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Xu L, Fan X, He Y, Xia X, Zhang J. Design, Synthesis, and Biological Evaluation of Lysine-Stapled Peptide Inhibitors of p53-MDM2/MDMX Interactions with Potent Antitumor Activity In Vivo. J Med Chem 2024; 67:17893-17904. [PMID: 39300610 DOI: 10.1021/acs.jmedchem.4c01939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
We introduce novel lysine-stapled peptide inhibitors targeting p53-MDM2/MDMX interactions. Leveraging the model peptides pDI (LTFEHYWAQLTS) and PMI-M3 (LTFLEYWAQLMQ) as starting points, a series of lysine-stapled analogues were designed and synthesized. Through in vitro cell assay screening, two lead compounds, SPDI-48-T1 and SPMI-48-T3, were identified for their excellent antiproliferation activity. Fluorescence polarization assays revealed that both compounds exhibited strong binding affinities against MDM2 and MDMX, ascertained by Kd values within the low micromolar spectrum. Further characterization of SPDI-48-T1 and SPMI-48-T3 demonstrated that SPDI-48-T1 possessed superior cell permeability and serum stability. Notably, SPDI-48-T1 displayed a dose-dependent suppression of tumor growth in an HCT116 xenograft mouse model. Our findings indicate that SPDI-48-T1 holds promise as a lead compound for further development as an anticancer agent by modulating p53-MDM2/MDMX interactions. Additionally, this study also proved that the lysine stapling strategy may serve as a robust approach for generating peptide ligands targeting other protein-protein interactions.
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Affiliation(s)
- Lei Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People's Republic of China
| | - Xin Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People's Republic of China
| | - Yi He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People's Republic of China
| | - Xuefeng Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People's Republic of China
| | - Jinqiang Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People's Republic of China
- Chongqing University Industrial Technology Research Institute, Chongqing 401329, People's Republic of China
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2
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Mak ECL, Chen Z, Lee LCC, Leung PKK, Yip AMH, Shum J, Yiu SM, Yam VWW, Lo KKW. Exploiting the Potential of Iridium(III) bis-Nitrone Complexes as Phosphorogenic Bifunctional Reagents for Phototheranostics. J Am Chem Soc 2024; 146:25589-25599. [PMID: 39248725 DOI: 10.1021/jacs.4c07251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Cross-linking strategies have found wide applications in chemical biology, enabling the labeling of biomolecules and monitoring of protein-protein interactions. Nitrone exhibits remarkable versatility and applicability in bioorthogonal labeling due to its high reactivity with strained alkynes via the strain-promoted alkyne-nitrone cycloaddition (SPANC) reaction. In this work, four cyclometalated iridium(III) polypyridine complexes functionalized with two nitrone units were designed as novel phosphorogenic bioorthogonal reagents for bioimaging and phototherapeutics. The complexes showed efficient emission quenching, which is attributed to an efficient nonradiative decay pathway via the low-lying T1/S0 minimum energy crossing point (MECP), as revealed by computational studies. However, the complexes displayed significant emission enhancement and lifetime extension upon reaction with (1R,8S,9s)-bicyclo[6.1.0]non-4-yne (BCN) derivatives. In particular, they showed a remarkably higher reaction rate toward a bis-cyclooctyne derivative (bis-BCN) compared with its monomeric counterpart (mono-BCN). Live-cell imaging and (photo)cytotoxicity studies revealed higher photocytotoxicity in bis-BCN-pretreated cells, which is ascribed to the enhanced singlet oxygen (1O2) photosensitization resulting from the elimination of the nitrone-associated quenching pathway. Importantly, the cross-linking properties and enhanced reactivity of the complexes make them highly promising candidates for the development of hydrogels and stapled/cyclized peptides, offering intriguing photophysical, photochemical, and biological properties. Notably, a nanosized hydrogel (2-gel) demonstrated potential as a drug delivery system, while a stapled peptide (2-bis-pDIKK) exhibited p53-Mdm2 inhibitory activity related to apoptosis and a cyclized peptide (2-bis-RGD) showed cancer selectivity.
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Affiliation(s)
- Eunice Chiu-Lam Mak
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Ziyong Chen
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Lawrence Cho-Cheung Lee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Units 1503-1511, 15/F, Building 17 W, Hong Kong Science Park, New Territories, Hong Kong, P. R. China
| | - Peter Kam-Keung Leung
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Alex Man-Hei Yip
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Units 1503-1511, 15/F, Building 17 W, Hong Kong Science Park, New Territories, Hong Kong, P. R. China
| | - Justin Shum
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Shek-Man Yiu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
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Philippe GJB, Huang YH, Mittermeier A, Brown CJ, Kaas Q, Ramlan SR, Wang CK, Lane D, Loewer A, Troeira Henriques S, Craik DJ. Delivery to, and Reactivation of, the p53 Pathway in Cancer Cells Using a Grafted Cyclotide Conjugated with a Cell-Penetrating Peptide. J Med Chem 2024; 67:1197-1208. [PMID: 38174919 DOI: 10.1021/acs.jmedchem.3c01682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Peptides are promising drug modalities that can modulate protein-protein interactions, but their application is hampered by their limited ability to reach intracellular targets. Here, we improved the cytosolic delivery of a peptide blocking p53:MDM2/X interactions using a cyclotide as a stabilizing scaffold. We applied several design strategies to improve intracellular delivery and found that the conjugation of the lead cyclotide to the cyclic cell-penetrating peptide cR10 was the most effective. Conjugation allowed cell internalization at micromolar concentration and led to elevated intracellular p53 levels in A549, MCF7, and MCF10A cells, as well as inducing apoptosis in A549 cells without causing membrane disruption. The lead peptide had >35-fold improvement in inhibitory activity and increased cellular uptake compared to a previously reported cyclotide p53 activator. In summary, we demonstrated the delivery of a large polar cyclic peptide in the cytosol and confirmed its ability to modulate intracellular protein-protein interactions involved in cancer.
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Affiliation(s)
- Grégoire Jean-Baptiste Philippe
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anna Mittermeier
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Christopher J Brown
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siti Radhiah Ramlan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Lane
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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4
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Zhang J, Liu J, Li X, Ju Y, Li Y, Zhang G, Li Y. Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine. J Am Chem Soc 2024; 146:2122-2131. [PMID: 38190443 DOI: 10.1021/jacs.3c11574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Bioconjugation chemistry has emerged as a powerful tool for the modification of diverse biomolecules under mild conditions. Tetrazole, initially proposed as a bioorthogonal photoclick handle for 1,3-dipolar cyclization with alkenes, was later demonstrated to possess broader photoreactivity with carboxylic acids, serving as a versatile bioconjugation and photoaffinity labeling probe. In this study, we unexpectedly discovered and validated the photoreactivity between tetrazole and primary amine to afford a new 1,2,4-triazole cyclization product. Given the significance of functionalized N-heterocycles in medicinal chemistry, we successfully harnessed the serendipitously discovered reaction to synthesize both pharmacologically relevant DNA-encoded chemical libraries (DELs) and small molecule compounds bearing 1,2,4-triazole scaffolds. Furthermore, the mild reaction conditions and stable 1,2,4-triazole linkage found broad application in photoinduced bioconjugation scenarios, spanning from intramolecular peptide macrocyclization and templated DNA reaction cross-linking to intermolecular photoaffinity labeling of proteins. Triazole cross-linking products on lysine side chains were identified in tetrazole-labeled proteins, refining the comprehensive understanding of the photo-cross-linking profiles of tetrazole-based probes. Altogether, this tetrazole-amine bioconjugation expands the current bioconjugation toolbox and creates new possibilities at the interface of medicinal chemistry and chemical biology.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Jinlu Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yunzhu Ju
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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5
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Cheng J, Yan Z, Jiang K, Liu C, Xu D, Lyu X, Hu X, Zhang S, Zhou Y, Li J, Zhao Y. Discovery of JN122, a Spiroindoline-Containing Molecule that Inhibits MDM2/p53 Protein-Protein Interaction and Exerts Robust In Vivo Antitumor Efficacy. J Med Chem 2023; 66:16991-17025. [PMID: 38062557 DOI: 10.1021/acs.jmedchem.3c01815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
MDM2 and MDM4 cooperatively and negatively regulate p53, while this pathway is often hijacked by cancer cells in favor of their survival. Blocking MDM2/p53 interaction with small-molecule inhibitors liberates p53 from MDM2 mediated degradation, which is an attractive strategy for drug discovery. We reported herein structure-based discovery of highly potent spiroindoline-containing MDM2 inhibitor (-)60 (JN122), which also exhibited moderate activities against MDM4/p53 interactions. In a panel of cancer cell lines harboring wild type p53, (-)60 efficiently promoted activation of p53 and its target genes, inhibited cell cycle progression, and induced cell apoptosis. Interestingly, (-)60 also promoted degradation of MDM4. More importantly, (-)60 exhibited good PK properties and exerted robust antitumor efficacies in a systemic mouse xenograft model of MOLM-13. Taken together, our study showcases a class of potent MDM2 inhibitors featuring a novel spiro-indoline scaffold, which is promising for future development targeting cancer cells with wild-type p53.
