Fc: the full three-helix Z-domain, a 34 amino acid two-helix version called Z34C and a 13 amino acid single helix stabilized with an exo-helix tether, called LH1.
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Affiliation(s)
- M Ultsch
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA
| | - A Braisted
- Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - H R Maun
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA
| | - C Eigenbrot
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA
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49
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Sawyer N, Watkins AM, Arora PS. Protein Domain Mimics as Modulators of Protein-Protein Interactions. Acc Chem Res 2017; 50:1313-1322. [PMID: 28561588 DOI: 10.1021/acs.accounts.7b00130] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Andrew M. Watkins
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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50
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Hypoxia inducible factor (HIF) as a model for studying inhibition of protein-protein interactions. Chem Sci 2017; 8:4188-4202. [PMID: 28878873 PMCID: PMC5576430 DOI: 10.1039/c7sc00388a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022] Open
Abstract
The state of the art in identifying protein–protein interaction inhibitors of hypoxia inducible factor – a promising target for anticancer drug design – is described.
The modulation of protein–protein interactions (PPIs) represents a major challenge in modern chemical biology. Current approaches (e.g. high-throughput screening, computer aided ligand design) are recognised as having limitations in terms of identification of hit matter. Considerable success has been achieved in terms of developing new approaches to PPI modulator discovery using the p53/hDM2 and Bcl-2 family of PPIs. However these important targets in oncology might be considered as “low-hanging-fruit”. Hypoxia inducible factor (HIF) is an emerging, but not yet fully validated target for cancer chemotherapy. Its role is to regulate the hypoxic response and it does so through a plethora of protein–protein interactions of varying topology, topography and complexity: its modulation represents an attractive approach to prevent development of new vasculature by hypoxic tumours.
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Affiliation(s)
- George M Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Adam Nelson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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