1
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Wang L, Kumar R, Winblad B, Pavlov PF. Structure-based discovery of small molecule inhibitors of FKBP51-Hsp90 protein-protein interaction. Eur J Med Chem 2024; 270:116356. [PMID: 38579621 DOI: 10.1016/j.ejmech.2024.116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024]
Abstract
The heat shock protein 90 kDa (Hsp90) molecular chaperone machinery is responsible for the folding and activation of hundreds of important clients such as kinases, steroid hormone receptors, transcription factors, etc. This process is dynamically regulated in an ATP-dependent manner by Hsp90 co-chaperones including a group of tetratricopeptide (TPR) motif proteins that bind to the C-terminus of Hsp90. Among these TPR containing co-chaperones, FK506-binding protein 51 kDa (FKBP51) is reported to play an important role in stress-related pathologies, psychiatric disorders, Alzheimer's disease, and cancer, making FKBP51-Hsp90 interaction a potential therapeutic target. In this study, we report identification of potent and selective inhibitors of FKBP51-Hsp90 protein-protein interaction using a structure-based virtual screening approach. Upon in vitro evaluation, the identified hits show a considerable degree of selectivity towards FKBP51 over other TPR proteins, particularly for highly homologous FKBP52. Tyr355 of FKBP51 emerged as an important contributor to inhibitor's specificity. Additionally, we demonstrate the impact of these inhibitors on cellular energy metabolism, and neurite outgrowth, which are subjects of FKBP51 regulation. Overall, the results from this study highlight a novel pharmacological approach towards regulation of FKBP51 function and more generally, Hsp90 function via its interaction with TPR co-chaperones.
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Affiliation(s)
- Lisha Wang
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden.
| | - Rajnish Kumar
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), 221005, Varanasi, India.
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Theme Inflammation and Aging, Karolinska University Hospital, 14186, Huddinge, Sweden
| | - Pavel F Pavlov
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden
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2
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Pinard M, Moursli A, Coulombe B. Drugs targeting the particle for arrangement of quaternary structure (PAQosome) and protein complex assembly. Expert Opin Drug Discov 2024; 19:57-71. [PMID: 37840283 DOI: 10.1080/17460441.2023.2267974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The PAQosome is a 12-subunit complex that acts as a co-factor of the molecular chaperones HSP90 and HSP70. This co-chaperone has been shown to participate in assembly and maturation of several protein complexes, including nuclear RNA polymerases, RNA processing factors, the ribosome, PIKKs, and others. Subunits of the PAQosome, adaptors, and clients have been reported to be involved in various diseases, making them interesting targets for drug discovery. AREA COVERED In this review, the authors cover the detailed mechanisms of PAQosome and chaperone function. Specifically, the authors summarize the status of the PAQosome and some related chaperones and co-chaperones as candidate targets for drug discovery. Indeed, a number of compounds are currently being tested for the development of treatments against diseases, such as cancers and neurodegenerative conditions. EXPERT OPINION Searching for new drugs targeting the PAQosome requires a better understanding of PAQosome subunit interactions and the discovery of new interaction partners. Thus, PAQosome subunit crystallization is an important experiment to initiate virtual screening against new target and the development of in silico tools such as AlphaFold-multimer could accelerate the search for new interaction partner and determine more rapidly the interaction pocket needed for virtual drug screening.
