1
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Zhou S, Nishimura F, Wada K, Fujii K, Kondo T, Watanabe K, Imai Y, Ohtsuki T, Kitamatsu M. Configuration of two cysteine residues in a ring within a stapled Bim peptide affects the secondary structure and apoptotic activity. Bioorg Med Chem Lett 2024; 112:129915. [PMID: 39127242 DOI: 10.1016/j.bmcl.2024.129915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Many reports have shown that stabilization of secondary structure by stapling functional peptides enhances the intracellular bioactivity. However, no report has discussed the correlation between stabilization and biological activity based on the configuration of amino acid residues used as anchors for stapling. To clarify this, we investigated the helix content and apoptotic efficiency of an apoptosis-inducing peptide, Bim, and four stapled Bim peptides containing stapling-related Cys residues introduced with different configurations within the sequence. The results demonstrated that the configuration of Cys residues in stapled Bim peptides affected the secondary structure and intracellular activity of the peptides, and furthermore, there was a correlation between these latter two variables.
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Affiliation(s)
- Shengli Zhou
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Fuka Nishimura
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuhaya Wada
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kaho Fujii
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takeshi Kondo
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Yoshitane Imai
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
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2
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Alboreggia G, Udompholkul P, Baggio C, Muzzarelli K, Assar Z, Pellecchia M. Histidine-Covalent Stapled Alpha-Helical Peptides Targeting hMcl-1. J Med Chem 2024; 67:8172-8185. [PMID: 38695666 PMCID: PMC11129181 DOI: 10.1021/acs.jmedchem.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024]
Abstract
Several novel and effective cysteine targeting (Cys) covalent drugs are in clinical use. However, the target area containing a druggable Cys residue is limited. Therefore, methods for creating covalent drugs that target different residues are being looked for; examples of such ligands include those that target the residues lysine (Lys) and tyrosine (Tyr). Though the histidine (His) side chain is more frequently found in protein binding locations and has higher desirable nucleophilicity, surprisingly limited research has been done to specifically target this residue, and there are not many examples of His-targeting ligands that have been rationally designed. In the current work, we created novel stapled peptides that are intended to target hMcl-1 His 252 covalently. We describe the in vitro (biochemical, NMR, and X-ray) and cellular design and characterization of such agents. Our findings further suggest that the use of electrophiles to specifically target His residues is warranted.
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Affiliation(s)
- Giulia Alboreggia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Kendall Muzzarelli
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Zahra Assar
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Maurizio Pellecchia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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3
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Li F, Liu J, Liu C, Liu Z, Peng X, Huang Y, Chen X, Sun X, Wang S, Chen W, Xiong D, Diao X, Wang S, Zhuang J, Wu C, Wu D. Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy. Nat Commun 2024; 15:1476. [PMID: 38368459 PMCID: PMC10874388 DOI: 10.1038/s41467-024-45848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 02/06/2024] [Indexed: 02/19/2024] Open
Abstract
Overexpressed pro-survival B-cell lymphoma-2 (BCL-2) family proteins BCL-2 and BCL-XL can render tumor cells malignant. Leukemia drug venetoclax is currently the only approved selective BCL-2 inhibitor. However, its application has led to an emergence of resistant mutations, calling for drugs with an innovative mechanism of action. Herein we present cyclic peptides (CPs) with nanomolar-level binding affinities to BCL-2 or BCL-XL, and further reveal the structural and functional mechanisms of how these CPs target two proteins in a fashion that is remarkably different from traditional small-molecule inhibitors. In addition, these CPs can bind to the venetoclax-resistant clinical BCL-2 mutants with similar affinities as to the wild-type protein. Furthermore, we identify a single-residue discrepancy between BCL-2 D111 and BCL-XL A104 as a molecular "switch" that can differently engage CPs. Our study suggests that CPs may inhibit BCL-2 or BCL-XL by delicately modulating protein-protein interactions, potentially benefiting the development of next-generation therapeutics.