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Affiliation(s)
- Jing Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, P. R. China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
| | - Kailong Jiang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, P. R. China
| | - Chen Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Dehua Xu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, P. R. China
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin 124000, P. R. China
| | - Xilin Lyu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
| | - Xiaobei Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, P. R. China
| | - Shiyan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, P. R. China
| | - Yubo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, P. R. China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, P. R. China
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin 124000, P. R. China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, P. R. China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, P. R. China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, P. R. China
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6
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Monti A, Vitagliano L, Caporale A, Ruvo M, Doti N. Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches. Int J Mol Sci 2023; 24:7842. [PMID: 37175549 PMCID: PMC10178479 DOI: 10.3390/ijms24097842] [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: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protein surfaces and the development of modulators of protein-protein interactions still represent a major challenge due to their highly dynamic and extensive interfacial areas. Over the years, multiple strategies including structural, computational, and combinatorial approaches have been developed to characterize PPI and to date, several successful examples of small molecules, antibodies, peptides, and aptamers able to modulate these interfaces have been determined. Notably, peptides are a particularly useful tool for inhibiting PPIs due to their exquisite potency, specificity, and selectivity. Here, after an overview of PPIs and of the commonly used approaches to identify and characterize them, we describe and evaluate the impact of chemical peptide libraries in medicinal chemistry with a special focus on the results achieved through recent applications of this methodology. Finally, we also discuss the role that this methodology can have in the framework of the opportunities, and challenges that the application of new predictive approaches based on artificial intelligence is generating in structural biology.
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Affiliation(s)
- Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), Strada Statale 14 km 163.5, Basovizza, 34149 Triese, Italy;
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
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7
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Zhang Y, Guo J, Cheng J, Zhang Z, Kang F, Wu X, Chu Q. High-Throughput Screening of Stapled Helical Peptides in Drug Discovery. J Med Chem 2023; 66:95-106. [PMID: 36580278 DOI: 10.1021/acs.jmedchem.2c01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
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Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
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8
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Gomari MM, Abkhiz S, Pour TG, Lotfi E, Rostami N, Monfared FN, Ghobari B, Mosavi M, Alipour B, Dokholyan NV. Peptidomimetics in cancer targeting. Mol Med 2022; 28:146. [PMID: 36476230 PMCID: PMC9730693 DOI: 10.1186/s10020-022-00577-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
The low efficiency of treatment strategies is one of the main obstacles to developing cancer inhibitors. Up to now, various classes of therapeutics have been developed to inhibit cancer progression. Peptides due to their small size and easy production compared to proteins are highly regarded in designing cancer vaccines and oncogenic pathway inhibitors. Although peptides seem to be a suitable therapeutic option, their short lifespan, instability, and low binding affinity for their target have not been widely applicable against malignant tumors. Given the peptides' disadvantages, a new class of agents called peptidomimetic has been introduced. With advances in physical chemistry and biochemistry, as well as increased knowledge about biomolecule structures, it is now possible to chemically modify peptides to develop efficient peptidomimetics. In recent years, numerous studies have been performed to the evaluation of the effectiveness of peptidomimetics in inhibiting metastasis, angiogenesis, and cancerous cell growth. Here, we offer a comprehensive review of designed peptidomimetics to diagnose and treat cancer.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- grid.411746.10000 0004 4911 7066Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shadi Abkhiz
- grid.411746.10000 0004 4911 7066Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Taha Ghantab Pour
- grid.411746.10000 0004 4911 7066Department of Anatomy, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Lotfi
- grid.411746.10000 0004 4911 7066Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Rostami
- grid.411425.70000 0004 0417 7516Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak, Iran
| | - Fatemeh Nafe Monfared
- grid.411705.60000 0001 0166 0922Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Ghobari
- grid.412831.d0000 0001 1172 3536Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mona Mosavi
- grid.411746.10000 0004 4911 7066Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behruz Alipour
- grid.411705.60000 0001 0166 0922Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nikolay V. Dokholyan
- grid.240473.60000 0004 0543 9901Department of Pharmacology, Penn State College of Medicine, Hershey, PA USA ,grid.240473.60000 0004 0543 9901Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA USA
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9
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Fenton M, Borcherds W, Chen L, Anbanandam A, Levy R, Chen J, Daughdrill G. The MDMX Acidic Domain Uses Allovalency to Bind Both p53 and MDMX. J Mol Biol 2022; 434:167844. [PMID: 36181774 PMCID: PMC9644833 DOI: 10.1016/j.jmb.2022.167844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 01/10/2023]
Abstract
Autoinhibition of p53 binding to MDMX requires two short-linear motifs (SLiMs) containing adjacent tryptophan (WW) and tryptophan-phenylalanine (WF) residues. NMR spectroscopy was used to show the WW and WF motifs directly compete for the p53 binding site on MDMX and circular dichroism spectroscopy was used to show the WW motif becomes helical when it is bound to the p53 binding domain (p53BD) of MDMX. Binding studies using isothermal titration calorimetry showed the WW motif is a stronger inhibitor of p53 binding than the WF motif when they are both tethered to p53BD by the natural disordered linker. We also investigated how the WW and WF motifs interact with the DNA binding domain (DBD) of p53. Both motifs bind independently to similar sites on DBD that overlap the DNA binding site. Taken together our work defines a model for complex formation between MDMX and p53 where a pair of disordered SLiMs bind overlapping sites on both proteins.
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Affiliation(s)
- Malissa Fenton
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Lihong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Asokan Anbanandam
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Jiandong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States.
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10
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Miki T, Namii K, Seko K, Kakehi S, Moro G, Mihara H. Pattern enrichment analysis for phage selection of stapled peptide ligands. Chem Sci 2022; 13:12634-12642. [PMID: 36519040 PMCID: PMC9645375 DOI: 10.1039/d2sc04058a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/11/2022] [Indexed: 08/22/2023] Open
Abstract
Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these difficulties, we devised a 'pattern enrichment analysis.' In this method, two samples (one obtained by affinity selection, the other simply amplified without selection) are prepared, and the two sequence datasets read on next-generation sequencer are compared to find the three-residue pattern most enriched in the selected sample. This allows us to compare two sequence datasets with high coverage and facilitates the identification of peptide sequences and the key residues for binding. We also demonstrated that this approach in the combination with structured peptide libraries allowed spatial mapping of the enriched sequence patterns. Here, we prepared a phage library displaying chemically stapled helical peptides with the X1C2X3X4X5X6X7X8C9X10 sequence, where X is any amino acid. To validate our method, we performed screening against the HDM2 protein. The results showed that the hydrophobic residues (Phe, Tyr, Trp and Leu) that are key to interactions with HDM2 were clearly identified by the pattern enrichment analysis. We also performed selection targeting the SARS-CoV-2 spike RBD in the same manner. The results showed that similar patterns were enriched among the hit peptides that inhibited the protein-protein interaction.
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Affiliation(s)
- Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Keigo Namii
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Kenta Seko
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Shota Kakehi
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Goshi Moro
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8501 Japan
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11
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Luo Z, Xu L, Tang X, Zhao X, He T, Lubell WD, Zhang J. Synthesis and biological evaluation of novel all-hydrocarbon cross-linked aza-stapled peptides. Org Biomol Chem 2022; 20:7963-7971. [PMID: 36190455 DOI: 10.1039/d2ob01496c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel all-hydrocarbon cross-linked aza-stapled peptides were designed and synthesized for the first time by ring-closing metathesis between two aza-alkenylglycine residues. Three aza-stapled peptidic analogues based on the peptide dual inhibitor of p53-MDM2/MDMX interactions were synthesized and screened for biological activities. Among the three aza-stapled peptides, aSPDI-411 displayed increased anti-tumor activity, binding affinities to both MDM2 and MDMX, and cell membrane permeability compared to its linear peptide counterpart.
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Affiliation(s)
- Zhihong Luo
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.
| | - Lei Xu
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.
| | - Xiaomin Tang
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.
| | - Xuejun Zhao
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.
| | - Tong He
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.
| | - William D Lubell
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada.
| | - Jinqiang Zhang
- Innovative Drug Research Centre (IDRC), Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China. .,Chongqing University Industrial Technology Research Institute, Chongqing 401329, People's Republic of China
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12
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Chatterjee C, Singh SK. Peptide and protein chemistry approaches to study the tumor suppressor protein p53. Org Biomol Chem 2022; 20:5500-5509. [PMID: 35786742 PMCID: PMC10112546 DOI: 10.1039/d2ob00902a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tumor suppressor and master gene regulator protein p53 has been the subject of intense investigation for several decades due to its mutation in about half of all human cancers. However, mechanistic studies of p53 in cells are complicated by its many dynamic binding partners and heterogeneous post-translational modifications. The design of therapeutics that rescue p53 functions in cells requires a mechanistic understanding of its protein-protein interactions in specific protein complexes and identifying changes in p53 activity by diverse post-translational modifications. This review highlights the important roles that peptide and protein chemistry have played in biophysical and biochemical studies aimed at elucidating p53 regulation by several key binding partners. The design of various peptide inhibitors that rescue p53 function in cells and new opportunities in targeting p53-protein interactions are discussed. In addition, the review highlights the importance of a protein semisynthesis approach to comprehend the role of site-specific PTMs in p53 regulation.