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Affiliation(s)
- Maxime Pinard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Asmae Moursli
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
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3
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Liao YT, Du XY, Wang M, Zheng CX, Li D, Chen CH, Li RT, Shao LD. A silicon-containing aryl/penta-1,4-dien-3-one/amine hybrid exhibits antiproliferative effects on breast cancer cells by targeting the HSP90 C-terminus without inducing heat-shock response. RSC Med Chem 2023; 14:2625-2639. [PMID: 38107168 PMCID: PMC10718586 DOI: 10.1039/d3md00431g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/11/2023] [Indexed: 12/19/2023] Open
Abstract
A pharmacophore-hybridized strategy based on previously reported HSP90 C-terminal inhibitors was utilized to prepare 32 aryl/penta-1,4-dien-3-one/amine hybrids. Among them, a silicon-containing compound 1z exhibited remarkable broad-spectrum antiproliferative effects on various human breast cancer cell lines. Through fluorescence polarization and AlphaScreen-based assays, we demonstrated that 1z specifically inhibited the HSP90 C-terminus without affecting HSP90 N-terminus. Furthermore, 1z effectively inhibited the HSP90 C-terminus without inducing heat-shock response (HSR), leading to the degradation of its client proteins HER2, pAKT, AKT, and CDK4, causing G1 arrest of MCF-7 and SKBr3 cells, and ultimately contributing to apoptosis of these cells through caspase-3, caspase-8, and caspase-9 activation. Additionally, the penta-1,4-dien-3-one linker in the hybrid, a large bulky lipophilic substitution in the aryl fragment at the 3'-site, and the presence of N-methylpiperazine as the amine fragment were identified as crucial factors that significantly contributed to the observed antiproliferative activity through structure-activity relationship (SAR) analysis. Lastly, we found that 1z exhibited superior thermostability compared to vibsanin B derivatives and good in vitro metabolic stability in simulated intestinal fluid, representing one of the few reported silicon-containing HSP90 C-terminal inhibitors.
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Affiliation(s)
- Yu-Ting Liao
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
| | - Xin-Ye Du
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
- Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming 650500 China
| | - Mei Wang
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
| | - Chun-Xia Zheng
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
| | - Dashan Li
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
| | - Chuan-Huizi Chen
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
| | - Rong-Tao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology Kunming 650500 China
| | - Li-Dong Shao
- Yunnan Key Laboratory of Southern Medicinal Resources, School of Chinese Materia Medica, Yunnan University of Chinese Medicine Kunming 650500 China
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4
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Xiang Y, Liu X, Sun Q, Liao K, Liu X, Zhao Z, Feng L, Liu Y, Wang B. The development of cancers research based on mitochondrial heat shock protein 90. Front Oncol 2023; 13:1296456. [PMID: 38098505 PMCID: PMC10720920 DOI: 10.3389/fonc.2023.1296456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondrial heat shock protein 90 (mtHsp90), including Tumor necrosis factor receptor-associated protein 1 (TRAP1) and Hsp90 translocated from cytoplasm, modulating cellular metabolism and signaling pathways by altering the conformation, activity, and stability of numerous client proteins, and is highly expressed in tumors. mtHsp90 inhibition results in the destabilization and eventual degradation of its client proteins, leading to interference with various tumor-related pathways and efficient control of cancer cell development. Among these compounds, gamitrinib, a specific mtHsp90 inhibitor, has demonstrated its safety and efficacy in several preclinical investigations and is currently undergoing evaluation in clinical trials. This review aims to provide a comprehensive overview of the present knowledge pertaining to mtHsp90, encompassing its structure and function. Moreover, our main emphasis is on the development of mtHsp90 inhibitors for various cancer therapies, to present a thorough overview of the recent pre-clinical and clinical advancements in this field.
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Affiliation(s)
- Yuchu Xiang
- West China Hospital of Sichuan University, Sichuan University, Chengdu, China
| | - Xudong Liu
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Qi Sun
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, Centre for Safe Medication Practice and Research, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaohan Liu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Zihui Zhao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lishuang Feng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yan Liu
- Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Bo Wang
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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5
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Amatya E, Blagg BSJ. Recent advances toward the development of Hsp90 C-terminal inhibitors. Bioorg Med Chem Lett 2023; 80:129111. [PMID: 36549397 PMCID: PMC9869726 DOI: 10.1016/j.bmcl.2022.129111] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Heat shock protein 90 (Hsp90) is a dynamic protein which serves to ensure proper folding of nascent client proteins, regulate transcriptional responses to environmental stress and guide misfolded and damaged proteins to destruction via ubiquitin proteasome pathway. Recent advances in the field of Hsp90 have been made through development of isoform selective inhibitors, Hsp90 C-terminal inhibitors and disruption of protein-protein interactions. These approaches have led to alleviation of adverse off-target effects caused by pan-inhibition of Hsp90 using N-terminal inhibitors. In this review, we provide an overview of relevant advances on targeting the Hsp90 C-terminal Domain (CTD) and the development of Hsp90 C-terminal inhibitors (CTIs) since 2015.
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Affiliation(s)
- Eva Amatya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN 46556, USA.