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Affiliation(s)
- Fengwei Li
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Junjie Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chao Liu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ziyan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xiangda Peng
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, China
| | - Yinyue Huang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoyu Chen
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiangnan Sun
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sen Wang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Chen
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, 200127, China
| | - Dan Xiong
- Xiamen Lifeint Technology Company Ltd., Xiamen, 361005, China
| | - Xiaotong Diao
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, China
| | - Jingjing Zhuang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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4
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Inhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function. Proc Natl Acad Sci U S A 2022; 119:e2209044119. [PMID: 36227917 PMCID: PMC9586281 DOI: 10.1073/pnas.2209044119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Therapies and preclinical probes designed to drug and better understand the specific functions of intracellular protein–protein interactions (PPIs) remain an area of unmet need. This study describes the development of prototype therapeutics against the FOXP3 homodimer, a PPI essential for regulatory T cell suppressive capacity. We demonstrate that hydrocarbon stapled peptides designed to block this interaction can dampen regulatory T cell (Treg cell) suppressive function and lead to genetic signatures of immune reactivation. This work provides strong scientific justification for continued development of FOXP3-specific peptide-based inhibitors and provides mechanistic insights into the design and delivery of specific inhibitors of the coiled-coil region of FOXP3. These studies ultimately could lead to new immunotherapeutic strategies to amplify immune responsiveness in a number of settings. Despite continuing advances in the development of novel cellular-, antibody-, and chemotherapeutic-based strategies to enhance immune reactivity, the presence of regulatory T cells (Treg cells) remains a complicating factor for their clinical efficacy. To overcome dosing limitations and off-target effects from antibody-based Treg cell deletional strategies or small molecule drugging, we investigated the ability of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3, the master transcription factor regulator of Treg cell development, maintenance, and suppressive function. Using the crystal structure of the FOXP3 homodimer as a guide, we developed SAHs in the likeness of a portion of the native FOXP3 antiparallel coiled-coil homodimerization domain (SAH-FOXP3) to block this key FOXP3 protein-protein interaction (PPI) through molecular mimicry. We describe the design, synthesis, and biochemical evaluation of single- and double-stapled SAHs covering the entire coiled-coil expanse. We show that lead SAH-FOXP3s bind FOXP3, are cell permeable and nontoxic to T cells, induce dose-dependent transcript and protein level alterations of FOXP3 target genes, impede Treg cell function, and lead to Treg cell gene expression changes in vivo consistent with FOXP3 dysfunction. These results demonstrate a proof of concept for rationally designed FOXP3-directed peptide therapeutics that could be used as approaches to amplify endogenous immune responsiveness.
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5
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Adak A, Das G, Gupta V, Khan J, Mukherjee N, Mondal P, Roy R, Barman S, Gharai PK, Ghosh S. Evolution of Potential Antimitotic Stapled Peptides from Multiple Helical Peptide Stretches of the Tubulin Heterodimer Interface: Helix-Mimicking Stapled Peptide Tubulin Inhibitors. J Med Chem 2022; 65:13866-13878. [PMID: 36240440 DOI: 10.1021/acs.jmedchem.2c01116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play a crucial role in microtubule dynamics. Microtubules are considered as a key target for the design and development of anticancer therapeutics, where inhibition of tubulin-tubulin interactions plays a crucial role. Here, we focused on a few key helical stretches at the interface of α,β-tubulin heterodimers and developed a structural mimic of these helical peptides, which can serve as potent inhibitors of microtubule polymerization. To induce helicity, we have made stapled analogues of these sequences. Thereafter, we modified the lead sequences of the antimitotic stapled peptides with halo derivatives. It is observed that halo-substituted stapled peptides follow an interesting trend for the electronegativity of halogen atoms in interaction patterns with tubulin and a correlation in the toxicity profile. Remarkably, we found that para-fluorophenylalanine-modified stapled peptide is the most potent inhibitors, which perturbs microtubule dynamics, induces apoptotic death, and inhibits the growth of melanoma.
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Affiliation(s)
- Anindyasundar Adak
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Varsha Gupta
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Juhee Khan
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Nabanita Mukherjee
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Surajit Barman
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Prabir Kumar Gharai
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India.,Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
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6
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Tian Y, Tirrell MV, LaBelle JL. Harnessing the Therapeutic Potential of Biomacromolecules through Intracellular Delivery of Nucleic Acids, Peptides, and Proteins. Adv Healthc Mater 2022; 11:e2102600. [PMID: 35285167 PMCID: PMC9232950 DOI: 10.1002/adhm.202102600] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/09/2022] [Indexed: 12/19/2022]
Abstract
Biomacromolecules have long been at the leading edge of academic and pharmaceutical drug development and clinical translation. With the clinical advances of new therapeutics, such as monoclonal antibodies and nucleic acids, the array of medical applications of biomacromolecules has broadened considerably. A major on-going effort is to expand therapeutic targets within intracellular locations. Owing to their large sizes, abundant charges, and hydrogen-bond donors and acceptors, advanced delivery technologies are required to deliver biomacromolecules effectively inside cells. In this review, strategies used for the intracellular delivery of three major forms of biomacromolecules: nucleic acids, proteins, and peptides, are highlighted. An emphasis is placed on synthetic delivery approaches and the major hurdles needed to be overcome for their ultimate clinical translation.