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Affiliation(s)
- Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sumeet K Singh
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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13
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de Araujo AD, Hoang HN, Lim J, Mak JYW, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022; 61:e202203995. [PMID: 35523729 PMCID: PMC9543247 DOI: 10.1002/anie.202203995] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 11/30/2022]
Abstract
Aromatic groups are key mediators of protein–membrane association at cell surfaces, contributing to hydrophobic effects and π‐membrane interactions. Here we show electrostatic and hydrophobic influences of aromatic ring substituents on membrane affinity and cell uptake of helical, cyclic and cell penetrating peptides. Hydrophobicity is important, but subtle changes in electrostatic surface potential, dipoles and polarizability also enhance association with phospholipid membranes and cell uptake. A combination of fluorine and sulfur substituents on an aromatic ring induces microdipoles that enhance cell uptake of 12‐residue peptide inhibitors of p53‐HDM2 interaction and of cell‐penetrating cyclic peptides. These aromatic motifs can be readily inserted into peptide sidechains to enhance their cell uptake.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Jeffrey Y. W. Mak
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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14
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Zhao X, Xiong D, Luo S, Duan L. Molecular investigation of the dual inhibition mechanism for targeted P53 regulator MDM2/MDMX inhibitors. Phys Chem Chem Phys 2022; 24:16799-16815. [PMID: 35775962 DOI: 10.1039/d2cp01780f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inhibitors that competitively bind MDM2/MDMX can block the inhibition of P53 by MDM2/MDMX and restart its tumor-suppressive effect. Molecular studies targeting MDM2/MDMX inhibitors have always been a hot topic in anticancer drug design. Although numerous inhibitors have been designed previously against MDM2/MDMX, their dual inhibition efficacy has not been demonstrated, and few studies assessed the general causes affecting the dual inhibition of MDM2/MDMX by these inhibitors. Here, molecular dynamics simulations and alanine scanning combined with the interaction entropy method were employed to precisely investigate whether 16 inhibitors could dually inhibit MDM2/MDMX and the similarities and differences in the interaction modes. Thereby addressing the key residue sites affecting dual inhibition. Residues L54/M53, I61/60, M62/61, Y67/66, and V93/92 of MDM2/MDMX, which are in corresponding positions in both protein structures, provide significant conditions for these inhibitors to bind to MDM2/MDMX tightly. In addition, most of these inhibitors prefer to bind MDM2 than MDMX, and residues H96 and I99 in MDM2 are attractive targets for inhibitors, resulting in inhibitors binding to MDM2/MDMX with different affinity. These key residues should be considered in the development of dual inhibitors. For these 16 inhibitors, most have dual inhibitory potential for MDM2/MDMX based on the binding affinity of the complexes. Still, it is questionable whether they can exert excellent dual inhibition considering the assessment of the hot-spots. At least their binding affinity for MDMX is not superior to that for MDM2 due to the difference in energy of the van der Waals interactions at the key sites. Furthermore, based on the analysis of three representative inhibitors (TUZ/HRH and HRQ with different binding preferences for MDM2/MDMX), 3-chloropyridine in TUZ leads to the differential binding affinity between the inhibitor and MDM2/MDMX. It readily forms hydrophobic interactions with the surrounding residues H96 and I99. But this phenomenon does not occur in the TUZ-MDMX system, implying the critical role of residues H96/P95 and I99/L98. And the completely different binding mechanism of HRQ binding to MDM2/MDMX explains its inability to inhibit MDM2 well. Thus, we are cautious about its dual inhibitory ability. Besides, HRH is more prone to strong van der Waals interactions with MDM2 than MDMX whereas its 2-chlorofluorobenzene is detrimental to this. We hope that these findings will provide reliable molecular insights for the screening and optimization of targeting MDM2/MDMX dual inhibitors.
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Affiliation(s)
- Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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15
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Lee P, Yim R, Miu KK, Fung SH, Liao JJ, Wang Z, Li J, Yung Y, Chu HT, Yip PK, Lee E, Tse E, Kwong YL, Gill H. Epigenetic Silencing of PTEN and Epi-Transcriptional Silencing of MDM2 Underlied Progression to Secondary Acute Myeloid Leukemia in Myelodysplastic Syndrome Treated with Hypomethylating Agents. Int J Mol Sci 2022; 23:5670. [PMID: 35628480 PMCID: PMC9144309 DOI: 10.3390/ijms23105670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/07/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
In myelodysplastic syndrome (MDS), resistance to hypomethylating agents (HMA) portends a poor prognosis, underscoring the importance of understanding the molecular mechanisms leading to HMA-resistance. In this study, P39 and Kasumi-1 cells and their azacitidine-resistant and decitabine-resistant sublines were evaluated comparatively with transcriptomic and methylomic analyses. Expression profiling and genome-wide methylation microarray showed downregulation of PTEN associated with DNA hypermethylation in P39 cell lines resistant to azacitidine and decitabine. This pattern of PTEN dysregulation was also confirmed in a cohort of patients failing treatment with HMA. DNA hypomethylation of MDM2 was detected with downregulation of MDM2 in HMA resistant cell lines. Long-read sequencing revealed significant RNA hypomethylation of MDM2 resulting in alternative splicing and production of a truncated MDM2 transcript in azacitidine-resistant P39 cells. The expression of this MDM2 truncated transcript was also significantly increased in HMA-resistant patients compared with HMA-responsive patients. In conclusion, epigenetic and epi-transcriptomic dysregulation of PTEN and MDM2 were associated with resistance to hypomethylating agents.
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Affiliation(s)
- Paul Lee
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Rita Yim
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Kai-Kei Miu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (K.-K.M.); (S.-H.F.); (Z.W.)
| | - Sin-Hang Fung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (K.-K.M.); (S.-H.F.); (Z.W.)
| | - Jason Jinyue Liao
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhangting Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (K.-K.M.); (S.-H.F.); (Z.W.)
| | - Jun Li
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, China;
| | - Yammy Yung
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Hiu-Tung Chu
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Pui-Kwan Yip
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Emily Lee
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Eric Tse
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Yok-Lam Kwong
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
| | - Harinder Gill
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (P.L.); (R.Y.); (Y.Y.); (H.-T.C.); (P.-K.Y.); (E.L.); (E.T.); (Y.-L.K.)
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16
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de Araujo AD, Hoang HN, Lim J, Mak J, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aline Dantes de Araujo
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Huy N Hoang
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Junxian Lim
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Jeffrey Mak
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - David P Fairlie
- Institute for Molecular Bioscience Division of Chemistry and Structural Biology The University of Queensland 4072 Brisbane AUSTRALIA
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17
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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18
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Zhang S, Yan Z, Li Y, Gong Y, Lyu X, Lou J, Zhang D, Meng X, Zhao Y. Structure-Based Discovery of MDM2/4 Dual Inhibitors that Exert Antitumor Activities against MDM4-Overexpressing Cancer Cells. J Med Chem 2022; 65:6207-6230. [PMID: 35420431 DOI: 10.1021/acs.jmedchem.2c00095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite recent clinical progress in peptide-based dual inhibitors of MDM2/4, small-molecule ones with robust antitumor activities remain challenging. To tackle this issue, 31 (YL93) was structure-based designed and synthesized, which had MDM2/4 binding Ki values of 1.1 and 642 nM, respectively. In three MDM4-overexpressing cancer cell lines harboring wild-type p53, 31 shows improved cell growth inhibition activities compared to RG7388, an MDM2-selective inhibitor in late-stage clinical trials. Mechanistic studies show that 31 increased cellular protein levels of p53 and p21 and upregulated the expression of p53-targeted genes in RKO cells with MDM4 amplification. In addition, 31 induced cell-cycle arrest and apoptosis in western blot and flow cytometry assays. Taken together, dual inhibition of MDM2/4 by 31 elicited stronger antitumor activities in vitro compared to selective MDM2 inhibitors in wild-type p53 and MDM4-overexpressing cancer cells.
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Affiliation(s)
- Shiyan Zhang
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yafang Li
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Yang Gong
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jianfeng Lou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Daizhou Zhang
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | - Xiangjing Meng
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.,Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
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19
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Yip AMH, Lai CKH, Yiu KSM, Lo KKW. Phosphorogenic Iridium(III) bis-Tetrazine Complexes for Bioorthogonal Peptide Stapling, Bioimaging, Photocytotoxic Applications, and the Construction of Nanosized Hydrogels. Angew Chem Int Ed Engl 2022; 61:e202116078. [PMID: 35119163 DOI: 10.1002/anie.202116078] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 12/28/2022]
Abstract
The dual functionality of 1,2,4,5-tetrazine as a bioorthogonal reactive unit and a luminescence quencher has shaped tetrazine-based probes as attractive candidates for luminogenic labeling of biomolecules in living systems. In this work, three cyclometalated iridium(III) complexes featuring two tetrazine units were synthesized and characterized. Upon photoexcitation, the complexes were non-emissive but displayed up to 3900-fold emission enhancement upon the inverse electron-demand Diels-Alder (IEDDA) [4+2] cycloaddition with (1R,8S,9s)-bicyclo[6.1.0]non-4-yne (BCN) substrates. The rapid reaction kinetics (k2 up to 1.47×104 M-1 s-1 ) of the complexes toward BCN substrates allowed effective peptide labeling. The complexes were also applied as live cell bioimaging reagents and photocytotoxic agents. One of the complexes was utilized in the preparation of luminescent nanosized hydrogels that exhibited interesting cargo delivery properties.