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6
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Hsp70/Hsp90 Organising Protein (Hop): Coordinating Much More than Chaperones. Subcell Biochem 2023; 101:81-125. [PMID: 36520304 DOI: 10.1007/978-3-031-14740-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Hsp70/Hsp90 organising protein (Hop, also known as stress-inducible protein 1/STI1/STIP1) has received considerable attention for diverse cellular functions in both healthy and diseased states. There is extensive evidence that intracellular Hop is a co-chaperone of the major chaperones Hsp70 and Hsp90, playing an important role in the productive folding of Hsp90 client proteins, although recent evidence suggests that eukaryotic Hop is regulatory within chaperone complexes rather than essential. Consequently, Hop is implicated in many key signalling pathways, including aberrant pathways leading to cancer. Hop is also secreted, and it is now well established that Hop interacts with the prion protein, PrPC, to mediate multiple signalling events. The intracellular and extracellular forms of Hop most likely represent two different isoforms, although the molecular determinants of these divergent functions are yet to be identified. There is also a growing body of research that reports the involvement of Hop in cellular activities that appear independent of either chaperones or PrPC. While the various cellular functions of Hop have been described, its biological function remains elusive. However, recent knockout studies in mammals suggest that Hop has an important role in embryonic development. This review provides a critical overview of the latest molecular, cellular and biological research on Hop, critically evaluating its function in healthy systems and how this function is adapted in diseased states.
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7
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Kho J, Pham PC, Kwon S, Huang AY, Rivers JP, Wang H, Ecroyd H, Donald WA, McAlpine SR. De Novo Design, Synthesis, and Mechanistic Evaluation of Short Peptides That Mimic Heat Shock Protein 27 Activity. ACS Med Chem Lett 2021; 12:713-719. [PMID: 34055216 DOI: 10.1021/acsmedchemlett.0c00609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/01/2021] [Indexed: 01/17/2023] Open
Abstract
We report the first small molecule peptides based on the N-terminal sequence of heat shock protein 27 (Hsp27, gene HSPB1) that demonstrates chaperone-like activity. The peptide, comprising the SWDPF sequence located at Hsp27's amino (N)-terminal domain, directly regulates protein aggregation events, maintaining the disaggregated state of the model protein, citrate synthase. While traditional inhibitors of protein aggregation act via regulation of a protein that facilitates aggregation or disaggregation, our molecules are the first small peptides between 5 and 8 amino acids in length that are based on the N-terminus of Hsp27 and directly control protein aggregation. The presented strategy showcases a new approach for developing small peptides that control protein aggregation in proteins with high aggregate levels, making them a useful approach in developing new drugs.
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Affiliation(s)
- Jessica Kho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - P. Chi Pham
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Suhyeon Kwon
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alana Y. Huang
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joel P. Rivers
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Huixin Wang
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Heath Ecroyd
- Department of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - W. Alexander Donald
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shelli R. McAlpine
- School of Chemistry, University of California Irvine, Irvine, California 92697, United States
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8
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Banerjee M, Hatial I, Keegan BM, Blagg BSJ. Assay design and development strategies for finding Hsp90 inhibitors and their role in human diseases. Pharmacol Ther 2021; 221:107747. [PMID: 33245994 PMCID: PMC8744950 DOI: 10.1016/j.pharmthera.2020.107747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/30/2022]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone that facilitates the maturation of its client proteins including protein kinases, transcription factors, and steroid hormone receptors which are structurally and functionally diverse. These client proteins are involved in various cellular signaling pathways, and Hsp90 is implicated in various human diseases including cancer, inflammation, and diseases associated with protein misfolding; thus making Hsp90 a promising target for drug discovery. Some of its client proteins are well-known cancer targets. Instead of targeting these client proteins individually, however, targeting Hsp90 is more practical for cancer drug development. Efforts have been invested in recognizing potential drugs for clinical use that inhibit Hsp90 activity and result in the prevention of Hsp90 client maturation and dampening of subsequent signaling cascades. Here, we discuss current assays and technologies used to find and characterize Hsp90 inhibitors that include biophysical, biochemical, cell-based assays and computational modeling. This review highlights recent discoveries that N-terminal isoform-selective compounds and inhibitors that target the Hsp90 C-terminus that may offer the potential to overcome some of the detriments observed with pan Hsp90 inhibitors. The tools and assays summarized in this review should be used to develop Hsp90-targeting drugs with high specificity, potency, and drug-like properties that may prove immensely useful in the clinic.