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Affiliation(s)
- Yu Tian
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 S Ellis Ave, Chicago, IL, 60637, USA
| | - Matthew V Tirrell
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 S Ellis Ave, Chicago, IL, 60637, USA
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
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7
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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8
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Gambini L, Udompholkul P, Baggio C, Muralidharan A, Kenjić N, Assar Z, Perry JJP, Pellecchia M. Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1. J Med Chem 2021; 64:4903-4912. [PMID: 33797903 DOI: 10.1021/acs.jmedchem.1c00005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Modulating disease-relevant protein-protein interactions (PPIs) using pharmacological tools is a critical step toward the design of novel therapeutic strategies. Over the years, however, targeting PPIs has proven a very challenging task owing to the large interfacial areas. Our recent efforts identified possible novel routes for the design of potent and selective inhibitors of PPIs using a structure-based design of covalent inhibitors targeting Lys residues. In this present study, we report on the design, synthesis, and characterizations of the first Lys-covalent BH3 peptide that has a remarkable affinity and selectivity for hMcl-1 over the closely related hBfl-1 protein. Our structural studies, aided by X-ray crystallography, provide atomic-level details of the inhibitor interactions that can be used to further translate these discoveries into novel generation, Lys-covalent pro-apoptotic agents.
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Affiliation(s)
- Luca Gambini
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Aruljothi Muralidharan
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Nikola Kenjić
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - J Jefferson P Perry
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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9
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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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10
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Assafa TE, Nandi S, Śmiłowicz D, Galazzo L, Teucher M, Elsner C, Pütz S, Bleicken S, Robin AY, Westphal D, Uson I, Stoll R, Czabotar PE, Metzler-Nolte N, Bordignon E. Biophysical Characterization of Pro-apoptotic BimBH3 Peptides Reveals an Unexpected Capacity for Self-Association. Structure 2020; 29:114-124.e3. [PMID: 32966763 DOI: 10.1016/j.str.2020.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/13/2020] [Accepted: 08/29/2020] [Indexed: 01/11/2023]
Abstract
Bcl-2 proteins orchestrate the mitochondrial pathway of apoptosis, pivotal for cell death. Yet, the structural details of the conformational changes of pro- and antiapoptotic proteins and their interactions remain unclear. Pulse dipolar spectroscopy (double electron-electron resonance [DEER], also known as PELDOR) in combination with spin-labeled apoptotic Bcl-2 proteins unveils conformational changes and interactions of each protein player via detection of intra- and inter-protein distances. Here, we present the synthesis and characterization of pro-apoptotic BimBH3 peptides of different lengths carrying cysteines for labeling with nitroxide or gadolinium spin probes. We show by DEER that the length of the peptides modulates their homo-interactions in the absence of other Bcl-2 proteins and solve by X-ray crystallography the structure of a BimBH3 tetramer, revealing the molecular details of the inter-peptide interactions. Finally, we prove that using orthogonal labels and three-channel DEER we can disentangle the Bim-Bim, Bcl-xL-Bcl-xL, and Bim-Bcl-xL interactions in a simplified interactome.
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Affiliation(s)
- Tufa E Assafa
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sukhendu Nandi
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Dariusz Śmiłowicz
- Chair of Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Christina Elsner
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefanie Pütz
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stephanie Bleicken
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Adeline Y Robin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Dana Westphal
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia; Department of Dermatology, Medical Faculty and University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Isabel Uson
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain; ICREA, Baldiri Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Nils Metzler-Nolte
- Chair of Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
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11
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Pham AT, Matile S. Peptide Stapling with Anion-π Catalysts. Chem Asian J 2020; 15:1562-1566. [PMID: 32311232 DOI: 10.1002/asia.202000309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/01/2020] [Indexed: 12/12/2022]
Abstract
We report design, synthesis and evaluation of a series of naphthalenediimides (NDIs) that are bridged with short peptides. Reminiscent of peptide stapling technologies, the macrocycles are conveniently accessible by a chromogenic nucleophilic aromatic substitution of two bromides in the NDI core with two thiols from cysteine sidechains. The dimension of core-bridged NDIs matches that of one turn of an α helix. NDI-stapled peptides exist as two, often separable atropisomers. Introduction of tertiary amine bases in amino-acid sidechains above the π-acidic NDI surface affords operational anion-π catalysts. According to an enolate chemistry benchmark reaction, anion-π catalysis next to peptides occurs with record chemoselectivity but weak enantioselectivity. Catalytic activity drops with increasing distance of the amine base to the NDI surface, looser homocysteine bridges, mismatched, shortened and elongated α-helix turns, and acyclic peptide controls. Elongation of isolated turns into short α helices significantly increases activity. This increase is consistent with remote control of anion-π catalysis from the α-helix macrodipole.