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Affiliation(s)
- Alex Man-Hei Yip
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Calvin Kin-Ho Lai
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Ken Shek-Man Yiu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China.,State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China.,Center for Functional Photonics, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
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20
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Feng X, Yan Z, Zhou F, Lou J, Lyu X, Ren X, Zeng Z, Liu C, Zhang S, Zhu D, Huang H, Yang J, Zhao Y. Discovery of a selective and covalent small-molecule inhibitor of BFL-1 protein that induces robust apoptosis in cancer cells. Eur J Med Chem 2022; 236:114327. [DOI: 10.1016/j.ejmech.2022.114327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/30/2022]
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21
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Yip AMH, Lai CKH, Yiu KSM, Lo KKW. Phosphorogenic Iridium(III) bis‐Tetrazine Complexes for Bioorthogonal Peptide Stapling, Bioimaging, Photocytotoxic Applications, and the Construction of Nanosized Hydrogels. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | | | - Kenneth Kam-Wing Lo
- City University of Hong Kong Department of Chemistry Tat Chee AvenueKowloon Tong N. A. Hong Kong HONG KONG
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22
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Affinity Selection from Synthetic Peptide Libraries Enabled by De Novo MS/MS Sequencing. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10370-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRecently, de novo MS/MS peptide sequencing has enabled the application of affinity selections to synthetic peptide mixtures that approach the diversity of phage libraries (> 108 random peptides). In conjunction with ‘split-mix’ solid phase synthesis to access equimolar peptide mixtures, this approach provides a straightforward means to examine synthetic peptide libraries of considerably higher diversity than has been feasible historically. Here, we offer a critical perspective on this work, report emerging data, and highlight opportunities for further methods refinement. With continued development, ‘affinity selection–mass spectrometry’ may become a complimentary approach to phage display, in vitro selection, and DNA-encoded libraries for the discovery of synthetic ligands that modulate protein function.
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23
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de Araujo AD, Lim J, Wu KC, Hoang HN, Nguyen HT, Fairlie DP. Landscaping macrocyclic peptides: stapling hDM2-binding peptides for helicity, protein affinity, proteolytic stability and cell uptake. RSC Chem Biol 2022; 3:895-904. [PMID: 35866171 PMCID: PMC9257625 DOI: 10.1039/d1cb00231g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
Surveying macrocycles for mimicking a helical tumor suppressor protein, resisting breakdown by proteases, and entering cancer cells.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T. Nguyen
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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24
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Li X, Gohain N, Chen S, Li Y, Zhao X, Li B, Tolbert WD, He W, Pazgier M, Hu H, Lu W. Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for P53 activation and tumor suppression. Acta Pharm Sin B 2021; 11:2655-2669. [PMID: 34589387 PMCID: PMC8463443 DOI: 10.1016/j.apsb.2021.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Peptide inhibition of the interactions of the tumor suppressor protein P53 with its negative regulators MDM2 and MDMX activates P53 in vitro and in vivo, representing a viable therapeutic strategy for cancer treatment. Using phage display techniques, we previously identified a potent peptide activator of P53, termed PMI (TSFAEYWNLLSP), with binding affinities for both MDM2 and MDMX in the low nanomolar concentration range. Here we report an ultrahigh affinity, dual-specificity peptide antagonist of MDM2 and MDMX obtained through systematic mutational analysis and additivity-based molecular design. Functional assays of over 100 peptide analogs of PMI using surface plasmon resonance and fluorescence polarization techniques yielded a dodecameric peptide termed PMI-M3 (LTFLEYWAQLMQ) that bound to MDM2 and MDMX with Kd values in the low picomolar concentration range as verified by isothermal titration calorimetry. Co-crystal structures of MDM2 and of MDMX in complex with PMI-M3 were solved at 1.65 and 3.0 Å resolution, respectively. Similar to PMI, PMI-M3 occupied the P53-binding pocket of MDM2/MDMX, which was dominated energetically by intermolecular interactions involving Phe3, Tyr6, Trp7, and Leu10. Notable differences in binding between PMI-M3 and PMI were observed at other positions such as Leu4 and Met11 with MDM2, and Leu1 and Met11 with MDMX, collectively contributing to a significantly enhanced binding affinity of PMI-M3 for both proteins. By adding lysine residues to both ends of PMI and PMI-M3 to improve their cellular uptake, we obtained modified peptides termed PMI-2K (KTSFAEYWNLLSPK) and M3-2K (KLTFLEYWAQLMQK). Compared with PMI-2K, M3-2K exhibited significantly improved antitumor activities in vitro and in vivo in a P53-dependent manner. This super-strong peptide inhibitor of the P53-MDM2/MDMX interactions may become, in its own right, a powerful lead compound for anticancer drug development, and can aid molecular design of other classes of P53 activators as well for anticancer therapy.
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Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Neelakshi Gohain
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Xiaoyuan Zhao
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Bo Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - William D. Tolbert
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wangxiao He
- Department of Talent Highland, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Marzena Pazgier
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Honggang Hu
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) of School of Basic Medical Sciences and Shanghai Institute of Infectious Disease and Biosecurity of School of Public Health, Fudan University, Shanghai 200032, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
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25
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Strizhak AV, Babii O, Afonin S, Bakanovich I, Pantelejevs T, Xu W, Fowler E, Eapen R, Sharma K, Platonov MO, Hurmach VV, Itzhaki L, Hyvönen M, Ulrich AS, Spring DR, Komarov IV. Diarylethene moiety as an enthalpy-entropy switch: photoisomerizable stapled peptides for modulating p53/MDM2 interaction. Org Biomol Chem 2021; 18:5359-5369. [PMID: 32390036 DOI: 10.1039/d0ob00831a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Analogs of the known inhibitor (peptide pDI) of the p53/MDM2 protein-protein interaction are reported, which are stapled by linkers bearing a photoisomerizable diarylethene moiety. The corresponding photoisomers possess significantly different affinities to the p53-interacting domain of the human MDM2. Apparent dissociation constants are in the picomolar-to-low nanomolar range for those isomers with diarylethene in the "open" configuration, but up to eight times larger for the corresponding "closed" isomers. Spectroscopic, structural, and computational studies showed that the stapling linkers of the peptides contribute to their binding. Calorimetry revealed that the binding of the "closed" isomers is mostly enthalpy-driven, whereas the "open" photoforms bind to the protein stronger due to their increased binding entropy. The results suggest that conformational dynamics of the protein-peptide complexes may explain the differences in the thermodynamic profiles of the binding.
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Affiliation(s)
- Alexander V Strizhak
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK. and Enamine Ltd, Vul. Chervonotkatska 78, 02094 Kyiv, Ukraine
| | - Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany.
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany.
| | - Iuliia Bakanovich
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK. and Enamine Ltd, Vul. Chervonotkatska 78, 02094 Kyiv, Ukraine
| | - Teodors Pantelejevs
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Wenshu Xu
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
| | - Elaine Fowler
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
| | - Rohan Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD Cambridge, UK
| | - Krishna Sharma
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
| | | | - Vasyl V Hurmach
- Enamine Ltd, Vul. Chervonotkatska 78, 02094 Kyiv, Ukraine and Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Laura Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany. and Institute of Organic Chemistry (IOC), KIT, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - David R Spring
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
| | - Igor V Komarov
- Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine and Lumobiotics GmbH, Auer Str. 2, 76227, Karlsruhe, Germany.
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26
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Zhang S, Lou J, Li Y, Zhou F, Yan Z, Lyu X, Zhao Y. Recent Progress and Clinical Development of Inhibitors that Block MDM4/p53 Protein-Protein Interactions. J Med Chem 2021; 64:10621-10640. [PMID: 34286973 DOI: 10.1021/acs.jmedchem.1c00940] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MDM4 is a homologue of MDM2, serving cooperatively as the negative regulator of tumor suppressor p53. Under the shadow of MDM2 inhibitors, limited efforts had been put into the discovery of MDM4 modulators. Recent studies of the experimental drug ALRN-6924, a dual MDM4 and MDM2 inhibitor, suggest that concurrent inhibition of MDM4 and MDM2 might be beneficial over only MDM2 inhibition. In view of the present research progress, we summarized published inhibitors of MDM4/p53 interactions including both peptide-based compounds and small molecules. Cocrystal structures of ligand/MDM4 complexes have been examined, and their structural features were compiled and compared in order to show the molecular basis required for high MDM4 binding affinities. Representative examples of small-molecule MDM4 inhibitors were discussed, followed by clinical results of ALRN-6924, together, providing a consolidated reference for further development of MDM4 inhibitors, either dual or selective.