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Affiliation(s)
- Monimoy Banerjee
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Ishita Hatial
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Bradley M Keegan
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Brian S J Blagg
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA.
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9
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Mak OW, Sharma N, Reynisson J, Leung IKH. Discovery of novel Hsp90 C-terminal domain inhibitors that disrupt co-chaperone binding. Bioorg Med Chem Lett 2021; 38:127857. [PMID: 33609661 DOI: 10.1016/j.bmcl.2021.127857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
Heat shock protein 90 (Hsp90) is an essential molecular chaperone that performs vital stress-related and housekeeping functions in cells and is a current therapeutic target for diseases such as cancers. Particularly, the development of Hsp90 C-terminal domain (CTD) inhibitors is highly desirable as inhibitors that target the N-terminal nucleotide-binding domain may cause unwanted biological effects. Herein, we report on the discovery of two drug-like novel Hsp90 CTD inhibitors by using virtual screening and intrinsic protein fluorescence quenching binding assays, paving the way for future development of new therapies that employ molecular chaperone inhibitors.
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Affiliation(s)
- Oi Wei Mak
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
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10
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McConnell JR, Dyson HJ, McAlpine SR. Using NMR to identify binding regions for N and C-terminal Hsp90 inhibitors using Hsp90 domains. RSC Med Chem 2021; 12:410-415. [PMID: 33898992 PMCID: PMC8044635 DOI: 10.1039/d0md00387e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/28/2021] [Indexed: 11/21/2022] Open
Abstract
We present the first NMR study of the interaction between heat shock protein 90 (Hsp90) and amino (N)-terminal inhibitors 17-AAG, and AUY922, and carboxy (C)-terminal modulators SM253, and LB51. We show that the two ATP mimics, 17-AAG and AUY922, bind deeply within the ATP binding pocket of the N-terminal domain, consistent with the crystal structures. In contrast, SM253, a C-terminal Hsp90 modulator, binds to the linker region between the N and middle domains. We also show that C-terminal inhibitor LB51 binds to the C-terminus with a more significant spectroscopic change than previously reported using NMR binding studies of C-terminal inhibitors novobiocin and silybin. These data provide key insights into how the allosteric inhibitor SM253 controls the C-terminal co-chaperones and confirms the binding domain of LB51.
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Affiliation(s)
- Jeanette R McConnell
- Work performed at School of Chemistry , University of New South Wales , Sydney , Australia .
| | - H Jane Dyson
- Work also performed at Scripps Research , 10550 North Torrey Pines Road , La Jolla , CA 92037 , USA .
| | - Shelli R McAlpine
- Work performed at School of Chemistry , University of New South Wales , Sydney , Australia .
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11
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Cipcigan F, Smith P, Crain J, Hogner A, De Maria L, Llinas A, Ratkova E. Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations. J Chem Inf Model 2020; 61:263-269. [PMID: 33350828 DOI: 10.1021/acs.jcim.0c00803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides have the potential to bind to challenging targets, which are undruggable with small molecules, but their application is limited by low membrane permeability. Here, using a series of cyclic pentapeptides, we showed that established physicochemical criteria of permeable peptides are heavily violated. We revealed that a dominant core conformation, stabilized by amides' shielding pattern, could guide the design of novel compounds. As a result, counter-intuitive strategies, such as incorporation of polar residues, can be beneficial for permeability. We further find that core globularity is a promising descriptor, which can extend the capability of standard predictive models.