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Affiliation(s)
- Anh-Tuan Pham
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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12
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Valiente PA, Becerra D, Kim PM. A Method to Calculate the Relative Binding Free Energy Differences of α-Helical Stapled Peptides. J Org Chem 2020; 85:1644-1651. [DOI: 10.1021/acs.joc.9b03067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pedro A Valiente
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E2, Canada
| | - David Becerra
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E2, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E2, Canada
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13
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Hadji A, Schmitt GK, Schnorenberg MR, Roach L, Hickey CM, Leak LB, Tirrell MV, LaBelle JL. Preferential targeting of MCL-1 by a hydrocarbon-stapled BIM BH3 peptide. Oncotarget 2019; 10:6219-6233. [PMID: 31692812 PMCID: PMC6817437 DOI: 10.18632/oncotarget.27262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 10/04/2019] [Indexed: 11/29/2022] Open
Abstract
BCL-2 family proteins are central regulators of apoptosis and represent prime therapeutic targets for overcoming cell death resistance in malignancies. However, plasticity of anti-apoptotic members, such as MCL-1, often allows for a switch in cell death dependency patterns that lie outside the binding profile of targeted BH3-mimetics. Therefore discovery of therapeutics that effectively inactivate all anti-apoptotic members is a high priority. To address this we tested the potency of a hydrocarbon stapled BIM BH3 peptide (BIM SAHBA) to overcome both BCL-2 and MCL-1 apoptotic resistance given BIM’s naturally wide ranging affinity for all BCL-2 family multidomain members. BIM SAHBA effectively killed diffuse large B-cell lymphoma (DLBCL) cell lines regardless of their anti-apoptotic dependence. Despite BIM BH3’s ability to bind all BCL-2 anti-apoptotic proteins, BIM SAHBA’s dominant intracellular target was MCL-1 and this specificity was exploited in sequenced combination BH3-mimetic treatments targeting BCL-2, BCL-XL, and BCL-W. Extending this MCL-1 functional dependence, mouse embryonic fibroblasts (MEFs) deficient in MCL-1 were resistant to mitochondrial changes induced by BIM SAHBA. This study demonstrates the importance of understanding BH3 mimetic functional intracellular affinities for optimized use and highlights the diagnostic and therapeutic promise of a BIM BH3 peptide mimetic as a potential MCL-1 inhibitor.
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Affiliation(s)
- Abbas Hadji
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Greta K Schmitt
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mathew R Schnorenberg
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA.,Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Lauren Roach
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Connie M Hickey
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Logan B Leak
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Matthew V Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation and Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
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14
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Activating the Intrinsic Pathway of Apoptosis Using BIM BH3 Peptides Delivered by Peptide Amphiphiles with Endosomal Release. MATERIALS 2019; 12:ma12162567. [PMID: 31408950 PMCID: PMC6719084 DOI: 10.3390/ma12162567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022]
Abstract
Therapeutic manipulation of the BCL-2 family using BH3 mimetics is an emerging paradigm in cancer treatment and immune modulation. For example, peptides mimicking the BIM BH3 helix can directly target the full complement of anti- and pro-apoptotic BCL-2 proteins to trigger apoptosis. This study has incorporated the potent BH3 α-helical death domain of BIM into peptide amphiphile (PA) nanostructures designed to facilitate cellular uptake and induce cell death. This study shows that these PA nanostructures are quickly incorporated into cells, are able to specifically bind BCL-2 proteins, are stable at physiologic temperatures and pH, and induce dose-dependent apoptosis in cells. The incorporation of a cathepsin B cleavable linker between the BIM BH3 peptide and the hydrophobic tail resulted in increased intracellular accumulation and mitochondrial co-localization of the BIM BH3 peptide while also improving BCL-2 family member binding and apoptotic reactivation. This PA platform represents a promising new strategy for intracellular therapeutic peptide delivery for the disruption of intracellular protein:protein interactions.
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15
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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16
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Flow Cytometry-Based Detection and Analysis of BCL-2 Family Proteins and Mitochondrial Outer Membrane Permeabilization (MOMP). Methods Mol Biol 2019; 1877:77-91. [PMID: 30535999 DOI: 10.1007/978-1-4939-8861-7_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The BCL-2 family of proteins orchestrates a complex signaling network that governs the balance between cellular survival and death. A comprehensive understanding of the mechanistic interactions between these proteins continues to evolve in normal and malignant cells. The functional variation by individual BCL-2 proteins in different cell types has driven clinical therapeutic development in targeting individual BCL-2 members with the goal of fine-tuning cell death in diseased cells. Given the importance of understanding and validating the effect of activating or inhibiting BCL-2 protein interactions in individual cells, the methods used to measure apoptotic cell death have undergone increased scrutiny. Here, we describe two in vitro flow cytometry-based methods that are useful in measuring BCL-2 proteins and mitochondrial-based cell death in complex cell populations.