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Affiliation(s)
- Shiyan Zhang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jianfeng Lou
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yafang Li
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu 215123, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Feilong Zhou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yujun Zhao
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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27
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Torner JM, Yang Y, Rooklin D, Zhang Y, Arora PS. Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics. ACS Chem Biol 2021; 16:1179-1183. [PMID: 34228913 DOI: 10.1021/acschembio.1c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.
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Affiliation(s)
- Justin M. Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yuwei Yang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - David Rooklin
- 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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28
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Nguyen TTT, Shingyoji M, Hanazono M, Zhong B, Morinaga T, Tada Y, Shimada H, Hiroshima K, Tagawa M. An MDM2 inhibitor achieves synergistic cytotoxic effects with adenoviruses lacking E1B55kDa gene on mesothelioma with the wild-type p53 through augmenting NFI expression. Cell Death Dis 2021; 12:663. [PMID: 34230456 PMCID: PMC8260618 DOI: 10.1038/s41419-021-03934-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
A majority of mesothelioma specimens were defective of p14 and p16 expression due to deletion of the INK4A/ARF region, and the p53 pathway was consequently inactivated by elevated MDM2 functions which facilitated p53 degradaton. We investigated a role of p53 elevation by MDM2 inhibitors, nutlin-3a and RG7112, in cytotoxicity of replication-competent adenoviruses (Ad) lacking the p53-binding E1B55kDa gene (Ad-delE1B). We found that a growth inhibition by p53-activating Ad-delE1B was irrelevant to p53 expression in the infected cells, but combination of Ad-delE1B and the MDM2 inhibitor produced synergistic inhibitory effects on mesothelioma with the wild-type but not mutated p53 genotype. The combination augmented p53 phosphorylation, activated apoptotic but not autophagic pathway, and enhanced DNA damage signals through ATM-Chk2 phosphorylation. The MDM2 inhibitors facilitated production of the Ad progenies through augmented expression of nuclear factor I (NFI), one of the transcriptional factors involved in Ad replications. Knocking down of p53 with siRNA did not increase the progeny production or the NFI expression. We also demonstrated anti-tumor effects by the combination of Ad-delE1B and the MDM2 inhibitors in an orthotopic animal model. These data collectively indicated that upregulation of wild-type p53 expression contributed to cytotoxicity by E1B55kDa-defective replicative Ad through NFI induction and suggested that replication-competent Ad together with augmented p53 levels was a therapeutic strategy for p53 wild-type mesothelioma.
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Affiliation(s)
- Thao Thi Thanh Nguyen
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan
- Department of Molecular Biology and Oncology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Division of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, 2374 National Highway 1, District 12, Ho Chi Minh, Vietnam
| | - Masato Shingyoji
- Division of Respirology, Chiba Cancer Center, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan
| | - Michiko Hanazono
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Boya Zhong
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan
- Department of Molecular Biology and Oncology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Takao Morinaga
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan
| | - Yuji Tada
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku©, Chiba, 260-8670, Japan
- Department of Respiratory Medicine, International University of Health and Welfare Atami Hospital, 13-1 Higasikaigan, Atami, 413-0012, Japan
| | - Hideaki Shimada
- Department of Surgery, Graduate School of Medicine, Toho University, 6-11-1 Oomori-nishi, Oota-ku, 143-8541, Tokyo, Japan
| | - Kenzo Hiroshima
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Department of Pathology, Tokyo Women's Medical University Yachiyo Medical Center, 477-96 Ohwadashinden, Yachiyo, 276-8524, Japan
| | - Masatoshi Tagawa
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba, 260-8717, Japan.
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
- Funabashi Orthopedic Hospital, 1-833 Hazama, Funabashi, 274-0822, Japan.
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29
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Evolution of KIPPIS as a versatile platform for evaluating intracellularly functional peptide aptamers. Sci Rep 2021; 11:11758. [PMID: 34083659 PMCID: PMC8175380 DOI: 10.1038/s41598-021-91287-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/18/2021] [Indexed: 11/18/2022] Open
Abstract
Chimeric proteins have been widely used to evaluate intracellular protein–protein interactions (PPIs) in living cells with various readouts. By combining an interleukin-3-dependent murine cells and chimeric proteins containing a receptor tyrosine kinase c-kit, we previously established a c-kit-based PPI screening (KIPPIS) system to evaluate and select protein binders. In the KIPPIS components, proteins of interest are connected with a chemically inducible helper module and the intracellular domain of the growth-signaling receptor c-kit, which detects PPIs based on cell proliferation as a readout. In this system, proteins of interest can be incorporated into chimeric proteins without any scaffold proteins, which would be advantageous for evaluating interaction between small peptides/domains. To prove this superiority, we apply KIPPIS to 6 peptide aptamer–polypeptide pairs, which are derived from endogenous, synthetic, and viral proteins. Consequently, all of the 6 peptide aptamer–polypeptide interactions are successfully detected by cell proliferation. The detection sensitivity can be modulated in a helper ligand-dependent manner. The assay results of KIPPIS correlate with the activation levels of Src, which is located downstream of c-kit-mediated signal transduction. Control experiments reveal that KIPPIS clearly discriminates interacting aptamers from non-interacting ones. Thus, KIPPIS proves to be a versatile platform for evaluating the binding properties of peptide aptamers.
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30
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Kashima D, Kageoka M, Kimura Y, Horikawa M, Miura M, Nakakido M, Tsumoto K, Nagamune T, Kawahara M. A Novel Cell-Based Intracellular Protein-Protein Interaction Detection Platform (SOLIS) for Multimodality Screening. ACS Synth Biol 2021; 10:990-999. [PMID: 33909409 DOI: 10.1021/acssynbio.0c00483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intervention in protein-protein interactions (PPIs) has tremendous effects in the molecular therapy of many diseases. To fulfill the requirements for targeting intracellular proteins, here we develop SOS-localization-based interaction screening (SOLIS), which elaborately mimics signaling via the Ras-mitogen-activated protein kinase pathway. SOLIS employs two chimeric proteins in which a membrane localization motif (CaaX) is fused at the C-terminus of a protein of interest and the catalytic domain of SOS is fused at the C-terminus of another protein of interest. Interaction between the two proteins of interest induces membrane localization of the SOS chimera and cell proliferation. Thus, the SOLIS system enables enrichment of superior binders based on cell proliferation in an intracellular PPI-dependent manner. This was verified by three major modalities against intracellular PPIs (small molecules, peptide aptamers, and intrabodies). The system worked over a broad range of affinities (KD = 0.32-140 nM). In a screening of a site-directed randomized library, novel intrabody clones were selected on the basis of the potency of cell proliferation. Three other PPI detection methods (NanoBiT, SPR, and pull-down assays) were employed to characterize the SOLIS system, and several intrabody clones were judged as false negatives in these assays. SOLIS signals would be less sensitive to the orientation/conformation of the chimeric proteins, and this feature emerges as the advantage of SOLIS as a mammalian cytosolic PPI detection system with few false negatives.
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Affiliation(s)
- Daiki Kashima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miho Kageoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yosuke Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makiko Horikawa
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masashi Miura
- Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka 567-0085, Japan
| | - Makoto Nakakido
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka 567-0085, Japan
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31
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Wu J, Ding W, Han G, You W, Gao W, Shen H, Tang J, Tang Q, Wang X. Nuclear delivery of dual anti-cancer drugs by molecular self-assembly. Biomater Sci 2021; 9:116-123. [PMID: 33325919 DOI: 10.1039/d0bm00971g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanomedicines generally suffer from poor accumulation in tumor cells, low anti-tumor efficacy, and drug resistance. In order to address these problems, we introduced a novel nanomedicine based on dual anti-cancer drugs, which showed good cell nuclear accumulation properties. The novel nanomedicine consisted of three components: (1) dual anti-cancer drugs, 10-hydroxycamptothecin (HCPT) and chlorambucil (CRB), whose targets are located in the cell nucleus, (2) a nuclear localizing dodecapeptide, PMI peptide (TSFAEYWNLLSP), which could activate p53 by binding with MDM2 and MDMX located in the cell nucleus, and (3) an efficient self-assembling tripeptide FFY. Our nanomedicine exhibited enhanced cellular uptake and nuclear accumulation properties, thus achieving an excellent anti-cancer capacity both in vitro and in vivo. Our study will provide an inspiration for the development of novel multifunctional nanomaterials for cancer diagnosis and therapy.