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Affiliation(s)
- Flaviu Cipcigan
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K
| | - Paul Smith
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K.,King's College London, London WC2R 2LS, U.K
| | - Jason Crain
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K.,Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (RI), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Antonio Llinas
- Inhalation Product Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Gothenburg 43150, Sweden
| | - Ekaterina Ratkova
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
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12
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Takenaka M, Takahashi Y, Takakura Y. Intercellular delivery of NF-κB inhibitor peptide utilizing small extracellular vesicles for the application of anti-inflammatory therapy. J Control Release 2020; 328:435-443. [DOI: 10.1016/j.jconrel.2020.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/11/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
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13
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Buckton LK, Rahimi MN, McAlpine SR. Cyclic Peptides as Drugs for Intracellular Targets: The Next Frontier in Peptide Therapeutic Development. Chemistry 2020; 27:1487-1513. [PMID: 32875673 DOI: 10.1002/chem.201905385] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Developing macrocyclic peptides that can reach intracellular targets is a significant challenge. This review discusses the most recent strategies used to develop cell permeable cyclic peptides that maintain binding to their biological target inside the cell. Macrocyclic peptides are unique from small molecules because traditional calculated physical properties are unsuccessful for predicting cell membrane permeability. Peptide synthesis and experimental membrane permeability is the only strategy that effectively differentiates between cell permeable and cell impermeable molecules. Discussed are chemical strategies, including backbone N-methylation and stereochemical changes, which have produced molecular scaffolds with improved cell permeability. However, these improvements often come at the expense of biological activity as chemical modifications alter the peptide conformation, frequently impacting the compound's ability to bind to the target. Highlighted is the most promising approach, which involves side-chain alterations that improve cell permeability without impact binding events.
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Affiliation(s)
- Laura K Buckton
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Marwa N Rahimi
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Shelli R McAlpine
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
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14
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Darby JF, Vidler LR, Simpson PJ, Al-Lazikani B, Matthews SJ, Sharp SY, Pearl LH, Hoelder S, Workman P. Solution structure of the Hop TPR2A domain and investigation of target druggability by NMR, biochemical and in silico approaches. Sci Rep 2020; 10:16000. [PMID: 32994435 PMCID: PMC7524759 DOI: 10.1038/s41598-020-71969-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/24/2020] [Indexed: 02/08/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone that plays an important role in tumour biology by promoting the stabilisation and activity of oncogenic 'client' proteins. Inhibition of Hsp90 by small-molecule drugs, acting via its ATP hydrolysis site, has shown promise as a molecularly targeted cancer therapy. Owing to the importance of Hop and other tetratricopeptide repeat (TPR)-containing cochaperones in regulating Hsp90 activity, the Hsp90-TPR domain interface is an alternative site for inhibitors, which could result in effects distinct from ATP site binders. The TPR binding site of Hsp90 cochaperones includes a shallow, positively charged groove that poses a significant challenge for druggability. Herein, we report the apo, solution-state structure of Hop TPR2A which enables this target for NMR-based screening approaches. We have designed prototype TPR ligands that mimic key native 'carboxylate clamp' interactions between Hsp90 and its TPR cochaperones and show that they block binding between Hop TPR2A and the Hsp90 C-terminal MEEVD peptide. We confirm direct TPR-binding of these ligands by mapping 1H-15N HSQC chemical shift perturbations to our new NMR structure. Our work provides a novel structure, a thorough assessment of druggability and robust screening approaches that may offer a potential route, albeit difficult, to address the chemically challenging nature of the Hop TPR2A target, with relevance to other TPR domain interactors.
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Affiliation(s)
- John F Darby
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Lewis R Vidler
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Peter J Simpson
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Bruker UK Ltd, Banner Lane, Coventry, CV4 9GH, UK
| | - Bissan Al-Lazikani
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Swee Y Sharp
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
- Division of Structural Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Swen Hoelder
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paul Workman
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
- Cancer Research UK Convergence Science Centre, The Institute of Cancer Research and Imperial College London, London, UK.
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15
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Huo Y, Buckton LK, Bennett JL, Smith EC, Byrne FL, Hoehn KL, Rahimi MN, McAlpine SR. Delivering bioactive cyclic peptides that target Hsp90 as prodrugs. J Enzyme Inhib Med Chem 2019; 34:728-739. [PMID: 30822267 PMCID: PMC6407599 DOI: 10.1080/14756366.2019.1580276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The most challenging issue facing peptide drug development is producing a molecule with optimal physical properties while maintaining target binding affinity. Masking peptides with protecting groups that can be removed inside the cell, produces a cell-permeable peptide, which theoretically can maintain its biological activity. Described are series of prodrugs masked using: (a) O-alkyl, (b) N-alkyl, and (c) acetyl groups, and their binding affinity for Hsp90. Alkyl moieties increased compound permeability, Papp, from 3.3 to 5.6, however alkyls could not be removed by liver microsomes or in-vivo and their presence decreased target binding affinity (IC50 of ≥10 µM). Thus, unlike small molecules, peptide masking groups cannot be predictably removed; their removal is related to the 3-D conformation. O-acetyl groups were cleaved but are labile, increasing challenges during synthesis. Utilising acetyl groups coupled with mono-methylated amines may decrease the polarity of a peptide, while maintaining binding affinity.