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17
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Peraro L, Deprey KL, Moser MK, Zou Z, Ball HL, Levine B, Kritzer JA. Cell Penetration Profiling Using the Chloroalkane Penetration Assay. J Am Chem Soc 2018; 140:11360-11369. [PMID: 30118219 PMCID: PMC6205923 DOI: 10.1021/jacs.8b06144] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotherapeutics are a promising class of molecules in drug discovery, but they are often limited to extracellular targets due to their poor cell penetration. High-throughput cell penetration assays are required for the optimization of biotherapeutics for enhanced cell penetration. We developed a HaloTag-based assay called the chloroalkane penetration assay (CAPA), which is quantitative, high-throughput, and compartment-specific. We demonstrate the ability of CAPA to profile extent of cytosolic penetration with respect to concentration, presence of serum, temperature, and time. We also used CAPA to investigate structure-penetration relationships for bioactive stapled peptides and peptides fused to cell-penetrating sequences. CAPA is not only limited to measuring cytosolic penetration. Using a cell line where HaloTag is localized to the nucleus, we show quantitative measurement of nuclear penetration. Going forward, CAPA will be a valuable method for measuring and optimizing the cell penetration of biotherapeutics.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, MA 02155
| | | | | | - Zhongju Zou
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75230
| | - Haydn L. Ball
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75230
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18
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Peraro L, Kritzer JA. Emerging Methods and Design Principles for Cell-Penetrant Peptides. Angew Chem Int Ed Engl 2018; 57:11868-11881. [PMID: 29740917 PMCID: PMC7184558 DOI: 10.1002/anie.201801361] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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19
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Peraro L, Kritzer JA. Neue Methoden und Designprinzipien für zellgängige Peptide. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leila Peraro
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
| | - Joshua A. Kritzer
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
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20
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Trypanothione reductase inhibition and anti-leishmanial activity of all-hydrocarbon stapled α-helical peptides with improved proteolytic stability. Eur J Med Chem 2018; 149:238-247. [DOI: 10.1016/j.ejmech.2018.02.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 12/24/2022]
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21
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IKKγ-Mimetic Peptides Block the Resistance to Apoptosis Associated with Kaposi's Sarcoma-Associated Herpesvirus Infection. J Virol 2017; 91:JVI.01170-17. [PMID: 28931678 PMCID: PMC5686756 DOI: 10.1128/jvi.01170-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/31/2017] [Indexed: 11/20/2022] Open
Abstract
Primary effusion lymphoma (PEL) is a lymphogenic disorder associated with Kaposi's sarcoma-associated herpesvirus (KSHV) infection. Key to the survival and proliferation of PEL is the canonical NF-κB pathway, which becomes constitutively activated following overexpression of the viral oncoprotein KSHV vFLIP (ks-vFLIP). This arises from its capacity to form a complex with the modulatory subunit of the IκB kinase (IKK) kinase, IKKγ (or NEMO), resulting in the overproduction of proteins that promote cellular survival and prevent apoptosis, both of which are important drivers of tumorigenesis. Using a combination of cell-based and biophysical assays together with structural techniques, we showed that the observed resistance to cell death is largely independent of autophagy or major death receptor signaling pathways and demonstrated that direct targeting of the ks-vFLIP–IKKγ interaction both in cells and in vitro can be achieved using IKKγ-mimetic peptides. Our results further reveal that these peptides not only induce cell killing but also potently sensitize PEL to the proapoptotic agents tumor necrosis factor alpha and etoposide and are the first to confirm ks-vFLIP as a tractable target for the treatment of PEL and related disorders. IMPORTANCE KSHV vFLIP (ks-vFLIP) has been shown to have a crucial role in cellular transformation, in which it is vital for the survival and proliferation of primary effusion lymphoma (PEL), an aggressive malignancy associated with infection that is resistant to the majority of chemotherapeutic drugs. It operates via subversion of the canonical NF-κB pathway, which requires a physical interaction between ks-vFLIP and the IKK kinase modulatory subunit IKKγ. While this interaction has been directly linked to protection against apoptosis, it is unclear whether the suppression of other cell death pathways implicated in ks-vFLIP pathogenesis is an additional contributor. We demonstrate that the interaction between ks-vFLIP and IKKγ is pivotal in conferring resistance to apoptosis. Additionally, we show that the ks-vFLIP–IKKγ complex can be disrupted using peptides leading to direct killing and the sensitization of PEL cells to proapoptotic agents. Our studies thus provide a framework for future therapeutic interventions.