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Affiliation(s)
- Jindao Wu
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Hepatobiliary Center, Department of Breast Surgery, Department of Oncology, Department of Geriatric Digestion, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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32
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Liu C, Zhou F, Yan Z, Shen L, Zhang X, He F, Wang H, Lu X, Yu K, Zhao Y, Zhu D. Discovery of a novel, potent and selective small-molecule inhibitor of PD-1/PD-L1 interaction with robust in vivo anti-tumour efficacy. Br J Pharmacol 2021; 178:2651-2670. [PMID: 33768523 DOI: 10.1111/bph.15457] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE PD-1/PD-L1 antibodies have achieved great success in clinical treatment. However, monoclonal antibody drugs also have challenges, such as high manufacturing costs, poor diffusion, low oral bioavailability and limited penetration into tumour tissue. The development of small-molecule inhibitors of PD-1/PD-L1 interaction represents a promising perspective to overcome the above challenges in cancer immunotherapy. EXPERIMENTAL APPROACH We explored structural activity relationships and used biochemical assays to generate a lead compound (ZE132). CD8+ T-cells killing assay and Ifng expression assay were used to verify the in vitro cellular activity of ZE132. Off-target study was performed to verify the selectivity. Syngeneic mouse models were used to verify the in vivo activity of ZE132 in tumour immune microenvironment (TIME). We also performed pharmacokinetics profiling in mice and The Cancer Genome Atlas database analysis. KEY RESULTS ZE132 can effectively inhibit the PD-1/PD-L1 interactions in vitro, and it has a potent affinity to PD-L1. ZE132 shows robust anti-tumour effects in vivo, better than anti-PD-1 antibody. In the analysis of TIME, we found that ZE132 treatment promotes cytotoxic T-cell tumour infiltration and induces IL-2 expression. In addition, ZE132 elicits strong inhibitory effects on the mRNA expression of TGF-β, which may serve as a potential biomarker to predict responsiveness to PD-1/PD-L1 immunotherapies. CONCLUSION AND IMPLICATIONS We identified a new lead compound ZE132 targeting PD-1/PD-L1 interactions, not only showing favourable drug-like properties in vitro and in vivo but also showing the advantage of overcoming the barrier of TIME compared to anti-PD-1 antibody.
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Affiliation(s)
- Chenglong Liu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
| | - Feilong Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Lian Shen
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
| | - Xichen Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Fenglian He
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
| | - Heng Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ker Yu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Di Zhu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.,Key Laboratory of Smart Drug Delivery and Shanghai Engineering Research Center of Immune Therapy, Fudan University, Shanghai, China
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Wang H, Dawber RS, Zhang P, Walko M, Wilson AJ, Wang X. Peptide-based inhibitors of protein-protein interactions: biophysical, structural and cellular consequences of introducing a constraint. Chem Sci 2021; 12:5977-5993. [PMID: 33995995 PMCID: PMC8098664 DOI: 10.1039/d1sc00165e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/07/2021] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions (PPIs) are implicated in the majority of cellular processes by enabling and regulating the function of individual proteins. Thus, PPIs represent high-value, but challenging targets for therapeutic intervention. The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices. The approach can confer significant benefits including enhanced affinity, stability and cellular penetration and is ingrained in the premise that pre-organization simultaneously pays the entropic cost of binding, prevents a peptide from adopting a protease compliant β-strand conformation and shields the hydrophilic amides from the hydrophobic membrane. This conceptual blueprint for the empirical design of peptide-based PPI inhibitors is an exciting and potentially lucrative way to effect successful PPI inhibitor drug-discovery. However, a plethora of more subtle effects may arise from the introduction of a constraint that include changes to binding dynamics, the mode of recognition and molecular properties. In this review, we summarise the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour across a range of constraining chemistries and targets, to highlight the tremendous success that has been achieved with constrained peptides alongside emerging design opportunities and challenges.
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Affiliation(s)
- Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Nanjing 210023 Jiangsu China
| | - Robert S Dawber
- 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
| | - Peiyu Zhang
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Martin Walko
- 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
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- Department of Applied Chemistry and Engineering, University of Science and Technology of China Hefei 230026 China
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de Araujo AD, Nguyen HT, Fairlie DP. Late-Stage Hydrocarbon Conjugation and Cyclisation in Synthetic Peptides and Proteins. Chembiochem 2021; 22:1784-1789. [PMID: 33506598 DOI: 10.1002/cbic.202000796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/07/2021] [Indexed: 12/26/2022]
Abstract
The conventional S-alkylation of cysteine relies upon using activated electrophiles. Here we demonstrate high-yielding and selective S-alkylation and S-lipidation of cysteines in unprotected synthetic peptides and proteins by using weak electrophiles and a Zn2+ promoter. Linear or branched iodoalkanes can S-alkylate cysteine in an unprotected 38-residue Myc peptide fragment and in a 91-residue miniprotein Omomyc, thus highlighting selective late-stage synthetic modifications. Metal-assisted cysteine alkylation is also effective for incorporating dehydroalanine into unprotected peptides and for peptide cyclisation via aliphatic thioether crosslinks, including customising macrocycles to stabilise helical peptides for enhanced uptake and delivery to proteins inside cells. Chemoselective and efficient late-stage Zn2+ -promoted cysteine alkylation in unprotected peptides and proteins promises many useful applications.
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Affiliation(s)
- Aline D de Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T Nguyen
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Philippe GJB, Mittermeier A, Lawrence N, Huang YH, Condon ND, Loewer A, Craik DJ, Henriques ST. Angler Peptides: Macrocyclic Conjugates Inhibit p53:MDM2/X Interactions and Activate Apoptosis in Cancer Cells. ACS Chem Biol 2021; 16:414-428. [PMID: 33533253 DOI: 10.1021/acschembio.0c00988] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides are being developed as targeted anticancer drugs to modulate cytosolic protein-protein interactions involved in cancer progression. However, their use as therapeutics is often limited by their low cell membrane permeation and/or inability to reach cytosolic targets. Conjugation to cell penetrating peptides has been successfully used to improve the cytosolic delivery of high affinity binder peptides, but cellular uptake does not always result in modulation of the targeted pathway. To overcome this limitation, we developed "angler peptides" by conjugating KD3, a noncell permeable but potent and specific peptide inhibitor of p53:MDM2 and p53:MDMX interactions, with a set of cyclic cell-penetrating peptides. We examined their binding affinity for MDM2 and MDMX, the cell entry mechanism, and role in reactivation of the p53 pathway. We identified two angler peptides, cTAT-KD3 and cR10-KD3, able to activate the p53 pathway in cancer cells. cTAT-KD3 entered cells via endocytic pathways, escaped endosomes, and activated the p53 pathway in breast (MCF7), lung (A549), and colon (HCT116) cancer cell lines at concentrations in the range of 1-12 μM. cR10-KD3 reached the cytosol via direct membrane translocation and activated the p53 pathway at 1 μM in all the tested cell lines. Our work demonstrates that nonpermeable anticancer peptides can be delivered into the cytosol and inhibit intracellular cancer pathways when they are conjugated with stable cell penetrating peptides. The mechanistic studies suggest that direct translocation leads to less toxicity, higher cytosol delivery at lower concentrations, and lower dependencies on the membrane of the tested cell line than occurs for an endocytic pathway with endosomal escape. The angler strategy can rescue high affinity peptide binders identified from high throughput screening and convert them into targeted anticancer therapeutics, but investigation of their cellular uptake and cell death mechanisms is essential to confirming modulation of the targeted cancer pathways.
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Affiliation(s)
- Grégoire J.-B. Philippe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia T. Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland University of Technology, School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute, Brisbane, Queensland 4102, Australia
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Lawrence N, Philippe GJB, Harvey PJ, Condon ND, Benfield AH, Cheneval O, Craik DJ, Troeira Henriques S. Cyclic peptide scaffold with ability to stabilize and deliver a helical cell-impermeable cargo across membranes of cultured cancer cells. RSC Chem Biol 2020; 1:405-420. [PMID: 34458771 PMCID: PMC8386104 DOI: 10.1039/d0cb00099j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/01/2020] [Indexed: 12/31/2022] Open
Abstract
Cell penetrating peptides (CPPs) are valuable tools for developing anticancer therapies due to their ability to access intracellular targets, including protein–protein interactions. cPF4PD is a newly described CPP designed from a transduction domain of the human defense protein platelet factor 4 (PF4), that also has antimalarial activity. The cPF4PD peptide recapitulates the helical structure of the PF4 domain and maintains activity against intracellular malaria parasites via a selective membrane-active mechanism. We hypothesized that cPF4PD and PF4-derived peptide analogues would enter cancer cells and have utility as scaffolds for delivering a peptide dual inhibitor (pDI) sequence with ability to inhibit p53:MDM2/X interactions and reactivate the p53 pathway. Here we designed and produced PF4 peptide and PF4 peptide-pDI grafted analogues with low micromolar activity toward melanoma and leukemia. Two grafted analogues achieved a stable helical structure and inhibited interaction with MDM2 and MDMX. These peptides reached the cytoplasm of cells but were unable to reactivate the p53 pathway. Instead, the cytotoxic mechanism was attributed to peptide binding to mitochondrial membranes that perturbed function within two hours of treatment. These studies of PF4-derived CPPs suggest their potential as scaffolds for delivering cell-impermeable cargoes into the cytoplasm of cells and highlight the importance of characterizing the internalization and cell death mechanism of designer peptide-based drugs. A new helix-loop-helix peptide scaffold with dual ability to transport cargo across cancer cell membranes and disrupt mitochondrial membrane function.![]()
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Affiliation(s)
- Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - Grégoire J-B Philippe
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - Peta J Harvey
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - Nicholas D Condon
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - Aurélie H Benfield
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019.,Queensland University of Technology, School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute Brisbane Queensland 4102 Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland Brisbane Queensland 4072 Australia +61 7 34437342 +61 7 33462014 +61 7 33462019.,Queensland University of Technology, School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute Brisbane Queensland 4102 Australia
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Anananuchatkul T, Tsutsumi H, Miki T, Mihara H. hDM2 protein-binding peptides screened from stapled α-helical peptide phage display libraries with different types of staple linkers. Bioorg Med Chem Lett 2020; 30:127605. [PMID: 33038548 DOI: 10.1016/j.bmcl.2020.127605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/18/2022]
Abstract
Chemically modified peptide ligands were identified from α-helix peptide phage libraries with different types of staple linkers. The hDM2-protein was used as a representative target of protein-protein interactions to screen ligands for p53 binding sites in hDM2. Two types of staple linkers were used for the chemical modification of the peptide phage display libraries before affinity selection. The identified stapled peptides could bind to hDM2 competitively with the p53 peptide. The stapled peptide phage libraries developed in this study will improve the discovery of protein-protein interaction inhibitors through the synergistic effect of peptide units and staple linkers.