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Affiliation(s)
- Yuantao Huo
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Laura K Buckton
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Jack L Bennett
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Eloise C Smith
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Frances L Byrne
- b School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Kyle L Hoehn
- b School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Marwa N Rahimi
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Shelli R McAlpine
- a School of Chemistry, University of New South Wales , Sydney , Australia
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16
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Rahimi MN, Foster HG, Farazi SN, Chapman R, McAlpine SR. Polymer mediated transport of the Hsp90 inhibitor LB76, a polar cyclic peptide, produces an Hsp90 cellular phenotype. Chem Commun (Camb) 2019; 55:4515-4518. [PMID: 30920570 DOI: 10.1039/c9cc00890j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
LB76 is a cyclic peptide that shows great promise as a selective heat shock protein 90 (Hsp90) inhibitor. However despite strong binding to and inhibition of Hsp90 in cell lysate its polar structure prevents it from crossing the cell membrane. We have developed a pH responsive polymer nanoparticle that effectively encapsulates LB76 from solution without need for purification. The nanoparticle releases the molecule upon crossing the cell membrane. Treatment of human colon cancer HCT116 cells with nanoparticles laden with LB76 produces the typical phenotype associated with Hsp90 inhibition, providing evidence of a therapeutically active payload.
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Affiliation(s)
- Marwa N Rahimi
- School of Chemistry, University of New South Wales, Gate 2 High street, Dalton 219, Sydney, Australia.
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17
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Rahimi MN, McAlpine SR. Protein-protein inhibitor designed de novo to target the MEEVD region on the C-terminus of Hsp90 and block co-chaperone activity. Chem Commun (Camb) 2019; 55:846-849. [PMID: 30575826 DOI: 10.1039/c8cc07576j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions control all cellular functions. Presented is the first de novo designed protein-protein inhibitor that targets the C-terminus of heat shock protein 90 (Hsp90) and blocks co-chaperones from binding. Compound LB76, which was created from an Hsp90 co-chaperone, selectively pulls down Hsp90 from cell lysates, binds to Hsp90's C-terminal domain, and blocks the interactions between Hsp90 and TPR-containing co-chaperones. Through these interactions, LB76 inhibits the protein-folding function of Hsp90. Blocking these protein-protein interactions between Hsp90 and C-terminal co-chaperones regulate the cell's entire protein-folding machinery.
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Affiliation(s)
- Marwa N Rahimi
- School of Chemistry, Gate 2 High street, Dalton 219, University of New South Wales, Sydney, Australia.
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18
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Zaiter SS, Huo Y, Tiew FY, Gestwicki JE, McAlpine SR. Designing de Novo Small Molecules That Control Heat Shock Protein 70 (Hsp70) and Heat Shock Organizing Protein (HOP) within the Chaperone Protein-Folding Machinery. J Med Chem 2018; 62:742-761. [DOI: 10.1021/acs.jmedchem.8b01436] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Samantha S. Zaiter
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yuantao Huo
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Fong Y. Tiew
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neuro-degenerative Disease, University of California, San Francisco, San Francisco, California 94158, United States
| | - Shelli R. McAlpine
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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19
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Jiang Y, Long H, Zhu Y, Zeng Y. Macrocyclic peptides as regulators of protein-protein interactions. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Buckton LK, McAlpine SR. Improving the Cell Permeability of Polar Cyclic Peptides by Replacing Residues with Alkylated Amino Acids, Asparagines, and d-Amino Acids. Org Lett 2018; 20:506-509. [DOI: 10.1021/acs.orglett.7b03363] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Laura K. Buckton
- School of Chemistry, University of New South Wales, Sydney NSW 2051, Australia
| | - Shelli R. McAlpine
- School of Chemistry, University of New South Wales, Sydney NSW 2051, Australia
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