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22
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Klein M. Stabilized helical peptides: overview of the technologies and its impact on drug discovery. Expert Opin Drug Discov 2017; 12:1117-1125. [PMID: 28889766 DOI: 10.1080/17460441.2017.1372745] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Protein-protein interactions are predominant in the workings of all cells. Until now, there have been a few successes in targeting protein-protein interactions with small molecules. Peptides may overcome some of the challenges of small molecules in disrupting protein-protein interactions. However, peptides present a new set of challenges in drug discovery. Thus, the study of the stabilization of helical peptides has been extensive. Areas covered: Several technological approaches to helical peptide stabilization have been studied. In this review, stapled peptides, foldamers, and hydrogen bond surrogates are discussed. Issues regarding design principles are also discussed. Furthermore, this review introduces select computational techniques used to aid peptide design and discusses clinical trials of peptides in a more advanced stage of development. Expert opinion: Stabilized helical peptides hold great promise in a wide array of diseases. However, the field is still relatively new and new design principles are emerging. The possibilities of peptide modification are quite extensive and expanding, so the design of stabilized peptides requires great attention to detail in order to avoid a large number of failed lead peptides. The start of clinical trials with stapled peptides is a promising sign for the future.
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Affiliation(s)
- Mark Klein
- a Division of Hematology, Oncology, and Transplantation , University of Minnesota , Minneapolis , MN , USA.,b Hematology/Oncology Section , Minneapolis VA Healthcare System , Minneapolis , MN , USA
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23
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Wallbrecher R, Chène P, Ruetz S, Stachyra T, Vorherr T, Brock R. A critical assessment of the synthesis and biological activity of p53/human double minute 2-stapled peptide inhibitors. Br J Pharmacol 2017; 174:2613-2622. [PMID: 28436014 DOI: 10.1111/bph.13834] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 04/11/2017] [Accepted: 04/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND PURPOSE Helix stapling enhances the activity of peptides that interact with a target protein in a helical conformation. These staples are also supposed to change the pharmacokinetics of the molecules and promote cytoplasmic targeting. We assessed the extent to which the pharmacokinetic characteristics are a function of the staple for a peptide inhibiting the interaction of p53 with the human double minute 2 (Hdm2) protein and differ from those of the standard cationic cell-penetrating peptide nona-arginine. EXPERIMENTAL APPROACH Stapled peptides and linear counterparts were synthesized in free and fluorescently labelled forms. Activity was determined in biochemical time-resolved Förster resonance energy transfer experiments and cellular high-content assays. Cellular uptake and intracellular trafficking were visualized by confocal microscopy. KEY RESULTS Peptides showed sub-nanomolar potency. For short-time incubation, uptake efficiencies for the stapled and linear peptides were similar and both were taken up less efficiently than nona-arginine. Only for SJSA-1 cells expressing the Hdm2 target protein, the stapled peptides showed an enhanced cytoplasmic and nuclear accumulation after long-term incubation. This was also observed for the linear counterparts, albeit to a lesser degree. For HeLa cells, which lack target expression, no such accumulation was observed. CONCLUSION AND IMPLICATIONS Cytosolic and nuclear accumulation was not an intrinsic property of the stapled peptide, but resulted from capture by the target Hdm2 after endo-lysosomal release. Considering the rather poor uptake of stapled peptides, further development should focus on increasing the efficiency of uptake of these peptides.
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Affiliation(s)
- Rike Wallbrecher
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Patrick Chène
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Stephan Ruetz
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Thomas Vorherr
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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24
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Blood-brain-barrier spheroids as an in vitro screening platform for brain-penetrating agents. Nat Commun 2017; 8:15623. [PMID: 28585535 PMCID: PMC5467173 DOI: 10.1038/ncomms15623] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/07/2017] [Indexed: 12/24/2022] Open
Abstract
Culture-based blood–brain barrier (BBB) models are crucial tools to enable rapid screening of brain-penetrating drugs. However, reproducibility of in vitro barrier properties and permeability remain as major challenges. Here, we report that self-assembling multicellular BBB spheroids display reproducible BBB features and functions. The spheroid core is comprised mainly of astrocytes, while brain endothelial cells and pericytes encase the surface, acting as a barrier that regulates transport of molecules. The spheroid surface exhibits high expression of tight junction proteins, VEGF-dependent permeability, efflux pump activity and receptor-mediated transcytosis of angiopep-2. In contrast, the transwell co-culture system displays comparatively low levels of BBB regulatory proteins, and is unable to discriminate between the transport of angiopep-2 and a control peptide. Finally, we have utilized the BBB spheroids to screen and identify BBB-penetrant cell-penetrating peptides (CPPs). This robust in vitro BBB model could serve as a valuable next-generation platform for expediting the development of CNS therapeutics. In vitro blood-brain barrier (BBB) models are crucial tools for screening brain-penetrating compounds. Here the authors develop a self-assembling BBB spheroid model with superior performance to the standard transwell BBB model, and use their platform to identify cell-penetrating peptides that can cross the BBB.