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Affiliation(s)
- Teerapat Anananuchatkul
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroshi Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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38
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Huang Q, Chen L, Schonbrunn E, Chen J. MDMX inhibits casein kinase 1α activity and stimulates Wnt signaling. EMBO J 2020; 39:e104410. [PMID: 32511789 DOI: 10.15252/embj.2020104410] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Casein kinase 1 alpha (CK1α) is a serine/threonine kinase with numerous functions, including regulating the Wnt/β-catenin and p53 pathways. CK1α has a well-established role in inhibiting the p53 tumor suppressor by binding to MDMX and stimulating MDMX-p53 interaction. MDMX purified from cells contains near-stoichiometric amounts of CK1α, suggesting that MDMX may in turn regulate CK1α function. We present evidence that MDMX is a potent competitive inhibitor of CK1α kinase activity (Ki = 8 nM). Depletion of MDMX increases CK1α activity and β-catenin S45 phosphorylation, whereas ectopic MDMX expression inhibits CK1α activity and β-catenin phosphorylation. The MDMX acidic domain and zinc finger are necessary and sufficient for binding and inhibition of CK1α. P53 binding to MDMX disrupts an intramolecular auto-regulatory interaction and enhances its ability to inhibit CK1α. P53-null mice expressing the MDMXW 200S/W201G mutant, defective in CK1α binding, exhibit reduced Wnt/β-catenin target gene expression and delayed tumor development. Therefore, MDMX is a physiological inhibitor of CK1α and has a role in modulating cellular response to Wnt signaling. The MDMX-CK1α interaction may account for certain p53-independent functions of MDMX.
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Affiliation(s)
- Qingling Huang
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Lihong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Ernst Schonbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Jiandong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL, USA
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39
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Structure-based designing efficient peptides based on p53 binding site residues to disrupt p53-MDM2/X interaction. Sci Rep 2020; 10:11449. [PMID: 32651397 PMCID: PMC7351717 DOI: 10.1038/s41598-020-67510-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 06/09/2020] [Indexed: 12/23/2022] Open
Abstract
MDM2 and MDMX are known as overexpressed oncoproteins in several wild-type p53 cancer cells. The development of potent and dual antagonist peptides for p53-MDM2/X is a continuous challenge. In this study, we intended to investigate the pivotal structural points respecting the development of potent and dual inhibitors of MDM2/X. Correspondingly, MD simulation was performed on the experimentally confirmed peptides, comprising p53, pDI, pDIQ, PMI, and computationally screened mutant pDI and pDIQ. A follow-up secondary structure analysis showed the last three C-terminal residues provide the helicity reservation of peptides bound to MDM2/X. Furthermore, a delicate residue-residue examination displayed Met 11 and Ser12 in the modified peptides contribute significantly to dual inhibition of MDM2/X. Additionally, the peptides_MDM2/X complexes' ΔGbinding extracted by the umbrella sampling method were in agreement with the pattern of their experimental affinity values. It was concluded the screened pDI mutants were considered as suitable anti-MDM2/X peptides, and the data obtained could be exploited as the theoretical structure-based guide for rational peptide design. Taking account of results, the suitable C-terminal residues of p53-based peptides especially Met11, and Ser12, as well as higher umbrella sampling, generated ΔGbinding to MDM2/X would be considered as the positive structural markers of a promising anti-cancer agent.
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40
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Small-molecule MDM2/X inhibitors and PROTAC degraders for cancer therapy: advances and perspectives. Acta Pharm Sin B 2020; 10:1253-1278. [PMID: 32874827 PMCID: PMC7452049 DOI: 10.1016/j.apsb.2020.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/31/2019] [Accepted: 12/26/2019] [Indexed: 12/26/2022] Open
Abstract
Blocking the MDM2/X–P53 protein–protein interaction has been widely recognized as an attractive therapeutic strategy for the treatment of cancers. Numerous small-molecule MDM2 inhibitors have been reported since the release of the structure of the MDM2–P53 interaction in 1996, SAR405838, NVP-CGM097, MK-8242, RG7112, RG7388, DS-3032b, and AMG232 currently undergo clinical evaluation for cancer therapy. This review is intended to provide a comprehensive and updated overview of MDM2 inhibitors and proteolysis targeting chimera (PROTAC) degraders with a particular focus on how these inhibitors or degraders are identified from starting points, strategies employed, structure–activity relationship (SAR) studies, binding modes or co-crystal structures, biochemical data, mechanistic studies, and preclinical/clinical studies. Moreover, we briefly discuss the challenges of designing MDM2/X inhibitors for cancer therapy such as dual MDM2/X inhibition, acquired resistance and toxicity of P53 activation as well as future directions.
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Quartararo AJ, Gates ZP, Somsen BA, Hartrampf N, Ye X, Shimada A, Kajihara Y, Ottmann C, Pentelute BL. Ultra-large chemical libraries for the discovery of high-affinity peptide binders. Nat Commun 2020; 11:3183. [PMID: 32576815 PMCID: PMC7311396 DOI: 10.1038/s41467-020-16920-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/27/2020] [Indexed: 11/22/2022] Open
Abstract
High-diversity genetically-encoded combinatorial libraries (108-1013 members) are a rich source of peptide-based binding molecules, identified by affinity selection. Synthetic libraries can access broader chemical space, but typically examine only ~ 106 compounds by screening. Here we show that in-solution affinity selection can be interfaced with nano-liquid chromatography-tandem mass spectrometry peptide sequencing to identify binders from fully randomized synthetic libraries of 108 members-a 100-fold gain in diversity over standard practice. To validate this approach, we show that binders to a monoclonal antibody are identified in proportion to library diversity, as diversity is increased from 106-108. These results are then applied to the discovery of p53-like binders to MDM2, and to a family of 3-19 nM-affinity, α/β-peptide-based binders to 14-3-3. An X-ray structure of one of these binders in complex with 14-3-3σ is determined, illustrating the role of β-amino acids in facilitating a key binding contact.
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Affiliation(s)
- Anthony J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, Netherlands
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Arisa Shimada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, Netherlands
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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43
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Dowarha D, Chou RH, Yu C. S100A1 blocks the interaction between p53 and mdm2 and decreases cell proliferation activity. PLoS One 2020; 15:e0234152. [PMID: 32497081 PMCID: PMC7272100 DOI: 10.1371/journal.pone.0234152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/19/2020] [Indexed: 01/10/2023] Open
Abstract
About 50% of human cancers across the globe arise due to a mutation in the p53 gene which gives rise to its functional inactive form, and in the rest of the cancer the efficacy of active p53 (wild-type) is hindered by MDM2-mediated degradation. Breakdown of the p53-MDM2 association may constitute an effective strategy to stimulate or reinstate the activity of wild type p53, thereby reviving the p53 tumor suppressor capability. S100A1 has been revealed to associate with the N-terminal domain of MDM2 and p53 protein. We utilized NMR spectroscopy to study the interface amongst the S100A1 and N-terminal domain of MDM2. Additionally, the S100A1-MDM2 complex generated through the HADDOCK program was then superimposed with the p53 (peptide) -MDM2 complex reported earlier. The overlay indicated that a segment of S100A1 could block the interaction of p53 (peptide) -MDM2 complex significantly. To further justify our assumption, we performed HSQC-NMR titration for the S100A1 and p53 N-terminal domain (p53-TAD). The data obtained indicated that the S100A1 segment comprising nearly 17 residues have some common residues that interact with both MDM2 and p53-TAD. Further, we synthesized the 17-residue peptide derived from the S100A1 protein and attached it to the cell-penetrating HIV-TAT peptide. The HSQC-NMR competitive binding experiment revealed that Peptide 1 could successfully interfere with the p53-MDM2 interaction. Furthermore, functional effects of the peptide was validated in cancer cells. The results showed that Peptide 1 effectively inhibited cell proliferation, and increased the protein levels of p53 and its downstream p21 in MCF-7 cells. Treatment of Peptide 1 resulted in cell cycle arrest at G2/M phase, and also induced apoptotic cell death at higher concentration. Taken together, the results suggest that disruption of the interaction of p53 and MDM2 by Peptide 1 could activate normal p53 functions, leading to cell cycle arrest and apoptotic cell death in cancer cells. We proposed here that S100A1 could influence the p53-MDM2 interaction credibly and possibly reactivates the wild type p53 pathway.
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Affiliation(s)
- Deepu Dowarha
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Ruey-Hwang Chou
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Wufeng, Taichung, Taiwan
- * E-mail: (CY); (RHC)
| | - Chin Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (CY); (RHC)
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Datta A, Mishra S, Manna K, Saha KD, Mukherjee S, Roy S. Pro-Oxidant Therapeutic Activities of Cerium Oxide Nanoparticles in Colorectal Carcinoma Cells. ACS OMEGA 2020; 5:9714-9723. [PMID: 32391458 PMCID: PMC7203694 DOI: 10.1021/acsomega.9b04006] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/08/2020] [Indexed: 05/06/2023]
Abstract
Given that basal levels of reactive oxygen species (ROS) are higher in cancer cells, there is a growing school of thought that endorses pro-oxidants as potential chemotherapeutic agents. Intriguingly, cerium oxide (CeO2) nanoparticles can manifest either anti- or pro-oxidant activity as a function of differential pH of various subcellular localizations. In an acidic pH environment, for example, in extracellular milieu of cancer cells, CeO2 would function as a pro-oxidant. Based on this concept, the present study is designed to investigate the pro-oxidant activities of CeO2 in human colorectal carcinoma cell line (HCT 116). For comparison, we have also studied the effect of ceria nanoparticles on human embryonic kidney (HEK 293) cells. Dose-dependent viability of cancerous as well as normal cells has been assessed by treating them independently with CeO2 nanoparticles of different concentrations (5-100 μg/mL) in the culture media. The half maximal inhibitory concentration (IC50) of nanoceria for HCT 116 is found to be 50.48 μg/mL while that for the HEK 293 cell line is 92.03 μg/mL. To understand the intricate molecular mechanisms of CeO2-induced cellular apoptosis, a series of experiments have been conducted. The apoptosis-inducing ability of nanoceria has been investigated by Annexin V-FITC staining, caspase 3/9 analysis, cytochrome c release, intracellular ROS analysis, and mitochondrial membrane potential analysis using flow cytometry. Experimental data suggest that CeO2 treatment causes DNA fragmentation through enhanced generation of ROS, which ultimately leads to cellular apoptosis through the p53-dependent mitochondrial signaling pathway.
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Affiliation(s)
- Aparna Datta
- School of Materials Science and Nanotechnology, Jadavpur University, 188, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Snehasis Mishra
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Krishnendu Manna
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Krishna Das Saha
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Siddhartha Mukherjee
- Department of Metallurgical and Material Engineering, Jadavpur University, 188, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Somenath Roy
- CSIR-Central Glass and Ceramic Research Institute, 196 Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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45
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Identification of a Structural Determinant for Selective Targeting of HDMX. Structure 2020; 28:847-857.e5. [PMID: 32359398 DOI: 10.1016/j.str.2020.04.011] [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: 01/08/2020] [Revised: 03/11/2020] [Accepted: 04/11/2020] [Indexed: 11/21/2022]
Abstract
p53 is a critical tumor-suppressor protein that guards the human genome against mutations by inducing cell-cycle arrest or apoptosis. Cancer cells subvert p53 by deletion, mutation, or overexpression of the negative regulators HDM2 and HDMX. For tumors that retain wild-type p53, its reactivation by pharmacologic targeting of HDM2 and/or HDMX represents a promising strategy, with a series of selective small-molecule HDM2 inhibitors and a dual HDM2/HDMX stapled-peptide inhibitor being evaluated in clinical trials. Because selective HDM2 targeting can cause hematologic toxicity, selective HDMX inhibitors could provide an alternative p53-reactivation strategy, but clinical candidates remain elusive. Here, we applied a mutation-scanning approach to uncover p53-based stapled peptides that are selective for HDMX. Crystal structures of stapled-peptide/HDMX complexes revealed a molecular mechanism for the observed specificity, which was validated by HDMX mutagenesis. Thus, we provide a blueprint for the development of HDMX-selective inhibitors to dissect and target the p53/HDMX interaction.
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46
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An update on the central nervous system manifestations of Li-Fraumeni syndrome. Acta Neuropathol 2020; 139:669-687. [PMID: 31468188 DOI: 10.1007/s00401-019-02055-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022]
Abstract
Li-Fraumeni syndrome (LFS), caused by the germline mutations in the TP53 gene, leads to significant lifetime risk to cancer in the central nervous system. Recognition of LFS, and elucidating its underlying cause has had a remarkable effect on our knowledge of the biology of brain tumors and represents a significant opportunity for cancer surveillance and screening. In this review, we discuss the historical context of the LFS with an emphasis on the clinicopathologic implications in clincal diagnosis, germline testing, and clinical management of brain tumor patients.
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47
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity‐Driven Tool for the Development of Inhibitors of Protein–Protein Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel G. Ricardo
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Ameena M. Ali
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Jacek Plewka
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Ewa Surmiak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Constantinos G. Neochoritis
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Department of ChemistryUniversity of Crete Greece
| | - Jack Atmaj
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Faculty of ChemistryJagiellonian University Krakow Poland
| | | | - Ran Zhang
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Matthew Groves
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Daniel G. Rivera
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Alexander Dömling
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
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48
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2020; 59:5235-5241. [PMID: 31944488 DOI: 10.1002/anie.201916257] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein-protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.
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Affiliation(s)
- Manuel G Ricardo
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Ameena M Ali
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Department of Chemistry, University of, Crete, Greece
| | - Jack Atmaj
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ran Zhang
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Daniel G Rivera
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
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49
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Rasafar N, Barzegar A, Mehdizadeh Aghdam E. Design and development of high affinity dual anticancer peptide-inhibitors against p53-MDM2/X interaction. Life Sci 2020; 245:117358. [PMID: 32001262 DOI: 10.1016/j.lfs.2020.117358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
AIMS Inhibition of P53-MDM2/X interaction is known as an effective cancer therapy strategy. In this regard, pDI peptide was introduced previously with the potential of targeting MDM2. In this research, the large-scale peptide mutation screening was used to achieve the best sequence of pDI with the highest affinity for inhibition activity against MDM2/X. MAIN METHODS Three mutant peptides of pDI as dual inhibitor peptides including single mutations of pDIm/4W, pDIm/11M and double mutations of pDIdm/4W11M were presented with the high affinities to inhibit both MDM2/X. The selected mutants were then evaluated comprehensively to confirm their ability as potent MDM2/X inhibitors, using a theoretical simulation approach. KEY FINDINGS MD simulations analyses confirmed their dual inhibition potential against both MDM2/X interactions with p53 protein. The developed pDIm and mainly pDIdm peptides showed stable conformations over the simulation time with conserved secondary structure and effective interaction with MDM2/X by physical binding such as hydrogen bonding. Besides, umbrella sampling free energy calculation indicated higher binding energy, ΔGbinding, of pDIm-MDM2/X and pDIdm-MDM2/X compared to pDI-MDM2/X. SIGNIFICANCE The optimized and improved mutant pDI, pDIdm, with more effective ΔGbinding values of -30 and -25 kcal/mol to MDMX and MDM2, respectively, is recommended as a promising anticancer agent and suitable candidate for experimental evaluations.
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Affiliation(s)
- Nasim Rasafar
- Research Institute of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran.
| | - Elnaz Mehdizadeh Aghdam
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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50
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Sharma K, Strizhak AV, Fowler E, Xu W, Chappell B, Sore HF, Galloway WRJD, Grayson MN, Lau YH, Itzhaki LS, Spring DR. Functionalized Double Strain-Promoted Stapled Peptides for Inhibiting the p53-MDM2 Interaction. ACS OMEGA 2020; 5:1157-1169. [PMID: 31984273 PMCID: PMC6977200 DOI: 10.1021/acsomega.9b03459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
The Sondheimer dialkyne reagent has previously been employed in strain-promoted double-click cycloadditions with bis-azide peptides to generate stapled peptide inhibitors of protein-protein interactions. The substituted variants of the Sondheimer dialkyne can be used to generate functionalized stapled peptide inhibitors with improved biological properties; however, this remains a relatively underdeveloped field. Herein, we report the synthesis of new substituted variants of Sondheimer dialkyne and their application in the stapling of p53-based diazido peptides to generate potent stapled peptide-based inhibitors of the oncogenic p53-MDM2 interaction. The functionalized stapled peptide formed from a meta-fluoro-substituted Sondheimer dialkyne was found to be the most potent inhibitor. Furthermore, through experimental studies and density functional theory calculations, we investigated the impact of the substituent on the strain-promoted double-click reactivity of Sondheimer dialkyne.
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Affiliation(s)
- Krishna Sharma
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Alexander V. Strizhak
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Elaine Fowler
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Wenshu Xu
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - Ben Chappell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hannah F. Sore
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | | | - Matthew N. Grayson
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Yu Heng Lau
- School
of Chemistry, The University of Sydney, Eastern Avenue, Sydney, New South Wales 2006, Australia
| | - Laura S. Itzhaki
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - David R. Spring
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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