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25
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Tiwari G, Verma CS. Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041. J Phys Chem B 2017; 121:657-670. [PMID: 28048940 DOI: 10.1021/acs.jpcb.6b09900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactivation of tumor-suppressing activity of p53 protein by targeting its negative regulator MDM2/MDMX has been pursued as a potential anticancer strategy. A promising dual inhibitor of MDM2/MDMX that has been developed and is currently in clinical trials is the stapled peptide ATSP-7041. The activity of this molecule is reported to be modulated in the presence of serum. Albumin is the most abundant protein in serum and is known to bind reversibly to several molecules. To study this interaction, we develop a protocol combining molecular modeling, docking, and simulations. Exhaustive docking of the peptide with representative simulated structures of human serum albumin led to the identification of probable binding sites on the surface of the protein, including both known canonical and novel binding sites. Sequence differences at putative peptide-binding sites in human and mouse albumin result in differing interaction energies with the peptide and enable us to rationalize the observed differences in vivo. In general, the findings should help in guiding the design of features in such peptides that may affect their distribution and cell permeability, opening a new window in structure-guided design strategies.
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Affiliation(s)
- Garima Tiwari
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.,Department of Biological sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543, Singapore.,School of Biological sciences, Nanyang Technological University , 50 Nanyang Drive, Singapore 637551, Singapore
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26
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de Araujo AD, Lim J, Good AC, Skerlj RT, Fairlie DP. Electrophilic Helical Peptides That Bond Covalently, Irreversibly, and Selectively in a Protein-Protein Interaction Site. ACS Med Chem Lett 2017; 8:22-26. [PMID: 28105269 DOI: 10.1021/acsmedchemlett.6b00395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/15/2016] [Indexed: 12/28/2022] Open
Abstract
Protein-protein interactions mediate most physiological and disease processes. Helix-constrained peptides potently mimic or inhibit these interactions by making multiple contacts over large surface areas. However, despite high affinities, they typically have short lifetimes bound to the protein. Here we insert both a helix-inducing constraint and an adjacent electrophile into the native peptide ligand BIM to target the oncogenic protein Bcl2A1. The modified BIM peptide bonds covalently and irreversibly to one cysteine within the helix-binding groove of Bcl2A1, but not to two other exposed cysteines on its surface, and shows no covalent bonding to other Bcl2 proteins. It also penetrates cell membranes and bonds covalently to Bcl2A1 inside cells. This innovative approach to increasing receptor residence time of helical peptides demonstrates the potential to selectively silence a PPI inside cells, with selectivity over other nucleophilic sites on proteins.
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Affiliation(s)
- Aline Dantas de Araujo
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew C. Good
- Noliva Therapeutics, Newton, Massachusetts 02465, United States
| | | | - David P. Fairlie
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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27
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Abegg D, Gasparini G, Hoch DG, Shuster A, Bartolami E, Matile S, Adibekian A. Strained Cyclic Disulfides Enable Cellular Uptake by Reacting with the Transferrin Receptor. J Am Chem Soc 2016; 139:231-238. [DOI: 10.1021/jacs.6b09643] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Daniel Abegg
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Giulio Gasparini
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dominic G. Hoch
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Anton Shuster
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Eline Bartolami
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Alexander Adibekian
- School of Chemistry and Biochemistry,
National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
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Mechanistic validation of a clinical lead stapled peptide that reactivates p53 by dual HDM2 and HDMX targeting. Oncogene 2016; 36:2184-2190. [PMID: 27721413 PMCID: PMC5386833 DOI: 10.1038/onc.2016.361] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/03/2016] [Accepted: 08/10/2016] [Indexed: 01/02/2023]
Abstract
Hydrocarbon-stapled peptides that display key residues of the p53 transactivation domain have emerged as bona fide clinical candidates for reactivating the tumor suppression function of p53 in cancer by dual targeting of the negative regulators HDM2 and HDMX. A recent study questioned the mechanistic specificity of such stapled peptides based on interrogating their capacity to disrupt p53/HDM2 and p53/HDMX complexes in living cells using a new recombinase enhanced bimolecular luciferase complementation platform (ReBiL). Here, we directly evaluate the cellular uptake, intracellular targeting selectivity, and p53-dependent cytotoxicity of the clinical prototype ATSP-7041. We find that under standard serum-containing tissue culture conditions, ATSP-7041 achieves intracellular access without membrane disruption, dose-dependently dissociates both p53/HDM2 and p53/HDMX complexes but not an unrelated protein complex in long-term ReBiL experiments, and is selectively cytotoxic to cancer cells bearing wild-type p53 by inducing a surge in p53 protein level. These studies underscore the importance of a thorough step-wise approach, including consideration of the time-dependence of cellular uptake and intracellular distribution, in evaluating and advancing stapled peptides for clinical translation.
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29
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Bird GH, Mazzola E, Opoku-Nsiah K, Lammert MA, Godes M, Neuberg DS, Walensky LD. Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices. Nat Chem Biol 2016; 12:845-52. [PMID: 27547919 PMCID: PMC5055751 DOI: 10.1038/nchembio.2153] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/23/2016] [Indexed: 12/23/2022]
Abstract
Hydrocarbon-stapled peptides are a class of bioactive alpha-helical ligands developed to dissect and target protein interactions. While there is consensus that stapled peptides can be effective chemical tools for investigating protein regulation, their broader utility for therapeutic modulation of intracellular interactions remains an active area of study. In particular, the design principles for generating cell-permeable stapled peptides are empiric, yet consistent intracellular access is essential to in vivo application. Here, we used an unbiased statistical approach to determine which biophysical parameters dictate the uptake of stapled-peptide libraries. We found that staple placement at the amphipathic boundary combined with optimal hydrophobic and helical content are the key drivers of cellular uptake, whereas excess hydrophobicity and positive charge at isolated amino acid positions can trigger membrane lysis at elevated peptide dosing. Our results provide a design roadmap for maximizing the potential to generate cell-permeable stapled peptides with on-mechanism cellular activity.
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Affiliation(s)
- Gregory H. Bird
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Emanuele Mazzola
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Kwadwo Opoku-Nsiah
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Margaret A. Lammert
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Marina Godes
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Loren D. Walensky
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
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30
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Huhn AJ, Guerra RM, Harvey EP, Bird GH, Walensky LD. Selective Covalent Targeting of Anti-Apoptotic BFL-1 by Cysteine-Reactive Stapled Peptide Inhibitors. Cell Chem Biol 2016; 23:1123-1134. [PMID: 27617850 DOI: 10.1016/j.chembiol.2016.07.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/01/2016] [Accepted: 07/18/2016] [Indexed: 12/27/2022]
Abstract
Anti-apoptotic BCL-2 family proteins block cell death by trapping the critical α-helical BH3 domains of pro-apoptotic members in a surface groove. Cancer cells hijack this survival mechanism by overexpressing a spectrum of anti-apoptotic members, mounting formidable apoptotic blockades that resist chemotherapeutic treatment. Drugging the BH3-binding pockets of anti-apoptotic proteins has become a highest-priority goal, fueled by the clinical success of ABT-199, a selective BCL-2 inhibitor, in reactivating apoptosis in BCL-2-dependent cancers. BFL-1 is a BCL-2 homolog implicated in melanoma, lymphoma, and other cancers, and remains undrugged. A natural juxtaposition of two unique cysteines at the binding interface of the NOXA BH3 helix and BFL-1 pocket informed the development of stapled BH3 peptides bearing acrylamide warheads to irreversibly inhibit BFL-1 by covalent targeting. Given the frequent proximity of native cysteines to regulatory binding surfaces, covalent stapled peptide inhibitors provide a new therapeutic strategy for targeting pathologic protein interactions.
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Affiliation(s)
- Annissa J Huhn
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rachel M Guerra
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Edward P Harvey
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gregory H Bird
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Loren D Walensky
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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31
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Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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32
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Development of a lytic peptide derived from BH3-only proteins. Cell Death Discov 2016; 2:16008. [PMID: 27551502 PMCID: PMC4979451 DOI: 10.1038/cddiscovery.2016.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/28/2022] Open
Abstract
Despite great advances in cancer therapy, drug resistance is a difficult hurdle to overcome that requires development of anticancer agents with novel and effective modes of action. In a number of studies, lytic peptides have shown remarkable ability to eliminate cancer cells through a different way from traditional treatments. Lytic peptides are positively charged, amphiphilic, and are efficient at binding and disrupting the negatively charged cell membrane of cancer cells. In this study, we described the anticancer properties of a lytic peptide that was developed on the basis of the alignment of amphiphilic BH3 peptides. Our results demonstrated that the positive charge and conformation constraint were favourable for efficient cancer cell elimination. Artificial BCL-2 homology 3 peptides (ABH3) exhibited effective anticancer effects against a series of cancer cell lines in vitro and in HeLa human cervical tumour xenografts in vivo. ABH3 induced cell death in an apoptosis-independent manner through the lytic properties of the peptide that caused disruption of cell membrane. Our results showed that charge tuning and conformation constraining in a lytic peptide could be applied to optimise the anticancer activity of lytic peptides. These results also suggest that ABH3 may be a promising beginning for the development of additional lytic peptides as anticancer reagents.
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